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Temporal changes in the fecal bacterial community in Holstein dairy calves from birth through the transition to a solid diet

The development of a robust microbiome is critical to the health of dairy calves, but relatively little is known about the progression of the microbiome through the weaning transition. In this study, fecal samples were obtained from ten female Holstein calves at 6 timepoints between 2–13 weeks of ag...

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Autores principales: Hennessy, Meagan L., Indugu, Nagaraju, Vecchiarelli, Bonnie, Bender, Joseph, Pappalardo, Christa, Leibstein, Miranda, Toth, John, Katepalli, Ananya, Garapati, Satvik, Pitta, Dipti
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7478546/
https://www.ncbi.nlm.nih.gov/pubmed/32898158
http://dx.doi.org/10.1371/journal.pone.0238882
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author Hennessy, Meagan L.
Indugu, Nagaraju
Vecchiarelli, Bonnie
Bender, Joseph
Pappalardo, Christa
Leibstein, Miranda
Toth, John
Katepalli, Ananya
Garapati, Satvik
Pitta, Dipti
author_facet Hennessy, Meagan L.
Indugu, Nagaraju
Vecchiarelli, Bonnie
Bender, Joseph
Pappalardo, Christa
Leibstein, Miranda
Toth, John
Katepalli, Ananya
Garapati, Satvik
Pitta, Dipti
author_sort Hennessy, Meagan L.
collection PubMed
description The development of a robust microbiome is critical to the health of dairy calves, but relatively little is known about the progression of the microbiome through the weaning transition. In this study, fecal samples were obtained from ten female Holstein calves at 6 timepoints between 2–13 weeks of age. Calves were fed acidified milk until weaning at 8 weeks old and had access to starter grain throughout the study. Fecal samples were extracted for genomic DNA, PCR-amplified for the V1-V2 region of the 16S rRNA bacterial gene, sequenced on the Illumina MiSeq platform, and analyzed using the QIIME2 pipeline. Bacterial richness, estimated by number of observed species, and bacterial diversity, estimated by Shannon diversity index, both differed significantly between timepoints and both increased over time (P <0.05), with the largest increases occurring during weaning. Weighted and unweighted UniFrac analysis showed significant differences (P <0.05) between bacterial communities across timepoints; betadisper analysis revealed that the microbiomes of individual calves became more similar with time. Throughout the study, Firmicutes was the dominant phylum, followed by Bacteroidetes. Thirteen bacterial genera were found to be significantly influenced by time, including Faecalibacterium, Clostridium, unclassified S24-7, Collinsella, Sharpea, and Treponema. Unclassified Ruminococcaceae was the most prevalent genus at timepoints 1, 3, 5, and 6, but different amplicon sequence variants were detected at each timepoint suggesting the presence of different species of Ruminococcaceae at different times. Bacteroides was the most prevalent genus at timepoint 2, and Prevotella was most prevalent at timepoint 4. Our results indicate that there is considerable variation in the calf microbiome pre-weaning, but the microbial community stabilizes and becomes similar to the adult microbiome at weaning. Further studies to describe the phylogeny and functionality of core microbiota through the weaning transition are needed to improve health and reduce diarrhea in the neonatal period.
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spelling pubmed-74785462020-09-18 Temporal changes in the fecal bacterial community in Holstein dairy calves from birth through the transition to a solid diet Hennessy, Meagan L. Indugu, Nagaraju Vecchiarelli, Bonnie Bender, Joseph Pappalardo, Christa Leibstein, Miranda Toth, John Katepalli, Ananya Garapati, Satvik Pitta, Dipti PLoS One Research Article The development of a robust microbiome is critical to the health of dairy calves, but relatively little is known about the progression of the microbiome through the weaning transition. In this study, fecal samples were obtained from ten female Holstein calves at 6 timepoints between 2–13 weeks of age. Calves were fed acidified milk until weaning at 8 weeks old and had access to starter grain throughout the study. Fecal samples were extracted for genomic DNA, PCR-amplified for the V1-V2 region of the 16S rRNA bacterial gene, sequenced on the Illumina MiSeq platform, and analyzed using the QIIME2 pipeline. Bacterial richness, estimated by number of observed species, and bacterial diversity, estimated by Shannon diversity index, both differed significantly between timepoints and both increased over time (P <0.05), with the largest increases occurring during weaning. Weighted and unweighted UniFrac analysis showed significant differences (P <0.05) between bacterial communities across timepoints; betadisper analysis revealed that the microbiomes of individual calves became more similar with time. Throughout the study, Firmicutes was the dominant phylum, followed by Bacteroidetes. Thirteen bacterial genera were found to be significantly influenced by time, including Faecalibacterium, Clostridium, unclassified S24-7, Collinsella, Sharpea, and Treponema. Unclassified Ruminococcaceae was the most prevalent genus at timepoints 1, 3, 5, and 6, but different amplicon sequence variants were detected at each timepoint suggesting the presence of different species of Ruminococcaceae at different times. Bacteroides was the most prevalent genus at timepoint 2, and Prevotella was most prevalent at timepoint 4. Our results indicate that there is considerable variation in the calf microbiome pre-weaning, but the microbial community stabilizes and becomes similar to the adult microbiome at weaning. Further studies to describe the phylogeny and functionality of core microbiota through the weaning transition are needed to improve health and reduce diarrhea in the neonatal period. Public Library of Science 2020-09-08 /pmc/articles/PMC7478546/ /pubmed/32898158 http://dx.doi.org/10.1371/journal.pone.0238882 Text en © 2020 Hennessy et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Hennessy, Meagan L.
Indugu, Nagaraju
Vecchiarelli, Bonnie
Bender, Joseph
Pappalardo, Christa
Leibstein, Miranda
Toth, John
Katepalli, Ananya
Garapati, Satvik
Pitta, Dipti
Temporal changes in the fecal bacterial community in Holstein dairy calves from birth through the transition to a solid diet
title Temporal changes in the fecal bacterial community in Holstein dairy calves from birth through the transition to a solid diet
title_full Temporal changes in the fecal bacterial community in Holstein dairy calves from birth through the transition to a solid diet
title_fullStr Temporal changes in the fecal bacterial community in Holstein dairy calves from birth through the transition to a solid diet
title_full_unstemmed Temporal changes in the fecal bacterial community in Holstein dairy calves from birth through the transition to a solid diet
title_short Temporal changes in the fecal bacterial community in Holstein dairy calves from birth through the transition to a solid diet
title_sort temporal changes in the fecal bacterial community in holstein dairy calves from birth through the transition to a solid diet
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7478546/
https://www.ncbi.nlm.nih.gov/pubmed/32898158
http://dx.doi.org/10.1371/journal.pone.0238882
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