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González-Gragera E, García-López JD, Teso-Pérez C, Jiménez-Hernández I, Peralta-Sánchez JM, Valdivia E, Montalban-Lopez M, Martín-Platero AM, Baños A, Martínez-Bueno M. Genomic Characterization of Piscicolin CM22 Produced by Carnobacterium maltaromaticum CM22 Strain Isolated from Salmon (Salmo salar). Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10316-1. [PMID: 38958914 DOI: 10.1007/s12602-024-10316-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2024] [Indexed: 07/04/2024]
Abstract
Carnobacterium maltaromaticum is a species of lactic acid bacteria (LAB) that has been isolated from various natural environments. It is well-known for producing a diverse spectrum of bacteriocins with potential biotechnological applications. In the present study, a new psychrotolerant strain of C. maltaromaticum CM22 is reported, isolated from a salmon gut sample and producing a variant of the bacteriocin piscicolin 126 that has been named piscicolin CM22. After identification by 16S rRNA gene, this strain has been genomically characterized by sequencing and assembling its complete genome. Moreover, its bacteriocin was purified and characterized. In vitro tests demonstrated that both the strain and its bacteriocin possess antimicrobial activity against several Gram-positive bacteria of interest in human and animal health, such as Listeria monocytogenes, Clostridium perfringens, or Enterococcus faecalis. However, this bacteriocin did not produce any antimicrobial effect on Gram-negative species. The study of its genome showed the genetic structure of the gene cluster that encodes the bacteriocin, showing a high degree of homology to the gene cluster of piscicolin 126 described in other C. maltaromaticum. Although more studies are necessary concerning its functional properties, this new psychrotolerant strain C. maltaromaticum CM22 and its bacteriocin could be considered an interesting candidate with potential application in agri-food industry.
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Affiliation(s)
- Elías González-Gragera
- Department of Microbiology, University of Granada, Avda. Fuentenueva, S/N, 18071, Granada, Spain
| | - J David García-López
- Department of Microbiology, University of Granada, Avda. Fuentenueva, S/N, 18071, Granada, Spain
| | - Claudia Teso-Pérez
- Department of Microbiology, University of Granada, Avda. Fuentenueva, S/N, 18071, Granada, Spain
| | - Irene Jiménez-Hernández
- Department of Microbiology, University of Granada, Avda. Fuentenueva, S/N, 18071, Granada, Spain
| | | | - Eva Valdivia
- Department of Microbiology, University of Granada, Avda. Fuentenueva, S/N, 18071, Granada, Spain
- Institute of Biotechnology, University of Granada, 18071, Granada, Spain
| | - Manuel Montalban-Lopez
- Department of Microbiology, University of Granada, Avda. Fuentenueva, S/N, 18071, Granada, Spain
- Institute of Biotechnology, University of Granada, 18071, Granada, Spain
| | - Antonio M Martín-Platero
- Department of Microbiology, University of Granada, Avda. Fuentenueva, S/N, 18071, Granada, Spain
- Institute of Biotechnology, University of Granada, 18071, Granada, Spain
| | - Alberto Baños
- Department of Microbiology, University of Granada, Avda. Fuentenueva, S/N, 18071, Granada, Spain
| | - Manuel Martínez-Bueno
- Department of Microbiology, University of Granada, Avda. Fuentenueva, S/N, 18071, Granada, Spain.
- Institute of Biotechnology, University of Granada, 18071, Granada, Spain.
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Wang ZZ, Wang ZT, Wang WL, Lei KK, Zhou JS. Effects of Different Farming Modes on Salmo trutta fario Growth and Intestinal Microbial Community. Microorganisms 2024; 12:1082. [PMID: 38930465 PMCID: PMC11205959 DOI: 10.3390/microorganisms12061082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/23/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024] Open
Abstract
The gut microbiota plays a pivotal role in upholding intestinal health, fostering intestinal development, fortifying organisms against pathogen intrusion, regulating nutrient absorption, and managing the body's lipid metabolism. However, the influence of different cultivation modes on the growth indices and intestinal microbes of Salmo trutta fario remains underexplored. In this study, we employed high-throughput sequencing and bioinformatics techniques to scrutinize the intestinal microbiota in three farming modes: traditional pond aquaculture (TPA), recirculating aquaculture (RA), and flow-through aquaculture (FTA). We aimed to assess the impact of different farming methods on the water environment and Salmo trutta fario's growth performance. Our findings revealed that the final weight and weight gain rate in the FTA model surpassed those in the other two. Substantial disparities were observed in the composition, relative abundance, and diversity of Salmo trutta fario gut microbiota under different aquaculture modes. Notably, the dominant genera of Salmo trutta fario gut microbiota varied across farming modes: for instance, in the FTA model, the most prevalent genera were SC-I-84 (7.34%), Subgroup_6 (9.93%), and UTCFX1 (6.71%), while, under RA farming, they were Bacteroidetes_vadinHA17 (10.61%), MBNT15 (7.09%), and Anaeromyxoactor (6.62%). In the TPA model, dominant genera in the gut microbiota included Anaeromyxobacter (8.72%), Bacteroidetes_vadinHA17 (8.30%), and Geobacter (12.54%). From a comparative standpoint, the genus-level composition of the gut microbiota in the RA and TPA models exhibited relative similarity. The gut microbiota in the FTA model showcased the most intricate functional diversity, while TPA farming displayed a more intricate interaction pattern with the gut microbiota. Transparency, pH, dissolved oxygen, conductivity, total dissolved solids, and temperature emerged as pivotal factors influencing Salmo trutta fario gut microbiota under diverse farming conditions. These research findings offer valuable scientific insights for fostering healthy aquaculture practices and disease prevention and control measures for Salmo trutta fario, holding substantial significance for the sustainable development of the cold-water fish industry in the Qinghai-Tibet Plateau.
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Affiliation(s)
- Zhuang-Zhuang Wang
- Institute of Aquatic Sciences, Tibet Autonomous Region Academy of Agricultural and Animal Husbandry Sciences, Lasa 850032, China; (Z.-Z.W.); (W.-L.W.); (K.-K.L.)
- Key Laboratory of Fishery and Germplasm Resources Utilization of Xizang Autonomous Region, Lasa 850032, China
| | - Zhi-Tong Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Wan-Liang Wang
- Institute of Aquatic Sciences, Tibet Autonomous Region Academy of Agricultural and Animal Husbandry Sciences, Lasa 850032, China; (Z.-Z.W.); (W.-L.W.); (K.-K.L.)
- Key Laboratory of Fishery and Germplasm Resources Utilization of Xizang Autonomous Region, Lasa 850032, China
- Center for Research on Breeding and Utilization Techniques of Indigenous Fish Species in Xizang, Lasa 850032, China
| | - Kuan-Kuan Lei
- Institute of Aquatic Sciences, Tibet Autonomous Region Academy of Agricultural and Animal Husbandry Sciences, Lasa 850032, China; (Z.-Z.W.); (W.-L.W.); (K.-K.L.)
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Jian-She Zhou
- Institute of Aquatic Sciences, Tibet Autonomous Region Academy of Agricultural and Animal Husbandry Sciences, Lasa 850032, China; (Z.-Z.W.); (W.-L.W.); (K.-K.L.)
- Key Laboratory of Fishery and Germplasm Resources Utilization of Xizang Autonomous Region, Lasa 850032, China
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Louvado A, Coelho FJRC, Palma M, Magnoni LJ, Silva-Brito F, Ozório ROA, Cleary DFR, Viegas I, Gomes NCM. Study of the influence of tributyrin-supplemented diets on the gut bacterial communities of rainbow trout (Oncorhynchus mykiss). Sci Rep 2024; 14:5645. [PMID: 38454011 PMCID: PMC10920674 DOI: 10.1038/s41598-024-55660-y] [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: 01/23/2023] [Accepted: 02/26/2024] [Indexed: 03/09/2024] Open
Abstract
Dietary supplementation with triglyceride tributyrin (TBT), a butyrate precursor, has been associated with beneficial effects on fish health and improvements in the ability of carnivorous fish to tolerate higher levels of plant-based protein. In this study, we aimed to investigate the effects of a plant-based diet supplemented with TBT on the structural diversity and putative function of the digesta-associated bacterial communities of rainbow trout (Oncorhynchus mykiss). In addition to this, we also assessed the response of fish gut digestive enzyme activities and chyme metabolic profile in response to TBT supplementation. Our results indicated that TBT had no significant effects on the overall fish gut bacterial communities, digestive enzyme activities or metabolic profile when compared with non-supplemented controls. However, a more in-depth analysis into the most abundant taxa showed that diets at the highest TBT concentrations (0.2% and 0.4%) selectively inhibited members of the Enterobacterales order and reduced the relative abundance of a bacterial population related to Klebsiella pneumoniae, a potential fish pathogen. Furthermore, the predicted functional analysis of the bacterial communities indicated that increased levels of TBT were associated with depleted KEGG pathways related to pathogenesis. The specific effects of TBT on gut bacterial communities observed here are intriguing and encourage further studies to investigate the potential of this triglyceride to promote pathogen suppression in the fish gut environment, namely in the context of aquaculture.
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Affiliation(s)
- A Louvado
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - F J R C Coelho
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - M Palma
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - L J Magnoni
- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
- The New Zealand Institute for Plant and Food Research Limited, Nelson, New Zealand
| | - F Silva-Brito
- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
| | - R O A Ozório
- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
| | - D F R Cleary
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - I Viegas
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - N C M Gomes
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.
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Amill F, Gauthier J, Rautio M, Derome N. Characterization of gill bacterial microbiota in wild Arctic char ( Salvelinus alpinus) across lakes, rivers, and bays in the Canadian Arctic ecosystems. Microbiol Spectr 2024; 12:e0294323. [PMID: 38329329 PMCID: PMC10923216 DOI: 10.1128/spectrum.02943-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
Teleost gill mucus has a highly diverse microbiota, which plays an essential role in the host's fitness and is greatly influenced by the environment. Arctic char (Salvelinus alpinus), a salmonid well adapted to northern conditions, faces multiple stressors in the Arctic, including water chemistry modifications, that could negatively impact the gill microbiota dynamics related to the host's health. In the context of increasing environmental disturbances, we aimed to characterize the taxonomic distribution of transcriptionally active taxa within the bacterial gill microbiota of Arctic char in the Canadian Arctic in order to identify active bacterial composition that correlates with environmental factors. For this purpose, a total of 140 adult anadromous individuals were collected from rivers, lakes, and bays belonging to five Inuit communities located in four distinct hydrologic basins in the Canadian Arctic (Nunavut and Nunavik) during spring (May) and autumn (August). Various environmental factors were collected, including latitudes, water and air temperatures, oxygen concentration, pH, dissolved organic carbon (DOC), salinity, and chlorophyll-a concentration. The taxonomic distribution of transcriptionally active taxa within the gill microbiota was quantified by 16S rRNA gene transcripts sequencing. The results showed differential bacterial activity between the different geographical locations, explained by latitude, salinity, and, to a lesser extent, air temperature. Network analysis allowed the detection of a potential dysbiosis signature (i.e., bacterial imbalance) in fish gill microbiota from Duquet Lake in the Hudson Strait and the system Five Mile Inlet connected to the Hudson Bay, both showing the lowest alpha diversity and connectivity between taxa.IMPORTANCEThis paper aims to decipher the complex relationship between Arctic char (Salvelinus alpinus) and its symbiotic microbial consortium in gills. This salmonid is widespread in the Canadian Arctic and is the main protein and polyunsaturated fatty acids source for Inuit people. The influence of environmental parameters on gill microbiota in wild populations remains poorly understood. However, assessing the Arctic char's active gill bacterial community is essential to look for potential pathogens or dysbiosis that could threaten wild populations. Here, we concluded that Arctic char gill microbiota was mainly influenced by latitude and air temperature, the latter being correlated with water temperature. In addition, a dysbiosis signature detected in gill microbiota was potentially associated with poor fish health status recorded in these disturbed environments. With those results, we hypothesized that rapid climate change and increasing anthropic activities in the Arctic might profoundly disturb Arctic char gill microbiota, affecting their survival.
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Affiliation(s)
- Flora Amill
- Institute of Integrative and Systems Biology, Laval University, Quebec, Canada
| | - Jeff Gauthier
- Institute of Integrative and Systems Biology, Laval University, Quebec, Canada
| | - Milla Rautio
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Quebec, Canada
| | - Nicolas Derome
- Institute of Integrative and Systems Biology, Laval University, Quebec, Canada
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5
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Suhr M, Fichtner-Grabowski FT, Seibel H, Bang C, Franke A, Schulz C, Hornburg SC. Effects of plant-based proteins and handling stress on intestinal mucus microbiota in rainbow trout. Sci Rep 2023; 13:22563. [PMID: 38110473 PMCID: PMC10728151 DOI: 10.1038/s41598-023-50071-x] [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: 08/08/2023] [Accepted: 12/14/2023] [Indexed: 12/20/2023] Open
Abstract
Via 16S rRNA gene amplicon sequencing, this study explores whether the gut mucus microbiota of rainbow trout is affected by the interaction of a plant-protein-based diet and a daily handling stressor (chasing with a fishing net) across two genetic lines (A, B). Initial body weights of fish from lines A and B were 124.7 g and 147.2 g, respectively. Fish were fed 1.5% of body weight per day for 59 days either of two experimental diets, differing in their fish meal [fishmeal-based diet (F): 35%, plant-based diet (V): 7%] and plant-based protein content (diet F: 47%, diet V: 73%). No diet- or stress-related effect on fish performance was observed at the end of the trial. However, we found significantly increased observed ASVs in the intestinal mucus of fish fed diet F compared to diet V. No significant differences in Shannon diversity could be observed between treatments. The autochthonous microbiota in fish fed with diet V was dominated by representatives of the genera Mycoplasma, Cetobacterium, and Ruminococcaceae, whereas Enterobacteriaceae and Photobacterium were significantly associated with diet F. The mucus bacteria in both genetic lines were significantly separated by diet, but neither by stress nor an interaction, as obtained via PERMANOVA. However, pairwise comparisons revealed that the diet effect was only significant in stressed fish. Therefore, our findings indicate that the mucus-associated microbiota is primarily modulated by the protein source, but this modulation is mediated by the stress status of the fish.
