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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: 1517] [Impact Index Per Article: 379.3] [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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Wei YX, Gu CT. Lactobacillus yilanensis sp. nov., Lactobacillus bayanensis sp. nov., Lactobacillus keshanensis sp. nov., Lactobacillus kedongensis sp. nov., Lactobacillus baiquanensis sp. nov., Lactobacillus jidongensis sp. nov., Lactobacillus hulinensis sp. nov., Lactobacillus mishanensis sp. nov. and Lactobacillus zhongbaensis sp. nov., isolated from Chinese traditional pickle and yogurt. Int J Syst Evol Microbiol 2019; 69:3178-3190. [DOI: 10.1099/ijsem.0.003609] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Yu Xin Wei
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Chun Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
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Kim HJ, Lee HJ, Lim B, Kim E, Kim HY, Suh M, Hur M. Lactobacillus terrae sp. nov., a novel species isolated from soil samples in the Republic of Korea. Int J Syst Evol Microbiol 2018; 68:2906-2911. [PMID: 30010525 DOI: 10.1099/ijsem.0.002918] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strain, designated NIBRBAC000499792T, was isolated from a soil sample collected at Jukgye, Dongnam, Cheonan, Republic of Korea. Cells were Gram-positive, non-motile, non-spore-forming, rod-shaped, oxidase-negative and catalase-negative. Colonies grown on de Man, Rogosa and Sharpe agar were white, circular, raised and entire. Analysis of the 16S rRNA gene sequence analysis revealed that strain NIBRBAC000499792T belongs to the genus Lactobacillus (family Lactobacillaceae) and is most closely related to Lactobacillus nodensis DSM 19682T (96.1 % similarity) and Lactobacillus tucceti KCTC 21005T (96.7 %). The results of DNA-DNA hybridization experiments demonstrated that strain NIBRBAC000499792T represents a novel species. Major fatty acids are C18 : 1ω9c, C16 : 0 and unidentified 18.846 and/or C19 : 1ω6c and/or C19 : 0cyclo. The predominant respiratory quinones are menaquinone-8 and menaquinone-9. The major polar lipids are phosphatidylglycerol and diphosphatidylglycerol. The minor polar lipids are one unidentified aminophospholipid, one unidentified phospholipid, and four unidentified lipids. Next-generation sequencing analysis of strain NIBRBAC000499792T indicated that the total genome size was 1 548 794 bp with a G+C content of 33.1 mol%, 1586 coding sequences, 50 tRNAs and nine rRNAs. The most closely related genomes belonged to Lactobacillus species. Most metabolic pathways were related to carbon metabolism and carbon fixation. Based on this polyphasic analysis, strain NIBRBAC000499792T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus terrae sp. nov. is proposed, with the type strain NIBRBAC000499792T (=KCTC 21093T=JCM 32269T).
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Affiliation(s)
- Hyun-Joong Kim
- 1Institute of Life Sciences and Resources Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Hye Jin Lee
- 2Biological Resources Research Department, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Bora Lim
- 1Institute of Life Sciences and Resources Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Eiseul Kim
- 1Institute of Life Sciences and Resources Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Hae-Yeong Kim
- 1Institute of Life Sciences and Resources Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Minhwan Suh
- 2Biological Resources Research Department, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Moonsuk Hur
- 2Biological Resources Research Department, National Institute of Biological Resources, Incheon, Republic of Korea
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Lactobacillus metriopterae sp. nov., a novel lactic acid bacterium isolated from the gut of grasshopper Metrioptera engelhardti. Int J Syst Evol Microbiol 2018. [DOI: 10.1099/ijsem.0.002694] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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Jung MY, Lee SH, Lee M, Song JH, Chang JY. Lactobacillus allii sp. nov. isolated from scallion kimchi. Int J Syst Evol Microbiol 2017; 67:4936-4942. [PMID: 29043955 PMCID: PMC5845750 DOI: 10.1099/ijsem.0.002327] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A novel strain of lactic acid bacteria, WiKim39T, was isolated from a scallion kimchi sample consisting of fermented chili peppers and vegetables. The isolate was a Gram-positive, rod-shaped, non-motile, catalase-negative and facultatively anaerobic lactic acid bacterium. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain WiKim39T belonged to the genus Lactobacillus, and shared 97.1–98.2 % pair-wise sequence similarities with related type strains, Lactobacillus nodensis, Lactobacillus insicii, Lactobacillus versmoldensis, Lactobacillus tucceti and Lactobacillus furfuricola. The G+C content of the strain based on its genome sequence was 35.3 mol%. The ANI values between WiKim39T and the closest relatives were lower than 80 %. Based on the phenotypic, biochemical, and phylogenetic analyses, strain WiKim39T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus allii sp. nov. is proposed. The type strain is WiKim39T (=KCTC 21077T=JCM 31938T).
