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Koepper S, Clark KF, McClure JT, Revie CW, Stryhn H, Thakur KK. Differences in diversity and community composition of the shell microbiome of apparently healthy lobsters Homarus americanus across Atlantic Canada. Front Microbiol 2024; 15:1320812. [PMID: 38567078 PMCID: PMC10986177 DOI: 10.3389/fmicb.2024.1320812] [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: 11/10/2023] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Host-microbe dynamics are of increasing interest in marine research due to their role in host health and productivity. Changes in the shell microbiome of American lobsters have been associated with epizootic shell disease, a syndrome that is spreading northwards across the eastern U.S. and Canadian Atlantic coast. This study analyzed differences in alpha and beta diversity, as well as differentially abundant taxa, in the shell-associated bacterial community of apparently healthy lobsters from four lobster fishing areas (LFAs) in Atlantic Canada. Over 180 lobsters from New Brunswick, Nova Scotia and Prince Edward Island (PEI) were sampled during seven sampling events over four sampling months. The bacterial community was identified using novel PacBio long-read sequencing, while alpha and beta diversity parameters were analyzed using linear regression models and weighted UniFrac distances. The bacterial richness, diversity and evenness differed by sampling location, sampling month, and molt stage, but not by lobster sex or size, nor sampling depth. Similarly, based on LFA, sampling month, year and lobster molt stage, the shell microbiome differed in microbial community composition with up to 34 out of 162 taxa differing significantly in abundance between sampling groups. This large-scale microbial survey suggests that the shell microbial diversity of apparently healthy lobsters is influenced by spatial and temporal factors such as geographic location, as well as the length of time the carapace is exposed to the surrounding seawater.
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Affiliation(s)
- Svenja Koepper
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - K. Fraser Clark
- Department of Animal Sciences and Aquaculture, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - J. T. McClure
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Crawford W. Revie
- Department of Computer and Information Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Henrik Stryhn
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Krishna K. Thakur
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
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2
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Michnik ML, Semple SL, Joshi RN, Whittaker P, Barreda DR. The use of salmonid epithelial cells to characterize the toxicity of Tenacibaculum maritimum soluble extracellular products. J Appl Microbiol 2024; 135:lxae049. [PMID: 38409849 DOI: 10.1093/jambio/lxae049] [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: 11/23/2023] [Revised: 02/07/2024] [Accepted: 02/24/2024] [Indexed: 02/28/2024]
Abstract
AIMS This study assessed how the etiological agent of mouth rot in farmed Atlantic salmon, Tenacibaculum maritimum, induces toxicity in host salmonid barrier cells, and determined whether environmental changes are relevant for these effects. METHODS AND RESULTS Tenacibaculum maritimum soluble extracellular products (ECPs) were collected and used to treat Atlantic salmon and rainbow trout intestinal barrier cell lines as a comparative model of bacterial-salmonid cell interactions. Cellular assays that examine cell membrane integrity, marker expression, and metabolic activity revealed that T. maritimum ECPs induced salmonid epithelial cell death through an apoptosis mechanism. Changes in salinity (25, 29, and 33 ppt) and temperature (12°C, 18°C, and 24°C) within the natural ranges observed in Pacific Northwest aquaculture facilities affected bacterial growth and cytotoxicity of T. maritimum ECPs. CONCLUSIONS Our results suggest epithelial barriers as targets of T. maritimum-mediated toxicity in farmed mouth rot-infected Atlantic salmon. The induction of apoptosis by T. maritimum soluble ECPs may also help to explain the absence of overt inflammation typically reported for these fish.
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Affiliation(s)
- Matthew L Michnik
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Shawna L Semple
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Reema N Joshi
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Patrick Whittaker
- Grieg Seafood BC Ltd, Campbell River, British Columbia, V9W 5P7, Canada
| | - Daniel R Barreda
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
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3
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Jaramillo D, Busby BP, Bestbier M, Bennett P, Waddington Z. New Zealand rickettsia-like organism and Tenacibaculum maritimum vaccine efficacy study. JOURNAL OF FISH DISEASES 2024; 47:e13883. [PMID: 37975241 DOI: 10.1111/jfd.13883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023]
Abstract
A cohort of Chinook salmon juveniles was vaccinated, with an autogenous bivalent vaccine against New Zealand RLOs (NZ-RLO1) and Tenacibaculum maritimum. A proportion of the cohort was not vaccinated to act as controls. At smoltification, the fish were challenged with NZ-RLO1, NZ-RLO2, or T. maritimum. We found that challenge with T. maritimum by immersion in (7.5 × 105 cfu/mL of water) did not yield any pathology. Challenge with RLOs produced clinical signs that were more or less severe depending on the challenge route, dose or vaccination status. Survival was significantly higher for vaccinated fish within the groups challenged with NZ-RLO1 by intraperitoneal injection with a relative percent survival (RPS) of 48.84%. Survival was not significantly different between vaccinated and non-vaccinated fish for groups challenged with NZ-RLO2 by intraperitoneal injection or by NZ-RLO1 by immersion. Yet, anecdotally the clinical disease presentation (manifesting as haemorrhagic, ulcerative skin lesions) was more severe for the non-vaccinated fish. This study demonstrates that autogenous vaccine against NZ-RLO is protective against severe disease and death by NZ-RLO1 challenge which warrants implementation and further evaluation under field conditions. Yet, this study also highlights the importance of the route of administration and dose when evaluating pathogenicity and vaccine efficacy.
