{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T23:31:20Z","timestamp":1787959880539,"version":"build-2784847793"},"reference-count":106,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,6,26]],"date-time":"2023-06-26T00:00:00Z","timestamp":1687737600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100011129","name":"North Dakota Agricultural Experiment Station","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011129","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    Early life microbial colonization and factors affecting colonization patterns are gaining interest due to recent developments suggesting that early life microbiome may play a role in Developmental Origins of Health and Disease. In cattle, limited information exists on the early microbial colonization of anatomical sites involved in bovine health beyond the gastrointestinal tract. Here, we investigated 1) the initial microbial colonization of seven different anatomical locations in newborn calves and 2) whether these early life microbial communities and 3) serum cytokine profiles are influenced by prenatal vitamin and mineral (VTM) supplementation. Samples were collected from the hoof, liver, lung, nasal cavity, eye, rumen (tissue and fluid), and vagina of beef calves that were born from dams that either received or did not receive VTM supplementation throughout gestation (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u20097\/group). Calves were separated from dams immediately after birth and fed commercial colostrum and milk replacer until euthanasia at 30\u2009h post-initial colostrum feeding. The microbiota of all samples was assessed using 16S rRNA gene sequencing and qPCR. Calf serum was subjected to multiplex quantification of 15 bovine cytokines and chemokines. Our results indicated that the hoof, eye, liver, lung, nasal cavity, and vagina of newborn calves were colonized by site-specific microbiota, whose community structure differed from the ruminal-associated communities (0.64 \u2265\n                    <jats:italic>R<\/jats:italic>\n                    <jats:sup>2<\/jats:sup>\n                    \u2265 0.12,\n                    <jats:italic>p<\/jats:italic>\n                    \u2264 0.003). The ruminal fluid microbial community was the only one that differed by treatment (\n                    <jats:italic>p &amp;lt;<\/jats:italic>\n                    0.01). However, differences (\n                    <jats:italic>p<\/jats:italic>\n                    &amp;lt; 0.05) by treatment were detected in microbial richness (vagina); diversity (ruminal tissue, fluid, and eye); composition at the phylum and genus level (ruminal tissue, fluid, and vagina); and in total bacterial abundance (eye and vagina). From serum cytokines evaluated, concentration of chemokine IP-10 was greater (\n                    <jats:italic>p<\/jats:italic>\n                    = 0.02) in VTM calves compared to control calves. Overall, our results suggest that upon birth, the whole-body of newborn calves are colonized by relatively rich, diverse, and site-specific bacterial communities. Noticeable differences were observed in ruminal, vaginal, and ocular microbiota of newborn calves in response to prenatal VTM supplementation. These findings can derive future hypotheses regarding the initial microbial colonization of different body sites, and on maternal micronutrient consumption as a factor that may influence early life microbial colonization.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2023.1207601","type":"journal-article","created":{"date-parts":[[2023,6,26]],"date-time":"2023-06-26T06:38:22Z","timestamp":1687761502000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":27,"title":["Whole-body microbiota of newborn calves and their response to prenatal vitamin and mineral supplementation"],"prefix":"10.3389","volume":"14","author":[{"given":"Sarah M.","family":"Luecke","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Devin B.","family":"Holman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaycie N.","family":"Schmidt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine E.","family":"Gzyl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer L.","family":"Hurlbert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana Clara B.","family":"Menezes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kerri A.","family":"Bochantin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James D.","family":"Kirsch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Friederike","family":"Baumgaertner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin K.","family":"Sedivec","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kendall C.","family":"Swanson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carl R.","family":"Dahlen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samat","family":"Amat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,6,26]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"2838","DOI":"10.3168\/jds.S0022-0302(95)76914-4","article-title":"Effect of administration of bifidobacteria and lactic acid bacteria to newborn calves and piglets","volume":"78","author":"Abe","year":"1995","journal-title":"J. Dairy Sci."