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Affiliation(s)
- Marvin Suhr
- Institute of Animal Nutrition and Physiology, Christian-Albrechts-University Kiel, Hermann-Rodewald-Straße 9, 24118, Kiel, Germany.
| | | | - Henrike Seibel
- Fraunhofer Research Institution for Individualized and Cell-Based Medical Engineering (IMTE), Hafentörn 3, 25761, Büsum, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, University Hospital Schleswig-Holstein, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, University Hospital Schleswig-Holstein, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany
| | - Carsten Schulz
- Fraunhofer Research Institution for Individualized and Cell-Based Medical Engineering (IMTE), Hafentörn 3, 25761, Büsum, Germany
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Hermann-Rodewald-Straße 6, 24118, Kiel, Germany
| | - Stéphanie C Hornburg
- Institute of Animal Nutrition and Physiology, Christian-Albrechts-University Kiel, Hermann-Rodewald-Straße 9, 24118, Kiel, Germany
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Hasan I, Rimoldi S, Saroglia G, Terova G. Sustainable Fish Feeds with Insects and Probiotics Positively Affect Freshwater and Marine Fish Gut Microbiota. Animals (Basel) 2023; 13:1633. [PMID: 37238063 PMCID: PMC10215438 DOI: 10.3390/ani13101633] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Aquaculture is the fastest-growing agricultural industry in the world. Fishmeal is an essential component of commercial fish diets, but its long-term sustainability is a concern. Therefore, it is important to find alternatives to fishmeal that have a similar nutritional value and, at the same time, are affordable and readily available. The search for high-quality alternatives to fishmeal and fish oil has interested researchers worldwide. Over the past 20 years, different insect meals have been studied as a potential alternate source of fishmeal in aquafeeds. On the other hand, probiotics-live microbial strains-are being used as dietary supplements and showing beneficial effects on fish growth and health status. Fish gut microbiota plays a significant role in nutrition metabolism, which affects a number of other physiological functions, including fish growth and development, immune regulation, and pathogen resistance. One of the key reasons for studying fish gut microbiota is the possibility to modify microbial communities that inhabit the intestine to benefit host growth and health. The development of DNA sequencing technologies and advanced bioinformatics tools has made metagenomic analysis a feasible method for researching gut microbes. In this review, we analyze and summarize the current knowledge provided by studies of our research group on using insect meal and probiotic supplements in aquafeed formulations and their effects on different fish gut microbiota. We also highlight future research directions to make insect meals a key source of proteins for sustainable aquaculture and explore the challenges associated with the use of probiotics. Insect meals and probiotics will undoubtedly have a positive effect on the long-term sustainability and profitability of aquaculture.
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Affiliation(s)
- Imam Hasan
- Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant, 3-21100 Varese, Italy; (I.H.); (G.T.)
| | - Simona Rimoldi
- Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant, 3-21100 Varese, Italy; (I.H.); (G.T.)
| | - Giulio Saroglia
- Medical Devices Area, Institute of Digital Technologies for Personalized Healthcare-MeDiTech, Scuola Universitaria Professionale della Svizzera Italiana, Via La Santa 1, CH-6962 Lugano, Switzerland;
| | - Genciana Terova
- Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant, 3-21100 Varese, Italy; (I.H.); (G.T.)
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Zhu C, Liu G, Gu X, Zhang T, Xia A, Zheng Y, Yin J, Han M, Jiang Q. Effects of Quercetin on the Intestinal Microflora of Freshwater Dark Sleeper Odontobutis potamophila. Antioxidants (Basel) 2022; 11:antiox11102015. [PMID: 36290739 PMCID: PMC9598073 DOI: 10.3390/antiox11102015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/29/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
Flavonoids have antimicrobial and anti-oxidation properties. The effects of the flavonoid quercetin on the intestinal microflora of freshwater dark sleeper Odontobutis potamophila were tested for the first time. Odontobutis potamophila juveniles were treated with quercetin for 21 days at one of three concentrations (2.5, 5.0, or 10.0 mg/L) and compared with a control group that was not treated with quercetin. Quercetin improved the stability of the intestinal flora in O. potamophila and the probiotic bacteria Bacillus spp. and Lactobacillus spp. increased in species abundance after the low concentration quercetin treatments. Furthermore, the abundance of pathogenic bacteria Plesiomonas spp., Aeromonas spp., and Shewanella spp. decreased after the fish had been exposed to quercetin. Activity of hepatic antioxidant enzymes (superoxide dismutase, SOD), (glutathione S-transferase, GST), (glutathione peroxidase, GSH-Px), and (total antioxidant capacity, T-AOC) increased in the livers of O. potamophila treated with quercetin, thereby increasing their hepatic antioxidant capacity and their ability to scavenge free radicals.
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Affiliation(s)
- Chenxi Zhu
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
- Geography Section, School of Humanities, Universiti Sains Malaysia, Minden 11800, Malaysia
| | - Guoxing Liu
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiankun Gu
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Tongqing Zhang
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Aijun Xia
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - You Zheng
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Jiawen Yin
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Mingming Han
- Biology Program, School of Distance Education, Universiti Sains Malaysia, Minden 11800, Malaysia
| | - Qichen Jiang
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
- Correspondence:
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Suzuki A, Shirakata C, Anzai H, Sumiyama D, Suzuki M. Vitamin B 12 biosynthesis of Cetobacterium ceti isolated from the intestinal content of captive common bottlenose dolphins ( Tursiops truncatus). MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36178719 DOI: 10.1099/mic.0.001244] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In comparison with terrestrial mammals, dolphins require a large amount of haemoglobin in blood and myoglobin in muscle to prolong their diving time underwater and increase the depth they can dive. The genus Cetobacterium is a common gastrointestinal bacterium in dolphins and includes two species: C. somerae and C. ceti. Whilst the former produces vitamin B12, which is essential for the biosynthesis of haem, a component of haemoglobin and myoglobin, but not produced by mammals, the production ability of the latter remains unknown. The present study aimed to isolate C. ceti from dolphins and reveal its ability to biosynthesize vitamin B12. Three strains of C. ceti, identified by phylogenetic analyses with 16S rRNA gene and genome-based taxonomy assignment and biochemical features, were isolated from faecal samples collected from two captive common bottlenose dolphins (Tursiops truncatus). A microbioassay using Lactobacillus leichmannii ATCC 7830 showed that the average concentration of vitamin B12 produced by the three strains was 11 (standard deviation: 2) pg ml-1. The biosynthesis pathway of vitamin B12, in particular, adenosylcobalamin, was detected in the draft genome of the three strains using blastKOALA. This is the first study to isolate C. ceti from common bottlenose dolphins and reveal its ability of vitamin B12 biosynthesis, and our findings emphasize the importance of C. ceti in supplying haemoglobin and myoglobin to dolphins.
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Affiliation(s)
- Akihiko Suzuki
- Laboratory of Aquatic Animal Physiology, Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880 Japan
- National Institute for Environmental Studies, Tsukuba, Ibaraki, 305-8506 Japan
| | - Chika Shirakata
- Enoshima Aquarium, Fujisawa, Kanagawa, 251-0035 Japan
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-0054 Japan
| | - Hiroshi Anzai
- Laboratory of Biotechnology in Dairy Life, Department of Bioscience in Dairy Life, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880 Japan
| | - Daisuke Sumiyama
- Laboratory of Biotechnology in Dairy Life, Department of Bioscience in Dairy Life, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880 Japan
| | - Miwa Suzuki
- Laboratory of Aquatic Animal Physiology, Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880 Japan
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9
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Haque R, Das II, Sawant PB, Chadha NK, Sahoo L, Kumar R, Sundaray JK. Tenets in Microbial Endocrinology: A New Vista in Teleost Reproduction. Front Physiol 2022; 13:871045. [PMID: 36035477 PMCID: PMC9411670 DOI: 10.3389/fphys.2022.871045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Climate vulnerability and induced changes in physico-chemical properties of aquatic environment can bring impairment in metabolism, physiology and reproduction in teleost. Variation in environmental stimuli mainly acts on reproduction by interfering with steroidogenesis, gametogenesis and embryogenesis. The control on reproductive function in captivity is essential for the sustainability of aquaculture production. There are more than 3,000 teleost species across the globe having commercial importance; however, adequate quality and quantity of seed production have been the biggest bottleneck. Probiotics are widely used in aquaculture as a growth promoter, stress tolerance, pathogen inhibition, nutrient digestibility and metabolism, reproductive performance and gamete quality. As the gut microbiota exerts various effects on the intestinal milieu which influences distant organs and pathways, therefore it is considered to be a full-fledged endocrine organ. Researches on Gut-Brain-Gonad axis (GBG axis) and its importance on physiology and reproduction have already been highlighted for higher mammals; however, the study on fish physiology and reproduction is limited. While looking into the paucity of information, we have attempted to review the present status of microbiome and its interaction between the brain and gut. This review will address a process of the microbiome physiological mechanism involved in fish reproduction. The gut microbiota influences the BPG axis through a wide variety of compounds, including neuropeptides, neurotransmitter homologs and transmitters. Currently, research is being conducted to determine the precise process by which gut microbial composition influences brain function in fish. The gut-brain bidirectional interaction can influence brain biochemistry such as GABA, serotonin and tryptophan metabolites which play significant roles in CNS regulation. This review summarizes the fact, how microbes from gut, skin and other parts of the body influence fish reproduction through the Gut-Brain-Gonad axis.
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Affiliation(s)
- Ramjanul Haque
- Division of Aquaculture, ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - Ipsita Iswari Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | | | - Narinder Kumar Chadha
- Division of Aquaculture, ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - Lakshman Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Rajesh Kumar
- Aquaculture Production and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Jitendra Kumar Sundaray
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
- *Correspondence: Jitendra Kumar Sundaray,
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Liu Y, Li X, Li Y, Li J, Zhu S. Gut microbiomes of cyprinid fish exhibit host-species symbiosis along gut trait and diet. Front Microbiol 2022; 13:936601. [PMID: 36016786 PMCID: PMC9396210 DOI: 10.3389/fmicb.2022.936601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/18/2022] [Indexed: 11/15/2022] Open
Abstract
Teleost omnivorous fish that coexist partially sharing resources are likely to modify their gut traits and microbiome as a feedback mechanism between ecological processes and evolution. However, we do not understand how the core gut microbiome supports the metabolic capacity of the host and regulates digestive functions in specialized omnivorous fish gut traits. Therefore, we evaluated the gut microbiome of eight omnivorous fish from a single family (i.e., Cyprinidae) in the current study. We examined the correlation between host phylogeny, diet composition, and intestinal morphological traits related to the intestinal microbiome. The results indicated that cyprinid fish with similar relative gut lengths had considerable gut microbiome similarity. Notably, the SL (short relative gut length) group, as zoobenthos and zooplankton specialists, was abundant in Proteobacteria and was less abundant in Firmicutes than in the ML (medium relative gut length) and LL (long relative gut length) groups. These fish could extract nutrients from aquatic plants and algae. Additionally, we found the relative abundance of Clostridium and Romboutsia to be positively correlated with host relative gut length but negatively correlated with the relative abundance of Cetobacterium, Plesiomonas, Bacteroides, and Lactobacillus, and host-relative gut length. We also show a positive linear relationship between host gut microbiome carbohydrate metabolism and relative gut length, while the amino acid and lipid metabolism of the gut microbiome was negatively correlated with host-relative gut length. In addition, omnivorous species competing for resources improve their ecological adaptability through the specialization of gut length, which is closely related to variation in the synergy of the gut microbiome. Above all, specialized gut microbiota and associated gut morphologies enable fish to variably tolerate resource fluctuation and improve the utilization efficiency of nutrient extraction from challenging food resources.
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Affiliation(s)
- Yaqiu Liu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China
| | - Xinhui Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yuefei Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China
| | - Jie Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China
| | - Shuli Zhu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, China
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11
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Hu F, Zhang T, Liang J, Xiao J, Liu Z, Dahlgren RA. Impact of biochar on persistence and diffusion of antibiotic resistance genes in sediment from an aquaculture pond. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:57918-57930. [PMID: 35355188 DOI: 10.1007/s11356-022-19700-2] [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: 01/04/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Aquaculture sediments are a purported sizable pool of antibiotic resistance genes (ARGs). However, the pathways for transmission of ARGs from sediments to animals and humans remain unclear. We conducted an ARG survey in sediments from a bullfrog production facility located in Guangdong, China, and simulated zebrafish breeding systems were constructed, with or without biochar addition in sediments, to explore the effects of biochar on ARGs and their precursors of the sediment and zebrafish gut. After 60 days, 6 subtypes of ARGs and intI1 were detected, with sediments harboring more ARGs than zebrafish gut. The addition of biochar reduced the abundance of ARGs in the sediment and zebrafish gut, as well as suppressed the horizontal transmission of ARGs from sediment to zebrafish gut. Network analysis and partial least squares path modeling revealed that ARG enrichment was mainly affected by bacterial groups dominated by Nitrospirae, Gemmatimonades, Chloroflexi, and Cyanobacteria and intI1. Our findings provide insights into the transmission of ARGs from sediment to animals and highlight the efficacy of biochar amendments to aquaculture sediments to reduce the transmission of ARGs.
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Affiliation(s)
- Fengjie Hu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Taiping Zhang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, People's Republic of China.
