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Starr K, Montesanto F, Perisho E, Aluthge N, Pegg M, Fernando SC. Gut Microbial Composition of Cyprinella lutrensis (Red Shiner) and Notropis stramineus (Sand Shiner): Insights from Wild Fish Populations. MICROBIAL ECOLOGY 2024; 87:75. [PMID: 38775958 PMCID: PMC11111511 DOI: 10.1007/s00248-024-02386-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 04/27/2024] [Indexed: 05/25/2024]
Abstract
The gut microbiome is a highly intricate ecosystem that exerts a pivotal influence on the host's physiology. Characterizing fish microbiomes is critical to understanding fish physiology and health, but little is known about the ecology and colonization dynamics of microorganisms inhabiting fish species. In this study, we investigated the bacterial communities of two small-bodied fish species, Cyprinella lutrensis (red shiner) and Notropis stramineus (sand shiner), two fish species where gut microbiomes have not been investigated previously and surrounding waters, collected from rivers in Nebraska, USA. Our study focused on evaluating microbial diversity in small-bodied fish and identifying autochthonous microbes present within these species irrespective of location to better understand bacterial community composition and possible roles of such bacterial species. Our results revealed that both red shiner and sand shiner exhibited gut bacterial communities dominated by typical bacterial phyla found in freshwater fish. The phylum Bacteroidota was minimally abundant in both species and significantly lower in relative abundance compared to the surrounding water microbial community. Furthermore, we found that the gut microbiomes of red shiner and sand shiner differed from the microbial community in the surrounding water, suggesting that these fish species contain host-associated bacterial species that may provide benefits to the host such as nutrient digestion and colonization resistance of environmental pathogens. The fish gut bacterial communities were sensitive to environmental conditions such as turbidity, dissolved oxygen, temperature, and total nitrogen. Our findings also show bacterial community differences between fish species; although they shared notable similarities in bacterial taxa at phyla level composition, ASV level analysis of bacterial taxa displayed compositional differences. These findings contribute to a better understanding of the gut bacterial composition of wild, freshwater, small-bodied fish and highlight the influence of intrinsic (host) and environmental factors on shaping the bacterial composition.
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Affiliation(s)
- Krista Starr
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA
| | | | - Esther Perisho
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA
| | - Nirosh Aluthge
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA
| | - Mark Pegg
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA.
| | - Samodha C Fernando
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA.
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Wang XY, Yan J, Xie J. Coculture of Acinetobacter johnsonii and Shewanella putrefaciens Contributes to the ABC Transporter that Impacts Cold Adaption in the Aquatic Food Storage Environment. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10605-10615. [PMID: 38647030 DOI: 10.1021/acs.jafc.4c00885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Acinetobacter johnsonii and Shewanella putrefaciens were identified as specific spoilage organisms in aquatic food. The interactions among specific spoilage organisms under cold stress have a significant impact on the assembly of microbial communities, which play crucial roles in the spoilage and cold adaptation processes. The limited understanding of A. johnsonii and S. putrefaciens interactions in the cold adaptation mechanism hinders the elucidation of their roles in protein and metabolism levels. 4D quantitative proteomic analysis showed that the coculture of A. johnsonii and S. putrefaciens responds to low temperatures through ABC transporter proteins, resulting in phospholipid transport and inner membrane components. SapA and FtsX proteins were significantly upregulated, while LolC, LolD, LolE, PotD, PotA, PotB, and PotC proteins were significantly downregulated. Metabolome assays revealed that metabolites of glutathione and spermidine/putrescin were significantly upregulated, while metabolites of arginine/lysine/ornithine were significantly downregulated and involved in the ABC transporter metabolism. The results of ultramicroscopic analyses showed that the coculture of A. johnsonii and S. putrefaciens surface combined with the presence of the leakage of intracellular contents, suggesting that the bacteria were severely damaged and wrinkled to absorb metabolic nutrients and adapt to cold temperatures.
