{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T00:34:41Z","timestamp":1791333281476,"version":"4.3.1"},"reference-count":129,"publisher":"SAGE Publications","issue":"1","license":[{"start":{"date-parts":[[2015,7,28]],"date-time":"2015-07-28T00:00:00Z","timestamp":1438041600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["Vet Pathol"],"published-print":{"date-parts":[[2016,1]]},"abstract":"<jats:p>The microbiome is the complex collection of microorganisms, their genes, and their metabolites, colonizing the human and animal mucosal surfaces, digestive tract, and skin. It is now well known that the microbiome interacts with its host, assisting in digestion and detoxification, supporting immunity, protecting against pathogens, and maintaining health. Studies published to date have demonstrated that healthy individuals are often colonized with different microbiomes than those with disease involving various organ systems. This review covers a brief history of the development of the microbiome field, the main objectives of the Human Microbiome Project, and the most common microbiomes inhabiting the human respiratory tract, companion animal digestive tract, and skin in humans and companion animals. The main changes in the microbiomes in patients with pulmonary, gastrointestinal, and cutaneous lesions are described.<\/jats:p>","DOI":"10.1177\/0300985815595517","type":"journal-article","created":{"date-parts":[[2015,7,28]],"date-time":"2015-07-28T22:50:28Z","timestamp":1438123828000},"page":"10-21","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":99,"title":["The Microbiome"],"prefix":"10.1177","volume":"53","author":[{"given":"A. Rodrigues","family":"Hoffmann","sequence":"first","affiliation":[{"name":"Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L. M.","family":"Proctor","sequence":"additional","affiliation":[{"name":"National Human Genome Research Institute, National Institute of Health, Bethesda, MD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. G.","family":"Surette","sequence":"additional","affiliation":[{"name":"Department of Medicine, Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. S.","family":"Suchodolski","sequence":"additional","affiliation":[{"name":"Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"179","published-online":{"date-parts":[[2015,7,28]]},"reference":[{"key":"bibr1-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1096\/fj.12-220806"},{"issue":"2","key":"bibr2-0300985815595517","first-page":"61","volume":"5","author":"Abecia LH","year":"2010","journal-title":"International Journal of Probiotics and Prebiotics"},{"key":"bibr3-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1038\/ni1530"},{"key":"bibr4-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1186\/2049-2618-1-31"},{"key":"bibr5-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetmic.2010.05.025"},{"key":"bibr6-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/j.rmed.2007.05.007"},{"key":"bibr7-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1111\/j.1399-302X.1996.tb00180.x"},{"key":"bibr8-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1021\/pr3006809"},{"key":"bibr9-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/j.trsl.2012.02.005"},{"key":"bibr10-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0017035"},{"key":"bibr11-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1128\/9781555817947"},{"key":"bibr12-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2334-12-134"},{"key":"bibr13-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1038\/jid.2011.168"},{"key":"bibr14-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201104-0655OC"},{"key":"bibr15-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.62.5.1889-1895.1994"},{"key":"bibr16-0300985815595517","doi-asserted-by":"publisher","DOI":"10.4161\/gmic.29331"},{"key":"bibr17-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/j.cvsm.2011.01.003"},{"key":"bibr18-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1111\/j.0022-202X.2005.23935.x"},{"key":"bibr19-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/S0165-2427(01)00345-2"},{"issue":"1","key":"bibr20-0300985815595517","first-page":"120","volume":"137","author":"Desai AR","year":"2008","journal-title":"VetMicrobiol"},{"key":"bibr21-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1586\/ers.13.24"},{"key":"bibr22-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.2003.03803.x"},{"key":"bibr23-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1126\/science.1110591"},{"key":"bibr24-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002606"},{"key":"bibr25-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-3164.2009.00758.x"},{"key":"bibr26-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-3164.2009.00745.x"},{"key":"bibr27-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1007\/BF02412646"},{"key":"bibr28-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMra062477"},{"key":"bibr29-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1038\/nature12171"},{"key":"bibr30-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1038\/jid.2013.21"},{"key":"bibr31-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0041294"},{"key":"bibr32-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1155\/2013\/658373"},{"key":"bibr33-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1319284111"},{"key":"bibr34-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6941.2012.01331.x"},{"key":"bibr35-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkf506"},{"key":"bibr36-0300985815595517","doi-asserted-by":"publisher","DOI":"10.2337\/db12-0771"},{"key":"bibr37-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1111\/j.1939-1676.2003.tb01321.x"},{"key":"bibr38-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00481-13"},{"key":"bibr39-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1126\/science.1124234"},{"key":"bibr40-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1101\/gr.075549.107"},{"key":"bibr41-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2537"},{"key":"bibr42-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0127259"},{"key":"bibr43-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0053115"},{"key":"bibr44-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6941.2011.01058.x"},{"key":"bibr45-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1159\/000023899"},{"key":"bibr46-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1128\/9781555817947.ch12"},{"key":"bibr47-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00035-14"},{"key":"bibr48-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1126\/science.1183605"},{"key":"bibr49-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1038\/nature11209"},{"key":"bibr50-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1038\/nature11234"},{"key":"bibr51-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0034242"},{"key":"bibr52-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1019378108"},{"key":"bibr53-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1111\/j.1439-0396.2006.00640.x"},{"key":"bibr54-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2014.08.014"},{"key":"bibr55-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetmic.2007.10.014"},{"key":"bibr56-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/j.resmic.2007.09.004"},{"key":"bibr57-0300985815595517","doi-asserted-by":"publisher","DOI":"10.2460\/javma.2001.219.1247"},{"key":"bibr58-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro3199"},{"key":"bibr59-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1136\/vr.132.14.362"},{"key":"bibr60-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.aje.a116770"},{"issue":"12","key":"bibr61-0300985815595517","first-page":"1162","volume":"86","author":"Kasempimolporn