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Affiliation(s)
- D Jaramillo
- Biosecurity New Zealand, Ministry for Primary Industries, Wellington, New Zealand
| | - B P Busby
- Animal Health Laboratory, Ministry for Primary Industries, Upper Hutt, New Zealand
| | - M Bestbier
- Animal Health Laboratory, Ministry for Primary Industries, Upper Hutt, New Zealand
| | - P Bennett
- Animal Health Laboratory, Ministry for Primary Industries, Upper Hutt, New Zealand
| | - Z Waddington
- New Zealand King Salmon Ltd, Picton, New Zealand
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4
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Godoy M, Coca Y, Suárez R, Montes de Oca M, Bledsoe JW, Burbulis I, Caro D, Pontigo JP, Maracaja-Coutinho V, Arias-Carrasco R, Rodríguez-Córdova L, Sáez-Navarrete C. Salmo salar Skin and Gill Microbiome during Piscirickettsia salmonis Infection. Animals (Basel) 2023; 14:97. [PMID: 38200828 PMCID: PMC10778177 DOI: 10.3390/ani14010097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/13/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Maintaining the high overall health of farmed animals is a central tenant of their well-being and care. Intense animal crowding in aquaculture promotes animal morbidity especially in the absence of straightforward methods for monitoring their health. Here, we used bacterial 16S ribosomal RNA gene sequencing to measure bacterial population dynamics during P. salmonis infection. We observed a complex bacterial community consisting of a previously undescribed core pathobiome. Notably, we detected Aliivibrio wodanis and Tenacibaculum dicentrarchi on the skin ulcers of salmon infected with P. salmonis, while Vibrio spp. were enriched on infected gills. The prevalence of these co-occurring networks indicated that coinfection with other pathogens may enhance P. salmonis pathogenicity.
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Affiliation(s)
- Marcos Godoy
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Lago Panguipulli 1390, Puerto Montt 5480000, Región de Los Lagos, Chile; (M.M.d.O.); (D.C.)
- Laboratorio de Biotecnología, Facultad de Ciencias de la Naturaleza, Escuela de Medicina Veterinaria, Universidad San Sebastián, Sede Patagonia, Lago Panguipulli 1390, Puerto Montt 5480000, Región de Los Lagos, Chile
| | - Yoandy Coca
- Doctorado en Ciencias de la Ingeniería, Departamento de Ingeniería Química y Bioprocesos, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago 7820436, Macul, Chile;
| | - Rudy Suárez
- Programa de Magíster en Acuicultura, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo 1780000, Elqui, Chile;
| | - Marco Montes de Oca
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Lago Panguipulli 1390, Puerto Montt 5480000, Región de Los Lagos, Chile; (M.M.d.O.); (D.C.)
| | - Jacob W. Bledsoe
- Department of Animal, Veterinary, and Food Sciences, Aquaculture Research Institute, University of Idaho, Hagerman, ID 83332, USA;
| | - Ian Burbulis
- Facultad de Medicina y Ciencia, Centro de Investigación Biomédica, Universidad San Sebastián, Sede Patagonia, Lago Panguipulli 1390, Puerto Montt 5480000, Región de Los Lagos, Chile;
| | - Diego Caro
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Lago Panguipulli 1390, Puerto Montt 5480000, Región de Los Lagos, Chile; (M.M.d.O.); (D.C.)
| | - Juan Pablo Pontigo
- Laboratorio Institucional, Facultad de Ciencias de la Naturaleza, Escuela de Medicina Veterinaria, Universidad San Sebastián, Sede Patagonia, Lago Panguipulli 1390, Puerto Montt 5480000, Región de Los Lagos, Chile;
| | - Vinicius Maracaja-Coutinho
- Unidad de Genómica Avanzada, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 7820436, Macul, Chile;
- Centro de Modelamiento Molecular, Biofísica y Bioinformática (CM2B2), Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 7820436, Macul, Chile
- Beagle Bioinformatics, Santiago 7820436, Macul, Chile
| | - Raúl Arias-Carrasco
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago 7820436, Macul, Chile;
| | | | - César Sáez-Navarrete
- Departamento de Ingeniería Química y Bioprocesos, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Macul, Chile;
- Centro de Investigación en Nanotecnología y Materiales Avanzados (CIEN-UC), Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Macul, Chile
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Najafpour B, Pinto PIS, Sanz EC, Martinez-Blanch JF, Canario AVM, Moutou KA, Power DM. Core microbiome profiles and their modification by environmental, biological, and rearing factors in aquaculture hatcheries. MARINE POLLUTION BULLETIN 2023; 193:115218. [PMID: 37441915 DOI: 10.1016/j.marpolbul.2023.115218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/06/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023]
Abstract
16S rRNA gene sequencing and bacteria- and genus-specific quantitative PCR was used to profile microbial communities and their associated functions in water, live feed (microalgae, Artemia, and rotifer), and European sea bass and gilthead sea bream larvae from hatcheries in Greece and Italy. The transfer to larvae of genus containing potential pathogens of fish was more likely with Artemia and rotifer than with microalgae or water, irrespective of geographic location. The presence of potentially pathogenic bacteria (Vibrio and Pseudoalteromonas) in the core microbiota of water, live feed, and fish larvae, the enrichment of different bacterial resistance pathways and biofilm formation, and the overall low beneficial bacteria load during larval ontogeny emphasizes the risk for disease outbreaks. The present data characterizing microbiota in commercial aquaculture hatcheries provides a baseline for the design of strategies to manage disease and to model or remediate potential adverse environmental impacts.
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Affiliation(s)
- Babak Najafpour
- CCMAR - Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Edifício 7, 8005-139 Faro, Portugal
| | - Patricia I S Pinto
- CCMAR - Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Edifício 7, 8005-139 Faro, Portugal
| | - Eric Climent Sanz
- ADM Biopolis, Parc Cientific Universidad De Valencia, Paterna, Spain
| | | | - Adelino V M Canario
- CCMAR - Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Edifício 7, 8005-139 Faro, Portugal; Shanghai Ocean University International Center for Marine Studies, Shanghai, China
| | - Katerina A Moutou
- Department of Biochemistry & Biotechnology, University of Thessaly, Ploutonos 26, Larissa, Greece
| | - Deborah M Power
- CCMAR - Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Edifício 7, 8005-139 Faro, Portugal; Shanghai Ocean University International Center for Marine Studies, Shanghai, China.
