151
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Minich JJ, Zhu Q, Xu ZZ, Amir A, Ngochera M, Simwaka M, Allen EE, Zidana H, Knight R. Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus). Microbiologyopen 2018; 7:e00716. [PMID: 30168288 PMCID: PMC6291788 DOI: 10.1002/mbo3.716] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/15/2018] [Accepted: 08/01/2018] [Indexed: 01/19/2023] Open
Abstract
The majority of seafood is farmed, with most finfish coming from freshwater ponds. Ponds are often fertilized to promote microbial productivity as a natural feed source to fish. To understand if pond fertilization with livestock manure induces a probiotic or prebiotic effect, we communally reared tilapia (Oreochromis shiranus), and North African catfish (Clarias gariepinus), for 4 weeks under seven manure treatments including layer chicken, broiler chicken, guinea fowl, quail, pig, cow, vs. commercial feed to evaluate microbial community dynamics of the manure, pond water, and fish feces using 16S and 18S rRNA marker genes along with metagenome sequencing. Catfish growth, but not tilapia, was positively associated with plankton abundance (p = 0.0006, R2 = 0.4887) and greatest in ponds fertilized with quail manure (ANOVA, p < 0.05). Manure was unique and influenced the 16S microbiome in pond water, tilapia gut, and catfish gut and 18S community in pond water and catfish guts (PERMANOVA, p = 0.001). On average, 18.5%, 18.6%, and 45.3% of manure bacteria sOTUs, (sub‐operational taxonomic units), were present in the water column, catfish feces, and tilapia feces which comprised 3.7%, 12.8%, and 10.9% of the total microbial richness of the communities, respectively. Antibiotic resistance genes were highest in the manure and water samples followed by tilapia feces and lowest in catfish feces (p < 0.0001). In this study, we demonstrate how the bacterial and eukaryotic microbial composition of fish ponds are influenced by specific livestock manure inputs and that the gut microbiome of tilapia is more sensitive and responsive than catfish to these changes. We conclude that animal manure used as fertilizer induces a primarily prebiotic effect on the pond ecosystem rather than a direct probiotic effect on fish.
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Affiliation(s)
- Jeremiah J Minich
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, California
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California San Diego, La Jolla, California
| | - Amnon Amir
- Department of Pediatrics, University of California San Diego, La Jolla, California
| | - Maxon Ngochera
- Department of Fisheries, Fisheries Research Unit, Monkey Bay, Malawi
| | | | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California.,Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California
| | | | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California.,Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California
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152
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Jones J, DiBattista JD, Stat M, Bunce M, Boyce MC, Fairclough DV, Travers MJ, Huggett MJ. The Microbiome of the Gastrointestinal Tract of a Range-Shifting Marine Herbivorous Fish. Front Microbiol 2018; 9:2000. [PMID: 30210475 PMCID: PMC6121097 DOI: 10.3389/fmicb.2018.02000] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/08/2018] [Indexed: 01/01/2023] Open
Abstract
Globally, marine species’ distributions are being modified due to rising ocean temperatures. Increasing evidence suggests a circum-global pattern of poleward extensions in the distributions of many tropical herbivorous species, including the ecologically important rabbitfish Siganus fuscescens. Adaptability of a species to such new environments may be heavily influenced by the composition of their gastrointestinal microbe fauna, which is fundamentally important to animal health. Siganus fuscescens thus provides an opportunity to assess the stability of gastrointestinal microbes under varying environmental conditions. The gastrointestinal microbial communities of S. fuscescens were characterized over 2,000 km of Australia’s western coast, from tropical to temperate waters, including near its current southern distributional limit. Sequencing of the 16S rRNA gene demonstrated that each population had a distinct hindgut microbial community, and yet, 20 OTUs occurred consistently in all samples. These OTUs were considered the ‘core microbiome’ and were highly abundant, composing between 31 and 54% of each population. Furthermore, levels of short chain fatty acids, an indicator of microbial fermentation activity, were similar among tropical and temperate locations. These data suggest that flexibility in the hindgut microbiome may play a role in enabling such herbivores to colonize new environments beyond their existing range.
