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Ginevra L, Charlotte S, Hayley C, Fanny H, Deirdre B, Jean-François F, Graham CT, George IF. Do fish gut microbiotas vary across spatial scales? A case study of Diplodus vulgaris in the Mediterranean Sea. Anim Microbiome 2024; 6:32. [PMID: 38872229 DOI: 10.1186/s42523-024-00319-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/29/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Biogeography has been linked to differences in gut microbiota in several animals. However, the existence of such a relationship in fish is not clear yet. So far, it seems to depend on the fish species studied. However, most studies of fish gut microbiotas are based on single populations. In this study, we investigated the gut microbiota of fish from three wild populations of the two-banded sea bream Diplodus vulgaris (Geoffroy Saint-Hilaire, 1817) to determine whether its diversity, structure and potential functionality reflect the geographic origin of the fish, at large and small geographical scale. Additionally, we explored the host- and environmental-related factors explaining this relationship. RESULTS We showed that the taxonomy and potential functionality of the mucosa-associated gut microbiota of Diplodus vulgaris differ to varying degrees depending on the spatial scale considered. At large scale, we observed that both the taxonomical structure and the potential functionality of the fish microbiota differed significantly between populations. In contrast, the taxonomical diversity of the microbial community displayed a significant relationship with factors other than the geographic origin of the fish (i.e. sampling date). On the other hand, at small scale, the different composition and diversity of the microbiota differ according to the characteristics of the habitat occupied by the fish. Specifically, we identified the presence of Posidonia oceanica in the benthic habitat as predictor of both the microbiota composition and diversity. Lastly, we reported the enrichment of functions related to the metabolism of xenobiotics (i.e. drugs and 4-aminobenzoate) in a population and we indicated it as a potential target of future monitoring. CONCLUSIONS With this study, we confirmed the importance of investigating the gut microbiota of wild fish species using multiple populations, taking into account the different habitats occupied by the individuals. Furthermore, we underscored the use of the biodegradation potential of the gut microbiota as an alternative means of monitoring emerging contaminants in Mediterranean fish.
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Affiliation(s)
- Lilli Ginevra
- Laboratoire d'Ecologie des Systèmes Aquatiques (ESA), Université Libre de Bruxelles (ULB), 1050, Brussels, Belgium.
| | - Sirot Charlotte
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), University of Perpignan, Perpignan, France
| | - Campbell Hayley
- Marine and Freshwater Research Centre, Atlantic Technological University, Dublin Road, Galway, Ireland
| | - Hermand Fanny
- Laboratoire d'Ecologie des Systèmes Aquatiques (ESA), Université Libre de Bruxelles (ULB), 1050, Brussels, Belgium
| | - Brophy Deirdre
- Marine and Freshwater Research Centre, Atlantic Technological University, Dublin Road, Galway, Ireland
| | - Flot Jean-François
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels - (IB)², 1050, Brussels, Belgium
| | - Conor T Graham
- Marine and Freshwater Research Centre, Atlantic Technological University, Dublin Road, Galway, Ireland
| | - Isabelle F George
- Laboratoire d'Ecologie des Systèmes Aquatiques (ESA), Université Libre de Bruxelles (ULB), 1050, Brussels, Belgium
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2
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Ziab M, Chaganti SR, Heath DD. The effects of host quantitative genetic architecture on the gut microbiota composition of Chinook salmon (Oncorhynchus tshawytscha). Heredity (Edinb) 2023; 131:43-55. [PMID: 37179383 PMCID: PMC10313681 DOI: 10.1038/s41437-023-00620-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
The microbiota consists of microbes living in or on an organism and has been implicated in host health and function. Environmental and host-related factors were shown to shape host microbiota composition and diversity in many fish species, but the role of host quantitative architecture across populations and among families within a population is not fully characterized. Here, Chinook salmon were used to determine if inter-population differences and additive genetic variation within populations influenced the gut microbiota diversity and composition. Specifically, hybrid stocks of Chinook salmon were created by crossing males from eight populations with eggs from an inbred line created from self-fertilized hermaphrodite salmon. Based on high-throughput sequencing of the 16S rRNA gene, significant gut microbial community diversity and composition differences were found among the hybrid stocks. Furthermore, additive genetic variance components varied among hybrid stocks, indicative of population-specific heritability patterns, suggesting the potential to select for specific gut microbiota composition for aquaculture purposes. Determining the role of host genetics in shaping their gut microbiota has important implications for predicting population responses to environmental changes and will thus impact conservation efforts for declining populations of Chinook salmon.
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Affiliation(s)
- Mubarak Ziab
- Great Lakes Institute for Environmental Research (GLIER), University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research (GLIER), University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada.
- Department of Integrative Biology, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada.
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3
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Shi Q, Li Y, Deng S, Zhang H, Jiang H, Shen L, Pan T, Hong P, Wu H, Shu Y. The succession of gut microbiota in the concave-eared torrent frog ( Odorrana tormota) throughout developmental history. Ecol Evol 2023; 13:e10094. [PMID: 37214611 PMCID: PMC10199338 DOI: 10.1002/ece3.10094] [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: 03/13/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
The gut microbiota of amphibians plays a crucial role in maintaining health and adapting to various developmental stages. The composition of gut microbial community is influenced by the phylogeny, habitat, diet, and developmental stage of the host. The present study analyzed the microbiota in the intestine of O. tormota at 11 developmental stages (from the tadpole at Gosner stage 24 to the 3-year-old adult) using high-throughput 16S rRNA sequencing. Alpha diversity index analysis of the microbiota revealed that the index decreased from tadpole at Gosner stage 24 to adult frog stage, remained stable during the adult frog stages, but increased significantly at the early metamorphosis and hibernation preparation stages. The gut microbiota structure is similar in adult frogs but differs significantly in other developmental stages. Furthermore, the dominant phyla of gut microbiota in tadpoles were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, whereas those in adult frogs were Proteobacteria, Firmicutes, Bacteroidetes, and Verrucomicrobia. Host and environmental factors jointly affected the gut microbial diversity and community composition of O. tormota, but developmental stage, feeding habit, and habitat type had a more significant influence. The microbial community in the gut varies with the developmental stage of the host and constantly adapts to the survival requirements of the host. These findings advance our understanding of the evolutionary mechanism of amphibian gut microbiota in maintaining health homeostasis and adaptation.
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Affiliation(s)
- Qingkai Shi
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Yue Li
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Shuaitao Deng
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
- Shanghai Wildlife and Protected Natural Areas Research CenterShanghaiChina
| | - Huijuan Zhang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Huiling Jiang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Liang Shen
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Tao Pan
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Pei Hong
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Hailong Wu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Yilin Shu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
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Chouayekh H, Farhat-Khemakhem A, Karray F, Boubaker I, Mhiri N, Abdallah MB, Alghamdi OA, Guerbej H. Effects of Dietary Supplementation with Bacillus amyloliquefaciens US573 on Intestinal Morphology and Gut Microbiota of European Sea Bass. Probiotics Antimicrob Proteins 2023; 15:30-43. [PMID: 35933471 DOI: 10.1007/s12602-022-09974-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2022] [Indexed: 01/18/2023]
Abstract
Probiotics or direct-fed microbials (DFM) have proven strong potential for improving aquaculture sustainability. This study aims to evaluate the effects of dietary supplementation with the DFM Bacillus amyloliquefaciens US573 on growth performance, intestinal morphology, and gut microbiota (GM) of European sea bass. For this purpose, healthy fish were divided into two feeding trials in triplicate of 25 fish in each tank. The fish were fed with a control basal diet or a DFM-supplemented diet for 42 days. Results showed that, while no significant effects on growth performance were observed, the length and abundance of villi were higher in the DFM-fed group. The benefic effects of DFM supplementation included also the absence of cysts formation and the increase in number of goblet cells playing essential role in immune response. Through DNA metabarcoding analysis of GM, 5 phyla and 14 major genera were identified. At day 42, the main microbiome changes in response to B. amyloliquefaciens US573 addition included the significant decrease in abundance of Actinobacteria phylum that perfectly correlates with a decrease in Nocardia genus representatives which represent serious threat in marine and freshwater fish. On the contrary, an obvious dominance of Betaproteobacteria associated with the abundance in Variovorax genus members, known for their ability to metabolize numerous substrates, was recorded. Interestingly, Firmicutes, particularly species affiliated to the genus Sporosarcina with recent promising probiotic potential, were identified as the most abundant. These results suggest that B. amyloliquefaciens US573 can be effectively recommended as health-promoting DFM in European sea bass farming.
