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Lu X, Wu Y, Peng Y, Liu W, Liu M, Xu P, Tan K, Liang X, Cai X, Gong Q. Effects of Sophora flavescens dietary supplementation on the growth performance, haematological indices, and intestinal bacterial community of Oreochromis niloticus. JOURNAL OF FISH BIOLOGY 2024. [PMID: 39260822 DOI: 10.1111/jfb.15919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 08/13/2024] [Accepted: 08/13/2024] [Indexed: 09/13/2024]
Abstract
Sophora flavescens is considered to be of various medicinal and economic importance. Previous studies have shown that it has antibacterial, antioxidant, and immune-enhancing functions. To explore the full potential of S. flavescens in fish feed development, we investigated the effects of different levels of S. flavescens added to the diet on the growth performance, haematological indices, and the intestinal bacterial community of Nile tilapia (Oreochromis niloticus). The feeding trial lasted for 56 days, and the initial weight of the fish was 40.00 ± 5.00 g. Nile tilapia were randomly divided into six groups: a control group (CN) and five S. flavescens supplementation groups (0.02%, 0.04%, 0.08%, 0.16%, and 0.3% [w/w] of S. flavescens in diet). The growth performance of fish increased first and then decreased with the increase of S. flavescens supplemental level. Compared with other experimental groups, the growth performance of fish supplemented with 0.08% S. flavescens was significantly improved (p < 0.05). Haematological indices exhibited that erythrocyte (RBC), along with leucocyte (WBC) indices, exhibited a secondary trend of increasing and then decreasing with the increase of S. flavescens, reaching the highest level at 0.08% (p < 0.05). However, mean corpuscular volume (MCV), mean corpuscular haemoglobin (MCH), and mean corpuscular haemoglobin concentration (MCHC) exhibited a secondary trend of first decreasing and then increasing with the increase of S. flavescens and reached the lowest value at 0.08% (p < 0.05). Compared with the CN, alkaline phosphatase (AKP) significantly decreased and changed when the additional amount of S. flavescens was 0.04% in each treatment group (p < 0.05). In another way, the gut microbial profiles revealed that Bacteroides dominated the gut communities, and compared with the control group, two uncultured bacteria were suppressed. In addition, when the supplemental level of S. flavescens was more significant than 0.04%, the proliferation of Arcobacter cryaerophilus, Solibacillus silvestris, and Escherichia sp. in the gut of Nile tilapia was promoted. The results revealed that S. flavescens, as an additive to the Nile tilapia diet with levels ranging from 0.04% to 0.08%, can enhance the growth performance and immunity and promote the proliferation of intestinal beneficial bacteria of Nile tilapia.
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Affiliation(s)
- Xin Lu
- College of Marine Sciences, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, China
| | - Yingrui Wu
- College of Marine Sciences, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, China
| | - Yinhui Peng
- College of Marine Sciences, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, China
| | - Wenjie Liu
- College of Marine Sciences, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, China
| | - Ming Liu
- College of Marine Sciences, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, China
| | - Peng Xu
- College of Marine Sciences, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, China
| | - Kianann Tan
- College of Marine Sciences, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, China
| | - Xueying Liang
- College of Marine Sciences, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, China
| | - Xiaohui Cai
- College of Marine Sciences, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, China
| | - Qingfang Gong
- College of Marine Sciences, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, China
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Islam SI, Mahfuj S, Baqar Z, Asadujjaman M, Islam MJ, Alsiwiehri N, Almehmadi M, Sanjida S, Ahammad F. Bacterial diseases of Asian sea bass ( Lates calcarifer): A review for health management strategies and future aquaculture sustainability. Heliyon 2024; 10:e29793. [PMID: 38707314 PMCID: PMC11068540 DOI: 10.1016/j.heliyon.2024.e29793] [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: 12/23/2023] [Revised: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
The advent of aquaculture has been one of the most significant shifts in world food supply during the last century. Aquaculture has rapidly expanded and become a global food industry, spurred by population expansion, increased seafood consumption, and decreased captured fisheries. Nonetheless, the exponential growth of aquaculture has emerged as a significant contributor to anthropogenic changes. Unexpectedly, the result has focused in the emergence and spread of new diseases. The Asian sea bass (Lates calcarifer) is an economically important species in aquaculture, contributing significantly to the global seafood market. However, bacterial diseases have emerged as a major concern, affecting both wild and cultured populations of this species. The most prevalent bacterial pathogens are streptococcus, vibriosis, nocardiosis, tenacibaculosis, and pot-belly disease. Therefore, this review aims to comprehensively analyze both emerging and non-emerging bacterial diseases affecting L. calcarifer and explore potential management approaches for their control. Through an extensive literature survey and critical evaluation of research findings, this review highlights the current understanding of bacterial diseases in L. calcarifer and proposes strategies for better disease management. In addition, this review looks at the rise and characteristics of aquaculture, the major bacterial pathogens of L. calcarifer and their effects, and the specific attributes of disease emergence in an aquatic rather than terrestrial context. It also considers the potential for future disease emergence in L. calcarifer due to aquaculture expansion and climate changes.
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Affiliation(s)
- Sk Injamamul Islam
- Department of Fisheries and Marine Bioscience, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
- Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Sarower Mahfuj
- Department of Fisheries and Marine Bioscience, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Zulqarnain Baqar
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Md Asadujjaman
- Department of Aquaculture, Khulna Agricultural University, Khulna, 9100, Bangladesh
| | - Md Jakiul Islam
- Faculty of Fisheries, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Naif Alsiwiehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Mazen Almehmadi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Saloa Sanjida
- Department of Environmental Science and Technology, Faculty of Applied Science and Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Foysal Ahammad
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
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Palacios-Rodriguez AP, Espinoza-Culupú A, Durán Y, Sánchez-Rojas T. Antimicrobial Activity of Bacillus amyloliquefaciens BS4 against Gram-Negative Pathogenic Bacteria. Antibiotics (Basel) 2024; 13:304. [PMID: 38666980 PMCID: PMC11047741 DOI: 10.3390/antibiotics13040304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/08/2024] [Accepted: 03/15/2024] [Indexed: 04/29/2024] Open
Abstract
Worldwide, bacterial resistance is one of the most severe public health problems. Currently, the failure of antibiotics to counteract superbugs highlights the need to search for new molecules with antimicrobial potential to combat them. The objective of this research was to evaluate the antimicrobial activity of Bacillus amyloliquefaciens BS4 against Gram-negative bacteria. Thirty yeasts and thirty-two Bacillus isolates were tested following the agar well-diffusion method. Four Bacillus sp. strains (BS3, BS4, BS17, and BS21) showed antagonistic activity against E. coli ATCC 25922 using bacterial culture (BC) and the cell-free supernatant (CFS), where the BS4 strain stood out, showing inhibitory values of 20.50 ± 0.70 mm and 19.67 ± 0.58 mm for BC and CFS, respectively. The Bacillus sp. BS4 strain can produce antioxidant, non-hemolytic, and antimicrobial metabolites that exhibit activity against several microorganisms such as Salmonella enterica, Klebsiella pneumoniae, Shigella flexneri, Enterobacter aerogenes, Proteus vulgaris, Yersinia enterocolitica, Serratia marcescens, Aeromonas sp., Pseudomonas aeruginosa, Candida albicans, and Candida tropicalis. According to the characterization of the supernatant, the metabolites could be proteinaceous. The production of these metabolites is influenced by carbon and nitrogen sources. The most suitable medium to produce antimicrobial metabolites was TSB broth. The one-factor-at-a-time method was used to standardize parameters such as pH, agitation, temperature, carbon source, nitrogen source, and salts, resulting in the best conditions of pH 7, 150 rpm, 28 °C, starch (2.5 g/L), tryptone (20 g/L), and magnesium sulfate (0.2 g/L), respectively. Moreover, the co-culture was an excellent strategy to improve antimicrobial activity, achieving maximum antimicrobial activity with an inhibition zone of 21.85 ± 1.03 mm. These findings position the Bacillus amyloliquefaciens BS4 strain as a promising candidate for producing bioactive molecules with potential applications in human health.
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Affiliation(s)
- Ana Paula Palacios-Rodriguez
- Laboratory of Environmental Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru; (A.P.P.-R.); (Y.D.)
| | - Abraham Espinoza-Culupú
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
| | - Yerson Durán
- Laboratory of Environmental Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru; (A.P.P.-R.); (Y.D.)
| | - Tito Sánchez-Rojas
- Laboratory of Environmental Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru; (A.P.P.-R.); (Y.D.)
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Ruiz A, Torrecillas S, Kashinskaya E, Andree KB, Solovyev M, Gisbert E. Comparative study of the gut microbial communities collected by scraping and swabbing in a fish model: a comprehensive guide to promote non-lethal procedures for gut microbial studies. Front Vet Sci 2024; 11:1374803. [PMID: 38585300 PMCID: PMC10997143 DOI: 10.3389/fvets.2024.1374803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/12/2024] [Indexed: 04/09/2024] Open
Abstract
In the present study, we propose the use of swabs in non-lethal sampling procedures to collect the mucosa-adhered gut microbiota from the posterior intestine of fish, and therefore, we compare the bacterial communities collected by conventional scraping and by swabbing methods. For this purpose, samples of the posterior intestine of rainbow trout (Oncorhynchus mykiss) were collected first using the swabbing approach, and after fish euthanasia, by mucosa scraping. Finally, bacterial communities were compared by 16S rRNA gene Illumina sequencing. Results from the current study revealed that similar values of bacterial richness and diversity were found for both sampling procedures. Similarly, there were no differences between procedures when using qualitative metrics (Jaccard and unweighted UniFrac) for estimating inter-individual diversity, but the quantitative metrics (Bray-Curtis and weighted UniFrac) showed a higher dispersion when samples were obtained by swabbing compared to scraping. In terms of bacterial composition, there were differences in abundance for the phyla Firmicutes and Proteobacteria. The cause of these differential abundances may be the inability of the swab to access to certain areas, such as the basal region of the intestinal villi. Moreover, swabbing allowed a higher representation of low abundant taxa, which may also have an important role in host microbiome regardless of their low abundance. Overall, our results demonstrate that the sampling method is a factor to be considered in experimental design when studying gut bacterial communities to avoid potential biases in the interpretation or comparison of results from different studies. In addition, the advantages and disadvantages of each procedure (swabbing vs scraping) are discussed in detail, concluding that swabbing can be implemented as a reliable and non-lethal procedure for posterior gut microbiota studies, which is of particular interest for animal welfare and the 3Rs principle, and may offer a wide range of novel applications.
