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Laguna JG, Freitas ADS, Barroso FAL, De Jesus LCL, De Vasconcelos OAGG, Quaresma LS, Américo MF, Campos GM, Glória RDA, Dutra JDCF, Da Silva TF, Vital KD, Fernandes SO, Souza RO, Martins FDS, Ferreira E, Santos TM, Birbrair A, De Oliveira MFA, Faria AMC, Carvalho RDDO, Venanzi FM, Le Loir Y, Jan G, Guédon É, Azevedo VADC. Recombinant probiotic Lactococcus lactis delivering P62 mitigates moderate colitis in mice. Front Microbiol 2024; 15:1309160. [PMID: 38680913 PMCID: PMC11047439 DOI: 10.3389/fmicb.2024.1309160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/21/2024] [Indexed: 05/01/2024] Open
Abstract
Introduction and objective p62 is a human multifunctional adaptor protein involved in key cellular processes such as tissue homeostasis, inflammation, and cancer. It acts as a negative regulator of inflammasome complexes. It may thus be considered a good candidate for therapeutic use in inflammatory bowel diseases (IBD), such as colitis. Probiotics, including recombinant probiotic strains producing or delivering therapeutic biomolecules to the host mucosal surfaces, could help prevent and mitigate chronic intestinal inflammation. The objective of the present study was to combine the intrinsic immunomodulatory properties of the probiotic Lactococcus lactis NCDO2118 with its ability to deliver health-promoting molecules to enhance its protective and preventive effects in the context of ulcerative colitis (UC). Material and methods This study was realized in vivo in which mice were supplemented with the recombinant strain. The intestinal barrier function was analyzed by monitoring permeability, secretory IgA total levels, mucin expression, and tight junction genes. Its integrity was evaluated by histological analyses. Regarding inflammation, colonic cytokine levels, myeloperoxidase (MPO), and expression of key genes were monitored. The intestinal microbiota composition was investigated using 16S rRNA Gene Sequencing. Results and discussion No protective effect of L. lactis NCDO2118 pExu:p62 was observed regarding mice clinical parameters compared to the L. lactis NCDO2118 pExu: empty. However, the recombinant strain, expressing p62, increased the goblet cell counts, upregulated Muc2 gene expression in the colon, and downregulated pro-inflammatory cytokines Tnf and Ifng when compared to L. lactis NCDO2118 pExu: empty and inflamed groups. This recombinant strain also decreased colonic MPO activity. No difference in the intestinal microbiota was observed between all treatments. Altogether, our results show that recombinant L. lactis NCDO2118 delivering p62 protein protected the intestinal mucosa and mitigated inflammatory damages caused by dextran sodium sulfate (DSS). We thus suggest that p62 may constitute part of a therapeutic approach targeting inflammation.
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Affiliation(s)
- Juliana Guimarães Laguna
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Andria dos Santos Freitas
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Luís Cláudio Lima De Jesus
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Ludmila Silva Quaresma
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Monique Ferrary Américo
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Gabriela Munis Campos
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Rafael de Assis Glória
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Joyce da Cruz Ferraz Dutra
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Tales Fernando Da Silva
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Kátia Duarte Vital
- Department of Clinical Analysis and Toxicology, Federal University of Minas Gerais Belo Horizonte, Minas Gerais, Brazil
| | - Simone O. Fernandes
- Department of Clinical Analysis and Toxicology, Federal University of Minas Gerais Belo Horizonte, Minas Gerais, Brazil
| | - Ramon O. Souza
- Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Enio Ferreira
- Department of General Pathology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Túlio Marcos Santos
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Alexander Birbrair
- Department of General Pathology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Ana Maria Caetano Faria
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Franco Maria Venanzi
- School of Biosciences and Veterinary Medicine, University of Camerino, Matelica, Italy
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Laroute V, Aubry N, Audonnet M, Mercier-Bonin M, Daveran-Mingot ML, Cocaign-Bousquet M. Natural diversity of lactococci in γ-aminobutyric acid (GABA) production and genetic and phenotypic determinants. Microb Cell Fact 2023; 22:178. [PMID: 37689693 PMCID: PMC10492284 DOI: 10.1186/s12934-023-02181-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/18/2023] [Indexed: 09/11/2023] Open
Abstract
BACKGROUND γ-aminobutyric acid (GABA) is a bioactive compound produced by lactic acid bacteria (LAB). The diversity of GABA production in the Lactococcus genus is poorly understood. Genotypic and phenotypic approaches were therefore combined in this study to shed light on this diversity. A comparative genomic study was performed on the GAD-system genes (gadR, gadC and gadB) involved in GABA production in 36 lactococci including L. lactis and L. cremoris species. In addition, 132 Lactococcus strains were screened for GABA production in culture medium supplemented with 34 mM L-glutamic acid with or without NaCl (0.3 M). RESULTS Comparative analysis of the nucleotide sequence alignments revealed the same genetic organization of the GAD system in all strains except one, which has an insertion sequence element (IS981) into the PgadCB promoter. This analysis also highlighted several deletions including a 3-bp deletion specific to the cremoris species located in the PgadR promoter, and a second 39-bp deletion specific to L. cremoris strains with a cremoris phenotype. Phenotypic analysis revealed that GABA production varied widely, but it was higher in L. lactis species than in L. cremoris, with an exceptional GABA production of up to 14 and 24 mM in two L. lactis strains. Moreover, adding chloride increased GABA production in some L. cremoris and L. lactis strains by a factor of up to 16 and GAD activity correlated well with GABA production. CONCLUSIONS This genomic analysis unambiguously characterized the cremoris phenotype of L. cremoris species and modified GadB and GadR proteins explain why the corresponding strains do not produce GABA. Finally, we found that glutamate decarboxylase activity revealing GadB protein amount, varied widely between the strains and correlated well with GABA production both with and without chloride. As this protein level is associated to gene expression, the regulation of GAD gene expression was identified as a major contributor to this diversity.
