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Bu LK, Jia PP, Huo WB, Pei DS. Assessment of Probiotics' Impact on Neurodevelopmental and Behavioral Responses in Zebrafish Models: Implications for Autism Spectrum Disorder Therapy. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10335-y. [PMID: 39090455 DOI: 10.1007/s12602-024-10335-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder; the prevalence of which has been on the rise with unknown causes. Alterations in the gut-brain axis have been widely recognized in ASD patients, and probiotics are considered to potentially benefit the rescuing of autism-like behaviors. However, the effectiveness and mechanisms of multiple probiotics on zebrafish models are still not clearly revealed. This study aims to use the germ-free (GF) and conventionally raised (CR) AB wild-type zebrafish and the mutant Tbr1b-/- and Katnal2-/- lines as human-linked ASD animal models to evaluate the effects of multiple probiotics on mitigating developmental and behavioral defects. Results showed that the addition of probiotics increased the basic important developmental indexes, such as body length, weight, and survival rate of treated zebrafish. Moreover, the Lactobacillus plantarum and Lactobacillus rhamnosus affected the behavior of CR zebrafish by increasing their mobility, lowering the GF zebrafish manic, and mitigating transgenic zebrafish abnormal behavior. Moreover, the expression levels of key genes related to gamma-aminobutyric acid (GABA), dopamine (DA), and serotonin (5-HT) as important neuropathways to influence the appearance and development of autism-related disorders, including gad1b, tph1a, htr3a, th, and slc6a3, were significantly activated by some of the probiotics' treatment at some extent. Taken together, this study indicates the beneficial effects of different probiotics, which may provide a novel understanding of probiotic function in related diseases' therapy.
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Affiliation(s)
- Ling-Kang Bu
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
| | - Pan-Pan Jia
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
| | - Wen-Bo Huo
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China.
- Chongqing Miankai Biotechnology Research Institute Co., Ltd., Chongqing, 400025, China.
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2
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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; 133:54-66. [PMID: 38822131 PMCID: PMC11222526 DOI: 10.1038/s41437-024-00692-3] [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: 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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Zarantonello G, Cuenca A. Nanopore-Enabled Microbiome Analysis: Investigating Environmental and Host-Associated Samples in Rainbow Trout Aquaculture. Curr Protoc 2024; 4:e1069. [PMID: 38865207 DOI: 10.1002/cpz1.1069] [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] [Indexed: 06/14/2024]
Abstract
Microbiome sequencing is at the forefront of health management development, and as such, it is becoming of great interest to monitor the microbiome in the aquaculture industry as well. Oxford Nanopore Technologies (ONT) platforms are gaining popularity to study microbial communities, enabling faster sequencing, extended read length, and therefore, improved taxonomic resolution. Despite this, there is a lack of clear guidelines to perform a metabarcoding study, especially when dealing with samples from non-mammalian species, such as aquaculture-related samples. In this article, we provide general guidelines for sampling, nucleic acid extraction, and ONT-based library preparation for both environmental (water, sediment) and host-associated (gill or skin mucus, skin, gut content, or gut mucosa) microbiome analysis. Our procedures focus specifically on rainbow trout (Oncorhynchus mykiss) reared in experimental facilities. However, these protocols can also be transferred to alternative types of samples, such as environmental DNA (eDNA) monitoring from alternative water sources, or to different fish species. The additional challenge posed by the low biomass and limited bacterial diversity inherent in fish-associated microbiomes is addressed through the implementation of troubleshooting solutions. Furthermore, we describe a bioinformatic pipeline starting from raw reads and leading to taxonomic abundance tables using currently available tools and software. Finally, we provide a set of specific guidelines and considerations related to the strategic planning of a microbiome study within the context of aquaculture. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Environmental sample collection Basic Protocol 2: Host-associated sample collection Alternate Protocol: Host-associated sample collection: Alternative sample types Basic Protocol 3: Sample pre-treatment and nucleic acid extraction Basic Protocol 4: Quality control and preparation for 16S rRNA gene sequencing Support Protocol 1: Assessment of inhibition by quantitative PCR Support Protocol 2: Bioinformatic analysis from raw files to taxonomic abundance tables.
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Affiliation(s)
- Giulia Zarantonello
- National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Argelia Cuenca
- National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
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Barbacariu CA, Dumitru G, Rimbu CM, Horhogea CE, Dîrvariu L, Todirașcu-Ciornea E, Șerban DA, Burducea M. Inclusion of Sorghum in Cyprinus carpio L. Diet: Effects on Growth, Flesh Quality, Microbiota, and Oxidative Status. Animals (Basel) 2024; 14:1549. [PMID: 38891599 PMCID: PMC11171069 DOI: 10.3390/ani14111549] [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: 04/05/2024] [Revised: 05/15/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
This study investigates the impact of including sorghum in the diet of the common carp (Cyprinus carpio) on its growth, blood parameters, meat composition, intestinal microbiota, and oxidative stress. Experimental diets with varying sorghum content (0%-V0 or control, 10%-V1, 20%-V2, and 30%-V3) were administered to carp weighing 43 g initially. Notably, in the 30% variant, sorghum entirely replaced corn and barley in the diet. Chemical analysis of sorghum unveiled a protein content of 14% and a fat content of 3.9%. Sorghum inclusion led to a decline in final body weight and weight gain, particularly notable in the V3 group with 30% sorghum. However, other physiological parameters, such as feed conversion ratio, specific growth rate, and organ indices, remained unaffected. Protein and salt content in carp flesh increased with higher sorghum inclusion levels, while hematological parameters showed minimal variations. Analysis of the intestinal microbiota revealed increases in both aerobic and anaerobic bacterial populations with sorghum inclusion. Furthermore, sorghum concentration inversely correlated with glutathione levels and positively correlated with malondialdehyde content, indicating a disruption of antioxidant defense mechanisms and elevated oxidative stress.
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Affiliation(s)
- Cristian-Alin Barbacariu
- Research and Development Station for Aquaculture and Aquatic Ecology, “Alexandru Ioan Cuza” University, Carol I, 20A, 700505 Iasi, Romania; (C.-A.B.); (L.D.); (D.A.Ș.)
| | - Gabriela Dumitru
- Faculty of Biology, “Alexandru Ioan Cuza” University, Carol I, 20A, 700505 Iasi, Romania;
| | - Cristina Mihaela Rimbu
- Department of Public Health, Faculty of Veterinary Medicine, University of Life Sciences ‘’Ion Ionescu de la Brad’’ Iaşi, Mihail Sadoveanu Alley 6-8, 700490 Iasi, Romania; (C.M.R.)
| | - Cristina Elena Horhogea
- Department of Public Health, Faculty of Veterinary Medicine, University of Life Sciences ‘’Ion Ionescu de la Brad’’ Iaşi, Mihail Sadoveanu Alley 6-8, 700490 Iasi, Romania; (C.M.R.)
| | - Lenuța Dîrvariu
- Research and Development Station for Aquaculture and Aquatic Ecology, “Alexandru Ioan Cuza” University, Carol I, 20A, 700505 Iasi, Romania; (C.-A.B.); (L.D.); (D.A.Ș.)
| | | | - Dana Andreea Șerban
- Research and Development Station for Aquaculture and Aquatic Ecology, “Alexandru Ioan Cuza” University, Carol I, 20A, 700505 Iasi, Romania; (C.-A.B.); (L.D.); (D.A.Ș.)
- Faculty of Food and Animal Sciences, University of Life Sciences “Ion Ionescu de la Brad” Iaşi, Mihail Sadoveanu Alley 6-8, 700490 Iasi, Romania
| | - Marian Burducea
- Research and Development Station for Aquaculture and Aquatic Ecology, “Alexandru Ioan Cuza” University, Carol I, 20A, 700505 Iasi, Romania; (C.-A.B.); (L.D.); (D.A.Ș.)
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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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Sumithra TG, Sharma SRK, Suresh G, Gop AP, Surya S, Gomathi P, Anil MK, Sajina KA, Reshma KJ, Ebeneezar S, Narasimapallavan I, Gopalakrishnan A. Mechanistic insights into the early life stage microbiota of silver pompano ( Trachinotus blochii). Front Microbiol 2024; 15:1356828. [PMID: 38694807 PMCID: PMC11061439 DOI: 10.3389/fmicb.2024.1356828] [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: 12/16/2023] [Accepted: 03/13/2024] [Indexed: 05/04/2024] Open
Abstract
Introduction Deep investigations of host-associated microbiota can illuminate microbe-based solutions to improve production in an unprecedented manner. The poor larval survival represents the critical bottleneck in sustainable marine aquaculture practices. However, little is known about the microbiota profiles and their governing eco-evolutionary processes of the early life stages of marine teleost, impeding the development of suitable beneficial microbial management strategies. The study provides first-hand mechanistic insights into microbiota and its governing eco-evolutionary processes in early life stages of a tropical marine teleost model, Trachinotus blochii. Methods The microbiota profiles and their dynamics from the first day of hatching till the end of metamorphosis and that of fingerling's gut during the routine hatchery production were studied using 16S rRNA amplicon-based high-throughput sequencing. Further, the relative contributions of various external factors (rearing water, live feed, microalgae, and formulated feed) to the microbiota profiles at different ontogenies was also analyzed. Results A less diverse but abundant core microbial community (~58% and 54% in the whole microbiota and gut microbiota, respectively) was observed throughout the early life stages, supporting 'core microbiota' hypothesis. Surprisingly, there were two well-differentiated clusters in the whole microbiota profiles, ≤10 DPH (days post-hatching) and > 10 DPH samples. The levels of microbial taxonomic signatures of stress indicated increased stress in the early stages, a possible explanation for increased mortality during early life stages. Further, the results suggested an adaptive mechanism for establishing beneficial strains along the ontogenetic progression. Moreover, the highly transient microbiota in the early life stages became stable along the ontogenetic progression, hypothesizing that the earlier life stages will be the best window to influence the microbiota. The egg microbiota also crucially affected the microbial community. Noteworthily, both water and the feed microbiota significantly contributed to the early microbiota, with the feed microbiota having a more significant contribution to fish microbiota. The results illustrated that rotifer enrichment would be the optimal medium for the early larval microbiota manipulations. Conclusion The present study highlighted the crucial foundations for the microbial ecology of T. blochii during early life stages with implications to develop suitable beneficial microbial management strategies for sustainable mariculture production.
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Affiliation(s)
- T. G. Sumithra
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - S. R. Krupesha Sharma
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - Gayathri Suresh
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
- Cochin University of Science and Technology, Kochi, Kerala, India
| | - Ambarish P. Gop
- Vizhinjam Regional Centre of ICAR-Central Marine Fisheries Research Institute, Thiruvananthapuram, Kerala, India
| | - S. Surya
- Vizhinjam Regional Centre of ICAR-Central Marine Fisheries Research Institute, Thiruvananthapuram, Kerala, India
| | - P. Gomathi
- Vizhinjam Regional Centre of ICAR-Central Marine Fisheries Research Institute, Thiruvananthapuram, Kerala, India
| | - M. K. Anil
- Vizhinjam Regional Centre of ICAR-Central Marine Fisheries Research Institute, Thiruvananthapuram, Kerala, India
| | - K. A. Sajina
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - K. J. Reshma
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - Sanal Ebeneezar
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - Iyyapparaja Narasimapallavan
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - A. Gopalakrishnan
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
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Liang Y, Wang Z, Gao N, Qi X, Zeng J, Cui K, Lu W, Bai S. Variations and Interseasonal Changes in the Gut Microbial Communities of Seven Wild Fish Species in a Natural Lake with Limited Water Exchange during the Closed Fishing Season. Microorganisms 2024; 12:800. [PMID: 38674744 PMCID: PMC11052518 DOI: 10.3390/microorganisms12040800] [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: 03/23/2024] [Revised: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
The gut microbiota of fish is crucial for their growth, development, nutrient uptake, physiological balance, and disease resistance. Yet our knowledge of these microbial communities in wild fish populations in their natural ecosystems is insufficient. This study systematically examined the gut microbial communities of seven wild fish species in Chaohu Lake, a fishing-restricted area with minimal water turnover, across four seasons. We found significant variations in gut microbial community structures among species. Additionally, we observed significant seasonal and regional variations in the gut microbial communities. The Chaohu Lake fish gut microbial communities were predominantly composed of the phyla Firmicutes, Proteobacteria(Gamma), Proteobacteria(Alpha), Actinobacteriota, and Cyanobacteria. At the genus level, Aeromonas, Cetobacterium, Clostridium sensu stricto 1, Romboutsia, and Pseudomonas emerged as the most prevalent. A co-occurrence network analysis revealed that C. auratus, C. carpio, and C. brachygnathus possessed more complex and robust gut microbial networks than H. molitrix, C. alburnus, C. ectenes taihuensis, and A. nobilis. Certain microbial groups, such as Clostridium sensu stricto 1, Romboutsia, and Pseudomonas, were both dominant and keystone in the fish gut microbial network. Our study offers a new approach for studying the wild fish gut microbiota in natural, controlled environments. It offers an in-depth understanding of gut microbial communities in wild fish living in stable, limited water exchange natural environments.
