bluuebunny/crossref_metadata_2025 huggingface dataset:
Distinct Changes Occur in the Human Breast Milk Microbiome Between Early and Established Lactation in Breastfeeding Guatemalan Mothers
Authors: Gonzalez Emmanuel , Brereton Nicholas J. B. , Li Chen , Lopez Leyva Lilian , Solomons Noel W. , Agellon Luis B. , Scott Marilyn E. , Koski Kristine G.
Published: February 2021

Human breast milk contains a diverse community of bacteria, but as breast milk microbiome studies have largely focused on mothers from high income countries where few women breastfeed to 6 months, the temporal changes in the breast milk microbiome that occur during later lactation stages have not been explored. For this cross-sectional study, microbiota from breast milk samples ofMam-Mayan mothers living in eight remote rural communities in the Western Highlands of Guatemala were analyzed. All mothers delivered vaginally and breastfed their infants for 6 months. Breast milk from 76 unrelated mothers was used to compare two lactation stages, either “early” (6–46 days post-partum,n= 33) or “late” (109–184 days post-partum,n= 43). Breast milk microbial communities were assessed using 16S ribosomal RNA gene sequencing and lactation stages were compared using DESeq2 differential abundance analysis. A total of 1,505 OTUs were identified, including 287 which could be annotated as putative species. Among several maternal factors, lactation stage explained microbiome variance and inertia in ordination with the most significance (p< 0.001). Differential abundance analysis identified 137 OTUs as significantly higher in either early or late lactation. These included a general shift fromStaphylococcusandStreptococcusspecies in early lactation toSphingobiumandPseudomonasspecies in late lactation. Species enriched in early lactation included putative commensal bacteria known to colonize the infant oral and intestinal tracts whereas species enriched in late lactation had a uniform functional trait associated with aromatic compound degradation. Differentially abundant species also included several species which have not previously been reported within breast milk, such asJanthinobacterium agaricidamnosum,Novosphingobium clariflavum,Ottowia beijingensis, andFlavobacterium cucumis.These discoveries describe temporal changes to the breast milk microbiome of healthy Guatemalan mothers from early to late lactation. Collectively, these findings illustrate how studying under-represented human populations might advance our understanding of factors that modulate the human milk microbiome in low and middle income countries (LMIC).
Reciprocal Packaging of the Main Structural Proteins of Type 1 Fimbriae and Flagella in the Outer Membrane Vesicles of “Wild Type” Escherichia coli Strains
Authors: Blackburn Sarah A. , Shepherd Mark , Robinson Gary K.
Published: February 2021

Fundamental aspects of outer membrane vesicle (OMV) biogenesis and the engineering of producer strains have been major research foci for many in recent years. The focus of this study was OMV production in a variety of Escherichia coli strains including wild type (WT) (K12 and BW25113), mutants (from the Keio collection) and proprietary [BL21 and BL21 (DE3)] strains. The present study investigated the proteome and prospective mechanism that underpinned the key finding that the dominant protein present in E. coli K-12 WT OMVs was fimbrial protein monomer (FimA) (a polymerizable protein which is the key structural monomer from which Type 1 fimbriae are made). However, mutations in genes involved in fimbriae biosynthesis (ΔfimA, B, C, and F) resulted in the packaging of flagella protein monomer (FliC) (the major structural protein of flagella) into OMVs instead of FimA. Other mutations (ΔfimE, G, H, I, and ΔlrhA–a transcriptional regulator of fimbriation and flagella biosynthesis) lead to the packaging of both FimA and Flagellin into the OMVs. In the majority of instances shown within this research, the production of OMVs is considered in K-12 WT strains where structural appendages including fimbriae or flagella are temporally co-expressed throughout the growth curve as shown previously in the literature. The hypothesis, proposed and supported within the present paper, is that the vesicular packaging of the major FimA is reciprocally regulated with the major FliC in E. coli K-12 OMVs but this is abrogated in a range of mutated, non-WT E. coli strains. We also demonstrate, that a protein of interest (GFP) can be targeted to OMVs in an E. coli K-12 strain by protein fusion with FimA and that this causes normal packaging to be disrupted. The findings and underlying implications for host interactions and use in biotechnology are discussed.
Applying EEM- PARAFAC Analysis With Quantitative Real-Time PCR to Monitor Methanogenic Activity of High-Solid Anaerobic Digestion of Rice Straw
Authors: Deng Yuying , Li Weihua , Ruan Wenquan , Huang Zhenxing
Published: February 2021

