{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T06:20:29Z","timestamp":1791008429827,"version":"4.1.0"},"reference-count":52,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T00:00:00Z","timestamp":1774310400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004569","name":"Ministry of Science and Higher Education","doi-asserted-by":"publisher","award":["MEiN\/2023\/DPI\/2870"],"award-info":[{"award-number":["MEiN\/2023\/DPI\/2870"]}],"id":[{"id":"10.13039\/501100004569","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>The bovine milk microbiome is a complex and dynamic microbial ecosystem, comprising both commensal and pathogenic bacteria. Its composition is shaped by endogenous factors, including udder physiology, lactation stage, and health status, particularly mastitis, as well as by exogenous factors, such as housing conditions, farm infrastructure, milking practices, and post-milking processing. Mastitis not only alters milk quality but also induces persistent dysbiosis that may persist even after clinical recovery, highlighting the need for continuous microbiome monitoring to ensure milk safety. Advances in molecular and metagenomic techniques have enabled the detection of microbial taxa that are difficult to identify using traditional culture-based methods. However, challenges remain due to low microbial biomass, reagent contamination, and the inability to distinguish live from dead bacteria, all of which complicate accurate characterization. Environmental contamination from skin, air, and equipment, along with microbial shifts during transport, storage, pasteurization, and product separation, further modulate microbial communities. While mastitis-related changes in milk microbiota have been extensively studied, the effects of other bovine diseases and systemic health conditions remain largely unexplored, constituting a critical knowledge gap. Understanding the factors that shape milk microbial communities is essential for ensuring dairy product safety, optimizing herd management, and developing microbiome-based innovations in milk production.<\/jats:p>","DOI":"10.3390\/ani16070996","type":"journal-article","created":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T08:02:49Z","timestamp":1774339369000},"page":"996","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Microbiome of Bovine Milk and Factors Influencing Its Composition"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-4969-4431","authenticated-orcid":false,"given":"\u0141ukasz","family":"Szala","sequence":"first","affiliation":[{"name":"Department of Food Technology of Plant Origin, Faculty of Food Science and Nutrition, Poznan University of Life Sciences, Wojska Polskiego 31, 60-624 Poznan, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7675-1041","authenticated-orcid":false,"given":"Justyna","family":"Staninska-Pi\u0119ta","sequence":"additional","affiliation":[{"name":"Department of Food Technology of Plant Origin, Faculty of Food Science and Nutrition, Poznan University of Life Sciences, Wojska Polskiego 31, 60-624 Poznan, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2728-1303","authenticated-orcid":false,"given":"Agnieszka","family":"Piotrowska-Cyplik","sequence":"additional","affiliation":[{"name":"Department of Food Technology of Plant Origin, Faculty of Food Science and Nutrition, Poznan University of Life Sciences, Wojska Polskiego 31, 60-624 Poznan, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,3,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","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":"ref_2","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/s13567-017-0429-2","article-title":"Mammary microbiota of dairy ruminants: Fact or fiction?","volume":"48","author":"Rainard","year":"2017","journal-title":"Vet. Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"10609","DOI":"10.3168\/jds.2021-20480","article-title":"Both sampling seasonality and geographic origin contribute significantly to variations in raw milk microbiota, but sampling seasonality is the more determining factor","volume":"104","author":"Guo","year":"2021","journal-title":"J. Dairy Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.fm.2019.04.002","article-title":"Farm-to-fork profiling of bacterial communities associated with an artisan cheese production facility","volume":"83","author":"Falardeau","year":"2019","journal-title":"Food Microbiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"106293","DOI":"10.1016\/j.idairyj.2025.106293","article-title":"Changes in milk microbiota and spore content during milk processing unit operations","volume":"168","author":"Moscone","year":"2025","journal-title":"Int. Dairy J."