# Dysbiosis, malnutrition and enhanced gut-lung axis contribute to age-related respiratory diseases

Vinciane Saint-Criq, Geanncarlo Lugo-Villarino, Muriel Thomas

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Vinciane Saint-Criq, Geanncarlo Lugo-Villarino, Muriel Thomas. Dysbiosis, malnutrition and enhanced gut-lung axis contribute to age-related respiratory diseases. Ageing Research Reviews - ARR, 2021, 66, pp.101235. 10.1016/j.arr.2020.101235. hal-03129383

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DYSBIOSIS, MALNUTRITION AND ENHANCED GUT-LUNG AXIS CONTRIBUTE TO
AGE-RELATED RESPIRATORY DISEASES

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Vinciane Saint-Criq¹, Geanncarlo Lugo-Villarino², Muriel Thomas¹

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¹Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France

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²Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.

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HIGHLIGHTS

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* Older people are often malnourished and susceptible to develop lung diseases.

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* Ageing is associated with dysbiotic microbiota and alteration of the gut-lung axis.

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* Nutrition is an accessible lever affecting microbiota and ageing of the lung.

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* Gut and lung microbiota represent key players in the maintenance of healthy lungs.

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* Gut and lung microbiota are potential targets against ageing-related lung disease.

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32 Older people are at an increased risk of developing respiratory diseases such as chronic
33 obstructive pulmonary diseases, asthma, idiopathic pulmonary fibrosis or lung infections.

34 Susceptibility to these diseases is partly due to the intrinsic ageing process, characterized by
35 genomic, cellular and metabolic hallmarks and immunosenescence, and is associated with
36 changes in the intestinal microbiota. Importantly, in the lungs, ageing is also associated with
37 a dysbiosis and loss of resilience of the resident microbiota and alterations of the gut-lung
38 axis. Notably, as malnutrition is often observed in the elderly, nutrition is one of the most
39 accessible modifiable factors affecting both senescence and microbiota. This article reviews
40 the changes affecting the lung and its resident microbiota during ageing, as well as the
41 interconnections between malnutrition, senescence, microbiota, gut-lung axis and respiratory
42 health. As the communication along the gut-lung axis becomes more permissive with ageing,
43 this review also explores the evidence that the gut and lung microbiota are key players in the
44 maintenance of healthy lungs, and as such, are potential targets for nutrition-based
45 preventive strategies against lung disease in elderly populations.

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47 **Keywords:** Age-associated lung diseases, Microbiota, Nutrition, Gut-Lung axis, Ageing,
48 Respiratory infections.

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## 51 INTRODUCTION.

Population worldwide is getting older; more than 1 billion people are over 60 and this number will continue to increase in the future, especially in developing countries. Failing to ensure healthy ageing in these elderly populations would lead to multiple negative consequences (personal, economic and societal) and it is, therefore, essential to prepare societies to meet their specific needs. This has been made a priority of the World Health Organization (WHO), which has elaborated the plan for a Decade of Healthy Ageing 2020–2030.

Ageing reflects all the changes taking place over the course of life. Its process has a high inter-individual variability with respect to its rate and affected organs, and is characterized by a decrease in physical capacity, an increased vulnerability to environmental challenges, and a growing risk of disease and death. Physiologically, loss in muscle mass, decline in strength (Leong et al., 2015; Rantanen et al., 2003), and increased risk of fracture, are commonly associated with ageing. Impairments in sensory functions, increased frequency of infections, falls, pressure ulcers and deterioration in cognitive functions (Fernández-Garrido et al., 2014; Fried et al., 1991; Inouye et al., 2007), are negatively correlated with survival (Kane et al., 2012; Lordos et al., 2008). Particularly, the elderly population is at risk of developing lung infections. The prevalence of other pulmonary diseases, (e.g. tuberculosis, chronic obstructive pulmonary diseases, asthma), increases with age and contributes to morbidity and mortality in older individuals. At a cellular level, ageing is associated with immunosenescence (Lang et al., 2012) and with chronic low-level inflammation, known as inflamm-ageing (Ferrucci and Fabbri, 2018).

Malnutrition is defined by the European Society for Clinical Nutrition and Metabolism as “a state resulting from lack of intake or uptake of nutrition that leads to altered body composition (decreased fat free mass) and body cell mass leading to diminished physical and mental function and impaired clinical outcome from disease” (Cederholm et al., 2017). Importantly, it is also one of the first signs of a degrading health condition in the elderly population. Undernourished old people are at increased risk of falls, long hospital stays, infections,
78 impaired respiratory function and death (Rasheed and Woods, 2013; Tappenden et al., 79 2013). Interestingly, an early study by Heymsfield et al. showed an association between 80 malnutrition and the apparition of further pathologies, including bronchopneumonia 81 (Heymsfield et al., 1979). Thus, because nutrition is one of the most accessible modifiable 82 factors, it can be considered as a lever of action to promote healthy ageing in older people 83 (Rodgers and Collins, 2020).

84 Many clinical issues observed in ageing individuals are associated with changes in the 85 microbiota composition and functionality in the gut and other organs (Claesson et al., 2012, 86 2011; Jackson et al., 2016; Jeffery et al., 2016; O'Sullivan et al., 2011). Although there is a 87 very high inter-individual variability, multiple studies have shown that the diversity of gut 88 microbiota and genera such as *Bifidobacteria* and *Lactobacilli* are reduced in older 89 individuals, whereas certain opportunists (e.g. *Clostridioides difficile*) are increased 90 (Claesson et al., 2011; Milani et al., 2016; Rea et al., 2012). Moreover, specific microbial 91 profiles have been identified as longevity signatures in centenarians (Biagi et al., 2017; Cătoi 92 et al., 2020; Kong et al., 2016; Naito et al., 2019; Rampelli et al., 2020; Santoro et al., 2018; 93 N. Wang et al., 2019; Wu et al., 2020). In the lungs, due to the invasiveness of the 94 procedure, no study has been performed on lower respiratory tract microbiota and only a few 95 studies have described the composition of the upper respiratory tract (URT) microbiota in the 96 elderly (de Steenhuijsen Piters et al., 2016; J.-J. Lee et al., 2019; Stearns et al., 2015; 97 Whelan et al., 2014). It is not fully understood how the microbiota impacts ageing processes, 98 but it is likely that dysbiosis plays a central role in the progression of ageing-related disorders 99 and that restoration of eubiosis would promote healthy ageing (Figure 1).

100 Here, we review the hallmarks of the ageing lung and interconnections between malnutrition, 101 ageing, specifically cellular senescence, microbiota and lung health. The evidence of the gut- 102 lung axis and its specificities in the elderly population prompt us to propose that both gut and 103 lung microbiota are main players in the maintenance of healthy lungs and, therefore, are 104 central targets for nutrition based preventive strategies in elderly populations.
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# 1. AGEING IN THE LUNGS

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## 1.1. *The ageing lung and the most prevalent age-related pulmonary diseases*

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According to the European Respiratory Society (ERS), the status of lung function is considered a predictor of healthy ageing (Meiners et al., 2015). For instance, elder individuals with poor lung function are prone to develop cardiovascular disease, type 2 diabetes (T2D) and cognitive decline, when compared to those individuals with robust lung function (Bowdish, 2019; Hole et al., 1996; Lange et al., 1990; Weiss et al., 1995).

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Conversely, in older adults, a robust lung function correlates with a higher metabolic rate, which is a well-known parameter for fitness, activity and physical performance in the elderly (Bowdish, 2019; Choi and Pai, 2004; Simpson et al., 2005).

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Although the ageing of the lung is inevitable, and leads to a natural decline in its function, there are intrinsic (e.g., genetic components) and extrinsic (e.g., environment) factors that may accelerate or slow down this process. There are ten hallmarks thought to contribute to physiological changes associated with ageing and particularly with the ageing lung (Figure 2) (López-Otín et al., 2013; Meiners et al., 2015). These include 1) genomic instability, 2) telomere attrition, 3) epigenetic alterations, 4) loss of proteotasis, 5) deregulated nutrient sensing, 6) mitochondrial dysfunction, 7) cellular senescence, 8) stem cell exhaustion, 9) altered intercellular communication and 10) dysregulation of extracellular matrix (ECM). These alterations can occur in conducting airway epithelial cells, alveolar epithelial cells as well as airway smooth muscle cells and resident immune cells, and result in both structural and physiological changes. For instance, the increased apoptosis of epithelial cells, together with abnormalities of the microtubular structure of the cilia of multiciliated cells, the altered mucins and antioxidants content of the epithelium lining fluid and the decreased respiratory muscle and diaphragm strength, lead to defects in the mucociliary clearance machinery and a decreased ability of the lungs to clear mucus and inhaled particles and pathogens (Cho and Stout-Delgado, 2020; Ho et al., 2001; Wansleeben et al., 2014). The size of alveoli is also increased in the aged lungs, due to changes in the ECM and this leads to decreased elastic

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recoil and increased end expiratory lung volume (Cho and Stout-Delgado, 2020; Janssens et al., 1999). These physiological changes that occur in the ageing lung collectively lead to poor lung functional capacity and a decreased ability to maintain homeostasis.

As a consequence of the natural accumulation of age-related physiological changes in addition to exposure to toxic environmental factors, this organ becomes susceptible to chronic disorders such as Chronic Obstructive Pulmonary Disease (COPD), Idiopathic Pulmonary Fibrosis (IPF), Lung cancer and asthma, and infectious diseases like Community Acquired Pneumonia (CAP). In particular, the age-associated alterations of the immune system, called immunosenescence and discussed in the next section, are thought to be a key driver of asthma exacerbation in the elderly (Cho and Stout-Delgado, 2020; Z. Li et al., 2017; Metcalf et al., 2015; Shaw et al., 2011). Similarly, immunosenescence is thought to be the main culprit for predisposing the ageing lung to immunopathology in response to infectious stimuli (Chen et al., 2020; Cho and Stout-Delgado, 2020; Goldstein, 2012) and consequently, the ageing lung is more predisposed to secondary bacterial infections consecutive to viral pneumonia (Akgün et al., 2012; Castle et al., 2007; Chen et al., 2020; Cho and Stout-Delgado, 2020; Goldstein, 2012). According to the WHO-Europe, older adults are at a significant increased risk of severe disease from SARS-CoV-2 infection; over 95% of the reported fatalities occurred in those individuals over 60 years old and with comorbidities. Recent data indicate clear effects on the immune system, which may be worsen in older individuals (F. Wang et al., 2020).

## 1.2. Immunosenescence and its impact on age-related pulmonary diseases

Immunosenescence is defined as the age-associated decline in the immune system capacity to respond to infections and generate long-term immune memory (Cho and Stout-Delgado, 2020). As a consequence, older individuals are prone to infection, cancer, autoimmunity and chronic inflammation, and exhibit a poor vaccine response (Al-Alawi et al., 2014; Fulop et al., 2014; Murray and Chotirmall, 2015). Globally, immunosenescence has the following traits: poor capacity to respond to new antigens, accumulation of memory T cells in detriment of a
159 diminished naïve T cell repertoire, and chronic low-grade inflammation state known as
160 inflamm-ageing (Aiello et al., 2019). Both innate and adaptive immunity are affected by
161 immunosenescence.

162 Immunosenescence of alveolar macrophages causes a decrease in their total numbers and
163 capacity to perform phagocytosis and clearance of foreign particles, provoking susceptibility
164 to bacterial and viral infections causing CAP (Chen et al., 2020; Volkova et al., 2012; Wong
165 et al., 2017). It also diminishes the capacity of these cells to produce pro-resolution
166 mediators, such as resolvins (Arnardottir et al., 2014), antioxidant/detoxification factors in
167 response to cigarette smoke in COPD disease (Suzuki et al., 2008), or to clear away
168 apoptotic airway epithelial cells generated during COPD (Chen et al., 2020; Hodge et al.,
169 2003). Immunosenescence of airway mucosal Dendritic Cells (DCs) is reflected by lower
170 expression and function of Toll-like receptors (TLRs), decreased phagocytosis capacity, and
171 diminished/delayed migration potential towards draining lymph nodes upon activation
172 (Agrawal et al., 2007; Agrawal and Gupta, 2011; Volkova et al., 2012). In the context of viral
173 pneumonia, the capacity of DCs to prime naïve T cells against influenza is deficient due to a
174 delayed infiltration kinetics of DCs into the aged lungs, and a defect of DCs migration from
175 the lung into the draining lymph nodes (Valkenburg et al., 2012; Zhao et al., 2011). DCs also
176 display age-associated defects in their ability to prime CD8+ T cell responses through MHC-I-
177 dependent antigen presentation (Zacca et al., 2015), and inflammasome activation and
178 production of IL-1β (Chen et al., 2020; Stout-Delgado et al., 2012). Immunosenescence of
179 neutrophils, the most abundant innate immune leukocyte, provokes an unregulated
180 production of superoxide, deficient phagocytosis (Chen et al., 2014; Cho and Stout-Delgado,
181 2020; Corberand et al., 1981) and deficient formation of neutrophil extracellular traps (NETs)
182 that correlates with defective bacterial clearance (Brinkmann and Zychlinsky, 2007).
183 Immunosenescence also impacts neutrophil migration to the lung in response to stimuli but
184 these cells tend to accumulate and prolong their stay in this organ (Kahlich et al., 1975).
185 Together, these age-related alterations in neutrophil functions can have devastating
186 consequences, as best exemplified in the current SARS-CoV-2 pneumonia epidemic (Barnes
et al., 2020; Chen et al., 2020). Indeed, not only is the neutrophil accumulation well-documented across mouse and large animals during influenza infection, but COVID-19 patients who succumb, display a two-fold increase in neutrophilia, contributing to the age-enhanced mortality to SARS-CoV-2 infection (Barnes et al., 2020; Liu et al., 2020; D. Wang et al., 2020).

In the adaptive immune system, immunosenescence is best reflected in the T cell compartment, which increases the ratio of CD4+ to CD8+ T cells in the bronchoalveolar fluid, suggesting that the pool of lung resident memory CD4+ T cells also augments as a function of age (Haynes and Swain, 2006; Kovaiou and Grubeck-Loebenstein, 2006). The systemic and local increases in memory T cells are thought to contribute to the T cell-driven asthma in the elderly (Murray and Chotirmall, 2015). In viral-driven pneumonia, immunosenescence causes a decrease in the diversity of the CD8+ T cell compartment and in the global immune response to influenza infection (Zhang et al., 2002). In SARS-CoV-2 pneumonia, the total number of peripheral lymphocytes is reduced, displaying a clear defect in CD8+ T cell abundance, shifting the CD4+ to CD8+ T cell ratio (F. Wang et al., 2020). Beyond alteration in abundance, it appears that the function of CD8+ T cells in COVID-19 patients becomes exhausted (Zhang et al., 2019; Zheng et al., 2020). Immunosenescence also impairs B cell development at all stages, leading to a net reduction of the total numbers and diversity of immature B cells (Holodick and Rothstein, 2015). Consequently, the antibody specificity and antigen affinity are diminished, resulting in poor vaccination efficacy and susceptibility to lung infections in older people (Holodick and Rothstein, 2015). In SARS-CoV-2 pneumonia, the total number of peripheral B lymphocytes is reduced, a phenomenon that is reversed upon treatment (F. Wang et al., 2020). In the context of influenza infection, aged mice exhibit a defect in the cooperation between T follicular and B cells due to low expression of CD40L (Chen et al., 2020; Lefebvre et al., 2016). This is important because B cells require activation signalling through the CD40 receptor (by CD40L expressed in T cells) to undergo affinity maturation, class-switching, and differentiation into plasma cells (Chen et al., 2020; Lefebvre et al., 2016). Immunosenescence also induces B cell-intrinsic effects, such as low expression
215 of the transcription factors paired box 5 (Pax 5) and B-lymphocyte-induced maturation
216 protein 1 (Blimp1), which are crucial for the development and differentiation of these B
217 lymphocytes (Chen et al., 2020; Frasca et al., 2016; Nipper et al., 2018). Not too surprisingly,
218 there is a poor production of influenza-neutralizing antibodies in aged mice, non-human
219 primates and humans (Chen et al., 2020; Frasca et al., 2016; Josset et al., 2012; Toapanta
220 and Ross, 2009). Collectively, immunosenescence affects the humoral immunity in the
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1.3. Microbiota in the ageing lung
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224 The microorganisms populating this tissue have a low density, which appears to be critical
225 for the maintenance of healthy lungs (Mathieu et al., 2018) and these bacteria can exert
226 distinct effect on the pathogenesis of lung diseases such as asthma (Mathieu et al., 2018;
227 Remot et al., 2017). Due to the difficulty to access resident lung microbiota, to date, no study
228 has been performed on lower respiratory tract microbiota in the elderly population and only
229 few studies have compared the composition of the upper respiratory tract microbial
230 ecosystem in the elderly to the one in younger adults (Table 1, (de Steenhuijsen Piters et al.,
231 2016; J.-J. Lee et al., 2019; Stearns et al., 2015; Whelan et al., 2014)). Advanced age
232 decreased the relative abundance of *Corynebacterium* and *Propionibacterium* in the nose
233 and of *Prevotella* in the oropharynx. Importantly, Whelan *et al.* demonstrated that, although
234 the microbiota from the anterior nares is distinct from that of the oropharynx in mid-aged
235 adults, this distinction is abolished in elderly subjects (Stearns et al., 2015), suggesting that
236 ageing in the upper airways is accompanied by a loss in the geodistribution of the microbial
237 ecosystem. Another study by the same group, comparing URT microbiota from children to
238 that of adults, reported similar high inter-individual variability, as was shown in elderly
239 individuals. Therefore, it is possible that the absence of a more stable URT microbiota in
240 these aged groups is related to a higher susceptibility to respiratory infections and other lung
241 diseases, such as asthma as seen in children for whom the prevalence of these diseases is
also increased compared to adults. This is supported by mouse-based studies in which the age altered the recovery from pulmonary infection with *Streptococcus pneumoniae*. Indeed, older mice were less efficient to clear the pathogen and showed an increase in the abundance of OTUs from the *Firmicutes* phylum compared to the younger counterparts. The composition of URT microbiota from older mice also failed to return to their original composition, up to 4 weeks after the infection (Krone et al., 2014; Thevaranjan et al., 2016), suggesting a loss of resilience of their microbiota.

