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Gong J, Xu F, Li Y, He Y, Liang Z, Chen X, Zhang X, Liu L, Zhou L, Huang X. Metagenomic analysis of intestinal microbial function and key genes responsive to acute high-salinity stress in Nile tilapia (Oreochromis niloticus). Gene 2024; 913:148371. [PMID: 38485034 DOI: 10.1016/j.gene.2024.148371] [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: 11/21/2023] [Revised: 01/26/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
The intestinal microbiota is increasingly recognized as playing an important role in aquatic animals. To investigate the functional roles and mechanisms of the intestinal microbial genes/enzymes responding to salinity stress or osmotic pressure in fish, metagenomic analysis was carried out to evaluate the response of intestinal microbiota and especially their functional genes/enzymes from freshwater (the control group) to acute high salinity stress (the treatment group) in Nile tilapia. Our results showed that at the microbial community level, the intestinal microbiota in Nile tilapia generally underwent significant changes in diversity after acute high salinity stress. Among them, the shift in the bacterial community (mainly from Actinobacteria to Proteobacteria) dominated and had a large impact, the fungal community showed a very limited response, and other microbiota, such as phages, likely had a negligible response. At the functional level, the intestinal bacteriadecreased the normal physiological demand and processes, such as those of the digestive system and nervous system, but enhanced energy metabolism. Furthermore, at the gene level, some gene biomarkers, such as glutathione S-transferase, myo-inositol-1(or 4)-monophosphatase, glycine betaine/proline transport system permease protein, and some families of carbohydrate-active enzymes (GT4, GT2), were significantly enriched. However, GH15, GH23 and so on were significantly reduced. Exploring the functional details of the intestinal microbial genes/enzymes that respond to salinity stress in Nile tilapia sheds light on the mechanism of action of the intestinal microbiota with respect to the salinity adaptation of fish.
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Affiliation(s)
- Jiayi Gong
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Fengmeng Xu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China; Guangzhou Fishtech Biotechnology Co., Ltd., Guangzhou 510640, China
| | - Yao Li
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Yiyong He
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Zhizheng Liang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Xiao Chen
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Xiaoyong Zhang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Li Liu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Lei Zhou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China.
| | - Xiande Huang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China.
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Auclert LZ, Chhanda MS, Derome N. Interwoven processes in fish development: microbial community succession and immune maturation. PeerJ 2024; 12:e17051. [PMID: 38560465 PMCID: PMC10981415 DOI: 10.7717/peerj.17051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 02/13/2024] [Indexed: 04/04/2024] Open
Abstract
Fishes are hosts for many microorganisms that provide them with beneficial effects on growth, immune system development, nutrition and protection against pathogens. In order to avoid spreading of infectious diseases in aquaculture, prevention includes vaccinations and routine disinfection of eggs and equipment, while curative treatments consist in the administration of antibiotics. Vaccination processes can stress the fish and require substantial farmer's investment. Additionally, disinfection and antibiotics are not specific, and while they may be effective in the short term, they have major drawbacks in the long term. Indeed, they eliminate beneficial bacteria which are useful for the host and promote the raising of antibiotic resistance in beneficial, commensal but also in pathogenic bacterial strains. Numerous publications highlight the importance that plays the diversified microbial community colonizing fish (i.e., microbiota) in the development, health and ultimately survival of their host. This review targets the current knowledge on the bidirectional communication between the microbiota and the fish immune system during fish development. It explores the extent of this mutualistic relationship: on one hand, the effect that microbes exert on the immune system ontogeny of fishes, and on the other hand, the impact of critical steps in immune system development on the microbial recruitment and succession throughout their life. We will first describe the immune system and its ontogeny and gene expression steps in the immune system development of fishes. Secondly, the plurality of the microbiotas (depending on host organism, organ, and development stage) will be reviewed. Then, a description of the constant interactions between microbiota and immune system throughout the fish's life stages will be discussed. Healthy microbiotas allow immune system maturation and modulation of inflammation, both of which contribute to immune homeostasis. Thus, immune equilibrium is closely linked to microbiota stability and to the stages of microbial community succession during the host development. We will provide examples from several fish species and describe more extensively the mechanisms occurring in zebrafish model because immune system ontogeny is much more finely described for this species, thanks to the many existing zebrafish mutants which allow more precise investigations. We will conclude on how the conceptual framework associated to the research on the immune system will benefit from considering the relations between microbiota and immune system maturation. More precisely, the development of active tolerance of the microbiota from the earliest stages of life enables the sustainable establishment of a complex healthy microbial community in the adult host. Establishing a balanced host-microbiota interaction avoids triggering deleterious inflammation, and maintains immunological and microbiological homeostasis.
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Affiliation(s)
- Lisa Zoé Auclert
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Mousumi Sarker Chhanda
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
- Department of Aquaculture, Faculty of Fisheries, Hajee Mohammad Danesh Science and Technology University, Basherhat, Bangladesh
| | - Nicolas Derome
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
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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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Brealey JC, Kodama M, Rasmussen JA, Hansen SB, Santos-Bay L, Lecaudey LA, Hansen M, Fjære E, Myrmel LS, Madsen L, Bernhard A, Sveier H, Kristiansen K, Gilbert MTP, Martin MD, Limborg MT. Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon. mSystems 2024; 9:e0104323. [PMID: 38294254 PMCID: PMC10886447 DOI: 10.1128/msystems.01043-23] [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: 09/27/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
Animals and their associated microbiota share long evolutionary histories. However, it is not always clear how host genotype and microbiota interact to affect phenotype. We applied a hologenomic approach to explore how host-microbiota interactions shape lifetime growth and parasite infection in farmed Atlantic salmon (Salmo salar). Multi-omics data sets were generated from the guts of 460 salmon, 82% of which were naturally infected with an intestinal cestode. A single Mycoplasma bacterial strain, MAG01, dominated the gut metagenome of large, non-parasitized fish, consistent with previous studies showing high levels of Mycoplasma in the gut microbiota of healthy salmon. While small and/or parasitized salmon also had high abundance of MAG01, we observed increased alpha diversity in these individuals, driven by increased frequency of low-abundance Vibrionaceae and other Mycoplasma species that carried known virulence genes. Colonization by one of these cestode-associated Mycoplasma strains was associated with host individual genomic variation in long non-coding RNAs. Integrating the multi-omic data sets revealed coordinated changes in the salmon gut mRNA transcriptome and metabolome that correlated with shifts in the microbiota of smaller, parasitized fish. Our results suggest that the gut microbiota of small and/or parasitized fish is in a state of dysbiosis that partly depends on the host genotype, highlighting the value of using a hologenomic approach to incorporate the microbiota into the study of host-parasite dynamics.IMPORTANCEStudying host-microbiota interactions through the perspective of the hologenome is gaining interest across all life sciences. Intestinal parasite infections are a huge burden on human and animal health; however, there are few studies investigating the role of the hologenome during parasite infections. We address this gap in the largest multi-omics fish microbiota study to date using natural cestode infection of farmed Atlantic salmon. We find a clear association between cestode infection, salmon lifetime growth, and perturbation of the salmon gut microbiota. Furthermore, we provide the first evidence that the genetic background of the host may partly determine how the gut microbiota changes during parasite-associated dysbiosis. Our study therefore highlights the value of a hologenomic approach for gaining a more in-depth understanding of parasitism.
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Affiliation(s)
- Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Miyako Kodama
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Jacob A Rasmussen
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
- Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Copenhagen, Denmark
| | - Søren B Hansen
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Luisa Santos-Bay
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Laurène A Lecaudey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Aquaculture Department, SINTEF Ocean, Trondheim, Norway
| | - Martin Hansen
- Department of Environmental Science, Environmental Metabolomics Lab, Aarhus University, Roskilde, Denmark
| | - Even Fjære
- Institute of Marine Research, Bergen, Norway
| | | | - Lise Madsen
- Institute of Marine Research, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Norway, Bergen, Norway
| | | | | | - Karsten Kristiansen
- Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
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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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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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Wang J, Li Y, Jaramillo-Torres A, Einen O, Jakobsen JV, Krogdahl Å, Kortner TM. Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics. Anim Microbiome 2023; 5:47. [PMID: 37789427 PMCID: PMC10548677 DOI: 10.1186/s42523-023-00269-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/24/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND The importance of the gut microbiota for physiological processes in mammals is well established, but the knowledge of their functional roles in fish is still limited. The aims of this study were to investigate associations between variation in taxonomical composition of the gut microbiota and gut health status in Atlantic salmon and to explore possible modulatory effects of dietary prebiotics in one net-pen farm in open water. The fish with initial mean body weight of around 240 g were fed diets based on the same basal composition, either without (Ref diet) or with (Test diet) yeast cell wall based-prebiotics, during the marine production phase from December to September the following year. Sampling was conducted at three sampling time points: January, April, and September, with average water temperature of 3.9 ℃, 3.4 ℃ and 9.6 ℃, respectively. RESULTS As the fish progressed towards September, growth, brush border membrane enzyme activities, and the expression in the gut of most of the observed genes involved in immune (e.g., il8, cd4a, myd88, il1b, gilt, tgfb, cd8b and cd3), barrier (e.g., zo1, occludin, ecad, claudin25b and claudin15), and metabolism increased significantly. Lipid accumulation in pyloric enterocytes decreased remarkably, suggesting improvement of gut health condition. The growth of the fish did not differ between dietary treatments. Further, dietary prebiotics affected the gut health only marginally regardless of duration of administration. Regarding gut microbiota composition, a decrease in alpha diversity (Observed species, Pielou and Shannon) over time was observed, which was significantly associated with an increase in the relative abundance of genus Mycoplasma and decrease in 32 different taxa in genus level including lactic acid bacteria (LAB), such as Lactobacillus, Leuconostoc, and Lactococcus. This indicates that developmental stage of Atlantic salmon is a determinant for microbial composition. Multivariate association analysis revealed that the relative abundance of Mycoplasma was positively correlated with gut barrier gene expression, negatively correlated with plasma glucose levels, and that its relative abundance slightly increased by exposure to prebiotics. Furthermore, certain LAB (e.g., Leuconostoc), belonging to the core microbiota, showed a negative development with time, and significant associations with plasma nutrients levels (e.g., triglyceride and cholesterol) and gene expression related to gut immune and barrier function. CONCLUSIONS As Atlantic salmon grew older under large-scale, commercial farm settings, the Mycoplasma became more prominent with a concomitant decline in LAB. Mycoplasma abundance correlated positively with time and gut barrier genes, while LAB abundance negatively correlated to time. Dietary prebiotics affected gut health status only marginally.
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Affiliation(s)
- Jie Wang
- National Aquafeed Safety Assessment Center, Institute of Feed Research, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St, Beijing, China.
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, Ås, 1432, Norway.
| | - Yanxian Li
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, Ås, 1432, Norway
| | | | - Olai Einen
- Cermaq Group AS, Dronning Eufemias gate 16, Oslo, 0191, Norway
| | - Jan Vidar Jakobsen
- Cargill Aqua Nutrition, Prof. Olav Hanssensvei 7A, Stavanger, 4021, Norway
| | - Åshild Krogdahl
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, Ås, 1432, Norway
| | - Trond M Kortner
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, Ås, 1432, Norway
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Chakraborty M, Acharya D, Dutta TK. Diversity analysis of hilsa (Tenualosa ilisha) gut microbiota using culture-dependent and culture-independent approaches. J Appl Microbiol 2023; 134:lxad208. [PMID: 37699793 DOI: 10.1093/jambio/lxad208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 09/14/2023]
Abstract
AIMS The bacterial communities associated with the gastrointestinal (GI) tract are primarily involved in digestion, physiology, and the immune response against pathogenic bacteria for the overall development and health of the host. Hilsa shad (Tenualosa ilisha), a tropical anadromous fish, found predominantly in Bangladesh and India, has so far been poorly investigated for its gut bacterial communities. In this study, both culture-based and metagenomic approaches were used to detect intestinal isolates of hilsa, captured from both freshwater and seawater to investigate the community structure of intestinal microbiota. METHODS AND RESULTS Culture-dependent approach allowed to isolate a total of 23 distinct bacterial species comprising 16 Gram-negative, and 7 Gram-positive isolates, where Proteobacteria and Firmicutes were identified as the two most dominant phyla. While metagenomic approach explored a wide range of important GI bacteria, primarily dominated by Proteobacteria, Firmicutes, and Bacteroidetes, with Proteobacteria and Firmicutes, being the most abundant in freshwater and seawater samples, respectively. CONCLUSIONS A combination of these approaches provided the differential GI-associated bacterial diversity in freshwater and seawater hilsa with the prediction of overall functional potential. IMPACT STATEMENT The study explored the diversity of gut microbiota in hilsa, one of the most preferred nutritious dietary fish, captured from freshwater and seawater habitats, which may encourage to comprehend the composition of the gut microbiome in relation to the migratory behavior and polyunsaturated fatty acid profile of anadromous fish in general.
