{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T01:41:57Z","timestamp":1791855717819,"version":"4.3.4"},"reference-count":108,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,8,25]],"date-time":"2022-08-25T00:00:00Z","timestamp":1661385600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002322","name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"CNPq","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Mastitis, mainly caused by bacterial intramammary infections, is the main problem in the breeding of dairy animals. The inflammations of the mammary gland is separated by types of mastitis, being subclinical, clinical, and the most severe, gangrenous mastitis. Here, we used 16S rRNA amplicon sequencing to characterize the bacterial microbiota of goat milk in the different types of goat mastitis caused by bacteria. We used 72 goat milk samples from a region of the state of Minas Gerais in Brazil, of which 12 were from clinically healthy animals, 42 from animals diagnosed with subclinical mastitis, 16 from animals with clinical mastitis, and 2 from animals with gangrenous mastitis. The group related to gangrenous mastitis was the most divergent in terms of alpha and beta diversity. The most abundant genus among samples of the groups was <jats:italic>Staphylococcus<\/jats:italic> spp., and we found a high abundance of <jats:italic>Mycoplasma<\/jats:italic> sp. in the milk of animals diagnosed with clinical mastitis. The most statistically relevant microorganisms among the groups were <jats:italic>Prevotella<\/jats:italic> sp., <jats:italic>Ruminococcaceae<\/jats:italic>, <jats:italic>Prevotella ruminicola<\/jats:italic> sp., and <jats:italic>Providencia<\/jats:italic> sp. We highlight a new association of bacterial agents in gangrenous mastitis among <jats:italic>Escherichia<\/jats:italic> sp.\/<jats:italic>Shigella<\/jats:italic> sp. and <jats:italic>Enterococcus<\/jats:italic> sp. and provide the second report of the genus <jats:italic>Alkalibacterium<\/jats:italic> sp., in milk samples. Only the taxa <jats:italic>Staphylococcus<\/jats:italic> sp., <jats:italic>Bacteroides<\/jats:italic> sp., <jats:italic>Enterococcus<\/jats:italic>, and <jats:italic>Brevidabacterium<\/jats:italic> sp., were present in all groups. The superpathway of L-tryptophan biosynthesis metabolites and the sucrose degradation III (sucrose invertase) pathway were the most prominent ones among the groups. In this study, we demonstrate how a rich microbiota of goat milk from healthy animals can be altered during the aggravation of different types of mastitis, in addition to demonstrating new bacterial genera in milk not previously detected in other studies as well as new associations between agents.<\/jats:p>","DOI":"10.3389\/fmicb.2022.918706","type":"journal-article","created":{"date-parts":[[2022,8,25]],"date-time":"2022-08-25T08:10:47Z","timestamp":1661415047000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":25,"title":["Distinguishing the milk microbiota of healthy goats and goats diagnosed with subclinical mastitis, clinical mastitis, and gangrenous mastitis"],"prefix":"10.3389","volume":"13","author":[{"given":"Richard Costa","family":"Polveiro","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pedro Marcus Pereira","family":"Vidigal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiago Ant\u00f4nio","family":"de Oliveira Mendes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ricardo Seiti","family":"Yamatogi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luciana Saraiva","family":"da Silva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juliana Miwa","family":"Fujikura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mateus Matiuzzi","family":"Da Costa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Aparecida Scatamburlo","family":"Moreira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2022,8,25]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/0378-1135(95)00043-A","article-title":"Evaluation of phenotypic and genotypic methods for epidemiological typing of Staphylococcus aureus isolates from bovine mastitis in Denmark","volume":"45","author":"Aarestrup","year":"1995","journal-title":"Vet. Microbiol."},{"key":"ref2","first-page":"281","article-title":"Studies on gangrenous mastitis in goats","volume":"78","author":"Abu-Samra","year":"1988","journal-title":"Cornell Vet."