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Cabezas MP, Fonseca NA, Muñoz-Mérida A. MIMt: a curated 16S rRNA reference database with less redundancy and higher accuracy at species-level identification. ENVIRONMENTAL MICROBIOME 2024; 19:88. [PMID: 39522045 PMCID: PMC11550520 DOI: 10.1186/s40793-024-00634-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 10/31/2024] [Indexed: 11/16/2024]
Abstract
MOTIVATION Accurate determination and quantification of the taxonomic composition of microbial communities, especially at the species level, is one of the major issues in metagenomics. This is primarily due to the limitations of commonly used 16S rRNA reference databases, which either contain a lot of redundancy or a high percentage of sequences with missing taxonomic information. This may lead to erroneous identifications and, thus, to inaccurate conclusions regarding the ecological role and importance of those microorganisms in the ecosystem. RESULTS The current study presents MIMt, a new 16S rRNA database for archaea and bacteria's identification, encompassing 47 001 sequences, all precisely identified at species level. In addition, a MIMt2.0 version was created with only curated sequences from RefSeq Targeted loci with 32 086 sequences. MIMt aims to be updated twice a year to include all newly sequenced species. We evaluated MIMt against Greengenes, RDP, GTDB and SILVA in terms of sequence distribution and taxonomic assignments accuracy. Our results showed that MIMt contains less redundancy, and despite being 20 to 500 times smaller than existing databases, outperforms them in completeness and taxonomic accuracy, enabling more precise assignments at lower taxonomic ranks and thus, significantly improving species-level identification.
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Affiliation(s)
- M Pilar Cabezas
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Nuno A Fonseca
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Antonio Muñoz-Mérida
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, 4485-661, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
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Xavier R, Pérez-Losada M, Silva SM, Lino M, Faleiro MJ, Canada P. Lymphocystis viral disease impacts the diversity and functional profiles of the skin microbiome in gilthead seabream. Front Microbiol 2024; 15:1470572. [PMID: 39498134 PMCID: PMC11532066 DOI: 10.3389/fmicb.2024.1470572] [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: 07/25/2024] [Accepted: 09/30/2024] [Indexed: 11/07/2024] Open
Abstract
Lymphocystis viral disease (LVD) is a highly transmissible disease known to affect multiple fishes worldwide. Although this disease is usually benign, mortalities can occur in cases where infection is severe or secondary infection with bacterial pathogens and parasites occur. However, little is known about the bacterial dynamics of fish with LVD or what bacterial pathogens may be responsible for secondary infections. Here we assessed the effects of LVD on the skin microbiome of gilthead seabream by comparing 30 symptomatic, asymptomatic and recovered (three weeks after infection) fish using 16S rRNA high-throughput sequencing. Our results show that LVD is associated with significant changes in microbiome structure and function. Importantly, fish pathogens like Tenacibaculum maritimum and some Vibrio species increased their abundance. Moreover, microbial metabolic activities of the commensal microbiota that may confer some protection to fish were suppressed in diseased fish. After reducing fish cage density to treat symptoms and three weeks of recovery, the abundance of pathogens was significantly reduced and microbiome functionality was recovered, although community structure remained significantly different. These results show that LVD can severely disrupt the bacterial communities of the skin of the gilthead seabream, leading to an increase in bacterial pathogens responsible for relevant diseases in gilthead seabream farms.