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Affiliation(s)
- Alberto Ruiz
- Aquaculture Program, Centre de La Ràpita, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), La Ràpita, Spain
| | - Silvia Torrecillas
- Aquaculture Program, Centre de La Ràpita, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), La Ràpita, Spain
| | - Elena Kashinskaya
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Karl B. Andree
- Aquaculture Program, Centre de La Ràpita, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), La Ràpita, Spain
| | - Mikhail Solovyev
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
- Biological Institute, Tomsk State University, Tomsk, Russia
| | - Enric Gisbert
- Aquaculture Program, Centre de La Ràpita, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), La Ràpita, Spain
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5
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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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Pang A, Peng C, Xie R, Wang Z, Tan B, Wang T, Zhang W. Effects of fermented soybean meal substitution for fish meal on intestinal flora and intestinal health in pearl gentian grouper. Front Physiol 2023; 14:1194071. [PMID: 37469566 PMCID: PMC10352108 DOI: 10.3389/fphys.2023.1194071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 05/25/2023] [Indexed: 07/21/2023] Open
Abstract
This study explored the role of replacing fish meal protein with fermented soybean meal (FSBM) protein on the growth performance and intestinal morphology, immunity, and microbiota of the pearl gentian grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂). Three isonitrogenous and isolipidic diets with increasing levels of FSBM (0%, 20% and 40%; referred to as FM, FSBM20 and FSBM40 diets, respectively) as a replacement for fish meal were selected for this study. The pearl gentian grouper were fed these diets for 10 weeks. The findings revealed that the growth of fish fed the FSBM diets (FSBM20 and FSBM40) were remarkably lower than the fish fed the FM diet. Pathological manifestations of intestinal inflammation, such as shortened intestinal mucosal folds and thickened lamina propria, were observed in the fish fed the FSBM diets. Moreover, the gene expression levels of IL1β, IL12, IL17, and TNFα were remarkably upregulated in fish fed the FSBM40 diet, in contrast to the gene expression levels of IL4, IL5, IL10, and TGFβ1, which were remarkably downregulated (p < 0.05). The FSBM diets significantly affected the stability of the fish gut microbiota. Photobacterium was the dominant phylum in all experimental groups, and the proportion of these bacteria gradually decreased with increasing FSBM substitution. The composition of intestinal flora at the genus level was not the same in the three experimental groups, with a richer composition of intestinal bacteria detected in the FSBM20 and FSBM40 groups (p < 0.05). The correlation between intestinal flora balance and immune gene expression revealed that only Photobacterium was negatively correlated with the above upregulated genes, while other bacteria were positively correlated with these pro-inflammatory factors (p < 0.05). Photobacterium was positively correlated with the above downregulated genes, while other bacteria were negatively correlated with these anti-inflammatory factors (p < 0.05). In conclusion, high levels of substitution of FSBM for fish meal causes intestinal inflammation in pearl gentian grouper. This is likely associated with changes to the intestinal flora. More attention should be paid to the negative role of dietary FSBM on intestinal flora.
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Affiliation(s)
- Aobo Pang
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
- Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, Guangdong, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, Guangdong, China
| | - Cong Peng
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
- Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, Guangdong, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, Guangdong, China
| | - Ruitao Xie
- Guangdong Evergreen Feed Industry Co, Ltd., Zhangjiang, China
| | - Zhuoduo Wang
- Guangdong Evergreen Feed Industry Co, Ltd., Zhangjiang, China
| | - Beiping Tan
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
- Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, Guangdong, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, Guangdong, China
| | - Tingting Wang
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
- Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, Guangdong, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, Guangdong, China
| | - Wei Zhang
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
- Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, Guangdong, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, Guangdong, China
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Gaughan S, Kyndt JA, Haas JD, Steffensen KD, Kočovský PM, Pope KL. Using the Gut Microbiome to Assess Stocking Efforts of the Endangered Pallid Sturgeon, Scaphirhynchus albus. Life (Basel) 2023; 13:life13020309. [PMID: 36836665 PMCID: PMC9967686 DOI: 10.3390/life13020309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
The endangered Pallid Sturgeon, Scaphirhynchus albus, has been actively managed to prevent population declines, including stocking of hatchery-raised fish. The gut microbiome plays an innate role in an organism's absorption of nutrients by increasing nutrient availability and can provide new insights for Pallid Sturgeon management. In this study, the Pallid Sturgeon's microbiome is dominated by the phyla Proteobacteria, Firmicutes, Actinobacteria and Fusobacteria. It was also determined that the gut bacterial diversity in hatchery-raised Pallid Sturgeon was not significantly different from wild Pallid Sturgeon, supporting that hatchery-raised Pallid Sturgeon are transitioning effectively to wild diets. There is also a high degree of intraspecific variation in the bacterial and eukaryotic sequences amongst individual Pallid Sturgeon microbiomes, suggesting the Pallid Sturgeon may be omnivorous. This study demonstrated that genetic markers may be used to effectively describe the dietary requirements for wild Pallid Sturgeon and provides the first genetic evidence that Pallid Sturgeons are effectively transitioning from hatchery-raised environments to the wild.
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Affiliation(s)
- Sarah Gaughan
- College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA
| | - John A Kyndt
- College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA
| | - Justin D Haas
- Nebraska Game and Parks Commission, Lincoln, NE 68501, USA
| | | | | | - Kevin L Pope
- U.S. Geological Survey-Nebraska Cooperative Fish and Wildlife Research Unit, School of Natural Resources, Lincoln, NE 68583, USA
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8
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Ramírez C, Gutiérrez MS, Venegas L, Sapag C, Araya C, Caruffo M, López P, Reyes-Jara A, Toro M, González-Rocha G, Yáñez JM, Navarrete P. Microbiota composition and susceptibility to florfenicol and oxytetracycline of bacterial isolates from mussels (Mytilus spp.) reared on different years and distance from salmon farms. ENVIRONMENTAL RESEARCH 2022; 204:112068. [PMID: 34547250 DOI: 10.1016/j.envres.2021.112068] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/05/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Chilean aquaculture mainly produces salmonids and molluscs. Salmonid production has been questioned by its excessive use of antimicrobials. This study aimed to investigate the bacterial microbiota composition of Mytilus spp. cultivated near salmonid farms and to determine the minimum inhibitory concentration (MIC) to florfenicol and oxytetracycline of its culturable bacteria. Seven Mytilus farming sites classified according to their proximity to salmon farms as close (CSF) or distant (DSF) were sampled in two years. We analyzed Mytilus microbiota composition through culture-independent methods, and isolated culturable bacteria, and identified those isolates with MIC values ≥ 64 μg mL-1 to florfenicol or oxytetracycline. Results revealed that the alpha diversity was affected by sampling year but not by Mytilus farming site location or its interaction. Nevertheless, in 2018, we observed a significant negative correlation between the alpha diversity of Mytilus microbiota in each farm sites and the tonnes of florfenicol reported for each phytosanitary management area. We detected significant differences in beta diversity and relative abundance of specific bacterial taxa in Mytilus microbiota depending on the proximity to salmon farms and years. A higher proportion of isolates with MIC values ≥ 64 μg mL-1 to both antibiotics was detected in 2019 compared to 2018, but not significant differences were detected according to Mytilus farming site location. However, in 2019, isolates from CSF sites showed higher MIC values for both antibiotics than those from DSF. Bacterial genera corresponding to isolates with MIC values ≥ 64 μg mL-1 represented a low proportion of Mytilus microbiota identified with the culture-independent approach, reflecting the need to implement new methodologies in the study of antimicrobial resistance. These results suggest that the proximity to salmonid farms and sampling year influence the Mytilus microbiota and MIC values of their bacterial isolates; however, other environmental variables should be considered in further studies.
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Affiliation(s)
- Carolina Ramírez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - María Soledad Gutiérrez
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile; ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Chile
| | - Lucas Venegas
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile; Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile
| | | | - Carolina Araya
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Mario Caruffo
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile
| | - Paulina López
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile; Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile
| | - Angélica Reyes-Jara
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile
| | - Magaly Toro
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile; Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - José Manuel Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile; Núcleo Milenio INVASAL, Concepción, Chile
| | - Paola Navarrete
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile; ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Chile.
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Wang S, Li X, Zhang M, Jiang H, Wang R, Qian Y, Li M. Ammonia stress disrupts intestinal microbial community and amino acid metabolism of juvenile yellow catfish (Pelteobagrus fulvidraco). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 227:112932. [PMID: 34700169 DOI: 10.1016/j.ecoenv.2021.112932] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/01/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Ammonia has adverse effects on aquatic animals, which is also widely distributed in natural aquatic environments and intensive aquaculture systems. The intestine is a primary defensive line for aquatic animals, the accumulation of ammonia in the aquatic environment can cause irreversible damage to intestinal function. In this study, we investigated the effects of acute ammonia stress on the reaction characteristics of digestive function, amino acid metabolism, and the variation in the intestinal microbiota of juvenile yellow catfish (Pelteobagrus fulvidraco). Thus, the yellow catfish was placed in water with the addition of ammonia at 0 (control), 14.6, and 146 mg/L total ammonia nitrogen for 96-h. The present study observed that ammonia accumulated in the intestine and muscle (ammonia contents in the intestine and muscle increased) and induced the activities of protein digestive enzymes dysfunction (pepsin increased while trypsin decreased). Ammonia stress changed various amino acids composition (proline, arginine, lysine, histidine, phenylalanine, tyrosine, leucine, isoleucine, valine, alanine, glutamic acid, tyrosine, and aspartic acid contents were increased in muscle) and increased the activities of alanine aminotransferase and aspartate aminotransferase in muscle. Furthermore, through 16 S rRNA gene analysis, ammonia stress-induced reduction in diversity, richness, and evenness and structure of microbiota alteration in the intestine. At the phylum level, the abundance of Fusobacteria increased while Firmicutes and Actinobacteria decreased significantly. At the genus level, the abundance of beneficial microbiota Cetobacterium significantly increased after ammonia stress. In conclusion, activation of amino acid synthesis in muscle may be involved in ammonia detoxification after severe ammonia stress. The accumulation of ammonia can disrupt the intestinal digestive function and intestinal microbiota community. The Cetobacterium may be a new potential positive factor in the resistance of ammonia toxicity.
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Affiliation(s)
- Shidong Wang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Xue Li
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Muzi Zhang
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Haibo Jiang
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Rixin Wang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Yunxia Qian
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Ming Li
- School of Marine Sciences, Ningbo University, Ningbo 315211, China.
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10
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Kim PS, Shin NR, Lee JB, Kim MS, Whon TW, Hyun DW, Yun JH, Jung MJ, Kim JY, Bae JW. Host habitat is the major determinant of the gut microbiome of fish. MICROBIOME 2021; 9:166. [PMID: 34332628 PMCID: PMC8325807 DOI: 10.1186/s40168-021-01113-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/14/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Our understanding of the gut microbiota of animals is largely based on studies of mammals. To better understand the evolutionary basis of symbiotic relationships between animal hosts and indigenous microbes, it is necessary to investigate the gut microbiota of non-mammalian vertebrate species. In particular, fish have the highest species diversity among groups of vertebrates, with approximately 33,000 species. In this study, we comprehensively characterized gut bacterial communities in fish. RESULTS We analyzed 227 individual fish representing 14 orders, 42 families, 79 genera, and 85 species. The fish gut microbiota was dominated by Proteobacteria (51.7%) and Firmicutes (13.5%), different from the dominant taxa reported in terrestrial vertebrates (Firmicutes and Bacteroidetes). The gut microbial community in fish was more strongly shaped by host habitat than by host taxonomy or trophic level. Using a machine learning approach trained on the microbial community composition or predicted functional profiles, we found that the host habitat exhibited the highest classification accuracy. Principal coordinate analysis revealed that the gut bacterial community of fish differs significantly from those of other vertebrate classes (reptiles, birds, and mammals). CONCLUSIONS Collectively, these data provide a reference for future studies of the gut microbiome of aquatic animals as well as insights into the relationship between fish and their gut bacteria, including the key role of host habitat and the distinct compositions in comparison with those of mammals, reptiles, and birds. Video Abstract.