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Affiliation(s)
- Jacquelyn Jones
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Joseph D DiBattista
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth WA, Australia.,Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Michael Stat
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth WA, Australia.,Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth WA, Australia
| | - Mary C Boyce
- Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - David V Fairclough
- Department of Primary Industries and Regional Development, Fisheries Division, Government of Western Australia, Hillarys, WA, Australia
| | - Michael J Travers
- Department of Primary Industries and Regional Development, Fisheries Division, Government of Western Australia, Hillarys, WA, Australia
| | - Megan J Huggett
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA, Australia.,Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, WA, Australia.,School of Environmental and Life Sciences, University of Newcastle, Ourimbah, NSW, Australia
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153
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Talwar C, Nagar S, Lal R, Negi RK. Fish Gut Microbiome: Current Approaches and Future Perspectives. Indian J Microbiol 2018; 58:397-414. [PMID: 30262950 DOI: 10.1007/s12088-018-0760-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/17/2018] [Indexed: 12/13/2022] Open
Abstract
In recent years, investigations of microbial flora associated with fish gut have deepened our knowledge of the complex interactions occurring between microbes and host fish. The gut microbiome not only reinforces the digestive and immune systems in fish but is itself shaped by several host-associated factors. Unfortunately, in the past, majority of studies have focused upon the structure of fish gut microbiome providing little knowledge of effects of these factors distinctively and the immense functional potential of the gut microbiome. In this review, we have highlighted the recently gained insights into the diversity and functions of the fish gut microbiome. We have also delved on the current approaches that are being employed to study the fish gut microbiome with an aim to collate all the knowledge gained and make accurate conclusions for their application based perspectives. The literature reviewed indicated that the future research should shift towards functional microbiomics to improve the maximum sustainable yield in aquaculture.
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Affiliation(s)
- Chandni Talwar
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Shekhar Nagar
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, 110007 India
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154
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Ringø E, Hoseinifar SH, Ghosh K, Doan HV, Beck BR, Song SK. Lactic Acid Bacteria in Finfish-An Update. Front Microbiol 2018; 9:1818. [PMID: 30147679 PMCID: PMC6096003 DOI: 10.3389/fmicb.2018.01818] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/19/2018] [Indexed: 12/17/2022] Open
Abstract
A complex and dynamic community of microorganisms, play important roles within the fish gastrointestinal (GI) tract. Of the bacteria colonizing the GI tract, are lactic acid bacteria (LAB) generally considered as favorable microorganism due to their abilities to stimulating host GI development, digestive function, mucosal tolerance, stimulating immune response, and improved disease resistance. In early finfish studies, were culture-dependent methods used to enumerate bacterial population levels within the GI tract. However, due to limitations by using culture methods, culture-independent techniques have been used during the last decade. These investigations have revealed the presence of Lactobacillus, Lactococcus, Leuconostoc, Enterococcus, Streptococcus, Carnobacterium, Weissella, and Pediococcus as indigenous species. Numerous strains of LAB isolated from finfish are able to produce antibacterial substances toward different potential fish pathogenic bacteria as well as human pathogens. LAB are revealed be the most promising bacterial genera as probiotic in aquaculture. During the decade numerous investigations are performed on evaluation of probiotic properties of different genus and species of LAB. Except limited contradictory reports, most of administered strains displayed beneficial effects on both, growth-and reproductive performance, immune responses and disease resistance of finfish. This eventually led to industrial scale up and introduction LAB-based commercial probiotics. Pathogenic LAB belonging to the genera Streptococcus, Enterococcus, Lactobacillus, Carnobacterium, and Lactococcus have been detected from ascites, kidney, liver, heart, and spleen of several finfish species. These pathogenic bacteria will be addressed in present review which includes their impacts on finfish aquaculture, possible routes for treatment. Finfish share many common structures and functions of the immune system with warm-blooded animals, although apparent differences exist. This similarity in the immune system may result in many shared LAB effects between finfish and land animals. LAB-fed fish show an increase in innate immune activities leading to disease resistances: neutrophil activity, lysozyme secretion, phagocytosis, and production of pro-inflammatory cytokines (IL-1β, IL-6, IL-8, and TNF-α). However, some LAB strains preferentially induces IL-10 instead, a potent anti-inflammatory cytokine. These results indicate that LAB may vary in their immunological effects depending on the species and hosts. So far, the immunological studies using LAB have been focused on their effects on innate immunity. However, these studies need to be further extended by investigating their involvement in the modulation of adaptive immunity. The present review paper focuses on recent findings in the field of isolation and detection of LAB, their administration as probiotic in aquaculture and their interaction with fish immune responses. Furthermore, the mode of action of probiotics on finfish are discussed.