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6
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Fiedler AW, Drågen MKR, Lorentsen ED, Vadstein O, Bakke I. The stability and composition of the gut and skin microbiota of Atlantic salmon throughout the yolk sac stage. Front Microbiol 2023; 14:1177972. [PMID: 37485532 PMCID: PMC10358989 DOI: 10.3389/fmicb.2023.1177972] [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: 03/02/2023] [Accepted: 06/19/2023] [Indexed: 07/25/2023] Open
Abstract
The bacterial colonization of newly hatched fish is important for the larval development and health. Still, little is known about the ontogeny of the early microbiota of fish. Here, we conducted two independent experiments with yolk sac fry of Atlantic salmon that were (1) either reared conventionally, with the eggs as the only source for bacteria (egg-derived microbiota; EDM) or (2) hatched germ-free and re-colonized using lake water (lake-derived microbiota; LDM). First, we characterized the gut and skin microbiota at 6, 9, and 13 weeks post hatching based on extracted RNA. In the second experiment, we exposed fry to high doses of either a fish pathogen or a commensal bacterial isolate and sampled the microbiota based on extracted DNA. The fish microbiota differed strongly between EDM and LDM treatments. The phyla Proteobacteria, Bacteroidetes, and Actinobacteria dominated the fry microbiota, which was found temporarily dynamic. Interestingly, the microbiota of EDM fry was more stable, both between replicate rearing flasks, and over time. Although similar, the skin and gut microbiota started to differentiate during the yolk sac stage, several weeks before the yolk was consumed. Addition of high doses of bacterial isolates to fish flasks had only minor effects on the microbiota.
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7
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Samsing F, Zhang W, Zadoks RN, Whittington R, Venturini C, Giles C, Carson J, Becker JA. Cold temperature stress and damaged skin induced high mortality in barramundi (Lates calcarifer) challenged with Vibrio harveyi. JOURNAL OF FISH DISEASES 2023; 46:751-766. [PMID: 36966382 DOI: 10.1111/jfd.13784] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 06/07/2023]
Abstract
Most diseases in aquaculture are caused by opportunistic pathogens. One of them, Vibrio harveyi, is a widespread Gram-negative bacterium that has become an important pathogen of aquatic species in marine environments. Here, we propose the use of the causal pie model as a framework to conceptualize the causation of vibriosis in juvenile barramundi (Lates calcarifer) and to establish an effective challenge model. In the model, a sufficient cause, or the causal pie, is a constellation of component causes that lead to an outcome (e.g. vibriosis). In the pilot study, a high cumulative mortality (63.3% ± 10.0%, mean ± SE) was observed when V. harveyi was administered by intraperitoneal injection using a high challenge dose [107 colony-forming units (CFU) fish-1 ], but low or no mortality was observed in fish subject to cold stress or fish with intact skin when challenged by immersion. We, therefore, tested the use of a skin lesion (induced with a 4-mm biopsy punch) combined with cold temperature stress to induce vibriosis following the causal pie model. After challenge, fish were immediately subject to cold stress (22°C) or placed at an optimal temperature of 30°C. All groups were challenged with 108 CFU mL-1 for 60 min. A considerably higher mortality level (72.7% ± 13.9%) was observed in fish challenged with both a skin lesion and cold stress compared with mortality in fish only having a skin lesion (14.6% ± 2.8%). V. harveyi was re-isolated from all moribund fish and was detected by species-specific real-time PCR in gills, head kidney and liver, regardless of challenge treatment confirming vibriosis as the cause of disease. Parenchymal tissues had histopathological changes consistent with vibriosis. Whole-genome sequence (WGS) is provided for the Vibrio harveyi isolate examined in this study. Overall, the causal pie model was a useful framework to conceptualize the design of the experimental challenge model, in which both cold stress and skin damage were identified as component causes of vibriosis with high mortality. This conceptual framework can be applied to other opportunistic pathogens in aquaculture or to the study of co-infections in fish.