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"2359","DOI":"10.1039\/c6mb00217j","article-title":"The bovine milk microbiota: insights and perspectives from -omics studies","volume":"12","author":"Addis","year":"2016","journal-title":"Mol. BioSyst."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"2348","DOI":"10.3389\/FIMMU.2019.02348","article-title":"Bifidobacterial dialogue with its human host and consequent modulation of the immune system","volume":"10","author":"Alessandri","year":"2019","journal-title":"Front. Immunol."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1016\/0921-4488(94)90080-9","article-title":"Gangrenous caprine coliform mastitis","volume":"13","author":"Ameh","year":"1994","journal-title":"Small Rumin. Res."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1890\/0012-9658(2003)084[0511:CAOPCA]2.0.CO;2","article-title":"Canonical analysis of principal coordinates: a useful method of constrained ordination for ecology","volume":"84","author":"Anderson","year":"2003","journal-title":"Ecology"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"11381","DOI":"10.1038\/S41598-020-68305-7","article-title":"Exploring bacteria diversity in commercialized table olive biofilms by metataxonomic and compositional data analysis","volume":"10","author":"Ben\u00edtez-Cabello","year":"2020","journal-title":"Sci. Rep."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"639","DOI":"10.1111\/J.1365-2672.2012.05244.X","article-title":"Milk microbiome signatures of subclinical mastitis-affected cattle analysed by shotgun sequencing","volume":"112","author":"Bhatt","year":"2012","journal-title":"J. Appl. Microbiol."},{"key":"ref001","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1099\/00207713-41-1-163","article-title":"Bifidobacterium ruminantium sp. nov. and Bifidobacterium merycicum sp. nov. from the rumens of cattle","volume":"41","author":"Biavati","year":"1991","journal-title":"Int. J. Syst. Bacteriol"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"18521","DOI":"10.1038\/s41598-020-74719-0","article-title":"Human milk microbiota in sub-acute lactational mastitis induces inflammation and undergoes changes in composition, diversity and load","volume":"10","author":"Boix-Amor\u00f3s","year":"2020","journal-title":"Sci. Rep."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"8067","DOI":"10.1038\/s41598-017-08790-5","article-title":"Milk microbiome and bacterial load following dry cow therapy without antibiotics in dairy cows with healthy mammary gland","volume":"7","author":"Bonsaglia","year":"2017","journal-title":"Sci. Rep."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1016\/j.smallrumres.2005.06.003","article-title":"The role of the goat in society: past, present and perspectives for the future","volume":"60","author":"Boyazoglu","year":"2005","journal-title":"Small Rumin. Res."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"325","DOI":"10.2307\/1942268","article-title":"An ordination of the upland Forest communities of Southern Wisconsin","volume":"27","author":"Bray","year":"1957","journal-title":"Ecol. Monogr."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/0167-5877(95)00518-8","article-title":"Effect of milk sample collection strategy on the sensitivity and specificity of bacteriologic culture and somatic cell count for detection of Staphylococcus aureus intramammary infection in dairy cattle","volume":"26","author":"Buelow","year":"1996","journal-title":"Prev. Vet. Med."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"2639","DOI":"10.1038\/ismej.2017.119","article-title":"Exact sequence variants should replace operational taxonomic units in marker-gene data analysis","volume":"11","author":"Callahan","year":"2017","journal-title":"ISME J."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"1621","DOI":"10.1038\/ismej.2012.8","article-title":"Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms","volume":"6","author":"Caporaso","year":"2012","journal-title":"ISME J."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"D633","DOI":"10.1093\/nar\/gkx935","article-title":"The MetaCyc database of metabolic pathways and enzymes","volume":"46","author":"Caspi","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"e0184710","DOI":"10.1371\/JOURNAL.PONE.0184710","article-title":"The microbiota of water buffalo milk during mastitis","volume":"12","author":"Catozzi","year":"2017","journal-title":"PLoS One"},{"key":"ref19","first-page":"265","article-title":"Nonparametric estimation of the number of classes in a population","volume":"11","author":"Chao","year":"1984","journal-title":"Scand. J. Stat."