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Characterizing Core Microbiota and Regulatory Functions of the Pig Gut Microbiome.

ISME Journal(2024)SCI 1区

National Key Laboratory of Agricultural Microbiology

Cited 4|Views66
Abstract
Domestic pigs (Sus scrofa) are the leading terrestrial animals used for meat production. The gut microbiota significantly affect host nutrition, metabolism, and immunity. Hence, characterization of the gut microbial structure and function will improve our understanding of gut microbial resources and the mechanisms underlying host-microbe interactions. Here, we investigated the gut microbiomes of seven pig breeds using metagenomics and 16S rRNA gene amplicon sequencing. We established an expanded gut microbial reference catalog comprising 17 020 160 genes and identified 4910 metagenome-assembled genomes. We also analyzed the gut resistome to provide an overview of the profiles of the antimicrobial resistance genes in pigs. By analyzing the relative abundances of microbes, we identified three core-predominant gut microbes (Phascolarctobacterium succinatutens, Prevotella copri, and Oscillibacter valericigenes) in pigs used in this study. Oral administration of the three core-predominant gut microbes significantly increased the organ indexes (including the heart, spleen, and thymus), but decreased the gastrointestinal lengths in germ-free mice. The three core microbes significantly enhanced intestinal epithelial barrier function and altered the intestinal mucosal morphology, as was evident from the increase in crypt depths in the duodenum and ileum. Furthermore, the three core microbes significantly affected several metabolic pathways (such as "steroid hormone biosynthesis," "primary bile acid biosynthesis," "phenylalanine, tyrosine and tryptophan biosynthesis," and "phenylalanine metabolism") in germ-free mice. These findings provide a panoramic view of the pig gut microbiome and insights into the functional contributions of the core-predominant gut microbes to the host.
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gut microbiome,pig,core gut microbes,gene catalog,germ-free mice
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要点】:通过对七种猪品种的肠道微生物组进行研究,建立了具有17,020,160个基因的肠道微生物组参考目录,并鉴定了4,910个微生物组装基因组。实验发现,在本研究中所使用的猪中,存在三种核心主导的肠道微生物(Phascolarctobacterium succinatutens, Prevotella copri, and Oscillibacter valericigenes)。这三种核心微生物的口服给药显著增加了无菌(GF)小鼠的器官指数(包括心脏、脾脏和胸腺),但减少了胃肠道的长度。此外,这三种核心微生物显著增强了肠道上皮屏障功能,并改变了肠道粘膜形态学,表现为十二指肠和回肠的小肠深度增加。此外,这三种核心微生物显著影响了GF小鼠的几个代谢途径(如“类固醇激素生物合成”、“主要胆酸生物合成”、“苯丙氨酸、酪氨酸和色氨酸生物合成”和“苯丙氨酸代谢”)。这些发现提供了猪肠道微生物组的全景视图,并揭示了核心主导微生物对宿主的功能贡献。

方法】:使用了16S rRNA基因测序和宏基因组学技术对七种猪品种的肠道微生物组进行分析,建立了肠道微生物组参考目录,并鉴定了微生物组装基因组。

实验】:口服给药了三种核心主导的肠道微生物,并观察到它们显著增强了无菌小鼠的器官指数,但减少了胃肠道的长度。此外,这三种微生物还显著改变了肠道上皮屏障功能和肠道粘膜形态学,并影响了多个代谢途径。