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Song ST, Li CY, Gu CT. Lacticaseibacillus jixiensis sp. nov., Isolated from Traditional Chinese Pickle. Curr Microbiol 2024; 81:374. [PMID: 39316138 DOI: 10.1007/s00284-024-03902-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Accepted: 09/15/2024] [Indexed: 09/25/2024]
Abstract
A novel lactic acid bacterial strain (designated N163-3-2T), isolated from traditional Chinese pickle ('Suan cai'), was characterized using a polyphasic approach. Strain N163-3-2T was most closely related to the type strains of Lacticaseibacillus baoqingensis, Lacticaseibacillus manihotivorans, and Lacticaseibacillus porcinae, having 97.9-98.4% 16S rRNA gene, 82.0-85.1% pheS, 87.5-87.8% rpoA, and 85.8-86.7% concatenated pheS and rpoA sequence similarities. Strain N163-3-2T had 74.4-81.7% ANI, 22.6-23.9% dDDH, and 74.0-75.1% AAI values with L. baoqingensis 47-3T, L. manihotivorans DSM 13343T and L. porcinae JCM 19617T, less than the threshold for species demarcation (95-96%, 70% and 95-96%, respectively), indicating that strain N163-3-2T represented a novel species of the genus Lacticaseibacillus. Based upon the data obtained in the present study, a novel species, Lacticaseibacillus jixiensis sp. nov., is proposed, and the type strain is N163-3-2T (= CCTCC AB 2024125T = JCM 36999T).
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Affiliation(s)
- Si-Tong Song
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, PR China
| | - Chun Yan Li
- College of Food Science, 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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Choi H, Kim Y, Kim S, Kwon SW, Lee D, Han BH, Hong SB, Naito H, Yamada T, Hamada M, Heo J. Lacticaseibacillus pabuli sp. nov., isolated from fermented cattle feed. Int J Syst Evol Microbiol 2024; 74. [PMID: 38446021 DOI: 10.1099/ijsem.0.006277] [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: 03/07/2024] Open
Abstract
Strain BSF-3MT is a Gram-stain-positive, non-flagellated, facultative anaerobic and rod-shaped bacterium that was isolated from fermented feed collected at a cattle farm in the Daejeon region of the Republic of Korea. It was studied using polyphasic taxonomic methods. Using 16S rRNA gene sequences and the resulting phylogenetic tree, the strain was primarily identified as a member of the genus Lacticaseibacillus. Strain BSF-3MT contained a chromosome of 2.5 Mbp and a plasmid of 33.4 kbp. The G+C content of genomic DNA was 51.3 mol%. Strain BSF-3MT had the highest ortho-average nucleotide identity value of 73.7 % with Lacticaseibacillus songhuajiangensis 7-19T, its closest relative in the phylogenetic tree based on the 16S rRNA gene sequences and the phylogenomic tree based on up-to-date bacterial core genes. Based on the results of a polyphasic taxonomic study, strain BSF-3MT represents a novel species in the genus Lacticaseibacillus, for which the name Lacticaseibacillus pabuli sp. nov. is proposed. The type strain is BSF-3MT (=KACC 23028T=NBRC 116014T).
