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ORIGINAL RESEARCH article

Front. Microbiol.
Sec. Microbial Symbioses
Volume 15 - 2024 | doi: 10.3389/fmicb.2024.1482925

Multi-omics analysis reveals interactions between host and microbes in Bama miniature pigs during weaning

Provisionally accepted
Wen Ma Wen Ma 1Li Yin Li Yin 2Ying Hu Ying Hu 1Xu Liu Xu Liu 1ZhengHong Guo ZhengHong Guo 3Bingyang Zhong Bingyang Zhong 2Haofeng Qiu Haofeng Qiu 2Jing Li Jing Li 1*
  • 1 Sichuan University, Chengdu, China
  • 2 Chengdu Dossy Experimental Animal Co., Ltd, Chengdu, China
  • 3 Dossy Biological Engineering (Chongqing) Co., Ltd, Chongqing, China

The final, formatted version of the article will be published soon.

    There are complex interactions between host and gut microbes during weaning, many of the mechanisms are not yet fully understood. To reveal these interactions in Bama miniature piglets that were weaned 30 days after birth, we collected samples on days 25 and 36 for metabolomics, transcriptomics, and microgenomics analysis. The average daily weight gain of piglets during weaning was only 58.1% and 40.6% of that during 0-25 days and 36-60 days. Metabolomic results identified 61 significantly different metabolites (SDMs), of which, the most significantly increased and decreased SDMs after weaning were ectoine and taurocholate, respectively, indicating the occurrence of inflammation. Metagenomic analysis identified 23 significantly different microbes before and after weaning. Bacteria related to decreasing intestinal inflammation, such as Megasphaera, Alistipes and Bifidobacterium, were enriched before weaning. While bacteria related to infection such as Chlamydia, Clostridium, Clostridioides, and Blautia were enriched after weaning.The carbohydrate enzymes CBM91, CBM13, GH51_1, and GH94 increase after weaning, which may contribute to the digestion of complex plant fibers. Furthermore, we found the composition of antibiotic resistance genes (ARGs) changed during weaning. Transcriptomic analysis identified 147 significantly differentially expressed genes (DEGs). The upregulated genes after weaning were enriched in immune response categories, whereas downregulated genes were enriched in eprotein degradation. Combining multi-omics data, we identified significant positive correlations between gene MZB1, genera Alistipes and metabolite stachydrine, which involve anti-inflammatory functions.The reduced abundance of bacteria Dialister after weaning had strong correlations with the decreased 2-AGPE metabolite and the downregulated expression of RHBDF1 gene. Altogether, the multi-omics study reflects dietary changes and gut inflammation during weaning, highlighting complex interactions between gut microbes, host genes and metabolites.

    Keywords: Weaning1, Multi-omics2, Interactions3, gut microbes4, metabolites5, gene expression5

    Received: 19 Aug 2024; Accepted: 27 Nov 2024.

    Copyright: © 2024 Ma, Yin, Hu, Liu, Guo, Zhong, Qiu and Li. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Jing Li, Sichuan University, Chengdu, China

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