{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T05:39:16Z","timestamp":1771479556690,"version":"3.50.1"},"reference-count":55,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,9,26]],"date-time":"2022-09-26T00:00:00Z","timestamp":1664150400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Donkeys\u2019 gut microbe is critical for their health and adaptation to the environment. Little research has been conducted on the donkey gut microbiome compared with other domestic animals. The Tibetan Plateau is an extreme environment. In this study, 6 Qinghai donkeys (QH) from the Tibetan Plateau and 6 Dezhou donkeys (DZ) were investigated, and the contents of 4 parts\u2014stomach, small intestine, cecum, and rectum\u2014were collected. 16S rRNA sequencing and metagenomic sequencing were used to analyze the composition and diversity of gut microbial communities in donkeys. The results showed that the flora diversity and richness of the hindgut were significantly higher than those of the foregut (<jats:italic>p<\/jats:italic>\u2009&amp;lt;\u20090.01), with no sex differences, and the community structure and composition of the same or adjacent regions (stomach, small intestine, cecum, and rectum) were similar. Besides, the flora diversity and richness of QH on the Tibetan Plateau were significantly higher than those of DZ (<jats:italic>p<\/jats:italic>\u2009&amp;lt;\u20090.05). The major pathways associated with QH were signal transduction mechanisms and carbohydrate transport and metabolism, and <jats:italic>Bacteroidales<\/jats:italic> were the major contributors to these functions. Our study provides novel insights into the contribution of microbiomes to the adaptive evolution of donkeys.<\/jats:p>","DOI":"10.3389\/fmicb.2022.964799","type":"journal-article","created":{"date-parts":[[2022,9,26]],"date-time":"2022-09-26T09:21:50Z","timestamp":1664184110000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":14,"title":["Comparison of gut microflora of donkeys in high and low altitude areas"],"prefix":"10.3389","volume":"13","author":[{"given":"Rong","family":"Guo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuer","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianxing","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Shen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guoliang","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junjie","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fali","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qingjie","family":"Pan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Taifeng","family":"Xie","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Deqiang","family":"Ai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianbao","family":"Dong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiajia","family":"Suo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yujiang","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuqin","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2022,9,26]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1016\/j.cveq.2009.04.005","article-title":"The bacterial community of the horse gastrointestinal tract and its relation to fermentative acidosis, laminitis, colic, and stomach ulcers","volume":"25","author":"Al","year":"2009","journal-title":"Vet. Clin. North Am. Equine Pract."},{"key":"ref2","first-page":"E469","article-title":"Interrelationship of Na, HCO3, and volatile fatty acid transport by equine large intestine","volume":"233","author":"Argenzio","year":"1977","journal-title":"Am. J. Phys."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1152\/ajplegacy.1974.226.5.1043","article-title":"Sites of organic acid production and absorption in the equine gastrointestinal tract","volume":"226","author":"Argenzio","year":"1974","journal-title":"Am. J. Phys."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"1230","DOI":"10.1002\/ejlt.201100393","article-title":"Effect of lactobacillus plantarum P-8 on lipid metabolism in hyperlipidemic rat model","volume":"114","author":"Bao","year":"2012","journal-title":"Eur. J. Lipid Sci. Technol."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1038\/ncb3124","article-title":"Metabolic pathways promoting cancer cell survival and growth","volume":"17","author":"Boroughs","year":"2015","journal-title":"Nat. Cell Biol."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"1948","DOI":"10.1073\/pnas.0806191105","article-title":"Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases","volume":"106","author":"Brulc","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"1360","DOI":"10.1016\/j.cell.2015.11.004","article-title":"Gut microbiota orchestrates energy homeostasis during cold","volume":"163","author":"Chevalier","year":"2015","journal-title":"Cell"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1016\/j.tvjl.2015.03.018","article-title":"Characterization and comparison of the bacterial microbiota in different gastrointestinal tract compartments in horses","volume":"205","author":"Costa","year":"2015","journal-title":"Vet. J."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"12727","DOI":"10.1038\/s41598-018-30932-6","article-title":"Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions","volume":"8","author":"Crespo-Piazuelo","year":"2018","journal-title":"Sci. Rep."},{"key":"ref12","first-page":"460","article-title":"Gut microbiota and its possible relationship with obesity","author":"DiBaise","year":"2008"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1038\/nmeth.2604","article-title":"UPARSE: highly accurate OTU sequences from microbial amplicon reads","volume":"10","author":"Edgar","year":"2013","journal-title":"Nat. Methods"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1016\/j.tim.2005.12.007","article-title":"Beyond diversity: functional microbiomics of the human colon","volume":"14","author":"Egert","year":"2006","journal-title":"Trends Microbiol."