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An Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Domestic Animals Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0028122. [PMID: 36533907 PMCID: PMC9945509 DOI: 10.1128/jcm.00281-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Novel bacterial taxonomy and nomenclature revisions can have significant impacts on clinical practice, disease epidemiology, and veterinary microbiology laboratory operations. Expansion of research on the microbiota of humans, animals, and insects has significant potential impacts on the taxonomy of organisms of clinical interest. Implications of taxonomic changes may be especially important when considering zoonotic diseases. Here, we address novel taxonomy and nomenclature revisions of veterinary significance. Noteworthy discussion centers around descriptions of novel mastitis pathogens in Streptococcaceae, Staphylococcaceae, and Actinomycetaceae; bovine reproductive tract pathogens in Corynebacteriaceae; novel members of Mannheimia spp., Leptospira spp., and Mycobacterium spp.; the transfer of Ochrobactrum spp. to Brucella spp.; and revisions to the genus Mycoplasma.
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Rahman MS, Lee Y, Park DS, Kim YS. Bifidobacterium bifidum DS0908 and Bifidobacterium longum DS0950 Culture-Supernatants Ameliorate Obesity-Related Characteristics in Mice with High-Fat Diet-Induced Obesity. J Microbiol Biotechnol 2023; 33:96-105. [PMID: 36457182 PMCID: PMC9899789 DOI: 10.4014/jmb.2210.10046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022]
Abstract
Probiotic supplements have promising therapeutic effects on chronic diseases. In this study, we demonstrated the anti-obesity effects of two potential probiotics, Bifidobacterium bifidum DS0908 (DS0908) and Bifidobacterium longum DS0950 (DS0950). Treatment with DS0908 and DS0950 postbiotics significantly induced the expression of the brown adipocyte-specific markers UCP1, PPARγ, PGC1α, PRDM16 and beige adipocyte-specific markers CD137, FGF21, P2RX5, and COX2 in C3H10T1/2 mesenchymal stem cells (MSCs). In mice with high-fat diet (HFD)-induced obesity, both potential probiotics and postbiotics noticeably reduced body weight and epididymal fat accumulation without affecting food intake. DS0908 and DS0950 also improved insulin sensitivity and glucose use in mice with HFD-induced obesity. In addition, DS0908 and DS0950 improved the plasma lipid profile, proved by reduced triglyceride, low-density lipoprotein, and cholesterol levels. Furthermore, DS0908 and DS0950 improved mitochondrial respiratory function, confirmed by the high expression of oxidative phosphorylation proteins, during thermogenesis induction in the visceral and epididymal fat in mice with HFD-induced obesity. Notably, the physiological and metabolic changes were more significant after treatment with potential probiotic culture-supernatants than those with the bacterial pellet. Finally, gene knockdown and co-treatment with inhibitor-mediated mechanistic analyses showed that both DS0908 and DS0950 exerted anti-obesity-related effects via the PKA/p38 MAPK signaling activation in C3H10T1/2 MSCs. Our observations suggest that DS0908 and DS0950 could potentially alleviate obesity as dietary supplements.
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Affiliation(s)
- M. Shamim Rahman
- Institute of Tissue Regeneration, College of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Department of Microbiology, College of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea
| | - Youri Lee
- Institute of Tissue Regeneration, College of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Department of Microbiology, College of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea
| | - Doo-Sang Park
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Yong-Sik Kim
- Institute of Tissue Regeneration, College of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Department of Microbiology, College of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Corresponding author Phone: +82-41-570-2413 Fax: +82-41-575-2412 E-mail:
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Lee H, Jung KB, Kwon O, Son YS, Choi E, Yu WD, Son N, Jeon JH, Jo H, Yang H, Son YR, Yun CS, Cho HS, Kim SK, Kim DS, Park DS, Son MY. Limosilactobacillus reuteri DS0384 promotes intestinal epithelial maturation via the postbiotic effect in human intestinal organoids and infant mice. Gut Microbes 2022; 14:2121580. [PMID: 36130031 PMCID: PMC9519030 DOI: 10.1080/19490976.2022.2121580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Little is known about the modulatory capacity of the microbiota in early intestinal development. We examined various intestinal models that respond to gut microbial metabolites based on human pluripotent stem cell-derived human intestinal organoids (hIOs): physiologically relevant in vitro fetal-like intestine, intestinal stem cell, and intestinal disease models. We found that a newly isolated Limosilactobacillus reuteri strain DS0384 accelerated maturation of the fetal intestine using 3D hIO with immature fetal characteristics. Comparative metabolomic profiling analysis revealed that the secreted metabolite N-carbamyl glutamic acid (NCG) is involved in the beneficial effect of DS0384 cell-free supernatants on the intestinal maturation of hIOs. Experiments in an intestinal stem cell spheroid model and hIO-based intestinal inflamed model revealed that the cell-free supernatant from DS0384 comprising NCG promoted intestinal stem cell proliferation and was important for intestinal protection against cytokine-induced intestinal epithelial injury. The probiotic properties of DS0384 were also evaluated, including acid and bile tolerance and ability to adhere to human intestinal cells. Seven-day oral administration of DS0384 and cell-free supernatant promoted the intestinal development of newborn mice. Moreover, NCG exerted a protective effect on experimental colitis in mice. These results suggest that DS0384 is a useful agent for probiotic applications and therapeutic treatment for disorders of early gut development and for preventing intestinal barrier dysfunction.
