{"paper_id":"3006894c-d1a0-4e0f-bee8-4b5255fea3bf","body_text":"The Gut Microbiome Profile of Lions in EtoshaNational Park, Namibia | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article The Gut Microbiome Profile of Lions in EtoshaNational Park, Namibia Carl Belger, Jakob Wirbel, Dylan Maghini, Nadia Carstens, Ansia van Coller, and 6 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9092464/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 7 You are reading this latest preprint version Abstract Background: The gut microbiome plays a crucial role in carnivore ecology, diet, and health, yet remains poorly characterised in African lions (Panthera leo melanochaita). Previous studies of lion microbiomes have primarily focused on small numbers of captive individuals maintained on controlled diets of Asian origin, reporting Fusobacteriota and Firmicutes as dominant phyla. Some recent literature has begun to describe microbiome composition in free-living African lions; however, genome-resolved analyses and detailed functional characterisation of the wild African lion gut microbiome remain lacking. Results: We present the first comprehensive gut microbiome analysis of free-living African lions, including novel MAGs generated from examining 23 fresh faecal samples from 20 individuals in Etosha National Park, Namibia. The African lion gut was dominated by Bacteroides (22.1%) and Phocaeicola (13.3%) - two related genera - contrasting sharply with the captive lions where Fusobacterium (Bhopal, India) and Firmicutes (Rotterdam, Netherlands) predominate. This divergence likely reflects dietary differences, captivity effects and possibly allopatric separation. While recent work has begun to characterise taxonomic composition in wild African lions, our study extends these findings through the reconstruction of 318 bacterial and 102 viral metagenome-assembled genomes (MAGs) from combined short- and long-read sequencing data. Most MAGs shared <95% average nucleotide identity with existing reference genomes, indicating largely novel species. Supplementing the GTDB database with these MAGs reduced unclassified reads from 24.5% to 9.2%, demonstrating the substantial gaps in existing carnivore gut microbiome databases. Functional analysis revealed metabolic pathway enrichment, particularly for purine metabolism—critical for processing the lions’ high-purine diet—with nearly complete pathways for degrading adenine and guanine to urea. Conclusions: This study provides the first in depth description of the microbial taxa in the African lion gut microbiome. Genera in the Bacteroidaceae family dominated. There are large differences with the metagenomics of the n = 3, 4 hybrid and Asiatic lions on controlled diets reported in prior studies. The discovery of over 300 novel MAGs significantly expands microbial reference databases and underscores the unique and understudied nature of apex carnivore microbiomes. These findings show critical microbial contributions to carnivore nutrition and establish a foundation for microbiome-based approaches to wildlife health monitoring and conservation management of threatened lion population. Panthera Leo microbiome Namibia conservation metagenomics Full Text Additional Declarations No competing interests reported. Supplementary Files Supplementaryfiguresandtables.pdf Cite Share Download PDF Status: Under Review Version 1 posted Reviews received at journal 09 May, 2026 Reviewers agreed at journal 30 Apr, 2026 Reviewers agreed at journal 28 Apr, 2026 Reviewers invited by journal 28 Apr, 2026 Editor assigned by journal 14 Apr, 2026 Submission checks completed at journal 08 Apr, 2026 First submitted to journal 08 Apr, 2026 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {\"props\":{\"pageProps\":{\"initialData\":{\"identity\":\"rs-9092464\",\"acceptedTermsAndConditions\":true,\"allowDirectSubmit\":false,\"archivedVersions\":[],\"articleType\":\"Research Article\",\"associatedPublications\":[],\"authors\":[{\"id\":632567571,\"identity\":\"a6e76f5b-8107-43a4-afd4-61a7db3a42ac\",\"order_by\":0,\"name\":\"Carl