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Schwob G, Cabrol L, Saucède T, Gérard K, Poulin E, Orlando J. Unveiling the co-phylogeny signal between plunderfish Harpagifer spp. and their gut microbiomes across the Southern Ocean. Microbiol Spectr 2024; 12:e0383023. [PMID: 38441978 PMCID: PMC10986581 DOI: 10.1128/spectrum.03830-23] [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: 11/01/2023] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
Understanding the factors that sculpt fish gut microbiome is challenging, especially in natural populations characterized by high environmental and host genomic complexity. However, closely related hosts are valuable models for deciphering the contribution of host evolutionary history to microbiome assembly, through the underscoring of phylosymbiosis and co-phylogeny patterns. Here, we propose that the recent diversification of several Harpagifer species across the Southern Ocean would allow the detection of robust phylogenetic congruence between the host and its microbiome. We characterized the gut mucosa microbiome of 77 individuals from four field-collected species of the plunderfish Harpagifer (Teleostei, Notothenioidei), distributed across three biogeographic regions of the Southern Ocean. We found that seawater physicochemical properties, host phylogeny, and geography collectively explained 35% of the variation in bacterial community composition in Harpagifer gut mucosa. The core microbiome of Harpagifer spp. gut mucosa was characterized by a low diversity, mostly driven by selective processes, and dominated by a single Aliivibrio Operational Taxonomic Unit (OTU) detected in more than 80% of the individuals. Nearly half of the core microbiome taxa, including Aliivibrio, harbored co-phylogeny signal at microdiversity resolution with host phylogeny, indicating an intimate symbiotic relationship and a shared evolutionary history with Harpagifer. The clear phylosymbiosis and co-phylogeny signals underscore the relevance of the Harpagifer model in understanding the role of fish evolutionary history in shaping the gut microbiome assembly. We propose that the recent diversification of Harpagifer may have led to the diversification of Aliivibrio, exhibiting patterns that mirror the host phylogeny. IMPORTANCE Although challenging to detect in wild populations, phylogenetic congruence between marine fish and its microbiome is critical, as it highlights intimate associations between hosts and ecologically relevant microbial symbionts. Our study leverages a natural system of closely related fish species in the Southern Ocean to unveil new insights into the contribution of host evolutionary trajectory on gut microbiome assembly, an underappreciated driver of the global marine fish holobiont. Notably, we unveiled striking evidence of co-diversification between Harpagifer and its microbiome, demonstrating both phylosymbiosis of gut bacterial communities and co-phylogeny of some specific bacterial symbionts, mirroring the host diversification patterns. Given Harpagifer's significance as a trophic resource in coastal areas and its vulnerability to climatic and anthropic pressures, understanding the potential evolutionary interdependence between the hosts and its microbiome provides valuable microbial candidates for future monitoring, as they may play a pivotal role in host species acclimatization to a rapidly changing environment.
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Affiliation(s)
- Guillaume Schwob
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Department of Ecological Sciences, Faculty of Sciences, University of Chile, Santiago, Chile
- Institute of Ecology and Biodiversity, Santiago, Chile
| | - Léa Cabrol
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Institute of Ecology and Biodiversity, Santiago, Chile
- Aix Marseille University, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France, Marseille, France
| | - Thomas Saucède
- UMR 6282 Biogeosciences, University Bourgogne Franche-Comté, CNRS, EPHE, Dijon, France
| | - Karin Gérard
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Laboratory of Antarctic and Subantarctic Marine Ecosystems, Faculty of Sciences, University of Magallanes, Punta Arenas, Chile
- Cape Horn International Center, Puerto Williams, Chile
| | - Elie Poulin
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Department of Ecological Sciences, Faculty of Sciences, University of Chile, Santiago, Chile
- Institute of Ecology and Biodiversity, Santiago, Chile
| | - Julieta Orlando
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Department of Ecological Sciences, Faculty of Sciences, University of Chile, Santiago, Chile
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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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3
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Soh M, Tay YC, Lee CS, Low A, Orban L, Jaafar Z, Seedorf H. The intestinal digesta microbiota of tropical marine fish is largely uncultured and distinct from surrounding water microbiota. NPJ Biofilms Microbiomes 2024; 10:11. [PMID: 38374184 PMCID: PMC10876542 DOI: 10.1038/s41522-024-00484-x] [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: 03/28/2023] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
Studying the gut microbes of marine fishes is an important part of conservation as many fish species are increasingly threatened by extinction. The gut microbiota of only a small fraction of the more than 32,000 known fish species has been investigated. In this study we analysed the intestinal digesta microbiota composition of more than 50 different wild fish species from tropical waters. Our results show that the fish harbour intestinal digesta microbiota that are distinct from that of the surrounding water and that location, domestication status, and host intrinsic factors are strongly associated with the microbiota composition. Furthermore, we show that the vast majority (~97%) of the fish-associated microorganisms do not have any cultured representative. Considering the impact of the microbiota on host health and physiology, these findings underpin the call to also preserve the microbiota of host species, especially those that may be exposed to habitat destruction.
