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Kawser AQMR, Hoque MN, Rahman MS, Sakif TI, Coffey TJ, Islam T. Unveiling the gut bacteriome diversity and distribution in the national fish hilsa (Tenualosa ilisha) of Bangladesh. PLoS One 2024; 19:e0303047. [PMID: 38691556 PMCID: PMC11062526 DOI: 10.1371/journal.pone.0303047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/09/2024] [Indexed: 05/03/2024] Open
Abstract
The field of fish microbiome research has rapidly been advancing, primarily focusing on farmed or laboratory fish species rather than natural or marine fish populations. This study sought to reveal the distinctive gut bacteriome composition and diversity within the anadromous fish species Tenualosa ilisha (hilsa), which holds the status of being the national fish of Bangladesh. We conducted an analysis on 15 gut samples obtained from 15 individual hilsa fishes collected from three primary habitats (e.g., freshwater = 5, brackish water = 5 and marine water = 5) in Bangladesh. The analysis utilized metagenomics based on 16S rRNA gene sequencing targeting the V3-V4 regions. Our comprehensive identification revealed a total of 258 operational taxonomic units (OTUs). The observed OTUs were represented by six phyla, nine classes, 19 orders, 26 families and 40 genera of bacteria. Our analysis unveiled considerable taxonomic differences among the habitats (freshwater, brackish water, and marine water) of hilsa fishes, as denoted by a higher level of shared microbiota (p = 0.007, Kruskal-Wallis test). Among the identified genera in the gut of hilsa fishes, including Vagococcus, Morganella, Enterobacter, Plesiomonas, Shigella, Clostridium, Klebsiella, Serratia, Aeromonas, Macrococcus, Staphylococcus, Proteus, and Hafnia, several are recognized as fish probiotics. Importantly, some bacterial genera such as Sinobaca, Synechococcus, Gemmata, Serinicoccus, Saccharopolyspora, and Paulinella identified in the gut of hilsa identified in this study have not been reported in any aquatic or marine fish species. Significantly, we observed that 67.50% (27/40) of bacterial genera were found to be common among hilsa fishes across all three habitats. Our findings offer compelling evidence for the presence of both exclusive and communal bacteriomes within the gut of hilsa fishes, exhibiting potential probiotic properties. These observations could be crucial for guiding future microbiome investigations in this economically significant fish species.
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Affiliation(s)
- A. Q. M. Robiul Kawser
- Department of Aquaculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - M. Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - M. Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Tahsin Islam Sakif
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, West Virginia, United States of America
| | - Tracey J. Coffey
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
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Knobloch S, Skirnisdóttir S, Dubois M, Mayolle L, Kolypczuk L, Leroi F, Leeper A, Passerini D, Marteinsson VÞ. The gut microbiome of farmed Arctic char ( Salvelinus alpinus) is shaped by feeding stage and nutrient presence. FEMS MICROBES 2024; 5:xtae011. [PMID: 38745980 PMCID: PMC11092275 DOI: 10.1093/femsmc/xtae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/06/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
The gut microbiome plays an important role in maintaining health and productivity of farmed fish. However, the functional role of most gut microorganisms remains unknown. Identifying the stable members of the gut microbiota and understanding their functional roles could aid in the selection of positive traits or act as a proxy for fish health in aquaculture. Here, we analyse the gut microbial community of farmed juvenile Arctic char (Salvelinus alpinus) and reconstruct the metabolic potential of its main symbionts. The gut microbiota of Arctic char undergoes a succession in community composition during the first weeks post-hatch, with a decrease in Shannon diversity and the establishment of three dominant bacterial taxa. The genome of the most abundant bacterium, a Mycoplasma sp., shows adaptation to rapid growth in the nutrient-rich gut environment. The second most abundant taxon, a Brevinema sp., has versatile metabolic potential, including genes involved in host mucin degradation and utilization. However, during periods of absent gut content, a Ruminococcaceae bacterium becomes dominant, possibly outgrowing all other bacteria through the production of secondary metabolites involved in quorum sensing and cross-inhibition while benefiting the host through short-chain fatty acid production. Whereas Mycoplasma is often present as a symbiont in farmed salmonids, we show that the Ruminococcaceae species is also detected in wild Arctic char, suggesting a close evolutionary relationship between the host and this symbiotic bacterium.