The methanogenic activity is an important indicator to assess the efficiency of high-solid anaerobic digestion. However, it is not yet elucidated clearly how to detect the parameter rapidly and reliably in the rice straw feeding reactor. Co-inoculated with ruminal digesta and anaerobic sludge, the digestion performance was studied at three different organic loading rates (OLRs). The excitation emission matrix–parallel factor analysis (EEM–PARAFAC) was used to detect dynamic changes in the characteristic of fluorescence components. Our results revealed that CH4 productivity reached 280.90 mL/g volatile solid (VS) with a 54.39% CH4 content under the OLR of 2.26 g/(L⋅d), which amount to 80.29% of its theoretical value. At the OLR of 2.47 g/(L⋅d), the average accumulated NH4+ concentration was 1082.63 mg/L, which resulted in the hydrogenotrophic Methanobacteriales decreasing from 1.70 × 109 to 1.04 × 106 copies/g in the solid residues, whereas the acetotrophic Methanosarcinales increased from 7.89 × 106 to 9.44 × 106 copies/g. The dynamics of the methanogenic community consequently influenced the bioconversion efficiency of rice straw, and CH4 productivity was reduced to 256.54 mL/g VS. The three fluorescent components, at the excitation/emission wavelength of 420 nm/470 nm, 340 nm/430 nm, and 280 nm/340 nm, were decomposed by PARAFAC model in the digestate. Fluorescence intensities of coenzyme F420 and NADH reflected the dynamic changes of CH4-producing activity and anaerobic digestion efficiency, respectively. The coenzyme F420, unique to hydrogenotrophic methanogens, was correlated with methane yield, suggesting they played a dominant role in the anaerobic reactor. This study demonstrates that the EEM–PARAFAC combined with Q-PCR can be used to characterize methanogenic activity variation during the high-solid anaerobic digestion of rice straw with 15% total solid (TS).
The Genomic Capabilities of Microbial Communities Track Seasonal Variation in Environmental Conditions of Arctic Lagoons
Authors: Baker Kristina D. , Kellogg Colleen T. E. , McClelland James W. , Dunton Kenneth H. , Crump Byron C.
Published: February 2021

In contrast to temperate systems, Arctic lagoons that span the Alaska Beaufort Sea coast face extreme seasonality. Nine months of ice cover up to ∼1.7 m thick is followed by a spring thaw that introduces an enormous pulse of freshwater, nutrients, and organic matter into these lagoons over a relatively brief 2–3 week period. Prokaryotic communities link these subsidies to lagoon food webs through nutrient uptake, heterotrophic production, and other biogeochemical processes, but little is known about how the genomic capabilities of these communities respond to seasonal variability. Replicate water samples from two lagoons and one coastal site near Kaktovik, AK were collected in April (full ice cover), June (ice break up), and August (open water) to represent winter, spring, and summer, respectively. Samples were size fractionated to distinguish free-living and particle-attached microbial communities. Multivariate analysis of metagenomes indicated that seasonal variability in gene abundances was greater than variability between size fractions and sites, and that June differed significantly from the other months. Spring (June) gene abundances reflected the high input of watershed-sourced nutrients and organic matter via spring thaw, featuring indicator genes for denitrification possibly linked to greater organic carbon availability, and genes for processing phytoplankton-derived organic matter associated with spring blooms. Summer featured fewer indicator genes, but had increased abundances of anoxygenic photosynthesis genes, possibly associated with elevated light availability. Winter (April) gene abundances suggested low energy inputs and autotrophic bacterial metabolism, featuring indicator genes for chemoautotrophic carbon fixation, methane metabolism, and nitrification. Winter indicator genes for nitrification belonged to Thaumarchaeota and Nitrosomonadales, suggesting these organisms play an important role in oxidizing ammonium during the under-ice period. This study shows that high latitude estuarine microbial assemblages shift metabolic capabilities as they change phylogenetic composition between these extreme seasons, providing evidence that these communities may be resilient to large hydrological events in a rapidly changing Arctic.
Temperature Stress Induces Shift From Co-Existence to Competition for Organic Carbon in Microalgae-Bacterial Photobioreactor Community – Enabling Continuous Production of Microalgal Biomass
Authors: Sörenson Eva , Capo Eric , Farnelid Hanna , Lindehoff Elin , Legrand Catherine
Published: February 2021

To better predict the consequences of environmental change on aquatic microbial ecosystems it is important to understand what enables community resilience. The mechanisms by which a microbial community maintain its overall function, for example, the cycling of carbon, when exposed to a stressor, can be explored by considering three concepts: biotic interactions, functional adaptations, and community structure. Interactions between species are traditionally considered as, e.g., mutualistic, parasitic, or neutral but are here broadly defined as either coexistence or competition, while functions relate to their metabolism (e.g., autotrophy or heterotrophy) and roles in ecosystem functioning (e.g., oxygen production, organic matter degradation). The term structure here align with species richness and diversity, where a more diverse community is though to exhibit a broader functional capacity than a less diverse community. These concepts have here been combined with ecological theories commonly used in resilience studies, i.e., adaptive cycles, panarchy, and cross-scale resilience, that describe how the status and behavior at one trophic level impact that of surrounding levels. This allows us to explore the resilience of a marine microbial community, cultivated in an outdoor photobioreactor, when exposed to a naturally occurring seasonal stress. The culture was monitored for 6weeks during which it was exposed to two different temperature regimes (21 ± 2 and 11 ± 1°C). Samples were taken for metatranscriptomic analysis, in order to assess the regulation of carbon uptake and utilization, and for amplicon (18S and 16S rRNA gene) sequencing, to characterize the community structure of both autotrophs (dominated by the green microalgaeMychonastes) and heterotrophs (associated bacterioplankton). Differential gene expression analyses suggested that community function at warm temperatures was based on concomitant utilization of inorganic and organic carbon assigned to autotrophs and heterotrophs, while at colder temperatures, the uptake of organic carbon was performed primarily by autotrophs. Upon the shift from high to low temperature, community interactions shifted from coexistence to competition for organic carbon. Network analysis indicated that the community structure showed opposite trends for autotrophs and heterotrophs in having either high or low diversity. Despite an abrupt change of temperature, the microbial community as a whole responded in a way that maintained the overall level of diversity and function within and across autotrophic and heterotrophic levels. This is in line with cross-scale resilience theory describing how ecosystems may balance functional overlaps within and functional redundancy between levels in order to be resilient to environmental change (such as temperature).
Trp-Containing Antibacterial Peptides Impair Quorum Sensing and Biofilm Development in Multidrug-Resistant Pseudomonas aeruginosa and Exhibit Synergistic Effects With Antibiotics
Authors: Shang Dejing , Han Xue , Du Wanying , Kou Zhiru , Jiang Fengquan
Published: February 2021

