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At least 91 records · Page 5

Field expedient stool collection methods for gut microbiome analysis in deployed military environments

ABSTRACT Field expedient devices and protocols for the collection, storage, and shipment of stool samples in deployed settings are needed for the advancement of microbiome research in military health. Relevant assessments include the evaluation of microbiome signatures associated with susceptibility to travelers’ diarrhea and recovery of gut function following infection. However, inherent biases in microbial measurements due to preservatives and sampling methods are unclear and should be assessed for an accurate evaluation of the microbiome. We performed shotgun metagenomic sequencing and compared the microbiome composition in paired fecal samples collected using Flinters Technology Associates (FTA) cards and OMNIgene (OG) Gut tubes, prior to and during international travel, from 49 adult participants, 39 of whom remained asymptomatic and 10 experienced travelers’ diarrhea. Higher concentrations of nucleic acid and sequencing libraries were observed in OG samples. A majority of genera (82.9%) were detected with both methods, and detections of genera limited to one collection method were not highly prevalent across samples and were present in extremely low relative abundances (<0.01%). Differences in beta diversity were largely explained by inter-individuality of microbiome composition, followed by the effect of collection method and timepoint-disease states. Differential abundance analysis indicated that Corynebacterium and Blautia were consistently higher in abundance across all groups with FTA and OG collection, respectively. The observed differences in microbiome composition between methods suggest the need for consistent and standardized protocols within a study. Overall, the data presented here could help guide the future design of fecal microbiome study protocols in field and military deployment settings. IMPORTANCE The assessment of field-deployable methods for fecal sample collection and storage is required to reliably capture samples collected in remote and austere locations. This study describes a comparative metagenomics analysis between samples collected by two different commercially available methods in a military-deployed setting. The results presented here are foundational for the future design of fecal microbiome study protocols in an operational context.

field study↗

Fungal diversity and function in metagenomes sequenced from extreme environments

Fungi are increasingly recognized as key players in various extreme environments. Here we present an analysis of publicly-sourced metagenomes from global extreme environments, focusing on fungal taxonomy and function. The majority of 855 selected metagenomes contained scaffolds assigned to fungi. Relative abundance of fungi was as high as 10% of protein-coding genes with taxonomic annotation, with up to 289 fungal genera per sample. Despite taxonomic clustering by environment, fungal communities were more dissimilar than archaeal and bacterial communities, both for within- and between-environment comparisons. Relatively abundant fungal classes in extreme environments included Dothideomycetes, Eurotiomycetes, Leotiomycetes, Pezizomycetes, Saccharomycetes, and Sordariomycetes. Broad generalists and prolific aerial spore formers were the most relatively abundant fungal genera detected in most of the extreme environments, bringing up the question of whether they are actively growing in those environments or just surviving as spores. More specialized fungi were common in some environments, such as zoosporic taxa in cryosphere water and hot springs. Relative abundances of genes involved in adaptation to general, thermal, oxidative, and osmotic stress were greatest in soda lake, acid mine drainage, and cryosphere water samples.

60 APPLIED LIFE SCIENCES↗

Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale

The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. The analysis was conducted using metagenomes and metagenome-assembled genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs. The microbial community structure in the coral SML varied according to the local environment, both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and those that are related to higher levels of microbial activity, competition, and stress response. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome, potentially increasing holobiont resilience to environmental changes and disease.

59 BASIC BIOLOGICAL SCIENCES↗

A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse

Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.

