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Toxqui-Rodríguez S, Estensoro I, Domingo-Bretón R, Del Pozo R, Pérez-Sánchez J, Sipkema D, Sitjà-Bobadilla A, Piazzon MC. Interactions between gilthead seabream intestinal transcriptome and microbiota upon Enteromyxum leei infection: a multi-omic approach. Anim Microbiome 2025; 7:22. [PMID: 40050956 PMCID: PMC11884135 DOI: 10.1186/s42523-025-00388-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Accepted: 02/25/2025] [Indexed: 03/09/2025] Open
Abstract
BACKGROUND The enteric myxozoan parasite Enteromyxum leei is an important problem in gilthead seabream aquaculture invading the intestinal epithelium and leading to chronic intestinal inflammation, poor food conversion rates, cachexia, and mortalities, with no treatments available, resulting in significant economic losses. It is known that myxozoan infections are affected by factors such as temperature, duration of exposure, stocking densities, and seasonality. Gut microbiota has key effects on host health, including disease resistance and immune system training and development, tightly interacting with the host, affecting systemic and local physiological functions. This study aimed to gain insights into the host-microbiota-parasite interactions integrating metataxonomics, host transcriptomics, and metatranscriptomics within this disease model. RESULTS Exposure to E. leei together with temperature and age differences led to alterations in gilthead seabream intestinal microbiota. Samples from 240 g fish kept at 18ºC during a winter trial at 10 weeks post-parasite exposure showed the highest significant changes in their microbial composition with Proteobacteria increasing in abundance from 32.3% in the control group up to 89.8% in the infected group, while Firmicutes and Actinobacteria significantly decreased in relative abundance from 23% and 37.8-2.4% and 1.1%, respectively. After LEfSe analysis, Acinetobacter was identified as the best biomarker for the parasite-exposed group. Parasite exposure also altered the expression of 935 host genes, highlighting genes involved in immune responses such as pathways related to Interleukins, MHCI and Interferons. Microbial transcripts, also showed significant changes upon parasite infection. Integration of the results revealed differential effects on the host induced directly by the parasite or indirectly by parasite-induced microbial shift. CONCLUSIONS Intestinal microbiota and local host gene expression showed significant changes upon en enteromyxosis. The detected activation of the host immune response was not exclusively linked to the parasite infection but also to changes in microbiota, demonstrating the key role of the different components of the mucosal system during disease. These results provided different datasets of bacterial taxa and microbial and host transcripts that will allow a better understanding of host-microbiota-parasite interactions and can serve as starting points for studying and evaluating mucosal health in aquaculture during parasitosis or other diseases.
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Affiliation(s)
- Socorro Toxqui-Rodríguez
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS, CSIC), Castellón, Spain
- Nutrigenomics and Fish Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS, CSIC), Castellón, Spain
| | - Itziar Estensoro
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS, CSIC), Castellón, Spain
| | - Ricardo Domingo-Bretón
- Nutrigenomics and Fish Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS, CSIC), Castellón, Spain
| | - Raquel Del Pozo
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS, CSIC), Castellón, Spain
| | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS, CSIC), Castellón, Spain
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS, CSIC), Castellón, Spain
| | - M Carla Piazzon
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS, CSIC), Castellón, Spain.
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Varela JL, Nikouli E, Medina A, Papaspyrou S, Kormas K. The gills and skin microbiota of five pelagic fish species from the Atlantic Ocean. Int Microbiol 2025; 28:95-105. [PMID: 38740652 PMCID: PMC11775069 DOI: 10.1007/s10123-024-00524-8] [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: 02/16/2024] [Revised: 04/25/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024]
Abstract
The gills and skin microbiota and microbiome of wild fish remain far more under-investigated compared to that of farmed fish species, despite that these animal-microbe interactions hold the same ecophysiological roles in both cases. In this study, the gills and skin bacterial microbiota profiles and their presumptive bacterial metabolisms were investigated in five open-sea fishes: bullet tuna (Auxis sp.), common dolphinfish (Coryphaena hippurus), Atlantic little tunny (Euthynnus alletteratus), Atlantic bonito (Sarda sarda) and Atlantic white marlin (Kajikia albida). Gills and skin tissues were collected from two to three individuals per species, from specimens caught by recreational trolling during summer of 2019, and their bacterial 16S rRNA gene diversity was analysed by high-throughput sequencing. The gills bacterial communities among the five species were clearly different but not the skin bacterial microbiota. The dominant operational taxonomic units belonged to the Moraxellaceae, Pseudomonadaceae, Rhodobacteraceae, Staphylococcaceae and Vibrionaceae families. Despite the differences in taxonomic composition, the presumptive bacterial metabolisms between the gills and skin of the five fishes investigated here were ≥ 94% similar and were dominated by basic metabolism, most likely reflecting the continuous exposure of these tissues in the surrounding seawater.
