{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T03:42:36Z","timestamp":1792035756772,"version":"4.4.0"},"reference-count":75,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,8,19]],"date-time":"2025-08-19T00:00:00Z","timestamp":1755561600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,8,19]],"date-time":"2025-08-19T00:00:00Z","timestamp":1755561600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BBS\/E\/RL\/230001A"],"award-info":[{"award-number":["BBS\/E\/RL\/230001A"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BBS\/E\/RL\/230001A"],"award-info":[{"award-number":["BBS\/E\/RL\/230001A"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The Game and Wildlife Conservation Trust","award":["Fundraising from the private sector"],"award-info":[{"award-number":["Fundraising from the private sector"]}]},{"name":"The Game and Wildlife Conservation Trust","award":["Fundraising from the private sector"],"award-info":[{"award-number":["Fundraising from the private sector"]}]},{"DOI":"10.13039\/501100000848","name":"University of Edinburgh","doi-asserted-by":"publisher","award":["Chancellor\u2019s Fellowship"],"award-info":[{"award-number":["Chancellor\u2019s Fellowship"]}],"id":[{"id":"10.13039\/501100000848","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Microbiol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      The avian caecal microbiota plays a vital role in host nutrition, enabling non-digestible, fibrous material to be converted into compounds that can be absorbed and used as an energy source by the host. The diet of adult red grouse (\n                      <jats:italic>Lagopus scotica<\/jats:italic>\n                      ) is dominated by heather (\n                      <jats:italic>Calluna vulgaris<\/jats:italic>\n                      ), which is particularly high in fibre. It is therefore likely that the caecal microbiota plays a key role in enabling grouse to thrive on this diet. In this study, we present the first characterisation of the caecal microbiota of red grouse using modern sequencing methods.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We performed metagenomic sequencing on caecal content samples from fifteen red grouse from three upland estates in Scotland. From this data, we constructed and characterised twelve high-quality, species-level metagenome assembled genomes (MAGs). Eleven of these MAGs could not be assigned a taxonomic label at species level, indicating that they may be novel species. MAGs belonged to diverse taxa (5 phyla) and several encoded genes and pathways for the digestion of fibres, including cellulose, hemi-cellulose, xylooligosaccharides and pectin. Several MAGs also contained antimicrobial resistance genes, predominantly related to vancomycin resistance.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>This study is the first to reconstruct commensal microbial genomes from red grouse. The caeca contain diverse, often novel, microbial taxa capable of fermenting various fibres, potentially aiding in the digestion of the red grouse\u2019s high-fibre diet. Further research is necessary to explore how these bacteria support red grouse nutrition and health.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12866-025-04280-1","type":"journal-article","created":{"date-parts":[[2025,8,19]],"date-time":"2025-08-19T11:48:14Z","timestamp":1755604094000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Metagenomics reveals fibre fermentation and AMR pathways in red grouse (Lagopus scotica) microbiota"],"prefix":"10.1186","volume":"25","author":[{"given":"Anum Ali","family":"Ahmad","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathy","family":"Fletcher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas","family":"Hesford","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Glendinning","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,8,19]]},"reference":[{"key":"4280_CR1","doi-asserted-by":"publisher","first-page":"934272","DOI":"10.3389\/fmicb.2022.934272","volume":"13","author":"F Sun","year":"2022","unstructured":"Sun F, Chen J, Liu K, Tang M, Yang Y. The avian gut microbiota: diversity, influencing factors, and future directions. Front Microbiol. 