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da Silva Santos D, Freitas NSA, de Morais MA, Mendonça AA. Liquorilactobacillus: A Context of the Evolutionary History and Metabolic Adaptation of a Bacterial Genus from Fermentation Liquid Environments. J Mol Evol 2024:10.1007/s00239-024-10189-6. [PMID: 39017924 DOI: 10.1007/s00239-024-10189-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 07/09/2024] [Indexed: 07/18/2024]
Abstract
In the present work, we carried out a comparative genomic analysis to trace the evolutionary trajectory of the bacterial species that make up the Liquorilactobacillus genus, from the identification of genes and speciation/adaptation mechanisms in their unique characteristics to the identification of the pattern grouping these species. We present phylogenetic relationships between Liquorilactobacillus and related taxa such as Bacillus, basal lactobacilli and Ligilactobacillus, highlighting evolutionary divergences and lifestyle transitions across different taxa. The species of this genus share a core genome of 1023 genes, distributed in all COGs, which made it possible to characterize it as Liquorilactobacillus sensu lato: few amino acid auxotrophy, low genes number for resistance to antibiotics and general and specific cellular reprogramming mechanisms for environmental responses. These species were divided into four clades, with diversity being enhanced mainly by the diversity of genes involved in sugar metabolism. Clade 1 presented lower (< 70%) average amino acid identity with the other clades, with exclusive or absent genes, and greater distance in the genome compared to clades 2, 3 and 4. The data pointed to an ancestor of clades 2, 3 and 4 as being the origin of the genus Ligilactobacillus, while the species of clade 1 being closer to the ancestral Bacillus. All these traits indicated that the species of clade 1 could be soon separated in a distinct genus.
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Affiliation(s)
- Dayane da Silva Santos
- Department of Genetics, Federal University of Pernambuco, Av. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | | | - Marcos Antonio de Morais
- Department of Genetics, Federal University of Pernambuco, Av. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil.
| | - Allyson Andrade Mendonça
- Department of Genetics, Federal University of Pernambuco, Av. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil.
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Qiao N, Bechtner J, Cnockaert M, Depoorter E, Díaz-Muñoz C, Vandamme P, De Vuyst L, Gänzle MG. Comparative genomic analysis of Periweissella and the characterization of novel motile species. Appl Environ Microbiol 2023; 89:e0103423. [PMID: 37728921 PMCID: PMC10617413 DOI: 10.1128/aem.01034-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/14/2023] [Indexed: 09/22/2023] Open
Abstract
The genus Periweissella was proposed as a novel genus in the Lactobacillaceae in 2022. However, the phylogenetic relationship between Periweissella and other heterofermentative lactobacilli, and the genetic and physiological properties of this genus remain unclear. This study aimed to determine the phylogenetic relationship between Periweissella and the two closest genera, Weissella and Furfurilactobacillus, by the phylogenetic analysis and calculation of (core gene) pairwise average amino acid identity. Targeted genomic analysis showed that fructose bisphosphate aldolase was only present in the genome of Pw. cryptocerci. Mannitol dehydrogenase was found in genomes of Pw. beninensis, Pw. fabaria, and Pw. fabalis. Untargeted genomic analysis identified the presence of flagellar genes in Periweissella but not in other closely related genera. Phenotypes related to carbohydrate fermentation and motility matched the genotypes. Motility genes were organized in a single operon and the proteins shared a high amino acid similarity in the genus Periweissella. The relatively low similarity of motility operons between Periweissella and other motile lactobacilli indicated the acquisition of motility by the ancestral species. Our findings facilitate the phylogenetic, genetic, and phenotypic understanding of the genus Periweissella.ImportanceThe genus Periweissella is a heterofermentative genus in the Lactobacillaceae which includes predominantly isolates from cocoa fermentations in tropical climates. Despite the relevance of the genus in food fermentations, genetic and physiological properties of the genus are poorly characterized and genome sequences became available only after 2020. This study characterized strains of the genus by functional genomic analysis, and by determination of metabolic and physiological traits. Phylogenetic analysis revealed that Periweissella is the evolutionary link between rod-shaped heterofermentative lactobacilli and the coccoid Leuconostoc clade with the genera Weissella and Furfurilactobacillus as closest relatives. Periweissella is the only heterofermentative genus in the Lactobacillaceae which comprises predominantly motile strains. The genomic, physiological, and metabolic characterization of Periweissella may facilitate the potential use of strains of the genus as starter culture in traditional or novel food fermentations.