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Affiliation(s)
- José Luis Varela
- Department of Biology, University of Cádiz, Puerto Real, 11510, Cádiz, Spain
| | - Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece
| | - Antonio Medina
- Department of Biology, University of Cádiz, Puerto Real, 11510, Cádiz, Spain
| | - Sokratis Papaspyrou
- Department of Biology, University of Cádiz, Puerto Real, 11510, Cádiz, Spain
| | - Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece.
- Agricultural Development Institute, University Research and Innovation Centre "IASON", Argonafton & Filellinon, 382 21, Volos, Greece.
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Afful P, Abotsi GK, Adu-Gyamfi CO, Benyem G, Katawa G, Kyei S, Arndts K, Ritter M, Asare KK. Schistosomiasis-Microbiota Interactions: A Systematic Review and Meta-Analysis. Pathogens 2024; 13:906. [PMID: 39452777 PMCID: PMC11510367 DOI: 10.3390/pathogens13100906] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 10/10/2024] [Accepted: 10/12/2024] [Indexed: 10/26/2024] Open
Abstract
INTRODUCTION Schistosomiasis, a tropical disease affecting humans and animals, affected 251.4 million people in 2021. Schistosoma mansoni, S. haematobium, S. intercalatum, and S. japonicum are primary human schistosomes, causing tissue damage, granulomas, ulceration, hemorrhage, and opportunistic pathogen entry. The gut and urinary tract microbiota significantly impact a host's susceptibility to schistosomiasis, disrupting microbial balance; however, this relationship is not well understood. This systematic review and meta-analysis explores the intricate relationship between schistosomiasis and the host's microbiota, providing crucial insights into disease pathogenesis and management. METHODS This systematic review used PRISMA guidelines to identify peer-reviewed articles on schistosomiasis and its interactions with the host microbiome, using multiple databases and Google Scholar, providing a robust dataset for analysis. The study utilized Meta-Mar v3.5.1; descriptive tests, random-effects models, and subgroups were analyzed for the interaction between Schistosomiasis and the microbiome. Forest plots, Cochran's Q test, and Higgins' inconsistency statistic (I2) were used to assess heterogeneity. RESULTS The human Schistosoma species were observed to be associated with various bacterial species isolated from blood, stool, urine, sputum, skin, and vaginal or cervical samples. A meta-analysis of the interaction between schistosomiasis and the host microbiome, based on 31 studies, showed 29,784 observations and 5871 events. The pooled estimates indicated a significant association between schistosomiasis and changes in the microbiome of infected individuals. There was considerable heterogeneity with variance effect sizes (p < 0.0001). Subgroup analysis of Schistosoma species demonstrated that S. haematobium was the most significant contributor to the overall heterogeneity, accounting for 62.1% (p < 0.01). S. mansoni contributed 13.0% (p = 0.02), and the coinfection of S. haematobium and S. mansoni accounted for 16.8% of the heterogeneity (p < 0.01), contributing to the variability seen in the pooled analysis. Similarly, praziquantel treatment (RR = 1.68, 95% CI: 1.07-2.64) showed high heterogeneity (Chi2 = 71.42, df = 11, p < 0.01) and also indicated that Schistosoma infections in males (RR = 1.46, 95% CI: 0.00 to 551.30) and females (RR = 2.09, 95% CI: 0.24 to 18.31) have a higher risk of altering the host microbiome. CONCLUSIONS Schistosomiasis significantly disrupts the host microbiota across various bodily sites, leading to increased susceptibility to different bacterial taxa such as E. coli, Klebsiella, Proteus, Pseudomonas, Salmonella, Staphylococcus, Streptococcus, and Mycobacterium species (M. tuberculosis and M. leprae). This disruption enables these bacteria to produce toxic metabolites, which in turn cause inflammation and facilitate the progression of disease. The impact of schistosomiasis on the vaginal microbiome underscores the necessity for gender-specific approaches to treatment and prevention. Effective management of female genital schistosomiasis (FGS) requires addressing both the parasitic infection and the resulting microbiome imbalances. Additionally, praziquantel-treated individuals have different microbiome compositions compared to individuals with no praziquantel treatment. This suggests that combining praziquantel treatment with probiotics could potentially decrease the disease severity caused by an altered microbiome.
