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Cao Y, Bi L, Chen Q, Liu Y, Zhao H, Jin L, Peng R. Understanding the links between micro/nanoplastics-induced gut microbes dysbiosis and potential diseases in fish: A review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 352:124103. [PMID: 38734053 DOI: 10.1016/j.envpol.2024.124103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
At present, the quantity of micro/nano plastics in the environment is steadily rising, and their pollution has emerged as a global environmental issue. The tendency of their bioaccumulation in aquatic organisms (especially fish) has intensified people's attention to their persistent ecotoxicology. This review critically studies the accumulation of fish in the intestines of fish through active or passive intake of micro/nano plastics, resulting in their accumulation in intestinal organs and subsequent disturbance of intestinal microflora. The key lies in the complex toxic effect on the host after the disturbance of fish intestinal microflora. In addition, this review pointed out the characteristics of micro/nano plastics and the effects of their combined toxicity with adsorbed pollutants on fish intestinal microorganisms, in order to fully understand the characteristics of micro/nano plastics and emphasize the complex interaction between MNPs and other pollutants. We have an in-depth understanding of MNPs-induced intestinal flora disorders and intestinal dysfunction, affecting the host's systemic system, including immune system, nervous system, and reproductive system. The review also underscores the imperative for future research to investigate the toxic effects of prolonged exposure to MNPs, which are crucial for evaluating the ecological risks posed by MNPs and devising strategies to safeguard aquatic organisms.
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Affiliation(s)
- Yu Cao
- Institute of Life Sciences & Biomedicine Collaborative Innovation Center of Zhejiang province, College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Liuliu Bi
- Institute of Life Sciences & Biomedicine Collaborative Innovation Center of Zhejiang province, College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Qianqian Chen
- Institute of Life Sciences & Biomedicine Collaborative Innovation Center of Zhejiang province, College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Yinai Liu
- Institute of Life Sciences & Biomedicine Collaborative Innovation Center of Zhejiang province, College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Haiyang Zhao
- Institute of Life Sciences & Biomedicine Collaborative Innovation Center of Zhejiang province, College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Libo Jin
- Institute of Life Sciences & Biomedicine Collaborative Innovation Center of Zhejiang province, College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Renyi Peng
- Institute of Life Sciences & Biomedicine Collaborative Innovation Center of Zhejiang province, College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China.
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Burgos FA, Cai W, Arias CR. Gut dysbiosis induced by florfenicol increases susceptibility to Aeromonas hydrophila infection in Zebrafish Danio rerio after the recommended withdrawal period. JOURNAL OF AQUATIC ANIMAL HEALTH 2024; 36:113-127. [PMID: 38060422 DOI: 10.1002/aah.10211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/27/2023] [Accepted: 11/25/2023] [Indexed: 02/18/2024]
Abstract
OBJECTIVE Florfenicol (FFC) is a broad-spectrum antibiotic approved by the U.S. Food and Drug Administration to treat both systemic and external bacterial infections in food fish. The objective of this study was to evaluate the effect of FFC-medicated feed on the gut microbiota of Zebrafish Danio danio to determine (1) if the therapeutic dose of FFC-medicated feed induces dysbiosis and (2) if fish with altered gut microbiota were more susceptible to subsequent infection by the common opportunistic fish pathogen Aeromonas hydrophila. METHODS Zebrafish that were treated with regular and FFC-medicated feeds were artificially challenged with A. hydrophila at the end of the recommended 15-day antibiotic withdrawal period. The gut microbiota of the Zebrafish at different stages was analyzed using 16S ribosomal RNA gene sequencing. RESULT Our results found that FFC-medicated feed induced disruption of the gut microbiota. Dysbiosis was observed in all treated groups, with a significant increase in bacterial diversity, and was characterized by a remarkable bloom of Proteobacteria and a drastic decline of Mycoplasma and Cetobacterium in treated animals but without noticeable clinical signs or mortalities. In addition, the increase of Proteobacteria was not significantly reduced after the recommended 15-day withdrawal period, and the Zebrafish treated with FFC-medicated feed exhibited a significantly higher mortality rate when they were subsequently challenged with A. hydrophila compared to the control (regular feed) groups. Interestingly, the most dramatic changes in the gut microbiome composition occurred at the transition time between the late stage of the medicated treatment and the beginning of the withdrawal period instead of the time during the Aeromonas infection. CONCLUSION The administration of FFC-medicated feed at the recommended dose induced gut dysbiosis in Zebrafish, and fish did not recover to the baseline after the recommended withdrawal period. Our findings suggest that the use of antibiotics in fish elicits a response similar to those previously described in mammals and possibly makes the host more susceptible to subsequent infections of opportunistic pathogens. This study using a controlled model system suggests that antibiotics in aquaculture may have long-term effects on the general well-being of the fish.
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Affiliation(s)
- Francisca A Burgos
- Facultad de Ingeniería Marítima y Ciencias del Mar, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Wenlong Cai
- Department of Infectious Diseases and Public Health, State Key Lab of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Covadonga R Arias
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama, USA
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3
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Mes W, Lücker S, Jetten MSM, Siepel H, Gorissen M, van Kessel MAHJ. Feeding strategy and feed protein level affect the gut microbiota of common carp (Cyprinus carpio). ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13262. [PMID: 38725141 PMCID: PMC11082430 DOI: 10.1111/1758-2229.13262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/06/2024] [Indexed: 05/13/2024]
Abstract
Common carp (Cyprinus carpio) were fed food with different protein concentrations following different feeding regimes, which were previously shown to affect growth, nitrogen excretion and amino acid catabolism. 16S rRNA gene amplicon sequencing was performed to investigate the gut microbiota of these fish. Lower dietary protein content increased microbial richness, while the combination of demand feeding and dietary protein content affected the composition of the gut microbiota. Hepatic glutamate dehydrogenase (GDH) activity was correlated to the composition of the gut microbiota in all dietary treatments. We found that demand-fed carp fed a diet containing 39% protein had a significantly higher abundance of Beijerinckiaceae compared to other dietary groups. Network analysis identified this family and two Rhizobiales families as hubs in the microbial association network. In demand-fed carp, the microbial association network had significantly fewer connections than in batch-fed carp. In contrast to the large effects of the feeding regime and protein content of the food on growth and nitrogen metabolism, it had only limited effects on gut microbiota composition. However, correlations between gut microbiota composition and liver GDH activity showed that host physiology and gut microbiota are connected, which warrants functional studies into the role of the gut microbiota in fish physiology.
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Affiliation(s)
- Wouter Mes
- Department of Microbiology, Radboud Institute for Biological and Environmental SciencesRadboud UniversityNijmegenThe Netherlands
- Department of Plant and Animal Biology, Radboud Institute for Biological and Environmental SciencesRadboud UniversityNijmegenThe Netherlands
| | - Sebastian Lücker
- Department of Microbiology, Radboud Institute for Biological and Environmental SciencesRadboud UniversityNijmegenThe Netherlands
| | - Mike S. M. Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental SciencesRadboud UniversityNijmegenThe Netherlands
| | - Henk Siepel
- Department of Plant and Animal Biology, Radboud Institute for Biological and Environmental SciencesRadboud UniversityNijmegenThe Netherlands
| | - Marnix Gorissen
- Department of Plant and Animal Biology, Radboud Institute for Biological and Environmental SciencesRadboud UniversityNijmegenThe Netherlands
| | - Maartje A. H. J. van Kessel
- Department of Microbiology, Radboud Institute for Biological and Environmental SciencesRadboud UniversityNijmegenThe Netherlands
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4
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Sadeghi J, Zaib F, Heath DD. Genetic architecture and correlations between the gut microbiome and gut gene transcription in Chinook salmon (Oncorhynchus tshawytscha). Heredity (Edinb) 2024:10.1038/s41437-024-00692-3. [PMID: 38822131 DOI: 10.1038/s41437-024-00692-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 06/02/2024] Open
Abstract
Population divergence through selection can drive local adaptation in natural populations which has implications for the effective restoration of declining and extirpated populations. However, adaptation to local environmental conditions is complicated when both the host and its associated microbiomes must respond via co-evolutionary change. Nevertheless, for adaptation to occur through selection, variation in both host and microbiome traits should include additive genetic effects. Here we focus on host immune function and quantify factors affecting variation in gut immune gene transcription and gut bacterial community composition in early life-stage Chinook salmon (Oncorhynchus tshawytscha). Specifically, we utilized a replicated factorial breeding design to determine the genetic architecture (sire, dam and sire-by-dam interaction) of gut immune gene transcription and microbiome composition. Furthermore, we explored correlations between host gut gene transcription and microbiota composition. Gene transcription was quantified using nanofluidic qPCR arrays (22 target genes) and microbiota composition using 16 S rRNA gene (V5-V6) amplicon sequencing. We discovered limited but significant genetic architecture in gut microbiota composition and transcriptional profiles. We also identified significant correlations between gut gene transcription and microbiota composition, highlighting potential mechanisms for functional interactions between the two. Overall, this study provides support for the co-evolution of host immune function and their gut microbiota in Chinook salmon, a species recognized as locally adapted. Thus, the inclusion of immune gene transcription profile and gut microbiome composition as factors in the development of conservation and commercial rearing practices may provide new and more effective approaches to captive rearing.
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Affiliation(s)
- Javad Sadeghi
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
- Department of Physical & Environmental Sciences, University of Toronto-Scarborough, Toronto, ON, Canada
| | - Farwa Zaib
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada.
- Department of Integrative Biology, University of Windsor, Ontario, ON, Canada.
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Wu DG, Harris CR, Kalis KM, Biddle JF, Farag IF. Comparative metagenomics of tropical reef fishes show conserved core gut functions across hosts and diets with diet-related functional gene enrichments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595191. [PMID: 38826274 PMCID: PMC11142082 DOI: 10.1101/2024.05.21.595191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Fish gut microbial communities are important for the breakdown and energy harvesting of the host diet. Microbes within the fish gut are selected by environmental and evolutionary factors. To understand how fish gut microbial communities are shaped by diet, three tropical fish species (hawkfish, Paracirrhites arcatus; yellow tang, Zebrasoma flavescens; and triggerfish, Rhinecanthus aculeatus) were fed piscivorous (fish meal pellets), herbivorous (seaweed), and invertivorous (shrimp) diets, respectively. From fecal samples, a total of 43 metagenome assembled genomes (MAGs) were recovered from all fish diet treatments. Each host-diet treatment harbored distinct microbial communities based on taxonomy, with Proteobacteria, Bacteroidota, and Firmicutes being the most represented. Based on their metagenomes, microbial communities from all three host-diet treatments demonstrated a baseline ability to degrade proteinaceous, fatty acid, and simple carbohydrate inputs and carry out central carbon metabolism, lactate and formate fermentation, acetogenesis, nitrate respiration, and B vitamin synthesis. The herbivorous yellow tang harbored a more functionally diverse microbial community with some complex polysaccharide degradation specialists, while the piscivorous hawkfish's gut community was more specialized for the degradation of proteins. The invertivorous triggerfish's gut microbiome lacked many carbohydrate degrading capabilities, resulting in a more specialized, functionally uniform community. Across all treatments, several MAGs were able to participate in only individual steps of the degradation of complex polysaccharides, suggestive of microbial community networks that degrade complex inputs. These data suggest the existence of a functional core microbiome that is common among fish species, although the specific taxonomic identities of the associated bacteria may differ.
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Affiliation(s)
- Derek G. Wu
- School of Marine Science and Policy, University of Delaware, Lewes DE 19958 USA
| | - Cassandra R. Harris
- School of Marine Science and Policy, University of Delaware, Lewes DE 19958 USA
| | - Katie M. Kalis
- School of Marine Science and Policy, University of Delaware, Lewes DE 19958 USA
| | - Jennifer F. Biddle
- School of Marine Science and Policy, University of Delaware, Lewes DE 19958 USA
| | - Ibrahim F. Farag
- School of Marine Science and Policy, University of Delaware, Lewes DE 19958 USA
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Varela JL, Nikouli E, Medina A, Papaspyrou S, Kormas K. The gills and skin microbiota of five pelagic fish species from the Atlantic Ocean. Int Microbiol 2024:10.1007/s10123-024-00524-8. [PMID: 38740652 DOI: 10.1007/s10123-024-00524-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/25/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024]
Abstract
The gills and skin microbiota and microbiome of wild fish remain far more under-investigated compared to that of farmed fish species, despite that these animal-microbe interactions hold the same ecophysiological roles in both cases. In this study, the gills and skin bacterial microbiota profiles and their presumptive bacterial metabolisms were investigated in five open-sea fishes: bullet tuna (Auxis sp.), common dolphinfish (Coryphaena hippurus), Atlantic little tunny (Euthynnus alletteratus), Atlantic bonito (Sarda sarda) and Atlantic white marlin (Kajikia albida). Gills and skin tissues were collected from two to three individuals per species, from specimens caught by recreational trolling during summer of 2019, and their bacterial 16S rRNA gene diversity was analysed by high-throughput sequencing. The gills bacterial communities among the five species were clearly different but not the skin bacterial microbiota. The dominant operational taxonomic units belonged to the Moraxellaceae, Pseudomonadaceae, Rhodobacteraceae, Staphylococcaceae and Vibrionaceae families. Despite the differences in taxonomic composition, the presumptive bacterial metabolisms between the gills and skin of the five fishes investigated here were ≥ 94% similar and were dominated by basic metabolism, most likely reflecting the continuous exposure of these tissues in the surrounding seawater.
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Affiliation(s)
- José Luis Varela
- Department of Biology, University of Cádiz, Puerto Real, 11510, Cádiz, Spain
| | - Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece
| | - Antonio Medina
- Department of Biology, University of Cádiz, Puerto Real, 11510, Cádiz, Spain
| | - Sokratis Papaspyrou
- Department of Biology, University of Cádiz, Puerto Real, 11510, Cádiz, Spain
| | - Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece.
- Agricultural Development Institute, University Research and Innovation Centre "IASON", Argonafton & Filellinon, 382 21, Volos, Greece.