},{"key":"ref15","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1007\/978-1-4615-2391-8_7","article-title":"Fermentation of acetate","volume-title":"Methanogenesis","author":"Ferry","year":"1993"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"289","DOI":"10.4161\/gmic.19897","article-title":"Microbial degradation of complex carbohydrates in the gut","volume":"3","author":"Flint","year":"2012","journal-title":"Gut Microbes"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1126\/science.1124234","article-title":"Metagenomic analysis of the human distal gut microbiome","volume":"312","author":"Gill","year":"2006","journal-title":"Science"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"1316","DOI":"10.1016\/0006-291X(82)91921-0","article-title":"Electron transport components from methanogenic bacteria: the ferredoxin from Methanosarcina barkeri (strain Fusaro)","volume":"109","author":"Hatchikian","year":"1982","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"1532","DOI":"10.1038\/s41591-018-0164-x","article-title":"Regional variation limits applications of healthy gut microbiome reference ranges and disease models","volume":"24","author":"He","year":"2018","journal-title":"Nat. Med."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1016\/j.bbrc.2005.11.155","article-title":"Anabolic five subunit-type pyruvate:ferredoxin oxidoreductase from Hydrogenobacter thermophilus TK-6","volume":"340","author":"Ikeda","year":"2006","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"109","DOI":"10.4172\/1745-7580.10000109","article-title":"Influence of gut microbiota on inflammation and pathogenesis of sugar rich diet induced diabetes","volume":"12","author":"Jena","year":"2016","journal-title":"Immunome Res."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"647","DOI":"10.1007\/s00792-007-0094-x","article-title":"Characterization of cofactor-dependent and cofactor-independent phosphoglycerate mutases from Archaea","volume":"11","author":"Johnsen","year":"2007","journal-title":"Extremophiles"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1089\/ham.2020.0062","article-title":"Effect of Synbiotics on amelioration of intestinal inflammation under hypobaric hypoxia","volume":"22","author":"Khanna","year":"2021","journal-title":"High Alt. Med. Biol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"1779","DOI":"10.1111\/j.1365-294X.2012.05502.x","article-title":"Ecological drift and local exposures drive enteric bacterial community differences within species of Galapagos iguanas","volume":"21","author":"Lankau","year":"2012","journal-title":"Mol. Ecol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"2720","DOI":"10.1016\/j.celrep.2019.02.015","article-title":"Microbiota depletion impairs thermogenesis of Brown adipose tissue and Browning of white adipose tissue","volume":"26","author":"Li","year":"","journal-title":"Cell Rep."},{"key":"ref27","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.02125","article-title":"Characterization and comparison of microbiota in the gastrointestinal tracts of the goat (Capra hircus) during preweaning development","volume":"10","author":"Li","year":"","journal-title":"Front. Microbiol."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"713","DOI":"10.1093\/bioinformatics\/btn025","article-title":"SOAP: short oligonucleotide alignment program","volume":"24","author":"Li","year":"2008","journal-title":"Bioinformatics"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"e0226186","DOI":"10.1371\/journal.pone.0226186","article-title":"Microbial diversity within the digestive tract contents of Dezhou donkeys","volume":"14","author":"Liu","year":"2019","journal-title":"PLoS One"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"e9032","DOI":"10.7717\/peerj.9032","article-title":"Comparative study of gut microbiota in Tibetan wild asses (Equus kiang) and domestic donkeys (Equus asinus) on the Qinghai-Tibet plateau","volume":"8","author":"Liu","year":"2020","journal-title":"PeerJ."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"3240","DOI":"10.1093\/molbev\/msu257","article-title":"Genetic differentiation of hypothalamus parentally biased transcripts in populations of the house mouse implicate the Prader\u2013Willi syndrome imprinted region as a possible source of behavioral divergence","volume":"31","author":"Lorenc","year":"2014","journal-title":"Mol. Biol."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1016\/j.ebiom.2018.11.010","article-title":"Chronic intermittent hypoxia disrupts cardiorespiratory homeostasis and gut microbiota composition in adult male Guinea-pigs","volume":"38","author":"Lucking","year":"2018","journal-title":"EBioMedicine"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","article-title":"FLASH: fast length adjustment of short reads to improve genome assemblies","volume":"27","author":"Magoc","year":"2011","journal-title":"Bioinformatics"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"5859","DOI":"10.1073\/pnas.0901529106","article-title":"Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla","volume":"106","author":"Mahowald","year":"2009","journal-title":"Proc. Natl. Acad. Sci."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"16116","DOI":"10.1038\/srep16116","article-title":"Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function","volume":"5","author":"Mao","year":"2015","journal-title":"Sci. Rep."