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Affiliation(s)
- Hichem Chouayekh
- Department of Biological Sciences, College of Science, University of Jeddah, Asfan Road, 21959, P.O. Box 34, Jeddah, Kingdom of Saudi Arabia. .,Laboratory of Microbial Biotechnology, Enzymatic and Biomolecules (LMBEB), Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, Road Sidi Mansour 6 km, Sfax, 3018, Tunisia.
| | - Ameny Farhat-Khemakhem
- Laboratory of Microbial Biotechnology, Enzymatic and Biomolecules (LMBEB), Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, Road Sidi Mansour 6 km, Sfax, 3018, Tunisia
| | - Fatma Karray
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, Road Sidi Mansour 6 km, Sfax, 3018, Tunisia
| | - Insaf Boubaker
- Laboratory of Microbial Biotechnology, Enzymatic and Biomolecules (LMBEB), Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, Road Sidi Mansour 6 km, Sfax, 3018, Tunisia
| | - Najla Mhiri
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, Road Sidi Mansour 6 km, Sfax, 3018, Tunisia
| | - Manel Ben Abdallah
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, Road Sidi Mansour 6 km, Sfax, 3018, Tunisia
| | - Othman A Alghamdi
- Department of Biological Sciences, College of Science, University of Jeddah, Asfan Road, 21959, P.O. Box 34, Jeddah, Kingdom of Saudi Arabia
| | - Hamadi Guerbej
- National Institute of Sea Sciences and Technologies, Monastir, Tunisia
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Kormas K, Nikouli E, Kousteni V, Damalas D. Midgut Bacterial Microbiota of 12 Fish Species from a Marine Protected Area in the Aegean Sea (Greece). MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02154-x. [PMID: 36529834 DOI: 10.1007/s00248-022-02154-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Fish microbiome science is progressing fast, but it is biased toward farmed or laboratory fish species against natural fish populations, which remain considerably underinvestigated. We analyzed the midgut bacterial microbiota of 45 specimens of 12 fish species collected from the Gyaros Island marine protected area (Aegean Sea, Greece). The species belong to seven taxonomic families and are either herbivores or omnivores. Mucosa midgut bacterial diversity was assessed by amplicon metabarcoding of the 16S rRNA V3-V4 gene region. A total of 854 operational taxonomic units (OTUs) were identified. In each fish species, between 2 and 18 OTUs dominated with cumulative relative abundance ≥ 70%. Most of the dominating bacterial taxa have been reported to occur both in wild and farmed fish populations. The midgut bacterial communities were different among the 12 fish species, except for Pagrus pagrus and Pagellus erythrinus, which belong to the Sparidae family. No differentiation of the midgut bacterial microbiota was found based on feeding habits, i.e., omnivorous vs. carnivorous. Comparing wild and farmed P. pagrus midgut bacterial microbiota revealed considerable variation between them. Our results expand the gut microbiota of wild fish and support the host species effect as the more likely factor shaping intestinal bacterial microbiota.
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Affiliation(s)
- Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, 384 46, Volos, Greece.
| | - Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, University of Thessaly, 384 46, Volos, Greece
| | - Vasiliki Kousteni
- Institute of Marine Biological Resources and Inland Waters, Hellenic Centre for Marine Research, 710 03, Heraklion, Greece
- Fisheries Research Institute, Hellenic Agricultural Organization - Demeter, 640 07, Nea Peramos, Greece
| | - Dimitrios Damalas
- Institute of Marine Biological Resources and Inland Waters, Hellenic Centre for Marine Research, 710 03, Heraklion, Greece
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Al-Ashhab A, Alexander-Shani R, Avrahami Y, Ehrlich R, Strem RI, Meshner S, Shental N, Sharon G. Sparus aurata and Lates calcarifer skin microbiota under healthy and diseased conditions in UV and non-UV treated water. Anim Microbiome 2022; 4:42. [PMID: 35729615 PMCID: PMC9210813 DOI: 10.1186/s42523-022-00191-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/10/2022] [Indexed: 11/15/2022] Open
Abstract
Background The welfare of farmed fish is influenced by numerous environmental and management factors. Fish skin is an important site for immunity and a major route by which infections are acquired. The objective of this study was to characterize bacterial composition variability on skin of healthy, diseased, and recovered Gilthead Seabream (Sparus aurata) and Barramundi (Lates calcarifer). S. aurata, which are highly sensitive to gram-negative bacteria, were challenged with Vibrio harveyi. In addition, and to provide a wider range of infections, both fish species (S. aurata and L. calcarifer) were infected with gram-positive Streptococcus iniae, to compare the response of the highly sensitive L. calcarifer to that of the more resistant S. aurata. All experiments also compared microbial communities found on skin of fish reared in UV (a general practice used in aquaculture) and non-UV treated water tanks. Results Skin swab samples were taken from different areas of the fish (lateral lines, abdomen and gills) prior to controlled infection, and 24, 48 and 72 h, 5 days, one week and one-month post-infection. Fish skin microbial communities were determined using Illumina iSeq100 16S rDNA for bacterial sequencing. The results showed that naturally present bacterial composition is similar on all sampled fish skin sites prior to infection, but the controlled infections (T1 24 h post infection) altered the bacterial communities found on fish skin. Moreover, when the naturally occurring skin microbiota did not quickly recover, fish mortality was common following T1 (24 h post infection). We further confirmed the differences in bacterial communities found on skin and in the water of fish reared in non-UV and UV treated water under healthy and diseased conditions. Conclusions Our experimental findings shed light on the fish skin microbiota in relation to fish survival (in diseased and healthy conditions). The results can be harnessed to provide management tools for commercial fish farmers; predicting and preventing fish diseases can increase fish health, welfare, and enhance commercial fish yields. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00191-y.
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7
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Naya-Català F, Piazzon MC, Torrecillas S, Toxqui-Rodríguez S, Calduch-Giner JÀ, Fontanillas R, Sitjà-Bobadilla A, Montero D, Pérez-Sánchez J. Genetics and Nutrition Drive the Gut Microbiota Succession and Host-Transcriptome Interactions through the Gilthead Sea Bream ( Sparus aurata) Production Cycle. BIOLOGY 2022; 11:1744. [PMID: 36552254 PMCID: PMC9774573 DOI: 10.3390/biology11121744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
Fish genetically selected for growth (GS) and reference (REF) fish were fed with CTRL (15% FM, 5-7% FO) or FUTURE (7.5% FM, 10% poultry meal, 2.2% poultry oil + 2.5% DHA-algae oil) diets during a 12-months production cycle. Samples from initial (t0; November 2019), intermediate (t1; July 2020) and final (t2; November 2020) sampling points were used for Illumina 16S rRNA gene amplicon sequencing of the adherent microbiota of anterior intestine (AI). Samples from the same individuals (t1) were also used for the gene expression profiling of AI by RNA-seq, and subsequent correlation analyses with microbiota abundances. Discriminant analyses indicated the gut bacterial succession along the production cycle with the proliferation of some valuable taxa for facing seasonality and different developmental stages. An effect of genetic background was evidenced along time, decreasing through the progression of the trial, namely the gut microbiota of GS fish was less influenced by changes in diet composition. At the same time, these fish showed wider transcriptomic landmarks in the AI to cope with these changes. Our results highlighted an enhanced intestinal sphingolipid and phospholipid metabolism, epithelial turnover and intestinal motility in GS fish, which would favour their improved performance despite the lack of association with changes in gut microbiota composition. Furthermore, in GS fish, correlation analyses supported the involvement of different taxa with the down-regulated expression of pro-inflammatory markers and the boosting of markers of extracellular remodelling and response to bacterium. Altogether, these findings support the combined action of the gut microbiome and host transcriptionally mediated effects to preserve and improve gut health and function in a scenario of different growth performance and potentiality.
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Affiliation(s)
- Fernando Naya-Català
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | - M Carla Piazzon
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | - Silvia Torrecillas
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Crta. Taliarte s/n, 35214 Telde, Las Palmas, Canary Islands, Spain
| | - Socorro Toxqui-Rodríguez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | - Josep À Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | | | - Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | - Daniel Montero
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Crta. Taliarte s/n, 35214 Telde, Las Palmas, Canary Islands, Spain
| | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
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Draft Genome Sequence of Delftia tsuruhatensis Strain 45.2.2, Colonizer of Zebrafish, Danio rerio, Skin Mucus. Microbiol Resour Announc 2022; 11:e0066622. [PMCID: PMC9670938 DOI: 10.1128/mra.00666-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Delftia tsuruhatensis strain 45.2.2 is a member of the zebrafish, Danio rerio, skin mucus microbiota. Its genome is similar in size and GC content to those of other Delftia strains.