2022;13:934272. https:\/\/doi.org\/10.3389\/fmicb.2022.934272.","journal-title":"Front Microbiol"},{"key":"4280_CR2","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1016\/j.tim.2021.07.003","volume":"30","author":"KH Bodawatta","year":"2022","unstructured":"Bodawatta KH, Hird SM, Grond K, Poulsen M, J\u00f8nsson KA. Avian gut microbiomes taking flight. Trends Microbiol. 2022;30:268\u201380. https:\/\/doi.org\/10.1016\/j.tim.2021.07.003.","journal-title":"Trends Microbiol"},{"key":"4280_CR3","doi-asserted-by":"publisher","first-page":"424","DOI":"10.1111\/1755-0998.12744","volume":"18","author":"E Videvall","year":"2018","unstructured":"Videvall E, Strandh M, Engelbrecht A, Cloete S, Cornwallis CK. Measuring the gut Microbiome in birds: comparison of faecal and cloacal sampling. Mol Ecol Resour. 2018;18:424\u201334. https:\/\/doi.org\/10.1111\/1755-0998.12744.","journal-title":"Mol Ecol Resour"},{"key":"4280_CR4","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1186\/s12866-015-0388-6","volume":"15","author":"D Stanley","year":"2015","unstructured":"Stanley D, Geier MS, Chen H, Hughes RJ, Moore RJ. Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences. BMC Microbiol. 2015;15:51. https:\/\/doi.org\/10.1186\/s12866-015-0388-6.","journal-title":"BMC Microbiol"},{"key":"4280_CR5","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1080\/01584197.2022.2114088","volume":"122","author":"MIA Matheen","year":"2022","unstructured":"Matheen MIA, GM R, Dudaniec RY. Dominant factors shaping the gut microbiota of wild birds. Emu. 2022;122:255\u201368. https:\/\/doi.org\/10.1080\/01584197.2022.2114088.","journal-title":"Emu"},{"key":"4280_CR6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.aninu.2019.11.004","volume":"6","author":"T Mahmood","year":"2020","unstructured":"Mahmood T, Guo Y. Dietary fiber and chicken Microbiome interaction: where will it lead to? Anim Nutr. 2020;6:1\u20138. https:\/\/doi.org\/10.1016\/j.aninu.2019.11.004.","journal-title":"Anim Nutr"},{"key":"4280_CR7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.anifeedsci.2003.09.007","volume":"113","author":"D J\u00f3zefiak","year":"2004","unstructured":"J\u00f3zefiak D, Rutkowski A, Martin SA. Carbohydrate fermentation in the avian ceca: A review. Anim Feed Sci Technol. 2004;113:1\u201315. https:\/\/doi.org\/10.1016\/j.anifeedsci.2003.09.007.","journal-title":"Anim Feed Sci Technol"},{"key":"4280_CR8","doi-asserted-by":"publisher","first-page":"4243","DOI":"10.1038\/s41598-019-40822-0","volume":"9","author":"A Hunt","year":"2019","unstructured":"Hunt A, Al-Nakkash L, Lee AH, Smith HF. Phylogeny and herbivory are related to avian cecal size. Sci Rep. 2019;9:4243. https:\/\/doi.org\/10.1038\/s41598-019-40822-0.","journal-title":"Sci Rep"},{"key":"4280_CR9","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1079\/BJN19720093","volume":"27","author":"R Moss","year":"1972","unstructured":"Moss R, Parkinson JA. The digestion of Heather (Calluna vulgaris) by red Grouse (Lagopus lagopus scoticus). Br J Nutr. 1972;27:285\u201398. https:\/\/doi.org\/10.1079\/BJN19720093.","journal-title":"Br J Nutr"},{"key":"4280_CR10","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1080\/00071668708416939","volume":"28","author":"R Moss","year":"1987","unstructured":"Moss R, Trenholm IB. Food intake, digestibility and gut size in red Grouse. Br Poult Sci. 1987;28:81\u20139. https:\/\/doi.org\/10.1080\/00071668708416939.","journal-title":"Br Poult Sci"},{"key":"4280_CR11","doi-asserted-by":"publisher","first-page":"754","DOI":"10.1038\/s41564-023-01351-9","volume":"8","author":"DGJ Larsson","year":"2023","unstructured":"Larsson DGJ, Gaze WH, Laxminarayan R, Topp E. AMR, one health and the environment. Nat Microbiol. 2023;8:754\u20135. https:\/\/doi.org\/10.1038\/s41564-023-01351-9.","journal-title":"Nat Microbiol"},{"key":"4280_CR12","doi-asserted-by":"publisher","first-page":"e2540","DOI":"10.1002\/vetr.2540","volume":"192","author":"C Bain","year":"2023","unstructured":"Bain C, Rathor G, Jones BP, Hassan MM, Papke P, et al. \u03b2-Lactam resistance genes present in UK pheasants and red-legged partridges. Vet Rec. 2023;192:e2540. https:\/\/doi.org\/10.1002\/vetr.2540.","journal-title":"Vet Rec"},{"key":"4280_CR13","doi-asserted-by":"crossref","unstructured":"Chintoan-Uta C, Seguino A. Antimicrobial resistance of Campylobacter spp. in wild game pheasants (Phasia nus colchicus) in Scotland. Microbiology Society Annual Conference; 