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1702","DOI":"10.1111\/1462-2920.15407","article-title":"How multiple farming conditions correlate with the composition of the raw cow\u2019s milk lactic microbiome","volume":"23","author":"Nikoloudaki","year":"2021","journal-title":"Environ. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"6346","DOI":"10.3168\/jds.2017-14212","article-title":"Influence of sampling technique and bedding type on the milk microbiota: Results of a pilot study","volume":"101","author":"Metzger","year":"2018","journal-title":"J. Dairy Sci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2536","DOI":"10.3168\/jds.2016-11540","article-title":"The microbiome of bulk tank milk: Characterization and associations with somatic cell count and bacterial count","volume":"100","author":"Rodrigues","year":"2017","journal-title":"J. Dairy Sci."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Vel\u00e1zquez-Ordo\u00f1ez, V., Valladares-Carranza, B., Tenorio-Borroto, E., Talavera-Rojas, M., Antonio Varela-Guerrero, J., Acosta-Dibarrat, J., Puigvert, F., Grille, L., Gonz\u00e1lez Revello, \u00c1., and Pareja, L. (2019). Microbial Contamination in Milk Quality and Health Risk of the Consumers of Raw Milk and Dairy Products. Nutrition in Health and Disease\u2014Our Challenges Now and Forthcoming Time, IntechOpen.","DOI":"10.5772\/intechopen.86182"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"109045","DOI":"10.1016\/j.ijfoodmicro.2021.109045","article-title":"Role prediction of Gram-negative species in the resistome of raw cow\u2019s milk","volume":"340","author":"Nikoloudaki","year":"2021","journal-title":"Int. J. Food Microbiol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"7016","DOI":"10.3168\/jds.2016-11041","article-title":"Characterization of the indigenous microflora in raw and pasteurized buffalo milk during storage at refrigeration temperature by high-throughput sequencing","volume":"99","author":"Li","year":"2016","journal-title":"J. Dairy Sci."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1016\/j.cvfa.2018.06.003","article-title":"Understanding the Milk Microbiota","volume":"34","author":"Metzger","year":"2018","journal-title":"Vet. Clin. N. Am.\u2014Food Anim. Pract."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Oikonomou, G., Bicalho, M.L., Meira, E., Rossi, R.E., Foditsch, C., Machado, V.S., Teixeira, A.G.V., Santisteban, C., Schukken, Y.H., and Bicalho, R.C. (2014). Microbiota of Cow\u2019s Milk; Distinguishing Healthy, Sub-Clinically and Clinically Diseased Quarters. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0085904"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Kuehn, J.S., Gorden, P.J., Munro, D., Rong, R., Dong, Q., Plummer, P.J., Wang, C., and Phillips, G.J. (2013). Bacterial Community Profiling of Milk Samples as a Means to Understand Culture-Negative Bovine Clinical Mastitis. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0061959"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1017\/S0022029920000837","article-title":"Metataxonomics contributes to unravel the microbiota of a Brazilian dairy","volume":"87","author":"Frazilio","year":"2020","journal-title":"J. Dairy Res."},{"key":"ref_16","doi-asserted-by":"crossref","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":"ref_17","doi-asserted-by":"crossref","unstructured":"Hornik, B., Czarny, J., Staninska-Pi\u0119ta, J., Wolko, \u0141., Cyplik, P., and Piotrowska-Cyplik, A. (2021). The Raw Milk Microbiota from Semi-Subsistence Farms Characteristics by NGS Analysis Method. Molecules, 26.","DOI":"10.3390\/molecules26165029"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"106708","DOI":"10.1016\/j.domaniend.2021.106708","article-title":"The bovine milk microbiome\u2014An evolving science","volume":"79","author":"Ruegg","year":"2022","journal-title":"Domest. Anim. Endocrinol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"e00619-21","DOI":"10.1128\/mSystems.00619-21","article-title":"DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid","volume":"6","author":"Ganda","year":"2021","journal-title":"mSystems"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"3031","DOI":"10.3168\/jds.2016-11604","article-title":"The bovine colostrum microbiome and its association with clinical mastitis","volume":"100","author":"Lima","year":"2017","journal-title":"J. Dairy Sci."