1
|
Wang TY, Gu CT. Elevation of Lentilactobacillus rapi subsp. dabitei Li et al. 2022 to the species level as Lentilactobacillus dabitei sp. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37917542 DOI: 10.1099/ijsem.0.006149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
Lentilactobacillus rapi subsp. dabitei was proposed by Li et al. in 2022. The type strains of L. rapi subsp. dabitei and L. rapi subsp. rapi shared 93.1 % average nucleotide identity and 52.8 % digital DNA-DNA hybridization values. Strain IMAU80584T was proposed as a novel subspecies of L. rapi rather than a novel species of the genus Lentilactobacillus on the basis of similar phenotypic characteristics (including growth temperature and pH, tolerance to NaCl and features based on API 50CH and API ZYM). However, the phenotypic investigation performed by Li et al. was insufficient because some physiological and biochemical characteristics recommended by Mattarelli et al. were not included. In the present study, the taxonomic relationship between L. rapi subsp. dabitei and L. rapi subsp. rapi was re-evaluated. Based upon the data obtained in the present study, we propose to elevate L. rapi subsp. dabitei to the species level as Lentilactobacillus dabitei sp. nov. The type strain is IMAU80584T (=GDMCC 1.2566T=JCM 34647T).
Collapse
Affiliation(s)
- Ting-Yu Wang
- 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
| |
Collapse
|
2
|
Ren Q, Hill JE. Rapid and accurate taxonomic classification of cpn60 amplicon sequence variants. ISME COMMUNICATIONS 2023; 3:77. [PMID: 37479852 PMCID: PMC10362019 DOI: 10.1038/s43705-023-00283-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/23/2023]
Abstract
The "universal target" region of the gene encoding the 60 kDa chaperonin protein (cpn60, also known as groEL or hsp60) is a proven sequence barcode for bacteria and a useful target for marker gene amplicon-based studies of complex microbial communities. To date, identification of cpn60 sequence variants from microbiome studies has been accomplished by alignment of queries to a reference database. Naïve Bayesian classifiers offer an alternative identification method that provides variable rank classification and shorter analysis times. We curated a set of cpn60 barcode sequences to train the RDP classifier and tested its performance on data from previous human microbiome studies. Results showed that sequences accounting for 79%, 86% and 92% of the observations (read counts) in saliva, vagina and infant stool microbiome data sets were classified to the species rank. We also trained the QIIME 2 q2-feature-classifier on cpn60 sequence data and demonstrated that it gives results consistent with the standalone RDP classifier. Successful implementation of a naïve Bayesian classifier for cpn60 sequences will facilitate future microbiome studies and open opportunities to integrate cpn60 amplicon sequence identification into existing analysis pipelines.
Collapse
Affiliation(s)
- Qingyi Ren
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Janet E Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada.
| |
Collapse
|
3
|
Munson E, Lawhon SD, Burbick CR, Zapp A, Villaflor M, Thelen E. 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] [MESH Headings] [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.
Collapse
Affiliation(s)
- Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Sara D. Lawhon
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Claire R. Burbick
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Amanda Zapp
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Maia Villaflor
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Elizabeth Thelen
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| |
Collapse
|
4
|
Shukla I, Hill JE. cpn60 barcode sequences accurately identify newly defined genera within the Lactobacillaceae. Can J Microbiol 2022; 68:457-464. [PMID: 35230911 DOI: 10.1139/cjm-2021-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The cpn60 barcode sequence is established as an informative target for microbial species identification. Applications of cpn60 barcode sequencing are supported by the availability of "universal" PCR primers for its amplification and a curated reference database of cpn60 sequences, cpnDB. A recent reclassification of lactobacilli involving the definition of 23 new genera provided an opportunity to update cpnDB and to determine if the cpn60 barcode could be used for accurate identification of species consistent with the new framework. Analysis of 275 cpn60 sequences representing 258/269 of the validly named species in Lactobacillus, Paralactobacillus and the 23 newer genera showed that cpn60-based sequence relationships were generally consistent with the whole-genome-based phylogeny. Aligning or mapping full length barcode sequences or a 150 bp subsequence resulted in accurate and unambiguous species identification in almost all cases. Taken together, our results show that the combination of available reference sequence data, "universal" barcode amplification primers, and the inherent sequence diversity within the cpn60 barcode make it a useful target for the detection and identification of lactobacilli as defined by the latest taxonomic framework.
Collapse
Affiliation(s)
- Ishika Shukla
- University of Saskatchewan, 7235, Veterinary Microbiology, Saskatoon, Saskatchewan, Canada;
| | - Janet E Hill
- University of Saskatchewan, 7235, Veterinary Microbiology, Saskatoon, Saskatchewan, Canada;
| |
Collapse
|
5
|
Shin Y, Paek J, Kim H, Kook JK, Chang YH. Faecalicatena absiana sp. nov., an obligately anaerobic bacterium from a pig farm faeces dump. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005238] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An obligately anaerobic, Gram-stain-positive, spore-forming, short-rod-shaped bacterium, designated strain YH-C36aT, was isolated from a pig farm faeces dump. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus
Faecalicatena
and is most closely related to
Faecalicatena contorta
KCTC 5831T,
Faecalicatena fissicatena
KCTC 15010T and
Faecalicatena orotica
KCTC 15331T, with 96.3, 96.2, and 96.0 % sequence similarity, respectively. The average nucleotide identity values for strain YH-C36aT and the closest related strains were lower than 72 %. The G+C content of the isolate was 43.0 mol%. The cell-wall peptidoglycan was A1γ type and contained meso-diaminopimelic acid. The predominant fatty acids were C16 : 0, C18 : 1
cis 9, C16 : 0 DMA, C18 : 0 DMA and C18:0. The major end products of glucose fermentation were lactate, formate and acetate. Based on its phenotypic, phylogenetic and chemotaxonomic properties, a novel species, named Faecalicatena absiana sp. nov., is proposed for strain YH-C36aT (=KCTC 25106T=NBRC 114768T).
