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ODFM, an omics data resource from microorganisms associated with fermented foods. Sci Data 2021; 8:113. [PMID: 33879798 PMCID: PMC8058077 DOI: 10.1038/s41597-021-00895-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 03/23/2021] [Indexed: 11/08/2022] Open
Abstract
ODFM is a data management system that integrates comprehensive omics information for microorganisms associated with various fermented foods, additive ingredients, and seasonings (e.g. kimchi, Korean fermented vegetables, fermented seafood, solar salt, soybean paste, vinegar, beer, cheese, sake, and yogurt). The ODFM archives genome, metagenome, metataxonome, and (meta)transcriptome sequences of fermented food-associated bacteria, archaea, eukaryotic microorganisms, and viruses; 131 bacterial, 38 archaeal, and 28 eukaryotic genomes are now available to users. The ODFM provides both the Basic Local Alignment Search Tool search-based local alignment function as well as average nucleotide identity-based genetic relatedness measurement, enabling gene diversity and taxonomic analyses of an input query against the database. Genome sequences and annotation results of microorganisms are directly downloadable, and the microbial strains registered in the archive library will be available from our culture collection of fermented food-associated microorganisms. The ODFM is a comprehensive database that covers the genomes of an entire microbiome within a specific food ecosystem, providing basic information to evaluate microbial isolates as candidate fermentation starters for fermented food production.
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Silva WM, Sousa CS, Oliveira LC, Soares SC, Souza GF, Tavares GC, Resende CP, Folador EL, Pereira FL, Figueiredo H, Azevedo V. Comparative proteomic analysis of four biotechnological strains Lactococcus lactis through label-free quantitative proteomics. Microb Biotechnol 2019; 12:265-274. [PMID: 30341804 PMCID: PMC6389847 DOI: 10.1111/1751-7915.13305] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 06/25/2018] [Accepted: 07/21/2018] [Indexed: 12/12/2022] Open
Abstract
Lactococcus lactis is a bacteria with high biotechnological potential, where is frequently used in the amino acid production and production of fermented dairy products, as well as drug delivery systems and mucosal vaccine vector. The knowledge of a functional core proteome is important extremely for both fundamental understanding of cell functions and for synthetic biology applications. In this study, we characterized the L. lacits proteome from proteomic analysis of four biotechnological strains L. lactis: L. lactis subsp. lactis NCDO2118, L. lactis subsp. lactis IL1403, L. lactis subsp. cremoris NZ9000 and L. lactis subsp. cremoris MG1363. Our label-free quantitative proteomic analysis of the whole bacterial lysates from each strains resulted in the characterization of the L. lactis core proteome that was composed by 586 proteins, which might contribute to resistance of this bacterium to different stress conditions as well as involved in the probiotic characteristic of L. lactis. Kegg enrichment analysis shows that ribosome, metabolic pathways, pyruvate metabolism and microbial metabolism in diverse environments were the most enriched. According to our quantitative proteomic analysis, proteins related to translation process were the more abundant in the core proteome, which represent an important step in the synthetic biology. In addition, we identified a subset of conserved proteins that are exclusive of the L. lactis subsp. cremoris or L. lactis subsp. lactis, which some are related to metabolic pathway exclusive. Regarding specific proteome of NCDO2118, we detected 'strain-specific proteins'. Finally, proteogenomics analysis allows the identification of proteins, which were not previously annotated in IL1403 and MG1363. The results obtained in this study allowed to increase our knowledge about the biology of L. lactis, which contributes to the implementation of strategies that make it possible to increase the biotechnological potential of this bacterium.