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Affiliation(s)
- Melissa Soh
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore
| | - Ywee Chieh Tay
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore
| | - Co Sin Lee
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore
| | - Adrian Low
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, MD6-Centre for Translational Medicine, 14 Medical Drive, Singapore, 117599, Singapore
| | - Laszlo Orban
- Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, Keszthely, 8360, Hungary
| | - Zeehan Jaafar
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Henning Seedorf
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.
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4
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Paralika V, Kokou F, Karapanagiotis S, Makridis P. Characterization of Host-Associated Microbiota and Isolation of Antagonistic Bacteria from Greater Amberjack ( Seriola dumerili, Risso, 1810) Larvae. Microorganisms 2023; 11:1889. [PMID: 37630449 PMCID: PMC10456766 DOI: 10.3390/microorganisms11081889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Greater amberjack (Seriola dumerili) is a new species in marine aquaculture with high mortalities at the larval stages. The microbiota of amberjack larvae was analyzed using 16S rDNA sequencing in two groups, one added copepod nauplii (Acartia tonsa) in the diet, and one without copepods (control). In addition, antagonistic bacteria were isolated from amberjack larvae and live food cultures. Proteobacteria was the most abundant phylum followed by Bacteroidota in amberjack larvae. The composition and diversity of the microbiota were influenced by age, but not by diet. Microbial community richness and diversity significantly increased over time. Rhodobacteraceae was the most dominant family followed by Vibrionaceae, which showed the highest relative abundance in larvae from the control group 31 days after hatching. Alcaligenes and Thalassobius genera exhibited a significantly higher relative abundance in the copepod group. Sixty-two antagonistic bacterial strains were isolated and screened for their ability to inhibit four fish pathogens (Aeromonas veronii, Vibrio harveyi, V. anguillarum, V. alginolyticus) using a double-layer test. Phaeobacter gallaeciensis, Phaeobacter sp., Ruegeria sp., and Rhodobacter sp. isolated from larvae and Artemia sp. inhibited the fish pathogens. These antagonistic bacteria could be used as host-derived probiotics to improve the growth and survival of the greater amberjack larvae.