Collapse
Affiliation(s)
- Yeseul Shin
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hongik Kim
- Vitabio Inc., Daejeon, 305-500, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| |
Collapse
|
6
|
Tohno M, Tanizawa Y, Kojima Y, Sakamoto M, Ohkuma M, Kobayashi H. Lentilactobacillus fungorum sp. nov., isolated from spent mushroom substrates. Int J Syst Evol Microbiol 2021; 71. [PMID: 34913426 DOI: 10.1099/ijsem.0.005184] [Citation(s) in RCA: 5] [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
In Japan, during a screening of lactic acid bacteria in spent mushroom substrates, an unknown bacterium was isolated and could not be assigned to any known species. Strain YK48GT is Gram-stain-positive, rod-shaped, non-motile, non-spore-forming and catalase-negative. The isolate grew in 0-4 % (w/v) NaCl, at 15-37 °C (optimum, 30 °C) and at pH 4.0-8.0 (optimum, pH 6.0). The genomic DNA G+C content of strain YK48GT was 42.5 mol%. Based on its 16S rRNA gene sequence, strain YK48GT represented a member of the genus Lentilactobacillus and showed the highest pairwise similarity to Lentilactobacillus rapi DSM 19907T (97.86 %). Phylogenetic analyses based on amino acid sequences of 466 shared protein-encoding genes also revealed that the strain was phylogenetically positioned in the genus Lentilactobacillus but did not suggest an affiliation with previously described species. The average nucleotide identity and digital DNA-DNA hybridization values between strain YK48GT and the type strains of phylogenetically related species were 72.2-76.6% and 19.0-21.2 %, respectively, indicating that strain YK48GT represents a novel species within the genus Lentilactobacillus. Phenotypic data further confirmed the differentiation of strain YK48GT from other members of the genus Lentilactobacillus. According to the results of the polyphasic characterization presented in this study, strain YK48GT represents a novel species of the genus Lentilactobacillus, for which the name Lentilactobacillus fungorum sp. nov. is proposed. The type strain is YK48GT (=JCM 32598T=DSM 107968T).
Collapse
Affiliation(s)
- Masanori Tohno
- Institute of Livestock and Grassland Science, NARO, Nasushiobara, Tochigi 329-2793, Japan.,Research Center of Genetic Resources, Core Technology Research Headquarters, NARO, Tsukuba, Ibaraki, 305-8632, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yoichiro Kojima
- Central Region Agricultural Research Center, NARO, Nasushiobara, Tochigi 329-2793, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Hisami Kobayashi
- Institute of Livestock and Grassland Science, NARO, Nasushiobara, Tochigi 329-2793, Japan
| |
Collapse
|
7
|
Chiou TY, Suda W, Oshima K, Hattori M, Matsuzaki C, Yamamoto K, Takahashi T. Lentilactobacillus kosonis sp. nov., isolated from kôso, a Japanese sugar-vegetable fermented beverage. Int J Syst Evol Microbiol 2021; 71. [PMID: 34779759 DOI: 10.1099/ijsem.0.005128] [Citation(s) in RCA: 5] [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 lactic acid-producing, Gram-stain-positive, catalase-negative and rod-shaped strain, designated as strain C06_No.73T, was isolated from a traditional Japanese fermented beverage called kôso. According to the results of phylogenetic analysis based on 16S rRNA gene sequences, strain C06_No.73T belongs to the genus Lentilactobacillus. The closest type strain was Lentilactobacillus curieae CCTCC M 2011381T, with a sequence identity of 98.1 %. The identity values with other strains were all below 97 %. The isolate propagated under the conditions of 18-39 °C (optimum, 27 °C for 48 h incubation) and pH 4.0-7.0 (optimum, pH 6.5). The G+C content of its genomic DNA was determined to be 37.9 mol%. The main fatty acids were C16 : 0, C18 : 1 ω7c, C18 : 1 ω9c and C19 : 0 cyclopropane 11,12. The major polar lipid was identified as phosphatidylglycerol. No isoprenoid quinone was detected. The predominant cell-wall amino acids were lysine, alanine, glutamic acid and aspartic acid. Neither meso-diaminopimelic acid nor ornithine were detected. On the basis of this polyphasic taxonomic study, the isolate is concluded to represent a novel species, for which the name Lentilactobacillus kosonis sp. nov. is proposed. The type strain is C06_No.73T (=NBRC 111893T=BCRC 81282T).
Collapse
Affiliation(s)
- Tai-Ying Chiou
- Department of Biotechnology and Environmental Chemistry, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido, Japan
| | - Wataru Suda
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences,1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Kenshiro Oshima
- School of Pharmacy, Kitasato University, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa, Japan
| | - Masahira Hattori
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences,1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Chiaki Matsuzaki
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Japan
| | - Kenji Yamamoto
- Center for Innovative and Joint Research, Wakayama University, Sakaedani 930, Wakayama, Wakayama, Japan
| | - Tomoya Takahashi
- ARSOA Research & Development Center, ARSOA Keioh Group Corporation, 2961 Kobuchisawa-cho, Hokuto, Yamanashi, Japan
| |
Collapse
|