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"1002","DOI":"10.1164\/rccm.201911-2127LE","article-title":"Human fetal Lungs Harbor a microbiome signature","volume":"201","author":"Al Alam","year":"2020","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"skab076","DOI":"10.1093\/jas\/skab076","article-title":"Bacterial community analysis of purulent material from liver abscesses of crossbred cattle and Holstein steers fed finishing diets with or without tylosin","volume":"99","author":"Amachawadi","year":"2021","journal-title":"J. Anim. Sci."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"854453","DOI":"10.3389\/fmicb.2022.854453","article-title":"Bovine animal model for studying the maternal microbiome","volume":"13","author":"Amat","year":"","journal-title":"Front. Microbiol."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"771832","DOI":"10.3389\/fmicb.2021.771832","article-title":"Characterization of the microbiota associated with 12-week-old bovine fetuses exposed to divergent","volume":"12","author":"Amat","year":"","journal-title":"Front. Microbiol."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"2011","DOI":"10.3390\/microorganisms9102011","article-title":"The nasopharyngeal, ruminal, and vaginal microbiota and the Core taxa shared across these microbiomes in virgin yearling heifers exposed to divergent in utero nutrition during their first trimester of gestation and in pregnant beef heifers in response to mineral supplementation","volume":"9","author":"Amat","year":"","journal-title":"Microorganisms"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"e0101622","DOI":"10.1128\/msystems.01016-22","article-title":"A single intranasal dose of bacterial therapeutics to calves confers longitudinal modulation of the nasopharyngeal microbiota","volume":"8","author":"Amat","year":"","journal-title":"mSystems"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"427","DOI":"10.3389\/fimmu.2014.00427","article-title":"The intestinal microbiome in early life: health and disease","volume":"5","author":"Arrieta","year":"2014","journal-title":"Front. Immunol."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"1757","DOI":"10.3390\/ani12141757","article-title":"Vitamin and mineral supplementation and rate of gain in beef heifers I: effects on dam hormonal and metabolic status, fetal tissue and organ mass, and concentration of glucose and fructose in fetal fluids at d 83 of gestation","volume":"12","author":"Menezes","year":"2022","journal-title":"Animals (Basel)"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1186\/s42523-020-00049-1","article-title":"Maternal influences on oral and faecal microbiota maturation in neonatal calves in beef and dairy production systems","volume":"2","author":"Barden","year":"2020","journal-title":"Anim Microbiome"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1186\/s42523-021-00079-3","article-title":"Longitudinal assessment of the bovine ocular bacterial community dynamics in calves","volume":"3","author":"Bartenslager","year":"2021","journal-title":"Anim Microbiome"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"5047","DOI":"10.3168\/jds.2019-18002","article-title":"Inoculation with rumen fluid in early life as a strategy to optimize the weaning process in intensive dairy goat systems","volume":"103","author":"Belanche","year":"2020","journal-title":"J. Dairy Sci."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"6803","DOI":"10.3390\/ijms22136803","article-title":"Bioaccessibility and bioavailability of minerals in relation to a healthy gut microbiome","volume":"22","author":"Bielik","year":"2021","journal-title":"Int. J. Mol. Sci."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"813","DOI":"10.1093\/nutrit\/nuz101","article-title":"Safety and efficacy of supplements in pregnancy","volume":"78","author":"Brown","year":"2020","journal-title":"Nutr. Rev."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1111\/j.1939-1676.1998.tb02120.x","article-title":"Infectious bovine keratoconjunctivitis: a review","volume":"12","author":"Brown","year":"1998","journal-title":"J. Vet. Intern. Med."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"e0070821","DOI":"10.1128\/mSystems.00708-21","article-title":"Identification and quantification of bovine digital dermatitis-associated microbiota across lesion stages in feedlot beef cattle","volume":"6","author":"Caddey","year":"2021","journal-title":"mSystems"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1016\/j.tem.2019.07.021","article-title":"Maternal microbiome and metabolic health program microbiome development and health of the offspring","volume":"30","author":"Calatayud","year":"2019","journal-title":"Trends Endocrinol. Metab."