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Cardoso MD, Maciel OLDC, de Souza ALM, Roges EM, Gonçalves VD, Siciliano S, Rodrigues DDP, Hauser-Davis RA. Smelly shark, smelly ray: what is infecting you? J Appl Microbiol 2024; 135:lxae068. [PMID: 38486350 DOI: 10.1093/jambio/lxae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/15/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024]
Abstract
AIMS Although elasmobranchs are consumed worldwide, bacteriological assessments for this group are still sorely lacking. In this context, this study assessed bacteria of sharks and rays from one of the most important landing ports along the Rio de Janeiro coast. METHODS AND RESULTS Bacteria were isolated from the cloacal swabs of the sampled elasmobranchs. They were cultured, and Vibrio, Aeromonas, and Enterobacterales were isolated and identified. The isolated bacteria were then biochemically identified and antimicrobial susceptibility assays were performed. Antigenic characterizations were performed for Salmonella spp. and Polymerase Chain Reaction (PCR) assays were performed to identify Escherichia coli pathotypes. Several bacteria of interest in the One Health context were detected. The most prevalent Enterobacterales were Morganella morganii and Citrobacter freundii, while Vibrio harveyi and Vibrio fluvialis were the most prevalent among Vibrio spp. and Aeromonas allosacharophila and Aeromonas veronii bv. veronii were the most frequent among Aeromonas spp. Several bacteria also displayed antimicrobial resistance, indicative of Public Health concerns. A total of 10% of Vibrio strains were resistant to trimethoprim-sulfamethoxazole and 40% displayed intermediate resistance to cefoxitin. Salmonella enterica strains displayed intermediate resistance to ciprofloxacin, nalidixic acid and streptomycin. All V. cholerae strains were identified as non-O1/non-O139. The detected E. coli strains did not exhibit pathogenicity genes. This is the first study to perform serology assessments for S. enterica subsp. enterica isolated from elasmobranchs, identifying the zoonotic Typhimurium serovar. Salmonella serology evaluations are, therefore, paramount to identify the importance of elasmobranchs in the epidemiological salmonellosis chain. CONCLUSIONS The detection of several pathogenic and antibiotic-resistant bacteria may pose significant Public Health risks in Brazil, due to high elasmobranch consumption rates, indicating the urgent need for further bacteriological assessments in this group.
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Affiliation(s)
- Maíra Duarte Cardoso
- Fundação Instituto de Pesca do Estado do Rio de Janeiro (FIPERJ). Pç. Fonseca Ramos s/n - Terminal Rodoviário Roberto Silveira, sobreloja, 24030-020 Centro, Niterói, RJ, Brazil
| | - Oswaldo Luiz de C Maciel
- Fundação Instituto de Pesca do Estado do Rio de Janeiro (FIPERJ). Pç. Fonseca Ramos s/n - Terminal Rodoviário Roberto Silveira, sobreloja, 24030-020 Centro, Niterói, RJ, Brazil
- Programa de Pós-Graduação em Geociências (Geoquímica), Departamento de Geoquímica, Instituto de Química, Universidade Federal Fluminense (UFF). Outeiro São João Baptista s/n, 24020-141 Centro, Niterói, RJ, RJ, Brazil
| | - André Luiz Medeiros de Souza
- Secretaria de Estado de Desenvolvimento Econômico, Indústria, Comércio e Serviços do Rio de Janeiro (SEDEICS-RJ). Rua Pinheiro Machado s/n, Anexo, Andar 3, 22231-090 Laranjeiras, Rio de Janeiro, RJ, Brazil
| | - Emily Moraes Roges
- Laboratório de Referência Nacional de Enteroinfecções Bacterianas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz. Av. Brasil 4365, Manguinhos 21040-900, Rio de Janeiro, RJ, Brazil
| | - Verônica Dias Gonçalves
- Laboratório de Referência Nacional de Enteroinfecções Bacterianas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz. Av. Brasil 4365, Manguinhos 21040-900, Rio de Janeiro, RJ, Brazil
| | - Salvatore Siciliano
- Escola Nacional de Saúde Pública/Fiocruz, Departamento de Ciências Biológicas. Rua Leopoldo Bulhões 1.480 - sala 10, 21040-900 Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Dália Dos Prazeres Rodrigues
- Laboratório de Referência Nacional de Enteroinfecções Bacterianas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz. Av. Brasil 4365, Manguinhos 21040-900, Rio de Janeiro, RJ, Brazil
| | - Rachel Ann Hauser-Davis
- Laboratório de Avaliação e Promoção da Saúde Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz. Av. Brasil 4365, Manguinhos 21040-900, Rio de Janeiro, RJ, Brazil
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Fronton F, Villemur R, Robert D, St-Pierre Y. Divergent bacterial landscapes: unraveling geographically driven microbiomes in Atlantic cod. Sci Rep 2024; 14:6088. [PMID: 38480867 PMCID: PMC10938007 DOI: 10.1038/s41598-024-56616-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/08/2024] [Indexed: 03/17/2024] Open
