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Zhao R, Symonds JE, Walker SP, Steiner K, Carter CG, Bowman JP, Nowak BF. Relationship between gut microbiota and Chinook salmon ( Oncorhynchus tshawytscha) health and growth performance in freshwater recirculating aquaculture systems. Front Microbiol 2023; 14:1065823. [PMID: 36825086 PMCID: PMC9941681 DOI: 10.3389/fmicb.2023.1065823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/06/2023] [Indexed: 02/10/2023] Open
Abstract
Gut microbiota play important roles in fish health and growth performance and the microbiome in fish has been shown to be a biomarker for stress. In this study, we surveyed the change of Chinook salmon (Oncorhynchus tshawytscha) gut and water microbiota in freshwater recirculating aquaculture systems (RAS) for 7 months and evaluated how gut microbial communities were influenced by fish health and growth performance. The gut microbial diversity significantly increased in parallel with the growth of the fish. The dominant gut microbiota shifted from a predominance of Firmicutes to Proteobacteria, while Proteobacteria constantly dominated the water microbiota. Photobacterium sp. was persistently the major gut microbial community member during the whole experiment and was identified as the core gut microbiota for freshwater farmed Chinook salmon. No significant variation in gut microbial diversity and composition was observed among fish with different growth performance. At the end of the trial, 36 out of 78 fish had fluid in their swim bladders. These fish had gut microbiomes containing elevated proportions of Enterococcus, Stenotrophomonas, Aeromonas, and Raoultella. Our study supports the growing body of knowledge about the beneficial microbiota associated with modern salmon aquaculture systems and provides additional information on possible links between dysbiosis and gut microbiota for Chinook salmon.
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Affiliation(s)
- Ruixiang Zhao
- Institute for Marine and Antarctic Studies, University of Tasmania, Newnham, TAS, Australia,*Correspondence: Ruixiang Zhao, ✉
| | - Jane E. Symonds
- Cawthron Institute, Nelson, New Zealand,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | | | | | - Chris G. Carter
- Institute for Marine and Antarctic Studies, University of Tasmania, Newnham, TAS, Australia,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - John P. Bowman
- Centre for Food Safety and Innovation, Tasmanian Institute of Agriculture, Hobart, TAS, Australia
| | - Barbara F. Nowak
- Institute for Marine and Antarctic Studies, University of Tasmania, Newnham, TAS, Australia,Barbara F. Nowak, ✉
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Parshukov AN, Fokina NN, Sukhovskaya IV, Kantserova NP, Lysenko LA. Infection and antibiotic treatment have prolonged effect on gut microbiota, muscle and hepatic fatty acids in rainbow trout (Oncorhynchus mykiss). J Appl Microbiol 2022; 133:1709-1724. [PMID: 35717574 DOI: 10.1111/jam.15674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/23/2022] [Accepted: 06/15/2022] [Indexed: 11/27/2022]
Abstract
AIMS The aim of the present study was to investigate the gastrointestinal (GI) microbiota and bacterium-specific fatty acid occurrence in the muscle and hepatic lipids of rainbow trout Oncorhynchus mykiss (Walbaum, 1792), both healthy and those naturally infected with bacterial pathogens. METHODS AND RESULTS From June 2017 (L1) to September 2018 (L8), 74 specimens of rainbow trout Oncorhynchus mykiss (with the average weight from 139.2 ± 7.1 g (L1) to 2191.7 ± 85.1 g (L8)) were studied. Amplicon sequencing targeted to the V3-V4 region of 16S rRNA gene fragments is used for identification of taxonomic composition of gut bacterial communities. Firmicutes, Bacteroidetes, Proteobacteria, Tenericutes, and Fusobacteria were the major phyla. Besides behavioural and physiological manifestations of the bacterial mixed disease (yersiniosis, pseudomonosis, and flavobacteriosis), some disorders induced both the infection and followed antibiotic treatment were detected in the host organism, including (1) a progressive decrease in the content of odd-chain saturated fatty acids of bacterial origin within the trout lipid molecules and (2) abnormalities in trout GI tract microbiota, such as the elimination of LAB and progressive occurrence of certain bacterial taxa, particularly Mycoplasmataceae. CONCLUSIONS The GI bacterial flora varied principally due to Mycoplasmataceae and Lactobacillaceae, which could be considered in the search for bioindicators. The content of specific bacterium-derived fatty acids incorporated into the lipids of trout muscle and hepatic seems to be related to the prevalence of bacterial taxa, and their deficit could be regarded as an early warning sign of microbiota disturbance. SIGNIFICANCE AND IMPACT OF STUDY Our results demonstrated that infectious disease and antibiotic treatment of reared species can cause pertinent imbalance in their gut microbiota and reduce the abundance of specific fatty acids. This can be useful for the sustainable aquaculture industry due to development of early indication technologies for rapid disease diagnosis.
