{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T12:48:09Z","timestamp":1789735689766,"version":"4.0.1"},"reference-count":59,"publisher":"American Society for Microbiology","issue":"9","license":[{"start":{"date-parts":[[2018,5,1]],"date-time":"2018-05-01T00:00:00Z","timestamp":1525132800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100005825","name":"USDA | National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["WIS01729"],"award-info":[{"award-number":["WIS01729"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"USDA | National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2015-67015-23246"],"award-info":[{"award-number":["2015-67015-23246"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"MCTI | Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["157168\/2012-3"],"award-info":[{"award-number":["157168\/2012-3"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"MCTI | Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["PVE 313792\/2014-3"],"award-info":[{"award-number":["PVE 313792\/2014-3"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002322","name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","doi-asserted-by":"publisher","award":["PE 99999.002493\/2014-04"],"award-info":[{"award-number":["PE 99999.002493\/2014-04"]}],"id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Appl Environ Microbiol"],"published-print":{"date-parts":[[2018,5]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Microbial communities play critical roles in the gastrointestinal tracts (GIT) of preruminant calves by influencing performance and health. However, little is known about the establishment of microbial communities in the calf GIT or their dynamics during development. In this study, next-generation sequencing was used to assess changes in the bacterial communities of the rumen, jejunum, cecum, and colon in 26 crossbred calves at four developmental stages (7, 28, 49, and 63 days old). Alpha diversity differed among GIT regions with the lowest diversity and evenness in the jejunum, whereas no changes in alpha diversity were observed across developmental stage. Beta diversity analysis showed both region and age effects, with low numbers of operational taxonomic units (OTUs) shared between regions within a given age group or between ages in a given region. Taxonomic analysis revealed that several taxa coexisted in the rumen, jejunum, cecum, and colon but that their abundances differed considerably by GIT region and age. As calves aged, we observed lower abundances of taxa such as\n                    <jats:named-content content-type=\"genus-species\">Bacteroides<\/jats:named-content>\n                    ,\n                    <jats:named-content content-type=\"genus-species\">Parabacteroides<\/jats:named-content>\n                    , and\n                    <jats:named-content content-type=\"genus-species\">Paraprevotella<\/jats:named-content>\n                    with higher abundances of\n                    <jats:named-content content-type=\"genus-species\">Bulleidia<\/jats:named-content>\n                    and\n                    <jats:named-content content-type=\"genus-species\">Succiniclasticum<\/jats:named-content>\n                    in the rumen. The jejunum also displayed taxonomic changes with increases in\n                    <jats:named-content content-type=\"genus-species\">Clostridiaceae<\/jats:named-content>\n                    and\n                    <jats:named-content content-type=\"genus-species\">Turicibacter<\/jats:named-content>\n                    taxa in older calves. In the lower gut, taxa such as\n                    <jats:named-content content-type=\"genus-species\">Lactobacillus<\/jats:named-content>\n                    ,\n                    <jats:named-content content-type=\"genus-species\">Blautia<\/jats:named-content>\n                    , and\n                    <jats:named-content content-type=\"genus-species\">Faecalibacterium<\/jats:named-content>\n                    decreased and S24-7,\n                    <jats:named-content content-type=\"genus-species\">Paraprevotella<\/jats:named-content>\n                    , and\n                    <jats:named-content content-type=\"genus-species\">Prevotella<\/jats:named-content>\n                    increased as calves aged. These data support a model whereby early and successive colonization by bacteria occurs across the GIT of calves and provides insights into the temporal dynamics of the GIT microbiota of dairy calves during preweaning development.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>IMPORTANCE<\/jats:bold>\n                    The gastrointestinal tracts (GIT) of ruminants, such as dairy cows, house complex microbial communities that contribute to their overall health and support their ability to produce milk. For example, the rumen microbiota converts feed into usable nutrients, while the jejunal microbiota provides access to protein. Thus, establishing a properly functioning GIT microbiota in dairy calves is critical to their productivity as adult cows. However, little is known about the establishment, maintenance, and dynamics of the calf GIT microbiota in early life. In this study, we evaluated the bacterial communities in the rumen, jejunum, cecum, and colon in dairy calves across preweaning development and show that they are highly variable early on in life before transitioning to a stable community. Understanding the dairy calf GIT microbiota has implications for ensuring proper health during early life and will aid in efforts to develop strategies for improving downstream production.