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Affiliation(s)
- Einar Ringø
- Faculty of Bioscience, Fisheries and Economics, Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Seyed Hossein Hoseinifar
- Department of Fisheries, Faculty of Fisheries and Environmental Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Koushik Ghosh
- Aquaculture Laboratory, Department of Zoology, The University of Burdwan, Bardhaman, India
| | - Hien Van Doan
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
| | - Bo Ram Beck
- School of Life Science, Handong University, Pohang, South Korea
| | - Seong Kyu Song
- School of Life Science, Handong University, Pohang, South Korea
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155
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Zheng Y, Wu W, Hu G, Qiu L, Meng S, Song C, Fan L, Zhao Z, Bing X, Chen J. Gut microbiota analysis of juvenile genetically improved farmed tilapia (Oreochromis niloticus) by dietary supplementation of different resveratrol concentrations. FISH & SHELLFISH IMMUNOLOGY 2018; 77:200-207. [PMID: 29574130 DOI: 10.1016/j.fsi.2018.03.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 03/05/2018] [Accepted: 03/20/2018] [Indexed: 06/08/2023]
Abstract
The genetically improved farmed tilapia (GIFT, Oreochromis niloticus) is cultured widely for production of freshwater fish in China, while streptococcosis, likely related to pathogenic infections, occurs frequently in juvenile, mother, and operated GIFT. The gut microbiota plays an important role in nutrient digestibility in animals, and resveratrol (RES) has been used in feed for different freshwater fish species. Therefore, understanding changes in the tilapia gut microbiota across different concentrations of dietary RES supplementation is extremely important. The gut microbiota population in tilapia at 45 d after supplementation with different concentrations (0, 0.025, 0.05, 0.1 g/kg) of dietary RES was assessed by 16S rDNA gene sequencing. A total of 5445 operational taxonomic units were identified from all samples, and 14 phyla and 81 families were identified from all fecal samples. The bacteria of the phylum Firmicutes were significantly enriched in the 0.025 g/kg RES group when compared with the controls. Proteobacteria, Firmicutes and Cyanobacteria were the most dominant three phyla in all samples. With the increasing concentrations, the proportion of beneficial microbial taxa (Acetobacteraceae and Methylobacteriaceae) increased, whereas the proportion of harmful microbial taxa decreased, eg. Streptococcaceae except for 0.1 g/kg RES groups. RES did not affect the richness and diversity in tilapia gut microbiota. These findings provide information on the diversity and differences in GIFT gut microbiota database, and may contribute to developing strategies for management of diseases and long-term sustainability of O. niloticus culture.
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Affiliation(s)
- Yao Zheng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Evironment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu, 214081, PR China
| | - Wei Wu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Evironment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu, 214081, PR China
| | - Gengdong Hu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Evironment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu, 214081, PR China
| | - Liping Qiu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Evironment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu, 214081, PR China
| | - Shunlong Meng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Evironment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu, 214081, PR China
| | - Chao Song
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Evironment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu, 214081, PR China
| | - Limin Fan
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Evironment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu, 214081, PR China
| | - Zhixiang Zhao
- Wuxi Fishery College, Nanjing Agricultural University, Wuxi, Jiangsu, 214081, PR China
| | - Xuwen Bing
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Evironment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu, 214081, PR China; Wuxi Fishery College, Nanjing Agricultural University, Wuxi, Jiangsu, 214081, PR China.
| | - Jiazhang Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Evironment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu, 214081, PR China; Wuxi Fishery College, Nanjing Agricultural University, Wuxi, Jiangsu, 214081, PR China; Key Laboratory of Control of Quality and Safety for Aquatic Products, Ministry of Agriculture, PR China.
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156
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Egerton S, Culloty S, Whooley J, Stanton C, Ross RP. The Gut Microbiota of Marine Fish. Front Microbiol 2018; 9:873. [PMID: 29780377 PMCID: PMC5946678 DOI: 10.3389/fmicb.2018.00873] [Citation(s) in RCA: 343] [Impact Index Per Article: 57.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/16/2018] [Indexed: 12/19/2022] Open
Abstract
The body of work relating to the gut microbiota of fish is dwarfed by that on humans and mammals. However, it is a field that has had historical interest and has grown significantly along with the expansion of the aquaculture industry and developments in microbiome research. Research is now moving quickly in this field. Much recent focus has been on nutritional manipulation and modification of the gut microbiota to meet the needs of fish farming, while trying to maintain host health and welfare. However, the diversity amongst fish means that baseline data from wild fish and a clear understanding of the role that specific gut microbiota play is still lacking. We review here the factors shaping marine fish gut microbiota and highlight gaps in the research.