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Affiliation(s)
- Xin-Yun Wang
- International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200300, China
- College of Food Science & Technology, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquatic Product Processing & Preservation, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Professional Technology Service Platform on Cold Chain Equipment Performance and Energy Saving Evaluation, Shanghai Ocean University, Shanghai 201306, China
| | - Jun Yan
- College of Food Science & Technology, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquatic Product Processing & Preservation, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Professional Technology Service Platform on Cold Chain Equipment Performance and Energy Saving Evaluation, Shanghai Ocean University, Shanghai 201306, China
- National Experimental Teaching Demonstration Center for Food Science and Engineering Shanghai Ocean University, Shanghai 201306, China
| | - Jing Xie
- College of Food Science & Technology, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquatic Product Processing & Preservation, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Professional Technology Service Platform on Cold Chain Equipment Performance and Energy Saving Evaluation, Shanghai Ocean University, Shanghai 201306, China
- National Experimental Teaching Demonstration Center for Food Science and Engineering Shanghai Ocean University, Shanghai 201306, China
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Wang LC, Chen LH, Chiu YC, Liou CY, Chen HC, Lu CY, Chen JL. Teleost skin microbiome: An intimate interplay between the environment and the host immunity. FISH & SHELLFISH IMMUNOLOGY 2023; 139:108869. [PMID: 37285875 DOI: 10.1016/j.fsi.2023.108869] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/22/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
The mucosal microbiome plays a role in regulating host health. The research conducted in humans and mice has governed and detailed the information on microbiome-host immunity interactions. Teleost fish, different from humans and mice, lives in and relies on the aquatic environment and is subjected to environmental variation. The growth of teleost mucosal microbiome studies, the majority in the gastrointestinal tract, has emphasized the essential role of the teleost microbiome in growth and health. However, research in the teleost external surface microbiome, as the skin microbiome, has just started. In this review, we examine the general findings in the colonization of the skin microbiome, how the skin microbiome is subjected to environmental change and the reciprocal regulation with the host immune system, and the current challenges that potential study models can address. The information collected from teleost skin microbiome-host immunity research would help future teleost culturing from the potential parasitic infestation and bacterial infection as foreseeing growing threats.
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Affiliation(s)
- Liang-Chun Wang
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan; Committee of Fisheries Extension Service, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan.
| | - Li-Hsuan Chen
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan; Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | - Yu-Che Chiu
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Chung-Yi Liou
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Han-Chung Chen
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Chia-Yun Lu
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Jian-Lin Chen
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
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Al-Ashhab A, Alexander-Shani R, Avrahami Y, Ehrlich R, Strem RI, Meshner S, Shental N, Sharon G. Sparus aurata and Lates calcarifer skin microbiota under healthy and diseased conditions in UV and non-UV treated water. Anim Microbiome 2022; 4:42. [PMID: 35729615 PMCID: PMC9210813 DOI: 10.1186/s42523-022-00191-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/10/2022] [Indexed: 11/15/2022] Open
Abstract
Background The welfare of farmed fish is influenced by numerous environmental and management factors. Fish skin is an important site for immunity and a major route by which infections are acquired. The objective of this study was to characterize bacterial composition variability on skin of healthy, diseased, and recovered Gilthead Seabream (Sparus aurata) and Barramundi (Lates calcarifer). S. aurata, which are highly sensitive to gram-negative bacteria, were challenged with Vibrio harveyi. In addition, and to provide a wider range of infections, both fish species (S. aurata and L. calcarifer) were infected with gram-positive Streptococcus iniae, to compare the response of the highly sensitive L. calcarifer to that of the more resistant S. aurata. All experiments also compared microbial communities found on skin of fish reared in UV (a general practice used in aquaculture) and non-UV treated water tanks. Results Skin swab samples were taken from different areas of the fish (lateral lines, abdomen and gills) prior to controlled infection, and 24, 48 and 72 h, 5 days, one week and one-month post-infection. Fish skin microbial communities were determined using Illumina iSeq100 16S rDNA for bacterial sequencing. The results showed that naturally present bacterial composition is similar on all sampled fish skin sites prior to infection, but the controlled infections (T1 24 h post infection) altered the bacterial communities found on fish skin. Moreover, when the naturally occurring skin microbiota did not quickly recover, fish mortality was common following T1 (24 h post infection). We further confirmed the differences in bacterial communities found on skin and in the water of fish reared in non-UV and UV treated water under healthy and diseased conditions. Conclusions Our experimental findings shed light on the fish skin microbiota in relation to fish survival (in diseased and healthy conditions). The results can be harnessed to provide management tools for commercial fish farmers; predicting and preventing fish diseases can increase fish health, welfare, and enhance commercial fish yields. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00191-y.
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Gallet A, Yao EK, Foucault P, Bernard C, Quiblier C, Humbert JF, Coulibaly JK, Troussellier M, Marie B, Duperron S. Fish gut-associated bacterial communities in a tropical lagoon (Aghien lagoon, Ivory Coast). Front Microbiol 2022; 13:963456. [PMID: 36246274 PMCID: PMC9556852 DOI: 10.3389/fmicb.2022.963456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Aghien lagoon (Ivory Coast) is a eutrophic freshwater lagoon that harbors high biomasses of phytoplankton. Despite Increasing interest in fish gut microbiomes diversity and functions, little data is currently available regarding wild species from tropical west African lakes. Here, gut-associated bacterial communities are investigated in four fish species that are consumed by locale populations, namely the Cichlidae Hemichromis fasciatus, Tilapia guineensis and Sarotherodon melanotheron, and the Claroteidae Chrysichthys nigrodigitatus. Species-related differences are identified, that can be attributed to host phylogeny and diet. Important variations throughout the year are observed in T. guineensis and C. nigrodigitatus. This result emphasized the importance of time-series sampling and comparison with environmental variables even in tropical regions, that are not often conducted in wild populations. Effects of environmental factors (anthropogenic or not) on the microbiota and potential outcomes for fish health and populations sustainability need to be further explored. Interestingly, fish appear as major reservoirs of bacterial diversity, suggesting that they could contribute to the overall stability and resilience of bacterial communities present in the Aghien lagoon.