},{"key":"ref18","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":"ref19","doi-asserted-by":"publisher","first-page":"976","DOI":"10.1093\/tas\/txy127","article-title":"Maternal nutrition and programming of offspring energy requirements","volume":"3","author":"Caton","year":"2019","journal-title":"Transl Anim Sci"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"952473","DOI":"10.3389\/fmicb.2022.952473","article-title":"Ocular surface microbiota: ophthalmic infectious disease and probiotics","volume":"13","author":"Chiang","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1159\/000499144","article-title":"Microbiota and neurodevelopmental trajectories: role of maternal and early-life nutrition","volume":"74","author":"Codagnone","year":"2019","journal-title":"Ann. Nutr. Metab."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"148","DOI":"10.3390\/life11020148","article-title":"When a neonate is born, so is a microbiota","volume":"11","author":"Coscia","year":"2021","journal-title":"Life (Basel)"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"696","DOI":"10.3390\/metabo12080696","article-title":"Vitamin and mineral supplementation and rate of weight gain during the first trimester of gestation in beef heifers alters the fetal liver amino acid, carbohydrate, and energy profile at day 83 of gestation","volume":"12","author":"Crouse","year":"2022","journal-title":"Meta"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"483","DOI":"10.3168\/jds.S0022-0302(96)76389-0","article-title":"Effect of Lactobacillus acidophilus supplementation of milk replacer on preweaning performance of calves","volume":"79","author":"Cruywagen","year":"1996","journal-title":"J. Dairy Sci."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"11668","DOI":"10.3390\/ijms222111668","article-title":"Programming of embryonic development","volume":"22","author":"Dahlen","year":"2021","journal-title":"Int. J. Mol. Sci."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"1744","DOI":"10.3390\/nu7031744","article-title":"Micronutrients in pregnancy in low- and middle-income countries","volume":"7","author":"Darnton-Hill","year":"2015","journal-title":"Nutrients"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"385","DOI":"10.3390\/genes12030385","article-title":"Maternal vitamin and mineral supplementation and rate of maternal weight gain affects placental expression of energy metabolism and transport-related genes","volume":"12","author":"Diniz","year":"2021","journal-title":"Genes (Basel)"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"772863","DOI":"10.3389\/fmicb.2021.772863","article-title":"The gut microbiota of newborn calves and influence of potential probiotics on reducing diarrheic disease by inhibition of pathogen colonization","volume":"12","author":"Fan","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"4213","DOI":"10.4049\/jimmunol.1202246","article-title":"Il-4 in the brain: a cytokine to remember","volume":"189","author":"Gadani","year":"2012","journal-title":"J. Immunol."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"11786","DOI":"10.3168\/jds.2019-17106","article-title":"Symposium review: the uterine microbiome associated with the development of uterine disease in dairy cows","volume":"102","author":"Galv\u00e3o","year":"2019","journal-title":"J. Dairy Sci."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"1558","DOI":"10.3389\/fimmu.2020.01558","article-title":"Biology of Interleukin-17 and its pathophysiological significance in Sepsis","volume":"11","author":"Ge","year":"2020","journal-title":"Front. Immunol."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"3349","DOI":"10.3390\/ani11123349","article-title":"The maternal Milk microbiome in mammals of different types and its potential role in the neonatal gut microbiota composition","volume":"11","author":"Ge","year":"2021","journal-title":"Animals (Basel)"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1016\/j.cvfa.2010.04.004","article-title":"Bacterial pathogens of the bovine respiratory disease complex","volume":"26","author":"Griffin","year":"2010","journal-title":"Vet. Clin. North Am. Food Anim. Pract."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1111\/j.1574-6968.2008.01343.x","article-title":"Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle's feed efficiency","volume":"288","author":"Guan","year":"2008","journal-title":"FEMS Microbiol. Lett."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"17712","DOI":"10.1038\/s41598-020-74677-7","article-title":"A pioneer calf foetus microbiome","volume":"10","author":"Guzman","year":"2020","journal-title":"Sci. Rep."