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Wang C, Li Z, Huang X, Xu X, Xu X, Zhang K, Zhou Y, Bai J, Liu Z, Jiang Y, Tang Y, Deng X, Li S, Hu E, Peng W, Xiong L, Xiao Q, Yang Y, Qin Q, Liu S. Multi-Omic Analysis Reveals the Potential Anti-Disease Mechanism of Disease-Resistant Grass Carp. Int J Mol Sci 2025; 26:3619. [PMID: 40332099 PMCID: PMC12027461 DOI: 10.3390/ijms26083619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2025] [Revised: 03/31/2025] [Accepted: 04/04/2025] [Indexed: 05/08/2025] Open
Abstract
The gut-liver axis is essential in animal disease and health. However, the role of the gut-liver axis in the anti-disease mechanism of disease-resistant grass carp (DRGC) derived from the backcross of female gynogenetic grass carp (GGC) and male grass carp (GC) remains unclear. This study analyzed the changes in gut histopathology, fecal intestinal microflora and metabolites, and liver transcriptome between GC and DRGC. Histological analysis revealed significant differences in the gut between DRGC and GC. In addition, microbial community analyses indicated that hybridization induced gut microbiome variation by significantly increasing the proportion of Firmicutes and Bacteroidota in DRGC. Metabolomic data revealed that the hybridization-induced metabolic change was probably characterized by being related to taurocholate and sphinganine in DRGC. Transcriptome analysis suggested that the enhanced disease resistance of DRGC was primarily attributed to immune-related genes (SHMT2, GOT1, ACACA, DLAT, GPIA, TALDO1, G6PD, and FASN). Spearman's correlation analysis revealed a significant association between the gut microbiota, immune-related genes, and metabolites. Collectively, the gut-liver axis, through the interconnected microbiome-metabolite-gene pathway, may play a crucial role in the mechanism of greater disease resistance in DRGC, offering valuable insights for advancing the grass carp cultivation industry.
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Affiliation(s)
- Chongqing Wang
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
- Nansha-South China Agricultural University Fishery Research Institute, Guangzhou 511457, China
| | - Zeyang Li
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
| | - Xu Huang
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
| | - Xidan Xu
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
| | - Xiaowei Xu
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
| | - Kun Zhang
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
| | - Yue Zhou
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
| | - Jinhai Bai
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
| | - Zhengkun Liu
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
| | - Yuchen Jiang
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
| | - Yan Tang
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
| | - Xinyi Deng
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
| | - Siyang Li
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
| | - Enkui Hu
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
| | - Wanjing Peng
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
| | - Ling Xiong
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
| | - Qian Xiao
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
| | - Yuhan Yang
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
| | - Qinbo Qin
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
- Nansha-South China Agricultural University Fishery Research Institute, Guangzhou 511457, China
| | - Shaojun Liu
- Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education, Ministry, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (C.W.); (Z.L.); (X.H.); (X.X.); (X.X.); (K.Z.); (Y.Z.); (J.B.); (Z.L.); (Y.J.); (Y.T.); (X.D.); (S.L.); (E.H.); (W.P.); (L.X.); (Q.X.); (Y.Y.); (S.L.)
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Mathisen AJH, Gómez de la Torre Canny S, Gundersen MS, Østensen MA, Olsen Y, Vadstein O, Bakke I. Community assembly of gut microbiomes in yolk sac fry of Atlantic salmon: host genetics, environmental microbiomes, and ecological processes. FEMS Microbiol Ecol 2025; 101:fiaf007. [PMID: 39824653 PMCID: PMC11797051 DOI: 10.1093/femsec/fiaf007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 10/28/2024] [Accepted: 01/16/2025] [Indexed: 01/20/2025] Open
Abstract
In this study, we investigated the influence of host genetics and environmental microbiomes on the early gut microbiome of Atlantic salmon. We aimed at rearing the fish in either r- or K-selected environments, where the r-selected environment would be expected to be dominated by fast-growing opportunistic bacteria and thus represent more detrimental microbial environment than the K-selected water. Eggs from both wild and aquaculture strains of Atlantic salmon were hatched under germ-free conditions. One week after hatching, rearing flasks were inoculated with either r- or K-selected water communities. Three weeks after hatching, no effect of host strain on the gut microbiomes were observed. r-selection was found to take place in the rearing water of all flasks, including in the flasks added K-selected water. Still, the water microbiomes differed significantly between the flasks that had been added r- and K-selected water (Add-r and Add-K flasks, respectively). Lower alpha diversity and higher abundances of Pseudomonas were observed for the Add-K flasks, indicating a potential unfavorable microbial environment. Selection in the host structured the gut microbiomes, but an extensive interindividual variation was explained by stochastic processes in community assembly. The gut microbiomes also differed significantly between the Add-r and Add-K flasks. In Add-K flasks, they had higher similarities to the rearing water microbiomes, and the assembly of gut communities was less influenced by stochastic processes. The fish in Add-K flasks had lower growth rates than in Add-r flasks, probably as a result of negative host-microbe interactions. These findings highlight the importance of, but also the challenges related to, managing the microbial environment when cultivating fish.
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Affiliation(s)
- Amalie Johanne Horn Mathisen
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Sol Gómez de la Torre Canny
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway
- Skretting Aquaculture Innovation (AI), 4016 Stavanger, Norway
| | - Madeleine S Gundersen
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Mari-Ann Østensen
- Department of Biology, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Yngvar Olsen
- Department of Biology, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Olav Vadstein
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Ingrid Bakke
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway
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Li X, Han B, Liu D, Wang S, Wang L, Pei Q, Zhang Z, Zhao J, Huang B, Zhang F, Zhao K, Tian D. Whole-genome resequencing to investigate the genetic diversity and mechanisms of plateau adaptation in Tibetan sheep. J Anim Sci Biotechnol 2024; 15:164. [PMID: 39639384 PMCID: PMC11622566 DOI: 10.1186/s40104-024-01125-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Accepted: 11/06/2024] [Indexed: 12/07/2024] Open
Abstract
INTRODUCTION Tibetan sheep, economically important animals on the Qinghai-Tibet Plateau, have diversified into numerous local breeds with unique characteristics through prolonged environmental adaptation and selective breeding. However, most current research focuses on one or two breeds, and lacks a comprehensive representation of the genetic diversity across multiple Tibetan sheep breeds. This study aims to fill this gap by investigating the genetic structure, diversity and high-altitude adaptation of 6 Tibetan sheep breeds using whole-genome resequencing data. RESULTS Six Tibetan sheep breeds were investigated in this study, and whole-genome resequencing data were used to investigate their genetic structure and population diversity. The results showed that the 6 Tibetan sheep breeds exhibited distinct separation in the phylogenetic tree; however, the levels of differentiation among the breeds were minimal, with extensive gene flow observed. Population structure analysis broadly categorized the 6 breeds into 3 distinct ecological types: plateau-type, valley-type and Euler-type. Analysis of unique single-nucleotide polymorphisms (SNPs) and selective sweeps between Argali and Tibetan sheep revealed that Tibetan sheep domestication was associated primarily with sensory and signal transduction, nutrient absorption and metabolism, and growth and reproductive characteristics. Finally, comprehensive analysis of selective sweep and transcriptome data suggested that Tibetan sheep breeds inhabiting different altitudes on the Qinghai-Tibet Plateau adapt by enhancing cardiopulmonary function, regulating body fluid balance through renal reabsorption, and modifying nutrient digestion and absorption pathways. CONCLUSION In this study, we investigated the genetic diversity and population structure of 6 Tibetan sheep breeds in Qinghai Province, China. Additionally, we analyzed the domestication traits and investigated the unique adaptation mechanisms residing varying altitudes in the plateau region of Tibetan sheep. This study provides valuable insights into the evolutionary processes of Tibetan sheep in extreme environments. These findings will also contribute to the preservation of genetic diversity and offer a foundation for Tibetan sheep diversity preservation and plateau animal environmental adaptation mechanisms.
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Affiliation(s)
- Xue Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, China
| | - Buying Han
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dehui Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Song Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Wang
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, Qinghai, 812300, China
| | - Quanbang Pei
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, Qinghai, 812300, China
| | - Zian Zhang
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, Qinghai, 812300, China
| | - Jincai Zhao
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, Qinghai, 812300, China
| | - Bin Huang
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, Qinghai, 812300, China
| | - Fuqiang Zhang
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, Qinghai, 812300, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, China
| | - Dehong Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, China.
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Zhao H, Fang DA, Wang Y, Zhang M, Wang A, Xu Y, Xu D. A high-quality chromosome-level genome assembly of the topmouth culter (Culter alburnus Basilewsky, 1855). Sci Data 2024; 11:910. [PMID: 39174585 PMCID: PMC11341867 DOI: 10.1038/s41597-024-03657-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 07/18/2024] [Indexed: 08/24/2024] Open
Abstract
Culter alburnus is extensively distributed in various rivers and lakes across China. As a widely adaptive fish species, it has significant economic values and special ecological roles. To meet research demands and provide better genomic resources, in this research, a chromosome-level genome assembly was constructed using HiFi long-reads and Hi-C sequencing data. Compared with the published versions, our genome assembly is of higher quality with only 31 gaps and closer to its true structure and sequence. The genome size was 1.052 Gb, with a contig N50 of 32.92 Mb and a scaffold N50 of 43.09 Mb. 55 contigs were anchored to 24 chromosomes on the basis of Hi-C data. A total of 598.23 Mb of repetitive sequences were annotated and 28,228 protein-coding genes were predicted. Additionally, BUSCO assessment indicated assembly and annotation scores of 98.3% and 99.2%, respectively. This high-quality genome will provide scientific support for excavating the species characteristics of C. alburnus and exploring its molecular mechanisms in response to environmental changes and stress.