<table><caption>**Table 1: Summary of the results of publications comparing respiratory tract microbiome from elderly to younger adults.** Arrows indicate an increase (↗) or decrease (↘) in relative abundance of the microbiome</caption><thead><tr><th>Study [ref]</th><th>N</th><th>Population</th><th>Age</th><th>Sample origin</th><th>Results</th></tr></thead><tbody><tr><td rowspan="2">Whelan (2014) (Whelan et al., 2014)</td><td>18</td><td>Elderly</td><td>68-96</td><td>Anterior nares and oropharynx</td><td>Elderly vs. mid-aged</td></tr><tr><td>242</td><td>Publicly available data (NIH's Human Microbiome Project)</td><td>18-40</td><td>Anterior nares and throats</td><td>No clustering based sample origin (anterior nares or oropharynx) in elderly<br/>Streptococcus (both locations)<br/>in anterior nares:<br/>Corynebacterium, Propionibacterium, Staphylococcus<br/>Prevotella, Veillonella<br/>in oropharynx:<br/>Prevotella, Lachnospiraceae</td></tr><tr><td rowspan="4">de Steenhuijsen (2016) (de Steenhuijsen Pitters et al., 2016)</td><td>100</td><td>Elderly pneumonia (EP) patients</td><td>75.7</td><td>Oropharynx</td><td>HE vs. YH</td></tr><tr><td>91</td><td>Healthy elderly (HE)</td><td>75.3</td><td></td><td>EP vs. HE<br/>&amp;<br/>YP vs. YH</td></tr><tr><td>27</td><td>Young adult pneumonia (YP) patients</td><td>46.4</td><td></td><td> overall bacterial density<br/> species richness (not in young cohorts)<br/> Shannon diversity indices (not in young cohorts)<br/> Streptococcus (pseudo)pneumoniae, several Streptococcus OTUs, Rothia<br/> Gemellales, Prevotella melaninogenica, Veillonella dispar, Parascardovia and Leptotrichia</td></tr><tr><td>187</td><td>Young healthy adults (YH)</td><td>34.4</td><td></td><td></td></tr><tr><td rowspan="3">Lee (2019) (J.-J. Lee et al., 2019)</td><td>10</td><td>Healthy elderly (HE)</td><td>67.3 ± 3.5</td><td>Nasopharynx</td><td>HE vs. HA</td></tr><tr><td>30</td><td>Asthmatic elderly (AE)</td><td>72.5 ± 5.4</td><td></td><td>AE vs. AA</td></tr><tr><td>10</td><td>Healthy adults (HA)</td><td>25.4 ± 6.2</td><td></td><td>AA vs. HA</td></tr></tbody></table>
<table><tr><td></td><td>30</td><td>Asthmatic adults (AA)</td><td>34.1 ± 7.0</td><td></td><td>AE vs. HE</td><td>No significant relative abundances of phyla</td></tr><tr><td rowspan="2">Lee (2019) (S. Y. Lee et al., 2019)</td><td>24</td><td>Elderly</td><td>63</td><td rowspan="2">Sputum</td><td rowspan="2">Elderly vs. young</td><td>☑ Firmicutes</td></tr><tr><td>24</td><td>Young</td><td>29</td><td>☐ Proteobacteria</td></tr><tr><td colspan="7">Fusobacteria and Leptotrichia associated with arterial stiffness in elderly subjects</td></tr></table>

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## 2. IMPACT OF NUTRITION ON AGEING/SENESCENCE AND ROLE OF THE MICROBIOTA

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Lifestyle and more particularly certain diets/dietary patterns have been associated with changes in Years of Life Lost (YLL) and Years Lost due to Disability (YLD), thus modulating Disability-Adjusted Life Years (DALYs), which represents years of healthy life (GBD 2017 Diet Collaborators, 2019; May et al., 2015; Struijk et al., 2014).

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### 2.1. Nutrition and cellular senescence

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As described above, at the cellular level, the ageing process, called senescence is characterized, among others, by shortening of telomeres and the SASP (Senescence-Associated Secretory Phenotype). One current area of interest is whether diet can influence senescence process. This has now been studied by many groups and reviewed recently (Balan et al., 2018), although no consensus has emerged. Some studies have reported a positive association between a longer telomere length, measured in leukocytes, and certain types of food, including nuts, seaweed, fruits or coffee, whereas consumption of alcohol, and red or processed meat was associated with a shorter leukocyte telomere length (Balan et al., 2018; Lee et al., 2015; Leung et al., 2014; Liu et al., 2016; Pavanello et al., 2011; Tucker, 2018). Consumption of certain diets, foods and nutrients have also been positively or negatively associated SASP in different tissues (Sone and Kagawa, 2005; S.-Y. Wang et al., 2019; Yang et al., 2020). On the other hand, a meta-analysis from 2017 (Pérez et al., 2017), which included 533 participants under 9 different diets in 5 randomized controlled trials, showed that there was no effect of diet on telomere length. However, there was a high heterogeneity in the types, length of studies and in the dietary interventions, which might
have affected the conclusion of this meta-analysis. One of the hypotheses that could explain how diet impacts senescence process is through the regulation of ROS production and oxidative stress coming from endogenous and exogenous sources. Indeed, it is known, for example, that unhealthy diets, such as high fat diets, can induce an increase in ROS production in certain tissues (Matsuzawa-Nagata et al., 2008; Vial et al., 2011). Of interest, a healthy diet with reduced calorie intake (calorie restriction diet – CR), reduced mitochondrial activity and ROS production, and this has shown some promising results in certain studies. In animals, CR diet delayed the onset on some ageing-associated diseases such as diabetes (Cheng et al., 2017; Colman et al., 2009), cardiovascular diseases (Colman et al., 2009) or cancer (Weindruch et al., 1986), and it even prolonged life in non-human primates (Colman et al., 2014, 2009), although it did not appear to affect telomere length (Smith et al., 2011). In humans, while such studies are difficult to implement, similar health benefits have been reported in certain population, such as the Okinawan adult population. This population eats an average of 17% less calorie-intake compared to that of the rest of Japan, and has a higher rate of centenarian people and a lower mortality due to cardiovascular diseases, cancer and other diseases around the globe (Kagawa, 1978; Suzuki et al., 2001). The CALERIE 1 & 2 studies have also demonstrated the beneficial effect of a CR diet on general health and the prevention of ageing associated diseases (Most et al., 2018; Redman et al., 2018; Weiss et al., 2006). Interestingly, intermittent fasting has also been shown to reduce insulin resistance and cholesterol levels in humans, suggesting that this type of diet could also be beneficial against the development of ageing associated pathologies by modulating oxidative stress associated with ageing (Harvie et al., 2013, 2011; Klempel et al., 2012; Stekovic et al., 2019; Varady et al., 2015).

## 2.2. Involvement of the microbiota in the effect of nutrition on ageing processes

It is now widely accepted that the composition and function of the gut microbiota are clearly influenced by dietary intake and can be modulated by specific diets (e.g., meat, vegetarians, rich in fiber) and the type of food matrices, which includes both the composition and
interactions between the constituents (Aguilera, 2019; David et al., 2014; Derrien and Veiga, 2017; Duncan et al., 2007; Ley et al., 2006; Muegge et al., 2011; Walker et al., 2011; Wu et al., 2011). Consequently, the effect of particular diets on molecular and cellular processes involved in ageing could be mediated by the modulation of microbiota.

### 2.2.1. Impact of nutrition on microbiota

Our diet feeds the microbiota by supplying substrates for microorganisms, especially non-digestible sugars, known as prebiotics (Gibson et al., 2017). Food is also a source of microorganisms, seeding our ecosystems in the gut and the lung. The overall microbial biomass ingested per day has been estimated around $10^{10}$ (Derrien and van Hylckama Vlieg, 2015), ranging from $10^9$ to $10^{12}$ in function of the diet considered. In addition to fermented foods, that are especially rich in microorganisms, it is important to realize that raw food we ingest (e.g., fruits, vegetables) also contains their own microbial communities that could impact the composition and functionality of gut microbiota. Thus, modifying the diet for elderly people also impacts the microorganisms they ingest. Since the early 2010's, it is known that these food microorganisms survive through the GI tract and associate, at least temporarily, with the resident gut microbiota (David et al., 2014; Walker et al., 2011), although whether they "durably" colonize the digestive tract remains uncertain (McNulty et al., 2011).

Distinct types of food, such as non-digestible starch, and particular diets like the Mediterranean diet, affect the microbiota composition in a specific manner. It has been extensively reviewed in recent years (Barber et al., 2020; Burr et al., 2020; Dogra et al., 2020; Fassarella et al., 2020; Kolodziejczyk et al., 2019; Vandeputte and Joossens, 2020). Although there exists a very high inter-individual variability, due to host and microbe own characteristics, the microbiota appears as a strong malleable therapeutic target that can be reshaped using specific diets. For instance, a high-fat and low-fibre diet in mice decreased microbiota composition in *Bacteroidetes* and increased *Firmicutes* and *Proteobacteria* (Hildebrandt et al., 2009). The consumption of poly-unsaturated fatty acids increased
bacteria, such as *Bifidobacterium*, *Lachnospira*, *Roseburia* and *Lactobacillus*, in humans (Watson et al., 2018). Of interest for the ageing population as they often show protein deficiency, the source of this nutrient also affects the microbiota composition (Zhu et al., 2015). Soybean and peanut proteins induced modulation of the abundance of beneficial bacteria in the gut; a diet enriched with 20% peanut protein increased *Bifidobacteria*, and reduced *Enterobacteria* and *Clostridium perfringens* in rats (Peng et al., 2015). On the other hand, animal derived proteins induced a *Bacteroides* enterotype (Wu et al., 2011). Gut bacteria can convert L-carnitine and phosphatidylcholine, which are present in red meats, into trimethylamine N-oxide (TMAO), which is associated with the development of cardiovascular diseases, linking, here as well, the impact of diet on microbiota and the host physiology. Strikingly, a recent study showed that in older individuals, consumption of Mediterranean diet was associated with specific changes in microbiota composition and function; adherence to this diet was associated with a lower decline in microbiota diversity, an increase in taxa negatively associated with inflammation and positively associated with SCFA production (Ghosh et al., 2020).

In addition to diet composition, food supplements or additives also impact gut microbiota composition. In recent years, studies have investigated the effect of probiotics - ingested as food supplements - or fermented foods, which both have a high microbial load, on the survival of these microorganisms their residence time in the host's digestive environment and their direct impact on the microbiota. Although fermented foods have shown to beneficially impact human health (Marco et al., 2017; Tamang et al., 2016), a detectable modification of the intestinal microbiota was not consistently observed in these studies, and it is therefore important to dissociate the direct effects of food microorganisms and associated bioactive compounds from those linked to the matrix itself. A recent study from Taylor *et al.* showed that, in stool samples from over 6000 individuals, there was a small significant change in beta diversity as well as differential taxa between people consuming fermented foods and non-consumers (Taylor et al., 2020). Finally, in one of the first reports on fermented foods effects on microbiota, McNulty *et al.* demonstrated the impact of these foods on the intestinal
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physiology of an individual without necessarily modification of the composition of their
microbiota (McNulty et al., 2011). Even though microbial food ecosystems might have very
little influence on the diversity, composition and stability of the gut microbiota, they are
thought to impact the host physiology.

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Whether food, via substrates or microorganisms, is able to modify the lung microbiota is not
known so far. A main trend of changes observed in gut microbiota in elderly populations is a
decreasing abundance of beneficial microbes, like *Lactobacillus* and *Bifidobacterium*.

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Therefore, we assume that a diet enriched with these microorganisms or promoting their
growth should be beneficial to counter-balance the loss. A better knowledge of the evolution
of lung microbiota with age would help to define nutritional enrichment by specific microbes
to preserve the lung microbiota.

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2.2.2. Impact of microbiota on cellular senescence

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As food modulates microbiota composition and function as well as molecular ageing
processes, it is believed that one of the possible mechanisms of action of diets on ageing
processes is through their action on microbiota, particularly the gut microbial ecosystem. This
can occur through the metabolites they secrete or their interactions with the immune system
and the epithelial barriers. Indeed, it has been shown that metabolites and secreted products
from the microbiota are able to affect cellular senescence, either promoting or reducing it. In
a healthy context, senescence can be detrimental, whereas in a carcinogenic context, for
example, the induction of senescence can eliminate cancerous cells. For example, colibactin,
a genotoxin from *E. coli*, has been shown to induce senescence, thus promoting colon tumor
growth (Dalmasso et al., 2014). Other metabolites such as Cdtb (Cytolethal distending toxin
subunit B) of *Helicobacter hepaticus*, Trimethylamine-N-oxide or Urolithin A can also induce
senescence, although mechanisms of action vary from one metabolite to another (Giménez-
Bastida et al., 2020; Ke et al., 2018; Péré-Védrenne et al., 2017). In the case of Urolithin A, it
is of interest to note that the induction of senescence actually served to prevent irreversible,
cell cycle progression of colon cancer cells. On the other hand, and of particular interest in
the search for molecules promoting healthy ageing, certain bacterial metabolites can also reduce or prevent senescent process. This is the case of secreted products from *Lactobacillus fermentum*, for example, which protects the 3T3-L1 preadipocytes *in vitro* against oxidative stress-induced senescence by inhibiting the mTOR pathway (Kumar et al., 2019). Although the responsible molecules have not been identified in this case, this study provided a *proof-of-concept* that metabolites from probiotics may possess anti-ageing properties. Depending on the diet and type of food intake, gut microorganisms can also produce a family of metabolites termed short-chain fatty acids (SCFA). These are end products of bacterial fermentation that happens in the gut and play important roles at local and distant sites. In 2012, O'Callaghan *et al.* showed that a red meat rich diet was linked to a decreased telomere length in rat colonic cells and could be prevented by adding resistant starch to the diet. Interestingly, they found an association between the absolute telomere length and the caecal levels of two SCFAs, acetate and propionate (O'Callaghan et al., 2012).

It is now well established that the gut microbiome plays an important role in the development and maturation of the immune system throughout life. In healthy individuals, commensal bacteria rarely cross the physical barrier constituted by the epithelial cells and the mucus layer. However, when this happens, bacteria are rapidly killed by macrophages. Others can survive inside DCs but these cells only go as far as the mesenteric lymph nodes, restricting the bacterial challenge to the mucosal immune system (Macpherson and Uhr, 2004). As the epithelium becomes leaky with age, it is inferred that more commensals or bacterial components can cross that barrier and may induce aberrant immune responses (Man et al., 2014; Thevaranjan et al., 2017). The immune system may then react against native microflora as well as inappropriately control invading pathogens. Additionally, the decline in gut microbiota diversity, observed in older individuals, may also impact the immune system at the local and systemic levels. This could be due, at least partly, to the reduction in growth control of distinct groups of potentially pathogenic bacteria. Together, this may participate in
410 the establishment of the low-grade inflammation observed in ageing individuals (Rehman,
411 2012), as well as the onset of age-related illnesses.

412 Taken together, these studies show that diets modulate molecular mechanisms involved in
413 ageing through their actions on gut microbiota. Thus, in older people, nutrition represents a
414 mean of action to maintain a balanced gut microbiota that will positively impact senescence
415 and ageing, at the local and systemic levels.

416

417 3. THE GUT-LUNG AXIS AND AGEING LUNGS

418 In the literature, the first papers supporting the existence of an intestine-lung axis, trace back
419 to the early 1990's and referred to the occurrence of ARDS (Acute respiratory distress
420 syndrome) following septic shock and translocation of bacterial products from the lumen of
421 the intestine to the blood stream (Pugin and Chevrolet, 1991). It was actually mainly known
422 as the gut-liver-lung axis as the ARDS was caused by degranulation of neutrophils that was
423 triggered by inflammatory factors secreted by the liver (Pugin and Chevrolet, 1991). Using a
424 bone marrow transplantation mouse model, Cooke et al. later proposed that controlling gut
425 toxicity and specifically the translocation of lipopolysaccharide (LPS) across the intestinal
426 epithelium could reduce idiopathic pneumonia syndrome, demonstrating the existence of a
427 gut-lung axis of inflammation (Cooke et al., 2000). It is now known that certain acute and
428 chronic lung diseases are associated with dysbiotic microbial communities in the lung and
429 gut, and with gut symptoms or disorders. This relationship is bi-directional and, although
430 evidence for the lung-gut axis is not as abundant as data on the gut-lung axis, it is now well
431 established that chronic and acute lung disease induce changes in the gut microbiology and
432 physiology. One of the striking recent evidence supporting this is the presence of
433 gastrointestinal symptoms in 10 to 18 % of patients infected by the SARS-CoV-2, according
434 to the most recent meta-analyses (Trottein and Sokol, 2020), for which, although all age
435 groups can contract the virus, older people (60+) are at increased risk of developing severe
436 illness. Here, we present the physiological similarities between the two tissues, and the
437

anatomical features enabling the gut-lung axis, and review the evidence of the reciprocal
regulation of the microbial ecosystems and epithelial physiology between the airways and the
gastrointestinal (GI) tract.

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3.1. *The anatomical continuum between the lungs and gut is more permissive to exchanges in the elderly*

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In the gut and lungs, the epithelium serves a crucial role of barrier that is at the same time,
physical, chemical and physiological. Interestingly, the permeability of both the lung and gut
epithelia is increased in aged individuals or ageing animal models (César Machado and da
Silva, 2016; Parrish, 2017; Tankersley et al., 2003), suggesting an impaired barrier function
of these tissues with old age. These structures are in permanent contact with exogenous
particles and microorganisms with a potential for pathogenicity and by regulating their
permeability through their tight junctions; they allow selective transfer of materials across this
physical barrier. They also take part in the innate immune response to pathogens, acting as
a chemical barrier, by secreting soluble factors that will either have antimicrobial activity
(direct response) or signal to the immune system their presence, and thus trigger the
appropriate innate and adaptive immune responses. Both epithelial structures are also able
to tightly regulate ion and fluid transport via the expression of many ion channels and
transporters common to both organs, which are of particular importance in the regulation of
the composition and pH of the luminal environment in which the microbiota live. These
barriers become ‘leakier’ with age, but up to now there is no evidence this is a cause or
consequence of microbiota dysbiosis. However, it is plausible that an impaired epithelial
barrier would allow for less stringent regulation of the trans-epithelial transport of microbes
and microbial metabolites, and therefore an enhanced and unfiltered communication along
the gut-lung axis that would lead to a loss in compartmentalisation of the microbiota.