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"294","DOI":"10.1097\/MPG.0000000000000597","article-title":"Why is initial bacterial colonization of the intestine important to infants' and children's health?","volume":"60","author":"Houghteling","year":"2015","journal-title":"J. Pediatr. Gastroenterol. Nutr."},{"key":"ref001","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1093\/jas\/skac313.021","article-title":"Impacts of Vitamin and Mineral Supplementation to Beef Heifers During Gestation on Performance Measures of the Neonatal Calf, Trace Mineral Status, and Organ Weights at 30 Hours After Birth","volume":"100","author":"Hurlbert","year":"2022","journal-title":"Journal of Animal Sci."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"2161","DOI":"10.3389\/fmicb.2018.02161","article-title":"Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future","volume":"9","author":"Huws","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"e60","DOI":"10.1038\/emi.2013.58","article-title":"Il-17 cytokines in immunity and inflammation","volume":"2","author":"Jin","year":"2013","journal-title":"Emerg Microbes Infect"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"eaaw8429","DOI":"10.1126\/science.aaw8429","article-title":"Maternal gut microbiota in pregnancy influences offspring metabolic phenotype in mice","volume":"367","author":"Kimura","year":"2020","journal-title":"Science"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"e0231013","DOI":"10.1371\/journal.pone.0231013","article-title":"Interferon gamma-induced protein 10 (Ip-10) and cardiovascular disease in African Americans","volume":"15","author":"Leavitt","year":"2020","journal-title":"PLoS One"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"819958","DOI":"10.3389\/fmicb.2022.819958","article-title":"Healthy vaginal microbiota and influence of probiotics across the female life span","volume":"13","author":"Lehtoranta","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"e151725","DOI":"10.1172\/JCI151725","article-title":"Intrahepatic microbes govern liver immunity by programming NKT cells","volume":"132","author":"Leinwand","year":"2022","journal-title":"J. Clin. Invest."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1111\/j.1462-2920.2011.02543.x","article-title":"Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools","volume":"14","author":"Li","year":"2012","journal-title":"Environ. Microbiol."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.1093\/infdis\/jiaa155","article-title":"Vertical transmission of gut microbiome and antimicrobial resistance genes in infants exposed to antibiotics at birth","volume":"224","author":"Li","year":"2021","journal-title":"J. Infect. Dis."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1016\/j.cytogfr.2011.06.001","article-title":"Cxcl10\/Ip-10 in infectious diseases pathogenesis and potential therapeutic implications","volume":"22","author":"Liu","year":"2011","journal-title":"Cytokine Growth Factor Rev."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"812861","DOI":"10.3389\/fvets.2022.812861","article-title":"Rumen microbiome and metabolome of high and low residual feed intake Angus heifers","volume":"9","author":"Liu","year":"2022","journal-title":"Front Vet Sci"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1186\/s40104-021-00599-7","article-title":"Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers","volume":"12","author":"Lopes","year":"2021","journal-title":"J Anim Sci Biotechnol"},{"key":"ref48","doi-asserted-by":"publisher","first-page":"1029128","DOI":"10.3389\/fmicb.2022.1029128","article-title":"Seminal and vagino-uterine microbiome and their individual and interactive effects on cattle fertility","volume":"13","author":"Luecke","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"999","DOI":"10.1038\/nmeth.2634","article-title":"Practical innovations for high-throughput amplicon sequencing","volume":"10","author":"Lundberg","year":"2013","journal-title":"Nat. Methods"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"R188","DOI":"10.1186\/ar4378","article-title":"Interferon-gamma inducible protein-10 as a potential biomarker in localized scleroderma","volume":"15","author":"Magee","year":"2013","journal-title":"Arthritis Res. Ther."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"e1009442","DOI":"10.1371\/journal.pcbi.1009442","article-title":"Multivariable association discovery in population-scale meta-omics studies","volume":"17","author":"Mallick","year":"2021","journal-title":"PLoS Comput. Biol."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1038\/nrmicro.2017.14","article-title":"The microbiota of the respiratory tract: gatekeeper to respiratory health","volume":"15","author":"Man","year":"2017","journal-title":"Nat. Rev. Microbiol."