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Affiliation(s)
- Yangyang Liang
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China; (Y.L.); (N.G.); (K.C.); (W.L.)
| | - Zijia Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Z.W.); (X.Q.); (J.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Gao
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China; (Y.L.); (N.G.); (K.C.); (W.L.)
| | - Xiaoxue Qi
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Z.W.); (X.Q.); (J.Z.)
| | - Juntao Zeng
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Z.W.); (X.Q.); (J.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Cui
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China; (Y.L.); (N.G.); (K.C.); (W.L.)
| | - Wenxuan Lu
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China; (Y.L.); (N.G.); (K.C.); (W.L.)
| | - Shijie Bai
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Z.W.); (X.Q.); (J.Z.)
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Kelly LA, Yost CK, Cooke SJ. Opportunities and challenges with transitioning to non-lethal sampling of wild fish for microbiome research. JOURNAL OF FISH BIOLOGY 2024; 104:912-919. [PMID: 38226503 DOI: 10.1111/jfb.15650] [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: 12/04/2023] [Accepted: 12/19/2023] [Indexed: 01/17/2024]
Abstract
The microbial communities of fish are considered an integral part of maintaining the overall health and fitness of their host. Research has shown that resident microbes reside on various mucosal surfaces, such as the gills, skin, and gastrointestinal tract, and play a key role in various host functions, including digestion, immunity, and disease resistance. A second, more transient group of microbes reside in the digesta, or feces, and are primarily influenced by environmental factors such as the host diet. The vast majority of fish microbiome research currently uses lethal sampling to analyse any one of these mucosal and/or digesta microbial communities. The present paper discusses the various opportunities that non-lethal microbiome sampling offers, as well as some inherent challenges, with the ultimate goal of creating a sound argument for future researchers to transition to non-lethal sampling of wild fish in microbiome research. Doing so will reduce animal welfare and population impacts on fish while creating novel opportunities to link host microbial communities to an individual's behavior and survival across space and time (e.g., life-stages, seasons). Current lethal sampling efforts constrain our ability to understand the mechanistic ecological consequences of variation in microbiome communities in the wild. Transitioning to non-lethal sampling will open new frontiers in ecological and microbial research.
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Affiliation(s)
- Lisa A Kelly
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Institute of Environmental and Interdisciplinary Science, Carleton University, Ottawa, Ontario, Canada
| | - Christopher K Yost
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan, Canada
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Institute of Environmental and Interdisciplinary Science, Carleton University, Ottawa, Ontario, Canada
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Zhao Z, Zhao H, Wang X, Zhang L, Mou C, Huang Z, Ke H, Duan Y, Zhou J, Li Q. Effects of different temperatures on Leiocassis longirostris gill structure and intestinal microbial composition. Sci Rep 2024; 14:7150. [PMID: 38532085 DOI: 10.1038/s41598-024-57731-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/21/2024] [Indexed: 03/28/2024] Open
Abstract
Fish are poikilothermic vertebrates and their physiological activities are affected by water temperature. In recent years, extreme weather has occurred frequently, and temperature changes have adversely affected the growth of farmed fish. To explore the changes in gill tissue structure caused by changing the water temperature and the relationship between the intestinal microbiota and the Leiocassis longirostris host adaptation mechanism, gill tissue sections and intestinal microbial 16S rRNA amplicon sequencing were conducted under different temperature stress (low temperature 4 °C, normal temperature 26 °C and high temperature 32 °C). The results showed that heat stress and cold stress caused injury and swelling, terminal congestion, cell vacuolation, and necrosis of the gill tissue of L. longirostris. For intestinal microbiota, the abundances of Pseudomonadota and Bacillota increased at the cold stress, while the abundances of Fusobacteriota and Bacteroidota increased at the heat stress. The number of opportunistic bacteria, mainly Aeromonas and Acinetobacter, was the highest under cold stress. In addition, the richness of the intestinal microbiota decreased significantly at heat and cold stresses, while evenness increased. Prediction of intestinal microbiota function showed that most common functions, such as metabolism of cofactors and vitamins, energy metabolism and replication and repair, were decreased significantly at heat stress and cold stress, and phylogenetic relationship analysis revealed significant differences among the groups. In conclusion, the change of temperature altered the gill tissue structure, and affected the structure and homeostasis of the intestinal microbiota, thus affecting the survival time of L. longirostris, and cold stress had a greater effect than heat stress.
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Affiliation(s)
- Zhongmeng Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Han Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Xiongyan Wang
- Sichuan Water Conservancy Vocational College, Chongzhou, Sichuan, China
| | - Lu Zhang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Chengyan Mou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Zhipeng Huang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Hongyu Ke
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Yuanliang Duan
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Jian Zhou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Qiang Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China.
- , 1611 Xiyuan Avenue, Chengdu, China.
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10
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Amill F, Gauthier J, Rautio M, Derome N. Characterization of gill bacterial microbiota in wild Arctic char ( Salvelinus alpinus) across lakes, rivers, and bays in the Canadian Arctic ecosystems. Microbiol Spectr 2024; 12:e0294323. [PMID: 38329329 PMCID: PMC10923216 DOI: 10.1128/spectrum.02943-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
Teleost gill mucus has a highly diverse microbiota, which plays an essential role in the host's fitness and is greatly influenced by the environment. Arctic char (Salvelinus alpinus), a salmonid well adapted to northern conditions, faces multiple stressors in the Arctic, including water chemistry modifications, that could negatively impact the gill microbiota dynamics related to the host's health. In the context of increasing environmental disturbances, we aimed to characterize the taxonomic distribution of transcriptionally active taxa within the bacterial gill microbiota of Arctic char in the Canadian Arctic in order to identify active bacterial composition that correlates with environmental factors. For this purpose, a total of 140 adult anadromous individuals were collected from rivers, lakes, and bays belonging to five Inuit communities located in four distinct hydrologic basins in the Canadian Arctic (Nunavut and Nunavik) during spring (May) and autumn (August). Various environmental factors were collected, including latitudes, water and air temperatures, oxygen concentration, pH, dissolved organic carbon (DOC), salinity, and chlorophyll-a concentration. The taxonomic distribution of transcriptionally active taxa within the gill microbiota was quantified by 16S rRNA gene transcripts sequencing. The results showed differential bacterial activity between the different geographical locations, explained by latitude, salinity, and, to a lesser extent, air temperature. Network analysis allowed the detection of a potential dysbiosis signature (i.e., bacterial imbalance) in fish gill microbiota from Duquet Lake in the Hudson Strait and the system Five Mile Inlet connected to the Hudson Bay, both showing the lowest alpha diversity and connectivity between taxa.IMPORTANCEThis paper aims to decipher the complex relationship between Arctic char (Salvelinus alpinus) and its symbiotic microbial consortium in gills. This salmonid is widespread in the Canadian Arctic and is the main protein and polyunsaturated fatty acids source for Inuit people. The influence of environmental parameters on gill microbiota in wild populations remains poorly understood. However, assessing the Arctic char's active gill bacterial community is essential to look for potential pathogens or dysbiosis that could threaten wild populations. Here, we concluded that Arctic char gill microbiota was mainly influenced by latitude and air temperature, the latter being correlated with water temperature. In addition, a dysbiosis signature detected in gill microbiota was potentially associated with poor fish health status recorded in these disturbed environments. With those results, we hypothesized that rapid climate change and increasing anthropic activities in the Arctic might profoundly disturb Arctic char gill microbiota, affecting their survival.
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Affiliation(s)
- Flora Amill
- Institute of Integrative and Systems Biology, Laval University, Quebec, Canada
| | - Jeff Gauthier
- Institute of Integrative and Systems Biology, Laval University, Quebec, Canada
| | - Milla Rautio
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Quebec, Canada
| | - Nicolas Derome
- Institute of Integrative and Systems Biology, Laval University, Quebec, Canada
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11
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Talwar C, Nagar S, Negi RK. Comparative analyses of gut microbiota reveal ammonia detoxification and nitrogen assimilation in Cyprinus carpio var. specularis. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01151-6. [PMID: 38367166 DOI: 10.1007/s12223-024-01151-6] [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: 08/29/2023] [Accepted: 02/08/2024] [Indexed: 02/19/2024]
Abstract
The complex niche of fish gut is often characterized by the associated microorganisms that have implications in fish gut-health nexus. Although efforts to distinguish the microbial communities have highlighted their disparate structure along the gut length, remarkably little information is available about their distinct structural and functional profiles in different gut compartments in different fish species. Here, we performed comparative taxonomic and predictive functional analyses of the foregut and hindgut microbiota in an omnivorous freshwater fish species, Cyprinus carpio var. specularis, commonly known as mirror carp. Our analyses showed that the hindgut microbiota could be distinguished from foregut based on the abundance of ammonia-oxidizing, denitrifying, and nitrogen-fixing commensals of families such as Rhodospirillaceae, Oxalobacteraceae, Nitrosomonadaceae, and Nitrospiraceae. Functionally, unique metabolic pathways such as degradation of lignin, 2-nitrobenzoate, vanillin, vanillate, and toluene predicted within hindgut also hinted at the ability of hindgut microbiota for assimilation of nitrogen and detoxification of ammonia. The study highlights a major role of hindgut microbiota in assimilating nitrogen, which remains to be one of the limiting nutrients within the gut of mirror carp.
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Affiliation(s)
- Chandni Talwar
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
- Department of Pathology & Immunology, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 770030, USA
| | - Shekhar Nagar
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
- Department of Zoology, Deshbandhu College, Kalkaji, New Delhi, 110019, India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India.
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12
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Lokesh J, Siriyappagouder P, Fernandes JMO. Unravelling the temporal and spatial variation of fungal phylotypes from embryo to adult stages in Atlantic salmon. Sci Rep 2024; 14:981. [PMID: 38200059 PMCID: PMC10781754 DOI: 10.1038/s41598-023-50883-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: 07/14/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Early microbial colonization has a profound impact on host physiology during different stages of ontogeny. Although several studies have focused on early bacterial colonization and succession, the composition and role of fungal communities are poorly known in fish. Here, we sequenced the internal transcribed spacer 2 (ITS2) region of fungi to profile the mycobiome associated with the eggs, hatchlings and intestine of Atlantic salmon at various freshwater and marine stages. In most of the stages studied, fungal diversity was lower than bacterial diversity. There were several stage-specific fungal phylotypes belonging to different stages of ontogeny but some groups, such as Candida tropicalis, Saccharomyces cerevisiae, Alternaria metachromatica, Davidiella tassiana and Humicola nigrescens, persisted during successive stages of ontogeny. We observed significant changes in the intestinal fungal communities during the first feeding. Prior to first feeding, Humicola nigrescens dominated, but Saccharomyces cerevisiae (10 weeks post hatch) and Candida tropicalis (12 weeks post hatch) became dominant subsequently. Seawater transfer resulted in a decrease in alpha diversity and an increase in Candida tropicalis abundance. We also observed notable variations in beta diversity and composition between the different farms. Overall, the present study sheds light on the fungal communities of Atlantic salmon from early ontogeny to adulthood. These novel findings will also be useful in future studies investigating host-microbiota interactions in the context of developing better nutritional and health management strategies for Atlantic salmon farming.
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Affiliation(s)
- Jep Lokesh
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
- Université de Pau et des Pays de l'Adour, E2S UPPA. INRAE, NUMEA, Saint-Pée-Sur-Nivelle, France.
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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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Simakov YG, Ponomarev AK, Nikiforov-Nikishin DL, Kochetkov NI. Histological examination of the young Oncorhynchus mykiss intestines using the feed with chelated and probiotic supplements. BRAZ J BIOL 2024; 84:e265121. [DOI: 10.1590/1519-6984.265121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/26/2022] [Indexed: 11/22/2022] Open
Abstract
Abstract Macronutrient and micronutrient deficiencies in the fish diet can affect fish growth rate, ability to resist disease, and fillet quality. Determination of effective dose of developed feed additives consisting of chelate compounds of biogenic elements and probiotic preparation based on Bacillus subtilis. Young rainbow trout were divided into four groups consisting of 100 fish each. The control group received standard food; the experimental groups received food with chelates and probiotics in different concentrations. At the end of the experiment (30 days), the middle intestine histology and morphometric parameters were studied. The use of chelated compounds alone affected the state of the intestinal villi and the infiltration of the epithelium by lymphocytes. The addition of a probiotic had a positive effect on the migration of immune cells in the intestinal villi; however, the probiotic in high concentrations contributed to a decrease in the number and area of goblet cells. Synergistic effects of chelated compounds and probiotic preparations on the morphometric parameters of the medium intestine were observed. In the proper doses, the studied feed additives might be recommended for rainbow trout farming under industrial aquaculture conditions.