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Affiliation(s)
- Megha Chakraborty
- Department of Microbiology, Bose Institute, Kolkata 700091, West Bengal, India
| | - Debarun Acharya
- Department of Microbiology, Bose Institute, Kolkata 700091, West Bengal, India
| | - Tapan K Dutta
- Department of Microbiology, Bose Institute, Kolkata 700091, West Bengal, India
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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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10
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Lorgen-Ritchie M, Uren Webster T, McMurtrie J, Bass D, Tyler CR, Rowley A, Martin SAM. Microbiomes in the context of developing sustainable intensified aquaculture. Front Microbiol 2023; 14:1200997. [PMID: 37426003 PMCID: PMC10327644 DOI: 10.3389/fmicb.2023.1200997] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023] Open
Abstract
With an ever-growing human population, the need for sustainable production of nutritional food sources has never been greater. Aquaculture is a key industry engaged in active development to increase production in line with this need while remaining sustainable in terms of environmental impact and promoting good welfare and health in farmed species. Microbiomes fundamentally underpin animal health, being a key part of their digestive, metabolic and defense systems, in the latter case protecting against opportunistic pathogens in the environment. The potential to manipulate the microbiome to the advantage of enhancing health, welfare and production is an intriguing prospect that has gained considerable traction in recent years. In this review we first set out what is known about the role of the microbiome in aquaculture production systems across the phylogenetic spectrum of cultured animals, from invertebrates to finfish. With a view to reducing environmental footprint and tightening biological and physical control, investment in "closed" aquaculture systems is on the rise, but little is known about how the microbial systems of these closed systems affect the health of cultured organisms. Through comparisons of the microbiomes and their dynamics across phylogenetically distinct animals and different aquaculture systems, we focus on microbial communities in terms of their functionality in order to identify what features within these microbiomes need to be harnessed for optimizing healthy intensified production in support of a sustainable future for aquaculture.
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Affiliation(s)
| | - Tamsyn Uren Webster
- Centre for Sustainable Aquatic Research, Swansea University, Swansea, United Kingdom
| | - Jamie McMurtrie
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - David Bass
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, United Kingdom
| | - Charles R. Tyler
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Andrew Rowley
- Department of Biosciences, Faculty of Science and Engineering, Swansea University, Swansea, United Kingdom
| | - Samuel A. M. Martin
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
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11
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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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12
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Foysal MJ. Host habitat shapes the core gut bacteria of decapod crustaceans: A meta-analysis. Heliyon 2023; 9:e16511. [PMID: 37274665 PMCID: PMC10238905 DOI: 10.1016/j.heliyon.2023.e16511] [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: 12/29/2022] [Revised: 05/13/2023] [Accepted: 05/18/2023] [Indexed: 06/06/2023] Open
Abstract
Gut microbiota is an essential determinant factor that drives the physiological, immunological, and metabolic functions of animals. A few meta-analysis studies identified crucial information about the gut microbiota of vertebrate animals in different habitats including fish while no report is yet available for the commercially cultured decapod crustaceans (DC). This meta-analysis investigated the gut microbiota of 11 commercially cultured DC species from five different groups-crab, crayfish, lobster, prawn, and shrimp to gain an overview of microbial diversity and composition and to find out core genera under two different host habitats: freshwater and saltwater. The analysis of 627 Illumina datasets from 25 published studies revealed selective patterns of diversity and compositional differences among groups and between freshwater and saltwater culture systems. The study found a salinity-dependent heterogeneous response of gut microbiota, specifically Vibrio in saltwater for white shrimp, a species that can be cultured with and without salt. Overall, the genera reared in freshwater showed higher diversity in the gut microbial communities than those reared in saltwater. An overwhelming abundance of Candidatus Bacilloplasma and Vibrio were identified for species cultured in freshwater and saltwater system, respectively and these two species were identified as the main core genera for nine out of 11 DC species, except freshwater prawn and river prawn. Together, these results demonstrate the effectiveness of the meta-analysis in identifying the robust and reproducible features of DC gut microbiota for different groups and host habitats. The diversity information curated here could be used as a reference for future studies to differentiate various DC species under two different rearing environments.
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13
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Kusumawaty D, Augustine SMN, Aryani A, Effendi Y, Emran TB, Tallei TE. Configuration of gut bacterial community profile and their potential functionality in the digestive tract of the wild and cultivated Indonesian shortfin elver-phase eels ( Anguilla bicolor bicolor McClelland, 1844). 3 Biotech 2023; 13:153. [PMID: 37131968 PMCID: PMC10148933 DOI: 10.1007/s13205-023-03561-8] [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] [Received: 06/21/2022] [Accepted: 04/15/2023] [Indexed: 05/04/2023] Open
Abstract
This study aimed to explore the bacteria present in the digestive tracts of wild and cultivated Indonesian shortfin eel during the elver phase. The eel has high export potential due to its vitamin and micronutrient content, but slow growth and vulnerability to collapse in farm conditions hinder its cultivation. The microbiota in the eel's digestive tract is crucial for its health, particularly during the elver phase. This study used Next Generation Sequencing to analyze the community structure and diversity of bacteria in the eels' digestive tracts, focusing on the V3-V4 regions of the 16S rRNA gene. Mothur software was used for data analysis and PAST v.3.26 was used to calculate alpha diversity. The results showed that Proteobacteria (64.18%) and Firmicutes (33.55%) were the predominant phyla in the digestive tract of cultivated eels, while Bacteroidetes (54.16%), Firmicutes (14.71%), and Fusobacteria (10.56%) were predominant in wild eels. The most prevalent genera in cultivated and wild elver were Plesiomonas and Cetobacterium, respectively. The microbiota in the digestive tract of cultivated eels was diverse despite uneven distribution. The KEGG database analysis revealed that the primary function of the microbiome was to facilitate the eel's absorption of nutrients by contributing significantly to the metabolism of carbohydrates and amino acids. This study's findings can aid in assessing eel health and improving eel farming conditions.
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Affiliation(s)
- Diah Kusumawaty
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung, 40154 Indonesia
| | - Stella Melbournita Noor Augustine
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung, 40154 Indonesia
| | - Any Aryani
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung, 40154 Indonesia
| | - Yunus Effendi
- Department of Biology, Faculty of Science and Technology, Al-Azhar Indonesia University, Jakarta, 12110 Indonesia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381 Bangladesh
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, 95115 North Sulawesi Indonesia
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14
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Agboola JO, Rocha SDC, Mensah DD, Hansen JØ, Øyås O, Lapeña D, Mydland LT, Arntzen MØ, Horn SJ, Øverland M. Effect of yeast species and processing on intestinal microbiota of Atlantic salmon (Salmo salar) fed soybean meal-based diets in seawater. Anim Microbiome 2023; 5:21. [PMID: 37016467 PMCID: PMC10074822 DOI: 10.1186/s42523-023-00242-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] [Received: 02/11/2022] [Accepted: 03/20/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Yeasts are gaining attention as alternative ingredients in aquafeeds. However, the impact of yeast inclusion on modulation of intestinal microbiota of fish fed plant-based ingredients is limited. Thus, the present study investigates the effects of yeast and processing on composition, diversity and predicted metabolic capacity of gut microbiota of Atlantic salmon smolt fed soybean meal (SBM)-based diet. Two yeasts, Cyberlindnera jadinii (CJ) and Wickerhamomyces anomalus (WA), were produced in-house and processed by direct heat-inactivation with spray-drying (ICJ and IWA) or autolyzed at 50 °C for 16 h, followed by spray-drying (ACJ and AWA). In a 42-day feeding experiment, fish were fed one of six diets: a fishmeal (FM)-based diet, a challenging diet with 30% SBM and four other diets containing 30% SBM and 10% of each of the four yeast products (i.e., ICJ, ACJ, IWA and AWA). Microbial profiling of digesta samples was conducted using 16S rRNA gene sequencing, and the predicted metabolic capacities of gut microbiota were determined using genome-scale metabolic models. RESULTS The microbial composition and predicted metabolic capacity of gut microbiota differed between fish fed FM diet and those fed SBM diet. The digesta of fish fed SBM diet was dominated by members of lactic acid bacteria, which was similar to microbial composition in the digesta of fish fed the inactivated yeasts (ICJ and IWA diets). Inclusion of autolyzed yeasts (ACJ and AWA diets) reduced the richness and diversity of gut microbiota in fish. The gut microbiota of fish fed ACJ diet was dominated by the genus Pediococcus and showed a predicted increase in mucin O-glycan degradation compared with the other diets. The gut microbiota of fish fed AWA diet was highly dominated by the family Bacillaceae. CONCLUSIONS The present study showed that dietary inclusion of FM and SBM differentially modulate the composition and predicted metabolic capacity of gut microbiota of fish. The inclusion of inactivated yeasts did not alter the modulation caused by SBM-based diet. Fish fed ACJ diet increased relative abundance of Pediococcus, and mucin O-glycan degradation pathway compared with the other diets.
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Affiliation(s)
- Jeleel O Agboola
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway.
| | - Sérgio D C Rocha
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Dominic D Mensah
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Jon Ø Hansen
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Ove Øyås
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - David Lapeña
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Liv T Mydland
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Svein J Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Margareth Øverland
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway.
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15
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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] [MESH Headings] [Grants] [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)
| | | | | | | | | | - Ingrid Bakke
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
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16
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Morshed SM, Chen YY, Lin CH, Chen YP, Lee TH. Freshwater transfer affected intestinal microbiota with correlation to cytokine gene expression in Asian sea bass. Front Microbiol 2023; 14:1097954. [PMID: 37089546 PMCID: PMC10117908 DOI: 10.3389/fmicb.2023.1097954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/22/2023] [Indexed: 04/25/2023] Open
Abstract
As a catadromous fish, Asian sea bass (Lates calcarifer) juveniles migrate from seawater (SW) to freshwater (FW) for growth and development. During migration, they undergo physiological changes to acclimate to environmental salinity. Thus, it is crucial to understand how SW-to-FW migration affects the gut microbiota of catadromous fish. To the best of our knowledge, no study has revealed the effects of transfer to hypotonic environments on a catadromous fish microbiota. In this study, we aimed to determine the effects of FW transfer on the microbiota and cytokine gene expression in the intestines of juvenile catadromous Asian sea bass. The relationship between the water and the gut microbiota of this euryhaline species was also examined. We found that FW transfer affected both mucosa- and digesta-associated microbiota of Asian sea bass. Plesiomonas and Cetobacterium were dominant in both the mucosa- and digesta-associated microbiota of FW-acclimated sea bass. The pathogenic genera Vibrio, Staphylococcus, and Acinetobacter were dominant in the SW group. Although dominant fish microbes were present in the water, fish had their own unique microbes. Vitamin B6 metabolism was highly expressed in the FW fish microbiota, whereas arginine, proline, and lipid metabolism were highly expressed in the SW fish microbiota. Additionally, the correlation between cytokine gene expression and microbiota was found to be affected by FW transfer. Taken together, our results demonstrated that FW transfer altered the composition and functions of mucosa- and digesta-associated microbiota of catadromous Asian sea bass intestines, which correlated with cytokine gene expression.
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Affiliation(s)
- Syed Monzur Morshed
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Yi Chen
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
| | - Chia-Hao Lin
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan
| | - Yen-Po Chen
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
- *Correspondence: Yen-Po Chen,
| | - Tsung-Han Lee
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Tsung-Han Lee,
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17
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Morales-Rivera MF, Valenzuela-Miranda D, Nuñez-Acuña G, Benavente BP, Gallardo-Escárate C, Valenzuela-Muñoz V. Atlantic Salmon ( Salmo salar) Transfer to Seawater by Gradual Salinity Changes Exhibited an Increase in The Intestinal Microbial Abundance and Richness. Microorganisms 2022; 11:microorganisms11010076. [PMID: 36677368 PMCID: PMC9865641 DOI: 10.3390/microorganisms11010076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022] Open
Abstract
The host's physiological history and environment determine the microbiome structure. In that sense, the strategy used for the salmon transfer to seawater after parr-smolt transformation may influence the Atlantic salmon's intestinal microbiota. Therefore, this study aimed to explore the diversity and abundance of the Atlantic salmon intestinal microbiota and metagenome functional prediction during seawater transfer under three treatments. One group was exposed to gradual salinity change (GSC), the other to salinity shock (SS), and the third was fed with a functional diet (FD) before the seawater (SW) transfer. The microbial profile was assessed through full-16S rRNA gene sequencing using the Nanopore platform. In addition, metagenome functional prediction was performed using PICRUSt2. The results showed an influence of salinity changes on Atlantic salmon gut microbiota richness, diversity, and taxonomic composition. The findings reveal that GSC and the FD increased the Atlantic salmon smolt microbiota diversity, suggesting a positive association between the intestinal microbial community and fish health during seawater transfer. The reported knowledge can be applied to surveil the microbiome in smolt fish production, improving the performance of Atlantic salmon to seawater transfer.