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Affiliation(s)
- Hyorim Choi
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
- Division of Biotechnology, Jeonbuk National University, Jeollabuk-do, Republic of Korea
| | - Yiseul Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Seunghwan Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Daseul Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Byeong-Hak Han
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Seung-Beom Hong
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Hanako Naito
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomomi Yamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriyuki Hamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
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Stephen JM, Saleh AM. Homofermentative Lactobacilli isolated from organic sources exhibit potential ability of lactic acid production. Front Microbiol 2023; 14:1297036. [PMID: 38179457 PMCID: PMC10764624 DOI: 10.3389/fmicb.2023.1297036] [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: 09/19/2023] [Accepted: 12/01/2023] [Indexed: 01/06/2024] Open
Abstract
There has been an increasing interest in recent years in lactic acid bacteria that are derived from organic sources for lactic acid production. This research article presents the isolation and identification of homofermentative lactic acid bacteria from various novel organic sources, followed by qualitative and quantitative analyses of lactic acid produced. A total of 32 isolates were identified initially from various sources, such as curd (C1, C2), probiotics (P1, P2, and P3), silage (Si1 and Si2), soil samples (S1, S2, and S3), vermicompost (V1 and V2), and Farmyard manure. Biochemical tests such as Gram's staining, catalase test, and oxidase test were conducted for preliminary identification of lactic acid bacteria using De Man, Rogosa, and Sharpe agar (MRS) media. Through selection and identification, based on colony morphology and biochemical characteristics, 18 isolates were identified as lactic acid bacteria. The subsequent analysis included a tube test, screening for organic acid production, and homofermentative screening using homofermentative-heterofermentative differential (HHD) medium for qualitative analysis of lactic acid. The results revealed that 9 out of 18 selected strains were homofermentative and had promising potential for the production of lactic acid. Furthermore, six isolates (P1-1, S1-3, C2-1, V2-3, P2-1, and C1-1) from all of the nine positive strains were subjected to pH testing (0, 24, 48, and 72 h) and titrimetric assay for estimation of % crude lactic acid present. The presence of lactic acid was confirmed using thin-layer chromatography (TLC). L (+)-Lactic acid was quantified using a K-LATE enzymatic assay kit, for the best three isolates (P1-1, S1-3, C2-1). Finally, the strains were subjected to 16SrRNA sequencing and were identified as Lactobacilli. Based on the findings of the study, it could be concluded that homofermentative lactic acid bacteria with significant LA-producing ability can be obtained from different organic sources and may prove to be useful in the successful production of lactic acid for biotechnological applications.
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Affiliation(s)
- Jain Maria Stephen
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
- VIT School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, India
| | - Arabi Mohammed Saleh
- VIT School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, India
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Bai L, Paek J, Shin Y, Kim H, Kim SH, Shin JH, Kook JK, Chang YH. Lacticaseibacillus parakribbianus sp. nov., isolated from a pig farm faeces dump. Int J Syst Evol Microbiol 2023; 73. [PMID: 36943347 DOI: 10.1099/ijsem.0.005758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
A lactic acid bacterium isolated from pig faeces was characterized using a polyphasic approach. The strain was Gram-stain-positive, rod-shaped, and facultative anaerobic. Phylogenetic analysis of the 16S rRNA gene sequence indicated that the isolate belonged to the genus Lacticaseibacillus. The multi-locus sequence tree revealed that the strain formed a sub-cluster adjacent to Lacticaseibacillus kribbianus. The main fatty acids were C16 : 0 and C18 : 1ω9c. The average nucleotide identity value, average amino acid identity, and genome-to-genome distance for YH-lacS6T and its most closely related strain, L. kribbianus, were 85.4, 85.2 and 29.2 %, respectively. The G+C content of the genomic DNA was 61.6 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, aminophospholipids and phospholipids. The cell-wall peptidoglycan did not contain meso-diaminopimelic acid. Thus, YH-lacS6T (=KCTC 21186T=JCM 34954T) represents a novel species. The name Lacticaseibacillus parakribbianus sp. nov. is proposed.
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Affiliation(s)
- Lu Bai
- 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
| | - Yeseul Shin
- 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
| | - Si Hyun Kim
- Department of Clinical Laboratory Science, Semyung University, Jecheon, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan 614-735, 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
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Paek J, Bai L, Shin Y, Kim H, Kook JK, Kim SH, Shin JH, Chang YH. Lacticaseibacillus kribbianus sp. nov., isolated from pig farm faeces dump. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748483 DOI: 10.1099/ijsem.0.005617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
A lactic acid bacteria isolated from pig faeces was characterized using a polyphasic approach. Cells of the strain were Gram-stain-positive, rod-shaped and facultative anaerobic. Phylogenetic analysis of 16S rRNA gene sequence indicated that the isolate belonged to the genus Lacticaseibacillus; however, the similarity to other homologues within the genus was <98 %. Analysis of housekeeping gene sequences (pheS and recA) revealed that the strain formed a sub-cluster adjacent to Lacticaseibacillus absianus and Lacticaseibacillus daqingensis. The main fatty acids of the strain is the C18 : 1ω9c and C16 : 0. The G+C content of the genomic DNA was 62.8 mol %. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, aminophospholipids and phospholipids. The cell-wall peptidoglycan did not contain meso-diaminopimelic acid. Thus, YH-lac21T (=KCTC 21185=JCM 34953) represents a novel species. The name Lacticaseibacillus kribbianus sp. nov. is proposed.
