Wu Lin, Liu Yuxin, Chen Congying, Gao Jun
National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, China.
Front Microbiol. 2025 Jun 25;16:1578236. doi: 10.3389/fmicb.2025.1578236. eCollection 2025.
Fecal samples have often been used as a proxy for studying the gut microbiota. However, the fecal microbiota does not fully reflect the gut microbiota composition. To elucidate the biogeographical characteristics and interaction networks of porcine gut microbiota, we systematically determined the compositions and co-abundance networks of gut microbiota from small to large intestine using 2,955 microbial samples from ileum, cecum, and feces of F6 (715) and F7 (687) pigs which were slaughtered at the age of 240 days from an experimentally designed heterogeneous pig population by crossing eight divergent breeds using 16S rRNA gene sequencing. The gut microbial composition showed significant spatial heterogeneity. The diversity of the gut microbiota progressively increased along the intestinal tract. Significantly spatial heterogeneity was also observed in the co-abundance networks. The numbers of OTUs showing co-abundance correlations with other OTUs were increased from ileum to cecum and feces. We found that the stronger the co-abundance correlation, the higher the gut location specificity of the co-abundance relationships. Only 644 (0.2%) co-abundance relationships among OTUs existed in all three gut locations. had the highest number of stable co-abundance relationships, followed by Bacteroidales, , , and Lachnospiraceae. Topological analysis found that the co-abundance network of OTUs in the ileum showed random network characteristics, while the co-abundance networks of OTUs in the cecum and feces showed the scale-free network characteristics in both pig populations. Compared with the co-abundance networks in the cecum and feces, the networks in the ileum had fewer nodes, but more edges, indicating that the ileum microbiota was a microbial ecosystem with a smaller number of microbial species, but closer interactions. However, the pairwise co-abundance correlations between OTUs were more independent in the cecum. The co-abundance network in the ileum had the lowest stability, but the highest vulnerability, while the co-abundance network in the cecum exhibited the highest stability, but low vulnerability. Finally, we characterized the gut location-specific microbial co-abundance relationships. Characterizing the different phylogenetic structures of gut microbiota in different intestinal biogeographic niches would help to explore the spatial heterogeneity of microbial physiological functions and to develop the strategy regulating gut microbiota targeting to specific gut locations.
粪便样本常被用作研究肠道微生物群的替代物。然而，粪便微生物群并不能完全反映肠道微生物群的组成。为了阐明猪肠道微生物群的生物地理特征和相互作用网络，我们使用来自F6（715头）和F7（687头）猪的回肠、盲肠和粪便的2955个微生物样本，通过16S rRNA基因测序，系统地确定了从十二指肠到大肠的肠道微生物群的组成和共丰度网络。这些猪是通过杂交八个不同品种从一个实验设计的异质猪群中挑选出来的，在240日龄时屠宰。肠道微生物组成显示出显著的空间异质性。肠道微生物群的多样性沿肠道逐渐增加。在共丰度网络中也观察到显著的空间异质性。与其他OTU显示共丰度相关性的OTU数量从回肠到盲肠和粪便逐渐增加。我们发现，共丰度相关性越强，共丰度关系的肠道位置特异性越高。在所有三个肠道位置中，OTU之间只有644（0.2%）个共丰度关系。 具有最高数量的稳定共丰度关系，其次是拟杆菌目、 、 和毛螺菌科。拓扑分析发现，回肠中OTU的共丰度网络显示出随机网络特征，而盲肠和粪便中OTU的共丰度网络在两个猪群中均显示出无标度网络特征。与盲肠和粪便中的共丰度网络相比，回肠中的网络节点较少，但边较多，这表明回肠微生物群是一个微生物物种数量较少但相互作用更密切的微生物生态系统。然而，OTU之间的成对共丰度相关性在盲肠中更独立。回肠中的共丰度网络稳定性最低，但脆弱性最高，而盲肠中的共丰度网络稳定性最高，但脆弱性较低。最后，我们对肠道位置特异性微生物共丰度关系进行了表征。表征不同肠道生物地理生态位中肠道微生物群的不同系统发育结构，将有助于探索微生物生理功能的空间异质性，并制定针对特定肠道位置调节肠道微生物群的策略。