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Affiliation(s)
- Nanzhen Qiao
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Julia Bechtner
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Margo Cnockaert
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Laboratory of Microbiology, Ghent, Belgium
| | - Eliza Depoorter
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Laboratory of Microbiology, Ghent, Belgium
| | - Christian Díaz-Muñoz
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Laboratory of Microbiology, Ghent, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Michael G. Gänzle
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
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Miotto SPS, Fensterseifer LC, de Souza Hassemer G, Martins G, Ficagna E, Steffens J, Puton BMS, Backes GT, Valduga E, Cansian RL. Malolactic fermentation of lactic acid bacteria isolated from southern Brazilian red wine. World J Microbiol Biotechnol 2023; 39:201. [PMID: 37202540 DOI: 10.1007/s11274-023-03645-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023]
Abstract
The objective was to isolate lactic acid bacteria (LAB) from southern Brazil's wines and investigate their potential as starter cultures for malolactic fermentation (MLF) in Merlot (ME) and Cabernet Sauvignon (CS) wines through the fermentative capacity. The LAB were isolated from CS, ME, and Pinot Noir (PN) wines in the 2016 and 2017 harvests and evaluated for morphological (color and shape of the colonies), genetic, fermentative (increase in pH, acidity reduction, preservation of anthocyanins, decarboxylation of L-malic acid, yield of L-lactic acid, and content of reduced sugars), and sensory characteristics. Four strains were identified as Oenococcus oeni [CS(16)3B1, ME(16)1A1, ME(17)26, and PN(17)65], one as Lactiplantibacillus plantarum [PN(17)75], and one as Paucilactobacillus suebicus [CS(17)5]. Isolates were evaluated in the MLF and compared to a commercial strain (O. oeni), as well as a control (without inoculation and spontaneous MLF), and standard (without MLF). CS(16)3B1 and ME(17)26 isolates finished the MLF for CS and ME wines, respectively, after 35 days, similar to the commercial strain, and CS(17)5 and ME(16)1A1 isolates ended the MLF in 45 days. In the sensory analysis, ME wines with isolated strains received better scores for flavor and overall quality than the control. Compared to the commercial strain, CS(16)3B1 isolate obtained the highest scores for buttery flavor and taste persistence. CS(17)5 isolate received the higher scores for a fruity flavor and overall quality and the lowest for a buttery flavor. The native LAB displayed MLF potential, regardless of the year and grape species from which they were isolated.
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Affiliation(s)
- Shana Paula Segala Miotto
- Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul, Campus Bento Gonçalves. Av. Osvaldo Aranha, 540. Zip code, Bento Gonçalves, 95700-000, RS, Brazil
| | - Letícia Caroline Fensterseifer
- Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul, Campus Bento Gonçalves. Av. Osvaldo Aranha, 540. Zip code, Bento Gonçalves, 95700-000, RS, Brazil
| | - Guilherme de Souza Hassemer
- Universidade Regional Integrada do Alto Uruguai e das Missões, Campus Erechim. Av. Sete de Setembro, 1621. Zip code, Erechim, 99709-910, RS, Brazil
| | - Guilherme Martins
- Institut des Sciences de la Vigne et du Vin - ISVV, Université de Bordeaux. 210 Chem. de Leysotte, Villenave-d'Ornon, 33140, France
| | - Evandro Ficagna
- Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul, Campus Bento Gonçalves. Av. Osvaldo Aranha, 540. Zip code, Bento Gonçalves, 95700-000, RS, Brazil
| | - Juliana Steffens
- Universidade Regional Integrada do Alto Uruguai e das Missões, Campus Erechim. Av. Sete de Setembro, 1621. Zip code, Erechim, 99709-910, RS, Brazil
| | - Bruna Maria Saorin Puton
- Universidade Regional Integrada do Alto Uruguai e das Missões, Campus Erechim. Av. Sete de Setembro, 1621. Zip code, Erechim, 99709-910, RS, Brazil.