2018. https:\/\/www.research.ed.ac.uk\/en\/publications\/antimicrobial-resistance-of-campylobacter-spp-in-wild-game-pheasa.","DOI":"10.1016\/j.fm.2018.04.002"},{"key":"4280_CR14","doi-asserted-by":"publisher","first-page":"127372","DOI":"10.1016\/j.micres.2023.127372","volume":"271","author":"JA Rasmussen","year":"2023","unstructured":"Rasmussen JA, Chua PYS. Genome-resolving metagenomics reveals wild Western capercaillies (Tetrao urogallus) as avian hosts for antibiotic-resistance bacteria and their interactions with the gut-virome community. Microbiol Res. 2023;271:127372. https:\/\/doi.org\/10.1016\/j.micres.2023.127372.","journal-title":"Microbiol Res"},{"key":"4280_CR15","doi-asserted-by":"publisher","first-page":"542","DOI":"10.1016\/j.syapm.2011.06.003","volume":"34","author":"T Wienemann","year":"2011","unstructured":"Wienemann T, Schmitt-Wagner D, Meuser K, Segelbacher G, Schink B, et al. The bacterial microbiota in the Ceca of capercaillie (Tetrao urogallus) differs between wild and captive birds. Syst Appl Microbiol. 2011;34:542\u201351. https:\/\/doi.org\/10.1016\/j.syapm.2011.06.003.","journal-title":"Syst Appl Microbiol"},{"key":"4280_CR16","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1186\/s42523-019-0002-6","volume":"1","author":"SV Drovetski","year":"2019","unstructured":"Drovetski SV, O\u2019Mahoney MJV, Matterson KO, Schmidt BK, Graves GR. Distinct microbiotas of anatomical gut regions display idiosyncratic seasonal variation in an avian folivore. Anim Microbiome. 2019;1:2. https:\/\/doi.org\/10.1186\/s42523-019-0002-6.","journal-title":"Anim Microbiome"},{"key":"4280_CR17","doi-asserted-by":"publisher","first-page":"fnw144","DOI":"10.1093\/femsle\/fnw144","volume":"363","author":"KD Kohl","year":"2016","unstructured":"Kohl KD, Connelly JW, Dearing MD, Forbey JS. Microbial detoxification in the gut of a specialist avian herbivore, the greater Sage-Grouse. FEMS Microbiol Lett. 2016;363:fnw144. https:\/\/doi.org\/10.1093\/femsle\/fnw144.","journal-title":"FEMS Microbiol Lett"},{"key":"4280_CR18","doi-asserted-by":"publisher","first-page":"coae052","DOI":"10.1093\/conphys\/coae052","volume":"12","author":"E Vaasjo","year":"2024","unstructured":"Vaasjo E, Stothart MR, Black SR, Poissant J, Whiteside DP. The impact of management on the fecal Microbiome of endangered greater sage-grouse (Centrocercus urophasianus) in a zoo-based conservation program. Conserv Physiol. 2024;12:coae052. https:\/\/doi.org\/10.1093\/conphys\/coae052.","journal-title":"Conserv Physiol"},{"key":"4280_CR19","doi-asserted-by":"publisher","first-page":"119418","DOI":"10.1016\/j.envpol.2022.119418","volume":"306","author":"SV Drovetski","year":"2022","unstructured":"Drovetski SV, Schmidt BK, Lai JE, Gross MS, Hladik ML, et al. Exposure to crop production alters cecal prokaryotic microbiota, inflates virulome and resistome in wild prairie Grouse. Environ Pollut. 2022;306:119418. https:\/\/doi.org\/10.1016\/j.envpol.2022.119418.","journal-title":"Environ Pollut"},{"key":"4280_CR20","doi-asserted-by":"publisher","first-page":"e0213503","DOI":"10.1371\/journal.pone.0213503","volume":"14","author":"A Salgado-Flores","year":"2019","unstructured":"Salgado-Flores A, Tveit AT, Wright A-D, Pope PB, Sundset MA. Characterization of the cecum Microbiome from wild and captive rock ptarmigans Indigenous to Arctic Norway. PLoS ONE. 2019;14:e0213503. https:\/\/doi.org\/10.1371\/journal.pone.0213503.","journal-title":"PLoS ONE"},{"key":"4280_CR21","doi-asserted-by":"publisher","first-page":"101","DOI":"10.3390\/d17020101","volume":"17","author":"E Durnova","year":"2025","unstructured":"Durnova E, Karmanova E, Sorokina T, Mayorova K, Aksenov A. Bacterial diversity and composition in the internal organs of Taiga bean goose, greater White-Fronted Goose and Willow ptarmigan as a new tools in the Arctic biomonitoring system. Diversity. 2025;17:101. https:\/\/doi.org\/10.3390\/d17020101.","journal-title":"Diversity"},{"key":"4280_CR22","doi-asserted-by":"publisher","first-page":"231518","DOI":"10.1098\/rsos.231518","volume":"11","author":"EW Ingvaldsen","year":"2024","unstructured":"Ingvaldsen EW, \u00d8stnes JE, Kleven O, Davey M, Foss\u00f8y F, Nilsen EB. Fecal DNA metabarcoding reveals seasonal and annual variation in Willow ptarmigan diet. R Soc Open Sci. 2024;11:231518. https:\/\/doi.org\/10.1098\/rsos.231518.","journal-title":"R Soc Open Sci"},{"key":"4280_CR23","doi-asserted-by":"publisher","unstructured":"Dunn JC, Clegg SR. High prevalence of multi-drug resistant bacteria in faecal samples from UK passerine birds. BioRxiv. 