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Lokesh J, Siriyappagouder P, Fernandes JMO. Unravelling the temporal and spatial variation of fungal phylotypes from embryo to adult stages in Atlantic salmon. Sci Rep 2024; 14:981. [PMID: 38200059 PMCID: PMC10781754 DOI: 10.1038/s41598-023-50883-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Early microbial colonization has a profound impact on host physiology during different stages of ontogeny. Although several studies have focused on early bacterial colonization and succession, the composition and role of fungal communities are poorly known in fish. Here, we sequenced the internal transcribed spacer 2 (ITS2) region of fungi to profile the mycobiome associated with the eggs, hatchlings and intestine of Atlantic salmon at various freshwater and marine stages. In most of the stages studied, fungal diversity was lower than bacterial diversity. There were several stage-specific fungal phylotypes belonging to different stages of ontogeny but some groups, such as Candida tropicalis, Saccharomyces cerevisiae, Alternaria metachromatica, Davidiella tassiana and Humicola nigrescens, persisted during successive stages of ontogeny. We observed significant changes in the intestinal fungal communities during the first feeding. Prior to first feeding, Humicola nigrescens dominated, but Saccharomyces cerevisiae (10 weeks post hatch) and Candida tropicalis (12 weeks post hatch) became dominant subsequently. Seawater transfer resulted in a decrease in alpha diversity and an increase in Candida tropicalis abundance. We also observed notable variations in beta diversity and composition between the different farms. Overall, the present study sheds light on the fungal communities of Atlantic salmon from early ontogeny to adulthood. These novel findings will also be useful in future studies investigating host-microbiota interactions in the context of developing better nutritional and health management strategies for Atlantic salmon farming.
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Affiliation(s)
- Jep Lokesh
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
- Université de Pau et des Pays de l'Adour, E2S UPPA. INRAE, NUMEA, Saint-Pée-Sur-Nivelle, France.
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Keiz K, Ulrich S, Wenderlein J, Keferloher P, Wiesinger A, Neuhaus K, Lagkouvardos I, Wedekind H, Straubinger RK. The Development of the Bacterial Community of Brown Trout ( Salmo trutta) during Ontogeny. Microorganisms 2023; 11:211. [PMID: 36677503 PMCID: PMC9863972 DOI: 10.3390/microorganisms11010211] [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: 12/22/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Brown trout (Salmo trutta) is an important aquaculture species in Germany, but its production faces challenges due to global warming and a high embryo mortality. Climate factors might influence the fish's bacterial community (BC) and thus increase embryo mortality. Yet, knowledge of the physiological BC during ontogeny in general is scarce. In this project, the BC of brown trout has been investigated in a period from unfertilized egg to 95 days post fertilization (dpf) using 16S rRNA gene amplicon sequencing. Developmental changes differed between early and late ontogeny and major differences in BC occurred especially during early developmental stages. Thus, analysis was conducted separately for 0 to 67 dpf and from 67 to 95 dpf. All analyzed stages were sampled in toto to avoid bias due to different sampling methods in different developmental stages. The most abundant phylum in the BC of all developmental stages was Pseudomonadota, while only two families (Comamonadaceae and Moraxellaceae) occurred in all developmental stages. The early developmental stages until 67 dpf displayed greater shifts in their BC regarding bacterial richness, microbial diversity, and taxonomic composition. Thereafter, in the fry stages, the BC seemed to stabilize and changes were moderate. In future studies, a reduction in the sampling time frames during early development, an increase in sampling numbers, and an attempt for biological reproduction in order to characterize the causes of these variations is recommended.