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Affiliation(s)
- María F. Morales-Rivera
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Diego Valenzuela-Miranda
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
- Centro de Biotecnología, Universidad de Concepción, Concepcion 4030000, Chile
| | - Gustavo Nuñez-Acuña
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Bárbara P. Benavente
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
- Centro de Biotecnología, Universidad de Concepción, Concepcion 4030000, Chile
- Correspondence: ; Tel.: +56-41-2204402
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18
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Bertucci A, Hoede C, Dassié E, Gourves PY, Suin A, Le Menach K, Budzinski H, Daverat F. Impact of environmental micropollutants and diet composition on the gut microbiota of wild european eels (Anguilla anguilla). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120207. [PMID: 36165828 DOI: 10.1016/j.envpol.2022.120207] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/22/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
In fish, the gut microbiome plays a crucial role in homeostasis and health and is affected by several organic and inorganic environmental contaminants. Amphidromous fish are sentinel species, particularly exposed to these stressors. We used whole metagenome sequencing to characterize the gut microbiome of wild European eels (Anguilla anguilla) at a juvenile stage captured from three sites with contrasted pollution levels in term of heavy metals and persistent organic pollutants. The objectives were to identify what parameters could alter the gut microbiome of this catadromous fish and to explore the potential use of microbiota as bioindicators of environment quality. We identified a total of 1079 microbial genera. Overall, gut microbiome was dominated by Proteobacteria, Firmicutes and Actinobacteria. Alpha and beta diversity were different amongst sites and could be explained by a reduced number of environmental and biological factors, specifically the relative abundance of fish preys in eels' diet, PCB101, γHCH (lindane), transnonachlor and arsenic. Furthermore, we identified a series of indicator taxa with differential abundance between the three sites. Changes in the microbial communities in the gut caused by environmental pollutants were previously undocumented in European eels. Our results indicate that microbiota might represent another route by which pollutants affect the health of these aquatic sentinel organisms.
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Affiliation(s)
| | - Claire Hoede
- Université de Toulouse, INRAE, UR MIAT, PF GenoToul Bioinfo, 31320, Castanet-Tolosan, France; Université Fédérale de Toulouse, INRAE, BioinfOmics, GenoToul Bioinformatics Facility, 31326, Castanet-Tolosan, France
| | - Emilie Dassié
- Univ. Bordeaux, CNRS, EPOC, EPHE, UMR 5805, 33600, Pessac, France
| | | | - Amandine Suin
- Genome & Transcriptome - Plateforme GeT-PlaGe, INRAE, 31326, Castanet-Tolosan, France
| | - Karine Le Menach
- Univ. Bordeaux, CNRS, EPOC, EPHE, UMR 5805, 33600, Pessac, France
| | - Hélène Budzinski
- Univ. Bordeaux, CNRS, EPOC, EPHE, UMR 5805, 33600, Pessac, France
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19
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Cathers HS, Mane SP, Tawari NR, Balakuntla J, Plata G, Krishnamurthy M, MacDonald A, Wolter M, Baxter N, Briones J, Nagireddy A, Millman G, Martin RE, Kumar Mahajan A, Gangaiah D. In silico, in vitro and in vivo characterization of host-associated Latilactobacillus curvatus strains for potential probiotic applications in farmed Atlantic salmon (Salmo salar). Sci Rep 2022; 12:18417. [PMID: 36319729 PMCID: PMC9626465 DOI: 10.1038/s41598-022-23009-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/21/2022] [Indexed: 11/07/2022] Open
Abstract
Salmon aquaculture is the fastest growing animal protein production system in the world; however, intensive farming leads to poor weight gain, stress, and disease outbreaks. Probiotics offer the potential to enhance growth performance and feed efficiency in Atlantic salmon, as well as immunostimulate fish against common pathogens, benefitting farmers and consumers with more efficient production. Here, we isolated and identified 900 native microbial isolates including 18 Lactobacilli from the farmed salmon intestines. Based on whole-genome sequencing and phylogenetic analysis, the Lactobacillus candidates belonged to Latilactobacillus curvatus (L. curvatus) species and formed two distinct phylogenetic groups. Using bioinformatics and in vitro analyses, we selected two candidates L. curvatus ATCC PTA-127116 and L. curvatus ATCC PTA-127117, which showed desirable safety and probiotic properties. The two L. curvatus candidates were evaluated for safety and efficacy (higher final weight) in Atlantic salmon alongside spore-forming Bacilli isolated from salmon, poultry, and swine. All the tested candidates were safe to salmon with no adverse effects. While we did not see efficacy in any Bacillus supplemented groups, compared to untreated group, the group administered with the two L. curvatus strains consortium in feed for seven weeks in freshwater showed indicators of improvement in final body weight by 4.2%. Similarly, the two L. curvatus candidates were also evaluated for safety and efficacy in Atlantic salmon in saltwater; the group administered with the two L. curvatus strains consortium in feed for 11 weeks showed indicators of improvement in final body weight by 4.7%. Comprehensive metabolomics analyses in the presence of different prebiotics and/or additives identified galactooligosaccharide as a potential prebiotic to enhance the efficacy of two L. curvatus candidates. All together, these data provide comprehensive genomic, phenotypic and metabolomic evidence of safety and desirable probiotic properties as well as indicators of in vivo efficacy of two novel endogenous L. curvatus candidates for potential probiotic applications in Atlantic salmon. The in vivo findings need to be confirmed in larger performance studies, including field trials.
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Affiliation(s)
- Hannah S Cathers
- Elanco Animal Health, 2500 Innovation Way, Greenfield, IN, 46140, USA
| | | | - Nilesh R Tawari
- Elanco Innovation and Alliance Centre, 22, 3Rd Cross Rd, SR Layout, Murgesh Pallya, Bengaluru, Karnataka, India
| | - Jayanth Balakuntla
- Elanco Innovation and Alliance Centre, 22, 3Rd Cross Rd, SR Layout, Murgesh Pallya, Bengaluru, Karnataka, India
| | - Germán Plata
- BiomEdit, LLC, 10100 Lantern Road, Fishers, IN, 46037, USA
| | | | - Alicia MacDonald
- Elanco Animal Health, 37 McCarville St, Charlottetown, PEI, Canada
| | - Marilyn Wolter
- Elanco Animal Health, Inc., Ruta 5 Sur Km 1012, Puerto Varas, Los Lagos, Chile
| | - Niel Baxter
- BiomEdit, LLC, 10100 Lantern Road, Fishers, IN, 46037, USA
| | - Julian Briones
- Elanco Animal Health, Inc., Ruta 5 Sur Km 1012, Puerto Varas, Los Lagos, Chile
| | - Akshitha Nagireddy
- Elanco Innovation and Alliance Centre, 22, 3Rd Cross Rd, SR Layout, Murgesh Pallya, Bengaluru, Karnataka, India
| | - Gregory Millman
- Elanco Animal Health, 2500 Innovation Way, Greenfield, IN, 46140, USA
| | - Roberto E Martin
- Elanco Animal Health, Inc., Ruta 5 Sur Km 1012, Puerto Varas, Los Lagos, Chile
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20
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Li D, Sun W, Lei H, Li X, Hou L, Wang Y, Chen H, Schlenk D, Ying GG, Mu J, Xie L. Cyclophosphamide alters the behaviors of adult Zebrafish via neurotransmitters and gut microbiota. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 250:106246. [PMID: 35917676 DOI: 10.1016/j.aquatox.2022.106246] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Cyclophosphamide, one of the earliest prescribed alkylating anticancer drugs, has been frequently detected in aquatic environments. However, its effects on fish behavior and associated mechanisms remain largely unknown. In this study, the behaviors, neurochemicals, and gut microbiota of adult zebrafish were investigated after 2 months of exposure to CP at 0.05, 0.5, 5, and 50 µg/L. Behavioral assays revealed that CP increased locomotion and anxiety, and decreased the cognition of zebrafish. The alteration of neurotransmitters and related gene expressions in the dopamine and gamma-aminobutyric acid pathways induced by CP may be responsible for the observed changes in locomotion and cognition of adult zebrafish. Meanwhile, CP increased the anxiety of adult zebrafish through the serotonin, acetylcholine, and histamine pathways in the brain. In addition, increased abundances of Fusobacteriales, Reyanellales, Staphylococcales, Rhodobacterals, and Patescibateria in the intestine at the CP-50 treatment were observed. The study has demonstrated that CP affects the locomotion, anxiety, and cognition in zebrafish, which might be linked with the dysfunction of neurochemicals in the brain. This study further suggests that the gut-brain axis might interact to modulate fish behaviors upon exposure to CP (maybe other organic pollutants). Further research is warranted to test this hypothesis.
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Affiliation(s)
- Dan Li
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Weijun Sun
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Haojun Lei
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Xiao Li
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Liping Hou
- School of Life Sciences, Guangzhou University, Guangzhou 510655, China
| | - Yongzhuang Wang
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Nanning Normal University, Ministry of Education, Nanning 530001, China
| | - Hongxing Chen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Daniel Schlenk
- Department of Environmental Sciences, University of California Riverside, Riverside, CA 92507, USA
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Jingli Mu
- College of Geography and Oceanography, Minjiang University, Fuzhou 350108, PR China
| | - Lingtian Xie
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
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21
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Dietary carbohydrate-to-protein ratio influences growth performance, hepatic health and dynamic of gut microbiota in atlantic salmon (Salmo salar). ANIMAL NUTRITION 2022; 10:261-279. [PMID: 35785253 PMCID: PMC9234083 DOI: 10.1016/j.aninu.2022.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 01/11/2022] [Accepted: 04/10/2022] [Indexed: 11/24/2022]
Abstract
Atlantic salmon (Salmo salar) fed a carbohydrate-rich diet exhibit suboptimal growth performance, along with other metabolic disturbances. It is well known that gut microbes play a pivotal role in influencing metabolism of the host, and these microbes can be modified by the diet. The main goal of the present study was to determine the effect of feeding graded levels of digestible carbohydrates to Atlantic salmon on the distal intestine digesta microbiota at 3 sampling times (i.e., weeks 4, 8 and 12), during a 12-week trial. A low carbohydrate-to-high protein diet (LC/HP, 0% wheat starch), a medium carbohydrate-to-medium protein diet (MC/MP, 15% wheat starch) or a high carbohydrate-to-low protein diet (HC/LP, 30% wheat starch) was fed to triplicate fish tanks (27 to 28 fish per tank). We performed an in-depth characterization of the distal intestine digesta microbiota. Further, growth parameters, liver histology and the expression of genes involved in hepatic neolipogenesis in fish were measured. Fish fed a HC/LP diet showed greater hepatosomatic and viscerosomatic indexes (P = 0.026 and P = 0.018, respectively), lower final weight (P = 0.005), weight gain (P = 0.003), feed efficiency (P = 0.033) and growth rate (P = 0.003) compared with fish fed the LC/HP diet. Further, feeding salmon a high digestible carbohydrate diet caused greater lipid vacuolization, steatosis index (P = 0.007) and expression of fatty acid synthase (fas) and delta-6 fatty acyl desaturase (d6fad) (P = 0.001 and P = 0.001, respectively) in the liver compared with fish fed the LC/HP diet. Although, the major impact of feeding a carbohydrate-rich diet to Atlantic salmon in beta diversity of distal intestine digesta microbiota was observed at week 4 (HC/LP vs MC/MP and HC/LP vs LC/HP; P = 0.007 and P = 0.008, respectively) and week 8 (HC/LP vs MC/MP; P = 0.04), no differences between experimental groups were detected after 12 weeks of feeding. Finally, at the end of the trial, there was a negative correlation between lactic acid bacteria (LAB) members, including Leuconostoc and Lactobacillus, with hepatic steatosis level, the hepatosomatic and viscerosomatic indexes as well as the expression of fas and d6fad. Weissella showed negative correlation with hepatic steatosis level and the hepatosomatic index. Finally, further research to explore the potential use of LAB as probiotics to improve liver health in carnivorous fish fed fatty liver-induced diet is warranted.