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Affiliation(s)
- Y. G. Simakov
- Moscow State University of Technologies and Management, Russia
| | - A. K. Ponomarev
- Moscow State University of Technologies and Management, Russia
| | | | - N. I. Kochetkov
- Moscow State University of Technologies and Management, Russia
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15
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Mozanzadeh MT, Mohammadian T, Ahangarzadeh M, Houshmand H, Najafabadi MZ, Oosooli R, Seyyedi S, Mehrjooyan S, Saghavi H, Sephdari A, Mirbakhsh M, Osroosh E. Feeding Strategies with Multi-Strain Probiotics Affect Growth, Health Condition, and Disease Resistance in Asian Seabass (Lates calcarifer). Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10207-x. [PMID: 38135810 DOI: 10.1007/s12602-023-10207-x] [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: 12/14/2023] [Indexed: 12/24/2023]
Abstract
A 16-week feeding trial was done to examine the impacts of continuous feeding (CF) or pulse-feeding (PF) of multi-strain probiotics on Asian seabass (Lates calcarifer, 30.0 ± 0.1 g) juveniles. In this study, three different multi-strain probiotic mixtures were added to a basal diet, including (I) a mixture of different strains of Lactobacillus plantarum, (II) a mixture of the first probiotic (I) + L. delbrueckii sub bulgaricus, L. rhamnosus and L. acidophilus, and (III) a mixture of the second probiotic (II) + two quorum quenching (QQ) bacteria (Bacillus thuringiensis QQ1 and B. cereus QQ2). CF (every day) or PF (every two weeks) strategies were applied for using the abovementioned probiotics to design seven experimental groups including C (control, without probiotics), CF-I (continuous feeding of fish with the probiotic mixture I), CF-II (continuous feeding of fish with the probiotic mixture II), CF-III (continuous feeding of fish with the probiotic mixture III), PF-I (pulse-feeding of fish with the probiotic mixture I), PF-II (pulse-feeding of fish with the probiotic mixture II), and PF-III (pulse-feeding of fish with the probiotic mixture III). Four hundred and twenty fish were stocked into 21 circular polyethylene tanks with 220 L volume (20 fish/tank). Each dietary treatment had three replicates. Tanks were supplied with seawater (temperature = 30.5 °C, salinity = 45 g L-1) in a flow-throw system. Fish in CF-I, CF-II, and CF-III had higher growth rate (ca. 113-145%) and better feed conversion ratio than fish fed C and PF-I (P < 0.05). Fish in the CF-III group had the highest protease activity. Continuous feeding strategy resulted in a higher amount of glutathione and catalase activities in both the liver and plasma as well as higher superoxide dismutase activity in the liver of fish. Pulse-feeding strategy resulted in lower plasma lactate dehydrogenase and aspartate aminotransferase levels than the CF strategy. Regardless of feeding strategy, different probiotic mixtures significantly enhanced blood hemoglobin and hematocrit levels compared to the control. Continuous feeding with the multi-strain probiotics resulted in a higher survival rate against Vibrio harveyi than the PF method. Continuous feeding induced higher mRNA transcription levels of granulocyte-macrophage colony-forming cells and interleukin 10 genes in the gut of fish than PF strategy. In conclusion, continuous feeding with multi-strain probiotics is better than pulse-feeding on growth, feed utilization, antioxidant capacity, and the gut's immune-related genes and led to higher resistance of L. calcarifer in challenge with V. harveyi.
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Affiliation(s)
- Mansour Torfi Mozanzadeh
- South Iran Aquaculture Research Centre, Iranian Fisheries Science Research Institute (IFSRI), Agricultural Research, Education and Extension Organization (AREEO), Ahwaz, Iran.
| | - Takavar Mohammadian
- Department of livestock, Poultry and Aquatic Animal Health, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
- Member of Excellence Center of Warm Water Fish Health, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
| | - Mina Ahangarzadeh
- South Iran Aquaculture Research Centre, Iranian Fisheries Science Research Institute (IFSRI), Agricultural Research, Education and Extension Organization (AREEO), Ahwaz, Iran
| | - Hossein Houshmand
- South Iran Aquaculture Research Centre, Iranian Fisheries Science Research Institute (IFSRI), Agricultural Research, Education and Extension Organization (AREEO), Ahwaz, Iran
| | - Mojtaba Zabayeh Najafabadi
- South Iran Aquaculture Research Centre, Iranian Fisheries Science Research Institute (IFSRI), Agricultural Research, Education and Extension Organization (AREEO), Ahwaz, Iran
| | - Rahim Oosooli
- South Iran Aquaculture Research Centre, Iranian Fisheries Science Research Institute (IFSRI), Agricultural Research, Education and Extension Organization (AREEO), Ahwaz, Iran
| | - Sadra Seyyedi
- Behbahan Khatam Alanbia University of Technology, Behbahan, Iran
| | - Shapour Mehrjooyan
- South Iran Aquaculture Research Centre, Iranian Fisheries Science Research Institute (IFSRI), Agricultural Research, Education and Extension Organization (AREEO), Ahwaz, Iran
| | - Hamid Saghavi
- South Iran Aquaculture Research Centre, Iranian Fisheries Science Research Institute (IFSRI), Agricultural Research, Education and Extension Organization (AREEO), Ahwaz, Iran
| | - Abolfazl Sephdari
- Iranian Fisheries Science Research Institute, Agricultural Research Education and Extension Organization (AREEO), Tehran, Iran
| | - Maryam Mirbakhsh
- Iranian Fisheries Science Research Institute, Agricultural Research Education and Extension Organization (AREEO), Tehran, Iran
| | - Elham Osroosh
- Department of livestock, Poultry and Aquatic Animal Health, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- Member of Excellence Center of Warm Water Fish Health, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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16
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Suhr M, Fichtner-Grabowski FT, Seibel H, Bang C, Franke A, Schulz C, Hornburg SC. Effects of plant-based proteins and handling stress on intestinal mucus microbiota in rainbow trout. Sci Rep 2023; 13:22563. [PMID: 38110473 PMCID: PMC10728151 DOI: 10.1038/s41598-023-50071-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/14/2023] [Indexed: 12/20/2023] Open
Abstract
Via 16S rRNA gene amplicon sequencing, this study explores whether the gut mucus microbiota of rainbow trout is affected by the interaction of a plant-protein-based diet and a daily handling stressor (chasing with a fishing net) across two genetic lines (A, B). Initial body weights of fish from lines A and B were 124.7 g and 147.2 g, respectively. Fish were fed 1.5% of body weight per day for 59 days either of two experimental diets, differing in their fish meal [fishmeal-based diet (F): 35%, plant-based diet (V): 7%] and plant-based protein content (diet F: 47%, diet V: 73%). No diet- or stress-related effect on fish performance was observed at the end of the trial. However, we found significantly increased observed ASVs in the intestinal mucus of fish fed diet F compared to diet V. No significant differences in Shannon diversity could be observed between treatments. The autochthonous microbiota in fish fed with diet V was dominated by representatives of the genera Mycoplasma, Cetobacterium, and Ruminococcaceae, whereas Enterobacteriaceae and Photobacterium were significantly associated with diet F. The mucus bacteria in both genetic lines were significantly separated by diet, but neither by stress nor an interaction, as obtained via PERMANOVA. However, pairwise comparisons revealed that the diet effect was only significant in stressed fish. Therefore, our findings indicate that the mucus-associated microbiota is primarily modulated by the protein source, but this modulation is mediated by the stress status of the fish.
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Affiliation(s)
- Marvin Suhr
- Institute of Animal Nutrition and Physiology, Christian-Albrechts-University Kiel, Hermann-Rodewald-Straße 9, 24118, Kiel, Germany.
| | | | - Henrike Seibel
- Fraunhofer Research Institution for Individualized and Cell-Based Medical Engineering (IMTE), Hafentörn 3, 25761, Büsum, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, University Hospital Schleswig-Holstein, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, University Hospital Schleswig-Holstein, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany
| | - Carsten Schulz
- Fraunhofer Research Institution for Individualized and Cell-Based Medical Engineering (IMTE), Hafentörn 3, 25761, Büsum, Germany
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Hermann-Rodewald-Straße 6, 24118, Kiel, Germany
| | - Stéphanie C Hornburg
- Institute of Animal Nutrition and Physiology, Christian-Albrechts-University Kiel, Hermann-Rodewald-Straße 9, 24118, Kiel, Germany
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17
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Colorado Gómez MA, Melo-Bolívar JF, Ruíz Pardo RY, Rodriguez JA, Villamil LM. Unveiling the Probiotic Potential of the Anaerobic Bacterium Cetobacterium sp. nov. C33 for Enhancing Nile Tilapia ( Oreochromis niloticus) Cultures. Microorganisms 2023; 11:2922. [PMID: 38138066 PMCID: PMC10745334 DOI: 10.3390/microorganisms11122922] [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: 09/19/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023] Open
Abstract
The bacterium strain Cetobacterium sp. C33 was isolated from the intestinal microbial content of Nile tilapia (O. niloticus) under anaerobic conditions. Given that Cetobacterium species are recognized as primary constituents of the intestinal microbiota in cultured Nile tilapia by culture-independent techniques, the adaptability of the C33 strain to the host gastrointestinal conditions, its antibacterial activity against aquaculture bacterial and its antibiotic susceptibility were assessed. The genome of C33 was sequenced, assembled, annotated, and subjected to functional inference, particularly regarding pinpointed probiotic activities. Furthermore, phylogenomic comparative analyses were performed including closely reported strains/species relatives. Comparative genomics with closely related species disclosed that the isolate is not phylogenetically identical to other Cetobacterium species, displaying an approximately 5% sequence divergence from C. somerae and a 13% sequence divergence from Cetobacterium ceti. It can be distinguished from other species through physiological and biochemical criteria. Whole-genome annotation highlighted that Cetobacterium sp. nov. C33 possesses a set of genes that may contribute to antagonism against competing bacteria and has specific symbiotic adaptations in fish. Additional in vivo experiments should be carried out to verify favorable features, reinforcing its potential as a probiotic bacterium.
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Affiliation(s)
- Mario Andrés Colorado Gómez
- Doctorado en Biociencias, Facultad de Ingeniería, Universidad de La Sabana, Chía 250001, Colombia; (M.A.C.G.); (J.F.M.-B.); (R.Y.R.P.); (J.A.R.)
- Fundación Clínica Shaio, Bogotá 110121, Colombia
| | - Javier Fernando Melo-Bolívar
- Doctorado en Biociencias, Facultad de Ingeniería, Universidad de La Sabana, Chía 250001, Colombia; (M.A.C.G.); (J.F.M.-B.); (R.Y.R.P.); (J.A.R.)
| | - Ruth Yolanda Ruíz Pardo
- Doctorado en Biociencias, Facultad de Ingeniería, Universidad de La Sabana, Chía 250001, Colombia; (M.A.C.G.); (J.F.M.-B.); (R.Y.R.P.); (J.A.R.)
| | - Jorge Alberto Rodriguez
- Doctorado en Biociencias, Facultad de Ingeniería, Universidad de La Sabana, Chía 250001, Colombia; (M.A.C.G.); (J.F.M.-B.); (R.Y.R.P.); (J.A.R.)
| | - Luisa Marcela Villamil
- Doctorado en Biociencias, Facultad de Ingeniería, Universidad de La Sabana, Chía 250001, Colombia; (M.A.C.G.); (J.F.M.-B.); (R.Y.R.P.); (J.A.R.)
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18
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Siddik MAB, Francis P, Rohani MF, Azam MS, Mock TS, Francis DS. Seaweed and Seaweed-Based Functional Metabolites as Potential Modulators of Growth, Immune and Antioxidant Responses, and Gut Microbiota in Fish. Antioxidants (Basel) 2023; 12:2066. [PMID: 38136186 PMCID: PMC10740464 DOI: 10.3390/antiox12122066] [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: 09/09/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Seaweed, also known as macroalgae, represents a vast resource that can be categorized into three taxonomic groups: Rhodophyta (red), Chlorophyta (green), and Phaeophyceae (brown). They are a good source of essential nutrients such as proteins, minerals, vitamins, and omega-3 fatty acids. Seaweed also contains a wide range of functional metabolites, including polyphenols, polysaccharides, and pigments. This study comprehensively discusses seaweed and seaweed-derived metabolites and their potential as a functional feed ingredient in aquafeed for aquaculture production. Past research has discussed the nutritional role of seaweed in promoting the growth performance of fish, but their effects on immune response and gut health in fish have received considerably less attention in the published literature. Existing research, however, has demonstrated that dietary seaweed and seaweed-based metabolite supplementation positively impact the antioxidant status, disease resistance, and stress response in fish. Additionally, seaweed supplementation can promote the growth of beneficial bacteria and inhibit the proliferation of harmful bacteria, thereby improving gut health and nutrient absorption in fish. Nevertheless, an important balance remains between dietary seaweed inclusion level and the resultant metabolic alteration in fish. This review highlights the current state of knowledge and the associated importance of continued research endeavors regarding seaweed and seaweed-based functional metabolites as potential modulators of growth, immune and antioxidant response, and gut microbiota composition in fish.
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Affiliation(s)
- Muhammad A. B. Siddik
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3216, Australia; (P.F.); (T.S.M.); (D.S.F.)
| | - Prue Francis
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3216, Australia; (P.F.); (T.S.M.); (D.S.F.)
| | - Md Fazle Rohani
- Department of Aquaculture, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh;
| | | | - Thomas S. Mock
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3216, Australia; (P.F.); (T.S.M.); (D.S.F.)
| | - David S. Francis
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3216, Australia; (P.F.); (T.S.M.); (D.S.F.)