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7
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Fang C, Zeng F, Chen S, Li S, Yang Y, Lin W, Liu Y, Peng C, Yang H. Gender Impacted Gut Microbiota and Growth Performance in the Blotched Snakehead ( Channa maculata). Microorganisms 2024; 12:871. [PMID: 38792700 PMCID: PMC11124158 DOI: 10.3390/microorganisms12050871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
The blotched snakehead Channa maculata is an important economical freshwater species in East Asia. However, there has been relatively little research conducted on the correlation between gender and gut microbes. In this study, 36 of 1000 blotched snakeheads were randomly selected for growth performance measurement and gut microbiota high-throughput sequencing. Results showed that microbial diversity, composition, and metabolic functions were altered by gender and growth performance except the microbial network. In our study, Proteobacteria were the most abundant phylum, with Fusobacteria showing enrichment in males and Bacteroidetes in females. Notably, phylum Deinococcus-Thermus was identified as a significant biomarker. The Cetobacterium was the most abundant genus-level taxon. Furthermore, gut microbes specializing in the production of gut-healthy substances, such as coenzymes and vitamins, were identified as biomarkers in the fast-growing group. Our investigation highlighted the impact of gender on the composition and abundance of gut microbial biomarkers in both males and females, thereby influencing differential growth performance through the modulation of specific metabolic functions.
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Affiliation(s)
- Chang Fang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (C.F.); (F.Z.); (S.C.); (Y.Y.); (W.L.)
- Zhongshan Innovation Center, South China Agricultural University, Zhongshan 528400, China
| | - Fang Zeng
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (C.F.); (F.Z.); (S.C.); (Y.Y.); (W.L.)
- Zhongshan Innovation Center, South China Agricultural University, Zhongshan 528400, China
| | - Shijun Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (C.F.); (F.Z.); (S.C.); (Y.Y.); (W.L.)
- Zhongshan Innovation Center, South China Agricultural University, Zhongshan 528400, China
| | - Shuisheng Li
- Laboratory for Aquatic Economic Animals, Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China; (S.L.); (Y.L.)
| | - Yuting Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (C.F.); (F.Z.); (S.C.); (Y.Y.); (W.L.)
- Zhongshan Innovation Center, South China Agricultural University, Zhongshan 528400, China
| | - Wanjing Lin
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (C.F.); (F.Z.); (S.C.); (Y.Y.); (W.L.)
- Zhongshan Innovation Center, South China Agricultural University, Zhongshan 528400, China
| | - Yun Liu
- Laboratory for Aquatic Economic Animals, Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China; (S.L.); (Y.L.)
| | - Cheng Peng
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
- Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Huirong Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (C.F.); (F.Z.); (S.C.); (Y.Y.); (W.L.)
- Zhongshan Innovation Center, South China Agricultural University, Zhongshan 528400, China
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Knobloch S, Skirnisdóttir S, Dubois M, Mayolle L, Kolypczuk L, Leroi F, Leeper A, Passerini D, Marteinsson VÞ. The gut microbiome of farmed Arctic char ( Salvelinus alpinus) is shaped by feeding stage and nutrient presence. FEMS MICROBES 2024; 5:xtae011. [PMID: 38745980 PMCID: PMC11092275 DOI: 10.1093/femsmc/xtae011] [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: 01/02/2024] [Revised: 03/06/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
The gut microbiome plays an important role in maintaining health and productivity of farmed fish. However, the functional role of most gut microorganisms remains unknown. Identifying the stable members of the gut microbiota and understanding their functional roles could aid in the selection of positive traits or act as a proxy for fish health in aquaculture. Here, we analyse the gut microbial community of farmed juvenile Arctic char (Salvelinus alpinus) and reconstruct the metabolic potential of its main symbionts. The gut microbiota of Arctic char undergoes a succession in community composition during the first weeks post-hatch, with a decrease in Shannon diversity and the establishment of three dominant bacterial taxa. The genome of the most abundant bacterium, a Mycoplasma sp., shows adaptation to rapid growth in the nutrient-rich gut environment. The second most abundant taxon, a Brevinema sp., has versatile metabolic potential, including genes involved in host mucin degradation and utilization. However, during periods of absent gut content, a Ruminococcaceae bacterium becomes dominant, possibly outgrowing all other bacteria through the production of secondary metabolites involved in quorum sensing and cross-inhibition while benefiting the host through short-chain fatty acid production. Whereas Mycoplasma is often present as a symbiont in farmed salmonids, we show that the Ruminococcaceae species is also detected in wild Arctic char, suggesting a close evolutionary relationship between the host and this symbiotic bacterium.
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Affiliation(s)
- Stephen Knobloch
- Matís ohf., Microbiology Research Group, Vínlandsleið 12, 113 Reykjavík, Iceland
- Department of Food Technology, University of Applied Sciences Fulda, Leipziger Strasse 123, 36037 Fulda, Germany
| | | | - Marianne Dubois
- ESBS/University of Strasbourg, 300 Bd Sébastien Brant, 67085 Strasbourg, France
| | - Lucie Mayolle
- University of Technology of Compiègne, Rue Roger Couttolenc, 60203 Compiègne, France
| | - Laetitia Kolypczuk
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, BP 21105, F-44000 Nantes, France
| | - Françoise Leroi
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, BP 21105, F-44000 Nantes, France
| | - Alexandra Leeper
- Matís ohf., Microbiology Research Group, Vínlandsleið 12, 113 Reykjavík, Iceland
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Arboretveien 6, 1430 Ås, Norway
- Iceland Ocean Cluster, Department of Research and Innovation, Grandagarður 16, 101 Reykjavík, Iceland
| | - Delphine Passerini
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, BP 21105, F-44000 Nantes, France
| | - Viggó Þ Marteinsson
- Matís ohf., Microbiology Research Group, Vínlandsleið 12, 113 Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Sæmundargata 2, 101 Reykjavik, Iceland
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Liu H, Wei M, Tan B, Dong X, Xie S. The Supplementation of Berberine in High-Carbohydrate Diets Improves Glucose Metabolism of Tilapia ( Oreochromis niloticus) via Transcriptome, Bile Acid Synthesis Gene Expression and Intestinal Flora. Animals (Basel) 2024; 14:1239. [PMID: 38672387 PMCID: PMC11047455 DOI: 10.3390/ani14081239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Berberine is an alkaloid used to treat diabetes. This experiment aimed to investigate the effects of berberine supplementation in high-carbohydrate diets on the growth performance, glucose metabolism, bile acid synthesis, liver transcriptome, and intestinal flora of Nile tilapia. The six dietary groups were the C group with 29% carbohydrate, the H group with 44% carbohydrate, and the HB1-HB4 groups supplemented with 25, 50, 75, and 100 mg/kg of berberine in group H. The results of the 8-week trial showed that compared to group C, the abundance of Bacteroidetes was increased in group HB2 (p < 0.05). The cholesterol-7α-hydroxylase (CYP7A1) and sterol-27-hydroxylase (CYP27A1) activities were decreased and the expression of FXR was increased in group HB4 (p < 0.05). The pyruvate carboxylase (PC) and phosphoenolpyruvate carboxykinase (PEPCK) activities was decreased in group HB4 (p < 0.05). The liver transcriptome suggests that berberine affects carbohydrate metabolic pathways and primary bile acid synthesis pathways. In summary, berberine affects the glucose metabolism in tilapia by altering the intestinal flora structure, enriching differentially expressed genes (DEGs) in the bile acid pathway to stimulate bile acid production so that it promotes glycolysis and inhibits gluconeogenesis. Therefore, 100 mg/kg of berberine supplementation in high-carbohydrate diets is beneficial to tilapia.
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Affiliation(s)
- Hongyu Liu
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (H.L.); (M.W.); (X.D.); (S.X.)
- Aquatic Animals Precision Nutrition and High-Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang 524088, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524088, China
| | - Menglin Wei
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (H.L.); (M.W.); (X.D.); (S.X.)
- Aquatic Animals Precision Nutrition and High-Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang 524088, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524088, China
| | - Beiping Tan
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (H.L.); (M.W.); (X.D.); (S.X.)
- Aquatic Animals Precision Nutrition and High-Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang 524088, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524088, China
| | - Xiaohui Dong
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (H.L.); (M.W.); (X.D.); (S.X.)
- Aquatic Animals Precision Nutrition and High-Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang 524088, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524088, China
| | - Shiwei Xie
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (H.L.); (M.W.); (X.D.); (S.X.)
- Aquatic Animals Precision Nutrition and High-Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang 524088, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524088, China
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10
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Kato A, Pipil S, Ota C, Kusakabe M, Watanabe T, Nagashima A, Chen AP, Islam Z, Hayashi N, Wong MKS, Komada M, Romero MF, Takei Y. Convergent gene losses and pseudogenizations in multiple lineages of stomachless fishes. Commun Biol 2024; 7:408. [PMID: 38570609 PMCID: PMC10991444 DOI: 10.1038/s42003-024-06103-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 03/25/2024] [Indexed: 04/05/2024] Open
Abstract
The regressive evolution of independent lineages often results in convergent phenotypes. Several teleost groups display secondary loss of the stomach, and four gastric genes, atp4a, atp4b, pgc, and pga2 have been co-deleted in agastric (stomachless) fish. Analyses of genotypic convergence among agastric fishes showed that four genes, slc26a9, kcne2, cldn18a, and vsig1, were co-deleted or pseudogenized in most agastric fishes of the four major groups. kcne2 and vsig1 were also deleted or pseudogenized in the agastric monotreme echidna and platypus, respectively. In the stomachs of sticklebacks, these genes are expressed in gastric gland cells or surface epithelial cells. An ohnolog of cldn18 was retained in some agastric teleosts but exhibited an increased non-synonymous substitution when compared with gastric species. These results revealed novel convergent gene losses at multiple loci among the four major groups of agastric fish, as well as a single gene loss in the echidna and platypus.
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Affiliation(s)
- Akira Kato
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Japan.
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Japan.
- Department of Physiology & Biomedical Engineering, Mayo Clinic College of Medicine & Science, Rochester, MN, USA.
| | - Supriya Pipil
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Chihiro Ota
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Makoto Kusakabe
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
- Department of Biological Sciences, Faculty of Science, Shizuoka University, Shizuoka, Japan
| | - Taro Watanabe
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Ayumi Nagashima
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - An-Ping Chen
- Department of Physiology & Biomedical Engineering, Mayo Clinic College of Medicine & Science, Rochester, MN, USA
| | - Zinia Islam
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Japan
| | - Naoko Hayashi
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Japan
| | - Marty Kwok-Shing Wong
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
- Department of Biomolecular Science, Toho University, Funabashi, Japan
| | - Masayuki Komada
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Michael F Romero
- Department of Physiology & Biomedical Engineering, Mayo Clinic College of Medicine & Science, Rochester, MN, USA
- Department of Nephrology & Hypertension, Mayo Clinic College of Medicine & Science, Rochester, MN, USA
| | - Yoshio Takei
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
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11
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Lima ECSDE, Souza FPDE, Furlan-Murari PJ, Pandolfi VCF, Leite NG, Mainardi RM, Chideroli RT, Pereira UP, Araújo EJA, Pupim ACE, Koch JFA, Lopera-Barrero NM. Effects of dietary β-glucans on the productive performance, blood parameters, and intestinal microbiota of angelfish (Pterophyllum scalare) juveniles. AN ACAD BRAS CIENC 2024; 96:e20231006. [PMID: 38451599 DOI: 10.1590/0001-3765202420231006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/29/2023] [Indexed: 03/08/2024] Open
Abstract
Among the potential feed additives, β-glucans are known to positively affect the growth performance, blood parameters, and intestinal microbiota of fish, even the ornamental species. Therefore, the present study evaluated the effects of the dietary supplementation of different Saccharomyces cerevisiae β-glucans concentrations (0, 0.05, 0.1, and 0.2%) in juvenile angelfish (Pterophyllum scalare) over a 42-day period. Regarding growth performance, no effects were observed on most parameters. However, 0.2% β-glucans supplementation produced higher condition factor values, indicating a better nutritional status. Furthermore, β-glucans supplementation did not affect blood parameters. Regarding intestinal microbiota, β-glucans supplementation increased the abundance of the potentially beneficial bacterial genus Phascolarctobacterium. The high abundance of bacteria from the phylum Bacteroidetes, which can degrade β-glucans, may be attributed to the increased abundance of Phascolarctobacterium spp. In addition, 0.2% β-glucans supplementation produced more operational taxonomic units and higher Sobs (observed species richness), indicating effects on the overall bacterial community structure. These results demonstrate the potential application of β-glucans as a dietary supplement to improve the performance and modulate the intestinal microbiota of angelfish.
