Composition and evolutionary characterization of the gut microbiota in pigs
-
Published:2023-11-20
Issue:
Volume:
Page:
-
ISSN:1618-1905
-
Container-title:International Microbiology
-
language:en
-
Short-container-title:Int Microbiol
Author:
Zhang Shuhong,Zhang Huan,Zhang Cheng,Wang Guan,Shi Chuanxing,Li Zhiqiang,Gao Fengyi,Cui Yanyan,Li Ming,Yang Guangli
Abstract
AbstractThe intestinal microbiota plays significant role in the physiology and functioning of host organisms. However, there is limited knowledge of the composition and evolution of microbiota-host relationships from wild ancestors to modern domesticated species. In this study, the 16S rRNA gene V3–V4 in the intestinal contents of different pig breeds was analyzed and was compared using high-throughput sequencing. This identified 18 323 amplicon sequence variants, of which the Firmicutes and Actinobacteria phyla and Bifidobacterium and Allobaculum genera were most prevalent in wild pigs (WP). In contrast, Proteobacteria and Firmicutes predominated in Chinese Shanxi Black pigs (CSB), while Firmicutes were the most prevalent phylum in Large White pigs (LW) and Iberian pigs (IB), followed by Bacteroidetes in IB and Proteobacteria in LW. At the genus level, Shigella and Lactobacillus were most prevalent in CSB and LW, while Actinobacillus and Sarcina predominated in IB. Differential gene expression together with phylogenetic and functional analyses indicated significant differences in the relative abundance of microbial taxa between different pig breeds. Although many microbial taxa were common to both wild and domestic pigs, significant diversification was observed in bacterial genes that potentially influence host phenotypic traits. Overall, these findings suggested that both the composition and functions of the microbiota were closely associated with domestication and the evolutionary changes in the host. The members of the microbial communities were vertically transmitted in pigs, with evidence of co-evolution of both the hosts and their intestinal microbial communities. These results enhance our understanding and appreciation of the complex interactions between intestinal microbes and hosts and highlight the importance of applying this knowledge in agricultural and microbiological research.
Funder
the Foundation of Industry University Research Cooperation Project of He’nan Science and Technology Committee of China the Key R&D and Promotion Program in Henan Province of China
Publisher
Springer Science and Business Media LLC
Subject
Microbiology (medical),Microbiology
Reference88 articles.
1. Asnicar F, Weingart G, Tickle TL, Huttenhower C, Segata N (2015) Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ 3:e1029 2. Baldwin J, Collins B, Wolf PG, Martinez K, Shen W, Chuang CC, Zhong W, Cooney P, Cockrell C, Chang E, Gaskins HR, McIntosh MK (2016) Table grape consumption reduces adiposity and markers of hepatic lipogenesis and alters gut microbiota in butter fat-fed mice. J Nutr Biochem 27:123–135 3. Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, Huttley GA, Caporaso JG (2018) Optimizing taxonomic classification of marker-gene amplicon sequences with Qiime 2´s q2-feature-classifier plugin. Microbiome 6:90 4. Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet C, Al-Ghalith GA, Caporaso JG (2018) QIIME 2: reproducible, interactive, scalable, and extensible microbiome data science. Peer J Preprints 6:e27295v2 5. Bonder MJ, Kurilshikov A, Tigchelaar EF, Mujagic Z, Imhann F, Vila AV, Deelen P, Vatanen T, Schirmer M, Smeekens SP, Zhernakova DV, Jankipersadsing SA, Jaeger M, Oosting M, Cenit MC, Masclee AAM, Swertz MA, Li Y, Kumar V, Joosten L, Harmsen H, Weersma RK, Franke L, Hofker MH, Xavier RJ, Jonkers D, Netea MG, Wijmenga C, Fu J, Zhernakova A (2016) The effect of host genetics on the gut microbiome. Nat Genet 48(11):1407–1412
|
|