Abstract
Establishing microbiome signatures is now recognized as a critical step toward identifying genetic and environmental factors shaping animal-associated microbiomes and informing the health status of a given host. In the present work, we prospectively collected 63 blood samples of the Atlantic cod population of the Southern Gulf of Saint Lawrence (GSL) and characterized their 16S rRNA circulating microbiome signature. Our results revealed that the blood microbiome signature was dominated at the phylum level by Proteobacteria, Bacteroidetes, Acidobacteria and Actinobacteria, a typical signature for fish populations inhabiting the GSL and other marine ecosystems. At the genus level, however, we identified two distinct cod groups. While the microbiome signature of the first group was dominated by Pseudoalteromonas, a genus we previously found in the microbiome signature of Greenland and Atlantic halibut populations of the GSL, the second group had a microbiome signature dominated by Nitrobacter and Sediminibacterium (approximately 75% of the circulating microbiome). Cods harboring a Nitrobacter/Sediminibacterium-rich microbiome signature were localized in the most southern part of the GSL, just along the northern coast of Cape Breton Island. Atlantic cod microbiome signatures did not correlate with the weight, length, relative condition, depth, temperature, sex, and salinity, as previously observed in the halibut populations. Our study provides, for the first time, a unique snapshot of the circulating microbiome signature of Atlantic cod populations and the potential existence of dysbiotic signatures associated with the geographical distribution of the population, probably linked with the presence of nitrite in the environment.
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Affiliation(s)
- Fanny Fronton
- INRS-Center Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Richard Villemur
- INRS-Center Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Dominique Robert
- Institut des Sciences de la Mer, Université du Québec à Rimouski, 310, allée des Ursulines, C.P. 3300, Rimouski, QC, G5L 3A1, Canada
| | - Yves St-Pierre
- INRS-Center Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada.
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Kerr EN, Papudeshi B, Haggerty M, Wild N, Goodman AZ, Lima LFO, Hesse RD, Skye A, Mallawaarachchi V, Johri S, Parker S, Dinsdale EA. Stingray epidermal microbiomes are species-specific with local adaptations. Front Microbiol 2023; 14:1031711. [PMID: 36937279 PMCID: PMC10017458 DOI: 10.3389/fmicb.2023.1031711] [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: 08/30/2022] [Accepted: 02/07/2023] [Indexed: 03/06/2023] Open
Abstract
Marine host-associated microbiomes are affected by a combination of species-specific (e.g., host ancestry, genotype) and habitat-specific features (e.g., environmental physiochemistry and microbial biogeography). The stingray epidermis provides a gradient of characteristics from high dermal denticles coverage with low mucus to reduce dermal denticles and high levels of mucus. Here we investigate the effects of host phylogeny and habitat by comparing the epidermal microbiomes of Myliobatis californica (bat rays) with a mucus rich epidermis, and Urobatis halleri (round rays) with a mucus reduced epidermis from two locations, Los Angeles and San Diego, California (a 150 km distance). We found that host microbiomes are species-specific and distinct from the water column, however composition of M. californica microbiomes showed more variability between individuals compared to U. halleri. The variability in the microbiome of M. californica caused the microbial taxa to be similar across locations, while U. halleri microbiomes were distinct across locations. Despite taxonomic differences, Shannon diversity is the same across the two locations in U. halleri microbiomes suggesting the taxonomic composition are locally adapted, but diversity is maintained by the host. Myliobatis californica and U. halleri microbiomes maintain functional similarity across Los Angeles and San Diego and each ray showed several unique functional genes. Myliobatis californica has a greater relative abundance of RNA Polymerase III-like genes in the microbiome than U. halleri, suggesting specific adaptations to a heavy mucus environment. Construction of Metagenome Assembled Genomes (MAGs) identified novel microbial species within Rhodobacteraceae, Moraxellaceae, Caulobacteraceae, Alcanivoracaceae and Gammaproteobacteria. All MAGs had a high abundance of active RNA processing genes, heavy metal, and antibiotic resistant genes, suggesting the stingray mucus supports high microbial growth rates, which may drive high levels of competition within the microbiomes increasing the antimicrobial properties of the microbes.