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Moreover, microbiota from the gut, the nose and throat, have recently been shown to
develop in a coordinated way during the first year of life (Grier et al., 2018). Both the GI and

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464 respiratory tracts share a common entry point for microorganisms – the oral cavity. In this
465 organ, the microbiota has been shown to share significant overlaps with both the gut and
466 lung ecosystems (Bassis et al., 2015; Segata et al., 2012), and it is able to modulate
467 inflammation in bronchial cells *in vitro* (Mathieu et al., 2020). A study from the Human
468 Microbiome Project revealed a 45 % overlap between the microbiota from the oral cavity and
469 stool samples (Segata et al., 2012). Interestingly, Bassis *et al.* demonstrated that, using
470 redundancy analysis of the microbiota from the mouth, nose and broncho-alveolar lavage
471 (BALs), the microbial community from the BALs were closer to that of the mouth instead of
472 that found in the nose, although the indices of intra-subject similarity ranged from dissimilar
473 to highly dissimilar. When looking at bacterial Operational Taxonomic Units (OTUs), the
474 bacterial communities of the lung showed a significant overlap with the ones from the mouth,
475 but they differed considerably from those found in the nose (Bassis et al., 2015). Therefore,
476 this establishes an anatomical continuum for microorganisms from the mouth to colonize
477 both the respiratory and GI tracts (Figure 3). Microorganisms from the mouth migrate to the
478 GI tract by swallowing, whereas they colonize the lungs through micro-aspirations and
479 inhalation of micro-aerosols. The elimination of microorganisms from the lungs occurs *via* the
480 mucociliary escalator, in which the coordinated movement of the cilia together with the
481 secretion of mucus, ion and water, allows to move the mucus up towards the pharynx, where
482 it will be swallowed or expectorated. By contrast, microbes present in the stomach may move
483 back to the mouth *via* the oesophagus in cases of gastroesophageal reflux and be inhaled in
484 the lungs. This is supported by the fact that the composition of the lung microbiome more
485 closely resembles that of the oropharynx than the nasopharynx (Bassis et al., 2015; Dickson
486 and Huffnagle, 2015). Additionally, a study by Rosen *et al.* showed that the concentration of
487 some bacteria in the lung was correlated with full-column non-acid reflux burden in patients
488 receiving acid-suppression therapy, supporting the fact that gastric microbiota can alter lung
489 microbiota (Duvallet et al., 2019; Rosen et al., 2014). The prevalence of gastroesophageal
490 reflux disease increases with age (Poh et al., 2010; Zhu et al., 1993), suggesting that transfer
491 of microbiota from the stomach to the lungs might happen more easily in older individuals,
492 providing here as well, an enhanced and unchecked communication pathway between the gut and the lung. Moreover, some studies have shown that the coordinated response to 493 certain stresses or pathogens in the lungs and the gut are mediated through the modulation 494 of the immune system and the transport, in the blood, of bacterial metabolites (Figure 3). 495

496 3.2. From the lungs to the gut – impact of lung infections on gut health

497 Although it is difficult to establish a causal link between certain lung diseases and a dysbiotic 498 gut microbiota in humans, animal models have strongly contributed to this field in recent 499 years. The pioneering work from Sze et al. demonstrated that, in mice, acute lung injury 500 induced by LPS caused an increase in bacterial load in the blood and caecum, whereas lung 501 total 16S was slightly reduced in BALs and changes in abundance of certain bacterial 502 species occurred (Sze et al., 2014). Another model of lung injury in mice, induced by 503 cigarette smoke, further detailed the impact of acute exposure to stress on gut inflammation, 504 and it identified the Th17-dependent pathway as a main player in the communication 505 between the two tissues (Kim et al., 2019). In this study, mice were exposed to cigarette 506 smoke and then to an intestinal inflammatory challenge (2 % DSS in drinking water for 6 507 days). DSS-induced weight loss was more pronounced in mice exposed to cigarette smoke, 508 and this was accompanied by increased histological damage and immune cell infiltration at 509 the intestine level (Kim et al., 2019). This study did not report on the composition of the lung 510 and gut microbiota. However, it is possible that cigarette smoke-induced changes in the lung 511 microbial community that drove the local and systemic immune responses.

512 Of interest, especially in elderly people, is the impact of respiratory infections on gut 513 microbial and physiological homeostasis. As previously mentioned, older people are at 514 higher risk of complications when infected by certain respiratory viruses or bacteria (see 515 chapter 2). To date, no study has specifically reported the effect of respiratory bacterial or 516 viral infections on the gut microbiota in older human populations. However, studies in 517 younger human populations and in mouse models have provided accumulating evidence
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supporting a central role for acute infections in modulating gut microbiota and impacting its

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homeostasis (Table 2).

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<caption>**Table 2: Impact of respiratory pathogens on gut microbiota, mechanisms of action and consequences.**</caption>

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Arrows indicate an increase (↗) or decrease (↘) in relative abundance of the microbiome

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<table><thead><tr><th>Study [ref]</th><th>Animal / Microbiota Analysis method</th><th>Infectious agent</th><th>Effect on gut microbiota</th><th>Mode of Action and consequences</th></tr></thead><tbody><tr><td colspan="5">Viruses</td></tr><tr><td>Wang (2014)<br>(Wang et al., 2014)</td><td>Mouse /<br>Real-time PCR and selective culture</td><td>Influenza A/PR/8/34 (PR8), 0.1 HA of PR8, intranasally</td><td>No change in number of total bacteria<br>↘ Segmented filamentous bacteria (SFB)<br>↘ Lactobacillus/Lactococcus<br>↗ Enterobacteriaceae (E. coli)</td><td>Lung-derived CD4<sup>+</sup> T cells -> IFN-γ<br>CCL25-CCR9 axis: recruitment of CCR9<sup>+</sup>CD4<sup>+</sup> cells to the intestine -> gut microbiota dysbiosis</td></tr><tr><td>Qin (2015) (Qin et al., 2015)</td><td>Human /<br>Illumina TruSeq</td><td>H7N9</td><td>↗ Proteobacteria<br>↘ Eubacterium, Ruminococcus, Bifidobacterium and Roseburia<br>↗ Escherichia, Salmonella, Enterococcus, Veillonella</td><td>N/A</td></tr><tr><td>Yu (2015) (Yu et al., 2015)</td><td>Mouse /<br>Bacterial colony plate counts</td><td>Influenza A/FM1/1/47 20% Lethal Dose 50 intranasally</td><td>↘ E. coli<br>↘ Anaerobic bacteria<br>↗ Bifidobacterium and Lactobacillus</td><td>N/A</td></tr><tr><td>Deriu (2016)<br>(Deriu et al., 2016)</td><td>Mouse /<br>MiSeq Illumina</td><td>Influenza A /Puerto Rico/8/34 (PR8) – 200 PFU – intra-tracheal</td><td>↗ Proteobacteria<br>↗ Escherichia</td><td>↗ IFN-Is (Ifnar1<sup>-/-</sup>) mice<br>IAV leads to enhanced susceptibility to secondary enteric infections</td></tr><tr><td>Bartley (2017)<br>(Bartley et al., 2017)</td><td>Mouse /<br>MiSeq Illumina</td><td>Influenza virus A/PR/8/34 (PR8), 400 EID50 intranasally</td><td>↗ Proteobacteria<br>↗ Verrucomicrobia</td><td>N/A</td></tr><tr><td>Groves (2018)<br>(Groves et al., 2018)</td><td>Mouse /<br>MiSeq Illumina</td><td>RSV-A2, 2 × 10<sup>5</sup> PFU/ml</td><td>No change in total fecal bacterial load, total observed OTU, alpha diversity<br>↗ Bacteroidetes (Bacteroidaceae)<br>↘ Firmicutes (Lachnospiraceae, Lactobacillaceae)</td><td>↗ in MUC5AC provides a source of energy to Bacteroidetes</td></tr><tr><td>Yildiz (2018)<br>(Yildiz et al., 2018)</td><td>Mouse /<br>MiSeq Illumina</td><td>Influenza A/Eng/195/2009, 4 × 10<sup>4</sup> PFU/ml</td><td>↗ Bacteroidetes (Porphyromonadaceae)<br>↘ Firmicutes</td><td>N/A<br>IAV leads to enhanced susceptibility to secondary enteric infections</td></tr></tbody></table>
<table><tr><td>2018)</td><td>MiSeq Illumina</td><td>intranasal</td><td>▷ Firmicutes in small intestine at 7dpi<br>▷ Bacteroidetes in small intestine at 7dpi<br>No change in fecal bacteria</td><td>infections</td></tr><tr><td>Sencio (2020)<br>(Sencio et al., 2020)</td><td>Mouse (C57BL/6J) /<br>• MiSeq Illumina</td><td>• Influenza H3N2 IAV<br>Scotland/20/197 4, 30 pfu, intranasally<br>• Influenza H1N1 WSN/1933, 200 pfu, intranasally<br>• Influenza H1N1 California/04/2009, (pdm09), 100 pfu intranasally</td><td>▷ Verrucomicrobia (Akkermansia), Cyanobacteria<br>▷ Parabacteroidetes and Odoribacter<br>▷ Bacteroidales S24-7<br>▷ Clostridiales (unaffiliated), Ruminococcaceae, and Mogibacteriaceae<br>▷ Lachnospiraceae family, Dehalobacterium and Lactobacillus genera<br>▷ Alphaproteobacteria Gammaproteobacteria (Escherichia genus)<br>▷ Betaproteobacteria (Sutterella genus)</td><td>IAV infection leads to decreased food intake, less production of Short chain fatty acids, particularly acetate</td></tr><tr><td colspan="5">Bacteria</td></tr><tr><td colspan="5">Mycobacterium tuberculosis</td></tr><tr><td>Winglee (2014)<br>(Winglee et al., 2014)</td><td>Mouse (Balb/c) /<br>454 FLX pyro-sequencing</td><td>Mycobacterium tuberculosis<br>CDC1551 or H37Rv., aerosol (Middlebrook inhalation exposure system)</td><td>▷ Diversity<br>▷ Bacteroidetes<br>▷ Actinobacteria<br>▷ Lactobacillus<br>▷ Lachnospiraceae<br>▷ Ruminococcaceae</td><td>N/A</td></tr><tr><td>Luo (2017)<br>(Luo et al., 2017)</td><td>Human (adults) /<br>MiSeq Illumina</td><td></td><td>▷ Bacteroidetes<br>▷ Proteobacteria (Escherichia), Actinobacteria (Collinsella)<br>▷ Prevotella, Lachnospira, Roseburia, Coprococcu (Firmicutes)</td><td>N/A</td></tr><tr><td>Hu (2019)<br>(Yongfei Hu et al., 2019)</td><td>Human (adults) /<br>HiSeq 2500 Illumina</td><td>Mycobacterium tuberculosis</td><td>▷ Alpha-diversity<br>▷ Coprobacillus bacterium and Clostridium bolteae<br>▷ Haemophilus parainfluenzae, Roseburia inulinivorans, Eubacterium eligens, Roseburia hominis, Roseburia intestinalis, Megamonas unclassified, Eubacterium rectale, Ruminococcus obeum, Dora formicigenerans, Coprococcus sp_ART55/1, Megamonas funiformis, Sutterella wadsworthensis, Bifidobacterium adolescensis, Megamonas hypermegale, Collinsella aerofaciens, Bifidobacterium longum, Akkermancia muciniphila, Megamonas rupellensis, Coprococcus comes, Lachnospiraceae bacterium</td><td>N/A</td></tr></table>
<table><tr><td></td><td></td><td></td><td>1_157FAA, Ruminococcus lactaris, Bifidobacterium pseudocatenulatum, Dorea longicatena</td><td></td></tr><tr><td>Hu (2019) (Yongfeng Hu et al., 2019)</td><td>Human (adults) / HiSeq 2500 Illumina</td><td>Mycobacterium tuberculosis</td><td>No significant difference</td><td>N/A</td></tr><tr><td>Huang (2019) (Huang et al., 2019)</td><td>Human (adults) / MiSeq Illumina</td><td>Mycobacterium tuberculosis</td><td>☞ Bacteroidetes<br/>☞ Bifidobacteriaceae</td><td>Correlation between gut F/B ratio blood IL-1β</td></tr><tr><td>Li (2019) (Li et al., 2019)</td><td>Human (children) / MiSeq Illumina</td><td>Mycobacterium tuberculosis</td><td>☞ Diversity (Simpson index)<br/>☞ Enterococcaceae, Prevotellaceae<br/>☞ Rikenellaceae, Bifidobacteriaceae, Lachnospiraceae, Ruminococcaceae,<br/>☞ Enterococcus, Prevotella<br/>☞ Faecalibacterium, Bacteroides Ruminococcus, Dorea</td><td>N/A</td></tr><tr><td>Namasivayam (2019) (Namasivayam et al., 2018)</td><td>Rhesus macaques / Illumina NextSeq (V4 region)</td><td>Mycobacterium tuberculosis Erdman strain, &lt;10 CFU, intrabronchial instillation</td><td>Minor changes<br/>Severe diseases associated with:<br/>☞ Roseburia intestinalis (family Lachnospiraceae), Succinivibrio dextrinosolvens, certain Ruminococcaceae, and Weissella (family Leuconostocaceae)<br/>☞ Streptococcus equinus (family Streptococcaceae)</td><td>N/A</td></tr><tr><td>Streptococcus pneumoniae</td><td></td><td></td><td></td><td></td></tr><tr><td>Dabrowski (2019) (Dabrowski et al., 2019)</td><td>Mouse (BALB/c) / MiSeq Illumina</td><td>Streptococcus pneumonia, NCTC 7978, 10<sup>5</sup> cfu</td><td>☞ Lachnospiraceae, Ruminococcaceae<br/>☞ Bacteroidales S24-7, Lactobacillaceae, Coriobacteriaceae</td><td>N/A</td></tr><tr><td>Fungi</td><td></td><td></td><td></td><td></td></tr><tr><td>Samuelson (2016) (Samuelson et al., 2016)</td><td>Mouse (C57BL/6j) / MiSeq Illumina</td><td>Pneumocystis murina (2 &times; 10<sup>6</sup> cysts/mL (intratracheal))</td><td>☞ α-diversity<br/>☞ Lactobacillus, Ruminococcus bromii<br/>☞ Turicibacter, Lachnospiraceae<br/>Oscillospira,</td><td>N/A</td></tr></table>

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Of note, respiratory pathogens, however diverse they are, trigger common shifts in microbiota composition; species from the *Firmicute* phylum and *Clostridiales* order, including *Lachnospiraceae*, *Faecalibacterium* and *Ruminococcus*, are generally decreased as are *Bifidobacteria* from the *Actinobacteria* phylum. By contrast, *Proteobacteria*, especially *E. coli* species are found increased in the gut of individuals or animals infected with respiratory
pathogens. As studies are sparse for certain types of pathogens such as fungi or certain
bacteria commonly responsible for pneumonia in elderly people, it is, at the time of writing,
impossible to identify specific patterns associated with specific types of pathogens.

Most studies that have searched for gut colonization of the respiratory pathogen have not
found any evidence that this occurs, suggesting that there exist other lines of communication
responsible for the dysbiosis observed in the gut. Mechanisms of action involved in
transducing the signal of infection from the lungs to the GI tract are not yet fully understood,
although certain pathways have been identified. For instance, Wang et al. showed that after
Influenza A virus (IAV) infection, lung-derived CD4+ T cells activate the CCL25-CCR9 axis to
induce the recruitment of CCR9+CD4+ T cells to the intestine and thus inducing gut
microbiota dysbiosis. Likewise, a recent study by Liu et al. showed that mast cells might also
be key players in transducing the signal of infection from the lungs to the gut (Liu et al.,
2019).

### 3.3. From the gut to the lungs – Impact of gut microbiota and food intake/diet on lung health

As previously described, respiratory infections can impact the composition and diversity of
gut microbiota either by modulating local immune populations that are then recruited to the
gut, or by inducing anorexia, thus decreasing food intake and nutrient availability.
Interestingly, these changes in microbiota feed back to the respiratory tract and increase the
susceptibility to secondary infections, as in the case of Influenza virus infections (Sencio et
al., 2020). There are now multiple reports supporting the role of intestinal microbiota in the
maintenance of healthy lungs, as well as its responses to respiratory infections and vaccines
(Dumas et al., 2018; Hanada et al., 2018). Many studies have used oral antibiotics
administration in order to investigate the role of gut microbiota in other tissue responses to
various stressors (e.g. infection, inflammation). However, the impact of such treatment on
distal microbiota such as the pulmonary microbiota has rarely been investigated and thus
requires further exploration. For example, early studies demonstrated that antibiotics
treatment increased mortality of animals that were infected with IAV (Abt et al., 2012; Ichinohe et al., 2011) or *S. pneumoniae* (Schuijt et al., 2016). Although the effect of oral antibiotics on lung microbiota cannot be excluded, several studies have reported different means of communication between the gut and the lungs. This communication along this gut-lung axis can be mediated by (i) the immune system, (ii) transfer of microbes, or (iii) microbial and host metabolites in the blood from one tissue to the other. Since the gut microbiota plays a major role in shaping the immune system, it affects both local and systemic (in the lungs) responses to pathogens.

### 3.3.1. Communication via the immune system.

Depleting gut microbiota with antibiotics modulated the degree of the macrophage response to respiratory IAV infection by decreasing the expression of macrophage-associated antiviral response genes in these circulating leukocytes, particularly genes related to IFN-dependent responses (Abt et al., 2012). Schuijt et al. also reported that alveolar macrophages and whole-blood neutrophils displayed a decreased phagocytic activity against *S. pneumoniae*, and a decreased inflammatory profile in response to stimulation with TLR ligands (Schuijt et al., 2016). Interestingly, in the latter study, faecal transfer of a microbiota from healthy animals restored pulmonary bacterial clearance and certain cytokines levels in the lungs (Schuijt et al., 2016). Another study reported the pivotal role of Granulocyte-macrophage colony-stimulating factor (GM-CSF) and IL-17A in the bacterial clearance of *S. pneumoniae* and *Klebsiella pneumoniae*. Both cytokine levels were impacted by oral antibiotics administration and neutralising antibodies increased bacterial burden in non-antibiotic-treated mice. Moreover, by orally or intra-nasally administering a consortium of bacteria that were strong Nod2 activators, it was shown that the restitution of either microbiota could rescue defects in pulmonary clearance of *S. pneumoniae* or *K. pneumonia* (Brown et al., 2017). In the case of viral infections with IAV, Ichinohe et al. demonstrated that antibiotics treatment altered B cells, CD4+ and CD8+ T cells, as well as DC homeostasis; mediastinal lymph nodes DC numbers were reduced and showed an impaired presentation of viral antigen peptide,
making them unable to activate antigen specific CD8+ T cells (Ichinohe et al., 2011). Finally, Gauguet et al. showed that gut microbiota also impacts responses to pulmonary infections by modulating the Th17 cell-mediated immunity. Particularly, they found that the presence of the commensal segmented filamentous bacteria (SFB) in murine GI tract protected against Methicillin-resistant Staphylococcus aureus (MRSA) pneumonia and increased mucosal immunity (specifically type-3 immune effectors) in the lung. This was linked to higher levels of IL-22 and larger numbers of IL-22+TCRβ+ cells in BAL fluids (Gauguet et al., 2015). Taken together, these studies demonstrate that gut microbiota can impact innate and adaptive immunity by allowing the trafficking of immune cells between the gut and the lungs, which further modulate responses to respiratory pathogens. This suggests that this axis of communication, if functional, might play a beneficial role in the fight against pulmonary bacterial and viral infections. We infer that altered microbiota in the ageing gut decreases its protective role.

### 3.3.2. Communication via soluble components and metabolites.

In addition to directly modulating the host immune system, the microbial ecosystems also produce soluble mediators that can be detected by the host. This is the case of SCFA, which have been shown, in several studies, to exert a crucial role in shaping the local (gut) immune system (reviewed in (Parada Venegas et al., 2019)). The three major SCFAs are butyrate, propionate and acetate, and these have been shown to exert positive effect against respiratory tract infections. Specifically, in 2018, Trompette and colleagues showed that upon reaching the bone marrow, butyrate increased the production of a certain subtype of macrophages (Ly6c⁻) that decreased the recruitment of neutrophils in the mouse lungs. In parallel, the SCFA also increased CD8+ T cell effector function, and together these protected the animals against Influenza virus lung damage (Trompette et al., 2018). Interestingly, Haak et al. showed that in patients that had received allogenic hematopoietic stem cell transplantation, a high abundance of butyrate-producing bacteria in faecal samples was associated to a decreased risk of developing viral lower respiratory tract infections (LRTI)
611 (Haak et al., 2018). The effect of butyrate is not specific to viruses as it was effective in 612 increasing survival of mice infected with *K. pneumoniae* (Chakraborty et al., 2017). Acetate 613 protected mice against Respiratory syncytial virus (RSV) infection as observed by a lower 614 weight loss, and a decreased lung viral load and inflammation (Antunes et al., 2019). Galvao 615 *et al.* also demonstrated that acetate, *via* the activation of its receptor, free fatty acid receptor 616 2 (FFAR, also known as GPR43), was protective against *K. pneumoniae* infection also by 617 controlling bacterial load and inflammation levels (Galvão et al., 2018). Finally, the study by 618 Sencio *et al.* also reported that acetate protected against secondary lung infections. This 619 group primarily infected mice with IAV followed by a secondary pulmonary infection with *S.* 620 *pneumoniae*. They found that supplementation with acetate restored IAV-induced impairment 621 of alveolar macrophages bacterial killing activity as well as prolonged mice survival following 622 bacterial infection (Sencio et al., 2020). Taken together, these studies demonstrate the 623 protective function of gut microbial metabolites against respiratory infection.