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Quero GM, Piredda R, Basili M, Maricchiolo G, Mirto S, Manini E, Seyfarth AM, Candela M, Luna GM. Host-associated and Environmental Microbiomes in an Open-Sea Mediterranean Gilthead Sea Bream Fish Farm. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02120-7. [PMID: 36205738 DOI: 10.1007/s00248-022-02120-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Gilthead seabream is among the most important farmed fish species in the Mediterranean Sea. Several approaches are currently applied to assure a lower impact of diseases and higher productivity, including the exploration of the fish microbiome and its manipulation as a sustainable alternative to improve aquaculture practices. Here, using 16S rRNA gene high-throughput sequencing, we explored the microbiome of farmed seabream to assess similarities and differences among microbial assemblages associated to different tissues and compare them with those in the surrounding environment. Seabream had distinct associated microbiomes according to the tissue and compared to the marine environment. The gut hosted the most diverse microbiome; different sets of dominant ASVs characterized the environmental and fish samples. The similarity between fish and environmental microbiomes was higher in seawater than sediment (up to 7.8 times), and the highest similarity (3.9%) was observed between gill and seawater, suggesting that gills are more closely interacting with the environment. We finally analyzed the potential connections occurring among microbiomes. These connections were relatively low among the host's tissues and, in particular, between the gut and the others fish-related microbiomes; other tissues, including skin and gills, were found to be the most connected microbiomes. Our results suggest that, in mariculture, seabream microbiomes reflect only partially those in their surrounding environment and that the host is the primary driver shaping the seabream microbiome. These data provide a step forward to understand the role of the microbiome in farmed fish and farming environments, useful to enhance disease control, fish health, and environmental sustainability.
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Affiliation(s)
- Grazia Marina Quero
- Institute for Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy.
| | - Roberta Piredda
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano (Bari), Italy
| | - Marco Basili
- Institute for Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
- Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Giulia Maricchiolo
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Messina, Italy
| | - Simone Mirto
- Institute of Anthropic Impacts and Sustainability in Marine Environment, National Research Council (IAS-CNR), Palermo, Italy
| | - Elena Manini
- Institute for Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
| | - Anne Mette Seyfarth
- Department of Global Surveillance, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Marco Candela
- Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Gian Marco Luna
- Institute for Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
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Floris R, Sanna G, Mura L, Fiori M, Culurgioni J, Diciotti R, Rizzo C, Lo Giudice A, Laganà P, Fois N. Isolation and Identification of Bacteria with Surface and Antibacterial Activity from the Gut of Mediterranean Grey Mullets. Microorganisms 2021; 9:microorganisms9122555. [PMID: 34946156 PMCID: PMC8703445 DOI: 10.3390/microorganisms9122555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 11/27/2022] Open
Abstract
Fish gut represents a peculiar ecological niche where bacteria can transit and reside to play vital roles by producing bio-compounds with nutritional, immunomodulatory and other functions. This complex microbial ecosystem reflects several factors (environment, feeding regimen, fish species, etc.). The objective of the present study was the identification of intestinal microbial strains able to produce molecules called biosurfactants (BSs), which were tested for surface and antibacterial activity in order to select a group of probiotic bacteria for aquaculture use. Forty-two bacterial isolates from the digestive tracts of twenty Mediterranean grey mullets were screened for testing emulsifying (E-24), surface and antibiotic activities. Fifty percent of bacteria, ascribed to Pseudomonas aeruginosa, Pseudomonas sp., P. putida and P. anguilliseptica, P. stutzeri, P. protegens and Enterobacter ludwigii were found to be surfactant producers. Of the tested strains, 26.6% exhibited an antibacterial activity against Staphylococcus aureus (10.0 ± 0.0–14.5 ± 0.7 mm inhibition zone), and among them, 23.3% of isolates also showed inhibitory activity vs. Proteus mirabilis (10.0 ± 0.0–18.5 ± 0.7 mm inhibition zone) and 6.6% vs. Klebsiella pneumoniae (11.5 ± 0.7–17.5 ± 0.7 mm inhibition zone). According to preliminary chemical analysis, the bioactive compounds are suggested to be ascribed to the class of glycolipids. This works indicated that fish gut is a source of bioactive compounds which deserves to be explored.
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Affiliation(s)
- Rosanna Floris
- AGRIS-Sardegna, Agricultural Research Agency of Sardinia, Bonassai, 07100 Sassari, Italy; (G.S.); (L.M.); (M.F.); (J.C.); (R.D.); (N.F.)
- Correspondence: ; Tel.: +39-079-284-2331
| | - Gabriele Sanna
- AGRIS-Sardegna, Agricultural Research Agency of Sardinia, Bonassai, 07100 Sassari, Italy; (G.S.); (L.M.); (M.F.); (J.C.); (R.D.); (N.F.)
| | - Laura Mura
- AGRIS-Sardegna, Agricultural Research Agency of Sardinia, Bonassai, 07100 Sassari, Italy; (G.S.); (L.M.); (M.F.); (J.C.); (R.D.); (N.F.)
| | - Myriam Fiori
- AGRIS-Sardegna, Agricultural Research Agency of Sardinia, Bonassai, 07100 Sassari, Italy; (G.S.); (L.M.); (M.F.); (J.C.); (R.D.); (N.F.)
| | - Jacopo Culurgioni
- AGRIS-Sardegna, Agricultural Research Agency of Sardinia, Bonassai, 07100 Sassari, Italy; (G.S.); (L.M.); (M.F.); (J.C.); (R.D.); (N.F.)
| | - Riccardo Diciotti
- AGRIS-Sardegna, Agricultural Research Agency of Sardinia, Bonassai, 07100 Sassari, Italy; (G.S.); (L.M.); (M.F.); (J.C.); (R.D.); (N.F.)
| | - Carmen Rizzo
- Stazione Zoologica Anton Dohrn-Ecosustainable Marine Biotechnology Department, Sicily Marine Centre, Villa Pace, Contrada Porticatello 29, 98167 Messina, Italy;
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council (ISP-CNR), 98122 Messina, Italy;
| | - Pasqualina Laganà
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Torre Biologica 3p, AOU ‘G. Martino, Via C. Valeria, s.n.c., 98125 Messina, Italy;
| | - Nicola Fois
- AGRIS-Sardegna, Agricultural Research Agency of Sardinia, Bonassai, 07100 Sassari, Italy; (G.S.); (L.M.); (M.F.); (J.C.); (R.D.); (N.F.)
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11
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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: 3] [Impact Index Per Article: 1.0] [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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12
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Effects of Dietary Fishmeal Replacement by Poultry By-Product Meal and Hydrolyzed Feather Meal on Liver and Intestinal Histomorphology and on Intestinal Microbiota of Gilthead Seabream (Sparus aurata). APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11198806] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The effects on liver and intestinal histomorphology and on intestinal microbiota in gilthead seabream (Sparus aurata) fed diets that contained poultry by-product meal (PBM) and hydrolyzed feather meal (HFM) as fishmeal replacements were studied. Fish fed on a series of isonitrogenous and isoenergetic diets, where fishmeal protein of the control diet (FM diet) was replaced by either PBM or by HFM at 25%, 50% and 100% without amino acid supplementation (PBM25, PBM50, PBM100, HFM25, HFM50 and HFM100 diets) or supplemented with lysine and methionine (PBM25+, PBM50+, HFM25+ and HFM50+ diets). The use of PBM and HFM at 25% fishmeal replacement generated a similar hepatic histomorphology to FM-fed fish, indicating that both land animal proteins are highly digestible at low FM replacement levels. However, 50% and 100% FM replacement levels by either PBM or HFM resulted in pronounced hepatic alterations in fish with the latter causing more severe degradation of the liver. Dietary amino acid supplementation delivered an improved tissue histology signifying their importance at high FM replacement levels. Intestinal microbiota was dominated by Proteobacteria (58.8%) and Actinobacteria (32.4%) in all dietary groups, but no specific pattern was observed among them at any taxonomic level. This finding was probably driven by the high inter-individual variability observed.
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13
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Haro-Moreno JM, Coutinho FH, Zaragoza-Solas A, Picazo A, Almagro-Moreno S, López-Pérez M. Dysbiosis in marine aquaculture revealed through microbiome analysis: reverse ecology for environmental sustainability. FEMS Microbiol Ecol 2021; 96:6027483. [PMID: 33289802 DOI: 10.1093/femsec/fiaa218] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/11/2020] [Indexed: 01/18/2023] Open
Abstract
The increasing demand for products for human consumption is leading to the fast-growing expansion of numerous food sectors such as marine aquaculture (mariculture). However, excessive input of nutrients and pollutants modifies marine ecosystems. Here, we applied a metagenomic approach to investigate these perturbations in samples from marine farms of gilthead seabream cultures. Results revealed dysbiosis and functional imbalance within the net cage with a unique structure, with little interference with samples from the fish microbiota or those collected far away from the coast. Remarkably, below the cage the prokaryotic community was highly similar to the marine microbiome of photic offshore samples. We recovered 48 novel metagenome-assembled genomes. Metagenomic recruitment revealed a significant change in the microbial community which was dominated by several Proteobacteria orders (Sphingomonadales, Pseudomonadales, Caudobacterales and Rhizobiales). Genomic potential for bioremediation processes, including nitrate removal through aerobic denitrification, and degradation of aromatic compounds and other toxic products were enriched in these microbes. The detrimental side effects were the increased number of antimicrobial resistance genes and the presence of potentially emergent pathogens. Knowledge of this metabolic diversity and the microbes involved in ecological balance recovery can be used to reduce the environmental impact of these practices.