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Affiliation(s)
- A N Parshukov
- Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences, Petrozavodsk, Russia
| | - N N Fokina
- Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences, Petrozavodsk, Russia
| | - I V Sukhovskaya
- Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences, Petrozavodsk, Russia
| | - N P Kantserova
- Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences, Petrozavodsk, Russia
| | - L A Lysenko
- Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences, Petrozavodsk, Russia
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3
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Zhang T, Zhang C, Zhang J, Lin J, Song D, Zhang P, Liu Y, Chen L, Zhang L. Cadmium impairs zebrafish swim bladder development via ROS mediated inhibition of the Wnt / Hedgehog pathway. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 247:106180. [PMID: 35490551 DOI: 10.1016/j.aquatox.2022.106180] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/15/2022] [Accepted: 04/23/2022] [Indexed: 06/14/2023]
Abstract
The posterior swim bladder is an important organ in teleost fishes, that primarily maintains buoyancy and motility for swimming and survival. In this study, we examined the molecular mechanisms of the toxicity of cadmium (Cd) on the early development of the swim bladder in zebrafish. Embryonic Cd exposure resulted in the non-inflation of the swim bladder when the ambient Cd concentration was greater than or equal to 0.25 mg/L. Cd disturbed surfactant lipid distribution and inhibited the formation of all three tissue layers in the swim bladder. Additionally, excessive Cd down-regulated Wnt (fzd3, nkd1, fzd7 and axin2) and Hedgehog (ihh, shh, ptc1 and ptc2) signaling pathways. Conversely, Wnt signaling activation partially neutralized Cd-induced swim bladder developmental defects. Moreover, ROS scavenger reduced Glutathione (GSH) effectively recovered Cd induced defects in swim bladder and Wnt/Hedgehog signaling. Taken together, our results first revealed that Cd caused swim bladder developmental defects via ROS-mediated inhibition of the Wnt and Hedgehog pathways. These results herein provide important data for future toxicological studies and risk assessments of Cd.
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Affiliation(s)
- Ting Zhang
- Key Laboratory of Tropical Marine Bio-resourcesand Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Canchuan Zhang
- Key Laboratory of Tropical Marine Bio-resourcesand Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Jin Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jiangtian Lin
- Key Laboratory of Tropical Marine Bio-resourcesand Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Dongdong Song
- Key Laboratory of Tropical Marine Bio-resourcesand Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Peng Zhang
- Key Laboratory of Tropical Marine Bio-resourcesand Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Yang Liu
- Key Laboratory of Tropical Marine Bio-resourcesand Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Lizhao Chen
- Key Laboratory of Tropical Marine Bio-resourcesand Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Li Zhang
- Key Laboratory of Tropical Marine Bio-resourcesand Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China.