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Affiliation(s)
- Pil Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Na-Ri Shin
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Jeollabuk-do 56212 Republic of Korea
| | - Jae-Bong Lee
- Distant-water Fisheries Resources Division, National Institute of Fisheries Science, Gijang-eup, Busan, 46083 Republic of Korea
| | - Min-Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Tae Woong Whon
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Dong-Wook Hyun
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Ji-Hyun Yun
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Mi-Ja Jung
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Joon Yong Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Jin-Woo Bae
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
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11
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Haro-Moreno JM, Coutinho FH, Zaragoza-Solas A, Picazo A, Almagro-Moreno S, López-Pérez M. Dysbiosis in marine aquaculture revealed through microbiome analysis: reverse ecology for environmental sustainability. FEMS Microbiol Ecol 2021; 96:6027483. [PMID: 33289802 DOI: 10.1093/femsec/fiaa218] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/11/2020] [Indexed: 01/18/2023] Open
Abstract
The increasing demand for products for human consumption is leading to the fast-growing expansion of numerous food sectors such as marine aquaculture (mariculture). However, excessive input of nutrients and pollutants modifies marine ecosystems. Here, we applied a metagenomic approach to investigate these perturbations in samples from marine farms of gilthead seabream cultures. Results revealed dysbiosis and functional imbalance within the net cage with a unique structure, with little interference with samples from the fish microbiota or those collected far away from the coast. Remarkably, below the cage the prokaryotic community was highly similar to the marine microbiome of photic offshore samples. We recovered 48 novel metagenome-assembled genomes. Metagenomic recruitment revealed a significant change in the microbial community which was dominated by several Proteobacteria orders (Sphingomonadales, Pseudomonadales, Caudobacterales and Rhizobiales). Genomic potential for bioremediation processes, including nitrate removal through aerobic denitrification, and degradation of aromatic compounds and other toxic products were enriched in these microbes. The detrimental side effects were the increased number of antimicrobial resistance genes and the presence of potentially emergent pathogens. Knowledge of this metabolic diversity and the microbes involved in ecological balance recovery can be used to reduce the environmental impact of these practices.
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Affiliation(s)
- Jose M Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan 03550, Alicante, Spain
| | - Felipe Hernandes Coutinho
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan 03550, Alicante, Spain
| | - Asier Zaragoza-Solas
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan 03550, Alicante, Spain
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Burjassot, E-46100 Valencia, Spain
| | - Salvador Almagro-Moreno
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL, USA
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan 03550, Alicante, Spain
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12
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Characterization of a Novel Variant of the Quinolone-Resistance Gene qnrB ( qnrB89) Carried by a Multi-Drug Resistant Citrobacter gillenii Strain Isolated from Farmed Salmon in Chile. Antibiotics (Basel) 2021; 10:antibiotics10030236. [PMID: 33652626 PMCID: PMC7996913 DOI: 10.3390/antibiotics10030236] [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: 01/16/2021] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 11/17/2022] Open
Abstract
The main objective of this study was to characterize using whole-genome sequencing analysis, a new variant of the qnrB gene (qnrB89) carried by a fluoroquinolone-susceptible bacterium isolated from mucus of farmed Salmo salar fingerling in Chile. Citrobacter gillenii FP75 was identified by using biochemical tests and 16S ribosomal gene analysis. Nucleotide and amino acid sequences of the qnrB89 gene exhibited an identity to qnrB of 81.24% and 91.59%, respectively. The genetic environment of qnrB89 was characterized by the upstream location of a sequence encoding for a protein containing a heavy metal-binding domain and a gene encoding for a N-acetylmuramoyl-L-alanine amidase protein, whereas downstream to qnrB89 gene were detected the csp and cspG genes, encoding cold-shock proteins. The qnrB89 gene was located on a large chromosomal contig of the FP75 genome and was not associated with the 10-kb plasmid and class 1 integron harbored by the FP75 strain. This study reports for the first time the carriage of a qnrB gene by the C. gillenii species, and its detection in a bacterial strain isolated from farmed salmon in Chile.
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13
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Xu C, Zhong XQ, Li XF, Shi HJ, Liu WB. Regulation of growth, intestinal microflora composition and expression of immune-related genes by dietary supplementation of Streptococcus faecalis in blunt snout bream (Megalobrama amblycephala). FISH & SHELLFISH IMMUNOLOGY 2020; 105:195-202. [PMID: 32652298 DOI: 10.1016/j.fsi.2020.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
A 10-week feeding trial was performed to investigate the effects of Streptococcus faecalis on the growth, intestinal microflora composition and expression of immune-related genes of blunt snout bream (Megalobrama amblycephala). Fish (46.32 ± 0.09 g) were fed four experimental diets containing 0 cfu/g (SF0, control), 1 × 105 cfu/g (SF1), 1 × 106 cfu/g (SF2) and 1 × 107 cfu/g (SF3) of S. faecalis, respectively. Results showed that daily growth index (DGI), feed efficiency ratio (FER), plasma glucose level, plasma contents of total protein and albumin as well as intestinal serous layer (SL), muscular layer (ML), submucous layer (SML), villi thickness (VT) and lamina propria (LP) were all no significant difference among all the treatments, whereas their (except plasma albumin content and intestinal ML) relatively high values were found in the SF2 group. Meanwhile, the intake of the SF2 diets significantly increased plasma globulin content and intestinal digestive enzymes activities, the opposite was true for the activities of plasma aspartate aminotransferase (AST) and alanine transaminase (ALT). In addition, the analysis of the intestinal microbiota showed that fish fed the SF2 diet have the highest values of intestinal alpha diversity and intestinal abundances of Actinobacteria, Chlamydiae, Firmicutes, Planctomycetes, Verrucomicrobia, Clostridium and Synechococcus, while the opposite was true for intestinal abundances of Acinetobacter, Anoxybacillus, Flavobacterium, Planctomyces, Plesiomonas, Pseudomonas, Staphylococcus and Clostridium perfringens. At the molecular level, the expression levels of tumour necrosis factor α (TNF α), interleukin 1β (IL 1β) and heat shock proteins 7 (HSP 70) in head kidney and spleen were all decreased significantly with the increasing S. faecalis levels up to 1 × 106 cfu/g, and then they were increased with further increasing S. faecalis levels. Overall, dietary supplementation of S. faecalis at 1 × 106 cfu/g could improve the intestinal health and innate immunity of blunt snout bream.
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Affiliation(s)
- Chao Xu
- College of Marine Sciences of South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Xiao-Qun Zhong
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Xiang-Fei Li
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China.
| | - Hua-Juan Shi
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Wen-Bin Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
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14
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Hossain TJ, Chowdhury SI, Mozumder HA, Chowdhury MNA, Ali F, Rahman N, Dey S. Hydrolytic Exoenzymes Produced by Bacteria Isolated and Identified From the Gastrointestinal Tract of Bombay Duck. Front Microbiol 2020; 11:2097. [PMID: 32983064 PMCID: PMC7479992 DOI: 10.3389/fmicb.2020.02097] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022] Open
Abstract
Bacteria producing hydrolytic exoenzymes are of great importance considering their contribution to the host metabolism as well as for their various applications in industrial bioprocesses. In this work hydrolytic capacity of bacteria isolated from the gastrointestinal tract of Bombay duck (Harpadon nehereus) was analyzed and the enzyme-producing bacteria were genetically characterized. A total of twenty gut-associated bacteria, classified into seventeen different species, were isolated and screened for the production of protease, lipase, pectinase, cellulase and amylase enzymes. It was found that thirteen of the isolates could produce at least one of these hydrolytic enzymes among which protease was the most common enzyme detected in ten isolates; lipase in nine, pectinase in four, and cellulase and amylase in one isolate each. This enzymatic array strongly correlated to the previously reported eating behavior of Bombay duck. 16S rRNA gene sequence-based taxonomic classification of the enzyme-producing isolates revealed that the thirteen isolates were grouped into three different classes of bacteria consisting of eight different genera. Staphylococcus, representing ∼46% of the isolates, was the most dominant genus. Measurement of enzyme-production via agar diffusion technique revealed that one of the isolates which belonged to the genus Exiguobacterium, secreted the highest amount of lipolytic and pectinolytic enzymes, whereas a Staphylococcus species produced highest proteolytic activity. The Exiguobacterium sp. expressing a maximum of four hydrolases, appeared to be the most promising isolate of all.
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Affiliation(s)
- Tanim J. Hossain
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
| | - Sumaiya I. Chowdhury
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
| | - Halima A. Mozumder
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
| | - Mohammad N. A. Chowdhury
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
| | - Ferdausi Ali
- Department of Microbiology, University of Chittagong, Chattogram, Bangladesh
| | - Nabila Rahman
- Department of Biology, Chittagong Sunshine College, Chattogram, Bangladesh
| | - Sujan Dey
- Department of Microbiology, University of Chittagong, Chattogram, Bangladesh
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15
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Jia Z, Bai W, Li X, Fang T, Li C. Assessing the growth of Listeria monocytogenes in salmon with or without the competition of background microflora -- A one-step kinetic analysis. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Isolation and Partial Characterization of Lactic Acid Bacteria from the Gut Microbiota of Marine Fishes for Potential Application as Probiotics in Aquaculture. Probiotics Antimicrob Proteins 2020; 11:569-579. [PMID: 29959637 DOI: 10.1007/s12602-018-9439-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
With the increase of antimicrobial resistances due to the widespread use of antibiotics, the search of new probiotics to control aquaculture diseases has a growing public interest. The aim of this study was to isolate bacteria with antimicrobial effect from the gut of marine healthy fishes and select lactic acid bacteria (LAB) as potential probiotics, being strains considered as generally regarded as safe (GRAS) by the European Food Safety Agency (EFSA). Of a total of 45 Gram-positive strains with antimicrobial activity found in a screening of the gut microbiota of 13 marine fishes, nine were identified as LAB by 16S rRNA gene sequencing. LAB strains (five Lactococcus lactis subsp. lactis, two Enterococcus spp., one Lactobacillus plantarum, and one Leuconostoc mesenteroides subsp. mesenteroides) also showed a broad-spectrum antibacterial activity against aquaculture pathogens such as Vibrio harveyi, V. splendidus, and Photobacterium damselae and survived in experimental gastrointestinal conditions when grown in culture media modified with different values of pH and bile salts. These results showed the potential of LAB obtained from the indigenous microbiota of wild marine fishes for use as probiotics in aquaculture.
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17
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Qiao G, Xu C, Sun Q, Xu DH, Zhang M, Chen P, Li Q. Effects of dietary poly-β-hydroxybutyrate supplementation on the growth, immune response and intestinal microbiota of soiny mullet (Liza haematocheila). FISH & SHELLFISH IMMUNOLOGY 2019; 91:251-263. [PMID: 31121290 DOI: 10.1016/j.fsi.2019.05.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/10/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
Soiny mullet (Liza haematocheila) is an important economic fish species in China, but stress and diseases have seriously restricted its culture. There are no effective methods including vaccines to prevent or control these diseases. Alternative methods should be employed, such as using novel immunostimulant poly-β-hydroxybutyrate (PHB). The present study aimed to evaluate effects of dietary PHB supplementation on the growth, antioxidant enzymes activity, immune-related genes expression and intestinal microbiota in soiny mullet. The fish was fed for 30 or 60 days with six diets at different PHB supplementation of 0, 0.5, 1, 2, 4 and 8%, named as groups P0, P0.5, P1, P2, P4 and P8. The results showed that the weight gain and specific growth rate of fish in P2 and P0.5 groups were significantly higher than those in control P0 group at 30 and 60 days, respectively (P < 0.05). The antioxidant enzymes activity of catalase and superoxide dismutase in serum were significantly increased in P0.5/P1/P2 groups after 30 days. The transcriptional levels of penicillin-binding protein A and interleukin-8 analyzed by qRT-PCR were significantly upregulated in P2 and P4 groups compared to those in P0/P0.5/P1/P8 groups at 30 days. The transcriptional level of major histocompatibility complex class II in P2 group was significantly upregulated, and aldehyde oxidase downregulated compared to P0 group. Intestinal microbiota analysis by Illumina high-throughput sequencing showed that the microbiota diversity was not changed significantly, but the microbiota structure shifted significantly post PHB treatment. At the phyla level, Firmicutes and Proteobacteria were predominant in both P0 and P2 groups. At the genus level, the relative abundance of Bacillus spp. in P2 group increased significantly, and abundance of Achromobacter spp. decreased significantly. KEGG pathway analysis by PICRUSt showed that oral administration PHB significantly upregulated abundances of genes responsible for 10 pathways and downregulated genes involved in 17 pathways. In conclusion, soiny mullet fed with 2% PHB supplemental diets for 30 days showed better growth performance, higher antioxidant enzymes activity and immune-related genes expression. Their regulation of growth and immunity might be related with the intestinal microbiota change post PHB supplementation. It will provide very useful basic information to study the regulation mechanism of PHB in aquatic animals, and provide good green method to prevent disease in soiny mullet.