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Affiliation(s)
- Francisca Samsing
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, New South Wales, Australia
| | - William Zhang
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camden, New South Wales, Australia
| | - Ruth N Zadoks
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, New South Wales, Australia
| | - Richard Whittington
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, New South Wales, Australia
| | - Carola Venturini
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, New South Wales, Australia
| | - Carla Giles
- Centre for Aquatic Animal Health and Vaccines, Department of Natural Resources and Environment Tasmania, Launceston, Tasmania, Australia
| | - Jeremy Carson
- Carson BioConsulting, Launceston, Tasmania, Australia
| | - Joy A Becker
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camden, New South Wales, Australia
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Almeida DB, Semedo M, Magalhães C, Blanquet I, Mucha AP. Sole microbiome progression in a hatchery life cycle, from egg to juvenile. Front Microbiol 2023; 14:1188876. [PMID: 37434707 PMCID: PMC10331008 DOI: 10.3389/fmicb.2023.1188876] [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: 03/17/2023] [Accepted: 06/05/2023] [Indexed: 07/13/2023] Open
Abstract
Recirculating aquaculture systems (RAS) pose unique challenges in microbial community management since they rely on a stable community with key target groups, both in the RAS environment and in the host (in this case, Solea senegalensis). Our goal was to determine how much of the sole microbiome is inherited from the egg stage, and how much is acquired during the remainder of the sole life cycle in an aquaculture production batch, especially regarding potentially probiotic and pathogenic groups. Our work comprises sole tissue samples from 2 days before hatching and up to 146 days after hatching (-2 to 146 DAH), encompassing the egg, larval, weaning, and pre-ongrowing stages. Total DNA was isolated from the different sole tissues, as well as from live feed introduced in the first stages, and 16S rRNA gene was sequenced (V6-V8 region) using the Illumina MiSeq platform. The output was analysed with the DADA2 pipeline, and taxonomic attribution with SILVAngs version 138.1. Using the Bray-Curtis dissimilarity index, both age and life cycle stage appeared to be drivers of bacterial community dissimilarity. To try to distinguish the inherited (present since the egg stage) from the acquired community (detected at later stages), different tissues were analysed at 49, 119 and 146 DAH (gill, intestine, fin and mucus). Only a few genera were inherited, but those that were inherited accompany the sole microbiome throughout the life cycle. Two genera of potentially probiotic bacteria (Bacillus and Enterococcus) were already present in the eggs, while others were acquired later, in particularly, forty days after live feed was introduced. The potentially pathogenic genera Tenacibaculum and Vibrio were inherited from the eggs, while Photobacterium and Mycobacterium seemed to be acquired at 49 and 119 DAH, respectively. Significant co-occurrence was found between Tenacibaculum and both Photobacterium and Vibrio. On the other hand, significantly negative correlations were detected between Vibrio and Streptococcus, Bacillus, Limosilactobacillus and Gardnerella. Our work reinforces the importance of life cycle studies, which can contribute to improve production husbandry strategies. However, we still need more information on this topic as repetition of patterns in different settings is essential to confirm our findings.
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Affiliation(s)
- Diana Bastos Almeida
- ICBAS – Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- SEA EIGHT - Safiestela S.A., Estela, Portugal
| | - Miguel Semedo
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Catarina Magalhães
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- FCUP – Faculty of Sciences, University of Porto, Porto, Portugal
| | | | - Ana Paula Mucha
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- FCUP – Faculty of Sciences, University of Porto, Porto, Portugal
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Lorgen-Ritchie M, Uren Webster T, McMurtrie J, Bass D, Tyler CR, Rowley A, Martin SAM. Microbiomes in the context of developing sustainable intensified aquaculture. Front Microbiol 2023; 14:1200997. [PMID: 37426003 PMCID: PMC10327644 DOI: 10.3389/fmicb.2023.1200997] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023] Open
Abstract
With an ever-growing human population, the need for sustainable production of nutritional food sources has never been greater. Aquaculture is a key industry engaged in active development to increase production in line with this need while remaining sustainable in terms of environmental impact and promoting good welfare and health in farmed species. Microbiomes fundamentally underpin animal health, being a key part of their digestive, metabolic and defense systems, in the latter case protecting against opportunistic pathogens in the environment. The potential to manipulate the microbiome to the advantage of enhancing health, welfare and production is an intriguing prospect that has gained considerable traction in recent years. In this review we first set out what is known about the role of the microbiome in aquaculture production systems across the phylogenetic spectrum of cultured animals, from invertebrates to finfish. With a view to reducing environmental footprint and tightening biological and physical control, investment in "closed" aquaculture systems is on the rise, but little is known about how the microbial systems of these closed systems affect the health of cultured organisms. Through comparisons of the microbiomes and their dynamics across phylogenetically distinct animals and different aquaculture systems, we focus on microbial communities in terms of their functionality in order to identify what features within these microbiomes need to be harnessed for optimizing healthy intensified production in support of a sustainable future for aquaculture.
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Affiliation(s)
| | - Tamsyn Uren Webster
- Centre for Sustainable Aquatic Research, Swansea University, Swansea, United Kingdom
| | - Jamie McMurtrie
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - David Bass
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, United Kingdom
| | - Charles R. Tyler
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Andrew Rowley
- Department of Biosciences, Faculty of Science and Engineering, Swansea University, Swansea, United Kingdom
| | - Samuel A. M. Martin
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
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10
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Satyam R, Ahmad S, Raza K. Comparative genomic assessment of members of genus Tenacibaculum: an exploratory study. Mol Genet Genomics 2023:10.1007/s00438-023-02031-3. [PMID: 37225902 DOI: 10.1007/s00438-023-02031-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 05/04/2023] [Indexed: 05/26/2023]
Abstract
Tenacibaculosis is an ulcerative skin disorder that affects finfish. It is caused by members of the genus Tenacibaculum, resulting in eccentric behavioural changes, including anorexia, lethargy, and abnormal swimming patterns that often result in mortality. Currently, species suspected of causing fish mortality include T. ovolyticum, T. gallaicum, T. discolor, T. finnmarkense, T. mesophilum, T. soleae, T. dicentrarchi, and T. maritimum. However, pathogenic members and the mechanisms involved in disease causation, progression, and transmission are limited due to the inadequate sequencing efforts in the past decade. In this study, we use a comparative genomics approach to investigate the characteristic features of 26 publicly available genomes of Tenacibaculum and report our observations. We propose the reclassification of "T. litoreum HSC 22" to the singaporense species and assignment of "T. sp. 4G03" to the species discolor (species with quotation marks have not been appropriately named). We also report the co-occurrence of several antimicrobial resistance/virulence genes and genes private to a few members. Finally, we mine several non-B DNA forming regions, operons, tandem repeats, high-confidence putative effector proteins, and sortase that might play a pivotal role in bacterial evolution, transcription, and pathogenesis.
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Affiliation(s)
- Rohit Satyam
- Computational Intelligence and Bioinformatics Laboratory, Department of Computer Science, Jamia Millia Islamia, New Delhi, 110025, India
| | - Shaban Ahmad
- Computational Intelligence and Bioinformatics Laboratory, Department of Computer Science, Jamia Millia Islamia, New Delhi, 110025, India
| | - Khalid Raza
- Computational Intelligence and Bioinformatics Laboratory, Department of Computer Science, Jamia Millia Islamia, New Delhi, 110025, India.