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Affiliation(s)
- Stephen Knobloch
- Matís ohf., Microbiology Research Group, Vínlandsleið 12, 113 Reykjavík, Iceland
- Department of Food Technology, University of Applied Sciences Fulda, Leipziger Strasse 123, 36037 Fulda, Germany
| | | | - Marianne Dubois
- ESBS/University of Strasbourg, 300 Bd Sébastien Brant, 67085 Strasbourg, France
| | - Lucie Mayolle
- University of Technology of Compiègne, Rue Roger Couttolenc, 60203 Compiègne, France
| | - Laetitia Kolypczuk
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, BP 21105, F-44000 Nantes, France
| | - Françoise Leroi
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, BP 21105, F-44000 Nantes, France
| | - Alexandra Leeper
- Matís ohf., Microbiology Research Group, Vínlandsleið 12, 113 Reykjavík, Iceland
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Arboretveien 6, 1430 Ås, Norway
- Iceland Ocean Cluster, Department of Research and Innovation, Grandagarður 16, 101 Reykjavík, Iceland
| | - Delphine Passerini
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, BP 21105, F-44000 Nantes, France
| | - Viggó Þ Marteinsson
- Matís ohf., Microbiology Research Group, Vínlandsleið 12, 113 Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Sæmundargata 2, 101 Reykjavik, Iceland
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Auclert LZ, Chhanda MS, Derome N. Interwoven processes in fish development: microbial community succession and immune maturation. PeerJ 2024; 12:e17051. [PMID: 38560465 PMCID: PMC10981415 DOI: 10.7717/peerj.17051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 02/13/2024] [Indexed: 04/04/2024] Open
Abstract
Fishes are hosts for many microorganisms that provide them with beneficial effects on growth, immune system development, nutrition and protection against pathogens. In order to avoid spreading of infectious diseases in aquaculture, prevention includes vaccinations and routine disinfection of eggs and equipment, while curative treatments consist in the administration of antibiotics. Vaccination processes can stress the fish and require substantial farmer's investment. Additionally, disinfection and antibiotics are not specific, and while they may be effective in the short term, they have major drawbacks in the long term. Indeed, they eliminate beneficial bacteria which are useful for the host and promote the raising of antibiotic resistance in beneficial, commensal but also in pathogenic bacterial strains. Numerous publications highlight the importance that plays the diversified microbial community colonizing fish (i.e., microbiota) in the development, health and ultimately survival of their host. This review targets the current knowledge on the bidirectional communication between the microbiota and the fish immune system during fish development. It explores the extent of this mutualistic relationship: on one hand, the effect that microbes exert on the immune system ontogeny of fishes, and on the other hand, the impact of critical steps in immune system development on the microbial recruitment and succession throughout their life. We will first describe the immune system and its ontogeny and gene expression steps in the immune system development of fishes. Secondly, the plurality of the microbiotas (depending on host organism, organ, and development stage) will be reviewed. Then, a description of the constant interactions between microbiota and immune system throughout the fish's life stages will be discussed. Healthy microbiotas allow immune system maturation and modulation of inflammation, both of which contribute to immune homeostasis. Thus, immune equilibrium is closely linked to microbiota stability and to the stages of microbial community succession during the host development. We will provide examples from several fish species and describe more extensively the mechanisms occurring in zebrafish model because immune system ontogeny is much more finely described for this species, thanks to the many existing zebrafish mutants which allow more precise investigations. We will conclude on how the conceptual framework associated to the research on the immune system will benefit from considering the relations between microbiota and immune system maturation. More precisely, the development of active tolerance of the microbiota from the earliest stages of life enables the sustainable establishment of a complex healthy microbial community in the adult host. Establishing a balanced host-microbiota interaction avoids triggering deleterious inflammation, and maintains immunological and microbiological homeostasis.