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Affiliation(s)
- Valérie Laroute
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Nathalie Aubry
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Marjorie Audonnet
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Muriel Mercier-Bonin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Marie-Line Daveran-Mingot
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Muriel Cocaign-Bousquet
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
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3
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Alves JL, Lemos L, Rodrigues NM, Pereira VB, Barros PAV, Canesso MCC, Guimarães MAF, Cara DC, Miyoshi A, Azevedo VA, Maioli TU, Gomes-Santos AC, Faria AMC. Immunomodulatory effects of different strains of Lactococcus lactis in DSS-induced colitis. Braz J Microbiol 2023; 54:1203-1215. [PMID: 36821043 PMCID: PMC10234881 DOI: 10.1007/s42770-023-00928-0] [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: 12/12/2021] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are gastrointestinal disorders characterized by a breakdown in intestinal homeostasis by inflammatory immune responses to luminal antigens. Novel strategies for ameliorating IBD have been proposed in many studies using animal models. Our group has demonstrated that administration of Lactococcus lactis NCDO 2118 can improve clinical parameters of colitis induced by oral administration of dextran sulphate sodium (DSS). However, it is not clear whether other strains of L. lactis can yield the same effect. The objective of present study was to analyze the effects of three different L. lactis strains (NCDO2118, IL1403 and MG1363) in the development of DSS-induced colitis in C57BL/6 mice. Acute colitis was induced in C57/BL6 mice by the administration of 2% DSS during 7 consecutive days. Body weight loss and shortening of colon length were observed in DSS-treated mice, and none of L. lactis strains had an impact in these clinical signs of colitis. On the other hand, all strains improved the global macroscopical disease index and prevented goblet cells depletion as well as the increase of intestinal permeability. TNF-α production was reduced in gut mucosa of L. lactis DSS-treated mice indicating a modulation of a critical pro-inflammatory response by all strains tested. However, only L. lactis NCDO2118 and MG1363 induced a higher frequency of CD11c+CD11b-CD103+ tolerogenic dendritic cells in lymphoid organs of mice at steady state. We conclude that all tested strains of L. lactis improved the clinical scores and parameters of colitis, which confirm their anti-inflammatory properties in this model of colitis.
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Affiliation(s)
- Juliana Lima Alves
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil.
| | - Luisa Lemos
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Nubia Morais Rodrigues
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Vanessa Bastos Pereira
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Ecologia E Evolução, Belo Horizonte, MG, Brazil
| | - Patrícia A Vieira Barros
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Maria Cecília Campos Canesso
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Mauro A F Guimarães
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Denise Carmona Cara
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Anderson Miyoshi
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Ecologia E Evolução, Belo Horizonte, MG, Brazil
| | - Vasco Ariston Azevedo
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Ecologia E Evolução, Belo Horizonte, MG, Brazil
| | - Tatiani Uceli Maioli
- Departamento de Nutrição, Escola de Enfermagem, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Ana Cristina Gomes-Santos
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Ana Maria Caetano Faria
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil.
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Laroute V, Beaufrand C, Gomes P, Nouaille S, Tondereau V, Daveran-Mingot ML, Theodorou V, Eutamene H, Mercier-Bonin M, Cocaign-Bousquet M. Lactococcus lactis NCDO2118 exerts visceral antinociceptive properties in rat via GABA production in the gastro-intestinal tract. eLife 2022; 11:77100. [PMID: 35727704 PMCID: PMC9213000 DOI: 10.7554/elife.77100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 06/01/2022] [Indexed: 12/01/2022] Open
Abstract
Gut disorders associated to irritable bowel syndrome (IBS) are combined with anxiety and depression. Evidence suggests that microbially produced neuroactive molecules, like γ-aminobutyric acid (GABA), can modulate the gut-brain axis. Two natural strains of Lactococcus lactis and one mutant were characterized in vitro for their GABA production and tested in vivo in rat by oral gavage for their antinociceptive properties. L. lactis NCDO2118 significantly reduced visceral hypersensitivity induced by stress due to its glutamate decarboxylase (GAD) activity. L. lactis NCDO2727 with similar genes for GABA metabolism but no detectable GAD activity had no in vivo effect, as well as the NCDO2118 ΔgadB mutant. The antinociceptive effect observed for the NCDO2118 strain was mediated by the production of GABA in the gastro-intestinal tract and blocked by GABAB receptor antagonist. Only minor changes in the faecal microbiota composition were observed after the L. lactis NCDO2118 treatment. These findings reveal the crucial role of the microbial GAD activity of L. lactis NCDO2118 to deliver GABA into the gastro-intestinal tract for exerting antinociceptive properties in vivo and open avenues for this GRAS (Generally Recognized As safe) bacterium in the management of visceral pain and anxious profile of IBS patients.