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Rieder J, Kapopoulou A, Bank C, Adrian-Kalchhauser I. Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems. ENVIRONMENTAL MICROBIOME 2023; 18:8. [PMID: 36788626 PMCID: PMC9930364 DOI: 10.1186/s40793-023-00459-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 01/02/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND Microbial communities in recirculating aquaculture systems (RAS) play a role in system success, nutrient cycling, and water quality. Considering the increasing socio-economic role of fish farming, e.g., regarding food security, an in-depth understanding of aquaculture microbial communities is also relevant from a management perspective, especially regarding the growth, development, and welfare of the farmed animal. However, the current data on the composition of microbial communities within RAS is patchy, which is partly attributable to diverging method choices that render comparative analyses challenging. Therefore, there is a need for accurate, standardized, and user-friendly methods to study microbial communities in aquaculture systems. RESULTS We compared sequencing approach performances (3 types of 16S short amplicon sequencing, PacBio long-read amplicon sequencing, and amplification-free shotgun metagenomics) in the characterization of microbial communities in two commercial RAS fish farms. Results showed that 16S primer choice and amplicon length affect some values (e.g., diversity measures, number of assigned taxa or distinguishing ASVs) but have no impact on spatio-temporal patterns between sample types, farms and time points. This implies that 16S rRNA approaches are adequate for community studies. The long-read amplicons underperformed regarding the quantitative resolution of spatio-temporal patterns but were suited to identify functional services, e.g., nitrification cycling and the detection of pathogens. Finally, shotgun metagenomics extended the picture to fungi, viruses, and bacteriophages, opening avenues for exploring inter-domain interactions. All sequencing datasets agreed on major prokaryotic players, such as Actinobacteriota, Bacteroidota, Nitrospirota, and Proteobacteria. CONCLUSION The different sequencing approaches yielded overlapping and highly complementary results, with each contributing unique data not obtainable with the other approaches. We conclude that a tiered approach constitutes a strategy for obtaining the maximum amount of information on aquaculture microbial communities and can inform basic research on community evolution dynamics. For specific and/or applied questions, single-method approaches are more practical and cost-effective and could lead to better farm management practices.
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Affiliation(s)
- Jessica Rieder
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, Institute for Fish and Wildlife Health, University of Bern, Länggasstrasse 122, 3001 Bern, Switzerland
- Division of Theoretical Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, 1015 Lausanne, Switzerland
| | - Adamandia Kapopoulou
- Division of Theoretical Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, 1015 Lausanne, Switzerland
| | - Claudia Bank
- Division of Theoretical Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, 1015 Lausanne, Switzerland
| | - Irene Adrian-Kalchhauser
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, Institute for Fish and Wildlife Health, University of Bern, Länggasstrasse 122, 3001 Bern, Switzerland
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12
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Galindo-Villegas J, Bossier P, Reyes-López FE. Editorial: Oral Immune-Enhancing Research in Fish. Front Immunol 2022; 13:850026. [PMID: 35371028 PMCID: PMC8967974 DOI: 10.3389/fimmu.2022.850026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jorge Galindo-Villegas
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- *Correspondence: Jorge Galindo-Villegas, ; Peter Bossier, ; Felipe E. Reyes-López,
| | - Peter Bossier
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Science and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- *Correspondence: Jorge Galindo-Villegas, ; Peter Bossier, ; Felipe E. Reyes-López,
| | - Felipe E. Reyes-López
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Chile
- *Correspondence: Jorge Galindo-Villegas, ; Peter Bossier, ; Felipe E. Reyes-López,
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13
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Abdelhafiz Y, Fernandes JMO, Stefani E, Albanese D, Donati C, Kiron V. Power Play of Commensal Bacteria in the Buccal Cavity of Female Nile Tilapia. Front Microbiol 2021; 12:773351. [PMID: 34867911 PMCID: PMC8636895 DOI: 10.3389/fmicb.2021.773351] [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: 09/09/2021] [Accepted: 10/14/2021] [Indexed: 01/29/2023] Open
Abstract
Fish are widely exposed to higher microbial loads compared to land and air animals. It is known that the microbiome plays an essential role in the health and development of the host. The oral microbiome is vital in females of different organisms, including the maternal mouthbrooding species such as Nile tilapia (Oreochromis niloticus). The present study reports for the first time the microbial composition in the buccal cavity of female and male Nile tilapia reared in a recirculating aquaculture system. Mucus samples were collected from the buccal cavity of 58 adult fish (∼1 kg), and 16S rRNA gene amplicon sequencing was used to profile the microbial communities in females and males. The analysis revealed that opportunistic pathogens such as Streptococcus sp. were less abundant in the female buccal cavity. The power play of certain bacteria such as Acinetobacter, Acidobacteria (GP4 and GP6), and Saccharibacteria that have known metabolic advantages was evident in females compared to males. Association networks inferred from relative abundances showed few microbe–microbe interactions of opportunistic pathogens in female fish. The findings of opportunistic bacteria and their interactions with other microbes will be valuable for improving Nile tilapia rearing practices. The presence of bacteria with specific functions in the buccal cavity of female fish points to their ability to create a protective microbial ecosystem for the offspring.