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Affiliation(s)
- Jose M Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan 03550, Alicante, Spain
| | - Felipe Hernandes Coutinho
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan 03550, Alicante, Spain
| | - Asier Zaragoza-Solas
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan 03550, Alicante, Spain
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Burjassot, E-46100 Valencia, Spain
| | - Salvador Almagro-Moreno
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL, USA
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan 03550, Alicante, Spain
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14
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Meng KF, Ding LG, Wu S, Wu ZB, Cheng GF, Zhai X, Sun RH, Xu Z. Interactions Between Commensal Microbiota and Mucosal Immunity in Teleost Fish During Viral Infection With SVCV. Front Immunol 2021; 12:654758. [PMID: 33897703 PMCID: PMC8058427 DOI: 10.3389/fimmu.2021.654758] [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: 01/17/2021] [Accepted: 03/17/2021] [Indexed: 12/11/2022] Open
Abstract
The mucosa of vertebrates is a particularly complex but dynamic environment in which the host constantly interacts with trillions of commensal microorganisms and pathogens. Although the internal and external mucosal microbiomes with immune defense of mammals have been well investigated, the relationship between mucosal microbes and their host’s immune responses has not been systematically understood in the early vertebrates. In this study, we compared the composition and distribution of mucosal microbiota in common carp (Cyprinus carpio), and found that there were significant differences of microbiota between in the internal (gut) and external mucosal (buccal mucosa, gills and skin) tissues. Next, we successfully constructed an infection model with spring viremia of carp virus (SVCV). Specifically, following viral infection, the immune and antiviral related genes showed different up-regulation in all selected mucosal tissues while significant morphological changes were only found in external tissues including buccal mucosa, gills and skin. Using 16S rRNA gene sequence, we revealed that the abundance of Proteobacteria in mucosal tissues including buccal mucosa, gills and gut showed increased trend after viral infection, whereas the abundance of Fusobacteria significantly decreased in gut. In addition, the loss of dominant commensal microorganisms and increased colonization of opportunistic bacteria were discovered in the mucosal surfaces indicating that a secondary bacterial infection might occur in these mucosal tissues after viral infection. Overall, our results firstly point out the distribution of internal and external mucosal microbiota and analyze the changes of mucosal microbiota in common carp after SVCV infection, which may indicated that the potential role of mucosal microbiota in the antiviral process in early vertebrates.
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Affiliation(s)
- Kai-Feng Meng
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Li-Guo Ding
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Sha Wu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Zheng-Ben Wu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Gao-Feng Cheng
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Xue Zhai
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Ru-Han Sun
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Zhen Xu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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15
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Panteli N, Mastoraki M, Lazarina M, Chatzifotis S, Mente E, Kormas KA, Antonopoulou E. Configuration of Gut Microbiota Structure and Potential Functionality in Two Teleosts under the Influence of Dietary Insect Meals. Microorganisms 2021; 9:microorganisms9040699. [PMID: 33800578 PMCID: PMC8067204 DOI: 10.3390/microorganisms9040699] [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: 02/09/2021] [Revised: 03/03/2021] [Accepted: 03/25/2021] [Indexed: 11/16/2022] Open
Abstract
Insect meals are considered promising, eco-friendly, alternative ingredients for aquafeed. Considering the dietary influence on establishment of functioning gut microbiota, the effect of the insect meal diets on the microbial ecology should be addressed. The present study assessed diet- and species-specific shifts in gut resident bacterial communities of juvenile reared Dicentrarchus labrax and Sparus aurata in response to three experimental diets with insect meals from three insects (Hermetia illucens, Tenebrio molitor, Musca domestica), using high-throughput Illumina sequencing of the V3–V4 region of the 16S rRNA gene. The dominant phyla were Firmicutes, Proteobacteria and Actinobacteria in all dietary treatments. Anaerococcus sp., Cutibacterium sp. and Pseudomonas sp. in D. labrax, and Staphylococcus sp., Hafnia sp. and Aeromonas sp. in S. aurata were the most enriched shared species, following insect-meal inclusion. Network analysis of the dietary treatments highlighted diet-induced changes in the microbial community assemblies and revealed unique and shared microbe-to-microbe interactions. PICRUSt-predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly differentiated, including genes associated with metabolic pathways. The present findings strengthen the importance of diet in microbiota configuration and underline that different insects as fish feed ingredients elicit species-specific differential responses of structural and functional dynamics in gut microbial communities.
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Affiliation(s)
- Nikolas Panteli
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (N.P.); (M.M.)
| | - Maria Mastoraki
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (N.P.); (M.M.)
| | - Maria Lazarina
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Stavros Chatzifotis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, 71003 Heraklion, Greece;
| | - Eleni Mente
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece; (E.M.); (K.A.K.)
| | - Konstantinos Ar. Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece; (E.M.); (K.A.K.)
| | - Efthimia Antonopoulou
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (N.P.); (M.M.)
- Correspondence: ; Tel.: +30-231-099-8563
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16
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Knobloch S, Philip J, Ferrari S, Benhaïm D, Bertrand M, Poirier I. The effect of ultrasonic antifouling control on the growth and microbiota of farmed European sea bass (Dicentrarchus labrax). MARINE POLLUTION BULLETIN 2021; 164:112072. [PMID: 33529875 DOI: 10.1016/j.marpolbul.2021.112072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/14/2021] [Accepted: 01/16/2021] [Indexed: 05/11/2023]
Abstract
Biofouling is a serious threat to marine renewable energy structures and marine aquaculture operations alike. As an alternative to toxic surface coatings, ultrasonic antifouling control has been proposed as an environmentally friendly means to reduce biofouling. However, the impact of ultrasound on fish farmed in offshore structures or in marine multi-purpose platforms, combining renewable energy production and aquaculture, has not yet been assessed. Here we study the impact of ultrasound on the growth and microbiota of farmed European sea bass (Dicentrarchus labrax) under laboratory conditions. Whereas growth and survival were not reduced by ultrasound exposure, microbiological analysis using plate counts and 16S rRNA gene based metataxonomics showed a perturbation of the gill and skin microbiota, including an increase in putative pathogenic bacteria. This warrants further research into the long-term effects of ultrasonic antifouling control on the health and wellbeing of farmed fish.
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Affiliation(s)
- Stephen Knobloch
- Matís ohf., Microbiology Group, Vínlandsleid 12, 113 Reykjavík, Iceland
| | - Joris Philip
- Hólar University, Department of Aquaculture and Fish Biology, Háeyri 1, 550 Saudárkrókur, Iceland
| | - Sébastien Ferrari
- Conservatoire National des Arts et Métiers, Institut National des Sciences et Techniques de la Mer, EPN8, Boulevard Collignon, Tourlaville, 50110 Cherbourg en Cotentin, France; Laboratoire Universitaire des Sciences Appliquées de Cherbourg, EA4253, Normandie Université, UNICAEN, 50130 Cherbourg en Cotentin, France
| | - David Benhaïm
- Hólar University, Department of Aquaculture and Fish Biology, Háeyri 1, 550 Saudárkrókur, Iceland; Conservatoire National des Arts et Métiers, Institut National des Sciences et Techniques de la Mer, EPN8, Boulevard Collignon, Tourlaville, 50110 Cherbourg en Cotentin, France
| | - Martine Bertrand
- Conservatoire National des Arts et Métiers, Institut National des Sciences et Techniques de la Mer, EPN8, Boulevard Collignon, Tourlaville, 50110 Cherbourg en Cotentin, France; Laboratoire Universitaire des Sciences Appliquées de Cherbourg, EA4253, Normandie Université, UNICAEN, 50130 Cherbourg en Cotentin, France
| | - Isabelle Poirier
- Conservatoire National des Arts et Métiers, Institut National des Sciences et Techniques de la Mer, EPN8, Boulevard Collignon, Tourlaville, 50110 Cherbourg en Cotentin, France; Laboratoire Universitaire des Sciences Appliquées de Cherbourg, EA4253, Normandie Université, UNICAEN, 50130 Cherbourg en Cotentin, France.