| | - Geciane Toniazzo Backes
- Universidade Regional Integrada do Alto Uruguai e das Missões, Campus Erechim. Av. Sete de Setembro, 1621. Zip code, Erechim, 99709-910, RS, Brazil
| | - Eunice Valduga
- Universidade Regional Integrada do Alto Uruguai e das Missões, Campus Erechim. Av. Sete de Setembro, 1621. Zip code, Erechim, 99709-910, RS, Brazil
| | - Rogério Luis Cansian
- Universidade Regional Integrada do Alto Uruguai e das Missões, Campus Erechim. Av. Sete de Setembro, 1621. Zip code, Erechim, 99709-910, RS, Brazil
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Puertas AI, Llamas-Arriba MG, Etxebeste O, Berregi I, Pardo MÁ, Prieto A, López P, Dueñas MT. Characterization of the heteropolysaccharides produced by Liquorilactobacillus sicerae CUPV261 and Secundilactobacillus collinoides CUPV237 isolated from cider. Int J Food Microbiol 2023; 397:110199. [PMID: 37086527 DOI: 10.1016/j.ijfoodmicro.2023.110199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 04/24/2023]
Abstract
Some lactic acid bacteria (LAB) strains isolated from alcoholic beverages are able to produce exopolysaccharides (EPS). The present work focuses on the physico-chemical characterization of the heteropolysaccharides (HePS) produced by Liquorilactobacillus sicerae CUPV261T (formerly known as Lactobacillus sicerae) and Secundilactobacillus collinoides CUPV237 (formerly known as Lactobacillus collinoides) strains isolated from cider. Genome sequencing and assembly enabled the identification of at least four putative HePS gene clusters in each strain, which correlated with the ability of both strains to secrete EPS. The crude EPS preparation from CUPV261T contained glucose, galactose and rhamnose, and that of CUPV237 was composed of glucose, galactose and N-acetylglucosamine. Both EPS were mixtures of HePS of different composition, with two major soluble components of average molecular weights (Mw) in the range of 106 and 104 g.mol-1. These HePS were resistant to gastric stress conditions in an in vitro model, and they significantly reduced zebrafish larvae mortality in an in vivo model of inflammatory bowel disease.
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Affiliation(s)
- Ana Isabel Puertas
- Faculty of Chemistry, University of the Basque Country, UPV/EHU, Manuel de Lardizabal 3, 20018, San Sebastián, Spain
| | - Mª Goretti Llamas-Arriba
- Faculty of Chemistry, University of the Basque Country, UPV/EHU, Manuel de Lardizabal 3, 20018, San Sebastián, Spain
| | - Oier Etxebeste
- Faculty of Chemistry, University of the Basque Country, UPV/EHU, Manuel de Lardizabal 3, 20018, San Sebastián, Spain
| | - Iñaki Berregi
- Faculty of Chemistry, University of the Basque Country, UPV/EHU, Manuel de Lardizabal 3, 20018, San Sebastián, Spain
| | - Miguel Ángel Pardo
- Food Research Unit, Food and Marine Research Technology Centre AZTI, Parque Tecnológico de Bizkaia, Astondo Bidea, Building 609, 48160 Derio, Bizkaia, Spain
| | - Alicia Prieto
- Margarita Salas Biological Research Centre, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Paloma López
- Margarita Salas Biological Research Centre, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Mª Teresa Dueñas
- Faculty of Chemistry, University of the Basque Country, UPV/EHU, Manuel de Lardizabal 3, 20018, San Sebastián, Spain.
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Torres-Guardado R, Esteve-Zarzoso B, Reguant C, Bordons A. Microbial interactions in alcoholic beverages. Int Microbiol 2021; 25:1-15. [PMID: 34347199 DOI: 10.1007/s10123-021-00200-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022]
Abstract
This review examines the different types of interactions between the microorganisms involved in the fermentation processes of alcoholic beverages produced all over the world from cereals or fruit juices. The alcoholic fermentation converting sugars into ethanol is usually carried out by yeasts, mainly Saccharomyces cerevisiae, which can grow directly using fruit sugars, such as those in grapes for wine or apples for cider, or on previously hydrolyzed starch of cereals, such as for beers. Some of these beverages, or the worts obtained from cereals, can be distilled to obtain spirits. Besides S. cerevisiae, all alcoholic beverages can contain other microorganisms and especially in spontaneous fermentation when starter cultures are not used. These other microbes are mostly lactic acid bacteria and other yeasts-the non-Saccharomyces yeasts. The interactions between all these microorganisms are very diverse and complex, as in any natural occurring ecosystem, including food fermentations. To describe them, we have followed a simplified ecological classification of the interactions. The negative ones are amensalism, by which a metabolic product of one species has a negative effect on others, and antagonism, by which one microbe competes directly with others. The positive interactions are commensalism, by which one species has benefits but no apparent effect on others, and synergism, by which there are benefits for all the microbes and also for the final product. The main interactions in alcoholic beverages are between S. cerevisiae and non-Saccharomyces and between yeasts and lactic acid bacteria. These interactions can be related to metabolites produced by fermentation such as ethanol, or to secondary metabolites such as proteinaceous toxins, or are feed-related, either by competition for nutrients or by benefit from released compounds during yeast autolysis. The positive or negative effects of these interactions on the organoleptic qualities of the final product are also revised. Focusing mainly on the alcoholic beverages produced by spontaneous fermentations, this paper reviews the interactions between the different yeasts and lactic acid bacteria in wine, cider, beer, and in spirits such as tequila, mezcal and cachaça.