624 The evidence of this Gut-Lung axis has led to the hypothesis that respiratory infections might 625 be prevented, or at least dampened, by modulating the intestinal microbial ecosystem 626 through changes in food intake or supplementation with pre- and probiotics. Particular diets 627 have been associated, in animal models as well as in humans, with either the exacerbation 628 or the improvement of lung health in acute and chronic diseases. Particularly, fiber-rich diet 629 has been associated with lower risk of developing COPD (Vaughan et al., 2019), improved 630 response to viral infection (Trompette et al., 2018), and decreased severity of allergic airway 631 disease (Trompette et al., 2014). It has been shown that probiotics can impact the course of 632 respiratory diseases. Using a mouse model and the probiotic *Lactobacillus plantarum* 633 CIRM653, Vareille-Delarbre reported a reduced response to intra nasal infection with *K.* 634 *pneumonia* (Vareille-Delarbre et al., 2019). Results from randomised control trials and meta- 635 analyses generally show improvement of lung health following probiotics supplementation, 636 whether it impact the incidence of certain infections, the duration, or the severity of the 637 disease (de Vrese et al., 2006; Hao et al., 2015; Wang et al., 2016).

638
639 **4. DISCUSSION**

640 As described in this review, recent studies have provided evidence for the modulation of
641 respiratory health by diets and/or shifts in microbiota composition and function (Sencio et al.,
642 2020; Trompette et al., 2018, 2014; Vaughan et al., 2019). These studies have mainly been
643 carried out on animal models at a young or adult age. The ageing process is influenced by
644 both intrinsic and external factors. In addition to replicative senescence, events along
645 people's lifespan might have long-lasting impacts on their own physiology, as well as on their
646 microbiota. Repetitive courses of antibiotics, for example, disrupt the gut microbial
647 ecosystem, and we can assume that it is also the case for the lung microbiota. Considering
648 the physiological characteristics of the elderly population, it is now important to investigate
649 the interactions between diet, gut and lung microbiota, and lung health and disease, in
650 models mimicking more closely the physiological changes happening in older human adults.
651 This would involve either aged wild-type animals or genetically modified animal models of
652 accelerated ageing. The *Terc*⁻/⁻ mice, for example, are deficient in the RNA subunit of the
653 telomerase, and have shown a higher susceptibility to bacterial pneumonia (Kang et al.,
654 2018), while the *Klotho*⁻/⁻ mice, which develop premature-ageing syndrome, also develop
655 emphysema (Nakatani et al., 2009). It also appears that the lines of communication between
656 the gut and the lungs might be enhanced by the impairment of the barrier function of both
657 epithelial structures. Establishing models that will mimic these features will allow the study of
658 the impact of the loss of topography of the microbiota in the susceptibility and pathogenesis
659 of pulmonary diseases. Interestingly, a loss of compartmentalisation of the microbiota has
660 been reported in chronically malnourished children (Vonaesch et al., 2018). Extrapolating to
661 elderly individuals, malnutrition could also lead to the loss of topography of the microbiota,
662 exacerbating the communication between the lung and the gut and thus increasing the
663 susceptibility to respiratory diseases. Although mammalian lungs from different species
664 share extensive characteristics, there exist differences, particularly between rodents and
665 humans, which can impact responses to inhaled particles and pathogens. This is particularly
the case for ion channels and transporters that actively participate in the mucociliary escalator to remove particulate matter trapped in the mucus, and are therefore playing a central role in the barrier function of the airway epithelium (Cutting, 2015; Tanner and Beeton, 2018). Consequently, although difficult to implement, it will be crucial to further investigate the impact of diet, probiotics and prebiotics on respiratory health in human older adults. Thus, investigating the regulatory pathways between what we eat and how we breathe, will not only expand the basic knowledge and understanding of the gut-lung axis, but it will also help develop nutritional strategies to prevent the development of respiratory pathologies in the elderly.

Older individuals are often malnourished; dietary needs evolve with age while nutrient intake does not always change appropriately. It is thus critical to optimize nutrient intake and adapt food matrices in order to elaborate personalized diets allowing the maintenance of adequate nutritional health. In addition, as elderly people present dysbiotic microbiota, it appears necessary to provide food supplements that will restore microbial balance (Figure 4). These supplements can be probiotics, prebiotics or synbiotics, a combination of prebiotics with probiotics that improve the survival and implantation of the microorganisms in the GI tract (de Vrese and Schrezenmeir, 2008). It is now essential to confirm the emerging evidence of the impact of specific diets and supplements on respiratory health that suggests that nutrition may be the most accessible lever of action to prevent the development of lung diseases. The potential use of microbiota in clinical applications for preventing lung pathologies in older populations is of particular interest.

It is well known that viral respiratory infections such as influenza, SARS or RSV, can cause serious illness in elderly patients and are often associated with changes in gastro-intestinal homeostasis and gut dysbiosis. Strikingly, older patients infected with SARS-CoV-2 who were hospitalized, frequently presented comorbidities, with hypertension and T2D being amongst the most prevalent ones (Guan et al., 2020; Richardson et al., 2020). These two conditions have also been associated with gut dysbiosis (Gurung et al., 2020; J. Li et al., 2017) and taken together, this points out to a central role of the microbiota in the physiology
694 of the elderly and the pathophysiology and disease course of airway diseases. As clinical
695 studies have shown that probiotics can decrease the duration and severity of symptoms of
696 respiratory viral infections (de Vrese et al., 2006), we argue that developing personalized
697 nutritional plans specifically reinforcing a symbiotic microbiota will help in the fight against
698 respiratory pathogens (Figure 4).

699

700 CONCLUSIONS

701 Older age is associated with dysbiotic gut and lung microbiota along with a loss of resilience
702 and compartmentalisation of microbial species in both tissues. In this review article, we
703 propose the existence of an enhanced bidirectional communication between the gut and the
704 lung, which could link the nutritional status to the susceptibility to respiratory diseases in
705 older individuals. Collectively, the studies presented here highlight a central role for the gut-
706 lung axis and the corresponding local microbiota communities in the maintenance of healthy
707 lungs in older individuals.

708

709 LIST OF ABBREVIATIONS

710 AECII: Alveolar epithelial type II cells

711 AMDC: airway mucosal DC

712 ARDS: acute respiratory distress syndrome

713 ATP: adenosine triphosphate

714 BAL: bronchoalveolar lavage

715 BCR: B cell receptor

716 Blimp: B-lymphocyte-induced maturation protein

717 CAF: cancer-associated fibroblast
718 CAP: Community Acquired Pneumonia

719 COPD: Chronic Obstructive Pulmonary Disease

720 COVID-19: coronavirus disease 2019

721 CR: Calorie restriction

722 Cx43: connexin 43

723 DALY: Disability-Adjusted Life Years

724 DC: Dendritic cell

725 DDR: DNA damage response

726 DKC1: dyskerin 1

727 ECM: extracellular matrix

728 ER: endoplasmic reticulum

729 ERS: European Respiratory Society

730 EV: extracellular vesicles

731 FFAR: Free fatty acid receptor

732 FOXO: forkhead box "O"

733 GATA4: GATA binding protein 4

734 GI: gastrointestinal

735 GM-CSF: Granulocyte-macrophage colony-stimulating factor

736 IAV: influenza A virus

737 IFN: interferon

738 Ig: immunoglobulin
739 IGF-1: insulin-like growth factor 1

740 IIS: insulin and IGF-1 signaling

741 IL: interleukin

742 IPF: Idiopathic Pulmonary Fibrosis

743 IRP2: iron-regulatory protein

744 LPS: lipopolysaccharide

745 LRTI: lower respiratory tract infections

746 MHC: major histocompatibility complex

747 miRNA: microRNA

748 MRSA: Methicillin-resistant Staphylococcus aureus

749 mTOR: mammalian target of rapamycin

750 NET: neutrophil extracellular trap

751 NF-κB: nuclear factor kappa-light-chain-enhancer of activated B cells

752 NO: nitric oxide

753 NSCLC: non-small cell lung cancer

754 OTU: Operational Taxonomic Units

755 Pax: paired box

756 PI3K: phosphoinositide 3-kinase

757 PINK1: PTEN-induced putative kinase I

758 PTEN: phosphatase and tensin homolog

759 ROS: reactive oxygen species
760 RSV: Respiratory syncytial virus

761 SAMP: senescence-accelerated prone

762 SAMR: senescence-accelerated resistant

763 SARS-CoV-2: severe acute respiratory syndrome coronavirus 2

764 SASP: senescence-associated secretory phenotype

765 SCFA: short-chain fatty acids

766 SFB: segmented filamentous bacteria

767 SP: surfactant protein

768 T2D: Type 2 Diabetes

769 Tc: cytotoxic effector T cell

770 TCR: T cell receptor

771 TGF: Transforming growth factor

772 TLR: toll-like receptor

773 TNM: tumor, node, metastasis

774 Treg: regulatory T cell

775 UPR: unfolded protein response

776 URT: upper respiratory tract

777 WHO: World Health Organization

778 YDL: Years Lost to Disability

779 YLL: Years of Life Lost

780
781 DECLARATIONS

782 Declaration of Competing Interests

783 None of the authors of this paper have a financial or personal relationship with people or
784 organizations that could inappropriately influence or bias the content of the paper.

785 Funding

786 This work was supported by two grants from the Agence Nationale de la Recherche, [grant
787 numbers ANR-15-CE15-0012 (MMI-TB) to G. L-V and ANR-18-CE14-0011-03 (SevAsthma
788 children) to M.T].

789 CRediT authorship contribution statement

790 Vinciane Saint-Criq: Conceptualization, Writing - original draft, Writing - review & editing;

791 **Geanncarlo Lugo-Villarino:** Writing - original draft, Writing - review & editing, Funding acquisition; **Muriel Thomas:** Conceptualization, Writing - review & editing, Funding acquisition. All co-authors actively contributed to the critical discussions. All co-authors read and approved the final manuscript.

795 Acknowledgements

796 The authors thank Dr. M.A. Gray for his critical reading of the manuscript.

797

798 REFERENCES

799 Abt, M.C., Osborne, L.C., Monticelli, L.A., Doering, T.A., Alenghat, T., Sonnenberg,
800 G.F., Paley, M.A., Antenus, M., Williams, K.L., Erikson, J., Wherry, E.J., Artis, D.,
801 2012. Commensal bacteria calibrate the activation threshold of innate antiviral
802 immunity. Immunity 37, 158–170. https://doi.org/10.1016/j.immuni.2012.04.011

803 Agrawal, A., Agrawal, S., Cao, J.-N., Su, H., Osann, K., Gupta, S., 2007. Altered
804 innate immune functioning of dendritic cells in elderly humans: a role of
805 phosphoinositide 3-kinase-signaling pathway. J. Immunol. 178, 6912–6922.
806 https://doi.org/10.4049/jimmunol.178.11.6912

807 Agrawal, A., Gupta, S., 2011. Impact of aging on dendritic cell functions in humans.
808 Ageing Res. Rev. 10, 336–345. https://doi.org/10.1016/j.arr.2010.06.004

809 Aguilera, J.M., 2019. The food matrix: implications in processing, nutrition and health.

810 Crit Rev Food Sci Nutr 59, 3612–3629.

811 https://doi.org/10.1080/10408398.2018.1502743

812 Aiello, A., Farzaneh, F., Candore, G., Caruso, C., Davinelli, S., Gambino, C.M.,

813 Ligotti, M.E., Zareian, N., Accardi, G., 2019. Immunosenescence and Its Hallmarks:

814 How to Oppose Aging Strategically? A Review of Potential Options for Therapeutic

815 Intervention. Front Immunol 10, 2247. https://doi.org/10.3389/fimmu.2019.02247

816 Akgün, K.M., Crothers, K., Pisani, M., 2012. Epidemiology and management of

817 common pulmonary diseases in older persons. J. Gerontol. A Biol. Sci. Med. Sci. 67,

818 276–291. https://doi.org/10.1093/gerona/glr251

819 Al-Alawi, M., Hassan, T., Chotirmall, S.H., 2014. Advances in the diagnosis and

820 management of asthma in older adults. Am. J. Med. 127, 370–378.

821 https://doi.org/10.1016/j.amjmed.2013.12.013

822 Antunes, K.H., Fachi, J.L., de Paula, R., da Silva, E.F., Pral, L.P., Dos Santos, A.Á.,

823 Dias, G.B.M., Vargas, J.E., Puga, R., Mayer, F.Q., Maito, F., Zárate-Bladés, C.R.,

824 Ajami, N.J., Sant'Ana, M.R., Candreva, T., Rodrigues, H.G., Schmiele, M., Silva

825 Clerici, M.T.P., Proença-Modena, J.L., Vieira, A.T., Mackay, C.R., Mansur, D.,

826 Caballero, M.T., Marzec, J., Li, J., Wang, X., Bell, D., Polack, F.P., Kleeberger, S.R.,

827 Stein, R.T., Vinolo, M.A.R., de Souza, A.P.D., 2019. Microbiota-derived acetate

828 protects against respiratory syncytial virus infection through a GPR43-type 1

829 interferon response. Nat Commun 10, 3273. https://doi.org/10.1038/s41467-019-

830 11152-6

831 Arnardottir, H.H., Dalli, J., Colas, R.A., Shinohara, M., Serhan, C.N., 2014. Aging

832 delays resolution of acute inflammation in mice: reprogramming the host response

833 with novel nano-proresolving medicines. J. Immunol. 193, 4235–4244.

834 https://doi.org/10.4049/jimmunol.1401313

835 Balan, E., Decottignies, A., Deldicque, L., 2018. Physical Activity and Nutrition: Two

836 Promising Strategies for Telomere Maintenance? Nutrients 10.

837 https://doi.org/10.3390/nu10121942

838 Barber, T.M., Kabisch, S., Pfeiffer, A.F.H., Weickert, M.O., 2020. The Health Benefits
839 of Dietary Fibre. Nutrients 12. https://doi.org/10.3390/nu12103209

840 Barnes, B.J., Adrover, J.M., Baxter-Stoltzfus, A., Borczuk, A., Cools-Lartigue, J.,

841 Crawford, J.M., Daßler-Plenker, J., Guerci, P., Huynh, C., Knight, J.S., Loda, M.,

842 Looney, M.R., McAllister, F., Rayes, R., Renaud, S., Rousseau, S., Salvatore, S.,

843 Schwartz, R.E., Spicer, J.D., Yost, C.C., Weber, A., Zuo, Y., Egeblad, M., 2020.

844 Targeting potential drivers of COVID-19: Neutrophil extracellular traps. J. Exp. Med.

845 217. https://doi.org/10.1084/jem.20200652

846 Bartley, J.M., Zhou, X., Kuchel, G.A., Weinstock, G.M., Haynes, L., 2017. Impact of

847 Age, Caloric Restriction, and Influenza Infection on Mouse Gut Microbiome: An

848 Exploratory Study of the Role of Age-Related Microbiome Changes on Influenza

849 Responses. Front Immunol 8, 1164. https://doi.org/10.3389/fimmu.2017.01164

850 Bassis, C.M., Erb-Downward, J.R., Dickson, R.P., Freeman, C.M., Schmidt, T.M.,

851 Young, V.B., Beck, J.M., Curtis, J.L., Huffnagle, G.B., 2015. Analysis of the upper

852 respiratory tract microbiotas as the source of the lung and gastric microbiotas in

853 healthy individuals. mBio 6, e00037. https://doi.org/10.1128/mBio.00037-15

854 Biagi, E., Rampelli, S., Turroni, S., Quercia, S., Candela, M., Brigidi, P., 2017. The

855 gut microbiota of centenarians: Signatures of longevity in the gut microbiota profile.

856 Mech. Ageing Dev. 165, 180-184. https://doi.org/10.1016/j.mad.2016.12.013

857 Bowdish, D.M.E., 2019. The Aging Lung: Is Lung Health Good Health for Older

858 Adults? Chest 155, 391-400. https://doi.org/10.1016/j.chest.2018.09.003

859 Brinkmann, V., Zychlinsky, A., 2007. Beneficial suicide: why neutrophils die to make

860 NETs. Nat. Rev. Microbiol. 5, 577-582. https://doi.org/10.1038/nrmicro1710

861 Brown, R.L., Sequeira, R.P., Clarke, T.B., 2017. The microbiota protects against

862 respiratory infection via GM-CSF signaling. Nat Commun 8, 1512.