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Affiliation(s)
- Lisa Zoé Auclert
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Mousumi Sarker Chhanda
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
- Department of Aquaculture, Faculty of Fisheries, Hajee Mohammad Danesh Science and Technology University, Basherhat, Bangladesh
| | - Nicolas Derome
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
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Amill F, Gauthier J, Rautio M, Derome N. Characterization of gill bacterial microbiota in wild Arctic char ( Salvelinus alpinus) across lakes, rivers, and bays in the Canadian Arctic ecosystems. Microbiol Spectr 2024; 12:e0294323. [PMID: 38329329 PMCID: PMC10923216 DOI: 10.1128/spectrum.02943-23] [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: 09/07/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
Teleost gill mucus has a highly diverse microbiota, which plays an essential role in the host's fitness and is greatly influenced by the environment. Arctic char (Salvelinus alpinus), a salmonid well adapted to northern conditions, faces multiple stressors in the Arctic, including water chemistry modifications, that could negatively impact the gill microbiota dynamics related to the host's health. In the context of increasing environmental disturbances, we aimed to characterize the taxonomic distribution of transcriptionally active taxa within the bacterial gill microbiota of Arctic char in the Canadian Arctic in order to identify active bacterial composition that correlates with environmental factors. For this purpose, a total of 140 adult anadromous individuals were collected from rivers, lakes, and bays belonging to five Inuit communities located in four distinct hydrologic basins in the Canadian Arctic (Nunavut and Nunavik) during spring (May) and autumn (August). Various environmental factors were collected, including latitudes, water and air temperatures, oxygen concentration, pH, dissolved organic carbon (DOC), salinity, and chlorophyll-a concentration. The taxonomic distribution of transcriptionally active taxa within the gill microbiota was quantified by 16S rRNA gene transcripts sequencing. The results showed differential bacterial activity between the different geographical locations, explained by latitude, salinity, and, to a lesser extent, air temperature. Network analysis allowed the detection of a potential dysbiosis signature (i.e., bacterial imbalance) in fish gill microbiota from Duquet Lake in the Hudson Strait and the system Five Mile Inlet connected to the Hudson Bay, both showing the lowest alpha diversity and connectivity between taxa.IMPORTANCEThis paper aims to decipher the complex relationship between Arctic char (Salvelinus alpinus) and its symbiotic microbial consortium in gills. This salmonid is widespread in the Canadian Arctic and is the main protein and polyunsaturated fatty acids source for Inuit people. The influence of environmental parameters on gill microbiota in wild populations remains poorly understood. However, assessing the Arctic char's active gill bacterial community is essential to look for potential pathogens or dysbiosis that could threaten wild populations. Here, we concluded that Arctic char gill microbiota was mainly influenced by latitude and air temperature, the latter being correlated with water temperature. In addition, a dysbiosis signature detected in gill microbiota was potentially associated with poor fish health status recorded in these disturbed environments. With those results, we hypothesized that rapid climate change and increasing anthropic activities in the Arctic might profoundly disturb Arctic char gill microbiota, affecting their survival.
