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Diversity and compositional changes in the gut microbiota of wild and captive vertebrates: a meta-analysis
<p>Bioinformatic code, data files, raw figures and data accessibility table associated to the manuscript "Diversity and compositional changes in the gut microbiota of wild and captive vertebrates: a meta-analysis".</p>
Resources from: Gut microbiome composition better reflects host phylogeny than diet diversity in breeding wood-warblers
<p>Understanding the factors that shape microbiomes can provide insight on the importance of host-symbiont interactions and on co-evolutionary dynamics. Unlike for mammals, previous studies have found little or no support for an influence of host evolutionary history on avian gut microbiome diversity and instead have suggested a greater influence of the environment or diet due to fast gut turnover. Because effects of different factors may be conflated by captivity and sampling design, examining natural variation using large sample sizes is important. Our goal was to overcome these limitations by sampling wild birds to compare environmental, dietary, and evolutionary influences on gut microbiome structure. We performed fecal metabarcoding to characterize both the gut microbiome and diet of fifteen wood-warbler species across a four-year period and from two geographic localities. We find host taxonomy generally explained ~10% of the variation between individuals, which is ~6-fold more variation of any other factor considered, including diet diversity. Further, gut microbiome similarity was more congruent with the host phylogeny than with host diet similarity and we found little association between diet diversity and microbiome diversity. Together, our results suggest evolutionary history is the strongest predictor of gut microbiome differentiation among wood-warblers. Although the phylogenetic signal of the warbler gut microbiome is not very strong, our data suggest that a stronger influence of diet (as measured by diet diversity) does not account for this pattern. The mechanism underlying this phylogenetic signal is not clear, but we argue host traits may filter colonization and maintenance of microbes.</p>
Degenerative Cervical Myelopathy (DCM) induces sex-specific dysbiosis in the mouse gut bacterial microbiome, altering abundance and function
<p><strong>Background:</strong> Degenerative cervical myelopathy (DCM) represents the commonest cause of spinal cord impairment induced by non-traumatic events in the elderly population. It describes a spectrum of disorders that cause progressive spinal cord compression, neurological impairment, loss of bladder and bowel functions, as well as gastrointestinal dysfunction. The gut microbiota has been increasingly recognized as an environmental factor that can modulate both the central nervous system and immune response through the microbiota-gut-brain axis. Changes in gut microbiota composition or in the microbiota producing factors have been linked in the progression and development of several different pathologies such as traumatic spinal cord injury (SCI). Little is known about the molecular mechanisms that trigger DCM manifestation, and the potential role of the gut microbiota.</p> <p><strong>Results: </strong>Herein DCM was induced in female and male C57BL/6 mice by implanting an aromatic polyether material underneath the C5-6 laminae. The extent of DCM-induced changes in microbiota composition, also known as dysbiosis, was assessed by 16S rRNA sequencing from fecal samples at 3 different time points (6, 9 and 12 weeks after DCM induction). Several bacterial members were identified based on BLAST against the largest collection of metagenome-derived genomes from the mouse gut up to date. In both, female and males DCM caused gut dysbiosis compared with the sham group. However, dysbiosis was more pronounced in males than females, where several bacterial members of the families <em>Lachnospiraceae</em> and <em>Muribaculaceae</em> were significantly altered in the DCM group. These changes were also associated with altered immune cell composition in gut-associated lymphoid tissue, blood, and microbe-derived metabolic changes in propionate, butyrate, and lactate-producing bacterial members.</p> <p><strong>Conclusions: </strong>Our results demonstrate for the first time that DCM causes dynamic changes over time in the gut microbiota. Furthermore, we identify specie-specific abundance changes during DCM progression. DCM strongly reduces the abundance of butyrate-producing bacteria, and lactate-producing bacteria in much less extent. Sequence-based pangenomics cores were not resolved between the latter bacteria, but the gap-filling reactions and metabolic modelling successfully identified pyruvate-to-butanoate and pyruvate-to-propionate genes such as Buk and ACH1, respectively. These results aid to better understand markers and the molecular mechanisms that over time trigger DCM manifestation in females and males.</p>