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17
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Serra CR, Oliva-Teles A, Enes P, Tavares F. Gut microbiota dynamics in carnivorous European seabass (Dicentrarchus labrax) fed plant-based diets. Sci Rep 2021; 11:447. [PMID: 33432059 PMCID: PMC7801451 DOI: 10.1038/s41598-020-80138-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 12/15/2020] [Indexed: 12/19/2022] Open
Abstract
A healthy gastrointestinal microbiota is essential for host fitness, and strongly modulated by host diet. In aquaculture, a current challenge is to feed carnivorous fish with plant-feedstuffs in substitution of fish meal, an unsustainable commodity. Plants have a limited nutritive value due to the presence of non-starch polysaccharides (NSP) which are not metabolized by fish. In this work we assessed the effects of NSP-enriched diets on European seabass gut microbiota and evaluate the selective pressure of plant feedstuffs towards gut microbes with NSP-hydrolytic potential, i.e. capable to convert indigestible dietary constituents in fish metabolites. Triplicate groups of European seabass juveniles were fed a fish meal-based diet (control) or three plant-based diets (SBM, soybean meal; RSM, rapeseed meal; SFM, sunflower meal) for 6 weeks, before recovering intestinal samples for microbiota analysis, using the Illumina's MiSeq platform. Plant-based diets impacted differently digesta and mucosal microbiota. A decrease (p = 0.020) on species richness, accompanied by a decline on the relative abundance of specific phyla such as Acidobacteria (p = 0.030), was observed in digesta samples of SBM and RSM experimental fish, but no effects were seen in mucosa-associated microbiota. Plant-based diets favored the Firmicutes (p = 0.01), in particular the Bacillaceae (p = 0.017) and Clostridiaceae (p = 0.007), two bacterial families known to harbor carbohydrate active enzymes and thus putatively more prone to grow in high NSP environments. Overall, bacterial gut communities of European seabass respond to plant-feedstuffs with adjustments in the presence of transient microorganisms (allochthonous) with carbohydrolytic potential, while maintaining a balanced core (autochthonous) microbiota.
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Affiliation(s)
- Cláudia R Serra
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, Universidade do Porto, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.
| | - Aires Oliva-Teles
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, Universidade do Porto, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre S/N, Ed. FC4, 4169-007, Porto, Portugal
| | - Paula Enes
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, Universidade do Porto, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre S/N, Ed. FC4, 4169-007, Porto, Portugal
| | - Fernando Tavares
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre S/N, Ed. FC4, 4169-007, Porto, Portugal
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
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18
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Keating C, Bolton-Warberg M, Hinchcliffe J, Davies R, Whelan S, Wan AHL, Fitzgerald RD, Davies SJ, Ijaz UZ, Smith CJ. Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae. Anim Microbiome 2021; 3:7. [PMID: 33500003 PMCID: PMC7934267 DOI: 10.1186/s42523-020-00065-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/24/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Aquaculture successfully meets global food demands for many fish species. However, aquaculture production of Atlantic cod (Gadus morhua) is just 2.5% of total market production. For cod farming to be a viable economic venture specific challenges on how to increase growth, health and farming productivity need to be addressed. Feed ingredients play a key role here. Macroalgae (seaweeds) have been suggested as a functional feed supplement with both health and economic benefits for terrestrial farmed animals and fish. The impact of such dietary supplements to cod gut integrity and microbiota, which contribute to overall fish robustness is unknown. The objective of this study was to supplement the diet of juvenile Atlantic cod with macroalgae and determine the impacts on fish condition and growth, gut morphology and hindgut microbiota composition (16S rRNA amplicon sequencing). Fish were fed one of three diets: control (no macroalgal inclusion), 10% inclusion of either egg wrack (Ascophyllum nodosum) or sea lettuce (Ulva rigida) macroalgae in a 12-week trial. RESULTS The results demonstrated there was no significant difference in fish condition, gut morphology or hindgut microbiota between the U. rigida supplemented fish group and the control group at any time-point. This trend was not observed with the A. nodosum treatment. Fish within this group were further categorised as either 'Normal' or 'Lower Growth'. 'Lower Growth' individuals found the diet unpalatable resulting in reduced weight and condition factor combined with an altered gut morphology and microbiome relative to the other treatments. Excluding this group, our results show that the hindgut microbiota was largely driven by temporal pressures with the microbial communities becoming more similar over time irrespective of dietary treatment. The core microbiome at the final time-point consisted of the orders Vibrionales (Vibrio and Photobacterium), Bacteroidales (Bacteroidetes and Macellibacteroides) and Clostridiales (Lachnoclostridium). CONCLUSIONS Our study indicates that U. rigida macroalgae can be supplemented at 10% inclusion levels in the diet of juvenile farmed Atlantic cod without any impact on fish condition or hindgut microbial community structure. We also conclude that 10% dietary inclusion of A. nodosum is not a suitable feed supplement in a farmed cod diet.
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Affiliation(s)
- C Keating
- Department of Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, H91 TK33, Ireland.
- Water and Environment Group, Infrastructure and Environment Division, James Watt School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK.
| | - M Bolton-Warberg
- Carna Research Station, Ryan Institute, National University of Ireland Galway, Carna, Co, Galway, H91 V8Y1, Ireland
| | - J Hinchcliffe
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - R Davies
- AquaBioTech Group, Central Complex, Naggar Street, Targa Gap, Mosta, G.C, MST 1761, Malta
| | - S Whelan
- Carna Research Station, Ryan Institute, National University of Ireland Galway, Carna, Co, Galway, H91 V8Y1, Ireland
| | - A H L Wan
- Irish Seaweed Research Group, Ryan Institute and School of Natural Sciences, National University of Ireland Galway, Galway, H91 TK33, Ireland
- Aquaculture Nutrition and Aquafeed Research Unit, Carna Research Station, Ryan Institute and School of Natural Sciences, National University of Ireland Galway, Carna, Co, Galway, H91 V8Y1, Ireland
| | - R D Fitzgerald
- Carna Research Station, Ryan Institute, National University of Ireland Galway, Carna, Co, Galway, H91 V8Y1, Ireland
| | - S J Davies
- Department of Animal Production, Welfare and Veterinary Science, Harper Adams University, Newport, Shropshire, TF10 8NB, UK
| | - U Z Ijaz
- Water and Environment Group, Infrastructure and Environment Division, James Watt School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK.
| | - C J Smith
- Department of Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, H91 TK33, Ireland.
- Water and Environment Group, Infrastructure and Environment Division, James Watt School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK.
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19
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Piazzon MC, Naya-Català F, Perera E, Palenzuela O, Sitjà-Bobadilla A, Pérez-Sánchez J. Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream. MICROBIOME 2020; 8:168. [PMID: 33228779 PMCID: PMC7686744 DOI: 10.1186/s40168-020-00922-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/09/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND The key effects of intestinal microbiota in animal health have led to an increasing interest in manipulating these bacterial populations to improve animal welfare. The aquaculture sector is no exception and in the last years, many studies have described these populations in different fish species. However, this is not an easy task, as intestinal microbiota is composed of very dynamic populations that are influenced by different factors, such as diet, environment, host age, and genetics. In the current study, we aimed to determine whether the genetic background of gilthead sea bream (Sparus aurata) influences the intestinal microbial composition, how these bacterial populations are modulated by dietary changes, and the effect of selection by growth on intestinal disease resistance. To that aim, three different groups of five families of gilthead sea bream that were selected during two generations for fast, intermediate, or slow growth (F3 generation) were kept together in the same open-flow tanks and fed a control or a well-balanced plant-based diet during 9 months. Six animals per family and dietary treatment were sacrificed and the adherent bacteria from the anterior intestinal portion were sequenced. In parallel, fish of the fast- and slow-growth groups were infected with the intestinal parasite Enteromyxum leei and the disease signs, prevalence, intensity, and parasite abundance were evaluated. RESULTS No differences were detected in alpha diversity indexes among families, and the core bacterial architecture was the prototypical composition of gilthead sea bream intestinal microbiota, indicating no dysbiosis in any of the groups. The plant-based diet significantly changed the microbiota in the intermediate- and slow-growth families, with a much lower effect on the fast-growth group. Interestingly, the smaller changes detected in the fast-growth families potentially accounted for more changes at the metabolic level when compared with the other families. Upon parasitic infection, the fast-growth group showed significantly lower disease signs and parasite intensity and abundance than the slow-growth animals. CONCLUSIONS These results show a clear genome-metagenome interaction indicating that the fast-growth families harbor a microbiota that is more flexible upon dietary changes. These animals also showed a better ability to cope with intestinal infections. Video Abstract.