S","year":"2003","journal-title":"J Med Assoc Thai"},{"key":"bibr62-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0030117"},{"key":"bibr63-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1136\/vr.d5380"},{"key":"bibr64-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1038\/nature10213"},{"key":"bibr65-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/j.it.2005.04.008"},{"key":"bibr66-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1000081107"},{"key":"bibr67-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/j.molmed.2011.01.013"},{"key":"bibr68-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1101\/gr.131029.111"},{"key":"bibr69-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1038\/jid.2011.417"},{"key":"bibr70-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.25.14547"},{"key":"bibr71-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.82.20.6955"},{"key":"bibr72-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1038\/nature10434"},{"key":"bibr73-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1126\/science.288.5464.287"},{"issue":"3","key":"bibr74-0300985815595517","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00129-10","volume":"1","author":"Lemon KP","year":"2010","journal-title":"MBio"},{"key":"bibr75-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0032118"},{"key":"bibr76-0300985815595517","doi-asserted-by":"publisher","DOI":"10.21037\/jtd.2018.01.65"},{"key":"bibr77-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201211-2145OC"},{"key":"bibr78-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetimm.2009.08.014"},{"key":"bibr79-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a009738"},{"key":"bibr80-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1097\/MCG.0b013e31822fecfe"},{"key":"bibr81-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1111\/jvim.12020"},{"key":"bibr82-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2180-10-59"},{"issue":"3","key":"bibr83-0300985815595517","first-page":"765","volume":"26","author":"Markel M","year":"2012","journal-title":"J Vet Intern Med"},{"key":"bibr84-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/j.rmed.2004.05.010"},{"key":"bibr85-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-3164.2011.00967.x"},{"key":"bibr86-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetimm.2009.11.012"},{"key":"bibr87-0300985815595517","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.53"},{"key":"bibr88-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetmic.2014.10.005"},{"key":"bibr89-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2014.997612"},{"key":"bibr90-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201210-1913OC"},{"key":"bibr91-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms2441"},{"key":"bibr92-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1101\/gr.159467.113"},{"key":"bibr93-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1159\/000331884"},{"key":"bibr94-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1097\/QCO.0b013e32832a8a5d"},{"key":"bibr95-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0050177"},{"key":"bibr96-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2011.10.001"},{"key":"bibr97-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1097\/MCP.0b013e328358d49a"},{"key":"bibr98-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1111\/jvim.12261"},{"key":"bibr99-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0083197"},{"key":"bibr100-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01324-09"},{"key":"bibr101-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0094699"},{"key":"bibr102-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2008.76"},{"key":"bibr103-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1902\/jop.1999.70.7.793"},{"key":"bibr104-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1186\/2049-2618-1-19"},{"key":"bibr105-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000184"},{"key":"bibr106-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00067-06"},{"key":"bibr107-0300985815595517","first-page":"327","volume":"385","author":"Smith AM","year":"2014","journal-title":"Curr Top Microbiol Immunol"},{"key":"bibr108-0300985815595517","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.00458"},{"key":"bibr109-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2540"},{"key":"bibr110-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2014.250"},{"key":"bibr111-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1038\/srep00170"},{"key":"bibr112-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetmic.2012.11.018"},{"key":"bibr113-0300985815595517","doi-asserted-by":"publisher","DOI":"10.2527\/jas.2010-3377"},{"key":"bibr114-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2180-9-210"},{"key":"bibr115-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0039333"},{"key":"bibr116-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0127378"},{"key":"bibr117-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0051907"},{"key":"bibr118-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetmic.2008.05.017"},{"key":"bibr119-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetmic.2009.11.002"},{"key":"bibr120-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1513\/AnnalsATS.201306-159MG"},{"key":"bibr121-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2010.162"},{"key":"bibr122-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1016\/j.mimet.2012.01.001"},{"key":"bibr123-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-micro-090110-102830"},{"key":"bibr124-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1038\/jid.2010.328"},{"key":"bibr125-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1513\/AnnalsATS.201310-351OC"},{"key":"bibr126-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6941.2008.00556.x"},{"key":"bibr127-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1021\/pr500936p"},{"key":"bibr128-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-015-0153-3"},{"key":"bibr129-0300985815595517","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2012-13-11-r101"}],"container-title":["Veterinary Pathology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1177\/0300985815595517","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/full-xml\/10.1177\/0300985815595517","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1177\/0300985815595517","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T18:56:07Z","timestamp":1777661767000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/10.1177\/0300985815595517"}},"subtitle":["The Trillions of Microorganisms That Maintain Health and Cause Disease in Humans and Companion Animals"],"short-title":[],"issued":{"date-parts":[[2015,7,28]]},"references-count":129,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2016,1]]}},"alternative-id":["10.1177\/0300985815595517"],"URL":"https:\/\/doi.org\/10.1177\/0300985815595517","relation":{},"ISSN":["0300-9858","1544-2217"],"issn-type":[{"value":"0300-9858","type":"print"},{"value":"1544-2217","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,7,28]]}}}