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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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20
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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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21
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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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22
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Bharti M, Nagar S, Negi RK. Riverine pollution influences the intraspecific variation in the gut microbiome of an invasive fish, Cyprinus carpio (Linn., 1758). 3 Biotech 2023; 13:320. [PMID: 37649590 PMCID: PMC10462599 DOI: 10.1007/s13205-023-03747-0] [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: 01/25/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
Humans are significantly impacting riverine systems worldwide, prompting us to investigate the effects of water pollution on the gut microbiome of Cyprinus carpio (common carp). Using 16S rRNA gene sequencing, we compared the gut microbiomes of common carp from two sites along river Yamuna with different pollution levels. Water pollution significantly altered the fish gut microbiome structure and microbial composition. Proteobacteria dominated in both sampling sites, while Bacteroidota prevailed in polluted water samples, indicating sewage and fecal contamination. Less polluted samples exhibited Verrucomicrobiae and Planctomycetes, negatively correlated with pollution levels. The polluted site had higher prevalence of potentially pathogenic and heavy metal-resistant bacteria, as well as microbial communities associated with wastewater treatment systems. Functional prediction highlighted the significant role of the gut microbiome in digestion and metabolism, with active enzymes for breaking down various organic substances. Biosynthetic pathways for leucine, valine, and isoleucine were present in both sites, known to be involved fish immunity. The host maintained a stable and diverse bacterial consortium, while microbial diversity became more specialized due to human activities, adapting to anthropogenic stress and selection pressures. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03747-0.
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Affiliation(s)
- Meghali Bharti
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, North Campus, Delhi, 110007 India
| | - Shekhar Nagar
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, North Campus, Delhi, 110007 India
- Department of Zoology, Deshbandhu College, Kalkaji, New Delhi, 110019 India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, North Campus, Delhi, 110007 India
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23
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Sagada G, Wang L, Xu B, Sun Y, Shao Q. Interactive Effect of Dietary Heat-Killed Lactobacillus Plantarum L-137 and Berberine Supplementation on Intestinal Mucosa and Microbiota of Juvenile Black Sea Bream (Acanthopagrus Schlegelii). Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10153-8. [PMID: 37740880 DOI: 10.1007/s12602-023-10153-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2023] [Indexed: 09/25/2023]
Abstract
To compare the synergistic impact of dietary heat-killed Lactobacillus plantarum and berberine supplementation on intestinal health of juvenile black sea bream, the test fish (5.67 ± 0.05 g) were fed three diets: a basal control diet designated as Con; basal diet supplemented with 400 mg/kg L. plantarum, labelled LP; and basal diet supplemented with 400 mg/kg L. plantarum + 50 mg/k berberine, labelled LPBB. After 56 days of feeding, the control fish had significantly lower intestinal villus height (VH), villus surface area (VSA), and muscularis mucosae (MS) thickness than the rest of the groups (P < 0.05). The LPBB fish had significantly higher VH than the control fish, and wider MS and VSA than the rest of the groups (P < 0.05). Occludin was significantly upregulated in the LPBB fish, and heat shock protein 90 was upregulated in the control fish (P < 0.05). The abundance of Proteobacteria family was significantly higher in the intestinal microbiome of the control and LP fish, the LPBB fish had higher abundance of Cyanobacteria and Spirochaetes, and the LP group had higher Bacteroidetes abundance (P < 0.05). Potentially beneficial Delftia and Brevinema were the significantly abundant genera in the LP and LPBB fish, respectively; potentially pathogenic Elizabethkingia was abundant in the LP fish; and the control fish had higher abundance of potentially pathogenic Burkholderia-Caballeronia-Paraburkholderia (P < 0.05). According to these results, there is possible synergy between L. plantarum and berberine as dietary supplements in fostering healthy intestine for black sea bream than L. plantarum alone.
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Affiliation(s)
- Gladstone Sagada
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lei Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241000, China
| | - Bingying Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yuxiao Sun
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qingjun Shao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
- Ocean Academy, Zhejiang University, Zhoushan, 316021, China.
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24
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Rigas D, Grivas N, Nelli A, Gouva E, Skoufos I, Kormas K, Tzora A, Lagkouvardos I. Persistent Dysbiosis, Parasite Rise and Growth Impairment in Aquacultured European Seabass after Oxytetracycline Treatment. Microorganisms 2023; 11:2302. [PMID: 37764146 PMCID: PMC10534334 DOI: 10.3390/microorganisms11092302] [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: 08/11/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
The use of antibiotics in open-water aquaculture is often unavoidable when faced with pathogens with high mortality rates. In addition, seasonal pathogen surges have become more common and more intense over the years. Apart from the apparent cost of antibiotic treatment, it has been observed that, in aquaculture practice, the surviving fish often display measurable growth impairment. To understand the role of gut microbiota on the observed growth impairment, in this study, we follow the incidence of Photobacterium damselae subsp. piscicida in a seabass commercial open-water aquaculture setting in Galaxidi (Greece). Fish around 10 months of age were fed with feed containing oxytetracycline (120 mg/kg/day) for twelve days, followed by a twelve-day withdrawal period, and another eighteen days of treatment. The fish were sampled 19 days before the start of the first treatment and one month after the end of the second treatment cycle. Sequencing of the 16S rRNA gene was used to measure changes in the gut microbiome. Overall, the gut microbiota community, even a month after treatment, was highly dysbiotic and characterized by very low alpha diversity. High abundances of alkalophilic bacteria in the post-antibiotic-treated fish indicated a rise in pH that was coupled with a significant increase in gut parasites. This study's results indicate that oxytetracycline (OTC) treatment causes persistent dysbiosis even one month after withdrawal and provides a more suitable environment for an increase in parasites. These findings highlight the need for interventions to restore a healthy and protective gut microbiome.
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Affiliation(s)
| | - Nikos Grivas
- Galaxidi Marine Farm S.A., 33200 Galaxidi, Greece
| | - Aikaterini Nelli
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, School of Agriculture, University of Ioannina, 47100 Arta, Greece
| | - Evangelia Gouva
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, School of Agriculture, University of Ioannina, 47100 Arta, Greece
| | - Ioannis Skoufos
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, School of Agriculture, University of Ioannina, 47100 Arta, Greece
| | - Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, 38446 Volos, Greece
- Agricultural Development Institute, University Research and Innovation Centre "IASON", Argonafton & Filellinon, 38221 Volos, Greece
| | - Athina Tzora
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, School of Agriculture, University of Ioannina, 47100 Arta, Greece
| | - Ilias Lagkouvardos
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, School of Agriculture, University of Ioannina, 47100 Arta, Greece
- Department of Microbiology and Microbial Pathogenesis, School of Medicine, University of Crete, 71500 Heraklion, Greece
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25
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Melo-Bolívar JF, Ruiz Pardo RY, Quintanilla-Carvajal MX, Díaz LE, Alzate JF, Junca H, Rodríguez Orjuela JA, Villamil Diaz LM. Evaluation of dietary single probiotic isolates and probiotic multistrain consortia in growth performance, gut histology, gut microbiota, immune regulation, and infection resistance of Nile tilapia, Oreochromis niloticus, shows superior monostrain performance. FISH & SHELLFISH IMMUNOLOGY 2023; 140:108928. [PMID: 37423403 DOI: 10.1016/j.fsi.2023.108928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 05/15/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
The probiotic potential of a designed bacterial consortia isolated from a competitive exclusion culture originally obtained from the intestinal contents of tilapia juveniles were evaluated on Nile tilapia alevins. The growth performance, intestinal histology, microbiota effects, resistance to Streptococcus agalactiae challenge, and immune response were assessed. In addition, the following treatments were included in a commercial feed: A12+M4+M10 (Lactococcus lactis A12, Priestia megaterium M4, and Priestia sp. M10), M4+M10 (P. megaterium M4, and Priestia sp. M10) and the single bacteria as controls; A12 (L. lactis A12), M4 (P. megaterium M4), M10 (Priestia sp. M10), also a commercial feed without any probiotic addition was included as a control. The results showed that all probiotic treatments improved the growth performance, intestinal histology, and resistance during experimental infection with S. agalactiae in comparison to the control fish. Also, the administration of probiotics resulted in the modulation of genes associated with the innate and adaptive immune systems that were non-dependent on microbial colonization. Surprisingly, L. lactis A12 alone induced benefits in fish compared to the microbial consortia, showing the highest increase in growth rate, survival during experimental infection with S. agalactiae, increased intestinal fold length, and the number of differentially expressed genes. Lastly, we conclude that a competitive exclusion culture is a reliable source of probiotics, and monostrain L. lactis A12 has comparable or even greater probiotic potential than the bacterial consortia.
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Affiliation(s)
- Javier Fernando Melo-Bolívar
- Universidad de La Sabana, Doctorado en Biociencias, Campus del Puente del Común, Km. 7, Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
| | - Ruth Yolanda Ruiz Pardo
- Universidad de La Sabana, Doctorado en Biociencias, Campus del Puente del Común, Km. 7, Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
| | - María Ximena Quintanilla-Carvajal
- Universidad de La Sabana, Doctorado en Biociencias, Campus del Puente del Común, Km. 7, Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
| | - Luis Eduardo Díaz
- Universidad de La Sabana, Doctorado en Biociencias, Campus del Puente del Común, Km. 7, Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica- CNSG, Sede de Investigación Universitaria SIU, Grupo Pediaciencias, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Howard Junca
- Microbiomas Foundation, Div. Ecogenomics & Holobionts, RG Microbial Ecology: Metabolism, Genomics & Evolution, Chía, Colombia
| | - Jorge Alberto Rodríguez Orjuela
- Universidad de La Sabana, Doctorado en Biociencias, Campus del Puente del Común, Km. 7, Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
| | - Luisa Marcela Villamil Diaz
- Universidad de La Sabana, Doctorado en Biociencias, Campus del Puente del Común, Km. 7, Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia.
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26
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Leeper A, Sauphar C, Berlizot B, Ladurée G, Koppe W, Knobloch S, Skírnisdóttir S, Björnsdóttir R, Øverland M, Benhaïm D. Enhancement of Soybean Meal Alters Gut Microbiome and Influences Behavior of Farmed Atlantic Salmon ( Salmo salar). Animals (Basel) 2023; 13:2591. [PMID: 37627382 PMCID: PMC10451335 DOI: 10.3390/ani13162591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/05/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Atlantic salmon (Salmo salar) is one of the worlds most domesticated fish. As production volumes increase, access to high quality and sustainable protein sources for formulated feeds of this carnivorous fish is required. Soybean meal (SBM) and soy-derived proteins are the dominant protein sources in commercial aquafeeds due to their low-cost, availability and favorable amino acid profile. However, for Atlantic salmon, the inclusion of soybean meal (SBM), and soy protein concentrate (SPC) in certain combinations can impact gut health, which has consequences for immunity and welfare, limiting the use of soy products in salmonid feeds. This study sought to address this challenge by evaluating two gut health-targeted enhancements of SBM for inclusion in freshwater phase salmon diets: enzyme pre-treatment (ETS), and addition of fructose oligosaccharide (USP). These were compared with untreated soybean meal (US) and fish meal (FM). This study took a multi-disciplinary approach, investigating the effect on growth performance, gut microbiome, and behaviors relevant to welfare in aquaculture. This study suggests that both enhancements of SBM provide benefits for growth performance compared with conventional SBM. Both SBM treatments altered fish gut microbiomes and in the case of ETS, increased the presence of the lactic acid bacteria Enterococcus. For the first time, the effects of marine protein sources and plant protein sources on the coping style of salmon were demonstrated. Fish fed SBM showed a tendency for more reactive behavior compared with those fed the FM-based control. All fish had a similar low response to elicited stress, although ETS-fed fish responded more actively than US-fed fish for a single swimming measure. Furthermore, SBM-fed fish displayed lower repeatability of behavior, which may indicate diminished welfare for intensively farmed fish. The implications of these findings for commercial salmonid aquaculture are discussed.