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Affiliation(s)
- Jayoung Paek
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Lu Bai
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yeseul Shin
- 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
| | - Si Hyun Kim
- Department of Clinical Laboratory Science, Semyung University, Jecheon, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan 614-735, Republic of Korea
| | - Young Hyo Chang
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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Huang K, Chen H, Liu Y, Hong Q, Yang B, Wang J. Lactic acid bacteria strains selected from fermented total mixed rations improve ensiling and in vitro rumen fermentation characteristics of corn stover silage. Anim Biosci 2022; 35:1379-1389. [PMID: 34991191 PMCID: PMC9449406 DOI: 10.5713/ab.21.0461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 12/30/2021] [Indexed: 11/27/2022] Open
Abstract
Objective This study identified the major lactic acid bacteria (LAB) strains from different fermented total mixed rations (FTMRs) via metataxonomic analysis and evaluated the ability of their standard strain as ensiling inoculants for corn stover silage. Methods The bacterial composition of eight FTMRs were analyzed by 16S rDNA sequencing. Corn stover was ensiled without LAB inoculation (control) or with 1×106 cfu/g LAB standard strain (Lactobacillus vaginalis, Lactobacillus reuteri, Lactobacillus helveticus, or Lactobacillus paralimentarius) selected from the FTMRs or 10 g/t commercial silage inoculant (CSI) around 25°C for 56 days. For each inoculation, a portion of the silage was sampled to analyze ensiling characteristics at time intervals of 0, 1, 3, 7, 14, 28, and 56 days, gas production (GP), microbial crude protein and volatile fatty acids as the measurements of rumen fermentation characteristics were evaluated in vitro with the silages of 56 days after 72 h incubation. Results Lactobacillus covered >85% relative abundance of all FTMRs, in which L. pontis, L. vaginalis, L. reuteri, L. helveticus, and L. paralimentarius showed >4% in specific FTMRs. CSI, L. helveticus, and L. paralimentarius accelerated the decline of silage pH. Silage inoculated with L. paralimentarius and CSI produced more lactic acid the early 14 days. Silage inoculated with L. paralimentarius produced less acetic acid and butyric acid. For the in vitro rumen fermentation, silage inoculated with CSI produced more potential GP, isobutyric acid, and isovaleric acid; silage inoculated with L. helveticus produced more potential GP and isovaleric acid, silage inoculated with L. paralimentarius or L. reuteri produced more potential GP only. Conclusion The standard strain L. paralimentarius (DSM 13238) is a promising ensiling inoculant for corn stover silage. The findings provide clues on strategies to select LAB to improve the quality of silage.
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Affiliation(s)
- Kailang Huang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hongwei Chen
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yalu Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qihua Hong
- The Experimental Teaching Center, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Bin Yang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiakun Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
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Evaluation of bacterial communities of Grana Padano cheese by DNA metabarcoding and DNA fingerprinting analysis. Food Microbiol 2020; 93:103613. [PMID: 32912585 DOI: 10.1016/j.fm.2020.103613] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/20/2022]
Abstract
The composition of the bacterial community of Grana Padano (GP) cheese was evaluated by an amplicon-based metagenomic approach (DNA metabarcoding) and RAPD-PCR fingerprinting. One hundred eighteen cheeses, which included 118 dairies located in the production area of GP, were collected. Two hundred fifty-four OTUs were detected, of which 82 were further discriminated between dominant (32 OTUs; > 1% total reads) and subdominant (50 OTUs; between 0.1% and 1% total reads) taxa. Lactobacillus (L.) delbrueckii, Lacticaseibacillus (Lact.) rhamnosus, Lact. casei, Limosilactobacillus fermentum, Lactococcus (Lc.) raffinolactis, L. helveticus, Streptococcus thermophilus, and Lc. lactis were the major dominant taxa ('core microbiota'). The origin of samples significantly impacted on both richness, evenness, and the relative abundance of bacterial species, with peculiar pattern distribution among the five GP production regions. A differential analysis allowed to find bacterial species significantly associated with specific region pairings. The analysis of pattern similarity among RAPD-PCR profiles highlighted the presence of a 'core' community banding pattern present in all the GP samples, which was strictly associated with the core microbiota highlighted by DNA metabarcoding. A trend to group samples according to the five production regions was also observed. This study widened our knowledge on the bacterial composition and ecology of Grana Padano cheese.