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Affiliation(s)
- M. Carla Piazzon
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Fernando Naya-Català
- Nutrigenomics and Fish Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Erick Perera
- 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
| | - Oswaldo Palenzuela
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Ariadna Sitjà-Bobadilla
- 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
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20
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Tong Q, Cui LY, Hu ZF, Du XP, Abid HM, Wang HB. Environmental and host factors shaping the gut microbiota diversity of brown frog Rana dybowskii. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 741:140142. [PMID: 32615421 DOI: 10.1016/j.scitotenv.2020.140142] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/18/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
Symbiotic microbial communities are common in amphibians, and the composition of gut microbial communities varies with factors such as host phylogeny, life stage, ecology, and diet. However, little is known regarding how amphibians acquire their microbiota or how their growth, development, and environmental factors affect the diversity of their microbiotas. We sampled the gut microbiota during different developmental stages of brown frog Rana dybowskii, including tadpoles (T), frogs in metamorphosis (M), frogs just post-metamorphosis and after eating (F), juvenile frogs in summer (Js), adult frogs in summer (As), adult frogs in autumn (Aa), and hibernating frogs (Ah). We recorded data on the environmental (ambient temperature, fasting status, habitat, and season) and host (body mass and developmental period) factors. We investigated whether the gut microbiota diversity of R. dybowskii differs according to the host developmental stage via high-throughput Illumina sequencing and whether the gut microbiota diversity is affected by environmental and host factors. We found that alpha and beta diversity varied significantly during different developmental stages. The linear discriminant analysis effect size (LEfSe) analysis identified eight phyla exhibiting significant differences: Cyanobacteria (T group), Proteobacteria (M group), Fusobacteria (F group), Firmicutes (As group), Actinobacteria (Aa group), Verrucomicrobia (Aa group), Tenericutes (Aa group), and Bacteroidetes (Ah group). The Venn diagrams showed that 49 shared OTUs were present during all stages of development, whereas 10 OTUs were present in >90% of the samples. The environmental and host factors were significantly correlated with microbial community changes. Furthermore, the AIC-based model results suggested that development was the only variable that needed inclusion in the redundancy analysis (RDA) to explain the variance in taxa. These results have broad implications for our understanding of gut microbiota development and its associations with amphibian development and environmental factors.
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Affiliation(s)
- Qing Tong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China; Hejiang Forestry Research Institute of Heilongjiang Province, Jiamusi, China
| | - Li-Yong Cui
- Hejiang Forestry Research Institute of Heilongjiang Province, Jiamusi, China
| | - Zong-Fu Hu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Xiao-Peng Du
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Hayat Muhammad Abid
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Hong-Bin Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.
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21
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Su S, Munganga BP, Du F, Yu J, Li J, Yu F, Wang M, He X, Li X, Bouzoualegh R, Xu P, Tang Y. Relationship Between the Fatty Acid Profiles and Gut Bacterial Communities of the Chinese Mitten Crab ( Eriocheir sinensis) From Ecologically Different Habitats. Front Microbiol 2020; 11:565267. [PMID: 33178151 PMCID: PMC7593381 DOI: 10.3389/fmicb.2020.565267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 08/31/2020] [Indexed: 12/11/2022] Open
Abstract
The gut microbiota plays an important role in a variety of physiological functions such as intestinal digestion, metabolic homeostasis, immune response, and responses to disease treatment. Whether there is a relationship between gut microbial communities and fatty acid (FA) profiles of Chinese mitten crab is unclear. Hence, we analyzed the relationship between FA profiles and the gut bacterial communities of six Chinese mitten crab (Eriocheir sinensis) populations from different lakes. The crabs were sampled from six different lakes in Jiangsu Province, China. The FA profiles of these crab populations were compared and clustered, and then used to determine the relationship between geographic location and FA composition. We also characterized the gut microbial communities of these crabs using 16S rRNA high-throughput gene sequencing. The FA profiles varied significantly (P < 0.05) between crabs from different geographical locations. A similar trend was also observed in the gut microbial communities, which also varied significantly based on their geographical origin (P < 0.05). Furthermore, alpha diversity, cluster analysis, and matching bacterial community structures with specific locations revealed patterns that significantly linked FA profiles to the gut microbiota. Further analysis of FA profiles and gut microbial community generated patterns that linked the two parameters. Hence, it was observed that the gut microbial community seems to contribute significantly to the FA composition of the Chinese mitten crab. However, further studies need to be conducted to investigate the interactions between gut microbial communities and the biochemical composition of the Chinese mitten crab, which will ultimately unravel the complexity of microbial ecosystems for potential applications in aquaculture and species conservation.
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Affiliation(s)
- Shengyan Su
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | | | - Fukuan Du
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Juhua Yu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Jianlin Li
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Fan Yu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Meiyao Wang
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Xinjin He
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Xinyuan Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Raouf Bouzoualegh
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Pao Xu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Yongkai Tang
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
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22
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Pérez-Pascual D, Estellé J, Dutto G, Rodde C, Bernardet JF, Marchand Y, Duchaud E, Przybyla C, Ghigo JM. Growth Performance and Adaptability of European Sea Bass ( Dicentrarchus labrax) Gut Microbiota to Alternative Diets Free of Fish Products. Microorganisms 2020; 8:microorganisms8091346. [PMID: 32899237 PMCID: PMC7565124 DOI: 10.3390/microorganisms8091346] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 01/17/2023] Open
Abstract
Innovative fish diets made of terrestrial plants supplemented with sustainable protein sources free of fish-derived proteins could contribute to reducing the environmental impact of the farmed fish industry. However, such alternative diets may influence fish gut microbial community, health, and, ultimately, growth performance. Here, we developed five fish feed formulas composed of terrestrial plant-based nutrients, in which fish-derived proteins were substituted with sustainable protein sources, including insect larvae, cyanobacteria, yeast, or recycled processed poultry protein. We then analyzed the growth performance of European sea bass (Dicentrarchus labrax L.) and the evolution of gut microbiota of fish fed the five formulations. We showed that replacement of 15% protein of a vegetal formulation by insect or yeast proteins led to a significantly higher fish growth performance and feed intake when compared with the full vegetal formulation, with feed conversion ratio similar to a commercial diet. 16S rRNA gene sequencing monitoring of the sea bass gut microbial community showed a predominance of Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes phyla. The partial replacement of protein source in fish diets was not associated with significant differences on gut microbial richness. Overall, our study highlights the adaptability of European sea bass gut microbiota composition to changes in fish diet and identifies promising alternative protein sources for sustainable aquafeeds with terrestrial vegetal complements.
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Affiliation(s)
- David Pérez-Pascual
- Unité de Génétique des Biofilms, Institut Pasteur, UMR CNRS2001, 75015 Paris, France;
| | - Jordi Estellé
- AgroParisTech, GABI, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France;
| | - Gilbert Dutto
- Laboratoire Service d’Expérimentations Aquacoles, Ifremer, 34250 Palavas les flots, France;
| | - Charles Rodde
- MARBEC, IRD, IFREMER, Univ Montpellier, CNRS, Laboratoire Adaptation, adaptabilité, des animaux et des systèmes Ifremer, 34250 Palavas les flots, France;
| | - Jean-François Bernardet
- Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (J.-F.B.); (E.D.)
| | | | - Eric Duchaud
- Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (J.-F.B.); (E.D.)
| | - Cyrille Przybyla
- MARBEC, IRD, IFREMER, Univ Montpellier, CNRS, Laboratoire Adaptation, adaptabilité, des animaux et des systèmes Ifremer, 34250 Palavas les flots, France;
- Correspondence: (C.P.); (J.-M.G.)
| | - Jean-Marc Ghigo
- Unité de Génétique des Biofilms, Institut Pasteur, UMR CNRS2001, 75015 Paris, France;
- Correspondence: (C.P.); (J.-M.G.)
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23
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Panteli N, Mastoraki M, Nikouli E, Lazarina M, Antonopoulou E, Kormas KA. Imprinting statistically sound conclusions for gut microbiota in comparative animal studies: A case study with diet and teleost fishes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100738. [PMID: 32896688 DOI: 10.1016/j.cbd.2020.100738] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Despite the technical progress in high-throughput sequencing technologies, defining the sample size which is capable of yielding representative inferences in metabarcoding analysis still remains debatable. The present study addresses the influence of individual variability in assessing dietary effects on fish gut microbiota parameters and estimates the biological sample size that is sufficient to imprint a statistically secure outcome. European sea bass (Dicentrarchus labrax) and gilthead sea bream (Sparus aurata) were fed three alternative animal protein diets and a fishmeal control diet. Gut microbiota data from 12 individuals per diet, derived from Illumina sequencing of the V3-V4 region of the 16S rRNA gene, were randomized in all possible combinations of n-1 individuals. Results in this study showcased that increasing the sample size can limit the prevalence of individuals with high microbial load on the outcome and can ensure the statistical confidence required for an accurate validation of dietary-induced microbe shifts. Inter-individual variability was evident in the four dietary treatments where consequently misleading inferences arose from insufficient biological replication. These findings have critical implications for the design of future metabarcoding studies and highlight the urgency in selecting an adequate sample size able to safely elucidate the dietary effects on fish gut microbial communities.