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4
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Donati VL, Madsen L, Middelboe M, Strube ML, Dalsgaard I. The Gut Microbiota of Healthy and Flavobacterium psychrophilum-Infected Rainbow Trout Fry Is Shaped by Antibiotics and Phage Therapies. Front Microbiol 2022; 13:771296. [PMID: 35620089 PMCID: PMC9128845 DOI: 10.3389/fmicb.2022.771296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 03/07/2022] [Indexed: 01/15/2023] Open
Abstract
In the aquaculture sector, there is an increased interest in developing environmentally friendly alternatives to antibiotics in the treatment and prevention of bacterial infections. This requires an understanding of the effects of different treatments on the fish microbiota as a measure for improving the fish health status. In this study, we focused on the freshwater pathogen Flavobacterium psychrophilum and investigated the effects of antibiotics (florfenicol) and phage therapies on the gut microbiota of healthy and infected rainbow trout fry (1–2 g). Florfenicol-coated feed was administered for 10 days, starting two days after the infection procedure. A two-component mix of phage targeting F. psychrophilum (FpV4 and FPSV-D22) was continuously delivered by feed with a prophylactic period of 12 days. Samples of the distal intestine were collected over time (day -1 and 1, 8, and 33 days post-infection) and analyzed by community analysis targeting the 16S rRNA gene (V3–V4 region). Results showed the dysbiosis effect caused both by the infection and by florfenicol administration. Shifts in the overall composition were detected by β-diversity analysis, and changes in specific populations were observed during taxonomic mapping. Measures of α-diversity were only affected in infected fish (large variation observed 1 and 8 dpi). These community alterations disappeared again when fish recovered from the infection and the antibiotic treatment was terminated (33 dpi). Interestingly, phage addition altered the microbiota of the fish independently of the presence of their target bacterium. The overall gut bacterial community in fish fed phage-treated feed was different from the controls at each time point as revealed by β-diversity analysis. However, it was not possible to identify specific bacterial populations responsible for these changes except for an increase of lactic acid bacteria 33 dpi. Overall, the results indicate that the administered phages might affect the complex network of phage-bacteria interactions in the fish gut. Nevertheless, we did not observe negative effects on fish health or growth, and further studies should be directed in understanding if these changes are beneficial or not for the fish health with an additional focus on the host immune response.
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Affiliation(s)
- Valentina Laura Donati
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lone Madsen
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mathias Middelboe
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Inger Dalsgaard
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
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5
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Exploring the gut microbiota composition of Indian major carp, rohu (Labeo rohita), under diverse culture conditions. Genomics 2022; 114:110354. [PMID: 35364266 DOI: 10.1016/j.ygeno.2022.110354] [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: 04/21/2021] [Revised: 02/10/2022] [Accepted: 03/27/2022] [Indexed: 01/14/2023]
Abstract
Gut microbiota of freshwater carps are often investigated for their roles in nutrient absorption, enzyme activities and probiotic properties. However, little is known about core microbiota, assembly pattern and the environmental influence on the gut microbiota of the Indian major carp, rohu. The gut microbial composition of rohu reared in different culture conditions was analysed by 16S rRNA amplicon sequencing. There was variation on gut microbial diversity and composition. A significant negative correlation between dissolved oxygen content (DO) and alpha diversity was observed, thus signifying DO content as one of the key environmental factors that regulated the diversity of rohu gut microbial community. A significant positive correlation was observed between phosphate concentration and abundance of Actinobacteria in different culture conditions. Two phyla, Proteobacteria and Actinobacteria along with OTU750868 (Streptomyces) showed significant (p < 0.05) differences in their abundance among all culture conditions. The Non-metric multidimensional scaling ordination (NMDS) analysis using Bray-Curtis distances, showed the presence of unique gut microbiota in rohu compared to other herbivorous fish. Based on niche breadth, 3 OTUs were identified as core generalists, persistent across all the culture conditions whereas the specialists dominated in the rohu gut microbiota assembly. Co-occurrence network analysis revealed positive interaction within core members while mutual exclusion between core and non-core members. Predicted microbiota function revealed that different culture conditions affected the metabolic capacity of gut microbiota of rohu. The results overall indicated the significant effect of different rearing environments on gut microbiota structure, assembly and inferred community function of rohu which might be useful for effective manipulation of gut microbial communities of rohu to promote better health and growth under different husbandry settings.