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Xu D, Wang N, Rinne M, Ke W, Weinberg ZG, Da M, Bai J, Zhang Y, Li F, Guo X. The bacterial community and metabolome dynamics and their interactions modulate fermentation process of whole crop corn silage prepared with or without inoculants. Microb Biotechnol 2020; 14:561-576. [PMID: 32627363 PMCID: PMC7936295 DOI: 10.1111/1751-7915.13623] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/11/2020] [Accepted: 06/11/2020] [Indexed: 01/14/2023] Open
Abstract
Multi‐omics approach was adopted to investigate the modulation of bacterial microbiota and metabolome as well as their interactions in whole crop corn ensiling systems by inoculating homofermentative Lactobacillus plantarum or heterofermentative Lactobacillus buchneri. Inoculations of the two different inoculants resulted in substantial differences in microbial community and metabolic composition as well as their dynamics in ensiled corn. Inoculants also altered the correlations of microbiota in different manners, and various keystone species were identified in corn silages with different treatments. Many metabolites with biofunctional activities like bacteriostatic, antioxidant, central nervous system inhibitory and anti‐inflammatory were found in the present silage. A constitutive difference in microbiota dynamics was found for several pathways, which were upregulated by specific taxa in middle stage of fermentation, and widespread associations between metabolites with biofunctions and the species of lactic acid bacteria dominated in silage were observed. Multiple microbial and metabolic structures and dynamics were correlated and affected the fermentation process of the corn ensiling systems. Results of the current study improve our understanding of the complicated biological process underlying silage fermentation and provide a framework to re‐evaluate silages with biofunctions, which may contribute to target‐based regulation methods to produce functional silage for animal production.
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Affiliation(s)
- Dongmei Xu
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Center, Lanzhou University, Lanzhou, 730000, China
| | - Nian Wang
- Nextomics Biosciences Institute, Wuhan, 430000, China
| | - Marketta Rinne
- Natural Resources Institute Finland (Luke) Animale, Jokioinen, 31600, Finland
| | - Wencan Ke
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Center, Lanzhou University, Lanzhou, 730000, China
| | - Zwika G Weinberg
- Microbial Food-Safety Research Unit, Department of Food Quality and Safety, The Volcani Center, Agriculture Research Organization, Institute for Postharvest and Food Sciences, Derech HaMaccabim Road 68, POB 15159, Rishon-LeZion, 7528809, Israel
| | - Mi Da
- Nextomics Biosciences Institute, Wuhan, 430000, China
| | - Jie Bai
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Center, Lanzhou University, Lanzhou, 730000, China
| | - Yixin Zhang
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Center, Lanzhou University, Lanzhou, 730000, China
| | - Fuhou Li
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Center, Lanzhou University, Lanzhou, 730000, China
| | - Xusheng Guo
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Center, Lanzhou University, Lanzhou, 730000, China
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Tse TJ, Shen J, Shim YY, Reaney MJT. Changes in Bacterial Populations and Their Metabolism over 90 Sequential Cultures on Wheat-Based Thin Stillage. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4717-4729. [PMID: 32138511 DOI: 10.1021/acs.jafc.9b07414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Wheat-based thin stillage (W-TS) is a liquid co-product of wheat fermentation for ethanol production, which typically contains substantial amounts of glycerol. Two-stage fermentation, via endemic microorganisms, can be used in processes to convert this compound to more valuable products and simplify the enrichment process through the clarification of the medium and concentration of particles as a protein-rich concentrate. We recultured bacteria 90 times (72 h at 37 °C) on fresh W-TS to determine the stability of the culture and metabolic processes. Next-generation sequencing of W-TS revealed the presence of a predominant Lactobacillus community that rapidly displaced competing microorganisms (e.g., Pediococcus) in subsequent fermentations. These organisms produced bacteriocins (e.g., helveticin J, interpreted through the presence of bacteriocin genes) and acidified the fermentation broth (through the production of succinic acid: 1.7 g/L, lactic acid: 1.8 g/L, and acetic acid: 4.1 g/L). Furthermore, the microbial community produced cobalamin (inferred through sequencing) and converted glycerol (10 g/L reduced to 3.5 g/L after 72 h) to 1,3-propanediol (6.1 g/L after 72 h). Altogether, Lactobacilli were identified as the predominant endemic microorganisms in W-TS after the first 10 cultures. The community was stable and provided a novel approach to increase the value of organic solutes in W-TS.