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Zhu, H., Miao, R., Tao, X., Wu, J., Liu, L., Qu, J., Liu, H., Sun, Y., Li, L., and Qu, Y. (2023). Longitudinal Changes in Milk Microorganisms in the First Two Months of Lactation of Primiparous and Multiparous Cows. Animals, 13.","DOI":"10.3390\/ani13121923"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"36350","DOI":"10.1038\/s41598-025-20111-9","article-title":"Exploring colostrum microbiota and its influence on early calf gut microbiota development using full-length 16S rRNA gene metabarcoding","volume":"15","author":"Ocejo","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1186\/s40168-018-0586-1","article-title":"Association of bovine major histocompatibility complex (BoLA) gene polymorphism with colostrum and milk microbiota of dairy cows during the first week of lactation","volume":"6","author":"Derakhshani","year":"2018","journal-title":"Microbiome"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Gathinji, P.K., Yousofi, Z., Akada, K., Wali, A., Nishino, N., Gathinji, P.K., Yousofi, Z., Akada, K., Wali, A., and Nishino, N. (2023). Monitoring the Milk Composition, Milk Microbiota, and Blood Metabolites of Jersey Cows Throughout a Lactation Period. Vet. Sci., 10.","DOI":"10.3390\/vetsci10030226"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Metzger, S.A., Hernandez, L.L., Skarlupka, J.H., Walker, T.M., Suen, G., and Ruegg, P.L. (2018). A cohort study of the milk microbiota of healthy and inflamed bovine mammary glands from dryoff through 150 days in milk. Front. Vet. Sci., 5.","DOI":"10.3389\/fvets.2018.00247"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Breitenwieser, F., Doll, E.V., Clavel, T., Scherer, S., and Wenning, M. (2020). Complementary Use of Cultivation and High-Throughput Amplicon Sequencing Reveals High Biodiversity Within Raw Milk Microbiota. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.01557"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"6532","DOI":"10.3168\/jds.2015-10811","article-title":"The effect of sampling technique on PCR-based bacteriological results of bovine milk samples","volume":"99","author":"Simojoki","year":"2016","journal-title":"J. Dairy Sci."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Oikonomou, G., Addis, M.F., Chassard, C., Nader-Macias, M.E.F., Grant, I., Delb\u00e8s, C., Bogni, C.I., Le Loir, Y., and Even, S. (2020). Milk Microbiota: What Are We Exactly Talking About?. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.00060"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"fuab011","DOI":"10.1093\/femsre\/fuab011","article-title":"Can we modulate the breastfed infant gut microbiota through maternal diet?","volume":"45","author":"Sindi","year":"2021","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.jare.2023.06.016","article-title":"Bovine milk microbiota: Key players, origins, and potential contributions to early-life gut development","volume":"59","author":"Guo","year":"2024","journal-title":"J. Adv. Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e888","DOI":"10.7717\/peerj.888","article-title":"Transfer of intestinal bacterial components to mammary secretions in the cow","volume":"3","author":"Young","year":"2015","journal-title":"PeerJ"},{"key":"ref_32","first-page":"2","article-title":"Production of Milk and Bovine Mastitis","volume":"5","author":"Izquierdo","year":"2017","journal-title":"Adv. Dairy Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1186\/s42523-024-00345-0","article-title":"Unravelling the complexity of bovine milk microbiome: Insights into mastitis through enterotyping using full-length 16S-metabarcoding","volume":"6","author":"Ocejo","year":"2024","journal-title":"Anim. Microbiome"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Pang, M., Xie, X., Bao, H., Sun, L., He, T., Zhao, H., Zhou, Y., Zhang, L., Zhang, H., and Wei, R. (2018). Insights into the bovine milk microbiota in dairy farms with different incidence rates of subclinical mastitis. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.02379"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Kaczorowski, \u0141., Powierska-Czarny, J., Wolko, \u0141., Piotrowska-Cyplik, A., Cyplik, P., and Czarny, J. (2022). The Influence of Bacteria Causing Subclinical Mastitis on the Structure of the Cow\u2019s Milk Microbiome. Molecules, 27.","DOI":"10.3390\/molecules27061829"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/s44280-025-00105-y","article-title":"Differences in milk microbiota between healthy cows and those with recurring Klebsiella mastitis","volume":"3","author":"Yang","year":"2025","journal-title":"One Health Adv."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"10220","DOI":"10.3168\/jds.2025-26401","article-title":"Changes in the milk and fecal microbiota in Holstein cows with subclinical intramammary infection","volume":"108","author":"Secchi","year":"2025","journal-title":"J. Dairy Sci."