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Affiliation(s)
- Ed C S DE Lima
- Programa de Pós-Graduação em Ciência Animal, Universidade Estadual de Londrina (UEL), Centro de Ciências Agrárias (CCA), Rodovia Celso Garcia Cid, PR 445 Km 380, 86057-970 Londrina, PR, Brazil
| | - Felipe P DE Souza
- Programa de Pós-Graduação em Ciência Animal, Universidade Estadual de Londrina (UEL), Centro de Ciências Agrárias (CCA), Rodovia Celso Garcia Cid, PR 445 Km 380, 86057-970 Londrina, PR, Brazil
| | - Pâmela Juliana Furlan-Murari
- Programa de Pós-Graduação em Ciência Animal, Universidade Estadual de Londrina (UEL), Centro de Ciências Agrárias (CCA), Rodovia Celso Garcia Cid, PR 445 Km 380, 86057-970 Londrina, PR, Brazil
| | - Victor César F Pandolfi
- Programa de Pós-Graduação em Ciência Animal, Universidade Estadual de Londrina (UEL), Centro de Ciências Agrárias (CCA), Rodovia Celso Garcia Cid, PR 445 Km 380, 86057-970 Londrina, PR, Brazil
| | - Natália G Leite
- Programa de Pós-Graduação em Ciência Animal, Universidade Estadual de Londrina (UEL), Centro de Ciências Agrárias (CCA), Rodovia Celso Garcia Cid, PR 445 Km 380, 86057-970 Londrina, PR, Brazil
| | - Raffaella M Mainardi
- Programa de Pós-Graduação em Ciência Animal, Universidade Estadual de Londrina (UEL), Centro de Ciências Agrárias (CCA), Rodovia Celso Garcia Cid, PR 445 Km 380, 86057-970 Londrina, PR, Brazil
| | - Roberta T Chideroli
- Programa de Pós-Graduação em Ciência Animal, Universidade Estadual de Londrina (UEL), Centro de Ciências Agrárias (CCA), Rodovia Celso Garcia Cid, PR 445 Km 380, 86057-970 Londrina, PR, Brazil
| | - Ulisses P Pereira
- Universidade Estadual de Londrina (UEL), Departamento de Medicina Veterinária Preventiva, Centro de Ciências Agrárias (CCA), Rodovia Celso Garcia Cid, PR 445 Km 380, 86057-970 Londrina, PR, Brazil
| | - Eduardo José A Araújo
- Universidade Estadual de Londrina (UEL), Departamento de Histologia, Centro de Ciência Biológicas (CCB), Rodovia Celso Garcia Cid, PR 445 Km 380, 86057-970 Londrina, PR, Brazil
| | - Andréia Carla E Pupim
- Universidade Estadual de Londrina (UEL), Departamento de Histologia, Centro de Ciência Biológicas (CCB), Rodovia Celso Garcia Cid, PR 445 Km 380, 86057-970 Londrina, PR, Brazil
| | - João Fernando A Koch
- Biorigin Brasil, Rua Quinze de Novembro, 865, Centro, 18680-900 Lençóis Paulista, SP, Brazil
| | - Nelson Mauricio Lopera-Barrero
- Universidade Estadual de Londrina (UEL), Departamento de Zootecnia, Centro de Ciências Agrárias (CCA), Rodovia Celso Garcia Cid, PR 445 Km 380, 86057-970 Londrina, PR, Brazil
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12
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Yang JH, Park JW, Kim HS, Lee S, Yerke AM, Jaiswal YS, Williams LL, Hwang S, Moon KH. Effects of Antibiotic Residues on Fish Gut Microbiome Dysbiosis and Mucosal Barrier-Related Pathogen Susceptibility in Zebrafish Experimental Model. Antibiotics (Basel) 2024; 13:82. [PMID: 38247641 PMCID: PMC10812462 DOI: 10.3390/antibiotics13010082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/05/2024] [Accepted: 01/13/2024] [Indexed: 01/23/2024] Open
Abstract
The symbiotic community of microorganisms in the gut plays an important role in the health of the host. While many previous studies have been performed on the interactions between the gut microbiome and the host in mammals, studies in fish are still lacking. In this study, we investigated changes in the intestinal microbiome and pathogen susceptibility of zebrafish (Danio rerio) following chronic antibiotics exposure. The chronic antibiotics exposure assay was performed on zebrafish for 30 days using oxytetracycline (Otc), sulfamethoxazole/trimethoprim (Smx/Tmp), or erythromycin (Ery), which are antibiotics widely used in the aquaculture industry. The microbiome analysis indicated that Fusobacteria, Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla in the gut microbiome of the zebrafish used in this study. However, in Smx/Tmp-treated zebrafish, the compositions of Fusobacteria and Proteobacteria were changed significantly, and in Ery-treated zebrafish, the compositions of Proteobacteria and Firmicutes were altered significantly. Although alpha diversity analysis showed that there was no significant difference in the richness, beta diversity analysis revealed a community imbalance in the gut microbiome of all chronically antibiotics-exposed zebrafish. Intriguingly, in zebrafish with dysbiosis in the gut microbiome, the pathogen susceptibility to Edwardsiella piscicida, a representative Gram-negative fish pathogen, was reduced. Gut microbiome imbalance resulted in a higher count of goblet cells in intestinal tissue and an upregulation of genes related to the intestinal mucosal barrier. In addition, as innate immunity was enhanced by the increased mucosal barrier, immune and stress-related gene expression in the intestinal tissue was downregulated. In this study, we provide new insight into the effect of gut microbiome dysbiosis on pathogen susceptibility.
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Affiliation(s)
- Jun Hyeok Yang
- Laboratory of Marine Microbiology, Division of Convergence of Marine Science, Korea Maritime & Ocean University, Busan 49112, Republic of Korea; (J.H.Y.); (J.W.P.); (H.S.K.)
- Department of Marine Bioscience and Environment, Korea Maritime & Ocean University, Busan 49112, Republic of Korea
| | - Jeong Woo Park
- Laboratory of Marine Microbiology, Division of Convergence of Marine Science, Korea Maritime & Ocean University, Busan 49112, Republic of Korea; (J.H.Y.); (J.W.P.); (H.S.K.)
- Department of Convergence Study on the Ocean Science and Technology, Ocean Science and Technology School, Korea Maritime & Ocean University, Busan 49112, Republic of Korea
| | - Ho Sung Kim
- Laboratory of Marine Microbiology, Division of Convergence of Marine Science, Korea Maritime & Ocean University, Busan 49112, Republic of Korea; (J.H.Y.); (J.W.P.); (H.S.K.)
- Department of Convergence Study on the Ocean Science and Technology, Ocean Science and Technology School, Korea Maritime & Ocean University, Busan 49112, Republic of Korea
| | - Seungki Lee
- National Institute of Biological Resources, Environmental Research Complex, Incheon 22689, Republic of Korea;
| | - Aaron M. Yerke
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA;
| | - Yogini S. Jaiswal
- Center for Excellence in Post Harvest Technologies, North Carolina Agricultural and Technical State University, The North Carolina Research Campus, 500 Laureate Way, Kannapolis, NC 28081, USA; (Y.S.J.); (L.L.W.)
| | - Leonard L. Williams
- Center for Excellence in Post Harvest Technologies, North Carolina Agricultural and Technical State University, The North Carolina Research Campus, 500 Laureate Way, Kannapolis, NC 28081, USA; (Y.S.J.); (L.L.W.)
| | - Sungmin Hwang
- Division of Practical Research, Honam National Institute Biological Resources, Mokpo-si 58762, Republic of Korea
| | - Ki Hwan Moon
- Laboratory of Marine Microbiology, Division of Convergence of Marine Science, Korea Maritime & Ocean University, Busan 49112, Republic of Korea; (J.H.Y.); (J.W.P.); (H.S.K.)
- Department of Marine Bioscience and Environment, Korea Maritime & Ocean University, Busan 49112, Republic of Korea
- Department of Convergence Study on the Ocean Science and Technology, Ocean Science and Technology School, Korea Maritime & Ocean University, Busan 49112, Republic of Korea
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13
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Bellec L, Milinkovitch T, Dubillot E, Pante É, Tran D, Lefrancois C. Fish gut and skin microbiota dysbiosis induced by exposure to commercial sunscreen formulations. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2024; 266:106799. [PMID: 38113619 DOI: 10.1016/j.aquatox.2023.106799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/03/2023] [Accepted: 12/08/2023] [Indexed: 12/21/2023]
Abstract
UV filters (organic or mineral) present in sunscreen products are emerging contaminants of coastal aquatic environments. There is an urgent need to understand marine organisms responses to these compounds. In this study, we investigated the effect of exposure to dilutions of commercial sunscreen formulations on bacterial communities of mullet (Chelon sp.). The gut and skin mucus microbial communities were characterized using a metabarcoding approach targeting the 16S rRNA gene. Our results revealed that mullets had its own bacterial communities that differ from their surrounding habitats and specific to tissue. The dilutions of commercial sunscreens modified the relative abundance of Actinobacteroita, Bacteriodota and Proteobacteria for both gut and skin microbiota. They also allowed to bacteria affiliated to Mycobacterium, Nocardia and Tenacibaculum genera, known to house pathogenic species, to colonize the epithelium which may have implications for fish host health.
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Affiliation(s)
- Laure Bellec
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France.
| | | | - Emmanuel Dubillot
- La Rochelle Univ., CNRS, LIENSs, UMR 7266, La Rochelle F-17000, France
| | - Éric Pante
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, IUEM, F-29280 Plouzané, France
| | - Damien Tran
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
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14
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Biswas S, Foysal MJ, Mannan A, Sharifuzzaman SM, Tanzina AY, Tanni AA, Sharmen F, Hossain MM, Chowdhury MSN, Tay ACY, Islam SMR. Microbiome pattern and diversity of an anadromous fish, hilsa shad (Tenualosa ilisha). Mol Biol Rep 2023; 51:38. [PMID: 38158480 DOI: 10.1007/s11033-023-08965-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 10/30/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND The host-microbe interactions are complex, dynamic and context-dependent. In this regard, migratory fish species like hilsa shad (Tenualosa ilisha), which migrates from seawater to freshwater for spawning, provides a unique system for investigating the microbiome under an additional change in fish's habitat. This work was undertaken to detect taxonomic variation of microbiome and their function in the migration of hilsa. METHODS AND RESULTS The study employed 16S rRNA amplicon-based metagenomic analysis to scrutinize bacterial diversity in hilsa gut, skin mucus and water. Thus, a total of 284 operational taxonomic units (OTUs), 9 phyla, 35 orders and 121 genera were identified in all samples. More than 60% of the identified bacteria were Proteobacteria with modest abundance (> 5%) of Firmicutes, Bacteroidetes and Actinobacteria. Leucobacter in gut and Serratia in skin mucus were the core bacterial genera, while Acinetobacter, Pseudomonas and Psychrobacter exhibited differential compositions in gut, skin mucus and water. CONCLUSIONS Representative fresh-, brackish- and seawater samples of hilsa habitats were primarily composed of Vibrio, Serratia and Psychrobacter, and their diversity in seawater was significantly higher (P < 0.05) than freshwater. Overall, salinity and water microbiota had an influence on the microbial composition of hilsa shad, contributing to host metabolism and adaptation processes. This pioneer exploration of hilsa gut and skin mucus bacteria across habitats will advance our insights into microbiome assembly in migratory fish populations.
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Affiliation(s)
- Sabuj Biswas
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Adnan Mannan
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - S M Sharifuzzaman
- Institute of Marine Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Afsana Yeasmin Tanzina
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Afroza Akter Tanni
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Farjana Sharmen
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Md Mobarok Hossain
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | | | - Alfred Chin-Yen Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - S M Rafiqul Islam
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh.
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh.
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15
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Berggren H, Nordahl O, Yıldırım Y, Larsson P, Tibblin P, Forsman A. Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish. Proc Biol Sci 2023; 290:20231608. [PMID: 38113936 PMCID: PMC10730295 DOI: 10.1098/rspb.2023.1608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Abstract
Variation in the composition of skin-associated microbiomes has been attributed to host species, geographical location and habitat, but the role of intraspecific phenotypic variation among host individuals remains elusive. We explored if and how host environment and different phenotypic traits were associated with microbiome composition. We conducted repeated sampling of dorsal and ventral skin microbiomes of carp individuals (Cyprinus carpio) before and after translocation from laboratory conditions to a semi-natural environment. Both alpha and beta diversity of skin-associated microbiomes increased substantially within and among individuals following translocation, particularly on dorsal body sites. The variation in microbiome composition among hosts was significantly associated with body site, sun-basking, habitat switch and growth, but not temperature gain while basking, sex, personality nor colour morph. We suggest that the overall increase in the alpha and beta diversity estimates among hosts were induced by individuals expressing greater variation in behaviours and thus exposure to potential colonizers in the pond environment compared with the laboratory. Our results exemplify how biological diversity at one level of organization (phenotypic variation among and within fish host individuals) together with the external environment impacts biological diversity at a higher hierarchical level of organization (richness and composition of fish-associated microbial communities).
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Affiliation(s)
- Hanna Berggren
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Oscar Nordahl
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Yeşerin Yıldırım
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Per Larsson
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Petter Tibblin
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Anders Forsman
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
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16
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Abasubong KP, Jiang GZ, Guo HX, Wang X, Li XF, Yan-Zou D, Liu WB, Desouky HE. High-fat diet alters intestinal microbiota and induces endoplasmic reticulum stress via the activation of apoptosis and inflammation in blunt snout bream. FISH PHYSIOLOGY AND BIOCHEMISTRY 2023; 49:1079-1095. [PMID: 37831370 DOI: 10.1007/s10695-023-01240-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/16/2023] [Indexed: 10/14/2023]
Abstract
The primary organ for absorbing dietary fat is the gut. High dietary lipid intake negatively affects health and absorption by causing fat deposition in the intestine. This research explores the effect of a high-fat diet (HFD) on intestinal microbiota and its connections with endoplasmic reticulum stress and inflammation. 60 fish (average weight: 45.84 ± 0.07 g) were randomly fed a control diet (6% fat) and a high-fat diet (12 % fat) in four replicates for 12 weeks. From the result, hepatosomatic index (HSI), Visceralsomatic index (VSI), abdominal fat (ADF), Intestosomatic index (ISI), mesenteric fat (MFI), Triglycerides (TG), total cholesterol (TC), non-esterified fatty acid (NEFA) content were substantially greater on HFD compared to the control diet. Moreover, fish provided the HFD significantly obtained lower superoxide dismutase (SOD) and glutathione peroxidase (GPX) activities. In contrast, an opposite result was seen in malondialdehyde (MDA) content in comparison to the control. HFD significantly altered intestinal microbiota in blunt snout bream, characterized by an increased abundance of Aeromonas, Plesiomonas proteobacteria, and firmicutes with a reduced abundance of Cetobacterium and ZOR0006. The transcriptional levels of glucose-regulated protein 78 (grp78), inositol requiring enzyme 1 (ire1), spliced X box-binding protein 1 (xbp1), DnaJ heat shock protein family (Hsp40) member B9 (dnajb9), tumor necrosis factor alpha (tnf-α), nuclear factor-kappa B (nf-κb), monocyte chemoattractant protein-1 (mcp-1), and interleukin-6 (il-6) in the intestine were markedly upregulated in fish fed HFD than the control group. Also, the outcome was similar in bax, caspases-3, and caspases-9, ZO-1, Occludin-1, and Occludin-2 expressions. In conclusion, HFD could alter microbiota and facilitate chronic inflammatory signals via activating endoplasmic reticulum stress.
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Affiliation(s)
- Kenneth Prudence Abasubong
- 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
- National Laboratory of Animal Science, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Guang-Zhen Jiang
- 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
- National Laboratory of Animal Science, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Hui-Xing Guo
- 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
- National Laboratory of Animal Science, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Xi Wang
- 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
- National Laboratory of Animal Science, 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
- National Laboratory of Animal Science, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Dong Yan-Zou
- 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
- National Laboratory of Animal Science, 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.
- National Laboratory of Animal Science, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China.
| | - Hesham Eed Desouky
- 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
- National Laboratory of Animal Science, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
- Department of Animal and Poultry Production, Faculty of Agriculture, Damanhour University, Damanhour, Beheria, 22713, Egypt
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17
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Scheifler M, Magnanou E, Sanchez-Brosseau S, Desdevises Y. Host-microbiota-parasite interactions in two wild sparid fish species, Diplodus annularis and Oblada melanura (Teleostei, Sparidae) over a year: a pilot study. BMC Microbiol 2023; 23:340. [PMID: 37974095 PMCID: PMC10652623 DOI: 10.1186/s12866-023-03086-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/23/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The microbiota in fish external mucus is mainly known for having a role in homeostasis and protection against pathogens, but recent evidence suggests it is also involved in the host-specificity of some ectoparasites. In this study, we investigated the influence of seasonality and environmental factors on both fish external microbiota and monogenean gill ectoparasites abundance and diversity and assessed the level of covariations between monogenean and bacterial communities across seasons. To do so, we assessed skin and gill microbiota of two sparid species, Oblada melanura and Diplodus annularis, over a year and collected their specific monogenean ectoparasites belonging to the Lamellodiscus genus. RESULTS Our results revealed that diversity and structure of skin and gill mucus microbiota were strongly affected by seasonality, mainly by the variations of temperature, with specific fish-associated bacterial taxa for each season. The diversity and abundance of parasites were also influenced by seasonality, with the abundance of some Lamellodiscus species significantly correlated to temperature. Numerous positive and negative correlations between the abundance of given bacterial genera and Lamellodiscus species were observed throughout the year, suggesting their differential interaction across seasons. CONCLUSIONS The present study is one of the first to demonstrate the influence of seasonality and related abiotic factors on fish external microbiota over a year. We further identified potential interactions between gill microbiota and parasite occurrence in wild fish populations, improving current knowledge and understanding of the establishment of host-specificity.
