Dynamic changes in fecal bacterial microbiota of dairy cattle across the production line

Lei Zhao; Xunde Li; Edward R Atwill; Sharif S Aly; Deniece R Williams; Zhengchang Su

doi:10.1186/s12866-022-02549-3

Dynamic changes in fecal bacterial microbiota of dairy cattle across the production line

BMC Microbiol. 2022 May 14;22(1):132. doi: 10.1186/s12866-022-02549-3.

Authors

Lei Zhao¹, Xunde Li^{2

3}, Edward R Atwill⁴, Sharif S Aly^{4

5}, Deniece R Williams^{4

5}, Zhengchang Su⁶

Affiliations

¹ Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, Charlotte, North Carolina, USA.
² Western Institute for Food Safety and Security, University of California, Davis, California, USA. xdli@ucdavis.edu.
³ Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA. xdli@ucdavis.edu.
⁴ Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA.
⁵ Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, CA, USA.
⁶ Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, Charlotte, North Carolina, USA. zcsu@uncc.edu.

Abstract

Background: Microbiota play important roles in the gastrointestinal tract (GIT) of dairy cattle as the communities are responsible for host health, growth, and production performance. However, a systematic characterization and comparison of microbial communities in the GIT of cattle housed in different management units on a modern dairy farm are still lacking. We used 16S rRNA gene sequencing to evaluate the fecal bacterial communities of 90 dairy cattle housed in 12 distinctly defined management units on a modern dairy farm.

Results: We found that cattle from management units 5, 6, 8, and 9 had similar bacterial communities while the other units showed varying levels of differences. Hutch calves had a dramatically different bacterial community than adult cattle, with at least 10 genera exclusively detected in their samples but not in non-neonatal cattle. Moreover, we compared fecal bacteria of cattle from every pair of the management units and detailed the number and relative abundance of the significantly differential genera. Lastly, we identified 181 pairs of strongly correlated taxa in the community, showing possible synergistic or antagonistic relationships.

Conclusions: This study assesses the fecal microbiota of cattle from 12 distinctly defined management units along the production line on a California dairy farm. The results highlight the similarities and differences of fecal microbiota between cattle from each pair of the management units. Especially, the data indicate that the newborn calves host very different gut bacterial communities than non-neonatal cattle, while non-neonatal cattle adopt one of the two distinct types of gut bacterial communities with subtle differences among the management units. The gut microbial communities of dairy cattle change dramatically in bacterial abundances at different taxonomic levels along the production line. The findings provide a reference for research and practice in modern dairy farm management.

Keywords: 16S rRNA; Bioinformatics; Dairy cattle; Gastrointestinal; Microbiome; Production line.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

Animals
Bacteria / genetics
Cattle
Feces / microbiology
Gastrointestinal Tract / microbiology
Microbiota*
RNA, Ribosomal, 16S / genetics

Substances

RNA, Ribosomal, 16S

Grants and funding

R01 GM106013/GM/NIGMS NIH HHS/United States