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou, 510006, People's Republic of China.
| | - Jinni Liang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Jiahui Xiao
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Zidan Liu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Randy A Dahlgren
- Department of Land, Air and Water Resources, University of California, Davis, CA, 95616, USA
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12
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Brealey JC, Lecaudey LA, Kodama M, Rasmussen JA, Sveier H, Dheilly NM, Martin MD, Limborg MT. Microbiome "Inception": an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host. mBio 2022; 13:e0067922. [PMID: 35502903 PMCID: PMC9239044 DOI: 10.1128/mbio.00679-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/04/2022] [Indexed: 11/20/2022] Open
Abstract
The concept of a holobiont, a host organism and its associated microbial communities, encapsulates the vital role the microbiome plays in the normal functioning of its host. Parasitic infections can disrupt this relationship, leading to dysbiosis. However, it is increasingly recognized that multicellular parasites are themselves holobionts. Intestinal parasites share space with the host gut microbiome, creating a system of nested microbiomes within the primary host. However, how the parasite, as a holobiont, interacts with the host holobiont remains unclear, as do the consequences of these interactions for host health. Here, we used 16S amplicon and shotgun metagenomics sequencing to characterize the microbiome of the intestinal cestode Eubothrium and its effect on the gut microbiome of its primary host, Atlantic salmon. Our results indicate that cestode infection is associated with salmon gut dysbiosis by acting as a selective force benefiting putative pathogens and potentially introducing novel bacterial species to the host. Our results suggest that parasitic cestodes may themselves be holobionts nested within the microbial community of their holobiont host, emphasizing the importance of also considering microbes associated with parasites when studying intestinal parasitic infections. IMPORTANCE The importance of the parasite microbiome is gaining recognition. Of particular concern is understanding how these parasite microbiomes influence host-parasite interactions and parasite interactions with the vertebrate host microbiome as part of a system of nested holobionts. However, there are still relatively few studies focusing on the microbiome of parasitic helminths in general and almost none on cestodes in particular, despite the significant burden of disease caused by these parasites globally. Our study provides insights into a system of significance to the aquaculture industry, cestode infections of Atlantic salmon and, more broadly, expands our general understanding of parasite-microbiome-host interactions and introduces a new element, the microbiome of the parasite itself, which may play a critical role in modulating the host microbiome, and, therefore, the host response, to parasite infection.
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Affiliation(s)
- Jaelle C. Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Laurène A. Lecaudey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Miyako Kodama
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jacob A. Rasmussen
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Nolwenn M. Dheilly
- UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health Laboratory, Maisons-Alfort, France
| | - Michael D. Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Morten T. Limborg
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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13
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Clavere-Graciette AG, McWhirt ME, Hoopes LA, Bassos-Hull K, Wilkinson KA, Stewart FJ, Pratte ZA. Microbiome differences between wild and aquarium whitespotted eagle rays (Aetobatus narinari). Anim Microbiome 2022; 4:34. [PMID: 35606841 PMCID: PMC9128078 DOI: 10.1186/s42523-022-00187-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 05/09/2022] [Indexed: 11/15/2022] Open
Abstract
Background Animal-associated microbiomes can be influenced by both host and environmental factors. Comparing wild animals to those in zoos or aquariums can help disentangle the effects of host versus environmental factors, while also testing whether managed conditions foster a ‘natural’ host microbiome. Focusing on an endangered elasmobranch species—the whitespotted eagle ray Aetobatus narinari—we compared the skin, gill, and cloaca microbiomes of wild individuals to those at Georgia Aquarium. Whitespotted eagle ray microbiomes from Georgia Aquarium were also compared to those of cownose rays (Rhinoptera bonasus) in the same exhibit, allowing us to explore the effect of host identity on the ray microbiome.
Results Long-term veterinary monitoring indicated that the rays in managed care did not have a history of disease and maintained health parameters consistent with those of wild individuals, with one exception. Aquarium whitespotted eagle rays were regularly treated to control parasite loads, but the effects on animal health were subclinical. Microbiome α- and β-diversity differed between wild versus aquarium whitespotted eagle rays at all body sites, with α-diversity significantly higher in wild individuals. β-diversity differences in wild versus aquarium whitespotted eagle rays were greater for skin and gill microbiomes compared to those of the cloaca. At each body site, we also detected microbial taxa shared between wild and aquarium eagle rays. Additionally, the cloaca, skin, and gill microbiomes of aquarium eagle rays differed from those of cownose rays in the same exhibit. Potentially pathogenic bacteria were at low abundance in all wild and aquarium rays.
Conclusion For whitespotted eagle rays, managed care was associated with a microbiome differing significantly from that of wild individuals. These differences were not absolute, as the microbiome of aquarium rays shared members with that of wild counterparts and was distinct from that of a cohabitating ray species. Eagle rays under managed care appear healthy, suggesting that their microbiomes are not associated with compromised host health. However, the ray microbiome is dynamic, differing with both environmental factors and host identity. Monitoring of aquarium ray microbiomes over time may identify taxonomic patterns that co-vary with host health. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00187-8.
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Affiliation(s)
| | - Mary E McWhirt
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Lisa A Hoopes
- Department of Research and Conservation, Georgia Aquarium, Atlanta, GA, USA
| | - Kim Bassos-Hull
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA.,Chicago Zoological Society's Sarasota Dolphin Research Program, c/o Mote Marine Laboratory, Sarasota, FL, USA
| | - Krystan A Wilkinson
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA.,Chicago Zoological Society's Sarasota Dolphin Research Program, c/o Mote Marine Laboratory, Sarasota, FL, USA
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, USA
| | - Zoe A Pratte
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, USA.
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14
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Chen X, Sun C, Dong J, Li W, Tian Y, Hu J, Ye X. Comparative Analysis of the Gut Microbiota of Mandarin Fish ( Siniperca chuatsi) Feeding on Compound Diets and Live Baits. Front Genet 2022; 13:797420. [PMID: 35664316 PMCID: PMC9158118 DOI: 10.3389/fgene.2022.797420] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Siniperca chuatsi feeds on live fry throughout their life. The sustainable development of its farming industry has urgently necessitated the development of artificial diets to substitute live baits. It has been demonstrated that gut microbiota assists in feed adaptation and improves the feed conversion rate in fish. Therefore, this study aimed to understand the potential role of intestinal microorganisms in the domestication of S. chuatsi with a compound diet. Accordingly, we performed 16S rRNA sequencing of the gut microbial communities in S. chuatsi groups that were fed a compound diet (including large and small individuals) and live baits. A total of 2,471 OTUs were identified, and the large individual group possessed the highest number of unique OTUs. The α-diversity index of the gut microbiota in groups that were fed a compound diet was significantly higher (p < 0.05) than that in the live bait group. There were no significant differences in the α-diversity between the large and small individual groups. However, relatively higher numbers of Lactococcus, Klebsiella, and Woeseia were observed in the intestines of the large individual group. Prediction of the metabolic function of the microbiota among these three fish groups by Tax4Fun revealed that most metabolic pathways, such as glycan metabolism and amino acid metabolism, were typically more enriched for the larger individuals. The results indicated that certain taxa mentioned above exist in large individuals and may be closely related to the digestion and absorption of compound diets. The present study provides a basis for understanding the utilization mechanism of artificial feed by S. chuatsi.
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Affiliation(s)
- Xiao Chen
- Key Laboratory of Tropical and Subtropical Fisheries Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
| | - Chengfei Sun
- Key Laboratory of Tropical and Subtropical Fisheries Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Junjian Dong
- Key Laboratory of Tropical and Subtropical Fisheries Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Wuhui Li
- Key Laboratory of Tropical and Subtropical Fisheries Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yuanyuan Tian
- Key Laboratory of Tropical and Subtropical Fisheries Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jie Hu
- Key Laboratory of Tropical and Subtropical Fisheries Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Xing Ye
- Key Laboratory of Tropical and Subtropical Fisheries Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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15
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Gut Microbial Composition of Pacific Salmonids Differs across Oregon River Basins and Hatchery Ancestry. Microorganisms 2022; 10:microorganisms10050933. [PMID: 35630377 PMCID: PMC9144809 DOI: 10.3390/microorganisms10050933] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/16/2022] [Accepted: 04/23/2022] [Indexed: 01/04/2023] Open
Abstract
The gut microbiome may represent a relatively untapped resource in the effort to manage and conserve threatened or endangered fish populations, including wild and hatchery-reared Pacific salmonids. To clarify this potential, we defined how steelhead trout gut microbiome composition varies across watersheds and as a function of ancestry. First, we measured this variation across watersheds using wild steelhead trout sampled from nine locations spanning three river basins. While gut microbial composition differs across basins, there exist bacterial clades that are ubiquitous across all populations. Correlating the phylogenetic composition of clades with geographic distance reveals 395 clades of bacteria whose ecological distribution implicates their co-diversification with steelheads. Second, we quantified how microbiome composition varies between first generation hatchery-reared steelhead and traditional hatchery-reared steelhead. Despite being subject to the same hatchery management strategies, fish bred from wild parents carry distinct microbiomes from those bred from hatchery broodstock, implicating the role of genotype on microbiome composition. Finally, we integrated all data from both studies to reveal two distinct, yet robust clusters of community composition. Collectively, our study documents for the first time how the steelhead gut microbiome varies by geography or broodstock and uncovers microbial taxa that may indicate the watershed or hatchery from which an individual was sourced.
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16
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Nyholm L, Odriozola I, Martin Bideguren G, Aizpurua O, Alberdi A. Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish. PeerJ 2022; 10:e12992. [PMID: 35223211 PMCID: PMC8877339 DOI: 10.7717/peerj.12992] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/02/2022] [Indexed: 01/11/2023] Open
Abstract
The microbial gut communities of fish are receiving increased attention for their relevance, among others, in a growing aquaculture industry. The members of these communities are often split into resident (long-term colonisers specialised to grow in and adhere to the mucus lining of the gut) and transient (short-term colonisers originated from food items and the surrounding water) microorganisms. Separating these two communities in small fish are impeded by the small size and fragility of the gastrointestinal tract. With the aim of testing whether it is possible to recover two distinct communities in small species of fish using a simple sampling technique, we used 16S amplicon sequencing of paired intestinal wall and digesta samples from three small Cyprinodontiformes fish. We examined the diversity and compositional variation of the two recovered communities, and we used joint species distribution modelling to identify microbes that are most likely to be a part of the resident community. For all three species we found that the diversity of intestinal wall samples was significantly lower compared to digesta samples and that the community composition between sample types was significantly different. Across the three species we found seven unique families of bacteria to be significantly enriched in samples from the intestinal wall, encompassing most of the 89 ASVs enriched in intestinal wall samples. We conclude that it is possible to characterise two different microbial communities and identify potentially resident microbes through separately analysing samples from the intestinal wall and digesta from small species of fish. We encourage researchers to be aware that different sampling procedures for gut microbiome characterization will capture different parts of the microbiome and that this should be taken into consideration when reporting results from such studies on small species of fish.
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Affiliation(s)
- Lasse Nyholm
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Iñaki Odriozola
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Garazi Martin Bideguren
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
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17
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Pinto ACSM, De Pierri CR, Evangelista AG, Gomes ASDLPB, Luciano FB. Deoxynivalenol: Toxicology, Degradation by Bacteria, and Phylogenetic Analysis. Toxins (Basel) 2022; 14:toxins14020090. [PMID: 35202118 PMCID: PMC8876347 DOI: 10.3390/toxins14020090] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/27/2023] Open
Abstract
Deoxynivalenol (DON) is a toxic secondary metabolite produced by fungi that contaminates many crops, mainly wheat, maize, and barley. It affects animal health, causing intestinal barrier impairment and immunostimulatory effect in low doses and emesis, reduction in feed conversion rate, and immunosuppression in high doses. As it is very hard to completely avoid DON’s production in the field, mitigatory methods have been developed. Biodegradation has become a promising method as new microorganisms are studied and new enzymatic routes are described. Understanding the common root of bacteria with DON degradation capability and the relationship with their place of isolation may bring insights for more effective ways to find DON-degrading microorganisms. The purpose of this review is to bring an overview of the occurrence, regulation, metabolism, and toxicology of DON as addressed in recent publications focusing on animal production, as well as to explore the enzymatic routes described for DON’s degradation by microorganisms and the phylogenetic relationship among them.
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Affiliation(s)
- Anne Caroline Schoch Marques Pinto
- Graduate Program in Animal Science, School of Life Sciences, Pontifícia Universidade Católica do Paraná, 1155 Imaculada Conceição Street, Prado Velho, Curitiba 80215-901, Brazil; (A.C.S.M.P.); (A.G.E.); (A.S.d.L.P.B.G.)
| | - Camilla Reginatto De Pierri
- Graduate Program in Sciences—Biochemistry, Department of Biochemistry and Molecular Biology, Federal University of Paraná, 100 Coronel Francisco H. dos Santos Avenue, Jardim das Américas, Curitiba 81530-000, Brazil;
| | - Alberto Gonçalves Evangelista
- Graduate Program in Animal Science, School of Life Sciences, Pontifícia Universidade Católica do Paraná, 1155 Imaculada Conceição Street, Prado Velho, Curitiba 80215-901, Brazil; (A.C.S.M.P.); (A.G.E.); (A.S.d.L.P.B.G.)
| | - Ana Silvia de Lara Pires Batista Gomes
- Graduate Program in Animal Science, School of Life Sciences, Pontifícia Universidade Católica do Paraná, 1155 Imaculada Conceição Street, Prado Velho, Curitiba 80215-901, Brazil; (A.C.S.M.P.); (A.G.E.); (A.S.d.L.P.B.G.)
| | - Fernando Bittencourt Luciano
- Graduate Program in Animal Science, School of Life Sciences, Pontifícia Universidade Católica do Paraná, 1155 Imaculada Conceição Street, Prado Velho, Curitiba 80215-901, Brazil; (A.C.S.M.P.); (A.G.E.); (A.S.d.L.P.B.G.)
