title: Environmental filtering decreases with fish development for the assembly of gut microbiota.
abstract: Gut microbiota typically occupy habitats with definable limits/borders that are comparable to oceanic islands. The gut therefore can be regarded as an 'island' for the assembly of microbial communities within the 'sea' of surrounding environments. This study aims to reveal the ecological mechanisms that govern microbiota in the fish gut 'island' ecosystem. Taxonomic compositions, phylogenetic diversity, and community turnover across host development were analyzed via the high-throughput sequencing of 16S rRNA gene amplicons. The results indicate that the Shannon diversity of gut microbiota in the three examined freshwater fish species all significantly decreased with host development, and the dominant bacterial taxa also changed significantly during host development. Null model and phylogenetic-based mean nearest taxon distance (MNTD) analyses suggest that host gut environmental filtering led to the assembly of microbial communities in the fish gut 'island'. However, the phylogenetic clustering of local communities and deterministic processes that governed community turnover became less distinct as the fish developed. The observed mechanisms that shaped fish gut microbiota seemed to be mainly shaped by the gut environment and by some other selective changes accompanying the host development process. These findings greatly enhance our understanding of stage-specific community assembly patterns in the fish gut ecosystem.
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
authors.forename: Qingyun
authors.initials: Q
authors.lastname: Yan
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.|Qilu Normal University, Jinan, 250013, China.
authors.forename: Jinjin
authors.initials: J
authors.lastname: Li
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
authors.forename: Yuhe
authors.initials: Y
authors.lastname: Yu
authors.affiliation: Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.|State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
authors.forename: Jianjun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
authors.forename: Zhili
authors.initials: Z
authors.lastname: He
authors.affiliation: Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
authors.forename: Joy D
authors.initials: JD
authors.lastname: Van Nostrand
authors.affiliation: Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
authors.forename: Megan L
authors.initials: ML
authors.lastname: Kempher
authors.affiliation: Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
authors.forename: Liyou
authors.initials: L
authors.lastname: Wu
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
authors.forename: Yaping
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
authors.forename: Lanjie
authors.initials: L
authors.lastname: Liao
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.|Graduate University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Xinghao
authors.initials: X
authors.lastname: Li
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
authors.forename: Shu
authors.initials: S
authors.lastname: Wu
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.|State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou, 510070, China.
authors.forename: Jiajia
authors.initials: J
authors.lastname: Ni
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.|Graduate University of Chinese Academy of Sciences, Beijing, 100049, China.|Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
authors.forename: Chun
authors.initials: C
authors.lastname: Wang
authors.affiliation: Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.|State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.|Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
mesh_terms: D000818:Animals; D017753:Ecosystem; D005399:Fishes / Q000382:microbiology*; D005618:Fresh Water; D000069196:Gastrointestinal Microbiome; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S