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Affiliation(s)
- Yousri Abdelhafiz
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Erika Stefani
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Davide Albanese
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Claudio Donati
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Viswanath Kiron
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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14
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Slinger J, Wynne JW, Adams MB. Profiling Branchial Bacteria of Atlantic Salmon (Salmo salar L.) Following Exposure to Antimicrobial Agents. FRONTIERS IN ANIMAL SCIENCE 2021. [DOI: 10.3389/fanim.2021.756101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microbial gill diseases caused by either opportunistic or specific pathogens are an emerging area of concern for aquaculture producers in part due to their sometimes complex and/or cryptic nature. Many antimicrobial treatments used in aquacultural settings are broad spectrum in nature. The effect of such therapeutics upon reduction and recolonization of commensal or pathogenic microbiota post-treatment has received little attention to date. Commensal bacteria are an integral component of the barrier function of mucosal surfaces in animals. This study evaluated the effect of several commercially relevant antimicrobial treatments upon the diversity and composition of branchial bacteria of Atlantic salmon. Here we exposed Atlantic salmon smolt to a number of commercially relevant antimicrobial treatments including chemotherapeutants (chloramine-t and hydrogen peroxide) and antibiotics (oxytetracycline and florfenicol) in vivo. Subsequently we examined the change in bacterial load, 16S rRNA gene expression, and taxonomic diversity post-treatment upon the gills. Results revealed a decrease in cultivable bacterial colonies after antimicrobial treatment, and a downstream decrease in bacterial richness and abundance post-treatment, with colonization of several prominent pathogenic taxa including Vibrio and Tenacibaculum. Temporal tracing over a 14-day period demonstrated that the bacteriome of gill mucus is sensitive to change, and altered by antimicrobial treatment and handling. This study identified candidate antimicrobial treatments which could be implemented in future studies to illustrate the effect of dysbiosis on microbial gill diseases.
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15
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Clinton M, Wyness AJ, Martin SAM, Brierley AS, Ferrier DEK. Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs. BMC Microbiol 2021; 21:313. [PMID: 34758745 PMCID: PMC8579561 DOI: 10.1186/s12866-021-02374-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/25/2021] [Indexed: 12/20/2022] Open
Abstract
Background Understanding the influence of methodology on results is an essential consideration in experimental design. In the expanding field of fish microbiology, many best practices and targeted techniques remain to be refined. This study aimed to compare microbial assemblages obtained from Atlantic salmon (Salmo salar) gills by swabbing versus biopsy excision. Results demonstrate the variation introduced by altered sampling strategies and enhance the available knowledge of the fish gill microbiome. Results The microbiome was sampled using swabs and biopsies from fish gills, with identical treatment of samples for 16S next generation Illumina sequencing. Results show a clear divergence in microbial communities obtained through the different sampling strategies, with swabbing consistently isolating a more diverse microbial consortia, and suffering less from the technical issue of host DNA contamination associated with biopsy use. Sequencing results from biopsy-derived extractions, however, hint at the potential for more cryptic localisation of some community members. Conclusions Overall, results demonstrate a divergence in the obtained microbial community when different sampling methodology is used. Swabbing appears a superior method for sampling the microbiota of mucosal surfaces for broad ecological research in fish, whilst biopsies might be best applied in exploration of communities beyond the reach of swabs, such as sub-surface and intracellular microbes, as well as in pathogen diagnosis. Most studies on the external microbial communities of aquatic organisms utilise swabbing for sample collection, likely due to convenience. Much of the ultrastructure of gill tissue in live fish is, however, potentially inaccessible to swabbing, meaning swabbing might fail to capture the full diversity of gill microbiota. This work therefore also provides valuable insight into partitioning of the gill microbiota, informing varied applications of different sampling methods in experimental design for future research. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02374-0.
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Affiliation(s)
- Morag Clinton
- Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK. .,Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA.
| | - Adam J Wyness
- Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK.,Coastal Research Group, Department of Zoology and Entomology, Rhodes University, Makhanda (Grahamstown), 6139, South Africa
| | - Samuel A M Martin
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Andrew S Brierley
- Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK
| | - David E K Ferrier
- Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK.
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16
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Nowlan JP, Britney SR, Lumsden JS, Russell S. Experimental Induction of Tenacibaculosis in Atlantic Salmon ( Salmo salar L.) Using Tenacibaculum maritimum, T. dicentrarchi, and T. finnmarkense. Pathogens 2021; 10:pathogens10111439. [PMID: 34832595 PMCID: PMC8623880 DOI: 10.3390/pathogens10111439] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 12/31/2022] Open
Abstract
There is a limited understanding of the pathogenesis of tenacibaculosis in Atlantic salmon (Salmo salar L.) and there are few reproducible exposure models for comparison. Atlantic salmon were exposed via bath to Tenacibaculum maritimum, T. dicentrarchi, or T. finnmarkense, and were then grouped with naïve cohabitants. Mortalities had exaggerated clinical signs of mouthrot, a presentation of tenacibaculosis characterized by epidermal ulceration and yellow plaques, on the mouth and less frequently on other tissues. Histopathology showed tissue spongiosis, erosion, ulceration, and necrosis ranging from mild to marked, locally to regionally extensive with mats of intralesional bacteria on the rostrum, vomer, gill rakers, gill filaments, and body surface. Exposure to T. maritimum resulted in less than a 0.4 probability of survival for both exposed and cohabitants until Day 21. Exposures to T. dicentrarchi resulted in 0 and 0.55 (exposed), and 0.8 and 0.9 (cohabitant) probability of survival to Day 12 post-exposure, while T. finnmarkense had a 0.9 probability of survival to Day 12 for all groups. This experimental infection model will be useful to further investigate the pathogenesis of tenacibaculosis, its treatment, and immunity to Tenacibaculum species.
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Affiliation(s)
- Joseph P. Nowlan
- Center for Innovation in Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada; (S.R.B.); (S.R.)
- Correspondence:
| | - Scott R. Britney
- Center for Innovation in Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada; (S.R.B.); (S.R.)