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Affiliation(s)
- Flora Amill
- Institute of Integrative and Systems Biology, Laval University, Quebec, Canada
| | - Jeff Gauthier
- Institute of Integrative and Systems Biology, Laval University, Quebec, Canada
| | - Milla Rautio
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Quebec, Canada
| | - Nicolas Derome
- Institute of Integrative and Systems Biology, Laval University, Quebec, Canada
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Bell AG, McMurtrie J, Bolaños LM, Cable J, Temperton B, Tyler CR. Influence of host phylogeny and water physicochemistry on microbial assemblages of the fish skin microbiome. FEMS Microbiol Ecol 2024; 100:fiae021. [PMID: 38366921 PMCID: PMC10903987 DOI: 10.1093/femsec/fiae021] [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: 12/05/2023] [Revised: 01/10/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024] Open
Abstract
The skin of fish contains a diverse microbiota that has symbiotic functions with the host, facilitating pathogen exclusion, immune system priming, and nutrient degradation. The composition of fish skin microbiomes varies across species and in response to a variety of stressors, however, there has been no systematic analysis across these studies to evaluate how these factors shape fish skin microbiomes. Here, we examined 1922 fish skin microbiomes from 36 studies that included 98 species and nine rearing conditions to investigate associations between fish skin microbiome, fish species, and water physiochemical factors. Proteobacteria, particularly the class Gammaproteobacteria, were present in all marine and freshwater fish skin microbiomes. Acinetobacter, Aeromonas, Ralstonia, Sphingomonas and Flavobacterium were the most abundant genera within freshwater fish skin microbiomes, and Alteromonas, Photobacterium, Pseudoalteromonas, Psychrobacter and Vibrio were the most abundant in saltwater fish. Our results show that different culturing (rearing) environments have a small but significant effect on the skin bacterial community compositions. Water temperature, pH, dissolved oxygen concentration, and salinity significantly correlated with differences in beta-diversity but not necessarily alpha-diversity. To improve study comparability on fish skin microbiomes, we provide recommendations for approaches to the analyses of sequencing data and improve study reproducibility.
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Affiliation(s)
- Ashley G Bell
- College of Life and Environmental Sciences, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
- Sustainable Aquaculture Futures, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
| | - Jamie McMurtrie
- College of Life and Environmental Sciences, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
- Sustainable Aquaculture Futures, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
| | - Luis M Bolaños
- College of Life and Environmental Sciences, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
| | - Jo Cable
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, United Kingdom
| | - Ben Temperton
- College of Life and Environmental Sciences, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
| | - Charles R Tyler
- College of Life and Environmental Sciences, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
- Sustainable Aquaculture Futures, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
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Biswas S, Foysal MJ, Mannan A, Sharifuzzaman SM, Tanzina AY, Tanni AA, Sharmen F, Hossain MM, Chowdhury MSN, Tay ACY, Islam SMR. Microbiome pattern and diversity of an anadromous fish, hilsa shad (Tenualosa ilisha). Mol Biol Rep 2023; 51:38. [PMID: 38158480 DOI: 10.1007/s11033-023-08965-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 10/30/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND The host-microbe interactions are complex, dynamic and context-dependent. In this regard, migratory fish species like hilsa shad (Tenualosa ilisha), which migrates from seawater to freshwater for spawning, provides a unique system for investigating the microbiome under an additional change in fish's habitat. This work was undertaken to detect taxonomic variation of microbiome and their function in the migration of hilsa. METHODS AND RESULTS The study employed 16S rRNA amplicon-based metagenomic analysis to scrutinize bacterial diversity in hilsa gut, skin mucus and water. Thus, a total of 284 operational taxonomic units (OTUs), 9 phyla, 35 orders and 121 genera were identified in all samples. More than 60% of the identified bacteria were Proteobacteria with modest abundance (> 5%) of Firmicutes, Bacteroidetes and Actinobacteria. Leucobacter in gut and Serratia in skin mucus were the core bacterial genera, while Acinetobacter, Pseudomonas and Psychrobacter exhibited differential compositions in gut, skin mucus and water. CONCLUSIONS Representative fresh-, brackish- and seawater samples of hilsa habitats were primarily composed of Vibrio, Serratia and Psychrobacter, and their diversity in seawater was significantly higher (P < 0.05) than freshwater. Overall, salinity and water microbiota had an influence on the microbial composition of hilsa shad, contributing to host metabolism and adaptation processes. This pioneer exploration of hilsa gut and skin mucus bacteria across habitats will advance our insights into microbiome assembly in migratory fish populations.