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Affiliation(s)
- Sian Egerton
- School of Microbiology, University College Cork, Cork, Ireland.,School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Sarah Culloty
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Jason Whooley
- Bio-marine Ingredients Ireland Ltd., Killybegs, Ireland
| | - Catherine Stanton
- Teagasc Research Centre, Fermoy, Ireland.,APC Microbiome Ireland, Teagasc and University College Cork, Cork, Ireland
| | - R Paul Ross
- School of Microbiology, University College Cork, Cork, Ireland.,Teagasc Research Centre, Fermoy, Ireland.,APC Microbiome Ireland, Teagasc and University College Cork, Cork, Ireland
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157
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Tapia-Paniagua ST, Ceballos-Francisco D, Balebona MC, Esteban MÁ, Moriñigo MÁ. Mucus glycosylation, immunity and bacterial microbiota associated to the skin of experimentally ulcered gilthead seabream (Sparus aurata). FISH & SHELLFISH IMMUNOLOGY 2018; 75:381-390. [PMID: 29421587 DOI: 10.1016/j.fsi.2018.02.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 01/24/2018] [Accepted: 02/02/2018] [Indexed: 05/25/2023]
Abstract
Interest in fish skin immunity and its associated microbiota has greatly increased among immunologists. The objective of this study is to know if skin ulcers may be associated with changes in the mucus composition and microbial diversity. The abundance of terminal carbohydrates, several enzymes (protease, antiprotease, peroxidase, lysozyme) and total immunoglobulin M levels were evaluated in skin mucus of experimentally ulcered gilthead seabream (Sparus aurata L.). Furthermore, the composition of the microbiota of ulcered and non-ulcered skin has been determined using Illumina Miseq technology. Significant decreases of terminal abundance of α-D-mannose, α-D-glucose and N-acetyl-galactosamine in skin mucus of ulcered fish, compared to control fish were detected. The levels of IgM and all the tested enzymes in mucus were decreased in ulcered fish (compared to control fish) although the observed decreases were only statistically significant for proteases and antiproteases. Concomitantly, the analysis of the composition of the skin microbiota showed clear differences between ulcered and non-ulcered areas. The genus taxonomic analysis showed that Staphylococcus and Lactobacillus were more abundant in non-ulcered skin whereas in ulcered area were Streptococcus and Granulicatella. Important decreases of the number of sequences related to Alteromonas, Thalassabius and Winogradskyella were detected in ulcered skin whilst slight increases of sequences related to Flavobacterium, Chryseobacterium and Tenacibaculum genera were observed. Overall these results demonstrated that the presence of skin ulcers provide microenvironments that perturb both the mucus composition and microbial biodiversity of this important external surface which seem to be more vulnerable to diseases.
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Affiliation(s)
- Silvana Teresa Tapia-Paniagua
- Group of Prophylaxis and Biocontrol of Fish Diseases, Departamento de Microbiología, Campus de Teatinos s/n, Universidad de Málaga, 29071 Málaga, Spain
| | - Diana Ceballos-Francisco
- Department of Cell Biology and Histology, Faculty of Biology, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", University of Murcia, 30100, Murcia, Spain
| | - M Carmen Balebona
- Group of Prophylaxis and Biocontrol of Fish Diseases, Departamento de Microbiología, Campus de Teatinos s/n, Universidad de Málaga, 29071 Málaga, Spain
| | - María Ángeles Esteban
- Department of Cell Biology and Histology, Faculty of Biology, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", University of Murcia, 30100, Murcia, Spain
| | - Miguel Ángel Moriñigo
- Group of Prophylaxis and Biocontrol of Fish Diseases, Departamento de Microbiología, Campus de Teatinos s/n, Universidad de Málaga, 29071 Málaga, Spain.