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Affiliation(s)
- Guo Qiao
- Department of Marine Technology, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| | - Chen Xu
- Department of Marine Technology, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| | - Qirui Sun
- Department of Marine Technology, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| | - De-Hai Xu
- U.S. Department of Agriculture, Agricultural Research Service, Aquatic Animal Health Research Unit, 990 Wire Road, Auburn, AL, 36832, USA
| | - Mingming Zhang
- Department of Marine Technology, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| | - Peng Chen
- Department of Marine Technology, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| | - Qiang Li
- Department of Marine Technology, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China.
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18
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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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19
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Rojas R, Miranda CD, Romero J, Barja JL, Dubert J. Isolation and Pathogenic Characterization of Vibrio bivalvicida Associated With a Massive Larval Mortality Event in a Commercial Hatchery of Scallop Argopecten purpuratus in Chile. Front Microbiol 2019; 10:855. [PMID: 31133994 PMCID: PMC6524457 DOI: 10.3389/fmicb.2019.00855] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/03/2019] [Indexed: 12/16/2022] Open
Abstract
The VPAP30 strain was isolated as the highly predominant bacteria from an episode of massive larval mortality occurring in a commercial culture of the Chilean scallop Argopecten purpuratus. The main aims of this study were, to characterize and identify the pathogenic strain using biochemical and molecular methods, to demonstrate its pathogenic activity on scallop larvae, to characterize its pathogenic properties and to describe the chronology of the pathology. The pathogenic strain was identified as Vibrio bivalvicida based on its phenotypic properties, the multilocus sequence analysis (MLSA) of eight housekeeping genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, and topA) and different in silico genome-to-genome comparisons. When triplicate cultures of healthy 10 days old scallop larvae were challenged with 1 × 105 colony forming units (CFU) mL-1 of the VPAP30 strain, percentages of larval survival of 78.9 ± 3.3%, 34.3 ± 4.9%, and 0% were observed at 12, 2,4 and 36 h, respectively, whereas uninfected larval cultures showed survival rates of 97.4 ± 1.2% after of 48 h. Clinical symptoms exhibited by the scallop larvae infected with the VPAP30 strain include the accumulation of bacteria around the scallop larvae, velum disruption and necrosis of digestive gland. The 50% lethal dose (LD50) of VPAP30 strain at 24 and 48 h was 1.3 × 104 and 1.2 × 103 CFU mL-1, respectively. The invasive pathogenic activity of the VPAP30 strain was investigated with staining of the bacterial pathogen with 5-DTAF and analyzing bacterial invasion using epifluorescence, and a complete bacterial dissemination inside the larvae at 24 h post-infection was observed. When scallop larvae were inoculated with cell-free extracellular products (ECPs) of VPAP30, the larval survival rate was 59.5 ± 1.7%, significantly (P < 0.001) lower than the control group (97.4 ± 1.2%) whereas larvae treated with heat-treated ECPs exhibited a survival rate of 61.6 ± 1.8% after 48 h of exposure. V. bivalvicida VPAP30 exhibits high pathogenic activity on scallop larvae, mediated both by bacterial invasion and the production of toxigenic heat-stable compounds. This report constitutes the first isolation of V. bivalvicida out of Europe and extends the host range of this species, having demonstrated its pathogenic activity on the Chilean scallop larvae (A. purpuratus). These results supporting the pathogenic potential of V. bivalvicida to kill the larvae of a broad range of bivalve species reared in hatcheries located in the Atlantic and the Pacific coasts.
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Affiliation(s)
- Rodrigo Rojas
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo, Chile.,Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Centro AquaPacífico, Coquimbo, Chile
| | - Claudio D Miranda
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo, Chile.,Centro AquaPacífico, Coquimbo, Chile
| | - Jaime Romero
- Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Centro AquaPacífico, Coquimbo, Chile
| | - Juan L Barja
- Departamento de Microbiología y Parasitología, CIBUS - Facultad de Biología, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Javier Dubert
- Departamento de Microbiología y Parasitología, CIBUS - Facultad de Biología, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
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20
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Li X, Zhu Y, Ringø E, Wang X, Gong J, Yang D. Intestinal microbiome and its potential functions in bighead carp ( Aristichthys nobilis) under different feeding strategies. PeerJ 2018; 6:e6000. [PMID: 30533302 PMCID: PMC6283038 DOI: 10.7717/peerj.6000] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/25/2018] [Indexed: 01/06/2023] Open
Abstract
Bighead carps (Aristichthys nobilis) were divided into four groups with different feeding strategies: group A, nature live food only (fertiliser only, 200 g urea + 160 g ethylamine phosphate + 250 g Huangjintai bio-fertiliser); group B, nature live food + 1/2 formulated feed; group C, nature live food + formulated feed; and group D, formulated feed only. The intestinal microbiomes of the different groups were compared through the Illumina MiSeq sequencing of the bacterial 16S rRNA gene. The specific growth rate (SGR), survival and blood biochemical factors of the fish were also investigated. Results showed that feeding treatment influenced the intestinal communities in the fish. In specific, more bacterial phyla dominated in groups A and B (phyla Bacteroidetes, Fusobacteria, Firmicutes and Proteobacteria in group A, phyla Proteobacteria and Fusobacteria in group B) than in groups C and D (phylum Proteobacteria). The diversity was also lower in groups C and D than in groups A and B. Unweighted pair-group method analysis revealed a clear difference in intestinal microbiota among the different feeding treatments. No difference in survival rate was found among the treatment groups, but the SGR was significantly higher (P < 0.01) in groups B, C and D than in group A. Functional analysis showed that the intestinal bacteria correlated with fish glucose metabolism in group A but with lipid metabolic activity in groups B, C and D. In summary, the intestinal microbiomes and their potential functions vary in bighead carp under different feeding treatments. This study provides new insights into the gut microbiomes of filter-feeding and formulated diet-fed fish.
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Affiliation(s)
- Xuemei Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Areas of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Yongjiu Zhu
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Areas of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Einar Ringø
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Xuge Wang
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Areas of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Jinling Gong
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Areas of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Deguo Yang
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Areas of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
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21
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Higuera-Llantén S, Vásquez-Ponce F, Barrientos-Espinoza B, Mardones FO, Marshall SH, Olivares-Pacheco J. Extended antibiotic treatment in salmon farms select multiresistant gut bacteria with a high prevalence of antibiotic resistance genes. PLoS One 2018; 13:e0203641. [PMID: 30204782 PMCID: PMC6133359 DOI: 10.1371/journal.pone.0203641] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/26/2018] [Indexed: 01/31/2023] Open
Abstract
The high use of antibiotics for the treatment of bacterial diseases is one of the main problems in the mass production of animal protein. Salmon farming in Chile is a clear example of the above statement, where more than 5,500 tonnes of antibiotics have been used over the last 10 years. This has caused a great impact both at the production level and on the environment; however, there are still few works in relation to it. In order to demonstrate the impact of the high use of antibiotics on fish gut microbiota, we have selected four salmon farms presenting a similar amount of fish of the Atlantic salmon species (Salmo salar), ranging from 4,500 to 6,000 tonnes. All of these farms used treatments with high doses of antibiotics. Thus, 15 healthy fish were selected and euthanised in order to isolate the bacteria resistant to the antibiotics oxytetracycline and florfenicol from the gut microbiota. In total, 47 bacterial isolates resistant to florfenicol and 44 resistant to oxytetracycline were isolated, among which isolates with Minimum Inhibitory Concentrations (MIC) exceeding 2048 μg/mL for florfenicol and 1024 μg/mL for oxytetracycline were found. In addition, another six different antibiotics were tested in order to demonstrate the multiresistance phenomenon. In this regard, six isolates of 91 showed elevated resistance values for the eight tested antibiotics, including florfenicol and oxytetracycline, were found. These bacteria were called “super-resistant” bacteria. This phenotypic resistance was verified at a genotypic level since most isolates showed antibiotic resistance genes (ARGs) to florfenicol and oxytetracycline. Specifically, 77% of antibiotic resistant bacteria showed at least one gene resistant to florfenicol and 89% showed at least one gene resistant to oxytetracycline. In the present study, it was demonstrated that the high use of the antibiotics florfenicol and oxytetracycline has, as a consequence, the selection of multiresistant bacteria in the gut microbiota of farmed fish of the Salmo salar species at the seawater stage. Also, the phenotypic resistance of these bacteria can be correlated with the presence of antibiotic resistance genes.
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MESH Headings
- Animals
- Anti-Bacterial Agents/pharmacology
- Aquaculture
- Bacteria/drug effects
- Bacteria/genetics
- Bacteria/isolation & purification
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Gastrointestinal Microbiome/drug effects
- Intestines/microbiology
- Microbial Sensitivity Tests
- Oxytetracycline/pharmacology
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Salmo salar
- Thiamphenicol/analogs & derivatives
- Thiamphenicol/pharmacology
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Affiliation(s)
- Sebastián Higuera-Llantén
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, CP, Chile
| | - Felipe Vásquez-Ponce
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, CP, Chile
| | - Beatriz Barrientos-Espinoza
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, CP, Chile
| | - Fernando O. Mardones
- Escuela de Medicina Veterinaria, Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Republica 252, CP, Santiago, Chile
| | - Sergio H. Marshall
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, CP, Chile
| | - Jorge Olivares-Pacheco
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, CP, Chile
- Millenium Nucleus on Interdisciplinary approach to Antimicrobial Resistance, Lo Barnechea, Santiago, CP, Chile
- * E-mail:
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22
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Catalán N, Villasante A, Wacyk J, Ramírez C, Romero J. Fermented Soybean Meal Increases Lactic Acid Bacteria in Gut Microbiota of Atlantic Salmon (Salmo salar). Probiotics Antimicrob Proteins 2018; 10:566-576. [PMID: 29274013 DOI: 10.1007/s12602-017-9366-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The main goal of the present study was to address the effect of feeding fermented soybean meal-based diet to Atlantic salmon on gut microbiota. Further, expression of genes of interest, including cathelicidin antimicrobial peptide (cath), mucin 2 (muc2), aquaporin (aqp8ab), and proliferating cell nuclear antigen (pcna), in proximal intestine of fish fed either experimental diet was analyzed. Three experimental diets, including a control fishmeal (30% FM), soybean meal (30% SBM), or fermented soybean meal diet (30% FSBM) were randomly assigned to triplicate tanks during a 50-day trial. The PCR-TTGE showed microbiota composition was influenced by experimental diets. Bands corresponding to genus Lactobacillus and Pediococcus were characteristic in fish fed the FSBM-based diet. On the other hand, bands corresponding to Isoptericola, Cellulomonas, and Clostridium sensu stricto were only observed in fish FM-based diet, while Acinetobacter and Altererythrobacter were detected in fish fed SBM-based diet. The expression of muc2 and aqp8ab were significantly greater in fish fed the FSBM-based diet compared with the control group. Our results suggest feeding FSBM to Atlantic salmon may (1) boost health and growth physiology in fish by promoting intestinal lactic acid bacteria growth, having a prebiotic-like effect, (2) promote proximal intestine health by increasing mucin production, and (3) boost intestinal trans-cellular uptake of water. Further research to better understands the effects of bioactive compounds derived from the fermentation process of plant feedstuff on gut microbiota and the effects on health and growth in fish is required.