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Affiliation(s)
- Huali Zhao
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Di-An Fang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China.
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Yuan Wang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Minying Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Anqi Wang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Yuanfeng Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Dongpo Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
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Maritan E, Quagliariello A, Frago E, Patarnello T, Martino ME. The role of animal hosts in shaping gut microbiome variation. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230071. [PMID: 38497257 PMCID: PMC10945410 DOI: 10.1098/rstb.2023.0071] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/10/2023] [Indexed: 03/19/2024] Open
Abstract
Millions of years of co-evolution between animals and their associated microbial communities have shaped and diversified the nature of their relationship. Studies continue to reveal new layers of complexity in host-microbe interactions, the fate of which depends on a variety of different factors, ranging from neutral processes and environmental factors to local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics and mathematical modelling to disentangle the individual contribution of ecological factors to microbiome evolution. Within this framework, host factors are known to be among the dominant drivers of microbiome composition in different animal species. However, the extent to which they shape microbiome assembly and evolution remains unclear. In this review, we summarize our understanding of how host factors drive microbial communities and how these dynamics are conserved and vary across taxa. We conclude by outlining key avenues for research and highlight the need for implementation of and key modifications to existing theory to fully capture the dynamics of host-associated microbiomes. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- Elisa Maritan
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Andrea Quagliariello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Enric Frago
- CIRAD, UMR CBGP, INRAE, Institut Agro, IRD, Université Montpellier, 34398 Montpellier, France
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Maria Elena Martino
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
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Liang Y, Wang Z, Gao N, Qi X, Zeng J, Cui K, Lu W, Bai S. Variations and Interseasonal Changes in the Gut Microbial Communities of Seven Wild Fish Species in a Natural Lake with Limited Water Exchange during the Closed Fishing Season. Microorganisms 2024; 12:800. [PMID: 38674744 PMCID: PMC11052518 DOI: 10.3390/microorganisms12040800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
The gut microbiota of fish is crucial for their growth, development, nutrient uptake, physiological balance, and disease resistance. Yet our knowledge of these microbial communities in wild fish populations in their natural ecosystems is insufficient. This study systematically examined the gut microbial communities of seven wild fish species in Chaohu Lake, a fishing-restricted area with minimal water turnover, across four seasons. We found significant variations in gut microbial community structures among species. Additionally, we observed significant seasonal and regional variations in the gut microbial communities. The Chaohu Lake fish gut microbial communities were predominantly composed of the phyla Firmicutes, Proteobacteria(Gamma), Proteobacteria(Alpha), Actinobacteriota, and Cyanobacteria. At the genus level, Aeromonas, Cetobacterium, Clostridium sensu stricto 1, Romboutsia, and Pseudomonas emerged as the most prevalent. A co-occurrence network analysis revealed that C. auratus, C. carpio, and C. brachygnathus possessed more complex and robust gut microbial networks than H. molitrix, C. alburnus, C. ectenes taihuensis, and A. nobilis. Certain microbial groups, such as Clostridium sensu stricto 1, Romboutsia, and Pseudomonas, were both dominant and keystone in the fish gut microbial network. Our study offers a new approach for studying the wild fish gut microbiota in natural, controlled environments. It offers an in-depth understanding of gut microbial communities in wild fish living in stable, limited water exchange natural environments.
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Affiliation(s)
- Yangyang Liang
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China; (Y.L.); (N.G.); (K.C.); (W.L.)
| | - Zijia Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Z.W.); (X.Q.); (J.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Gao
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China; (Y.L.); (N.G.); (K.C.); (W.L.)
| | - Xiaoxue Qi
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Z.W.); (X.Q.); (J.Z.)
| | - Juntao Zeng
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Z.W.); (X.Q.); (J.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Cui
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China; (Y.L.); (N.G.); (K.C.); (W.L.)
| | - Wenxuan Lu
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China; (Y.L.); (N.G.); (K.C.); (W.L.)
| | - Shijie Bai
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Z.W.); (X.Q.); (J.Z.)
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Dong Y, Li Y, Ge M, Takatsu T, Wang Z, Zhang X, Ding D, Xu Q. Distinct gut microbial communities and functional predictions in divergent ophiuroid species: host differentiation, ecological niches, and adaptation to cold-water habitats. Microbiol Spectr 2023; 11:e0207323. [PMID: 37889056 PMCID: PMC10715168 DOI: 10.1128/spectrum.02073-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Gastrointestinal microorganisms are critical to the survival and adaptation of hosts, and there are few studies on the differences and functions of gastrointestinal microbes in widely distributed species. This study investigated the gut microbes of two ophiuroid species (Ophiura sarsii and its subspecies O. sarsii vadicola) in cold-water habitats of the Northern Pacific Ocean. The results showed that a combination of host and environmental factors shapes the intestinal microbiota of ophiuroids. There was a high similarity in microbial communities between the two groups living in different regions, which may be related to their similar ecological niches. These microorganisms played a vital role in the ecological success of ophiuroids as the foundation for their adaptation to cold-water environments. This study revealed the complex relationship between hosts and their gut microbes, providing insights into the role they play in the adaptation and survival of marine species.
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Affiliation(s)
- Yue Dong
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Yixuan Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Meiling Ge
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Tetsuya Takatsu
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Zongling Wang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Xuelei Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Dewen Ding
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Qinzeng Xu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
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8
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Porretta D, Canestrelli D. The ecological importance of hybridization. Trends Ecol Evol 2023; 38:1097-1108. [PMID: 37620217 DOI: 10.1016/j.tree.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023]
Abstract
Hybridization as an evolutionary process has been studied in depth over the past few decades. Research has focused on its role in shaping reproductive barriers, its adaptive value, and its genomic consequences. In contrast, our knowledge of ecological dimensions of hybridization is still in its infancy, despite hybridization being an inherently ecological interaction. Using examples from various organisms, we show that hybridization can affect and be affected by non-reproductive interactions, including predation, competition, parasitism, mutualism, commensalism, and organism-environment interactions, with significant implications for community structure and ecosystem functioning. However, since these dimensions of hybridization have mostly been revealed from studies designed to decipher other evolutionary processes, we argue that much of the eco-evolutionary importance of hybridization is yet to be discovered.
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Affiliation(s)
- Daniele Porretta
- Department of Environmental Biology, Sapienza University of Rome, Italy.
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9
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Lokesh J, Delaygues M, Defaix R, Le Bechec M, Pigot T, Dupont-Nivet M, Kerneis T, Labbé L, Goardon L, Terrier F, Panserat S, Ricaud K. Interaction between genetics and inulin affects host metabolism in rainbow trout fed a sustainable all plant-based diet. Br J Nutr 2023; 130:1105-1120. [PMID: 36690577 DOI: 10.1017/s0007114523000120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Inulin affects nutrition and metabolism in many animals. Although inulin is widely used in the diet of teleosts, its mechanism of action is unknown. Here, we investigated the effect of inulin (2 %) on the intestinal microbiome and metabolism in rainbow trout (Oncorhynchus mykiss) selected for growth and survival when fed a 100 % plant-based diet (suave) and a control line (temoin). Metabolic responses to the two factors (line and inulin) in liver, intestine, muscle and adipose were tissue-specific, with line and interaction between the two factors influencing overall expression in liver. In the intestine, inulin and line and in muscle, line influenced the expression of metabolic genes. Microbiota between the mucus and digestive contents was significantly different, with genera from Proteobacteria being more abundant in the mucus, whereas genera from the Firmicutes and Planctomycetes being more abundant in contents. Effect of inulin and interaction between factors on the microbiome was evident in contents. The significant taxa of control and inulin-fed groups differed greatly with Streptococcus and Weissella being significantly abundant in the inulin-fed group. There was a general trend showing higher levels of all SCFA in temoin group with propionic acid levels being significantly higher. An operational taxonomic unit (OTU) belonging to the Ruminococcaceae was significantly abundant in suave. The tissue-specific correlations between OTU and gene expression may indicate the link between microbiome and metabolism. Together, these results suggest that line and inulin impact the gene expression in a tissue-specific manner, possibly driven by specific OTUs enriched in inulin-fed groups and suave.