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Affiliation(s)
- Min Young Jung
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Se Hee Lee
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Moeun Lee
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Jung Hee Song
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Ji Yoon Chang
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
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Fernández Ramírez MD, Kostopoulos I, Smid EJ, Nierop Groot MN, Abee T. Quantitative assessment of viable cells of Lactobacillus plantarum strains in single, dual and multi-strain biofilms. Int J Food Microbiol 2017; 244:43-51. [DOI: 10.1016/j.ijfoodmicro.2016.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 12/17/2022]
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Ehrmann MA, Kröckel L, Lick S, Radmann P, Bantleon A, Vogel RF. Lactobacillus insicii sp. nov., isolated from fermented raw meat. Int J Syst Evol Microbiol 2016; 66:236-242. [DOI: 10.1099/ijsem.0.000705] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Matthias A. Ehrmann
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Weihenstephaner Steig 16, 85350 Freising, Germany
| | - Lothar Kröckel
- Department of Safety and Quality of Meat, E.-C.-Baumann- Strasse 20, D-95326, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Kulmbach, Germany
| | - Sonja Lick
- Department of Safety and Quality of Meat, E.-C.-Baumann- Strasse 20, D-95326, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Kulmbach, Germany
| | - Pia Radmann
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Weihenstephaner Steig 16, 85350 Freising, Germany
| | - Annegret Bantleon
- VFG Labor GmbH & Co. KG, Nordfeldstr. 19, D-33775, Versmold, Germany
| | - Rudi. F. Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Weihenstephaner Steig 16, 85350 Freising, Germany
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Fernández Ramírez MD, Smid EJ, Abee T, Nierop Groot MN. Characterisation of biofilms formed by Lactobacillus plantarum WCFS1 and food spoilage isolates. Int J Food Microbiol 2015; 207:23-9. [PMID: 25965141 DOI: 10.1016/j.ijfoodmicro.2015.04.030] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 02/25/2015] [Accepted: 04/19/2015] [Indexed: 12/25/2022]
Abstract
Lactobacillus plantarum has been associated with food spoilage in a wide range of products and the biofilm growth mode has been implicated as a possible source of contamination. In this study we analysed the biofilm forming capacity of L. plantarum WCFS1 and six food spoilage isolates. Biofilm formation as quantified by crystal violet staining and colony forming units was largely affected by the medium composition, growth temperature and maturation time and by strain specific features. All strains showed highest biofilm formation in Brain Heart Infusion medium supplemented with manganese and glucose. For L. plantarum biofilms the crystal violet (CV) assay, that is routinely used to quantify total biofilm formation, correlates poorly with the number of culturable cells in the biofilm. This can in part be explained by cell death and lysis resulting in CV stainable material, conceivably extracellular DNA (eDNA), contributing to the extracellular matrix. The strain to strain variation may in part be explained by differences in levels of eDNA, likely as result of differences in lysis behaviour. In line with this, biofilms of all strains tested, except for one spoilage isolate, were sensitive to DNase treatment. In addition, biofilms were highly sensitive to treatment with Proteinase K suggesting a role for proteins and/or proteinaceous material in surface colonisation. This study shows the impact of a range of environmental factors and enzyme treatments on biofilm formation capacity for selected L. plantarum isolates associated with food spoilage, and may provide clues for disinfection strategies in food industry.
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Affiliation(s)
- Mónica D Fernández Ramírez
- Top Institute Food and Nutrition (TIFN), Nieuwe Kanaal 9A, 6709 PA Wageningen, The Netherlands; Laboratory of Food Microbiology, Wageningen University and Research Centre, Bornse Weilanden 9, 6700 AA Wageningen, The Netherlands
| | - Eddy J Smid
- Top Institute Food and Nutrition (TIFN), Nieuwe Kanaal 9A, 6709 PA Wageningen, The Netherlands; Laboratory of Food Microbiology, Wageningen University and Research Centre, Bornse Weilanden 9, 6700 AA Wageningen, The Netherlands
| | - Tjakko Abee
- Top Institute Food and Nutrition (TIFN), Nieuwe Kanaal 9A, 6709 PA Wageningen, The Netherlands; Laboratory of Food Microbiology, Wageningen University and Research Centre, Bornse Weilanden 9, 6700 AA Wageningen, The Netherlands.
| | - Masja N Nierop Groot
- Top Institute Food and Nutrition (TIFN), Nieuwe Kanaal 9A, 6709 PA Wageningen, The Netherlands; Wageningen UR Food and Biobased Research, Bornse Weilanden 9, 6700 AA Wageningen, The Netherlands
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Lactobacillus
bombi sp. nov., from the digestive tract of laboratory-reared bumblebee queens (Bombus terrestris). Int J Syst Evol Microbiol 2014; 64:2611-2617. [DOI: 10.1099/ijs.0.063602-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three bacterial strains belonging to the genus
Lactobacillus
were isolated from the digestive tracts of laboratory-reared bumblebee queens (Bombus terrestris) using MRS agar under anaerobic conditions. The isolates were identified according to 16S rRNA gene sequence analysis as undescribed members of the genus
Lactobacillus
, with the highest 16S rRNA gene sequence similarity (96.9 %) to the uncharacterized bacterial strain Lactobacillus sp. Mboho2r2 isolated from the stomach of a European honeybee (Apis mellifera).