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Affiliation(s)
- Valérie Laroute
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Catherine Beaufrand
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Pedro Gomes
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.,Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Sébastien Nouaille
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Valérie Tondereau
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | | | - Vassilia Theodorou
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Hélène Eutamene
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Muriel Mercier-Bonin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Muriel Cocaign-Bousquet
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
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5
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Fatahi-Bafghi M, Naseri S, Alizehi A. Genome analysis of probiotic bacteria for antibiotic resistance genes. Antonie van Leeuwenhoek 2022; 115:375-389. [PMID: 34989942 DOI: 10.1007/s10482-021-01703-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 12/21/2021] [Indexed: 12/30/2022]
Abstract
To date, probiotic bacteria are used in the diet and have various clinical applications. There are reports of antibiotic resistance genes in these bacteria that can transfer to other commensal and pathogenic bacteria. The aim of this study was to use whole-genome sequence analysis to identify antibiotic resistance genes in a group of bacterial with probiotic properties. Also, this study followed existing issues about the importance and presence of antibiotic resistance genes in these bacteria and the dangers that may affect human health in the future. In the current study, a collection of 126 complete probiotic bacterial genomes was analyzed for antibiotic resistance genes. The results of the current study showed that there are various resistance genes in these bacteria that some of them are transferable to other bacteria. The tet(W) tetracycline resistance gene was more than other antibiotic resistance genes in these bacteria and this gene was found in Bifidobacterium and Lactobacillus. In our study, the most numbers of antibiotic resistance genes were transferred with mobile genetic elements. We propose that probiotic companies before the use of a micro-organism as a probiotic, perform an antibiotic susceptibility testing for a large number of antibiotics. Also, they perform analysis of complete genome sequence for prediction of antibiotic resistance genes.
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Affiliation(s)
- Mehdi Fatahi-Bafghi
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran. .,Zoonotic Diseases Research Center, Department of Food Hygiene and Safety, School of Public Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Sara Naseri
- Zoonotic Diseases Research Center, Department of Food Hygiene and Safety, School of Public Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Ali Alizehi
- International Campus, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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Ardalani O, Motamedian E, Hamedi J. Reconstruction and validation of genome-scale metabolic model of L. lactis subsp. lactis NCDO 2118 and in silico analysis for succinate and Gamma-aminobutyric acid overproduction. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Cordeiro BF, Alves JL, Belo GA, Oliveira ER, Braga MP, da Silva SH, Lemos L, Guimarães JT, Silva R, Rocha RS, Jan G, Le Loir Y, Silva MC, Freitas MQ, Esmerino EA, Gala-García A, Ferreira E, Faria AMC, Cruz AG, Azevedo V, do Carmo FLR. Therapeutic Effects of Probiotic Minas Frescal Cheese on the Attenuation of Ulcerative Colitis in a Murine Model. Front Microbiol 2021; 12:623920. [PMID: 33737918 PMCID: PMC7960676 DOI: 10.3389/fmicb.2021.623920] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/18/2021] [Indexed: 01/14/2023] Open
Abstract
Inflammatory bowel diseases (IBDs) constitute disturbances of gastrointestinal tract that cause irreversible changes in the structure and function of tissues. Ulcerative colitis (UC), the most frequent IBD in the population, is characterized by prominent inflammation of the human colon. Functional foods containing probiotic bacteria have been studied as adjuvants to the treatment or prevention of IBDs. The selected probiotic strain Lactococcus lactis NCDO 2118 (L. lactis NCDO 2118) exhibits immunomodulatory effects, with promising results in UC mouse model induced by dextran sodium sulfate (DSS). Additionally, cheese is a dairy food that presents high nutritional value, besides being a good delivery system that can be used to improve survival and enhance the therapeutic effects of probiotic bacteria in the host. Therefore, this work investigated the probiotic therapeutic effects of an experimental Minas Frescal cheese containing L. lactis NCDO 2118 in DSS-induced colitis in mice. During colitis induction, mice that consumed the probiotic cheese exhibited reduced in the severity of colitis, with attenuated weight loss, lower disease activity index, limited shortening of the colon length, and reduced histopathological score. Moreover, probiotic cheese administration increased gene expression of tight junctions’ proteins zo-1, zo-2, ocln, and cln-1 in the colon and increase IL-10 release in the spleen and lymph nodes. In this way, this work demonstrates that consumption of probiotic Minas Frescal cheese, containing L. lactis NCDO 2118, prevents the inflammatory process during DSS-induced colitis in mice, opening perspectives for the development of new probiotic functional foods for personalized nutrition in the context of IBD.