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Affiliation(s)
- Sabuj Biswas
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Adnan Mannan
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - S M Sharifuzzaman
- Institute of Marine Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Afsana Yeasmin Tanzina
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Afroza Akter Tanni
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Farjana Sharmen
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Md Mobarok Hossain
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | | | - Alfred Chin-Yen Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - S M Rafiqul Islam
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh.
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh.
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The Involvement of Public Higher Education Institutions (HEIs) in Poland in the Promotion of the Sustainable Development Goals (SDGs) in the Age of Social Media. INFORMATION 2022. [DOI: 10.3390/info13100473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The aim of this paper is to present the involvement of public Higher Education Institutions (HEIs) in Poland in promoting the Sustainable Development Goals (SDGs) in 2021. The reason for undertaking the research was a noticeable lack of studies in the literature on the engagement of universities in the concept of sustainability. The research conducted was mainly qualitative in nature. The aim was realized using three groups of research methods: collection of empirical data, data processing, and the presentation of study outcomes. The study used 16 indicators, constructed from data taken from SciVal and RAD-on reports. These indicators presented the number of publications promoting each of the SDGs in 2021 per academic staff and other persons carrying out and participating in teaching or research activities. The research was conducted on 57 universities from Poland. Four clusters were distinguished as a result of the cluster analysis that was performed. The first cluster comprised only universities of life sciences. This group had the highest publication productivity for the following goals: SDG2, SDG3, SDG6, SDG11, SDG12, SDG13, SDG14, SDG15, and SDG16. The universities that made up cluster 2 (predominantly universities of technology) specialized in publications related to goals such as SDG7 and SDG9. The highest publication productivity for SDG1, SDG4, SDG5, SDG8, SDG10, and SDG16 belonged to cluster 3 (consisting mainly of universities of economics). The HEIs (mainly universities of physical education) that made up cluster 4 did not have the highest publication productivity in any of the SDGs. Therefore, it can be concluded that, in 2021, there was a correlation between the profile of a public HEI in Poland and the SDGs it was involved in promoting.
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Moniz K, Walker VK, Shah V. Antibiotic resistance in mucosal bacteria from high Arctic migratory salmonids. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:385-390. [PMID: 34109745 PMCID: PMC9292178 DOI: 10.1111/1758-2229.12975] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/17/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Two related salmonids, Arctic char (Salvelinus alpinus) and lake whitefish (Coregonus clupeaformis) sampled from the high Arctic region of Nunavut, Canada are anadromous fish, migrating annually from the same ice-covered freshwater waterbodies to spend summers in the marine waters of the Arctic Ocean. Microbiota associated with the skin-associated mucus undergo community change coincident with migration, and irrespective of this turnover, antibiotic resistance was detected in mixed bacterial cultures initiated with mucus samples. Although as expected most bacteria were unculturable, however, 5/7 isolates showed susceptibility to a panel of five common antibiotics. The fish were sampled under severe conditions and at remote locations far from human habitation. Regardless, two isolates, 'Carnobacterium maltaromaticum sm-2' and 'Arthrobacter citreus sm', showed multi-resistance to two or more antibiotics including ampicillin and streptomycin indicating multiple resistance genes. It is unknown if these fish bacteria have 'natural' resistance phenotypes or if resistance has been acquired. As result of these observations, we urge long-term monitoring of drug-resistant bacteria in the region and caution the assumption of a lack of drug-resistant organisms even in such extreme environments.