Belger\",\"email\":\"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA70lEQVRIiWNgGAWjYHACxgOMDQwyIMYDIMHDR4wekBYeIM1sANLCRooWNgkQj6AW/vazDw7z7rDhkXfvfVb5NcdOho2B+eGjG3i0SJxJNzjMeyaNx/DMcbPbstuSgQ5jMzbOwaPFgCGN4XBu22EewxlpbLcltzEDtfCwSePVwv8MpOU/j+H8Z2zFktvqidAiAbblAI+8BBsb48dthwlrkbgBtOXvmWQeA540ZmnGbcd52JgJ+IW/P43x4cwddnLy7ccYP/7cVm3Pz9788DE+LQgXHgDGJSh2GJiJUQ4C8g3AFPODWNWjYBSMglEwogAAbONDlyU4UHEAAAAASUVORK5CYII=\",\"orcid\":\"\",\"institution\":\"University of the Witwatersrand\",\"correspondingAuthor\":true,\"prefix\":\"\",\"firstName\":\"Carl\",\"middleName\":\"\",\"lastName\":\"Belger\",\"suffix\":\"\"},{\"id\":632567572,\"identity\":\"e1bec11e-2323-4ef2-8382-5c777ac88734\",\"order_by\":1,\"name\":\"Jakob Wirbel\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"Stanford University\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Jakob\",\"middleName\":\"\",\"lastName\":\"Wirbel\",\"suffix\":\"\"},{\"id\":632567573,\"identity\":\"d31aceb8-655f-4946-b7b0-9343f90b803d\",\"order_by\":2,\"name\":\"Dylan Maghini\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"University of the Witwatersrand\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Dylan\",\"middleName\":\"\",\"lastName\":\"Maghini\",\"suffix\":\"\"},{\"id\":632567574,\"identity\":\"c630a66a-1828-42cd-a56a-06a0e1c597a4\",\"order_by\":3,\"name\":\"Nadia Carstens\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"South African Medical Research Council\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Nadia\",\"middleName\":\"\",\"lastName\":\"Carstens\",\"suffix\":\"\"},{\"id\":632567575,\"identity\":\"cacfdaad-bc37-41d8-8d2e-aab21b34aa9c\",\"order_by\":4,\"name\":\"Ansia van Coller\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"South African Medical Research Council\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Ansia\",\"middleName\":\"van\",\"lastName\":\"Coller\",\"suffix\":\"\"},{\"id\":632567576,\"identity\":\"4a36b6c8-ea2d-40f0-aa2a-91715bcc91ab\",\"order_by\":5,\"name\":\"James C. 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Berkman\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"University of the Witwatersrand\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Aaron\",\"middleName\":\"Y.\",\"lastName\":\"Berkman\",\"suffix\":\"\"},{\"id\":632567579,\"identity\":\"3a02e906-60bc-456f-8388-d14511a55f27\",\"order_by\":8,\"name\":\"Willem Maartin Strauss\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"University of South Africa\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Willem\",\"middleName\":\"Maartin\",\"lastName\":\"Strauss\",\"suffix\":\"\"},{\"id\":632567580,\"identity\":\"3fefcfd2-79f0-4791-82a3-1cc22c6fe1da\",\"order_by\":9,\"name\":\"Robyn S. 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Previous studies of lion microbiomes have primarily focused on small numbers of captive individuals maintained on controlled diets of Asian origin, reporting Fusobacteriota and Firmicutes as dominant phyla. Some recent literature has begun to describe microbiome composition in free-living African lions; however, genome-resolved analyses and detailed functional characterisation of the wild African lion gut microbiome remain lacking.\\u003c/p\\u003e\\n\\u003cp\\u003e\\u003cstrong\\u003eResults: \\u003c/strong\\u003eWe present the first comprehensive gut microbiome analysis of free-living African lions, including novel MAGs generated from examining 23 fresh faecal samples from 20 individuals in Etosha National Park, Namibia. The African lion gut was dominated by Bacteroides (22.1%) and Phocaeicola (13.3%) - two related genera - contrasting sharply with the captive lions where Fusobacterium (Bhopal, India) and Firmicutes (Rotterdam, Netherlands) predominate. This divergence likely reflects dietary differences, captivity effects and possibly allopatric separation. While recent work has begun to characterise taxonomic composition in wild African lions, our study extends these findings through the reconstruction of 318 bacterial and 102 viral metagenome-assembled genomes (MAGs) from combined short- and long-read sequencing data. Most MAGs shared \\u0026lt;95% average nucleotide identity with existing reference genomes, indicating largely novel species. Supplementing the GTDB database with these MAGs reduced unclassified reads from 24.5% to 9.2%, demonstrating the substantial gaps in existing carnivore gut microbiome databases. Functional analysis revealed metabolic pathway enrichment, particularly for purine metabolism—critical for processing the lions’ high-purine diet—with nearly complete pathways for degrading adenine and guanine to urea.