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Affiliation(s)
- Hana Lee
- Stem Cell Research Convergence Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Kwang Bo Jung
- Stem Cell Research Convergence Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Ohman Kwon
- Stem Cell Research Convergence Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Ye Seul Son
- Stem Cell Research Convergence Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Eunho Choi
- Stem Cell Research Convergence Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Won Dong Yu
- Stem Cell Research Convergence Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Naeun Son
- Stem Cell Research Convergence Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Jun Hyoung Jeon
- Korean Collection for Type Cultures, Biological Resource Center, KRIBB, Jeongeup, Republic of Korea
| | - Hana Jo
- Korean Collection for Type Cultures, Biological Resource Center, KRIBB, Jeongeup, Republic of Korea
| | - Haneol Yang
- Korean Collection for Type Cultures, Biological Resource Center, KRIBB, Jeongeup, Republic of Korea
| | - Yeong Rak Son
- Korean Collection for Type Cultures, Biological Resource Center, KRIBB, Jeongeup, Republic of Korea
| | - Chan-Seok Yun
- Korean Collection for Type Cultures, Biological Resource Center, KRIBB, Jeongeup, Republic of Korea
| | - Hyun-Soo Cho
- KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea,Digital Biotech Innovation Center, KRIBB, Daejeon, Republic of Korea
| | - Sang Kyu Kim
- Laboratory of Efficacy Research, Korea Ginseng Corp., Daejeon, Republic of Korea
| | - Dae-Soo Kim
- KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea,Digital Biotech Innovation Center, KRIBB, Daejeon, Republic of Korea
| | - Doo-Sang Park
- Korean Collection for Type Cultures, Biological Resource Center, KRIBB, Jeongeup, Republic of Korea,Doo-Sang Park Korean Collection for Type Cultures, Biological Resource Center, KRIBB, Jeongeup, 56212, Republic of Korea
| | - Mi-Young Son
- Stem Cell Research Convergence Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea,CONTACT Mi-Young Son Stem Cell Research Convergence Center, KRIBB, Daejeon, 34141, Republic of Korea
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Tohno M, Tanizawa Y, Kojima Y, Sakamoto M, Ohkuma M, Kobayashi H. Lactobacillus corticis sp. nov., isolated from hardwood bark. Int J Syst Evol Microbiol 2021; 71. [PMID: 34264810 DOI: 10.1099/ijsem.0.004882] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a study on the biodiversity of bacteria that inhabit woody biomass, we isolated a strain coded B40T from hardwood bark used as a compost ingredient in Japan. The strain, characterized as B40T, is a Gram-stain-positive, rod-shaped, non-motile, non-spore-forming and catalase-negative bacterium. This novel isolate showed growth at 30-50 °C, at pH 3.5-7.5 and in the presence of up to 4 % (w/v) NaCl. Its major fatty acids include C16:0, C18:1 ω9c and summed feature 8. The genomic DNA G+C content of strain B40T is 42.2 mol%. Results of 16S rRNA gene sequence-based phylogenetic analysis indicated that strain B40T belongs to the genus Lactobacillus and the closest neighbours of strain B40T are Lactobacillus gigeriorum 202T (95.7 %), Lactobacillus pasteurii CRBIP 24.76T (95.6 %), Lactobacillus psittaci DSM 15354T (95.4 %), Lactobacillus fornicalis TV1018T (95.4 %) and Lactobacillus jensenii ATCC 25258T (95.2 %). The amino acid sequence-based phylogenetic analyses of 489 shared protein-encoding genes showed that the strain forms a phylogenetically independent lineage in the genus Lactobacillus but could not be assigned to any known species. Strain B40T has an average nucleotide identify of <70.2 % and a digital DNA-DNA hybridization value of 19.2 % compared with the strains of other closely related Lactobacillus species. Differential genomic, phenotypic and chemotaxonomic properties, in addition to phylogenetic analyses, indicated that strain B40T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus corticis sp. nov. is proposed. The strain type is B40T (=JCM 32597T=DSM 107967T).