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Affiliation(s)
- Timothy J Tse
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Jianheng Shen
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Youn Young Shim
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan S7N 5A8, Canada
- Prairie Tide Diversified Inc., 102 Melville Street, Saskatoon Saskatchewan S7J 0R1, Canada
- Guangdong Saskatchewan Oilseed Joint Laboratory, Department of Food Science and Engineering, Jinan University, 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
- Department of Integrative Biotechnology, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, Korea
| | - Martin J T Reaney
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan S7N 5A8, Canada
- Prairie Tide Diversified Inc., 102 Melville Street, Saskatoon Saskatchewan S7J 0R1, Canada
- Guangdong Saskatchewan Oilseed Joint Laboratory, Department of Food Science and Engineering, Jinan University, 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
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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: 1547] [Impact Index Per Article: 386.8] [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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11
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Long GY, Wei YX, Tu W, Gu CT. Lactobacillus hegangensis sp. nov., Lactobacillus suibinensis sp. nov., Lactobacillus daqingensis sp. nov., Lactobacillus yichunensis sp. nov., Lactobacillus mulanensis sp. nov., Lactobacillus achengensis sp. nov., Lactobacillus wuchangensis sp. nov., Lactobacillus gannanensis sp. nov., Lactobacillus binensis sp. nov. and Lactobacillus angrenensis sp. nov., isolated from Chinese traditional pickle and yogurt. Int J Syst Evol Microbiol 2020; 70:2467-2484. [DOI: 10.1099/ijsem.0.004060] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Fourteen Gram-stain-positive bacterial strains were isolated from Chinese traditional pickle and yogurt. The strains were characterized using a polyphasic taxonomic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, fatty acid methyl ester analysis, determination of DNA G+C content, determination of average nucleotide identity (ANI), in silico DNA–DNA hybridization (isDDH) and an analysis of phenotypic features. The data demonstrated that the 14 strains represented ten novel species belonging to the genus
Lactobacillus
, strains 73-4T, 247-3T, 143-4(a)T, 33-1T, 143-6T, 247-4T, 17-4T, 143-1T, 735-2T and M1530-1T were designated as the type strains. Strains 73-4T and 247-3T were phylogenetically related to the type strains of
Lactobacillus camelliae
and
Lactobacillus jixianensis
, having 97.0–98.9 % 16S rRNA gene sequence similarities, 83.9–87.2 % pheS gene sequence similarities and 86.8–93.3 % rpoA gene sequence similarities. Strains 143-4(a)T and 33-1T were phylogenetically related to the type strains of
Lactobacillus rhamnosus
,
Lactobacillus paracasei
and
Lactobacillus casei
, having 93.6–96.5 % 16S rRNA gene sequence similarities, 73.9–77.2 % pheS gene sequence similarities and 76.1–77.6 % rpoA gene sequence similarities. Strains 143-6T, 247-4T, 17-4T and 143-1T were phylogenetically related to the type strains of
Lactobacillus concavus
,
Lactobacillus dextrinicus
and
Lactobacillus bayanensis
, exhibiting 95.5–99.9 % 16S rRNA gene sequence similarities, 76.5–83.1 % pheS gene sequence similarities and 83.6–98.3 % rpoA gene sequence similarities. Strain 735-2T was phylogenetically related to the type strains of
Lactobacillus zhaoyuanensis
,
Lactobacillus jiayinensis
and
Lactobacillus coryniformis
, having 98.2–99.1 % 16S rRNA gene sequence similarities, 82.8–84.1 % pheS gene sequence similarities and 93.0–93.9 % rpoA gene sequence similarities. Strain M1530-1T was phylogenetically related to the type strains of Lactobacillus suantsaiihabitans and
Lactobacillus brevis
, having 99.5 and 99.0 % 16S rRNA gene sequence similarities, 90.3 and 81.7 % pheS gene sequence similarities and 97.7 and 91.1 % rpoA gene sequence similarities. The ANI and isDDH values between strains 73-4T, 247-3T, 143-4(a)T, 33-1T, 143-6T, 247-4T, 17-4T, 143-1T, 735-2T, M1530-1T and type strains of phylogenetically related species were less than 86.8 % and 33.9 % respectively, confirming that they represent ten novel species within the genus