Pseudomonas aeruginosa uses quorum sensing (QS) to control virulence, biofilm formation and antibiotic efflux pump expression. The development of effective small molecules targeting the QS system and biofilm formation represents a novel attractive strategy. In this present study, the effects of a series of Trp-containing peptides on the QS-regulated virulence and biofilm development of multidrug-resistant P. aeruginosa, as well as their synergistic antibacterial activity with three classes of traditional chemical antibiotics were investigated. The results showed that Trp-containing peptides at low concentrations reduced the production of QS-regulated virulence factors by downregulating the gene expression of both the las and rhl systems in the strain MRPA0108. Biofilm formation was inhibited in a concentration-dependent manner, which was associated with extracellular polysaccharide production inhibition by downregulating pelA, algD, and pslA transcription. These changes correlated with alterations in the extracellular production of pseudomonal virulence factors and swarming motility. In addition, the combination of Trp-containing peptides at low concentration with the antibiotics ceftazidime and piperacillin provided synergistic effects. Notably, L11W and L12W showed the highest synergy with ceftazidime and piperacillin. A mechanistic study demonstrated that the Trp-containing peptides, especially L12W, significantly decreased β-lactamase activity and expression of efflux pump genes OprM, MexX, and MexA, resulting in a reduction in antibiotic efflux from MRPA0108 cells and thus increasing the antibacterial activity of these antibiotics against MRPA0108.
Intercropping With Aromatic Plants Increased the Soil Organic Matter Content and Changed the Microbial Community in a Pear Orchard
Authors: Zhang Yan , Han Mingzheng , Song Mengni , Tian Ji , Song Beizhou , Hu Yujing , Zhang Jie , Yao Yuncong
Published: February 2021

Intercropping influences the soil microbiota via litter and root exudate inputs, but the mechanisms by which root exudates mediate the soil microbial community and soil organic matter (SOM) are still unclear. In this study, we selected three aromatic plants (Ocimum basilicum, Tr1;Satureja hortensis, Tr2;Ageratum houstonianum, Tr3) as intercrops that separately grew between rows of pear trees, and no plants were grown as the control in a pear orchard during the spring–summer season for 3 years. The soil from each plot was collected using a stainless-steel corer by five-point sampling between rows of pear trees. The bacterial and fungal communities of the different aromatic intercrops were analyzed by 16S and ITS rRNA gene amplicon sequencing; their functional profiles were predicted by PICRUSt and FUNGuild analyses. The root exudates of the aromatic plants were analyzed by a liquid chromatography-tandem mass spectrometry (LC-MS) system. Compared with the control treatment, all intercropping treatments with aromatic plants significantly increased SOM and soil water content and decreased pH values. The contents of total nitrogen and alkali-hydrolyzable nitrogen in Tr1 and Tr2 were higher than those in Tr3. In Tr3 soil, the relative content of saccharides increased little, whereas the changes in amine (increases) and alcohols (decreases) were rapid.Ageratum houstonianumintercropping decreased the microbial community diversity and significantly influenced the relative abundances of the dominant microbiota (Actinobacteria, Verrucomicrobia, Gemmatimonadetes, Cyanobacteria, Ascomycota, and Basidiomycota) at the phylum, class, and order levels, which increased the assemblage of functional groups (nitrite ammonification, nitrate ammonification, and ureolysis groups). Our study suggested that the main root exudates from aromatic plants shaped the microbial diversity, structure, and functional groups related to the N cycle during SOM mineralization and that intercropping with aromatic plants (especially basil and summer savory) increased N release in the orchard soil.
Multifaceted Mechanism of Amicoumacin A Inhibition of Bacterial Translation
Authors: Maksimova Elena M. , Vinogradova Daria S. , Osterman Ilya A. , Kasatsky Pavel S. , Nikonov Oleg S. , Milón Pohl , Dontsova Olga A. , Sergiev Petr V. , Paleskava Alena , Konevega Andrey L.
Published: February 2021

Amicoumacin A (Ami) halts bacterial growth by inhibiting the ribosome during translation. The Ami binding site locates in the vicinity of the E-site codon of mRNA. However, Ami does not clash with mRNA, rather stabilizes it, which is relatively unusual and implies a unique way of translation inhibition. In this work, we performed a kinetic and thermodynamic investigation of Ami influence on the main steps of polypeptide synthesis. We show that Ami reduces the rate of the functional canonical 70S initiation complex (IC) formation by 30-fold. Additionally, our results indicate that Ami promotes the formation of erroneous 30S ICs; however, IF3 prevents them from progressing towards translation initiation. During early elongation steps, Ami does not compromise EF-Tu-dependent A-site binding or peptide bond formation. On the other hand, Ami reduces the rate of peptidyl-tRNA movement from the A to the P site and significantly decreases the amount of the ribosomes capable of polypeptide synthesis. Our data indicate that Ami progressively decreases the activity of translating ribosomes that may appear to be the main inhibitory mechanism of Ami. Indeed, the use of EF-G mutants that confer resistance to Ami (G542V, G581A, or ins544V) leads to a complete restoration of the ribosome functionality. It is possible that the changes in translocation induced by EF-G mutants compensate for the activity loss caused by Ami.
Microbial Communities in Flexible Biomethanation of Hydrogen Are Functionally Resilient Upon Starvation
Authors: Logroño Washington , Popp Denny , Nikolausz Marcell , Kluge Paul , Harms Hauke , Kleinsteuber Sabine
Published: February 2021