Gut microbiome composition associated with Plasmodium infection in the Eurasian tree sparrow
<p>Recent expansion of microbiome research has uncovered connections between resident microbial communities and blood parasite risk, establishing the potential for microbial disease treatments such as probiotics in the future. However, this field has largely focused on humans and model organisms, leaving much unknown about how microbial communities might directly or indirectly impact parasite infection in wild populations and non-mammals. To contribute to this knowledge base in wild birds, we collected fecal and blood samples from wild Eurasian tree sparrows (<em>Passer montanus</em>) in the United States to test for associations between blood parasite infection and the gut microbiome. We used a widespread molecular approach to test 81 samples from peripheral blood for <em>Plasmodium</em> and <em>Haemoproteus</em>, and we characterized the gut microbiome using fecal samples as a proxy. Neither alpha nor beta diversity significantly varied with detected <em>Plasmodium</em> infection. However, differential abundance analysis highlighted a number of significantly varying bacteria, with the greatest representation within the phyla <em>Proteobacteria</em> and <em>Firmicutes</em> in <em>Plasmodium</em>-infected birds. These differentially abundant taxa offer a starting point for experimental work establishing the relationship between microbial abundance and <em>Plasmodium</em> infection.</p>
MAGs and gapseq models for auxotrophy predictions in the human gut microbiome
<p>This dataset contains MAGs, their DNA sequence, genome statistics, quantification per sample, and their metabolic model reconstructions from two human population cohorts from northern Germany.</p>
Individual variation in the avian gut microbiota: The influence of host state and environmental heterogeneity
<div class="abstract-group metis-abstract"> <div class="article-section__content en main"> <p>The gut microbiota have important consequences for host biological processes and there is some evidence that they also affect fitness. However, the complex, interactive nature of ecological factors that influence the gut microbiota has scarcely been investigated in natural populations. We sampled the gut microbiota of wild great tits (<em>Parus major</em>) at different life stages allowing us to evaluate how microbiota varied with respect to a diverse range of key ecological factors of two broad types: (1) host state, namely age and sex, and the life history variables, timing of breeding, fecundity and reproductive success; and (2) the environment, including habitat type, the distance of the nest to the woodland edge, and the general nest and woodland site environments. The gut microbiota varied with life history and the environment in many ways that were largely dependent on age. Nestlings were far more sensitive to environmental variation than adults, pointing to a high degree of flexibility at an important time in development. As nestlings developed their microbiota from one to two weeks of life, they retained consistent (i.e., repeatable) among-individual differences. However these apparent individual differences were driven entirely by the effect of sharing the same nest. Our findings point to important early windows during development in which the gut microbiota are most sensitive to a variety of environmental drivers at multiple scales, and suggest reproductive timing, and hence potentially parental quality or food availability, are linked with the microbiota. Identifying and explicating the various ecological sources that shape an individual's gut bacteria is of vital importance for understanding the gut microbiota's role in animal fitness.</p> </div> </div> <div class="pb-dropzone"> </div>
Disentangling relationships between physiology, morphology, diet, and gut microbial diversity in American Kestrel nestlings