Lactobacillus
. Based upon the data of polyphasic characterization obtained in the present study, ten novel species, Lactobacillus hegangensis sp. nov., Lactobacillus suibinensis sp. nov., Lactobacillus daqingensis sp. nov., Lactobacillus yichunensis sp. nov., Lactobacillus mulanensis sp. nov., Lactobacillus achengensis sp. nov., Lactobacillus wuchangensis sp. nov., Lactobacillus gannanensis sp. nov., Lactobacillus binensis sp. nov. and Lactobacillus angrenensis sp. nov., are proposed and the type strains are 73-4T (=NCIMB 15177T=CCM 8912T=CCTCC AB 2018407T), 247-3T (=NCIMB 15176T=JCM 33275T), 143-4(a)T (=NCIMB 15173T=CCM 8948T=JCM 33273T=CCTCC AB 2018390T), 33-1T (=NCIMB 15169T=CCM 8947T=JCM 33272T=CCTCC AB 2018405T), 143-6T (=NCIMB 15162T=CCM 8951T=JCM 33274T=CCTCC AB 2018411T), 247-4T (=NCIMB 15155T=CCM 8897T=LMG 31059T=CCTCC AB 2018410T), 17-4T (=NCIMB 15161T=CCM 8946T=JCM 33271T=CCTCC AB 2018406T), 143-1T (=NCIMB 15157T=CCM 8937T=CCTCC AB 2018409T), 735-2T (=NCIMB 15190T=CCM 8925T=LMG 31186T) and M1530-1T (=NCIMB 15150T=CCM 8893T=LMG 31046T=CCTCC AB 2018402T), respectively.
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Affiliation(s)
- Guang Yun Long
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Yu Xin Wei
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Wan Tu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
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12
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Nazari-Vanani R, Sattarahmady N, Yadegari H, Khatami M, Heli H. Electrochemical biosensing of 16s rRNA gene sequence of Enterococcus faecalis. Biosens Bioelectron 2019; 142:111541. [DOI: 10.1016/j.bios.2019.111541] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 12/11/2022]
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13
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Long GY, Gu CT. Lactobacillus jixianensis sp. nov., Lactobacillus baoqingensis sp. nov., Lactobacillus jiayinensis sp. nov., Lactobacillus zhaoyuanensis sp. nov., Lactobacillus lindianensis sp. nov., Lactobacillus huananensis sp. nov., Lactobacillus tangyuanensis sp. nov., Lactobacillus fuyuanensis sp. nov., Lactobacillus tongjiangensis sp. nov., Lactobacillus fujinensis sp. nov. and Lactobacillus mulengensis sp. nov., isolated from Chinese traditional pickle. Int J Syst Evol Microbiol 2019; 69:2340-2353. [DOI: 10.1099/ijsem.0.003474] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Guang Yun Long
- 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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14
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Tohno M, Tanizawa Y, Kojima Y, Sakamoto M, Nakamura Y, Ohkuma M, Kobayashi H. Lactobacillus salitolerans sp. nov., a novel lactic acid bacterium isolated from spent mushroom substrates. Int J Syst Evol Microbiol 2019; 69:964-969. [DOI: 10.1099/ijsem.0.003224] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study of a Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, catalase-negative bacterium, strain YK43T, isolated from spent mushroom substrates stored in Nagano, Japan was performed. Growth was detected at 15–45 °C, pH 5.0–8.5, and 0–10 % (w/v) NaCl. The genomic DNA G+C content of strain YK43T was 43.6 mol%. The predominant fatty acids were C16 : 0, C18 : 1 ω9c and summed feature 8. Based on 16S rRNA gene sequence analysis, the type strains of
Lactobacillus acidipiscis
(sequence similarity, 97.6 %) and
Lactobacillus pobuzihii
(97.4 %) were most closely related to YK43T. The average nucleotide identities were 74.1 % between strain YK43T and
L. acidipiscis
DSM 15836T and 74.0 % between YK43T and
L. pobuzihii
E100301T. Based on a multilocus sequence analysis, comparative genomic analysis and a range of phenotypic and chemotaxonomic characteristics, strain YK43T represents a novel species of the genus
Lactobacillus
, for which the name
Lactobacillus
salitolerans sp. nov. is proposed. The type strain is YK43T (=JCM 31331T = DSM 103433T).
