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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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Jiang XR, Dai YY, Wang YR, Guo K, Du Y, Gao JF, Lin LH, Li P, Li H, Ji X, Qu YF. Dietary and Sexual Correlates of Gut Microbiota in the Japanese Gecko, Gekko japonicus (Schlegel, 1836). Animals (Basel) 2023; 13:ani13081365. [PMID: 37106928 PMCID: PMC10134999 DOI: 10.3390/ani13081365] [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: 03/01/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Numerous studies have demonstrated that multiple intrinsic and extrinsic factors shape the structure and composition of gut microbiota in a host. The disorder of the gut microbiota may trigger various host diseases. Here, we collected fecal samples from wild-caught Japanese geckos (Gekko japonicus) and captive conspecifics fed with mealworms (mealworm-fed geckos) and fruit flies (fly-fed geckos), aiming to examine the dietary and sexual correlates of the gut microbiota. We used 16S rRNA gene sequencing technology to determine the composition of the gut microbiota. The dominant phyla with a mean relative abundance higher than 10% were Verrucomicrobiota, Bacteroidota, and Firmicutes. Gut microbial community richness and diversity were higher in mealworm-fed geckos than in wild geckos. Neither community evenness nor beta diversity of gut microbiota differed among wild, mealworm-fed, and fly-fed geckos. The beta rather than alpha diversity of gut microbiota was sex dependent. Based on the relative abundance of gut bacteria and their gene functions, we concluded that gut microbiota contributed more significantly to the host's metabolic and immune functions. A higher diversity of gut microbiota in mealworm-fed geckos could result from higher chitin content in insects of the order Coleoptera. This study not only provides basic information about the gut microbiota of G. japonicus but also shows that gut microbiota correlates with dietary habits and sex in the species.
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Affiliation(s)
- Xin-Ru Jiang
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ying-Yu Dai
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yu-Rong Wang
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Kun Guo
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China
| | - Yu Du
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China
| | - Jian-Fang Gao
- Herpetological Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Long-Hui Lin
- Herpetological Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Peng Li
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Hong Li
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Xiang Ji
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China
| | - Yan-Fu Qu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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Martyniuk CJ, Buerger AN, Vespalcova H, Rudzanova B, Sohag SR, Hanlon AT, Ginn PE, Craft SL, Smetanova S, Budinska E, Bisesi JH, Adamovsky O. Sex-dependent host-microbiome dynamics in zebrafish: Implications for toxicology and gastrointestinal physiology. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100993. [PMID: 35533547 DOI: 10.1016/j.cbd.2022.100993] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 03/04/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
The physiology of males and females can be vastly different, complicating interpretation of toxicological and physiological data. The objectives of this study were to elucidate the sex differences in the microbiome-gastrointestinal (GI) transcriptome of adult zebrafish. We compared microbial composition and diversity in both males and females fed the same diet and housed in the same environment. There were no sex-specific differences in weight gain nor gastrointestinal morphology based on histopathology. There was no difference in gut microbial diversity, richness (Shannon and Chao1 index) nor predicted functional composition of the microbiome between males and females. Prior to post-hoc correction, male zebrafish showed higher abundance for the bacterial families Erythrobacteraceae and Lamiaceae, both belonging to the phyla Actinobacteria and Proteobacteria. At the genus level, Lamia and Altererythrobacter were more dominant in males and an unidentified genus in Bacteroidetes was more abundant in females. There were 16 unique differentially expressed transcripts in the gastrointestinal tissue between male and female zebrafish (FDR corrected, p < 0.05). Relative to males, the mRNA expression for trim35-9, slc25a48, chchd3b, csad, and hsd17b3 were lower in female GI while cyp2k6, adra2c, and bckdk were higher in the female GI. Immune and lipid-related gene network expression differed between the sexes (i.e., cholesterol export and metabolism) as well as networks related to gastric motility, gastrointestinal system absorption and digestion. Such data provide clues as to putative differences in gastrointestinal physiology between male and female zebrafish. This study identifies host-transcriptome differences that can be considered when interpreting the microgenderome of zebrafish in studies investigating GI physiology and toxicology of fishes.
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Affiliation(s)
- Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, UF Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Amanda N Buerger
- Department of Environmental and Global Health and Center for Environmental and Human Toxicology, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Hana Vespalcova
- Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 753/5, Brno, Czech Republic
| | - Barbora Rudzanova
- Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 753/5, Brno, Czech Republic
| | - Shahadur R Sohag
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, UF Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Amy T Hanlon
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, UF Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Pamela E Ginn
- Department of Comparative, Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Serena L Craft
- Department of Comparative, Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Sona Smetanova
- Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 753/5, Brno, Czech Republic
| | - Eva Budinska
- Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 753/5, Brno, Czech Republic
| | - Joseph H Bisesi
- Department of Environmental and Global Health and Center for Environmental and Human Toxicology, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Ondrej Adamovsky
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, UF Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA; Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 753/5, Brno, Czech Republic.
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Liu C, Zhao LP, Shen YQ. A systematic review of advances in intestinal microflora of fish. FISH PHYSIOLOGY AND BIOCHEMISTRY 2021; 47:2041-2053. [PMID: 34750711 DOI: 10.1007/s10695-021-01027-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 10/13/2021] [Indexed: 05/26/2023]
Abstract
Intestinal flora is closely related to the health of organisms and the occurrence and development of diseases. The study of intestinal flora will provide a reference for the research and treatment of disease pathogenesis. Upon hatching, fish begin to acquire a microbial community in the intestine. In response to the environment and the host itself, the fish gut eventually develops a unique set of microflora, with some microorganisms being common to different fish. The existence of intestinal microorganisms creates an excellent microecological environment for the host, while the fish symbiotically provides conditions for the growth and reproduction of intestinal microflora. The intestinal flora and the host are interdependent and mutually restrictive. This review mainly describes the formation of fish intestinal flora, the function of normal intestinal flora, factors affecting intestinal flora, and a series of fish models.