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22
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Brealey JC, Lecaudey LA, Kodama M, Rasmussen JA, Sveier H, Dheilly NM, Martin MD, Limborg MT. Microbiome "Inception": an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host. mBio 2022; 13:e0067922. [PMID: 35502903 PMCID: PMC9239044 DOI: 10.1128/mbio.00679-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/04/2022] [Indexed: 11/20/2022] Open
Abstract
The concept of a holobiont, a host organism and its associated microbial communities, encapsulates the vital role the microbiome plays in the normal functioning of its host. Parasitic infections can disrupt this relationship, leading to dysbiosis. However, it is increasingly recognized that multicellular parasites are themselves holobionts. Intestinal parasites share space with the host gut microbiome, creating a system of nested microbiomes within the primary host. However, how the parasite, as a holobiont, interacts with the host holobiont remains unclear, as do the consequences of these interactions for host health. Here, we used 16S amplicon and shotgun metagenomics sequencing to characterize the microbiome of the intestinal cestode Eubothrium and its effect on the gut microbiome of its primary host, Atlantic salmon. Our results indicate that cestode infection is associated with salmon gut dysbiosis by acting as a selective force benefiting putative pathogens and potentially introducing novel bacterial species to the host. Our results suggest that parasitic cestodes may themselves be holobionts nested within the microbial community of their holobiont host, emphasizing the importance of also considering microbes associated with parasites when studying intestinal parasitic infections. IMPORTANCE The importance of the parasite microbiome is gaining recognition. Of particular concern is understanding how these parasite microbiomes influence host-parasite interactions and parasite interactions with the vertebrate host microbiome as part of a system of nested holobionts. However, there are still relatively few studies focusing on the microbiome of parasitic helminths in general and almost none on cestodes in particular, despite the significant burden of disease caused by these parasites globally. Our study provides insights into a system of significance to the aquaculture industry, cestode infections of Atlantic salmon and, more broadly, expands our general understanding of parasite-microbiome-host interactions and introduces a new element, the microbiome of the parasite itself, which may play a critical role in modulating the host microbiome, and, therefore, the host response, to parasite infection.
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Affiliation(s)
- Jaelle C. Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Laurène A. Lecaudey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Miyako Kodama
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jacob A. Rasmussen
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Nolwenn M. Dheilly
- UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health Laboratory, Maisons-Alfort, France
| | - Michael D. Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Morten T. Limborg
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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23
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Shao C, Zhao W, Li N, Li Y, Zhang H, Li J, Xu Z, Wang J, Gao T. Gut Microbiome Succession in Chinese Mitten Crab Eriocheir sinensis During Seawater-Freshwater Migration. Front Microbiol 2022; 13:858508. [PMID: 35432227 PMCID: PMC9005979 DOI: 10.3389/fmicb.2022.858508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/15/2022] [Indexed: 11/20/2022] Open
Abstract
Biological migration is usually associated with disturbances and environmental changes that are key drivers in determining the diversity, community compositions, and function of gut microbiome. However, little is known about how gut microbiome is affected by disturbance such as salinity changes during migration from seawater to freshwater. Here, we tracked the gut microbiome succession of Chinese mitten crabs (Eriocheir sinensis) during their migrations from seawater to freshwater and afterward using 16S rDNA sequencing for 127 days, and explored the temporal patterns in microbial diversity and the underlying environmental factors. The species richness of gut microbiome showed a hump-shaped trend over time during seawater–freshwater migration. The community dissimilarities of gut microbiome increased significantly with day change. The turnover rate of gut microbiome community was higher during seawater–freshwater transition (1–5 days) than that in later freshwater conditions. Salinity was the major factor leading to the alpha diversity and community dissimilarity of gut microbiome during seawater–freshwater transition, while the host selection showed dominant effects during freshwater stage. The transitivity, connectivity, and average clustering coefficient of gut microbial co-occurrence networks showed decreased trends, while modularity increased during seawater–freshwater migration. For metabolic pathways, “Amino Acid Metabolism” and “Lipid Metabolism” were higher during seawater–freshwater transition than in freshwater. This study advances our mechanistic understanding of the assembly and succession of gut microbiota, which provides new insights into the gut ecology of other aquatic animals.
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Affiliation(s)
- Chenxi Shao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| | - Wenqian Zhao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Nannan Li
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| | - Yinkang Li
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| | - Huiming Zhang
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Jingjing Li
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| | - Zhiqiang Xu
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Tianheng Gao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
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24
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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: 7] [Impact Index Per Article: 3.5] [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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25
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Berggren H, Tibblin P, Yıldırım Y, Broman E, Larsson P, Lundin D, Forsman A. Fish Skin Microbiomes Are Highly Variable Among Individuals and Populations but Not Within Individuals. Front Microbiol 2022; 12:767770. [PMID: 35126324 PMCID: PMC8813977 DOI: 10.3389/fmicb.2021.767770] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/13/2021] [Indexed: 12/31/2022] Open
Abstract
Fish skin-associated microbial communities are highly variable among populations and species and can impact host fitness. Still, the sources of variation in microbiome composition, and particularly how they vary among and within host individuals, have rarely been investigated. To tackle this issue, we explored patterns of variation in fish skin microbiomes across different spatial scales. We conducted replicate sampling of dorsal and ventral body sites of perch (Perca fluviatilis) from two populations and characterized the variation of fish skin-associated microbial communities with 16S rRNA gene metabarcoding. Results showed a high similarity of microbiome samples taken from the left and right side of the same fish individuals, suggesting that fish skin microbiomes can be reliably assessed and characterized even using a single sample from a specific body site. The microbiome composition of fish skin differed markedly from the bacterioplankton communities in the surrounding water and was highly variable among individuals. No ASV was present in all samples, and the most prevalent phyla, Actinobacteria, Bacteroidetes, and Proteobacteria, varied in relative abundance among fish hosts. Microbiome composition was both individual- and population specific, with most of the variation explained by individual host. At the individual level, we found no diversification in microbiome composition between dorsal and ventral body sites, but the degree of intra-individual heterogeneity varied among individuals. To identify how genetic and phenotypic characteristics of fish hosts impact the rate and nature of intra-individual temporal dynamics of the skin microbiome, and thereby contribute to the host-specific patterns documented here, remains an important task for future research.
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Affiliation(s)
- Hanna Berggren
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Petter Tibblin
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Yeşerin Yıldırım
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Per Larsson
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Daniel Lundin
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Anders Forsman
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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26
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Weththasinghe P, Rocha SDC, Øyås O, Lagos L, Hansen JØ, Mydland LT, Øverland M. Modulation of Atlantic salmon (Salmo salar) gut microbiota composition and predicted metabolic capacity by feeding diets with processed black soldier fly (Hermetia illucens) larvae meals and fractions. Anim Microbiome 2022; 4:9. [PMID: 35033208 PMCID: PMC8760679 DOI: 10.1186/s42523-021-00161-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/30/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Black soldier fly (Hermetia illucens) is a promising insect species to use as a novel ingredient in fish feeds. Black soldier fly larvae consists of three major fractions, namely protein, lipid, and exoskeleton. These fractions contain bioactive compounds that can modulate the gut microbiota in fish such as antimicrobial peptides, lauric acid, and chitin. However, it is not certain how, or which fractions of black solider fly would affect gut microbiota in fish. In the present study, black soldier fly larvae were processed into three different meals (full-fat, defatted and de-chitinized) and two fractions (oil and exoskeleton), and included in diets for Atlantic salmon (Salmo salar). Atlantic salmon pre-smolts were fed with these diets in comparison with a commercial-like control diet for eight weeks to investigate the effects of insect meals and fractions on the composition and predicted metabolic capacity of gut microbiota. The gut microbiota was profiled by 16S rRNA gene sequencing, and the predicted metabolic capacities of gut microbiota were determined using genome-scale metabolic models. RESULTS The inclusion of insect meals and fractions decreased abundance of Proteobacteria and increased abundance of Firmicutes in salmon gut. The diets that contained insect chitin, i.e., insect meals or exoskeleton diets, increased abundance of chitinolytic bacteria including lactic acid bacteria and Actinomyces in salmon gut, with fish fed full-fat meal diet showing the highest abundances. The diets that contained insect lipids, i.e., insect meals and oil diets enriched Bacillaceae in fish gut. The fish fed diets containing full-fat insect meal had a unique gut microbiota composition dominated by beneficial lactic acid bacteria and Actinomyces, and showed a predicted increase in mucin degradation compared to the other diets. CONCLUSIONS The present results showed that the dietary inclusion of insect meals and fractions can differently modulate the composition and predicted metabolic capacity of gut microbiota in Atlantic salmon pre-smolts. The use of full-fat black soldier fly larvae meal in diets for salmon is more favorable for beneficial modulation of gut microbiota than larvae processed by separation of lipid or exoskeleton fractions.
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Affiliation(s)
- Pabodha Weththasinghe
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Sérgio D. C. Rocha
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Ove Øyås
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Leidy Lagos
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Jon Ø. Hansen
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Liv T. Mydland
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Margareth Øverland
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
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27
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Leeper A, Ekmay R, Knobloch S, Skírnisdóttir S, Varunjikar M, Dubois M, Smárason BÖ, Árnason J, Koppe W, Benhaïm D. Torula yeast in the diet of Atlantic salmon Salmo salar and the impact on growth performance and gut microbiome. Sci Rep 2022; 12:567. [PMID: 35022439 PMCID: PMC8755733 DOI: 10.1038/s41598-021-04413-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/08/2021] [Indexed: 01/04/2023] Open
Abstract
Atlantic salmon aquaculture is expanding, and with it, the need to find suitable replacements for conventional protein sources used in formulated feeds. Torula yeast (Cyberlindnera jadinii), has been identified as a promising alternative protein for feed and can be sustainably cultivated on lignocellulosic biomasses. The present study investigated the impact of torula yeast on the growth performance and gut microbiome of freshwater Atlantic salmon. A marine protein base diet and a mixed marine and plant protein base diet were tested, where conventional proteins were replaced with increasing inclusion levels of torula yeast, (0%, 10%, 20%). This study demonstrated that 20% torula yeast can replace fish meal without alteration to growth performance while leading to potential benefits for the gut microbiome by increasing the presence of bacteria positively associated with the host. However, when torula yeast replaced plant meal in a mixed protein diet, results suggested that 10% inclusion of yeast produced the best growth performance results but at the 20% inclusion level of yeast, potentially negative changes were observed in the gut microbial community, such as a decrease in lactic acid bacteria. This study supports the continued investigation of torula yeast for Atlantic salmon as a partial replacement for conventional proteins.
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Affiliation(s)
- Alexandra Leeper
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box, 1420, Ås, Norway. .,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
| | | | - Madhushri Varunjikar
- Department of Research and Innovation, Matís Ltd, 12, Vínlandsleid, 113, Reykjavik, Iceland
| | - Marianne Dubois
- Department of Research and Innovation, Matís Ltd, 12, Vínlandsleid, 113, Reykjavik, Iceland
| | - Birgir Örn Smárason
- Department of Research and Innovation, Matís Ltd, 12, Vínlandsleid, 113, Reykjavik, Iceland
| | - Jón Árnason
- Department of Research and Innovation, Matís Ltd, 12, Vínlandsleid, 113, Reykjavik, Iceland
| | - Wolfgang Koppe
- Department of Research and Innovation, Matís Ltd, 12, Vínlandsleid, 113, Reykjavik, Iceland
| | - David Benhaïm
- Department of Aquaculture and Fish Biology, Hólar University, Haeyri 1, 551, Saudárkrókur, Iceland
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28
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Abstract
The term "core microbiome" has become widely used in microbial ecology over the last decade. Broadly, the core microbiome refers to any set of microbial taxa, or the genomic and functional attributes associated with those taxa, that are characteristic of a host or environment of interest. Most commonly, core microbiomes are measured as the microbial taxa shared among two or more samples from a particular host or environment. Despite the popularity of this term and its growing use, there is little consensus about how a core microbiome should be quantified in practice. Here, we present a brief history of the core microbiome concept and use a representative sample of the literature to review the different metrics commonly used for quantifying the core. Empirical analyses have used a wide range of metrics for quantifying the core microbiome, including arbitrary occurrence and abundance cutoff values, with the focal taxonomic level of the core ranging from phyla to amplicon sequence variants. However, many of these metrics are susceptible to sampling and other biases. Developing a standardized set of metrics for quantifying the core that accounts for such biases is necessary for testing specific hypotheses about the functional and ecological roles of core microbiomes.
