SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
EMG produced TPA metagenomics assembly of PRJEB35524 data set (A low-digestibility protein supplementation during an energy-restricted diet reduces visceral fat and stimulates gut microbiota aminoacid metabolism in subjects with metabolic syndrome).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB35524, and was assembled with megahit v1.2.9. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system
EMG produced TPA metagenomics assembly of PRJEB17643 data set (A randomized trial of bread consumption: Personal glycemic responses and effects on clinical parameters and gut microbiome).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB17643, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system
The effect of RSV-A M37 infection on the respiratory microbiome of adults

Human volunteer challenge studies uniquely allow investigation of factors with pre-dispose to infection and study of the pre-symptomatic phase of disease. Patients were exposed to RSV on day 0 and throat swabs were collected over the course of infection for quantitative PCR and 16S rRNA sequencing analysis.

Biome: root:Host-associated:Human:Digestive system:Oral:Throat
Viral respiratory tract infections and oropharyngeal microbiome interactions in wheezing children

Early life exposure to both environmental and infectious microorganisms have been implicated as major risk factors in future disease susceptibility. Acute viral infections resulting in respiratory wheeze are not only a major reason for hospital admission in children but also a risk factor for development of asthma. To investigate if the microbiota in the lungs of children was associated with wheeze respiratory samples from children attending a paediatric hospital in Perth were compared to healthy controls using viral PCR and 16s rRNA gene qPCR and sequencing. No significant difference in bacterial diversity was observed between samples from those with wheeze and healthy controls. Within the wheeze cohort, attendance at kindergarten or preschool was associated with increased bacterial diversity. Bacterial biomass was a significant factor in explaining the variation in beta diversity.  Human rhinovirus (HRV) infection was not found to have a significant effect on bacterial alpha or beta diversity.  A significant difference in bacterial richness was observed between HRV-A and HRV-C, however this is likely due to the differences in age group between the to patient cohorts. Random forest models were unable to successfully predict individual OTU’s associated with wheeze or viral infection in this dataset due to the variation in the bacterial community.  The bacterial community within the lungs was found to be diverse and heterogeneous. Age and contact with children at day care or kindergarten were important factors in driving bacterial diversity. However, wheeze and viral infection were not found to show significant differences in the bacterial community.

Biome: root:Host-associated:Human:Respiratory system:Nasopharyngeal
Healthy human lung microbiome from 15 volunteers

Lung metagenomes from 15 healthy volunteers were sequenced (16S V3-V4 region)

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Human lung microbiome in Cystic Fibrosis - 3D reconstruction

explant or post-mortem lung lobes from human with Cystic Fibrosis

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Comparison of the upper and lower airway microbiota

TS and lower airway samples (bronchoalveolar lavage fluid (BALF), bronchial brushings or both) were prospectively collected from 49 children undergoing a clinically indicated fibreoptic bronchoscopy.  Bacterial DNA was extracted for sequencing of the V4 region of the 16S rRNA gene using the Illumina MiSeq.

Biome: root:Host-associated:Human:Respiratory system:Nasopharyngeal
EMG produced TPA metagenomics assembly of the PRJNA397112 data set (Indian Human Gut Microbiome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA397112.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine.

Biome: root:Host-associated:Human:Digestive system
Longitudinal changes in gut microbiome are associated with BMI: insights from a digital therapeutics-based intervention

This study aimed to identify changes in the gut microbiome associated with a reduction in BMI after a dietary and lifestyle intervention for weight loss.

Biome: root:Host-associated:Human:Digestive system
IBD and gut microbiome

Using current knowledge of dietary patterns and components and their relationships to systemic inflammation in IBD this study aimed to describe the mechanistic relationship between dietary intake and gut microbiome composition and function in patients with luminal CD in remission. The first study objective was to characterize the differences in microbiome composition and function in patients consuming a diversified dietary pattern (DD) compared to a nondiversified dietary pattern (NDD). The second study objective was to compare microbiome composition and function between patients in the DD group to patients in the NDD group who received a structured dietary intervention using whole foods over 12 weeks.