- Correspondence:
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18
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Extremophilic Fungi from Marine Environments: Underexplored Sources of Antitumor, Anti-Infective and Other Biologically Active Agents. Mar Drugs 2022; 20:md20010062. [PMID: 35049917 PMCID: PMC8781577 DOI: 10.3390/md20010062] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/07/2023] Open
Abstract
Marine environments are underexplored terrains containing fungi that produce a diversity of natural products given unique environmental pressures and nutrients. While bacteria are commonly the most studied microorganism for natural products in the marine world, marine fungi are also abundant but remain an untapped source of bioactive metabolites. Given that their terrestrial counterparts have been a source of many blockbuster antitumor agents and anti-infectives, including camptothecin, the penicillins, and cyclosporin A, marine fungi also have the potential to produce new chemical scaffolds as leads to potential drugs. Fungi are more phylogenetically diverse than bacteria and have larger genomes that contain many silent biosynthetic gene clusters involved in making bioactive compounds. However, less than 5% of all known fungi have been cultivated under standard laboratory conditions. While the number of reported natural products from marine fungi is steadily increasing, their number is still significantly lower compared to those reported from their bacterial counterparts. Herein, we discuss many varied cytotoxic and anti-infective fungal metabolites isolated from extreme marine environments, including symbiotic associations as well as extreme pressures, temperatures, salinity, and light. We also discuss cultivation strategies that can be used to produce new bioactive metabolites or increase their production. This review presents a large number of reported structures though, at times, only a few of a large number of related structures are shown.
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19
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Barik A, Patel GD, Sen SK, Rajhans G, Nayak C, Raut S. Probiotic Characterization of Indigenous Kocuria flava Y4 Strain Isolated from Dioscorea villosa Leaves. Probiotics Antimicrob Proteins 2021; 15:614-629. [PMID: 34825308 DOI: 10.1007/s12602-021-09877-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 12/19/2022]
Abstract
This aim of the study was to isolate and screen potential probiotics from Dioscorea villosa leaves. The potential isolate Y4 was obtained from the Dioscorea villosa leaves, and its ability to grow in a medium containing high NaCl concentrations (2-10%) indicated its negative hemolytic activity. Furthermore, Y4 demonstrated inhibitory activity against human pathogens, such as Klebsiella pneumonia, Staphylococcus aureus, Citrobacter koseri, and Vibrio cholerae, as well as towards a plant pathogen isolate OR-2 (obtained from Citrus sinensis). Some biologically important functional groups of Y4 metabolites, such as sulfoxide; aliphatic ether; 1, 2, 3-trisubstituted, tertiary alcohol: vinyl ether; aromatic amine; carboxylic acid; nitro compound; alkene mono-substituted; and alcohol, were identified through FTIR analysis. The 16S rRNA sequencing and subsequent phylogenetic tree analysis indicated that Y4 and OR-2 are the closest neighbors to Kocuria flava (GenBank accession no. MT773277) and Pantoea dispersa (GenBank accession no. MT766308), respectively. The potential isolate Y4 was found to exhibit adhesion, auto-aggregation, co-aggregation, and weak biofilm activity. It also exhibited a high level of antimicrobial activity and antibiotic susceptibility. The safety of K. flava Y4 isolate, which is proposed to be a probiotic, was evaluated through acute oral toxicity test and biogenic amine production test. Moreover, the preservation potential of isolate Y4 was assessed through application on fruits under different temperatures. Thus, our results confirmed that Kocuria flava Y4 is a prospective probiotic and could also be used for the preservation of fruits.
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Affiliation(s)
- Adyasa Barik
- Center for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed To Be University), Bhubaneswar, 751003, Odisha, India
| | - Gaurav D Patel
- Center for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed To Be University), Bhubaneswar, 751003, Odisha, India
| | | | - Geetanjali Rajhans
- Center for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed To Be University), Bhubaneswar, 751003, Odisha, India
| | - Chirasmita Nayak
- Orissa University of Agriculture and Technology, Bhubaneswar, 751003, India
| | - Sangeeta Raut
- Center for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed To Be University), Bhubaneswar, 751003, Odisha, India.
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20
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Han Q, Hu Y, Lu Z, Wang J, Chen H, Mo Z, Luo X, Li A, Dan X, Li Y. Study on the characterization of grouper (Epinephelus coioides) immunoglobulin T and its positive cells. FISH & SHELLFISH IMMUNOLOGY 2021; 118:102-110. [PMID: 34481975 DOI: 10.1016/j.fsi.2021.08.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 08/10/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Immunoglobulins (Igs) play a vital role in the adaptive immunity of gnathostomes. IgT, a particular Ig class in teleost fishes, receives much attention concerning the mucosal immunity. While, the characteristic and function of Epinephelus coioides IgT is still unknown. In our study, a polyclonal antibody was first prepared with grouper IgT heavy chain recombinant protein. IgT was revealed to be polymeric in serum and mucus. In normal groupers, IgT had high expression level in head kidney and spleen, while little amount in gills, thymus, gut and liver. The number of IgT-positive cells in different tissues was in line with their IgT expression. Furthermore, IgT could coat fractional bacteria in the mucus. In conclusion, this research revealed the protein characteristic, basal expression and bacterial coverage of grouper IgT. This is the first study to identify the characteristic of grouper IgT and demonstrate the capacity of coating microbes.
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Affiliation(s)
- Qing Han
- College of Marine Science, South China Agricultural University, Guangzhou, 510640, China
| | - Yingtong Hu
- College of Marine Science, South China Agricultural University, Guangzhou, 510640, China
| | - Zijun Lu
- College of Marine Science, South China Agricultural University, Guangzhou, 510640, China
| | - Jiule Wang
- College of Marine Science, South China Agricultural University, Guangzhou, 510640, China
| | - Hongping Chen
- College of Marine Science, South China Agricultural University, Guangzhou, 510640, China
| | - Zequan Mo
- College of Marine Science, South China Agricultural University, Guangzhou, 510640, China
| | - Xiaochun Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Anxing Li
- State Key Laboratory of Biocontrol/Guangdong Provincial Key Lab for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong Province, China
| | - Xueming Dan
- College of Marine Science, South China Agricultural University, Guangzhou, 510640, China.
| | - Yanwei Li
- College of Marine Science, South China Agricultural University, Guangzhou, 510640, China.
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21
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Wang Y, Wang Q, Lian S, Yue Y, Gao Q, Peng S. Dietary jellyfish affect digestive enzyme activities and gut microbiota of Pampus argenteus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 40:100923. [PMID: 34634570 DOI: 10.1016/j.cbd.2021.100923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/25/2021] [Accepted: 09/28/2021] [Indexed: 10/20/2022]
Abstract
For many years, jellyfish were described as 'dead ends' in marine food webs, due to their high-water content and low nutritional value. However, it has been confirmed that silver pomfret (Pampus argenteus) has a particular preference for preying on jellyfish. In this study, we determined the effect of consuming jellyfish on the intestinal microbes of silver pomfret. Analysis of bacterial 16S rRNA gene amplicons showed that jellyfish had a dramatic impact on the composition of the gut microbiota. The content of Proteobacteria was reduced from 99% to 51%, while Firmicutes, Bacteroidetes and Actinobacteria increased, accounting for 35%, 9% and 2% of the total flora, respectively. At the genus level, the content of Photobacterium decreased sharply to <1% of the total flora. By contrast, Lactobacillus, Burkholderia and Sphingomonas increased to 12%, 9% and 7% of the total flora, respectively. After feeding jellyfish, the functions of intestinal microbes and the activity of digestive enzymes also changed, resulting in better digestion and absorption of jellyfish. The results provide insights into the specific bacterial taxa within the silver pomfret intestinal microbiome that are impacted by jellyfish. Silver pomfret can better digest and absorb jellyfish by adjusting the intestinal microbial composition. The findings provide a theoretical basis for the digestive mechanism by which silver pomfret consume jellyfish.
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Affiliation(s)
- Yabing Wang
- Key Laboratory of Marine and Estuarine Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, People's Republic of China
| | - Qian Wang
- Key Laboratory of Marine and Estuarine Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, People's Republic of China
| | - Shiya Lian
- Key Laboratory of Marine and Estuarine Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, People's Republic of China
| | - Yanfeng Yue
- Key Laboratory of Marine and Estuarine Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, People's Republic of China
| | - Quanxin Gao
- College of Life Science, Huzhou University, Huzhou 313000, People's Republic of China
| | - Shiming Peng
- Key Laboratory of Marine and Estuarine Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, People's Republic of China; College of Life Science, Huzhou University, Huzhou 313000, People's Republic of China.
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22
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Diwan AD, Harke SN, Gopalkrishna, Panche AN. Aquaculture industry prospective from gut microbiome of fish and shellfish: An overview. J Anim Physiol Anim Nutr (Berl) 2021; 106:441-469. [PMID: 34355428 DOI: 10.1111/jpn.13619] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/17/2021] [Accepted: 07/20/2021] [Indexed: 12/17/2022]
Abstract
The microbiome actually deals with micro-organisms that are associated with indigenous body parts and the entire gut system in all animals, including human beings. These microbes are linked with roles involving hereditary traits, defence against diseases and strengthening overall immunity, which determines the health status of an organism. Considerable efforts have been made to find out the microbiome diversity and their taxonomic identification in finfish and shellfish and its importance has been correlated with various physiological functions and activities. In recent past due to the availability of advanced molecular tools, some efforts have also been made on DNA sequencing of these microbes to understand the environmental impact and other stress factors on their genomic structural profile. There are reports on the use of next-generation sequencing (NGS) technology, including amplicon and shot-gun approaches, and associated bioinformatics tools to count and classify commensal microbiome at the species level. The microbiome present in the whole body, particularly in the gut systems of finfish and shellfish, not only contributes to digestion but also has an impact on nutrition, growth, reproduction, immune system and vulnerability of the host fish to diseases. Therefore, the study of such microbial communities is highly relevant for the development of new and innovative bio-products which will be a vital source to build bio and pharmaceutical industries, including aquaculture. In recent years, attempts have been made to discover the chemical ingredients present in these microbes in the form of biomolecules/bioactive compounds with their functions and usefulness for various health benefits, particularly for the treatment of different types of disorders in animals. Therefore, it has been speculated that microbiomes hold great promise not only as a cure for ailments but also as a preventive measure for the number of infectious diseases. This kind of exploration of new breeds of microbes with their miraculous ingredients will definitely help to accelerate the development of the drugs, pharmaceutical and other biological related industries. Probiotic research and bioinformatics skills will further escalate these opportunities in the sector. In the present review, efforts have been made to collect comprehensive information on the finfish and shellfish microbiome, their diversity and functional properties, relationship with diseases, health status, data on species-specific metagenomics, probiotic research and bioinformatics skills. Further, emphasis has also been made to carry out microbiome research on priority basis not only to keep healthy environment of the fish farming sector but also for the sustainable growth of biological related industries, including aquaculture.
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Affiliation(s)
- Arvind D Diwan
- Mahatma Gandhi Mission's (MGM) Institute of Biosciences and Technology, MGM University, Aurangabad, Maharashtra, India
| | - Sanjay N Harke
- Mahatma Gandhi Mission's (MGM) Institute of Biosciences and Technology, MGM University, Aurangabad, Maharashtra, India
| | - Gopalkrishna
- Central Institute of Fisheries Education (CIFE, Deemed University), ICAR, Mumbai, India
| | - Archana N Panche
- Mahatma Gandhi Mission's (MGM) Institute of Biosciences and Technology, MGM University, Aurangabad, Maharashtra, India
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23
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Morris MT, Hauton C, Baylay AJ, Peruzza L, Targett TE, Ciotti BJ. Spatial variation in the gastrointestinal microbiome, diet, and nutritional condition of a juvenile flatfish among coastal habitats. MARINE ENVIRONMENTAL RESEARCH 2021; 170:105413. [PMID: 34284178 DOI: 10.1016/j.marenvres.2021.105413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/30/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Gut microbiota are important for the health, fitness and development of animal hosts, but little is known about these assemblages in wild populations of fish. Such knowledge is particularly important for juvenile life stages where nutritional intake critically determines early development, growth, and ultimately recruitment. We characterise the microbiome inhabiting the gut of young-of-the-year European plaice ('YOY plaice') on sandy beaches, their key juvenile habitat, and examine how these microbial communities vary spatially in relation to diet and nutritional condition of their plaice hosts. Body size, diet (stomach fullness and eukaryotic 18S ribosomal sequencing), nutritional condition (RNA:DNA) and gut microbiota (16S prokaryotic ribosomal sequencing) were compared in fish at two spatial scales: between beaches separated by 10s of kilometres and between sites at different depths on the same beach, separated by 10s of metres. The main microbial phyla in YOY plaice guts were Proteobacteria, Spirochaetes, Tenericutes and Verrucomicrobiae. Within the Proteobacteria there was an unusual dominance of Alphaproteobacteria. Differences in body size, diet and nutritional condition of YOY plaice between beaches were accompanied by differences in gut microbial assemblage structure. Notably, substantially reduced nutritional condition and size at one of the beaches was associated with lower stomach fullness, reduced consumption of annelids and differences in the abundance and presence of specific microbial taxa. Differences were also detected in microbial assemblages, body size, and diet between depths within the same nursery beach, although stomach fullness and nutritional condition did not vary significantly. The functional links between the environment, gut microbiota, and their hosts are potentially important mediators of the development of young fish through critical life stages. Our study indicates that these links need to be addressed at 10 km and even 10 m scales to capture the variability observed in wild populations of juvenile fish.
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Affiliation(s)
- Marc T Morris
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre Southampton, European Way, Southampton, SO14 3ZH, UK; Present address: Australian Centre for Ecogenomics, University of Queensland, Brisbane, St Lucia, 4072, Australia
| | - Chris Hauton
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre Southampton, European Way, Southampton, SO14 3ZH, UK
| | - Alison J Baylay
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre Southampton, European Way, Southampton, SO14 3ZH, UK
| | - Luca Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Timothy E Targett
- School of Marine Science and Policy, University of Delaware, Lewes, DE 19958, USA
| | - Benjamin J Ciotti
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK.