2024: 2024.07.24.604896.\u00a0https:\/\/doi.org\/10.1101\/2024.07.24.604896.","DOI":"10.1101\/2024.07.24.604896"},{"key":"4280_CR24","doi-asserted-by":"publisher","first-page":"692","DOI":"10.1111\/j.1096-3642.1910.tb01911.x","volume":"80","author":"HB Fantham","year":"1910","unstructured":"Fantham HB. Observations on the parasitic protozoa of the red Grouse (Lagopus scoticus), with a note on the Grouse fly. Proc Zool Soc Lond. 1910;80:692\u2013708. https:\/\/doi.org\/10.1111\/j.1096-3642.1910.tb01911.x.","journal-title":"Proc Zool Soc Lond"},{"key":"4280_CR25","unstructured":"FastQC. A quality control analysis tool for high throughput sequencing data.https:\/\/github.com\/s-andrews\/FastQC."},{"key":"4280_CR26","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","volume":"32","author":"P Ewels","year":"2016","unstructured":"Ewels P, Magnusson M, Lundin S, K\u00e4ller M, MultiQC. Summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32:3047\u20138. https:\/\/doi.org\/10.1093\/bioinformatics\/btw354.","journal-title":"Bioinformatics"},{"key":"4280_CR27","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","volume":"34","author":"S Chen","year":"2018","unstructured":"Chen S, Zhou Y, Chen Y, Gu J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884\u201390. https:\/\/doi.org\/10.1093\/bioinformatics\/bty560.","journal-title":"Bioinformatics"},{"key":"4280_CR28","doi-asserted-by":"publisher","first-page":"612","DOI":"10.2307\/3798870","volume":"34","author":"DS Eastman","year":"1970","unstructured":"Eastman DS, Jenkins D. Comparative food habits of red Grouse in Northeast scotland, using fecal analysis. J Wildl Manag. 1970;34:612\u201320. https:\/\/doi.org\/10.2307\/3798870.","journal-title":"J Wildl Manag"},{"key":"4280_CR29","doi-asserted-by":"publisher","first-page":"3997","DOI":"10.48550\/arXiv.1303.3997","volume":"1303","author":"H Li","year":"2013","unstructured":"Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv. 2013;1303:3997. https:\/\/doi.org\/10.48550\/ArXiv.1303.3997.","journal-title":"ArXiv"},{"key":"4280_CR30","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. The sequence alignment\/map format and samtools. Bioinformatics. 2009;25:2078\u20139. https:\/\/doi.org\/10.1093\/bioinformatics\/btp352.","journal-title":"Bioinformatics"},{"key":"4280_CR31","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","volume":"20","author":"DE Wood","year":"2019","unstructured":"Wood DE, Lu J, Langmead B. Improved metagenomic analysis with kraken 2. Genome Biol. 2019;20:257. https:\/\/doi.org\/10.1186\/s13059-019-1891-0.","journal-title":"Genome Biol"},{"key":"4280_CR32","doi-asserted-by":"publisher","first-page":"e104","DOI":"10.7717\/peerj-cs.104","volume":"3","author":"J Lu","year":"2017","unstructured":"Lu J, Breitwieser FP, Thielen P, Salzberg SL, Bracken. Estimating species abundance in metagenomics data. PeerJ Comput Sci. 2017;3:e104. https:\/\/doi.org\/10.7717\/peerj-cs.104.","journal-title":"PeerJ Comput Sci"},{"key":"4280_CR33","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","volume":"31","author":"D Li","year":"2015","unstructured":"Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31:1674\u20136. https:\/\/doi.org\/10.1093\/bioinformatics\/btv033.","journal-title":"Bioinformatics"},{"key":"4280_CR34","doi-asserted-by":"publisher","unstructured":"Aroney ST, Newell RJ, Nissen JN, Camargo AP, Tyson GW, Woodcroft BJ. CoverM: read alignment statistics for metagenomics. Bioinformatics. 2025;41:btaf147. https:\/\/doi.org\/10.1093\/bioinformatics\/btaf147.","DOI":"10.1093\/bioinformatics\/btaf147"},{"key":"4280_CR35","doi-asserted-by":"publisher","first-page":"e7359","DOI":"10.7717\/peerj.7359","volume":"7","author":"DD Kang","year":"2019","unstructured":"Kang DD, Li F, Kirton E, Thomas A, Egan R, et al. MetaBAT 2: an adaptive Binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019;7:e7359. https:\/\/doi.org\/10.7717\/peerj.7359.","journal-title":"PeerJ"},{"key":"4280_CR36","doi-asserted-by":"publisher","first-page":"1203","DOI":"10.1038\/s41592-023-01940-w","volume":"20","author":"A Chklovski","year":"2023","unstructured":"Chklovski A, Parks DH, Woodcroft BJ, Tyson GW. CheckM2: A rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat Methods. 