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Affiliation(s)
- Jep Lokesh
- Université de Pau et des Pays de l'Adour, E2S UPPA. INRAE, NUMEA, Saint-Pée-sur-Nivelle, France
| | - Marine Delaygues
- Université de Pau et des Pays de l'Adour, E2S UPPA. INRAE, NUMEA, Saint-Pée-sur-Nivelle, France
| | - Raphaël Defaix
- Université de Pau et des Pays de l'Adour, E2S UPPA. INRAE, NUMEA, Saint-Pée-sur-Nivelle, France
| | - Mickael Le Bechec
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IMT Mines Ales, IPREM, Pau, France; Institut des sciences analytiques et de Physicochimie pour l'environnement et les Matériaux, UMR5254, Hélioparc, 2 avenue Président Angot, 64 053 PAU cedex 9, France
| | - Thierry Pigot
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IMT Mines Ales, IPREM, Pau, France; Institut des sciences analytiques et de Physicochimie pour l'environnement et les Matériaux, UMR5254, Hélioparc, 2 avenue Président Angot, 64 053 PAU cedex 9, France
| | | | | | | | | | - Frédéric Terrier
- Université de Pau et des Pays de l'Adour, E2S UPPA. INRAE, NUMEA, Saint-Pée-sur-Nivelle, France
| | - Stéphane Panserat
- Université de Pau et des Pays de l'Adour, E2S UPPA. INRAE, NUMEA, Saint-Pée-sur-Nivelle, France
| | - Karine Ricaud
- Université de Pau et des Pays de l'Adour, E2S UPPA. INRAE, NUMEA, Saint-Pée-sur-Nivelle, France
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10
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Ding X, Zhang Y, Li D, Xu J, Wu C, Cui X, Sun Y. Comparative transcriptomic analysis of reproductive characteristics of reciprocal hybrid lineages derived from hybridization between Megalobrama amblycephala and Culter alburnus. BMC Genom Data 2023; 24:45. [PMID: 37573319 PMCID: PMC10422732 DOI: 10.1186/s12863-023-01141-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/21/2023] [Indexed: 08/14/2023] Open
Abstract
BACKGROUND Distant hybridization is an important breeding technique for creating new strains with superior traits by integrating two different genomes. Successful hybridization of Megalobrama amblycephala (Blunt snout bream, BSB, 2n = 48) and Culter alburnus (Topmouth culter, TC, 2n = 48) was achieved to establish hybrid lineages (BT and TB), which provide valuable materials for exploring the mechanisms of distant hybridization fertility. In this study, the gonadal tissue transcriptomes of BSB, TC, BT-F1, and TB-F1 were sequenced using Illumina high-throughput sequencing technology to analyze the reproductive characteristics of BT and TB. RESULTS Differential gene expression analysis showed that the differentially expressed genes in BT vs BSB and BT vs TC were mainly enriched in signaling pathways not directly associated with meiosis. While, the differentially expressed genes of TB vs BSB and TB vs TC were mainly enriched in pathways related to meiosis, and most of them were down-regulated, indicating that meiosis is suppressed in TB. Under-dominance (UD) genes were enriched in pathways related to meiosis and DNA repair in TB. Over-dominance (OD) genes were enriched in MAPK signaling pathway, expression level dominance-BSB (ELD-B) genes were enriched in pathways related to steroid hormone synthesis and expression level dominance-TC (ELD-T) genes were not significantly enriched in any pathway in both BT and TB. CONCLUSIONS These results suggest that meiotic progression may not be affected in BT, whereas it is clearly inhibited in TB. Offspring of M. amblycephala maternal parent may have better genomic compatibility and fertility. Our study provides important information on the molecular mechanisms of breaking reproductive isolation in distantly hybridized fertile lineages.
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Affiliation(s)
- Xue Ding
- School of Life Science and Health, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Yifei Zhang
- School of Life Science and Health, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Die Li
- School of Life Science and Health, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Jia Xu
- School of Life Science and Health, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fishes, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Xiaojuan Cui
- School of Life Science and Health, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China.
| | - Yuandong Sun
- School of Life Science and Health, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China.
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11
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Ziab M, Chaganti SR, Heath DD. The effects of host quantitative genetic architecture on the gut microbiota composition of Chinook salmon (Oncorhynchus tshawytscha). Heredity (Edinb) 2023; 131:43-55. [PMID: 37179383 PMCID: PMC10313681 DOI: 10.1038/s41437-023-00620-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
The microbiota consists of microbes living in or on an organism and has been implicated in host health and function. Environmental and host-related factors were shown to shape host microbiota composition and diversity in many fish species, but the role of host quantitative architecture across populations and among families within a population is not fully characterized. Here, Chinook salmon were used to determine if inter-population differences and additive genetic variation within populations influenced the gut microbiota diversity and composition. Specifically, hybrid stocks of Chinook salmon were created by crossing males from eight populations with eggs from an inbred line created from self-fertilized hermaphrodite salmon. Based on high-throughput sequencing of the 16S rRNA gene, significant gut microbial community diversity and composition differences were found among the hybrid stocks. Furthermore, additive genetic variance components varied among hybrid stocks, indicative of population-specific heritability patterns, suggesting the potential to select for specific gut microbiota composition for aquaculture purposes. Determining the role of host genetics in shaping their gut microbiota has important implications for predicting population responses to environmental changes and will thus impact conservation efforts for declining populations of Chinook salmon.
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Affiliation(s)
- Mubarak Ziab
- Great Lakes Institute for Environmental Research (GLIER), University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research (GLIER), University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada.
- Department of Integrative Biology, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada.
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12
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Li W, Zhou Z, Li H, Wang S, Ren L, Hu J, Liu Q, Wu C, Tang C, Hu F, Zeng L, Zhao R, Tao M, Zhang C, Qin Q, Liu S. Successional Changes of Microbial Communities and Host-Microbiota Interactions Contribute to Dietary Adaptation in Allodiploid Hybrid Fish. MICROBIAL ECOLOGY 2023; 85:1190-1201. [PMID: 35366074 DOI: 10.1007/s00248-022-01993-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/07/2022] [Indexed: 05/10/2023]
Abstract
Host-microbiota interactions play critical roles in host development, immunity, metabolism, and behavior. However, information regarding host-microbiota interactions is limited in fishes due to their complex living environment. In the present study, an allodiploid hybrid fish derived from herbivorous Megalobrama amblycephala (♀) × carnivorous Culter alburnus (♂) was used to investigate the successional changes of the microbial communities and host-microbiota interactions during herbivorous and carnivorous dietary adaptations. The growth level was not significantly different in any developmental stage between the two diet groups of fish. The diversity and composition of the dominant microbial communities showed similar successional patterns in the early developmental stages, but significantly changed during the two dietary adaptations. A large number of bacterial communities coexisted in all developmental stages, whereas the abundance of some genera associated with metabolism, including Acinetobacter, Gemmobacter, Microbacterium, Vibrio, and Aeromonas, was higher in either diet groups of fish. Moreover, the abundance of phylum Firmicutes, Actinobacteria, and Chloroflexi was positively correlated with the host growth level. In addition, Spearman's correlation analysis revealed that the differentially expressed homologous genes in the intestine associated with cell growth, immunity, and metabolism were related to the dominant gut microbiota. Our results present evidence that host genetics-gut microbiota interactions contribute to dietary adaptation in hybrid fish, which also provides basic data for understanding the diversity of dietary adaptations and evolution in fish.
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Affiliation(s)
- Wuhui Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Zexun Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Hongqing Li
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Jie Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Qingfeng Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Fangzhou Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Lei Zeng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Rulong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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13
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Gong D, Wang X, Yang J, Liang J, Tao M, Hu F, Wang S, Liu Z, Tang C, Luo K, Zhang C, Ma M, Wang Y, Liu S. Protection and utilization status of Parabramis and Megalobrama germplasm resources. REPRODUCTION AND BREEDING 2023. [DOI: 10.1016/j.repbre.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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Host Hybridization Dominates over Cohabitation in Affecting Gut Microbiota of Intrageneric Hybrid Takifugu Pufferfish. mSystems 2023; 8:e0118122. [PMID: 36815841 PMCID: PMC10134855 DOI: 10.1128/msystems.01181-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Microbial symbionts are of great importance for macroscopic life, including fish, and both collectively comprise an integrated biological entity known as the holobiont. Yet little is known as to how the normal balance within the fish holobiont is maintained and how it responds to biotic and/or abiotic influences. Here, through amplicon profiling, the genealogical relationship between artificial F1 hybrid pufferfish with growth heterosis, produced from crossing female Takifugu obscurus with male Takifugu rubripes and its maternal halfsibling purebred, was well recapitulated by their gut microbial community similarities, indicating an evident parallelism between host phylogeny (hybridity) and microbiota relationships therein. Interestingly, modest yet significant fish growth promotion and gut microbiota alteration mediated by hybrid-purebred cohabitation were observed, in comparison with their respective monoculture cohorts that share common genetic makeups, implying a certain degree of environmental influences. Moreover, the underlying assemblage patterns of gut microbial communities were found associated with a trade-off between variable selection and dispersal limitation, which are plausibly driven by the augmented social interactions between hybrid and purebred cohabitants differing in behaviors. Results from this study not only can enrich, from a microbial perspective, the sophisticated understanding of complex and dynamic assemblage of the fish holobiont, but will also provide deeper insights into the ecophysiological factors imposed on the diversity-function relationships thereof. Our findings emphasize the intimate associations of gut microbiota in host genetics-environmental interactions and would have deeper practical implications for microbial contributions to optimize performance prediction and to improve the production of farmed fishes. IMPORTANCE Microbial symbionts are of great importance for macroscopic life, including fish, and yet little is known as to how the normal balance within the fish holobiont is maintained and how it responds to the biotic and/or abiotic influences. Through gut microbiota profiling, we show that host intrageneric hybridization and cohabitation can impose a strong disturbance upon pufferfish gut microbiota. Moreover, marked alterations in the composition and function of gut microbiota in both hybrid and purebred pufferfish cohabitants were observed, which are potentially correlated with different metabolic priorities and behaviors between host genealogy. These results can enrich, from a microbial perspective, the sophisticated understanding of the complex and dynamic assemblage of the fish holobiont and would have deeper practical implications for microbial contributions to optimize performance prediction and to improve farmed fish production.
