School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Lab, The University of Hong Kong, Hong Kong, China.
Mol Ecol. 2020 Dec;29(24):5019-5034. doi: 10.1111/mec.15699. Epub 2020 Nov 9.
Microorganisms in the gastrointestinal tract of animals play vital roles in food digestion, homeostasis and immune response regulation. Globally, there are 33,700 fish species, representing almost half of all vertebrate diversity and a wide range of physiologies, ecologies and life histories. To investigate gut microbiomes with high coverage, we performed 16S rRNA gene amplicon sequencing with 115 samples of 20 common marine fish species. The fish gut microbiome is a remarkably simple community with low microbial diversity (a maximum of 300 amplicon sequence variants only) and has up to 70% of unknown species in some fish species. The gut microbial community structure was significantly shaped by the combined influence of host-associated factors, including the fish taxon (p < .001, R = 0.16, ω = 0.04), feeding habit (p < .001, R = 0.06, ω = 0.02) and trophic level (p < .01, R = 0.04, ω = 0.01), although the influence was subtle with a small effect size. The core gut microbiomes of different feeding habits were also previously discovered in animal-associated and corresponding habitat samples. Certain energy metabolism pathways were enriched in herbivore/omnivore and zooplanktivore/zoobenthivore fishes, whereas lipid metabolism and glycan metabolism were enriched in zoobenthivore/piscivore fishes. Moreover, substantial taxonomic variability was found between the gut microbiomes of fish and animals, indicated by their low degree of shared microbiota. The data and observations reported herein pave the way for further investigations on the co-evolution of fish gut microbiomes and their hosts, the physiological functions of gut microorganisms and the development of probiotics for improving the nutrition and health of aquaculture fish species.
动物胃肠道中的微生物在食物消化、体内平衡和免疫反应调节中发挥着重要作用。全球有 33700 种鱼类，占所有脊椎动物多样性的近一半，具有广泛的生理学、生态学和生活史。为了进行高覆盖率的肠道微生物组研究，我们对 20 种常见海洋鱼类的 115 个样本进行了 16S rRNA 基因扩增子测序。鱼类肠道微生物组是一个非常简单的群落，微生物多样性低（最多只有 300 个扩增子序列变异），在一些鱼类中，高达 70%的物种是未知的。宿主相关因素的综合影响显著塑造了肠道微生物群落结构，包括鱼类分类群（p<.001，R=0.16，ω=0.04）、摄食习性（p<.001，R=0.06，ω=0.02）和营养级（p<.01，R=0.04，ω=0.01），尽管影响微弱，效应大小较小。不同摄食习性的核心肠道微生物组也在动物相关和相应生境样本中被发现。某些能量代谢途径在草食性/杂食性和浮游动物/底栖动物鱼类中富集，而脂质代谢和聚糖代谢在底栖动物/肉食性鱼类中富集。此外，鱼类和动物的肠道微生物组之间存在大量的分类学变异性，这表明它们的共享微生物组数量较少。本文报告的数据和观察结果为进一步研究鱼类肠道微生物组与其宿主的共同进化、肠道微生物的生理功能以及开发益生菌以改善水产养殖鱼类的营养和健康状况铺平了道路。