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1186\/1471-2105-12-35","article-title":"VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R","volume":"12","author":"Chen","year":"2011","journal-title":"BMC Bioinformat."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1016\/S0301-6226(02)00172-0","article-title":"The role of intramammary pathogens in dairy goats","volume":"79","author":"Contreras","year":"2003","journal-title":"Livest. Prod. Sci."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1016\/j.smallrumres.2006.09.011","article-title":"Mastitis in small ruminants","volume":"68","author":"Contreras","year":"2007","journal-title":"Small Rumin. Res."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"67","DOI":"10.3389\/FIMMU.2020.00067\/BIBTEX","article-title":"Tryptophan co-metabolism at the host-pathogen Interface","volume":"11","author":"Costantini","year":"2020","journal-title":"Front. Immunol."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"4727","DOI":"10.3168\/jds.2018-15272","article-title":"Symposium review: features of Staphylococcus aureus mastitis pathogenesis that guide vaccine development strategies","volume":"102","author":"C\u00f4t\u00e9-Gravel","year":"2019","journal-title":"J. Dairy Sci."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1016\/0378-1135(95)92532-G","article-title":"Staphylococcus spp. as mastitis-related pathogens in goat milk","volume":"43","author":"Deinhofer","year":"1995","journal-title":"Vet. Microbiol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"10605","DOI":"10.3168\/jds.2018-14860","article-title":"Invited review: microbiota of the bovine udder: contributing factors and potential implications for udder health and mastitis susceptibility","volume":"101","author":"Derakhshani","year":"2018","journal-title":"J. Dairy Sci."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1016\/j.smallrumres.2016.07.010","article-title":"Survey on small ruminant bacterial mastitis in Italy, 2013\u20132014","volume":"141","author":"Dore","year":"2016","journal-title":"Small Rumin. Res."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1038\/s41587-020-0548-6","article-title":"PICRUSt2 for prediction of metagenome functions","volume":"38","author":"Douglas","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"8","DOI":"10.3390\/MICROORGANISMS9010008","article-title":"Exploring the ecology of bifidobacteria and their genetic adaptation to the mammalian gut","volume":"9","author":"Duranti","year":"2020","journal-title":"Microorganisms"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"23971","DOI":"10.1038\/srep23971","article-title":"Evaluation of genetic diversity among strains of the human gut commensal Bifidobacterium adolescentis","volume":"6","author":"Duranti","year":"2016","journal-title":"Sci. Rep."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1038\/s41576-020-0212-5","article-title":"A systems approach to infectious disease","volume":"21","author":"Eckhardt","year":"2020","journal-title":"Nat. Rev. Genet."},{"key":"ref32","volume-title":"Overview of Global Dairy market Developments in 2018","year":"2019"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"689","DOI":"10.3389\/FCIMB.2020.586667\/BIBTEX","article-title":"The microbiota of the human mammary ecosystem","volume":"10","author":"Fern\u00e1ndez","year":"2020","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"e72801","DOI":"10.7554\/eLife.72801","article-title":"Multi-omics investigation of Clostridioides difficile-colonized patients reveals pathogen and commensal correlates of C. difficile pathogenesis","volume":"11","author":"Fishbein","year":"2022","journal-title":"elife"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"e1005404","DOI":"10.1371\/journal.pcbi.1005404","article-title":"Metacoder: an R package for visualization and manipulation of community taxonomic diversity data","volume":"13","author":"Foster","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"16353","DOI":"10.1038\/s41598-019-52820-3","article-title":"The replication-transmission relativity theory for multiscale Modelling of infectious disease systems","volume":"9","author":"Garira","year":"2019","journal-title":"Sci. Rep."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"15968","DOI":"10.1038\/s41598-018-34371-1","article-title":"Distinct phenotypic traits of Staphylococcus aureus are associated with persistent, contagious bovine intramammary infections","volume":"8","author":"Grunert","year":"2018","journal-title":"Sci. Rep."