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Affiliation(s)
| | - Fotini Kokou
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, 6700 AH Wageningen, The Netherlands;
| | | | - Pavlos Makridis
- Department of Biology, University of Patras, 26504 Rio, Greece;
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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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Liu H, Chen G, Li L, Lin Z, Tan B, Dong X, Yang Q, Chi S, Zhang S, Zhou X. Supplementing artemisinin positively influences growth, antioxidant capacity, immune response, gut health and disease resistance against Vibrio parahaemolyticus in Litopenaeus vannamei fed cottonseed protein concentrate meal diets. FISH & SHELLFISH IMMUNOLOGY 2022; 131:105-118. [PMID: 36198380 DOI: 10.1016/j.fsi.2022.09.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/13/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Artemisinin (ART) is a kind of Chinese herbal medicine worth exploring, which obtains various physiological activities. In order to study the prebiotic effect of ART on Litopenaeus vannamei fed cottonseed protein concentrate meal diets, six groups of isonitrogenous and isolipid diets were prepared (including the fish meal control group, FM; cottonseed protein concentrate replacing 30% fishmeal protein and supplementing ART groups: ART0, ART0.3, ART0.6, ART0.9, and ART1.2). The feeding trials was lasted for 56 days. The results showed that the final body weight, weight gain and specific growth rate of the ART0.6 group were the highest, yet the feed coefficient rate of the ART0.6 group was the lowest significantly (P < 0.05). There was no significant difference in survival rate among treatments (P > 0.05). In serum, the content of malondialdehyde in ART0 group was the highest (P < 0.05); the activities of superoxide dismutase, catalase, phenol oxidase and lysozyme increased firstly and then decreased among the ARTs groups (P < 0.05). The activities of intestinal digestive enzymes (including the trypsin, lipase and amylase) showed an upward trend among the ARTs groups (P < 0.05). The histological sections showed that the intestinal muscle thickness, fold height and fold width in the FM group were significantly better than those in the ART0 group; while the mentioned above morphological indexes in the ART0 group were significantly lowest among the ARTs groups (P < 0.05). Sequencing of intestinal microbiota suggested that the microbial richness indexes firstly increased and then decreased (P < 0.05); the bacterial community structure of each treatment group was almost close; the relative abundance of pathogenic bacteria decreased significantly (P < 0.05), such as the Proteobacteria and Cyanobacteria at phylum level, besides the Vibrio and Candidatus Bacilloplasma at genus level. In intestinal tissue, the relative expression levels of TOLL1, TRAF6 and Pehaeidih3 showed up-regulated trends, while the expression of Crustin and LZM firstly up-regulated and then down-regulated (P < 0.05). The challenge experiment suggested that the cumulative mortality of FM group was significantly lower than that of ART0 group; besides the cumulative mortality firstly increased and then decreased between the ARTs groups (P < 0.05). In conclusion, the dietary supplementation of ART can improve the growth, antioxidant capacity, immune response, gut health and disease resistance of the shrimp. To be considered as a dietary immune enhancer, the recommended supplementation level of ART in shrimp's cottonseed protein concentrate meal diets is 0.43%.
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Affiliation(s)
- Hongyu Liu
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China; Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, Guangdong, China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, Guangdong, 524000, China
| | - Guofeng Chen
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China; Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, Guangdong, China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, Guangdong, 524000, China
| | - Lixian Li
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China; Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, Guangdong, China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, Guangdong, 524000, China
| | - Zhixuan Lin
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China; Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, Guangdong, China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, Guangdong, 524000, China
| | - Beiping Tan
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China; Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, Guangdong, China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, Guangdong, 524000, China.
| | - Xiaohui Dong
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China; Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, Guangdong, China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, Guangdong, 524000, China
| | - Qihui Yang
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China; Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, Guangdong, China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, Guangdong, 524000, China
| | - Shuyan Chi
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China; Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, Guangdong, China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, Guangdong, 524000, China
| | - Shuang Zhang
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China; Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, Guangdong, China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, Guangdong, 524000, China
| | - Xiaoqiu Zhou
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
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Zhang Z, Fan Z, Yi M, Liu Z, Ke X, Gao F, Cao J, Wang M, Chen G, Lu M. Characterization of the core gut microbiota of Nile tilapia (Oreochromis niloticus): indication of a putative novel Cetobacterium species and analysis of its potential function on nutrition. Arch Microbiol 2022; 204:690. [DOI: 10.1007/s00203-022-03301-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/27/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
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8
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Gallet A, Yao EK, Foucault P, Bernard C, Quiblier C, Humbert JF, Coulibaly JK, Troussellier M, Marie B, Duperron S. Fish gut-associated bacterial communities in a tropical lagoon (Aghien lagoon, Ivory Coast). Front Microbiol 2022; 13:963456. [PMID: 36246274 PMCID: PMC9556852 DOI: 10.3389/fmicb.2022.963456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Aghien lagoon (Ivory Coast) is a eutrophic freshwater lagoon that harbors high biomasses of phytoplankton. Despite Increasing interest in fish gut microbiomes diversity and functions, little data is currently available regarding wild species from tropical west African lakes. Here, gut-associated bacterial communities are investigated in four fish species that are consumed by locale populations, namely the Cichlidae Hemichromis fasciatus, Tilapia guineensis and Sarotherodon melanotheron, and the Claroteidae Chrysichthys nigrodigitatus. Species-related differences are identified, that can be attributed to host phylogeny and diet. Important variations throughout the year are observed in T. guineensis and C. nigrodigitatus. This result emphasized the importance of time-series sampling and comparison with environmental variables even in tropical regions, that are not often conducted in wild populations. Effects of environmental factors (anthropogenic or not) on the microbiota and potential outcomes for fish health and populations sustainability need to be further explored. Interestingly, fish appear as major reservoirs of bacterial diversity, suggesting that they could contribute to the overall stability and resilience of bacterial communities present in the Aghien lagoon.