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15
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Wakade G, Lin S, Saha P, Kumari U, Daniell H. Abatement of microfibre pollution and detoxification of textile dye - Indigo by engineered plant enzymes. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:302-316. [PMID: 36208023 PMCID: PMC9884014 DOI: 10.1111/pbi.13942] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Microfibres (diameter <5 mm) and textile dyes released from textile industries are ubiquitous, cause environmental pollution, and harm aquatic flora, fauna, animals and human life. Therefore, enzymatic abatement of microfibre pollution and textile dye detoxification is essential. Microbial enzymes for such application present major challenges of scale and affordability to clean up large scale pollution. Therefore, enzymes required for the biodegradation of microfibres and indigo dye were expressed in transplastomic tobacco plants through chloroplast genetic engineering. Integration of laccase and lignin peroxidase genes into the tobacco chloroplast genomes and homoplasmy was confirmed by Southern blots. Decolorization (up to 86%) of samples containing indigo dye (100 mg/L) was obtained using cp-laccase (0.5% plant enzyme powder). Significant (8-fold) reduction in commercial microbial cellulase cocktail was achieved in pretreated cotton fibre hydrolysis by supplementing cost effective cellulases (endoglucanases, ß-glucosidases) and accessory enzymes (swollenin, xylanase, lipase) and ligninases (laccase lignin peroxidase) expressed in chloroplasts. Microfibre hydrolysis using cocktail of Cp-cellulases and Cp-accessory enzymes along with minimal dose (0.25% and 0.5%) of commercial cellulase blend (Ctec2) showed 88%-89% of sugar release from pretreated cotton and microfibres. Cp-ligninases, Cp-cellulases and Cp-accessory enzymes were stable in freeze dried leaves up to 15 and 36 months respectively at room temperature, when protected from light. Use of plant powder for decolorization or hydrolysis eliminated the need for preservatives, purification or concentration or cold chain. Evidently, abatement of microfibre pollution and textile dye detoxification using Cp-enzymes is a novel and cost-effective approach to prevent their environmental pollution.
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Affiliation(s)
- Geetanjali Wakade
- Department of Basic and Translational Sciences, School of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Shina Lin
- Department of Basic and Translational Sciences, School of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Prasenjit Saha
- Department of Basic and Translational Sciences, School of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Uma Kumari
- Department of Basic and Translational Sciences, School of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Henry Daniell
- Department of Basic and Translational Sciences, School of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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16
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Gu Q, Yuan H, Zhong H, Wei Z, Shu Y, Wang J, Ren L, Gong D, Liu S. Spatiotemporal characteristics of the pharyngeal teeth in interspecific distant hybrids of cyprinid fish: Phylogeny and expression of the initiation marker genes. Front Genet 2022; 13:983444. [PMID: 36051700 PMCID: PMC9424816 DOI: 10.3389/fgene.2022.983444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
As an important feeding organ and taxonomical characteristic, the pharyngeal teeth of cyprinid fish have very high morphological diversity and exhibit species-specific numbers and arrangements. Many genes have been verified to regulate the pharyngeal teeth development and act as the initiation marker for teeth. Six initiation marker genes for pharyngeal teeth were used as RNA probes to investigate the expression pattern, and these genes were further used to construct a phylogenetic tree for cyprinid fish including some distant hybrids. The results from in situ hybridization showed that similarities and differences existed in the expression of dlx2b, dlx4b, dlx5a, pitx2, fth1b, and scpp5 in the pharyngeal region of the hybrids (BT) by the crosses of blunt snout bream (BSB, ♀) × topmouth culter (TC, ♂). Particularly, we found a high specificity marker gene scpp5 for the early development of pharyngeal teeth. The Scpp5 expression pattern established a clear graphic representation on the spatiotemporal characteristics of the early morphogenesis of pharyngeal teeth in BT and BSB. Our results suggested that the scpp5 expression in 4V1, 3V1, and 5V1 in BT occurred earlier than that in BSB, while the replacement rate of pharyngeal teeth (4V2, 3V2, and 5V2) was faster in BSB. Phylogenetic analysis revealed that the six marker genes were highly conserved and could be used as the molecular marker for identifying the parents of the distant hybrids in cyprinid fish. The expression patterns of the scpp5 gene was examined in various tissues, including the brain, gill, heart, liver, muscle, skin, fins, gonad, eye, and kidney, showing that the scpp5 gene was ubiquitously expressed, indicating its important role in cyprinid fish.
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Affiliation(s)
- Qianhong Gu
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Hui Yuan
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Hui Zhong
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Zehong Wei
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yuqin Shu
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jing Wang
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Li Ren
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Dingbin Gong
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Shaojun Liu
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- *Correspondence: Shaojun Liu,
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17
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Gong D, Tao M, Xu L, Hu F, Wei Z, Wang S, Wang Y, Liu Q, Wu C, Luo K, Tang C, Zhou R, Zhang C, Wang Y, Liu S. An improved hybrid bream derived from a hybrid lineage of Megalobrama amblycephala (♀)×Culter alburnus (♂). SCIENCE CHINA. LIFE SCIENCES 2022; 65:1213-1221. [PMID: 34757543 DOI: 10.1007/s11427-021-2005-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Distant hybridization is an important technique in fish genetic breeding. In this study, based on the establishment of an allodiploid fish lineage (BT, 2n=48, F1-F6) derived from distant hybridization between female Megalobrama amblycephala (BSB, 2n=48) and male Culter alburnus (TC, 2n=48), and the backcross progeny (BTB, 2n=48) derived by backcrossing female F1 of BT to male BSB, an improved hybrid bream (BTBB, 2n=48) was obtained by backcrossing BTB (♀) to BSB (♂). Moreover, the morphological and genetic characteristics of BTBB individuals were investigated; BTBB was similar to BSB in appearance but had a higher body height than BSB. The study results regarding chromosome numbers and DNA content indicated that BTBB is a diploid hybrid fish. The 5S rDNA and Hox gene of BTBB were inherited from the original parents. Gonadal development in BTBB was normal. On the other hand, BTBB had a faster growth rate, higher muscle protein level, and lower muscle carbohydrate level than BSB. Hence, bisexual fertile BTBB is promoted and can be applied as a high-quality fish, and it can also be used as a new fish germplasm resource to develop high-quality fish further. Thus, this study is of great significance for fish genetic breeding.
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Affiliation(s)
- Dingbin Gong
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Lihui Xu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Fangzhou Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Zehong Wei
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yude Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Qingfeng Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Kaikun Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Rong Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yuequn Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
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18
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Cui X, Zhang Q, Zhang Q, Zhang Y, Chen H, Liu G, Zhu L. Research Progress of the Gut Microbiome in Hybrid Fish. Microorganisms 2022; 10:891. [PMID: 35630336 PMCID: PMC9146865 DOI: 10.3390/microorganisms10050891] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 02/07/2023] Open
Abstract
Fish, including hybrid species, are essential components of aquaculture, and the gut microbiome plays a vital role in fish growth, behavior, digestion, and immune health. The gut microbiome can be affected by various internal and/or external factors, such as host development, diet, and environment. We reviewed the effects of diet and dietary supplements on intestinal microorganisms in hybrid fish and the difference in the gut microbiome between the hybrid and their hybrids that originate. Then, we summarized the role of the gut microbiome in the speciation and ecological invasion of hybrid fish. Finally, we discussed possible future studies on the gut microbiome in hybrid fish, including the potential interaction with environmental microbiomes, the effects of the gut microbiome on population expansion, and fish conservation and management.
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Affiliation(s)
- Xinyuan Cui
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, China; (X.C.); (Q.Z.); (Q.Z.); (Y.Z.)
| | - Qinrong Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, China; (X.C.); (Q.Z.); (Q.Z.); (Y.Z.)
| | - Qunde Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, China; (X.C.); (Q.Z.); (Q.Z.); (Y.Z.)
| | - Yongyong Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, China; (X.C.); (Q.Z.); (Q.Z.); (Y.Z.)
| | - Hua Chen
- Mingke Biotechnology, Hangzhou 310000, China; (H.C.); (G.L.)
| | - Guoqi Liu
- Mingke Biotechnology, Hangzhou 310000, China; (H.C.); (G.L.)
| | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, China; (X.C.); (Q.Z.); (Q.Z.); (Y.Z.)
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19
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Bereded NK, Abebe GB, Fanta SW, Curto M, Waidbacher H, Meimberg H, Domig KJ. The gut bacterial microbiome of Nile tilapia (Oreochromis niloticus) from lakes across an altitudinal gradient. BMC Microbiol 2022; 22:87. [PMID: 35379180 PMCID: PMC8978401 DOI: 10.1186/s12866-022-02496-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/17/2022] [Indexed: 12/27/2022] Open
Abstract
Background Microorganisms inhabiting the gut play a significant role in supporting fundamental physiological processes of the host, which contributes to their survival in varied environments. Several studies have shown that altitude affects the composition and diversity of intestinal microbial communities in terrestrial animals. However, little is known about the impact of altitude on the gut microbiota of aquatic animals. The current study examined the variations in the gut microbiota of Nile tilapia (Oreochromis niloticus) from four lakes along an altitudinal gradient in Ethiopia by using 16S rDNA Illumina MiSeq high-throughput sequencing. Results The results indicated that low-altitude samples typically displayed greater alpha diversity. The results of principal coordinate analysis (PCoA) showed significant differences across samples from different lakes. Firmicutes was the most abundant phylum in the Lake Awassa and Lake Chamo samples whereas Fusobacteriota was the dominant phylum in samples from Lake Hashengie and Lake Tana. The ratio of Firmicutes to Bacteroidota in the high-altitude sample (Lake Hashengie, altitude 2440 m) was much higher than the ratio of Firmicutes to Bacteroidota in the low altitude population (Lake Chamo, altitude 1235 m). We found that the relative abundances of Actinobacteriota, Chloroflexi, Cyanobacteria, and Firmicutes were negatively correlated with altitude, while Fusobacteriota showed a positive association with altitude. Despite variability in the abundance of the gut microbiota across the lakes, some shared bacterial communities were detected. Conclusions In summary, this study showed the indirect influence of altitude on gut microbiota. Altitude has the potential to modulate the gut microbiota composition and diversity of Nile tilapia. Future work will be needed to elucidate the functional significance of gut microbiota variations based on the geographical environment. Significance and impact of the study Our study determined the composition and diversity of the gut microbiota in Nile tilapia collected from lakes across an altitude gradient. Our findings greatly extend the baseline knowledge of fish gut microbiota in Ethiopian lakes that plays an important role in this species sustainable aquaculture activities and conservation. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02496-z.