Ex situ biomethanation allows the conversion of hydrogen produced from surplus electricity to methane. The flexibility of the process was recently demonstrated, yet it is unknown how intermittent hydrogen feeding impacts the functionality of the microbial communities. We investigated the effect of starvation events on the hydrogen consumption and methane production rates (MPRs) of two different methanogenic communities that were fed with hydrogen and carbon dioxide. Both communities showed functional resilience in terms of hydrogen consumption and MPRs upon starvation periods of up to 14 days. The origin of the inoculum, community structure and dominant methanogens were decisive for high gas conversion rates. Thus, pre-screening a well performing inoculum is essential to ensure the efficiency of biomethanation systems operating under flexible gas feeding regimes. Our results suggest that the type of the predominant hydrogenotrophic methanogen (here: Methanobacterium) is important for an efficient process. We also show that flexible biomethanation of hydrogen and carbon dioxide with complex microbiota is possible while avoiding the accumulation of acetate, which is relevant for practical implementation. In our study, the inoculum from an upflow anaerobic sludge blanket reactor treating wastewater from paper industry performed better compared to the inoculum from a plug flow reactor treating cow manure and corn silage. Therefore, the implementation of the power-to-gas concept in wastewater treatment plants of the paper industry, where biocatalytic biomass is readily available, may be a viable option to reduce the carbon footprint of the paper industry.
Transcriptomic Analysis of Wheat Seedling Responses to the Systemic Acquired Resistance Inducer N-Hydroxypipecolic Acid
Authors: Zhang Eric T. , Zhang Hao , Tang Weihua
Published: February 2021

The fungal pathogenFusarium graminearumcan cause destructive diseases on wheat, such as Fusarium head blight and Fusarium crown rot. However, a solution is still unavailable. Recently, N-hydroxypipecolic acid (NHP) was identified as a potent signaling molecule that is capable of inducing systemic acquired resistance to bacterial, oomycete, and fungal infection in several plant species. However, it is not clear whether NHP works in wheat to resistF. graminearuminfection or how NHP affects wheat gene expression. In this report, we showed that pretreatment with NHP moderately increased wheat seedling resistance toF. graminearum. Using RNA sequencing, we found that 17% of wheat-expressed genes were significantly affected by NHP treatment. The genes encoding nucleotide-binding leucine-rich repeat immune receptors were significantly overrepresented in the group of genes upregulated by NHP treatment, while the genes encoding receptor-like kinases were not. Our results suggested that NHP treatment sensitizes a subset of the immune surveillance system in wheat seedlings, thereby facilitating wheat defense againstF. graminearuminfection.
Cytophaga hutchinsonii SprA and SprT Are Essential Components of the Type IX Secretion System Required for Ca2+ Acquisition, Cellulose Degradation, and Cell Motility
Authors: Gao Lijuan , Tan Yahong , Zhang Weican , Qi Qingsheng , Lu Xuemei
Published: February 2021

The type IX secretion system (T9SS) is a novel protein secretion system, which is found in and confined to the phylumBacteroidetes. T9SS is involved in the secretion of virulence factors, cell surface adhesins, and complex biopolymer degrading enzymes to the cell surface or extracellular medium.Cytophaga hutchinsoniiis a widely distributed bacterium, which is able to efficiently digest cellulose and rapidly glide along the solid surfaces.C. hutchinsoniihas a full set of orthologs of T9SS components. However, the functions of most homologous proteins have not been verified. InC.hutchinsonii, CHU_0029 and CHU_2709 are similar in sequence toFlavobacterium johnsoniaeT9SS components SprA and SprT, respectively. In this study, the single deletion mutants ofchu_0029(sprA) andchu_2709(sprT) were obtained using a complex medium with the addition of Ca2+and Mg2+. Single deletion ofsprAorsprTresulted in defects in cellulose utilization and gliding motility. Moreover, the ΔsprAand ΔsprTmutants showed growth defects in Ca2+- and Mg2+-deficient media. The results of ICP-MS test showed that both the whole cell and intracellular concentrations of Ca2+were dramatically reduced in the ΔsprAand ΔsprTmutants, indicating that SprA and SprT are both important for the assimilation of trace amount of Ca2+. While the assimilation of Mg2+was not obviously influenced in the ΔsprAand ΔsprTmutants. Through proteomics analysis of the cell surface proteins of the wild type and mutants, we found that the ΔsprAand ΔsprTmutants were defective in secretion of the majority of T9SS substrates. Together, these results indicate that SprA and SprT are both essential components ofC.hutchinsoniiT9SS, which is required for protein secretion, Ca2+acquisition, cellulose degradation, and gliding motility inC. hutchinsonii.Our study shed more light on the functions of SprA and SprT in T9SS, and further proved the link between the T9SS and Ca2+uptake system.
Fungal G-Protein-Coupled Receptors: A Promising Mediator of the Impact of Extracellular Signals on Biosynthesis of Ochratoxin A
Authors: Gao Jing , Xu Xinge , Huang Kunlun , Liang Zhihong
Published: February 2021