\n                  <\/jats:p>","DOI":"10.1128\/aem.02675-17","type":"journal-article","created":{"date-parts":[[2018,4,13]],"date-time":"2018-04-13T06:39:26Z","timestamp":1523601566000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":114,"title":["Bacterial Community Dynamics across the Gastrointestinal Tracts of Dairy Calves during Preweaning Development"],"prefix":"10.1128","volume":"84","author":[{"given":"Juliana","family":"Dias","sequence":"first","affiliation":[{"name":"Department of Animal Science, Universidade Federal de Vi\u00e7osa, Vi\u00e7osa, MG, Brazil"},{"name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior, Minist\u00e9rio da Educa\u00e7\u00e3o, Bras\u00edlia, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcos In\u00e1cio","family":"Marcondes","sequence":"additional","affiliation":[{"name":"Department of Animal Science, Universidade Federal de Vi\u00e7osa, Vi\u00e7osa, MG, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shirley","family":"Motta de Souza","sequence":"additional","affiliation":[{"name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior, Minist\u00e9rio da Educa\u00e7\u00e3o, Bras\u00edlia, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barbara","family":"Cardoso da Mata e Silva","sequence":"additional","affiliation":[{"name":"Universidade Jos\u00e9 do Ros\u00e1rio Vellano, Alfenas, MG, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melline","family":"Fontes Noronha","sequence":"additional","affiliation":[{"name":"Division of Microbial Resources, Research Centre for Chemistry, Biology and Agriculture, University of Campinas, Campinas, SP, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafael","family":"Tassinari Resende","sequence":"additional","affiliation":[{"name":"Department of Forestry, Universidade Federal de Vi\u00e7osa, Vi\u00e7osa, MG, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fernanda Samarini","family":"Machado","sequence":"additional","affiliation":[{"name":"Embrapa Dairy Cattle, Juiz de Fora, MG, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3481-5318","authenticated-orcid":false,"given":"Hil\u00e1rio","family":"Cuquetto Mantovani","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Universidade Federal de Vi\u00e7osa, Vi\u00e7osa, MG, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kimberly A.","family":"Dill-McFarland","sequence":"additional","affiliation":[{"name":"Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Garret","family":"Suen","sequence":"additional","affiliation":[{"name":"Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-133-7-1835"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1111\/jam.12405"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0133048"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1017\/S1466252312000096"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1021\/jf60067a003"},{"key":"e_1_3_3_7_2","first-page":"35","article-title":"Influence of the gastrointestinal microbiota on development of the immune system in young animals","volume":"7","author":"Bauer E","year":"2006","unstructured":"Bauer E, Williams BA, Smidt H, Verstegen MWA, Mosenthin R. 2006. Influence of the gastrointestinal microbiota on development of the immune system in young animals. Curr Issues Intest Microbiol 7:35\u201351.","journal-title":"Curr Issues Intest Microbiol"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.3168\/jds.S0022-0302(04)70061-2"},{"key":"e_1_3_3_9_2","first-page":"37","article-title":"Gastrointestinal tract and digestion in the young ruminant: ontogenesis, adaptations, consequences and manipulations","volume":"60","author":"Guilloteau P","year":"2009","unstructured":"Guilloteau P, Zabielski R, Blum JW. 2009. Gastrointestinal tract and digestion in the young ruminant: ontogenesis, adaptations, consequences and manipulations. J Physiol Pharmacol 60:37\u201346.","journal-title":"J Physiol Pharmacol"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.3168\/jds.2015-9975"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2013.2"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1472-765X.2010.02937.x"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1038\/srep40864"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2015.00036"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.00296"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.00720-15"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2016.62"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.3168\/jds.2017-12746"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.03864-13"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1111\/asj.12429"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01043-13"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2011.02543.x"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0063157"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0151220"},{"key":"e_1_3_3_25_2","unstructured":"Linz AA. 2016. OTUtable: north temperate lakes\u2014microbial observatory 16S time series data and functions. R package version 1.0.0. https:\/\/CRAN.R-project.org\/package=OTUtable."