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Affiliation(s)
- Bárbara F Cordeiro
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Juliana L Alves
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Giovanna A Belo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Emiliano R Oliveira
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Marina P Braga
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Sara H da Silva
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Luisa Lemos
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil.,Department of Infectious Diseases, Harvard Medical School, Massachusetts General Hospital, Boston, MA, United States
| | - Jonas T Guimarães
- Faculdade de Medicina Veterinária, Universidade Federal Fluminense (UFF), Niterói, Brazil
| | - Ramon Silva
- Faculdade de Medicina Veterinária, Universidade Federal Fluminense (UFF), Niterói, Brazil.,Departamento de Alimentos, Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro (IFRJ), Rio de Janeiro, Brazil
| | - Ramon S Rocha
- Faculdade de Medicina Veterinária, Universidade Federal Fluminense (UFF), Niterói, Brazil.,Departamento de Alimentos, Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro (IFRJ), Rio de Janeiro, Brazil
| | - Gwénaël Jan
- INRAE, STLO, Institut Agro, Agrocampus Ouest, Rennes, France
| | - Yves Le Loir
- INRAE, STLO, Institut Agro, Agrocampus Ouest, Rennes, France
| | - Marcia Cristina Silva
- Departamento de Alimentos, Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro (IFRJ), Rio de Janeiro, Brazil
| | - Mônica Q Freitas
- Faculdade de Medicina Veterinária, Universidade Federal Fluminense (UFF), Niterói, Brazil
| | - Erick A Esmerino
- Faculdade de Medicina Veterinária, Universidade Federal Fluminense (UFF), Niterói, Brazil
| | - Alfonso Gala-García
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Enio Ferreira
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Ana Maria C Faria
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Adriano G Cruz
- Departamento de Alimentos, Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro (IFRJ), Rio de Janeiro, Brazil
| | - Vasco Azevedo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Fillipe L R do Carmo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil.,INRAE, STLO, Institut Agro, Agrocampus Ouest, Rennes, France
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Román Naranjo D, Callanan M, Thierry A, McAuliffe O. Superior esterolytic activity in environmental Lactococcus lactis strains is linked to the presence of the SGNH hydrolase family of esterases. JDS COMMUNICATIONS 2020; 1:25-28. [PMID: 36341150 PMCID: PMC9623632 DOI: 10.3168/jdsc.2020-0003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/02/2020] [Indexed: 12/28/2022]
Abstract
Lactococcus lactis from environmental niches show high esterolytic activity Higher metabolic diversity is seen in environmental versus dairy L. lactis strains SGNH hydrolase family of esterases may be linked to high esterolytic activity
Lactococcus lactis strains are widely used in the dairy industry in fermentation processes for production of cheese and fermented milks. However, the esterolytic activity of L. lactis is not generally considered high. For this reason, purified microbial lipases and esterases are often added in certain dairy processes to generate specific flavors in the final food product. This work demonstrates the superior esterolytic activity of a collection of L. lactis strains isolated from different environmental sources compared with that of dairy-derived strains. It provides further evidence of the more diverse metabolic capabilities displayed by L. lactis strains from environmental sources compared to their domesticated dairy counterparts. Furthermore, the presence of a 1,287-bp gene encoding a 428-amino acid SGNH hydrolase in the high-esterolytic environmental strains suggests a possible link between superior esterolytic activity and the presence of the esterase from the SGNH hydrolase family.
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Affiliation(s)
- Desirée Román Naranjo
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- Cork Institute of Technology, Cork, Ireland
| | - Michael Callanan
- Cork Institute of Technology, Cork, Ireland
- VistaMilk SFI Research Centre, Moorepark, Fermoy, Cork, Ireland
| | | | - Olivia McAuliffe
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- VistaMilk SFI Research Centre, Moorepark, Fermoy, Cork, Ireland
- Corresponding author
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Liu J, Meng F, Du Y, Nelson E, Zhao G, Zhu H, Caiyin Q, Zhang Z, Qiao J. Co-production of Nisin and γ-Aminobutyric Acid by Engineered Lactococcus lactis for Potential Application in Food Preservation. Front Microbiol 2020; 11:49. [PMID: 32063895 PMCID: PMC7000361 DOI: 10.3389/fmicb.2020.00049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 01/10/2020] [Indexed: 02/05/2023] Open
Abstract
Microbiological contamination and oxidative damage are the two main challenges in maintaining quality and improving shelf-life of foods. Here, we developed a Lactococcus lactis fermentation system that could simultaneously produce nisin, an antimicrobial peptide, and γ-aminobutyric acid (GABA), an antioxidant agent. In this system, we metabolically engineered a nisin producing strain L. lactis F44 for GABA production by expression of glutamate decarboxylase and glutamate/GABA antiporter. GABA biosynthesis could facilitate nisin production through enhancing acid resistance of the strain. By applying a two-stage pH-control fermentation strategy, the engineered strain yielded up to 9.12 g/L GABA, which was 2.2 times higher than that of pH-constant fermentation. Furthermore, we demonstrated the potential application of the freeze-dried fermentation product as a preservative to improve the storage performance of meat and fruit. These results suggested that the fermentation product of nisin-GABA co-producing strain could serve as a cost-effective, easily prepared, and high-performance food preservative.