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Affiliation(s)
- Alexandra Leeper
- Department of Research and Innovation, Iceland Ocean Cluster, Grandagardur 16, 101 Reykjavik, Iceland
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1420 Aas, Norway
- Department of Research and Innovation, Matís Ltd., 12, Vínlandsleid, 113 Reykjavik, Iceland
| | - Clara Sauphar
- Department of Research and Innovation, Matís Ltd., 12, Vínlandsleid, 113 Reykjavik, Iceland
- Department of Aquaculture and Fish Biology, Hólar University, 551 Hólar, Iceland
- Department of Biological Sciences Ålesund, Norwegian University of Science and Technology, 6025 Ålesund, Norway
| | - Benoit Berlizot
- Department of Aquaculture and Fish Biology, Hólar University, 551 Hólar, Iceland
| | - Gabrielle Ladurée
- Department of Aquaculture and Fish Biology, Hólar University, 551 Hólar, Iceland
| | - Wolfgang Koppe
- Department of Research and Innovation, Matís Ltd., 12, Vínlandsleid, 113 Reykjavik, Iceland
| | - Stephen Knobloch
- Department of Research and Innovation, Matís Ltd., 12, Vínlandsleid, 113 Reykjavik, Iceland
- Department of Food Technology, Fulda University of Applied Sciences, 36037 Fulda, Germany
| | | | - Rannveig Björnsdóttir
- Faculty of Natural Resource Sciences, University of Akureyi, Nordurslod, 600 Akureyi, Iceland
| | - Margareth Øverland
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1420 Aas, Norway
| | - David Benhaïm
- Department of Aquaculture and Fish Biology, Hólar University, 551 Hólar, Iceland
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27
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Wang LC, Chen LH, Chiu YC, Liou CY, Chen HC, Lu CY, Chen JL. Teleost skin microbiome: An intimate interplay between the environment and the host immunity. FISH & SHELLFISH IMMUNOLOGY 2023; 139:108869. [PMID: 37285875 DOI: 10.1016/j.fsi.2023.108869] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/22/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
The mucosal microbiome plays a role in regulating host health. The research conducted in humans and mice has governed and detailed the information on microbiome-host immunity interactions. Teleost fish, different from humans and mice, lives in and relies on the aquatic environment and is subjected to environmental variation. The growth of teleost mucosal microbiome studies, the majority in the gastrointestinal tract, has emphasized the essential role of the teleost microbiome in growth and health. However, research in the teleost external surface microbiome, as the skin microbiome, has just started. In this review, we examine the general findings in the colonization of the skin microbiome, how the skin microbiome is subjected to environmental change and the reciprocal regulation with the host immune system, and the current challenges that potential study models can address. The information collected from teleost skin microbiome-host immunity research would help future teleost culturing from the potential parasitic infestation and bacterial infection as foreseeing growing threats.
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Affiliation(s)
- Liang-Chun Wang
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan; Committee of Fisheries Extension Service, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan.
| | - Li-Hsuan Chen
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan; Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | - Yu-Che Chiu
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Chung-Yi Liou
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Han-Chung Chen
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Chia-Yun Lu
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Jian-Lin Chen
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
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28
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Oliveira MME, Lopes AP, Pinto TN, da Costa GL, Goes-Neto A, Hauser-Davis RA. A Novel One Health Approach concerning Yeast Present in the Oral Microbiome of the Endangered Rio Skate ( Rioraja agassizii) from Southeastern Brazil. Microorganisms 2023; 11:1969. [PMID: 37630528 PMCID: PMC10459090 DOI: 10.3390/microorganisms11081969] [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: 07/04/2023] [Revised: 07/22/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
The current climate change scenario caused by anthropogenic activities has resulted in novel environmental pressures, increasing the occurrence and severity of fungal infections in the marine environment. Research on fungi in several taxonomic groups is widespread although not the case for elasmobranchs (sharks and rays). In this context, the aim of the present study was to screen the oral fungal microbiota present in artisanally captured Rioraja agassizii, a batoid that, although endangered, is highly fished and consumed worldwide. Oropharyngeal samples were obtained by swabbing and the samples were investigated using morphological and phenotypic methods by streaking on Sabouraud Dextrose Agar (SDA) and subculturing onto CHROMagar Candida (BD Difco) and CHROMagar Candida Plus (CHROMagarTM), as well as molecular techniques by amplification of the ITS1-5.8S-ITS2 ribosomal DNA region and a MALDI-TOF MS assessment. The findings indicated the presence of Candida parapsilosis (seven isolates), Candida duobushaemulonii (one isolate) and Rhodotorula mucilaginosa (three isolates), several of these reported for the first time in Rioraja agassizii. In addition, a 100% agreement between the MALDI-TOF results and partial ITS region sequencing was noted, demonstrating that the MALDI-TOF MS is a rapid and effective alternative for yeast identification in Rioraja agassizii isolates and potentially in other elasmobranch species. These findings highlight the need for further research to determine the potential impact on elasmobranch health, ecology, and commercial fisheries. Furthermore, this research is paramount in a One Health framework and may be employed to predict elasmobranch responses to an evolving ocean, keep healthy populations in check, monitor species, and assess the public health consequences of consuming these species.
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Affiliation(s)
- Manoel Marques Evangelista Oliveira
- Laboratory of Taxonomy, Biochemistry and Bioprospecting of Fungi, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040360, RJ, Brazil
| | - Amanda Pontes Lopes
- Laboratório de Avaliação e Promoção da Saúde Ambiental, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040360, RJ, Brazil
| | - Tatiane Nobre Pinto
- Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 30130100, MG, Brazil (A.G.-N.)
| | - Gisela Lara da Costa
- Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 30130100, MG, Brazil (A.G.-N.)
| | - Aristóteles Goes-Neto
- Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 30130100, MG, Brazil (A.G.-N.)
| | - Rachel Ann Hauser-Davis
- Laboratório de Avaliação e Promoção da Saúde Ambiental, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040360, RJ, Brazil
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Nayak A, Harshitha M, Dubey S, Munang'andu HM, Chakraborty A, Karunasagar I, Maiti B. Evaluation of Probiotic Efficacy of Bacillus subtilis RODK28110C3 Against Pathogenic Aeromonas hydrophila and Edwardsiella tarda Using In Vitro Studies and In Vivo Gnotobiotic Zebrafish Gut Model System. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10127-w. [PMID: 37486455 DOI: 10.1007/s12602-023-10127-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2023] [Indexed: 07/25/2023]
Abstract
The indiscriminate use of antibiotics in aquaculture has led to the emergence of resistance; hence, eco-friendly, host-specific alternatives to mitigate bacterial infections have become imminent. In this study, bacteria that could possibly serve as probiotics were isolated and evaluated for their efficacy with in vitro experiments and in vivo zebrafish gut model. One isolate from each of the 23 rohu fish (Labeo rohita) was shortlisted after preliminary screening of several isolates and tested for their ability to inhibit two important warm water bacterial fish pathogens, Aeromonas hydrophila, and Edwardsiella tarda. An isolate (RODK28110C3) that showed broad-spectrum inhibitory activity against a battery of different isolates of the two fish pathogens included in this study and maintained in our repository was selected for further characterization. The culture was identified phenotypically as Bacillus subtilis and confirmed by 16S rDNA sequencing. The isolate was able to hydrolyze fish feed constituents that include starch, protein, and cellulose. Further in vitro tests ensured that the potential isolate with probiotic attributes could tolerate different gut conditions, which included a range of pH, salinity, and varying concentrations of bile salt. Exposure of 4 days post fertilization zebrafish embryos to the RFP-tagged isolate confirmed the colonization of B. subtilis in the gut of the zebrafish embryo, which is an important attribute of a probiotic. The isolate was able to inhibit both A. hydrophila and E. tarda in gnotobiotic zebrafish embryo in triplicate. The study demonstrates the probiotic characteristics of the B. subtilis isolated from L. rohita and its ability to inhibit A. hydrophila and E. tarda using in vitro conditions and in the zebrafish gut and could serve as an effective alternative to antibiotics in aquaculture.
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Grants
- INT/NOR/RCN/BIO/P-01/2018 Department of Science and Technology, Ministry of Science and Technology, India
- INT/NOR/RCN/BIO/P-01/2018 Department of Science and Technology, Ministry of Science and Technology, India
- INT/NOR/RCN/BIO/P-01/2018 Department of Science and Technology, Ministry of Science and Technology, India
- INT/NOR/RCN/BIO/P-01/2018 Department of Science and Technology, Ministry of Science and Technology, India
- INT/NOR/RCN/BIO/P-01/2018 Department of Science and Technology, Ministry of Science and Technology, India
- INT/NOR/RCN/BIO/P-01/2018 Department of Science and Technology, Ministry of Science and Technology, India
- INT/NOR/RCN/BIO/P-01/2018 Department of Science and Technology, Ministry of Science and Technology, India
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Affiliation(s)
- Ashwath Nayak
- Division of Infectious Diseases, Nitte (Deemed to be University), Nitte University Centre for Science Education and Research, Paneer Campus, Deralakatte, Mangaluru, 575018, India
| | - Mave Harshitha
- Division of Infectious Diseases, Nitte (Deemed to be University), Nitte University Centre for Science Education and Research, Paneer Campus, Deralakatte, Mangaluru, 575018, India
| | - Saurabh Dubey
- Faculty of Veterinary Medicine, Department of Production Animal Clinical Sciences, Section of Experimental Biomedicine, Norwegian University of Life Sciences, Ås, Norway
| | | | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte (Deemed to be University), Nitte University Centre for Science Education and Research, Paneer Campus, Deralakatte, Mangaluru, 575018, India
| | - Indrani Karunasagar
- Nitte (Deemed to be University), DST Technology Enabling Centre, Paneer Campus, Deralakatte, Mangaluru, 575018, India
| | - Biswajit Maiti
- Division of Infectious Diseases, Nitte (Deemed to be University), Nitte University Centre for Science Education and Research, Paneer Campus, Deralakatte, Mangaluru, 575018, India.
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Najafpour B, Pinto PIS, Sanz EC, Martinez-Blanch JF, Canario AVM, Moutou KA, Power DM. Core microbiome profiles and their modification by environmental, biological, and rearing factors in aquaculture hatcheries. MARINE POLLUTION BULLETIN 2023; 193:115218. [PMID: 37441915 DOI: 10.1016/j.marpolbul.2023.115218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/06/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023]
Abstract
16S rRNA gene sequencing and bacteria- and genus-specific quantitative PCR was used to profile microbial communities and their associated functions in water, live feed (microalgae, Artemia, and rotifer), and European sea bass and gilthead sea bream larvae from hatcheries in Greece and Italy. The transfer to larvae of genus containing potential pathogens of fish was more likely with Artemia and rotifer than with microalgae or water, irrespective of geographic location. The presence of potentially pathogenic bacteria (Vibrio and Pseudoalteromonas) in the core microbiota of water, live feed, and fish larvae, the enrichment of different bacterial resistance pathways and biofilm formation, and the overall low beneficial bacteria load during larval ontogeny emphasizes the risk for disease outbreaks. The present data characterizing microbiota in commercial aquaculture hatcheries provides a baseline for the design of strategies to manage disease and to model or remediate potential adverse environmental impacts.
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Affiliation(s)
- Babak Najafpour
- CCMAR - Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Edifício 7, 8005-139 Faro, Portugal
| | - Patricia I S Pinto
- CCMAR - Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Edifício 7, 8005-139 Faro, Portugal
| | - Eric Climent Sanz
- ADM Biopolis, Parc Cientific Universidad De Valencia, Paterna, Spain
| | | | - Adelino V M Canario
- CCMAR - Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Edifício 7, 8005-139 Faro, Portugal; Shanghai Ocean University International Center for Marine Studies, Shanghai, China
| | - Katerina A Moutou
- Department of Biochemistry & Biotechnology, University of Thessaly, Ploutonos 26, Larissa, Greece
| | - Deborah M Power
- CCMAR - Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Edifício 7, 8005-139 Faro, Portugal; Shanghai Ocean University International Center for Marine Studies, Shanghai, China.
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Fiedler AW, Drågen MKR, Lorentsen ED, Vadstein O, Bakke I. The stability and composition of the gut and skin microbiota of Atlantic salmon throughout the yolk sac stage. Front Microbiol 2023; 14:1177972. [PMID: 37485532 PMCID: PMC10358989 DOI: 10.3389/fmicb.2023.1177972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/19/2023] [Indexed: 07/25/2023] Open
Abstract
The bacterial colonization of newly hatched fish is important for the larval development and health. Still, little is known about the ontogeny of the early microbiota of fish. Here, we conducted two independent experiments with yolk sac fry of Atlantic salmon that were (1) either reared conventionally, with the eggs as the only source for bacteria (egg-derived microbiota; EDM) or (2) hatched germ-free and re-colonized using lake water (lake-derived microbiota; LDM). First, we characterized the gut and skin microbiota at 6, 9, and 13 weeks post hatching based on extracted RNA. In the second experiment, we exposed fry to high doses of either a fish pathogen or a commensal bacterial isolate and sampled the microbiota based on extracted DNA. The fish microbiota differed strongly between EDM and LDM treatments. The phyla Proteobacteria, Bacteroidetes, and Actinobacteria dominated the fry microbiota, which was found temporarily dynamic. Interestingly, the microbiota of EDM fry was more stable, both between replicate rearing flasks, and over time. Although similar, the skin and gut microbiota started to differentiate during the yolk sac stage, several weeks before the yolk was consumed. Addition of high doses of bacterial isolates to fish flasks had only minor effects on the microbiota.