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Affiliation(s)
- Natalia Catalán
- Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Alejandro Villasante
- Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Jurij Wacyk
- Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Carolina Ramírez
- Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Jaime Romero
- Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile.
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23
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Hornick KM, Buschmann AH. Insights into the diversity and metabolic function of bacterial communities in sediments from Chilean salmon aquaculture sites. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1317-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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24
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Villasante A, Ramirez C, Catalán N, Romero J. First Report of Swim Bladder-Associated Microbiota in Rainbow Trout (Oncorhynchus mykiss). Microbes Environ 2017; 32:386-389. [PMID: 29033407 PMCID: PMC5745024 DOI: 10.1264/jsme2.me17071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The aim of the present study was to identify major bacteria associated with the swim bladder in the rainbow trout, Oncorhynchus mykiss. We extracted DNA from the swim bladder and gut contents in order to perform a temporal temperature gradient gel electrophoresis (TTGE) analysis of 16S rRNA amplicons for bacterial identification to further compare both profiles. Arthrobacter and Cellulosimicrobium were the major genera observed in the swim bladder in fish, but were not present in fish gut contents; Mycoplasma were instead observed in these samples. Further research to investigate the possible symbiotic roles of the swim bladder-associated microbiota in salmonids is needed.
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Affiliation(s)
- Alejandro Villasante
- Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile Avda
| | - Carolina Ramirez
- Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile Avda
| | - Natalia Catalán
- Laboratorio de Biotecnología, Unidad de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile Avda
| | - Jaime Romero
- Laboratorio de Biotecnología, Unidad de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile Avda
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25
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Ceppa F, Faccenda F, De Filippo C, Albanese D, Pindo M, Martelli R, Marconi P, Lunelli F, Fava F, Parisi G. Influence of essential oils in diet and life-stage on gut microbiota and fillet quality of rainbow trout (Oncorhynchus mykiss). Int J Food Sci Nutr 2017; 69:318-333. [PMID: 28859525 DOI: 10.1080/09637486.2017.1370699] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Developing fish farming to meet the demands of food security and sustainability in the 21st century will require new farming systems and improved feeds. Diet and microbe interactions in the gut is an important variable with the potential to make a significant impact on future fish farming diets and production systems. It was monitored the gut microbiota of farmed rainbow trout using 16S rRNA profiling over 51 weeks during standard rearing conditions and feeding diet with supplementation of an essential oils (MixOil) mixture from plants (at a concentration in diet of 200 mg/kg). Gut microbiota 16S rRNA profiling indicated that the fish gut was dominated by Actinobacteria, Proteobacteria, Bacteroidetes and Firmicutes. Although the dietary supplementation with MixOil had no impact on either the composition or architecture of gut microbiota, significant changes in alpha and beta diversity and relative abundance of groups of gut bacteria were evident during growth stages on test feeds, especially upon prolonged growth on finishing feed. Fish fillet quality to guarantee palatability and safety for human consumption was also evaluated. Significant differences within the gut microbiota of juvenile and adult trout under the same rearing conditions were observed, The addition of essential oil blend affected some physicochemical characteristics of trout fillets, including their resistance to oxidative damage and their weight loss (as liquid loss and water holding capacity) during the first period of storage, that are two important parameters related to product shelf life and susceptibility to spoilage. The results highlighted the need for further studies concern dietary microbiome modulation at different life stages and its influence on animal health, growth performance and final product quality.
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Affiliation(s)
- Florencia Ceppa
- a Department of Food Quality and Nutrition, Nutrition and Nutrigenomics Unit, Research and Innovation Center , Fondazione Edmund Mach , Trento , Italy
| | - Filippo Faccenda
- b Technology Transfer Centre, Experiment and Technological Services Department , Fondazione Edmund Mach , Trento , Italy
| | - Carlotta De Filippo
- c Institute of Biometeorology , National Research Council (IBIMET-CNR) , Firenze , Italy
| | - Davide Albanese
- d Computational Biology Department, Research and Innovation Center , Fondazione Edmund Mach , Trento , Italy
| | - Massimo Pindo
- e Genomics Platform, Genomics and Biology of Fruit Crop Department, Research and Innovation Center , Fondazione Edmund Mach , Trento , Italy
| | - Roberta Martelli
- f Department of Agri-Food Production and Environmental Sciences, Section of Animal Sciences , University of Firenze , Firenze , Italy
| | - Paola Marconi
- g Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri , Firenze , Italy
| | - Fernando Lunelli
- b Technology Transfer Centre, Experiment and Technological Services Department , Fondazione Edmund Mach , Trento , Italy
| | - Francesca Fava
- a Department of Food Quality and Nutrition, Nutrition and Nutrigenomics Unit, Research and Innovation Center , Fondazione Edmund Mach , Trento , Italy
| | - Giuliana Parisi
- f Department of Agri-Food Production and Environmental Sciences, Section of Animal Sciences , University of Firenze , Firenze , Italy
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26
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Lobos O, Barrera A, Padilla C. Microorganisms of the Intestinal Microbiota of Oncorhynchus Mykiss Produce Antagonistic Substances Against Bacteria Contaminating Food and Causing Disease in Humans. Ital J Food Saf 2017; 6:6240. [PMID: 28713788 PMCID: PMC5505081 DOI: 10.4081/ijfs.2017.6240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 05/31/2017] [Accepted: 05/31/2017] [Indexed: 11/23/2022] Open
Abstract
The objective was to analyse the antibacterial ability of members of the intestinal microbiota of Oncorhynchus mykiss specimens on several bacterial target strains that contaminate food and cause disease in humans. Bacterial colonies from an intestinal portion of the 20 specimens of O. mykiss were obtained in different culture media. Several of the colonies showed antibacterial action on different target strains. The bacterial species with the highest antagonistic capacity were Hafnia alvei and Lactococcus lactis and the more susceptible target strains were Aeromonas hydrophila, Listeria monocytogenes and Escherichia coli. Moreover, it was shown that all the antibacterial substances were susceptible to the action of various proteolytic enzymes. The detection of substances of a proteinaceous nature, possibly bacteriocins produced by bacteria of the intestinal microbiota of O. mykiss, allows further study of these products to establish biotechnological developments in the area of health protection and food biopreservation.
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Affiliation(s)
- Olga Lobos
- Department of Microbiology, University of Talca, Talca, Chile
| | - Andrea Barrera
- Department of Microbiology, University of Talca, Talca, Chile
| | - Carlos Padilla
- Department of Microbiology, University of Talca, Talca, Chile
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27
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Gonçalves AT, Gallardo-Escárate C. Microbiome dynamic modulation through functional diets based on pre- and probiotics (mannan-oligosaccharides and Saccharomyces cerevisiae) in juvenile rainbow trout (Oncorhynchus mykiss). J Appl Microbiol 2017; 122:1333-1347. [PMID: 28256031 DOI: 10.1111/jam.13437] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/06/2017] [Accepted: 02/25/2017] [Indexed: 12/26/2022]
Abstract
AIMS This study used high-throughput sequencing to evaluate the intestinal microbiome dynamics in rainbow trout (Oncorhynchus mykiss) fed commercial diets supplemented with either pre- or probiotics (0·6% mannan-oligosaccharides and 0·5% Saccharomyces cerevisiae respectively) or the mixture of both. METHODS AND RESULTS A total of 57 fish whole intestinal mucosa and contents bacterial communities were characterized by high-throughput sequencing and analysis of the V3-V4 region of the 16S rRNA gene, as well as the relationship between plasma biochemical health indicators and microbiome diversity. This was performed at 7, 14 and 30 days after start feeding functional diets, and microbiome diversity increased when fish fed functional diets after 7 days and it was positively correlated with plasma cholesterol levels. Dominant phyla were, in descending order, Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria, Bacteroidetes and Fusobacteria. However, functional diets reduced the abundance of Gammaproteobacteria to favour abundances of organisms from Firmicutes and Fusobacteria, two phyla with members that confer beneficial effects. A dynamic shift of the microbiome composition was observed with changes after 7 days of feeding and the modulation by functional diets tend to cluster the corresponding groups apart from CTRL group. The core microbiome showed an overall stability with functional diets, except genus such as Escherichia-Shigella that suffered severe reductions on their abundances when feeding any of the functional diets. CONCLUSIONS Functional diets based on pre- or probiotics dynamically modulate intestinal microbiota of juvenile trout engaging taxonomical abundance shifts that might impact fish physiological performance. SIGNIFICANCE AND IMPACT OF THE STUDY This study shows for the first time the microbiome modulation dynamics by functional diets based on mannan-oligosaccharides and S. cerevisiae and their synergy using culture independent high-throughput sequencing technology, revealing the complexity behind the dietary modulation with functional feeds in aquatic organisms.
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Affiliation(s)
- A T Gonçalves
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
| | - C Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
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28
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Dehler CE, Secombes CJ, Martin SA. Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr ( Salmo salar L.). AQUACULTURE (AMSTERDAM, NETHERLANDS) 2017; 467:149-157. [PMID: 28111483 PMCID: PMC5142738 DOI: 10.1016/j.aquaculture.2016.07.017] [Citation(s) in RCA: 192] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 07/07/2016] [Accepted: 07/14/2016] [Indexed: 05/11/2023]
Abstract
Gut microbes are key players in host immune system priming, protection and development, as well as providing nutrients to the host that would be otherwise unavailable. Due to this importance, studies investigating the link between host and microbe are being initiated in farmed fish. The establishment, maintenance and subsequent changes of the intestinal microbiota are central to define fish physiology and nutrition in the future. In fish, unlike mammals, acquiring intestinal microbes is believed to occur around the time of first feeding mainly from the water surrounding them and their microbial composition over time is shaped therefore by their habitat. Here we compare the distal intestine microbiota of Atlantic salmon parr reared in a recirculating laboratory aquarium with that of age matched parr maintained in cage culture in an open freshwater loch environment of a commercial fish farm to establish the microbial profiles in the gut at the freshwater stage and investigate if there is a stable subset of bacteria present regardless of habitat type. We used deep sequencing across two variable regions of the 16S rRNA gene, with a mean read depth of 180,144 ± 12,096 raw sequences per sample. All individual fish used in this study had a minimum of 30,000 quality controlled reads, corresponding to an average of 342 ± 19 Operational Taxonomic Units (OTUs) per sample, which predominantly mapped to the phyla Firmicutes, Proteobacteria, and Tenericutes. The results indicate that species richness is comparable between both treatment groups, however, significant differences were found in the compositions of the gut microbiota between the rearing groups. Furthermore, a core microbiota of 19 OTUs was identified, shared by all samples regardless of treatment group, mainly consisting of members of the phyla Proteobacteria, Bacteroidetes and Firmicutes. Core microbiotas of the individual rearing groups were determined (aquarium fish: 19 + 4 (total 23) OTUs, loch fish: 19 + 13 (total 32) OTUs), indicating that microbe acquisition or loss is occurring differently in the two habitats, but also that selective forces are acting within the host, offering niches to specific bacterial taxa. The new information gathered in this study by the Illumina MiSeq approach will be useful to understand and define the gut microbiota of healthy Atlantic salmon in freshwater and expand on previous studies using DGGE, TGGE and T-RFPL. Monitoring deviations from these profiles, especially the core microbes which are present regardless of habitat type, might be used in the future as early indicator for intestinal health issues caused by sub optimal feed or infectious diseases in the farm setting. STATEMENT OF RELEVANCE The Microbiome is central to gut health, local immune function and nutrient up take. We have used deep sequencing approach to show differences in rearing conditions of Atlantic salmon. This work is of interest to aquaculture nutritionists.
