Zhang Mingyue, Zhou Yanan, Cui Xinyuan, Zhu Lifeng
College of Life Sciences, Nanjing Normal University, Nanjing 210098, China.
Microorganisms. 2024 Mar 31;12(4):713. doi: 10.3390/microorganisms12040713.
Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host's physiological development and immune health. A phage is a virus that directly infects bacteria, and phages' close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem. Here, we utilized 99 published metagenomic datasets from 38 mammalian species to investigate the relationship (diversity and composition) and potential interactions between gut bacterial and phage communities and the impact of diet and phylogeny on these communities. Our results highlight the co-evolutionary potential of bacterial-phage interactions within the mammalian gut. We observed a higher alpha diversity in gut bacteria than in phages and identified positive correlations between bacterial and phage compositions. Furthermore, our study revealed the significant influence of diet and phylogeny on mammalian gut bacterial and phage communities. We discovered that the impact of dietary factors on these communities was more pronounced than that of phylogenetic factors at the order level. In contrast, phylogenetic characteristics had a more substantial influence at the family level. The similar omnivorous dietary preference and closer phylogenetic relationship (family Ursidae) may contribute to the similarity of gut bacterial and phage communities between captive giant panda populations (GPCD and GPYA) and omnivorous animals (OC; including Sun bear, brown bear, and Asian black bear). This study employed co-occurrence microbial network analysis to reveal the potential interaction patterns between bacteria and phages. Compared to other mammalian groups (carnivores, herbivores, and omnivores), the gut bacterial and phage communities of bamboo-eating species (giant pandas and red pandas) exhibited a higher level of interaction. Additionally, keystone species and modular analysis showed the potential role of phages in driving and maintaining the interaction patterns between bacteria and phages in captive giant pandas. In sum, gaining a comprehensive understanding of the interaction between the gut microbiota and phages in mammals is of great significance, which is of great value in promoting healthy and sustainable mammals and may provide valuable insights into the conservation of wildlife populations, especially endangered animal species.
细菌和噬菌体是肠道微生物群中最丰富的两种生物实体，饮食和宿主系统发育是影响肠道微生物群的两个最关键因素。稳定的肠道细菌群落对宿主的生理发育和免疫健康起着关键作用。噬菌体是一种直接感染细菌的病毒，噬菌体与细菌的密切关联和相互作用对于维持肠道细菌群落和整个微生物生态系统的稳定性至关重要。在此，我们利用来自38种哺乳动物的99个已发表的宏基因组数据集，研究肠道细菌和噬菌体群落之间的关系（多样性和组成）以及潜在相互作用，以及饮食和系统发育对这些群落的影响。我们的结果突出了哺乳动物肠道内细菌 - 噬菌体相互作用的共同进化潜力。我们观察到肠道细菌的α多样性高于噬菌体，并确定了细菌和噬菌体组成之间的正相关关系。此外，我们的研究揭示了饮食和系统发育对哺乳动物肠道细菌和噬菌体群落的重大影响。我们发现，在目水平上，饮食因素对这些群落的影响比系统发育因素更明显。相比之下，系统发育特征在科水平上有更大的影响。圈养大熊猫种群（GPCD和GPYA）与杂食动物（OC；包括马来熊、棕熊和亚洲黑熊）之间相似的杂食性饮食偏好和更密切的系统发育关系（熊科）可能导致它们肠道细菌和噬菌体群落的相似性。本研究采用共现微生物网络分析来揭示细菌和噬菌体之间的潜在相互作用模式。与其他哺乳动物群体（食肉动物、食草动物和杂食动物）相比，食竹物种（大熊猫和小熊猫）的肠道细菌和噬菌体群落表现出更高水平的相互作用。此外，关键物种和模块分析显示了噬菌体在驱动和维持圈养大熊猫中细菌和噬菌体相互作用模式方面的潜在作用。总之，全面了解哺乳动物肠道微生物群与噬菌体之间的相互作用具有重要意义，这对于促进哺乳动物的健康和可持续发展具有重要价值，并且可能为野生动物种群，特别是濒危动物物种的保护提供有价值的见解。