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Affiliation(s)
- Alison Gallet
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Eric Kouamé Yao
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
- Institut Pasteur de Côte d’Ivoire, Abidjan, Côte d’Ivoire
| | - Pierre Foucault
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Cécile Bernard
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Catherine Quiblier
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
- Université Paris Cité, UFR Sciences du Vivant, Paris, France
| | | | | | - Marc Troussellier
- MARBEC, Centre National de la Recherche Scientifique, Université Montpellier, IFREMER, IRD, Montpellier, France
| | - Benjamin Marie
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Sébastien Duperron
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
- *Correspondence: Sébastien Duperron,
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9
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Escalas A, Auguet JC, Avouac A, Belmaker J, Dailianis T, Kiflawi M, Pickholtz R, Skouradakis G, Villéger S. Shift and homogenization of gut microbiome during invasion in marine fishes. Anim Microbiome 2022; 4:37. [PMID: 35659312 PMCID: PMC9167558 DOI: 10.1186/s42523-022-00181-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 04/04/2022] [Indexed: 11/17/2022] Open
Abstract
Biological invasion is one of the main components of global changes in aquatic ecosystems. Unraveling how establishment in novel environments affects key biological features of animals is a key step towards understanding invasion. Gut microbiome of herbivorous animals is important for host health but has been scarcely assessed in invasive species. Here, we characterized the gut microbiome of two invasive marine herbivorous fishes (Siganus rivulatus and Siganus luridus) in their native (Red Sea) and invaded (Mediterranean Sea) ranges. The taxonomic and phylogenetic diversity of the microbiome increased as the fishes move away from the native range and its structure became increasingly different from the native microbiome. These shifts resulted in homogenization of the microbiome in the invaded range, within and between the two species. The shift in microbial diversity was associated with changes in its functions related with the metabolism of short-chain fatty acids. Altogether, our results suggest that the environmental conditions encountered by Siganidae during their expansion in Mediterranean ecosystems strongly modifies the composition of their gut microbiome along with its putative functions. Further studies should pursue to identify the precise determinants of these modifications (e.g. changes in host diet or behavior, genetic differentiation) and whether they participate in the ecological success of these species.