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Affiliation(s)
- Mathilde Scheifler
- Sorbonne Université, CNRS, Biologie Intégrative Des Organismes Marins, BIOM, Banyuls-sur-Mer, F-66650, France.
| | - Elodie Magnanou
- Sorbonne Université, CNRS, Biologie Intégrative Des Organismes Marins, BIOM, Banyuls-sur-Mer, F-66650, France
| | - Sophie Sanchez-Brosseau
- Sorbonne Université, CNRS, Biologie Intégrative Des Organismes Marins, BIOM, Banyuls-sur-Mer, F-66650, France
| | - Yves Desdevises
- Sorbonne Université, CNRS, Biologie Intégrative Des Organismes Marins, BIOM, Banyuls-sur-Mer, F-66650, France
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18
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Kakakhel MA, Narwal N, Kataria N, Johari SA, Zaheer Ud Din S, Jiang Z, Khoo KS, Xiaotao S. Deciphering the dysbiosis caused in the fish microbiota by emerging contaminants and its mitigation strategies-A review. ENVIRONMENTAL RESEARCH 2023; 237:117002. [PMID: 37648194 DOI: 10.1016/j.envres.2023.117002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/01/2023]
Abstract
The primary barrier to nutrient absorption in fish is the intestinal epithelium, followed by a community of microorganisms known as the gut microbiota, which can be thought of as a hidden organ. The gastrointestinal microbiota of fish plays a key role in the upholding of overall health by maintaining the homeostasis and disease resistance of the host. However, emerging contaminants as the result of anthropogenic activities have significantly led to disruptions and intestinal dysbiosis in fish. Which probably results in fish mortalities and disrupts the balance of an ecosystem. Therefore, we comprehensively seek to compile the effects and consequences of emerging contaminations on fish intestinal microbiota. Additionally, the mitigation strategies including prebiotics, probiotics, plant-based diet, and Biofloc technology are being outlined. Biofloc technology (BFT) can treat toxic materials, i.e., nitrogen components, and convert them into a useful product such as proteins and demonstrated promising elevating technique for the fish intestinal bacterial composition. However, it remains unclear whether the bacterial isolate is primarily responsible for the BFT's removal of nitrate and ammonia and the corresponding removal mechanism. To answer this, real time polymerase chain reaction (RT-PCR) with metagenomics, transcriptomics, and proteomics techniques probably provides a possible solution.
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Affiliation(s)
- Mian Adnan Kakakhel
- Hubei International Science and Technology Cooperation Base of Fish Passage, Three Gorges University, Yichang, 443002, Hubei, China; College of Hydraulic & Environmental Engineering, Three Gorges University, Yichang, 443002, Hubei, China
| | - Nishita Narwal
- University School of Environment Management, Guru Gobind Singh Indraprastha University, New Delhi, 110078, India
| | - Navish Kataria
- Department of Environmental Sciences, J.C. Bose University of Science and Technology, YMCA, Faridabad, Haryana, 121006, India
| | - Seyed Ali Johari
- Department of Fisheries, Faculty of Natural Resources, University of Kurdistan, Sanandaj, Kurdistan, Iran
| | - Syed Zaheer Ud Din
- International School for Optoelectronic Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Zewen Jiang
- Hubei International Science and Technology Cooperation Base of Fish Passage, Three Gorges University, Yichang, 443002, Hubei, China; College of Hydraulic & Environmental Engineering, Three Gorges University, Yichang, 443002, Hubei, China
| | - Kuan Shiong Khoo
- Department of Chemical Engineering and Materials Science, Yuan Ze University, Taoyuan, Taiwan
| | - Shi Xiaotao
- Hubei International Science and Technology Cooperation Base of Fish Passage, Three Gorges University, Yichang, 443002, Hubei, China; College of Hydraulic & Environmental Engineering, Three Gorges University, Yichang, 443002, Hubei, China.
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19
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Rankins DR, Herrera MJ, Christensen MP, Chen A, Hood NZ, Heras J, German DP. When digestive physiology doesn't match "diet": Lumpenus sagitta (Stichaeidae) is an "omnivore" with a carnivorous gut. Comp Biochem Physiol A Mol Integr Physiol 2023; 285:111508. [PMID: 37625480 DOI: 10.1016/j.cbpa.2023.111508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/21/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023]
Abstract
What an animal ingests and what it digests can be different. Thus, we examined the nutritional physiology of Lumpenus sagitta, a member of the family Stichaeidae, to better understand whether it could digest algal components like its better studied algivorous relatives. Although L. sagitta ingests considerable algal content, we found little evidence of algal digestion. This fish species has a short gut that doesn't show positive allometry with body size, low amylolytic activity that actually decreases as the fish grow, no ontogenetic changes in digestive enzyme gene expression, elevated N-acetyl-glucosaminidase activity (indicative of chitin breakdown), and an enteric microbial community that is consistent with carnivory and differs from members of its family that consume and digest algae. Hence, we are left concluding that L. sagitta is not capable of digesting the algae it consumes, and instead, are likely targeting epibionts on the algae itself, and other invertebrates consumed with the algae. Our study expands the coverage of dietary and digestive information for the family Stichaeidae, which is becoming a model for fish digestive physiology and genomics, and shows the power of moving beyond gut content analyses to better understand what an animal can actually digest and use metabolically.
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Affiliation(s)
- Daniel R Rankins
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA.
| | - Michelle J Herrera
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Michelle P Christensen
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Alisa Chen
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Newton Z Hood
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Joseph Heras
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Donovan P German
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
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20
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Mes W, Lücker S, Jetten MSM, Siepel H, Gorissen M, van Kessel MAHJ. Comparison of the gill and gut microbiomes of common carp (Cyprinus carpio) and zebrafish (Danio rerio) and their RAS environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165212. [PMID: 37391154 DOI: 10.1016/j.scitotenv.2023.165212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/12/2023] [Accepted: 06/27/2023] [Indexed: 07/02/2023]
Abstract
Recirculating aquaculture systems (RAS) are increasingly being used to grow fish, as intensive water reuse reduces water consumption and environmental impact. RAS use biofilters containing nitrogen-cycling microorganisms that remove ammonia from the aquaculture water. Knowledge of how RAS microbial communities relate to the fish-associated microbiome is limited, as is knowledge of fish-associated microbiota in general. Recently, nitrogen-cycling bacteria have been discovered in zebrafish and carp gills and shown to detoxify ammonia in a manner similar to the RAS biofilter. Here, we compared RAS water and biofilter microbiomes with fish-associated gut and gill microbial communities in laboratory RAS housing either zebrafish (Danio rerio) or common carp (Cyprinus carpio) using 16S rRNA gene amplicon sequencing. The phylogeny of ammonia-oxidizing bacteria in the gills and the RAS environment was investigated in more detail by phylogenetic analysis of the ammonia monooxygenase subunit A (amoA). The location from which the microbiome was sampled (RAS compartments and gills or gut) had a stronger effect on community composition than the fish species, but species-specific differences were also observed. We found that carp- and zebrafish-associated microbiomes were highly distinct from their respective RAS microbiomes, characterized by lower overall diversity and a small core microbiome consisting of taxa specifically adapted to the respective organ. The gill microbiome was also defined by a high proportion of unique taxa. Finally, we found that amoA sequences from the gills were distinct from those from the RAS biofilter and water. Our results showed that the gut and gill microbiomes of carp and zebrafish share a common and species-specific core microbiome that is distinct from the microbially-rich RAS environment.
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Affiliation(s)
- Wouter Mes
- Cluster Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, the Netherlands; Cluster Ecology & Physiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, the Netherlands
| | - Sebastian Lücker
- Cluster Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, the Netherlands
| | - Mike S M Jetten
- Cluster Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, the Netherlands
| | - Henk Siepel
- Cluster Ecology & Physiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, the Netherlands
| | - Marnix Gorissen
- Cluster Ecology & Physiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, the Netherlands
| | - Maartje A H J van Kessel
- Cluster Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, the Netherlands.
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21
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Pisaniello A, Handley KM, White WL, Angert ER, Boey JS, Clements KD. Host individual and gut location are more important in gut microbiota community composition than temporal variation in the marine herbivorous fish Kyphosus sydneyanus. BMC Microbiol 2023; 23:275. [PMID: 37773099 PMCID: PMC10540440 DOI: 10.1186/s12866-023-03025-2] [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: 03/23/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Gut microbiota play a key role in the nutrition of many marine herbivorous fishes through hindgut fermentation of seaweed. Gut microbiota composition in the herbivorous fish Kyphosus sydneyanus (family Kyphosidae) varies between individuals and gut sections, raising two questions: (i) is community composition stable over time, especially given seasonal shifts in storage metabolites of dietary brown algae, and (ii) what processes influence community assembly in the hindgut? RESULTS We examined variation in community composition in gut lumen and mucosa samples from three hindgut sections of K. sydneyanus collected at various time points in 2020 and 2021 from reefs near Great Barrier Island, New Zealand. 16S rRNA gene analysis was used to characterize microbial community composition, diversity and estimated density. Differences in community composition between gut sections remained relatively stable over time, with little evidence of temporal variation. Clostridia dominated the proximal hindgut sections and Bacteroidia the most distal section. Differences were detected in microbial composition between lumen and mucosa, especially at genus level. CONCLUSIONS High variation in community composition and estimated bacterial density among individual fish combined with low variation in community composition temporally suggests that initial community assembly involved environmental selection and random sampling/neutral effects. Community stability following colonisation could also be influenced by historical contingency, where early colonizing members of the community may have a selective advantage. The impact of temporal changes in the algae may be limited by the dynamics of substrate depletion along the gut following feeding, i.e. the depletion of storage metabolites in the proximal hindgut. Estimated bacterial density, showed that Bacteroidota has the highest density (copies/mL) in distal-most lumen section V, where SCFA concentrations are highest. Bacteroidota genera Alistipes and Rikenella may play important roles in the breakdown of seaweed into useful compounds for the fish host.
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Affiliation(s)
- Alessandro Pisaniello
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.
| | - Kim M Handley
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - W Lindsey White
- School of Science, Auckland University of Technology, Private Bag 92006, Auckland, New Zealand
| | - Esther R Angert
- Department of Microbiology, Cornell University, 123 Wing Drive, Ithaca, NY, 14853, USA
| | - Jian Sheng Boey
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Kendall D Clements
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.
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22
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Chakraborty M, Acharya D, Dutta TK. Diversity analysis of hilsa (Tenualosa ilisha) gut microbiota using culture-dependent and culture-independent approaches. J Appl Microbiol 2023; 134:lxad208. [PMID: 37699793 DOI: 10.1093/jambio/lxad208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 09/14/2023]
Abstract
AIMS The bacterial communities associated with the gastrointestinal (GI) tract are primarily involved in digestion, physiology, and the immune response against pathogenic bacteria for the overall development and health of the host. Hilsa shad (Tenualosa ilisha), a tropical anadromous fish, found predominantly in Bangladesh and India, has so far been poorly investigated for its gut bacterial communities. In this study, both culture-based and metagenomic approaches were used to detect intestinal isolates of hilsa, captured from both freshwater and seawater to investigate the community structure of intestinal microbiota. METHODS AND RESULTS Culture-dependent approach allowed to isolate a total of 23 distinct bacterial species comprising 16 Gram-negative, and 7 Gram-positive isolates, where Proteobacteria and Firmicutes were identified as the two most dominant phyla. While metagenomic approach explored a wide range of important GI bacteria, primarily dominated by Proteobacteria, Firmicutes, and Bacteroidetes, with Proteobacteria and Firmicutes, being the most abundant in freshwater and seawater samples, respectively. CONCLUSIONS A combination of these approaches provided the differential GI-associated bacterial diversity in freshwater and seawater hilsa with the prediction of overall functional potential. IMPACT STATEMENT The study explored the diversity of gut microbiota in hilsa, one of the most preferred nutritious dietary fish, captured from freshwater and seawater habitats, which may encourage to comprehend the composition of the gut microbiome in relation to the migratory behavior and polyunsaturated fatty acid profile of anadromous fish in general.
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Affiliation(s)
- Megha Chakraborty
- Department of Microbiology, Bose Institute, Kolkata 700091, West Bengal, India
| | - Debarun Acharya
- Department of Microbiology, Bose Institute, Kolkata 700091, West Bengal, India
| | - Tapan K Dutta
- Department of Microbiology, Bose Institute, Kolkata 700091, West Bengal, India
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23
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Pan X, Raaijmakers JM, Carrión VJ. Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning. Trends Microbiol 2023; 31:959-971. [PMID: 37173204 DOI: 10.1016/j.tim.2023.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 05/15/2023]
Abstract
Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.
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Affiliation(s)
- Xinya Pan
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands; Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain; Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Málaga, Spain.
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24
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Paralika V, Kokou F, Karapanagiotis S, Makridis P. Characterization of Host-Associated Microbiota and Isolation of Antagonistic Bacteria from Greater Amberjack ( Seriola dumerili, Risso, 1810) Larvae. Microorganisms 2023; 11:1889. [PMID: 37630449 PMCID: PMC10456766 DOI: 10.3390/microorganisms11081889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Greater amberjack (Seriola dumerili) is a new species in marine aquaculture with high mortalities at the larval stages. The microbiota of amberjack larvae was analyzed using 16S rDNA sequencing in two groups, one added copepod nauplii (Acartia tonsa) in the diet, and one without copepods (control). In addition, antagonistic bacteria were isolated from amberjack larvae and live food cultures. Proteobacteria was the most abundant phylum followed by Bacteroidota in amberjack larvae. The composition and diversity of the microbiota were influenced by age, but not by diet. Microbial community richness and diversity significantly increased over time. Rhodobacteraceae was the most dominant family followed by Vibrionaceae, which showed the highest relative abundance in larvae from the control group 31 days after hatching. Alcaligenes and Thalassobius genera exhibited a significantly higher relative abundance in the copepod group. Sixty-two antagonistic bacterial strains were isolated and screened for their ability to inhibit four fish pathogens (Aeromonas veronii, Vibrio harveyi, V. anguillarum, V. alginolyticus) using a double-layer test. Phaeobacter gallaeciensis, Phaeobacter sp., Ruegeria sp., and Rhodobacter sp. isolated from larvae and Artemia sp. inhibited the fish pathogens. These antagonistic bacteria could be used as host-derived probiotics to improve the growth and survival of the greater amberjack larvae.