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Affiliation(s)
- Masanori Tohno
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Yasuhiro Tanizawa
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yoichiro Kojima
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
| | - Yasukazu Nakamura
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Hisami Kobayashi
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
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15
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A novel and ultrasensitive electrochemical DNA biosensor based on an ice crystals-like gold nanostructure for the detection of Enterococcus faecalis gene sequence. Colloids Surf B Biointerfaces 2018; 166:245-253. [DOI: 10.1016/j.colsurfb.2018.03.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 02/22/2018] [Accepted: 03/18/2018] [Indexed: 12/13/2022]
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16
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Kaur J, Sharma A, Lee S, Park YS. Molecular typing of Lactobacillus brevis isolates from Korean food using repetitive element-polymerase chain reaction. FOOD SCI TECHNOL INT 2018; 24:341-350. [PMID: 29350065 DOI: 10.1177/1082013217753993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Lactobacillus brevis is a part of a large family of lactic acid bacteria that are present in cheese, sauerkraut, sourdough, silage, cow manure, feces, and the intestinal tract of humans and rats. It finds its use in food fermentation, and so is considered a "generally regarded as safe" organism. L. brevis strains are extensively used as probiotics and hence, there is a need for identifying and characterizing these strains. For identification and discrimination of the bacterial species at the subspecific level, repetitive element-polymerase chain reaction method is a reliable genomic fingerprinting tool. The objective of the present study was to characterize 13 strains of L. brevis isolated from various fermented foods using repetitive element-polymerase chain reaction. Repetitive element-polymerase chain reaction was performed using three primer sets, REP, Enterobacterial Repetitive Intergenic Consensus (ERIC), and (GTG)5, which produced different fingerprinting patterns that enable us to distinguish between the closely related strains. Fingerprinting patterns generated band range in between 150 and 5000 bp with REP, 200-7500 bp with ERIC, and 250-2000 bp with (GTG)5 primers, respectively. The Jaccard's dissimilarity matrices were used to obtain dendrograms by the unweighted neighbor-joining method using genetic dissimilarities based on repetitive element-polymerase chain reaction fingerprinting data. Repetitive element-polymerase chain reaction proved to be a rapid and easy method that can produce reliable results in L. brevis species.
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Affiliation(s)
- Jasmine Kaur
- Department of Food Science and Biotechnology, Gachon University, Seongnam, South Korea
| | - Anshul Sharma
- Department of Food Science and Biotechnology, Gachon University, Seongnam, South Korea
| | - Sulhee Lee
- Department of Food Science and Biotechnology, Gachon University, Seongnam, South Korea
| | - Young-Seo Park
- Department of Food Science and Biotechnology, Gachon University, Seongnam, South Korea
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17
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Suryavanshi MV, Paul D, Doijad SP, Bhute SS, Hingamire TB, Gune RP, Shouche YS. Draft genome sequence of Lactobacillus plantarum strains E2C2 and E2C5 isolated from human stool culture. Stand Genomic Sci 2017; 12:15. [PMID: 28163824 PMCID: PMC5282701 DOI: 10.1186/s40793-017-0222-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 12/07/2016] [Indexed: 11/28/2022] Open
Abstract
Probiotic Lactobacillus species offer various health benefits, thus have been employed in treatment and prevention of various diseases. Due to the differences in the isolation source and the site of action, most of the lactobacilli tested in-vitro for probiotics properties fail to extend similar effects in-vivo. Consequently, the search of autochthonous, efficacious and probably population specific probiotics is a high priority in the probiotics research. In this regards, whole genome sequencing of as many Lactobacillus as possible will help to deepen our understanding of biology and their health effects. Here, we provide the genomic insights of two coherent oxalic acid tolerant Lactobacillus species (E2C2 and E2C5) isolated from two different healthy human gut flora. These two isolates were found to have higher tolerance towards oxalic acid (300 mM sodium oxalate). The draft genome of strain E2C2 consists of 3,603,563 bp with 3289 protein-coding genes, 94 RNA genes, and 43.99% GC content, while E2C5 contained 3,615,168 bp, 3293 coding genes (93.4% of the total genes), 95 RNA genes and 43.97% GC content. Based on 16S rRNA gene sequence analysis followed by in silico DNA-DNA hybridization studies, both the strains were identified as Lactobacillus plantarum belonging to family Lactobacillaceae within the phylum Firmicutes. Both the strains were genomically identical, sharing 99.99% CDS that showed 112 SNPs. Both the strains also exhibited deconjugation activity for the bile salts while genome analysis revealed that the L. plantarum strains E2C2 and E2C5 also have the ability to produce vitamins, biotin, alpha- and beta- glucosidase suggesting potential probiotic activities of the isolates. The description presented here is based on the draft genomes of strains E2C2 and E2C5 which are submitted to GenBank under the accession numbers LSST00000000.1 and LTCD00000000.1, respectively.
