{"doi":"10.1111/mec.17685","title":"Culture‐Independent Species‐Level Taxonomic and Functional Characterisation of\n                    <i>Bacteroides</i>\n                    , the Core Bacterial Genus Within Reptile Guts","abstract":"<jats:title>ABSTRACT</jats:title>\n                  <jats:p>\n                    The genus\n                    <jats:italic>Bacteroides</jats:italic>\n                    is a widespread and abundant bacterial taxon associated with gut microbiotas. Species within\n                    <jats:italic>Bacteroides</jats:italic>\n                    fill many niches, including as mutualists, commensals and pathogens for their hosts. Within many reptiles,\n                    <jats:italic>Bacteroides</jats:italic>\n                    is a dominant, ‘core’ gut bacterium that sometimes exhibits increased abundance in times of food scarcity, such as during hibernation. Here, we take a two‐pronged approach to better characterise\n                    <jats:italic>Bacteroides</jats:italic>\n                    populations in reptile guts. Firstly, we leverage published 16S rRNA gene sequence datasets to determine the species‐level distributions of\n                    <jats:italic>Bacteroides</jats:italic>\n                    members in reptile hosts. Secondly, we mine publicly available metagenomes to extract data for\n                    <jats:italic>Bacteroides</jats:italic>\n                    from reptiles, birds, amphibians and mammals, to compare the functional potential of\n                    <jats:italic>Bacteroides</jats:italic>\n                    in different host taxa. The 16S rRNA gene analyses revealed that\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>B. acidifaciens</jats:italic>\n                    </jats:styled-content>\n                    is the most common\n                    <jats:italic>Bacteroides</jats:italic>\n                    species in reptile guts, and that different orders of reptiles differ in which\n                    <jats:italic>Bacteroides</jats:italic>\n                    species they harbour. The taxonomy of\n                    <jats:italic>Bacteroides</jats:italic>\n                    species recovered from metagenomic assembly did not differ between reptile orders or substantially across birds, amphibians and mammals. Metagenome‐assembled genomes for\n                    <jats:italic>Bacteroides</jats:italic>\n                    species were marginally more related when their hosts were more closely related, with reptile hosts in particular harbouring markedly more unique\n                    <jats:italic>Bacteroides</jats:italic>\n                    MAGs compared to other hosts. Our findings indicate that hosts harbour similar profiles of\n                    <jats:italic>Bacteroides</jats:italic>\n                    species across broad comparisons, but with some differences between reptile groups, and that\n                    <jats:italic>Bacteroides</jats:italic>\n                    appears to perform largely similar roles in vertebrate host guts regardless of host relatedness.\n                  </jats:p>","journal":"Molecular Ecology","year":2025,"id":684215,"datarank":0.32958368660043297,"base_score":2.1972245773362196,"endowment":2.1972245773362196,"self_citation_contribution":0.32958368660043297,"citation_network_contribution":0.0,"self_endowment_contribution":0.32958368660043297,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":8,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1778561,"name":"Danielle M. R. L. Middleton","orcid":null,"position":1,"is_corresponding":false},{"id":1787492,"name":"Jessica A. Wallbank","orcid":null,"position":2,"is_corresponding":false},{"id":1787493,"name":"Jian S. Boey","orcid":null,"position":3,"is_corresponding":false},{"id":612027,"name":"Michael W. Taylor","orcid":"0000-0002-0463-7813","position":4,"is_corresponding":false},{"id":1778560,"name":"Carmen Hoffbeck","orcid":"0000-0002-0685-8505","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Culture‐Independent Species‐Level Taxonomic and Functional Characterisation of\n                    <i>Bacteroides</i>\n                    , the Core Bacterial Genus Within Reptile Guts","abstract":"<jats:title>ABSTRACT</jats:title>\n                  <jats:p>\n                    The genus\n                    <jats:italic>Bacteroides</jats:italic>\n                    is a widespread and abundant bacterial taxon associated with gut microbiotas. Species within\n                    <jats:italic>Bacteroides</jats:italic>\n                    fill many niches, including as mutualists, commensals and pathogens for their hosts. Within many reptiles,\n                    <jats:italic>Bacteroides</jats:italic>\n                    is a dominant, ‘core’ gut bacterium that sometimes exhibits increased abundance in times of food scarcity, such as during hibernation. Here, we take a two‐pronged approach to better characterise\n                    <jats:italic>Bacteroides</jats:italic>\n                    populations in reptile guts. Firstly, we leverage published 16S rRNA gene sequence datasets to determine the species‐level distributions of\n                    <jats:italic>Bacteroides</jats:italic>\n                    members in reptile hosts. Secondly, we mine publicly available metagenomes to extract data for\n                    <jats:italic>Bacteroides</jats:italic>\n                    from reptiles, birds, amphibians and mammals, to compare the functional potential of\n                    <jats:italic>Bacteroides</jats:italic>\n                    in different host taxa. The 16S rRNA gene analyses revealed that\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>B. acidifaciens</jats:italic>\n                    </jats:styled-content>\n                    is the most common\n                    <jats:italic>Bacteroides</jats:italic>\n                    species in reptile guts, and that different orders of reptiles differ in which\n                    <jats:italic>Bacteroides</jats:italic>\n                    species they harbour. The taxonomy of\n                    <jats:italic>Bacteroides</jats:italic>\n                    species recovered from metagenomic assembly did not differ between reptile orders or substantially across birds, amphibians and mammals. Metagenome‐assembled genomes for\n                    <jats:italic>Bacteroides</jats:italic>\n                    species were marginally more related when their hosts were more closely related, with reptile hosts in particular harbouring markedly more unique\n                    <jats:italic>Bacteroides</jats:italic>\n                    MAGs compared to other hosts. Our findings indicate that hosts harbour similar profiles of\n                    <jats:italic>Bacteroides</jats:italic>\n                    species across broad comparisons, but with some differences between reptile groups, and that\n                    <jats:italic>Bacteroides</jats:italic>\n                    appears to perform largely similar roles in vertebrate host guts regardless of host relatedness.\n                  </jats:p>","is_dataset_classified":null,"base_score":2.1972245773362196,"endowment":2.1972245773362196,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"39917835","pmcid":"PMC11874691","openalex_id":"https://openalex.org/W4407257791","authors":[],"funders":[],"total_grants":0,"fwci":3.0805,"citation_percentile":0.91210635,"influential_citations":0,"citation_trend":[{"year":2025,"count":4},{"year":2026,"count":4}],"oa_status":"hybrid","license":"cc-by-nc","oa_locations":[{"url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/mec.17685","host_type":"journal"},{"url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/mec.17685","host_type":"publisher"},{"url":"https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.17685","host_type":"publisher"},{"url":"https://doi.org/10.1111/mec.17685","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/39917835","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11874691","host_type":"repository"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11874691/pdf/MEC-34-e17685.pdf","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC11874691","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC11874691?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Gut microbiota and health","Aquaculture disease management and microbiota","Bacterial Identification and Susceptibility Testing"],"mesh_terms":["Gastrointestinal Microbiome","Animals","Bacteroides","Phylogeny","Reptiles","RNA, Ribosomal, 16S","Metagenome","Metagenomics"],"keywords":["Biology","Bacteroides","Genus","Zoology","Ecology","Evolutionary biology","Bacteria","Paleontology","Metagenomics","Microbiome","Metabarcoding","Reptile Microbiome"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life below water"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-18T13:34:53.176748Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}