G-protein-coupled receptors (GPCRs) are transmembrane receptors involved in transducing signals from the external environment inside the cell, which enables fungi to coordinate cell transport, metabolism, and growth to promote their survival, reproduction, and virulence. There are 14 classes of GPCRs in fungi involved in sensing various ligands. In this paper, the synthesis of mycotoxins that are GPCR-mediated is discussed with respect to ligands, environmental stimuli, and intra-/interspecific communication. Despite their apparent importance in fungal biology, very little is known about the role of ochratoxin A (OTA) biosynthesis byAspergillus ochraceusand the ligands that are involved. Fortunately, increasing evidence shows that the GPCR that involves the AF/ST (sterigmatocystin) pathway in fungi belongs to the same genus. Therefore, we speculate that GPCRs play an important role in a variety of environmental signals and downstream pathways in OTA biosynthesis. The verification of this inference will result in a more controllable GPCR target for control of fungal contamination in the future.
Microbial Communities Under Distinct Thermal and Geochemical Regimes in Axial and Off-Axis Sediments of Guaymas Basin
Authors: Teske Andreas , Wegener Gunter , Chanton Jeffrey P. , White Dylan , MacGregor Barbara , Hoer Daniel , de Beer Dirk , Zhuang Guangchao , Saxton Matthew A. , Joye Samantha B. , Lizarralde Daniel , Soule S. Adam , Ruff S. Emil
Published: February 2021

Cold seeps and hydrothermal vents are seafloor habitats fueled by subsurface energy sources. Both habitat types coexist in Guaymas Basin in the Gulf of California, providing an opportunity to compare microbial communities with distinct physiologies adapted to different thermal regimes. Hydrothermally active sites in the southern Guaymas Basin axial valley, and cold seep sites at Octopus Mound, a carbonate mound with abundant methanotrophic cold seep fauna at the Central Seep location on the northern off-axis flanking regions, show consistent geochemical and microbial differences between hot, temperate, cold seep, and background sites. The changing microbial actors include autotrophic and heterotrophic bacterial and archaeal lineages that catalyze sulfur, nitrogen, and methane cycling, organic matter degradation, and hydrocarbon oxidation. Thermal, biogeochemical, and microbiological characteristics of the sampling locations indicate that sediment thermal regime and seep-derived or hydrothermal energy sources structure the microbial communities at the sediment surface.
Organic Waste Substrates Induce Important Shifts in Gut Microbiota of Black Soldier Fly (Hermetia illucens L.): Coexistence of Conserved, Variable, and Potential Pathogenic Microbes
Authors: Tanga Chrysantus M. , Waweru Jacqueline Wahura , Tola Yosef Hamba , Onyoni Abel Anyega , Khamis Fathiya M. , Ekesi Sunday , Paredes Juan C.
Published: February 2021

The sustainable utilization of black soldier fly (BSF) for recycling organic waste into nutrient-rich biomass, such as high-quality protein additive, is gaining momentum, and its microbiota is thought to play important roles in these processes. Several studies have characterized the BSF gut microbiota in different substrates and locations; nonetheless, in-depth knowledge on community stability, consistency of member associations, pathogenic associations, and microbe–microbe and host–microbe interactions remains largely elusive. In this study, we characterized the bacterial and fungal communities of BSF larval gut across four untreated substrates (brewers’ spent grain, kitchen food waste, poultry manure, and rabbit manure) using 16S and ITS2 amplicon sequencing. Results demonstrated that substrate impacted larval weight gain from 30 to 100% gain differences among diets and induced an important microbial shift in the gut of BSF larvae: fungal communities were highly substrate dependent with Pichia being the only prevalent genus across 96% of the samples; bacterial communities also varied across diets; nonetheless, we observed six conserved bacterial members in 99.9% of our samples, namely, Dysgonomonas, Morganella, Enterococcus, Pseudomonas, Actinomyces, and Providencia. Among these, Enterococcus was highly correlated with other genera including Morganella and Providencia. Additionally, we showed that diets such as rabbit manure induced a dysbiosis with higher loads of the pathogenic bacteria Campylobacter. Together, this study provides the first comprehensive analysis of bacterial and fungal communities of BSF gut across untreated substrates and highlights conserved members, potential pathogens, and their interactions. This information will contribute to the establishment of safety measures for future processing of BSF larval meals and the creation of legislation to regulate their use in animal feeds.
The Alternative Sigma Factor RpoE2 Is Involved in the Stress Response to Hypochlorite and in vivo Survival of Haemophilus influenzae
Authors: Nasreen Marufa , Fletcher Aidan , Hosmer Jennifer , Zhong Qifeng , Essilfie Ama-Tawiah , McEwan Alastair G. , Kappler Ulrike
Published: February 2021

Extracytoplasmic function (ECF) sigma factors underpin the ability of bacteria to adapt to changing environmental conditions, a process that is particularly relevant in human pathogens that inhabit niches where human immune cells contribute to high levels of extracellular stress. Here, we have characterized the previously unstudied RpoE2 ECF sigma factor from the human respiratory pathogen H. influenzae (Hi) and its role in hypochlorite-induced stress. Exposure of H. influenzae to oxidative stress (HOCl, H2O2) increased rpoE2 gene expression, and the activity of RpoE2 was controlled by a cytoplasmic 67-aa anti-sigma factor, HrsE. RpoE2 regulated the expression of the periplasmic MsrAB peptide methionine sulfoxide reductase that, in H. influenzae, is required for HOCl resistance, thus linking RpoE2 to HOCl stress. Interestingly, a HiΔrpoE2 strain had wild-type levels of resistance to oxidative stress in vitro, but HiΔrpoE2 survival was reduced 26-fold in a mouse model of lung infection, demonstrating the relevance of this sigma factor for H. influenzae pathogenesis. The HiRpoE2 system has some similarity to the ECF sigma factors described in Streptomyces and Neisseria sp. that also control the expression of msr genes. However, HiRpoE2 regulation extended to genes encoding other periplasmic damage repair proteins, an operon containing a DoxX-like protein, and also included selected OxyR-controlled genes. Based on our results, we propose that the highly conserved HiRpoE2 sigma factor is a key regulator of H. influenzae responses to oxidative damage in the cell envelope region that controls a variety of target genes required for survival in the host.
Development of a Virus-Based Reporter System for Functional Analysis of Plant rRNA Gene Promoter
Authors: Xu Li , Li Zhiying , Wang Sheng
Published: February 2021