Biome: root:Host-associated:Human:Digestive system
Three dimensional cartography of microbiome and metabolome data onto radiological images of the human lung

Our understanding of spatial variation of the chemical and microbial make-up of an entire human organ remains limited, in part due to the size and heterogeneity of human organs and the complexity of the associated metabolome and microbiome. To address this challenge we developed a workflow, including the adaptation of a software, to enable the cartography of metabolomics and microbiome data onto a three dimensional (3D) organ reconstruction built off radiological images. Our methodology enabled for the first time the visualization of the microbial and chemical makeup of a human lung from a cystic fibrosis patient. We detected host-derived molecules, microbial metabolites, different medications, and regiospecific metabolism of medications. Consequently, metabolomics data can now be understood in the context of microbial distributions in the lung. Our tool, which allows visualization of omics data on an organ in 3D and the browsable maps of the first 3D microbiome/metabolome reconstruction on a radiological image of a human lung are an interactive resource for the scientific community.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Tackling the human archaeome: specific archaea detection in the gastrointestinal tract, lung, nose and on skin

Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea have been found to be regular commensals of the human gut, and represent keystone species in metabolic processes.Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with other parts of the human body, besides the gastro-intestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable to characterize the full spectrum of Archaea.The goal of this study was to critically assess PCR-based methods for specific Archaea detection in human tissue samples. We tested approaches to specifically detect M. smithii, M. stadtmanae and M. luminyensis, and to assess the overall archaeal abundance and diversity using next generation sequencing based technology. To test our established protocols, we determined the archaeal diversity associated with human skin, lung (bronchoalveolar lavage), gastrointestinal tract, stool and nose.Detection of Archaea was highly dependent on primer selection and sequence processing pipeline. Our proposed protocol enabled us to retrieve a novel picture of the human archaeome, as we identified for the first time Methanobacterium and Woesearchaeota (DPANN superphylum) to be associated with the human gastrointestinal tract and the human lung, respectively. Similar to bacteria, human-associated archaeal communities were found to group biogeographically, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal GIT, (iii) a mixed skin/GIT landscape for the nose, and (iv) a woesearchaeal lung landscape.Our study highlights the importance of primer and bioinformatics pipeline choice for studying the human archaeome. We were able to establish protocols that enlightened the presence of yet undetected Archaea in all investigated tissue samples and to detect biogeographic patterns of the human archaeome in respiratory tract, the gastrointestinal tract and on skin. Our results are a solid basis for further investigation of the human archaeome, and in the long term to uncover the potential  archaeal role in human health and disease.

Biome: root:Mixed
The Impact of Persistent Bacterial Bronchitis on the Pulmonary Microbiome of Children.

Persistent bacterial bronchitis (PBB) is a leading cause of chronic wet cough in young children. This study aimed to characterise the respiratory bacterial microbiota of healthy children and to assess the impact of the changes associated with the development of PBB. Blind, protected brushings were obtained from 20 healthy controls and 24 children with PBB, with an additional directed sample obtained from PBB patients. DNA was extracted, quantified using a 16S rRNA gene quantitative PCR assay prior to microbial community analysis by 16S rRNA gene sequencing. No significant difference in bacterial diversity or community composition (R2 = 0.01, P = 0.36) was observed between paired blind and non-blind brushes, showing that blind brushings are a valid means of accessing the airway microbiota in PBB A significant decrease in bacterial diversity (P < 0.001) and change in community composition (R2 = 0.08, P = 0.004) was observed between controls and patients. Bacterial communities within patients with PBB were dominated by Proteobacteria, and indicator species analysis showed that Haemophilus and Neisseria were significantly associated with the patient group.  In 15 (52.9%) cases the dominant organism by sequencing was not identified by standard routine clinical culture.The bacteria present in the lungs of patients with PBB were less diverse in terms of richness and evenness. The results validate the clinical diagnosis, and suggest that more attention to bacterial communities in children with chronic cough may lead to more rapid recognition of this condition with earlier treatment and reduction in disease burden.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
The lung microbiota and bacterial abundance in patients with bronchiectasis when clinically stable and during exacerbation