2023;20:1203\u201312. https:\/\/doi.org\/10.1038\/s41592-023-01940-w.","journal-title":"Nat Methods"},{"key":"4280_CR37","doi-asserted-by":"publisher","unstructured":"Olm MR, Brown CT, Brooks B, Banfield JF, dRep. A tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017;11:2864\u20138. https:\/\/doi.org\/10.1038\/ismej.2017.126.","DOI":"10.1038\/ismej.2017.126"},{"key":"4280_CR38","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1186\/s40168-020-00990-y","volume":"9","author":"J Guo","year":"2021","unstructured":"Guo J, Bolduc B, Zayed AA, Varsani A, Dominguez-Huerta G, et al. VirSorter2: A multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome. 2021;9:37. https:\/\/doi.org\/10.1186\/s40168-020-00990-y.","journal-title":"Microbiome"},{"key":"4280_CR39","doi-asserted-by":"publisher","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","volume":"36","author":"P-A Chaumeil","year":"2019","unstructured":"Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: A toolkit to classify genomes with the genome taxonomy database. Bioinformatics. 2019;36:1925\u20137. https:\/\/doi.org\/10.1093\/bioinformatics\/btz848.","journal-title":"Bioinformatics"},{"key":"4280_CR40","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/s40168-021-01213-8","volume":"10","author":"Z Zhou","year":"2022","unstructured":"Zhou Z, Tran PQ, Breister AM, Liu Y, Kieft K, et al. High-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. Microbiome. 2022;10:33. https:\/\/doi.org\/10.1186\/s40168-021-01213-8.","journal-title":"Microbiome"},{"key":"4280_CR41","doi-asserted-by":"publisher","first-page":"D690","DOI":"10.1093\/nar\/gkac920","volume":"51","author":"BP Alcock","year":"2022","unstructured":"Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya Amogelang R, et al. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database. Nucleic Acids Res. 2022;51:D690\u20139. https:\/\/doi.org\/10.1093\/nar\/gkac920.","journal-title":"Nucleic Acids Res"},{"key":"4280_CR42","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v021.i12","volume":"21","author":"H Wickham","year":"2007","unstructured":"Wickham H. Reshaping data with the reshape package. J Stat Softw. 2007;21:1\u201320. https:\/\/doi.org\/10.18637\/jss.v021.i12.","journal-title":"J Stat Softw"},{"key":"4280_CR43","unstructured":"Wilke CO. cowplot: Streamlined plot theme and plot annotations for \u2018ggplot2\u2019. 2024. https:\/\/cran.r-project.org\/web\/packages\/cowplot\/index.html"},{"key":"4280_CR44","unstructured":"Wickham H, Fran\u00e7ois R, Henry L, M\u00fcller K, Vaughan D. dplyr: A grammar of data manipulation. 2023. https:\/\/cran.r-project.org\/web\/packages\/dplyr\/index.html"},{"key":"4280_CR45","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: elegant graphics for data analysis","author":"H Wickham","year":"2016","unstructured":"Wickham H. ggplot2: elegant graphics for data analysis. New York: Springer-; 2016."},{"key":"4280_CR46","doi-asserted-by":"publisher","first-page":"1686","DOI":"10.21105\/joss.01686","volume":"4","author":"H Wickham","year":"2019","unstructured":"Wickham H, Averick M, Bryan J, Chang W, McGowan LDA, et al. Welcome to the tidyverse. J Open Source Softw. 2019;4:1686. https:\/\/doi.org\/10.21105\/joss.01686.","journal-title":"J Open Source Softw"},{"key":"4280_CR47","doi-asserted-by":"publisher","first-page":"2500","DOI":"10.1038\/s41467-020-16366-7","volume":"11","author":"F Asnicar","year":"2020","unstructured":"Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, et al. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat Commun. 2020;11:2500. https:\/\/doi.org\/10.1038\/s41467-020-16366-7.","journal-title":"Nat Commun"},{"key":"4280_CR48","unstructured":"Figtree https:\/\/github.com\/rambaut\/figtree."},{"key":"4280_CR49","doi-asserted-by":"publisher","unstructured":"Pallen MJ, Ponsero AJ, Telatin A, Moss CJ, Baker D, et al. Faecal metagenomes of great Tits and blue Tits provide insights into host, diet, pathogens and microbial biodiversity. Access Microbiol. 