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29
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Ou W, Yu G, Zhang Y, Mai K. Recent progress in the understanding of the gut microbiota of marine fishes. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:434-448. [PMID: 37073265 PMCID: PMC10077274 DOI: 10.1007/s42995-021-00094-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 01/12/2021] [Indexed: 05/03/2023]
Abstract
As the significance of the gut microbiota has become increasingly realized, a large number of related studies have emerged. With respect to the gut microbial composition of fish, the predominant gut microbes and core gut microbiota have been reported by many researchers. Our understanding of fish gut microbiota, especially its functional roles, has fallen far behind that of terrestrial vertebrates, although previous studies using gnotobiotic zebrafish models have revealed that the gut microbiota performs a significant role in gut development, nutrient metabolism and immune responses. Given that environmental factors of marine habitats are very different from those of freshwater habitats, a distinct difference may exist in the gut microbiota between freshwater and marine fish. Therefore, this review aims to address the advances in marine fish gut microbiota in terms of methodologies, the gut microbial composition, and gnotobiotic models of marine fish, the important factors (host genotype and three environmental factors: temperature, salinity and diet) that drive marine fish gut microbiota, and significant roles of the gut microbiota in marine fish.
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Affiliation(s)
- Weihao Ou
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) and the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003 China
| | - Guijuan Yu
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) and the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003 China
| | - Yanjiao Zhang
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) and the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Kangsen Mai
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) and the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237 China
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30
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Aizpurua O, Nyholm L, Morris E, Chaverri G, Herrera Montalvo LG, Flores-Martinez JJ, Lin A, Razgour O, Gilbert MTP, Alberdi A. The role of the gut microbiota in the dietary niche expansion of fishing bats. Anim Microbiome 2021; 3:76. [PMID: 34711286 PMCID: PMC8555116 DOI: 10.1186/s42523-021-00137-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 10/04/2021] [Indexed: 01/04/2023] Open
Abstract
Background Due to its central role in animal nutrition, the gut microbiota is likely a relevant factor shaping dietary niche shifts. We analysed both the impact and contribution of the gut microbiota to the dietary niche expansion of the only four bat species that have incorporated fish into their primarily arthropodophage diet. Results We first compared the taxonomic and functional features of the gut microbiota of the four piscivorous bats to that of 11 strictly arthropodophagous species using 16S rRNA targeted amplicon sequencing. Second, we increased the resolution of our analyses for one of the piscivorous bat species, namely Myotis capaccinii, and analysed multiple populations combining targeted approaches with shotgun sequencing. To better understand the origin of gut microorganisms, we also analysed the gut microbiota of their fish prey (Gambusia holbrooki). Our analyses showed that piscivorous bats carry a characteristic gut microbiota that differs from that of their strict arthropodophagous counterparts, in which the most relevant bacteria have been directly acquired from their fish prey. This characteristic microbiota exhibits enrichment of genes involved in vitamin biosynthesis, as well as complex carbohydrate and lipid metabolism, likely providing their hosts with an enhanced capacity to metabolise the glycosphingolipids and long-chain fatty acids that are particularly abundant in fish. Conclusions Our results depict the gut microbiota as a relevant element in facilitating the dietary transition from arthropodophagy to piscivory. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00137-w.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark.
| | - Lasse Nyholm
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark
| | - Evie Morris
- University of Exeter, Streatham Campus, Biosciences, Exeter, EX4 4PS, UK
| | - Gloriana Chaverri
- Sede del Sur, Universidad de Costa Rica, #4000 Alamedas, Golfito, 60701, Costa Rica.,Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, República de Panamá
| | - L Gerardo Herrera Montalvo
- Estación de Biología Chamela, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 21, San Patricio, 48980, Jalisco, Mexico
| | - José Juan Flores-Martinez
- Laboratorio de Sistemas de Información Geográfica, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Aiqing Lin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China
| | - Orly Razgour
- University of Exeter, Streatham Campus, Biosciences, Exeter, EX4 4PS, UK
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark
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31
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Naya-Català F, do Vale Pereira G, Piazzon MC, Fernandes AM, Calduch-Giner JA, Sitjà-Bobadilla A, Conceição LEC, Pérez-Sánchez J. Cross-Talk Between Intestinal Microbiota and Host Gene Expression in Gilthead Sea Bream ( Sparus aurata) Juveniles: Insights in Fish Feeds for Increased Circularity and Resource Utilization. Front Physiol 2021; 12:748265. [PMID: 34675821 PMCID: PMC8523787 DOI: 10.3389/fphys.2021.748265] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/02/2021] [Indexed: 01/03/2023] Open
Abstract
New types of fish feed based on processed animal proteins (PAPs), insect meal, yeast, and microbial biomasses have been used with success in gilthead sea bream. However, some drawback effects on feed conversion and inflammatory systemic markers were reported in different degrees with PAP- and non-PAP-based feed formulations. Here, we focused on the effects of control and two experimental diets on gut mucosal-adherent microbiota, and how it correlated with host transcriptomics at the local (intestine) and systemic (liver and head kidney) levels. The use of tissue-specific PCR-arrays of 93 genes in total rendered 13, 12, and 9 differentially expressed (DE) genes in the intestine, liver, and head kidney, respectively. Illumina sequencing of gut microbiota yielded a mean of 125,350 reads per sample, assigned to 1,281 operational taxonomic unit (OTUs). Bacterial richness and alpha diversity were lower in fish fed with the PAP diet, and discriminant analysis displayed 135 OTUs driving the separation between groups with 43 taxa correlating with 27 DE genes. The highest expression of intestinal pcna and alpi was achieved in PAP fish with intermediate values in non-PAP, being the pro-inflammatory action of alpi associated with the presence of Psychrobacter piscatorii. The intestinal muc13 gene was down-regulated in non-PAP fish, with this gene being negatively correlated with anaerobic (Chloroflexi and Anoxybacillus) and metal-reducing (Pelosinus and Psychrosinus) bacteria. Other inflammatory markers (igm, il8, tnfα) were up-regulated in PAP fish, positively correlating the intestinal igm gene with the inflammasome activator Escherichia/Shigella, whereas the systemic expression of il8 and tnfα was negatively correlated with the Bacilli class in PAP fish and positively correlated with Paracoccus yeei in non-PAP fish. Overall changes in the expression pattern of il10, galectins (lgals1, lgals8), and toll-like receptors (tlr2, tlr5, tlr9) reinforced the anti-inflammatory profile of fish fed with the non-PAP diet, with these gene markers being associated with a wide range of OTUs. A gut microbiota-liver axis was also established, linking the microbial generation of short chain fatty acids with the fueling of scd1- and elovl6-mediated lipogenesis. In summary, by correlating the microbiome with host gene expression, we offer new insights in the evaluation of fish diets promoting gut and metabolism homeostasis, and ultimately, the health of farmed fish.
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Affiliation(s)
- Fernando Naya-Català
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS-CSIC), Castellón, Spain
| | | | - M Carla Piazzon
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Ana Margarida Fernandes
- SPAROS Lda, Area Empresarial de Marim, Olhăo, Portugal.,Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Josep Alvar Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS-CSIC), Castellón, Spain
| | | | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS-CSIC), Castellón, Spain
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32
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Cheaib B, Yang P, Kazlauskaite R, Lindsay E, Heys C, Dwyer T, De Noa M, Schaal P, Sloan W, Ijaz U, Llewellyn M. Genome erosion and evidence for an intracellular niche - exploring the biology of mycoplasmas in Atlantic salmon. AQUACULTURE (AMSTERDAM, NETHERLANDS) 2021; 541:736772. [PMID: 34471330 PMCID: PMC8192413 DOI: 10.1016/j.aquaculture.2021.736772] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/15/2021] [Accepted: 04/12/2021] [Indexed: 05/09/2023]
Abstract
Mycoplasmas are the smallest autonomously self-replicating life form on the planet. Members of this bacterial genus are known to parasitise a wide array of metazoans including vertebrates. Whilst much research has been significant targeted at parasitic mammalian mycoplasmas, very little is known about their role in other vertebrates. In the current study, we aim to explore the biology of mycoplasmas in Atlantic Salmon, a species of major significance for aquaculture, including cellular niche, genome size structure and gene content. Using fluorescent in-situ hybridisation (FISH), mycoplasmas were targeted in epithelial tissues across the digestive tract (stomach, pyloric caecum and midgut) from different development stages (eggs, parr, subadult) of farmed Atlantic salmon (Salmo salar), and we present evidence for an intracellular niche for some of the microbes visualised. Via shotgun metagenomic sequencing, a nearly complete, albeit small, genome (~0.57 MB) as assembled from a farmed Atlantic salmon subadult. Phylogenetic analysis of the recovered genome revealed taxonomic proximity to other salmon derived mycoplasmas, as well as to the human pathogen Mycoplasma penetrans (~1.36 Mb). We annotated coding sequences and identified riboflavin pathway encoding genes and sugar transporters, the former potentially consistent with micronutrient provisioning in salmonid development. Our study provides insights into mucosal adherence, the cellular niche and gene catalog of Mycoplasma in the gut ecosystem of the Atlantic salmon, suggesting a high dependency of this minimalist bacterium on its host. Further study is required to explore and functional role of Mycoplasma in the nutrition and development of its salmonid host.
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Affiliation(s)
- B. Cheaib
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
- School of Engineering, University of Glasgow, Glasgow G12 8QQ, United Kingdom
- Corresponding author at: Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom.
| | - P. Yang
- Laboratory of Aquaculture, nutrition and feed, Fisheries College, Ocean University of China, Hongdao Rd, Shinan District, Qingdao, Shandong, China
| | - R. Kazlauskaite
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - E. Lindsay
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - C. Heys
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - T. Dwyer
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - M. De Noa
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Patrick Schaal
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - W. Sloan
- School of Engineering, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - U.Z. Ijaz
- School of Engineering, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - M.S. Llewellyn
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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33
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Zhu P, Wong MKS, Lin X, Chan TF, Wong CKC, Lai KP, Tse WKF. Changes of the intestinal microbiota along the gut of Japanese Eel (Anguilla japonica). Lett Appl Microbiol 2021; 73:529-541. [PMID: 34265084 DOI: 10.1111/lam.13539] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/21/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
Fish intestine contains different types of microbiomes, and bacteria are the dominant microbiota in fishes. Studies have identified various core gut bacteria in fishes. However, little is known about the composition and their relative functions of gut microbial community along the intestine. To explore this, the current study investigated the microbial community distribution along the gut in Anguilla japonica. By 16S rRNA gene sequencing, we profiled the gut microbiota in eel along the three regions (anterior intestine (AI), the middle intestine (MI) and the posterior intestine (PI)). Results suggested that the three regions did not have significant differences on the observed species and diversities. The cluster tree analysis showed that the bacteria community in MI was closer to PI than the AI. The dominant bacteria in AI were the Proteobacteria, in which the majority was graduated replaced by Bacteroidetes along the gut to PI region. Through PICRUSt analysis, shifts in the bacterial community along the gut were found to affect the genetic information processing pathways. Higher levels of translation and transcriptional pathway activities were found in MI and PI than in AI. The dominant bacterial species were different among the regions and contributed to various biological functions along the gut.
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Affiliation(s)
- P Zhu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi, PR China
| | - M K-S Wong
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - X Lin
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - T F Chan
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - C K C Wong
- Department of Biology, Croucher Institute for Environmental Sciences, Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong Baptist University, Kowloon, Hong Kong
| | - K P Lai
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi, PR China.,Department of Biology, Croucher Institute for Environmental Sciences, Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong Baptist University, Kowloon, Hong Kong.,Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, PR China
| | - W K F Tse
- Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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34
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Rosado D, Xavier R, Cable J, Severino R, Tarroso P, Pérez-Losada M. Longitudinal sampling of external mucosae in farmed European seabass reveals the impact of water temperature on bacterial dynamics. ISME COMMUNICATIONS 2021; 1:28. [PMID: 36739461 PMCID: PMC9723769 DOI: 10.1038/s43705-021-00019-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
Fish microbiota are intrinsically linked to health and fitness, but they are highly variable and influenced by both biotic and abiotic factors. Water temperature particularly limits bacterial adhesion and growth, impacting microbial diversity and bacterial infections on the skin and gills. Aquaculture is heavily affected by infectious diseases, especially in warmer months, and industry practices often promote stress and microbial dysbiosis, leading to an increased abundance of potentially pathogenic bacteria. In this regard, fish mucosa health is extremely important because it provides a primary barrier against pathogens. We used 16 rRNA V4 metataxonomics to characterize the skin and gill microbiota of the European seabass, Dicentrarchus labrax, and the surrounding water over 12 months, assessing the impact of water temperature on microbial diversity and function. We show that the microbiota of external mucosae are highly dynamic with consistent longitudinal trends in taxon diversity. Several potentially pathogenic genera (Aliivibrio, Photobacterium, Pseudomonas, and Vibrio) were highly abundant, showing complex interactions with other bacterial genera, some of which with recognized probiotic activity, and were also significantly impacted by changes in temperature. The surrounding water temperature influenced fish microbial composition, structure and function over time (days and months). Additionally, dysbiosis was more frequent in warmer months and during transitions between cold/warm months. We also detected a strong seasonal effect in the fish microbiota, which is likely to result from the compound action of several unmeasured environmental factors (e.g., pH, nutrient availability) beyond temperature. Our results highlight the importance of performing longitudinal studies to assess the impact of environmental factors on fish microbiotas.