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Affiliation(s)
| | | | - Samuel A.M. Martin
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen AB24 2TZ, UK
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29
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Muziasari WI, Pitkänen LK, Sørum H, Stedtfeld RD, Tiedje JM, Virta M. The Resistome of Farmed Fish Feces Contributes to the Enrichment of Antibiotic Resistance Genes in Sediments below Baltic Sea Fish Farms. Front Microbiol 2017; 7:2137. [PMID: 28111573 PMCID: PMC5216021 DOI: 10.3389/fmicb.2016.02137] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/19/2016] [Indexed: 12/12/2022] Open
Abstract
Our previous studies showed that particular antibiotic resistance genes (ARGs) were enriched locally in sediments below fish farms in the Northern Baltic Sea, Finland, even when the selection pressure from antibiotics was negligible. We assumed that a constant influx of farmed fish feces could be the plausible source of the ARGs enriched in the farm sediments. In the present study, we analyzed the composition of the antibiotic resistome from the intestinal contents of 20 fish from the Baltic Sea farms. We used a high-throughput method, WaferGen qPCR array with 364 primer sets to detect and quantify ARGs, mobile genetic elements (MGE), and the 16S rRNA gene. Despite a considerably wide selection of qPCR primer sets, only 28 genes were detected in the intestinal contents. The detected genes were ARGs encoding resistance to sulfonamide (sul1), trimethoprim (dfrA1), tetracycline [tet(32), tetM, tetO, tetW], aminoglycoside (aadA1, aadA2), chloramphenicol (catA1), and efflux-pumps resistance genes (emrB, matA, mefA, msrA). The detected genes also included class 1 integron-associated genes (intI1, qacEΔ1) and transposases (tnpA). Importantly, most of the detected genes were the same genes enriched in the farm sediments. This preliminary study suggests that feces from farmed fish contribute to the ARG enrichment in farm sediments despite the lack of contemporaneous antibiotic treatments at the farms. We observed that the intestinal contents of individual farmed fish had their own resistome compositions. Our result also showed that the total relative abundances of transposases and tet genes were significantly correlated (p = 0.001, R2 = 0.71). In addition, we analyzed the mucosal skin and gill filament resistomes of the farmed fish but only one multidrug-efflux resistance gene (emrB) was detected. To our knowledge, this is the first study reporting the resistome of farmed fish using a culture-independent method. Determining the possible sources of ARGs, especially mobilized ARGs, is essential for controlling the occurrence and spread of ARGs at fish farming facilities and for lowering the risk of ARG spread from the farms to surrounding environments.
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Affiliation(s)
- Windi I Muziasari
- Department of Food and Environmental Sciences, University of Helsinki Helsinki, Finland
| | - Leena K Pitkänen
- Department of Food and Environmental Sciences, University of Helsinki Helsinki, Finland
| | - Henning Sørum
- Department of Food Safety and Infection Biology, Norwegian University of Life Sciences Oslo, Norway
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Center for Microbial Ecology, Michigan State University Michigan, MI, USA
| | - James M Tiedje
- Department of Civil and Environmental Engineering, Center for Microbial Ecology, Michigan State University Michigan, MI, USA
| | - Marko Virta
- Department of Food and Environmental Sciences, University of Helsinki Helsinki, Finland
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30
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Rojas R, Miranda CD, Santander J, Romero J. First Report of Vibrio tubiashii Associated with a Massive Larval Mortality Event in a Commercial Hatchery of Scallop Argopecten purpuratus in Chile. Front Microbiol 2016; 7:1473. [PMID: 27703450 PMCID: PMC5029309 DOI: 10.3389/fmicb.2016.01473] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/05/2016] [Indexed: 01/20/2023] Open
Abstract
The VPAP30 strain was isolated as the highly predominant bacteria from an episode of massive larval mortality occurring in a commercial culture of the Chilean scallop Argopecten purpuratus. The main aims of this study were, to characterize and identify the pathogenic strain using biochemical and molecular methods to demonstrate its pathogenic activity on scallop larvae, to characterize its pathogenic properties and to describe the chronology of this pathology. The pathogenic strain was identified as Vibrio tubiashii based on its phenotypic properties and the sequence analysis of its 16S rRNA and housekeeping genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA and topA). When triplicate cultures of healthy 10–day–old scallop larvae were challenged with 1 × 105 colony forming units (CFU) mL-1 of the VPAP30 strain, percentages of larval survival of 78.87 ± 3.33%, 34.32 ± 4.94%, and 0% were observed at 12, 24, and 36 h, respectively; whereas uninfected larval cultures showed survival rates of 97.4 ± 1.24% after of 48 h. Clinical symptoms exhibited by the scallop larvae infected with the VPAP30 strain include the accumulation of bacteria around the scallop larvae, velum disruption and necrosis of digestive gland. The 50% lethal dose (LD50) of VPAP30 strain at 24 and 48 h was 1.3 × 104 and 1.2 × 103 CFU mL-1, respectively. The invasive pathogenic activity of the VPAP30 strain was investigated with staining of the bacterial pathogen with 5-DTAF and analyzing bacterial invasion using epifluorescence, and a complete bacterial dissemination inside the larvae at 24 h post-infection was observed. When scallop larvae were inoculated with cell-free extracellular products (ECPs) of VPAP30, the larval survival rate was 59.5 ± 1.66%, significantly (P < 0.001) lower than the control group (97.4 ± 1.20%) whereas larvae treated with heat-treated ECPs exhibited a survival rate of 61.6 ± 1.84% after 48 h of exposure. This is the first report of the isolation of V. tubiashii from the diseased larvae of the scallop A. purpuratus, occurring in a commercial culture in Chile, and it was demonstrated that the VPAP30 strain exhibits high pathogenic activity on scallop larvae, mediated both by bacterial invasion and the production of toxigenic heat-stable compounds.
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Affiliation(s)
- Rodrigo Rojas
- Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile; Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del NorteCoquimbo, Chile; Centro AquapacíficoCoquimbo, Chile
| | - Claudio D Miranda
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del NorteCoquimbo, Chile; Centro AquapacíficoCoquimbo, Chile
| | - Javier Santander
- Laboratorio de Patogénesis Microbiana y Vacunación, Facultad de Ciencias, Universidad Mayor Santiago, Chile
| | - Jaime Romero
- Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile; Centro AquapacíficoCoquimbo, Chile
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A high-resolution map of the gut microbiota in Atlantic salmon (Salmo salar): A basis for comparative gut microbial research. Sci Rep 2016; 6:30893. [PMID: 27485205 PMCID: PMC4971465 DOI: 10.1038/srep30893] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/08/2016] [Indexed: 02/08/2023] Open
Abstract
Gut health challenges, possibly related to alterations in gut microbiota, caused by plant ingredients in the diets, cause losses in Atlantic salmon production. To investigate the role of the microbiota for gut function and health, detailed characterization of the gut microbiota is needed. We present the first in-depth characterization of salmon gut microbiota based on high-throughput sequencing of the 16S rRNA gene's V1-V2 region. Samples were taken from five intestinal compartments: digesta from proximal, mid and distal intestine and of mucosa from mid and distal intestine of 67.3 g salmon kept in seawater (12-14 °C) and fed a commercial diet for 4 weeks. Microbial richness and diversity differed significantly and were higher in the digesta than the mucosa. In mucosa, Proteobacteria dominated the microbiota (90%), whereas in digesta both Proteobacteria (47%) and Firmicutes (38%) showed high abundance. Future studies of diet and environmental impacts on gut microbiota should therefore differentiate between effects on mucosa and digesta in the proximal, mid and the distal intestine. A core microbiota, represented by 22 OTUs, was found in 80% of the samples. The gut microbiota of Atlantic salmon showed similarities with that of mammals.
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Estruch G, Collado MC, Peñaranda DS, Tomás Vidal A, Jover Cerdá M, Pérez Martínez G, Martinez-Llorens S. Impact of Fishmeal Replacement in Diets for Gilthead Sea Bream (Sparus aurata) on the Gastrointestinal Microbiota Determined by Pyrosequencing the 16S rRNA Gene. PLoS One 2015; 10:e0136389. [PMID: 26317431 PMCID: PMC4552794 DOI: 10.1371/journal.pone.0136389] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 08/04/2015] [Indexed: 11/18/2022] Open
Abstract
Recent studies have demonstrated the impact of diet on microbiota composition, but the essential need for the optimization of production rates and costs forces farms and aquaculture production to carry out continuous dietary tests. In order to understand the effect of total fishmeal replacement by vegetable-based feed in the sea bream (Sparus aurata), the microbial composition of the stomach, foregut, midgut and hindgut was analysed using high-throughput 16S rDNA sequencing, also considering parameters of growth, survival and nutrient utilisation indices.A total of 91,539 16S rRNA filtered-sequences were analysed, with an average number of 3661.56 taxonomically assigned, high-quality sequences per sample. The dominant phyla throughout the whole gastrointestinal tract were Actinobacteria, Protebacteria and Firmicutes. A lower diversity in the stomach in comparison to the other intestinal sections was observed. The microbial composition of the Recirculating Aquaculture System was totally different to that of the sea bream gastrointestinal tract. Total fishmeal replacement had an important impact on microbial profiles but not on diversity. Streptococcus (p-value: 0.043) and Photobacterium (p-value: 0.025) were highly represented in fish fed with fishmeal and vegetable-meal diets, respectively. In the stomach samples with the vegetable diet, reads of chloroplasts and mitochondria from vegetable dietary ingredients were rather abundant. Principal Coordinate Analysis showed a clear differentiation between diets in the microbiota present in the gut, supporting the presence of specific bacterial consortia associated with the diet.Although differences in growth and nutritive parameters were not observed, a negative effect of the vegetable diet on the survival rate was determined. Further studies are required to shed more light on the relationship between the immune system and sea bream gastrointestinal tract microbiota and should consider the modulation of the microbiota to improve the survival rate and nutritive efficacy when using plant-based diets.