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Casadei E, Mani A, Cisco M, Vågnes Ø, Salinas I, Patel S. Sex-dependent effects of mechanical delousing on the skin microbiome of broodstock Atlantic salmon (Salmo salar L.). Sci Rep 2023; 13:10824. [PMID: 37402791 DOI: 10.1038/s41598-023-37670-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 06/26/2023] [Indexed: 07/06/2023] Open
Abstract
Delousing strategies, including mechanical delousing, are typically used to treat Atlantic salmon (Salmo salar) sea lice infestations. In this study, we evaluate the impact of mechanical delousing (Hydrolicer) on the skin bacterial microbiome of broodstock female and male Atlantic salmon. 16S rDNA sequencing of salmon skin microbial communities was performed immediately before delousing, right after delousing and 2 and 13 days post-delousing (dpd). The skin bacterial community of female salmon was more diverse than that of males at the start of the experiment. Overall, hydrolycer caused losses in alpha diversity in females and increases in alpha diversity in males. Hydrolicer also caused rapid shifts in the skin microbial community composition immediately after delicing in a sex-specific manner. There was a decrease in abundance of Proteobacteria and Bacteriodetes in both female and male salmon, whereas Firmicutes and Tenericutes abundances increased. Interestingly, the female community recovered faster, while the male community remained dysbiotic 13 dpd due to expansions in Bacteroidetes (Pseudomonadaceae) and Firmicutes. Our data suggest that female broodstock are more resilient to Hydrolicer treatment due to their more diverse skin microbiota community, and that sex influences the skin microbial community and therefore host health outcomes during common farming manipulations.
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Affiliation(s)
- Elisa Casadei
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Amir Mani
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Mariela Cisco
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Øyvind Vågnes
- Vaxxinova Norway, Kong Christian Frederiks Plass 3, 5006, Bergen, Norway
- Blue Analytics AS, Kong Christian Frederiks Plass 3, 5006, Bergen, Norway
| | - Irene Salinas
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Sonal Patel
- Vaxxinova Norway, Kong Christian Frederiks Plass 3, 5006, Bergen, Norway.
- Norwegian Veterinary Institute, Thormøhlens Gate 53C, 5006, Bergen, Norway.
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Ziab M, Chaganti SR, Heath DD. The effects of host quantitative genetic architecture on the gut microbiota composition of Chinook salmon (Oncorhynchus tshawytscha). Heredity (Edinb) 2023; 131:43-55. [PMID: 37179383 PMCID: PMC10313681 DOI: 10.1038/s41437-023-00620-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: 12/29/2022] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
The microbiota consists of microbes living in or on an organism and has been implicated in host health and function. Environmental and host-related factors were shown to shape host microbiota composition and diversity in many fish species, but the role of host quantitative architecture across populations and among families within a population is not fully characterized. Here, Chinook salmon were used to determine if inter-population differences and additive genetic variation within populations influenced the gut microbiota diversity and composition. Specifically, hybrid stocks of Chinook salmon were created by crossing males from eight populations with eggs from an inbred line created from self-fertilized hermaphrodite salmon. Based on high-throughput sequencing of the 16S rRNA gene, significant gut microbial community diversity and composition differences were found among the hybrid stocks. Furthermore, additive genetic variance components varied among hybrid stocks, indicative of population-specific heritability patterns, suggesting the potential to select for specific gut microbiota composition for aquaculture purposes. Determining the role of host genetics in shaping their gut microbiota has important implications for predicting population responses to environmental changes and will thus impact conservation efforts for declining populations of Chinook salmon.
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Affiliation(s)
- Mubarak Ziab
- Great Lakes Institute for Environmental Research (GLIER), University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research (GLIER), University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada.
- Department of Integrative Biology, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada.
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Suhr M, Fichtner-Grabowski FT, Seibel H, Bang C, Franke A, Schulz C, Hornburg SC. The microbiota knows: handling-stress and diet transform the microbial landscape in the gut content of rainbow trout in RAS. Anim Microbiome 2023; 5:33. [PMID: 37386608 DOI: 10.1186/s42523-023-00253-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/16/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND The aim of the present study was to characterize the effects of handling stress on the microbiota in the intestinal gut contents of rainbow trout (Oncorhynchus mykiss) fed a plant-based diet from two different breeding lines (initial body weights: A: 124.69 g, B: 147.24 g). Diets were formulated in accordance with commercial trout diets differing in their respective protein sources: fishmeal (35% in fishmeal-based diet F, 7% in plant protein-based diet V) and plant-based proteins (47% in diet F, 73% in diet V). Experimental diets were provided for 59 days to all female trout in two separate recirculating aquaculture systems (RASs; mean temperature: A: 15.17 °C ± 0.44, B: 15.42 °C ± 0.38). Half of the fish in each RAS were chased with a fishing net twice per day to induce long-term stress (Group 1), while the other half were not exposed to stress (Group 0). RESULTS No differences in performance parameters were found between the treatment groups. By using 16S rRNA amplicon sequencing of the hypervariable region V3/V4, we examined the microbial community in the whole intestinal content of fish at the end of the trial. We discovered no significant differences in alpha diversity induced by diet or stress within either genetic trout line. However, the microbial composition was significantly driven by the interaction of stress and diet in trout line A. Otherwise, in trout line B, the main factor was stress. The communities of both breeding lines were predominantly colonized by bacteria from the phyla Fusobacteriota, Firmicutes, Proteobacteria, Actinobacteriota, and Bacteroidota. The most varying and abundant taxa were Firmicutes and Fusobacteriota, whereas at the genus level, Cetobacterium and Mycoplasma were key components in terms of adaptation. In trout line A, Cetobacterium abundance was affected by factor stress, and in trout line B, it was affected by the factor diet. CONCLUSION We conclude that microbial gut composition, but neither microbial diversity nor fish performance, is highly influenced by stress handling, which also interacts with dietary protein sources. This influence varies between different genetic trout lines and depends on the fish's life history.
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Affiliation(s)
- Marvin Suhr
- Institute of Animal Nutrition and Physiology, Christian-Albrechts-University Kiel, Hermann-Rodewald-Straße 9, 24118, Kiel, Germany.
| | | | - Henrike Seibel
- Fraunhofer Research Institution for Individualized and Cell-Based Medical Engineering, Hafentörn 3, 25761, Büsum, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, University Hospital Schleswig-Holstein, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, University Hospital Schleswig-Holstein, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany
| | - Carsten Schulz
- Fraunhofer Research Institution for Individualized and Cell-Based Medical Engineering, Hafentörn 3, 25761, Büsum, Germany
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Hermann-Rodewald-Straße 6, 24118, Kiel, Germany
| | - Stéphanie Céline Hornburg
- Institute of Animal Nutrition and Physiology, Christian-Albrechts-University Kiel, Hermann-Rodewald-Straße 9, 24118, Kiel, Germany
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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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Liang Y, Liu H, Zhai S, Huang L, Huang W, Huang B, Xu J, Xiong J, Wang B. Effects of weaning American glass eels ( Anguilla rostrata) with the formula diet on intestinal microbiota and inflammatory cytokines genes expression. Heliyon 2023; 9:e16965. [PMID: 37346341 PMCID: PMC10279831 DOI: 10.1016/j.heliyon.2023.e16965] [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: 11/20/2022] [Revised: 04/27/2023] [Accepted: 06/02/2023] [Indexed: 06/23/2023] Open
Abstract
This study aimed to investigate the effects of weaning American glass eels (Anguilla rostrata) with the formula diet on intestinal microbiota and the expression of inflammatory cytokines genes. During the feeding trial, the control group (termed IF group) was fed with initial feed for 34 days, and the experimental group (termed FF group) was fed with initial feed for 30 days, and then weaned with the formula diet for 4 days. After feeding trial, intestines were subjected to microbiota analysis using 16S rDNA high-throughput sequencing, and expression of three inflammatory cytokines genes in gut were examined by qPCR. The results indicated that the species richness and diversity of intestinal microbiota exhibited significantly higher in FF group than that in IF group (P < 0.05). At the phylum level, the core intestinal microflora was the same for two groups. The most abundant phylum was Firmicutes in IF group, while it was Proteobacteria in FF group. Five genera were significantly higher in the IF group compared with the FF group, and Bacillus was the most major enriched biomarker at genus level. Nine genera were significantly higher in the FF group compared with the IF group, and Acidovorax was the most major enriched biomarker. Weaning from initial feeding diet to formula feeding diet enhanced the expression levels of TNF-α and IL-8, and there was no significant change in IL-1β expression between the two groups. These findings would be very useful to improve the diet formulation for weaning stage of American glass eels.
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Affiliation(s)
- Ying Liang
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, Guangdong, 524088, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, PR China, Xiamen, Fujian, 361021, China
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China, Xiamen, Fujian, 361021, China
| | - Haizi Liu
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China, Xiamen, Fujian, 361021, China
| | - Shaowei Zhai
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China, Xiamen, Fujian, 361021, China
| | - Lixing Huang
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
| | - Wenshu Huang
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China, Xiamen, Fujian, 361021, China
| | - Bei Huang
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China, Xiamen, Fujian, 361021, China
| | - Jisong Xu
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China, Xiamen, Fujian, 361021, China
| | - Jing Xiong
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China, Xiamen, Fujian, 361021, China
| | - Bei Wang
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, Guangdong, 524088, China
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Zhao Z, Zhao H, Zhang L, Huang Z, Ke H, Liu Y, Duan Y, Li H, Wang X, Li Q. Integrated analysis of how gender and body weight affect the intestinal microbial diversity of Gymnocypris chilianensis. Sci Rep 2023; 13:8811. [PMID: 37258553 DOI: 10.1038/s41598-023-35600-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 05/20/2023] [Indexed: 06/02/2023] Open
Abstract
Intestinal microorganisms that living in the mucosa and contents of the gastrointestinal tract of animals, have close links with their hosts over a long evolutionary history. The community structure of the fish intestinal microbiota is associated with food, living environment, and the growth stage. To screen for potential probiotics that can be used for regulating breeding behaviors, this study focused on the diversity of fish intestinal microorganisms. This study aimed to investigate the effects of sex and body weight on the intestinal microbial diversity of Gymnocypris chilianensis in the wild. The results showed that the significant high diversity and richness of intestinal microbiota were fould in heavier individuals, and males. The dominant bacterial phyla of G. chilianensis were Proteobacteria, Firmicutes, and Bacteroidetes. In addition, the abundance of Firmicutes varied significantly among different body weights. The genus profile revealed that small individuals were dominated by Weissella, while females were dominated by Aeromonas, and both large individuals and males were dominated by other genera. Phylogenetic relationships and UPGMA clustering analysis showed significant differences among the groups. In general, the two main factors that have an effect on the intestinal microbiota diversity of wild G. chilianensis are sex and body weight.
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Affiliation(s)
- Zhongmeng Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Han Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Lu Zhang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Zhipeng Huang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Hongyu Ke
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Ya Liu
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Yuanliang Duan
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Huadong Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Xiongyan Wang
- Sichuan Water Conservancy Vocational College, Chongzhou, Sichuan, China
| | - Qiang Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China.
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Gallet A, Halary S, Duval C, Huet H, Duperron S, Marie B. Disruption of fish gut microbiota composition and holobiont's metabolome during a simulated Microcystis aeruginosa (Cyanobacteria) bloom. MICROBIOME 2023; 11:108. [PMID: 37194081 DOI: 10.1186/s40168-023-01558-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/26/2023] [Indexed: 05/18/2023]
Abstract
BACKGROUND Cyanobacterial blooms are one of the most common stressors encountered by metazoans living in freshwater lentic systems such as lakes and ponds. Blooms reportedly impair fish health, notably through oxygen depletion and production of bioactive compounds including cyanotoxins. However, in the times of the "microbiome revolution", it is surprising that so little is still known regarding the influence of blooms on fish microbiota. In this study, an experimental approach is used to demonstrate that blooms affect fish microbiome composition and functions, as well as the metabolome of holobionts. To this end, the model teleost Oryzias latipes is exposed to simulated Microcystis aeruginosa blooms of various intensities in a microcosm setting, and the response of bacterial gut communities is evaluated in terms of composition and metabolome profiling. Metagenome-encoded functions are compared after 28 days between control individuals and those exposed to highest bloom level. RESULTS The gut bacterial community of O. latipes exhibits marked responses to the presence of M. aeruginosa blooms in a dose-dependent manner. Notably, abundant gut-associated Firmicutes almost disappear, while potential opportunists increase. The holobiont's gut metabolome displays major changes, while functions encoded in the metagenome of bacterial partners are more marginally affected. Bacterial communities tend to return to original composition after the end of the bloom and remain sensitive in case of a second bloom, reflecting a highly reactive gut community. CONCLUSION Gut-associated bacterial communities and holobiont functioning are affected by both short and long exposure to M. aeruginosa, and show evidence of post-bloom resilience. These findings point to the significance of bloom events to fish health and fitness, including survival and reproduction, through microbiome-related effects. In the context of increasingly frequent and intense blooms worldwide, potential outcomes relevant to conservation biology as well as aquaculture warrant further investigation. Video Abstract.
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Affiliation(s)
- Alison Gallet
- UMR7245 Molécules de Communication et Adaptation des Micro-organismes, Muséum National d'Histoire Naturelle, CNRS, Paris, France
| | - Sébastien Halary
- UMR7245 Molécules de Communication et Adaptation des Micro-organismes, Muséum National d'Histoire Naturelle, CNRS, Paris, France
| | - Charlotte Duval
- UMR7245 Molécules de Communication et Adaptation des Micro-organismes, Muséum National d'Histoire Naturelle, CNRS, Paris, France
| | - Hélène Huet
- UMR1161 Virologie, École Nationale Vétérinaire d'Alfort, INRA - ANSES - ENVA, Maisons-Alfort, France
| | - Sébastien Duperron
- UMR7245 Molécules de Communication et Adaptation des Micro-organismes, Muséum National d'Histoire Naturelle, CNRS, Paris, France.