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158
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Obregón C, Lyndon AR, Barker J, Christiansen H, Godley BJ, Kurland S, Piccolo JJ, Potts R, Short R, Tebb A, Mariani S. Valuing and understanding fish populations in the Anthropocene: key questions to address. JOURNAL OF FISH BIOLOGY 2018; 92:828-845. [PMID: 29411379 DOI: 10.1111/jfb.13536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/09/2017] [Indexed: 06/08/2023]
Abstract
Research on the values of fish populations and fisheries has primarily focused on bio-economic aspects; a more nuanced and multidimensional perspective is mostly neglected. Although a range of social aspects is increasingly being considered in fisheries research, there is still no clear understanding as to how to include these additional values within management policies nor is there a cogent appreciation of the major knowledge gaps that should be tackled by future research. This paper results from a workshop held during the 50th anniversary symposium of the Fisheries Society of the British Isles at the University of Exeter, UK, in July 2017. Here, we aim to highlight the current knowledge gaps on the values of fish populations and fisheries thus directing future research. To this end, we present eight questions that are deeply relevant to understanding the values of fish populations and fisheries. These can be applied to all habitats and fisheries, including freshwater, estuarine and marine.
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Affiliation(s)
- C Obregón
- Estuaries & Wetlands Conservation Programmes, Conservation Programmes Department, Zoological Society of London, Regents Park, London NW1 4RY, U.K
- Centre for Fish and Fisheries Research, Department of Biological Sciences, Murdoch University, 90 South Street, Murdoch, Western Australia 6150, Australia
| | - A R Lyndon
- Centre for Marine Biodiversity and Biotechnology, Institute of Life and Earth Sciences, John Muir Building, Heriot-Watt University, Edinburgh, EH14 4AS, U.K
| | - J Barker
- Estuaries & Wetlands Conservation Programmes, Conservation Programmes Department, Zoological Society of London, Regents Park, London NW1 4RY, U.K
| | - H Christiansen
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Charles Deberiotstraat 32 - Box 2439, 3000 Leuven, Belgium
| | - B J Godley
- Centre for Ecology and Conservation, Daphne du Maurier Building, College of Life and Environmental Sciences, Department of Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, U.K
| | - S Kurland
- Populations genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - J J Piccolo
- Institution for Environmental and Life Science, River Ecology and Management Group, Department of Environmental and Life Sciences, Karlstad University, Karlstad, Sweden
| | - R Potts
- Biosciences, College of Life and Environmental Sciences, Department of Biosciences, University of Exeter, Stocker Road, Exeter, Devon EX4 4QD, U.K
| | - R Short
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, U.K
| | - A Tebb
- Sussex Inshore Fisheries and Conservation Authority, Shoreham-by-Sea, West Sussex, BN43 6RE, U.K
| | - S Mariani
- School of Environment and Life Sciences, Peel Building, University of Salford, Salford, M5 4WT, U.K
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159
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Wu Z, Gatesoupe FJ, Li T, Wang X, Zhang Q, Feng D, Feng Y, Chen H, Li A. Significant improvement of intestinal microbiota of gibel carp (Carassius auratus gibelio
) after traditional Chinese medicine feeding. J Appl Microbiol 2018; 124:829-841. [DOI: 10.1111/jam.13674] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/27/2017] [Accepted: 12/12/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Z.B. Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
| | - F.-J. Gatesoupe
- NUMEA; INRA; University of Pau and Pays de l'Adour; Saint Pée sur Nivelle France
| | - T.T. Li
- Department of Applied Biology; College of Biotechnology and Bioengineering; Zhejiang University of Technology; Hangzhou China
| | - X.H. Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
| | - Q.Q. Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- Freshwater Aquaculture Collaborative Innovation Centre of Hubei Province; Huazhong Agricultural University; Wuhan China
| | - D.Y. Feng
- National Fisheries Technical Extension Centre; Ministry of Agriculture; Beijing China
| | - Y.Q. Feng
- State Key Laboratory of Freshwater Ecology and Biotechnology; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
| | - H. Chen
- Fisheries Technical Extension Centre of Jiangsu Province; Nanjing China
| | - A.H. Li
- State Key Laboratory of Freshwater Ecology and Biotechnology; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- Freshwater Aquaculture Collaborative Innovation Centre of Hubei Province; Huazhong Agricultural University; Wuhan China
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160
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Rudi K, Angell IL, Pope PB, Vik JO, Sandve SR, Snipen LG. Stable Core Gut Microbiota across the Freshwater-to-Saltwater Transition for Farmed Atlantic Salmon. Appl Environ Microbiol 2018; 84:e01974-17. [PMID: 29101198 PMCID: PMC5752857 DOI: 10.1128/aem.01974-17] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/01/2017] [Indexed: 12/21/2022] Open