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Affiliation(s)
- Kristy Moniz
- Department of Biology and School of Environmental StudiesQueen's UniversityKingstonOntarioK7L 3N6Canada
| | - Virginia K. Walker
- Department of Biology and School of Environmental StudiesQueen's UniversityKingstonOntarioK7L 3N6Canada
| | - Vishal Shah
- College of the Sciences and MathematicsWest Chester UniversityWest ChesterPennsylvaniaUSA
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Ou W, Yu G, Zhang Y, Mai K. Recent progress in the understanding of the gut microbiota of marine fishes. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:434-448. [PMID: 37073265 PMCID: PMC10077274 DOI: 10.1007/s42995-021-00094-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 01/12/2021] [Indexed: 05/03/2023]
Abstract
As the significance of the gut microbiota has become increasingly realized, a large number of related studies have emerged. With respect to the gut microbial composition of fish, the predominant gut microbes and core gut microbiota have been reported by many researchers. Our understanding of fish gut microbiota, especially its functional roles, has fallen far behind that of terrestrial vertebrates, although previous studies using gnotobiotic zebrafish models have revealed that the gut microbiota performs a significant role in gut development, nutrient metabolism and immune responses. Given that environmental factors of marine habitats are very different from those of freshwater habitats, a distinct difference may exist in the gut microbiota between freshwater and marine fish. Therefore, this review aims to address the advances in marine fish gut microbiota in terms of methodologies, the gut microbial composition, and gnotobiotic models of marine fish, the important factors (host genotype and three environmental factors: temperature, salinity and diet) that drive marine fish gut microbiota, and significant roles of the gut microbiota in marine fish.
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Affiliation(s)
- Weihao Ou
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) and the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003 China
| | - Guijuan Yu
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) and the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003 China
| | - Yanjiao Zhang
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) and the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Kangsen Mai
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) and the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237 China
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10
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Gomez JA, Primm TP. A Slimy Business: the Future of Fish Skin Microbiome Studies. MICROBIAL ECOLOGY 2021; 82:275-287. [PMID: 33410931 DOI: 10.1007/s00248-020-01648-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/16/2020] [Indexed: 05/10/2023]
Abstract
Fish skin contains a mucosal microbiome for the largest and oldest group of vertebrates, a location ideal for microbial community ecology and practical applications in agriculture and veterinary medicine. These selective microbiomes are dominated by Proteobacteria, with compositions different from the surrounding water. Core taxa are a small percentage of those present and are currently functionally uncharacterized. Methods for skin sampling, DNA extraction and amplification, and sequence data processing are highly varied across the field, and reanalysis of recent studies using a consistent pipeline revealed that some conclusions did change in statistical significance. Further, the 16S gene sequencing approaches lack quantitation of microbes and copy number adjustment. Thus, consistency in the field is a serious limitation in comparing across studies. The most significant area for future study, requiring metagenomic and metabolomics data, is the biochemical pathways and functions within the microbiome community, the interactions between members, and the resulting effects on fish host health being linked to specific nutrients and microbial species. Genes linked to skin colonization, such as those for attachment or mucin degradation, need to be uncovered and explored. Skin immunity factors need to be directly linked to microbiome composition and individual taxa. The basic foundation has been laid, and many exciting future discoveries remain.
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Affiliation(s)
- Javier A Gomez
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, 77320, USA
| | - Todd P Primm
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, 77320, USA.