Kordia↗

KBase Narrative - Timberlake Metagenomes

This narrative contains the MAG Analysis from: Clifton P Bueno de Mesquita, Wyatt H Hartman, Marcelo Ardón, Susannah G Tringe, Disentangling the effects of sulfate and other seawater ions on microbial communities and greenhouse gas emissions in a coastal forested wetland, ISME Communications, 2024; ycae040, https://doi.org/10.1093/ismeco/ycae040 Metagenomes were uploaded to IMG/M for other analyses.

de Mesquita, Clifton Bueno↗

Genome-Resolved Metagenomics and Detailed Geochemical Speciation Analyses Yield New Insights into Microbial Mercury Cycling in Geothermal Springs

Geothermal systems emit substantial amounts of aqueous, gaseous, and methylated mercury, but little is known about microbial influences on mercury speciation. Here, we report results from genome-resolved metagenomics and mercury speciation analysis of acidic warm springs in the Ngawha Geothermal Field (< 55°C, pH < 4.5), Northland Region, Aotearoa New Zealand. Our aim was to identify the microorganisms genetically equipped for mercury methylation, demethylation, or Hg(II) reduction to volatile Hg(0) in these springs. Dissolved total and methylated mercury concentrations in two adjacent springs with different mercury speciation ranked among the highest reported from natural sources (250 to 16,000 ng liter -1 and 0.5 to 13.9 ng liter -1 , respectively). Total solid mercury concentrations in spring sediments ranged from 1,274 to 7,000 μg g -1 . In the context of such ultrahigh mercury levels, the geothermal microbiome was unexpectedly diverse and dominated by acidophilic and mesophilic sulfur- and iron-cycling bacteria, mercury- and arsenic-resistant bacteria, and thermophilic and acidophilic archaea. By integrating microbiome structure and metagenomic potential with geochemical constraints, we constructed a conceptual model for biogeochemical mercury cycling in geothermal springs. The model includes abiotic and biotic controls on mercury speciation and illustrates how geothermal mercury cycling may couple to microbial community dynamics and sulfur and iron biogeochemistry.

59 BASIC BIOLOGICAL SCIENCES↗

Metagenomic Insights Into the Microbial Iron Cycle of Subseafloor Habitats

Microbial iron cycling influences the flux of major nutrients in the environment (e.g., through the adsorptive capacity of iron oxides) and includes biotically induced iron oxidation and reduction processes. The ecological extent of microbial iron cycling is not well understood, even with increased sequencing efforts, in part due to limitations in gene annotation pipelines and limitations in experimental studies linking phenotype to genotype. This is particularly true for the marine subseafloor, which remains undersampled, but represents the largest contiguous habitat on Earth. To address this limitation, we used FeGenie, a database and bioinformatics tool that identifies microbial iron cycling genes and enables the development of testable hypotheses on the biogeochemical cycling of iron. Herein, we survey the microbial iron cycle in diverse subseafloor habitats, including sediment-buried crustal aquifers, as well as surficial and deep sediments. We inferred the genetic potential for iron redox cycling in 32 of the 46 metagenomes included in our analysis, demonstrating the prevalence of these activities across underexplored subseafloor ecosystems. We show that while some processes (e.g., iron uptake and storage, siderophore transport potential, and iron gene regulation) are near-universal, others (e.g., iron reduction/oxidation, siderophore synthesis, and magnetosome formation) are dependent on local redox and nutrient status. Additionally, we detected niche-specific differences in strategies used for dissimilatory iron reduction, suggesting that geochemical constraints likely play an important role in dictating the dominant mechanisms for iron cycling. Overall, our survey advances the known distribution, magnitude, and potential ecological impact of microbe-mediated iron cycling and utilization in sub-benthic ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗

Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost

While wetlands are major sources of biogenic methane (CH 4 ), our understanding of resident microbial metabolism is incomplete, which compromises the prediction of CH 4 emissions under ongoing climate change. Here, we employed genome-resolved multi-omics to expand our understanding of methanogenesis in the thawing permafrost peatland of Stordalen Mire in Arctic Sweden. In quadrupling the genomic representation of the site’s methanogens and examining their encoded metabolism, we revealed that nearly 20% of the metagenome-assembled genomes (MAGs) encoded the potential for methylotrophic methanogenesis. Further, 27% of the transcriptionally active methanogens expressed methylotrophic genes; for Methanosarcinales and Methanobacteriales MAGs, these data indicated the use of methylated oxygen compounds (e.g., methanol), while for Methanomassiliicoccales, they primarily implicated methyl sulfides and methylamines. In addition to methanogenic methylotrophy, >1,700 bacterial MAGs across 19 phyla encoded anaerobic methylotrophic potential, with expression across 12 phyla. Metabolomic analyses revealed the presence of diverse methylated compounds in the Mire, including some known methylotrophic substrates. Active methylotrophy was observed across all stages of a permafrost thaw gradient in Stordalen, with the most frozen non-methanogenic palsa found to host bacterial methylotrophy and the partially thawed bog and fully thawed fen seen to house both methanogenic and bacterial methylotrophic activities. Methanogenesis across increasing permafrost thaw is thus revised from the sole dominance of hydrogenotrophic production and the appearance of acetoclastic at full thaw to consider the co-occurrence of methylotrophy throughout. Collectively, these findings indicate that methanogenic and bacterial methylotrophy may be an important and previously underappreciated component of carbon cycling and emissions in these rapidly changing wetland habitats.

59 BASIC BIOLOGICAL SCIENCES↗

Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism

Abstract Background Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling. Results Sulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa , dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L 2,3 edges show that filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that they are sulfur oxidizers, likely Thiothrix . Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b [NiFe]-hydrogenase, putatively a sulfhydrogenase, potentially linked to sulfur metabolism via redox cofactors. This complex could potentially contribute to symbioses, for example, with sulfur-oxidizing bacteria such as Thiothrix that is based on cryptic sulfur cycling. One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite. We find similar conserved genomic architecture associated with CPR bacteria from other sulfur-rich subsurface ecosystems. Conclusions Our combined metagenomic, geochemical, spectromicroscopic, and structural bioinformatics analyses of biofilms growing in sulfide-rich springs revealed consortia that contain CPR bacteria and sulfur-oxidizing Proteobacteria, including Thiothrix , and bacteria from a new family within Beggiatoales. We infer roles for CPR bacteria in sulfur and hydrogen cycling.

59 BASIC BIOLOGICAL SCIENCES↗

Metagenome-assembled genomes from microbial communities producing lactic acid from dairy residues

To advance the knowledge of microbial communities capable of fermenting agro-industrial residues into value-added products, we report metagenomes of microbial communities from four anaerobic bioreactors fed a mixture of ultra-filtered milk permeate and cottage cheese acid whey. This analysis produced 42 unique metagenome-assembled genomes (MAGs) that represent distinct taxa.

59 BASIC BIOLOGICAL SCIENCES↗

BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes

Secondary metabolites are compounds not essential for an organism’s development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗

Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC

Large amounts of metagenomically-derived data are submitted to PATRIC for analysis. In the future, we expect even more jobs submitted to PATRIC will use metagenomic data. One in-demand use case is the extraction of near-complete draft genomes from assembled contigs of metagenomic origin. The PATRIC metagenome binning service utilizes the PATRIC database to furnish a large, diverse set of reference genomes. We provide a new service for supervised extraction and annotation of high-quality, near-complete genomes from metagenomically-derived contigs. Reference genomes are assigned to putative draft genome bins based on the presence of single-copy universal marker roles in the sample, and contigs are sorted into these bins by their similarity to reference genomes in PATRIC. Each set of binned contigs represents a draft genome that will be annotated by RASTtk in PATRIC. A structured-language binning report is provided containing quality measurements and taxonomic information about the contig bins. The PATRIC metagenome binning service emphasizes extraction of high-quality genomes for downstream analysis using other PATRIC tools and services. Due to its supervised nature, the binning service is not appropriate for mining novel or extremely low-coverage genomes from metagenomic samples.