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Affiliation(s)
- Daniela Rosado
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal.
| | - Raquel Xavier
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal.
| | - Jo Cable
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Ricardo Severino
- Piscicultura Vale da Lama, Sapal do Vale da Lama, Odiáxere, Lagos, Portugal
| | - Pedro Tarroso
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Marcos Pérez-Losada
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
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35
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Rasmussen JA, Villumsen KR, Duchêne DA, Puetz LC, Delmont TO, Sveier H, Jørgensen LVG, Præbel K, Martin MD, Bojesen AM, Gilbert MTP, Kristiansen K, Limborg MT. Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts. Commun Biol 2021; 4:579. [PMID: 33990699 PMCID: PMC8121932 DOI: 10.1038/s42003-021-02105-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/14/2021] [Indexed: 11/08/2022] Open
Abstract
Salmonids are important sources of protein for a large proportion of the human population. Mycoplasma species are a major constituent of the gut microbiota of salmonids, often representing the majority of microbiota. Despite the frequent reported dominance of salmonid-related Mycoplasma species, little is known about the phylogenomic placement, functions and potential evolutionary relationships with their salmonid hosts. In this study, we utilise 2.9 billion metagenomic reads generated from 12 samples from three different salmonid host species to I) characterise and curate the first metagenome-assembled genomes (MAGs) of Mycoplasma dominating the intestines of three different salmonid species, II) establish the phylogeny of these salmonid candidate Mycoplasma species, III) perform a comprehensive pangenomic analysis of Mycoplasma, IV) decipher the putative functionalities of the salmonid MAGs and reveal specific functions expected to benefit the host. Our data provide a basis for future studies examining the composition and function of the salmonid microbiota.
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Affiliation(s)
- Jacob A Rasmussen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Kasper R Villumsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Copenhagen, Denmark
| | - David A Duchêne
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lara C Puetz
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tom O Delmont
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | - Louise von Gersdorff Jørgensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Parasitology and Aquatic Pathobiology, Copenhagen, Denmark
| | - Kim Præbel
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Anders M Bojesen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Institute of Metagenomics, BGI-Shenzhen, Shenzhen, China
| | - Morten T Limborg
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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36
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Dias D, Dardengo GM, Engrola S, Navarro-Guillén C. Characterization and comparison of the digestive physiology of two scombrids, Katsuwonus pelamis and Sarda sarda, in the Gulf of Cádiz. PLoS One 2021; 16:e0249541. [PMID: 33852608 PMCID: PMC8046184 DOI: 10.1371/journal.pone.0249541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/20/2021] [Indexed: 11/25/2022] Open
Abstract
Fish and other marine animals have a unique and intimate interaction with their surrounding environment. Diet type or trophic level play significant roles in modulating species digestive physiology. However, little is known about how the trophic niche influences digestive activity and gut microbiota in scombrids species. The aim of the present study was to analyse and describe the digestive physiology of the skipjack tuna (Katsuwonus pelamis) and the Atlantic bonito (Sarda sarda) as bioindicator of the feeding ecology and trophic niche for both species in the Gulf of Cádiz (Spain). For that, fish proximate composition, pH of digestive organs and digestive enzymes activity levels were analysed in 10 individuals of each species to gain insight into the digestive physiological adaptations of the two species of scombrids. In addition, intestinal microbiota composition was determined for the skipjack tuna. The integration of the results suggested a clear trophic niche segregation between both species. Stomach pH was associated in both species with infrequent feeding events. Body proximate composition and digestive lipases activity patterns pointed to a high predominance of lipids in the Atlantic bonito diet, suggesting oily fish as main prey. On the other hand, results supported the skipjack tuna as a highly opportunistic feeder with a more varied diet, including fish but also crustaceans as preys. The gut microbial community in the latter species is dominated by Firmicutes and Tenericutes at phylum level, and by Mycoplasma, Blautia and Dorea at genus level. The present study contributes to advance the knowledge on the feeding behaviour and physiology diversity in fish species as a result of adaptation to a particular habitat.
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Affiliation(s)
- Diogo Dias
- Aquaculture Research Group, Centro de Ciências do Mar do Algarve (CCMAR), Faro, Portugal
| | - Gian Marco Dardengo
- Aquaculture Research Group, Centro de Ciências do Mar do Algarve (CCMAR), Faro, Portugal
| | - Sofia Engrola
- Aquaculture Research Group, Centro de Ciências do Mar do Algarve (CCMAR), Faro, Portugal
| | - Carmen Navarro-Guillén
- Aquaculture Research Group, Centro de Ciências do Mar do Algarve (CCMAR), Faro, Portugal
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37
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Jin Y, Harvey TN, Bartosova Z, Hassani S, Bruheim P, Sandve SR, Vik JO. Diet and Life Stage-Associated Lipidome Remodeling in Atlantic Salmon. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3787-3796. [PMID: 33754702 PMCID: PMC8041299 DOI: 10.1021/acs.jafc.0c07281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/05/2021] [Accepted: 03/15/2021] [Indexed: 05/07/2023]
Abstract
Salmon is an important source of long-chain highly unsaturated fatty acids (LC-HUFAs) such as 22:6n-3 [docosahexaenoic acid (DHA)]. In the present study, we conducted two identical experiments on salmon in freshwater (FW) and seawater (SW) stages, with a diet switch from fish oil (high in LC-HUFA) to vegetable oil (low in LC-HUFA) and vice versa. Our aim was to investigate the diet and life stage-specific features of lipid uptake (gut), processing (liver), and deposition (muscle). The lipid composition changed much faster in the gut of SW fish relative to FW fish, suggesting that the former had a higher rate of lipid absorption and transport. SW fish also had higher expression of phospholipid synthesis and lipoprotein formation genes in the gut, whereas FW fish had higher expression of lipid synthesis genes in the liver. All phospholipids except PC-44:12 and PE-44:12 were less abundant in SW, suggesting that SW fish have a higher requirement for DHA.
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Affiliation(s)
- Yang Jin
- Center
of Integrative Genetics (CIGENE), Norwegian
University of Life Sciences, 1430 Aas, Norway
| | - Thomas Nelson Harvey
- Center
of Integrative Genetics (CIGENE), Norwegian
University of Life Sciences, 1430 Aas, Norway
| | - Zdenka Bartosova
- Department
of Biotechnology and Food Science, Norwegian
University of Science and Technology, 7491 Trondheim, Norway
| | - Sahar Hassani
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Aas, Norway
| | - Per Bruheim
- Department
of Biotechnology and Food Science, Norwegian
University of Science and Technology, 7491 Trondheim, Norway
| | - Simen Rød Sandve
- Center
of Integrative Genetics (CIGENE), Norwegian
University of Life Sciences, 1430 Aas, Norway
| | - Jon Olav Vik
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Aas, Norway
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Bateman AW, Schulze AD, Kaukinen KH, Tabata A, Mordecai G, Flynn K, Bass A, Di Cicco E, Miller KM. Descriptive multi-agent epidemiology via molecular screening on Atlantic salmon farms in the northeast Pacific Ocean. Sci Rep 2021; 11:3466. [PMID: 33568681 PMCID: PMC7876018 DOI: 10.1038/s41598-020-78978-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/24/2020] [Indexed: 02/07/2023] Open
Abstract
Rapid expansion of salmon aquaculture has resulted in high-density populations that host diverse infectious agents, for which surveillance and monitoring are critical to disease management. Screening can reveal infection diversity from which disease arises, differential patterns of infection in live and dead fish that are difficult to collect in wild populations, and potential risks associated with agent transmission between wild and farmed hosts. We report results from a multi-year infectious-agent screening program of farmed salmon in British Columbia, Canada, using quantitative PCR to assess presence and load of 58 infective agents (viruses, bacteria, and eukaryotes) in 2931 Atlantic salmon (Salmo salar). Our analysis reveals temporal trends, agent correlations within hosts, and agent-associated mortality signatures. Multiple agents, most notably Tenacibaculum maritimum, were elevated in dead and dying salmon. We also report detections of agents only recently shown to infect farmed salmon in BC (Atlantic salmon calicivirus, Cutthroat trout virus-2), detection in freshwater hatcheries of two marine agents (Kudoa thyrsites and Tenacibaculum maritimum), and detection in the ocean of a freshwater agent (Flavobacterium psychrophilum). Our results provide information for farm managers, regulators, and conservationists, and enable further work to explore patterns of multi-agent infection and farm/wild transmission risk.
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Affiliation(s)
- Andrew W Bateman
- Pacific Salmon Foundation, Vancouver, Canada. .,Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.
| | - Angela D Schulze
- Molecular Genetics, Fisheries and Oceans Canada, Nanaimo, Canada
| | - Karia H Kaukinen
- Molecular Genetics, Fisheries and Oceans Canada, Nanaimo, Canada
| | - Amy Tabata
- Molecular Genetics, Fisheries and Oceans Canada, Nanaimo, Canada
| | - Gideon Mordecai
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Kelsey Flynn
- Molecular Genetics, Fisheries and Oceans Canada, Nanaimo, Canada
| | - Arthur Bass
- Pacific Salmon Foundation, Vancouver, Canada.,Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
| | | | - Kristina M Miller
- Molecular Genetics, Fisheries and Oceans Canada, Nanaimo, Canada.,Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
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Wang J, Jaramillo-Torres A, Li Y, Kortner TM, Gajardo K, Brevik ØJ, Jakobsen JV, Krogdahl Å. Microbiota in intestinal digesta of Atlantic salmon (Salmo salar), observed from late freshwater stage until one year in seawater, and effects of functional ingredients: a case study from a commercial sized research site in the Arctic region. Anim Microbiome 2021; 3:14. [PMID: 33509296 PMCID: PMC7841887 DOI: 10.1186/s42523-021-00075-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/08/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The importance of the gut microbiota for health and wellbeing is well established for humans and some land animals. The gut microbiota is supposedly as important for fish, but existing knowledge has many gaps, in particular for fish in the Arctic areas. This study addressed the dynamics of Atlantic salmon digesta-associated gut microbiota assemblage and its associations with host responses from freshwater to seawater life stages under large-scale, commercial conditions in the Arctic region of Norway, and explored the effects of functional ingredients. The microbiota was characterized by 16S rRNA gene sequencing in distal intestinal digesta at four time points: 2 weeks before seawater transfer (in May, FW); 4 weeks after seawater transfer (in June, SW1); in November (SW2), and in April (SW3) the following year. Two series of diets were fed, varying throughout the observation time in nutrient composition according to the requirements of fish, one without (Ref diet), and the other with functional ingredients (Test diet). The functional ingredients, i.e. nucleotides, yeast cell walls, one prebiotic and essential fatty acids, were supplemented as single or mixtures based on the strategies from the feed company. RESULTS Overall, the fish showed higher microbial richness and lactic acid bacteria (LAB) abundance after seawater transfer, while Simpson's diversity decreased throughout the observation period. At SW1, the gut microbiota was slightly different from those at FW, and was dominated by the genera Lactobacillus and Photobacterium. As the fish progressed towards SW2 and SW3, the genera Lactobacillus and Mycoplasma became more prominent, with a corresponding decline in genus Photobacterium. The overall bacterial profiles at these time points showed a clear distinction from those at FW. A significant effect of functional ingredients (a mixture of nucleotides, yeast cell walls and essential fatty acids) was observed at SW2, where Test-fed fish showed lower microbial richness, Shannon's diversity, and LAB abundance. The multivariate association analysis identified differentially abundant taxa, especially Megasphaera, to be significantly associated with gut immune and barrier gene expressions, and plasma nutrients. CONCLUSIONS The gut microbiota profile varied during the observation period, and the Mycoplasma became the dominating bacteria with time. Megasphaera abundance was associated with gut health and plasma nutrient biomarkers. Functional ingredients modulated the gut microbiota profile during an important ongrowing stage.