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24
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Processed Animal Proteins from Insect and Poultry By-Products in a Fish Meal-Free Diet for Rainbow Trout: Impact on Intestinal Microbiota and Inflammatory Markers. Int J Mol Sci 2021; 22:ijms22115454. [PMID: 34064267 PMCID: PMC8196822 DOI: 10.3390/ijms22115454] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/13/2022] Open
Abstract
Sustainability of aquaculture is tied to the origin of feed ingredients. In search of sustainable fish meal-free formulations for rainbow trout, we evaluated the effect of Hermetia illucens meal (H) and poultry by-product meal (P), singly (10, 30, and 60% of either H or P) or in combination (10% H + 50% P, H10P50), as partial replacement of vegetable protein (VM) on gut microbiota (GM), inflammatory, and immune biomarkers. Fish fed the mixture H10P50 had the best growth performance. H, P, and especially the combination H10P50 partially restored α-diversity that was negatively affected by VM. Diets did not differ in the Firmicutes:Proteobacteria ratio, although the relative abundance of Gammaproteobacteria was reduced in H and was higher in P and in the fishmeal control. H had higher relative abundance of chitin-degrading Actinomyces and Bacillus, Dorea, and Enterococcus. Actinomyces was also higher in H feed, suggesting feed-chain microbiome transmission. P increased the relative abundance of protein degraders Paeniclostridium and Bacteroidales. IL-1β, IL-10, TGF-β, COX-2, and TCR-β gene expression in the midgut and head kidney and plasma lipopolysaccharide (LPS) revealed that the diets did not compromise the gut barrier function or induce inflammation. H, P, and H10P50 therefore appear valid protein sources in fishmeal-free aquafeeds.
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25
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Liu Y, Li X, Li J, Chen W. The gut microbiome composition and degradation enzymes activity of black Amur bream ( Megalobrama terminalis) in response to breeding migratory behavior. Ecol Evol 2021; 11:5150-5163. [PMID: 34025998 PMCID: PMC8131771 DOI: 10.1002/ece3.7407] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 01/04/2023] Open
Abstract
Black Amur bream (Megalobrama terminalis), a dominant species, resides in the Pearl River basin, known for its high plasticity in digestive ability. During spawning season, M. terminalis individuals with large body size and high fertility undergo a spawn migratory phase, while other smaller individuals prefer to settlement over migration. It is well known that gut microbial community often underpins the metabolic capability and regulates a wide variety of important functions in fish. However, little was known about how the gut microbiomes affect fish breeding migration. To investigate the variations in the gut microbiome of M. terminalis during the migration, we used high-throughput 16S rRNA gene sequencing to reveal the distinct composition and diversity of the whole gut microbiome of migrated and nonmigrated population during period of peak reproduction, respectively. Our results indicated that nonmigrated population in estuary had a higher alpha diversity than that of migrated population in main stem. Additionally, an obvious abundant taxa shift between the gut microbiota community of nonmigrated and migrated M. terminalis was also observed. Change of dominant gut taxa from nonmigrated to migrated population was thought to be closely related to their degradation enzymes. Our results suggested that amino acid metabolism and lipid metabolism in migrated population were higher than that in nonmigrated population, providing a line of evidence for that M. terminalis change from partial herbivorous to partial carnivorous diet during breeding migration. We further concluded that, in order to digest foods of higher nutrition to supply energy to spawning migration, M. terminalis regulate activities of the gut microbiome and degradation enzymes, considered to be a key physiological strategy for reproduction.
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Affiliation(s)
- Yaqiu Liu
- Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Middle and Lower Reaches of Pearl RiverMinistry of Agriculture and Rural AffairsGuangzhouChina
| | - Xinhui Li
- Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Middle and Lower Reaches of Pearl RiverMinistry of Agriculture and Rural AffairsGuangzhouChina
| | - Jie Li
- Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Middle and Lower Reaches of Pearl RiverMinistry of Agriculture and Rural AffairsGuangzhouChina
| | - Weitao Chen
- Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Middle and Lower Reaches of Pearl RiverMinistry of Agriculture and Rural AffairsGuangzhouChina
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26
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Bozzi D, Rasmussen JA, Carøe C, Sveier H, Nordøy K, Gilbert MTP, Limborg MT. Salmon gut microbiota correlates with disease infection status: potential for monitoring health in farmed animals. Anim Microbiome 2021; 3:30. [PMID: 33879261 PMCID: PMC8056536 DOI: 10.1186/s42523-021-00096-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 04/04/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Infectious diseases cause significant production losses in aquaculture every year. Since the gut microbiota plays an essential role in regulating the host immune system, health and physiology, altered gut microbiota compositions are often associated with a diseased status. However, few studies have examined the association between disease severity and degree of gut dysbiosis, especially when the gut is not the site of the primary infection. Moreover, there is a lack of knowledge on whether bath treatment with formalin, a disinfectant commonly used in aquaculture to treat external infections, might affect the gut microbiome as a consequence of formalin ingestion. Here we investigate, through 16S rRNA gene metabarcoding, changes in the distal gut microbiota composition of a captive-reared cohort of 80 Atlantic salmon (Salmo salar L.), in consequence of an external bacterial skin infection due to a natural outbreak and subsequent formalin treatment. RESULTS We identified Tenacibaculum dicentrarchi as the causative disease pathogen and we show that the distal gut of diseased salmon presented a different composition from that of healthy individuals. A new, yet undescribed, Mycoplasma genus characterized the gut of healthy salmon, while in the sick fish we observed an increase in terms of relative abundance of Aliivibrio sp., a strain regarded as opportunistic. We also noticed a positive correlation between fish weight and Mycoplasma sp. relative abundance, potentially indicating a beneficial effect for its host. Moreover, we observed that the gut microbiota of fish treated with formalin was more similar to those of sick fish than healthy ones. CONCLUSIONS We conclude that external Tenacibaculum infections have the potential of indirectly affecting the host gut microbiota. As such, treatment optimization procedures should account for that. Formalin treatment is not an optimal solution from a holistic perspective, since we observe an altered gut microbiota in the treated fish. We suggest its coupling with a probiotic treatment aimed at re-establishing a healthy community. Lastly, we have observed a positive correlation of Mycoplasma sp. with salmon health and weight, therefore we encourage further investigations towards its potential utilization as a biomarker for monitoring health in salmon and potentially other farmed fish species.
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Affiliation(s)
- Davide Bozzi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark
| | - Jacob A Rasmussen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark
| | | | | | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark.
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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27
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Yang C, Jiang M, Lu X, Wen H. Effects of Dietary Protein Level on the Gut Microbiome and Nutrient Metabolism in Tilapia ( Oreochromis niloticus). Animals (Basel) 2021; 11:1024. [PMID: 33916356 PMCID: PMC8066363 DOI: 10.3390/ani11041024] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 11/23/2022] Open
Abstract
Dietary protein is one of the most important nutritional factors in aquaculture. The aim of this study was to examine the effects of dietary protein levels on the gut microbiome and the liver and serum levels of metabolites in tilapia. Tilapia were fed a diet with a low (20%), moderate (30%), or high (40%) content of crude protein, and the homeostasis of the gut microbiome and metabolic profile of the liver and serum were analyzed. The results showed no significant differences in the diversity and richness of the gut microbiome among the groups; however, there were differences in the microbial composition of the gut. The metabolome analysis of liver samples revealed a difference in the glucose level among the groups, with the highest glucose level in fish fed a high protein diet. In addition, there were significant differences in the levels of tyrosine, guanosine, and inosine among the metabolome analysis of serum samples of these groups. In summary, diets with different protein levels could affect the composition of gut microbiota and the dynamic balance of microbial communities. Dietary protein content can also affect glycolysis and amino acid metabolism in tilapia.
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Affiliation(s)
- Changgeng Yang
- Life Science & Technology School, Lingnan Normal University, Zhanjiang 524048, China;
| | - Ming Jiang
- Fish Nutrition and Feed Division, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (X.L.); (H.W.)
| | - Xin Lu
- Fish Nutrition and Feed Division, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (X.L.); (H.W.)
| | - Hua Wen
- Fish Nutrition and Feed Division, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (X.L.); (H.W.)
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28
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Sehnal L, Brammer-Robbins E, Wormington AM, Blaha L, Bisesi J, Larkin I, Martyniuk CJ, Simonin M, Adamovsky O. Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health. Front Microbiol 2021; 12:567408. [PMID: 33776947 PMCID: PMC7995652 DOI: 10.3389/fmicb.2021.567408] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/05/2021] [Indexed: 01/03/2023] Open
Abstract
Aquatic ecosystems are under increasing stress from global anthropogenic and natural changes, including climate change, eutrophication, ocean acidification, and pollution. In this critical review, we synthesize research on the microbiota of aquatic vertebrates and discuss the impact of emerging stressors on aquatic microbial communities using two case studies, that of toxic cyanobacteria and microplastics. Most studies to date are focused on host-associated microbiomes of individual organisms, however, few studies take an integrative approach to examine aquatic vertebrate microbiomes by considering both host-associated and free-living microbiota within an ecosystem. We highlight what is known about microbiota in aquatic ecosystems, with a focus on the interface between water, fish, and marine mammals. Though microbiomes in water vary with geography, temperature, depth, and other factors, core microbial functions such as primary production, nitrogen cycling, and nutrient metabolism are often conserved across aquatic environments. We outline knowledge on the composition and function of tissue-specific microbiomes in fish and marine mammals and discuss the environmental factors influencing their structure. The microbiota of aquatic mammals and fish are highly unique to species and a delicate balance between respiratory, skin, and gastrointestinal microbiota exists within the host. In aquatic vertebrates, water conditions and ecological niche are driving factors behind microbial composition and function. We also generate a comprehensive catalog of marine mammal and fish microbial genera, revealing commonalities in composition and function among aquatic species, and discuss the potential use of microbiomes as indicators of health and ecological status of aquatic ecosystems. We also discuss the importance of a focus on the functional relevance of microbial communities in relation to organism physiology and their ability to overcome stressors related to global change. Understanding the dynamic relationship between aquatic microbiota and the animals they colonize is critical for monitoring water quality and population health.
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Affiliation(s)
- Ludek Sehnal
- RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Elizabeth Brammer-Robbins
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, United States
- Department of Physiological Sciences, University of Florida, Gainesville, FL, United States
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Alexis M. Wormington
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
| | - Ludek Blaha
- RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Joe Bisesi
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
| | - Iske Larkin
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, United States
| | - Christopher J. Martyniuk
- Department of Physiological Sciences, University of Florida, Gainesville, FL, United States
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Marie Simonin
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
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Endosymbiotic pathogen-inhibitory gut bacteria in three Indian Major Carps under polyculture system: A step toward making a probiotics consortium. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2020.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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30
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Nikouli E, Meziti A, Smeti E, Antonopoulou E, Mente E, Kormas KA. Gut Microbiota of Five Sympatrically Farmed Marine Fish Species in the Aegean Sea. MICROBIAL ECOLOGY 2021; 81:460-470. [PMID: 32840670 DOI: 10.1007/s00248-020-01580-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
In this study, we hypothesized that sympatrically grown farmed fish, i.e. fish which experience similar environmental conditions and nutritionally similar diets, would have more convergent gut microbiota. Using a "common garden" approach, we identified the core microbiota and bacterial community structure differences between five fish species farmed in the same aquaculture site on the west coast of the Aegean Sea, Greece. The investigated individuals were at similar developmental stages and reared in adjacent (< 50 m) aquaculture cages; each cage had 15 kg fish m-3. The diets were nutritionally similar to support optimal growth for each fish species. DNA from the midgut of 3-6 individuals per fish species was extracted and sequenced for the V3-V4 region of the bacterial 16S rRNA. Only 3.9% of the total 181 operational taxonomic units (OTUs) were shared among all fish. Between 5 and 74 OTUs were unique to each fish species. Each of the investigated fish species had a distinct profile of dominant OTUs, i.e. cumulative relative abundance of ≥ 80%. Co-occurrence network analysis for each fish species showed that all networks were strongly dominated by positive correlations between the abundances of their OTUs. However, each fish species had different network characteristics suggesting the differential significance of the OTUs in each of the five fish species midgut. The results of the present study may provide evidence that adult fish farmed in the Mediterranean Sea have a rather divergent and species-specific gut microbiota profile, which are shaped independently of the similar environmental conditions under which they grow.
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Affiliation(s)
- Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece
| | - Alexandra Meziti
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece
| | - Evangelia Smeti
- Institute of Marine Biological Resources and Inland Waters, Hellenic Centre for Marine Research (HCMR), 46.7km Athens-Sounio Ave., Anavyssos, 19013, Athens, Greece
| | - Efthimia Antonopoulou
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece
| | - Eleni Mente
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece
| | - Konstantinos Ar Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece.
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Gu H, Feng Y, Zhang Y, Yin D, Yang Z, Tang W. Differential study of the Parabramis pekinensis intestinal microbiota according to different habitats and different parts of the intestine. ANN MICROBIOL 2021. [DOI: 10.1186/s13213-020-01614-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Abstract
Purpose
To identify the differences in gut bacterial community of Parabramis pekinensis under different growth conditions, and the effect of the diet in a controlled habitat on the community structure, aiming to provide a comprehensive survey of how the gut microbiota in P. pekinensis varies depending on habitat.
Methods
A total of 73 P. pekinensis from Yangtze River (W), rivers in the outskirts of Jingjiang (Jiangsu province, China, R), and farms (C) were collected to analyze the intestinal microbiota using high-throughput sequencing of the V3-V4 16S ribosomal RNA gene. We also subdivided the gut into the foregut (F), midgut (M), and hindgut (B) to analyze the differences between them.
