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. 2018 Mar 27;6(1):62.
doi: 10.1186/s40168-018-0447-y.

Assessment of microbiome changes after rumen transfaunation: implications on improving feed efficiency in beef cattle

Mi Zhou  1 , Yong-Jia Peng  2 , Yanhong Chen  1 , Christen M Klinger  1 , Masahito Oba  1 , Jian-Xin Liu  2 , Le Luo Guan  3
Affiliations

Assessment of microbiome changes after rumen transfaunation: implications on improving feed efficiency in beef cattle

Mi Zhou et al. Microbiome. .

Abstract

Background: Understanding the host impact on its symbiotic microbiota is important in redirecting the rumen microbiota and thus improving animal performance. The current study aimed to understand how rumen microbiota were altered and re-established after being emptied and receiving content from donor, thus to understand the impact of such process on rumen microbial fermentation and to explore the microbial phylotypes with higher manipulation potentials.

Results: Individual animal had strong effect on the re-establishment of the bacterial community according to the observed profiles detected by both fingerprinting and pyrosequencing. Most of the bacterial profile recovery patterns and extents at genus level varied among steers; and each identified bacterial genus responded to transfaunation differently within each host. Coriobacteriaceae, Coprococcus, and Lactobacillus were found to be the most responsive and tunable genera by exchanging rumen content. Besides, the association of 18 bacterial phylotypes with host fermentation parameters suggest that these phylotypes should also be considered as the regulating targets in improving host feed efficiency. In addition, the archaeal community had different re-establishment patterns for each host as determined by fingerprint profiling: it was altered after receiving non-native microbiome in some animals, while it resumed its original status after the adaptation period in the other ones.

Conclusions: The highly individualized microbial re-establishment process suggested the importance of considering host genetics, microbial functional genomics, and host fermentation/performance assessment when developing effective and selective microbial manipulation methods for improving animal feed efficiency.

Keywords: Adaptation; Beef cattle; Rumen microbiota; Transfaunation.

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Conflict of interest statement

Ethics approval

All of the animals used for the current study were obtained from Roy Berg Kinsella Research Ranch, University of Alberta, and were cared for following the guidelines of the Canadian Council of Animal Care (ISBN: 978-0-919087-50-7) (2009, Ottawa, ON, Canada). The animals were transferred to Metabolic Units at Edmonton Research Station, University of Alberta, and the animal study was proved by Animal Care Use Committee Livestock, University of Alberta (Protocol No. AUP00000116).

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Microbial community dynamics in control animals. a Bacterial phyla identified along the experiment. b PCoA plot of the bacterial profiles from 454 sequencing
Fig. 2
Fig. 2
PCoA plot of bacterial profiles of D0 from 454 pyrosequencing
Fig. 3
Fig. 3
Recovery patterns of the bacterial communities. a Clustering of bacterial profiles at D0, D1, D7, and D28 with different classifications. b Bacterial community alteration along experiment at phylum level. c Bacterial diversity alteration along experiment at genus level
Fig. 4
Fig. 4
Changes in the observed OTUs along the re-establishment process
Fig. 5
Fig. 5
Common and distinctive bacterial genera among the samples by Venn’s diagram. a Genera distribution among the four exchange types. b Genera distribution among individuals belonging to the same transfaunation type
See this image and copyright information in PMC

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