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Affiliation(s)
- Raquel Xavier
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Marcos Pérez-Losada
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Sofia Marques Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Marilia Lino
- Department of Computer Sciences, Faculty of Sciences, University of Porto, Porto, Portugal
| | | | - Paula Canada
- CIIMAR/CIMAR-LA–Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
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Thomsson KA, Benktander J, Toxqui-Rodríguez S, Piazzon MC, Linden SK. Gilthead seabream mucus glycosylation is complex, differs between epithelial sites and carries unusual poly N-acetylhexosamine motifs. FISH & SHELLFISH IMMUNOLOGY 2024; 153:109864. [PMID: 39216712 DOI: 10.1016/j.fsi.2024.109864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 08/26/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Gilthead seabream (Sparus aurata) is a marine finfish of economic importance in aquaculture. Despite its adaptability to varying culture conditions, gilthead seabream culture can be affected by viral, bacterial or parasitic diseases. The main route of entry of pathogens is through mucosal surfaces. Teleost external and internal surfaces are covered by mucus, mainly comprised of highly glycosylated proteins called mucins. The mucin glycans regulate pathogen growth, adhesion, virulence and inter and intra species communication. Here, we characterized the gilthead seabream mucus glycosylation, compared it to previously described species and investigated associations with microbiota. 214 glycans were identified. The majority of the glycans were found at more than one epithelial surface, but 27, 22 and 89 O-glycan structures were unique to skin, gill and intestinal sample groups, respectively. Six O-glycan core types were observed. The majority of the seabream skin and gill O-glycans were neutral with unusual poly HexNAc motifs. In contrast, seabream intestinal O-glycans were highly acidic and not of the 'poly HexNAc' type observed in skin and gill. Furthermore, gilthead seabream gill mucosa had less oligomannose and more complex N-glycans compared to skin and intestine. The concentration and diversity of bacteria was similar in skin, gill and intestine, but the bacterial species differed between epithelia and co-varied with glycan epitopes. The presence of a complex mucus glycosylation with plenty of glycan epitopes for bacterial foraging, suggest that the skin mucosal defense in seabream includes an abundant resident microbiota. This large library of structures provides a platform for further studies, for example aiming to identifying glycans to use for diagnostic purposes, to study host-microbe interactions or disease intervention therapies.
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Affiliation(s)
- Kristina A Thomsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9C, 405 30, Gothenburg, Sweden
| | - John Benktander
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9C, 405 30, Gothenburg, Sweden
| | - Socorro Toxqui-Rodríguez
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), Ribera de Cabanes s/n, 12595, Cabanes, Castellón, Spain; Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), Ribera de Cabanes s/n, 12595, Cabanes, Castellón, Spain
| | - M Carla Piazzon
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), Ribera de Cabanes s/n, 12595, Cabanes, Castellón, Spain
| | - Sara K Linden
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9C, 405 30, Gothenburg, Sweden.
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Ruiz A, Gisbert E, Andree KB. Impact of the diet in the gut microbiota after an inter-species microbial transplantation in fish. Sci Rep 2024; 14:4007. [PMID: 38369563 PMCID: PMC10874947 DOI: 10.1038/s41598-024-54519-6] [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: 10/31/2023] [Accepted: 02/13/2024] [Indexed: 02/20/2024] Open
Abstract
Inter-species microbial transplantations offer the possibility of transferring species-specific microbes and their associated functionality. As a conceptual approach, an intestinal microbiota transplant (IMT) between two marine carnivorous fish species that thrive in different environmental conditions was conducted: from donor Atlantic salmon (Salmo salar) to recipient gilthead seabream (Sparus aurata), after obliterating its basal microbiota with an antibiotic treatment. To confirm that the gut microbiota was able to recover after antibiotics without the influence of the diet, a group of gilthead seabream not submitted to the IMT was kept fasted as an internal control. To assess the effect of the diet after the IMT, two groups of gilthead seabream were respectively fed with their typical diet and with Atlantic salmon diet. At 36 days post-IMT, the gut of the individuals fed with their typical diet was dominated by the feed-associated bacteria, while those fed with the salmon diet had developed a unique microbiota from the convergence of the diet, donor, and recipient microbiota. These results suggested that an intestinal microbiota transplantation may be effective if the basal microbiota from the gut is first cleared and a targeted dietary modification is provided to maintain and enrich the novel bacteria species over time.
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Affiliation(s)
- Alberto Ruiz
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de La Ràpita, Crta. Poble Nou, km 5.5, 43540, La Ràpita, Spain.
| | - Enric Gisbert
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de La Ràpita, Crta. Poble Nou, km 5.5, 43540, La Ràpita, Spain
| | - Karl B Andree
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de La Ràpita, Crta. Poble Nou, km 5.5, 43540, La Ràpita, Spain
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