Sparagon Wesley J, Gentry Emily C, Minich Jeremiah J, Vollbrecht Lisa, Laurens Lieve M L, Allen Eric E, Sims Neil A, Dorrestein Pieter C, Kelly Linda Wegley, Nelson Craig E
Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, University of Hawai'i at Mānoa, 1950 East West Road, Honolulu, HI, 96822, USA.
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Anim Microbiome. 2022 May 23;4(1):33. doi: 10.1186/s42523-022-00182-z.
Gut microorganisms aid in the digestion of food by providing exogenous metabolic pathways to break down organic compounds. An integration of longitudinal microbial and chemical data is necessary to illuminate how gut microorganisms supplement the energetic and nutritional requirements of animals. Although mammalian gut systems are well-studied in this capacity, the role of microbes in the breakdown and utilization of recalcitrant marine macroalgae in herbivorous fish is relatively understudied and an emerging priority for bioproduct extraction. Here we use a comprehensive survey of the marine herbivorous fish gut microbial ecosystem via parallel 16S rRNA gene amplicon profiling (microbiota) and untargeted tandem mass spectrometry (metabolomes) to demonstrate consistent transitions among 8 gut subsections across five fish of the genus of Kyphosus.
Integration of microbial phylogenetic and chemical diversity data reveals that microbial communities and metabolomes covaried and differentiated continuously from stomach to hindgut, with the midgut containing multiple distinct and previously uncharacterized microenvironments and a distinct hindgut community dominated by obligate anaerobes. This differentiation was driven primarily by anaerobic gut endosymbionts of the classes Bacteroidia and Clostridia changing in concert with bile acids, small peptides, and phospholipids: bile acid deconjugation associated with early midgut microbiota, small peptide production associated with midgut microbiota, and phospholipid production associated with hindgut microbiota.
The combination of microbial and untargeted metabolomic data at high spatial resolution provides a new view of the diverse fish gut microenvironment and serves as a foundation to understand functional partitioning of microbial activities that contribute to the digestion of complex macroalgae in herbivorous marine fish.
肠道微生物通过提供外源代谢途径来分解有机化合物，从而辅助食物消化。整合纵向的微生物和化学数据对于阐明肠道微生物如何补充动物的能量和营养需求至关重要。尽管哺乳动物的肠道系统在这方面已得到充分研究，但微生物在草食性鱼类中对顽固海洋大型藻类的分解和利用作用相对研究较少，且是生物产品提取领域新出现的重点研究方向。在此，我们通过平行的16S rRNA基因扩增子分析（微生物群）和非靶向串联质谱分析（代谢组），对海洋草食性鱼类肠道微生物生态系统进行了全面调查，以证明驼背鱼属五种鱼类的8个肠道亚段之间存在一致的转变。
微生物系统发育和化学多样性数据的整合表明，微生物群落和代谢组从胃到后肠持续协变并分化，中肠包含多个不同且以前未被表征的微环境，后肠群落则由专性厌氧菌主导。这种分化主要由拟杆菌纲和梭菌纲的厌氧肠道内共生菌与胆汁酸、小肽和磷脂协同变化驱动：胆汁酸去结合与中肠早期微生物群相关，小肽产生与中肠微生物群相关，磷脂产生与后肠微生物群相关。
高空间分辨率下微生物和非靶向代谢组学数据的结合，为多样的鱼类肠道微环境提供了新视角，并为理解有助于草食性海洋鱼类消化复杂大型藻类的微生物活动功能分区奠定了基础。