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1016\/0012-1606(92)90056-M","article-title":"Differential transcription of Pgk genes during spermatogenesis in the mouse","volume":"154","author":"McCarrey","year":"1992","journal-title":"Dev. Biol."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"13768","DOI":"10.1073\/pnas.1700122114","article-title":"Dispersal limitation promotes the diversification of the mammalian gut microbiota","volume":"114","author":"Moeller","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"1752605","DOI":"10.1080\/19490976.2020.1752605","article-title":"Metagenomics reveals impact of geography and acute diarrheal disease on the central Indian human gut microbiome","volume":"12","author":"Monaghan","year":"2020","journal-title":"Gut Microbes"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1007\/s11154-019-09523-x","article-title":"The gut microbiota modulates both browning of white adipose tissue and the activity of brown adipose tissue","volume":"20","author":"Moreno-Navarrete","year":"2019","journal-title":"Rev. Endocr. Metab. Disord."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"5623","DOI":"10.1093\/nar\/gkl723","article-title":"MetaGene: prokaryotic gene finding from environmental genome shotgun sequences","volume":"34","author":"Noguchi","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"2617","DOI":"10.1111\/j.1365-294X.2012.05568.x","article-title":"Microbiome analysis among bats describes influences of host phylogeny, life history, physiology and geography","volume":"21","author":"Phillips","year":"2012","journal-title":"Mol. Ecol."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1111\/j.1574-6968.2002.tb11467.x","article-title":"The microbiology of butyrate formation in the human colon","volume":"217","author":"Pryde","year":"2002","journal-title":"FEMS Microbiol. Lett."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1038\/nature25973","article-title":"Environment dominates over host genetics in shaping human gut microbiota","volume":"555","author":"Rothschild","year":"2018","journal-title":"Nature"},{"key":"ref46","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1023\/A:1012058205158","article-title":"Recognition and degradation of chitin by streptomycetes","volume":"79","author":"Schrempf","year":"2001","journal-title":"Antonie Van Leeuwenhoek"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"7287","DOI":"10.1007\/s00253-019-10012-z","article-title":"Glycan utilisation system in Bacteroides and Bifidobacteria and their roles in gut stability and health","volume":"103","author":"Singh","year":"2019","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"846","DOI":"10.1099\/00207713-44-4-846","article-title":"Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology","volume":"44","author":"Stackebrandt","year":"1994","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"6134","DOI":"10.1111\/mec.12027","article-title":"Geographical and ecological stability of the symbiotic mid-gut microbiota in European firebugs, Pyrrhocoris apterus (Hemiptera, Pyrrhocoridae)","volume":"21","author":"Sudakaran","year":"2012","journal-title":"Mol. Ecol."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"3363","DOI":"10.1111\/j.1365-294X.2012.05552.x","article-title":"Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis","volume":"21","author":"Sullam","year":"2012","journal-title":"Mol. Ecol."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"1332","DOI":"10.1038\/bjc.2015.114","article-title":"Phosphoglycerate kinase-1 is a predictor of poor survival and a novel prognostic biomarker of chemoresistance to paclitaxel treatment in breast cancer","volume":"112","author":"Sun","year":"2015","journal-title":"Br. J. Cancer"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1016\/j.tim.2017.10.001","article-title":"Glycan utilization and cross-feeding activities by bifidobacteria","volume":"26","author":"Turroni","year":"2018","journal-title":"Trends Microbiol."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"1348886","DOI":"10.1080\/16512235.2017.1348886","article-title":"Modulation of the gut microbiota by prebiotic fibres and bacteriocins","volume":"28","author":"Umu","year":"2017","journal-title":"Microb. Ecol. Health Dis."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"5261","DOI":"10.1128\/AEM.00062-07","article-title":"Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy","volume":"73","author":"Wang","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"114","DOI":"10.3389\/fmicb.2018.00114","article-title":"The divergence in bacterial components associated with Bactrocera dorsalis across developmental stages","volume":"9","author":"Zhao","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"753","DOI":"10.1002\/mbo3.367","article-title":"Cecal microbiota of Tibetan chickens from five geographic regions were determined by 16S rRNA sequencing","volume":"5","author":"Zhou","year":"2016","journal-title":"Microbiology"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"1216","DOI":"10.1016\/j.cmet.2016.05.001","article-title":"Altered microbiota contributes to reduced diet-induced obesity upon cold exposure","volume":"23","author":"Zietak","year":"2016","journal-title":"Cell Metab."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2022.964799\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,26]],"date-time":"2022-09-26T09:21:54Z","timestamp":1664184114000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2022.964799\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,9,26]]},"references-count":55,"alternative-id":["10.3389\/fmicb.2022.964799"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2022.964799","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,9,26]]},"article-number":"964799"}}