Reporter gene-based expression systems have been intensively used in plants for monitoring the activity of gene promoters. However, rRNA transcripts are unable to efficiently express a reporter gene due to a lack of a 5' cap. Because of this obstacle, plant rRNA gene promoters are less well characterized to this day. We developed a virus-based reporter system to characterize the Nicotiana benthamiana rRNA (NbrRNA) gene promoter. The system utilizes the cap-independent translation strategy of viral genomic mRNA and uses the virus-expressed green fluorescent protein (GFP) as an indicator of the rRNA gene promoter activity in virus-infected plants. Based on the reporter system, some characteristics of the N. benthamiana rRNA gene promoter were revealed. The results showed that the strength of the NbrRNA gene promoter was lower than that of the cauliflower mosaic virus (CaMV) 35S promoter, a well-characterized polymerase II promoter. The sequences between −77 and +42 are sufficient for the NbrRNA gene promoter-mediated transcription and the NbrRNA gene promoter may lack the functional upstream control element (UCE). Interestingly, NbrRNA gene promoter activity was increased when the 35S enhancer was introduced. An intron-excision mediated assay revealed that the NbrRNA gene promoter can be inefficiently used by RNA polymerase II in N. benthamiana cells. This virus-based reporter system is easier to operate and more convenient when compared with the previously Pol I promoter assays. And it offers a promising solution to analyzing the functional architecture of plant rRNA gene promoter.
Methylacidimicrobium thermophilum AP8, a Novel Methane- and Hydrogen-Oxidizing Bacterium Isolated From Volcanic Soil on Pantelleria Island, Italy
Authors: Picone Nunzia , Blom Pieter , Wallenius Anna J. , Hogendoorn Carmen , Mesman Rob , Cremers Geert , Gagliano Antonina L. , D’Alessandro Walter , Quatrini Paola , Jetten Mike S. M. , Pol Arjan , Op den Camp Huub J. M.
Published: February 2021

The Favara Grande is a geothermal area located on Pantelleria Island, Italy. The area is characterized high temperatures in the top layer of the soil (60°C), low pH (3–5) and hydrothermal gas emissions mainly composed of carbon dioxide (CO2), methane (CH4), and hydrogen (H2). These geothermal features may provide a suitable niche for the growth of chemolithotrophic thermoacidophiles, including the lanthanide-dependent methanotrophs of the phylum Verrucomicrobia. In this study, we started enrichment cultures inoculated with soil of the Favara Grande at 50 and 60°C with CH4 as energy source and medium containing sufficient lanthanides at pH 3 and 5. From these cultures, a verrucomicrobial methanotroph could be isolated via serial dilution and floating filters techniques. The genome of strain AP8 was sequenced and based on phylogenetic analysis we propose to name this new species Methylacidimicrobium thermophilum AP8. The transcriptome data at μmax (0.051 ± 0.001 h−1, doubling time ~14 h) of the new strain showed a high expression of the pmoCAB2 operon encoding the membrane-bound methane monooxygenase and of the gene xoxF1, encoding the lanthanide-dependent methanol dehydrogenase. A second pmoCAB operon and xoxF2 gene were not expressed. The physiology of strain AP8 was further investigated and revealed an optimal growth in a pH range of 3–5 at 50°C, representing the first thermophilic strain of the genus Methylacidimicrobium. Moreover, strain AP8 had a KS(app) for methane of 8 ± 1 μM. Beside methane, a type 1b [NiFe] hydrogenase enabled hydrogen oxidation at oxygen concentrations up to 1%. Taken together, our results expand the knowledge on the characteristics and adaptations of verrucomicrobial methanotrophs in hydrothermal environments and add a new thermophilic strain to the genus Methylacidimicrobium.
Applications of CRISPR/Cas9 in the Synthesis of Secondary Metabolites in Filamentous Fungi
Authors: Jiang Chunmiao , Lv Gongbo , Tu Yayi , Cheng Xiaojie , Duan Yitian , Zeng Bin , He Bin
Published: February 2021

Filamentous fungi possess the capacity to produce a wide array of secondary metabolites with diverse biological activities and structures, such as lovastatin and swainsonine. With the advent of the post-genomic era, increasing amounts of cryptic or uncharacterized secondary metabolite biosynthetic gene clusters are continually being discovered. However, owing to the longstanding lack of versatile, comparatively simple, and highly efficient genetic manipulation techniques, the broader exploration of industrially important secondary metabolites has been hampered thus far. With the emergence of CRISPR/Cas9-based genome editing technology, this dilemma may be alleviated, as this advanced technique has revolutionized genetic research and enabled the exploitation and discovery of new bioactive compounds from filamentous fungi. In this review, we introduce the CRISPR/Cas9 system in detail and summarize the latest applications of CRISPR/Cas9-mediated genome editing in filamentous fungi. We also briefly introduce the specific applications of the CRISPR/Cas9 system and CRISPRa in the improvement of secondary metabolite contents and discovery of novel biologically active compounds in filamentous fungi, with specific examples noted. Additionally, we highlight and discuss some of the challenges and deficiencies of using the CRISPR/Cas9-based genome editing technology in research on the biosynthesis of secondary metabolites as well as future application of CRISPR/Cas9 strategy in filamentous fungi are highlighted and discussed.
Low Levels of Natural Anti-α-N-Acetylgalactosamine (Tn) Antibodies Are Associated With COVID-19
Authors: Breiman Adrien , Ruvoën-Clouet Nathalie , Deleers Marie , Beauvais Tiffany , Jouand Nicolas , Rocher Jézabel , Bovin Nicolai , Labarrière Nathalie , El Kenz Hanane , Le Pendu Jacques
Published: February 2021