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Affiliation(s)
- Jiaheng Liu
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Furong Meng
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Yuhui Du
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, Beijing, China
| | - Edwina Nelson
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Guangrong Zhao
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Hongji Zhu
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Qinggele Caiyin
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Zhijun Zhang
- Key Laboratory of Storage of Agricultural Products, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Jianjun Qiao
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
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10
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Marques Da Silva W, Oliveira LC, Soares SC, Sousa CS, Tavares GC, Resende CP, Pereira FL, Ghosh P, Figueiredo H, Azevedo V. Quantitative Proteomic Analysis of the Response of Probiotic Putative Lactococcus lactis NCDO 2118 Strain to Different Oxygen Availability Under Temperature Variation. Front Microbiol 2019; 10:759. [PMID: 31031733 PMCID: PMC6470185 DOI: 10.3389/fmicb.2019.00759] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/26/2019] [Indexed: 02/06/2023] Open
Abstract
Lactococcus lactis is a gram positive facultative anaerobe widely used in the dairy industry and human health. L. lactis subsp. lactis NCDO 2118 is a strain that exhibits anti-inflammatory and immunomodulatory properties. In this study, we applied a label-free shotgun proteomic approach to characterize and quantify the NCDO 2118 proteome in response to variations of temperature and oxygen bioavailability, which constitute the environmental conditions found by this bacterium during its passage through the host gastro-intestinal tract and in other industrial processes. From this proteomic analysis, a total of 1,284 non-redundant proteins of NCDO 2118 were characterized, which correspond to approximately 54% of its predicted proteome. Comparative proteomic analysis identified 149 and 136 proteins in anaerobic (30°C and 37°C) and non-aerated (30°C and 37°C) conditions, respectively. Our label-free proteomic analysis quantified a total of 1,239 proteins amongst which 161 proteins were statistically differentially expressed. Main differences were observed in cellular metabolism, stress response, transcription and proteins associated to cell wall. In addition, we identified six strain-specific proteins of NCDO 2118. Altogether, the results obtained in our study will help to improve the understanding about the factors related to both physiology and adaptive processes of L. lactis NCDO 2118 under changing environmental conditions.
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Affiliation(s)
- Wanderson Marques Da Silva
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Leticia Castro Oliveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triangulo Mineiro, Uberaba, Brazil
| | - Siomar Castro Soares
- Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triangulo Mineiro, Uberaba, Brazil
| | - Cassiana Severiano Sousa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Felipe Luis Pereira
- AQUACEN, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Henrique Figueiredo
- AQUACEN, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vasco Azevedo
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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11
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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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12
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Frantzen CA, Kleppen HP, Holo H. Lactococcus lactis Diversity in Undefined Mixed Dairy Starter Cultures as Revealed by Comparative Genome Analyses and Targeted Amplicon Sequencing of epsD. Appl Environ Microbiol 2018; 84:e02199-17. [PMID: 29222100 PMCID: PMC5772235 DOI: 10.1128/aem.02199-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/10/2017] [Indexed: 12/20/2022] Open
Abstract
Undefined mesophilic mixed (DL) starter cultures are used in the production of continental cheeses and contain unknown strain mixtures of Lactococcus lactis and leuconostocs. The choice of starter culture affects the taste, aroma, and quality of the final product. To gain insight into the diversity of Lactococcus lactis strains in starter cultures, we whole-genome sequenced 95 isolates from three different starter cultures. Pan-genomic analyses, which included 30 publically available complete genomes, grouped the strains into 21 L. lactis subsp. lactis and 28 L. lactis subsp. cremoris lineages. Only one of the 95 isolates grouped with previously sequenced strains, and the three starter cultures showed no overlap in lineage distributions. The culture diversity was assessed by targeted amplicon sequencing using purR, a core gene, and epsD, present in 93 of the 95 starter culture isolates but absent in most of the reference strains. This enabled an unprecedented discrimination of starter culture Lactococcus lactis and revealed substantial differences between the three starter cultures and compositional shifts during the cultivation of cultures in milk.IMPORTANCE In contemporary cheese production, standardized frozen seed stock starter cultures are used to ensure production stability, reproducibility, and quality control of the product. The dairy industry experiences significant disruptions of cheese production due to phage attacks, and one commonly used countermeasure to phage attack is to employ a starter rotation strategy, in which two or more starters with minimal overlap in phage sensitivity are used alternately. A culture-independent analysis of the lactococcal diversity in complex undefined starter cultures revealed large differences between the three starter cultures and temporal shifts in lactococcal composition during the production of bulk starters. A better understanding of the lactococcal diversity in starter cultures will enable the development of more robust starter cultures and assist in maintaining the efficiency and stability of the production process by ensuring the presence of key bacteria that are important to the characteristics of the product.
