Dai Qinlong, Ding Jingjing, Cui Xinyuan, Zhu Yudong, Chen Hua, Zhu Lifeng
Sichuan Liziping National Natural Reserve Shimian China.
Jiangsu Academy of Forest Nanjing China.
Ecol Evol. 2023 Feb 22;13(2):e9829. doi: 10.1002/ece3.9829. eCollection 2023 Feb.
Numerous gut microbial studies have focused on bacteria. However, archaea, viruses, fungi, protists, and nematodes are also regular residents of the gut ecosystem. Little is known about the composition and potential interactions among these six kingdoms in the same samples. Here, we unraveled the complex connection among them using approximately 123 gut metagenomes from 42 mammalian species (including carnivores, omnivores, and herbivores). We observed high variation in bacterial and fungal families and relatively low variation in archaea, viruses, protists, and nematodes. We found that some fungi in the mammalian intestine might come from environmental sources (e.g., soil and dietary plants), and some might be native to the intestine (e.g., the occurrence of ). The and families (archaea and protozoa, respectively) were predominant in these metagenomes, whereas and were the two most common nematodes, and and the two most common virus families in these mammalian gut metagenomes. Interestingly, most of the pairwise co-occurrence patterns were significantly positive among these six kingdoms, and significantly negative networks mainly occurred between fungi and prokaryotes (both bacteria and archaea). Our study revealed some inconvenient characteristics in the mammalian gut microorganism ecosystem: (1) the community formed by members of the analyzed kingdoms reflects the life history of the host and the potential threat posed by pathogenic protists and nematodes in mammals; and (2) the networks suggest the existence of predicted mutualism among members of these six kingdoms and of the predicted competition, mainly among fungi and other kingdoms.
众多肠道微生物研究都聚焦于细菌。然而，古菌、病毒、真菌、原生生物和线虫也是肠道生态系统的常住居民。对于同一样本中这六个生物界的组成及潜在相互作用，我们了解甚少。在此，我们利用来自42种哺乳动物（包括食肉动物、杂食动物和食草动物）的约123个肠道宏基因组，揭示了它们之间的复杂联系。我们观察到细菌和真菌家族的变化很大，而古菌、病毒、原生生物和线虫的变化相对较小。我们发现哺乳动物肠道中的一些真菌可能来自环境源（如土壤和食用植物），有些可能是肠道原生的（如 的出现）。在这些宏基因组中， 家族（分别为古菌和原生动物）占主导地位，而 和 是两种最常见的线虫， 和 是这些哺乳动物肠道宏基因组中两种最常见的病毒家族。有趣的是，在这六个生物界中，大多数成对共现模式呈显著正相关，而显著的负相关网络主要出现在真菌与原核生物（细菌和古菌）之间。我们的研究揭示了哺乳动物肠道微生物生态系统中的一些特点：（1）由所分析生物界成员组成的群落反映了宿主的生活史以及哺乳动物中致病原生生物和线虫带来的潜在威胁；（2）这些网络表明这六个生物界成员之间存在预测的互利共生关系，以及预测的竞争关系，主要存在于真菌与其他生物界之间。