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Affiliation(s)
- Negash Kabtimer Bereded
- University of Natural Resources and Life Sciences, Vienna, Austria. .,Department of Food Science and Technology, Institute of Food Science, Muthgasse 18, 1190, Vienna, Austria. .,Department of Biology, Bahir Dar University, Post Code 79, Bahir Dar, Ethiopia.
| | | | - Solomon Workneh Fanta
- Faculty of Chemical and Food Engineering, Bahir Dar Institute of Technology, Bahir Dar University, Post Code 26, Bahir Dar, Ethiopia
| | - Manuel Curto
- Department of Integrative Biology and Biodiversity Research, Institute for Integrative Nature Conservation Research, Gregor Mendel Strasse 33, 1180, Vienna, Austria.,MARE-Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1049-001, Lisboa, Portugal
| | - Herwig Waidbacher
- Department of Water, Atmosphere and Environment, Institute of Hydrobiology and Aquatic Ecosystem Management, Gregor Mendel Strasse 33, 1180, Vienna, Austria
| | - Harald Meimberg
- Department of Integrative Biology and Biodiversity Research, Institute for Integrative Nature Conservation Research, Gregor Mendel Strasse 33, 1180, Vienna, Austria
| | - Konrad J Domig
- University of Natural Resources and Life Sciences, Vienna, Austria.,Department of Food Science and Technology, Institute of Food Science, Muthgasse 18, 1190, Vienna, Austria
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20
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Miller AK, Westlake CS, Cross KL, Leigh BA, Bordenstein SR. The microbiome impacts host hybridization and speciation. PLoS Biol 2021; 19:e3001417. [PMID: 34699520 PMCID: PMC8547693 DOI: 10.1371/journal.pbio.3001417] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Microbial symbiosis and speciation profoundly shape the composition of life's biodiversity. Despite the enormous contributions of these two fields to the foundations of modern biology, there is a vast and exciting frontier ahead for research, literature, and conferences to address the neglected prospects of merging their study. Here, we survey and synthesize exemplar cases of how endosymbionts and microbial communities affect animal hybridization and vice versa. We conclude that though the number of case studies remain nascent, the wide-ranging types of animals, microbes, and isolation barriers impacted by hybridization will likely prove general and a major new phase of study that includes the microbiome as part of the functional whole contributing to reproductive isolation. Though microorganisms were proposed to impact animal speciation a century ago, the weight of the evidence supporting this view has now reached a tipping point.
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Affiliation(s)
- Asia K. Miller
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
- Vanderbilt University, Vanderbilt Microbiome Innovation Center, Nashville, Tennessee, United States of America
| | - Camille S. Westlake
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
- Vanderbilt University, Vanderbilt Microbiome Innovation Center, Nashville, Tennessee, United States of America
| | - Karissa L. Cross
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
- Vanderbilt University, Vanderbilt Microbiome Innovation Center, Nashville, Tennessee, United States of America
| | - Brittany A. Leigh
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
- Vanderbilt University, Vanderbilt Microbiome Innovation Center, Nashville, Tennessee, United States of America
| | - Seth R. Bordenstein
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
- Vanderbilt University, Vanderbilt Microbiome Innovation Center, Nashville, Tennessee, United States of America
- Vanderbilt University Medical Center, Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, Tennessee, United States of America
- Vanderbilt University Medical Center, Department of Pathology, Microbiology & Immunology, Nashville, Tennessee, United States of America
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21
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Ücker M, Ansorge R, Sato Y, Sayavedra L, Breusing C, Dubilier N. Deep-sea mussels from a hybrid zone on the Mid-Atlantic Ridge host genetically indistinguishable symbionts. THE ISME JOURNAL 2021; 15:3076-3083. [PMID: 33972724 PMCID: PMC8443746 DOI: 10.1038/s41396-021-00927-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/26/2021] [Accepted: 02/03/2021] [Indexed: 02/04/2023]
Abstract
The composition and diversity of animal microbiomes is shaped by a variety of factors, many of them interacting, such as host traits, the environment, and biogeography. Hybrid zones, in which the ranges of two host species meet and hybrids are found, provide natural experiments for determining the drivers of microbiome communities, but have not been well studied in marine environments. Here, we analysed the composition of the symbiont community in two deep-sea, Bathymodiolus mussel species along their known distribution range at hydrothermal vents on the Mid-Atlantic Ridge, with a focus on the hybrid zone where they interbreed. In-depth metagenomic analyses of the sulphur-oxidising symbionts of 30 mussels from the hybrid zone, at a resolution of single nucleotide polymorphism analyses of ~2500 orthologous genes, revealed that parental and hybrid mussels (F2-F4 generation) have genetically indistinguishable symbionts. While host genetics does not appear to affect symbiont composition in these mussels, redundancy analyses showed that geographic location of the mussels on the Mid-Atlantic Ridge explained most of the symbiont genetic variability compared to the other factors. We hypothesise that geographic structuring of the free-living symbiont population plays a major role in driving the composition of the microbiome in these deep-sea mussels.
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Affiliation(s)
- Merle Ücker
- grid.419529.20000 0004 0491 3210Max Planck Institute for Marine Microbiology, Bremen, Germany ,grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences of the University of Bremen, Bremen, Germany
| | - Rebecca Ansorge
- grid.419529.20000 0004 0491 3210Max Planck Institute for Marine Microbiology, Bremen, Germany ,grid.40368.390000 0000 9347 0159Quadram Institute Bioscience, Norwich, Norfolk UK
| | - Yui Sato
- grid.419529.20000 0004 0491 3210Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Lizbeth Sayavedra
- grid.419529.20000 0004 0491 3210Max Planck Institute for Marine Microbiology, Bremen, Germany ,grid.40368.390000 0000 9347 0159Quadram Institute Bioscience, Norwich, Norfolk UK
| | - Corinna Breusing
- grid.20431.340000 0004 0416 2242University of Rhode Island, Graduate School of Oceanography, Narragansett, RI USA
| | - Nicole Dubilier
- grid.419529.20000 0004 0491 3210Max Planck Institute for Marine Microbiology, Bremen, Germany ,grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences of the University of Bremen, Bremen, Germany
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22
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Li W, Wang S, Hu J, Tang C, Wu C, Liu J, Ren L, Sun C, Dong J, Liu S, Ye X. Asymmetric expression of homoeologous genes contributes to dietary adaption of an allodiploid hybrid fish derived from Megalobrama amblycephala (♀) × Culter alburnus (♂). BMC Genomics 2021; 22:362. [PMID: 34011285 PMCID: PMC8132401 DOI: 10.1186/s12864-021-07639-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 04/21/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Hybridization, which can quickly merge two or more divergent genomes and form new allopolyploids, is an important technique in fish genetic breeding. However, the merged subgenomes must adjust and coexist with one another in a single nucleus, which may cause subgenome interaction and dominance at the gene expression level and has been observed in some allopolyploid plants. In our previous studies, newly formed allodiploid hybrid fish derived from herbivorous Megalobrama amblycephala (♀) × carnivorous Culter alburnus (♂) had herbivorous characteristic. It is thus interesting to further characterize whether the subgenome interaction and dominance derive dietary adaptation of this hybrid fish. RESULTS Differential expression, homoeolog expression silencing and bias were investigated in the hybrid fish after 70 days of adaptation to carnivorous and herbivorous diets. A total of 2.65 × 108 clean reads (74.06 Gb) from the liver and intestinal transcriptomes were mapped to the two parent genomes based on specific SNPs. A total of 2538 and 4385 differentially expressed homoeologous genes (DEHs) were identified in the liver and intestinal tissues between the two groups of fish, respectively, and these DEHs were highly enriched in fat digestion and carbon metabolism, amino acid metabolism and steroid biosynthesis. Furthermore, subgenome dominance were observed in tissues, with paternal subgenome was more dominant than maternal subgenome. Moreover, subgenome expression dominance controlled functional pathways in metabolism, disease, cellular processes, environment and genetic information processing during the two dietary adaptation processes. In addition, few but sturdy villi in the intestine, significant fat accumulation and a higher concentration of malondialdehyde in the liver were observed in fish fed carnivorous diet compared with fish fed herbivorous diet. CONCLUSIONS Our results indicated that diet drives phenotypic and genetic variation, and the asymmetric expression of homoeologous genes (including differential expression, expression silencing and bias) may play key roles in dietary adaptation of hybrid fish. Subgenome expression dominance may contribute to uncovering the mechanistic basis of heterosis and also provide perspectives for fish genetic breeding and application.
