{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T10:28:30Z","timestamp":1781778510310,"version":"3.54.5"},"reference-count":48,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2020,7,24]],"date-time":"2020-07-24T00:00:00Z","timestamp":1595548800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Early microbial colonization in the gut impacts animal performance and lifelong health. However, research on gut microbial colonization and development in young ruminants, especially after weaning, is currently limited. In this study, next-generation sequencing technology was performed to investigate the temporal dynamic changes of the microbial community in the jejunum and colon of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days (d) of age. As age increased, significant increases in microbial diversity, including the number of Observed OTUs and the Shannon Index, were observed in both the jejunum and colon. Regarding beta diversity, significant shifts in community membership and structure from d1 to d84 were observed based on both Bray\u2013Curtis and Jaccard distances. With increasing age, dominant genera in the jejunum shifted from Lactobacillus to unclassified Ruminococcaceae, unclassified Lachnospiraceae and unclassified Clostridiales through starter supplementation, whereas colonic dominant genera changed from Lactobacillus and Butyricicoccus, within d1\u2013d28, to unclassified Ruminococcaceae, unclassified Clostridiales and Campylobacter after solid diet supplementation. The linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed bacterial features that are stage-specific in the jejunum and colon, respectively. In the jejunum and colon, a significantly distinct structure and membership of the microbiota was observed across all ages. The growth stage-associated microbiota in each gut compartment was also identified as a marker for biogeography. Our data indicate the temporal and spatial differences of the gut microbiota in goats are important for their performance and health. Early microbial colonization can influence microbial composition in later life (e.g., post-weaning phase). This study provides insights that the temporal dynamics of gut microbiota development from newborn to post-weaning can aid in developing feeding strategies to improve goat health and production.<\/jats:p>","DOI":"10.3390\/microorganisms8081111","type":"journal-article","created":{"date-parts":[[2020,7,24]],"date-time":"2020-07-24T09:06:09Z","timestamp":1595581569000},"page":"1111","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":43,"title":["Longitudinal Investigation of the Gut Microbiota in Goat Kids from Birth to Postweaning"],"prefix":"10.3390","volume":"8","author":[{"given":"Yimin","family":"Zhuang","sequence":"first","affiliation":[{"name":"Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9341-9932","authenticated-orcid":false,"given":"Jianmin","family":"Chai","sequence":"additional","affiliation":[{"name":"Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China"},{"name":"Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai","family":"Cui","sequence":"additional","affiliation":[{"name":"Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanliang","family":"Bi","sequence":"additional","affiliation":[{"name":"Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8037-1471","authenticated-orcid":false,"given":"Qiyu","family":"Diao","sequence":"additional","affiliation":[{"name":"Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenqin","family":"Huang","sequence":"additional","affiliation":[{"name":"Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hunter","family":"Usdrowski","sequence":"additional","affiliation":[{"name":"Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6272-7553","authenticated-orcid":false,"given":"Naifeng","family":"Zhang","sequence":"additional","affiliation":[{"name":"Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,7,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2333","DOI":"10.1111\/1462-2920.14614","article-title":"Feeding modes shape the acquisition and structure of the initial gut microbiota in newborn lambs","volume":"21","author":"Bi","year":"2019","journal-title":"Environ. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1186\/s40168-017-0296-0","article-title":"(Dis)Trust your gut: The gut microbiome in age-related inflammation, health, and disease","volume":"5","author":"Buford","year":"2017","journal-title":"Microbiome"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1186\/s40168-019-0721-7","article-title":"Longitudinal investigation of the swine gut microbiome from birth to market reveals stage and growth performance associated bacteria","volume":"7","author":"Wang","year":"2019","journal-title":"Microbiome"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"skaa093","DOI":"10.1093\/jas\/skaa093","article-title":"Influences of starter NDF level on growth performance and rumen development in lambs fed isocaloric and isonitrogenous diets","volume":"98","author":"Xie","year":"2020","journal-title":"J. Anim. Sci."