Results
The dominant bacterial phyla in P. pekinensis were Fusobacteria, Firmicutes, Proteobacteria, and Actinobacteria; meanwhile, Cyanobacteria, Bacteroidetes, Chloroflexi, and Verrucomicrobia were also highly abundant. It is worth noting that the abundance of Fusobacteria Cetobacterium was also very high. The abundance and diversity of the intestinal microbiota structure of fish taken from breeding farm were significantly lower than those taken from Yangtze river and Suburban river, and the abundance of Aeromonas in the gut of fish taken from Yangtze river was much higher than that of fish taken from Suburban river. Compared to midgut, foregut and hindgut have similar microbiota structures, but did not differ significantly in them.
Conclusions
The core intestinal microbiota of P. pekinensis is the same to other herbivorous and partially omnivorous fish. There were significant differences in the intestinal microbiota structure of P. pekinensis from different habitats, but no significant differences in the microbiota abundance and diversity between the different parts of the intestine.
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Huang Q, Sham RC, Deng Y, Mao Y, Wang C, Zhang T, Leung KMY. Diversity of gut microbiomes in marine fishes is shaped by host-related factors. Mol Ecol 2020; 29:5019-5034. [PMID: 33084100 PMCID: PMC7756402 DOI: 10.1111/mec.15699] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 12/25/2022]
Abstract
Microorganisms in the gastrointestinal tract of animals play vital roles in food digestion, homeostasis and immune response regulation. Globally, there are 33,700 fish species, representing almost half of all vertebrate diversity and a wide range of physiologies, ecologies and life histories. To investigate gut microbiomes with high coverage, we performed 16S rRNA gene amplicon sequencing with 115 samples of 20 common marine fish species. The fish gut microbiome is a remarkably simple community with low microbial diversity (a maximum of 300 amplicon sequence variants only) and has up to 70% of unknown species in some fish species. The gut microbial community structure was significantly shaped by the combined influence of host-associated factors, including the fish taxon (p < .001, R2 = 0.16, ω2 = 0.04), feeding habit (p < .001, R2 = 0.06, ω2 = 0.02) and trophic level (p < .01, R2 = 0.04, ω2 = 0.01), although the influence was subtle with a small effect size. The core gut microbiomes of different feeding habits were also previously discovered in animal-associated and corresponding habitat samples. Certain energy metabolism pathways were enriched in herbivore/omnivore and zooplanktivore/zoobenthivore fishes, whereas lipid metabolism and glycan metabolism were enriched in zoobenthivore/piscivore fishes. Moreover, substantial taxonomic variability was found between the gut microbiomes of fish and animals, indicated by their low degree of shared microbiota. The data and observations reported herein pave the way for further investigations on the co-evolution of fish gut microbiomes and their hosts, the physiological functions of gut microorganisms and the development of probiotics for improving the nutrition and health of aquaculture fish species.
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Affiliation(s)
- Qi Huang
- School of Biological SciencesThe University of Hong KongHong KongChina
- Department of Civil EngineeringEnvironmental Microbiome Engineering and Biotechnology LabThe University of Hong KongHong KongChina
| | - Ronia C. Sham
- School of Biological SciencesThe University of Hong KongHong KongChina
| | - Yu Deng
- Department of Civil EngineeringEnvironmental Microbiome Engineering and Biotechnology LabThe University of Hong KongHong KongChina
| | - Yanping Mao
- Department of Civil EngineeringEnvironmental Microbiome Engineering and Biotechnology LabThe University of Hong KongHong KongChina
- College of Chemistry and Environmental EngineeringShenzhen UniversityShenzhenChina
| | - Chunxiao Wang
- Department of Civil EngineeringEnvironmental Microbiome Engineering and Biotechnology LabThe University of Hong KongHong KongChina
| | - Tong Zhang
- Department of Civil EngineeringEnvironmental Microbiome Engineering and Biotechnology LabThe University of Hong KongHong KongChina
| | - Kenneth M. Y. Leung
- School of Biological SciencesThe University of Hong KongHong KongChina
- State Key Laboratory of Marine Pollution and Department of ChemistryCity University of Hong KongHong KongChina
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Piazzon MC, Naya-Català F, Perera E, Palenzuela O, Sitjà-Bobadilla A, Pérez-Sánchez J. Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream. MICROBIOME 2020; 8:168. [PMID: 33228779 PMCID: PMC7686744 DOI: 10.1186/s40168-020-00922-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/09/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND The key effects of intestinal microbiota in animal health have led to an increasing interest in manipulating these bacterial populations to improve animal welfare. The aquaculture sector is no exception and in the last years, many studies have described these populations in different fish species. However, this is not an easy task, as intestinal microbiota is composed of very dynamic populations that are influenced by different factors, such as diet, environment, host age, and genetics. In the current study, we aimed to determine whether the genetic background of gilthead sea bream (Sparus aurata) influences the intestinal microbial composition, how these bacterial populations are modulated by dietary changes, and the effect of selection by growth on intestinal disease resistance. To that aim, three different groups of five families of gilthead sea bream that were selected during two generations for fast, intermediate, or slow growth (F3 generation) were kept together in the same open-flow tanks and fed a control or a well-balanced plant-based diet during 9 months. Six animals per family and dietary treatment were sacrificed and the adherent bacteria from the anterior intestinal portion were sequenced. In parallel, fish of the fast- and slow-growth groups were infected with the intestinal parasite Enteromyxum leei and the disease signs, prevalence, intensity, and parasite abundance were evaluated. RESULTS No differences were detected in alpha diversity indexes among families, and the core bacterial architecture was the prototypical composition of gilthead sea bream intestinal microbiota, indicating no dysbiosis in any of the groups. The plant-based diet significantly changed the microbiota in the intermediate- and slow-growth families, with a much lower effect on the fast-growth group. Interestingly, the smaller changes detected in the fast-growth families potentially accounted for more changes at the metabolic level when compared with the other families. Upon parasitic infection, the fast-growth group showed significantly lower disease signs and parasite intensity and abundance than the slow-growth animals. CONCLUSIONS These results show a clear genome-metagenome interaction indicating that the fast-growth families harbor a microbiota that is more flexible upon dietary changes. These animals also showed a better ability to cope with intestinal infections. Video Abstract.
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Affiliation(s)
- M. Carla Piazzon
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Fernando Naya-Català
- Nutrigenomics and Fish Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Erick Perera
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
- Nutrigenomics and Fish 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 Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
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Fong JJ, Sung YH, Ding L. Comparative Analysis of the Fecal Microbiota of Wild and Captive Beal's Eyed Turtle ( Sacalia bealei) by 16S rRNA Gene Sequencing. Front Microbiol 2020; 11:570890. [PMID: 33240228 PMCID: PMC7677423 DOI: 10.3389/fmicb.2020.570890] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/09/2020] [Indexed: 11/13/2022] Open
Abstract
The Beal’s eyed turtle (Sacalia bealei) is threatened with extinction due to hunting for large-scale trade. In Hong Kong, there are some of the world’s remaining wild populations of S. bealei, as well as a breeding colony. This breeding colony is at the core of conservation efforts (captive breeding, reintroduction programs). Therefore, we would like to know how captivity, in particular diet, affects the gut microbiota. Using high-throughput 16S rRNA gene sequencing, we comparatively analyzed the fecal microbiota of wild and captive S. bealei. We found that wild S. bealei have higher alpha diversity than captive S. bealei, but the difference was not significant. Significant differences were found in β-diversity; at the phylum level, wild S. bealei have higher relative abundances of Proteobacteria and captive S. bealei have higher relative abundances of Firmicutes. At the genus level, Cetobacterium and Citrobacter are more abundant in wild S. bealei, while Clostridium spp. are significantly more abundant in captive S. bealei. These results suggest conditions in captivity, with diet being a major factor, influence the gut microbiota of S. bealei. The connection between diet and health has always been considered for captive animals, and in this study we use the gut microbiota as an another tool to assess health.
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Affiliation(s)
| | - Yik-Hei Sung
- Science Unit, Lingnan University, Hong Kong, China
| | - Li Ding
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
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Roux N, Salis P, Lee SH, Besseau L, Laudet V. Anemonefish, a model for Eco-Evo-Devo. EvoDevo 2020; 11:20. [PMID: 33042514 PMCID: PMC7539381 DOI: 10.1186/s13227-020-00166-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/18/2020] [Indexed: 12/20/2022] Open
Abstract
Anemonefish, are a group of about 30 species of damselfish (Pomacentridae) that have long aroused the interest of coral reef fish ecologists. Combining a series of original biological traits and practical features in their breeding that are described in this paper, anemonefish are now emerging as an experimental system of interest for developmental biology, ecology and evolutionary sciences. They are small sized and relatively easy to breed in specific husbandries, unlike the large-sized marine fish used for aquaculture. Because they live in highly structured social groups in sea anemones, anemonefish allow addressing a series of relevant scientific questions such as the social control of growth and sex change, the mechanisms controlling symbiosis, the establishment and variation of complex color patterns, and the regulation of aging. Combined with the use of behavioral experiments, that can be performed in the lab or directly in the wild, as well as functional genetics and genomics, anemonefish provide an attractive experimental system for Eco-Evo-Devo.
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Affiliation(s)
- Natacha Roux
- Sorbonne Université, CNRS, UMR « Biologie Intégrative Des Organismes Marins », BIOM, 1, 66650 Banyuls-sur-Mer, France
| | - Pauline Salis
- Sorbonne Université, CNRS, UMR « Biologie Intégrative Des Organismes Marins », BIOM, 1, 66650 Banyuls-sur-Mer, France
| | - Shu-Hua Lee
- Lab of Marine Eco-Evo-Devo, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Laurence Besseau
- Sorbonne Université, CNRS, UMR « Biologie Intégrative Des Organismes Marins », BIOM, 1, 66650 Banyuls-sur-Mer, France
| | - Vincent Laudet
- Lab of Marine Eco-Evo-Devo, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.,Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna son, Okinawa, 904-0495 Japan
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36
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Attaya A, Secombes CJ, Wang T. Effective isolation of GALT cells: Insights into the intestine immune response of rainbow trout (Oncorhynchus mykiss) to different bacterin vaccine preparations. FISH & SHELLFISH IMMUNOLOGY 2020; 105:378-392. [PMID: 32615166 DOI: 10.1016/j.fsi.2020.06.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
The teleost gut is a multifunction complex structure that plays a pivotal immunological role in homeostasis and the maintenance of health, in addition to digestion of food and/or nutrient absorption. In vitro examination of the intestine leucocyte repertoire has the potential to aid our understanding of gut immune competence and allows a rapid screen of host-microorganism interactions in different immunological contexts. To explore this possibility, in the present study we investigated the response of isolated gut leucocytes to 4 bacterins of Aeromonas salmonicida, prepared from different strains, combinations and strains grown in different environments, in comparison to a Yersinia ruckeri bacterin for which a commercial/effective oral booster vaccine has been developed. To aid this study we also optimized further our method of GALT cell isolation from rainbow trout, so as to avoid mechanical clearance of the intestine contents. This drastically increased the cell yield from ~12 × 106 to ~210 × 106/fish with no change in the percent cell viability over time or presence of transcripts typical of the key leucocyte types needed for the study of immune modulation (i.e. T- and B-cells, dendritic cells and macrophages). A wide array of immune transcripts were modulated by the bacterins, demonstrating the diversity of GALT cell responses to bacterial stimulation. Indeed, the GALT leucocyte responses were sensitive enough to distinguish the different bacterial species, strains and membrane proteins, as seen by distinct kinetics of immune gene expression. However, the response of the GALT cells was often relatively slow and of a low magnitude compared to those of PBL. These results enhance our knowledge of the gut biocapacity and help validate the use of this model for screening of oral vaccine candidates.
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Affiliation(s)
- Ahmed Attaya
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, AB24 2TZ, UK.
| | - Christopher J Secombes
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, AB24 2TZ, UK.
| | - Tiehui Wang
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, AB24 2TZ, UK.
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Roh H, Kim BS, Lee MK, Park CI, Kim DH. Genome-wide comparison of Carnobacterium maltaromaticum derived from diseased fish harbouring important virulence-related genes. JOURNAL OF FISH DISEASES 2020; 43:1029-1037. [PMID: 32627213 DOI: 10.1111/jfd.13208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 05/07/2023]
Abstract
Although Carnobacterium maltaromaticum has been used as a probiotic in fish, it was reported to cause disease for the first time in Korea. The objective of this study was to understand the differences between pathogenic and non-pathogenic strains. Pathogenicity was tested by challenging rainbow trout with C. maltaromaticum ATCC35586 and 18ISCm isolated from diseased fish, and DSM20342 isolated from a dairy product. We also compared 24 genomes of C. maltaromaticum strains plus the genome of our isolate 18ISCm sequenced in this study. Only the strains from diseased fish caused high mortality with severe histopathological changes. Although all strains shared more than 90% of Ko_id, wecC and xtmA were found only in strains from diseased fish. Interestingly, only strains from diseased fish harboured two wecC paralogs involved in the production of D-mannosaminuronic acid which is a major component of a well-known virulence factor, teichuronic acid. Two wecC paralogs of 18ISCm were increased when they were co-cultured with trout blood cells, suggesting that wecC genes might play a role in virulence. The results of this study show that strains isolated from diseased fish are different from strains derived from food in terms of pathogenicity to fish and the presence of virulence-related genes.