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Affiliation(s)
- Nikolas Panteli
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Maria Mastoraki
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
| | - Maria Lazarina
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Efthimia Antonopoulou
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece.
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
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24
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Khurana H, Singh DN, Singh A, Singh Y, Lal R, Negi RK. Gut microbiome of endangered Tor putitora (Ham.) as a reservoir of antibiotic resistance genes and pathogens associated with fish health. BMC Microbiol 2020; 20:249. [PMID: 32787773 PMCID: PMC7425606 DOI: 10.1186/s12866-020-01911-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 07/19/2020] [Indexed: 01/16/2023] Open
Abstract
Background Tor putitora, the largest freshwater fish of the Indian subcontinent, is an endangered species. Several factors have been attributed towards its continuous population decrease, but very little is known about the gut microbiome of this fish. Also, the fish gut microbiome serves as a reservoir of virulence factors and antibiotic resistance determinants. Therefore, the shotgun metagenomic approach was employed to investigate the taxonomic composition and functional potential of microbial communities present in the gut of Tor putitora, as well as the detection of virulence and antibiotic resistance genes in the microbiome. Results The analysis of bacterial diversity showed that Proteobacteria was predominant phylum, followed by Chloroflexi, Bacteroidetes, and Actinobacteria. Within Proteobacteria, Aeromonas and Caulobacter were chiefly present; also, Klebsiella, Escherichia, and plant symbionts were noticeably detected. Functional characterization of gut microbes endowed the virulence determinants, while surveillance of antibiotic resistance genes showed the dominance of β-lactamase variants. The antibiotic-resistant Klebsiella pneumoniae and Escherichia coli pathovars were also detected. Microbial genome reconstruction and comparative genomics confirmed the presence of Aeromonads, the predominant fish pathogens. Conclusions Gut microbiome of endangered Tor putitora consisted of both commensals and opportunistic pathogens, implying that factors adversely affecting the non-pathogenic population would allow colonization and proliferation of pathogens causing diseased state in asymptomatic Tor putitora. The presence of virulence factors and antibiotic resistance genes suggested the potential risk of dissemination to other bacteria due to horizontal gene transfer, thereby posing a threat to fish and human health. The preservation of healthy gut microflora and limited use of antibiotics are some of the prerequisites for the conservation of this imperilled species.
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Affiliation(s)
- Himani Khurana
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India.,Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Durgesh Narain Singh
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India.,Laboratory of Microbial Pathogenesis, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Anoop Singh
- Laboratory of Microbial Pathogenesis, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Yogendra Singh
- Laboratory of Microbial Pathogenesis, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Rup Lal
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India. .,Present address: The Energy and Resources Institute Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003, India.
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India.
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25
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Pereira AC, Bandeira V, Fonseca C, Cunha MV. Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose ( Herpestes ichneumon) Gut Microbiome. Microorganisms 2020; 8:E808. [PMID: 32471180 PMCID: PMC7355707 DOI: 10.3390/microorganisms8060808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/10/2020] [Accepted: 05/26/2020] [Indexed: 02/07/2023] Open
Abstract
Recently, we unveiled taxonomical and functional differences in Egyptian mongoose (Herpestes ichneumon) gut microbiota across sex and age classes by microbial profiling. In this study, we generate, through culturomics, extended baseline information on the culturable bacterial and fungal microbiome of the species using the same specimens as models. Firstly, this strategy enabled us to explore cultivable microbial community differences across sexes and to ascertain the influence exerted by biological and environmental contexts of each host in its microbiota signature. Secondly, it permitted us to compare the culturomics and microbial profiling approaches and their ability to provide information on mongoose gut microbiota. In agreement with microbial profiling, culturomics showed that the core gut cultivable microbiota of the mongoose is dominated by Firmicutes and, as previously found, is able to distinguish sex- and age class-specific genera. Additional information could be obtained by culturomics, with six new genera unveiled. Richness indices and the Shannon index were concordant between culture-dependent and culture-independent approaches, highlighting significantly higher values when using microbial profiling. However, the Simpson index underlined higher values for the culturomics-generated data. These contrasting results were due to a differential influence of dominant and rare taxa on those indices. Beta diversity analyses of culturable microbiota showed similarities between adults and juveniles, but not in the data series originated from microbial profiling. Additionally, whereas the microbial profiling indicated that there were several bioenvironmental features related to the bacterial gut microbiota of the Egyptian mongoose, a clear association between microbiota and bioenvironmental features could not be established through culturomics. The discrepancies found between the data generated by the two methodologies and the underlying inferences, both in terms of β-diversity and role of bioenvironmental features, confirm that culture-independent, sequence-based methods have a higher ability to assess, at a fine scale, the influence of abiotic and biotic factors on the microbial community composition of mongoose' gut. However, when used in a complementary perspective, this knowledge can be expanded by culturomics.
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Affiliation(s)
- André C. Pereira
- National Institute for Agrarian and Veterinary Research (INIAV, IP), Wildlife, Hunting and Biodiversity R&D Unit, 2780-157 Oeiras, Portugal;
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Victor Bandeira
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal; (V.B.); (C.F.)
| | - Carlos Fonseca
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal; (V.B.); (C.F.)
| | - Mónica V. Cunha
- National Institute for Agrarian and Veterinary Research (INIAV, IP), Wildlife, Hunting and Biodiversity R&D Unit, 2780-157 Oeiras, Portugal;
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
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Basili D, Lutfi E, Falcinelli S, Balbuena-Pecino S, Navarro I, Bertolucci C, Capilla E, Carnevali O. Photoperiod Manipulation Affects Transcriptional Profile of Genes Related to Lipid Metabolism and Apoptosis in Zebrafish (Danio rerio) Larvae: Potential Roles of Gut Microbiota. MICROBIAL ECOLOGY 2020; 79:933-946. [PMID: 31820072 DOI: 10.1007/s00248-019-01468-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
Gut microbiota plays a fundamental role in maintaining host's health by controlling a wide range of physiological processes. Administration of probiotics and manipulation of photoperiod have been suggested as modulators of microbial composition and are currently undergoing an extensive research in aquaculture as a way to improve health and quality of harvested fish. However, our understanding regarding their effects on physiological processes is still limited. In the present study we investigated whether manipulation of photoperiod and/or probiotic administration was able to alter microbial composition in zebrafish larvae at hatching stage. Our findings show that probiotic does not elicit effects while photoperiod manipulation has a significant impact on microbiota composition. Moreover, we successfully predicted lipid biosynthesis and apoptosis to be modulated by microbial communities undergoing continuous darkness. Interestingly, expression levels of caspase 3 gene (casp3) and lipid-related genes (hnf4a, npc1l1, pparγ, srebf1, agpat4 and fitm2) were found to be significantly overexpressed in dark-exposed larvae, suggesting an increase in the occurrence of apoptotic processes and a lipid metabolism impairment, respectively (p < 0.05). Our results provide the evidence that microbial communities in zebrafish at early life stages are not modulated by a short administration of probiotics and highlight the significant effect that dark photoperiod elicits on zebrafish microbiota and potentially on health.
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Affiliation(s)
- Danilo Basili
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Esmail Lutfi
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Norwegian Institute of Food, Fisheries and Aquaculture Research, P.O. Box 210, 1431, Ås, Norway
| | - Silvia Falcinelli
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Sara Balbuena-Pecino
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Isabel Navarro
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Cristiano Bertolucci
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy
| | - Encarnación Capilla
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Oliana Carnevali
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy.
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27
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Gao YM, Zou KS, Zhou L, Huang XD, Li YY, Gao XY, Chen X, Zhang XY. Deep Insights into Gut Microbiota in Four Carnivorous Coral Reef Fishes from the South China Sea. Microorganisms 2020; 8:microorganisms8030426. [PMID: 32197354 PMCID: PMC7143975 DOI: 10.3390/microorganisms8030426] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/16/2020] [Accepted: 03/16/2020] [Indexed: 12/31/2022] Open
Abstract
Investigations of gut microbial diversity among fish to provide baseline data for wild marine fish, especially the carnivorous coral reef fishes of the South China Sea, are lacking. The present study investigated the gut microbiota of four carnivorous coral reef fishes, including Oxycheilinus unifasciatus, Cephalopholis urodeta, Lutjanus kasmira, and Gnathodentex aurolineatus, from the South China Sea for the first time using high-throughput Illumina sequencing. Proteobacteria, Firmicutes, and Bacteroidetes constituted 98% of the gut microbiota of the four fishes, and 20 of the gut microbial genera recovered in this study represent new reports from marine fishes. Comparative analysis indicated that the four fishes shared a similar microbial community, suggesting that diet type (carnivorous) might play a more important role in shaping the gut microbiota of coral reef fishes than the species of fish. Furthermore, the genera Psychrobacter, Escherichia-Shigella, and Vibrio constituted the core microbial community of the four fishes, accounting for 61–91% of the total sequences in each fish. The lack of the genus Epulopiscium in the four fishes was in sharp contrast to what has been found in coral reef fishes from the Red Sea, in which Epulopiscium was shown to be the most dominant gut microbial genus in seven herbivorous coral reef fishes. In addition, while unique gut microbial genera accounted for a small proportion (8–13%) of the total sequences, many such genera were distributed in each coral reef fish species, including several genera (Endozoicomonas, Clostridium, and Staphylococcus) that are frequently found in marine fishes and 11 new reports of gut microbes in marine fishes. The present study expands our knowledge of the diversity and specificity of gut microbes associated with coral reef fishes.