863 https://doi.org/10.1038/s41467-017-01803-x

864 Burr, A.H.P., Bhattacharjee, A., Hand, T.W., 2020. Nutritional Modulation of the

865 Microbiome and Immune Response. J Immunol 205, 1479-1487.

866 https://doi.org/10.4049/jimmunol.2000419

867 Castle, S.C., Uyemura, K., Fulop, T., Makinodan, T., 2007. Host resistance and

868 immune responses in advanced age. Clin. Geriatr. Med. 23, 463-479, v.
869 https://doi.org/10.1016/j.cger.2007.03.005

870 Cederholm, T., Barazzoni, R., Austin, P., Ballmer, P., Biolo, G., Bischoff, S.C.,
871 Compher, C., Correia, I., Higashiguchi, T., Holst, M., Jensen, G.L., Malone, A.,
872 Muscaritoli, M., Nyulasi, I., Pirlich, M., Rothenberg, E., Schindler, K., Schneider, S.M.,
873 de van der Schueren, M. a. E., Sieber, C., Valentini, L., Yu, J.C., Van Gossum, A.,
874 Singer, P., 2017. ESPEN guidelines on definitions and terminology of clinical
875 nutrition. Clin Nutr 36, 49–64. https://doi.org/10.1016/j.clnu.2016.09.004

876 César Machado, M.C., da Silva, F.P., 2016. Intestinal Barrier Dysfunction in Human
877 Pathology and Aging. Curr. Pharm. Des. 22, 4645–4650.
878 https://doi.org/10.2174/1381612822666160510125331

879 Chakraborty, K., Raundhal, M., Chen, B.B., Morse, C., Tyurina, Y.Y., Khare, A.,
880 Oriss, T.B., Huff, R., Lee, J.S., St Croix, C.M., Watkins, S., Mallampalli, R.K., Kagan,
881 V.E., Ray, A., Ray, P., 2017. The mito-DAMP cardiolipin blocks IL-10 production
882 causing persistent inflammation during bacterial pneumonia. Nat Commun 8, 13944.
883 https://doi.org/10.1038/ncomms13944

884 Chen, J., Kelley, W.J., Goldstein, D.R., 2020. Role of Aging and the Immune
885 Response to Respiratory Viral Infections: Potential Implications for COVID-19. J.
886 Immunol. https://doi.org/10.4049/jimmunol.2000380

887 Chen, M.M., Palmer, J.L., Plackett, T.P., Deburghgraeve, C.R., Kovacs, E.J., 2014.
888 Age-related differences in the neutrophil response to pulmonary pseudomonas
889 infection. Exp. Gerontol. 54, 42–46. https://doi.org/10.1016/j.exger.2013.12.010

890 Cheng, C.-W., Villani, V., Buono, R., Wei, M., Kumar, S., Yilmaz, O.H., Cohen, P.,
891 Sneddon, J.B., Perin, L., Longo, V.D., 2017. Fasting-Mimicking Diet Promotes Ngn3-
892 Driven β-Cell Regeneration to Reverse Diabetes. Cell 168, 775-788.e12.
893 https://doi.org/10.1016/j.cell.2017.01.040

894 Cho, S.J., Stout-Delgado, H.W., 2020. Aging and Lung Disease. Annu. Rev. Physiol.
895 82, 433–459. https://doi.org/10.1146/annurev-physiol-021119-034610

896 Choi, J.W., Pai, S.H., 2004. Brief communication: Respiratory function is closely
897 associated with basal metabolic rate in elderly persons. Ann. Clin. Lab. Sci. 34, 99–
898 102.
Claesson, M.J., Cusack, S., O'Sullivan, O., Greene-Diniz, R., de Weerd, H., Flannery, E., Marchesi, J.R., Falush, D., Dinan, T., Fitzgerald, G., Stanton, C., van Sinderen, D., O'Connor, M., Harnedy, N., O'Connor, K., Henry, C., O'Mahony, D., Fitzgerald, A.P., Shanahan, F., Twomey, C., Hill, C., Ross, R.P., O'Toole, P.W., 2011. Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc. Natl. Acad. Sci. U.S.A. 108 Suppl 1, 4586-4591.
https://doi.org/10.1073/pnas.1000097107

Claesson, M.J., Jeffery, I.B., Conde, S., Power, S.E., O'Connor, E.M., Cusack, S., Harris, H.M.B., Coakley, M., Lakshminarayanan, B., O'Sullivan, O., Fitzgerald, G.F., Deane, J., O'Connor, M., Harnedy, N., O'Connor, K., O'Mahony, D., van Sinderen, D., Wallace, M., Brennan, L., Stanton, C., Marchesi, J.R., Fitzgerald, A.P., Shanahan, F., Hill, C., Ross, R.P., O'Toole, P.W., 2012. Gut microbiota composition correlates with diet and health in the elderly. Nature 488, 178-184.
https://doi.org/10.1038/nature11319

Colman, R.J., Anderson, R.M., Johnson, S.C., Kastman, E.K., Kosmatka, K.J., Beasley, T.M., Allison, D.B., Cruzen, C., Simmons, H.A., Kemnitz, J.W., Weindruch, R., 2009. Caloric restriction delays disease onset and mortality in rhesus monkeys. Science 325, 201-204. https://doi.org/10.1126/science.1173635

Colman, R.J., Beasley, T.M., Kemnitz, J.W., Johnson, S.C., Weindruch, R., Anderson, R.M., 2014. Caloric restriction reduces age-related and all-cause mortality in rhesus monkeys. Nat Commun 5, 3557. https://doi.org/10.1038/ncomms4557

Cooke, K.R., Hill, G.R., Gerbitz, A., Kobzik, L., Martin, T.R., Crawford, J.M., Brewer, J.P., Ferrara, J.L., 2000. Hyporesponsiveness of donor cells to lipopolysaccharide stimulation reduces the severity of experimental idiopathic pneumonia syndrome: potential role for a gut-lung axis of inflammation. J. Immunol. 165, 6612-6619.
https://doi.org/10.4049/jimmunol.165.11.6612

Corberand, J., Ngyen, F., Laharrague, P., Fontanilles, A.M., Gleyzes, B., Gyrard, E., Senegas, C., 1981. Polymorphonuclear functions and aging in humans. J Am Geriatr Soc 29, 391-397. https://doi.org/10.1111/j.1532-5415.1981.tb02376.x

Cutting, G.R., 2015. Cystic fibrosis genetics: from molecular understanding to clinical application. Nat. Rev. Genet. 16, 45-56. https://doi.org/10.1038/nrg3849
Cătoi, A.F., Corina, A., Katsiki, N., Vodnar, D.C., Andreicuţ, A.D., Stoian, A.P., Rizzo, M., Pérez-Martínez, P., 2020. Gut microbiota and aging-A focus on centenarians. 930 931
Biochim Biophys Acta Mol Basis Dis 1866, 165765. 932
https://doi.org/10.1016/j.bbadis.2020.165765 933

Dabrowski, A.N., Shrivastav, A., Conrad, C., Komma, K., Weigel, M., Dietert, K., 934
Gruber, A.D., Bertrams, W., Wilhelm, J., Schmeck, B., Reppe, K., N'Guessan, P.D., 935
Aly, S., Suttorp, N., Hain, T., Zahlten, J., 2019. Peptidoglycan Recognition Protein 4, 936
Limits Bacterial Clearance and Inflammation in Lungs by Control of the Gut 937
Microbiota. Front Immunol 10, 2106. https://doi.org/10.3389/fimmu.2019.02106 938

Dalmasso, G., Cougnoux, A., Delmas, J., Darfeuille-Michaud, A., Bonnet, R., 2014. 939
The bacterial genotoxin colibactin promotes colon tumor growth by modifying the 940
tumor microenvironment. Gut Microbes 5, 675-680. 941
https://doi.org/10.4161/19490976.2014.969989 942

David, L.A., Maurice, C.F., Carmody, R.N., Gootenberg, D.B., Button, J.E., Wolfe, 943
B.E., Ling, A.V., Devlin, A.S., Varma, Y., Fischbach, M.A., Biddinger, S.B., Dutton, 944
R.J., Turnbaugh, P.J., 2014. Diet rapidly and reproducibly alters the human gut 945
microbiome. Nature 505, 559-563. https://doi.org/10.1038/nature12820 946

de Steenhuijsen Piters, W.A.A., Huijskens, E.G.W., Wyllie, A.L., Biesbroek, G., van 947
den Bergh, M.R., Veenhoven, R.H., Wang, X., Trzciński, K., Bonten, M.J., Rossen, 948
J.W.A., Sanders, E.A.M., Bogaert, D., 2016. Dysbiosis of upper respiratory tract 949
microbiota in elderly pneumonia patients. ISME J 10, 97-108. 950
https://doi.org/10.1038/ismej.2015.99 951

de Vrese, M., Schrezenmeir, J., 2008. Probiotics, prebiotics, and synbiotics. Adv. 952
Biochem. Eng. Biotechnol. 111, 1-66. https://doi.org/10.1007/10_2008_097 953

de Vrese, M., Winkler, P., Rautenberg, P., Harder, T., Noah, C., Laue, C., Ott, S., 954
Hampe, J., Schreiber, S., Heller, K., Schrezenmeir, J., 2006. Probiotic bacteria 955
reduced duration and severity but not the incidence of common cold episodes in a 956
double blind, randomized, controlled trial. Vaccine 24, 6670-6674. 957
https://doi.org/10.1016/j.vaccine.2006.05.048 958

Deriu, E., Boxx, G.M., He, X., Pan, C., Benavidez, S.D., Cen, L., Rozengurt, N., Shi, 959
W., Cheng, G., 2016. Influenza Virus Affects Intestinal Microbiota and Secondary 960
961 Salmonella Infection in the Gut through Type I Interferons. PLoS Pathog. 12, 962 e1005572. https://doi.org/10.1371/journal.ppat.1005572

963 Derrien, M., van Hylckama Vlieg, J.E.T., 2015. Fate, activity, and impact of ingested 964 bacteria within the human gut microbiota. Trends Microbiol. 23, 354–366. 965 https://doi.org/10.1016/j.tim.2015.03.002

966 Derrien, M., Veiga, P., 2017. Rethinking Diet to Aid Human-Microbe Symbiosis. 967 Trends Microbiol. 25, 100–112. https://doi.org/10.1016/j.tim.2016.09.011

968 Dickson, R.P., Huffnagle, G.B., 2015. The Lung Microbiome: New Principles for 969 Respiratory Bacteriology in Health and Disease. PLoS Pathog. 11, e1004923. 970 https://doi.org/10.1371/journal.ppat.1004923

971 Dogra, S.K., Doré, J., Damak, S., 2020. Gut Microbiota Resilience: Definition, Link to 972 Health and Strategies for Intervention. Front Microbiol 11, 572921. 973 https://doi.org/10.3389/fmicb.2020.572921

974 Dumas, A., Bernard, L., Poquet, Y., Lugo-Villarino, G., Neyrolles, O., 2018. The role 975 of the lung microbiota and the gut-lung axis in respiratory infectious diseases. Cell. 976 Microbiol. 20, e12966. https://doi.org/10.1111/cmi.12966

977 Duncan, S.H., Belenguer, A., Holtrop, G., Johnstone, A.M., Flint, H.J., Lobley, G.E., 978 2007. Reduced dietary intake of carbohydrates by obese subjects results in 979 decreased concentrations of butyrate and butyrate-producing bacteria in feces. Appl. 980 Environ. Microbiol. 73, 1073–1078. https://doi.org/10.1128/AEM.02340-06

981 Duvallet, C., Larson, K., Snapper, S., Iosim, S., Lee, A., Freer, K., May, K., Alm, E., 982 Rosen, R., 2019. Aerodigestive sampling reveals altered microbial exchange 983 between lung, oropharyngeal, and gastric microbiomes in children with impaired 984 swallow function. PLoS One 14, e0216453. 985 https://doi.org/10.1371/journal.pone.0216453

986 Fassarella, M., Blaak, E.E., Penders, J., Nauta, A., Smidt, H., Zoetendal, E.G., 2020. 987 Gut microbiome stability and resilience: elucidating the response to perturbations in 988 order to modulate gut health. Gut. https://doi.org/10.1136/gutjnl-2020-321747

989 Fernández-Garrido, J., Ruiz-Ros, V., Buigues, C., Navarro-Martinez, R., Cauli, O., 990 2014. Clinical features of prefrail older individuals and emerging peripheral
991 biomarkers: a systematic review. Arch Gerontol Geriatr 59, 7-17.

992 https://doi.org/10.1016/j.archger.2014.02.008

993 Ferrucci, L., Fabbri, E., 2018. Inflammation: chronic inflammation in ageing,

994 cardiovascular disease, and frailty. Nat Rev Cardiol 15, 505-522.

995 https://doi.org/10.1038/s41569-018-0064-2

996 Frasca, D., Diaz, A., Romero, M., Blomberg, B.B., 2016. The generation of memory B

997 cells is maintained, but the antibody response is not, in the elderly after repeated

998 influenza immunizations. Vaccine 34, 2834-2840.

999 https://doi.org/10.1016/j.vaccine.2016.04.023

1000 Fried, L.P., Storer, D.J., King, D.E., Lodder, F., 1991. Diagnosis of illness

1001 presentation in the elderly. J Am Geriatr Soc 39, 117-123.

1002 https://doi.org/10.1111/j.1532-5415.1991.tb01612.x

1003 Fulop, T., Le Page, A., Fortin, C., Witkowski, J.M., Dupuis, G., Larbi, A., 2014.

1004 Cellular signaling in the aging immune system. Curr. Opin. Immunol. 29, 105-111.

1005 https://doi.org/10.1016/j.coi.2014.05.007

1006 Galvão, I., Tavares, L.P., Corrêa, R.O., Fachi, J.L., Rocha, V.M., Rungue, M., Garcia,

1007 C.C., Cassali, G., Ferreira, C.M., Martins, F.S., Oliveira, S.C., Mackay, C.R., Teixeira,

1008 M.M., Vinolo, M.A.R., Vieira, A.T., 2018. The Metabolic Sensor GPR43 Receptor

1009 Plays a Role in the Control of Klebsiella pneumoniae Infection in the Lung. Front

1010 Immunol 9, 142. https://doi.org/10.3389/fimmu.2018.00142

1011 Gauguet, S., D'Ortona, S., Ahnger-Pier, K., Duan, B., Surana, N.K., Lu, R., Cywes-

1012 Bentley, C., Gadjeva, M., Shan, Q., Priebe, G.P., Pier, G.B., 2015. Intestinal

1013 Microbiota of Mice Influences Resistance to Staphylococcus aureus Pneumonia.

1014 Infect. Immun. 83, 4003-4014. https://doi.org/10.1128/IAI.00037-15

1015 GBD 2017 Diet Collaborators, 2019. Health effects of dietary risks in 195 countries,

1016 1990-2017: a systematic analysis for the Global Burden of Disease Study 2017.

1017 Lancet 393, 1958-1972. https://doi.org/10.1016/S0140-6736(19)30041-8

1018 Ghosh, T.S., Rampelli, S., Jeffery, I.B., Santoro, A., Neto, M., Capri, M., Giampieri,

1019 E., Jennings, A., Candela, M., Turroni, S., Zoetendal, E.G., Hermes, G.D.A., Elodie,

1020 C., Meunier, N., Brugere, C.M., Pujos-Guillot, E., Berendsen, A.M., De Groot,

1021 L.C.P.G.M., Feskins, E.J.M., Kaluza, J., Pietruszka, B., Bielak, M.J., Comte, B.,
1022 Maijo-Ferre, M., Nicoletti, C., De Vos, W.M., Fairweather-Tait, S., Cassidy, A., Brigidi, P., Franceschi, C., O'Toole, P.W., 2020. Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries. Gut 69, 1218-1228.
1023
1024
1025
https://doi.org/10.1136/gutjnl-2019-319654

1027 Gibson, G.R., Hutkins, R., Sanders, M.E., Prescott, S.L., Reimer, R.A., Salminen, S.J., Scott, K., Stanton, C., Swanson, K.S., Cani, P.D., Verbeke, K., Reid, G., 2017. Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat Rev Gastroenterol Hepatol 14, 491-502.
1028
1029
1030
1031
https://doi.org/10.1038/nrgastro.2017.75

1033 Giménez-Bastida, J.A., Ávila-Gálvez, M.Á., Espín, J.C., González-Sarrías, A., 2020. The gut microbiota metabolite urolithin A, but not other relevant urolithins, induces p53-dependent cellular senescence in human colon cancer cells. Food Chem. Toxicol. 139, 111260. https://doi.org/10.1016/j.fct.2020.111260

1037 Goldstein, D.R., 2012. Role of aging on innate responses to viral infections. J. Gerontol. A Biol. Sci. Med. Sci. 67, 242-246. https://doi.org/10.1093/gerona/glr194

1039 Grier, A., McDavid, A., Wang, B., Qiu, X., Java, J., Bandyopadhyay, S., Yang, H., Holden-Wiltse, J., Kessler, H.A., Gill, A.L., Huyck, H., Falsey, A.R., Topham, D.J., Scheible, K.M., Caserta, M.T., Pryhuber, G.S., Gill, S.R., 2018. Neonatal gut and respiratory microbiota: coordinated development through time and space. Microbiome 6, 193. https://doi.org/10.1186/s40168-018-0566-5

1044 Groves, H.T., Cuthbertson, L., James, P., Moffatt, M.F., Cox, M.J., Tregoning, J.S., 2018. Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota. Front Immunol 9, 182. https://doi.org/10.3389/fimmu.2018.00182

1047 Guan, W.-J., Liang, W.-H., Zhao, Y., Liang, H.-R., Chen, Z.-S., Li, Y.-M., Liu, X.-Q., Chen, R.-C., Tang, C.-L., Wang, T., Ou, C.-Q., Li, L., Chen, P.-Y., Sang, L., Wang, W., Li, J.-F., Li, C.-C., Ou, L.-M., Cheng, B., Xiong, S., Ni, Z.-Y., Xiang, J., Hu, Y., Liu, L., Shan, H., Lei, C.-L., Peng, Y.-X., Wei, L., Liu, Y., Hu, Y.-H., Peng, P., Wang, J.-M., Liu, J.-Y., Chen, Z., Li, G., Zheng, Z.-J., Qiu, S.-Q., Luo, J., Ye, C.-J., Zhu, S.-Y., Cheng, L.-L., Ye, F., Li, S.-Y., Zheng, J.-P., Zhang, N.-F., Zhong, N.-S., He, J.-X.,
1053 China Medical Treatment Expert Group for COVID-19, 2020. Comorbidity and its impact on 1590 patients with COVID-19 in China: a nationwide analysis. Eur. Respir. J. 55. https://doi.org/10.1183/13993003.00547-2020

1056 Gurung, M., Li, Z., You, H., Rodrigues, R., Jump, D.B., Morgun, A., Shulzhenko, N., 2020. Role of gut microbiota in type 2 diabetes pathophysiology. EBioMedicine 51, 102590. https://doi.org/10.1016/j.ebiom.2019.11.051

1059 Haak, B.W., Littmann, E.R., Chaubard, J.-L., Pickard, A.J., Fontana, E., Adhi, F., Gyaltshen, Y., Ling, L., Morjaria, S.M., Peled, J.U., van den Brink, M.R., Geyer, A.I., Cross, J.R., Pamer, E.G., Taur, Y., 2018. Impact of gut colonization with butyrate-producing microbiota on respiratory viral infection following allo-HCT. Blood 131, 2978-2986. https://doi.org/10.1182/blood-2018-01-828996

1064 Hanada, S., Pirzadeh, M., Carver, K.Y., Deng, J.C., 2018. Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia. Front Immunol 9, 2640. https://doi.org/10.3389/fimmu.2018.02640

1067 Hao, Q., Dong, B.R., Wu, T., 2015. Probiotics for preventing acute upper respiratory tract infections. Cochrane Database Syst Rev CD006895. https://doi.org/10.1002/14651858.CD006895.pub3

1070 Harvie, M., Wright, C., Pegington, M., McMullan, D., Mitchell, E., Martin, B., Cutler, R.G., Evans, G., Whiteside, S., Maudsley, S., Camandola, S., Wang, R., Carlson, O.D., Egan, J.M., Mattson, M.P., Howell, A., 2013. The effect of intermittent energy and carbohydrate restriction v. daily energy restriction on weight loss and metabolic disease risk markers in overweight women. Br. J. Nutr. 110, 1534-1547. https://doi.org/10.1017/S0007114513000792

1076 Harvie, M.N., Pegington, M., Mattson, M.P., Frystyk, J., Dillon, B., Evans, G., Cuzick, J., Jebb, S.A., Martin, B., Cutler, R.G., Son, T.G., Maudsley, S., Carlson, O.D., Egan, J.M., Flyvbjerg, A., Howell, A., 2011. The effects of intermittent or continuous energy restriction on weight loss and metabolic disease risk markers: a randomized trial in young overweight women. Int J Obes (Lond) 35, 714-727. https://doi.org/10.1038/ijo.2010.171

1082 Haynes, L., Swain, S.L., 2006. Why aging T cells fail: implications for vaccination. Immunity 24, 663-666. https://doi.org/10.1016/j.immuni.2006.06.003
1084 Heymsfield, S.B., Bethel, R.A., Ansley, J.D., Nixon, D.W., Rudman, D., 1979. Enteral hyperalimentation: an alternative to central venous hyperalimentation. Ann. Intern. Med. 90, 63-71. https://doi.org/10.7326/0003-4819-90-1-63

1087 Hildebrandt, M.A., Hoffmann, C., Sherrill-Mix, S.A., Keilbaugh, S.A., Hamady, M., Chen, Y.-Y., Knight, R., Ahima, R.S., Bushman, F., Wu, G.D., 2009. High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology 137, 1716-1724.e1-2. https://doi.org/10.1053/j.gastro.2009.08.042