},{"key":"ref38","first-page":"1974","article-title":"Microbiota of Cow\u2019s milk with udder pathologies. microorganisms","author":"Gryaznova","year":"2021"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1577\/1548-8667(1998)010<0107:ROTHPA>2.0.CO;2","article-title":"Relationships of the host, pathogen, and environment: implications for diseases of cultured and wild fish populations","volume":"10","author":"Hedrick","year":"1998","journal-title":"J. Aquat. Anim. Health"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/srep14567","article-title":"Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range","volume":"5","author":"Henderson","year":"2015","journal-title":"Sci. Rep."},{"key":"ref41","author":"Hogan","year":"1999"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"13536","DOI":"10.1038\/S41598-019-49468-4","article-title":"Metagenomic deep sequencing reveals association of microbiome signature with functional biases in bovine mastitis","volume":"9","author":"Hoque","year":"2019","journal-title":"Sci. Rep."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"e0251221","DOI":"10.1128\/SPECTRUM.02512-21","article-title":"The rumen microbiota contributes to the Development of mastitis in dairy cows","volume":"10","author":"Hu","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"e21313","DOI":"10.1371\/journal.pone.0021313","article-title":"Characterization of the diversity and temporal stability of bacterial communities in human milk","volume":"6","author":"Hunt","year":"2011","journal-title":"PLoS One"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1111\/j.1472-765X.2006.02073.x","article-title":"Presence of halophilic and alkaliphilic lactic acid bacteria in various cheeses","volume":"44","author":"Ishikawa","year":"2007","journal-title":"Lett. Appl. Microbiol."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"1215","DOI":"10.1099\/IJS.0.65602-0","article-title":"Alkalibacterium thalassium sp. nov., Alkalibacterium pelagium sp. nov., Alkalibacterium putridalgicola sp. nov. and Alkalibacterium kapii sp. nov., slightly halophilic and alkaliphilic marine lactic acid bacteria isolated from marine organisms and salted foods collected in Japan and Thailand","volume":"59","author":"Ishikawa","year":"2009","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"1471","DOI":"10.1099\/ijs.0.042556-0","article-title":"Alkalibacterium gilvum sp. nov., slightly halophilic and alkaliphilic lactic acid bacterium isolated from soft and semi-hard cheeses","volume":"63","author":"Ishikawa","year":"","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"e61959","DOI":"10.1371\/journal.pone.0061959","article-title":"Bacterial community profiling of milk samples as a means to understand culture-negative bovine clinical mastitis","volume":"8","author":"Kuehn","year":"2013","journal-title":"PLoS One"},{"key":"ref49","first-page":"513","article-title":"Nutritional and nutraceutical properties of goat milk \u2013 a review","volume":"69","author":"Kumar","year":"2016","journal-title":"Indian J. Dairy Sci."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"2371","DOI":"10.1038\/s41598-018-20862-8","article-title":"Variation in raw milk microbiota throughout 12 months and the impact of weather conditions","volume":"8","author":"Li","year":"2018","journal-title":"Sci. Rep."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"3031","DOI":"10.3168\/JDS.2016-11604\/ATTACHMENT\/1CD6F623-1F98-4D24-9484-761316D3DD6D\/MMC1.PDF","article-title":"The bovine colostrum microbiome and its association with clinical mastitis","volume":"100","author":"Lima","year":"2017","journal-title":"J. Dairy Sci."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1186\/S40168-018-0578-1","article-title":"Cow-to-mouse fecal transplantations suggest intestinal microbiome as one cause of mastitis","volume":"6","author":"Ma","year":"2018","journal-title":"Microbiome"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2018\/3801479","article-title":"Prevalence, risk factors, and antibiogram of bacteria isolated from milk of goats with subclinical mastitis in Thika East Subcounty, Kenya","volume":"2018","author":"Mahlangu","year":"2018","journal-title":"J. Vet. Med."},{"key":"ref55","author":"Martinez Arbizu","year":"2020"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"836","DOI":"10.2460\/javma.242.6.836","article-title":"Gangrenous mastitis caused by Bacillus species in six goats","volume":"242","author":"Mavangira","year":"2013","journal-title":"J. Am. Vet. Med. Assoc."