\\u003c/p\\u003e\\n\\u003cp\\u003e\\u003cstrong\\u003eConclusions: \\u003c/strong\\u003eThis study provides the first in depth description of the microbial taxa in the African lion gut microbiome. Genera in the Bacteroidaceae family dominated. There are large differences with the metagenomics of the n = 3, 4 hybrid and Asiatic lions on controlled diets reported in prior studies. The discovery of over 300 novel MAGs significantly expands microbial reference databases and underscores the unique and understudied nature of apex carnivore microbiomes. These findings show critical microbial contributions to carnivore nutrition and establish a foundation for microbiome-based approaches to wildlife health monitoring and conservation management of threatened lion population.\\u003c/p\\u003e\",\"manuscriptTitle\":\"The Gut Microbiome Profile of Lions in EtoshaNational Park, Namibia\",\"msid\":\"\",\"msnumber\":\"\",\"nonDraftVersions\":[{\"code\":1,\"date\":\"2026-05-06 11:28:41\",\"doi\":\"10.21203/rs.3.rs-9092464/v1\",\"editorialEvents\":[{\"type\":\"communityComments\",\"content\":0},{\"type\":\"editorInvitedReview\",\"content\":\"\",\"date\":\"2026-05-09T08:38:53+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"reviewerAgreed\",\"content\":\"116064738414098567977156561307049674387\",\"date\":\"2026-04-30T09:24:22+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"reviewerAgreed\",\"content\":\"335807127454906634383899208453172900651\",\"date\":\"2026-04-28T15:07:43+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"reviewersInvited\",\"content\":\"\",\"date\":\"2026-04-28T08:55:37+00:00\",\"index\":\"\",\"fulltext\":\"\"},{\"type\":\"editorAssigned\",\"content\":\"\",\"date\":\"2026-04-14T21:29:42+00:00\",\"index\":\"\",\"fulltext\":\"\"},{\"type\":\"checksComplete\",\"content\":\"\",\"date\":\"2026-04-08T08:28:38+00:00\",\"index\":\"\",\"fulltext\":\"\"},{\"type\":\"submitted\",\"content\":\"Animal Microbiome\",\"date\":\"2026-04-08T06:54:08+00:00\",\"index\":\"\",\"fulltext\":\"\"}],\"status\":\"published\",\"journal\":{\"display\":true,\"email\":\"info@researchsquare.com\",\"identity\":\"animal-microbiome\",\"isNatureJournal\":false,\"hasQc\":true,\"allowDirectSubmit\":false,\"externalIdentity\":\"amic\",\"sideBox\":\"Learn more about [Animal Microbiome](http://animalmicrobiome.biomedcentral.com)\",\"snPcode\":\"42523\",\"submissionUrl\":\"https://submission.nature.com/new-submission/42523/3\",\"title\":\"Animal Microbiome\",\"twitterHandle\":\"@bmc\",\"acdcEnabled\":true,\"dfaEnabled\":true,\"editorialSystem\":\"em\",\"reportingPortfolio\":\"BMC/SO AJ\",\"inReviewEnabled\":true,\"inReviewRevisionsEnabled\":true}}],\"origin\":\"\",\"ownerIdentity\":\"cbe0ae3e-cb24-41a9-9baf-3013f3aed52c\",\"owner\":[],\"postedDate\":\"May 6th, 2026\",\"published\":true,\"recentEditorialEvents\":[{\"type\":\"editorInvitedReview\",\"content\":\"\",\"date\":\"2026-05-09T08:38:53+00:00\",\"index\":25,\"fulltext\":\"\"},{\"type\":\"reviewerAgreed\",\"content\":\"116064738414098567977156561307049674387\",\"date\":\"2026-04-30T09:24:22+00:00\",\"index\":23,\"fulltext\":\"\"}],\"rejectedJournal\":[],\"revision\":\"\",\"amendment\":\"\",\"status\":\"under-review\",\"subjectAreas\":[],\"tags\":[],\"updatedAt\":\"2026-05-06T11:28:41+00:00\",\"versionOfRecord\":[],\"versionCreatedAt\":\"2026-05-06 11:28:41\",\"video\":\"\",\"vorDoi\":\"\",\"vorDoiUrl\":\"\",\"workflowStages\":[]},\"version\":\"v1\",\"identity\":\"rs-9092464\",\"journalConfig\":\"researchsquare\"},\"__N_SSP\":true},\"page\":\"/article/[identity]/[[...version]]\",\"query\":{\"redirect\":\"/article/rs-9092464\",\"identity\":\"rs-9092464\",\"version\":[\"v1\"]},\"buildId\":\"XKTyCvWXoU3ODBz1xrDgd\",\"isFallback\":false,\"isExperimentalCompile\":false,\"dynamicIds\":[84888],\"gssp\":true,\"scriptLoader\":[]}","source_license":"CC-BY-4.0","license_restricted":false}