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Affiliation(s)
- Rafael Torres-Guardado
- Grup de Biotecnologia Enològica, Departament de Bioquímica i Biotecnologia, Facultat d´Enologia, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
| | - Braulio Esteve-Zarzoso
- Grup de Biotecnologia Enològica, Departament de Bioquímica i Biotecnologia, Facultat d´Enologia, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
| | - Cristina Reguant
- Grup de Biotecnologia Enològica, Departament de Bioquímica i Biotecnologia, Facultat d´Enologia, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
| | - Albert Bordons
- Grup de Biotecnologia Enològica, Departament de Bioquímica i Biotecnologia, Facultat d´Enologia, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain.
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Umegatani M, Takesue N, Asano S, Tadami H, Uemura K. Study of Beer Spoilage Lactobacillus nagelii Harboring Hop Resistance Gene horA. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2021. [DOI: 10.1080/03610470.2021.1915073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Minami Umegatani
- Research Laboratories for Alcohol Beverages, Asahi Breweries Ltd., Moriya, Japan
| | - Nobuchika Takesue
- Research Laboratories for Alcohol Beverages, Asahi Breweries Ltd., Moriya, Japan
| | - Shizuka Asano
- Research Laboratories for Alcohol Beverages, Asahi Breweries Ltd., Moriya, Japan
| | - Hideyo Tadami
- Research Laboratories for Alcohol Beverages, Asahi Breweries Ltd., Moriya, Japan
| | - Kazuhiko Uemura
- Research Laboratories for Alcohol Beverages, Asahi Breweries Ltd., Moriya, Japan
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Zheng J, Wittouck S, Salvetti E, Franz CMAP, Harris HMB, Mattarelli P, O'Toole PW, Pot B, Vandamme P, Walter J, Watanabe K, Wuyts S, Felis GE, Gänzle MG, Lebeer S. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int J Syst Evol Microbiol 2020; 70:2782-2858. [PMID: 32293557 DOI: 10.1099/ijsem.0.004107] [Citation(s) in RCA: 1536] [Impact Index Per Article: 384.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).
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Affiliation(s)
- Jinshui Zheng
- Huazhong Agricultural University, State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, PR China
| | - Stijn Wittouck
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Elisa Salvetti
- Dept. of Biotechnology, University of Verona, Verona, Italy
| | - Charles M A P Franz
- Max Rubner-Institut, Department of Microbiology and Biotechnology, Kiel, Germany
| | - Hugh M B Harris
- School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - Paola Mattarelli
- University of Bologna, Dept. of Agricultural and Food Sciences, Bologna, Italy
| | - Paul W O'Toole
- School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - Bruno Pot
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Jens Walter
- Department of Biological Sciences, University of Alberta, Edmonton, Canada.,Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada
| | - Koichi Watanabe
- Food Industry Research and Development Institute, Bioresource Collection and Research Center, Hsinchu, Taiwan, ROC.,National Taiwan University, Dept. of Animal Science and Technology, Taipei, Taiwan, ROC
| | - Sander Wuyts
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | | | - Michael G Gänzle
- Hubei University of Technology, College of Bioengineering and Food Science, Wuhan, Hubei, PR China.,Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada
| | - Sarah Lebeer
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
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Offret C, Jégou C, Mounier J, Fleury Y, Le Chevalier P. New insights into the haemo- and coelo-microbiota with antimicrobial activities from Echinodermata and Mollusca. J Appl Microbiol 2019; 126:1023-1031. [PMID: 30586216 DOI: 10.1111/jam.14184] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 12/05/2018] [Accepted: 12/08/2018] [Indexed: 11/26/2022]
Abstract