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Affiliation(s)
- G. Estruch
- Aquaculture and Biodiversity Research Group. Institute of Science and Animal Technology, (ICTA), Universitat Politècnica de València, Valencia (Valencia), Spain
| | - M. C. Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna (Valencia), Spain
| | - D. S. Peñaranda
- Aquaculture and Biodiversity Research Group. Institute of Science and Animal Technology, (ICTA), Universitat Politècnica de València, Valencia (Valencia), Spain
| | - A. Tomás Vidal
- Aquaculture and Biodiversity Research Group. Institute of Science and Animal Technology, (ICTA), Universitat Politècnica de València, Valencia (Valencia), Spain
| | - M. Jover Cerdá
- Aquaculture and Biodiversity Research Group. Institute of Science and Animal Technology, (ICTA), Universitat Politècnica de València, Valencia (Valencia), Spain
| | - G. Pérez Martínez
- Department of Biotechnology, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna (Valencia), Spain
| | - S. Martinez-Llorens
- Aquaculture and Biodiversity Research Group. Institute of Science and Animal Technology, (ICTA), Universitat Politècnica de València, Valencia (Valencia), Spain
- * E-mail:
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Cordero H, Guardiola FA, Tapia-Paniagua ST, Cuesta A, Meseguer J, Balebona MC, Moriñigo MÁ, Esteban MÁ. Modulation of immunity and gut microbiota after dietary administration of alginate encapsulated Shewanella putrefaciens Pdp11 to gilthead seabream (Sparus aurata L.). FISH & SHELLFISH IMMUNOLOGY 2015; 45:608-18. [PMID: 26003737 DOI: 10.1016/j.fsi.2015.05.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/28/2015] [Accepted: 05/05/2015] [Indexed: 05/13/2023]
Abstract
The potential benefits of probiotics when administering to fish could improve aquaculture production. The objective of this study was to examine the modulation of immune status and gut microbiota of gilthead seabream (Sparus aurata L.) specimens by a probiotic when administered encapsulated. Commercial diet was enriched with Shewanella putrefaciens Pdp11 (SpPdp11, at a concentration of 10(8) cfu g(-1)) before being encapsulated in calcium alginate beads. Fish were fed non-supplemented (control) or supplemented diet for 4 weeks. After 1, 2 and 4 weeks the main humoral and cellular immune parameters were determined. Furthermore, gene expression profile of five immune relevant genes (il1β, bd, mhcIIα, ighm and tcrβ) was studied by qPCR in head kidney. On the other hand, intestinal microbiota of fish was analysed at 7 and 30 days by DGGE. Results demonstrated that administration of alginate encapsulated SpPdp11 has immunostimulant properties on humoral parameters (IgM level and serum peroxidase activity). Although no immunostimulant effects were detected on leucocyte activities, significant increases were detected in the level of mRNA of head-kidney leucocytes for mhcIIα and tcrβ after 4 weeks of feeding the encapsulated-probiotic diet. The administration of SpPdp11 encapsulated in alginate beads produced important changes in the DGGE patterns corresponding to the intestinal microbiota. Predominant bands related to lactic acid bacteria, such as Lactococcus and Lactobacillus strains, were sequenced from the DGGE patterns of fish fed the probiotic diet, whereas they were not sequenced from fish receiving the control diet. The convenience or not of probiotic encapsulation is discussed.
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Affiliation(s)
- Héctor Cordero
- Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, 30100 Murcia, Spain
| | - Francisco A Guardiola
- Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, 30100 Murcia, Spain
| | - Silvana Teresa Tapia-Paniagua
- Group of Prophylaxis and Biocontrol of Fish Diseases, Department of Microbiology, Campus de Teatinos s/n, University of Malaga, 29071 Málaga, Spain
| | - Alberto Cuesta
- Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, 30100 Murcia, Spain
| | - José Meseguer
- Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, 30100 Murcia, Spain
| | - M Carmen Balebona
- Group of Prophylaxis and Biocontrol of Fish Diseases, Department of Microbiology, Campus de Teatinos s/n, University of Malaga, 29071 Málaga, Spain
| | - M Ángel Moriñigo
- Group of Prophylaxis and Biocontrol of Fish Diseases, Department of Microbiology, Campus de Teatinos s/n, University of Malaga, 29071 Málaga, Spain
| | - M Ángeles Esteban
- Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, 30100 Murcia, Spain.
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Miranda CD, Rojas R, Geisse J, Romero J, González-Rocha G. Scallop larvae hatcheries as source of bacteria carrying genes encoding for non-enzymatic phenicol resistance. MARINE POLLUTION BULLETIN 2015; 95:173-182. [PMID: 25956439 DOI: 10.1016/j.marpolbul.2015.04.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/21/2015] [Accepted: 04/11/2015] [Indexed: 06/04/2023]
Abstract
The main aim of the study was to evaluate the role of scallop hatcheries as source of the floR and cmlA genes. A number of 133 and 121 florfenicol-resistant strains were isolated from scallop larval cultures prior to their transfer to seawater and from effluent samples from 2 commercial hatcheries and identified by 16S rRNA gene sequence analysis, observing a predominance of the Pseudomonas, Pseudoalteromonas and Halomonas genera and exhibiting an important incidence of co-resistance to streptomycin, oxytetracycline and co-trimoxazole. A high percentage of strains from both hatcheries carried the floR gene (68.4% and 89.3% of strains), whereas a lower carriage of the cmlA gene was detected (27.1% and 54.5% of strains). The high prevalence of floR-carrying bacteria in reared scallop larvae and hatchery effluents contributes to enrich the marine resistome in marine environments, prompting the need of a continuous surveillance of these genes in the mariculture environments.
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Affiliation(s)
- Claudio D Miranda
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile; Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Larrondo 1281, Coquimbo, Chile.
| | - Rodrigo Rojas
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile
| | - Julieta Geisse
- Laboratorio de Antibióticos, Departamento de Microbiología, Universidad de Concepción, Concepción, Chile
| | - Jaime Romero
- Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Gerardo González-Rocha
- Laboratorio de Antibióticos, Departamento de Microbiología, Universidad de Concepción, Concepción, Chile
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Rojas R, Miranda CD, Opazo R, Romero J. Characterization and pathogenicity of Vibrio splendidus strains associated with massive mortalities of commercial hatchery-reared larvae of scallop Argopecten purpuratus (Lamarck, 1819). J Invertebr Pathol 2015; 124:61-9. [DOI: 10.1016/j.jip.2014.10.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 09/27/2014] [Accepted: 10/28/2014] [Indexed: 11/15/2022]
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He Y, Yang H. The gastrointestinal phage communities of the cultivated freshwater fishes. FEMS Microbiol Lett 2014; 362:fnu027. [DOI: 10.1093/femsle/fnu027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Tapia-Paniagua S, Lobo C, Moreno-Ventas X, de la Banda IG, Moriñigo MA, Balebona MC. Probiotic supplementation influences the diversity of the intestinal microbiota during early stages of farmed senegalese sole (Solea Senegalensis, Kaup 1858). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:716-728. [PMID: 25103323 DOI: 10.1007/s10126-014-9588-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 07/06/2014] [Indexed: 06/03/2023]
Abstract
Ingestion of bacteria at early stages results in establishment of a primary intestinal microbiota which likely undergoes several stages along fish life. The role of this intestinal microbiota regulating body functions is crucial for larval development. Probiotics have been proved to modulate this microbiota and exert antagonistic effects against fish pathogens. In the present study, we aimed to determine bacterial diversity along different developmental stages of farmed Senegalese sole (Solea senegalensis) after feeding probiotic (Shewanella putrefaciens Pdp11) supplemented diet for a short period (10-30 days after hatching, DAH). Intestinal lumen contents of sole larvae fed control and probiotic diets were collected at 23, 56, 87, and 119 DAH and DNA was amplified using 16S rDNA bacterial domain-specific primers. Amplicons obtained were separated by denaturing gradient gel electrophoresis (DGGE), cloned, and resulting sequences compared to sequences in GenBank. Results suggest that Shewanella putrefaciens Pdp11 induces a modulation of the dominant bacterial taxa of the intestinal microbiota from 23 DAH. DGGE patterns of larvae fed the probiotic diet showed a core of bands related to Lactobacillus helveticus, Pseudomonas acephalitica, Vibrio parahaemolyticus, and Shewanella genus, together with increased Vibrio genus presence. In addition, decreased number of clones related to Photobacterium damselae subsp piscicida at 23 and 56 DAH was observed in probiotic-fed larvae. A band corresponding to Shewanella putrefaciens Pdp11 was sequenced as predominant from 23 to 119 DAH samples, confirming the colonization by the probiotics. Microbiota modulation obtained via probiotics addition emerges as an effective tool to improve Solea senegalensis larviculture.
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Affiliation(s)
- Silvana Tapia-Paniagua
- Departamento de Microbiología, Universidad de Málaga, Campus de Teatinos s/n, 29071, Málaga, Spain
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Said MB, Hays S, Maucort-Boulch D, Oulmaati A, Hantova S, Loys CM, Jumas-Bilak E, Picaud JC. Gut microbiota in preterm infants with gross blood in stools: A prospective, controlled study. Early Hum Dev 2014; 90:579-85. [PMID: 25127287 DOI: 10.1016/j.earlhumdev.2014.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 07/06/2014] [Accepted: 07/08/2014] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Gross blood in stools is a peculiar entity in preterm infants, but little is known about its etiology. As gut microbiota can be distorted in preterm infants, we aimed to evaluate the gut microbiota in infants with gross blood in stools. STUDY DESIGN In a prospective, controlled, single-center study, we enrolled all infants born before 34 weeks of gestational age presenting gross blood in stools that was either completely isolated or associated with mild clinical symptoms or radiological signs. Each case was paired with two controls who were hospitalized in the same unit and were matched for gestational age and birth weight. The diversity of the gut microbiota was analyzed using 16S rRNA gene PCR and temporal temperature gel electrophoresis. We calculated a diversity score corresponding to the number of operational taxonomic units present in the microbiota. RESULTS Thirty-three preterm infants with gross blood in stools were matched with 57 controls. Clinical characteristics were similar in cases and controls. There was no statistically significant difference in the diversity score between the two groups, but microbiota composition differed. The proportion of infants with Escherichia coli was significantly higher in cases than in controls (p=0.045) and the opposite pattern occurred for Staphylococcus sp. (p=0.047). CONCLUSION Dysbiosis could be a risk factor for gross blood in stools in preterm infants. Additional, larger studies are needed to confirm the implications of the presence of different genotypes of E. coli and to evaluate preventive actions such as the prophylactic use of probiotics and/or prebiotics.
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Affiliation(s)
- Mohamed Ben Said
- Department of Neonatology, University Hospital Croix Rousse, Hospices Civils de Lyon, F-69004 Lyon, France; Faculty of Medicine of Tunis, University of Tunis El-Manar, 1007 Bab Saâdoun, Tunis, Tunisia
| | - Stephane Hays
- Department of Neonatology, University Hospital Croix Rousse, Hospices Civils de Lyon, F-69004 Lyon, France; Rhone-Alpes Human Nutrition Research Center, F-69310 Pierre Bénite, France
| | - Deplhine Maucort-Boulch
- Department of Biostatistics, Hospices Civils de Lyon, F-69003 Lyon, France; CNRS, Laboratoire Biostatistique Santé, UMR 5558, F-69310 Pierre Bénite, France; Lyon-Sud Charles Merieux Medical School, Claude Bernard University Lyon 1, F-69310 Pierre Bénite, France
| | - Abdallah Oulmaati
- Department of Neonatology, University Hospital Croix Rousse, Hospices Civils de Lyon, F-69004 Lyon, France
| | - Stefanyia Hantova
- University Montpellier 1, Laboratoire de Bacteriologie-Virologie, EA 3755 UM1, Faculte de Pharmacie, F-34093 Montpellier, France
| | - Claire-Marie Loys
- Department of Neonatology, University Hospital Croix Rousse, Hospices Civils de Lyon, F-69004 Lyon, France
| | - Estelle Jumas-Bilak
- University Montpellier 1, Laboratoire de Bacteriologie-Virologie, EA 3755 UM1, Faculte de Pharmacie, F-34093 Montpellier, France; Department of Hospital Hygiene, CHU de Montpellier, F-34000 Montpellier, France
| | - Jean-Charles Picaud
- Department of Neonatology, University Hospital Croix Rousse, Hospices Civils de Lyon, F-69004 Lyon, France; Rhone-Alpes Human Nutrition Research Center, F-69310 Pierre Bénite, France; Lyon-Sud Charles Merieux Medical School, Claude Bernard University Lyon 1, F-69310 Pierre Bénite, France.
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The gut microbial community of Midas cichlid fish in repeatedly evolved limnetic-benthic species pairs. PLoS One 2014; 9:e95027. [PMID: 24733403 PMCID: PMC3986361 DOI: 10.1371/journal.pone.0095027] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 03/22/2014] [Indexed: 12/22/2022] Open
Abstract
Gut bacterial communities are now known to influence a range of fitness related aspects of organisms. But how different the microbial community is in closely related species, and if these differences can be interpreted as adaptive is still unclear. In this study we compared microbial communities in two sets of closely related sympatric crater lake cichlid fish species pairs that show similar adaptations along the limnetic-benthic axis. The gut microbial community composition differs in the species pair inhabiting the older of two crater lakes. One major difference, relative to other fish, is that in these cichlids that live in hypersaline crater lakes, the microbial community is largely made up of Oceanospirillales (52.28%) which are halotolerant or halophilic bacteria. This analysis opens up further avenues to identify candidate symbiotic or co-evolved bacteria playing a role in adaptation to similar diets and life-styles or even have a role in speciation. Future functional and phylosymbiotic analyses might help to address these issues.