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Affiliation(s)
- HyeongJin Roh
- Department of Aquatic life medicine. College of Fisheries Science, Pukyong National University, Busan, Korea
| | - Bo Seong Kim
- Aquatic disease control division, National Institute of Fisheries Science (NIFS), Busan, Korea
| | - Mu Kun Lee
- Korean Aquatic Organism Disease Inspector Association, Busan, Korea
| | - Chan-Il Park
- Department of Marine Biology & Aquaculture, College of Marine Science, Gyeongsang National University, Tongyeong, Korea
| | - Do-Hyung Kim
- Department of Aquatic life medicine. College of Fisheries Science, Pukyong National University, Busan, Korea
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Wang R, Guo Z, Tang Y, Kuang J, Duan Y, Lin H, Jiang S, Shu H, Huang J. Effects on development and microbial community of shrimp Litopenaeus vannamei larvae with probiotics treatment. AMB Express 2020; 10:109. [PMID: 32504358 PMCID: PMC7275112 DOI: 10.1186/s13568-020-01041-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 05/27/2020] [Indexed: 12/30/2022] Open
Abstract
Shrimp production is the second ranked of the most-traded production in these decades and the whiteleg shrimp Litopenaeus vannamei is the sixth most cultured species. Probiotics are alternative strategy for the promotion of growth and prevention of diseases in aquaculture. To confirm the effects of the probiotics on development and microbial community of L. vannamei larvae during different development stages, five kinds of probiotics (108 ~ 109 CFU/g) were added into the rearing environment of shrimp larvae, and the effects of probiotics on bacterial community and water quality, larval growth and immune index were determined from nauplius larval stage to post larval stage. Results suggested that probiotics treated groups showed larger survival rate than the control groups from Z1 stage to P5 stage. Lactobacillus could improve the larvae's survival ability, especially in the larval stages M2, M3, P1, P5 stage. It was confirmed that probiotics could promote the growth and development of shrimp larvae and prevent the incomplete molting in their growing process, particularly for EM-treated group. Results suggested that all the probiotics-treated groups had shown significant decreasing trend in the quantity of vibrios, except for the SA-treated group. And different probiotics could inhibit vibrios during different life periods. Among these probiotics, LA, EM and PB had shown the best effects, including improving survival rate of the larvae, promoting the larval metamorphosis, reducing the quantity of vibrios and NH4-N and NO2-N levels, and increasing bacterial diversity.
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Rimoldi S, Torrecillas S, Montero D, Gini E, Makol A, Valdenegro V. V, Izquierdo M, Terova G. Assessment of dietary supplementation with galactomannan oligosaccharides and phytogenics on gut microbiota of European sea bass (Dicentrarchus Labrax) fed low fishmeal and fish oil based diet. PLoS One 2020; 15:e0231494. [PMID: 32298317 PMCID: PMC7162502 DOI: 10.1371/journal.pone.0231494] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/24/2020] [Indexed: 11/19/2022] Open
Abstract
There is an increasing interest from the aquafeed industry in functional feeds containing selected additives that improve fish growth performance and health status. Functional feed additives include probiotics, prebiotics, organic acids, and phytogenics (substances derived from plants and their extracts). This study evaluated the effects of dietary inclusion of a mucilage extract rich in galactomannan oligosaccharides (GMOS), a mixture of garlic and labiatae-plants oils (PHYTO), and a combination of them (GMOSPHYTO), on gut microbiota composition of European sea bass (Dicentrarchus labrax) fed with a low fishmeal (FM) and fish oil (FO) diet. Three experimental diets and a control diet (plant-based formulation with 10% FM and 6% FO) were tested in a 63-days feeding trial. To analyze the microbiota associated to feeds and the intestinal autochthonous (mucosa-adhered) and allochthonous (transient) microbial communities, the Illumina MiSeq platform for sequencing of 16S rRNA gene and QIIME2 pipeline were used. Metabarcoding analysis of feed-associated bacteria showed that the microbial communities of control (CTRL) feed deeply differed from those of experimental diets. The number of reads was significantly lower in CTRL feed than in other feeds. The OTU (operational taxonomic unit) number was instead similar between the feeds, ranging from 42 to 50 OTUs. The variation of resident gut microbiota induced by diet was lower than the variation of transient intestinal microbiota, because feedstuffs are a major source of allochthonous bacteria, which can temporarily integrate into the gut transient microbiome. However, the composition of transient bacterial communities was not simply a mirror of feed-borne bacteria. Indeed, the microbial profile of feeds was different from both faecal and mucosa profiles. Our findings suggest that the dietary inclusion of GMOS (0.5%) and PHYTO (0.02%) in a low FM and FO diet induces changes in gut microbiota composition of European sea bass. However, if on allochthonous microbiota the combined inclusion of GMOS and PHYTO showed an antagonistic effect on bactericidal activity against Vibrionales, at mucosa level, only GMOSPHYTO diet increased the relative abundance of Bacteroidales, Lactobacillales, and Clostridiales resident bacterial orders. The main beneficial effects of GMOS and PHYTO on gut microbiota are the reduction of coliforms and Vibrionales bacteria, which include several potentially pathogenic species for fish, and the enrichment of gut microbiota composition with butyrate producer taxa. Therefore, these functional ingredients have a great potential to be used as health-promoting agents in the farming of European sea bass and other marine fish.
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Affiliation(s)
- Simona Rimoldi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Silvia Torrecillas
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Telde, Las Palmas, Canary Islands, Spain
| | - Daniel Montero
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Telde, Las Palmas, Canary Islands, Spain
| | - Elisabetta Gini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Alex Makol
- Delacon Biotechnik GmbH, Steyregg, Austria
| | | | - Marisol Izquierdo
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Telde, Las Palmas, Canary Islands, Spain
| | - Genciana Terova
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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Jia J, Cheng M, Xue X, Guan Y, Wang Z. Characterization of tetracycline effects on microbial community, antibiotic resistance genes and antibiotic resistance of Aeromonas spp. in gut of goldfish Carassius auratus Linnaeus. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 191:110182. [PMID: 31958628 DOI: 10.1016/j.ecoenv.2020.110182] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 01/05/2020] [Accepted: 01/07/2020] [Indexed: 06/10/2023]
Abstract
The gut of aquatic animals was a significant niche for dissemination of antibiotic resistance genes (ARGs) and direct response of living conditions. In this study, the gut microbiota of goldfish Carassius auratus Linnaeus was sampled at 7 days and 21 days after treatment with tetracycline at 0.285 and 2.85 μg L-1 to investigate the influences on the microbial structure and antibiotic resistance. The proportion of tetracycline resistance bacteria was 1.02% in the control group, while increased to 23.00%, 38.43%, 62.05% in groups of high concentration for 7 days (H7), low concentration for 21 days (L21) and high concentration for 21 days (H21), respectively. Compared to the control group, the diversity of isolated Aeromonas spp. was decreased in the treatment groups and the minimal inhibitory concentration (MIC) of resistant isolates was enhanced from 32 to 256 μg mL-1 with the treatment of tetracycline in time- and dose-dependent manners. Furthermore, the abundance of most genes was increased in treatment groups and efflux genes mainly responded to the stress of tetracycline with an average level of 1.0 × 10-2. After treatment with tetracycline, the predominant species were changed both at phylum and genus levels. The present study explored the impact of tetracycline on gut microbiota of goldfish at environmentally realistic concentrations for the first time and our findings will provide a reference for characterizing the microbiome of fish in the natural environment.
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Affiliation(s)
- Jia Jia
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mengqian Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xue Xue
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yongjing Guan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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41
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Niu KM, Lee BJ, Kothari D, Lee WD, Hur SW, Lim SG, Kim KW, Kim KD, Kim NN, Kim SK. Dietary effect of low fish meal aquafeed on gut microbiota in olive flounder (Paralichthys olivaceus) at different growth stages. Microbiologyopen 2020; 9:e992. [PMID: 31925997 PMCID: PMC7066472 DOI: 10.1002/mbo3.992] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/04/2019] [Accepted: 12/16/2019] [Indexed: 12/13/2022] Open
Abstract
This study was conducted to investigate the long‐term effect of a low fish meal (FM) diet comprising plant‐based protein sources (PPS) on changes of gut microbial diversity in olive flounder (Paralichthys olivaceus) over the course of life. Two experimental diets were prepared to contain 74% FM (control) or 52% FM with 22% PPS (30% FM replacement, FM30). Fish were fed one of the two experimental diets for 8 months, and we collected the midgut contents to analyze the gut bacterial community by Illumina MiSeq based on the metagenomic sequences in the V3–V4 regions of 16S rRNA. We found that there were nine dominant phyla, which in turn presented Proteobacteria, Firmicutes, and Actinobacteria as the three major phyla in the gut microbiota of the flounder. At genus level, the dominant genera were Delftia, Prevotella, and Chthoniobacter at the juvenile stage (below 100 g/fish); Chthoniobacter, Bacillus, and Bradyrhizobium at the grower stage (400 g/fish); Chthoniobacter, Bacillus, and Delftia at the subadult stage (800 g/fish); and Lactobacillus and Prevotella at the adult stage (over 1,000 g/fish). The microbial diversity in olive flounders arched from the juvenile and subadult stage and reached a plateau thereafter. The fish fed the FM30 diet significantly had an increased abundance of Lactobacillus and Photobacterium and had less abundance of Prevotella and Paraprevotella than the control. However, the effect of dietary PPS was not significant on total microbial richness, indicating no negative effect as feed sources on the intestinal microbiota in olive flounder. These results indicate that the life stage of olive flounder is more important in modulating intestinal microbiota than is the diet. It could also be concluded that dietary PPS might be used as a potential fish meal alternative without any compromising effects on microbial diversity of olive flounder for long‐term feeding.
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Affiliation(s)
- Kai-Min Niu
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, China.,Department of Animal Science and Technology, Konkuk University, Seoul, Korea
| | - Bong-Joo Lee
- Aquafeed Research Center, National Institute of Fisheries Science, Pohang, Korea
| | - Damini Kothari
- Department of Animal Science and Technology, Konkuk University, Seoul, Korea
| | - Woo-Do Lee
- Department of Animal Science and Technology, Konkuk University, Seoul, Korea
| | - Sang-Woo Hur
- Aquafeed Research Center, National Institute of Fisheries Science, Pohang, Korea
| | - Sang-Gu Lim
- Aquafeed Research Center, National Institute of Fisheries Science, Pohang, Korea
| | - Kang-Woong Kim
- Aquaculture Management Division, National Institute of Fisheries Science, Busan, Korea
| | - Kyoung-Duck Kim
- Aquaculture Management Division, National Institute of Fisheries Science, Busan, Korea
| | - Na-Na Kim
- Inland Aquaculture Research Center, National Institute of Fisheries Science, Changwon, Korea
| | - Soo-Ki Kim
- Department of Animal Science and Technology, Konkuk University, Seoul, Korea
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42
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Fancello F, Multineddu C, Santona M, Deiana P, Zara G, Mannazzu I, Budroni M, Dettori S, Zara S. Bacterial Biodiversity of Extra Virgin Olive Oils and Their Potential Biotechnological Exploitation. Microorganisms 2020; 8:E97. [PMID: 31936728 PMCID: PMC7022595 DOI: 10.3390/microorganisms8010097] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/22/2019] [Accepted: 01/07/2020] [Indexed: 12/16/2022] Open
Abstract
Bacterial diversity of 15 extra virgin olive oils, obtained from different Italian varieties, including Frantoio, Coratina, Bosana, and Semidana, was analyzed in this study. All bacterial isolates were genotyped using RAPD and REP-PCR method and grouped by means of cluster analyses. Sequencing of 16S rDNA of 51 isolates, representative of 36 clusters, led to the identification of Bacillus spp., Brevibacillus spp., Micrococcus spp., Staphylococcus spp., Pantoea spp., Kocuria spp., Lysinbacillus spp., and Lactobacillus spp., most of which reported for first time in olive oils. Phenotypic characterization of the 51 isolates, some of which ascribed to potentially probiotic species, indicate that two of them have beta-glucosidase activity while 37% present lipolytic activity. Preliminary evaluation of probiotic potential indicates that 31% of the isolates show biofilm formation ability, 29% acidic pH resistance, and 25% bile salt resistance. Finally, 29% of the isolates were sensitive to antibiotics while the remaining 71%, that include bacterial species well-recognized for their ability to disseminate resistance genes in the environment, showed a variable pattern of antibiotic resistance. The results obtained underline that microbial diversity of extra virgin olive oils represents an unexpected sink of microbial diversity and poses safety issues on the possible biotechnological exploitation of this microbial biodiversity.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Severino Zara
- Dipartimento di Agraria, Viale Italia 39, University of Sassari, 07100 Sassari, Italy; (F.F.); (C.M.); (M.S.); (P.D.); (G.Z.); (I.M.); (M.B.); (S.D.)
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43
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Comparison of the intestinal microbiota composition and function in healthy and diseased Yunlong Grouper. AMB Express 2019; 9:187. [PMID: 31754862 PMCID: PMC6872706 DOI: 10.1186/s13568-019-0913-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/09/2019] [Indexed: 11/10/2022] Open
Abstract
Maintaining stabilization of the intestinal microbiota is important in preventing bacterial diseases in cultured fish. At present, there have been no reports on the composition and functional analysis of intestinal microbiota in Yunlong Grouper (Epinephelus moara♀ × Epinephelus lanceolatus♂). In this study we analyzed and compared the intestinal microbiota composition of healthy and diseased pond-reared fish to discern the functional profile of a healthy status. The richness and diversity of the intestinal microbiota did not differ significantly between diseased and healthy fish, yet the abundance of predominant phyla like the Proteobacteria were upregulated in the diseased Yunlong Grouper. At the genus level, a significant reduction of Cetobacterium was observed in the intestinal tracts of diseased fish, as Pseudomonas became the most dominant bacterium. To compare the intestinal microorganism abundances between the two health groups of fish, we first screened the gut bacteria and discerned 4 phyla and 12 genera to designate a healthy status in Yunlong Grouper. The environmental bacterial community influenced composition of the intestinal microbiota in Yunlong Grouper, and the intestinal microbiota of diseased fish was more susceptible to the influence of the culture water. In addition, the prediction of functional genes by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) indicated that the intestinal microbiota of Yunlong Grouper is related mainly to the terms "metabolism, environmental information processing, genetic information processing, human diseases, and cellular processing; moreover, the functions of the intestinal microbiota differed between the different health states of this fish. The overall results indicate that the occurrence of disease can affect the composition and function of the intestinal microbiota in a cultured fish.