Abstract
Gut microbiota associations through habitat transitions are fundamentally important yet poorly understood. One such habitat transition is the migration from freshwater to saltwater for anadromous fish, such as salmon. The aim of the current work was therefore to determine the freshwater-to-saltwater transition impact on the gut microbiota in farmed Atlantic salmon, with dietary interventions resembling freshwater and saltwater diets with respect to fatty acid composition. Using deep 16S rRNA gene sequencing and quantitative PCR, we found that the freshwater-to-saltwater transition had a major association with the microbiota composition and quantity, while diet did not show significant associations with the microbiota. In saltwater there was a 100-fold increase in bacterial quantity, with a relative increase of Firmicutes and a relative decrease of both Actinobacteria and Proteobacteria Irrespective of an overall shift in microbiota composition from freshwater to saltwater, we identified three core clostridia and one Lactobacillus-affiliated phylotype with wide geographic distribution that were highly prevalent and co-occurring. Taken together, our results support the importance of the dominating bacteria in the salmon gut, with the freshwater microbiota being immature. Due to the low number of potentially host-associated bacterial species in the salmon gut, we believe that farmed salmon can represent an important model for future understanding of host-bacterium interactions in aquatic environments.IMPORTANCE Little is known about factors affecting the interindividual distribution of gut bacteria in aquatic environments. We have shown that there is a core of four highly prevalent and co-occurring bacteria irrespective of feed and freshwater-to-saltwater transition. The potential host interactions of the core bacteria, however, need to be elucidated further.
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Affiliation(s)
- Knut Rudi
- Faculty of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
| | - Inga Leena Angell
- Faculty of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
| | - Jon Olav Vik
- Faculty of Biosciences, University of Life Sciences, Ås, Norway
| | | | - Lars-Gustav Snipen
- Faculty of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
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161
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Piazzon MC, Calduch-Giner JA, Fouz B, Estensoro I, Simó-Mirabet P, Puyalto M, Karalazos V, Palenzuela O, Sitjà-Bobadilla A, Pérez-Sánchez J. Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets. MICROBIOME 2017; 5:164. [PMID: 29282153 PMCID: PMC5745981 DOI: 10.1186/s40168-017-0390-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 12/18/2017] [Indexed: 05/15/2023]
Abstract
BACKGROUND The constant increase of aquaculture production and wealthy seafood consumption has forced the industry to explore alternative and more sustainable raw aquafeed materials, and plant ingredients have been used to replace marine feedstuffs in many farmed fish. The objective of the present study was to assess whether plant-based diets can induce changes in the intestinal mucus proteome, gut autochthonous microbiota and disease susceptibility of fish, and whether these changes could be reversed by the addition of sodium butyrate to the diets. Three different trials were performed using the teleostean gilthead sea bream (Sparus aurata) as model. In a first preliminary short-term trial, fish were fed with the additive (0.8%) supplementing a basal diet with low vegetable inclusion (D1) and then challenged with a bacteria to detect possible effects on survival. In a second trial, fish were fed with diets with greater vegetable inclusion levels (D2, D3) and the long-term effect of sodium butyrate at a lower dose (0.4%) added to D3 (D4 diet) was tested on the intestinal proteome and microbiome. In a third trial, the long-term effectiveness of sodium butyrate (D4) to prevent disease outcome after an intestinal parasite (Enteromyxum leei) challenge was tested. RESULTS The results showed that opposed forces were driven by dietary plant ingredients and sodium butyrate supplementation in fish diet. On the one hand, vegetable diets induced high parasite infection levels that provoked drops in growth performance, decreased intestinal microbiota diversity, induced the dominance of the Photobacterium genus, as well as altered the gut mucosal proteome suggesting detrimental effects on intestinal function. On the other hand, butyrate addition slightly decreased cumulative mortality after bacterial challenge, avoided growth retardation in parasitized fish, increased intestinal microbiota diversity with a higher representation of butyrate-producing bacteria and reversed most vegetable diet-induced changes in the gut proteome. CONCLUSIONS This integrative work gives insights on the pleiotropic effects of a dietary additive on the restoration of intestinal homeostasis and disease resilience, using a multifaceted approach.