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Affiliation(s)
- Wuhui Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081 Hunan China
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380 Guangdong China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081 Hunan China
| | - Jie Hu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380 Guangdong China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081 Hunan China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081 Hunan China
| | - Junmei Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081 Hunan China
| | - Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081 Hunan China
| | - Chengfei Sun
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380 Guangdong China
| | - Junjian Dong
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380 Guangdong China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081 Hunan China
| | - Xing Ye
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380 Guangdong China
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23
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Zhu L, Zhang Z, Chen H, Lamer JT, Wang J, Wei W, Fu L, Tang M, Wang C, Lu G. Gut microbiomes of bigheaded carps and hybrids provide insights into invasion: A hologenome perspective. Evol Appl 2021; 14:735-745. [PMID: 33767748 PMCID: PMC7980309 DOI: 10.1111/eva.13152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
Gut microbiomes play an essential role in host survival and local adaptation and thus can facilitate the invasion of host species. Biological invasions have been shown to be linked to the genetic properties of alien host species. It is thus plausible that the holobiont, the host, and its associated microbiome act as an entity to drive invasion success. The bighead carp and silver carp (bigheaded carps), invasive species that exhibit extensive hybridization in the Mississippi River Basin (MRB), provided a unique model to test the holobiont hypothesis of invasion. Here, we investigated the microbiomes of foreguts and hindguts in bigheaded carps and their reciprocal hybrids reared in aquaculture ponds using 16S amplicons and the associated gene prediction. We found an admixed pattern in the gut microbiome community in bigheaded carp hybrids. The hybrid gut microbiomes showed special characteristics such as relatively high alpha diversity in the foregut, an increasing dissimilarity between foreguts and hindguts, and a remarkable proportion of genes coding for putative enzymes related to their digestion of main food resources (Cyanobacteria, cellulose, and chitin). The pond-reared hybrids had advantageous features in genes coding for putative enzymes related to their diet. The above results collectively suggested that the gut microbiomes of hybrids could be beneficial to their local adaptation (e.g., food resource utilization), which might have facilitated their invasion in the MRB. The gut microbial findings, along with the intrinsic genomic features likely associated with life-history traits revealed in our recent study, provide preliminary evidence supporting the holobiont hypothesis of invasion.
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Affiliation(s)
- Lifeng Zhu
- College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Zheng Zhang
- College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Hua Chen
- Mingke Biotechnology CenterHangzhouChina
| | - James T. Lamer
- Department of Biological SciencesWestern Illinois UniversityMacombILUSA
| | - Jun Wang
- Key Laboratory of Freshwater Fisheries Germplasm ResourcesMinistry of Agriculture and Rural Affair/National Demonstration Center for Experimental Fisheries ScienceEducation/Shanghai Engineering Research Center of AquacultureShanghai Ocean UniversityShanghaiChina
| | - Wenzhi Wei
- College of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Lixia Fu
- College of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Minghu Tang
- Yangzhou Hanjiang National Carp Seed FarmYangzhouChina
| | - Chenghui Wang
- Key Laboratory of Freshwater Fisheries Germplasm ResourcesMinistry of Agriculture and Rural Affair/National Demonstration Center for Experimental Fisheries ScienceEducation/Shanghai Engineering Research Center of AquacultureShanghai Ocean UniversityShanghaiChina
| | - Guoqing Lu
- Department of BiologyUniversity of Nebraska at OmahaOmahaNEUSA
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24
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Bereded NK, Abebe GB, Fanta SW, Curto M, Waidbacher H, Meimberg H, Domig KJ. The Impact of Sampling Season and Catching Site (Wild and Aquaculture) on Gut Microbiota Composition and Diversity of Nile Tilapia ( Oreochromis niloticus). BIOLOGY 2021; 10:biology10030180. [PMID: 33804538 PMCID: PMC8001861 DOI: 10.3390/biology10030180] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 02/23/2021] [Indexed: 12/20/2022]
Abstract
Simple Summary The gut microbiota (all microbes in the intestine) of fishes is known to play an essential role in diverse aspects of their life. The gut microbiota of fish is affected by various environmental parameters, including temperature changes, salinity and diet. This study characterised the microbial composition in gut samples of Nile Tilapia collected from Lake Tana and the Bahir Dar aquaculture facility centre applying modern molecular techniques. The results show clear differences in the gut microbiota in fish from the Lake Tana and the ones from aquaculture. Further, also significant differences were observed on the composition of the gut microbiota across sampling months. Samples from the aquaculture centre displayed a higher diversity than the wild catch Nile tilapia from Lake Tana even though there is also an overlapping of the detected microbial groups. Overall, this is the first study on the effects of sampling season and catching site on the gut microbiota of Nile tilapia in Ethiopia. Future work will help to precisely explain the causes of these changes and their influence of the health and growth of Nile tilapia in Ethiopian lakes as well as under aquaculture conditions. Abstract The gut microbiota of fishes is known to play an essential role in diverse aspects of host biology. The gut microbiota of fish is affected by various environmental parameters, including temperature changes, salinity and diet. Studies of effect of environment on gut microbiota enables to have a further understanding of what comprises a healthy microbiota under different environmental conditions. However, there is insufficient understanding regarding the effects of sampling season and catching site (wild and aquaculture) on the gut microbiota of Nile tilapia. This study characterised gut microbial composition and diversity from samples collected from Lake Tana and the Bahir Dar aquaculture facility centre using 16S rDNA Illumina MiSeq platform sequencing. Firmicutes and Fusobacteria were the most dominant phyla in the Lake Tana samples, while Proteobacteria was the most dominant in the aquaculture samples. The results of differential abundance testing clearly indicated significant differences for Firmicutes, Fusobacteria, Bacteroidetes and Cyanobacteria across sampling months. However, Proteobacteria, Chloroflexi, Fusobacteria and Cyanobacteria were significantly enriched in the comparison of samples from the Lake Tana and aquaculture centre. Significant differences were observed in microbial diversity across sampling months and between wild and captive Nile tilapia. The alpha diversity clearly showed that samples from the aquaculture centre (captive) had a higher diversity than the wild Nile tilapia samples from Lake Tana. The core gut microbiota of all samples of Nile tilapia used in our study comprised Firmicutes, Proteobacteria and Fusobacteria. This study clearly showed the impact of sampling season and catching site (wild and aquaculture) on the diversity and composition of bacterial communities associated with the gut of Nile tilapia. Overall, this is the first study on the effects of sampling season and catching site on the gut microbiota of Nile tilapia in Ethiopia. Future work is recommended to precisely explain the causes of these changes using large representative samples of Nile tilapia from different lakes and aquaculture farms.
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Affiliation(s)
- Negash Kabtimer Bereded
- Institute of Food Science, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria;
- Department of Biology, Bahir Dar University, Bahir Dar, Post Code 79, Ethiopia;
- Correspondence:
| | | | - Solomon Workneh Fanta
- Faculty of Chemical and Food Engineering, Bahir Dar Institute of Technology, Bahir Dar University, Bahir Dar, Post Code 26, Ethiopia;
| | - Manuel Curto
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendle-Straße 33, 1180 Vienna, Austria; (M.C.); (H.M.)
- MARE−Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1049-001 Lisboa, Portugal
| | - Herwig Waidbacher
- Institute for Hydrobiology and Aquatic Ecosystems Management, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendle-Straße 33/DG, 1180 Vienna, Austria;
| | - Harald Meimberg
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendle-Straße 33, 1180 Vienna, Austria; (M.C.); (H.M.)
| | - Konrad J. Domig
- Institute of Food Science, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria;
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Xiao F, Zhu W, Yu Y, He Z, Wu B, Wang C, Shu L, Li X, Yin H, Wang J, Juneau P, Zheng X, Wu Y, Li J, Chen X, Hou D, Huang Z, He J, Xu G, Xie L, Huang J, Yan Q. Host development overwhelms environmental dispersal in governing the ecological succession of zebrafish gut microbiota. NPJ Biofilms Microbiomes 2021; 7:5. [PMID: 33469034 PMCID: PMC7815754 DOI: 10.1038/s41522-020-00176-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023] Open
Abstract
Clarifying mechanisms underlying the ecological succession of gut microbiota is a central theme of gut ecology. Under experimental manipulations of zebrafish hatching and rearing environments, we test our core hypothesis that the host development will overwhelm environmental dispersal in governing fish gut microbial community succession due to host genetics, immunology, and gut nutrient niches. We find that zebrafish developmental stage substantially explains the gut microbial community succession, whereas the environmental effects do not significantly affect the gut microbiota succession from larvae to adult fish. The gut microbiotas of zebrafish are clearly separated according to fish developmental stages, and the degree of homogeneous selection governing gut microbiota succession is increasing with host development. This study advances our mechanistic understanding of the gut microbiota assembly and succession by integrating the host and environmental effects, which also provides new insights into the gut ecology of other aquatic animals.
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Affiliation(s)
- Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510006, Guangzhou, China
| | - Wengen Zhu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, 430072, Wuhan, China
| | - Yuhe Yu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, 430072, Wuhan, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510006, Guangzhou, China
- College of Agronomy, Hunan Agricultural University, 410128, Changsha, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510006, Guangzhou, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510006, Guangzhou, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510006, Guangzhou, China
| | - Xinghao Li
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, 430072, Wuhan, China
| | - Huaqun Yin
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Philippe Juneau
- Department of Biological Science, GRIL, TOXEN, Ecotoxicology of Aquatic Microorganisms Laboratory, Université du Québec à Montréal, Succursale Centre-Ville, Montréal, QC, Canada
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510006, Guangzhou, China
| | - Yongjie Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510006, Guangzhou, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, 410128, Changsha, China
| | - Xiaojuan Chen
- Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, 430079, Wuhan, China
| | - Dongwei Hou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510006, Guangzhou, China
| | - Zhijian Huang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510006, Guangzhou, China
| | - Jianguo He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510006, Guangzhou, China
| | - Guohuan Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, 510070, Guangzhou, China
| | - Liwei Xie
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, 510070, Guangzhou, China
| | - Jie Huang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, 430072, Wuhan, China.