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Affiliation(s)
- Philip Afful
- Biomedical and Clinical Research Centre, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana; (P.A.); (G.K.A.); (C.O.A.-G.); (G.B.); (S.K.)
| | - Godwin Kwami Abotsi
- Biomedical and Clinical Research Centre, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana; (P.A.); (G.K.A.); (C.O.A.-G.); (G.B.); (S.K.)
| | - Czarina Owusua Adu-Gyamfi
- Biomedical and Clinical Research Centre, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana; (P.A.); (G.K.A.); (C.O.A.-G.); (G.B.); (S.K.)
| | - George Benyem
- Biomedical and Clinical Research Centre, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana; (P.A.); (G.K.A.); (C.O.A.-G.); (G.B.); (S.K.)
| | - Gnatoulma Katawa
- Unité de Recherche en Immunologie et Immunomodulation (UR2IM)/Laboratoire de Microbiologie et de Contrôle de Qualité des Denrées Alimentaires (LAMICODA), Ecole Supérieure des Techniques Biologiques et Alimentaires, Université de Lomé, Lomé, Togo;
| | - Samuel Kyei
- Biomedical and Clinical Research Centre, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana; (P.A.); (G.K.A.); (C.O.A.-G.); (G.B.); (S.K.)
- Department of Optometry and Vision Science, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Kathrin Arndts
- Institute for Medical Microbiology, Immunology, and Parasitology (IMMIP), University Hospital Bonn (UKB), 53127 Bonn, Germany;
- German-West African Centre for Global Health and Pandemic Prevention (G-WAC), Partner Site Bonn, 53127 Bonn, Germany
| | - Manuel Ritter
- Institute for Medical Microbiology, Immunology, and Parasitology (IMMIP), University Hospital Bonn (UKB), 53127 Bonn, Germany;
- German-West African Centre for Global Health and Pandemic Prevention (G-WAC), Partner Site Bonn, 53127 Bonn, Germany
| | - Kwame Kumi Asare
- Biomedical and Clinical Research Centre, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana; (P.A.); (G.K.A.); (C.O.A.-G.); (G.B.); (S.K.)