},{"key":"ref_5","first-page":"429","article-title":"Starter feeding supplementation alters colonic mucosal bacterial communities and modulates mucosal immune homeostasis in newborn lambs","volume":"8","author":"Liu","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Lv, X., Chai, J., Diao, Q., Huang, W., Zhuang, Y., and Zhang, N. (2019). The signature microbiota drive rumen function shifts in goat kids introduced to solid diet regimes. Microorganisms, 7.","DOI":"10.1101\/737775"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2125","DOI":"10.3389\/fmicb.2019.02125","article-title":"Characterization and comparison of microbiota in the gastrointestinal tracts of the goat (Capra hircus) during preweaning development","volume":"10","author":"Li","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1186\/s13059-019-1786-0","article-title":"Regulation of rumen development in neonatal ruminants through microbial metagenomes and host transcriptomes","volume":"20","author":"Malmuthuge","year":"2019","journal-title":"Genome Biol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"e02675-17","DOI":"10.1128\/AEM.02675-17","article-title":"Bacterial community dynamics across the gastrointestinal tracts of dairy calves during Preweaning development","volume":"84","author":"Dias","year":"2018","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.1038\/ismej.2013.2","article-title":"Exploring the bovine rumen bacterial community from birth to adulthood","volume":"7","author":"Mizrahi","year":"2013","journal-title":"ISME J."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1364","DOI":"10.3389\/fmicb.2016.01364","article-title":"Composition of Ileal Bacterial Community in grazing goats varies across non-rumination, transition and rumination stages of life","volume":"7","author":"Jiao","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"5112","DOI":"10.1128\/AEM.01043-13","article-title":"Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform","volume":"79","author":"Kozich","year":"2013","journal-title":"J. Appl. Environ. Microbiol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"D141","DOI":"10.1093\/nar\/gkn879","article-title":"The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis","volume":"37","author":"Cole","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"R60","DOI":"10.1186\/gb-2011-12-6-r60","article-title":"Metagenomic biomarker discovery and explanation","volume":"12","author":"Segata","year":"2011","journal-title":"Genome Biol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"S3","DOI":"10.1186\/1471-2164-14-S1-S3","article-title":"Expanding the boundaries of local similarity analysis","volume":"14","author":"Durno","year":"2013","journal-title":"BMC Genom."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"100","DOI":"10.5713\/ajas.16.0166","article-title":"Characterization of the microbial communities along the gastrointestinal tract of sheep by 454 pyrosequencing analysis","volume":"30","author":"Wang","year":"2017","journal-title":"Asian-Australas J. Anim. Sci."},{"key":"ref_17","doi-asserted-by":"crossref","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":"ref_18","doi-asserted-by":"crossref","unstructured":"Devine, A.A., Gonzalez, A., Speck, K.E., Knight, R., Helmrath, M., Lund, P.K., and Azcarate-Peril, M.A. (2013). Impact of ileocecal resection and concomitant antibiotics on the microbiome of the murine jejunum and colon. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0073140"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.anifeedsci.2011.12.022","article-title":"Nutrition and pathology of weaner pigs: Nutritional strategies to support barrier function in the gastrointestinal tract","volume":"173","author":"Kim","year":"2012","journal-title":"Anim. Feed Sci. Technol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"574","DOI":"10.3389\/fmicb.2018.00574","article-title":"Alfalfa intervention alters rumen microbial community development in Hu lambs during early life","volume":"9","author":"Yang","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"19","DOI":"10.3389\/fvets.2014.00019","article-title":"Characterization of the vaginal microbiota of ewes and cows reveals a unique microbiota with low levels of Lactobacilli and near-neutral pH","volume":"1","author":"Swartz","year":"2014","journal-title":"Front. Vet. Sci."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"8044","DOI":"10.3168\/jds.2015-9607","article-title":"Heat-treated colostrum feeding promotes beneficial bacteria colonization in the small intestine of neonatal calves","volume":"98","author":"Malmuthuge","year":"2015","journal-title":"J. Dairy Sci."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"3099","DOI":"10.3168\/jds.2017-13397","article-title":"Effect of delaying colostrum feeding on passive transfer and intestinal bacterial colonization in neonatal male Holstein calves","volume":"101","author":"Fischer","year":"2018","journal-title":"J. Dairy Sci."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1696","DOI":"10.3168\/jds.2008-1586","article-title":"Effect of colostrum immunoglobulin concentration on immunity in Majorera goat kids","volume":"92","author":"Castro","year":"2009","journal-title":"J. Dairy Sci."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1111\/pai.12232","article-title":"The first thousand days\u2014Intestinal microbiology of early life: Establishing a symbiosis","volume":"25","author":"Wopereis","year":"2015","journal-title":"Pediatr. Allergy Immunol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.chom.2018.06.005","article-title":"Mother-to-infant microbial transmission from different body sites shapes the developing infant gut Microbiome","volume":"24","author":"Ferretti","year":"2018","journal-title":"Cell Host Microbe"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1688","DOI":"10.3389\/fmicb.2017.01688","article-title":"The maturing development of gut microbiota in commercial piglets during the weaning transition","volume":"8","author":"Chen","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"e00036-17","DOI":"10.1128\/MMBR.00036-17","article-title":"The first microbial colonizers of the human gut: Composition, activities, and health implications of the infant gut microbiota","volume":"81","author":"Milani","year":"2017","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Finamore, A., Roselli, M., Imbinto, A., Seeboth, J., Oswald, I.P., and Mengheri, E. (2014). Lactobacillus amylovorus inhibits the TLR4 inflammatory signaling triggered by enterotoxigenic Escherichia coli via modulation of the negative regulators and involvement of TLR2 in intestinal Caco-2 cells and pig explants. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0094891"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1016\/j.jff.2012.09.001","article-title":"Lactobacillus fermentum and Lactobacillus amylovorus as probiotics alter body adiposity and gut microflora in healthy persons","volume":"5","author":"Omar","year":"2013","journal-title":"J. Funct. Foods"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"757","DOI":"10.3389\/fmicb.2018.00757","article-title":"Role of Lactobacillus reuteri in human health and diseases","volume":"9","author":"Mu","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"336","DOI":"10.3389\/fmicb.2020.00336","article-title":"Competition between butyrate fermenters and chain-elongating bacteria limits the efficiency of medium-chain carboxylate production","volume":"11","author":"Liu","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.smallrumres.2018.09.008","article-title":"Major and minor toxins of Clostridium perfringens isolated from healthy and diseased sheep","volume":"168","author":"Fahimeh","year":"2018","journal-title":"Small Rumiant Res."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1017\/S0950268811000859","article-title":"Molecular-based detection of non-culturable and emerging campylobacteria in patients presenting with gastroenteritis","volume":"140","author":"Bullman","year":"2012","journal-title":"Epidemiol. Infect."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1128\/AEM.01731-08","article-title":"Differential effects of Bifidobacterium pseudolongum strain Patronus and metronidazole in the rat gut","volume":"75","author":"Vasquez","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1016\/j.chom.2018.05.008","article-title":"The impact of dietary transition metals on host-bacterial interactions","volume":"23","author":"Lopez","year":"2018","journal-title":"Cell Host Microbe"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"236","DOI":"10.4161\/gmic.23998","article-title":"Some are more equal than others","volume":"4","author":"Ze","year":"2013","journal-title":"Gut Microbes"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Lugli, G.A., Duranti, S., Milani, C., Mancabelli, L., Turroni, F., Sinderen, D.V., and Ventura, M. (2019). Uncovering Bifidobacteria via targeted sequencing of the mammalian gut microbiota. Microorganisms, 7.","DOI":"10.3390\/microorganisms7110535"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"25909","DOI":"10.1073\/pnas.1916224116","article-title":"Division of labor in honey bee gut microbiota for plant polysaccharide digestion","volume":"116","author":"Zheng","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"627","DOI":"10.3390\/d5030627","article-title":"Untangling the genetic basis of fibrolytic specialization by Lachnospiraceae and Ruminococcaceae in diverse gut communities","volume":"5","author":"Biddle","year":"2013","journal-title":"Diversity"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1778","DOI":"10.1093\/jas\/sky109","article-title":"Microbiome profiling of commercial pigs from farrow to finish","volume":"96","author":"Youmans","year":"2018","journal-title":"J. Anim. Sci."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1016\/j.chom.2019.08.011","article-title":"Regional diversity of the gastrointestinal microbiome","volume":"26","author":"Leone","year":"2019","journal-title":"Cell Host Microbe"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Gerritsen, J., Hornung, B., Ritari, J., Paulin, L., Rijkers, G.T., Schaap, P.J., De Vos, W.M., and Smidt, H.J.B. (2019). A comparative and functional genomics analysis of the genus Romboutsia provides insight into adaptation to an intestinal lifestyle. BioRxiv.","DOI":"10.1101\/845511"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1038\/mi.2016.42","article-title":"Gut commensal Bacteroides acidifaciens prevents obesity and improves insulin sensitivity in mice","volume":"10","author":"Yang","year":"2017","journal-title":"Mucosal Immunol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1745","DOI":"10.1136\/gutjnl-2012-303611","article-title":"Butyricicoccus pullicaecorum in inflammatory bowel disease","volume":"62","author":"Eeckhaut","year":"2013","journal-title":"Gut"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1038\/s41587-019-0183-2","article-title":"Spatial metagenomic characterization of microbial biogeography in the gut","volume":"37","author":"Sheth","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1038\/ismej.2011.131","article-title":"Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows","volume":"6","author":"Goldfarb","year":"2012","journal-title":"ISME J."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/j.chom.2015.01.015","article-title":"Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque","volume":"17","author":"Yasuda","year":"2015","journal-title":"Cell Host Microbe"}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/8\/8\/1111\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T09:51:24Z","timestamp":1760176284000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/8\/8\/1111"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,7,24]]},"references-count":48,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2020,8]]}},"alternative-id":["microorganisms8081111"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms8081111","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,7,24]]}}}