1091 Ho, J.C., Chan, K.N., Hu, W.H., Lam, W.K., Zheng, L., Tipoe, G.L., Sun, J., Leung, R., Tsang, K.W., 2001. The effect of aging on nasal mucociliary clearance, beat frequency, and ultrastructure of respiratory cilia. American Journal of Respiratory and Critical Care Medicine 163, 983-988. https://doi.org/10.1164/ajrccm.163.4.9909121

1095 Hodge, S., Hodge, G., Scicchitano, R., Reynolds, P.N., Holmes, M., 2003. Alveolar macrophages from subjects with chronic obstructive pulmonary disease are deficient in their ability to phagocytose apoptotic airway epithelial cells. Immunol. Cell Biol. 81, 289-296. https://doi.org/10.1046/j.1440-1711.2003.t01-1-01170.x

1099 Hole, D.J., Watt, G.C., Davey-Smith, G., Hart, C.L., Gillis, C.R., Hawthorne, V.M., 1996. Impaired lung function and mortality risk in men and women: findings from the Renfrew and Paisley prospective population study. BMJ 313, 711-715; discussion 715-716. https://doi.org/10.1136/bmj.313.7059.711

1103 Holodick, N.E., Rothstein, T.L., 2015. B cells in the aging immune system: time to consider B-1 cells. Ann. N. Y. Acad. Sci. 1362, 176-187. https://doi.org/10.1111/nyas.12825

1106 Hu, Yongfei, Feng, Y., Wu, J., Liu, F., Zhang, Z., Hao, Y., Liang, S., Li, B., Li, J., Lv, N., Xu, Y., Zhu, B., Sun, Z., 2019. The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients. Front Cell Infect Microbiol 9, 90. https://doi.org/10.3389/fcimb.2019.00090

1110 Hu, Yongfeng, Yang, Q., Liu, B., Dong, J., Sun, L., Zhu, Y., Su, H., Yang, J., Yang, F., Chen, X., Jin, Q., 2019. Gut microbiota associated with pulmonary tuberculosis and dysbiosis caused by anti-tuberculosis drugs. J. Infect. 78, 317-322. https://doi.org/10.1016/j.jinf.2018.08.006

1114 Huang, S.-F., Yang, Y.-Y., Chou, K.-T., Fung, C.-P., Wang, F.-D., Su, W.-J., 2019.
1115 Systemic proinflammation after Mycobacterium tuberculosis infection was correlated
to the gut microbiome in HIV-uninfected humans. Eur. J. Clin. Invest. 49, e13068.
1116
1117 https://doi.org/10.1111/eci.13068

1118 Ichinohe, T., Pang, I.K., Kumamoto, Y., Peaper, D.R., Ho, J.H., Murray, T.S., Iwasaki, A., 2011. Microbiota regulates immune defense against respiratory tract influenza A virus infection. Proc. Natl. Acad. Sci. U.S.A. 108, 5354-5359.
1119
1120
1121 https://doi.org/10.1073/pnas.1019378108

1122 Inouye, S.K., Studenski, S., Tinetti, M.E., Kuchel, G.A., 2007. Geriatric syndromes: clinical, research, and policy implications of a core geriatric concept. J Am Geriatr Soc 55, 780-791. https://doi.org/10.1111/j.1532-5415.2007.01156.x

1125 Jackson, M.A., Jackson, M., Jeffery, I.B., Beaumont, M., Bell, J.T., Clark, A.G., Ley, R.E., O'Toole, P.W., Spector, T.D., Steves, C.J., 2016. Signatures of early frailty in the gut microbiota. Genome Med 8, 8. https://doi.org/10.1186/s13073-016-0262-7

1128 Janssens, J.P., Pache, J.C., Nicod, L.P., 1999. Physiological changes in respiratory function associated with ageing. The European Respiratory Journal 13, 197-205.
1129
1130 https://doi.org/10.1034/j.1399-3003.1999.13a36.x

1131 Jeffery, I.B., Lynch, D.B., O'Toole, P.W., 2016. Composition and temporal stability of the gut microbiota in older persons. ISME J 10, 170-182.
1132
1133 https://doi.org/10.1038/ismej.2015.88

1134 Josset, L., Engelmann, F., Haberthur, K., Kelly, S., Park, B., Kawoaka, Y., García-Sastre, A., Katze, M.G., Messaoudi, I., 2012. Increased viral loads and exacerbated innate host responses in aged macaques infected with the 2009 pandemic H1N1 influenza A virus. J. Virol. 86, 11115-11127. https://doi.org/10.1128/JVI.01571-12

1138 Kagawa, Y., 1978. Impact of Westernization on the nutrition of Japanese: changes in physique, cancer, longevity and centenarians. Prev Med 7, 205-217.
1139
1140 https://doi.org/10.1016/0091-7435(78)90246-3

1141 Kahlich, R., Kotlár, V., Skocil, V., 1975. Complex surveillance of Streptococcus pyogenes. I. Immunological surveys of anti-M antibodies and possibilities of long-term epidemiological prognosis. J Hyg Epidemiol Microbiol Immunol 19, 48-60.

1144 Kane, R.L., Shamliyan, T., Talley, K., Pacala, J., 2012. The association between
1145 geriatric syndromes and survival. J Am Geriatr Soc 60, 896-904.
1146 https://doi.org/10.1111/j.1532-5415.2012.03942.x

1147 Kang, Y., Zhang, H., Zhao, Y., Wang, Y., Wang, W., He, Y., Zhang, Wei, Zhang, Weiwei, Zhu, X., Zhou, Y., Zhang, L., Ju, Z., Shi, L., 2018. Telomere Dysfunction Disturbs Macrophage Mitochondrial Metabolism and the NLRP3 Inflammasome through the PGC-1α/TNFAIP3 Axis. Cell Rep 22, 3493-3506.
1151 https://doi.org/10.1016/j.celrep.2018.02.071

1152 Ke, Y., Li, D., Zhao, M., Liu, C., Liu, J., Zeng, A., Shi, X., Cheng, S., Pan, B., Zheng, L., Hong, H., 2018. Gut flora-dependent metabolite Trimethylamine-N-oxide accelerates endothelial cell senescence and vascular aging through oxidative stress. Free Radic. Biol. Med. 116, 88-100.
1156 https://doi.org/10.1016/j.freeradbiomed.2018.01.007

1157 Kim, M., Gu, B., Madison, M.C., Song, H.W., Norwood, K., Hill, A.A., Wu, W.-J., Corry, D., Kheradmand, F., Diehl, G.E., 2019. Cigarette Smoke Induces Intestinal Inflammation via a Th17 Cell-Neutrophil Axis. Front Immunol 10, 75.
1160 https://doi.org/10.3389/fimmu.2019.00075

1161 Klempel, M.C., Kroeger, C.M., Bhutani, S., Trepanowski, J.F., Varady, K.A., 2012. Intermittent fasting combined with calorie restriction is effective for weight loss and cardio-protection in obese women. Nutr J 11, 98. https://doi.org/10.1186/1475-2891-11-98

1165 Kolodziejczyk, A.A., Zheng, D., Elinav, E., 2019. Diet-microbiota interactions and personalized nutrition. Nat Rev Microbiol 17, 742-753.
1167 https://doi.org/10.1038/s41579-019-0256-8

1168 Kong, F., Hua, Y., Zeng, B., Ning, R., Li, Y., Zhao, J., 2016. Gut microbiota signatures of longevity. Curr. Biol. 26, R832-R833.
1170 https://doi.org/10.1016/j.cub.2016.08.015

1171 Kovaiou, R.D., Grubeck-Loebenstein, B., 2006. Age-associated changes within CD4+ T cells. Immunol. Lett. 107, 8-14. https://doi.org/10.1016/j.imlet.2006.07.006

1173 Krone, C.L., Biesbroek, G., Trzciński, K., Sanders, E.A.M., Bogaert, D., 2014. Respiratory microbiota dynamics following Streptococcus pneumoniae acquisition in young and elderly mice. Infect. Immun. 82, 1725-1731.
1175
1176 https://doi.org/10.1128/IAI.01290-13

1177 Kumar, R., Sharma, A., Gupta, M., Padwad, Y., Sharma, R., 2019. Cell-Free Culture

1178 Supernatant of Probiotic Lactobacillus fermentum Protects Against H2O2-Induced

1179 Premature Senescence by Suppressing ROS-Akt-mTOR Axis in Murine

1180 Preadipocytes. Probiotics Antimicrob Proteins. https://doi.org/10.1007/s12602-019-09576-z

1181

1182 Lang, P.-O., Mendes, A., Socquet, J., Assir, N., Govind, S., Aspinall, R., 2012.

1183 Effectiveness of influenza vaccine in aging and older adults: comprehensive analysis

1184 of the evidence. Clin Interv Aging 7, 55–64. https://doi.org/10.2147/CIA.S25215

1185 Lange, P., Nyboe, J., Appleyard, M., Jensen, G., Schnohr, P., 1990. Spirometric

1186 findings and mortality in never-smokers. J Clin Epidemiol 43, 867–873.

1187 https://doi.org/10.1016/0895-4356(90)90070-6

1188 Lee, J.-J., Kim, S.-H., Lee, M.-J., Kim, B.-K., Song, W.-J., Park, H.-W., Cho, S.-H.,

1189 Hong, S.-J., Chang, Y.-S., Kim, B.-S., 2019. Different upper airway microbiome and

1190 their functional genes associated with asthma in young adults and elderly individuals.

1191 Allergy 74, 709–719. https://doi.org/10.1111/all.13608

1192 Lee, J.-Y., Jun, N.-R., Yoon, D., Shin, C., Baik, I., 2015. Association between dietary

1193 patterns in the remote past and telomere length. Eur J Clin Nutr 69, 1048–1052.

1194 https://doi.org/10.1038/ejcn.2015.58

1195 Lee, S.Y., Mac Aogáin, M., Fam, K.D., Chia, K.L., Binte Mohamed Ali, N.A., Yap,

1196 M.M.C., Yap, E.P.H., Chotirmall, S.H., Lim, C.L., 2019. Airway microbiome

1197 composition correlates with lung function and arterial stiffness in an age-dependent

1198 manner. PLoS ONE 14, e0225636. https://doi.org/10.1371/journal.pone.0225636

1199 Lefebvre, J.S., Masters, A.R., Hopkins, J.W., Haynes, L., 2016. Age-related

1200 impairment of humoral response to influenza is associated with changes in antigen

1201 specific T follicular helper cell responses. Sci Rep 6, 25051.

1202 https://doi.org/10.1038/srep25051

1203 Leong, D.P., Teo, K.K., Rangarajan, S., Lopez-Jaramillo, P., Avezum, A., Orlandini,

1204 A., Seron, P., Ahmed, S.H., Rosengren, A., Kelishadi, R., Rahman, O.,

1205 Swaminathan, S., Iqbal, R., Gupta, R., Lear, S.A., Oguz, A., Yusoff, K., Zatonska, K.,

1206 Chifamba, J., Igumbor, E., Mohan, V., Anjana, R.M., Gu, H., Li, W., Yusuf, S.,
1207 Prospective Urban Rural Epidemiology (PURE) Study investigators, 2015. Prognostic
1208 value of grip strength: findings from the Prospective Urban Rural Epidemiology
1209 (PURE) study. Lancet 386, 266–273. https://doi.org/10.1016/S0140-6736(14)62000-6

1210 Leung, C.W., Laraia, B.A., Needham, B.L., Rehkopf, D.H., Adler, N.E., Lin, J.,
1211 Blackburn, E.H., Epel, E.S., 2014. Soda and cell aging: associations between sugar-
1212 sweetened beverage consumption and leukocyte telomere length in healthy adults
1213 from the National Health and Nutrition Examination Surveys. Am J Public Health 104,
1214 2425–2431. https://doi.org/10.2105/AJPH.2014.302151

1215 Ley, R.E., Turnbaugh, P.J., Klein, S., Gordon, J.I., 2006. Microbial ecology: human
gut microbes associated with obesity. Nature 444, 1022–1023.
1217 https://doi.org/10.1038/4441022a

1218 Li, J., Zhao, F., Wang, Y., Chen, J., Tao, J., Tian, G., Wu, S., Liu, W., Cui, Q., Geng,
1219 B., Zhang, W., Weldon, R., Auguste, K., Yang, L., Liu, X., Chen, L., Yang, X., Zhu,
1220 B., Cai, J., 2017. Gut microbiota dysbiosis contributes to the development of
1221 hypertension. Microbiome 5, 14. https://doi.org/10.1186/s40168-016-0222-x

1222 Li, W., Zhu, Y., Liao, Q., Wang, Z., Wan, C., 2019. Characterization of gut microbiota
1223 in children with pulmonary tuberculosis. BMC Pediatr 19, 445.
1224 https://doi.org/10.1186/s12887-019-1782-2

1225 Li, Z., Jiao, Y., Fan, E.K., Scott, M.J., Li, Y., Li, S., Billiar, T.R., Wilson, M.A., Shi, X.,
1226 Fan, J., 2017. Aging-Impaired Filamentous Actin Polymerization Signaling Reduces
1227 Alveolar Macrophage Phagocytosis of Bacteria. J. Immunol. 199, 3176–3186.
1228 https://doi.org/10.4049/jimmunol.1700140

1229 Liu, C., Yang, L., Han, Y., Ouyang, W., Yin, W., Xu, F., 2019. Mast cells participate in
1230 regulation of lung-gut axis during Staphylococcus aureus pneumonia. Cell Prolif. 52,
e12565. https://doi.org/10.1111/cpr.12565

1232 Liu, J., Liu, Y., Xiang, P., Pu, L., Xiong, H., Li, C., Zhang, M., Tan, J., Xu, Y., Song,
1233 R., Song, M., Wang, L., Zhang, W., Han, B., Yang, L., Wang, Xiaojing, Zhou, G.,
1234 Zhang, T., Li, B., Wang, Y., Chen, Z., Wang, Xianbo, 2020. Neutrophil-to-lymphocyte
1235 ratio predicts critical illness patients with 2019 coronavirus disease in the early stage.
1236 J Transl Med 18, 206. https://doi.org/10.1186/s12967-020-02374-0

1237 Liu, J.J., Crous-Bou, M., Giovannucci, E., De Vivo, I., 2016. Coffee Consumption Is
1238

Positively Associated with Longer Leukocyte Telomere Length in the Nurses' Health

1239

Study. J. Nutr. 146, 1373-1378. https://doi.org/10.3945/jn.116.230490

1240

López-Otín, C., Blasco, M.A., Partridge, L., Serrano, M., Kroemer, G., 2013. The

1241

hallmarks of aging. Cell 153, 1194-1217. https://doi.org/10.1016/j.cell.2013.05.039

1242

Lordos, E.F., Herrmann, F.R., Robine, J.-M., Balahoczky, M., Giannelli, S.V., Gold,

1243

G., Michel, J.-P., 2008. Comparative value of medical diagnosis versus physical

1244

functioning in predicting the 6-year survival of 1951 hospitalized old patients.

1245

Rejuvenation Res 11, 829-836. https://doi.org/10.1089/rej.2008.0721

1246

Luo, M., Liu, Y., Wu, P., Luo, D.-X., Sun, Q., Zheng, H., Hu, R., Pandol, S.J., Li, Q.-

1247

F., Han, Y.-P., Zeng, Y., 2017. Alternation of Gut Microbiota in Patients with

1248

Pulmonary Tuberculosis. Front Physiol 8, 822.

1249

https://doi.org/10.3389/fphys.2017.00822

1250

Macpherson, A.J., Uhr, T., 2004. Induction of protective IgA by intestinal dendritic

1251

cells carrying commensal bacteria. Science 303, 1662-1665.

1252

https://doi.org/10.1126/science.1091334

1253

Man, A.L., Gicheva, N., Nicoletti, C., 2014. The impact of ageing on the intestinal

1254

epithelial barrier and immune system. Cell Immunol 289, 112-118.

1255

https://doi.org/10.1016/j.cellimm.2014.04.001

1256

Marco, M.L., Heeney, D., Binda, S., Cifelli, C.J., Cotter, P.D., Foligné, B., Gänzle, M.,

1257

Kort, R., Pasin, G., Pihlanto, A., Smid, E.J., Hutkins, R., 2017. Health benefits of

1258

fermented foods: microbiota and beyond. Curr. Opin. Biotechnol. 44, 94-102.

1259

https://doi.org/10.1016/j.copbio.2016.11.010

1260

Mathieu, E., Escribano-Vazquez, U., Descamps, D., Cherbuy, C., Langella, P.,

1261

Riffault, S., Remot, A., Thomas, M., 2018. Paradigms of Lung Microbiota Functions in

1262

Health and Disease, Particularly, in Asthma. Front Physiol 9, 1168.

1263

https://doi.org/10.3389/fphys.2018.01168

1264

Mathieu, E., MacPherson, C.W., Belvis, J., Mathieu, O., Robert, V., Saint-Criq, V.,

1265

Langella, P., Tompkins, T.A., Thomas, M., 2020. Oral Primo-Colonizing Bacteria

1266

Modulate Inflammation and Gene Expression in Bronchial Epithelial Cells.