- Department of Biomedical Sciences, School of Allied Health Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
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Yuan S, Sun M, Ma D, Guo X, Wang Z, Niu J, Jiang W, He Y, Wei M, Qi J. Exploring the underlying mechanisms of enteritis impact on golden pompano (Trachinotus ovatus) through multi-omics analysis. FISH & SHELLFISH IMMUNOLOGY 2024; 150:109616. [PMID: 38734118 DOI: 10.1016/j.fsi.2024.109616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/28/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Enteritis posed a significant health challenge to golden pompano (Trachinotus ovatus) populations. In this research, a comprehensive multi-omics strategy was implemented to elucidate the pathogenesis of enteritis by comparing both healthy and affected golden pompano. Histologically, enteritis was characterized by villi adhesion and increased clustering after inflammation. Analysis of the intestinal microbiota revealed a significant increase (P < 0.05) in the abundance of specific bacterial strains, including Photobacterium and Salinivibrio, in diseased fish compared to the healthy group. Metabolomic analysis identified 5479 altered metabolites, with significant impacts on terpenoid and polyketide metabolism, as well as lipid metabolism (P < 0.05). Additionally, the concentrations of several compounds such as calcitetrol, vitamin D2, arachidonic acid, and linoleic acid were significantly reduced in the intestines of diseased fish post-enteritis (P < 0.05), with the detection of harmful substances such as Efonidipine. In transcriptomic profiling, enteritis induced 68 upregulated and 73 downregulated genes, predominantly affecting steroid hormone receptor activity (P < 0.05). KEGG pathway enrichment analysis highlighted upregulation of SQLE and CYP51 in steroidogenesis, while the HSV-1 associated MHC1 gene exhibited significant downregulation. Integration of multi-omics results suggested a potential pathogenic mechanism: enteritis may have resulted from concurrent infection of harmful bacteria, specifically Photobacterium and Salinivibrio, along with HSV-1. Efonidipine production within the intestinal tract may have blocked certain calcium ion channels, leading to downregulation of MHC1 gene expression and reduced extracellular immune recognition. Upregulation of SQLE and CYP51 genes stimulated steroid hormone synthesis within cells, which, upon binding to G protein-coupled receptors, influenced calcium ion transport, inhibited immune activation reactions, and further reduced intracellular synthesis of anti-inflammatory substances like arachidonic acid. Ultimately, this cascade led to inflammation progression, weakened intestinal peristalsis, and villi adhesion. This study utilized multi-level omics detection to investigate the pathological symptoms of enteritis and proposed a plausible pathogenic mechanism, providing innovative insights into enteritis verification and treatment in offshore cage culture of golden pompano.
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Affiliation(s)
- Shipeng Yuan
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute / MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China; Qingdao Marine Science and Technology Center, Qingdao, 266003, China
| | - Minmin Sun
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute / MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Di Ma
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute / MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Xiaodan Guo
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute / MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Zhuoyu Wang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute / MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Jingjing Niu
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute / MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Weiming Jiang
- Guangxi Academy of Fishery Sciences, No.8,Qingshan Load, Nanning, Guangxi, 530021, China
| | - Yan He
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute / MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Mingli Wei
- Guangxi Academy of Fishery Sciences, No.8,Qingshan Load, Nanning, Guangxi, 530021, China.
| | - Jie Qi
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute / MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
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Zou Y, Zhang Y, Wu D, Lu Z, Xiao J, Huang H, Fu Q, Guo Z. Multi-omics analysis revealed the differences in lipid metabolism of the gut between adult and juvenile yellowfin tuna ( Thunnus albacares). Front Microbiol 2024; 14:1326247. [PMID: 38274759 PMCID: PMC10808786 DOI: 10.3389/fmicb.2023.1326247] [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: 10/23/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction Tuna has a cost-effective energy supply to support the regional endothermic and high-speed swimming performance. The gut symbiotic microbiotas and their metabolites play essential roles in tuna's diet digestion, absorption, and energy acquirement, which are often highly related to the ontogenetic development of tuna. Methods We compared gut microbial compositions and metabolites, as well as mRNA expression of the intestine between juvenile and adult yellowfin tuna using 16S rRNA sequencing, metabolomic and transcriptomic, respectively. Results and discussion The results revealed that adults had a significantly higher microbial diversity and abundance of Acinetobacter than juveniles. Regarding the gut microbiota-derived metabolites, fatty acids, especially glycerophospholipid and sphingolipid, were significantly enriched in adults than in juveniles. Moreover, the short-chain fatty acid (butyrate and isobutyrate) contents were significantly higher in adults than in juveniles. To find the relationship between gut microbiotas and host physiology, intestinal transcriptome analysis demonstrated that the enriched pathways of differential expression genes (DEGs) in adult tuna were the lipid metabolism pathway, including "fat digestion and absorption," "cholesterol metabolism," "steroid hormone biosynthesis," "glycerolipid metabolism," and "glycerophospholipid metabolism." However, protein digestion and absorption and pancreatic secretion pathways were significantly enriched in the juveniles. The conjoint analysis indicated that the enriched pathways of both differential metabolites (DMs) and DEGs were remarkably related to the regulation of glycerophospholipids metabolism in adult tunas. This study highlights the role of gut microbiotas in fish nutrition metabolism. These findings provide new insights into the view of ontogenetic shifts of gut microbiotas and their metabolites on host health and gut function in endothermic and high-speed swimming marine fish species.