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"8214","DOI":"10.3168\/jds.2020-19941","article-title":"Effects of calfhood respiratory disease on health and performance of dairy cattle: A systematic review and meta-analysis","volume":"104","author":"Buczinski","year":"2021","journal-title":"J. Dairy Sci."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Tufarelli, V., Puva\u010da, N., Glamo\u010di\u0107, D., Pugliese, G., and Colonna, M.A. (2024). The Most Important Metabolic Diseases in Dairy Cattle During the Transition Period. Animals, 14.","DOI":"10.3390\/ani14050816"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Du, B., Meng, L., Liu, H., Zheng, N., Zhang, Y., Guo, X., Zhao, S., Li, F., and Wang, J. (2020). Impacts of Milking and Housing Environment on Milk Microbiota. Animals, 10.","DOI":"10.3390\/ani10122339"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Doyle, C.J., Gleeson, D., O\u2019Toole, P.W., and Cotter, P.D. (2017). Impacts of seasonal housing and teat preparation on raw milk microbiota: A high-throughput sequencing study. Appl. Environ. Microbiol., 83.","DOI":"10.1128\/AEM.02694-16"},{"key":"ref_42","doi-asserted-by":"crossref","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":"ref_43","doi-asserted-by":"crossref","first-page":"111579","DOI":"10.1016\/j.foodres.2022.111579","article-title":"Shotgun metagenomic sequencing of bulk tank milk filters reveals the role of Moraxellaceae and Enterobacteriaceae as carriers of antimicrobial resistance genes","volume":"158","author":"Rubiola","year":"2022","journal-title":"Food Res. Int."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Rubiola, S., Chiesa, F., Dalmasso, A., Di Ciccio, P., and Civera, T. (2020). Detection of Antimicrobial Resistance Genes in the Milk Production Environment: Impact of Host DNA and Sequencing Depth. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.01983"},{"key":"ref_45","first-page":"8120","article-title":"Biofilm Formation in Dairy: A Food Safety Concern\u2014Biofilms in the milking machine, from laboratory scale to on-farm results","volume":"108","author":"Desmousseaux","year":"2025","journal-title":"J. Dairy Sci."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Latorre, A.A., Oliva, R., Pugin, J., Estay, A., Nualart, F., Salazar, K., Garrido, N., and Mu\u00f1oz, M.A. (2022). Biofilms in hoses utilized to divert colostrum and milk on dairy farms: A report exploring their potential role in herd health, milk quality, and public health. Front. Vet. Sci., 9.","DOI":"10.3389\/fvets.2022.969455"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"110704","DOI":"10.1016\/j.ijfoodmicro.2024.110704","article-title":"Dynamics of microbiota and antimicrobial resistance in on-farm dairy processing plants using metagenomic and culture-dependent approaches","volume":"417","author":"Yi","year":"2024","journal-title":"Int. J. Food Microbiol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"109318","DOI":"10.1016\/j.ijfoodmicro.2021.109318","article-title":"Incidence of Bacillus cereus, Bacillus sporothermodurans and Geobacillus stearothermophilus in ultra-high temperature milk and biofilm formation capacity of isolates","volume":"354","author":"Alonso","year":"2021","journal-title":"Int. J. Food Microbiol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/mSystems.00226-20","article-title":"Tracking the Dairy Microbiota from Farm Bulk Tank to Skimmed Milk Powder","volume":"5","author":"McHugh","year":"2020","journal-title":"mSystems"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/mSystems.00052-16","article-title":"Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir","volume":"1","author":"Walsh","year":"2016","journal-title":"mSystems"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"2933","DOI":"10.1111\/1750-3841.16614","article-title":"Metagenomic analysis and antibacterial activity of kefir microorganisms","volume":"88","year":"2023","journal-title":"J. Food Sci."},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Korena, K., Krzyzankova, M., Florianova, M., Karasova, D., Babak, V., Strakova, N., and Juricova, H. (2023). Microbial Succession in the Cheese Ripening Process-Competition of the Starter Cultures and the Microbiota of the Cheese Plant Environment. Microorganisms, 11.","DOI":"10.3390\/microorganisms11071735"}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/7\/996\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T08:25:17Z","timestamp":1774340717000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/7\/996"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,24]]},"references-count":52,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2026,4]]}},"alternative-id":["ani16070996"],"URL":"https:\/\/doi.org\/10.3390\/ani16070996","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,24]]}}}