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Affiliation(s)
| | - Fotini Kokou
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, 6700 AH Wageningen, The Netherlands;
| | | | - Pavlos Makridis
- Department of Biology, University of Patras, 26504 Rio, Greece;
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25
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Morshed SM, Lee TH. The role of the microbiome on fish mucosal immunity under changing environments. FISH & SHELLFISH IMMUNOLOGY 2023:108877. [PMID: 37302678 DOI: 10.1016/j.fsi.2023.108877] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/13/2023]
Abstract
The environment is crucial for fish as their mucosal surfaces face continuous challenges in the water. Fish mucosal surfaces harbor the microbiome and mucosal immunity. Changes in the environment could affect the microbiome, thus altering mucosal immunity. Homeostasis between the microbiome and mucosal immunity is crucial for the overall health of fish. To date, very few studies have investigated mucosal immunity and its interaction with the microbiome in response to environmental changes. Based on the existing studies, we can infer that environmental factors can modulate the microbiome and mucosal immunity. However, we need to retrospectively examine the existing literature to investigate the possible interaction between the microbiome and mucosal immunity under specific environmental conditions. In this review, we summarize the existing literature on the effects of environmental changes on the fish microbiome and mucosal immunity. This review mainly focuses on temperature, salinity, dissolved oxygen, pH, and photoperiod. We also point out a gap in the literature and provide directions to go further in this research field. In-depth knowledge about mucosal immunity-microbiome interaction will also improve aquaculture practices by reducing loss during environmental stressful conditions.
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Affiliation(s)
- Syed Monzur Morshed
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan; The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Tsung-Han Lee
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan; The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.
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26
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Bera AK, Chowdhury H, Ghatak S, Malick RC, Chakraborty N, Chakraborty HJ, Swain HS, Hassan MA, Das BK. Microbiome analysis reveals potential for modulation of gut microbiota through polysaccharide-based prebiotic feeding in Oreochromis niloticus (Linnaeus, 1758). Front Physiol 2023; 14:1168284. [PMID: 37362433 PMCID: PMC10285058 DOI: 10.3389/fphys.2023.1168284] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
Characterization and functional profiling of the gut microbiota are essential for guiding nutritional interventions in fish and achieving favorable host-microbe interactions. Thus, we conducted a 30 days study to explore and document the gut microbial community of O. niloticus, as well as to evaluate the effects of a polysaccharide-based prebiotics with 0.5% and 0.75% Aloe vera extract on the gut microbiome through genomic analysis. The V3-V4 region of 16S rRNA was amplified and sequenced using Illumina HiSeq 2500, resulting in 1,000,199 reads for operational taxonomic unit (OTU) identification. Out of 8,894 OTUs, 1,181 were selected for further analysis. Our results revealed that Planctomycetes, Firmicutes, Proteobacteria, Verrucomicrobia, Actinobacteria, and Fusobacteria were the dominant phyla in both control and treatment samples. Higher doses of prebiotics were found to improve Planctomycetes and Firmicutes while decreasing Proteobacteria and Verrucomicrobia. We observed increasing trends in the abundance of Bacilli, Bacillaceae, and Bacillus bacteria at the class, family, and genus levels, respectively, in a dose-dependent manner. These findings were consistent with the conventional colony count data, which showed a higher prevalence of Bacillus in prebiotic-supplemented groups. Moreover, predicted functional analysis using PICRUSt indicated a dose-dependent upregulation in glycolysis V, superpathway of glycol metabolism and degradation, glucose and xylose degradation, glycolysis II, and sulfoglycolysis pathways. Most of the energy, protein, and amino acid synthesis pathways were upregulated only at lower doses of prebiotic treatment. Our findings suggest that the gut microbiome of O. niloticus can be optimized through nutritional interventions with plant-based polysaccharides for improved growth performance in commercial fish.
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Affiliation(s)
- Asit Kumar Bera
- Central Inland Fisheries Research Institute (ICAR), Bārākpur, India
| | | | - Sandeep Ghatak
- The ICAR Research Complex for North Eastern Hill Region (ICAR RC NEH), Umiam, India
| | | | | | | | | | - M. A. Hassan
- Central Inland Fisheries Research Institute (ICAR), Bārākpur, India
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27
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Chen J, Li Q, Tan C, Xie L, Yang X, Zhang Q, Deng X. Effects of enrofloxacin's exposure on the gut microbiota of Tilapia fish (Oreochromis niloticus). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 46:101077. [PMID: 37080057 DOI: 10.1016/j.cbd.2023.101077] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/02/2023] [Accepted: 04/09/2023] [Indexed: 04/22/2023]
Abstract
Enrofloxacin (ENFX) has a broad-spectrum antibiotic activity, which is widely used in aquaculture. The effect of different ENFX exposure ways on the gut microbiota of tilapia is unclear. This study was conducted to investigate the effects of ENFX exposure on the gut microbiota of tilapia fish (Oreochromis niloticus). Three methods of ENFX exposure were selected: injection (IEG), oral administration (OEG) and soaking (SEG). After 48 h of exposure period, the intestine of tilapia was collected for high-throughput sequencing. PCoA analysis revealed a distinct clustering of control group, and which was located rather far away from ENFX exposure groups. The dominant phyla in the gut microbiota of tilapia fish were Proteobacteria, Actinobacteriota, Fusobacteria and Firmicutes. Compared to the control group, phylum Fusobacteriota was increased in SEG and IEG while decreased in OEG. ENFX treatment led to a decline in Corynebacterium, Clostridium sensu stricto_3 and Bacillus in treated fish compared with control fish, accompanied by an increase in Akkermansia, Ralstonia and Romboutsia. IEG had the least effect on gut microbiota of tilapia because it retained more microbes among treatment groups. Alpha- diversity decreased the most in SEG, but retained more probiotics such as Cetobacterium and Akkermansia. We assessed the effect of enrofloxacin on tilapia by changes in intestinal flora. The result indicated that either exposure method significantly reduced the diversity of tilapia gut microbiota. It may provide basic data for the scientific use of ENFX in aquaculture.
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Affiliation(s)
- Jiayu Chen
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Jingming South Road No.727, Chenggong, Kunming, China
| | - Qiuyue Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Jingming South Road No.727, Chenggong, Kunming, China
| | - Chunyan Tan
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Jingming South Road No.727, Chenggong, Kunming, China
| | - Liqin Xie
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Jingming South Road No.727, Chenggong, Kunming, China
| | - Xuejiao Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Jingming South Road No.727, Chenggong, Kunming, China
| | - Qilin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Jingming South Road No.727, Chenggong, Kunming, China
| | - Xianyu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Jingming South Road No.727, Chenggong, Kunming, China.
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28
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Yue Z, Fan Z, Zhang H, Feng B, Wu C, Chen S, Ouyang J, Fan H, Weng P, Feng H, Chen S, Dong M, Xu A, Huang S. Differential roles of the fish chitinous membrane in gut barrier immunity and digestive compartments. EMBO Rep 2023; 24:e56645. [PMID: 36852962 PMCID: PMC10074124 DOI: 10.15252/embr.202256645] [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: 12/10/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 03/01/2023] Open
Abstract
The chitin-based peritrophic matrix (PM) is a structure critical for both gut immunity and digestion in invertebrates. PM was traditionally considered lost in all vertebrates, but a PM-like chitinous membrane (CM) has recently been discovered in fishes, which may increase the knowledge on vertebrate gut physiology and structural evolution. Here, we show that in zebrafish, the CM affects ingestion behavior, microbial homeostasis, epithelial renewal, digestion, growth, and longevity. Young mutant fish without CM appear healthy and are able to complete their life cycle normally, but with increasing age they develop gut inflammation, resulting in gut atrophy. Unlike mammals, zebrafish have no visible gel-forming mucin layers to protect their gut epithelia, but at least in young fish, the CM is not a prerequisite for the antibacterial gut immunity. These findings provide new insights into the role of the CM in fish prosperity and its eventual loss in tetrapods. These findings may also help to improve fish health and conservation, as well as to advance the understanding of vertebrate gut physiology and human intestinal diseases.
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Affiliation(s)
- Zirui Yue
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life SciencesSun Yat‐sen UniversityGuangdongChina#
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Zhaoyu Fan
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life SciencesSun Yat‐sen UniversityGuangdongChina#
| | - Hao Zhang
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life SciencesSun Yat‐sen UniversityGuangdongChina#
| | - Buhan Feng
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life SciencesSun Yat‐sen UniversityGuangdongChina#
| | - Chengyi Wu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life SciencesXiamen UniversityXiamenChina
| | - Shenghui Chen
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life SciencesSun Yat‐sen UniversityGuangdongChina#
| | - Jihua Ouyang
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life SciencesSun Yat‐sen UniversityGuangdongChina#
| | - Huiping Fan
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life SciencesSun Yat‐sen UniversityGuangdongChina#
| | - Panwei Weng
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life SciencesSun Yat‐sen UniversityGuangdongChina#
| | - Huixiong Feng
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life SciencesSun Yat‐sen UniversityGuangdongChina#
| | - Shangwu Chen
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life SciencesSun Yat‐sen UniversityGuangdongChina#
| | - Meiling Dong
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life SciencesSun Yat‐sen UniversityGuangdongChina#
| | - Anlong Xu
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life SciencesSun Yat‐sen UniversityGuangdongChina#
- School of Life SciencesBeijing University of Chinese MedicineBeijingChina
| | - Shengfeng Huang
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life SciencesSun Yat‐sen UniversityGuangdongChina#
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
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Van Doan H, Wangkahart E, Thaimuangphol W, Panase P, Sutthi N. Effects of Bacillus spp. Mixture on Growth, Immune Responses, Expression of Immune-Related Genes, and Resistance of Nile Tilapia Against Streptococcus agalactiae Infection. Probiotics Antimicrob Proteins 2023; 15:363-378. [PMID: 34596882 DOI: 10.1007/s12602-021-09845-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2021] [Indexed: 12/16/2022]
Abstract
The purpose of this study was to evaluate the effect of Bacillus spp. mixture (Bacillus subtilis TISTR001, Bacillus megaterium TISTR067, and Bacillus licheniformis DF001) (1 × 106 CFU/g) on growth, immune parameters, immune-related gene expression, and resistance of Nile tilapia against Streptococcus agalactiae AAHM04. Fish were fed different concentrations of Bacillus spp. 0 (control; T1), 1 (T2), 3 (T3), and 5 (T4) g/kg diets for 120 days. The results showed that weight gain, average daily gain, specific growth rate, feed conversion ratio in T3 diet were significantly higher than the control group and other tested diets (p < 0.05). Immune parameters, such as myeloperoxidase and lysozyme, were significantly higher in the T3 and T4 diets compared to the control group (p < 0.05). Similarly, IL-1β and TNF-α gene expressions in the spleen of fish fed T2, T3, and T4 diets were significantly higher than the control group (p < 0.05). However, no significant differences in survival rate, hematology, blood chemical indices, malondialdehyde (MDA) levels, body chemical composition, and organosomatic indices (p > 0.05) were noticed in all treatments. No significant differences in survival rate after the challenge test with S. agalactiae AAHM04 were found in fish fed Bacillus spp. mixture diets, except for the T3 diet. These results suggest that Bacillus spp. mixture diet at 3 g/kg diet (T3) could improve growth, immune response, and disease resistance of Nile tilapia.
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Affiliation(s)
- Hien Van Doan
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
- Science and Technology Research Institute, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Eakapol Wangkahart
- Department of Agricultural Technology, Faculty of Technology, Mahasarakham University, Maha Sarakham, 44150, Thailand
- Research Unit of Excellence for Tropical Fisheries and Technology, Faculty of Technology, Mahasarakham University, Maha Sarakham, 44150, Thailand
| | - Wipavee Thaimuangphol
- Department of Agricultural Technology, Faculty of Technology, Mahasarakham University, Maha Sarakham, 44150, Thailand
- Research Unit of Excellence for Tropical Fisheries and Technology, Faculty of Technology, Mahasarakham University, Maha Sarakham, 44150, Thailand
| | - Paiboon Panase
- Fisheries Division, School of Agriculture and Natural Resources, University of Phayao, Phayao, 56000, Thailand
- Unit of Excellence 2022 on Biodiversity and Natural Resources Management (FF65-UoE003), University of Phayao, Phayao, 56000, Thailand
| | - Nantaporn Sutthi
- Department of Agricultural Technology, Faculty of Technology, Mahasarakham University, Maha Sarakham, 44150, Thailand.
- Research Unit of Excellence for Tropical Fisheries and Technology, Faculty of Technology, Mahasarakham University, Maha Sarakham, 44150, Thailand.
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Elfidasari D, Rijal MS, Shalsabilla SE, Rahma Fadila DS, Cici A, Pikoli MR, Tetriana D, Sugoro I. Intestinal bacteria diversity of suckermouth catfish (Pterygoplichthys pardalis) in the Cd, Hg, and Pb contaminated Ciliwung River, Indonesia. Heliyon 2023; 9:e14842. [PMID: 37025814 PMCID: PMC10070546 DOI: 10.1016/j.heliyon.2023.e14842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/10/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
The contamination of aquatic environments with heavy metals poses a serious threat to fish, potentially leading to diseases or even death. Therefore, there is an urgent need for studies to investigate the adaptability of fish in heavy metal-contaminated environments. Several studies have explored the adaptability of suckermouth catfish (P. pardalis) to survive in the contaminated Ciliwung River. The findings obtained showed that the presence of intestinal bacteria helped these fish overcome the heavy metals in their intestines, thereby enabling the fish to survive. Analysis using the Next Generation Sequencing (NGS) technology has succeeded in identifying diversity of these bacteria in P. pardalis living in the Ciliwung River, which contaminated with Cd (0.3-1.6 ppm in the water & 0.9-1.6 ppm in the sediment), Hg (0.6-2 ppm in the water & 0.6-1.8 ppm in the sediment), and Pb (59.9-73.8 ppm in the water & 26.1-58.6 ppm in the sediment). Diversity index of intestinal bacteria in P. pardalis was relatively high, but it had a negative correlation with the presence of these contaminants. Actinobacteria, Firmicutes, and Proteobacteria were abundant in the intestines of P. pardalis from the upstream to downstream of the river, with an overall abundance range of 15-48%. Furthermore, Mycobacterium along with 6 other genera were identified as core intestinal bacteria. The presence of these bacterial communities in all the samples affected their survival in heavy metals-contaminated rivers. The fish's adaptability to live in this harsh environment indicated that it has the potential to be utilized as a bioremediator of heavy metals in river sediments.