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Affiliation(s)
- Chang Liu
- Wuxi Medical School of Jiangnan University, Wuxi, China
| | - Li-Ping Zhao
- Wuxi Medical School of Jiangnan University, Wuxi, China
| | - Yan-Qin Shen
- Wuxi Medical School of Jiangnan University, Wuxi, China.
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5
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Park J, Kim EB. Insights into the Gut and Skin Microbiome of Freshwater Fish, Smelt (Hypomesus nipponensis). Curr Microbiol 2021; 78:1798-1806. [PMID: 33738530 DOI: 10.1007/s00284-021-02440-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 03/01/2021] [Indexed: 12/19/2022]
Abstract
Freshwater smelt (Hypomesus nipponensis) is a planktivorous fish found in the river of South Korea, Japan, China, and Russia. Because of its specific characteristics living in the cold temperature, this species is economically valuable in the various countries that held winter festival. The body size of the smelt is too small, so people consumed raw smelt during the winter festival sometimes. However, the microbial studies of smelt are nonexistent. Here, we characterized and compared the bacterial communities in the gut and skin of freshwater smelts. We amplified, sequenced, and analyzed the V4 regions of bacterial 16S rRNA genes from freshwater smelts. The microbial diversity in the skin (375 OTUs) was much greater than that in the gut (250 OTUs). At the phylum level, Proteobacteria (gut: 51.5%; skin: 52.9%), Firmicutes (gut: 30.6%; skin: 25.4%), Bacteroidetes (gut: 7.7%; skin: 14.7%), and Actinobacteria (gut: 5.2%; skin: 3.8%) were predominant in both organs. At the genus level, Sphingomonas (gut: 24.9%; skin: 4.4%, P < 0.01) was more abundant in the gut, whereas Acinetobacter (gut: 0.8%; skin: 11.8%, P = 0.02) and Pseudomonas (gut: 0.3%; skin: 2.1%, P = 0.01) were more abundant in the skin. Both beneficial (Lactobacillus) and harmful (Staphylococcus and Streptococcus) bacteria were detected in both organs, even under freshwater conditions. These results revealed that smelts have their own unique microbial communities in the gut and skin. Our findings broaden the understanding of planktivorous freshwater fish microbiomes and provide new insights into fish microbiomes for ensuring food safety.
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Affiliation(s)
- Jongbin Park
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, 24341, Kangwon-do, Republic of Korea
| | - Eun Bae Kim
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, 24341, Kangwon-do, Republic of Korea. .,Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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Jiang M, Xu M, Ying C, Yin D, Dai P, Yang Y, Ye K, Liu K. The intestinal microbiota of lake anchovy varies according to sex, body size, and local habitat in Taihu Lake, China. Microbiologyopen 2019; 9:e00955. [PMID: 31782623 PMCID: PMC6957416 DOI: 10.1002/mbo3.955] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/21/2019] [Accepted: 09/21/2019] [Indexed: 12/16/2022] Open
Abstract
Lake anchovy (Coilia ectenes taihuensis) is a sedentary, dominant fish species that forms an unmanaged fishery in Taihu Lake, eastern China. The environment and developmental stage of lake anchovy are likely important drivers of their gut microbiome, which is linked to host health and development. To investigate the relationship between the gut microbiome and three defined factors (fish sex, fish body size, and the local habitat), high‐throughput sequencing of the 16S ribosomal RNA gene was used to study the microorganisms of 184 fish samples and four water samples collected in Taihu Lake. Four dominant bacterial phyla (Proteobacteria, Firmicutes, Planctomycetes, and Cyanobacteria) were present in all fish samples. We compared the microbial communities of males and females and found that the relative abundance of Corynebacteriaceae was significantly higher in males than in females, while the opposite trend was detected for Sphingomonadaceae. We also discovered that the relative abundance of Firmicutes was positively correlated with fish body size and that the proportions of Proteobacteria and Tenericutes were lower in larger fish than in fish of other sizes. Finally, we found that the difference in microbial richness between eastern and northern Taihu Lake was the most marked. Lake anchovy was rich in Lactobacillus and Clostridium in the eastern site, while those in the northern site had the highest abundance of Sphingomonas and Methylobacterium, suggesting that the local habitat may also influence the intestinal microbiome. These findings will not only help researchers understand the community composition of the intestinal microflora of lake anchovy but also contribute to the protection of fish resources in Lake Taihu and the sustainable use of lake anchovy.
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Affiliation(s)
- Min Jiang
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, WuXi, China
| | - Mengyuan Xu
- Wuxi Fishery College, Nanjing Agricultural University, Wuxi, China
| | - Congping Ying
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, WuXi, China
| | - Denghua Yin
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, WuXi, China
| | - Pei Dai
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, WuXi, China
| | - Yanping Yang
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, WuXi, China
| | - Kun Ye
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, WuXi, China
| | - Kai Liu
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, WuXi, China.,Wuxi Fishery College, Nanjing Agricultural University, Wuxi, China
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