AIMS The aim of this study was to investigate the diversity of bacteria with antimicrobial activity present in the coelomic fluid and haemolymph of wild and healthy echinodermata and mollusca. METHODS AND RESULTS Collection expeditions of healthy marine molluscs and echinoderms were conducted in the Glenan archipelago in spring 2014. Members of the culturable microbiota present in the haemolymph, (haemo-microbiota) of Haliotis tuberculata (gastropoda, abalone) and Mytilus edulis (bivalvia, mussel), as well as in the coelomic fluid (coelo-microbiota) of Echinus esculentus (echinoidea, sea urchin) and Holothuria forskali (Holothuroidea, holothurian) were screened for antimicrobial activity, and further identified using 16S rRNA sequencing. Except for E. esculentus, culturable bacteria in the internal fluids of all studied organisms (mussel, abalone and holothurian) were more abundant than in seawater. The haemo- and coelo-microbiota with antimicrobial activity differed significantly between host species, in terms of abundance and diversity. Indeed, higher numbers were isolated from mussel than from abalone haemolymph. Moreover, in mussels and holothurians, bacteria with antimicrobial activities were predominantly Vibrio spp. (respectively 55 and 45%), while Pseudoalteromonas spp. were the most abundant (50%) in abalone haemolymph. Nevertheless, the activity spectra of these bacteria mainly included marine pathogens affiliated to the Vibrio genus. CONCLUSION The haemo- and coelo-microbiota with antimicrobial activities were significantly related to their host species and differed in terms of abundance and diversity. These bacteria may play a key role in host homeostasis against pathogens. SIGNIFICANCE AND IMPACT OF THE STUDY This study brings new knowledge on the diversity of bacteria present in the internal fluids of two marine molluscs and two echinoderms and their antimicrobial activities towards marine pathogens.
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Affiliation(s)
- C Offret
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbiennes LUBEM EA3882, Université de Brest, Technopole Brest-Iroise, Plouzané, France.,Food Sciences Department, Pavillon Paul-Comtois, Université Laval, Québec, Canada
| | - C Jégou
- Laboratoire de Biotechnologie et Chimie Marines LBCM EA3884, Université de Brest, Institut Universitaire Européen de la Mer, IUT Quimper, Quimper, France
| | - J Mounier
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbiennes LUBEM EA3882, Université de Brest, Technopole Brest-Iroise, Plouzané, France
| | - Y Fleury
- Laboratoire de Biotechnologie et Chimie Marines LBCM EA3884, Université de Brest, Institut Universitaire Européen de la Mer, IUT Quimper, Quimper, France
| | - P Le Chevalier
- Laboratoire de Biotechnologie et Chimie Marines LBCM EA3884, Université de Brest, Institut Universitaire Européen de la Mer, IUT Quimper, Quimper, France
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Cousin FJ, Le Guellec R, Chuat V, Dalmasso M, Laplace JM, Cretenet M. Multiplex PCR for rapid identification of major lactic acid bacteria genera in cider and other fermented foods. Int J Food Microbiol 2018; 291:17-24. [PMID: 30428422 DOI: 10.1016/j.ijfoodmicro.2018.11.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/24/2018] [Accepted: 11/04/2018] [Indexed: 10/27/2022]
Abstract
Lactobacillus, Pediococcus, Oenococcus and Leuconostoc are the main Lactic Acid Bacteria (LAB) genera present in cider as they are able to survive this hostile environment. LAB play a significant role in cider quality, for example in the process of malolactic fermentation, even though they can also be involved in spoilage of cider (production of biogenic amines, exopolysaccharides, off-flavours…). In this context a better monitoring of the fermentation process is a matter of interest to guarantee cider quality. In the present study, we designed a genus-specific multiplex PCR for a rapid and simultaneous detection of the four main LAB genera involved in cider production. This multiplex PCR worked equally with purified genomic DNA of bacterial isolates and with colonies directly picked from agar plates. This new PCR method was also successfully extended to wine and dairy isolates, and thus constitutes an effective tool to quickly identify LAB associated with fermented foods. Moreover, many biodiversity studies would also benefit from this fast, cheap and reliable identification method.
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Affiliation(s)
- Fabien J Cousin
- Normandie Univ, UNICAEN, UNIROUEN, ABTE, 14000 Caen, France.
| | | | | | - Marion Dalmasso
- Normandie Univ, UNICAEN, UNIROUEN, ABTE, 14000 Caen, France.
| | | | - Marina Cretenet
- Normandie Univ, UNICAEN, UNIROUEN, ABTE, 14000 Caen, France.