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1111\/1751-7915.13685","article-title":"Defining how microorganisms benefit human health","volume":"14","author":"Marco","year":"2021","journal-title":"Microb. Biotechnol."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"Embnet J."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1080\/19490976.2018.1505176","article-title":"The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency","volume":"10","author":"Matthews","year":"2019","journal-title":"Gut Microbes"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"405","DOI":"10.3390\/pathogens10040405","article-title":"Characterization of ocular surface microbial profiles revealed discrepancies between conjunctival and corneal microbiota","volume":"10","author":"Matysiak","year":"2021","journal-title":"Pathogens"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"1925","DOI":"10.3390\/ani12151925","article-title":"Vitamin and mineral supplementation and rate of gain in beef heifers ii: effects on concentration of trace minerals in maternal liver and fetal liver, muscle, Allantoic, and amniotic fluids at day 83 of gestation","volume":"12","author":"McCarthy","year":"2022","journal-title":"Animals (Basel)"},{"key":"ref58","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1186\/s40168-020-00869-y","article-title":"Topography of the respiratory tract bacterial microbiota in cattle","volume":"8","author":"Mcmullen","year":"2020","journal-title":"Microbiome"},{"key":"ref59","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":"ref60","doi-asserted-by":"publisher","first-page":"424","DOI":"10.3390\/life12030424","article-title":"The maternal-fetal gut microbiota Axis: physiological changes, dietary influence, and modulation possibilities","volume":"12","author":"Miko","year":"2022","journal-title":"Life (Basel)"},{"key":"ref61","doi-asserted-by":"publisher","first-page":"2095","DOI":"10.3390\/microorganisms9102095","article-title":"Conjunctival sac microbiome in infectious conjunctivitis","volume":"9","author":"Mohamed","year":"2021","journal-title":"Microorganisms"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"287","DOI":"10.2527\/1998.761287x","article-title":"Liver abscesses in feedlot cattle: a review","volume":"76","author":"Nagaraja","year":"1998","journal-title":"J. Anim. Sci."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1111\/cei.13331","article-title":"Influence of maternal microbiota during pregnancy on infant immunity","volume":"198","author":"Nyangahu","year":"2019","journal-title":"Clin. Exp. Immunol."},{"key":"ref64","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1186\/s40168-018-0511-7","article-title":"Disruption of maternal gut microbiota during gestation alters offspring microbiota and immunity","volume":"6","author":"Nyangahu","year":"2018","journal-title":"Microbiome"},{"key":"ref65","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1146\/annurev-animal-021419-083952","article-title":"The role of the gut microbiome in cattle production and health: Driver or passenger?","volume":"8","author":"Ohara","year":"2020","journal-title":"Annu. Rev. Anim. Biosci."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"491","DOI":"10.3390\/nu12020491","article-title":"Vitamin and mineral supplementation during pregnancy on maternal, birth, child health and development outcomes in low- and middle-income countries: a systematic review and Meta-analysis","volume":"12","author":"Oh","year":"2020","journal-title":"Nutrients"},{"key":"ref67","author":"Oksanen","year":"2015"},{"key":"ref68","doi-asserted-by":"publisher","first-page":"377","DOI":"10.3945\/an.111.000570","article-title":"Nutritionally mediated programming of the developing immune system","volume":"2","author":"Palmer","year":"2011","journal-title":"Adv. Nutr."},{"key":"ref69","doi-asserted-by":"publisher","first-page":"lqaa001","DOI":"10.1093\/nargab\/lqaa001","article-title":"Host and body site-specific adaptation of","volume":"2","author":"Pan","year":"2020","journal-title":"Nar Genom. Bioinform."},{"key":"ref70","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/j.nutres.2021.09.001","article-title":"Vitamins, the gut microbiome and gastrointestinal health in humans","volume":"95","author":"Pham","year":"2021","journal-title":"Nutr. Res."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1016\/j.cvfa.2022.08.004","article-title":"The microbial ecology of liver abscesses in cattle","volume":"38","author":"Pinnell","year":"2022","journal-title":"Vet. Clin. North Am. Food Anim. Pract."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"882419","DOI":"10.3389\/fmicb.2022.882419","article-title":"Not all liver abscesses are created equal: the impact of Tylosin and antibiotic alternatives on bovine liver abscess microbial communities and a first look at Bacteroidetes-dominated communities","volume":"13","author":"Pinnell","year":"2022","journal-title":"Front. Microbiol."