},{"key":"ref57","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1016\/j.fm.2014.07.021","article-title":"Analysis of raw goat milk microbiota: impact of stage of lactation and lysozyme on microbial diversity","volume":"46","author":"McInnis","year":"2015","journal-title":"Food Microbiol."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","article-title":"Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data","volume":"8","author":"McMurdie","year":"2013","journal-title":"PLoS One"},{"key":"ref59","doi-asserted-by":"publisher","first-page":"e1003531","DOI":"10.1371\/journal.pcbi.1003531","article-title":"Waste not, want not: why rarefying microbiome data is inadmissible","volume":"10","author":"McMurdie","year":"2014","journal-title":"PLoS Comput. Biol."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1016\/S0749-0720(15)30032-3","article-title":"Mastitis of sheep and goats","volume":"17","author":"Menzies","year":"2001","journal-title":"Vet. Clin. N. Am. Food Anim. Pract."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"599","DOI":"10.3390\/MICROORGANISMS7120599","article-title":"Bifidobacterial distribution across Italian cheeses produced from raw milk","volume":"7","author":"Milani","year":"2019","journal-title":"Microorganisms"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"1161","DOI":"10.1099\/00207713-51-3-1161\/CITE\/REFWORKS","article-title":"Alkalibacterium olivoapovliticus gen. nov., sp. nov., a new obligately alkaliphilic bacterium isolated from edible-olive wash-waters","volume":"51","author":"Ntougias","year":"2001","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"60","DOI":"10.3389\/FMICB.2020.00060\/BIBTEX","article-title":"Milk microbiota: what are we exactly talking about?","volume":"11","author":"Oikonomou","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref64","doi-asserted-by":"publisher","first-page":"e85904","DOI":"10.1371\/journal.pone.0085904","article-title":"Microbiota of Cow\u2019s milk; distinguishing healthy, sub-clinically and clinically diseased quarters","volume":"9","author":"Oikonomou","year":"2014","journal-title":"PLoS One"},{"key":"ref65","doi-asserted-by":"publisher","first-page":"e47671","DOI":"10.1371\/journal.pone.0047671","article-title":"Microbial diversity of bovine mastitic milk as described by pyrosequencing of metagenomic 16s rDNA","volume":"7","author":"Oikonomou","year":"2012","journal-title":"PLoS One"},{"key":"ref66","author":"Oksanen","year":"2019"},{"key":"ref67","doi-asserted-by":"publisher","first-page":"3123","DOI":"10.1093\/bioinformatics\/btu494","article-title":"STAMP: statistical analysis of taxonomic and functional profiles","volume":"30","author":"Parks","year":"2014","journal-title":"Bioinformatics"},{"key":"ref68","doi-asserted-by":"publisher","first-page":"1825","DOI":"10.1099\/ijsem.0.002786","article-title":"LPSN\u2013list of prokaryotic names with standing in nomenclature (bacterio. net), 20 years on","volume":"68","author":"Parte","year":"2018","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref69","first-page":"92","article-title":"Studies on caprine gangrenous mastitis","volume":"13","author":"Peer","year":"2007","journal-title":"Indian J. Small Rumin."},{"key":"ref70","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1016\/s0921-4488(96)00990-x","article-title":"Relationships between California mastitis test (CMT) and somatic cell counts in dairy goats","volume":"26","author":"Perrin","year":"1997","journal-title":"Small Rumin. Res."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"4421","DOI":"10.1038\/s41598-020-61407-2","article-title":"Effects of enrofloxacin treatment on the bacterial microbiota of milk from goats with persistent mastitis","volume":"10","author":"Polveiro","year":"2020","journal-title":"Sci. Rep."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"21608","DOI":"10.1038\/s41598-020-77054-6","article-title":"A core microbiota dominates a rich microbial diversity in the bovine udder and may indicate presence of dysbiosis","volume":"10","author":"Porcellato","year":"2020","journal-title":"Sci. Rep."},{"key":"ref73","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref74","doi-asserted-by":"publisher","first-page":"664","DOI":"10.1111\/1574-6976.12030","article-title":"The complex microbiota of raw milk","volume":"37","author":"Quigley","year":"2013","journal-title":"FEMS Microbiol. Rev."