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Yu HN, Zhu J, Pan WS, Shen SR, Shan WG, Das UN. Effects of fish oil with a high content of n-3 polyunsaturated fatty acids on mouse gut microbiota. Arch Med Res 2014; 45:195-202. [PMID: 24681186 DOI: 10.1016/j.arcmed.2014.03.008] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Accepted: 01/29/2014] [Indexed: 01/15/2023]
Abstract
BACKGROUND AND AIMS Many studies show that fish oil with high content of n-3 polyunsaturated fatty acids (PUFAs) plays an important role in human health and disease. But the effects of fish oil with high content of PUFAs on gut microbiota, which are also known play a significant role in several human diseases, is not clear. In the present study we evaluated the effects of fish oil with high content of n-3 PUFAs on gut microbiota. METHODS Changes in gut microbiota in ICR mice after supplementation of fish oil (containing eicosapentaenoic acid and docosahexaenoic acid: ∼40 and 27% respectively) for 15 days was characterized using the hypervariable V3 region of the 16 rRNA gene-based polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) profiling, DNA sequencing, and phylogenetic analysis techniques. RESULTS Fish oil treatment resulted in a decrease in Helicobacter, Uncultured bacterium clone WD2_aaf07d12 (GenBank: EU511712.1), Clostridiales bacterium, Sphingomonadales bacterium and Pseudomonas species Firmicutes, and several uncultured bacteria. CONCLUSIONS Fish oil with a high content of n-3 PUFAs are capable of producing significant changes in the gut microbiota that may, at least in part, explain the health benefits or injury induced by fish oil use.
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Affiliation(s)
- Hai-Ning Yu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Jing Zhu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Wen-sheng Pan
- The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Sheng-Rong Shen
- School of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Wei-Guang Shan
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
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Filleron A, Simon M, Hantova S, Jacquot A, Cambonie G, Marchandin H, Jumas-Bilak E. tuf-PCR-temporal temperature gradient gel electrophoresis for molecular detection and identification of staphylococci: Application to breast milk and neonate gut microbiota. J Microbiol Methods 2014; 98:67-75. [DOI: 10.1016/j.mimet.2013.12.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 12/29/2013] [Accepted: 12/30/2013] [Indexed: 11/30/2022]
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Abstract
The gastrointestinal tract (GIT) microbiomes of production animals are now firmly established as a key feature underscoring animal health, development, and productivity. In particular, early gut colonization is critically important to the morphological and immunological development of the GIT, development of a functional fermentative environment, and neonatal resistance to pathogenic challenge. Although perturbations of an animal's GIT microbiome at any age can have profound consequences, perturbations during early GIT development can be particularly severe and result in significant and long-lasting sequelae. As the GIT microbiome matures, it exhibits significant diversity, ostensibly an important indicator of ecosystem health. Recognition of the immense importance of the GIT microbiota to the host has led to the development of probiotic and prebiotic feedstuffs with the express aim of ensuring animal health. We herein review the current collective understanding of the GIT microbiota of production animals.
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Affiliation(s)
- Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, Montana 59717-2900;
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Aquacultured rainbow trout (Oncorhynchus mykiss) possess a large core intestinal microbiota that is resistant to variation in diet and rearing density. Appl Environ Microbiol 2013; 79:4974-84. [PMID: 23770898 DOI: 10.1128/aem.00924-13] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
As global aquaculture fish production continues to expand, an improved understanding of how environmental factors interact in fish health and production is needed. Significant advances have been made toward economical alternatives to costly fishmeal-based diets, such as grain-based formulations, and toward defining the effect of rearing density on fish health and production. Little research, however, has examined the effects of fishmeal- and grain-based diets in combination with alterations in rearing density. Moreover, it is unknown whether interactions between rearing density and diet impact the composition of the fish intestinal microbiota, which might in turn impact fish health and production. We fed aquacultured adult rainbow trout (Oncorhynchus mykiss) fishmeal- or grain-based diets, reared them under high- or low-density conditions for 10 months in a single aquaculture facility, and evaluated individual fish growth, production, fin indices, and intestinal microbiota composition using 16S rRNA gene sequencing. We found that the intestinal microbiotas were dominated by a shared core microbiota consisting of 52 bacterial lineages observed across all individuals, diets, and rearing densities. Variations in diet and rearing density resulted in only minor changes in intestinal microbiota composition despite significant effects of these variables on fish growth, performance, fillet quality, and welfare. Significant interactions between diet and rearing density were observed only in evaluations of fin indices and the relative abundance of the bacterial genus Staphylococcus. These results demonstrate that aquacultured rainbow trout can achieve remarkable consistency in intestinal microbiota composition and suggest the possibility of developing novel aquaculture strategies without overtly altering intestinal microbiota composition.
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Makino L, Faustino F, Paes M, Beraldo-Massoli M, Cardozo M, Schocken-Iturrino R, Nakaghi L. Morfologia e quantificação da microbiota intestinal do curimbatá (Prochilodus lineatus) e do cascudo cinza (Pterygoplichthys anisitsi) cultivados em cativeiro. ARQ BRAS MED VET ZOO 2012. [DOI: 10.1590/s0102-09352012000400019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Todos os animais vivem em íntima associação com micro-organismos que desempenham importantes funções em seu desenvolvimento normal. Nos vertebrados, a mais populosa e complexa comunidade de micro-organismos reside no trato intestinal. O intuito do estudo foi quantificar, classificar e verificar morfologicamente a população microbiana intestinal de duas importantes espécies de peixes de água doce, o curimbatá (Prochilodus lineatus) e o cascudo cinza (Pterygoplichthys anisitsi). As amostras foram coletadas por meio de raspagens da mucosa intestinal, diluídas seriadamente até 10-4, semeadas em placas contendo ágar soja tripticaseína (TSA) e ágar chocolate (AC) para contagem de bactérias totais e identificação morfológica por Gram, em aerobiose e em anaerobiose facultativa, respectivamente. As contagens de bactérias totais mostraram resultados que variaram entre 10³ e 10(4)ufc.mL-1. Os tipos morfológicos encontrados foram cocos, leveduras e bastonetes Gram negativos e positivos. Estudos adicionais sobre os padrões de colonização microbiana e a morfologia dos micro-organismos aderidos à mucosa intestinal foram possíveis com o uso da microscopia eletrônica de varredura (MEV), sendo encontradas formas variadas de micro-organismos, tais como leveduras, formas cocoides e bacilares flageladas e não flageladas. A microbiota intestinal do curimbatá e a do cascudo cinza provaram ser bastante diversas e populosas, com o predomínio de micro-organismos Gram negativos.
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Navarrete P, Magne F, Araneda C, Fuentes P, Barros L, Opazo R, Espejo R, Romero J. PCR-TTGE analysis of 16S rRNA from rainbow trout (Oncorhynchus mykiss) gut microbiota reveals host-specific communities of active bacteria. PLoS One 2012; 7:e31335. [PMID: 22393360 PMCID: PMC3290605 DOI: 10.1371/journal.pone.0031335] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 01/06/2012] [Indexed: 01/30/2023] Open
Abstract
This study assessed the relative contributions of host genetics and diet in shaping the gut microbiota of rainbow trout. Full sibling fish from four unrelated families, each consisting of individuals derived from the mating of one male and one female belonging to a breeding program, were fed diets containing either vegetable proteins or vegetable oils for two months in comparison to a control diet consisting of only fish protein and fish oil. Two parallel approaches were applied on the same samples: transcriptionally active bacterial populations were examined based on RNA analysis and were compared with bacterial populations obtained from DNA analysis. Comparison of temporal temperature gradient gel electrophoresis (TTGE) profiles from DNA and RNA showed important differences, indicating that active bacterial populations were better described by RNA analysis. Results showed that some bacterial groups were significantly (P<0.05) associated with specific families, indicating that microbiota composition may be influenced by the host. In addition, the effect of diet on microbiota composition was dependent on the trout family.
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Affiliation(s)
- Paola Navarrete
- Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Región Metropolitana, Chile.
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Li X, Yu Y, Feng W, Yan Q, Gong Y. Host species as a strong determinant of the intestinal microbiota of fish larvae. J Microbiol 2012; 50:29-37. [DOI: 10.1007/s12275-012-1340-1] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 09/20/2011] [Indexed: 11/28/2022]
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Lan CC, Love DR. Molecular Characterisation of Bacterial Community Structure along the Intestinal Tract of Zebrafish (Danio rerio): A Pilot Study. ISRN MICROBIOLOGY 2012; 2012:590385. [PMID: 23724326 PMCID: PMC3658630 DOI: 10.5402/2012/590385] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Accepted: 11/06/2011] [Indexed: 11/23/2022]
Abstract
The bacterial composition along the intestinal tract of Danio rerio was investigated by cultivation-independent analysis of the 16S rRNA gene. Clone libraries were constructed for three compartments of the intestinal tract of individual fish. 566 individual clones were differentiated by amplified 16S rRNA gene restriction analysis (ARDRA), and clone representatives from each operational taxonomic unit (OTU) were sequenced. As reported in other studies, we found that Proteobacteria was the most prominent phylum among clone libraries from different fish. Data generated from this pilot study indicated some compositional differences in bacterial communities. Two dominant classes, Gammaproteobacteria and Bacilli, displayed different levels of abundance in different compartments; Gammaproteobacteria increased along the intestinal tract, while Bacilli decreased its abundance along the proximal-distal axis. Less obvious spatial patterns were observed for other classes. In general, bacterial diversity in the intestinal bulb was greater than that in the posterior intestine. Interindividual differences in bacterial diversity and composition were also noted in this study.
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Affiliation(s)
- Chuan-Ching Lan
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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Roeselers G, Mittge EK, Stephens WZ, Parichy DM, Cavanaugh CM, Guillemin K, Rawls JF. Evidence for a core gut microbiota in the zebrafish. ISME JOURNAL 2011; 5:1595-608. [PMID: 21472014 DOI: 10.1038/ismej.2011.38] [Citation(s) in RCA: 659] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Experimental analysis of gut microbial communities and their interactions with vertebrate hosts is conducted predominantly in domesticated animals that have been maintained in laboratory facilities for many generations. These animal models are useful for studying coevolved relationships between host and microbiota only if the microbial communities that occur in animals in lab facilities are representative of those that occur in nature. We performed 16S rRNA gene sequence-based comparisons of gut bacterial communities in zebrafish collected recently from their natural habitat and those reared for generations in lab facilities in different geographic locations. Patterns of gut microbiota structure in domesticated zebrafish varied across different lab facilities in correlation with historical connections between those facilities. However, gut microbiota membership in domesticated and recently caught zebrafish was strikingly similar, with a shared core gut microbiota. The zebrafish intestinal habitat therefore selects for specific bacterial taxa despite radical differences in host provenance and domestication status.
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Affiliation(s)
- Guus Roeselers
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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De Schryver P, Dierckens K, Bahn Thi QQ, Amalia R, Marzorati M, Bossier P, Boon N, Verstraete W. Convergent dynamics of the juvenile European sea bass gut microbiota induced by poly-β-hydroxybutyrate. Environ Microbiol 2011; 13:1042-51. [DOI: 10.1111/j.1462-2920.2010.02410.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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