- Institut Universitaire de France, Paris, France.
| | - Benjamin Marie
- UMR7245 Molécules de Communication et Adaptation des Micro-organismes, Muséum National d'Histoire Naturelle, CNRS, Paris, France.
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Hasan I, Rimoldi S, Saroglia G, Terova G. Sustainable Fish Feeds with Insects and Probiotics Positively Affect Freshwater and Marine Fish Gut Microbiota. Animals (Basel) 2023; 13:ani13101633. [PMID: 37238063 DOI: 10.3390/ani13101633] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Aquaculture is the fastest-growing agricultural industry in the world. Fishmeal is an essential component of commercial fish diets, but its long-term sustainability is a concern. Therefore, it is important to find alternatives to fishmeal that have a similar nutritional value and, at the same time, are affordable and readily available. The search for high-quality alternatives to fishmeal and fish oil has interested researchers worldwide. Over the past 20 years, different insect meals have been studied as a potential alternate source of fishmeal in aquafeeds. On the other hand, probiotics-live microbial strains-are being used as dietary supplements and showing beneficial effects on fish growth and health status. Fish gut microbiota plays a significant role in nutrition metabolism, which affects a number of other physiological functions, including fish growth and development, immune regulation, and pathogen resistance. One of the key reasons for studying fish gut microbiota is the possibility to modify microbial communities that inhabit the intestine to benefit host growth and health. The development of DNA sequencing technologies and advanced bioinformatics tools has made metagenomic analysis a feasible method for researching gut microbes. In this review, we analyze and summarize the current knowledge provided by studies of our research group on using insect meal and probiotic supplements in aquafeed formulations and their effects on different fish gut microbiota. We also highlight future research directions to make insect meals a key source of proteins for sustainable aquaculture and explore the challenges associated with the use of probiotics. Insect meals and probiotics will undoubtedly have a positive effect on the long-term sustainability and profitability of aquaculture.
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Affiliation(s)
- Imam Hasan
- Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant, 3-21100 Varese, Italy
| | - Simona Rimoldi
- Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant, 3-21100 Varese, Italy
| | - Giulio Saroglia
- Medical Devices Area, Institute of Digital Technologies for Personalized Healthcare-MeDiTech, Scuola Universitaria Professionale della Svizzera Italiana, Via La Santa 1, CH-6962 Lugano, Switzerland
| | - Genciana Terova
- Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant, 3-21100 Varese, Italy
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Li W, Zhou Z, Li H, Wang S, Ren L, Hu J, Liu Q, Wu C, Tang C, Hu F, Zeng L, Zhao R, Tao M, Zhang C, Qin Q, Liu S. Successional Changes of Microbial Communities and Host-Microbiota Interactions Contribute to Dietary Adaptation in Allodiploid Hybrid Fish. MICROBIAL ECOLOGY 2023; 85:1190-1201. [PMID: 35366074 DOI: 10.1007/s00248-022-01993-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/07/2022] [Indexed: 05/10/2023]
Abstract
Host-microbiota interactions play critical roles in host development, immunity, metabolism, and behavior. However, information regarding host-microbiota interactions is limited in fishes due to their complex living environment. In the present study, an allodiploid hybrid fish derived from herbivorous Megalobrama amblycephala (♀) × carnivorous Culter alburnus (♂) was used to investigate the successional changes of the microbial communities and host-microbiota interactions during herbivorous and carnivorous dietary adaptations. The growth level was not significantly different in any developmental stage between the two diet groups of fish. The diversity and composition of the dominant microbial communities showed similar successional patterns in the early developmental stages, but significantly changed during the two dietary adaptations. A large number of bacterial communities coexisted in all developmental stages, whereas the abundance of some genera associated with metabolism, including Acinetobacter, Gemmobacter, Microbacterium, Vibrio, and Aeromonas, was higher in either diet groups of fish. Moreover, the abundance of phylum Firmicutes, Actinobacteria, and Chloroflexi was positively correlated with the host growth level. In addition, Spearman's correlation analysis revealed that the differentially expressed homologous genes in the intestine associated with cell growth, immunity, and metabolism were related to the dominant gut microbiota. Our results present evidence that host genetics-gut microbiota interactions contribute to dietary adaptation in hybrid fish, which also provides basic data for understanding the diversity of dietary adaptations and evolution in fish.
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Affiliation(s)
- Wuhui Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Zexun Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Hongqing Li
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Jie Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Qingfeng Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Fangzhou Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Lei Zeng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Rulong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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Aly SM, Eissa AE, Abdel-Razek N, El-Ramlawy AO. The antibacterial activity and immunomodulatory effect of naturally synthesized chitosan and silver nanoparticles against Pseudomonas fluorescence infection in Nile tilapia (Oreochromis niloticus): An in vivo study. FISH & SHELLFISH IMMUNOLOGY 2023; 135:108628. [PMID: 36822383 DOI: 10.1016/j.fsi.2023.108628] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/05/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
A sixty-day feeding trial was conducted to assess the effects of silver nanoparticles (AgNPs) and chitosan nanoparticles (CNPs) on the growth and immunity of Nile tilapia (Oreochromis niloticus), compared with the control group. CNPs and AgNPs were green synthesized and added to a control diet (30% crude protein) at levels of 2.0 g CNPs/kg diet and 1.0 mg AgNPs/kg diet. One hundred and eighty fish (101 ± 3.98 g) were randomly distributed into nine fiberglass tanks (200 cm × 200 cm x 100 cm, twenty fish each) to represent three equal groups (60 fish per group). After one and two months of the feeding trial, parameters of water quality, growth indices, hematology, and liver and kidney biomarkers were evaluated. At the end of the experiment, 10 fish from each group were challenged experimentally via the intraperitoneal injection with Pseudomonas fluorescence and fish mortality was observed for further ten days. Then, specimens from the liver, kidney, spleen, and anterior intestine were examined to assess the histopathological alterations. Incorporating a 2.0 g CNPs/kg diet was a promising growth enhancer; however, a 1.0 mg AgNPs/kg diet had no effects on tilapia performance. Furthermore, AgNPs appeared to reduce water pollution, leading to water filtration via decreasing both total dissolved solids (TDS) and electrical conductivity (EC). A significant role of AgNPs in improving tilapia's erythrogram (RBCs number and Hb concentration) was evident. Compared with the control group, both groups of CNPs and AgNPs improved non-specific immune parameters and showed defense effects against P. fluorescence. The fish mortality after P. fluorescence infection in CNPs and AgNPs-fed fish groups revealed significant decreases (P < 0.05) of 10% and 25%; respectively, while the control group exhibited a mortality rate of 40%. The current investigation evoked that using dietary CNPs (2.0 g/kg feed) as an antibacterial agent against P. fluorescence infection in Nile tilapia culture was better than dietary AgNPs (1.0 mg/kg diet) which, induced cells inflammation causing tissues necrosis.
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Affiliation(s)
- Salah M Aly
- Department of Pathology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Alaa Eldin Eissa
- Department of Aquatic Animal Medicine & Management, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Nashwa Abdel-Razek
- Department of Fish Health and Management, Central Laboratory for Aquaculture Research, Agriculture Research Center, Abbassa, Abo-Hammad, Sharqia, 44662, Egypt
| | - Asmaa O El-Ramlawy
- Department of Aquaculture Diseases Control, Fish Farming and Technology Institute, Suez Canal University, Ismailia, Egypt.
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Zhang Y, Qi X, Zhang Z, Jin Z, Wang G, Ling F. Effects of dietary Cetobacterium somerae on the intestinal health, immune parameters and resistance against Nocardia seriolae of largemouth bass, Micropterus salmoides. FISH & SHELLFISH IMMUNOLOGY 2023; 135:108693. [PMID: 36940785 DOI: 10.1016/j.fsi.2023.108693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
Largemouth bass (Micropterus salmoides), one of the most important freshwater commercial fish species has been widely cultivated in China. In recent years, the nocardiosis caused by Nocardia seriolae has greatly damaged the M. salmoides industry and there is no effective treatment at present. Currently, Cetobacterium somerae, the predominant bacteria in the gut of many freshwater fishes has been reported to be associated with fish health. However, whether the native C. somerae could protect the host from N. seriolae is unclear. In this study, M. salmoides were fed with three different diets, including control diet (CD), low C. somerae diet (106 CFU/g as LD) and high C. somerae diet (108 CFU/g as HD). After 8-week feeding, growth performance, gut health index, serum enzyme activities and the expression of inflammation-related genes were tested. Results showed that the LD and HD diets had no adverse effects on the growth performance. Moreover, dietary HD enhanced gut barrier and reduced intestinal ROS and ORP, as well as increased serum enzyme activities including ACP, AKP, SOD and LZM compared to the CD group. In addition, the HD diet significantly up-regulated the expression of TNF-α, IL8, IL-1β and IL15, while down-regulating the expression of TGF-β1 and IL10 in kidney. Moreover, the expression of antibacterial genes was significantly increased in HD group after being challenged by N. seriolae. And the fish fed HD diet exhibited higher survival rate (57.5%) than that in CD (37.5%) and LD groups (42.5%). To summarize, our study demonstrates that dietary HD can enhance gut health, improve immune response and strengthen pathogen resistance, suggesting that C. somerae is a potential probiotic for defending against N. seriolae infection in M. salmoides.
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Affiliation(s)
- Yong Zhang
- Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China
| | - Xiaozhou Qi
- Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China
| | - Zhongyu Zhang
- Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China
| | - Zhanlin Jin
- Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China
| | - Gaoxue Wang
- Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China; Key Laboratory of Livestock Biology, Northwest A&F University, China.
| | - Fei Ling
- Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China; Key Laboratory of Livestock Biology, Northwest A&F University, China.
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Jang WJ, Lee KB, Jeon MH, Lee SJ, Hur SW, Lee S, Lee BJ, Lee JM, Kim KW, Lee EW. Characteristics and biological control functions of Bacillus sp. PM8313 as a host-associated probiotic in red sea bream ( Pagrus major) aquaculture. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2023; 12:20-31. [PMID: 36381063 PMCID: PMC9641168 DOI: 10.1016/j.aninu.2022.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 07/29/2022] [Accepted: 08/10/2022] [Indexed: 06/16/2023]
Abstract
Host-associated probiotics (HAPs) are bacteria originally isolated from rearing water or the host's gastrointestinal tract in order to enhance the host's growth and health. This study investigated the HAP potential of Bacillus sp. PM8313, isolated from wild red sea bream (Pagrus major), through characterization and feeding trials. Results based on in vitro tests showed that PM8313 is safe, confirming its hemolytic, cytotoxic, and antibiotic resistance. In addition, PM8313 showed advantages as a probiotic with high viability in the gastrointestinal model and a high cell adhesion rate. Whole-genome sequencing demonstrated that PM8313 has a 4,615,871 bp single circular chromosome and a guanine-cytosine content of 45.25%. It also showed the absence of genes encoding virulence factors, such as cytotoxin, enterotoxin, hemolysin, sphingomyelinase, and phospholipase. In the feeding trial, a supplemental diet of 1 × 108 CFU/g PM8313 positively altered the weight gain, digestive enzyme activity, and intestinal microbiota composition of red sea bream. Analysis of nonspecific immune parameters and immune-related gene expression, and a challenge test showed that PM8313 supplementation increases immunity and pathogenic bacteria resistance. Our findings suggest that PM8313 should be considered for application as a novel HAP to red sea bream aquaculture.