},{"key":"ref75","first-page":"986","article-title":"Veterinary microbiology and microbial disease","volume":"44","author":"Quinn","year":"2003","journal-title":"Can Vet J."},{"key":"ref76","volume-title":"Veterinary Microbiology and Microbial Disease","author":"Quinn","year":"2011"},{"key":"ref78","year":"2018"},{"key":"ref79","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1186\/s13567-018-0564-4","article-title":"Host factors determine the evolution of infection with Staphylococcus aureus to gangrenous mastitis in goats","volume":"49","author":"Rainard","year":"2018","journal-title":"Vet. Res."},{"key":"ref80","doi-asserted-by":"publisher","first-page":"810","DOI":"10.1590\/S0102-09352007000300037","article-title":"An unusual gangrenous goat mastitis caused by Staphylococcus aureus, Clostridium perfringens and Escherichia coli co-infection","volume":"59","author":"Ribeiro","year":"2007","journal-title":"Arq. Bras. Med. Vet. Zootec."},{"key":"ref81","doi-asserted-by":"publisher","first-page":"14","DOI":"10.3390\/MICROORGANISMS7010014","article-title":"What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases","volume":"7","author":"Rinninella","year":"2019","journal-title":"Microorganisms"},{"key":"ref82","doi-asserted-by":"publisher","DOI":"10.1155\/2017\/9351507","article-title":"Proteobacteria: a common factor in human diseases","volume":"2017","author":"Rizzatti","year":"2017","journal-title":"Biomed Res. Int."},{"key":"ref83","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1016\/J.IJFOODMICRO.2015.09.012","article-title":"Microbial diversity and dynamics throughout manufacturing and ripening of surface ripened semi-hard Danish Danbo cheeses investigated by culture-independent techniques","volume":"215","author":"Ryssel","year":"2015","journal-title":"Int. J. Food Microbiol."},{"key":"ref84","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/J.IJVSM.2015.02.001","article-title":"Unilateral mastectomy as an alternative treatment for gangrenous mastitis in a Saanen goat","volume":"3","author":"Sabuncu","year":"2015","journal-title":"Int. J. Vet. Sci. Med."},{"key":"ref85","doi-asserted-by":"publisher","first-page":"777","DOI":"10.5897\/AJMR12.1515","article-title":"Bovine mastitis: prevalence of bacterial pathogens and evaluation of early screening test","volume":"7","author":"Saidi","year":"2013","journal-title":"Afr. J. Microbiol. Res."},{"key":"ref86","doi-asserted-by":"publisher","first-page":"10899","DOI":"10.1038\/s41598-018-28966-x","article-title":"Potential of a polyherbal drug to prevent antimicrobial resistance in bacteria to antibiotics","volume":"8","author":"Sar","year":"2018","journal-title":"Sci. Rep."},{"key":"ref87","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1016\/j.vetimm.2011.08.022","article-title":"Host-response patterns of intramammary infections in dairy cows","volume":"144","author":"Schukken","year":"2011","journal-title":"Vet. Immunol. Immunopathol."},{"key":"ref88","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1002\/j.1538-7305.1948.tb00917.x","article-title":"A mathematical theory of communication","volume":"27","author":"Shannon","year":"1948","journal-title":"Bell Syst. Tech. J."},{"key":"ref89","doi-asserted-by":"publisher","first-page":"1401","DOI":"10.3390\/ANI11051401","article-title":"Comparative analysis of milk microbiomes and their association with bovine mastitis in two farms in Central Russia","volume":"11","author":"Sokolov","year":"2021","journal-title":"Animals"},{"key":"ref90","doi-asserted-by":"publisher","first-page":"3540","DOI":"10.3389\/FMICB.2020.590441\/BIBTEX","article-title":"Unravelling the role of rumen microbial communities, genes, and activities on milk fatty acid profile using a combination of Omics approaches","volume":"11","author":"Stergiadis","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref91","doi-asserted-by":"publisher","first-page":"377","DOI":"10.3389\/fmicb.2016.00377","article-title":"Review: diversity of microorganisms in global fermented foods and beverages","volume":"7","author":"Tamang","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref92","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S13567-019-0662-Y\/FIGURES\/4","article-title":"Bovine milk microbiome: a more complex issue than expected","volume":"50","author":"Taponen","year":"2019","journal-title":"Vet. Res."