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Affiliation(s)
- Arthur Escalas
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | | | - Amandine Avouac
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Jonathan Belmaker
- The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv-Yafo, Israel.,George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Thanos Dailianis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71003, Heraklion, Greece
| | - Moshe Kiflawi
- The Department of Life Sciences, Ben Gurion University, 84102, Beer Sheva, Israel.,The Inter-University Institute for Marine Sciences, 88103, Eilat, Israel
| | - Renanel Pickholtz
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv-Yafo, Israel.,The Inter-University Institute for Marine Sciences, 88103, Eilat, Israel
| | - Grigorios Skouradakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71003, Heraklion, Greece
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10
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Hieu DQ, Hang BTB, Lokesh J, Garigliany MM, Huong DTT, Yen DT, Liem PT, Tam BM, Hai DM, Son VN, Phuong NT, Farnir F, Kestemont P. Salinity significantly affects intestinal microbiota and gene expression in striped catfish juveniles. Appl Microbiol Biotechnol 2022; 106:3245-3264. [PMID: 35366085 DOI: 10.1007/s00253-022-11895-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/08/2022] [Accepted: 03/19/2022] [Indexed: 12/17/2022]
Abstract
In the present study, juvenile striped catfish (Pangasianodon hypophthalmus), a freshwater fish species, have been chronically exposed to a salinity gradient from freshwater to 20 psu (practical salinity unit) and were sampled at the beginning (D20) and the end (D34) of exposure. The results revealed that the intestinal microbial profile of striped catfish reared in freshwater conditions were dominated by the phyla Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. Alpha diversity measures (observed OTUs (operational taxonomic units), Shannon and Faith's PD (phylogenetic diversity)) showed a decreasing pattern as the salinities increased, except for the phylogenetic diversity at D34, which was showing an opposite trend. Furthermore, the beta diversity between groups was significantly different. Vibrio and Akkermansia genera were affected differentially with increasing salinity, the former being increased while the latter was decreased. The genus Sulfurospirillium was found predominantly in fish submitted to salinity treatments. Regarding the host response, the fish intestine likely contributed to osmoregulation by modifying the expression of osmoregulatory genes such as nka1a, nka1b, slc12a1, slc12a2, cftr, and aqp1, especially in fish exposed to 15 and 20 psu. The expression of heat shock proteins (hsp) hsp60, hsp70, and hsp90 was significantly increased in fish reared in 15 and 20 psu. On the other hand, the expression of pattern recognition receptors (PRRs) were inhibited in fish exposed to 20 psu at D20. In conclusion, the fish intestinal microbiota was significantly disrupted in salinities higher than 10 psu and these effects were proportional to the exposure time. In addition, the modifications of intestinal gene expression related to ion exchange and stressful responses may help the fish to adapt hyperosmotic environment. KEY POINTS: • It is the first study to provide detailed information on the gut microbiota of fish using the amplicon sequencing method. • Salinity environment significantly modified the intestinal microbiota of striped catfish. • Intestinal responses may help the fish adapt to hyperosmotic environment.
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Affiliation(s)
- Dang Quang Hieu
- Research Unit in Environmental and Evolutionary Biology, Institute of Life Earth & Environment (ILEE), University of Namur, Namur, Belgium.
| | - Bui Thi Bich Hang
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Jep Lokesh
- Université de Pau Et Des Pays de L'Adour, Saint-Pee-sur-Nivelle, E2S UPPA, INRAE, NuMéA, France
| | - Mutien-Marie Garigliany
- Department of Pathology, Faculty of Veterinary Medicine, University of Liège, Liege, Belgium
| | - Do Thi Thanh Huong
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Duong Thuy Yen
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Pham Thanh Liem
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Bui Minh Tam
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Dao Minh Hai
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam.,Department of Animal Production, Faculty of Veterinary Medicine, University of Liège, Liege, Belgium
| | - Vo Nam Son
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Nguyen Thanh Phuong
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Frédéric Farnir
- Department of Animal Production, Faculty of Veterinary Medicine, University of Liège, Liege, Belgium
| | - Patrick Kestemont
- Research Unit in Environmental and Evolutionary Biology, Institute of Life Earth & Environment (ILEE), University of Namur, Namur, Belgium.