Human serum contains large amounts of anti-carbohydrate antibodies, some of which may recognize epitopes on viral glycans. Here, we tested the hypothesis that such antibodies may confer protection against COVID-19 so that patients would be preferentially found among people with low amounts of specific anti-carbohydrate antibodies since individual repertoires vary considerably. After selecting glycan epitopes commonly represented in the human anti-carbohydrate antibody repertoire that may also be expressed on viral glycans, plasma levels of the corresponding antibodies were determined by ELISA in 88 SARS-CoV-2 infected individuals, including 13 asymptomatic, and in 82 non-infected controls. We observed that anti-Tn antibodies levels were significantly lower in patients as compared to non-infected individuals. This was not observed for any of the other tested carbohydrate epitopes, including anti-αGal antibodies used as a negative control since the epitope cannot be synthesized by humans. Owing to structural homologies with blood groups A and B antigens, we also observed that anti-Tn and anti-αGal antibodies levels were lower in blood group A and B, respectively. Analyses of correlations between anti-Tn and the other anti-carbohydrates tested revealed divergent patterns of correlations between patients and controls, suggesting qualitative differences in addition to the quantitative difference. Furthermore, anti-Tn levels correlated with anti-S protein levels in the patients’ group, suggesting that anti-Tn might contribute to the development of the specific antiviral response. Overall, this first analysis allows to hypothesize that natural anti-Tn antibodies might be protective against COVID-19.
Exosomal miR-590-5p in Serum as a Biomarker for the Diagnosis and Prognosis of Gastric Cancer
Authors: Zheng Guo-Dian , Xu Zhi-Yuan , Hu Can , Lv Hang , Xie Hua-Xia , Huang Ting , Zhang Yan-Qiang , Chen Gui-Ping , Fu Yu-Fei , Cheng Xiang-Dong
Published: February 2021

The purpose of this study is to explore the expression of miRNA-590-5p, an exosome of gastric cancer (GC), and to evaluate the suitability of miR-590-5p, an exosome with its own clinical characteristics. Serum samples from 168 gastric cancer patients and 50 matched controls were collected and exosomal RNAs were extracted. After that, miR-590-5p is analyzed by quantitative polymerase chain reaction (qRT-PCR), which is more related to clinical and pathological parameters and patient monitoring data. MGC-803 and HGC-27 cells were treated by miR-590-5p mimics, and then the changes of cell fluidity and invasiveness were monitored. The results showed that the expression level of miR-590-5p in exosomes of healthy observation group, early (I and II) stage group, and late stage (III) group was 30.34 ± 6.35, 6.19 ± 0.81, and 2.9 ± 0.19, respectively (all p < 0.05). ROC (receiver-operating characteristic curve) showed that the AUC (area under the curve) of exosomal miR-590-5p was 0.810 with 63.7% sensitivity and 86% specificity. The expression of exosomal miR-590-5p in serum was related to clinical stage (p = 0.008), infiltration depth, and the expression level of ki-67 (p < 0.001). In addition, Kaplan-Meier analysis showed that the decrease of explicit level of exosomal miR-590-5p was related to the decrease of overall survival rate (p < 0.001). Cox regression analysis showed that miR-590-5p can be used as an independent predictor. Furthermore, upregulation of miR-590-5p inhibited cell migration and invasion in MGC-803 cells and HGC-27 cells. The serum expression level of exosomal miR-590-5p may be a biomarker, which is potentially useful and noninvasive for early detection and prediction of GC. In addition, miR-590-5p can play a role in eliminating carcinogens by actively regulating the malignant potential of gastric cancer.
Body Temperature Is Associated With Cognitive Performance in Older Adults With and Without Mild Cognitive Impairment: A Cross-sectional Analysis
Authors: Eggenberger Patrick , Bürgisser Michael , Rossi René M. , Annaheim Simon
Published: February 2021