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6
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Kashinskaya EN, Simonov EP, Vlasenko PG, Markevich GN, Shokurova AV, Andree KB, Solovyev MM. The gut microbiota of Cystidicola farionis parasitizing the swim bladder of the nosed charr morph Salvelinus malma complex in Lake Kronotskoe (Kamchatka, Russia). J Nematol 2021; 53:e2021-106. [PMID: 34957411 PMCID: PMC8672423 DOI: 10.21307/jofnem-2021-106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Indexed: 12/23/2022] Open
Abstract
Using the approach of sequencing the V3–V4 region of the 16S rRNA gene, we have analyzed the bacterial diversity associated with the gut and “body” (other parts of nematode after dissection: cuticle, epidermis and longitudinal muscles, etc) of Cystidicola farionis parasitizing the swim bladder of different morphotypes of the nosed charr. Comparisons of the gut microbiota of nematodes with their “body” has revealed that the associated microbiota are closely related to each other. Taxonomic analysis indicated that the relative abundances of the dominant nematode-associated bacteria varied with individual fish. The common dominant microbiota of the gut and “body” of nematodes were represented by Aeromonas, Pseudomonas, Shewanella, and Yersinia, while the associated microbiota of the swim bladder of the nosed charr was dominated by Acinetobacter, Cetobacterium, Pajaroellobacter, Paracoccus, Pseudomonas, Shewanella. By comparing the associated microbiota of nematode parasitizing the different morphotypes of the nosed charr the difference in richness estimates (number of OTU’s and Chao1) were revealed between the N1g and N2 morphs.
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Affiliation(s)
- E N Kashinskaya
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia
| | - E P Simonov
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia.,University of Tyumen, Institute of Environmental and Agricultural Biology (X-BIO), 25 Lenina St., Tyumen, 625003, Russia
| | - P G Vlasenko
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia
| | | | - A V Shokurova
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia
| | - K B Andree
- Instituto de Investigación y Tecnología Agroalimentarias; Cultius Aquàtics; San Carlos de la Rapita, Tarragona, ES 08140, Spain
| | - M M Solovyev
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia.,Tomsk State University; Institute of Biology, Ecology, Soil Science, Agriculture, and Forestry; 36 Lenin Ave, Tomsk, 634050, Russia
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7
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Zhu P, Wong MKS, Lin X, Chan TF, Wong CKC, Lai KP, Tse WKF. Changes of the intestinal microbiota along the gut of Japanese Eel (Anguilla japonica). Lett Appl Microbiol 2021; 73:529-541. [PMID: 34265084 DOI: 10.1111/lam.13539] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/21/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
Fish intestine contains different types of microbiomes, and bacteria are the dominant microbiota in fishes. Studies have identified various core gut bacteria in fishes. However, little is known about the composition and their relative functions of gut microbial community along the intestine. To explore this, the current study investigated the microbial community distribution along the gut in Anguilla japonica. By 16S rRNA gene sequencing, we profiled the gut microbiota in eel along the three regions (anterior intestine (AI), the middle intestine (MI) and the posterior intestine (PI)). Results suggested that the three regions did not have significant differences on the observed species and diversities. The cluster tree analysis showed that the bacteria community in MI was closer to PI than the AI. The dominant bacteria in AI were the Proteobacteria, in which the majority was graduated replaced by Bacteroidetes along the gut to PI region. Through PICRUSt analysis, shifts in the bacterial community along the gut were found to affect the genetic information processing pathways. Higher levels of translation and transcriptional pathway activities were found in MI and PI than in AI. The dominant bacterial species were different among the regions and contributed to various biological functions along the gut.