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11
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Thépot V, Slinger J, Rimmer MA, Paul NA, Campbell AH. Is the Intestinal Bacterial Community in the Australian Rabbitfish Siganus fuscescens Influenced by Seaweed Supplementation or Geography? Microorganisms 2022; 10:microorganisms10030497. [PMID: 35336073 PMCID: PMC8954549 DOI: 10.3390/microorganisms10030497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/12/2022] [Accepted: 02/17/2022] [Indexed: 02/04/2023] Open
Abstract
We recently demonstrated that dietary supplementation with seaweed leads to dramatic improvements in immune responses in S. fuscescens, a candidate species for aquaculture development in Asia. Here, to assess whether the immunostimulatory effect was facilitated by changes to the gut microbiome, we investigated the effects of those same seaweed species and four commercial feed supplements currently used in aquaculture on the bacterial communities in the hindgut of the fish. Since we found no correlations between the relative abundance of any particular taxa and the fish enhanced innate immune responses, we hypothesised that S. fuscescens might have a core microbiome that is robust to dietary manipulation. Two recently published studies describing the bacteria within the hindgut of S. fuscescens provided an opportunity to test this hypothesis and to compare our samples to those from geographically distinct populations. We found that, although hindgut bacterial communities were clearly and significantly distinguishable between studies and populations, a substantial proportion (55 of 174 taxa) were consistently detected across all populations. Our data suggest that the importance of gut microbiota to animal health and the extent to which they can be influenced by dietary manipulations might be species-specific or related to an animals’ trophic level.
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Affiliation(s)
- Valentin Thépot
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD 4558, Australia; (M.A.R.); (N.A.P.)
- Correspondence:
| | - Joel Slinger
- CSIRO Agriculture and Food, Bribie Island Research Centre, Woorim, QLD 4507, Australia;
- Institute of Marine and Antarctic Studies, University of Tasmania, Launceston, TAS 7250, Australia
| | - Michael A. Rimmer
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD 4558, Australia; (M.A.R.); (N.A.P.)
| | - Nicholas A. Paul
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD 4558, Australia; (M.A.R.); (N.A.P.)
| | - Alexandra H. Campbell
- School of Health and Behavioural Sciences, University of the Sunshine Coast, Maroochydore DC, QLD 4558, Australia;
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12
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Yu C, Zhang C, Salisu A, Wang Y. Comparison of the Intestinal Bacteria Between Black Seabass Centropristis striata Reared in Recirculating Aquaculture System and Net Pen. Curr Microbiol 2022; 79:109. [PMID: 35175391 DOI: 10.1007/s00284-022-02789-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/26/2022] [Indexed: 11/03/2022]
Abstract
Determination of diversity and function of the bacteria in fish gut is essential to understanding the interaction between intestinal bacteria and their host organism. This study compared intestinal bacterial community of black seabass (Centropristis striata) hatched by the same breeding farm but reared in different aquaculture systems, an indoor recirculating aquaculture system (RAS) and an inshore net pen (INP). The fish were fed with formulated feed manufactured by same feed company. Bacteria in fish gut, formulated feed and seawater were identified by 16S rRNA high throughout sequencing (HTS). Total 1484 OTUs, which belonged to 34 phyla and 79 genera, were identified from fish gut, formulated feed and seawater. In fish gut, 24 phyla and 43 genera were identified. Proteobacteria, Fusobacteria, and Firmicutes dominated at the phylum level in fish gut in INP, while Proteobacteria and Firmicutes dominated in fish gut in RAS. Photobacterium, Vibrio, and Cetobacterium dominated at the genus level in fish gut in both INP and RAS. One OTU of Photobacterium occurred in all the fish gut samples, suggesting this bacterium might be the main component of the core microbiota. No significant difference was found in bacterial diversity in fish gut between INP and RAS, suggesting genetic background should be a primary factor determining intestinal bacterial community of black seabass. Bacterial diversity in seawater was high relative to that in fish gut and formulated feed, regardless in INP or RAS. The common OTU between fish gut and seawater was more than that between fish gut and formulated feed in INP, while the common OTU between fish gut and seawater was slightly less than that between fish gut and formulated feed in RAS. These results reveal that the bacteria in formulated feed and seawater could influence the bacteria in fish gut, and their priority in shaping intestinal bacterial community depended on the bacterial composition in feed and seawater. This study reveals that intestinal bacterial community of black seabass was influenced by both genetic background and environmental factors.