2025;7. https:\/\/doi.org\/10.1099\/acmi.0.000910.v3.","DOI":"10.1099\/acmi.0.000910.v3"},{"key":"4280_CR50","doi-asserted-by":"publisher","first-page":"595","DOI":"10.3967\/bes2023.087","volume":"36","author":"J Liu","year":"2023","unstructured":"Liu J, Li XY, Song WT, Zeng XX, Li H, et al. Metagenomic analysis of environmental samples from wildlife rescue station at Poyang lake, China. Biomed Environ Sci. 2023;36:595\u2013603. https:\/\/doi.org\/10.3967\/bes2023.087.","journal-title":"Biomed Environ Sci"},{"key":"4280_CR51","doi-asserted-by":"publisher","first-page":"1403932","DOI":"10.3389\/fvets.2024.1403932","volume":"11","author":"Y Wang","year":"2024","unstructured":"Wang Y, Zhai J, Tang B, Dong Y, Sun S, et al. Metagenomic comparison of gut communities between wild and captive Himalayan griffons. Front Vet Sci. 2024;11:1403932. https:\/\/doi.org\/10.3389\/fvets.2024.1403932.","journal-title":"Front Vet Sci"},{"key":"4280_CR52","doi-asserted-by":"publisher","first-page":"D726","DOI":"10.1093\/nar\/gkx967","volume":"46","author":"AL Mitchell","year":"2017","unstructured":"Mitchell AL, Scheremetjew M, Denise H, Potter S, Tarkowska A, et al. EBI metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies. Nucleic Acids Res. 2017;46:D726\u201335. https:\/\/doi.org\/10.1093\/nar\/gkx967.","journal-title":"Nucleic Acids Res"},{"key":"4280_CR53","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1186\/s40168-021-01078-x","volume":"9","author":"F Xie","year":"2021","unstructured":"Xie F, Jin W, Si H, Yuan Y, Tao Y, et al. An integrated gene catalog and over 10,000 metagenome-assembled genomes from the Gastrointestinal Microbiome of ruminants. Microbiome. 2021;9:137. https:\/\/doi.org\/10.1186\/s40168-021-01078-x.","journal-title":"Microbiome"},{"key":"4280_CR54","doi-asserted-by":"publisher","first-page":"e0305317","DOI":"10.1371\/journal.pone.0305317","volume":"19","author":"MB Bj\u00f8rnsen","year":"2024","unstructured":"Bj\u00f8rnsen MB, Valer\u00f3n NR, V\u00e1squez DP, Velasco EM, Hansen AJ, Hauptmann AL. Microbiota in the ptarmigan intestine\u2014An Inuit delicacy and its potential in popular cuisine. PLoS ONE. 2024;19:e0305317. https:\/\/doi.org\/10.1371\/journal.pone.0305317.","journal-title":"PLoS ONE"},{"key":"4280_CR55","doi-asserted-by":"publisher","first-page":"e10941","DOI":"10.7717\/peerj.10941","volume":"9","author":"R Gilroy","year":"2021","unstructured":"Gilroy R, Ravi A, Getino M, Pursley I, Horton DL, et al. Extensive microbial diversity within the chicken gut Microbiome revealed by metagenomics and culture. PeerJ. 2021;9:e10941. https:\/\/doi.org\/10.7717\/peerj.10941.","journal-title":"PeerJ"},{"key":"4280_CR56","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1016\/j.chom.2021.12.003","volume":"30","author":"BS Beresford-Jones","year":"2022","unstructured":"Beresford-Jones BS, Forster SC, Stares MD, Notley G, Viciani E, et al. The mouse Gastrointestinal bacteria catalogue enables translation between the mouse and human gut microbiotas via functional mapping. Cell Host Microbe. 2022;30:124\u2013e388. https:\/\/doi.org\/10.1016\/j.chom.2021.12.003.","journal-title":"Cell Host Microbe"},{"key":"4280_CR57","doi-asserted-by":"publisher","first-page":"eaaw4361","DOI":"10.1126\/science.aaw4361","volume":"365","author":"SP Rosshart","year":"2019","unstructured":"Rosshart SP, Herz J, Vassallo BG, Hunter A, Wall MK, et al. Laboratory mice born to wild mice have natural microbiota and model human immune responses. Science. 2019;365:eaaw4361. https:\/\/doi.org\/10.1126\/science.aaw4361.","journal-title":"Science"},{"key":"4280_CR58","doi-asserted-by":"publisher","first-page":"2909","DOI":"10.1016\/j.celrep.2020.02.036","volume":"30","author":"TR Lesker","year":"2020","unstructured":"Lesker TR, Durairaj AC, G\u00e1lvez EJC, Lagkouvardos I, Baines JF, et al. An integrated metagenome catalog reveals new insights into the murine gut Microbiome. Cell Rep. 2020;30:2909\u2013e226. https:\/\/doi.org\/10.1016\/j.celrep.2020.02.036.","journal-title":"Cell Rep"},{"key":"4280_CR59","doi-asserted-by":"publisher","first-page":"106469","DOI":"10.1016\/j.nbd.2024.106469","volume":"194","author":"A Riva","year":"2024","unstructured":"Riva A, Sahin E, Volpedo G, Petretto A, Lavarello C, et al. Identification of an epilepsy-linked gut microbiota signature in a pediatric rat model of acquired epilepsy. Neurobiol Dis. 2024;194:106469. https:\/\/doi.org\/10.1016\/j.nbd.2024.106469.","journal-title":"Neurobiol Dis"},{"key":"4280_CR60","doi-asserted-by":"publisher","first-page":"3555","DOI":"10.1038\/s41591-024-03280-4","volume":"30","author":"J Zheng","year":"2024","unstructured":"Zheng J, Sun Q, Zhang M, Liu C, Su Q, et al. Noninvasive, microbiome-based diagnosis of inflammatory bowel disease. Nat Med. 2024;30:3555\u201367. https:\/\/doi.org\/10.1038\/s41591-024-03280-4.","journal-title":"Nat Med"},{"key":"4280_CR61","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1111\/1462-2920.15858","volume":"24","author":"MDJ Blyton","year":"2022","unstructured":"Blyton MDJ, Soo RM, Hugenholtz P, Moore BD. Maternal inheritance of the Koala gut Microbiome and its compositional and functional maturation during juvenile development. Environ Microbiol. 