Lactobacillus tucceti
was found to be the closest related species with a validly published name, with 92.9 % 16S rRNA gene sequence similarity to the type strain. However, phylogenetic analyses based on different markers revealed that this species is phylogenetically very distant from the novel strains. The DNA G+C content of the proposed type strain BTLCH M1/2T is 37.8 mol%. The fatty acids C19 : 1ω6c and/or C19 : 0 cyclo ω10c/19ω6, C18 : 1ω9c and C16 : 0 were predominant in all strains. Diphosphatidylglycerol, phosphatidylglycerol, a phospholipid, seven glycolipids and two phosphoglycolipids were detected in the novel strains. Growth was observed at 47 °C. The peptidoglycan type A4α l-Lys–d-Asp was determined for strain BTLCH M1/2T. Genotypic characteristics and phylogenetic analyses based on the phylogenetic markers hsp60, pheS, rpoA and tuf as well as phenotypic characteristics and the results of chemotaxonomic analyses confirmed that the new isolates belong to a novel species of the genus
Lactobacillus
, for which the name Lactobacillus bombi sp. nov. is proposed. The type strain is BTLCH M1/2T ( = DSM 26517T = CCM 8440T).
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Irisawa T, Tanaka N, Kitahara M, Sakamoto M, Ohkuma M, Okada S. Lactobacillus furfuricola sp. nov., isolated from Nukadoko, rice bran paste for Japanese pickles. Int J Syst Evol Microbiol 2014; 64:2902-2906. [DOI: 10.1099/ijs.0.063933-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains of lactic acid bacteria, Nu27T and Nu29, were isolated from Nukadoko, rice bran paste for Japanese pickles. The isolates were Gram-stain-positive, rod-shaped, catalase-negative, non-motile and facultatively anaerobic lactic acid bacteria. The isolates showed identical 16S rRNA gene sequences. The closest relatives to strain Nu27T based on 16S rRNA gene sequence similarities were
Lactobacillus versmoldensis
KU-3T (98.9 % 16S rRNA gene sequence similarity),
Lactobacillus nodensis
iz4bT (96.3 %) and
Lactobacillus tucceti
CECT 5290T (97.2 %). DNA–DNA relatedness values revealed genotype separation of the two isolates from the above three species. Based on the physiological, biochemical and genotypic characteristics provided, the isolates represent a novel species of the genus
Lactobacillus
, for which name is Lactobacillus furfuricola proposed. The type strain is Nu 27T ( = JCM 18764T = NRIC 0900T = DSM 27174T).
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Affiliation(s)
- Tomohiro Irisawa
- NODAI Culture Collection Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Maki Kitahara
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Sanae Okada
- Department of Applied Biology and Chemistry, Faculty of Applied Bio-Science, Tokyo University of Agriculture, Tokyo 156-8502, Japan
- NODAI Culture Collection Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
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Lactobacillus ginsenosidimutans sp. nov., isolated from kimchi with the ability to transform ginsenosides. Antonie van Leeuwenhoek 2012; 103:867-76. [DOI: 10.1007/s10482-012-9868-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 12/20/2012] [Indexed: 11/25/2022]
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Lactobacillus aquaticus sp. nov., isolated from a Korean freshwater pond. Int J Syst Evol Microbiol 2009; 59:2215-8. [DOI: 10.1099/ijs.0.008276-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2009. [DOI: 10.1099/ijs.0.013961-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Manes-Lazaro R, Ferrer S, Rodas AM, Urdiain M, Pardo I. Lactobacillus bobalius sp. nov., a lactic acid bacterium isolated from Spanish Bobal grape must. Int J Syst Evol Microbiol 2008; 58:2699-703. [DOI: 10.1099/ijs.0.65695-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Mañes-Lázaro R, Ferrer S, Rosselló-Mora R, Pardo I. Lactobacillus uvarum sp. nov. – A new lactic acid bacterium isolated from Spanish Bobal grape must. Syst Appl Microbiol 2008; 31:425-33. [DOI: 10.1016/j.syapm.2008.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Indexed: 10/21/2022]
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