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Affiliation(s)
- María Carla Piazzon
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Josep Alvar Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Belén Fouz
- Department of Microbiology and Ecology, Faculty of Biology, University of Valencia, Valencia, Spain
| | - Itziar Estensoro
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Paula Simó-Mirabet
- Nutrigenomics and Fish Growth Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | | | | | - Oswaldo Palenzuela
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
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162
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de Bruijn I, Liu Y, Wiegertjes GF, Raaijmakers JM. Exploring fish microbial communities to mitigate emerging diseases in aquaculture. FEMS Microbiol Ecol 2017; 94:4675208. [DOI: 10.1093/femsec/fix161] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/28/2017] [Indexed: 12/21/2022] Open
Affiliation(s)
- Irene de Bruijn
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen 6708PB, The Netherlands
| | - Yiying Liu
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen 6708PB, The Netherlands
| | - Geert F Wiegertjes
- Cell Biology and Immunology group, Department of Animal Sciences, Wageningen University & Research, De Elst 1, Wageningen 6708WD, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen 6708PB, The Netherlands
- Institute of Biology (IBL), Leiden University, Sylviusweg 72, Leiden 2333 BE, Leiden, The Netherlands
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163
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Wu Y, Liu W, Li Q, Li Y, Yan Y, Huang F, Wu X, Zhou Q, Shu X, Ruan Z. Dietary chlorogenic acid regulates gut microbiota, serum-free amino acids and colonic serotonin levels in growing pigs. Int J Food Sci Nutr 2017; 69:566-573. [DOI: 10.1080/09637486.2017.1394449] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yi Wu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Wenhui Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Qi Li
- School of Public Health, Nanchang University, Nanchang, China
| | - Yafei Li
- Jiangxi Academy of Medical Science, College Community Hospital, Nanchang University, Nanchang, China
| | - Yali Yan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Fang Huang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Xin Wu
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Quancheng Zhou
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Xugang Shu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Zheng Ruan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Nanchang University, Nanchang, China
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164
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Ramírez C, Romero J. The Microbiome of Seriola lalandi of Wild and Aquaculture Origin Reveals Differences in Composition and Potential Function. Front Microbiol 2017; 8:1844. [PMID: 29018423 PMCID: PMC5622978 DOI: 10.3389/fmicb.2017.01844] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/08/2017] [Indexed: 11/16/2022] Open
Abstract
Seriola lalandi is an economically important species that is globally distributed in temperate and subtropical marine waters. Aquaculture production of this species has had problems associated with intensive fish farming, such as disease outbreaks or nutritional deficiencies causing high mortalities. Intestinal microbiota has been involved in many processes that benefit the host, such as disease control, stimulation of the immune response, and the promotion of nutrient metabolism, among others. However, little is known about the potential functionality of the microbiota and the differences in the composition between wild and aquacultured fish. Here, we assayed the V4-region of the 16S rRNA gene using high-throughput sequencing. Our results showed that there are significant differences between S. lalandi of wild and aquaculture origin (ANOSIM and PERMANOVA, P < 0.05). At the genus level, a total of 13 genera were differentially represented between the two groups, all of which have been described as beneficial microorganisms that have an antagonistic effect against pathogenic bacteria, improve immunological parameters and growth performance, and contribute to nutrition. Additionally, the changes in the presumptive functions of the intestinal microbiota of yellowtail were examined by predicting the metagenomes using PICRUSt. The most abundant functional categories were those corresponding to the metabolism of cofactors and vitamins, amino acid metabolism and carbohydrate metabolism, revealing differences in the contribution of the microbiota depending on the origin of the animals. To our knowledge, this is the first study to characterize and compare the intestinal microbiota of S. lalandi of wild and aquaculture origin using high-throughput sequencing.
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Affiliation(s)
- Carolina Ramírez
- Laboratorio de Biotecnología de los Alimentos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Doctorado en Acuicultura, Programa Cooperativo Universidad de Chile, Universidad Católica del Norte, Pontificia Universidad Católica de Valparaíso, Santiago, Chile
| | - Jaime Romero
- Laboratorio de Biotecnología de los Alimentos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
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