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The gut content microbiome of wild-caught rainbow darter is altered during laboratory acclimation. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100835. [PMID: 33894530 DOI: 10.1016/j.cbd.2021.100835] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 02/07/2023]
Abstract
An increasing number of laboratory studies are showing that environmental stressors and diet affect the fish gut microbiome. However, the application of these results to wild populations is uncertain as little is known about how the gut microbiome shifts when fish are transitioned from the field to the laboratory. To assess this, intestinal contents (i.e. digesta) of wild-caught rainbow darter (Etheostoma caeruleum) were sampled in the field and in the lab after 14- and 42-days acclimation. In addition, from days 15-42 some fish were exposed to waterborne triclosan, an antimicrobial found in aquatic ecosystems, or to dilutions of municipal wastewater effluents, to determine how these stressors affect the bacterial communities of gut contents. 16S rRNA gene amplicon sequencing was used to determine microbial community composition, alpha, and beta diversity present in the fish gut contents. In total, there was 8,074,658 reads and 11,853 amplicon sequence variants (ASVs) identified. The gut contents of wild fish were dominant in both Proteobacteria (35%) and Firmicutes (27%), while lab fish were dominant in Firmicutes (37-47%) and had lower alpha diversity. Wild fish had greater ASVs per sample (423-1304) compared to lab fish (19-685). Similarly, the beta-diversity of these bacterial communities differed between field and lab control fish; control fish were distinct from the 10% wastewater effluent and 100 ng/L TCS treatment groups. Results indicate that the gut microbiome of wild fish changes with the transition to laboratory environments; hence, prolonged acclimation to new settings may be required to achieve a stable gut content microbiome in wild-caught fish. Research is required to understand the length of time required to reach a stable fish gut microbiome.
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Restivo VE, Kidd KA, Surette MG, Servos MR, Wilson JY. Rainbow darter (Etheostoma caeruleum) from a river impacted by municipal wastewater effluents have altered gut content microbiomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141724. [PMID: 32889463 DOI: 10.1016/j.scitotenv.2020.141724] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
Municipal wastewater treatment plant (WWTP) effluent contains pharmaceuticals and personal care products known to affect fish health and reproduction. The microbiome is a community of bacteria integral in maintaining host health and is influenced by species, diet, and environment. This study investigated changes in the diversity and composition of the gut content microbiome of rainbow darter (Etheostoma caeruleum) at ten sites on the Grand River, Ontario, Canada. Gut contents were collected in fall 2018 from these fish at sites upstream and downstream of two municipal wastewater treatment plants (WWTPs; Waterloo and Kitchener). 16S rRNA genes were sequenced to determine the composition and diversity (alpha and beta) of microbial taxa present. Gut content bacterial alpha diversity increased downstream of both WWTP outfalls; dominance of bacterial amplicon sequence variants decreased compared to upstream fish. Fish collected at different sites had distinct bacterial communities, with upstream samples dominant in Proteobacteria and Firmicutes, and downstream samples increasingly abundant in Proteobacteria and Cyanobacteria. In mammals, increased abundance of Proteobacteria is indicative of microbial dysbiosis and has been linked to altered health outcomes, but this is not yet known for fish. This research indicates that the fish gut content microbiome was altered downstream of WWTP effluent outfalls and could lead to negative health outcomes.
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Affiliation(s)
| | - Karen A Kidd
- Department of Biology, McMaster University, Hamilton, Ontario, Canada; School of Earth, Environment and Society, McMaster University, Hamilton, Ontario, Canada.
| | - Michael G Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada; Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Joanna Y Wilson
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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Walker VK, Das P, Li P, Lougheed SC, Moniz K, Schott S, Qitsualik J, Koch I. Identification of Arctic Food Fish Species for Anthropogenic Contaminant Testing Using Geography and Genetics. Foods 2020; 9:foods9121824. [PMID: 33302601 PMCID: PMC7764770 DOI: 10.3390/foods9121824] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/27/2020] [Accepted: 12/03/2020] [Indexed: 02/07/2023] Open
Abstract
The identification of food fish bearing anthropogenic contaminants is one of many priorities for Indigenous peoples living in the Arctic. Mercury (Hg), arsenic (As), and persistent organic pollutants including polychlorinated biphenyls (PCBs) are of concern, and these are reported, in some cases for the first time, for fish sampled in and around King William Island, located in Nunavut, Canada. More than 500 salmonids, comprising Arctic char, lake trout, lake whitefish, and ciscoes, were assayed for contaminants. The studied species are anadromous, migrating to the ocean to feed in the summers and returning to freshwater before sea ice formation in the autumn. Assessments of muscle Hg levels in salmonids from fishing sites on King William Island showed generally higher levels than from mainland sites, with mean concentrations generally below guidelines, except for lake trout. In contrast, mainland fish showed higher means for As, including non-toxic arsenobetaine, than island fish. Lake trout were highest in As and PCB levels, with salmonid PCB congener analysis showing signatures consistent with the legacy of cold-war distant early warning stations. After DNA-profiling, only 4–32 Arctic char single nucleotide polymorphisms were needed for successful population assignment. These results support our objective to demonstrate that genomic tools could facilitate efficient and cost-effective cluster assignment for contaminant analysis during ocean residency. We further suggest that routine pollutant testing during the current period of dramatic climate change would be helpful to safeguard the wellbeing of Inuit who depend on these fish as a staple input to their diet. Moreover, this strategy should be applicable elsewhere.