Wearable devices for remote and continuous health monitoring in older populations frequently include sensors for body temperature measurements (i.e., skin and core body temperatures). Healthy aging is associated with core body temperatures that are in the lower range of age-related normal values (36.3 ± 0.6°C, oral temperature), while patients with Alzheimer’s disease (AD) exhibit core body temperatures above normal values (up to 0.2°C). However, the relation of body temperature measures with neurocognitive health in older adults remains unknown. This study aimed to explore the association of body temperature with cognitive performance in older adults with and without mild cognitive impairment (MCI). Eighty community-dwelling older adults (≥65 years) participated, of which 54 participants were cognitively healthy and 26 participants met the criteria for MCI. Skin temperatures at the rib cage and the scapula were measured in the laboratory (single-point measurement) and neuropsychological tests were conducted to assess general cognitive performance, episodic memory, verbal fluency, executive function, and processing speed. In a subgroup (n = 15, nine healthy, six MCI), skin and core body temperatures were measured continuously during 12 h of habitual daily activities (long-term measurement). Spearman’s partial correlation analyses, controlled for age, revealed that lower median body temperature and higher peak-to-peak body temperature amplitude was associated with better general cognitive performance and with better performance in specific domains of cognition; [e.g., rib median skin temperature (single-point) vs. processing speed: rs = 0.33, p = 0.002; rib median skin temperature (long-term) vs. executive function: rs = 0.56, p = 0.023; and peak-to-peak core body temperature amplitude (long-term) vs. episodic memory: rs = 0.51, p = 0.032]. Additionally, cognitively healthy older adults showed lower median body temperature and higher peak-to-peak body temperature amplitude compared to older adults with MCI (e.g., rib median skin temperature, single-point: p = 0.035, r = 0.20). We conclude that both skin and core body temperature measures are potential early biomarkers of cognitive decline and preclinical symptoms of MCI/AD. It may therefore be promising to integrate body temperature measures into multi-parameter systems for the remote and continuous monitoring of neurocognitive health in older adults.
Increased Plasma Heme Oxygenase-1 Levels in Patients With Early-Stage Parkinson’s Disease
Authors: Sun Wenhua , Zheng Jinhua , Ma Jianjun , Wang Zhidong , Shi Xiaoxue , Li Mingjian , Huang Shen , Hu Shiyu , Zhao Zhenxiang , Li Dongsheng
Published: February 2021

Introduction: Heme oxygenase-1 (HO-1) is a 32 kDa stress-response protein implicated in the pathogenesis of Parkinson’s disease (PD). Biliverdin is derived from heme through a reaction mediated by HO-1 and protects cells from oxidative stress. However, iron and carbon monoxide produced by the catabolism of HO-1 exert detrimental effects on patients with PD. The purpose of this study was to determine whether plasma HO-1 levels represent a biomarker of PD and to further explore the underlying mechanism of increased HO-1 levels by applying voxel-based morphometry (VBM).Methods: We measured plasma HO-1 levels using an enzyme-linked immunosorbent assay (ELISA) in 156 subjects, including 81 patients with early- and advanced-stage PD and 75 subjects without PD. The analyses were adjusted to control for confounders such as age, sex, and medication. We analyzed T1-weighted magnetic resonance imaging (MRI) data from 74 patients with PD using VBM to elucidate the association between altered brain volumes and HO-1 levels. Then, we compared performance on MMSE sub-items between PD patients with low and high levels of HO-1 using Mann-Whitney U tests.Results: Plasma HO-1 levels were significantly elevated in PD patients, predominantly those with early-stage PD, compared with controls (p < 0.05). The optimal cutoff value for patients with early PD was 2.245 ng/ml HO-1 [area under the curve (AUC) = 0.654]. Plasma HO-1 levels were unaffected by sex, age, and medications (p > 0.05). The right hippocampal volume was decreased in the subset of PD patients with high HO-1 levels (p < 0.05). A weak correlation was observed between right hippocampal volume and plasma HO-1 levels (r = −0.273, p = 0.018). There was no difference in total MMSE scores between the low- and high-HO-1 groups (p > 0.05), but the high-HO-1 group had higher language scores than the low-HO-1 group (p < 0.05).Conclusions: Plasma HO-1 levels may be a promising biomarker of early PD. Moreover, a high plasma concentration of the HO-1 protein is associated with a reduction in right hippocampal volume.
Blood Brain-Derived Neurotrophic Factor (BDNF) and Major Depression: Do We Have a Translational Perspective?
Authors: Arosio Beatrice , Guerini Franca Rosa , Voshaar Richard C. Oude , Aprahamian Ivan
Published: February 2021

Major depressive disorder (MDD) affects millions of people worldwide and is a leading cause of disability. Several theories have been proposed to explain its pathological mechanisms, and the “neurotrophin hypothesis of depression” involves one of the most relevant pathways. Brain-derived neurotrophic factor (BDNF) is an important neurotrophin, and it has been extensively investigated in both experimental models and clinical studies of MDD. Robust empirical findings have indicated an association between increased BDNF gene expression and peripheral concentration with improved neuronal plasticity and neurogenesis. Additionally, several studies have indicated the blunt expression of BDNF in carriers of the Val66Met gene polymorphism and lower blood BDNF (serum or plasma) levels in depressed individuals. Clinical trials have yielded mixed results with different treatment options, peripheral blood BDNF measurement techniques, and time of observation. Previous meta-analyses of MDD treatment have indicated that antidepressants and electroconvulsive therapy showed higher levels of blood BDNF after treatment but not with physical exercise, psychotherapy, or direct current stimulation. Moreover, the rapid-acting antidepressant ketamine has presented an early increase in blood BDNF concentration. Although evidence has pointed to increased levels of BDNF after antidepressant therapy, several factors, such as heterogeneous results, low sample size, publication bias, and different BDNF measurements (serum or plasma), pose a challenge in the interpretation of the relation between peripheral blood BDNF and MDD. These potential gaps in the literature have not been properly addressed in previous narrative reviews. In this review, current evidence regarding BDNF function, genetics and epigenetics, expression, and results from clinical trials is summarized, putting the literature into a translational perspective on MDD. In general, blood BDNF cannot be recommended for use as a biomarker in clinical practice. Moreover, future studies should expand the evidence with larger samples, use the serum or serum: whole blood concentration of BDNF as a more accurate measure of peripheral BDNF, and compare its change upon different treatment modalities of MDD.