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Affiliation(s)
- Ying Zou
- School of Life and Health Sciences, School of Marine Science and Engineering, School of Food Science and Engineering, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Yanjie Zhang
- School of Life and Health Sciences, School of Marine Science and Engineering, School of Food Science and Engineering, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Di Wu
- School of Life and Health Sciences, School of Marine Science and Engineering, School of Food Science and Engineering, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Zhiyuan Lu
- School of Life and Health Sciences, School of Marine Science and Engineering, School of Food Science and Engineering, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Juan Xiao
- School of Life and Health Sciences, School of Marine Science and Engineering, School of Food Science and Engineering, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Hai Huang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China
| | - Qiongyao Fu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Control of Tropical Diseases, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Zhiqiang Guo
- School of Life and Health Sciences, School of Marine Science and Engineering, School of Food Science and Engineering, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
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Ochoa-Sánchez M, Acuña Gomez EP, Ramírez-Fenández L, Eguiarte LE, Souza V. Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project. PeerJ 2023; 11:e15978. [PMID: 37810788 PMCID: PMC10557944 DOI: 10.7717/peerj.15978] [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: 03/28/2023] [Accepted: 08/07/2023] [Indexed: 10/10/2023] Open
Abstract
Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.
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Affiliation(s)
- Manuel Ochoa-Sánchez
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Lia Ramírez-Fenández
- Facultad de Recursos Naturales Renovables, Universidad Arturo Prat, Iquique, Chile
- Centro de Desarrollo de Biotecnología Industrial y Bioproductos, Antofagasta, Chile
| | - Luis E. Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Valeria Souza
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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Minich JJ, Härer A, Vechinski J, Frable BW, Skelton ZR, Kunselman E, Shane MA, Perry DS, Gonzalez A, McDonald D, Knight R, Michael TP, Allen EE. Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species. Nat Commun 2022; 13:6978. [PMID: 36396943 PMCID: PMC9671965 DOI: 10.1038/s41467-022-34557-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 10/28/2022] [Indexed: 11/18/2022] Open
Abstract
Fish are the most diverse and widely distributed vertebrates, yet little is known about the microbial ecology of fishes nor the biological and environmental factors that influence fish microbiota. To identify factors that explain microbial diversity patterns in a geographical subset of marine fish, we analyzed the microbiota (gill tissue, skin mucus, midgut digesta and hindgut digesta) from 101 species of Southern California marine fishes, spanning 22 orders, 55 families and 83 genera, representing ~25% of local marine fish diversity. We compare alpha, beta and gamma diversity while establishing a method to estimate microbial biomass associated with these host surfaces. We show that body site is the strongest driver of microbial diversity while microbial biomass and diversity is lowest in the gill of larger, pelagic fishes. Patterns of phylosymbiosis are observed across the gill, skin and hindgut. In a quantitative synthesis of vertebrate hindguts (569 species), we also show that mammals have the highest gamma diversity when controlling for host species number while fishes have the highest percent of unique microbial taxa. The composite dataset will be useful to vertebrate microbiota researchers and fish biologists interested in microbial ecology, with applications in aquaculture and fisheries management.