1267

Microorganisms 8. https://doi.org/10.3390/microorganisms8081094
1268 Matsuzawa-Nagata, N., Takamura, T., Ando, H., Nakamura, S., Kurita, S., Misu, H.,
1269 Ota, T., Yokoyama, M., Honda, M., Miyamoto, K., Kaneko, S., 2008. Increased
1270 oxidative stress precedes the onset of high-fat diet-induced insulin resistance and
1271 obesity. *Metab. Clin. Exp.* 57, 1071–1077.
1272 https://doi.org/10.1016/j.metabol.2008.03.010

1273 May, A.M., Struijk, E.A., Fransen, H.P., Onland-Moret, N.C., de Wit, G.A., Boer, J.M.A., van der Schouw, Y.T., Hoekstra, J., Bueno-de-Mesquita, H.B., Peeters, P.H.M., Beulens, J.W.J., 2015. The impact of a healthy lifestyle on Disability-Adjusted Life Years: a prospective cohort study. BMC Med 13, 39.
1277 https://doi.org/10.1186/s12916-015-0287-6

1278 McNulty, N.P., Yatsunenko, T., Hsiao, A., Faith, J.J., Muegge, B.D., Goodman, A.L.,
1279 Henrissat, B., Oozeer, R., Cools-Portier, S., Gobert, G., Chervaux, C., Knights, D.,
1280 Lozupone, C.A., Knight, R., Duncan, A.E., Bain, J.R., Muehlbauer, M.J., Newgard,
1281 C.B., Heath, A.C., Gordon, J.I., 2011. The Impact of a Consortium of Fermented Milk
1282 Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins. Science
1283 Translational Medicine 3, 106ra106-106ra106.
1284 https://doi.org/10.1126/scitranslmed.3002701

1285 Meiners, S., Eickelberg, O., Königshoff, M., 2015. Hallmarks of the ageing lung. Eur.
1286 Respir. J. 45, 807–827. https://doi.org/10.1183/09031936.00186914

1287 Metcalf, T.U., Cubas, R.A., Ghneim, K., Cartwright, M.J., Grevenynghe, J.V.,
1288 Richner, J.M., Olagnier, D.P., Wilkinson, P.A., Cameron, M.J., Park, B.S., Hiscott,
1289 J.B., Diamond, M.S., Wertheimer, A.M., Nikolich-Zugich, J., Haddad, E.K., 2015.
1290 Global analyses revealed age-related alterations in innate immune responses after
1291 stimulation of pathogen recognition receptors. Aging Cell 14, 421–432.
1292 https://doi.org/10.1111/acel.12320

1293 Milani, C., Ticinesi, A., Gerritsen, J., Nouvenne, A., Lugli, G.A., Mancabelli, L.,
1294 Turroni, F., Duranti, S., Mangifesta, M., Viappiani, A., Ferrario, C., Maggio, M.,
1295 Lauretani, F., De Vos, W., van Sinderen, D., Meschi, T., Ventura, M., 2016. Gut
1296 microbiota composition and Clostridium difficile infection in hospitalized elderly
1297 individuals: a metagenomic study. *Sci Rep* 6, 25945.
1298 https://doi.org/10.1038/srep25945
1299 Most, J., Gilmore, L.A., Smith, S.R., Han, H., Ravussin, E., Redman, L.M., 2018. Significant improvement in cardiometabolic health in healthy nonobese individuals during caloric restriction-induced weight loss and weight loss maintenance. Am. J. Physiol. Endocrinol. Metab. 314, E396-E405.
1303 https://doi.org/10.1152/ajpendo.00261.2017

1304 Muegge, B.D., Kuczynski, J., Knights, D., Clemente, J.C., González, A., Fontana, L., Henrissat, B., Knight, R., Gordon, J.I., 2011. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332, 970-974. https://doi.org/10.1126/science.1198719

1308 Murray, M.A., Chotirmall, S.H., 2015. The Impact of Immunosenescence on Pulmonary Disease. Mediators Inflamm. 2015, 692546.
1309 https://doi.org/10.1155/2015/692546

1311 Naito, Y., Takagi, T., Inoue, R., Kashiwagi, S., Mizushima, K., Tsuchiya, S., Itoh, Y., Okuda, K., Tsujimoto, Y., Adachi, A., Maruyama, N., Oda, Y., Matoba, S., 2019. Gut microbiota differences in elderly subjects between rural city Kyoto and urban city Kyoto: an age-gender-matched study. J Clin Biochem Nutr 65, 125-131. https://doi.org/10.3164/jcbn.19-26

1316 Nakatani, T., Sarraj, B., Ohnishi, M., Densmore, M.J., Taguchi, T., Goetz, R., Mohammadi, M., Lanske, B., Razzaque, M.S., 2009. In vivo genetic evidence for klotho-dependent, fibroblast growth factor 23 (FGF23) -mediated regulation of systemic phosphate homeostasis. FASEB J. 23, 433-441. https://doi.org/10.1096/fj.08-114397

1321 Namasivayam, S., Sher, A., Glickman, M.S., Wipperman, M.F., 2018. The Microbiome and Tuberculosis: Early Evidence for Cross Talk. mBio 9. https://doi.org/10.1128/mBio.01420-18

1324 Nipper, A.J., Smithey, M.J., Shah, R.C., Canaday, D.H., Landay, A.L., 2018. Diminished antibody response to influenza vaccination is characterized by expansion of an age-associated B-cell population with low PAX5. Clin. Immunol. 193, 80-87. https://doi.org/10.1016/j.clim.2018.02.003

1328 O'Callaghan, N.J., Toden, S., Bird, A.R., Topping, D.L., Fenech, M., Conlon, M.A., 2012. Colonocyte telomere shortening is greater with dietary red meat than white
meat and is attenuated by resistant starch. Clin Nutr 31, 60-64.
https://doi.org/10.1016/j.clnu.2011.09.003

O'Sullivan, Ó., Coakley, M., Lakshminarayanan, B., Claesson, M.J., Stanton, C., O'Toole, P.W., Ross, R.P., ELDERMET consortium (http://eldermet.ucc.ie), 2011.
Correlation of rRNA gene amplicon pyrosequencing and bacterial culture for microbial compositional analysis of faecal samples from elderly Irish subjects. J. Appl. Microbiol. 111, 467-473. https://doi.org/10.1111/j.1365-2672.2011.05067.x

Parada Venegas, D., De la Fuente, M.K., Landskron, G., González, M.J., Quera, R., Dijkstra, G., Harmsen, H.J.M., Faber, K.N., Hermoso, M.A., 2019. Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases. Front Immunol 10, 277.
https://doi.org/10.3389/fimmu.2019.00277

Parrish, A.R., 2017. The impact of aging on epithelial barriers. Tissue Barriers 5, e1343172. https://doi.org/10.1080/21688370.2017.1343172

Pavanello, S., Hoxha, M., Dioni, L., Bertazzi, P.A., Snenghi, R., Nalesso, A., Ferrara, S.D., Montisci, M., Baccarelli, A., 2011. Shortened telomeres in individuals with abuse in alcohol consumption. Int. J. Cancer 129, 983-992.
https://doi.org/10.1002/ijc.25999

Peng, M., Bitsko, E., Biswas, D., 2015. Functional properties of peanut fractions on the growth of probiotics and foodborne bacterial pathogens. J Food Sci 80, M635-641. https://doi.org/10.1111/1750-3841.12785

Péré-Védrenne, C., Prochazkova-Carlotti, M., Rousseau, B., He, W., Chambonnier, L., Sifré, E., Buissonnière, A., Dubus, P., Mégraud, F., Varon, C., Ménard, A., 2017.
The Cytolethal Distending Toxin Subunit CdtB of Helicobacter hepaticus Promotes Senescence and Endoreplication in Xenograft Mouse Models of Hepatic and Intestinal Cell Lines. Front Cell Infect Microbiol 7, 268.
https://doi.org/10.3389/fcimb.2017.00268

Pérez, L.M., Amaral, M.A., Mundstock, E., Barbé-Tuana, F.M., Guma, F.T.C.R., Jones, M.H., Machado, D.C., Sarria, E.E., Marques E Marques, M., Preto, L.T., Epifanio, M., Meinem Garbin, J.G., Mattiello, R., 2017. Effects of Diet on Telomere Length: Systematic Review and Meta-Analysis. Public Health Genomics 20, 286-
1361 292. https://doi.org/10.1159/000486586

1362 Poh, C.H., Navarro-Rodriguez, T., Fass, R., 2010. Review: treatment of
gastroesophageal reflux disease in the elderly. Am. J. Med. 123, 496-501.
1363
1364 https://doi.org/10.1016/j.amjmed.2009.07.036

1365 Pugin, J., Chevrolet, J.C., 1991. [ The intestine-liver-lung axis in septic syndrome].
1366 Schweiz Med Wochenschr 121, 1538-1544.

1367 Qin, N., Zheng, B., Yao, J., Guo, L., Zuo, J., Wu, L., Zhou, J., Liu, L., Guo, J., Ni, S.,
1368 Li, A., Zhu, Y., Liang, W., Xiao, Y., Ehrlich, S.D., Li, L., 2015. Influence of H7N9 virus
1369 infection and associated treatment on human gut microbiota. Sci Rep 5, 14771.
1370 https://doi.org/10.1038/srep14771

1371 Rampelli, S., Soverini, M., D'Amico, F., Barone, M., Tavella, T., Monti, D., Capri, M.,
1372 Astolfi, A., Brigidi, P., Biagi, E., Franceschi, C., Turroni, S., Candela, M., 2020.
1373 Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity
1374 and the Increasing Role of Xenobiotic Degradation. mSystems 5.
1375 https://doi.org/10.1128/mSystems.00124-20

1376 Rantanen, T., Volpato, S., Ferrucci, L., Heikkinen, E., Fried, L.P., Guralnik, J.M.,
1377 2003. Handgrip strength and cause-specific and total mortality in older disabled
1378 women: exploring the mechanism. J Am Geriatr Soc 51, 636-641.
1379 https://doi.org/10.1034/j.1600-0579.2003.00207.x

1380 Rasheed, S., Woods, R.T., 2013. Malnutrition and quality of life in older people: a
1381 systematic review and meta-analysis. Ageing Res. Rev. 12, 561-566.
1382 https://doi.org/10.1016/j.arr.2012.11.003

1383 Rea, M.C., O'Sullivan, O., Shanahan, F., O'Toole, P.W., Stanton, C., Ross, R.P., Hill,
1384 C., 2012. Clostridium difficile carriage in elderly subjects and associated changes in
1385 the intestinal microbiota. J. Clin. Microbiol. 50, 867-875.
1386 https://doi.org/10.1128/JCM.05176-11

1387 Redman, L.M., Smith, S.R., Burton, J.H., Martin, C.K., Il'yasova, D., Ravussin, E.,
1388 2018. Metabolic Slowing and Reduced Oxidative Damage with Sustained Caloric
1389 Restriction Support the Rate of Living and Oxidative Damage Theories of Aging. Cell
1390 Metab. 27, 805-815.e4. https://doi.org/10.1016/j.cmet.2018.02.019
1391 Rehman, T., 2012. Role of the gut microbiota in age-related chronic inflammation.
1392 Endocr Metab Immune Disord Drug Targets 12, 361–367.
1393 https://doi.org/10.2174/187153012803832620

1394 Remot, A., Descamps, D., Noordine, M.-L., Boukadiri, A., Mathieu, E., Robert, V.,
1395 Riffault, S., Lambrecht, B., Langella, P., Hammad, H., Thomas, M., 2017. Bacteria
1396 isolated from lung modulate asthma susceptibility in mice. ISME J 11, 1061–1074.
1397 https://doi.org/10.1038/ismej.2016.181

1398 Richardson, S., Hirsch, J.S., Narasimhan, M., Crawford, J.M., McGinn, T., Davidson,
1399 K.W., and the Northwell COVID-19 Research Consortium, Barnaby, D.P., Becker,
1400 L.B., Chelico, J.D., Cohen, S.L., Cookingham, J., Coppa, K., Diefenbach, M.A.,
1401 Dominello, A.J., Duer-Hefele, J., Falzon, L., Gitlin, J., Hajizadeh, N., Harvin, T.G.,
1402 Hirschwerk, D.A., Kim, E.J., Kozel, Z.M., Marrast, L.M., Mogavero, J.N., Osorio, G.A.,
1403 Qiu, M., Zanos, T.P., 2020. Presenting Characteristics, Comorbidities, and Outcomes
1404 Among 5700 Patients Hospitalized With COVID-19 in the New York City Area. JAMA.
1405 https://doi.org/10.1001/jama.2020.6775

1406 Rodgers, G.P., Collins, F.S., 2020. Precision Nutrition-the Answer to “What to Eat to
1407 Stay Healthy.” JAMA. https://doi.org/10.1001/jama.2020.13601

1408 Rosen, R., Amirault, J., Liu, H., Mitchell, P., Hu, L., Khatwa, U., Onderdonk, A., 2014.
1409 Changes in gastric and lung microflora with acid suppression: acid suppression and
1410 bacterial growth. JAMA Pediatr 168, 932–937.
1411 https://doi.org/10.1001/jamapediatrics.2014.696

1412 Samuelson, D.R., Charles, T.P., de la Rua, N.M., Taylor, C.M., Blanchard, E.E., Luo,
1413 M., Shellito, J.E., Welsh, D.A., 2016. Analysis of the intestinal microbial community
1414 and inferred functional capacities during the host response to Pneumocystis
1415 pneumonia. Exp. Lung Res. 42, 425–439.
1416 https://doi.org/10.1080/01902148.2016.1258442

1417 Santoro, A., Ostan, R., Candela, M., Biagi, E., Brigidi, P., Capri, M., Franceschi, C.,
1418 2018. Gut microbiota changes in the extreme decades of human life: a focus on
1419 centenarians. Cell. Mol. Life Sci. 75, 129–148. https://doi.org/10.1007/s00018-017-
1420 2674-y

1421 Schuijt, T.J., Lankelma, J.M., Scicluna, B.P., de Sousa e Melo, F., Roelofs, J.J.T.H.,
1422 de Boer, J.D., Hoogendijk, A.J., de Beer, R., de Vos, A., Belzer, C., de Vos, W.M.,
1423 van der Poll, T., Wiersinga, W.J., 2016. The gut microbiota plays a protective role in
1424 the host defence against pneumococcal pneumonia. Gut 65, 575–583.
1425 https://doi.org/10.1136/gutjnl-2015-309728

1426 Segata, N., Haake, S.K., Mannon, P., Lemon, K.P., Waldron, L., Gevers, D.,
1427 Huttenhower, C., Izard, J., 2012. Composition of the adult digestive tract bacterial
1428 microbiome based on seven mouth surfaces, tonsils, throat and stool samples.
1429 Genome Biol. 13, R42. https://doi.org/10.1186/gb-2012-13-6-r42

1430 Sencio, V., Barthelemy, A., Tavares, L.P., Machado, M.G., Soulard, D., Cuinat, C.,
1431 Queiroz-Junior, C.M., Noordine, M.-L., Salomé-Desnoulez, S., Deryuter, L., Foligné,
1432 B., Wahl, C., Frisch, B., Vieira, A.T., Paget, C., Milligan, G., Ulven, T., Wolowczuk, I.,
1433 Faveeuw, C., Le Goffic, R., Thomas, M., Ferreira, S., Teixeira, M.M., Trottein, F.,
1434 2020. Gut Dysbiosis during Influenza Contributes to Pulmonary Pneumococcal
1435 Superinfection through Altered Short-Chain Fatty Acid Production. Cell Rep 30,
1436 2934-2947.e6. https://doi.org/10.1016/j.celrep.2020.02.013

1437 Shaw, A.C., Panda, A., Joshi, S.R., Qian, F., Allore, H.G., Montgomery, R.R., 2011.
1438 Dysregulation of human Toll-like receptor function in aging. Ageing Res. Rev. 10,
1439 346–353. https://doi.org/10.1016/j.arr.2010.10.007

1440 Simpson, C.F., Punjabi, N.M., Wolfenden, L., Shardell, M., Shade, D.M., Fried, L.P.,
1441 2005. Relationship between lung function and physical performance in disabled older
1442 women. J. Gerontol. A Biol. Sci. Med. Sci. 60, 350–354.
1443 https://doi.org/10.1093/gerona/60.3.350

1444 Smith, D.L., Mattison, J.A., Desmond, R.A., Gardner, J.P., Kimura, M., Roth, G.S.,
1445 Ingram, D.K., Allison, D.B., Aviv, A., 2011. Telomere dynamics in rhesus monkeys:
1446 no apparent effect of caloric restriction. J. Gerontol. A Biol. Sci. Med. Sci. 66, 1163–
1447 1168. https://doi.org/10.1093/gerona/glr136

1448 Sone, H., Kagawa, Y., 2005. Pancreatic beta cell senescence contributes to the
1449 pathogenesis of type 2 diabetes in high-fat diet-induced diabetic mice. Diabetologia
1450 48, 58–67. https://doi.org/10.1007/s00125-004-1605-2

1451 Stearns, J.C., Davidson, C.J., McKeon, S., Whelan, F.J., Fontes, M.E., Schryvers,
1452 A.B., Bowdish, D.M.E., Kellner, J.D., Surette, M.G., 2015. Culture and molecular-
based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age. ISME J 9, 1246-1259. https://doi.org/10.1038/ismej.2014.250

Stekovic, S., Hofer, S.J., Tripolt, N., Aon, M.A., Royer, P., Pein, L., Stadler, J.T., Pendl, T., Prietl, B., Url, J., Schroeder, S., Tadic, J., Eisenberg, T., Magnes, C., Stumpe, M., Zuegner, E., Bordag, N., Riedl, R., Schmidt, A., Kolesnik, E., Verheyen, N., Springer, A., Madl, T., Sinner, F., de Cabo, R., Kroemer, G., Obermayer-Pietsch, B., Dengjel, J., Sourij, H., Pieber, T.R., Madeo, F., 2019. Alternate Day Fasting Improves Physiological and Molecular Markers of Aging in Healthy, Non-obese Humans. Cell Metab. 30, 462-476.e6. https://doi.org/10.1016/j.cmet.2019.07.016

Stout-Delgado, H.W., Vaughan, S.E., Shirali, A.C., Jaramillo, R.J., Harrod, K.S., 2012. Impaired NLRP3 inflammasome function in elderly mice during influenza infection is rescued by treatment with nigericin. J. Immunol. 188, 2815-2824. https://doi.org/10.4049/jimmunol.1103051

Struijk, E.A., Beulens, J.W.J., May, A.M., Fransen, H.P., Boer, J.M.A., de Wit, G.A., Onland-Moret, N.C., van der Schouw, Y.T., Hoekstra, J., Bueno-de-Mesquita, H.B., Peeters, P.H.M., 2014. Dietary patterns in relation to disease burden expressed in Disability-Adjusted Life Years. Am. J. Clin. Nutr. 100, 1158-1165. https://doi.org/10.3945/ajcn.113.082032

Suzuki, M., Betsuyaku, T., Ito, Y., Nagai, K., Nasuhara, Y., Kaga, K., Kondo, S., Nishimura, M., 2008. Down-regulated NF-E2-related factor 2 in pulmonary macrophages of aged smokers and patients with chronic obstructive pulmonary disease. Am. J. Respir. Cell Mol. Biol. 39, 673-682. https://doi.org/10.1165/rcmb.2007-0424OC

Suzuki, M., Wilcox, B.J., Wilcox, C.D., 2001. Implications from and for food cultures for cardiovascular disease: longevity. Asia Pac J Clin Nutr 10, 165-171. https://doi.org/10.1111/j.1440-6047.2001.00219.x

Sze, M.A., Tsuruta, M., Yang, S.-W.J., Oh, Y., Man, S.F.P., Hogg, J.C., Sin, D.D., 2014. Changes in the bacterial microbiota in gut, blood, and lungs following acute LPS instillation into mice lungs. PLoS ONE 9, e111228. https://doi.org/10.1371/journal.pone.0111228

Tamang, J.P., Shin, D.-H., Jung, S.-J., Chae, S.-W., 2016. Functional Properties of
1484 Microorganisms in Fermented Foods. Front. Microbiol. 7.
1485 https://doi.org/10.3389/fmicb.2016.00578

1486 Tankersley, C.G., Shank, J.A., Flanders, S.E., Soutiere, S.E., Rabold, R., Mitzner, W., Wagner, E.M., 2003. Changes in lung permeability and lung mechanics accompany homeostatic instability in senescent mice. J. Appl. Physiol. 95, 1681–1687. https://doi.org/10.1152/japplphysiol.00190.2003

1490 Tanner, M.R., Beeton, C., 2018. Differences in ion channel phenotype and function between humans and animal models. Front Biosci (Landmark Ed) 23, 43–64.
1491 https://doi.org/10.2741/4581

1493 Tappenden, K.A., Quatrara, B., Parkhurst, M.L., Malone, A.M., Fanjiang, G., Ziegler, T.R., 2013. Critical role of nutrition in improving quality of care: an interdisciplinary call to action to address adult hospital malnutrition. JPEN J Parenter Enteral Nutr 37, 482–497. https://doi.org/10.1177/0148607113484066

1497 Taylor, B.C., Lejzerowicz, F., Poirel, M., Shaffer, J.P., Jiang, L., Aksenov, A., Litwin, N., Humphrey, G., Martino, C., Miller-Montgomery, S., Dorrestein, P.C., Veiga, P., Song, S.J., McDonald, D., Derrien, M., Knight, R., 2020. Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome. mSystems 5. https://doi.org/10.1128/mSystems.00901-19