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Affiliation(s)
- Dewi Elfidasari
- Department of Biology, Faculty of Science and Technology, Al Azhar University Indonesia, Jakarta 12110, Indonesia
| | - Mohammad Syamsul Rijal
- Department of Biology, Faculty of Science and Technology, UIN Syarif Hidayatullah Jakarta, Banten 15412, Indonesia
| | - Syalwa Ersadiwi Shalsabilla
- Department of Biology, Faculty of Science and Technology, UIN Syarif Hidayatullah Jakarta, Banten 15412, Indonesia
| | - Diannisa Syahwa Rahma Fadila
- Department of Biology, Faculty of Science and Technology, UIN Syarif Hidayatullah Jakarta, Banten 15412, Indonesia
| | - Ade Cici
- Department of Biology, Faculty of Science and Technology, UIN Syarif Hidayatullah Jakarta, Banten 15412, Indonesia
| | - Megga Ratnasari Pikoli
- Department of Biology, Faculty of Science and Technology, UIN Syarif Hidayatullah Jakarta, Banten 15412, Indonesia
| | - Devita Tetriana
- National Research and Innovation Agency (BRIN), Jakarta 12440, Indonesia
| | - Irawan Sugoro
- National Research and Innovation Agency (BRIN), Jakarta 12440, Indonesia
- Corresponding author.
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31
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Sun Y, Meng X, Hu X, Liu R, Zhao Z, Wang S, Zhang R, Guo K, Luo L. Dietary supplementation with Lycium barbarum polysaccharides conducive to maintaining the health of Luciobarbus capito via the enhancement of enzyme activities and the modulation of gut microbiota. Int J Biol Macromol 2023; 232:123500. [PMID: 36736520 DOI: 10.1016/j.ijbiomac.2023.123500] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/08/2023] [Accepted: 01/28/2023] [Indexed: 02/01/2023]
Abstract
Lycium barbarum polysaccharide (LBP) is the main active component of Lycium barbarum (L. barbarum), which has important medicinal and nutritional value. However, the effect of LBP treatment on Luciobarbus capito (L. capito) still remains unknown. Given this, the current work aims to probe the underlying effect of different levels of LBP treatment (i.e. 0.10, 0.50 and 1.00 g/L) on L. capito in the context of enzymatic activity analysis, histological observations and gut microbiota analysis. Compared with control group, the activities of hepatic antioxidant enzymes, intestinal digestive enzymes and hepatic immune enzyme were found to be significantly increased after 0.10 g/L LBP and 0.50 g/L LBP treatment (P < 0.05). This result indicated that moderate levels of LBP treatment could dramatically enhance the immunity and antioxidant capacity of L. capito. Furthermore, the compositional structures of the gut microbiota in L. capito were found to be greatly shaped after LBP treatment, whereas the diversity and abundance of the gut microbiota were only found to be slightly changed (P > 0.05). No significant changes were screened in the morphologic structures of gut constructions. This work would provide theoretical and experimental basis for future application of LBP as supplement in the culture process of the farmed fish.
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Affiliation(s)
- Yuan Sun
- Center of Pharmaceutical Engineering and Technology, Harbin University of Commerce, Harbin 150076, PR China.
| | - Xianwei Meng
- Center of Pharmaceutical Engineering and Technology, Harbin University of Commerce, Harbin 150076, PR China; Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, PR China
| | - Xiaowei Hu
- Center of Pharmaceutical Engineering and Technology, Harbin University of Commerce, Harbin 150076, PR China; Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, PR China
| | - Rui Liu
- Center of Pharmaceutical Engineering and Technology, Harbin University of Commerce, Harbin 150076, PR China
| | - Zhigang Zhao
- Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, PR China
| | - Shihui Wang
- Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, PR China
| | - Rui Zhang
- Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, PR China
| | - Kun Guo
- Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, PR China
| | - Liang Luo
- Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, PR China.
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Zhu Z, Xu YM, Liang JH, Huang W, Chen JD, Wu ST, Huang XH, Huang YH, Zhang XY, Sun HY, Qin QW. Relationship of environmental factors in pond water and dynamic changes of gut microbes of sea bass Lateolabrax japonicus. Front Microbiol 2023; 14:1086471. [PMID: 37065157 PMCID: PMC10098083 DOI: 10.3389/fmicb.2023.1086471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/14/2023] [Indexed: 04/01/2023] Open
Abstract
The effect of structure of gut microbes on the health of host has attracted increasing attention. Sea bass Lateolabrax japonicus is an important farmed fish in China. The relationship of the dynamic changes of intestinal bacterial communities in L. japonicus and the cultural water environment is very important for healthy culture. Here, the diversity and abundance of the gut microbial communities of L. japonicus were evaluated during the culture using 16S rRNA Illumina sequencing. Both the opportunistic pathogens Aeromonas (1.68%), Vibrio (1.59%), and Acinetobacter (1.22%); and the potential probiotics Lactobacillus (2.27%), Bacillus (1.16%), and Lactococcus (0.37%) were distributed in the gut of L. japonicus. The increasing concentration of nitrogen of water environments with the increase of culture time significantly correlated with shifts in the microbial community structure: 40.04% of gut microbial changes due to nitrogen concentration. Higher concentrations of nitrogen showed a significantly negative correlation with intestinal probiotics in L. japonicus. The results indicate that the abundance of intestinal bacteria of L. japonicus is mainly driven by the changes of environmental factors (e.g., nitrogen), and it’s very important that the linking environmental parameters with bacterial data of guts could be used as an early warning indicator in L. japonicus heath culture.
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Affiliation(s)
- Zheng Zhu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yu-Min Xu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jun-Han Liang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Wei Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jin-Ding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - Si-Ting Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Xiao-Hong Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - You-Hua Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Xiao-Yang Zhang
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai Yueshun Aquaculture Co., Ltd., Zhuhai, China
| | - Hong-Yan Sun
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China
- *Correspondence: Hong-Yan Sun,
| | - Qi-Wei Qin
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai Yueshun Aquaculture Co., Ltd., Zhuhai, China
- Laboratory for Marine Biology and Biotechnology, Qingdao, China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Qi-Wei Qin,
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Yajima D, Fujita H, Hayashi I, Shima G, Suzuki K, Toju H. Core species and interactions prominent in fish-associated microbiome dynamics. MICROBIOME 2023; 11:53. [PMID: 36941627 PMCID: PMC10026521 DOI: 10.1186/s40168-023-01498-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND In aquatic ecosystems, the health and performance of fish depend greatly on the dynamics of microbial community structure in the background environment. Nonetheless, finding microbes with profound impacts on fish's performance out of thousands of candidate species remains a major challenge. METHODS We examined whether time-series analyses of microbial population dynamics could illuminate core components and structure of fish-associated microbiomes in the background (environmental) water. By targeting eel-aquaculture-tank microbiomes as model systems, we reconstructed the population dynamics of the 9605 bacterial and 303 archaeal species/strains across 128 days. RESULTS Due to the remarkable increase/decrease of constituent microbial population densities, the taxonomic compositions of the microbiome changed drastically through time. We then found that some specific microbial taxa showed a positive relationship with eels' activity levels even after excluding confounding effects of environmental parameters (pH and dissolved oxygen level) on population dynamics. In particular, a vitamin-B12-producing bacteria, Cetobacterium somerae, consistently showed strong positive associations with eels' activity levels across the replicate time series of the five aquaculture tanks analyzed. Network theoretical and metabolic modeling analyses further suggested that the highlighted bacterium and some other closely-associated bacteria formed "core microbiomes" with potentially positive impacts on eels. CONCLUSIONS Overall, these results suggest that the integration of microbiology, ecological theory, and network science allows us to explore core species and interactions embedded within complex dynamics of fish-associated microbiomes. Video Abstract.
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Affiliation(s)
- Daii Yajima
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan
| | - Hiroaki Fujita
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan
| | - Ibuki Hayashi
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan
| | - Genta Shima
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan
| | - Kenta Suzuki
- Integrated Bioresource Information Division, BioResource Research Center, RIKEN, Tsukuba, Ibaraki, 305-0074, Japan
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan.
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34
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Zhao C, Men X, Dang Y, Zhou Y, Ren Y. Probiotics Mediate Intestinal Microbiome and Microbiota-Derived Metabolites Regulating the Growth and Immunity of Rainbow Trout (Oncorhynchus mykiss). Microbiol Spectr 2023; 11:e0398022. [PMID: 36916965 PMCID: PMC10101061 DOI: 10.1128/spectrum.03980-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Emerging evidence confirms using probiotics in promoting growth and immunity of farmed fish. However, the molecular mechanisms underlying the host-microbiome interactions mediated by probiotics are not fully understood. In this study, we used rainbow trout (Oncorhynchus mykiss) as a model to investigate the internal mechanisms of host-microbiome interactions influenced by two probiotic bacteria, Bacillus velezensis and Lactobacillus sakei. We carried out experiments, including intestinal histology, serum physiology, and transcriptome and combined intestinal microbiome and metabolite profiling. Our results showed that both probiotics had a positive effect on growth, immunity, serum enzyme activity, the gut microbiome, and resistance to Aeromonas salmonicida in rainbow trout. Moreover, the intestinal microbial structure was reshaped with increased relative abundance of potential beneficial bacteria, such as Ruminococcus, Lachnospiraceae ucg-004, Leptotrichia, Bacillus coagulans, Porphyromonadaceae, Anaerococcus, and Photobacterium in the B. velezensis group and Paenibacillaceae and Eubacterium hallii in the L. sakei group. Metabolomic profiling and transcriptome analysis revealed upregulated metabolites as biomarkers, i.e., sucrose and l-malic acid in the B. velezensis group, and N-acetyl-l-phenylalanine, N-acetylneuraminic acid, and hydroxyproline in the L. sakei group. Additionally, a multiomics combined analysis illustrated significant positive correlations between the relative abundance of microflora, metabolites, and gene expression associated with immunity and growth. This study highlights the significant role of probiotics as effectors of intestinal microbial activity and shows that different probiotics can have a species-specific effect on the physiological regulation of the host. These findings contribute to a better understanding of the complex host-microbiome interactions in rainbow trout and may have implications for the use of probiotics in aquaculture. IMPORTANCE Probiotics are kinds of beneficial live microbes that impart beneficial effects on the host. Recent studies have proven that when given supplementation with probiotics, farmed fish showed improved disease prevention and growth promotion. However, the underlying metabolic functions regarding their involvement in regulating growth phenotypes, nutrient utilization, and immune response are not yet well understood in the aquaculture field. Given the active interactions between the gut microbiota and fish immune and growth performance, we conducted the supplementation experiments with the probiotics Bacillus velezensis and Lactobacillus sakei. The results showed that probiotics mediated intestinal microbiome- and microbiota-derived metabolites regulating the growth and immunity of fish, and different probiotics participated in the species-specific physiological regulation of the host. This study contributed to a better understanding of the functional interactions associated with host health and gut microbiota species.
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Affiliation(s)
- Chunyan Zhao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Xianhui Men
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Yongji Dang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Yangen Zhou
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Yichao Ren
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong, China
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35
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Chouayekh H, Farhat-Khemakhem A, Karray F, Boubaker I, Mhiri N, Abdallah MB, Alghamdi OA, Guerbej H. Effects of Dietary Supplementation with Bacillus amyloliquefaciens US573 on Intestinal Morphology and Gut Microbiota of European Sea Bass. Probiotics Antimicrob Proteins 2023; 15:30-43. [PMID: 35933471 DOI: 10.1007/s12602-022-09974-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2022] [Indexed: 01/18/2023]
Abstract
Probiotics or direct-fed microbials (DFM) have proven strong potential for improving aquaculture sustainability. This study aims to evaluate the effects of dietary supplementation with the DFM Bacillus amyloliquefaciens US573 on growth performance, intestinal morphology, and gut microbiota (GM) of European sea bass. For this purpose, healthy fish were divided into two feeding trials in triplicate of 25 fish in each tank. The fish were fed with a control basal diet or a DFM-supplemented diet for 42 days. Results showed that, while no significant effects on growth performance were observed, the length and abundance of villi were higher in the DFM-fed group. The benefic effects of DFM supplementation included also the absence of cysts formation and the increase in number of goblet cells playing essential role in immune response. Through DNA metabarcoding analysis of GM, 5 phyla and 14 major genera were identified. At day 42, the main microbiome changes in response to B. amyloliquefaciens US573 addition included the significant decrease in abundance of Actinobacteria phylum that perfectly correlates with a decrease in Nocardia genus representatives which represent serious threat in marine and freshwater fish. On the contrary, an obvious dominance of Betaproteobacteria associated with the abundance in Variovorax genus members, known for their ability to metabolize numerous substrates, was recorded. Interestingly, Firmicutes, particularly species affiliated to the genus Sporosarcina with recent promising probiotic potential, were identified as the most abundant. These results suggest that B. amyloliquefaciens US573 can be effectively recommended as health-promoting DFM in European sea bass farming.