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - John S. Lumsden
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Spencer Russell
- Center for Innovation in Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada; (S.R.B.); (S.R.)
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17
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Legrand T, Wos‐Oxley M, Wynne J, Weyrich L, Oxley A. Dead or alive: microbial viability treatment reveals both active and inactive bacterial constituents in the fish gut microbiota. J Appl Microbiol 2021; 131:2528-2538. [PMID: 33945191 PMCID: PMC8596808 DOI: 10.1111/jam.15113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/22/2021] [Accepted: 04/17/2021] [Indexed: 12/26/2022]
Abstract
AIMS This study evaluated the microbial viability of fish gut microbiota in both digesta (faecal) and mucosal samples using a modified propidium monoazide (PMA) protocol, followed by 16S ribosomal RNA (rRNA) gene sequencing. METHODS AND RESULTS Digesta and gut mucosal samples from farmed yellowtail kingfish (Seriola lalandi) were collected and a modified PMA treatment was applied prior to DNA extraction to differentiate both active and nonviable microbial cells in the samples. All samples were then sequenced using a standard 16S rRNA approach. The digesta and mucosal samples contained significantly different bacterial communities, with a higher diversity observed in digesta samples. In addition, PMA treatment significantly reduced the microbial diversity and richness of digesta and mucosal samples and depleted bacterial constituents typically considered to be important within fish, such as Lactobacillales and Clostridales taxa. CONCLUSIONS These findings suggest that important bacterial members may not be active in the fish gut microbiota. In particular, several beneficial lactic acid bacteria (LAB) were identified as nonviable bacterial cells, potentially influencing the functional potential of the fish microbiota. SIGNIFICANCE AND IMPACTS OF THE STUDY Standardizing the methods for characterizing the fish microbiota are paramount in order to compare studies. In this study, we showed that both sample type and PMA treatment influence the bacterial communities found in the fish gut microbiota. Our findings also suggest that several microbes previously described in the fish gut may not be active constituents. As a result, these factors should be considered in future studies to better evaluate the active bacterial communities associated with the host.
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Affiliation(s)
- T.P.R.A. Legrand
- School of Biological SciencesThe University of AdelaideAdelaideSAAustralia
- CSIRO, Agriculture and FoodHobartTasAustralia
- South Australian Research and Development InstituteAquatic Sciences CentreWest BeachSAAustralia
| | - M.L. Wos‐Oxley
- College of Science and EngineeringFlinders UniversityAdelaideSAAustralia
| | - J.W. Wynne
- CSIRO, Agriculture and FoodHobartTasAustralia
| | - L.S. Weyrich
- School of Biological SciencesThe University of AdelaideAdelaideSAAustralia
- Department of Anthropology and Huck Institutes of Life SciencesThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - A.P.A. Oxley
- Faculty of Science Engineering and Built EnvironmentSchool of Life and Environmental SciencesDeakin UniversityGeelongVic.Australia
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18
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Abdelhafiz Y, Fernandes JMO, Larger S, Albanese D, Donati C, Jafari O, Nedoluzhko AV, Kiron V. Breeding Strategy Shapes the Composition of Bacterial Communities in Female Nile Tilapia Reared in a Recirculating Aquaculture System. Front Microbiol 2021; 12:709611. [PMID: 34566914 PMCID: PMC8461179 DOI: 10.3389/fmicb.2021.709611] [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: 05/14/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
In industrial animal production, breeding strategies are essential to produce offspring of better quality and vitality. It is also known that host microbiome has a bearing on its health. Here, we report for the first time the influence of crossbreeding strategy, inbreeding or outbreeding, on the buccal and intestinal bacterial communities in female Nile tilapia (Oreochromis niloticus). Crossbreeding was performed within a family and between different fish families to obtain the inbred and outbred study groups, respectively. The genetic relationship and structure analysis revealed significant genetic differentiation between the inbred and outbred groups. We also employed a 16S rRNA gene sequencing technique to understand the significant differences between the diversities of the bacterial communities of the inbred and outbred groups. The core microbiota composition in the mouth and the intestine was not affected by the crossbreeding strategy but their abundance varied between the two groups. Furthermore, opportunistic bacteria were abundant in the buccal cavity and intestine of the outbred group, whereas beneficial bacteria were abundant in the intestine of the inbred group. The present study indicates that crossbreeding can influence the abundance of beneficial bacteria, core microbiome and the inter-individual variation in the microbiome.
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Affiliation(s)
- Yousri Abdelhafiz
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Simone Larger
- Unit of Computational Biology, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Davide Albanese
- Unit of Computational Biology, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Claudio Donati
- Unit of Computational Biology, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Omid Jafari
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.,International Sturgeon Research Institute, Iranian Fisheries Science Research Institute, Agricultural Research, Education and Extension Organization, Rasht, Iran
| | | | - Viswanath Kiron
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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19
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Slinger J, Adams MB, Stratford CN, Rigby M, Wynne JW. The Effect of Antimicrobial Treatment upon the Gill Bacteriome of Atlantic Salmon ( Salmo salar L.) and Progression of Amoebic Gill Disease (AGD) In Vivo. Microorganisms 2021; 9:987. [PMID: 34063289 PMCID: PMC8147422 DOI: 10.3390/microorganisms9050987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 01/04/2023] Open
Abstract
Branchial surfaces of finfish species contain a microbial layer rich in commensal bacteria which can provide protection through competitive colonization and production of antimicrobial products. Upon disturbance or compromise, pathogenic microbiota may opportunistically infiltrate this protective barrier and initiate disease. Amoebic gill disease (AGD) is a globally significant health condition affecting salmonid mariculture. The current study examined whether altering the diversity and/or abundance of branchial bacteria could influence the development of experimentally induced AGD. Here, we challenged Atlantic salmon (Salmo salar) with Neoparamoeba perurans in a number of scenarios where the bacterial community on the gill was altered or in a state of instability. Administration of oxytetracycline (in-feed) and chloramine-T (immersion bath) significantly altered the bacterial load and diversity of bacterial taxa upon the gill surface, and shifted the community profile appreciably. AGD severity was marginally higher in fish previously subjected to chloramine-T treatment following 21 days post-challenge. This research suggests that AGD progression and severity was not clearly linked to specific bacterial taxa present in these systems. However, we identified AGD associated taxa including known pathogenic genus (Aliivibrio, Tenacibaculum and Pseudomonas) which increased in abundance as AGD progressed. Elucidation of a potential role for these bacterial taxa in AGD development is warranted.