},{"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":"599","DOI":"10.1038\/s41591-020-0761-3","article-title":"Viable bacterial colonization is highly limited in the human intestine in utero","volume":"26","author":"Rackaityte","year":"2020","journal-title":"Nat. Med."},{"key":"ref75","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1016\/j.cvfa.2019.02.006","article-title":"Developmental programming of fetal growth and development","volume":"35","author":"Reynolds","year":"2019","journal-title":"Vet. Clin. North Am. Food Anim. Pract."},{"key":"ref76","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/j.tim.2018.09.008","article-title":"The human microbiome and child growth - first 1000 days and beyond","volume":"27","author":"Robertson","year":"2019","journal-title":"Trends Microbiol."},{"key":"ref77","doi-asserted-by":"publisher","first-page":"26050","DOI":"10.3402\/mehd.v26.26050","article-title":"The composition of the gut microbiota throughout life, with an emphasis on early life","volume":"26","author":"Rodr\u00edguez","year":"2015","journal-title":"Microb. Ecol. Health Dis."},{"key":"ref78","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1186\/s12915-014-0087-z","article-title":"Reagent and laboratory contamination can critically impact sequence-based microbiome analyses","volume":"12","author":"Salter","year":"2014","journal-title":"BMC Biol."},{"key":"ref79","doi-asserted-by":"publisher","first-page":"fiw182","DOI":"10.1093\/femsec\/fiw182","article-title":"Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies","volume":"92","author":"Santiago-Rodriguez","year":"2016","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref80","doi-asserted-by":"publisher","first-page":"1273","DOI":"10.3389\/fmicb.2018.01273","article-title":"Effectiveness of interventions to modulate the rumen microbiota composition and function in pre-ruminant and ruminant lambs","volume":"9","author":"Saro","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref81","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1177\/1753495X18775899","article-title":"The matter of the reproductive microbiome","volume":"12","author":"Schoenmakers","year":"2019","journal-title":"Obstet. Med."},{"key":"ref82","doi-asserted-by":"publisher","first-page":"2958","DOI":"10.1038\/ismej.2016.62","article-title":"Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants","volume":"10","author":"Shabat","year":"2016","journal-title":"ISME J."},{"key":"ref83","doi-asserted-by":"publisher","first-page":"450","DOI":"10.1136\/vr.105628","article-title":"Surveying bovine digital dermatitis and non-healing bovine foot lesions for the presence of","volume":"186","author":"Staton","year":"2020","journal-title":"Vet. Rec."},{"key":"ref84","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-018-0617-x","article-title":"Temporal development of the gut microbiome in early childhood from the teddy study","volume":"562","author":"Stewart","year":"2018","journal-title":"Nature"},{"key":"ref85","doi-asserted-by":"publisher","first-page":"e20172437","DOI":"10.1542\/peds.2017-2437","article-title":"The role of the microbiome in the developmental origins of health and disease","volume":"141","author":"Stiemsma","year":"2018","journal-title":"Pediatrics"},{"key":"ref86","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1017\/S2040174419000588","article-title":"Establishment of the early-life microbiome: a DohaD perspective","volume":"11","author":"Stinson","year":"2020","journal-title":"J. Dev. Orig. Health Dis."},{"key":"ref87","doi-asserted-by":"publisher","first-page":"1124","DOI":"10.3389\/fmicb.2019.01124","article-title":"The not-so-sterile womb: evidence that the human fetus is exposed to Bacteria prior to birth","volume":"10","author":"Stinson","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref88","doi-asserted-by":"publisher","first-page":"skab280","DOI":"10.1093\/jas\/skab280","article-title":"Characterization of bacterial Dna identified in abscessed and non-abscessed bovine hepatic tissue at the time of harvest","volume":"99","author":"Stotz","year":"2021","journal-title":"J. Anim. Sci."},{"key":"ref89","doi-asserted-by":"publisher","first-page":"713","DOI":"10.1038\/nm.4142","article-title":"The microbiome in early life: implications for health outcomes","volume":"22","author":"Tamburini","year":"2016","journal-title":"Nat. Med."},{"key":"ref90","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1186\/s12886-017-0612-2","article-title":"Bacterial profile of ocular infections: a systematic review","volume":"17","author":"Teweldemedhin","year":"2017","journal-title":"BMC Ophthalmol."