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Affiliation(s)
- Masanori Tohno
- Research Center of Genetic Resources, Core Technology Research Headquarters, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.,Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization Nasushiobara, Tochigi, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yoichiro Kojima
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Hisami Kobayashi
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization Nasushiobara, Tochigi, Japan
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Suzuki-Hashido N, Tsuchida S, Hayakawa T, Sakamoto M, Azumano A, Seino S, Matsuda I, Ohkuma M, Ushida K. Lactobacillus nasalidis sp. nov., isolated from the forestomach of a captive proboscis monkey ( Nasalis larvatus). Int J Syst Evol Microbiol 2021; 71. [PMID: 33906706 DOI: 10.1099/ijsem.0.004787] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three strains (YZ01T, YZ02 and YZ03) of Gram-stain-positive, facultatively anaerobic rods were isolated from the forestomach contents collected from a captive male proboscis monkey (Nasalis larvatus) at Yokohama Zoo in Japan. Phylogenetic analysis of the 16S rRNA gene sequences revealed that these strains belonged to the genus Lactobacillus. Based on the sequence similarity of the 16S rRNA gene, Lactobacillus delbrueckii subsp. indicus JCM 15610T was the closest phylogenetic neighbour to YZ01T. Sequence analyses of two partial concatenated housekeeping genes, the RNA polymerase alpha subunit (rpoA) and phenylalanyl-tRNA synthase alpha subunit (pheS) also indicated that the novel strains belonged to the genus Lactobacillus. The average nucleotide identity and digital DNA-DNA hybridization (dDDH) between L. delbrueckii subsp. indicus and YZ01T were 85.9 and 31.4 %, respectively. The phylogenetic tree based on the whole genomic data of strains YZ01T, YZ02 and YZ03 suggested that these three strains formed a single monophyletic cluster in the genus Lactobacillus, indicating that it belonged to a new species. The DNA G+C content of strain YZ01T was 51.6 mol%. The major fatty acids were C16 : 0 and C18 : 1 ω9c. Therefore, based on phylogenetic, phenotypic and physiological evidence, strains YZ01T, YZ02 and YZ03 represent a novel species of the genus Lactobacillus, for which the name Lactobacillus nasalidis sp. nov. is proposed with the type strain YZ01T (=JCM 33769T=DSM 110539T).