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Affiliation(s)
- Wanderson M. Silva
- Departamento de Biologia GeralInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteMinas GeraisBrasil
| | - Cassiana S. Sousa
- Departamento de Biologia GeralInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteMinas GeraisBrasil
| | - Leticia C. Oliveira
- Departamento de Biologia GeralInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteMinas GeraisBrasil
- Departamento de Microbiologia, Imunologia e ParasitologiaInstituto de Ciências Naturais e BiológicasUniversidade Federal do Triangulo MineiroUberabaMinas GeraisBrasil
| | - Siomar C. Soares
- Departamento de Microbiologia, Imunologia e ParasitologiaInstituto de Ciências Naturais e BiológicasUniversidade Federal do Triangulo MineiroUberabaMinas GeraisBrasil
| | - Gustavo F.M.H. Souza
- MS Applications LaboratoryWaters CorporationWaters Technologies BrazilAlphavilleSão PauloBrasil
| | - Guilherme C. Tavares
- AQUACENEscola de VeterináriaUniversidade Federal de Minas GeraisBelo HorizonteMinas GeraisBrasil
| | - Cristiana P. Resende
- AQUACENEscola de VeterináriaUniversidade Federal de Minas GeraisBelo HorizonteMinas GeraisBrasil
| | - Edson L. Folador
- Centro de BiotecnologiaUniversidade Federal da ParaíbaJoão PessoaParaíbaBrasil
| | - Felipe L. Pereira
- AQUACENEscola de VeterináriaUniversidade Federal de Minas GeraisBelo HorizonteMinas GeraisBrasil
| | - Henrique Figueiredo
- AQUACENEscola de VeterináriaUniversidade Federal de Minas GeraisBelo HorizonteMinas GeraisBrasil
| | - Vasco Azevedo
- Departamento de Biologia GeralInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteMinas GeraisBrasil
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Nóbrega MS, Silva BS, Leomil L, Tschoeke DA, Campeão ME, Garcia GD, Dias GA, Vieira VV, Thompson CC, Thompson FL. Description of Alteromonas abrolhosensis sp. nov., isolated from sea water of Abrolhos Bank, Brazil. Antonie van Leeuwenhoek 2018; 111:1131-1138. [PMID: 29349565 DOI: 10.1007/s10482-018-1016-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 01/10/2018] [Indexed: 11/29/2022]
Abstract
Two Gram-negative, motile, aerobic bacteria isolated from waters of the Abrolhos Bank were classified through a whole genome-based taxonomy. Strains PEL67ET and PEL68C shared 99% 16S rRNA and dnaK sequence identity with Alteromonas marina SW-47T and Alteromonas macleodii ATCC 27126T. In silico DNA-DNA Hybridization, i.e. genome-to-genome distance (GGD), average amino acid identity (AAI) and average nucleotide identity (ANI) showed that PEL67ET and PEL68C had identity values between 33-36, 86-88 and 83-84%, and 85-86 and 83%, respectively, towards their close neighbors A. macleodii ATCC 27126T and A. marina SW-47T. The DNA G + C contents of PEL67ET and PEL68C were 44.5%. The phenotypic features that differentiate PEL67ET and PEL68C strains from their close neighbors were assimilation of galactose and activity of phosphatase, and lack of mannitol, maltose, acetate, xylose and glycerol assimilation and lack of lipase, α and β-glucosidase activity. The new species Alteromonas abrolhosensis is proposed. The type strain is PEL67ET (= CBAS 610T = CAIM 1925T).
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Affiliation(s)
- Maria S Nóbrega
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Bruno S Silva
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Luciana Leomil
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Diogo Antonio Tschoeke
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil.,Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental de Macaé (NUPEM), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil.,SAGE-COPPE, Federal University of Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Mariana E Campeão
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Gizele D Garcia
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil.,Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
| | - Graciela A Dias
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | | | - Cristiane C Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil. .,CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Av. Carlos Chagas Filho 373. Sala 102, Bloco A, Rio de Janeiro, RJ, CEP 21941-599, Brazil.
| | - Fabiano L Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil. .,SAGE-COPPE, Federal University of Rio de Janeiro, Rio De Janeiro, RJ, Brazil. .,CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Av. Carlos Chagas Filho 373. Sala 102, Bloco A, Rio de Janeiro, RJ, CEP 21941-599, Brazil.
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Draft Genome Sequence of
Pseudoalteromonas
sp. Strain PAB 2.2 Isolated from Abrolhos Bank (Brazil). GENOME ANNOUNCEMENTS 2017; 5:5/10/e00016-17. [PMID: 28280012 PMCID: PMC5347232 DOI: 10.1128/genomea.00016-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We present here the draft genome sequence of Pseudoalteromonas sp. strain PAB 2.2, isolated from water of Parcel de Abrolhos coral reef (17°57′32.7″; 38°30′20.3″), on Abrolhos Bank, at a depth of 12 m. The assembly consists of 4,434,635 bp and contains 40 contigs, with a G+C content of 41.60%.
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