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Affiliation(s)
- Jie Wang
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Ås, Norway.
| | - Alexander Jaramillo-Torres
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Ås, Norway
| | - Yanxian Li
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Ås, Norway
| | - Trond M Kortner
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Ås, Norway
| | - Karina Gajardo
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Ås, Norway
| | | | - Jan Vidar Jakobsen
- Cargill Aqua Nutrition, Prof. Olav Hanssensvei 7A, 4021, Stavanger, Norway
| | - Åshild Krogdahl
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Ås, Norway
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Rosado D, Pérez-Losada M, Pereira A, Severino R, Xavier R. Effects of aging on the skin and gill microbiota of farmed seabass and seabream. Anim Microbiome 2021; 3:10. [PMID: 33499971 PMCID: PMC7934244 DOI: 10.1186/s42523-020-00072-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/29/2020] [Indexed: 12/15/2022] Open
Abstract
Background Important changes in microbial composition related to sexual maturation have been already reported in the gut of several vertebrates including mammals, amphibians and fish. Such changes in fish are linked to reproduction and growth during developmental stages, diet transitions and critical life events. We used amplicon (16S rRNA) high-throughput sequencing to characterize the skin and gill bacterial microbiota of farmed seabass and seabream belonging to three different developmental age groups: early and late juveniles and mature adults. We also assessed the impact of the surrounding estuarine water microbiota in shaping the fish skin and gill microbiota. Results Microbial diversity, composition and predicted metabolic functions varied across fish maturity stages. Alpha-diversity in the seabass microbiota varied significantly between age groups and was higher in older fish. Conversely, in the seabream, no significant differences were found in alpha-diversity between age groups. Microbial structure varied significantly across age groups; moreover, high structural variation was also observed within groups. Different bacterial metabolic pathways were predicted to be enriched in the microbiota of both species. Finally, we found that the water microbiota was significantly distinct from the fish microbiota across all the studied age groups, although a high percentage of ASVs was shared with the skin and gill microbiotas. Conclusions We report important microbial differences in composition and potential functionality across different ages of farmed seabass and seabream. These differences may be related to somatic growth and the onset of sexual maturation. Importantly, some of the inferred metabolic pathways could enhance the fish coping mechanisms during stressful conditions. Our results provide new evidence suggesting that growth and sexual maturation have an important role in shaping the microbiota of the fish external mucosae and highlight the importance of considering different life stages in microbiota studies. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-020-00072-2.
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Affiliation(s)
- Daniela Rosado
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, 4485-661, Porto, Portugal.
| | - Marcos Pérez-Losada
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, 4485-661, Porto, Portugal.,Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052-0066, USA
| | - Ana Pereira
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, 4485-661, Porto, Portugal
| | - Ricardo Severino
- Piscicultura Vale da Lama, Sapal do Vale da Lama, Odiáxere, 8600-258, Lagos, Portugal
| | - Raquel Xavier
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, 4485-661, Porto, Portugal.
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Li Y, Bruni L, Jaramillo-Torres A, Gajardo K, Kortner TM, Krogdahl Å. Differential response of digesta- and mucosa-associated intestinal microbiota to dietary insect meal during the seawater phase of Atlantic salmon. Anim Microbiome 2021; 3:8. [PMID: 33500000 PMCID: PMC7934271 DOI: 10.1186/s42523-020-00071-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/22/2020] [Indexed: 12/14/2022] Open
Abstract
Background Intestinal digesta is commonly used for studying responses of microbiota to dietary shifts, yet evidence is accumulating that it represents an incomplete view of the intestinal microbiota. The present work aims to investigate the differences between digesta- and mucosa-associated intestinal microbiota in Atlantic salmon (Salmo salar) and how they may respond differently to dietary perturbations. In a 16-week seawater feeding trial, Atlantic salmon were fed either a commercially-relevant reference diet or an insect meal diet containing ~ 15% black soldier fly (Hermetia illucens) larvae meal. The digesta- and mucosa-associated distal intestinal microbiota were profiled by 16S rRNA gene sequencing. Results Regardless of diet, we observed substantial differences between digesta- and mucosa-associated intestinal microbiota. Microbial richness and diversity were much higher in the digesta than the mucosa. The insect meal diet altered the distal intestinal microbiota resulting in higher microbial richness and diversity. The diet effect, however, depended on the sample origin. Digesta-associated intestinal microbiota showed more pronounced changes than the mucosa-associated microbiota. Multivariate association analyses identified two mucosa-enriched taxa, Brevinema andersonii and Spirochaetaceae, associated with the expression of genes related to immune responses and barrier function in the distal intestine, respectively. Conclusions Our data show that salmon intestinal digesta and mucosa harbor microbial communities with clear differences. While feeding insects increased microbial richness and diversity in both digesta- and mucosa-associated intestinal microbiota, mucosa-associated intestinal microbiota seems more resilient to variations in the diet composition. To fully unveil the response of intestinal microbiota to dietary changes, concurrent profiling of digesta- and mucosa-associated intestinal microbiota is recommended whenever feasible. Specific taxa enriched in the intestinal mucosa are associated to gene expression related to immune responses and barrier function. Detailed studies are needed on the ecological and functional significance of taxa associated to intestinal microbiota dwelling on the mucosa. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-020-00071-3.
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Affiliation(s)
- Yanxian Li
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway.
| | - Leonardo Bruni
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy
| | - Alexander Jaramillo-Torres
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Karina Gajardo
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Trond M Kortner
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Åshild Krogdahl
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
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42
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Huyben D, Rimoldi S, Ceccotti C, Montero D, Betancor M, Iannini F, Terova G. Effect of dietary oil from Camelina sativa on the growth performance, fillet fatty acid profile and gut microbiome of gilthead Sea bream ( Sparus aurata). PeerJ 2020; 8:e10430. [PMID: 33354421 PMCID: PMC7733328 DOI: 10.7717/peerj.10430] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In the last two decades, research has focused on testing cheaper and sustainable alternatives to fish oil (FO), such as vegetable oils (VO), in aquafeeds. However, FO cannot be entirely replaced by VOs due to their lack of omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA), particularly eicosapentaenoic (EPA; 20:5n-3) and docosahexaenoic (DHA; 22:6n-3) acids. The oilseed plant, Camelina sativa, may have a higher potential to replace FO since it can contains up to 40% of the omega-3 precursors α-linolenic acid (ALA; 18:3n-3) and linoleic acid (LA; 18:2n-6). METHODS A 90-day feeding trial was conducted with 600 gilthead sea bream (Sparus aurata) of 32.92 ± 0.31 g mean initial weight fed three diets that replaced 20%, 40% and 60% of FO with CO and a control diet of FO. Fish were distributed into triplicate tanks per diet and with 50 fish each in a flow-through open marine system. Growth performance and fatty acid profiles of the fillet were analysed. The Illumina MiSeq platform for sequencing of 16S rRNA gene and Mothur pipeline were used to identify bacteria in the faeces, gut mucosa and diets in addition to metagenomic analysis by PICRUSt. RESULTS AND CONCLUSIONS The feed conversion rate and specific growth rate were not affected by diet, although final weight was significantly lower for fish fed the 60% CO diet. Reduced final weight was attributed to lower levels of EPA and DHA in the CO ingredient. The lipid profile of fillets were similar between the dietary groups in regards to total saturated, monounsaturated, PUFA (n-3 and n-6), and the ratio of n-3/n-6. Levels of EPA and DHA in the fillet reflected the progressive replacement of FO by CO in the diet and the EPA was significantly lower in fish fed the 60% CO diet, while ALA was increased. Alpha and beta-diversities of gut bacteria in both the faeces and mucosa were not affected by any dietary treatment, although a few indicator bacteria, such as Corynebacterium and Rhodospirillales, were associated with the 60% CO diet. However, lower abundance of lactic acid bacteria, specifically Lactobacillus, in the gut of fish fed the 60% CO diet may indicate a potential negative effect on gut microbiota. PICRUSt analysis revealed similar predictive functions of bacteria in the faeces and mucosa, although a higher abundance of Corynebacterium in the mucosa of fish fed 60% CO diet increased the KEGG pathway of fatty acid synthesis and may act to compensate for the lack of fatty acids in the diet. In summary, this study demonstrated that up to 40% of FO can be replaced with CO without negative effects on growth performance, fillet composition and gut microbiota of gilthead sea bream.
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Affiliation(s)
- David Huyben
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
- Institute of Aquaculture, Faculty of Natural Sciences,, University of Stirling, Stirling, United Kingdom
| | - Simona Rimoldi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Chiara Ceccotti
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Daniel Montero
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Las Palmas, Canary Islands, Spain
| | - Monica Betancor
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Federica Iannini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Genciana Terova
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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Osborne P, Hall LJ, Kronfeld-Schor N, Thybert D, Haerty W. A rather dry subject; investigating the study of arid-associated microbial communities. ENVIRONMENTAL MICROBIOME 2020; 15:20. [PMID: 33902728 PMCID: PMC8067391 DOI: 10.1186/s40793-020-00367-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 11/12/2020] [Indexed: 05/08/2023]
Abstract
Almost one third of Earth's land surface is arid, with deserts alone covering more than 46 million square kilometres. Nearly 2.1 billion people inhabit deserts or drylands and these regions are also home to a great diversity of plant and animal species including many that are unique to them. Aridity is a multifaceted environmental stress combining a lack of water with limited food availability and typically extremes of temperature, impacting animal species across the planet from polar cold valleys, to Andean deserts and the Sahara. These harsh environments are also home to diverse microbial communities, demonstrating the ability of bacteria, fungi and archaea to settle and live in some of the toughest locations known. We now understand that these microbial ecosystems i.e. microbiotas, the sum total of microbial life across and within an environment, interact across both the environment, and the macroscopic organisms residing in these arid environments. Although multiple studies have explored these microbial communities in different arid environments, few studies have examined the microbiota of animals which are themselves arid-adapted. Here we aim to review the interactions between arid environments and the microbial communities which inhabit them, covering hot and cold deserts, the challenges these environments pose and some issues arising from limitations in the field. We also consider the work carried out on arid-adapted animal microbiotas, to investigate if any shared patterns or trends exist, whether between organisms or between the animals and the wider arid environment microbial communities. We determine if there are any patterns across studies potentially demonstrating a general impact of aridity on animal-associated microbiomes or benefits from aridity-adapted microbiomes for animals. In the context of increasing desertification and climate change it is important to understand the connections between the three pillars of microbiome, host genome and environment.
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Affiliation(s)
- Peter Osborne
- Earlham Institute, Norwich Research Park Innovation Centre, Colney Lane, Norwich, NR4 7UZ, UK.
| | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Chair of Intestinal Microbiome, School of Life Sciences, ZIEL - Institute for Food & Health, Technical University of Munich, 85354, Freising, Germany
| | | | - David Thybert
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park Innovation Centre, Colney Lane, Norwich, NR4 7UZ, UK
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44
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Yang S, Wu L, Wu B, Zhang Y, Wang H, Tan X. Diversity and structure of soil microbiota of the Jinsha earthen relic. PLoS One 2020; 15:e0236165. [PMID: 32697804 PMCID: PMC7375591 DOI: 10.1371/journal.pone.0236165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/30/2020] [Indexed: 12/02/2022] Open
Abstract
In order to define the diversity and composition of the microbial communities colonizing of the soil microbiome of the Jinsha earthen relic, we used high-throughput sequencing technology to identify and characterize the microbiota in 22 samples collected from the Jinsha earthen relic in China during 2017 and 2018. We compared the taxonomy of the microbial communities from samples taken at different times and different sites. Our results showed that the identity of the dominant bacterial phyla differed among the samples. Proteobacteria (23–86.2%) were the predominant bacterial phylum in all samples taken from site A in both 2017 and 2018. However, Actinobacteria (21–92.3%) were the most popular bacterial phylum in samples from sites B and C in 2017 and 2018. Ascomycota were identified as the only fungal phyla in samples in 2017. However, the group varied drastically in relative abundance between 2017 and 2018. Functional analysis of the soil bacterial community suggested that abundant members of the microbiota may be associated with metabolism and the specific environment. This report was the first high-throughput sequencing study of the soil of the Jinsha earthen relic microbiome. Since soil microbiota can damage soil and archeological structures, comprehensive analyses of the microbiomes at archeological sites may contribute to the understand of the influence of microorganisms on the degradation of soil, as well as to the identification of potentially beneficial or undesirable members of these microbial communities in archeological sites. The study will be helpful to provide effective data and guidance for the prevention and control of microbial corrosion of the Jinsha earthen relic.