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Affiliation(s)
- Nami Suzuki-Hashido
- Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo, 102-0083, Japan.,Chubu University Academy of Emerging Sciences, Kasugai, Aichi, 487-8501, Japan
| | - Sayaka Tsuchida
- Chubu University Academy of Emerging Sciences, Kasugai, Aichi, 487-8501, Japan
| | - Takashi Hayakawa
- Japan Monkey Centre, Inuyama, Aichi, 484-0081, Japan.,Faculty of Environmental Earth Science, Hokkaido University, Sapporo, 060-0810 Hokkaido, Japan
| | - Mitsuo Sakamoto
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan.,Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | | | - Satoru Seino
- Present address: Preservation and Research Center, City of Yokohama, Yokohama, Kanagawa, 241-0804, Japan.,Yokohama Zoo Zoorasia, Yokohama, Kanagawa, 241-0001, Japan
| | - Ikki Matsuda
- Wildlife Research Center, Kyoto University, Sakyo-ku, Kyoto, 606-8203, Japan.,Chubu University Academy of Emerging Sciences, Kasugai, Aichi, 487-8501, Japan.,Institute for Tropical Biology and Conservation, University Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia.,Japan Monkey Centre, Inuyama, Aichi, 484-0081, Japan
| | | | - Kazunari Ushida
- College of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, 487-8501, Japan.,Chubu University Academy of Emerging Sciences, Kasugai, Aichi, 487-8501, Japan
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Kim HS, Lee KC, Suh MK, Kim JS, Han KI, Eom MK, Shin YK, Lee JS. Mucilaginibacter mali sp. nov., isolated from rhizosphere soil of apple orchard. Int J Syst Evol Microbiol 2021; 71. [PMID: 33464201 DOI: 10.1099/ijsem.0.004617] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-negative bacterium, designated G2-14T, was isolated from rhizosphere soil sample collected from apple orchard in Chungju-si, Chungcheongbuk-do, Republic of Korea. Strain G2-14T was a strictly aerobic, non-spore-forming, non-motile and short-rod-shaped bacterium. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain G2-14T was closely related to Mucilaginibacter myungsuensis HMD1056T (96.9 %) and Mucilaginibacter boryungensis BDR-9T (96.8 %). The major cellular fatty acids (>10 %) of strain G2-14T were summed feature 3 (C16:1 ω6с and/or C16:1 ω7с) and iso-C15:0. The predominant quinone and the major polar lipid were menaquinone-7 and phosphatidylethanolamine, respectively. Strain G2-14T produced acetic acid. The DNA G+C content based on whole genome sequences was 46.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain G2-14T represents a novel species in the genus Mucilaginibacter, for which the name Mucilaginibacter mali sp. nov. is proposed. The type strain is G2-14T (=KCTC 72533T=NBRC 114179T).
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Affiliation(s)
- Han Sol Kim
- Semyung University, 65, Semyung -ro, Jecheon-si, Chungcheongbuk-do 27136, Republic of Korea.,Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Keun Chul Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Min Kuk Suh
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Ji-Sun Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Kook-Il Han
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Mi Kyung Eom
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Yong Kook Shin
- Semyung University, 65, Semyung -ro, Jecheon-si, Chungcheongbuk-do 27136, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea.,University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
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Son YS, Ki SJ, Thanavel R, Kim JJ, Lee MO, Kim J, Jung CR, Han TS, Cho HS, Ryu CM, Kim SH, Park DS, Son MY. Maturation of human intestinal organoids in vitro facilitates colonization by commensal lactobacilli by reinforcing the mucus layer. FASEB J 2020; 34:9899-9910. [PMID: 32602623 DOI: 10.1096/fj.202000063r] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/20/2020] [Accepted: 04/26/2020] [Indexed: 12/14/2022]
Abstract
Lactobacilli, which are probiotic commensal bacteria that mainly reside in the human small intestine, have attracted attention for their ability to exert health-promoting effects and beneficially modulate host immunity. However, host epithelial-commensal bacterial interactions are still largely unexplored because of limited access to human small intestinal tissues. Recently, we described an in vitro maturation technique for generating adult-like, mature human intestinal organoids (hIOs) from human pluripotent stem cells (hPSCs) that closely resemble the in vivo tissue structure and cellular diversity. Here, we established an in vitro human model to study the response to colonization by commensal bacteria using luminal microinjection into mature hIOs, allowing for the direct examination of epithelial-bacterial interactions. Lactobacillus reuteri and Lactobacillus plantarum were more likely to survive and colonize when microinjected into the lumen of mature hIOs than when injected into immature hIOs, as determined by scanning electron microscopy, colony formation assay, immunofluorescence, and real-time imaging with L plantarum expressing red fluorescent protein. The improved mature hIO-based host epithelium system resulted from enhanced intestinal epithelial integrity via upregulation of mucus secretion and tight junction proteins. Our study indicates that mature hIOs are a physiologically relevant in vitro model system for studying commensal microorganisms.
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Affiliation(s)
- Ye Seul Son
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Soo Jin Ki
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
| | - Rajangam Thanavel
- Center for Biomaterials, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Jong-Jin Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Mi-Ok Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Janghwan Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Cho-Rok Jung
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Tae-Su Han
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Hyun-Soo Cho
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Choong-Min Ryu
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Sang-Heon Kim
- Center for Biomaterials, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea.,Department of Biomedical Engineering, KIST school, UST, Daejeon, Republic of Korea
| | - Doo-Sang Park
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea.,Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
| | - Mi-Young Son
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
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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: 1520] [Impact Index Per Article: 380.0] [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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