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Affiliation(s)
- Cyril A Frantzen
- Laboratory of Microbial Gene Technology and Food Microbiology, Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Hans Petter Kleppen
- Laboratory of Microbial Gene Technology and Food Microbiology, Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- ACD Pharmaceuticals AS, Leknes, Norway
| | - Helge Holo
- Laboratory of Microbial Gene Technology and Food Microbiology, Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- TINE SA, Oslo, Norway
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13
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Golomb BL, Yu AO, Coates LC, Marco ML. The Lactococcus lactis KF147 nonribosomal peptide synthetase/polyketide synthase system confers resistance to oxidative stress during growth on plant leaf tissue lysate. Microbiologyopen 2017; 7. [PMID: 28921941 PMCID: PMC5822349 DOI: 10.1002/mbo3.531] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 07/24/2017] [Accepted: 08/01/2017] [Indexed: 01/07/2023] Open
Abstract
Strains of Lactococcus lactis isolated from plant tissues possess adaptations that support their survival and growth in plant‐associated microbial habitats. We previously demonstrated that genes coding for a hybrid nonribosomal peptide synthetase/polyketide synthase (NRPS/PKS) system involved in production of an uncharacterized secondary metabolite are specifically induced in L. lactis KF147 during growth on plant tissues. Notably, this NRPS/PKS has only been identified in plant‐isolated strains of L. lactis. Here, we show that the L. lactis KF147 NRPS/PKS genes have homologs in certain Streptococcus mutans isolates and the genetic organization of the NRPS/PKS locus is conserved among L. lactis strains. Using an L. lactis KF147 mutant deficient in synthesis of NrpC, a 4′‐phosphopantetheinyl transferase, we found that the NRPS/PKS system improves L. lactis during growth under oxidative conditions in Arapidopsis thaliana leaf lysate. The NRPS/PKS system also improves tolerance of L. lactis to reactive oxygen species and specifically H2O2 and superoxide radicals in culture medium. These findings indicate that this secondary metabolite provides a novel mechanism for reactive oxygen species detoxification not previously known for this species.
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Affiliation(s)
- Benjamin L Golomb
- Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Annabelle O Yu
- Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Laurynne C Coates
- Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Maria L Marco
- Department of Food Science and Technology, University of California, Davis, CA, USA
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14
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Oliveira LDC, Silveira AMM, Monteiro ADS, dos Santos VL, Nicoli JR, Azevedo VADC, Soares SDC, Dias-Souza MV, Nardi RMD. In silico Prediction, in vitro Antibacterial Spectrum, and Physicochemical Properties of a Putative Bacteriocin Produced by Lactobacillus rhamnosus Strain L156.4. Front Microbiol 2017; 8:876. [PMID: 28579977 PMCID: PMC5437165 DOI: 10.3389/fmicb.2017.00876] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 05/01/2017] [Indexed: 11/13/2022] Open
Abstract
A bacteriocinogenic Lactobacillus rhamnosus L156.4 strain isolated from the feces of NIH mice was identified by 16S rRNA gene sequencing and MALDI-TOF mass spectrometry. The entire genome was sequenced using Illumina, annotated in the PGAAP, and RAST servers, and deposited. Conserved genes associated with bacteriocin synthesis were predicted using BAGEL3, leading to the identification of an open reading frame (ORF) that shows homology with the L. rhamnosus GG (ATCC 53103) prebacteriocin gene. The encoded protein contains a conserved protein motif associated a structural gene of the Enterocin A superfamily. We found ORFs related to the prebacteriocin, immunity protein, ABC transporter proteins, and regulatory genes with 100% identity to those of L. rhamnosus HN001. In this study, we provide evidence of a putative bacteriocin produced by L. rhamnosus L156.4 that was further confirmed by in vitro assays. The antibacterial activity of the substances produced by this strain was evaluated using the deferred agar-spot and spot-on-the lawn assays, and a wide antimicrobial activity spectrum against human and foodborne pathogens was observed. The physicochemical characterization of the putative bacteriocin indicated that it was sensitive to proteolytic enzymes, heat stable and maintained its antibacterial activity in a pH ranging from 3 to 9. The activity against Lactobacillus fermentum, which was used as an indicator strain, was detected during bacterial logarithmic growth phase, and a positive correlation was confirmed between bacterial growth and production of the putative bacteriocin. After a partial purification from cell-free supernatant by salt precipitation, the putative bacteriocin migrated as a diffuse band of approximately 1.0-3.0 kDa by SDS-PAGE. Additional studies are being conducted to explore its use in the food industry for controlling bacterial growth and for probiotic applications.