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510006, Guangzhou, China.
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Piazzon MC, Naya-Català F, Perera E, Palenzuela O, Sitjà-Bobadilla A, Pérez-Sánchez J. Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream. MICROBIOME 2020; 8:168. [PMID: 33228779 PMCID: PMC7686744 DOI: 10.1186/s40168-020-00922-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/09/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND The key effects of intestinal microbiota in animal health have led to an increasing interest in manipulating these bacterial populations to improve animal welfare. The aquaculture sector is no exception and in the last years, many studies have described these populations in different fish species. However, this is not an easy task, as intestinal microbiota is composed of very dynamic populations that are influenced by different factors, such as diet, environment, host age, and genetics. In the current study, we aimed to determine whether the genetic background of gilthead sea bream (Sparus aurata) influences the intestinal microbial composition, how these bacterial populations are modulated by dietary changes, and the effect of selection by growth on intestinal disease resistance. To that aim, three different groups of five families of gilthead sea bream that were selected during two generations for fast, intermediate, or slow growth (F3 generation) were kept together in the same open-flow tanks and fed a control or a well-balanced plant-based diet during 9 months. Six animals per family and dietary treatment were sacrificed and the adherent bacteria from the anterior intestinal portion were sequenced. In parallel, fish of the fast- and slow-growth groups were infected with the intestinal parasite Enteromyxum leei and the disease signs, prevalence, intensity, and parasite abundance were evaluated. RESULTS No differences were detected in alpha diversity indexes among families, and the core bacterial architecture was the prototypical composition of gilthead sea bream intestinal microbiota, indicating no dysbiosis in any of the groups. The plant-based diet significantly changed the microbiota in the intermediate- and slow-growth families, with a much lower effect on the fast-growth group. Interestingly, the smaller changes detected in the fast-growth families potentially accounted for more changes at the metabolic level when compared with the other families. Upon parasitic infection, the fast-growth group showed significantly lower disease signs and parasite intensity and abundance than the slow-growth animals. CONCLUSIONS These results show a clear genome-metagenome interaction indicating that the fast-growth families harbor a microbiota that is more flexible upon dietary changes. These animals also showed a better ability to cope with intestinal infections. Video Abstract.
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Affiliation(s)
- M. Carla Piazzon
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Fernando Naya-Català
- Nutrigenomics and Fish Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Erick Perera
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
- Nutrigenomics and Fish Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Oswaldo Palenzuela
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
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Profile of Dr. Shaojun Liu. SCIENCE CHINA. LIFE SCIENCES 2020; 63:1283-1286. [PMID: 32700189 DOI: 10.1007/s11427-020-1746-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
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28
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Lv Y, Xu Q, Mao Y, Xu Y, Zhang R, Zhong H, Zhou Y, Xiao J, Du M, Song H, Liang Y, Yan J. TRAF3 of blunt snout bream participates in host innate immune response to pathogenic bacteria via NF-κB signaling pathway. FISH & SHELLFISH IMMUNOLOGY 2020; 104:592-604. [PMID: 32589928 DOI: 10.1016/j.fsi.2020.06.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
Tumor necrosis factor receptor-associated factor 3 (TRAF3) is a multifunctional adaptor protein primarily involved in both bacterial defense and antiviral immunity in living organisms. However, the knowledge on TRAF3 in blunt snout bream (Megalobrama amblycephala), a freshwater fish with economic values, remained unclear. In the present study, we identified and characterized successfully Traf3 gene from M. amblycephala (maTraf3). The maTraf3 cDNA contained a 1722 bp open reading frame that encoded a protein of 573 amino acid residues. The deduced amino acid sequence comprised of a RING finger domain, two zinc finger motifs, a coiled-coil region and a MATH domain. Analysis of the transcriptional patterns of maTraf3 revealed that it was ubiquitously distributed in various tissues tested from M. amblycephala, with the abundance of expression in spleen and muscle. Following a challenge with Aeromonas hydrophila and lipopolysaccharide stimulation, the expression of maTraf3 was strongly enhanced at different time points in vitro and in vivo. MaTRAF3 was identified as a cytosolic protein and suggested to form aggregates or be associated with vesicles scattering in the cytoplasm. NF-κB transcription was activated by maTraf3 in reporter assay. The overexpression of maTraf3 produced high levels of pro-inflammatory cytokines such as IL-1β, IL-6, IL-8 and TNF-α, implying its immune-regulatory role in M. amblycephala. Taken together, our results obtained in this study demonstrated the crucial role of maTraf3 in mediating host innate immune response to pathogen invasion via NF-κB signaling pathway, which might indicate a novel therapeutic approach to combat bacterial infection in fish.
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Affiliation(s)
- Yina Lv
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China; Department of Biology, Zhaoqing University, Zhaoqing, 526061, China
| | - Qian Xu
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China
| | - Ying Mao
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China
| | - Yandong Xu
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China
| | - Ru Zhang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China
| | - Huan Zhong
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, 530021, China
| | - Yi Zhou
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, 530021, China
| | - Jun Xiao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, 530021, China
| | - Mengke Du
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China
| | - Huiyang Song
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China
| | - Yinhua Liang
- Department of Operation, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - Jinpeng Yan
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China.
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29
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Perry WB, Lindsay E, Payne CJ, Brodie C, Kazlauskaite R. The role of the gut microbiome in sustainable teleost aquaculture. Proc Biol Sci 2020; 287:20200184. [PMID: 32372688 PMCID: PMC7282919 DOI: 10.1098/rspb.2020.0184] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
As the most diverse vertebrate group and a major component of a growing global aquaculture industry, teleosts continue to attract significant scientific attention. The growth in global aquaculture, driven by declines in wild stocks, has provided additional empirical demand, and thus opportunities, to explore teleost diversity. Among key developments is the recent growth in microbiome exploration, facilitated by advances in high-throughput sequencing technologies. Here, we consider studies on teleost gut microbiomes in the context of sustainable aquaculture, which we have discussed in four themes: diet, immunity, artificial selection and closed-loop systems. We demonstrate the influence aquaculture has had on gut microbiome research, while also providing a road map for the main deterministic forces that influence the gut microbiome, with topical applications to aquaculture. Functional significance is considered within an aquaculture context with reference to impacts on nutrition and immunity. Finally, we identify key knowledge gaps, both methodological and conceptual, and propose promising applications of gut microbiome manipulation to aquaculture, and future priorities in microbiome research. These include insect-based feeds, vaccination, mechanism of pro- and prebiotics, artificial selection on the hologenome, in-water bacteriophages in recirculating aquaculture systems (RAS), physiochemical properties of water and dysbiosis as a biomarker.
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Affiliation(s)
- William Bernard Perry
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Elle Lindsay
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | | | - Christopher Brodie
- Ecosystems and Environment Research Centre, University of Salford, Salford M5 4WT, UK.,School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool L3 5UG, UK
| | - Raminta Kazlauskaite
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
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30
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Houston RD, Bean TP, Macqueen DJ, Gundappa MK, Jin YH, Jenkins TL, Selly SLC, Martin SAM, Stevens JR, Santos EM, Davie A, Robledo D. Harnessing genomics to fast-track genetic improvement in aquaculture. Nat Rev Genet 2020; 21:389-409. [PMID: 32300217 DOI: 10.1038/s41576-020-0227-y] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2020] [Indexed: 12/12/2022]
Abstract
Aquaculture is the fastest-growing farmed food sector and will soon become the primary source of fish and shellfish for human diets. In contrast to crop and livestock production, aquaculture production is derived from numerous, exceptionally diverse species that are typically in the early stages of domestication. Genetic improvement of production traits via well-designed, managed breeding programmes has great potential to help meet the rising seafood demand driven by human population growth. Supported by continuous advances in sequencing and bioinformatics, genomics is increasingly being applied across the broad range of aquaculture species and at all stages of the domestication process to optimize selective breeding. In the future, combining genomic selection with biotechnological innovations, such as genome editing and surrogate broodstock technologies, may further expedite genetic improvement in aquaculture.