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Affiliation(s)
- Virginia K. Walker
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada; (P.D.); (P.L.); (S.C.L.); (K.M.); (I.K.)
- School of Environmental Studies, Queen’s University, Kingston, ON K7L 3N6, Canada
- Correspondence:
| | - Pranab Das
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada; (P.D.); (P.L.); (S.C.L.); (K.M.); (I.K.)
| | - Peiwen Li
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada; (P.D.); (P.L.); (S.C.L.); (K.M.); (I.K.)
| | - Stephen C. Lougheed
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada; (P.D.); (P.L.); (S.C.L.); (K.M.); (I.K.)
| | - Kristy Moniz
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada; (P.D.); (P.L.); (S.C.L.); (K.M.); (I.K.)
| | - Stephan Schott
- School of Public Policy and Administration, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - James Qitsualik
- Gjoa Haven Hunters and Trappers Association, Gjoa Haven, NU X0B 1J0, Canada;
| | - Iris Koch
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada; (P.D.); (P.L.); (S.C.L.); (K.M.); (I.K.)
- Royal Military College, Kingston, ON K7K 7B4, Canada
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Element G, Engel K, Neufeld JD, Casselman JM, van Coeverden de Groot P, Greer CW, Walker VK. Seasonal habitat drives intestinal microbiome composition in anadromous Arctic char (Salvelinus alpinus). Environ Microbiol 2020; 22:3112-3125. [PMID: 32363711 PMCID: PMC7496496 DOI: 10.1111/1462-2920.15049] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 04/25/2020] [Indexed: 12/13/2022]
Abstract
Intestinal microbial communities from 362 anadromous Arctic char (Salvelinus alpinus) from the high Arctic Kitikmeot region, Nunavut, Canada, were characterized using high-throughput 16S rRNA gene sequencing. The resulting bacterial communities were compared across four seasonal habitats that correspond to different stages of annual migration. Arctic char intestinal communities differed by sampling site, salinity and stages of freshwater residence. Although microbiota from fish sampled in brackish water were broadly consistent with taxa seen in other anadromous salmonids, they were enriched with putative psychrophiles, including the nonluminous gut symbiont Photobacterium iliopiscarium that was detected in >90% of intestinal samples from these waters. Microbiota from freshwater-associated fish were less consistent with results reported for other salmonids, and highly variable, possibly reflecting winter fasting behaviour of these char. We identified microbiota links to age for those fish sampled during the autumn upriver migration, but little impact of the intestinal content and water microbiota on the intestinal community. The strongest driver of intestinal community composition was seasonal habitat, and this finding combined with identification of psychrophiles suggested that water temperature and migratory behaviour are key to understanding the relationship between Arctic char and their symbionts.
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Affiliation(s)
- Geraint Element
- Department of Biology, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Katja Engel
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - John M Casselman
- Department of Biology, Queen's University, Kingston, ON, K7L 3N6, Canada
| | | | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montreal, QC, H4P 2R2, Canada
| | - Virginia K Walker
- Department of Biology, Queen's University, Kingston, ON, K7L 3N6, Canada.,School of Environmental Studies, Queen's University, Kingston, ON, K7L 3N6, Canada
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