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Evaluation of the infB and rpsB gene fragments as genetic markers intended for identification and phylogenetic analysis of particular representatives of the order Lactobacillales. Arch Microbiol 2018; 200:1427-1437. [PMID: 30039323 DOI: 10.1007/s00203-018-1554-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/28/2018] [Accepted: 07/17/2018] [Indexed: 10/28/2022]
Abstract
Detailed differentiation, classification, and phylogenetic analysis of the order Lactobacillales are performed using molecular techniques that involve the comparison of whole genomes, multilocus sequence analysis, DNA-DNA hybridisation, and 16S rRNA sequencing. Despite the wide application of the latter two techniques, issues associated with them are extensively discussed. Although complete genomic analyses are the most appropriate for phylogenetic studies, they are time-consuming and require high levels of expertise. Many phylogenetic/identification markers have been proposed for enterococci, lactobacilli, streptococci, and lactobacilli. However, none have been established for vagococci and some genera within the order Lactobacillales. The objective of the study was to find novel alternative housekeeping genes for classification, typing, and phylogenetic analysis of selected genera within the order Lactobacillales. We designed primers flanking variable regions of the infB (504 nt) and rpsB (333 nt) genes and amplified and sequenced them in 56 strains of different genera within the order Lactobacillales. Statistical analysis and characteristics of the gene regions suggested that they could be used for taxonomic purposes. Phylogenetic analyses, including assessment of (in)congruence between individual phylogenetic trees indicated the possibility of using the concatenation of the two genes as an alternative tool for the evaluation of phylogeny compared with the 16S rRNA gene representing the standard phylogenetic marker of prokaryotes. Moreover, infB, rpsB regions and their concatenate were phylogenetically consistent with two widely applied alternative genetic markers in taxonomy of particular Lactobacillales genera encoding the 60 kDa chaperonin protein (GroEL-hsp60) and phenylalanyl-tRNA synthetase, alpha subunit (pheS).
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Disclosing diversity of exopolysaccharide-producing lactobacilli from Spanish natural ciders. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2017.12.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Cousin FJ, Le Guellec R, Schlusselhuber M, Dalmasso M, Laplace JM, Cretenet M. Microorganisms in Fermented Apple Beverages: Current Knowledge and Future Directions. Microorganisms 2017; 5:E39. [PMID: 28757560 PMCID: PMC5620630 DOI: 10.3390/microorganisms5030039] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 12/18/2022] Open
Abstract
Production of fermented apple beverages is spread all around the world with specificities in each country. 'French ciders' refer to fermented apple juice mainly produced in the northwest of France and often associated with short periods of consumption. Research articles on this kind of product are scarce compared to wine, especially on phenomena associated with microbial activities. The wine fermentation microbiome and its dynamics, organoleptic improvement for healthy and pleasant products and development of starters are now widely studied. Even if both beverages seem close in terms of microbiome and process (with both alcoholic and malolactic fermentations), the inherent properties of the raw materials and different production and environmental parameters make research on the specificities of apple fermentation beverages worthwhile. This review summarizes current knowledge on the cider microbial ecosystem, associated activities and the influence of process parameters. In addition, available data on cider quality and safety is reviewed. Finally, we focus on the future role of lactic acid bacteria and yeasts in the development of even better or new beverages made from apples.
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Affiliation(s)
- Fabien J Cousin
- Aliments Bioprocédés Toxicologie Environnements, Normandie Univ., UNICAEN, UNIROUEN, 14000 Caen, France.
| | - Rozenn Le Guellec
- Aliments Bioprocédés Toxicologie Environnements, Normandie Univ., UNICAEN, UNIROUEN, 14000 Caen, France.
| | - Margot Schlusselhuber
- Aliments Bioprocédés Toxicologie Environnements, Normandie Univ., UNICAEN, UNIROUEN, 14000 Caen, France.
| | - Marion Dalmasso
- Aliments Bioprocédés Toxicologie Environnements, Normandie Univ., UNICAEN, UNIROUEN, 14000 Caen, France.
| | - Jean-Marie Laplace
- Aliments Bioprocédés Toxicologie Environnements, Normandie Univ., UNICAEN, UNIROUEN, 14000 Caen, France.
| | - Marina Cretenet
- Aliments Bioprocédés Toxicologie Environnements, Normandie Univ., UNICAEN, UNIROUEN, 14000 Caen, France.