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Affiliation(s)
- Hichem Chouayekh
- Department of Biological Sciences, College of Science, University of Jeddah, Asfan Road, 21959, P.O. Box 34, Jeddah, Kingdom of Saudi Arabia. .,Laboratory of Microbial Biotechnology, Enzymatic and Biomolecules (LMBEB), Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, Road Sidi Mansour 6 km, Sfax, 3018, Tunisia.
| | - Ameny Farhat-Khemakhem
- Laboratory of Microbial Biotechnology, Enzymatic and Biomolecules (LMBEB), Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, Road Sidi Mansour 6 km, Sfax, 3018, Tunisia
| | - Fatma Karray
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, Road Sidi Mansour 6 km, Sfax, 3018, Tunisia
| | - Insaf Boubaker
- Laboratory of Microbial Biotechnology, Enzymatic and Biomolecules (LMBEB), Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, Road Sidi Mansour 6 km, Sfax, 3018, Tunisia
| | - Najla Mhiri
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, Road Sidi Mansour 6 km, Sfax, 3018, Tunisia
| | - Manel Ben Abdallah
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, Road Sidi Mansour 6 km, Sfax, 3018, Tunisia
| | - Othman A Alghamdi
- Department of Biological Sciences, College of Science, University of Jeddah, Asfan Road, 21959, P.O. Box 34, Jeddah, Kingdom of Saudi Arabia
| | - Hamadi Guerbej
- National Institute of Sea Sciences and Technologies, Monastir, Tunisia
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Foyle L, Burnett M, Creaser A, Hens R, Keough J, Madin L, Price R, Smith H, Stone S, Kinobe RT. Prevalence and distribution of antimicrobial resistance in effluent wastewater from animal slaughter facilities: A systematic review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 318:120848. [PMID: 36563990 DOI: 10.1016/j.envpol.2022.120848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/18/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
The extensive use of antibiotics in food animal production and disposal of untreated wastewater from food animal slaughter facilities may create a shift in microbiomes of different ecosystems by generating reservoirs of antimicrobial resistance along the human-animal-environmental interface. This epidemiological problem has been studied, but its magnitude and impact on a global scale is poorly characterised. A systematic review was done to determine global prevalence and distribution patterns of antimicrobial resistance in effluent wastewater from animal slaughter facilities. Extracted data were stratified into rational groups for secondary analyses and presented as percentages. Culture and sensitivity testing was the predominant method; Escherichia spp., Enterococcus spp., and Staphylococcus aureus were the most targeted isolates. Variable incidences of resistance were detected against all major antimicrobial classes including reserved drugs such as ceftazidime, piperacillin, gentamicin, ciprofloxacin, and chloramphenicol; the median frequency and range in resistant Gram-negative isolates were: 11 (0-100), 62 (0-100), 8 (0-100), 14 (0-93) and 12 (0-62) respectively. Ciprofloxacin was the most tested drug with the highest incidences of resistance in livestock slaughterhouses in Iran (93%), Nigeria (50%) and China (20%), and poultry slaughterhouses in Germany (21-81%) and Spain (56%). Spatial global distribution patterns for antimicrobial resistance were associated with previously reported magnitude of antibiotic use in livestock or poultry farming and, the implicit existence of jurisdictional policies to regulate antibiotic use. These data indicate that anthropogenic activities in farming systems are a major contributor to the cause and dissemination of antimicrobial resistance into the environment via slaughterhouse effluents.
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Affiliation(s)
- Leo Foyle
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Solander Drive, Townsville, Queensland, 4811, Australia
| | - Matthew Burnett
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia
| | - Abbey Creaser
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia
| | - Rachel Hens
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia
| | - Julia Keough
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia
| | - Lauren Madin
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia
| | - Ruby Price
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia
| | - Hayley Smith
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia
| | - Samuel Stone
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia
| | - Robert T Kinobe
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia; Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Solander Drive, Townsville, Queensland, 4811, Australia.
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37
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The Development of the Bacterial Community of Brown Trout ( Salmo trutta) during Ontogeny. Microorganisms 2023; 11:microorganisms11010211. [PMID: 36677503 PMCID: PMC9863972 DOI: 10.3390/microorganisms11010211] [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: 12/22/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Brown trout (Salmo trutta) is an important aquaculture species in Germany, but its production faces challenges due to global warming and a high embryo mortality. Climate factors might influence the fish's bacterial community (BC) and thus increase embryo mortality. Yet, knowledge of the physiological BC during ontogeny in general is scarce. In this project, the BC of brown trout has been investigated in a period from unfertilized egg to 95 days post fertilization (dpf) using 16S rRNA gene amplicon sequencing. Developmental changes differed between early and late ontogeny and major differences in BC occurred especially during early developmental stages. Thus, analysis was conducted separately for 0 to 67 dpf and from 67 to 95 dpf. All analyzed stages were sampled in toto to avoid bias due to different sampling methods in different developmental stages. The most abundant phylum in the BC of all developmental stages was Pseudomonadota, while only two families (Comamonadaceae and Moraxellaceae) occurred in all developmental stages. The early developmental stages until 67 dpf displayed greater shifts in their BC regarding bacterial richness, microbial diversity, and taxonomic composition. Thereafter, in the fry stages, the BC seemed to stabilize and changes were moderate. In future studies, a reduction in the sampling time frames during early development, an increase in sampling numbers, and an attempt for biological reproduction in order to characterize the causes of these variations is recommended.
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38
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Morshed SM, Chen YY, Lin CH, Chen YP, Lee TH. Freshwater transfer affected intestinal microbiota with correlation to cytokine gene expression in Asian sea bass. Front Microbiol 2023; 14:1097954. [PMID: 37089546 PMCID: PMC10117908 DOI: 10.3389/fmicb.2023.1097954] [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: 11/14/2022] [Accepted: 03/22/2023] [Indexed: 04/25/2023] Open
Abstract
As a catadromous fish, Asian sea bass (Lates calcarifer) juveniles migrate from seawater (SW) to freshwater (FW) for growth and development. During migration, they undergo physiological changes to acclimate to environmental salinity. Thus, it is crucial to understand how SW-to-FW migration affects the gut microbiota of catadromous fish. To the best of our knowledge, no study has revealed the effects of transfer to hypotonic environments on a catadromous fish microbiota. In this study, we aimed to determine the effects of FW transfer on the microbiota and cytokine gene expression in the intestines of juvenile catadromous Asian sea bass. The relationship between the water and the gut microbiota of this euryhaline species was also examined. We found that FW transfer affected both mucosa- and digesta-associated microbiota of Asian sea bass. Plesiomonas and Cetobacterium were dominant in both the mucosa- and digesta-associated microbiota of FW-acclimated sea bass. The pathogenic genera Vibrio, Staphylococcus, and Acinetobacter were dominant in the SW group. Although dominant fish microbes were present in the water, fish had their own unique microbes. Vitamin B6 metabolism was highly expressed in the FW fish microbiota, whereas arginine, proline, and lipid metabolism were highly expressed in the SW fish microbiota. Additionally, the correlation between cytokine gene expression and microbiota was found to be affected by FW transfer. Taken together, our results demonstrated that FW transfer altered the composition and functions of mucosa- and digesta-associated microbiota of catadromous Asian sea bass intestines, which correlated with cytokine gene expression.
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Affiliation(s)
- Syed Monzur Morshed
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Yi Chen
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
| | - Chia-Hao Lin
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan
| | - Yen-Po Chen
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
- *Correspondence: Yen-Po Chen,
| | - Tsung-Han Lee
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Tsung-Han Lee,
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39
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Härer A, Rennison DJ. Quantifying (non)parallelism of gut microbial community change using multivariate vector analysis. Ecol Evol 2022; 12:e9674. [PMID: 36590339 PMCID: PMC9797641 DOI: 10.1002/ece3.9674] [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: 05/06/2022] [Revised: 11/26/2022] [Accepted: 12/09/2022] [Indexed: 12/30/2022] Open
Abstract
Parallel evolution of phenotypic traits is regarded as strong evidence for natural selection and has been studied extensively in a variety of taxa. However, we have limited knowledge of whether parallel evolution of host organisms is accompanied by parallel changes of their associated microbial communities (i.e., microbiotas), which are crucial for their hosts' ecology and evolution. Determining the extent of microbiota parallelism in nature can improve our ability to identify the factors that are associated with (putatively adaptive) shifts in microbial communities. While it has been emphasized that (non)parallel evolution is better considered as a quantitative continuum rather than a binary phenomenon, quantitative approaches have rarely been used to study microbiota parallelism. We advocate using multivariate vector analysis (i.e., phenotypic change vector analysis) to quantify direction and magnitude of microbiota changes and discuss the applicability of this approach for studying parallelism, and we compiled an R package for multivariate vector analysis of microbial communities ('multivarvector'). We exemplify its use by reanalyzing gut microbiota data from multiple fish species that exhibit parallel shifts in trophic ecology. We found that multivariate vector analysis results were largely consistent with other statistical methods, parallelism estimates were not affected by the taxonomic level at which the microbiota is studied, and parallelism might be stronger for gut microbiota function compared to taxonomic composition. This approach provides an analytical framework for quantitative comparisons across host lineages, thereby providing the potential to advance our capacity to predict microbiota changes. Hence, we emphasize that the development and application of quantitative measures, such as multivariate vector analysis, should be further explored in microbiota research in order to better understand the role of microbiota dynamics during their hosts' adaptive evolution, particularly in settings of parallel evolution.
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Affiliation(s)
- Andreas Härer
- School of Biological Sciences, Department of Ecology, Behavior, & EvolutionUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Diana J. Rennison
- School of Biological Sciences, Department of Ecology, Behavior, & EvolutionUniversity of California San DiegoLa JollaCaliforniaUSA
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40
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Kormas K, Nikouli E, Kousteni V, Damalas D. Midgut Bacterial Microbiota of 12 Fish Species from a Marine Protected Area in the Aegean Sea (Greece). MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02154-x. [PMID: 36529834 DOI: 10.1007/s00248-022-02154-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Fish microbiome science is progressing fast, but it is biased toward farmed or laboratory fish species against natural fish populations, which remain considerably underinvestigated. We analyzed the midgut bacterial microbiota of 45 specimens of 12 fish species collected from the Gyaros Island marine protected area (Aegean Sea, Greece). The species belong to seven taxonomic families and are either herbivores or omnivores. Mucosa midgut bacterial diversity was assessed by amplicon metabarcoding of the 16S rRNA V3-V4 gene region. A total of 854 operational taxonomic units (OTUs) were identified. In each fish species, between 2 and 18 OTUs dominated with cumulative relative abundance ≥ 70%. Most of the dominating bacterial taxa have been reported to occur both in wild and farmed fish populations. The midgut bacterial communities were different among the 12 fish species, except for Pagrus pagrus and Pagellus erythrinus, which belong to the Sparidae family. No differentiation of the midgut bacterial microbiota was found based on feeding habits, i.e., omnivorous vs. carnivorous. Comparing wild and farmed P. pagrus midgut bacterial microbiota revealed considerable variation between them. Our results expand the gut microbiota of wild fish and support the host species effect as the more likely factor shaping intestinal bacterial microbiota.
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Affiliation(s)
- Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, 384 46, Volos, Greece.
| | - Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, University of Thessaly, 384 46, Volos, Greece
| | - Vasiliki Kousteni
- Institute of Marine Biological Resources and Inland Waters, Hellenic Centre for Marine Research, 710 03, Heraklion, Greece
- Fisheries Research Institute, Hellenic Agricultural Organization - Demeter, 640 07, Nea Peramos, Greece
| | - Dimitrios Damalas
- Institute of Marine Biological Resources and Inland Waters, Hellenic Centre for Marine Research, 710 03, Heraklion, Greece
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41
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Puri P, Sharma JG, Singh R. Biotherapeutic microbial supplementation for ameliorating fish health: developing trends in probiotics, prebiotics, and synbiotics use in finfish aquaculture. Anim Health Res Rev 2022; 23:113-135. [PMID: 36597760 DOI: 10.1017/s1466252321000165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nutrition demands in aquaculture can be realized through quality aquafeeds as compounded diets that contribute to the growth and health of aquaculture species. Functional additives in feed, notably probiotics, prebiotics, and their admixture synbiotics, have been recently recognized for their biotherapeutic role as immunostimulants capable of conferring disease resistance, stress tolerance, and gastrointestinal health; counteracting the negative effects of anti-nutrients, pathogenic prevalence, and antimicrobials in finfish aquaculture. Formulated diets based on probiotics, prebiotics, and as a supplemental combination for synbiotics can significantly influence fish gut microbiomes, establishing the modalities of microbial dynamics to maximize host-associated benefits. These microbial functional-feed supplements are acclaimed to be biocompatible, biodegradable, and safe for dietary consumption as well as the environment. In fed fish aquaculture, prebiotic appended probiotic diet 'synbiotic' has propounded larger attention for its additional health and nutritional benefits. Synbiotic, prebiotic, and probiotic usage as functional feeds for finfish aquaculture thus provides promising prospects. Developing trends in their intended application are reviewed here forth.
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Affiliation(s)
- Parul Puri
- Department of Biotechnology, Delhi Technological University, Delhi, India
- Department of Zoology, Sri Aurobindo College, University of Delhi, Delhi, India
| | - Jai Gopal Sharma
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Ram Singh
- Department of Applied Chemistry, Delhi Technological University, Delhi, India
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42
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Gill SP, Learman DR, Annis ML, Woolnough DA. Freshwater mussels and host fish gut microbe community composition shifts after agricultural contaminant exposure. J Appl Microbiol 2022; 133:3645-3658. [PMID: 36056619 PMCID: PMC9825887 DOI: 10.1111/jam.15801] [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: 06/01/2022] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 01/11/2023]
Abstract
AIMS We examined the effects of a mixture of contaminants found in agricultural watersheds on the gut microbiota and physiology of both the freshwater mussel Lampsilis cardium, and L. cardium host fish Micropterus salmoides. METHODS AND RESULTS Lampsilis cardium and M. salmoides were exposed to three concentrations of agricultural contaminants for 60 days (observing behaviour daily) before being sampled for gut microbiota analyses. DNA was extracted from the gut samples, amplified via PCR, and sequenced using the Illumina Mi-Seq platform. Only L. cardium guts had differing microbiota across treatments, with an increase in potentially pathogenic Aeromonas. We also provide novel evidence of a core microbiota within L. cardium and M. salmoides. In terms of physiology, female L. cardium exhibited a decrease in movement and marsupial gill display in contaminant exposures. CONCLUSIONS Exposure to contaminants from agricultural watersheds may affect population recruitment within freshwater mussel communities over time. Specifically, increased pathogenic micro-organisms and altered behaviour can reduce the likelihood of glochidia dispersal. SIGNIFICANCE AND IMPACT OF THE STUDY This study supports emerging research that contaminants found in agricultural watersheds may be a factor in freshwater mussel population declines. It also provides novel evidence that unionids have a core gut microbiota.