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Affiliation(s)
- P Zhu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi, PR China
| | - M K-S Wong
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - X Lin
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - T F Chan
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - C K C Wong
- Department of Biology, Croucher Institute for Environmental Sciences, Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong Baptist University, Kowloon, Hong Kong
| | - K P Lai
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi, PR China.,Department of Biology, Croucher Institute for Environmental Sciences, Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong Baptist University, Kowloon, Hong Kong.,Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, PR China
| | - W K F Tse
- Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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8
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Sellyei B, Varga Z, Cech G, Varga Á, Székely C. Mycoplasma infections in freshwater carnivorous fishes in Hungary. JOURNAL OF FISH DISEASES 2021; 44:297-304. [PMID: 33128822 DOI: 10.1111/jfd.13283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 05/11/2023]
Abstract
The abundance of mycoplasma-like microorganisms seems to be common in the intestinal tract of fish, but their occurrence in other organs can be considered pathological. Isolation of piscine mycoplasmas is essential to prove their virulence. In this study, a total of 100 specimens of nine freshwater fish species collected from natural waters and fish farms were analysed for the prevalence of mycoplasmas in different extraintestinal organs. Our results demonstrate that mycoplasmas are present in carnivorous fish (pike, wels catfish, black bullhead and pike perch) than in cyprinids more frequently. Among the surveyed organs, they colonize mainly the gills, the kidney and the livers. Although mycoplasmas could be detected in one-fifth of samples by molecular assays, the isolation of mycoplasmas belonged to the M. sualvi cluster within the hominis group of Mycoplasmataceae, but was separate from M. mobile, has been successful only from some specimens originated from wels catfish that was feasible only by special preparation steps (prefreezing, filter sterilization and incubation conditions (long culturing period, etc.). The low-efficiency of isolation trials indicates an extensive gap in our knowledge about piscine mycoplasmas, especially in the field of their nutritional requirements.
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Affiliation(s)
- Boglárka Sellyei
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Zsuzsanna Varga
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Gábor Cech
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Ádám Varga
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Csaba Székely
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
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Effects of dietary organic acids and nature identical compounds on growth, immune parameters and gut microbiota of European sea bass. Sci Rep 2020; 10:21321. [PMID: 33288837 PMCID: PMC7721706 DOI: 10.1038/s41598-020-78441-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 11/19/2020] [Indexed: 11/08/2022] Open
Abstract
A 71-day study was conducted to explore the effect of increasing dietary levels (0, 250, 500, 1000 mg kg feed−1; D0, D250, D500 and D1000, respectively) of a blend of microencapsulated organic acids (OA, specifically citric and sorbic acid) and nature identical compounds (NIC, specifically thymol and vanillin), on growth, intestinal immune parameters and gut microbiota (GM) of European sea bass juveniles reared under normal and subsequently suboptimal environmental conditions (high temperature, 30.0 ± 0.4 °C and low oxygen, 4.6 ± 0.6 mg L−1). OA and NIC did not promote growth, feed utilisation and feed intake at the inclusion tested but induced a significantly upregulation of IL-8, IL-10 and TGFβ. GM analyzed by next-generation sequencing showed that OA and NIC were able to exert prebiotic properties stimulating the development of beneficial bacteria taxa such as Lactobacillus, Leuconostoc, and Bacillus sp. Picrust analyses displayed a significant potential functional reconfiguration of GM promoting a decrease in inflammation-promoting and homeostatic functions at increasing OA and NIC administration. For the first time on this species the exposure to suboptimal rearing conditions was able to modify GM structure reducing LAB and increasing Proteobacteria, findings which were consistent with the inflammatory process observed at mRNA level.
