Archaea: An under-estimated kingdom in livestock animals

Yunjuan Peng; Ting Xie; Zhuosui Wu; Wenxiao Zheng; Tao Zhang; Samantha Howe; Jianmin Chai; Feilong Deng; Ying Li; Jiangchao Zhao

doi:10.3389/fvets.2022.973508

Archaea: An under-estimated kingdom in livestock animals

Front Vet Sci. 2022 Jul 28:9:973508. doi: 10.3389/fvets.2022.973508. eCollection 2022.

Authors

Yunjuan Peng^{1

2}, Ting Xie^{1

2}, Zhuosui Wu^{1

2}, Wenxiao Zheng^{1

2}, Tao Zhang^{1

2}, Samantha Howe³, Jianmin Chai^{1

2

3}, Feilong Deng^{1

2

3}, Ying Li^{1

2}, Jiangchao Zhao³

Affiliations

¹ Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China.
² School of Life Science and Engineering, Foshan University, Foshan, China.
³ Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, United States.

Abstract

Archaea are considered an essential group of gut microorganisms in both humans and animals. However, they have been neglected in previous studies, especially those involving non-ruminants. In this study, we re-analyzed published metagenomic and metatranscriptomic data sequenced from matched samples to explore the composition and the expression activity of gut archaea in ruminants (cattle and sheep) and monogastric animals (pig and chicken). Our results showed that the alpha and beta diversity of each host species, especially cattle and chickens, calculated from metagenomic and metatranscriptomic data were significantly different, suggesting that metatranscriptomic data better represent the functional status of archaea. We detected that the relative abundance of 17 (cattle), 7 (sheep), 20 (pig), and 2 (chicken) archaeal species were identified in the top 100 archaeal taxa when analyzing the metagenomic datasets, and these species were classified as the "active archaeal species" for each host species by comparison with corresponding metatranscriptomic data. For example, The expressive abundance in metatranscriptomic dataset of Methanosphaera cuniculi and Methanosphaera stadtmanae were 30- and 27-fold higher than that in metagenomic abundance, indicating their potentially important function in the pig gut. Here we aim to show the potential importance of archaea in the livestock digestive tract and encourage future research in this area, especially on the gut archaea of monogastric animals.

Keywords: archaea; chicken; metagenome; metatranscriptome; monogastric animals; pig; ruminant.