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Affiliation(s)
- Yu-Miao Gao
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; (Y.-M.G.); (K.-S.Z.); (L.Z.); (X.-D.H.); (Y.-Y.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Ke-Shu Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; (Y.-M.G.); (K.-S.Z.); (L.Z.); (X.-D.H.); (Y.-Y.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, 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, 483 Wushan Road, Guangzhou 510642, China; (Y.-M.G.); (K.-S.Z.); (L.Z.); (X.-D.H.); (Y.-Y.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xian-De Huang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; (Y.-M.G.); (K.-S.Z.); (L.Z.); (X.-D.H.); (Y.-Y.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yi-Yang Li
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; (Y.-M.G.); (K.-S.Z.); (L.Z.); (X.-D.H.); (Y.-Y.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xiang-Yang Gao
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou 510642, 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, 483 Wushan Road, Guangzhou 510642, China; (Y.-M.G.); (K.-S.Z.); (L.Z.); (X.-D.H.); (Y.-Y.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Correspondence: (X.C.); (X.-Y.Z.); Tel.: +86-20-8757-1321(X.-Y.Z.)
| | - Xiao-Yong Zhang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; (Y.-M.G.); (K.-S.Z.); (L.Z.); (X.-D.H.); (Y.-Y.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou 510642, China;
- Correspondence: (X.C.); (X.-Y.Z.); Tel.: +86-20-8757-1321(X.-Y.Z.)
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Fonseca F, Cerqueira R, Fuentes J. Impact of Ocean Acidification on the Intestinal Microbiota of the Marine Sea Bream ( Sparus aurata L.). Front Physiol 2019; 10:1446. [PMID: 31849701 PMCID: PMC6893888 DOI: 10.3389/fphys.2019.01446] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/08/2019] [Indexed: 02/06/2023] Open
Abstract
Within a scenario of increasing atmospheric CO2 and ocean acidification (OA), it is highly relevant to investigate its impacts not only on fish performance but also on fish intestinal microbiome and how that reflects on host performance and health. The main objective of this study was to establish if the intestinal microbiota of the sea bream (Sparus aurata) was affected by high level of CO2 in line with the predictions for this century. The bacterial communities of the intestinal fluid were characterized in animals kept at the present-day level of CO2 (400 μatm) and in animals switched to high CO2 (1200 μatm) for 1 month. Bacterial taxa identification was based on molecular methods, using the DNA coding for the 16S ribosomal RNA and primers targeting the regions V1-V3. Amplicons obtained from DNA samples of animals in the same tank were combined, cloned to obtain a bacterial DNA library, and the clones were sequenced. No significant differences were found between the two treatments for alpha diversity. However, beta diversity analysis revealed distinct dysbiosis in response to hypercapnia, with phylum Firmicutes absent from the bacterial communities of fish exposed to 1200 μatm CO2, whereas Proteobacteria relative abundance was increased at elevated CO2, due to the presence of Gammaproteobacteria (Vibrionaceae and Alteromonadaceae), a class not present in the control samples. This study provides a first glimpse at the impact of OA in fish intestinal microbiota and highlights potential downstream effects to the general condition of fishes under hypercapnia.
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Affiliation(s)
- Filomena Fonseca
- Centro de Investigação Marinha e Ambiental, Universidade do Algarve, Faro, Portugal
| | - Ricardo Cerqueira
- Centro de Investigação Marinha e Ambiental, Universidade do Algarve, Faro, Portugal
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - Juan Fuentes
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
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29
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Piazzon MC, Naya-Català F, Simó-Mirabet P, Picard-Sánchez A, Roig FJ, Calduch-Giner JA, Sitjà-Bobadilla A, Pérez-Sánchez J. Sex, Age, and Bacteria: How the Intestinal Microbiota Is Modulated in a Protandrous Hermaphrodite Fish. Front Microbiol 2019; 10:2512. [PMID: 31736931 PMCID: PMC6834695 DOI: 10.3389/fmicb.2019.02512] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/18/2019] [Indexed: 12/11/2022] Open
Abstract
Intestinal microbiota is key for many host functions, such as digestion, nutrient metabolism, disease resistance, and immune function. With the growth of the aquaculture industry, there has been a growing interest in the manipulation of fish gut microbiota to improve welfare and nutrition. Intestinal microbiota varies with many factors, including host species, genetics, developmental stage, diet, environment, and sex. The aim of this study was to compare the intestinal microbiota of adult gilthead sea bream (Sparus aurata) from three groups of age and sex (1-year-old males and 2- and 4-year-old females) maintained under the same conditions and fed exactly the same diet. Microbiota diversity and richness did not differ among groups. However, bacterial composition did, highlighting the presence of Photobacterium and Vibrio starting at 2 years of age (females) and a higher presence of Staphylococcus and Corynebacterium in 1-year-old males. The core microbiota was defined by 14 Operational Taxonomic Units (OTUs) and the groups that showed more OTUs in common were 2- and 4-year-old females. Discriminant analyses showed a clear separation by sex and age, with bacteria belonging to the phyla Firmicutes, Proteobacteria and Actinobacteria driving the separation. Pathway analysis performed with the inferred metagenome showed significant differences between 1-year-old males and 4-year-old females, with an increase in infection-related pathways, nitrotoluene degradation and sphingolipid metabolism, and a significant decrease in carbohydrate metabolism pathways with age. These results show, for the first time, how intestinal microbiota is modulated in adult gilthead sea bream and highlight the importance of reporting age and sex variables in these type of studies in fish.
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Affiliation(s)
- M Carla Piazzon
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (CSIC), Castellón, Spain
| | - Fernando Naya-Català
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (CSIC), Castellón, Spain
| | - Paula Simó-Mirabet
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (CSIC), Castellón, Spain
| | - Amparo Picard-Sánchez
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (CSIC), Castellón, Spain
| | - Francisco J Roig
- Biotechvana S.L., Valencia, Spain.,Instituto de Medicina Genomica, S.L., Valencia, Spain
| | - Josep A Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (CSIC), Castellón, Spain
| | | | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (CSIC), Castellón, Spain
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30
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Kormas KA. Editorial for the Special Issue: Gut Microorganisms of Aquatic Animals. Microorganisms 2019; 7:E377. [PMID: 31546574 PMCID: PMC6843498 DOI: 10.3390/microorganisms7100377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 09/19/2019] [Indexed: 11/17/2022] Open
Abstract
Since the introduction of the term holobiont [...].
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Affiliation(s)
- Konstantinos Ar Kormas
- Department of Ichthyology & Aquatic Environment Faculty of Agricultural Sciences, University of Thessaly, Volos 382 21, Greece.
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31
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Host-Associated Bacterial Succession during the Early Embryonic Stages and First Feeding in Farmed Gilthead Sea Bream ( Sparus aurata). Genes (Basel) 2019; 10:genes10070483. [PMID: 31247994 PMCID: PMC6678923 DOI: 10.3390/genes10070483] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/07/2019] [Accepted: 06/21/2019] [Indexed: 02/07/2023] Open
Abstract
One of the most widely reared fish in the Mediterranean Sea is Sparus aurata. The succession of S. aurata whole-body microbiota in fertilized eggs, five, 15, 21 and 71 days post hatch (dph) larvae and the contribution of the rearing water and the provided feed (rotifers, Artemia sp. and commercial diet) to the host’s microbiota was investigated by 454 pyrosequencing of the 16S rRNA gene diversity. In total, 1917 bacterial operational taxonomic units (OTUs) were found in all samples. On average, between 93 ± 2.1 and 366 ± 9.2 bacterial OTUs per sample were found, with most of them belonging to Proteobacteria and Bacteroidetes. Ten OTUs were shared between all S. aurata stages and were also detected in the rearing water or diet. The highest OTU richness occurred at the egg stage and the lowest at the yolk sac stage (5 dph). The rearing water and diet microbial communities contributed in S. aurata microbiota without overlaps in their microbial composition and structure. The commercial diet showed higher contribution to the S. aurata microbiota than the rearing water. After stage D71 the observed microbiota showed similarities with that of adult S. aurata as indicated by the increased number of OTUs associated with γ-Proteobacteria and Firmicutes.
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