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10
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Khurana H, Singh DN, Singh A, Singh Y, Lal R, Negi RK. Gut microbiome of endangered Tor putitora (Ham.) as a reservoir of antibiotic resistance genes and pathogens associated with fish health. BMC Microbiol 2020; 20:249. [PMID: 32787773 PMCID: PMC7425606 DOI: 10.1186/s12866-020-01911-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 07/19/2020] [Indexed: 01/16/2023] Open
Abstract
Background Tor putitora, the largest freshwater fish of the Indian subcontinent, is an endangered species. Several factors have been attributed towards its continuous population decrease, but very little is known about the gut microbiome of this fish. Also, the fish gut microbiome serves as a reservoir of virulence factors and antibiotic resistance determinants. Therefore, the shotgun metagenomic approach was employed to investigate the taxonomic composition and functional potential of microbial communities present in the gut of Tor putitora, as well as the detection of virulence and antibiotic resistance genes in the microbiome. Results The analysis of bacterial diversity showed that Proteobacteria was predominant phylum, followed by Chloroflexi, Bacteroidetes, and Actinobacteria. Within Proteobacteria, Aeromonas and Caulobacter were chiefly present; also, Klebsiella, Escherichia, and plant symbionts were noticeably detected. Functional characterization of gut microbes endowed the virulence determinants, while surveillance of antibiotic resistance genes showed the dominance of β-lactamase variants. The antibiotic-resistant Klebsiella pneumoniae and Escherichia coli pathovars were also detected. Microbial genome reconstruction and comparative genomics confirmed the presence of Aeromonads, the predominant fish pathogens. Conclusions Gut microbiome of endangered Tor putitora consisted of both commensals and opportunistic pathogens, implying that factors adversely affecting the non-pathogenic population would allow colonization and proliferation of pathogens causing diseased state in asymptomatic Tor putitora. The presence of virulence factors and antibiotic resistance genes suggested the potential risk of dissemination to other bacteria due to horizontal gene transfer, thereby posing a threat to fish and human health. The preservation of healthy gut microflora and limited use of antibiotics are some of the prerequisites for the conservation of this imperilled species.
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Affiliation(s)
- Himani Khurana
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India.,Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Durgesh Narain Singh
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India.,Laboratory of Microbial Pathogenesis, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Anoop Singh
- Laboratory of Microbial Pathogenesis, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Yogendra Singh
- Laboratory of Microbial Pathogenesis, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Rup Lal
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India. .,Present address: The Energy and Resources Institute Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003, India.
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India.
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11
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Fish Skin and Gut Microbiomes Show Contrasting Signatures of Host Species and Habitat. Appl Environ Microbiol 2020; 86:AEM.00789-20. [PMID: 32503908 DOI: 10.1128/aem.00789-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/01/2020] [Indexed: 12/20/2022] Open
Abstract
Teleost fish represent an invaluable repertoire of host species to study the factors shaping animal-associated microbiomes. Several studies have shown that the phylogenetic structure of the fish gut microbiome is driven by species-specific (e.g., host ancestry, genotype, or diet) and habitat-specific (e.g., hydrochemical parameters and bacterioplankton composition) factors. However, our understanding of other host-associated microbial niches, such as the skin mucus microbiome, remains limited. The goal of our study was to explore simultaneously the phylogenetic structure of the fish skin mucus and gut microbiome and compare the effect of species- and habitat-specific drivers on the structure of microbial communities in both tissues. We sampled 114 wild fish from 6 populations of 3 ecologically and phylogenetically contrasting Amazonian teleost species. Water samples were collected at each site, and 10 physicochemical parameters were characterized. The skin mucus, gut, and water microbial communities were characterized using a metabarcoding approach targeting the V3-V4 regions of the 16S rRNA. Our results showed a significant distinction between the phylogenetic profile and diversity of the microbiome from each microbial niche. Skin mucus and bacterioplankton communities were significantly closer in composition than gut and free-living communities. Species-specific factors mostly modulated gut bacterial communities, while the skin mucus microbiome was predominantly associated with environmental physicochemistry and bacterioplankton community structure. These results suggest that the variable skin mucus community is a relevant target for the development of microbial biomarkers of environmental status, while the more conserved gut microbiome is better suited to study long-term host-microbe interactions over evolutionary time scales.IMPORTANCE Whether host-associated microbiomes are mostly shaped by species-specific or environmental factors is still unresolved. In particular, it is unknown to what extent microbial communities from two different host tissues from the same host respond to these factors. Our study is one of the first to focus on the microbiome of teleost fish to shed a light on this topic as we investigate how the phylogenetic structure of microbial communities from two distinct fish tissues are shaped by species- and habitat-specific factors. Our study showed that in contrast to the teleost gut microbiome, skin mucus communities are highly environment dependent. This result has various implications: (i) the skin mucus microbiome should be used, rather than the gut, to investigate bacterial biomarkers of ecosystem perturbance in the wild, and (ii) the gut microbiome is better suited for studies of the drivers of phylosymbiosis, or the coevolution of fish and their symbionts.
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