Characterization of bacterial populations in infectious respiratory diseases will provide a better understanding of the relationship between the lung microbiota, disease pathogenesis and treatment outcomes. Objectives: To comprehensively define lung microbiota composition during stable disease and exacerbation in bronchiectasis patients using both strict anaerobic culture and massively parallel pyrosequencing. Methods: Sputum was collected from bronchietasis patients when clinically stable and before and after completion of antibiotic treatment of pulmonary exacerbations. Bacterial abundance and community composition were analyzed using culture and 16S rDNA pyrosequencing. Measurements and Main Results: In clinically stable patients, aerobic and anaerobic bacteria were detected in 40/40 (100%) and 33/40 (83%) sputum samples, respectively. The dominant organisms cultured were P. aeruginosa (n=10 patients), H. influenzae (n=12), S. aureus(n=6), Prevotella (n=18) and Veillonella (n=13). Pyrosequencing generated over 150,000 sequences, representing 113 distinct microbial taxa; the majority of observed community richness resulted from taxa present in low abundance with similar patterns of phyla distribution in clinically stable patients and patients at the onset of exacerbation. Following antibiotic treatment of exacerbation, there was no change in total (p=0.925), aerobic(p=0.917) or anaerobic (p=0.683) viable counts and only a limited shift in community composition. There was also no correlation between lung function and microbial community diversity (ρ=0.123, p=0.549). Conclusions: A complex microbiota is present in the lungs of patients with bronchiectasis. Bacterial density and community diversity remain stable through treatment of exacerbations which suggests that changes in lung microbiota composition do not account for pulmonary exacerbations in patients with bronchiectasis.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Alterations of Microbiota in Urine from Interstitial Cystitis
                patients

Background: Interstitial Cystitis (IC) is a chronic inflammatory
                condition of the bladder with unknown etiology. The aim of this study was to
                characterize the microbial community present in the urine from IC female patients
                and compare this with the microbial profile of asymptomatic healthy female (HF)
                urine. Background: Interstitial Cystitis (IC) is a chronic inflammatory condition of
                the bladder with unknown etiology. The aim of this study was to characterize the
                microbial community present in the urine from IC female patients and compare this
                with the microbial profile of asymptomatic healthy female (HF) urine. Results: The
                composition and distribution of bacterial sequences differed between the urine
                microbiota of IC and HF. Reduced sequence richness and diversity were found for IC
                patient urine, and a significant difference in the community structure of IC urine
                in relation to HF urine was observed. More than 90% of the IC sequence reads were
                identified as belonging to the bacterial genus Lactobacillus, a marked increase
                compared to the 60% in the HF urine. Conclusion: The 16S rDNA sequence data
                demonstrates a shift in the bacterial composition of IC urine. The reduced microbial
                diversity and richness is accompanied by a higher abundance of the bacterial genus
                Lactobacillus, compared to HF urine. This study demonstrates that high throughput
                sequencing analysis of the urine microbiota in IC patients is a powerful tool
                towards a better understanding of this enigmatic disease.

Biome: root:Host-associated:Human:Excretory system:Urethra:Urine
The microbial pathology of asthma

The microbial pathology of asthma study (known as Celtic Fire) is a multi-centre cross-sectional study ofasthmatic subjects (ranging in severity from Global Initiative for Asthma [GINA] step 1 - 5) and healthy controls.Subjects were recruited via three sites in the British Isles: Connolly Hospital, Dublin; The Royal BromptonHospital, London; and Swansea University Medical School, Swansea. Data (demographic and clinical) andsamples were collected from each subject and sent to the central coordinating centre, the Asmarley Centrefor Genomic Medicine (ACGM), and its associated laboratories at the National Heart and Lung Institute (NHLI),Imperial College London (ICL). The target was to recruit 120 asthmatic subjects, 20 non-smoking controlsubjects and 20 smoking control subjects.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Soil bacterial communities under long-term organic production in Buenos Aires, Argentina

Soil bacterial communities under long-term organic production in Buenos Aires, Argentina

Biome: root:Environmental:Terrestrial:Soil
Organic management on soil bacteria, comparison of different type of soils in Buenos Aires, Argentina

Evaluation of organic management in soil bacteria, comparison of different type of soils in Buenos Aires, Argentina

Biome: root:Environmental:Terrestrial:Soil
Habitual dietary fibre intake and gut microbiota responsiveness

Presently, it is difficult to predict how the gut microbiota will respond to a particular dietary intervention. Therefore, the aim of this study was to determine what influence differing habitual dietary fibre intakes had on how the gut microbiota responded to an inulin-type fructan prebiotic

Biome: root:Host-associated:Human:Digestive system
Microbiota Brain Axis in Alzheimers Disease MIND Diet Induced Effects