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Affiliation(s)
- Emma N. Kerr
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
- *Correspondence: Emma N. Kerr,
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Miranda Haggerty
- California Department of Fish and Wildlife, San Diego, CA, United States
| | - Natasha Wild
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Asha Z. Goodman
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Lais F. O. Lima
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Ryan D. Hesse
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Amber Skye
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Shaili Johri
- Hopkins Maine Station, Stanford University, Stanford, CA, United States
| | - Sophia Parker
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Elizabeth A. Dinsdale
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
- Elizabeth A. Dinsdale,
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4
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Correia Costa I, Amorim de Oliveira M, Wosnick N, Ann Hauser-Davis R, Siciliano S, Nunes JLS. Elasmobranch-associated microbiota: a scientometric literature review. PeerJ 2022; 10:e14255. [PMID: 36345481 PMCID: PMC9636872 DOI: 10.7717/peerj.14255] [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: 02/07/2022] [Accepted: 09/26/2022] [Indexed: 11/07/2022] Open
Abstract
Elasmobranchs provide greatly relevant ecosystem services for the balance of the environments in which they are inserted. In recent decades, sharp population declines have been reported for many species in different regions worldwide, making this taxonomic group currently one of the most threatened with extinction. This scenario is almost entirely due to excessive fishing pressure, but any contributing factor that may cause additional mortality to populations must be mapped and monitored. In a fast-changing world, emerging marine pollution associated with climate change display the potential to increase the spread of infectious agents. These can, in turn, lead to mortality events, both directly and indirectly, by reducing immune responses and the physical and nutritional condition of affected individuals. In this context, the present study aimed to analyze data concerning elasmobranch-associated microbiota, identifying study trends and knowledge gaps in order to direct future studies on this topic of growing relevance for the health of wild populations, as well as individuals maintained in captivity, considering the zoonotic potential of these microorganisms.
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Affiliation(s)
- Ivana Correia Costa
- Laboratório de Organismos Aquáticos, Universidade Federal do Maranhão, São Luís, Maranhão, Brazil
| | - Mariene Amorim de Oliveira
- Laboratório de Genética e Biologia Molecular, Universidade Federal do Maranhão, São Luís, Maranhão, Brazil
| | - Natascha Wosnick
- Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Rachel Ann Hauser-Davis
- Laboratório de Avaliação e Promoção da Saúde Ambiental, Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Salvatore Siciliano
- Departamento de Ciências Biológicas, Escola Nacional de Saúde Pública/FIOCRUZ, Rio de Janeiro, Brazil
| | - Jorge Luiz Silva Nunes
- Laboratório de Organismos Aquáticos, Universidade Federal do Maranhão, São Luís, Maranhão, Brazil
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5
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Perry CT, Pratte ZA, Clavere-Graciette A, Ritchie KB, Hueter RE, Newton AL, Fischer GC, Dinsdale EA, Doane MP, Wilkinson KA, Bassos-Hull K, Lyons K, Dove ADM, Hoopes LA, Stewart FJ. Elasmobranch microbiomes: emerging patterns and implications for host health and ecology. Anim Microbiome 2021; 3:61. [PMID: 34526135 PMCID: PMC8444439 DOI: 10.1186/s42523-021-00121-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/21/2021] [Indexed: 12/20/2022] Open
Abstract
Elasmobranchs (sharks, skates and rays) are of broad ecological, economic, and societal value. These globally important fishes are experiencing sharp population declines as a result of human activity in the oceans. Research to understand elasmobranch ecology and conservation is critical and has now begun to explore the role of body-associated microbiomes in shaping elasmobranch health. Here, we review the burgeoning efforts to understand elasmobranch microbiomes, highlighting microbiome variation among gastrointestinal, oral, skin, and blood-associated niches. We identify major bacterial lineages in the microbiome, challenges to the field, key unanswered questions, and avenues for future work. We argue for prioritizing research to determine how microbiomes interact mechanistically with the unique physiology of elasmobranchs, potentially identifying roles in host immunity, disease, nutrition, and waste processing. Understanding elasmobranch–microbiome interactions is critical for predicting how sharks and rays respond to a changing ocean and for managing healthy populations in managed care.
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Affiliation(s)
- Cameron T Perry
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Zoe A Pratte
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Kim B Ritchie
- Department of Natural Sciences, University of South Carolina Beaufort, Beaufort, SC, USA
| | - Robert E Hueter
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA.,OCEARCH, Park City, UT, USA
| | - Alisa L Newton
- Disney's Animals, Science and Environment, Orlando, FL, USA
| | - G Christopher Fischer
- OCEARCH, Park City, UT, USA.,Marine Science Research Institute, Jacksonville University, Jacksonville, FL, USA
| | - Elizabeth A Dinsdale
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Michael P Doane
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Krystan A Wilkinson
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA.,Chicago Zoological Society's Sarasota Dolphin Research Program ℅ Mote Marine Laboratory, Sarasota, FL, USA
| | - Kim Bassos-Hull
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA
| | - Kady Lyons
- Research and Conservation Department, Georgia Aquarium, Atlanta, GA, USA
| | - Alistair D M Dove
- Research and Conservation Department, Georgia Aquarium, Atlanta, GA, USA
| | - Lisa A Hoopes
- Research and Conservation Department, Georgia Aquarium, Atlanta, GA, USA
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
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