},{"key":"ref91","doi-asserted-by":"publisher","first-page":"1373","DOI":"10.1136\/gutjnl-2019-320490","article-title":"Liver tissue microbiome in Nafld: next step in understanding the gut-liver axis?","volume":"69","author":"Tilg","year":"2020","journal-title":"Gut"},{"key":"ref92","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1016\/j.cvfa.2020.03.001","article-title":"Respiratory bacterial microbiota in cattle: from development to modulation to enhance respiratory health","volume":"36","author":"Timsit","year":"2020","journal-title":"Vet. Clin. North Am. Food Anim. Pract."},{"key":"ref93","doi-asserted-by":"publisher","first-page":"12171","DOI":"10.1038\/s41598-017-11699-8","article-title":"Microbiome profile of the amniotic fluid as a predictive biomarker of perinatal outcome","volume":"7","author":"Urushiyama","year":"2017","journal-title":"Sci. Rep."},{"key":"ref94","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1038\/s41586-020-2745-3","article-title":"The maternal microbiome modulates fetal neurodevelopment in mice","volume":"586","author":"Vuong","year":"2020","journal-title":"Nature"},{"key":"ref95","doi-asserted-by":"publisher","first-page":"19620","DOI":"10.1038\/s41598-019-56206-3","article-title":"Dynamics and stabilization of the rumen microbiome in yearling Tibetan sheep","volume":"9","author":"Wang","year":"2019","journal-title":"Sci. Rep."},{"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":"e0518022","DOI":"10.1128\/spectrum.05180-22","article-title":"A longitudinal characterization of the seminal microbiota and antibiotic resistance in yearling beef bulls subjected to different rates of gain","volume":"11","author":"Webb","year":"2023","journal-title":"Microbiol Spectr"},{"key":"ref98","doi-asserted-by":"publisher","first-page":"296","DOI":"10.3389\/fmicb.2015.00296","article-title":"Redundancy, resilience, and host specificity of the ruminal microbiota: implications for engineering improved ruminal fermentations","volume":"6","author":"Weimer","year":"2015","journal-title":"Front. Microbiol."},{"key":"ref99","doi-asserted-by":"publisher","first-page":"4520","DOI":"10.2527\/jas2017.1743","article-title":"Rapid communication: 16S ribosomal ribonucleic acid characterization of liver abscesses in feedlot cattle from three states in the United States","volume":"95","author":"Weinroth","year":"2017","journal-title":"J. Anim. Sci."},{"key":"ref100","doi-asserted-by":"publisher","first-page":"skac264","DOI":"10.1093\/jas\/skac264","article-title":"Calf rumen microbiome from birth to weaning and shared microbial properties to the maternal rumen microbiome","volume":"100","author":"Woodruff","year":"2022","journal-title":"J. Anim. Sci."},{"key":"ref101","doi-asserted-by":"publisher","first-page":"3197","DOI":"10.1038\/s41598-018-21440-8","article-title":"Biogeographical differences in the influence of maternal microbial sources on the early successional development of the bovine neonatal gastrointestinal tract","volume":"8","author":"Yeoman","year":"2018","journal-title":"Sci. Rep."},{"key":"ref102","doi-asserted-by":"publisher","first-page":"679135","DOI":"10.3389\/fmicb.2021.679135","article-title":"Age-related changes in the ruminal microbiota and their relationship with rumen fermentation in lambs","volume":"12","author":"Yin","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref103","doi-asserted-by":"publisher","first-page":"e33865","DOI":"10.1371\/journal.pone.0033865","article-title":"Evaluation of methods for the extraction and purification of Dna from the human microbiome","volume":"7","author":"Yuan","year":"2012","journal-title":"PLoS One"},{"key":"ref104","doi-asserted-by":"publisher","first-page":"1133","DOI":"10.3389\/fmicb.2015.01133","article-title":"Manipulating rumen microbiome and fermentation through interventions during early life: a review","volume":"6","author":"Y\u00e1\u00f1ez-Ruiz","year":"2015","journal-title":"Front. Microbiol."},{"key":"ref105","doi-asserted-by":"publisher","first-page":"753","DOI":"10.1016\/j.tim.2019.04.005","article-title":"Contribution of the mucosal microbiota to bovine respiratory health","volume":"27","author":"Zeineldin","year":"2019","journal-title":"Trends Microbiol."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2023.1207601\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,26]],"date-time":"2023-06-26T06:38:28Z","timestamp":1687761508000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2023.1207601\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,6,26]]},"references-count":106,"alternative-id":["10.3389\/fmicb.2023.1207601"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2023.1207601","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.03.21.533572","asserted-by":"object"}]},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,6,26]]},"article-number":"1207601"}}