{"doi":"10.1038/s41467-022-28402-9","title":"The microbiome of the buffalo digestive tract","abstract":"Buffalo is an important livestock species. Here, we present a comprehensive metagenomic survey of the microbial communities along the buffalo digestive tract. We analysed 695 samples covering eight different sites in three compartments (four-chambered stomach, intestine, and rectum). We mapped ~85% of the raw sequence reads to 4,960 strain-level metagenome-assembled genomes (MAGs) and 3,255 species-level MAGs, 90% of which appear to correspond to new species. In addition, we annotated over 5.8 million nonredundant proteins from the MAGs. In comparison with the rumen microbiome of cattle, the buffalo microbiota seems to present greater potential for fibre degradation and less potential for methane production. Our catalogue of microbial genomes and the encoded proteins provides insights into microbial functions and interactions at distinct sites along the buffalo digestive tract.","journal":"Nature Communications","year":2022,"id":11311,"datarank":2.2193740802648536,"base_score":4.499809670330265,"endowment":4.499809670330265,"self_citation_contribution":0.6749714505495399,"citation_network_contribution":1.544402629715314,"self_endowment_contribution":0.6749714505495399,"citer_contribution":1.544402629715314,"corpus_percentile":65.33767290480066,"corpus_rank":427,"citation_count":101,"citer_count":86,"citers_with_citation_signal":59,"citers_with_endowment":59,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.6768,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-02-10","fair_score":49.7917,"fair_percentile":77.9023746701847,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":39636,"name":"Teng Wang","orcid":"0000-0002-2850-6711","position":1,"is_corresponding":false},{"id":31693,"name":"Na L Gao","orcid":null,"position":2,"is_corresponding":false},{"id":91145,"name":"Ziying Liu","orcid":"0000-0001-7821-6723","position":3,"is_corresponding":false},{"id":91146,"name":"Kuiqing Cui","orcid":"0000-0002-9777-1084","position":4,"is_corresponding":false},{"id":91147,"name":"Yiqian Duan","orcid":"0000-0002-8046-9831","position":5,"is_corresponding":false},{"id":39633,"name":"Sicheng Wu","orcid":"0000-0002-5121-029X","position":6,"is_corresponding":false},{"id":91148,"name":"Yuhong Luo","orcid":"0000-0001-8273-8380","position":7,"is_corresponding":false},{"id":91149,"name":"Zhipeng Li","orcid":"0000-0003-3190-2253","position":8,"is_corresponding":false},{"id":91150,"name":"Chengjian Yang","orcid":"0000-0002-3000-1253","position":9,"is_corresponding":false},{"id":91151,"name":"Yixue Xu","orcid":"0000-0001-6683-6124","position":10,"is_corresponding":false},{"id":91152,"name":"Bo Lin","orcid":"0000-0002-5755-240X","position":11,"is_corresponding":false},{"id":91153,"name":"Liguo Yang","orcid":"0000-0002-0990-8694","position":12,"is_corresponding":false},{"id":91154,"name":"Alfredo Pauciullo","orcid":"0000-0002-3140-9373","position":13,"is_corresponding":false},{"id":91155,"name":"Deshun Shi","orcid":"0000-0002-8735-5925","position":14,"is_corresponding":false},{"id":91156,"name":"Guohua Hua","orcid":"0000-0002-6900-1023","position":15,"is_corresponding":false},{"id":23546,"name":"Wei-Hua Chen","orcid":"0000-0001-5160-4398","position":16,"is_corresponding":false},{"id":91157,"name":"Qingyou Liu","orcid":"0000-0003-3265-540X","position":17,"is_corresponding":false},{"id":31699,"name":"Na Gao","orcid":"0000-0002-9095-0987","position":18,"is_corresponding":false},{"id":91144,"name":"Feng Tong","orcid":"0000-0002-6056-0590","position":0,"is_corresponding":true}],"reference_count":110,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"35145088","pmcid":"PMC8831627","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":52.5,"fair_a":67.5,"fair_i":37.5,"fair_r":41.6667,"fair_zscore":0.4143,"fair_rationale":{"fair_score":49.79,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":52.5,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.25,"signal":null,"rationale":"The paper lacks structured, machine-readable metadata; metadata is buried in prose and HTML tags, not exposed in standards like DataCite or ISA-Tab."}]},"A":{"name":"Accessible","score":67.5,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":0.75,"signal":null,"rationale":"Data access is specified via NCBI SRA (PRJNA656389) and Figshare DOIs, and code via GitHub, which constitutes a clear access protocol, though no explicit statement on software dependencies or execution environment is provided."}]},"I":{"name":"Interoperable","score":37.5,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.75,"signal":null,"rationale":"The study uses standard formats (FASTQ, BAM, MAG files) and references standard databases (GTDB, CAZy, eggNOG), but does not formally declare use of community standards or ontologies (e.g., MIxS, OBO foundry)."}]},"R":{"name":"Reusable","score":41.67,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.667,"signal":null,"rationale":"Data are publicly archived under a CC-BY license and source data are provided, but the paper does not include a formal data-availability statement with license details for the code, nor describe reproducible computational environment (e.g., workflow managers, container)."}]}},"suggestions":["Add formal metadata descriptors (e.g., using DataCite schema or an ISA-Tab structured file) for the datasets and MAGs.","Include a clear data-availability statement with explicit licensing for both data and code (e.g., CC0 for data, MIT for code).","Provide a reproducible computational environment description (e.g., Docker/Singularity or a Conda environment file) alongside the GitHub repository.","Declare use of community standards for metadata reporting (e.g., MIxS for host-associated samples)."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:40:09.487294Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}