},{"key":"ref93","doi-asserted-by":"publisher","first-page":"315","DOI":"10.17221\/43\/2021-CJAS","article-title":"The presence of pathogens in milk of ewes in relation to the somatic cell count and subpopulations of leukocytes","volume":"66","author":"Tvaro\u017ekov\u00e1","year":"2021","journal-title":"Czech J. Anim. Sci."},{"key":"ref94","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S40168-015-0145-Y\/FIGURES\/3","article-title":"Human milk microbiota profiles in relation to birthing method, gestation and infant gender","volume":"4","author":"Urbaniak","year":"2016","journal-title":"Microbiome"},{"key":"ref95","doi-asserted-by":"crossref","DOI":"10.1128\/9781555816728","volume-title":"Manual of Clinical Microbiology","author":"Versalovic","year":"2011"},{"key":"ref96","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":"ref97","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1186\/s40168-017-0237-y","article-title":"Normalization and microbial differential abundance strategies depend upon data characteristics","volume":"5","author":"Weiss","year":"2017","journal-title":"Microbiome"},{"key":"ref98","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1016\/S0921-4488(99)00013-9","article-title":"Prevalence of mastitis pathogens in goat milk","volume":"33","author":"White","year":"1999","journal-title":"Small Rumin. Res."},{"key":"ref99","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot 2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2016"},{"key":"ref100","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1093\/FEMSRE\/FUAA010","article-title":"Insights into the reason of Human-Residential Bifidobacteria (HRB) being the natural inhabitants of the human gut and their potential health-promoting benefits","volume":"44","author":"Wong","year":"2020","journal-title":"FEMS Microbiol. Rev."},{"key":"ref101","doi-asserted-by":"publisher","first-page":"611413","DOI":"10.3389\/FMICB.2021.611413\/PDF","article-title":"Bacterial quorum-sensing systems and their role in intestinal bacteria-host crosstalk","volume":"12","author":"Wu","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref102","doi-asserted-by":"crossref","DOI":"10.1007\/978-981-13-1534-3","volume-title":"Statistical Analysis of Microbiome Data with R","author":"Xia","year":"2018"},{"key":"ref103","author":"Xu","year":"2020"},{"key":"ref104","doi-asserted-by":"publisher","first-page":"e1000465","DOI":"10.1371\/journal.pcbi.1000465","article-title":"A parsimony approach to biological pathway reconstruction\/inference for genomes and metagenomes","volume":"5","author":"Ye","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"ref105","doi-asserted-by":"publisher","first-page":"4923","DOI":"10.3168\/JDS.2017-14104","article-title":"Microbial community dynamics of a blue-veined raw milk cheese from the United Kingdom","volume":"101","author":"Yunita","year":"2018","journal-title":"J. Dairy Sci."},{"key":"ref106","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1080\/19490976.2020.1848158","article-title":"Gut Bacteroides species in health and disease","volume":"13","author":"Zafar","year":"2021","journal-title":"Gut Microbes"},{"key":"ref107","doi-asserted-by":"publisher","first-page":"5890","DOI":"10.1038\/s41598-018-24280-8","article-title":"Impact of sequencing depth on the characterization of the microbiome and resistome","volume":"8","author":"Zaheer","year":"2018","journal-title":"Sci. Rep."},{"key":"ref108","doi-asserted-by":"publisher","first-page":"7812","DOI":"10.3168\/jds.2017-13244","article-title":"Bacterial diversity in goat milk from the Guanzhong area of China","volume":"100","author":"Zhang","year":"2017","journal-title":"J. Dairy Sci."},{"key":"ref109","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3390\/MICROORGANISMS8122042","article-title":"Rumen and hindgut bacteria are potential indicators for mastitis of mid-lactating Holstein dairy cows","volume":"8","author":"Zhong","year":"2020","journal-title":"Microorganisms"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2022.918706\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,8,25]],"date-time":"2022-08-25T08:11:05Z","timestamp":1661415065000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2022.918706\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,8,25]]},"references-count":108,"alternative-id":["10.3389\/fmicb.2022.918706"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2022.918706","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,8,25]]},"article-number":"918706"}}