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Affiliation(s)
- Sheng Yang
- Chengdu Institute of Cultural Relics, Chengdu, PR China
| | - Linfeng Wu
- College of Life Sciences, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, PR China
| | - Bin Wu
- Jinsha Site Museum, Chengdu, PR China
| | - Yizheng Zhang
- College of Life Sciences, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, PR China
| | - Haiyan Wang
- College of Life Sciences, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, PR China
| | - Xuemei Tan
- College of Life Sciences, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, PR China
- * E-mail:
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Lai KP, Lin X, Tam N, Ho JCH, Wong MKS, Gu J, Chan TF, Tse WKF. Osmotic stress induces gut microbiota community shift in fish. Environ Microbiol 2020; 22:3784-3802. [PMID: 32618094 DOI: 10.1111/1462-2920.15150] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/29/2020] [Indexed: 12/11/2022]
Abstract
Alteration of the gut microbiota plays an important role in animal health and metabolic diseases. However, little is known with respect to the influence of environmental osmolality on the gut microbial community. The aim of the current study was to determine whether the reduction in salinity affects the gut microbiota and identify its potential role in salinity acclimation. Using Oryzias melastigma as a model organism to perform progressive hypotonic transfer experiments, we evaluated three conditions: seawater control (SW), SW to 50% sea water transfer (SFW) and SW to SFW to freshwater transfer (FW). Our results showed that the SFW and FW transfer groups contained higher operational taxonomic unit microbiota diversities. The dominant bacteria in all conditions constituted the phylum Proteobacteria, with the majority in the SW and SFW transfer gut comprising Vibrio at the genus level, whereas this population was replaced by Pseudomonas in the FW transfer gut. Furthermore, our data revealed that the FW transfer gut microbiota exhibited a reduced renin-angiotensin system, which is important in SW acclimation. In addition, induced detoxification and immune mechanisms were found in the FW transfer gut microbiota. The shift of the bacteria community in different osmolality environments indicated possible roles of bacteria in facilitating host acclimation.
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Affiliation(s)
- Keng Po Lai
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, 541004, China.,Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Xiao Lin
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Nathan Tam
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Jeff Cheuk Hin Ho
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Marty Kwok-Shing Wong
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8564, Japan
| | - Jie Gu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, 212000, China
| | - Ting Fung Chan
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - William Ka Fai Tse
- Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395, Japan
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Weinrauch AM, Folkerts EJ, Blewett TA, Bucking C, Anderson WG. Impacts of low salinity exposure and antibiotic application on gut transport activity in the Pacific spiny dogfish, Squalus acanthias suckleyi. J Comp Physiol B 2020; 190:535-545. [PMID: 32617717 DOI: 10.1007/s00360-020-01291-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/03/2020] [Accepted: 06/18/2020] [Indexed: 12/22/2022]
Abstract
The role of the marine elasmobranch gastrointestinal tract in nitrogen-recycling and osmotic homeostasis has become increasingly apparent, with the gut microbial community likely playing a significant role converting urea, an important osmolyte in elasmobranchs, into ammonia. The Pacific spiny dogfish can experience and tolerate reduced environmental salinities, yet how this environmental challenge may affect the microbiome, and consequently nitrogen transport across the gut, is as of yet unknown. In the present study, excised gut sac preparations were made from dogfish acclimated to the following: full-strength seawater (C), low salinity for 7 days (LS), and after acute transfer of LS-acclimated fish to full-strength SW for 6 h (AT). Significantly reduced microbial derived urease activity was observed in the mucosal saline of gut sac preparations from the LS (by 81%) and AT (by 89%) treatments relative to the C treatment. Microbial derived cellulase activity from mucosal saline samples tended to follow similar patterns. To further ensure an effective decrease in the spiral valve microbial population, an antibiotic cocktail was applied to the mucosal saline used for in vitro measurements of ion, water, and nitrogen flux in these gut sac preparations. This caused a further 57-61% decrease in the mucosal saline urease activity of the C and LS treatments. Overall, we observed relatively little flux across the stomach for all measured parameters aside from water movement, which switched from a net efflux in control fish to a net influx in acutely transferred fish, indicative of drinking. While no significant differences were observed in terms of nitrogen flux (urea or ammonia), we tended to see the accumulation of ammonia in the spiral valve lumen and a switch from efflux to influx of urea in control versus acutely transferred fish. The increased ammonia production likely occurs as a result of heightened metabolism in a challenging environment, while the retention and acquisition of urea is suggestive of nitrogen scavenging under nitrogen-limiting conditions.
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Affiliation(s)
- Alyssa M Weinrauch
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada. .,Bamfield Marine Sciences Centre, Bamfield, BC, V0R 1B0, Canada.
| | - Erik J Folkerts
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.,Bamfield Marine Sciences Centre, Bamfield, BC, V0R 1B0, Canada
| | - Tamzin A Blewett
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.,Bamfield Marine Sciences Centre, Bamfield, BC, V0R 1B0, Canada
| | - Carol Bucking
- Department of Biology, York University, Toronto, ON, M3J 1P3, Canada.,Bamfield Marine Sciences Centre, Bamfield, BC, V0R 1B0, Canada
| | - W Gary Anderson
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.,Bamfield Marine Sciences Centre, Bamfield, BC, V0R 1B0, Canada
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Variations and Potential Factors of Gut Prokaryotic Microbiome During Spawning Migration in Coilia nasus. Curr Microbiol 2020; 77:2802-2812. [PMID: 32583157 DOI: 10.1007/s00284-020-02088-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 06/12/2020] [Indexed: 02/01/2023]
Abstract
Coilia nasus is influenced by various external pressures during spawning migration and these anadromous transitions can lead to specific gut microbiome characteristics that affecting the host biological process. Therefore, the purpose of this study was to determine the variations of components and functions in the gut prokaryotic microbiome during spawning migration as well as the key factors that triggered the changes. The gut microbiome in C. nasus was mainly consisted of Proteobacteria, Bacteroidetes, Firmicutes, Deinococcus-Thermus and Fusobacteria via 16S rRNA Gene Amplicon Sequencing. The relative abundance of Acinetobacter and Clostridium increased, while Corynebacterium, Actinomyces, Bacillus, Klebsiella and Ochrobactrum decreased after entering freshwater, indicated the preference of C. nasus gut microbial members transferred from seawater to freshwater. Additionally, the proportion of Firmicutes significantly decreased and then increased, as well as the arise of some soil bacteria in gut, corresponding to the phenomenon that C. nasus are fasting during the upstream process and refeeding after entering the spawning grounds. The function prediction of gut microbiome was also consistent with the above results. The present study generally demonstrated the gut microbiome dynamics and the significant correlation between the gut microbiome and salinity and feeding behavior in the spawning migration of C. nasus.
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You L, Ying C, Liu K, Zhang X, Lin D, Yin D, Zhang J, Xu P. Changes in the fecal microbiome of the Yangtze finless porpoise during a short-term therapeutic treatment. Open Life Sci 2020; 15:296-310. [PMID: 33817218 PMCID: PMC7988435 DOI: 10.1515/biol-2020-0032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 02/15/2020] [Accepted: 02/18/2020] [Indexed: 01/15/2023] Open
Abstract
The fecal microbiome is an integral part of aquatic mammals, like an inner organ. But we know very little about this inner organ of the threatened aquatic species, Yangtze finless porpoise (YFP). Four YFPs were placed into a purse seine for skin ulceration treatment, and this opportunity was taken to nurse the animals closer. In particular, we collected the feces of the YFPs before and after the paired healing and therapeutic treatment, along with samples of their fish diet and water habitat, to explore the changes in their fecal microbiome. Firmicutes (20.9–96.1%), Proteobacteria (3.8–78.7%), Actinobacteria (0.1–35.0%) and Tenericutes (0.8–17.1%) were the most dominant phyla present in the feces. The proportion of Proteobacteria and Actinobacteria increased after the treatment. Firmicutes showed a significant decrease, and most potential pathogens were absent, which reflected the administration of ciprofloxacin hydrochloride. Moreover, environmental shifts can also contribute to changes in the fecal microbiome. These results indicate that certain microbial interactions can be affected by environmental shifts, dietary changes and health-care treatments, which can also help maintain the internal environment of YFPs. These findings will inform the future enhanced protection and management of endangered YFPs and other vulnerable aquatic animals.
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Affiliation(s)
- Lei You
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Congping Ying
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, Binhu District, Wuxi, Jiangsu, China
| | - Kai Liu
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, Binhu District, Wuxi, Jiangsu, China
| | - Xizhao Zhang
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, Binhu District, Wuxi, Jiangsu, China
| | - Danqing Lin
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, Binhu District, Wuxi, Jiangsu, China
| | - Denghua Yin
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, Binhu District, Wuxi, Jiangsu, China
| | - Jialu Zhang
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, Binhu District, Wuxi, Jiangsu, China
| | - Pao Xu
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, Binhu District, Wuxi, Jiangsu, China
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49
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Element G, Engel K, Neufeld JD, Casselman JM, van Coeverden de Groot P, Greer CW, Walker VK. Seasonal habitat drives intestinal microbiome composition in anadromous Arctic char (Salvelinus alpinus). Environ Microbiol 2020; 22:3112-3125. [PMID: 32363711 PMCID: PMC7496496 DOI: 10.1111/1462-2920.15049] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 04/25/2020] [Indexed: 12/13/2022]
Abstract
Intestinal microbial communities from 362 anadromous Arctic char (Salvelinus alpinus) from the high Arctic Kitikmeot region, Nunavut, Canada, were characterized using high-throughput 16S rRNA gene sequencing. The resulting bacterial communities were compared across four seasonal habitats that correspond to different stages of annual migration. Arctic char intestinal communities differed by sampling site, salinity and stages of freshwater residence. Although microbiota from fish sampled in brackish water were broadly consistent with taxa seen in other anadromous salmonids, they were enriched with putative psychrophiles, including the nonluminous gut symbiont Photobacterium iliopiscarium that was detected in >90% of intestinal samples from these waters. Microbiota from freshwater-associated fish were less consistent with results reported for other salmonids, and highly variable, possibly reflecting winter fasting behaviour of these char. We identified microbiota links to age for those fish sampled during the autumn upriver migration, but little impact of the intestinal content and water microbiota on the intestinal community. The strongest driver of intestinal community composition was seasonal habitat, and this finding combined with identification of psychrophiles suggested that water temperature and migratory behaviour are key to understanding the relationship between Arctic char and their symbionts.
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Affiliation(s)
- Geraint Element
- Department of Biology, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Katja Engel
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - John M Casselman
- Department of Biology, Queen's University, Kingston, ON, K7L 3N6, Canada
| | | | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montreal, QC, H4P 2R2, Canada
| | - Virginia K Walker
- Department of Biology, Queen's University, Kingston, ON, K7L 3N6, Canada.,School of Environmental Studies, Queen's University, Kingston, ON, K7L 3N6, Canada
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Microbial Ecology of Atlantic Salmon (Salmo salar) Hatcheries: Impacts of the Built Environment on Fish Mucosal Microbiota. Appl Environ Microbiol 2020; 86:AEM.00411-20. [PMID: 32303543 DOI: 10.1128/aem.00411-20] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/09/2020] [Indexed: 12/19/2022] Open
Abstract
Successful rearing of fish in hatcheries is critical for conservation, recreational fishing, commercial fishing through wild stock enhancements, and aquaculture production. Flowthrough (FT) hatcheries require more water than recirculating aquaculture systems (RAS), which enable up to 99% of their water to be recycled, thus significantly reducing environmental impacts. Here, we evaluated the biological and physical microbiome interactions of three Atlantic salmon hatcheries (RAS n = 2, FT n = 1). Gill, skin, and digesta from six juvenile fish along with tank biofilms and water were sampled from tanks in each of the hatcheries (60 fish across 10 tanks) to assess the built environment and mucosal microbiota using 16S rRNA gene sequencing. The water and tank biofilm had more microbial richness than fish mucus, while skin and digesta from RAS fish had 2 times the richness of FT fish. Body sites each had unique microbiomes (P < 0.001) and were influenced by hatchery system type (P < 0.001), with RAS being more similar. A strong association between the tank and fish microbiome was observed. Water and tank biofilm richness was positively correlated with skin and digesta richness. Strikingly, the gill, skin, and digesta communities were more similar to that in the origin tank biofilm than those in all other experimental tanks, suggesting that the tank biofilm has a direct influence on fish-associated microbial communities. Lastly, microbial diversity and mucous cell density were positively associated with fish growth and length. The results from this study provide evidence for a link between the tank microbiome and the fish microbiome, with the skin microbiome as an important intermediate.IMPORTANCE Atlantic salmon, Salmo salar, is the most farmed marine fish worldwide, with an annual production of 2,248 million metric tons in 2016. Salmon hatcheries are increasingly changing from flowthrough toward recirculating aquaculture system (RAS) design to accommodate more control over production along with improved environmental sustainability due to lower impacts on water consumption. To date, microbiome studies of hatcheries have focused either on the fish mucosal microbiota or on the built environment microbiota but have not combined the two to understand their interactions. Our study evaluates how the water and tank biofilm microbiota influences the fish microbiota across three mucosal environments (gill, skin, and digesta). Results from this study highlight how the built environment is a unique source of microbes to colonize fish mucus and, furthermore, how this can influence fish health. Further studies can use this knowledge to engineer built environments to modulate fish microbiota for beneficial phenotypes.
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