},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4757-2191-1_34"},{"key":"e_1_3_3_27_2","first-page":"1016","volume-title":"The Firmicutes","author":"Rainey F","year":"2009","unstructured":"Rainey F. 2009. Family VIII. Ruminococcaceae fam. nov., p 1016\u20131043. In Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer K-H, Whitman W (ed), Bergey's manual of systematic bacteriology, 2nd ed, vol 3. The Firmicutes. Springer Verlag, New York, NY.","edition":"2"},{"key":"e_1_3_3_28_2","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1007\/978-3-642-38954-2_131","volume-title":"The prokaryotes","author":"Rosenberg E","year":"2014","unstructured":"Rosenberg E. 2014. The Family Prevotellaceae, p 825\u2013827. In Rosenberg E, DeLong E, Lory S, Stackenbrandt E, Thomson F (ed), The prokaryotes, 4th ed. Springer Verlag, Berlin, Germany.","edition":"4"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetmic.2013.02.013"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1038\/srep16116"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40064-015-1201-6"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.2527\/jas.2015-9839"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0129174"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2016.03.006"},{"key":"e_1_3_3_35_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.01553"},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1099\/00207713-50-3-979"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1099\/00207713-52-4-1263"},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijs.0.008169-0"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00248-010-9692-8"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF01308340"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.3945\/jn.114.208595"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.00429"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.1128\/am.16.5.680-688.1968"},{"key":"e_1_3_3_44_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2012.00340"},{"key":"e_1_3_3_45_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0116465"},{"key":"e_1_3_3_46_2","doi-asserted-by":"publisher","DOI":"10.1017\/S0954422410000247"},{"key":"e_1_3_3_47_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00253-006-0802-y"},{"key":"e_1_3_3_48_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks808"},{"key":"e_1_3_3_49_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01541-09"},{"key":"e_1_3_3_50_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm864"},{"key":"e_1_3_3_51_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr381"},{"key":"e_1_3_3_52_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.03006-05"},{"key":"e_1_3_3_53_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-21706-2"},{"key":"e_1_3_3_54_2","volume-title":"Statistical methods","author":"Snedecor GW","year":"1989","unstructured":"Snedecor GW, Cochran WG. 1989. Statistical methods, 8th ed. Iowa State University Press, Ames, IA.","edition":"8"},{"key":"e_1_3_3_55_2","doi-asserted-by":"publisher","DOI":"10.1002\/bimj.200810425"},{"key":"e_1_3_3_56_2","volume-title":"Numerical ecology: developments in environmental modelling","author":"Legendre P","year":"1998","unstructured":"Legendre P, Legendre L. 1998. Numerical ecology: developments in environmental modelling, 2nd English ed. Elsevier, Amsterdam, Netherlands.","edition":"2"},{"key":"e_1_3_3_57_2","unstructured":"Chen H. 2015. VennDiagram: generate high-resolution Venn and Euler plots. R package version 1.6.18. https:\/\/CRAN.R-project.org\/package=VennDiagram."},{"key":"e_1_3_3_58_2","unstructured":"Oksanen J Guillaume Blanchet F Friendly M Kindt R Legendre P McGlinn D Minchin PR O'Hara RB Simpson GL Solymos P Stevens MHM Szoecs E Wagner H. 2016. vegan: community ecology package. R package version 2.3-4. https:\/\/CRAN.R-project.org\/package=vegan."},{"key":"e_1_3_3_59_2","doi-asserted-by":"crossref","unstructured":"Wickham H. 2009. ggplot2: elegant graphics for data analysis. Springer-Verlag New York NY. https:\/\/cran.r-project.org\/package=ggplot2.","DOI":"10.1007\/978-0-387-98141-3"},{"key":"e_1_3_3_60_2","doi-asserted-by":"publisher","DOI":"10.3168\/jds.S0022-0302(77)83975-1"}],"container-title":["Applied and Environmental Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/AEM.02675-17","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/AEM.02675-17","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T23:11:54Z","timestamp":1693609914000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/AEM.02675-17"}},"subtitle":[],"editor":[{"given":"Christopher A.","family":"Elkins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,5]]},"references-count":59,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2018,5]]}},"alternative-id":["10.1128\/AEM.02675-17"],"URL":"https:\/\/doi.org\/10.1128\/aem.02675-17","relation":{},"ISSN":["0099-2240","1098-5336"],"issn-type":[{"value":"0099-2240","type":"print"},{"value":"1098-5336","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,5]]},"assertion":[{"value":"2017-11-29","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2018-02-12","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2018-04-16","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e02675-17"}}