1502 Thevaranjan, N., Puchta, A., Schulz, C., Naidoo, A., Szamosi, J.C., Verschoor, C.P., Loukov, D., Schenck, L.P., Jury, J., Foley, K.P., Schertzer, J.D., Larché, M.J., Davidson, D.J., Verdú, E.F., Surette, M.G., Bowdish, D.M.E., 2017. Age-Associated Microbial Dysbiosis Promotes Intestinal Permeability, Systemic Inflammation, and Macrophage Dysfunction. Cell Host Microbe 21, 455-466.e4.
1507 https://doi.org/10.1016/j.chom.2017.03.002

1508 Thevaranjan, N., Whelan, F.J., Puchta, A., Ashu, E., Rossi, L., Surette, M.G., Bowdish, D.M.E., 2016. Streptococcus pneumoniae Colonization Disrupts the Microbial Community within the Upper Respiratory Tract of Aging Mice. Infect. Immun. 84, 906–916. https://doi.org/10.1128/IAI.01275-15

1512 Toapanta, F.R., Ross, T.M., 2009. Impaired immune responses in the lungs of aged mice following influenza infection. Respir. Res. 10, 112. https://doi.org/10.1186/1465-9921-10-112
1515 Trompette, A., Gollwitzer, E.S., Pattaroni, C., Lopez-Mejia, I.C., Riva, E., Pernot, J., 1516 Ubags, N., Fajas, L., Nicod, L.P., Marsland, B.J., 2018. Dietary Fiber Confers 1517 Protection against Flu by Shaping Ly6c- Patrolling Monocyte Hematopoiesis and 1518 CD8+ T Cell Metabolism. Immunity 48, 992-1005.e8. 1519 https://doi.org/10.1016/j.immuni.2018.04.022

1520 Trompette, A., Gollwitzer, E.S., Yadava, K., Sichelstiel, A.K., Sprenger, N., Ngom-1521 Bru, C., Blanchard, C., Junt, T., Nicod, L.P., Harris, N.L., Marsland, B.J., 2014. Gut 1522 microbiota metabolism of dietary fiber influences allergic airway disease and 1523 hematopoiesis. Nat. Med. 20, 159-166. https://doi.org/10.1038/nm.3444

1524 Trottein, F., Sokol, H., 2020. Potential Causes and Consequences of Gastrointestinal 1525 Disorders during a SARS-CoV-2 Infection. Cell Reports 107915. 1526 https://doi.org/10.1016/j.celrep.2020.107915

1527 Tucker, L.A., 2018. Dietary Fiber and Telomere Length in 5674 U.S. Adults: An 1528 NHANES Study of Biological Aging. Nutrients 10. 1529 https://doi.org/10.3390/nu10040400

1530 Valkenburg, S.A., Venturi, V., Dang, T.H.Y., Bird, N.L., Doherty, P.C., Turner, S.J., 1531 Davenport, M.P., Kedzierska, K., 2012. Early priming minimizes the age-related 1532 immune compromise of CD8+ T cell diversity and function. PLoS Pathog. 8, 1533 e1002544. https://doi.org/10.1371/journal.ppat.1002544

1534 Vandeputte, D., Joossens, M., 2020. Effects of Low and High FODMAP Diets on 1535 Human Gastrointestinal Microbiota Composition in Adults with Intestinal Diseases: A 1536 Systematic Review. Microorganisms 8. 1537 https://doi.org/10.3390/microorganisms8111638

1538 Varady, K.A., Dam, V.T., Klempel, M.C., Horne, M., Cruz, R., Kroeger, C.M., 1539 Santosa, S., 2015. Effects of weight loss via high fat vs. low fat alternate day fasting 1540 diets on free fatty acid profiles. Sci Rep 5, 7561. https://doi.org/10.1038/srep07561

1541 Vareille-Delarbre, M., Miquel, S., Garcin, S., Bertran, T., Balestrino, D., Evrard, B., 1542 Forestier, C., 2019. Immunomodulatory Effects of Lactobacillus plantarum on 1543 Inflammatory Response Induced by Klebsiella pneumoniae. Infect. Immun. 87. 1544 https://doi.org/10.1128/IAI.00570-19

1545 Vaughan, A., Frazer, Z.A., Hansbro, P.M., Yang, I.A., 2019. COPD and the gut-lung
axis: the therapeutic potential of fibre. J Thorac Dis 11, S2173-S2180.

https://doi.org/10.21037/jtd.2019.10.40

Vial, G., Dubouchaud, H., Couturier, K., Cottet-Rousselle, C., Taleux, N., Athias, A.,

Galinier, A., Casteilla, L., Leverve, X.M., 2011. Effects of a high-fat diet on energy
metabolism and ROS production in rat liver. J. Hepatol. 54, 348-356.

https://doi.org/10.1016/j.jhep.2010.06.044

Volkova, M., Zhang, Y., Shaw, A.C., Lee, P.J., 2012. The role of Toll-like receptors in

age-associated lung diseases. J. Gerontol. A Biol. Sci. Med. Sci. 67, 247-253.

https://doi.org/10.1093/gerona/glr226

Vonaesch, P., Morien, E., Andrianonimiadana, L., Sanke, H., Mbecko, J.-R., Huus,

K.E., Naharimanananirina, T., Gondje, B.P., Nigatoloum, S.N., Vondo, S.S., Kaleb

Kandou, J.E., Randremanana, R., Rakotondrainipiana, M., Mazel, F., Djorie, S.G.,

Gody, J.-C., Finlay, B.B., Rubbo, P.-A., Wegener Parfrey, L., Collard, J.-M.,

Sansonetti, P.J., Afribiota Investigators, 2018. Stunted childhood growth is
associated with decompartmentalization of the gastrointestinal tract and overgrowth
of oropharyngeal taxa. Proc. Natl. Acad. Sci. U.S.A. 115, E8489-E8498.

https://doi.org/10.1073/pnas.1806573115

Walker, A.W., Ince, J., Duncan, S.H., Webster, L.M., Holtrop, G., Ze, X., Brown, D.,

Stares, M.D., Scott, P., Bergerat, A., Louis, P., McIntosh, F., Johnstone, A.M.,

Lobley, G.E., Parkhill, J., Flint, H.J., 2011. Dominant and diet-responsive groups of
bacteria within the human colonic microbiota. ISME J 5, 220-230.

https://doi.org/10.1038/ismej.2010.118

Wang, D., Hu, B., Hu, C., Zhu, F., Liu, X., Zhang, J., Wang, B., Xiang, H., Cheng, Z.,

Xiong, Y., Zhao, Y., Li, Y., Wang, X., Peng, Z., 2020. Clinical Characteristics of 138

Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan,
China. JAMA. https://doi.org/10.1001/jama.2020.1585

Wang, F., Nie, J., Wang, H., Zhao, Q., Xiong, Y., Deng, L., Song, S., Ma, Z., Mo, P.,

Zhang, Y., 2020. Characteristics of Peripheral Lymphocyte Subset Alteration in
COVID-19 Pneumonia. J. Infect. Dis. 221, 1762-1769.

https://doi.org/10.1093/infdis/jiaa150

Wang, J., Li, F., Wei, H., Lian, Z.-X., Sun, R., Tian, Z., 2014. Respiratory influenza
1577 virus infection induces intestinal immune injury via microbiota-mediated Th17 cell-
1578 dependent inflammation. J. Exp. Med. 211, 2397-2410.
1579 https://doi.org/10.1084/jem.20140625

1580 Wang, N., Li, R., Lin, H., Fu, C., Wang, X., Zhang, Y., Su, M., Huang, P., Qian, J.,
1581 Jiang, F., Wang, H., Jiang, L., Yu, X., Liu, J., Chen, Y., Jiang, Q., 2019. Enriched
taxa were found among the gut microbiota of centenarians in East China. PLoS ONE
1582 14, e0222763. https://doi.org/10.1371/journal.pone.0222763
1583

1584 Wang, S.-Y., Wang, W.-J., Liu, J.-Q., Song, Y.-H., Li, P., Sun, X.-F., Cai, G.-Y.,
1585 Chen, X.-M., 2019. Methionine restriction delays senescence and suppresses the
senescence-associated secretory phenotype in the kidney through endogenous
1586 hydrogen sulfide. Cell Cycle 18, 1573-1587.
1587
1588 https://doi.org/10.1080/15384101.2019.1618124

1589 Wang, Y., Li, X., Ge, T., Xiao, Y., Liao, Y., Cui, Y., Zhang, Y., Ho, W., Yu, G., Zhang,
1590 T., 2016. Probiotics for prevention and treatment of respiratory tract infections in
1591 children: A systematic review and meta-analysis of randomized controlled trials.
1592 Medicine (Baltimore) 95, e4509. https://doi.org/10.1097/MD.0000000000004509

1593 Wansleeben, C., Bowie, E., Hotten, D.F., Yu, Y.-R.A., Hogan, B.L.M., 2014. Age-
1594 related changes in the cellular composition and epithelial organization of the mouse
1595 trachea. PloS One 9, e93496. https://doi.org/10.1371/journal.pone.0093496

1596 Watson, H., Mitra, S., Croden, F.C., Taylor, M., Wood, H.M., Perry, S.L., Spencer,
1597 J.A., Quirke, P., Toogood, G.J., Lawton, C.L., Dye, L., Loadman, P.M., Hull, M.A.,
2018. A randomised trial of the effect of omega-3 polyunsaturated fatty acid
1598 supplements on the human intestinal microbiota. Gut 67, 1974-1983.
1599
1600 https://doi.org/10.1136/gutjnl-2017-314968

1601 Weindruch, R., Walford, R.L., Fligiel, S., Guthrie, D., 1986. The retardation of aging
1602 in mice by dietary restriction: longevity, cancer, immunity and lifetime energy intake.
1603 J. Nutr. 116, 641-654. https://doi.org/10.1093/jn/116.4.641

1604 Weiss, E.P., Racette, S.B., Villareal, D.T., Fontana, L., Steger-May, K., Schechtman,
1605 K.B., Klein, S., Holloszy, J.O., Washington University School of Medicine CALERIE
1606 Group, 2006. Improvements in glucose tolerance and insulin action induced by
increasing energy expenditure or decreasing energy intake: a randomized controlled
1607
1608 trial. Am. J. Clin. Nutr. 84, 1033-1042. https://doi.org/10.1093/ajcn/84.5.1033
1609 Weiss, S.T., Segal, M.R., Sparrow, D., Wager, C., 1995. Relation of FEV1 and
1610 peripheral blood leukocyte count to total mortality. The Normative Aging Study. Am.
1611 J. Epidemiol. 142, 493-498; discussion 499-503.
1612 https://doi.org/10.1093/oxfordjournals.aje.a117665
1613 Whelan, F.J., Verschoor, C.P., Stearns, J.C., Rossi, L., Luinstra, K., Loeb, M.,
1614 Smieja, M., Johnstone, J., Surette, M.G., Bowdish, D.M.E., 2014. The loss of
1615 topography in the microbial communities of the upper respiratory tract in the elderly.
1616 Ann Am Thorac Soc 11, 513-521. https://doi.org/10.1513/AnnalsATS.201310-351OC
1617 Winglee, K., Eloe-Fadrosh, E., Gupta, S., Guo, H., Fraser, C., Bishai, W., 2014.
1618 Aerosol Mycobacterium tuberculosis infection causes rapid loss of diversity in gut
1619 microbiota. PLoS ONE 9, e97048. https://doi.org/10.1371/journal.pone.0097048
1620 Wong, C.K., Smith, C.A., Sakamoto, K., Kaminski, N., Koff, J.L., Goldstein, D.R.,
1621 2017. Aging Impairs Alveolar Macrophage Phagocytosis and Increases Influenza-
1622 Induced Mortality in Mice. J. Immunol. 199, 1060-1068.
1623 https://doi.org/10.4049/jimmunol.1700397
1624 Wu, G.D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.-Y., Keilbaugh, S.A., Bewtra,
1625 M., Knights, D., Walters, W.A., Knight, R., Sinha, R., Gilroy, E., Gupta, K.,
1626 Baldassano, R., Nessel, L., Li, H., Bushman, F.D., Lewis, J.D., 2011. Linking long-
1627 term dietary patterns with gut microbial enterotypes. Science 334, 105-108.
1628 https://doi.org/10.1126/science.1208344
1629 Wu, L., Zeng, T., Deligios, M., Milanesi, L., Langille, M.G.I., Zinellu, A., Rubino, S.,
1630 Carru, C., Kelvin, D.J., 2020. Age-Related Variation of Bacterial and Fungal
1631 Communities in Different Body Habitats across the Young, Elderly, and Centenarians
1632 in Sardinia. mSphere 5. https://doi.org/10.1128/mSphere.00558-19
1633 Yang, R., Chen, J., Zhang, J., Qin, R., Wang, R., Qiu, Y., Mao, Z., Goltzman, D.,
1634 Miao, D., 2020. 1,25-Dihydroxyvitamin D protects against age-related osteoporosis
1635 by a novel VDR-Ezh2-p16 signal axis. Aging Cell 19, e13095.
1636 https://doi.org/10.1111/acel.13095
1637 Yildiz, S., Mazel-Sanchez, B., Kandasamy, M., Manicassamy, B., Schmolke, M.,
1638 2018. Influenza A virus infection impacts systemic microbiota dynamics and causes
1639 quantitative enteric dysbiosis. Microbiome 6, 9. https://doi.org/10.1186/s40168-017-0386-z

1641 Yu, B., Dai, C., Chen, J., Deng, L., Wu, X., Wu, S., Zhao, C., Jiang, Z., Chen, X., 2015. Dysbiosis of gut microbiota induced the disorder of helper T cells in influenza virus-infected mice. Hum Vaccin Immunother 11, 1140-1146.
1644 https://doi.org/10.1080/21645515.2015.1009805

1645 Zacca, E.R., Crespo, M.I., Acland, R.P., Roselli, E., Núñez, N.G., Maccioni, M., Maletto, B.A., Pistoresi-Palencia, M.C., Morón, G., 2015. Aging Impairs the Ability of Conventional Dendritic Cells to Cross-Prime CD8+ T Cells upon Stimulation with a TLR7 Ligand. PLoS ONE 10, e0140672.
1649 https://doi.org/10.1371/journal.pone.0140672

1650 Zhang, C., Wang, X.-M., Li, S.-R., Twelkmeyer, T., Wang, W.-H., Zhang, S.-Y., Wang, S.-F., Chen, J.-Z., Jin, X., Wu, Y.-Z., Chen, X.-W., Wang, S.-D., Niu, J.-Q., Chen, H.-R., Tang, H., 2019. NKG2A is a NK cell exhaustion checkpoint for HCV persistence. Nat Commun 10, 1507. https://doi.org/10.1038/s41467-019-09212-y

1654 Zhang, Y., Wang, Y., Gilmore, X., Xu, K., Wyde, P.R., Mbawuike, I.N., 2002. An aged mouse model for RSV infection and diminished CD8(+) CTL responses. Exp. Biol. Med. (Maywood) 227, 133-140. https://doi.org/10.1177/153537020222700208

1657 Zhao, Jincun, Zhao, Jingxian, Legge, K., Perlman, S., 2011. Age-related increases in PGD(2) expression impair respiratory DC migration, resulting in diminished T cell responses upon respiratory virus infection in mice. J. Clin. Invest. 121, 4921-4930.
1660 https://doi.org/10.1172/JCI59777

1661 Zheng, M., Gao, Y., Wang, G., Song, G., Liu, S., Sun, D., Xu, Y., Tian, Z., 2020. Functional exhaustion of antiviral lymphocytes in COVID-19 patients. Cell. Mol. Immunol. 17, 533-535. https://doi.org/10.1038/s41423-020-0402-2

1664 Zhu, H., Pace, F., Sangaletti, O., Bianchi Porro, G., 1993. Features of symptomatic gastroesophageal reflux in elderly patients. Scand. J. Gastroenterol. 28, 235-238.
1666 https://doi.org/10.3109/00365529309096078

1667 Zhu, Y., Lin, X., Zhao, F., Shi, X., Li, H., Li, Y., Zhu, W., Xu, X., Li, C., Zhou, G., 2015. Meat, dairy and plant proteins alter bacterial composition of rat gut bacteria.
1669 Sci Rep 5, 15220. https://doi.org/10.1038/srep15220
1670

1671

1672

1673

1674 FIGURE LEGENDS

1675 **Figure 1: Microbiota is a central element connecting malnutrition and declining physiological functions in the elderly.** The decline in many physiological functions, occurring at an advanced age, are associated with changes in the microbiota structure and function in the gut and other organs. These aspects are affected by type and composition of food intake and diets.

1680 **Figure 2: Hallmarks of the ageing lung and key cellular players involved in senescence.**

1681
1682 **Figure 3: Continuum and basis for the communication pathways between the gut and lung microbiota.** The oral and nasal cavities are the major points of entry for microorganisms to colonise both the gastrointestinal and the respiratory tracts. In addition, transport of metabolites and immune cells through the blood and lymph circulatory systems allows for signal transduction between the two tissues.

1683
1684
1685
1686
1687 **Figure 4: The slippery slope of malnutrition in the elderly.** Malnutrition in the elderly leads to a sequence of reversible and irreversible pathophysiological changes leading to the degradation of the general state of the individual. One of the early signs of a degrading health is lung infection. We propose that targeting malnutrition, and more specifically gut microbiota, using probiotics containing foods, would help reverse this chain of events, thus preventing further health degradation.

1693

1694
Inadequate diet / malnutrition

<figure><img src="image_2.png" /></figure>

Gut/Lung Microbiota

Dysbiosis
Changes in composition, activity and topography

<figure><img src="image_3.png" /></figure>

Declining physiological functions

Cognitive

Memory deterioration
Dementia
Memory loss

Sensory

Taste, smell and
appetite deterioration

Immunity

Inflamm-ageing
Increased frequency of
infections
Immune exhaustion

Musculoskeletal

Loss in muscle mass
Loss in strength
Increased frailty and risk of fracture
## Aged lung

- Increased stiffness

- Decreased mucociliary clearance

- Loss in microbiota topography

- Enlarged alveoli

## Age-related lung diseases

- COPD

- Ilioidopathic pulmonary fibrosis

- Lung cancer

- Asthma

- Community acquired pneumonia

## Hallmarks of the ageing lung

<figure><img src="image_4.png" /></figure>

<figure><img src="image_5.png" /></figure>

<figure><img src="image_6.png" /></figure>

<figure><img src="image_7.png" /></figure>
Oral and nasal cavities

10³ (/nasal swab, nasal cavity)

10⁶ (/mL oral wash, oropharynx)

Lungs

10² (/mL bronchoalveolar lavage)

10⁴-10⁵ (/g tissue)

Blood and lymphcirculations

Metabolites,immune cells

<figure><img src="image_8.png" /></figure>

Colonisation frommouth and nose

<figure><img src="image_9.png" /></figure>

Mucociliary clearance

<figure><img src="image_10.png" /></figure>

Gastroesophagealreflux

Gastrointestinal tract

/g tissue)

10² (stomach) to

10¹² (colon)

<figure><img src="image_11.png" /></figure>
Malnutrition

Gut dysbiosis

Immunodeficiency

Respiratory tract infections

Lung dysbiosis

Urinary tract infections

Mental illness

Sarcopenia

Falls

Bedridden

Pressure ulcers

Death

Total or partial irreversibility

Reversibility

Gut eubiosis

<figure><img src="image_12.png" /></figure>

Adequate personalised nutrition

<figure><img src="image_13.png" /></figure>

Lung eubiosis