2022;24:475\u201393. https:\/\/doi.org\/10.1111\/1462-2920.15858.","journal-title":"Environ Microbiol"},{"key":"4280_CR62","doi-asserted-by":"publisher","first-page":"1802866","DOI":"10.1080\/19490976.2020.1802866","volume":"12","author":"A Mukherjee","year":"2020","unstructured":"Mukherjee A, Lordan C, Ross RP, Cotter PD. Gut microbes from the phylogenetically diverse genus Eubacterium and their various contributions to gut health. Gut Microbes. 2020;12:1802866. https:\/\/doi.org\/10.1080\/19490976.2020.1802866.","journal-title":"Gut Microbes"},{"key":"4280_CR63","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1186\/s13073-021-00950-7","volume":"13","author":"CY Kim","year":"2021","unstructured":"Kim CY, Lee M, Yang S, Kim K, Yong D, et al. Human reference gut Microbiome catalog including newly assembled genomes from under-represented Asian metagenomes. Genome Med. 2021;13:134. https:\/\/doi.org\/10.1186\/s13073-021-00950-7.","journal-title":"Genome Med"},{"key":"4280_CR64","doi-asserted-by":"publisher","first-page":"6389","DOI":"10.1038\/s41467-020-19929-w","volume":"11","author":"D Wylensek","year":"2020","unstructured":"Wylensek D, Hitch TCA, Riedel T, Afrizal A, Kumar N, et al. A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity. Nat Commun. 2020;11:6389. https:\/\/doi.org\/10.1038\/s41467-020-19929-w.","journal-title":"Nat Commun"},{"key":"4280_CR65","doi-asserted-by":"publisher","first-page":"fiac094","DOI":"10.1093\/femsec\/fiac094","volume":"98","author":"F IJdema","year":"2022","unstructured":"IJdema F, De Smet J, Crauwels S, Lievens B, Van Campenhout L. Meta-analysis of larvae of the black soldier fly (Hermetia illucens) microbiota based on 16S rRNA gene amplicon sequencing. FEMS Microbiol Ecol. 2022;98:fiac094. https:\/\/doi.org\/10.1093\/femsec\/fiac094.","journal-title":"FEMS Microbiol Ecol"},{"key":"4280_CR66","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1186\/s40168-024-01917-7","volume":"12","author":"JFM Salgado","year":"2024","unstructured":"Salgado JFM, Herv\u00e9 V, Vera MAG, Tokuda G, Brune A. Unveiling lignocellulolytic potential: a genomic exploration of bacterial lineages within the termite gut. Microbiome. 2024;12:201. https:\/\/doi.org\/10.1186\/s40168-024-01917-7.","journal-title":"Microbiome"},{"key":"4280_CR67","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1038\/s43705-021-00053-9","volume":"1","author":"KL Bowerman","year":"2021","unstructured":"Bowerman KL, Knowles SCL, Bradley JE, Baltr\u016bnait\u0117 L, Lynch MDJ, et al. Effects of laboratory domestication on the rodent gut Microbiome. ISME Commun. 2021;1:49. https:\/\/doi.org\/10.1038\/s43705-021-00053-9.","journal-title":"ISME Commun"},{"key":"4280_CR68","doi-asserted-by":"publisher","unstructured":"Betancur-Murillo CL, Aguilar-Mar\u00edn SB, Jovel J. Prevotella: A key player in ruminal metabolism. 2022;11:1.\u00a0https:\/\/doi.org\/10.3390\/microorganisms11010001.","DOI":"10.3390\/microorganisms11010001"},{"key":"4280_CR69","doi-asserted-by":"publisher","first-page":"1493","DOI":"10.1007\/bf02027727","volume":"22","author":"AH Murray","year":"1996","unstructured":"Murray AH, Iason GR, Stewart C. Effect of simple phenolic compounds of Heather (Calluna vulgaris) on rumen microbial activity in vitro. J Chem Ecol. 1996;22:1493\u2013504. https:\/\/doi.org\/10.1007\/bf02027727.","journal-title":"J Chem Ecol"},{"key":"4280_CR70","doi-asserted-by":"publisher","first-page":"654","DOI":"10.1002\/pro.3819","volume":"29","author":"PJ Stogios","year":"2020","unstructured":"Stogios PJ, Savchenko A. Molecular mechanisms of Vancomycin resistance. Protein Sci. 2020;29:654\u201369. https:\/\/doi.org\/10.1002\/pro.3819.","journal-title":"Protein Sci"},{"key":"4280_CR71","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1007\/978-3-319-39658-3_19","volume-title":"Efflux-mediated antimicrobial resistance in bacteria: mechanisms, regulation and clinical implications","author":"J Li","year":"2016","unstructured":"Li J, Li X-Z. Antimicrobial resistance and drug efflux pumps in Helicobacter. In: Li X-Z, Elkins CA, Zgurskaya HI, editors. Efflux-mediated antimicrobial resistance in bacteria: mechanisms, regulation and clinical implications. Springer International Publishing; 2016. p. 489\u2013513."