<p>Gut microbiota are increasingly recognized as important drivers of host health and fitness across vertebrate taxa. Given that gut microbial composition is directly influenced by the environment, gut microbiota may also serve as an eco-physiological mechanism connecting host ecology, such as diet, and physiology. Although gut microbiota have been well-studied in mammalian systems, little is known about how gut microbial diversity and composition impact morphological and physiological development in wild birds. Here, we characterized both diet and gut microbial diversity of free-living American kestrel (<em>Falco sparverius</em>) nestlings throughout development to test whether gut microbial diversity predicts host morphological and physiological traits in either contemporary or time-lagged manners. Gut microbial alpha diversity on day 21 of nestling development was positively correlated with diet alpha diversity representative of the majority of nestling development (days 5–20). Gut microbial alpha diversity early in development was negatively correlated with body mass in both contemporary and time-lagged manners. Gut microbial alpha diversity early in development was positively correlated with blood glucose later in development. As nestlings experience rapid growth demands in preparation to fledge, these time-lagged associations may indicate that gut microbial diversity at early critical developmental windows may determine the future trajectory of morphological and physiological traits underlying metabolism that ultimately impact fitness.</p>
Gut microbiota inter-species interactions shape the response of Clostridioides difficile to clinically relevant antibiotics
<p>In the human gut, the growth of <em>Clostridioides difficile </em>is impacted by a complex web of inter-species interactions with members of human gut microbiota. We investigate the contribution of inter-species interactions on the antibiotic response of <em>C. difficile </em>to clinically relevant antibiotics using bottom-up assembly of human gut communities. We discover two classes of microbial interactions that alter <em>C. </em>difficile’s antibiotic susceptibility: interactions resulting in increased <em>C. diffiicle </em>tolerance at high antibiotic concentrations (rare) and interactions resulting in <em>C. difficile </em>growth enhancement at low antibiotic concentrations (common). Based on genome-wide transcriptional profiling data, we demonstrate that metal sequestration due to hydrogen sulfide production by the prevalent gut species <em>Desulfovibrio piger </em>increases metronidazole tolerance of <em>C. difficile</em>. Competition with species that display higher sensitivity to the antibiotic than <em>C. difficile </em>leads to enhanced growth of <em>C. difficile </em>at low antibiotic concentrations. A dynamic computational model identifies the ecological design principles driving this effect. Our results provide a deeper understanding of ecological and molecular principles shaping <em>C. difficile</em>’s response to antibiotics, which could inform therapeutic interventions.In the human gut, the growth of <em>Clostridioides difficile </em>is impacted by a complex web of inter-species interactions with members of human gut microbiota. We investigate the contribution of inter-species interactions on the antibiotic response of <em>C. difficile </em>to clinically relevant antibiotics using bottom-up assembly of human gut communities. We discover two classes of microbial interactions that alter <em>C. </em>difficile’s antibiotic susceptibility: interactions resulting in increased <em>C. diffiicle </em>tolerance at high antibiotic concentrations (rare) and interactions resulting in <em>C. difficile </em>growth enhancement at low antibiotic concentrations (common). Based on genome-wide transcriptional profiling data, we demonstrate that metal sequestration due to hydrogen sulfide production by the prevalent gut species <em>Desulfovibrio piger </em>increases metronidazole tolerance of <em>C. difficile</em>. Competition with species that display higher sensitivity to the antibiotic than <em>C. difficile </em>leads to enhanced growth of <em>C. difficile </em>at low antibiotic concentrations. A dynamic computational model identifies the ecological design principles driving this effect. Our results provide a deeper understanding of ecological and molecular principles shaping <em>C. difficile</em>’s response to antibiotics, which could inform therapeutic interventions.</p>
Transcriptomes for Ranitomeya imitator and R. variabilis: Evidence for a Parabasalian Gut Symbiote in Egg-Feeding Poison Frog Tadpoles in Peru
<p>This dataset contains the assembled transcriptomes for our paper. The three assemblies are for <em>Ranitomeya imitator, R. variabilis, </em>and a merged assembly of the two species. For methodological details, see the published manuscript.</p>
Design, construction, and in vivo augmentation of a complex gut microbiome