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Affiliation(s)
- Cong Yu
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, People's Republic of China
| | - Chen Zhang
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, People's Republic of China
| | - Abba Salisu
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, People's Republic of China.,Department of Biological Sciences, Bayero University, Kano, PMB 3011, Nigeria
| | - Yan Wang
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, People's Republic of China.
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13
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Pardesi B, Roberton AM, Lee KC, Angert ER, Rosendale DI, Boycheva S, White WL, Clements KD. Distinct microbiota composition and fermentation products indicate functional compartmentalization in the hindgut of a marine herbivorous fish. Mol Ecol 2022; 31:2494-2509. [PMID: 35152505 PMCID: PMC9306998 DOI: 10.1111/mec.16394] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 11/28/2022]
Abstract
Many marine herbivorous fishes harbour diverse microbial communities in the hindgut that can play important roles in host health and nutrition. Kyphosus sydneyanus is a temperate marine herbivorous fish that feeds predominantly on brown seaweeds. We employed 16S rRNA gene amplicon sequencing and gas chromatography to characterize microbial communities and their metabolites in different hindgut regions of six K. sydneyanus. Measurements were confined to three distal sections of the intestine, labelled III, IV and V from anterior to posterior. A total of 625 operational taxonomic units from 20 phyla and 123 genera were obtained. Bacteroidota, Firmicutes and Proteobacteria were the major phyla in mean relative abundance, which varied along the gut. Firmicutes (76%) was the most dominant group in section III, whereas Bacteroidota (69.3%) dominated section V. Total short‐chain fatty acid (SCFA) concentration was highest in sections IV and V, confirming active fermentation in these two most distal sections. The abundance of Bacteroidota correlated with propionate concentration in section V, while Firmicutes positively correlated with formate in sections III and IV. Acetate levels were highest in sections IV and V, which correlated with abundance of Bacteroidota. Despite differences in gut microbial community composition, SCFA profiles were consistent between individual fish in the different hindgut regions of K. sydneyanus, although proportions of SCFAs differed among gut sections. These findings demonstrate functional compartmentalization of the hindgut microbial community, highlighting the need for regional sampling when interpreting overall microbiome function. These results support previous work suggesting that hindgut microbiota in marine herbivorous fish are important to nutrition in some host species by converting dietary carbohydrates into metabolically useful SCFAs.
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Affiliation(s)
- Bikiran Pardesi
- School of Biological Sciences University of Auckland Auckland New Zealand
| | | | - Kevin C. Lee
- Faculty of Health and Environmental Sciences Auckland University of Technology Auckland New Zealand
| | - Esther R. Angert
- Department of Microbiology Cornell University Ithaca NY 14853 USA
| | - Douglas I. Rosendale
- Plant & Food Research Ltd Palmerston North New Zealand
- Anagenix Ltd Parnell, Auckland 1052 New Zealand
| | - Svetlana Boycheva
- School of Biological Sciences University of Auckland Auckland New Zealand
- Biotelliga, Parnell, Auckland 1052 New Zealand
| | - William Lindsey White
- School of Science Faculty of Health and Environmental Sciences Auckland University of Technology Auckland New Zealand
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14
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Liu C, Zhao LP, Shen YQ. A systematic review of advances in intestinal microflora of fish. FISH PHYSIOLOGY AND BIOCHEMISTRY 2021; 47:2041-2053. [PMID: 34750711 DOI: 10.1007/s10695-021-01027-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 10/13/2021] [Indexed: 05/26/2023]
Abstract
Intestinal flora is closely related to the health of organisms and the occurrence and development of diseases. The study of intestinal flora will provide a reference for the research and treatment of disease pathogenesis. Upon hatching, fish begin to acquire a microbial community in the intestine. In response to the environment and the host itself, the fish gut eventually develops a unique set of microflora, with some microorganisms being common to different fish. The existence of intestinal microorganisms creates an excellent microecological environment for the host, while the fish symbiotically provides conditions for the growth and reproduction of intestinal microflora. The intestinal flora and the host are interdependent and mutually restrictive. This review mainly describes the formation of fish intestinal flora, the function of normal intestinal flora, factors affecting intestinal flora, and a series of fish models.