59 BASIC BIOLOGICAL SCIENCES↗

Systematic analysis of Baobaoqu fermentation starter for Wuliangye Baijiu by the combination of metagenomics and metabolomics

Baobaoqu (BBQ) is a traditional fermenting power, which is widely applied in Nong-flavor Baijiu brewing. There are two different types of BBQ (premium BBQ and normal BBQ) used in industrial manufacture, but the reasons for the significant differences between two kinds of BBQ have not been clearly illuminated. In this study, the combination of metagenomics and metabolomics was performed to compare the differences in the composition of microbial communities and the components of flavors between premium BBQ and normal BBQ. The results showed that the glycosidase-producing microorganisms are the biomarkers of premium BBQ, contributing a better ability of carbon source utilization than normal BBQ. In addition, several important flavors (ethyl hexanoate, phenylethanol, ethyl acetate) were rich in normal BBQ, which have a significant positive correlation with the biomarkers ( Lactobacillus and Pichia kudriavzevii ) of normal BBQ. It suggests that the microbial community has an advantage in utilizing raw materials in premium BBQ, while the community was inclined to form flavors in normal BBQ. The differences between two types of BBQ at the microbial and flavor level have theoretical and practical guiding significance in the application of premium and normal BBQ and in the further improvements of taste and quality of Baijiu.

Zhang, Qingmei↗

Methane-derived carbon flows into host–virus networks at different trophic levels in soil

Significance The impact of soil viruses on prokaryotic hosts and their functional processes is largely unknown. While metagenomic sequencing of soil microbial communities enables identification of linkages between viruses and hosts, this does not necessarily identify contemporary interactions. To enable a detailed analysis of active virus–host interactions between individual populations, we focused on the critical biogeochemical process of methane (CH 4 ) oxidation and followed the transfer of carbon from hosts to their associated viruses in situ. Analysis of 13 C-enriched metagenomic DNA demonstrated that CH 4 -derived carbon is transferred into viral biomass via both primary and secondary utilizers of CH 4 and suggests viral predation is an important mechanism for releasing CH 4 -derived organic carbon into the soil matrix.

Lee, Sungeun↗

Neotropical termite microbiomes as sources of novel plant cell wall degrading enzymes

In this study, we used shotgun metagenomic sequencing to characterise the microbial metabolic potential for lignocellulose transformation in the gut of two colonies of Argentine higher termite species with different feeding habits, Cortaritermes fulviceps and Nasutitermes aquilinus. Our goal was to assess the microbial community compositions and metabolic capacity, and to identify genes involved in lignocellulose degradation. Individuals from both termite species contained the same five dominant bacterial phyla (Spirochaetes, Firmicutes, Proteobacteria, Fibrobacteres and Bacteroidetes) although with different relative abundances. However, detected functional capacity varied, with C. fulviceps (a grass-wood-feeder) gut microbiome samples containing more genes related to amino acid metabolism, whereas N. aquilinus (a wood-feeder) gut microbiome samples were enriched in genes involved in carbohydrate metabolism and cellulose degradation. The C. fulviceps gut microbiome was enriched specifically in genes coding for debranching- and oligosaccharide-degrading enzymes. These findings suggest an association between the primary food source and the predicted categories of the enzymes present in the gut microbiomes of each species. To further investigate the termite microbiomes as sources of biotechnologically relevant glycosyl hydrolases, a putative GH10 endo-β-1,4-xylanase, Xyl10E, was cloned and expressed in Escherichia coli. Functional analysis of the recombinant metagenome-derived enzyme showed high specificity towards beechwood xylan (288.1 IU/mg), with the optimum activity at 50 °C and a pH-activity range from 5 to 10. These characteristics suggest that Xy110E may be a promising candidate for further development in lignocellulose deconstruction applications.