<p>Please cite: <a href="https://doi.org/10.1016/j.cell.2022.08.003">10.1016/j.cell.2022.08.003</a></p> <blockquote> <p>Cheng AG, Ho PY, Aranda-Díaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA. Design, construction, and in vivo augmentation of a complex gut microbiome. Cell. 2022 Sep 15;185(19):3617-3636.e19. doi: 10.1016/j.cell.2022.08.003. Epub 2022 Sep 6. PMID: 36070752; PMCID: PMC9691261.</p> </blockquote> <p>Original raw sequencing data is available in the BioProject: <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA746600">PRJNA746600</a></p> <p><strong>Article summary:</strong></p> <blockquote> <p>Efforts to model the human gut <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/microbiome">microbiome</a> in mice have led to important insights into the mechanisms of host-microbe interactions. However, the model communities studied to date have been defined or complex, but not both, limiting their utility. Here, we construct and characterize <em>in vitro</em> a defined community of 104 bacterial species composed of the most common taxa from the human <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/intestine-flora">gut microbiota</a> (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2. In <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/gnotobiotics">gnotobiotic mice</a>, hCom2 exhibited increased stability to fecal challenge and robust <a href="https://www.sciencedirect.com/topics/immunology-and-microbiology/colonisation-resistance">colonization resistance</a> against pathogenic <em>Escherichia coli</em>. Mice colonized by either hCom2 or a human fecal community are phenotypically similar, suggesting that this consortium will enable a mechanistic interrogation of species and genes on microbiome-associated phenotypes.</p> </blockquote> <p><strong>File Descriptions:</strong></p> <ul> <li><strong>hCom2.tar.gz:</strong> This dataset contains genomic sequences and <a href="https://github.com/oschwengers/bakta">bakta</a> annotations of members of the hCom2 community. Please note that these may not be identical to the ones used in the publication. For the exact versions used in the publication, please reach out to the authors. </li> <li> <p><strong>hCom2_20221117.ninjaIndex.tar.gz:</strong> This tarball contains the ninjamap index and the source files used to create this index. Please use this tarball if you wish to run <a href="https://github.com/FischbachLab/ninjaMap">NinjaMap</a> against the hCom2 community.</p> </li> </ul>
Enterosignatures define common bacterial guilds in the human gut microbiome (data)
<p>Additional data related to the manuscript <em>Enterosignatures define common bacterial guilds in the human gut microbiome.</em></p> <p>The deposit contains the following files:</p> <ul> <li>GMR_dataset.zip - data and results related to enterosignature computation in the GMR dataset: raw data, enterosignature composition, metabolic potentials of the associated metagenomic species</li> </ul> <p><strong>GMR_dataset</strong><br> ├── NMF_results <em># results of NMF decomposition, from k = 2 signatures to 10, 5 being the optimal number</em><br> │ ├── 10_H.tsv<br> │ ├── ....<br> │ ├── 9_W.tsv<br> │ └── README.txt<br> ├── age_metadata.tsv <em># age of individuals in the GMR dataset</em><br> ├── drama_MGS_gtdbtk_taxonomy.tsv <em># taxonomy of the MGS </em><br> ├── drama_genus_level_abundance.tsv <em># genus-level abundance table used for NMF</em><br> └── metabo_data <em># Metabolic potential of the MGS associated to the enterosignatures</em><br> ├── cazymes_by_genome.tsv <em># cazymes</em><br> ├── gene_numbers.tsv <em># number of genes</em><br> ├── kegg_metabolic_processes_by_genome.tsv <em># Kegg annotations</em><br> ├── level1_onto_metabolites.tsv <em># Metacyc classes of metabolites, highest level</em><br> ├── level2_onto_metabolites.tsv <em># Metacyc classes of metabolites, second level</em><br> ├── metabolic_producers_full_community.tsv <em># predicted producers of metabolites, all genomes considered</em><br> ├── metabolic_producers_withinES.tsv <em># predicted producers of metabolites, within an ES</em><br> └── westerndiet.sbml <em># nutrients considered for metabolic modelling</em></p> <ul> <li>BMIS_dataset.zip - data and results related to enterosignature computation in the BMIS dataset</li> </ul> <p><strong>BMIS_dataset</strong><br> ├── bmis_es_composition.tsv <em># ES assignments of BMIS samples (ES computed on the GMR dataset)</em><br> ├── bmis_es_et_assignments.tsv<em> # ES and enterotype assignments of BMIS samples</em><br> └── bmis_genus-level_abundance.tsv <em># genus-level abundance matrix used for ES abundance computation</em></p> <ul> <li>NonWestern_dataset.zip - data and results related to enterosignature computation in the non-western dataset</li> </ul> <p><strong>NonWestern_dataset</strong><br> ├── nonwestern_es_composition.tsv <em># ES assignments of Non-western samples (ES computed on the GMR dataset)</em><br> └── nonwestern_genus_abundance_normalised.tsv <em># genus-level abundance matrix used for ES abundance computation</em></p> <p>The data is also available in the following repository:<em> </em><a href="https://gitlab.inria.fr/cfrioux/enterosignature-paper/">https://gitlab.inria.fr/cfrioux/enterosignature-paper/</a>.</p> <p>See also <a href="https://enterosignatures.quadram.ac.uk/">https://enterosignatures.quadram.ac.uk/</a>.</p>