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Affiliation(s)
- Letícia de C. Oliveira
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Aline M. M. Silveira
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Andréa de S. Monteiro
- Laboratório de Microbiologia, Programa de Pós-graduação em Biologia Parasitária, Universidade CEUMASão Luís, Brazil
| | - Vera L. dos Santos
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Jacques R. Nicoli
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Vasco A. de C. Azevedo
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Siomar de C. Soares
- Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo MineiroUberaba, Brazil
| | - Marcus V. Dias-Souza
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Regina M. D. Nardi
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
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15
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Oliveira LC, Saraiva TDL, Silva WM, Pereira UP, Campos BC, Benevides LJ, Rocha FS, Figueiredo HCP, Azevedo V, Soares SC. Analyses of the probiotic property and stress resistance-related genes of Lactococcus lactis subsp. lactis NCDO 2118 through comparative genomics and in vitro assays. PLoS One 2017; 12:e0175116. [PMID: 28384209 PMCID: PMC5383145 DOI: 10.1371/journal.pone.0175116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/21/2017] [Indexed: 11/19/2022] Open
Abstract
Lactococcus lactis subsp. lactis NCDO 2118 was recently reported to alleviate colitis symptoms via its anti-inflammatory and immunomodulatory activities, which are exerted by exported proteins that are not produced by L. lactis subsp. lactis IL1403. Here, we used in vitro and in silico approaches to characterize the genomic structure, the safety aspects, and the immunomodulatory activity of this strain. Through comparative genomics, we identified genomic islands, phage regions, bile salt and acid stress resistance genes, bacteriocins, adhesion-related and antibiotic resistance genes, and genes encoding proteins that are putatively secreted, expressed in vitro and absent from IL1403. The high degree of similarity between all Lactococcus suggests that the Symbiotic Islands commonly shared by both NCDO 2118 and KF147 may be responsible for their close relationship and their adaptation to plants. The predicted bacteriocins may play an important role against the invasion of competing strains. The genes related to the acid and bile salt stresses may play important roles in gastrointestinal tract survival, whereas the adhesion proteins are important for persistence in the gut, culminating in the competitive exclusion of other bacteria. Finally, the five secreted and expressed proteins may be important targets for studies of new anti-inflammatory and immunomodulatory proteins. Altogether, the analyses performed here highlight the potential use of this strain as a target for the future development of probiotic foods.
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Affiliation(s)
- Letícia C. Oliveira
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Tessália D. L. Saraiva
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Wanderson M. Silva
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Ulisses P. Pereira
- Department of Preventive Veterinary Medicine, State University of Londrina, Londrina—PR, Brazil
| | - Bruno C. Campos
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Leandro J. Benevides
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Flávia S. Rocha
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Henrique C. P. Figueiredo
- Official Laboratory of Fisheries Ministry—Veterinary School, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Siomar C. Soares
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba—MG, Brazil
- * E-mail:
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16
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Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation. BMC Genomics 2017; 18:267. [PMID: 28356072 PMCID: PMC5372332 DOI: 10.1186/s12864-017-3650-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 03/21/2017] [Indexed: 01/07/2023] Open
Abstract
Background Lactococcus lactis is among the most widely studied lactic acid bacterial species due to its long history of safe use and economic importance to the dairy industry, where it is exploited as a starter culture in cheese production. Results In the current study, we report on the complete sequencing of 16 L. lactis subsp. lactis and L. lactis subsp. cremoris genomes. The chromosomal features of these 16 L. lactis strains in conjunction with 14 completely sequenced, publicly available lactococcal chromosomes were assessed with particular emphasis on discerning the L. lactis subspecies division, evolution and niche adaptation. The deduced pan-genome of L. lactis was found to be closed, indicating that the representative data sets employed for this analysis are sufficient to fully describe the genetic diversity of the taxon. Conclusions Niche adaptation appears to play a significant role in governing the genetic content of each L. lactis subspecies, while (differential) genome decay and redundancy in the dairy niche is also highlighted. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3650-5) contains supplementary material, which is available to authorized users.
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17
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Mariano DCB, Pereira FL, Aguiar EL, Oliveira LC, Benevides L, Guimarães LC, Folador EL, Sousa TJ, Ghosh P, Barh D, Figueiredo HCP, Silva A, Ramos RTJ, Azevedo VAC. SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology. BMC Bioinformatics 2016; 17:456. [PMID: 28105921 PMCID: PMC5249034 DOI: 10.1186/s12859-016-1344-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. RESULTS In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. CONCLUSION Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net .