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Affiliation(s)
- Stephanie P. Gill
- Biology Department and Institute for Great Lakes ResearchCentral Michigan UniversityMount PleasantMichiganUSA
| | - Deric R. Learman
- Biology Department and Institute for Great Lakes ResearchCentral Michigan UniversityMount PleasantMichiganUSA
| | - Mandy L. Annis
- US Fish & Wildlife Service, Michigan Ecological Services Field OfficeEast LansingMichiganUSA
| | - Daelyn A. Woolnough
- Biology Department and Institute for Great Lakes ResearchCentral Michigan UniversityMount PleasantMichiganUSA
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43
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Effects of dietary yeast culture on health status in digestive tract of juvenile Pacific white shrimp Litopenaeus Vannamei. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2022; 3:100065. [DOI: 10.1016/j.fsirep.2022.100065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/19/2022] Open
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44
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Bertucci A, Hoede C, Dassié E, Gourves PY, Suin A, Le Menach K, Budzinski H, Daverat F. Impact of environmental micropollutants and diet composition on the gut microbiota of wild european eels (Anguilla anguilla). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120207. [PMID: 36165828 DOI: 10.1016/j.envpol.2022.120207] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/22/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
In fish, the gut microbiome plays a crucial role in homeostasis and health and is affected by several organic and inorganic environmental contaminants. Amphidromous fish are sentinel species, particularly exposed to these stressors. We used whole metagenome sequencing to characterize the gut microbiome of wild European eels (Anguilla anguilla) at a juvenile stage captured from three sites with contrasted pollution levels in term of heavy metals and persistent organic pollutants. The objectives were to identify what parameters could alter the gut microbiome of this catadromous fish and to explore the potential use of microbiota as bioindicators of environment quality. We identified a total of 1079 microbial genera. Overall, gut microbiome was dominated by Proteobacteria, Firmicutes and Actinobacteria. Alpha and beta diversity were different amongst sites and could be explained by a reduced number of environmental and biological factors, specifically the relative abundance of fish preys in eels' diet, PCB101, γHCH (lindane), transnonachlor and arsenic. Furthermore, we identified a series of indicator taxa with differential abundance between the three sites. Changes in the microbial communities in the gut caused by environmental pollutants were previously undocumented in European eels. Our results indicate that microbiota might represent another route by which pollutants affect the health of these aquatic sentinel organisms.
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Affiliation(s)
| | - Claire Hoede
- Université de Toulouse, INRAE, UR MIAT, PF GenoToul Bioinfo, 31320, Castanet-Tolosan, France; Université Fédérale de Toulouse, INRAE, BioinfOmics, GenoToul Bioinformatics Facility, 31326, Castanet-Tolosan, France
| | - Emilie Dassié
- Univ. Bordeaux, CNRS, EPOC, EPHE, UMR 5805, 33600, Pessac, France
| | | | - Amandine Suin
- Genome & Transcriptome - Plateforme GeT-PlaGe, INRAE, 31326, Castanet-Tolosan, France
| | - Karine Le Menach
- Univ. Bordeaux, CNRS, EPOC, EPHE, UMR 5805, 33600, Pessac, France
| | - Hélène Budzinski
- Univ. Bordeaux, CNRS, EPOC, EPHE, UMR 5805, 33600, Pessac, France
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45
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Naya-Català F, Piazzon MC, Torrecillas S, Toxqui-Rodríguez S, Calduch-Giner JÀ, Fontanillas R, Sitjà-Bobadilla A, Montero D, Pérez-Sánchez J. Genetics and Nutrition Drive the Gut Microbiota Succession and Host-Transcriptome Interactions through the Gilthead Sea Bream ( Sparus aurata) Production Cycle. BIOLOGY 2022; 11:1744. [PMID: 36552254 PMCID: PMC9774573 DOI: 10.3390/biology11121744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
Fish genetically selected for growth (GS) and reference (REF) fish were fed with CTRL (15% FM, 5-7% FO) or FUTURE (7.5% FM, 10% poultry meal, 2.2% poultry oil + 2.5% DHA-algae oil) diets during a 12-months production cycle. Samples from initial (t0; November 2019), intermediate (t1; July 2020) and final (t2; November 2020) sampling points were used for Illumina 16S rRNA gene amplicon sequencing of the adherent microbiota of anterior intestine (AI). Samples from the same individuals (t1) were also used for the gene expression profiling of AI by RNA-seq, and subsequent correlation analyses with microbiota abundances. Discriminant analyses indicated the gut bacterial succession along the production cycle with the proliferation of some valuable taxa for facing seasonality and different developmental stages. An effect of genetic background was evidenced along time, decreasing through the progression of the trial, namely the gut microbiota of GS fish was less influenced by changes in diet composition. At the same time, these fish showed wider transcriptomic landmarks in the AI to cope with these changes. Our results highlighted an enhanced intestinal sphingolipid and phospholipid metabolism, epithelial turnover and intestinal motility in GS fish, which would favour their improved performance despite the lack of association with changes in gut microbiota composition. Furthermore, in GS fish, correlation analyses supported the involvement of different taxa with the down-regulated expression of pro-inflammatory markers and the boosting of markers of extracellular remodelling and response to bacterium. Altogether, these findings support the combined action of the gut microbiome and host transcriptionally mediated effects to preserve and improve gut health and function in a scenario of different growth performance and potentiality.
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Affiliation(s)
- Fernando Naya-Català
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | - M Carla Piazzon
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | - Silvia Torrecillas
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Crta. Taliarte s/n, 35214 Telde, Las Palmas, Canary Islands, Spain
| | - Socorro Toxqui-Rodríguez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | - Josep À Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | | | - Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | - Daniel Montero
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Crta. Taliarte s/n, 35214 Telde, Las Palmas, Canary Islands, Spain
| | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
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Gołaś I, Potorski JA. The Influence of Commercial Feed Supplemented with Carnobacterium maltaromaticum Environmental Probiotic Bacteria on the Rearing Parameters and Microbial Safety of Juvenile Rainbow Trout. Animals (Basel) 2022; 12:ani12233321. [PMID: 36496842 PMCID: PMC9741101 DOI: 10.3390/ani12233321] [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: 11/09/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
The aim of this study was to determine the effect of commercial feed (CF) supplemented with 0.1% of the Carnobacterium maltaromaticum environmental probiotic strain on the rearing parameters, apparent nutrient digestibility, and microbial safety of juvenile rainbow trout (Oncorhynchus mykiss). The fish were fed CF (control group, CG) and experimental feed (EF) supplemented with 0.1% of C. maltaromaticum (experimental group, EG) for 56 days. The final body weight and total body length of the fish were measured. The growth rate, condition factor, feed conversion ratio, viscerosomatic and hepatosomatic indices, and apparent digestibility coefficients of protein (PAD), lipids (LAD), ash (AAD), and nitrogen-free extract (NFEAD) were calculated. The total viable counts of C. maltaromaticum bacteria, mesophilic bacteria, hemolytic mesophilic bacteria, Pseudomonas fluorescens, Aeromonas hydrophila, Staphylococcus sp., and sulfite-reducing anaerobic spore-forming Clostridium sp. were determined in digestive tract contents and the skin of fish. Feed supplementation with C. maltaromaticum significantly affected most rearing parameters, as well as the PAD, LAD, AAD and NFE values, and bacterial counts. The principal component analysis (PCA) revealed significant positive correlations (p < 0.05) between fish growth rates, PAD and LAD values vs. C. maltaromaticum counts in the EF and in the digestive tract contents of the fish.
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Minich JJ, Härer A, Vechinski J, Frable BW, Skelton ZR, Kunselman E, Shane MA, Perry DS, Gonzalez A, McDonald D, Knight R, Michael TP, Allen EE. Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species. Nat Commun 2022; 13:6978. [PMID: 36396943 PMCID: PMC9671965 DOI: 10.1038/s41467-022-34557-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 10/28/2022] [Indexed: 11/18/2022] Open
Abstract
Fish are the most diverse and widely distributed vertebrates, yet little is known about the microbial ecology of fishes nor the biological and environmental factors that influence fish microbiota. To identify factors that explain microbial diversity patterns in a geographical subset of marine fish, we analyzed the microbiota (gill tissue, skin mucus, midgut digesta and hindgut digesta) from 101 species of Southern California marine fishes, spanning 22 orders, 55 families and 83 genera, representing ~25% of local marine fish diversity. We compare alpha, beta and gamma diversity while establishing a method to estimate microbial biomass associated with these host surfaces. We show that body site is the strongest driver of microbial diversity while microbial biomass and diversity is lowest in the gill of larger, pelagic fishes. Patterns of phylosymbiosis are observed across the gill, skin and hindgut. In a quantitative synthesis of vertebrate hindguts (569 species), we also show that mammals have the highest gamma diversity when controlling for host species number while fishes have the highest percent of unique microbial taxa. The composite dataset will be useful to vertebrate microbiota researchers and fish biologists interested in microbial ecology, with applications in aquaculture and fisheries management.
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Affiliation(s)
- Jeremiah J Minich
- The Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
| | - Andreas Härer
- School of Biological Sciences, Department of Ecology, Behavior, & Evolution, University of California San Diego, La Jolla, CA, 92093, USA
| | - Joseph Vechinski
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0244, USA
| | - Benjamin W Frable
- Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0244, USA
| | - Zachary R Skelton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - Emily Kunselman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0244, USA
| | - Michael A Shane
- Hubbs-SeaWorld Research Institute, 2595 Ingraham Street, San Diego, CA, 92109, USA
| | - Daniela S Perry
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
- Center for Microbiome Innovation, University of San Diego, California, La Jolla, CA, 92093, USA
- Department of Computer Science, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Todd P Michael
- The Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Eric E Allen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0244, USA
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
- Center for Microbiome Innovation, University of San Diego, California, La Jolla, CA, 92093, USA
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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48
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Response of Intestinal Microbiota to the Variation in Diets in Grass Carp (Ctenopharyngodon idella). Metabolites 2022; 12:metabo12111115. [PMID: 36422256 PMCID: PMC9698803 DOI: 10.3390/metabo12111115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/10/2022] [Accepted: 11/13/2022] [Indexed: 11/17/2022] Open
Abstract
The intestinal microbiota is important for the nutrient metabolism of fish and is significantly influenced by the host’s diet. The effect of ryegrass and commercial diets on the intestinal microbiota of grass carp was compared in this study. In comparison to ryegrass, artificial feed significantly reduced the microbial diversity in the intestine, which was measured by a decrease in the observed OTUs, ACE, Shannon, and the InvSimpson index. Although grass carp fed with ryegrass and artificial feed shared a dominant phyla Firmicutes and Proteobacteria, the microbial composition was clearly distinguishable between the two groups. In grass carp fed with ryegrass, Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria predominated, whereas Bacilli was significantly higher in the artificial feed group due to an increase in Weissella and an unassigned Bacillales bacteria, as well as a significant increase in a potential pathogen: Aeromonas australiensis. Grass carp fed with ryegrass exhibited a more complex ecological network performed by the intestinal bacterial community, which was dominated by cooperative interactions; this was also observed in grass carp fed with artificial feed. Despite this, the increase in A. australiensis increased the competitive interaction within this ecological network, which contributed to the vulnerable perturbation of the intestinal microbiota. The alteration of the microbial composition through diet can further affect microbial function. The intestinal microbial function in grass carp fed with ryegrass was rich in amino acids and exhibited an increased energy metabolism in order to compensate for a low-nutrient diet intake, while the artificial feed elevated the microbial lipid metabolism through the promotion of its synthesis in the primary and secondary bile acids, together with a notable enhancement of fatty acid biosynthesis. These results indicated that diet can affect the homeostasis of the intestinal microbiota by altering the microbial composition and the interspecific interactions, whilst microbial function can respond to a variation in diet.
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Chen CZ, Li P, Liu L, Li ZH. Exploring the interactions between the gut microbiome and the shifting surrounding aquatic environment in fisheries and aquaculture: A review. ENVIRONMENTAL RESEARCH 2022; 214:114202. [PMID: 36030922 DOI: 10.1016/j.envres.2022.114202] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/10/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
The rise of "new" sequencing technologies and the development of sophisticated bioinformatics tools have dramatically increased the study of the aquaculture microbiome. Microbial communities exist in complex and dynamic communities that play a vital role in the stability of healthy ecosystems. The gut microbiome contributes to multiple aspects of the host's physiological health status, ranging from nutritional regulation to immune modulation. Although studies of the gut microbiome in aquaculture are growing rapidly, the interrelationships between the aquaculture microbiome and its aquatic environment have not been discussed and summarized. In particular, few reviews have focused on the potential mechanisms driving the alteration of the gut microbiome by surrounding aquatic environmental factors. Here, we review current knowledge on the host gut microbiome and its interrelationship with the microbiome of the surrounding environment, mainly including the main methods for characterizing the gut microbiome, the composition and function of microbial communities, the dynamics of microbial interactions, and the relationship between the gut microbiome and the surrounding water/sediment microbiome. Our review highlights two potential mechanisms for how surrounding aquatic environmental factors drive the gut microbiome. This may deepen the understanding of the interactions between the microbiome and environmental factors. Lastly, we also briefly describe the research gaps in current knowledge and prospects for the future orientation of research. This review provides a framework for studying the complex relationship between the host gut microbiome and environmental stresses to better facilitate the widespread application of microbiome technologies in fisheries and aquaculture.
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Affiliation(s)
- Cheng-Zhuang Chen
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Ping Li
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Ling Liu
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Zhi-Hua Li
- Marine College, Shandong University, Weihai, Shandong, 264209, China.
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Links between host genetics, metabolism, gut microbiome and amoebic gill disease (AGD) in Atlantic salmon. Anim Microbiome 2022; 4:53. [PMID: 36109797 PMCID: PMC9479442 DOI: 10.1186/s42523-022-00203-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/30/2022] [Indexed: 12/02/2022] Open
Abstract
Background Rapidly spreading parasitic infections like amoebic gill disease (AGD) are increasingly problematic for Atlantic salmon reared in aquaculture facilities and potentially pose a risk to wild fish species in surrounding waters. Currently, it is not known whether susceptibility to AGD differs between wild and farmed salmon. Wild Atlantic salmon populations are declining and this emerging disease could represent an additional threat to their long-term viability. A better understanding of how AGD affects fish health is therefore relevant for the accurate assessment of the associated risk, both to farming and to the well-being of wild populations. In this study, we assessed the impact of natural exposure to AGD on wild, hybrid and farmed post-smolt Atlantic salmon reared in a sea farm together under common garden conditions. Results Wild fish showed substantially higher mortality levels (64%) than farmed fish (25%), with intermediate levels for hybrid fish (39%) suggesting that AGD susceptibility has an additive genetic basis. Metabolic rate measures representing physiological performance were similar among the genetic groups but were significantly lower in AGD-symptomatic fish than healthy fish. Gut microbial diversity was significantly lower in infected fish. We observed major shifts in gut microbial community composition in response to AGD infections. In symptomatic fish the relative abundance of key taxa Aliivibrio, Marinomonas and Pseudoalteromonas declined, whereas the abundance of Polaribacter and Vibrio increased compared to healthy fish. Conclusions Our results highlight the stress AGD imposes on fish physiology and suggest that low metabolic-rate fish phenotypes may be associated with better infection outcomes. We consider the role increased AGD outbreak events and a warmer future may have in driving secondary bacterial infections and in reducing performance in farmed and wild fish. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00203-x.
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