Andrang am Tisch der Entomologischen Gesellschaft Basel an der gut besuchten Zollinacht. (Foto Renato Joos) in Entomologische Gesellschaft Basel (EGB)
Andrang am Tisch der Entomologischen Gesellschaft Basel an der gut besuchten Zollinacht. (Foto Renato Joos)
MetaPep: A core peptide database for faster human gut metaproteomics database searches
<p>Metaproteomics has increasingly been applied to study functional changes in the human gut microbiome. And peptide identification is an important step in metaproteomics research. However, the large search space in metaproteomics studies causes significant challenges for peptide identification. Here, we constructed MetaPep, a core peptide database (including both collections of peptide sequences and tandem MS spectra) greatly accelerating the peptide identifications. Raw files from fifteen metaproteomics projects were re-analyzed and the identified peptide-spectrum matches (PSMs) were used to construct the MetaPep database. The constructed MetaPep database achieved rapid and accurate identification of peptides for human gut metaproteomics.</p>
Supplementary Material for publication "Bifidobacteria Define Gut Microbiome Profiles of Golden Lion Tamarin (Leontopithecus rosalia} and Marmoset Callithrix sp. Metagenomic Shotgun Pools
<p>Supplementary Tables and Figure for the publication "Bifidobacteria Define Gut Microbiome Profiles of Golden Lion Tamarin <em>Leontopithecus rosalia</em> and Marmoset <em>Callithrix</em> sp. Metagenomic Shotgun Pools"</p>
Data from: Seasonal restructuring facilitates compositional convergence of gut microbiota in free-ranging rodents
<p>Gut microbes provide essential services to their host and shifts in their composition can impact host fitness. However, despite advances in our understanding of how microbes are assembled in the gut, we understand little about the stability of these communities within individuals, nor what factors influence its composition over the life of an animal. For this reason, we conducted a longitudinal survey of the gut microbial communities of individual free-ranging woodrats (<em>Neotoma</em> spp.) across a hybrid zone in the Mojave Desert, USA, using amplicon sequencing approaches to characterize gut microbial profiles and diet. We found that gut microbial communities were individualized and experienced compositional restructuring as a result of seasonal transitions and changes in diet. Turnover of gut microbiota was highest amongst bacterial subspecies and was much lower at the rank of Family, suggesting there may be selection for conservation of core microbial functions in the woodrat gut. Lastly, we identified an abundant core gut bacterial community that may aid woodrats in metabolizing a diet of plants and their specialized metabolites. These results demonstrate that the gut microbial communities of woodrats are highly dynamic and experience seasonal restructuring which may facilitate adaptive plasticity in response to changes in diet. </p>
TableS1 of ML-based predictive gut microbiome analysis for health assessment
<p>Complete list of species associated with the COVID and Control cohort (ANOVA F score > 1). Comparison with respect to the original set of species used by Gupta <em>et al.</em>, and ANOVA-F values are reported.</p>
Comparative seagulls of gut microbiota by using metagenomics and 16S rDNA sequencing
<p><span>Shotgun</span><span> metagenomic and 16S rDNA sequencing are commonly used methods to identify the taxonomic composition of microbial communities. </span><span>We compared the metagenome and 16S rDNA amplicon results to demonstrate the features of this animal. </span><span>In general, </span><span>relatively </span><span>consistent patterns and reliability could be identified by both sequencing methods, but the results varied </span><span>following </span><span>the refinement of taxonomic levels. </span><span>Metagenomic </span><span>sequencing was more suitable for the discovery and detection of pathogenic bacteria of gut microbiota in seagulls.</span><span> Although there were large differences in the numbers and abundance of </span><span>bacterial </span><span>species of</span><span> the</span><span> two methods in terms of taxonomic levels, the patterns and reliability results of </span><span>the </span><span>samples were consistent.</span></p>
Gut Butyrate and Blood Pressure in African Americans
ClinicalTrials.gov study NCT04415333. IPD Sharing: YES. Countries: 1. Publications: 5.
Data from: Effects of manakin gut passage on germination of a neotropical melastome shrub (Melastomataceae)
Open the record for dataset details and reuse information.
Gut feeling: Host and habitat as drivers of the microbiome in blackbuck (Antilope cervicapra)
Open the record for dataset details and reuse information.
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