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Affiliation(s)
- Chang Liu
- Wuxi Medical School of Jiangnan University, Wuxi, China
| | - Li-Ping Zhao
- Wuxi Medical School of Jiangnan University, Wuxi, China
| | - Yan-Qin Shen
- Wuxi Medical School of Jiangnan University, Wuxi, China.
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15
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Borges N, Keller-Costa T, Sanches-Fernandes GMM, Louvado A, Gomes NCM, Costa R. Bacteriome Structure, Function, and Probiotics in Fish Larviculture: The Good, the Bad, and the Gaps. Annu Rev Anim Biosci 2020; 9:423-452. [PMID: 33256435 DOI: 10.1146/annurev-animal-062920-113114] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Aquaculture is the fastest-growing sector in food production worldwide. For decades, research on animal physiology, nutrition, and behavior established the foundations of best practices in land-based fish rearing and disease control. Current DNA sequencing, bioinformatics, and data science technologies now allow deep investigations of host-associated microbiomes in a tractable fashion. Adequate use of these technologies can illuminate microbiome dynamics and aid the engineering of microbiome-based solutions to disease prevention in an unprecedented manner. This review examines molecular studies of bacterial diversity, function, and host immunitymodulation at early stages of fish development, where microbial infections cause important economic losses. We uncover host colonization and virulence factors within a synthetic assemblage of fish pathogens using high-end comparative genomics and address the use of probiotics and paraprobiotics as applicable disease-prevention strategies in fish larval and juvenile rearing. We finally propose guidelines for future microbiome research of presumed relevance to fish larviculture.
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Affiliation(s)
- Nuno Borges
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; , , ,
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; , , ,
| | - Gracinda M M Sanches-Fernandes
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; , , ,
| | - António Louvado
- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; ,
| | - Newton C M Gomes
- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; ,
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; , , , .,Centre of Marine Sciences, Algarve University, 8005-139 Faro, Portugal.,Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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16
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Enteromorpha prolifera Diet Drives Intestinal Microbiome Composition in Siganus oramin. Curr Microbiol 2020; 78:229-237. [PMID: 33034768 DOI: 10.1007/s00284-020-02218-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 09/17/2020] [Indexed: 12/14/2022]
Abstract
Enteromorpha prolifera (E. prolifera) contains complex sulfated polysaccharides that are resistant to biological degradation. Most organisms cannot digest biomass of E. prolifera, except Siganus oramin (S. oramin). This study was conducted to identify the bacteria in the intestine of S. oramin facilitating the digestion of E. prolifera polysaccharides (EPP). Metagenomic sequencing analysis of the S. oramin intestinal microbiota revealed that E. prolifera diet increased the number of Firmicutes, replacing Proteobacteria to be the dominant bacteria. The proportion of Firmicutes increased from 38.8 to 58.6%, with Bacteroidetes increasing nearly fivefold from 5 to 23.7%. 16S rDNA high-throughput sequencing showed that EPP-induced Bacteroidetes increased significantly in the intestinal flora of S. oramin cultivated in vitro. Metatranscriptome analysis showed that EPP induced more transferase, polysaccharide hydrolase, glycoside hydrolase, and esterases expressed in vitro, and most of them were taxonomically annotated to Bacteroidetes. Compared with the aggregation of GH family genes in metagenomic sequencing analysis in vivo, EPP induced more CBM32, GH2, GT2, GT30, and GH30 families gene expression in vitro. In general, We found that the bacteria in intestinal tract of S. oramin responsible for digestion of E. prolifera were Firmicutes and Bacteroidetes, while Bacteroidetes was the dominant bacteria involved in EPP degradation in vitro cultures. Compared with in vivo experiments, only GH family genes were mostly involved, we detected a more complete and complex EPP degradation pathway in vitro. The results may benefit the further study of biodegradation of E. prolifera and has potential implications for the utilization of E. prolifera for biotechnology.
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