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44
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Piazzon MC, Naya-Català F, Simó-Mirabet P, Picard-Sánchez A, Roig FJ, Calduch-Giner JA, Sitjà-Bobadilla A, Pérez-Sánchez J. Sex, Age, and Bacteria: How the Intestinal Microbiota Is Modulated in a Protandrous Hermaphrodite Fish. Front Microbiol 2019; 10:2512. [PMID: 31736931 PMCID: PMC6834695 DOI: 10.3389/fmicb.2019.02512] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/18/2019] [Indexed: 12/11/2022] Open
Abstract
Intestinal microbiota is key for many host functions, such as digestion, nutrient metabolism, disease resistance, and immune function. With the growth of the aquaculture industry, there has been a growing interest in the manipulation of fish gut microbiota to improve welfare and nutrition. Intestinal microbiota varies with many factors, including host species, genetics, developmental stage, diet, environment, and sex. The aim of this study was to compare the intestinal microbiota of adult gilthead sea bream (Sparus aurata) from three groups of age and sex (1-year-old males and 2- and 4-year-old females) maintained under the same conditions and fed exactly the same diet. Microbiota diversity and richness did not differ among groups. However, bacterial composition did, highlighting the presence of Photobacterium and Vibrio starting at 2 years of age (females) and a higher presence of Staphylococcus and Corynebacterium in 1-year-old males. The core microbiota was defined by 14 Operational Taxonomic Units (OTUs) and the groups that showed more OTUs in common were 2- and 4-year-old females. Discriminant analyses showed a clear separation by sex and age, with bacteria belonging to the phyla Firmicutes, Proteobacteria and Actinobacteria driving the separation. Pathway analysis performed with the inferred metagenome showed significant differences between 1-year-old males and 4-year-old females, with an increase in infection-related pathways, nitrotoluene degradation and sphingolipid metabolism, and a significant decrease in carbohydrate metabolism pathways with age. These results show, for the first time, how intestinal microbiota is modulated in adult gilthead sea bream and highlight the importance of reporting age and sex variables in these type of studies in fish.
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Affiliation(s)
- M Carla Piazzon
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (CSIC), Castellón, Spain
| | - Fernando Naya-Català
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (CSIC), Castellón, Spain
| | - Paula Simó-Mirabet
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (CSIC), Castellón, Spain
| | - Amparo Picard-Sánchez
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (CSIC), Castellón, Spain
| | - Francisco J Roig
- Biotechvana S.L., Valencia, Spain.,Instituto de Medicina Genomica, S.L., Valencia, Spain
| | - Josep A Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (CSIC), Castellón, Spain
| | | | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (CSIC), Castellón, Spain
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45
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Wang C, Liu H, Mu G, Lu S, Wang D, Jiang H, Sun X, Han S, Liu Y. Effects of traditional Chinese medicines on immunity and culturable gut microflora to Oncorhynchus masou. FISH & SHELLFISH IMMUNOLOGY 2019; 93:322-327. [PMID: 31352114 DOI: 10.1016/j.fsi.2019.07.071] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/15/2019] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
The present study was conducted to evaluate the effect of dietary traditional Chinese medicines on the growth, immunity, and composition of culturable gut microflora in Oncorhynchus masou. Diets were formulated to contain no medicine (control), antitoxic decoction (A), general antiphlogistic decoction (B), or Herbae Artemisiae Capillariae decoction (C). Fish were manually fed twice daily till apparent satiation for 30 days. Compared with that in the control group, supplementation with the three kinds of Chinese herbal medicine enhanced fish growth significantly (P < 0.05). The activities of liver superoxide dismutase and glutathione peroxidase in the treatment groups were significantly higher compared with those in the control group (P < 0.05). The quantity of intestinal microflora was higher in the treatment groups compared with that in the control group. Moreover, there were some effects of dietary Chinese herbal medicine on the composition of intestinal microflora. Microflora of Pseudomonas sp., Psychrobacter sp., Microbacterium sp., Macrococcus sp., Burkholderia sp., and Arthrobacter sp. were found in the treatment groups, whereas there were none in the control group. There was a significant increase in their amounts in the treatment groups (P < 0.05). The three kinds of traditional Chinese medicines can improve the growth and immunity of Oncorhynchus masou and affect the quantity and composition of intestinal microflora.
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Affiliation(s)
- Chang'an Wang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
| | - Hongbai Liu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
| | - Guiqiang Mu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Shaoxia Lu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Di Wang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Haibo Jiang
- College of Animal Sciences, Guizhou University, Guiyang, China
| | - Xiao Sun
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Shicheng Han
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Yang Liu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
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46
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Fogarty C, Burgess CM, Cotter PD, Cabrera-Rubio R, Whyte P, Smyth C, Bolton DJ. Diversity and composition of the gut microbiota of Atlantic salmon (Salmo salar) farmed in Irish waters. J Appl Microbiol 2019; 127:648-657. [PMID: 31021487 DOI: 10.1111/jam.14291] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 04/01/2019] [Accepted: 04/04/2019] [Indexed: 12/25/2022]
Abstract
AIMS Information on the gut microbiota of salmon is essential for optimizing nutrition while maintaining host health and welfare. This study's objectives were to characterize the microbiota in the GI tract of Atlantic salmon (Salmo salar) farmed in waters off the west coast of Ireland and to investigate whether there is a difference in microbiota diversity between the proximal and distal regions of the intestine. METHODS AND RESULTS The microbiota from the proximal and distal intestine (PI and DI, respectively) of Atlantic salmon was examined using MiSeq Illumina high-throughput sequencing of the 16S ribosomal RNA gene. The PI region had greater bacterial diversity than the DI region. Six phyla were present in the DI samples, dominated by Tenericutes and Firmicutes. These six phyla were also amongst the 12 phyla detected in the PI samples. The PI microbiota was dominated by Tenericutes, Firmicutes, Bacteroidetes and Proteobacteria. A core microbiota of 20 operational taxonomic units (OTUs) common to both regions was observed. CONCLUSIONS It was concluded that Tenericutes were the dominant phylum in both PI and DI samples, and the PI region had greater Shannon and Simpson diversity of bacteria. However, further work is required to identify the functionality of the salmon microbiota. SIGNIFICANCE AND IMPACT OF THE STUDY Our study determined the composition and diversity of the intestinal microbiota in adult salmon from a commercial fishery and provides data to improve our understanding of their contributions to the nutrition, health and welfare of Atlantic salmon farmed in Irish waters.
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Affiliation(s)
- Colin Fogarty
- Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland.,School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | | | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, and APC Microbiome Ireland, Cork, Ireland
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, and APC Microbiome Ireland, Cork, Ireland
| | - Paul Whyte
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Conor Smyth
- Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland.,School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
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47
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Klūga A, Kačániová M, Terentjeva M. Identification and antibiotic susceptibility of bacterial microbiota of freshwater fish. POTRAVINARSTVO 2019. [DOI: 10.5219/1063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The fish meat is an essential part of human diet. However, fish may be contaminated with different microorganisms, including pathogens. Antimicrobial resistance of fish microbiota may facilitate the spread of resistant microorganisms causing serious consequences for human health. The aim of the present study was to detect bacterial contamination in fish gill, gut and skin and to determine antimicrobial susceptibility of the bacterial isolates. Rainbow trout (Oncorhynchus mykiss) and bream (Abramis bram) were obtained from the market in Jelgava city. Chub (Leuciscus cephalus), crucian carp (Carassius carassius) and tench (Tinca tinca) were collected from fishermen. Fish samples were examined for the total bacterial count (TBC), coliforms, Enterobacteriaceae, Pseudomonas spp. and Aeromonas spp. Testing was done in accordance with International Organization for Standardization (ISO) standards. Identification of all bacteria was accomplished with the Matrix Assisted Laser Desorption Ionization – Time of Flight Mass Spectrometry (MALDI-TOF MS) method. The disc diffusion method was used for the detection of antibiotic susceptibility of isolated bacterial species. TBC ranged from 2.70 to 7.00 log CFU.g-1, coliforms from 0 to 2.67 log CFU.g-1, Enterobacteriaceae from 0 to 2.85 log CFU.g-1. The highest contamination with Pseudomonas spp. and Aeromonas spp. was observed in chub gut samples with 1.60 log CFU.g-1 and 2.23 log CFU.g-1, respectively. Altogether, 16 microbial genera and 31 bacterial species were identified. The dominant bacterial species belonged to Pseudomonas spp. (54%) and Enterobacteriaceae. Pseudomonas spp. were resistant to ticarcillin, susceptibility to ciprofloxacin showed 88% of isolates. All Enterobacteriaceae isolates were susceptible to imipenem. The microbial quality of the fish was acceptable, but the presence of antibiotic resistant bacteria may further cause a negative impact on public health.
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48
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Parshukov AN, Kashinskaya EN, Simonov EP, Hlunov OV, Izvekova GI, Andree KB, Solovyev MM. Variations of the intestinal gut microbiota of farmed rainbow trout, Oncorhynchus mykiss (Walbaum), depending on the infection status of the fish. J Appl Microbiol 2019; 127:379-395. [PMID: 31066161 DOI: 10.1111/jam.14302] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/29/2019] [Accepted: 04/17/2019] [Indexed: 12/14/2022]
Abstract
AIMS The aim of the present study was to investigate the composition of the intestinal microbiota during the acute stage of a bacterial infection to understand how dysbiosis of the gut may influence overall taxonomic hierarchy and diversity, and determine if there exists a bacterial taxon(s) that serve as markers for healthy or diseased rainbow trout (Oncorhynchus mykiss). METHODS AND RESULTS From July to September 2015, 29 specimens of 3-year-old (an average weight from 240·9 ± 37·7 to 850·7 ± 70·1 g) rainbow trout O. mykiss were studied. Next-generation high-throughput sequencing of the 16S ribosomal RNA genes was applied to stomach and intestinal samples to compare the impact of infection status on the microbiota of rainbow trout O. mykiss (Walbaum) from the northwest part of Eurasia (Karelian region, Russia). The alpha diversity (Chao1, Simpson and Shannon index) of the microbial community of healthy rainbow trout was significantly higher than in unhealthy fish. The greatest contribution to the gut microbial composition of healthy fish was made by OTU's belonging to Bacillus, Serratia, Pseudomonas, Cetobacterium and Lactobacillus. Microbiota of unhealthy fish in most cases was represented by the genera Serratia, Bacillus and Pseudomonas. In microbiota of unhealthy fish there were also registered unique taxa such as bacteria from the family Mycoplasmataceae and Renibacterium. Analysis of similarities test revealed the significant dissimilarity between the microbiota of stomach and intestine (P ≤ 0·05). CONCLUSIONS A substantial finding was the absence of differences between microbial communities of the stomach and intestine in the unhealthy groups if compared with healthy fish. SIGNIFICANCE AND IMPACT OF THE STUDY These results demonstrated alterations of the gut microbiota of farmed rainbow trout, O. mykiss during co-infections and can be useful for the development of new strategies for disease control programs.
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Affiliation(s)
- A N Parshukov
- Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences, Petrozavodsk, Russia
| | - E N Kashinskaya
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - E P Simonov
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.,Laboratory for Genomic Research and Biotechnology, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk, Russia
| | - O V Hlunov
- LLC "FishForel", Lahdenpohja, Karelia, Russia
| | - G I Izvekova
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
| | - K B Andree
- IRTA-SCR, San Carlos de la Rapita, Tarragona, Spain
| | - M M Solovyev
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.,Tomsk State University, Tomsk, Russia
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49
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PASTRO DC, MARIOTTO S, SANTOS EC, FERREIRA DC, CHITARRA GS. Use of molecular techniques for the analysis of the microbiological quality of fish marketed in the municipality of Cuiabá, Mato Grosso, Brazil. FOOD SCIENCE AND TECHNOLOGY 2019. [DOI: 10.1590/fst.40217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
| | - Sandra MARIOTTO
- Instituto Federal de Educação, Ciência e Tecnologia de Mato Grosso, Brasil
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50
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Riiser ES, Haverkamp THA, Varadharajan S, Borgan Ø, Jakobsen KS, Jentoft S, Star B. Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod. Environ Microbiol 2019; 21:2576-2594. [PMID: 31091345 DOI: 10.1111/1462-2920.14652] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 05/07/2019] [Accepted: 05/09/2019] [Indexed: 12/29/2022]
Abstract
Atlantic cod (Gadus morhua) is an ecologically important species with a wide-spread distribution in the North Atlantic Ocean, yet little is known about the diversity of its intestinal microbiome in its natural habitat. No geographical differentiation in this microbiome was observed based on 16S rRNA amplicon analyses, yet such finding may result from an inherent lack of power of this method to resolve fine-scaled biological complexity. Here, we use metagenomic shotgun sequencing to investigate the intestinal microbiome of 19 adult Atlantic cod individuals from two coastal populations in Norway-located 470 km apart. Resolving the species community to unprecedented resolution, we identify two abundant species, Photobacterium iliopiscarium and Photobacterium kishitanii, which comprise over 50% of the classified reads. Interestingly, the intestinal P. kishitanii strains have functionally intact lux genes, and its high abundance suggests that fish intestines form an important part of its ecological niche. These observations support a hypothesis that bioluminescence plays an ecological role in the marine food web. Despite our improved taxonomical resolution, we identify no geographical differences in bacterial community structure, indicating that the intestinal microbiome of these coastal cod is colonized by a limited number of closely related bacterial species with a broad geographical distribution.
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Affiliation(s)
- Even Sannes Riiser
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
| | - Thomas H A Haverkamp
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
| | - Srinidhi Varadharajan
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
| | - Ørnulf Borgan
- Department of Mathematics, University of Oslo, PO Box 1053, Blindern, N-0316 Oslo, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
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