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Affiliation(s)
- Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK.
| | - Tim P Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Ye Hwa Jin
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Tom L Jenkins
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | | | | | - Jamie R Stevens
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Eduarda M Santos
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Andrew Davie
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
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31
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Zou S, Gong L, Khan TA, Pan L, Yan L, Li D, Cao L, Li Y, Ding X, Yi G, Sun Y, Hu S, Xia L. Comparative analysis and gut bacterial community assemblages of grass carp and crucian carp in new lineages from the Dongting Lake area. Microbiologyopen 2020; 9:e996. [PMID: 32175674 PMCID: PMC7221430 DOI: 10.1002/mbo3.996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/31/2019] [Accepted: 12/31/2019] [Indexed: 12/17/2022] Open
Abstract
Gut microbiota are known to play an important role in health and nutrition of the host and have been attracting an increasing attention. Farming of new lineages of grass carp and crucian carp has been developed rapidly as these species were found to outperform indigenous ones in terms of growth rate and susceptibility to diseases. Despite this rapid development, no studies have addressed the characteristics of their gut microbiota as a potential factor responsible for the improved characteristics. To reveal whether microbiomes of the new lineages are different from indigenous ones, and therefore could be responsible for improved growth features, intestinal microbiota from the new lineages were subjected to high-throughput sequencing. While the phyla Firmicutes, Fusobacteria and Proteobacteria were representing the core bacterial communities that comprised more than 75% in all fish intestinal samples, significant differences were found in the microbial community composition of the new linages versus indigenous fish populations, suggesting the possibility that results in the advantages of enhanced disease resistance and rapid growth for the new fish lineages. Bacterial composition was similar between herbivorous and omnivorous fish. The relative abundance of Bacteroidetes and Actinobacteria was significantly higher in omnivores compared to that of herbivores, whereas Cetobacterium_sp. was abundant in herbivores. We also found that the gut microbiota of freshwater fish in the Dongting lake area was distinct from those of other areas. Network graphs showed the reduced overall connectivity of gut bacteria in indigenous fish, whereas the bacteria of the new fish lineage groups showed hubs with more node degree. A phylogenetic investigation of communities by reconstruction of unobserved states inferred function profile showed several metabolic processes were more active in the new lineages compared to indigenous fish. Our findings suggest that differences in gut bacterial community composition may be an important factor contributing to the rapid growth and high disease resistance of the new fish lineages.
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Affiliation(s)
- Sheng Zou
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Liang Gong
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Tahir Ali Khan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Lifei Pan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Liang Yan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Dongjie Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Lina Cao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Yanping Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Xuezhi Ding
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Ganfeng Yi
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Yunjun Sun
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Shengbiao Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Liqiu Xia
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
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Chen X, Fang S, Wei L, Zhong Q. Systematic evaluation of the gut microbiome of swamp eel ( Monopterus albus) by 16S rRNA gene sequencing. PeerJ 2019; 7:e8176. [PMID: 31875148 PMCID: PMC6927349 DOI: 10.7717/peerj.8176] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 11/07/2019] [Indexed: 12/11/2022] Open
Abstract
Background The swamp eel (Monopterus albus) is a commercially important farmed species in China. The dysbiosis and homeostasis of gut microbiota has been suggested to be associated with the swamp eel’s disease pathogenesis and food digestion. Although the contributions of gut microbiome in fish growth and health has been increasingly recognized, little is known about the microbial community in the intestine of the swamp eel (Monopterus albus). Methods The intestinal microbiomes of the five distinct gut sections (midgut content and mucosa, hindgut content and mucosa, and stools) of swamp eel were compared using Illumina MiSeq sequencing of the bacterial 16S rRNA gene sequence and statistical analysis. Results The results showed that the number of observed OTUs in the intestine decreased proximally to distally. Principal coordinate analysis revealed significant separations among samples from different gut sections. There were 54 core OTUs shared by all gut sections and 36 of these core OTUs varied significantly in their abundances. Additionally, we discovered 66 section-specific enriched KEGG pathways. These section-specific enriched microbial taxa (e.g., Bacillus, Lactobacillus) and potential function capacities (e.g., amino acid metabolism, carbohydrate metabolism) might play vital roles in nutrient metabolism, immune modulation and host-microbe interactions of the swamp eel. Conclusions Our results showed that microbial diversity, composition and function capacity varied substantially across different gut sections. The gut section-specific enriched core microbial taxa and function capacities may perform important roles in swamp eel’s nutrient metabolism, immune modulation, and host-microbe interactions. This study should provide insights into the gut microbiome of the swamp eel.
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Affiliation(s)
- Xuan Chen
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Shaoming Fang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lili Wei
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Qiwang Zhong
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China
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Solovyev MM, Kashinskaya EN, Bochkarev NA, Andree KB, Simonov E. The effect of diet on the structure of gut bacterial community of sympatric pair of whitefishes ( Coregonus lavaretus): one story more. PeerJ 2019; 7:e8005. [PMID: 31824755 PMCID: PMC6896945 DOI: 10.7717/peerj.8005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 10/07/2019] [Indexed: 12/16/2022] Open
Abstract
In the Coregonus lavaretus complex may be found lacustrine sympatric pairs, which serves as an intriguing model for studying different aspects of fish evolutionary biology. One such sympatric whitefish pair inhabits Teletskoye Lake (West Siberia, Russia) and includes a “large” form (Coregonus lavaretus pidschian (Gmelin, 1789)) and a “small” form (C. l. pravdinellus (Dulkeit, 1949)). C. l. pravdinellus has a narrow trophic specialization and feeds on zooplankton, whereas the diet of C. l. pidschian is based on benthic prey. In the present study we aimed to address the question of how the gut microbial community reflects the divergence in diet of a sympatric pair of whitefish. Studied samples included the mucosa and content were collected for cardiac and pyloric stomach, anterior, middle, and posterior intestine, but only mucosa was collected for the pyloric caeca. In addition, water, sediment, macrophyte (environmental microbiota) and invertebrate (microbiota of prey) samples were collected in the same location. The V3–V4 region of the 16S rRNA genes was chosen for microbiome analysis and the software PICRUSt used to estimate the difference functional roles of the microbiota. The number of OTUs and Chao1 index in mucosa and content of cardiac and pyloric stomach were significantly different between whitefish. Significant differences were observed between whitefish for content from different parts of the intestine in terms of OTU number and Chao1 indices, whereas for mucosa from the same parts of intestine these differences were absent. No significant differences were found for diversity estimates of mucosa and content of different parts of the gut (there were a few exceptions) between whitefish. The form of whitefish and the segment of the digestive system were factors with a significant determinative effect on the structure of the microbiota from gut mucosa and content. The most dominant phyla in mucosa and content of cardiac and pyloric stomach was Proteobacteria (57.0–84.0%) for both whitefish. Throughout the intestine of C. l. pidschian the dominant phyla in mucosa were Proteobacteria (38.8%) and Firmicutes (15.6%), whereas for C. l. pravdinellus–Tenericutes (49.6%) and Proteobacteria (28.1%). For both forms, the phylum Spirochaetes was found in a significant amount (20.0–25.0%) in the mucosa of the posterior intestine. While for the content obtained from anterior, middle and posterior intestines, the dominant bacterial phyla were the same as those described for mucosa from the same parts of the intestine for both whitefish. The bacterial community of the prey and environment was significantly different from bacterial communities found for all parts of the gut mucosa for both whitefish, with the exception of the mucosa of the cardiac stomach. According to PICRUSt the highest level of differences between whitefish at the L3 level were found for the intestinal mucosa (75.3%), whereas the lowest one was registered for stomach content (38.8%).
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Affiliation(s)
- Mikhail M Solovyev
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Tomsk State University, Tomsk, Russia
| | - Elena N Kashinskaya
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Nickolai A Bochkarev
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Karl B Andree
- Instituto de Investigación y Tecnología Agroalimentarias, San Carlos de la Rapita, Tarragona, Spain
| | - Evgeniy Simonov
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Institute of Environmental and Agricultural Biology, Tyumen State University, Tyumen, Russia
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Ren L, Li W, Qin Q, Dai H, Han F, Xiao J, Gao X, Cui J, Wu C, Yan X, Wang G, Liu G, Liu J, Li J, Wan Z, Yang C, Zhang C, Tao M, Wang J, Luo K, Wang S, Hu F, Zhao R, Li X, Liu M, Zheng H, Zhou R, Shu Y, Wang Y, Liu Q, Tang C, Duan W, Liu S. The subgenomes show asymmetric expression of alleles in hybrid lineages of Megalobrama amblycephala × Culter alburnus. Genome Res 2019; 29:1805-1815. [PMID: 31649058 PMCID: PMC6836732 DOI: 10.1101/gr.249805.119] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 10/02/2019] [Indexed: 11/25/2022]
Abstract
Hybridization drives rapid speciation by shaping novel genotypic and phenotypic profiles. Genomic incompatibility and transcriptome shock have been observed in hybrids, although this is rarer in animals than in plants. Using the newly sequenced genomes of the blunt snout bream (Megalobrama amblycephala [BSB]) and the topmouth culter (Culter alburnus [TC]), we focused on the sequence variation and gene expression changes in the reciprocal intergeneric hybrid lineages (F1-F3) of BSB × TC. A genome-wide transcriptional analysis identified 145-974 expressed recombinant genes in the successive generations of hybrid fish, suggesting the rapid emergence of allelic variation following hybridization. Some gradual changes of gene expression with additive and dominance effects and various cis and trans regulations were observed from F1 to F3 in the two hybrid lineages. These asymmetric patterns of gene expression represent the alternative strategies for counteracting deleterious effects of the subgenomes and improving adaptability of novel hybrids. Furthermore, we identified positive selection and additive expression patterns in transforming growth factor, beta 1b (tgfb1b), which may account for the morphological variations of the pharyngeal jaw in the two hybrid lineages. Our current findings provide insights into the evolution of vertebrate genomes immediately following hybridization.
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Affiliation(s)
- Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Wuhui Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - He Dai
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Fengming Han
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Jun Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Xin Gao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Jialin Cui
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Xiaojing Yan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Guoliang Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Guiming Liu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jia Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Jiaming Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Zhong Wan
- School of Mathematics and Statistics, Central South University, Changsha 410083, China
| | - Conghui Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Jing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Kaikun Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Fangzhou Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Xuming Li
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Hongkun Zheng
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Rong Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Yuqin Shu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Yude Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Qinfeng Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Wei Duan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
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