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Affiliation(s)
- Joel Slinger
- CSIRO Agriculture and Food, Bribie Island Research Centre, Woorim, QLD 4507, Australia;
- Institute of Marine and Antarctic Studies, University of Tasmania, Launceston, TAS 7250, Australia;
| | - Mark B. Adams
- Institute of Marine and Antarctic Studies, University of Tasmania, Launceston, TAS 7250, Australia;
| | - Chris N. Stratford
- CSIRO Agriculture and Food, Bribie Island Research Centre, Woorim, QLD 4507, Australia;
| | - Megan Rigby
- CSIRO Agriculture and Food, Castray Esplanade, Hobart, TAS 7004, Australia; (M.R.); (J.W.W.)
| | - James W. Wynne
- CSIRO Agriculture and Food, Castray Esplanade, Hobart, TAS 7004, Australia; (M.R.); (J.W.W.)
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20
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Nowlan JP, Britney SR, Lumsden JS, Russell S. Application of Quantitative-PCR to Monitor Netpen Sites in British Columbia (Canada) for Tenacibaculum Species. Pathogens 2021; 10:pathogens10040414. [PMID: 33915806 PMCID: PMC8066307 DOI: 10.3390/pathogens10040414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/23/2021] [Accepted: 03/30/2021] [Indexed: 12/31/2022] Open
Abstract
Tenacibaculum are frequently detected from fish with tenacibaculosis at aquaculture sites; however, information on the ecology of these bacteria is sparse. Quantitative-PCR assays were used to detect T. maritimum and T. dicentrarchi at commercial Atlantic salmon (Salmo salar) netpen sites throughout several tenacibaculosis outbreaks. T. dicentrarchi and T. maritimum were identified in live fish, dead fish, other organisms associated with netpens, water samples and on inanimate substrates, which indicates a ubiquitous distribution around stocked netpen sites. Before an outbreak, T. dicentrarchi was found throughout the environment and from fish, and T. maritimum was infrequently identified. During an outbreak, increases in the bacterial load in were recorded and no differences were recorded after an outbreak supporting the observed recrudescence of mouthrot. More bacteria were recorded in the summer months, with more mortality events and antibiotic treatments, indicating that seasonality may influence tenacibaculosis; however, outbreaks occurred in both seasons. Relationships were identified between fish mortalities and antimicrobial use to water quality parameters (temperature, salinity, dissolved oxygen) (p < 0.05), but with low R2 values (<0.25), other variables are also involved. Furthermore, Tenacibaculum species appear to have a ubiquitous spatial and temporal distribution around stocked netpen sites, and with the potential to induce disease in Atlantic salmon, continued research is needed.
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Affiliation(s)
- Joseph P. Nowlan
- Center of Innovation for Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada; (S.R.B.); (S.R.)
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Correspondence:
| | - Scott R. Britney
- Center of Innovation for Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada; (S.R.B.); (S.R.)
| | - John S. Lumsden
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Spencer Russell
- Center of Innovation for Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada; (S.R.B.); (S.R.)
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21
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Nowlan JP, Lumsden JS, Russell S. Advancements in Characterizing Tenacibaculum Infections in Canada. Pathogens 2020; 9:pathogens9121029. [PMID: 33302445 PMCID: PMC7763822 DOI: 10.3390/pathogens9121029] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Tenacibaculum is a genus of gram negative, marine, filamentous bacteria, associated with the presence of disease (tenacibaculosis) at aquaculture sites worldwide; however, infections induced by this genus are poorly characterized. Documents regarding the genus Tenacibaculum and close relatives were compiled for a literature review, concentrating on ecology, identification, and impacts of potentially pathogenic species, with a focus on Atlantic salmon in Canada. Tenacibaculum species likely have a cosmopolitan distribution, but local distributions around aquaculture sites are unknown. Eight species of Tenacibaculum are currently believed to be related to numerous mortality events of fishes and few mortality events in bivalves. The clinical signs in fishes often include epidermal ulcers, atypical behaviors, and mortality. Clinical signs in bivalves often include gross ulcers and discoloration of tissues. The observed disease may differ based on the host, isolate, transmission route, and local environmental conditions. Species-specific identification techniques are limited; high sequence similarities using conventional genes (16S rDNA) indicate that new genes should be investigated. Annotating full genomes, next-generation sequencing, multilocus sequence analysis/typing (MLSA/MLST), matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF), and fatty acid methylesters (FAME) profiles could be further explored for identification purposes. However, each aforementioned technique has disadvantages. Since tenacibaculosis has been observed world-wide in fishes and other eukaryotes, and the disease has substantial economic impacts, continued research is needed.
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Affiliation(s)
- Joseph P. Nowlan
- Department of Pathobiology, University of Guelph, Guelph, OT N1G 2W1, Canada;
- Center for Innovation in Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada;
- Correspondence:
| | - John S. Lumsden
- Department of Pathobiology, University of Guelph, Guelph, OT N1G 2W1, Canada;
| | - Spencer Russell
- Center for Innovation in Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada;
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