59 BASIC BIOLOGICAL SCIENCES↗

Atmospheric methane consumption in arid ecosystems acts as a reverse chimney and is accelerated by plant-methanotroph biomes

Drylands cover one-third of the Earth’s surface and are one of the largest terrestrial sinks for methane. Understanding the structure–function interplay between members of arid biomes can provide critical insights into mechanisms of resilience toward anthropogenic and climate-change-driven environmental stressors—water scarcity, heatwaves, and increased atmospheric greenhouse gases. This study integrates in situ measurements with culture-independent and enrichment-based investigations of methane-consuming microbiomes inhabiting soil in the Anza-Borrego Desert, a model arid ecosystem in Southern California, United States. The atmospheric methane consumption ranged between 2.26 and 12.73 μmol m 2 h −1 , peaking during the daytime at vegetated sites. Metagenomic studies revealed similar soil-microbiome compositions at vegetated and unvegetated sites, with Methylocaldum being the major methanotrophic clade. Eighty-four metagenome-assembled genomes were recovered, six represented by methanotrophic bacteria (three Methylocaldum , two Methylobacter , and uncultivated Methylococcaceae ). The prevalence of copper-containing methane monooxygenases in metagenomic datasets suggests a diverse potential for methane oxidation in canonical methanotrophs and uncultivated Gammaproteobacteria. Five pure cultures of methanotrophic bacteria were obtained, including four Methylocaldum . Genomic analysis of Methylocaldum isolates and metagenome-assembled genomes revealed the presence of multiple stand-alone methane monooxygenase subunit C paralogs, which may have functions beyond methane oxidation. Furthermore, these methanotrophs have genetic signatures typically linked to symbiotic interactions with plants, including tryptophan synthesis and indole-3-acetic acid production. Based on in situ fluxes and soil microbiome compositions, we propose the existence of arid-soil reverse chimneys, an empowered methane sink represented by yet-to-be-defined cooperation between desert vegetation and methane-consuming microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗

Beyond microbial abundance: metadata integration enhances disease prediction in human microbiome studies

Multiple studies have highlighted the interaction of the human microbiome with physiological systems such as the gut, immune, liver, and skin, via key axes. Advances in sequencing technologies and high-performance computing have enabled the analysis of large-scale metagenomic data, facilitating the use of machine learning to predict disease likelihood from microbiome profiles. However, challenges such as compositionality, high dimensionality, sparsity, and limited sample sizes have hindered the development of actionable models. One strategy to improve these models is by incorporating key metadata from both the human host and sample collection/processing protocols. This remains challenging due to sparsity and inconsistency in metadata annotation and availability. In this paper, we introduce a machine learning-based pipeline for predicting human disease states by integrating host and protocol metadata with microbiome abundance profiles from 68 different studies, processed through a consistent pipeline. Our findings indicate that metadata can enhance machine learning predictions, particularly at higher taxonomic ranks like Kingdom and Phylum, though this effect diminishes at lower ranks. Our study leverages a large collection of microbiome datasets comprising 11,208 samples, therefore enhancing the robustness and statistical confidence of our findings. This work is a critical step toward utilizing microbiome and metadata for predicting diseases such as gastrointestinal infections, diabetes, cancer, and neurological disorders.

Mathematics and Computing↗

Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation

Bacteria and archaea possessing the hgcAB gene pair methylate inorganic mercury (Hg) to form highly toxic methylmercury. HgcA consists of a corrinoid binding domain and a transmembrane domain, and HgcB is a dicluster ferredoxin. However, their detailed structure and function have not been thoroughly characterized. We modeled the HgcAB complex by combining metagenome sequence data mining, coevolution analysis, and Rosetta structure calculations. In addition, we overexpressed HgcA and HgcB in Escherichia coli, confirmed spectroscopically that they bind cobalamin and [4Fe-4S] clusters, respectively, and incorporated these cofactors into the structural model. Surprisingly, the two domains of HgcA do not interact with each other, but HgcB forms extensive contacts with both domains. The model suggests that conserved cysteines in HgcB are involved in shuttling HgII, methylmercury, or both. These findings refine our understanding of the mechanism of Hg methylation and expand the known repertoire of corrinoid methyltransferases in nature.

59 BASIC BIOLOGICAL SCIENCES↗