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Affiliation(s)
- Diego C. B. Mariano
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Felipe L. Pereira
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Edgar L. Aguiar
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Letícia C. Oliveira
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Leandro Benevides
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Luís C. Guimarães
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Edson L. Folador
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Thiago J. Sousa
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Preetam Ghosh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, PurbaMedinipur WB-721172 India
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA USA
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, PurbaMedinipur WB-721172 India
| | - Henrique C. P. Figueiredo
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Artur Silva
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará Brazil
| | - Rommel T. J. Ramos
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará Brazil
| | - Vasco A. C. Azevedo
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
- Federal University of Minas Gerais, Institute of Biological Sciences, Antônio Carlos 6627, Pampulha, 30161-970 Belo Horizonte, Minas Gerais Brazil
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Laroute V, Yasaro C, Narin W, Mazzoli R, Pessione E, Cocaign-Bousquet M, Loubière P. GABA Production in Lactococcus lactis Is Enhanced by Arginine and Co-addition of Malate. Front Microbiol 2016; 7:1050. [PMID: 27458444 PMCID: PMC4934118 DOI: 10.3389/fmicb.2016.01050] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/22/2016] [Indexed: 11/13/2022] Open
Abstract
Lactococcus lactis NCDO 2118 was previously selected for its ability to decarboxylate glutamate to γ-aminobutyric acid (GABA), an interesting nutritional supplement able to improve mood and relaxation. Amino acid decarboxylation is generally considered as among the biochemical systems allowing lactic acid bacteria to counteracting acidic stress and obtaining metabolic energy. These strategies also include arginine deiminase pathway and malolactic fermentation but little is known about their possible interactions of with GABA production. In the present study, the effects of glutamate, arginine, and malate (i.e., the substrates of these acid-resistance pathways) on L. lactis NCDO 2118 growth and GABA production performances were analyzed. Both malate and arginine supplementation resulted in an efficient reduction of acidity and improvement of bacterial biomass compared to glutamate supplementation. Glutamate decarboxylation was limited to narrow environmental conditions (pH < 5.1) and physiological state (stationary phase). However, some conditions were able to improve GABA production or activate glutamate decarboxylation system even outside of this compass. Arginine clearly stimulated glutamate decarboxylation: the highest GABA production (8.6 mM) was observed in cultures supplemented with both arginine and glutamate. The simultaneous addition of arginine, malate, and glutamate enabled earlier GABA production (i.e., during exponential growth) at relatively high pH (6.5). As far as we know, no previous study has reported GABA production in such conditions. Although further studies are needed to understand the molecular basis of these phenomena, these results represent important keys suitable of application in GABA production processes.
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Affiliation(s)
- Valérie Laroute
- Laboratoire d’Ingénierie des Systéms Biologiques et des Procédés, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées, ToulouseFrance
| | - Chonthicha Yasaro
- Laboratoire d’Ingénierie des Systéms Biologiques et des Procédés, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées, ToulouseFrance
| | - Waranya Narin
- Laboratoire d’Ingénierie des Systéms Biologiques et des Procédés, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées, ToulouseFrance
| | - Roberto Mazzoli
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di TorinoTurin, Italy
| | - Enrica Pessione
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di TorinoTurin, Italy
| | - Muriel Cocaign-Bousquet
- Laboratoire d’Ingénierie des Systéms Biologiques et des Procédés, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées, ToulouseFrance
| | - Pascal Loubière
- Laboratoire d’Ingénierie des Systéms Biologiques et des Procédés, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées, ToulouseFrance
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Cui Y, Hu T, Qu X, Zhang L, Ding Z, Dong A. Plasmids from Food Lactic Acid Bacteria: Diversity, Similarity, and New Developments. Int J Mol Sci 2015; 16:13172-202. [PMID: 26068451 PMCID: PMC4490491 DOI: 10.3390/ijms160613172] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/09/2015] [Accepted: 05/22/2015] [Indexed: 12/24/2022] Open
Abstract
Plasmids are widely distributed in different sources of lactic acid bacteria (LAB) as self-replicating extrachromosomal genetic materials, and have received considerable attention due to their close relationship with many important functions as well as some industrially relevant characteristics of the LAB species. They are interesting with regard to the development of food-grade cloning vectors. This review summarizes new developments in the area of lactic acid bacteria plasmids and aims to provide up to date information that can be used in related future research.
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Affiliation(s)
- Yanhua Cui
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Tong Hu
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Xiaojun Qu
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin 150010, China.
| | - Lanwei Zhang
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Zhongqing Ding
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Aijun Dong
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
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Kelleher P, Murphy J, Mahony J, van Sinderen D. Next-generation sequencing as an approach to dairy starter selection. DAIRY SCIENCE & TECHNOLOGY 2015; 95:545-568. [PMID: 26798445 PMCID: PMC4712225 DOI: 10.1007/s13594-015-0227-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/25/2015] [Accepted: 04/02/2015] [Indexed: 02/06/2023]
Abstract
Lactococcal and streptococcal starter strains are crucial ingredients to manufacture fermented dairy products. As commercial starter culture suppliers and dairy producers attempt to overcome issues of phage sensitivity and develop new product ranges, there is an ever increasing need to improve technologies for the rational selection of novel starter culture blends. Whole genome sequencing, spurred on by recent advances in next-generation sequencing platforms, is a promising approach to facilitate rapid identification and selection of such strains based on gene-trait matching. This review provides a comprehensive overview of the available methodologies to analyse the technological potential of candidate starter strains and highlights recent advances in the area of dairy starter genomics.
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Affiliation(s)
- Philip Kelleher
- School of Microbiology, University College Cork, Cork, Ireland
| | - James Murphy
- School of Microbiology, University College Cork, Cork, Ireland
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, Cork, Ireland
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