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Affiliation(s)
- Jeremiah J Minich
- The Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
| | - Andreas Härer
- School of Biological Sciences, Department of Ecology, Behavior, & Evolution, University of California San Diego, La Jolla, CA, 92093, USA
| | - Joseph Vechinski
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0244, USA
| | - Benjamin W Frable
- Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0244, USA
| | - Zachary R Skelton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - Emily Kunselman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0244, USA
| | - Michael A Shane
- Hubbs-SeaWorld Research Institute, 2595 Ingraham Street, San Diego, CA, 92109, USA
| | - Daniela S Perry
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
- Center for Microbiome Innovation, University of San Diego, California, La Jolla, CA, 92093, USA
- Department of Computer Science, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Todd P Michael
- The Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Eric E Allen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0244, USA
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
- Center for Microbiome Innovation, University of San Diego, California, La Jolla, CA, 92093, USA
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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Succession of the intestinal bacterial community in Pacific bluefin tuna (Thunnus orientalis) larvae. PLoS One 2022; 17:e0275211. [PMID: 36201490 PMCID: PMC9536584 DOI: 10.1371/journal.pone.0275211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
We investigated the succession process of intestinal bacteria during seed production in full-cycle aquaculture of Pacific bluefin tuna (Thunnus orientalis). During the seed production, eggs, healthy fish, rearing water, and feeds from three experimental rounds in 2012 and 2013 were collected before transferring to offshore net cages and subjected to a fragment analysis of the bacterial community structure. We identified a clear succession of intestinal bacteria in bluefin tuna during seed production. While community structures of intestinal bacteria in the early stage of larvae were relatively similar to those of rearing water and feed, the bacterial community structures seen 17 days after hatching were different. Moreover, although intestinal bacteria in the late stage of larvae were less diverse than those in the early stage of larvae, the specific bacteria were predominant, suggesting that the developed intestinal environment of the host puts selection pressure on the bacteria in the late stage. The specific bacteria in the late stage of larvae, which likely composed 'core microbiota', were also found on the egg surface. The present study highlights that proper management of the seed production process, including the preparation of rearing water, feeds, and fish eggs, is important for the aquaculture of healthy fish.
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Gadoin E, Desnues C, d'Orbcastel ER, Bouvier T, Auguet JC, Dagorn L, Moroh JL, Adingra A, Bettarel Y. Fishing for the Microbiome of Tropical Tuna. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02096-4. [PMID: 35962839 DOI: 10.1007/s00248-022-02096-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Although tunas represent a significant part of the global fish economy and a major nutritional resource worldwide, their microbiome still remains poorly documented. Here, we conducted an analysis of the taxonomic composition of the bacterial communities inhabiting the gut, skin, and liver of two most consumed tropical tuna species (skipjack and yellowfin), from individuals caught in the Atlantic and Indian oceans. We hypothesized that each organ harbors a specific microbial assemblage whose composition might vary according to different biotic (sex, species) and/or abiotic (environmental) factors. Our results revealed that the composition of the tuna microbiome was totally independent of fish sex, regardless of the species and ocean considered. Instead, the main determinants of observed diversity were (i) tuna species for the gut and (ii) sampling site for the skin mucus layer and (iii) a combination of both parameters for the liver. Interestingly, 4.5% of all amplicon sequence variants (ASV) were shared by the three organs, highlighting the presence of a core-microbiota whose most abundant representatives belonged to the genera Mycoplasma, Cutibacterium, and Photobacterium. Our study also revealed the presence of a unique and diversified bacterial assemblage within the tuna liver, comprising a substantial proportion of potential histamine-producing bacteria, well known for their pathogenicity and their contribution to fish poisoning cases. These results indicate that this organ is an unexplored microbial niche whose role in the health of both the host and consumers remains to be elucidated.
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Affiliation(s)
- Elsa Gadoin
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Place Eugène Bataillon - Bat 24, 34095, Montpellier, France
| | - Christelle Desnues
- Institut Méditerranéen d'Océanologie (MIO), Aix-Marseille Université, Université de Toulon, CNRS, Campus Technologique Et Scientifique de Luminy, 163 avenue de Luminy - Bat. Méditerranée, 13288, Marseille, IRD, France
| | - Emmanuelle Roque d'Orbcastel
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Place Eugène Bataillon - Bat 24, 34095, Montpellier, France
| | - Thierry Bouvier
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Place Eugène Bataillon - Bat 24, 34095, Montpellier, France
| | - Jean-Christophe Auguet
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Place Eugène Bataillon - Bat 24, 34095, Montpellier, France
| | - Laurent Dagorn
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Place Eugène Bataillon - Bat 24, 34095, Montpellier, France
| | - Jean-Luc Moroh
- Université Peleforo Gbon Coulibaly, Korhogo, Ivory Coast
| | - Antoinette Adingra
- Centre de Recherches Océanologiques (CRO) - 29 rue des pêcheurs, Zone 3, Treichville, BP V 18 00225, Abidjan, Ivory Coast
| | - Yvan Bettarel
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Place Eugène Bataillon - Bat 24, 34095, Montpellier, France.
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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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