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Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y, Arita M. DFAST and DAGA: web-based integrated genome annotation tools and resources. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2016; 35:173-184. [PMID: 27867804 PMCID: PMC5107635 DOI: 10.12938/bmfh.16-003] [Citation(s) in RCA: 192] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/27/2016] [Indexed: 12/15/2022]
Abstract
Quality assurance and correct taxonomic affiliation of data submitted to public sequence databases have been an everlasting problem. The DDBJ Fast Annotation and Submission Tool (DFAST) is a newly developed genome annotation pipeline with quality and taxonomy assessment tools. To enable annotation of ready-to-submit quality, we also constructed curated reference protein databases tailored for lactic acid bacteria. DFAST was developed so that all the procedures required for DDBJ submission could be done seamlessly online. The online workspace would be especially useful for users not familiar with bioinformatics skills. In addition, we have developed a genome repository, DFAST Archive of Genome Annotation (DAGA), which currently includes 1,421 genomes covering 179 species and 18 subspecies of two genera, Lactobacillus and Pediococcus, obtained from both DDBJ/ENA/GenBank and Sequence Read Archive (SRA). All the genomes deposited in DAGA were annotated consistently and assessed using DFAST. To assess the taxonomic position based on genomic sequence information, we used the average nucleotide identity (ANI), which showed high discriminative power to determine whether two given genomes belong to the same species. We corrected mislabeled or misidentified genomes in the public database and deposited the curated information in DAGA. The repository will improve the accessibility and reusability of genome resources for lactic acid bacteria. By exploiting the data deposited in DAGA, we found intraspecific subgroups in Lactobacillus gasseri and Lactobacillus jensenii, whose variation between subgroups is larger than the well-accepted ANI threshold of 95% to differentiate species. DFAST and DAGA are freely accessible at https://dfast.nig.ac.jp.
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Affiliation(s)
- Yasuhiro Tanizawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan; Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Takatomo Fujisawa
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Eli Kaminuma
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Yasukazu Nakamura
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Masanori Arita
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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Draft Genome Sequence of Lactobacillus collinoides CUPV237, an Exopolysaccharide and Riboflavin Producer Isolated from Cider. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00506-16. [PMID: 27284133 PMCID: PMC4901224 DOI: 10.1128/genomea.00506-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Lactobacillus collinoides CUPV237 is a strain isolated from a Basque cider. Lactobacillus collinoides is one of the most frequent species found in cider from Spain, France, or England. A notable feature of the L. collinoides CUPV237 strain is its ability to produce exopolysaccharides.
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Detection and genomic characterization of motility in Lactobacillus curvatus: confirmation of motility in a species outside the Lactobacillus salivarius clade. Appl Environ Microbiol 2016; 81:1297-1308. [PMID: 25501479 DOI: 10.1128/aem.03594-14] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Lactobacillus is the largest genus within the lactic acid bacteria (LAB), with almost 180 species currently identified. Motility has been reported for at least 13 Lactobacillus species, all belonging to the Lactobacillus salivarius clade. Motility in lactobacilli is poorly characterized. It probably confers competitive advantages, such as superior nutrient acquisition and niche colonization, but it could also play an important role in innate immune system activation through flagellin–Toll-like receptor 5 (TLR5) interaction. We now report strong evidence of motility in a species outside the L. salivarius clade, Lactobacillus curvatus (strain NRIC0822). The motility of L. curvatus NRIC 0822 was revealed by phase-contrast microscopy and soft-agar motility assays. Strain NRIC 0822 was motile at temperatures between 15 °C and 37 °C, with a range of different carbohydrates, and under varying atmospheric conditions. We sequenced the L. curvatus NRIC 0822 genome, which revealed that the motility genes are organized in a single operon and that the products are very similar (>98.5% amino acid similarity over >11,000 amino acids) to those encoded by the motility operon of Lactobacillus acidipiscis KCTC 13900 (shown for the first time to be motile also). Moreover, the presence of a large number of mobile genetic elements within and flanking the motility operon of L. curvatus suggests recent horizontal transfer between members of two distinct Lactobacillus clades: L. acidipiscis in the L. salivarius clade and L. curvatus inthe L. sakei clade. This study provides novel phenotypic, genetic, and phylogenetic insights into flagellum-mediated motility in lactobacilli.
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