},{"key":"4280_CR72","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1016\/j.anaerobe.2018.10.004","volume":"55","author":"C Alauzet","year":"2019","unstructured":"Alauzet C, Lozniewski A, Marchandin H. Metronidazole resistance and Nim genes in anaerobes: A review. Anaerobe. 2019;55:40\u201353. https:\/\/doi.org\/10.1016\/j.anaerobe.2018.10.004.","journal-title":"Anaerobe"},{"key":"4280_CR73","doi-asserted-by":"publisher","first-page":"2033","DOI":"10.3390\/microorganisms12102033","volume":"12","author":"B Tang","year":"2024","unstructured":"Tang B, Wang Y, Dong Y, Cui Q, Zeng Z, et al. The catalog of microbial genes and metagenome-assembled genomes from the gut microbiomes of five typical crow species on the Qinghai-Tibetan Plateau. Microorganisms. 2024;12:2033. https:\/\/doi.org\/10.3390\/microorganisms12102033.","journal-title":"Microorganisms."},{"key":"4280_CR74","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1038\/s43705-023-00221-z","volume":"3","author":"R Eisenhofer","year":"2023","unstructured":"Eisenhofer R, Odriozola I, Alberdi A. Impact of microbial genome completeness on metagenomic functional inference. ISME Commun. 2023;3:12. https:\/\/doi.org\/10.1038\/s43705-023-00221-z.","journal-title":"ISME Commun"},{"key":"4280_CR75","doi-asserted-by":"publisher","first-page":"giaf004","DOI":"10.1093\/gigascience\/giaf004","volume":"14","author":"Y Gao","year":"2025","unstructured":"Gao Y, Luo H, Lyu H, Yang H, Yousuf S, et al. Benchmarking short-read metagenomics tools for removing host contamination. GigaScience. 2025;14:giaf004. https:\/\/doi.org\/10.1093\/gigascience\/giaf004.","journal-title":"GigaScience"}],"container-title":["BMC Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-025-04280-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12866-025-04280-1","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-025-04280-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T12:40:25Z","timestamp":1781613625000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12866-025-04280-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,19]]},"references-count":75,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["4280"],"URL":"https:\/\/doi.org\/10.1186\/s12866-025-04280-1","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.04.02.646739","asserted-by":"object"}]},"ISSN":["1471-2180"],"issn-type":[{"value":"1471-2180","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,8,19]]},"assertion":[{"value":"3 April 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 July 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 August 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Red grouse carcasses were privately owned by the estates on which the birds were shot. The Game Wildlife and Conservation Trust accessed and collected the gastrointestinal samples for this study. Informed consent was obtained from the owners to use these samples in our study. Field studies were conducted in accordance with local legislation. In the United Kingdom the birds listed in Schedule 2 of the Wildlife and Countryside Act 1981 (which include red grouse) are exempt from the general provision of protection. Any person is able to kill or \u2018take\u2019 a species listed outside of the close season for that bird. Therefore, red grouse can be legally taken between 12th August and 10th December within the United Kingdom. Red grouse were not killed for the purpose of providing samples for this study. Samples were collected from red grouse killed during legal game bird shoots within the open season in Scotland, from gastrointestinal samples that would normally be discarded as waste material. Therefore, approval for this study from an Animal Welfare and Ethical Review Body was not required.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"520"}}