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Affiliation(s)
- Won Je Jang
- Department of Biotechnology, Pukyong National University, Busan, 48513, South Korea
| | - Kyung-Bon Lee
- Department of Biology Education College of Education, Chonnam National University, Gwangju, 61186, South Korea
| | - Mi-Hyeon Jeon
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, Dong-Eui University, Busan, 47340, South Korea
| | - Su-Jeong Lee
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, Dong-Eui University, Busan, 47340, South Korea
| | - Sang Woo Hur
- Aquafeed Research Center, National Institute of Fisheries Science, Pohang, 37517, South Korea
| | - Seunghan Lee
- Aquafeed Research Center, National Institute of Fisheries Science, Pohang, 37517, South Korea
| | - Bong-Joo Lee
- Aquafeed Research Center, National Institute of Fisheries Science, Pohang, 37517, South Korea
- Department of Smart Fisheries Resources, College of Industrial Sciences, Kongju National University, Yesan, 32439, South Korea
| | - Jong Min Lee
- Department of Biotechnology, Pukyong National University, Busan, 48513, South Korea
| | - Kang-Woong Kim
- Aquafeed Research Center, National Institute of Fisheries Science, Pohang, 37517, South Korea
| | - Eun-Woo Lee
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, Dong-Eui University, Busan, 47340, South Korea
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Gómez de la Torre Canny S, Nordgård CT, Mathisen AJH, Degré Lorentsen E, Vadstein O, Bakke I. A novel gnotobiotic experimental system for Atlantic salmon ( Salmo salar L.) reveals a microbial influence on mucosal barrier function and adipose tissue accumulation during the yolk sac stage. Front Cell Infect Microbiol 2023; 12:1068302. [PMID: 36817693 PMCID: PMC9929952 DOI: 10.3389/fcimb.2022.1068302] [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: 10/12/2022] [Accepted: 12/05/2022] [Indexed: 02/04/2023] Open
Abstract
Gnotobiotic models have had a crucial role in studying the effect that commensal microbiota has on the health of their animal hosts. Despite their physiological and ecological diversity, teleost fishes are still underrepresented in gnotobiotic research. Moreover, a better understanding of host-microbe interactions in farmed fish has the potential to contribute to sustainable global food supply. We have developed a novel gnotobiotic experimental system that includes the derivation of fertilized eggs of farmed and wild Atlantic salmon, and gnotobiotic husbandry of fry during the yolk sac stage. We used a microscopy-based approach to estimate the barrier function of the skin mucus layer and used this measurement to select the derivation procedure that minimized adverse effects on the skin mucosa. We also used this method to demonstrate that the mucus barrier was reduced in germ-free fry when compared to fry colonized with two different bacterial communities. This alteration in the mucus barrier was preceded by an increase in the number of cells containing neutral mucosubstances in the anterior segment of the body, but without changes in the number of cells containing acidic substances in any of the other segments studied along the body axis. In addition, we showed how the microbial status of the fry temporarily affected body size and the utilization of internal yolk stores during the yolk sac stage. Finally, we showed that the presence of bacterial communities associated with the fry, as well as their composition, affected the size of adipose tissue. Fry colonized with water from a lake had a larger visceral adipose tissue depot than both conventionally raised and germ-free fry. Together, our results show that this novel gnotobiotic experimental system is a useful tool for the study of host-microbe interactions in this species of aquacultural importance.
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Affiliation(s)
| | - Catherine Taylor Nordgård
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Amalie Johanne Horn Mathisen
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Eirik Degré Lorentsen
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Olav Vadstein
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ingrid Bakke
- *Correspondence: Sol Gómez de la Torre Canny, ; Ingrid Bakke,
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Doane MP, Johnson CJ, Johri S, Kerr EN, Morris MM, Desantiago R, Turnlund AC, Goodman A, Mora M, Lima LFO, Nosal AP, Dinsdale EA. The Epidermal Microbiome Within an Aggregation of Leopard Sharks (Triakis semifasciata) Has Taxonomic Flexibility with Gene Functional Stability Across Three Time-points. MICROBIAL ECOLOGY 2023; 85:747-764. [PMID: 35129649 PMCID: PMC9957878 DOI: 10.1007/s00248-022-01969-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/17/2022] [Indexed: 05/06/2023]
Abstract
The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein-rich mucus that collectively, influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiome of the Triakis semifasciata (leopard shark) at three time-points collected across 4 years to identify links between microbial groups and host metabolism. Our aims include (1) describing the variation of microbiome taxa over time and identifying recurrent microbiome members (present across all time-points); (2) investigating the relationship between the recurrent and flexible taxa (those which are not found consistently across time-points); (3) describing the functional compositions of the microbiome which may suggest links with the host metabolism; and (4) identifying whether metabolic processes are shared across microbial genera or are unique to specific taxa. Microbial members of the microbiome showed high similarity between all individuals (Bray-Curtis similarity index = 82.7, where 0 = no overlap, 100 = total overlap) with the relative abundance of those members varying across sampling time-points, suggesting flexibility of taxa in the microbiome. One hundred and eighty-eight genera were identified as recurrent, including Pseudomonas, Erythrobacter, Alcanivorax, Marinobacter, and Sphingopxis being consistently abundant across time-points, while Limnobacter and Xyella exhibited switching patterns with high relative abundance in 2013, Sphingobium and Sphingomona in 2015, and Altermonas, Leeuwenhoekiella, Gramella, and Maribacter in 2017. Of the 188 genera identified as recurrent, the top 19 relatively abundant genera formed three recurrent groups. The microbiome also displayed high functional similarity between individuals (Bray-Curtis similarity index = 97.6) with gene function composition remaining consistent across all time-points. These results show that while the presence of microbial genera exhibits consistency across time-points, their abundances do fluctuate. Microbial functions however remain stable across time-points; thus, we suggest the leopard shark microbiomes exhibit functional redundancy. We show coexistence of microbes hosted in elasmobranch microbiomes that encode genes involved in utilizing nitrogen, but not fixing nitrogen, degrading urea, and resistant to heavy metal.
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Affiliation(s)
- Michael P. Doane
- College of Science and Engineering, Flinders University, Bedford Park, South Australia Australia
| | - Colton J. Johnson
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Shaili Johri
- Hopkins Marine Station, Stanford University, Pacific Grove, CA USA
| | - Emma N. Kerr
- College of Science and Engineering, Flinders University, Bedford Park, South Australia Australia
| | | | - Ric Desantiago
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Abigail C. Turnlund
- Australian Centre for Ecogenomics, University of Queensland, St Lucia, QLD Australia
| | - Asha Goodman
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Maria Mora
- Department of Biology, San Diego State University, San Diego, CA USA
| | | | - Andrew P. Nosal
- Department of Environmental and Ocean Sciences, University of San Diego, San Diego, CA USA
- Scripps Institution of Oceanography, University of California – San Diego, CA La Jolla, USA
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Duperron S, Foucault P, Duval C, Goto M, Gallet A, Colas S, Marie B. Multi-omics analyses from a single sample: prior metabolite extraction does not alter the 16S rRNA-based characterization of prokaryotic community in a diversity of sample types. FEMS Microbiol Lett 2023; 370:fnad125. [PMID: 37996396 DOI: 10.1093/femsle/fnad125] [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: 07/18/2023] [Revised: 10/27/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
Massive sequencing of the 16S rRNA gene has become a standard first step to describe and compare microbial communities from various samples. Parallel analysis of high numbers of samples makes it relevant to the statistical testing of the influence of natural or experimental factors and variables. However, these descriptions fail to document changes in community or ecosystem functioning. Nontargeted metabolomics are a suitable tool to bridge this gap, yet extraction protocols are different. In this study, prokaryotic community compositions are documented by 16S rRNA gene sequencing after direct DNA extraction or after metabolites extraction followed by DNA extraction. Results obtained using the V3-V4 region on nonaxenic cultures of cyanobacteria, lake water column, biofilm, and gut of wild and lab-reared fish indicate that prior extraction of metabolites does not influence the obtained image of prokaryotic communities. This validates sequential extraction of metabolites followed by DNA as a way to combine 16S rRNA sequencing with metabolome characterization from a single sample. This approach has the potential to complement community structure characterization with a proxy of their functioning, without the uncertainties associated with the use of separate samples.
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Affiliation(s)
- Sébastien Duperron
- UMR7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d'Histoire Naturelle, CNRS, 12 rue Buffon, 75005 Paris, France
| | - Pierre Foucault
- UMR7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d'Histoire Naturelle, CNRS, 12 rue Buffon, 75005 Paris, France
- UMR7618 iEES-Paris, Sorbonne Université, 4 place Jussieu, 75005 Paris, France
| | - Charlotte Duval
- UMR7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d'Histoire Naturelle, CNRS, 12 rue Buffon, 75005 Paris, France
| | - Midoli Goto
- UMR7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d'Histoire Naturelle, CNRS, 12 rue Buffon, 75005 Paris, France
| | - Alison Gallet
- UMR7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d'Histoire Naturelle, CNRS, 12 rue Buffon, 75005 Paris, France
| | - Simon Colas
- Université de Pau et des Pays de l'Adour, E2S-UPPA, CNRS, IPREM, 2 Av. du Président Pierre Angot, 64053 Pau, France
| | - Benjamin Marie
- UMR7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d'Histoire Naturelle, CNRS, 12 rue Buffon, 75005 Paris, France
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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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Sylvain FÉ, Leroux N, Normandeau É, Holland A, Bouslama S, Mercier PL, Luis Val A, Derome N. Genomic and Environmental Factors Shape the Active Gill Bacterial Community of an Amazonian Teleost Holobiont. Microbiol Spectr 2022; 10:e0206422. [PMID: 36445161 PMCID: PMC9769777 DOI: 10.1128/spectrum.02064-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
Fish bacterial communities provide functions critical for their host's survival in contrasting environments. These communities are sensitive to environmental-specific factors (i.e., physicochemical parameters, bacterioplankton), and host-specific factors (i.e., host genetic background). The relative contribution of these factors shaping Amazonian fish bacterial communities is largely unknown. Here, we investigated this topic by analyzing the gill bacterial communities of 240 wild flag cichlids (Mesonauta festivus) from 4 different populations (genetic clusters) distributed across 12 sites in 2 contrasting water types (ion-poor/acidic black water and ion-rich/circumneutral white water). Transcriptionally active gill bacterial communities were characterized by a 16S rRNA metabarcoding approach carried on RNA extractions. They were analyzed using comprehensive data sets from the hosts genetic background (Genotyping-By-Sequencing), the bacterioplankton (16S rRNA) and a set of 34 environmental parameters. Results show that the taxonomic structure of 16S rRNA gene transcripts libraries were significantly different between the 4 genetic clusters and also between the 2 water types. However, results suggest that the contribution of the host's genetic background was relatively weak in comparison to the environment-related factors in structuring the relative abundance of different active gill bacteria species. This finding was also confirmed by a mixed-effects modeling analysis, which indicated that the dissimilarity between the taxonomic structure of bacterioplanktonic communities possessed the best explicative power regarding the dissimilarity between gill bacterial communities' structure, while pairwise fixation indexes (FST) from the hosts' genetic data only had a weak explicative power. We discuss these results in terms of bacterial community assembly processes and flag cichlid fish ecology. IMPORTANCE Host-associated microbial communities respond to factors specific to the host physiology, genetic backgrounds, and life history. However, these communities also show different degrees of sensitivity to environment-dependent factors, such as abiotic physico-chemical parameters and ecological interactions. The relative importance of host- versus environment-associated factors in shaping teleost bacterial communities is still understudied and is paramount for their conservation and aquaculture. Here, we studied the relative importance of host- and environment-associated factors structuring teleost bacterial communities using gill samples from a wild Amazonian teleost model (Mesonauta festivus) sampled in contrasting habitats along a 1500 km section of the Amazonian basin, thus ensuring high genetic diversity. Results showed that the contribution of the host's genetic background was weak compared to environment-related bacterioplanktonic communities in shaping gill bacterial assemblages, thereby suggesting that our understanding of teleost microbiome assembly could benefit from further studies focused on the ecological interplay between host-associated and free-living communities.
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Affiliation(s)
| | - Nicolas Leroux
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Éric Normandeau
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Aleicia Holland
- La Trobe University, School of Life Science, Department of Ecology, Environment and Evolution, Centre for Freshwater Ecosystems, Wodonga, Victoria, Australia
| | - Sidki Bouslama
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Pierre-Luc Mercier
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Adalberto Luis Val
- Instituto Nacional de Pesquisas da Amazônia (INPA), Laboratório de Ecofisiologia e Evolução Molecular, Manaus, Amazonas, Brazil
| | - Nicolas Derome
- Instituto Nacional de Pesquisas da Amazônia (INPA), Laboratório de Ecofisiologia e Evolução Molecular, Manaus, Amazonas, Brazil
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Transcriptome and 16S rRNA Analyses Reveal That Hypoxic Stress Affects the Antioxidant Capacity of Largemouth Bass ( Micropterus salmoides), Resulting in Intestinal Tissue Damage and Structural Changes in Microflora. Antioxidants (Basel) 2022; 12:antiox12010001. [PMID: 36670863 PMCID: PMC9854696 DOI: 10.3390/antiox12010001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Dissolved oxygen (DO) is a key factor affecting the health of aquatic organisms in an intensive aquaculture environment. In this study, largemouth bass (Micropterus salmoides) were subjected to acute hypoxic stress for 96 h (DO: 1.00 mg/L) followed by recovery under sufficient DO conditions (DO: 7.50 mg/L) for 96 h. Serum biochemical indices, intestinal histomorphology, the transcriptome, and intestinal microbiota were compared between hypoxia-treated fish and those in a control group. The results showed that hypoxia caused oxidative stress, exfoliation of the intestinal villus epithelium and villus rupture, and increased cell apoptosis. Transcriptome analyses revealed that antioxidant-, inflammation-, and apoptosis-related pathways were activated, and that the MAPK signaling pathway played an important role under hypoxic stress. In addition, 16S rRNA sequencing analyses revealed that hypoxic stress significantly decreased bacterial richness and identified the dominant phyla (Proteobacteria, Firmicutes) and genera (Mycoplasma, unclassified Enterobacterales, Cetobacterium) involved in the intestinal inflammatory response of largemouth bass. Pearson's correlation analyses showed that differentially expressed genes in the MAPK signaling pathway were significantly correlated with some microflora. The results of this study will help to develop strategies to reduce damage caused by hypoxic stress in aquacultured fish.
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50
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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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