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Affiliation(s)
- Katharina Keiz
- Institute of Infectious Diseases and Zoonosis, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - Sebastian Ulrich
- Institute of Infectious Diseases and Zoonosis, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - Jasmin Wenderlein
- Institute of Infectious Diseases and Zoonosis, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - Patrick Keferloher
- Bavarian State Research Center for Agriculture (LfL), Institute for Fisheries (IFI), Weilheimer Straße 8, 82319 Starnberg, Germany
| | - Anna Wiesinger
- Institute of Infectious Diseases and Zoonosis, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - Klaus Neuhaus
- Core Facility Microbiome, ZIEL—Institute for Food & Health, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Ilias Lagkouvardos
- Core Facility Microbiome, ZIEL—Institute for Food & Health, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology and Aquaculture (IMBBC), 715 00 Heraklion, Greece
| | - Helmut Wedekind
- Bavarian State Research Center for Agriculture (LfL), Institute for Fisheries (IFI), Weilheimer Straße 8, 82319 Starnberg, Germany
| | - Reinhard K. Straubinger
- Institute of Infectious Diseases and Zoonosis, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, Veterinärstr. 13, 80539 Munich, Germany
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Najafpour B, Pinto PIS, Moutou KA, Canario AVM, Power DM. Factors Driving Bacterial Microbiota of Eggs from Commercial Hatcheries of European Seabass and Gilthead Seabream. Microorganisms 2021; 9:2275. [PMID: 34835401 PMCID: PMC8619918 DOI: 10.3390/microorganisms9112275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 02/07/2023] Open
Abstract
A comprehensive understanding of how bacterial community abundance changes in fishes during their lifecycle and the role of the microbiota on health and production is still lacking. From this perspective, the egg bacterial communities of two commercially farmed species, the European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata), from different aquaculture sites were compared, and the potential effect of broodstock water microbiota and disinfectants on the egg microbiota was evaluated. Moreover, 16S ribosomal RNA gene sequencing was used to profile the bacterial communities of the eggs and broodstock water from three commercial hatcheries. Proteobacteria were the most common and dominant phyla across the samples (49.7% on average). Vibrio sp. was the most highly represented genus (7.1%), followed by Glaciecola (4.8%), Pseudoalteromonas (4.4%), and Colwellia (4.2%), in eggs and water across the sites. Routinely used iodine-based disinfectants slightly reduced the eggs' bacterial load but did not significantly change their composition. Site, species, and type of sample (eggs or water) drove the microbial community structure and influenced microbiome functional profiles. The egg and seawater microbiome composition differed in abundance but shared similar functional profiles. The strong impact of site and species on egg bacterial communities indicates that disease management needs to be site-specific and highlights the need for species- and site-specific optimization of disinfection protocols.
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Affiliation(s)
- Babak Najafpour
- Centro de Ciências do Mar (CCMAR/CIIMAR), Universidade do Algarve, 8005-139 Faro, Portugal; (B.N.); (P.I.S.P.); (A.V.M.C.)
| | - Patricia I. S. Pinto
- Centro de Ciências do Mar (CCMAR/CIIMAR), Universidade do Algarve, 8005-139 Faro, Portugal; (B.N.); (P.I.S.P.); (A.V.M.C.)
| | - Katerina A. Moutou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41221 Larissa, Greece;
| | - Adelino V. M. Canario
- Centro de Ciências do Mar (CCMAR/CIIMAR), Universidade do Algarve, 8005-139 Faro, Portugal; (B.N.); (P.I.S.P.); (A.V.M.C.)
| | - Deborah M. Power
- Centro de Ciências do Mar (CCMAR/CIIMAR), Universidade do Algarve, 8005-139 Faro, Portugal; (B.N.); (P.I.S.P.); (A.V.M.C.)
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Bekaert M, Goffin N, McMillan S, Desbois AP. Essential Genes of Vibrio anguillarum and Other Vibrio spp. Guide the Development of New Drugs and Vaccines. Front Microbiol 2021; 12:755801. [PMID: 34745063 PMCID: PMC8564382 DOI: 10.3389/fmicb.2021.755801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/24/2021] [Indexed: 01/04/2023] Open
Abstract
Essential genes in bacterial pathogens are potential drug targets and vaccine candidates because disrupting their function is lethal. The development of new antibiotics, in addition to effective prevention measures such as vaccination, contributes to addressing the global problem of bacterial antibiotic resistance. The aim of this present study was to determine the essential genes of Vibrio anguillarum, a bacterial pathogen of aquatic animals, as a means to identify putative targets for novel drugs and to assist the prioritisation of potential vaccine candidates. Essential genes were characterised by a Tn-seq approach using the TnSC189 mariner transposon to construct a library of 52,662 insertion mutants. In total, 329 essential genes were identified, with 34.7% found within the core genome of this species; each of these genes represents a strong potential drug target. Seven essential gene products were predicted to reside in the cell membrane or be released extracellularly, thus serving as putative vaccine candidates. Comparison to essential gene data from five other studies of Vibrio species revealed 13 proteins to be conserved across the studies, while 25 genes were specific to V. anguillarum and not found to be essential in the other Vibrio spp. This study provides new information on the essential genes of Vibrio species and the methodology may be applied to other pathogens to guide the development of new drugs and vaccines, which will assist efforts to counter antibiotic resistance.
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Affiliation(s)
| | | | | | - Andrew P. Desbois
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
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