Alzheimers disease is a public health concern and the current study leverages a phase III randomized, interventional clinical trial to evaluate the ability of a dietary intervention to influence age associated cognitive decline in a population at risk for Alzheimers disease. Diet influences the intestinal microbiota, thus the current study investigated diet induced changes in the intestinal microbiota as a mechanism by which dietary interventions exert beneficial effects on cognition and Alzheimers disease pathogenesis. Subjects fecal baseline samples were analyzed using 16S rRNA gene amplicon sequencing. The relationship between the microbiota and baseline clinical and experimental variables were evaluated.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Modulatory Effects of Triphala and Manjistha Dietary Supplementation on Human Gut Microbiota: A Double-Blind, Randomized, Placebo-Controlled Pilot Study

We evaluated the impact of two medicinal herbs, triphala and manjistha on gut microbiota composition following a 4 week randomized, double blind placebo control intervention by profiling fecal communities by 16S rRNA profiling.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Gut microbiome alterations after high-fat low-carbohydrate weight reduction diet: pros and cons

OBJECTIVE The objectives were 1) determination of microbial composition of obese and normal weight subjects, 2) calculation of fiber composition of specially assigned low-calorie weight loss diet (WLD), 3) identification of microbial changes after WLD and improvements in health characteristics and associations of microbiota to fiber consumption profiles.METHODSA total of 19 overweight/obese participants with body mass index (BMI) of 28.9-44.4 kg/m2 were assigned to 20-40 % reduced calories high-fat low-carbohydrate diet for 4 weeks. Protein and fat content in composed diet was 1.5 times higher compared to that in average diet of normal weight group, while carbohydrate content was 2 times lower. Total fiber content was comparable to normal weight group. Food consumption data were obtained from assigned meals. Database of specific fiber composition of different food categories was developed and macronutrient, total and specific fiber consumption were calculated. Microbial composition was analysed before and after the intervention from 2 sequential samples by 16S rRNA sequencing. RESULTS:During intervention BMI reduced in average 2.5 ± 0.6 kg/m2 and stool frequency was normalized. Assigned diet induced significant changes in fecal microbiota. Abundance of bile resistant bacteria (Alistipes, Odoribacter splanchnicus), Ruminococcus bicirculans and Butyricimonas but also Enterobacteriaceae increased. Alistipes has been associated with lower BMI and Butyricimonas with higher values of HDL-cholesterol in blood. Importantly, abundance of bacteria often associated with inflammation such as Collinsella and Dorea decreased in parallel with decrease of BMI. Furthermore, the abundance of bifidobacteria decreased, which can be attributed to relatively low consumption of grains.  CONCLUSIONS:In conclusion, results showed that short intervention studies can alter microbial community structure and gave relevant insights into development of different dietary concepts.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
The dynamics of the pulmonary microbiome during mechanical ventilation in the intensive care unit and the association with occurrence of pneumonia.

Rationale: Mechanical ventilation is assumed to cause a shift in pulmonary microbial communities. Ventilator-associated pneumonia (VAP) is a frequent complication of prolonged mechanical ventilation and has a considerable morbidity and mortality. In this study we hypothesized that microbial diversity lowers with prolonged mechanical ventilation and as antibiotics are administrated; there was an effect of dominance  of a subset of well-adapted bacterial pathogens and these selection was more profound in patients that developed VAP. Methods: This is a case–control longitudinal study of patients that were originally included in an international multi–centre prospective observational cohort study of the predictive value of biological markers for development of VAP. Repeated sampling approach was applied during mechanical ventilation. Total DNA was extracted from endotracheal aspirates and variable regions 2 and 3 of bacterial 16S rRNA gene were amplified and sequenced. Results: Antibiotic use was not associated with  bacterial biodiversity decrease. There was an increase in relative abundance of Pseudomonadales, Enterobacteriales, Bacillales, and Burkholderiales within mechanical ventilation period, however it was not correlated with VAP development. In the microbial network potential pathogens Acinetobacter, Pseudomonas, Staphylococcus, Haemophilus tend to mutually exclude other species.  Conclusion: Repeated sampling approach is a useful tool to study respiratory microbiome. Together with characterization of host immune factors it will improve our understanding of microbiome dysbiosis caused by mechanical ventilation.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Trachea