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Affiliation(s)
- Alison Gallet
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Eric Kouamé Yao
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
- Institut Pasteur de Côte d’Ivoire, Abidjan, Côte d’Ivoire
| | - Pierre Foucault
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Cécile Bernard
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Catherine Quiblier
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
- Université Paris Cité, UFR Sciences du Vivant, Paris, France
| | | | | | - Marc Troussellier
- MARBEC, Centre National de la Recherche Scientifique, Université Montpellier, IFREMER, IRD, Montpellier, France
| | - Benjamin Marie
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Sébastien Duperron
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
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Huang Z, Zhan M, Cheng G, Lin R, Zhai X, Zheng H, Wang Q, Yu Y, Xu Z. IHNV Infection Induces Strong Mucosal Immunity and Changes of Microbiota in Trout Intestine. Viruses 2022; 14:v14081838. [PMID: 36016461 PMCID: PMC9415333 DOI: 10.3390/v14081838] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
The fish intestinal mucosa is among the main sites through which environmental microorganisms interact with the host. Therefore, this tissue not only constitutes the first line of defense against pathogenic microorganisms but also plays a crucial role in commensal colonization. The interaction between the mucosal immune system, commensal microbiota, and viral pathogens has been extensively described in the mammalian intestine. However, very few studies have characterized these interactions in early vertebrates such as teleosts. In this study, rainbow trout (Oncorhynchus mykiss) was infected with infectious hematopoietic necrosis virus (IHNV) via a recently developed immersion method to explore the effects of viral infection on gut immunity and microbial community structure. IHNV successfully invaded the gut mucosa of trout, resulting in severe tissue damage, inflammation, and an increase in gut mucus. Moreover, viral infection triggered a strong innate and adaptive immune response in the gut, and RNA−seq analysis indicated that both antiviral and antibacterial immune pathways were induced, suggesting that the viral infection was accompanied by secondary bacterial infection. Furthermore, 16S rRNA sequencing also revealed that IHNV infection induced severe dysbiosis, which was characterized by large increases in the abundance of Bacteroidetes and pathobiont proliferation. Moreover, the fish that survived viral infection exhibited a reversal of tissue damage and inflammation, and their microbiome was restored to its pre−infection state. Our findings thus demonstrated that the relationships between the microbiota and gut immune system are highly sensitive to the physiological changes triggered by viral infection. Therefore, opportunistic bacterial infection must also be considered when developing strategies to control viral infection.
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Affiliation(s)
- Zhenyu Huang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengting Zhan
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Gaofeng Cheng
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruiqi Lin
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xue Zhai
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Haiou Zheng
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingchao Wang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongyao Yu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhen Xu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- Correspondence:
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Antibacterial Effect of Dihydromyricetin on Specific Spoilage Organisms of Hybrid Grouper. J FOOD QUALITY 2021. [DOI: 10.1155/2021/5569298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
This study aimed to investigate the mechanism of antibacterial activity level inhibition of dihydromyricetin (DMY) against specific spoilage bacteria of grouper. Firstly, the specific spoilage bacteria of grouper in the cold storage process are Pseudomonas antarctica (P. antarctica), which are selected by calculating the spoilage metabolite yield factor. It was determined that the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of DMY against grouper spoilage bacteria were 2.0 mg/mL and 6.4 mg/mL, respectively. DMY was added to the matrix of chitosan and sodium alginate, and DMY emulsions of different concentrations (0 MIC, 1 MIC, 2 MIC, 4 MIC) were prepared and characterized by differential calorimetry methods. Through analyzing cell permeability, enzyme activity, and images of the confocal laser scanning microscope (CLSM), we further studied the antibacterial mechanism of DMY emulsion on specific spoilage bacteria. The results showed that, with the increase of DMY concentration in the treatment group, the leakage of nucleic acid and protein increased significantly, the activity of ATPase and three critical enzymes in the Embden-Meyerhof-Parnas (EMP) pathway decreased significantly, and the activity of AKPase did not decrease significantly, . The metabolic activity and viability are reduced considerably. Analysis of the above results shows that DMY inhibits the growth and reproduction of P. antarctica by interfering with the metabolic activity of bacteria and destroying the function of bacterial cell membranes but has no inhibitory effect on the activity of AKPase. This study proves that DMY could be an effective and natural antibacterial agent against specific spoilage bacteria in aquatic products.
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