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Affiliation(s)
- Mangesh V Suryavanshi
- Microbial Culture Collection, National Centre for Cell Science, Ganeshkhind, Pune, 411007 India
| | - Dhiraj Paul
- Microbial Culture Collection, National Centre for Cell Science, Ganeshkhind, Pune, 411007 India
| | - Swapnil P Doijad
- Institute of Medical Microbiology, Biomedizinisches Forschungszentrum Seltersberg, Schubertstr. 81, Giessen, 35392 Germany
| | - Shrikant S Bhute
- Department of Zoology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007 India
| | - Tejashri B Hingamire
- Biochemical Science Division, CSIR-National Chemical Laboratory, Homi Bhabha Road, Pune, 411008 India
| | - Rahul P Gune
- Department of Urology, RCSM Govt. Medical College, CPR Hospital Compound, Bhausingji Rd, Kolhapur, 416002 India
| | - Yogesh S Shouche
- Microbial Culture Collection, National Centre for Cell Science, Ganeshkhind, Pune, 411007 India
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18
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Sharma A, Kaur J, Lee S, Park YS. RAPD typing of Lactobacillus brevis isolated from various food products from Korea. Food Sci Biotechnol 2016; 25:1651-1655. [PMID: 30263458 DOI: 10.1007/s10068-016-0254-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/17/2016] [Accepted: 10/03/2016] [Indexed: 11/27/2022] Open
Abstract
In the present study, the fingerprinting technique, random amplified polymorphic DNA-PCR was evaluated to characterize 13 strains of Lactobacillus brevis, isolated from different vegetable products of South Korea. Two primers i.e. 239 and KAY3 were used. The primer 239 produced bands ranged from 500-4,000 bp and KAY3 primer produced bands with sizes from 600-4,000 bp. Both primers produced thirteen different RAPD profiles. Phylogenetic dendrogram showed that all the isolates could be divided into six major clusters both the primers. However, a few strains of L. brevis had similar profiles and were not well differentiated by RAPD.
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Affiliation(s)
- Anshul Sharma
- Department of Food Science and Biotechnology, Gachon University, Seongnam, Gyeonggi, 13120 Korea
| | - Jasmine Kaur
- Department of Food Science and Biotechnology, Gachon University, Seongnam, Gyeonggi, 13120 Korea
| | - Sulhee Lee
- Department of Food Science and Biotechnology, Gachon University, Seongnam, Gyeonggi, 13120 Korea
| | - Young-Seo Park
- Department of Food Science and Biotechnology, Gachon University, Seongnam, Gyeonggi, 13120 Korea
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19
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Pholsen S, Khota W, Pang H, Higgs D, Cai Y. Characterization and application of lactic acid bacteria for tropical silage preparation. Anim Sci J 2016; 87:1202-1211. [DOI: 10.1111/asj.12534] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/17/2015] [Accepted: 08/04/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Suradej Pholsen
- Faculty of Agriculture; Khon Kaen University; Khon Kaen Thailand
| | - Waroon Khota
- Faculty of Agriculture; Khon Kaen University; Khon Kaen Thailand
| | - Huili Pang
- Henan Provincial Key Laboratory of Ion Beam Bio-engineering; Zhengzhou University; Zhengzhou Henan China
| | - David Higgs
- Department of Human and Environmental Sciences; University of Hertfordshire; Hertfordshire UK
| | - Yimin Cai
- Japan International Research Center for Agricultural Sciences; Tsukuba Ibaraki Japan
- National Institute of Livestock and Grassland Science; Tsukuba Ibaraki Japan
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20
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Mikelsaar M, Sepp E, Štšepetova J, Songisepp E, Mändar R. Biodiversity of Intestinal Lactic Acid Bacteria in the Healthy Population. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 932:1-64. [DOI: 10.1007/5584_2016_3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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21
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Hoang VA, Kim YJ, Nguyen NL, Kim SK, Yang DC. Lactobacillus vespulae sp. nov., isolated from gut of a queen wasp (Vespula vulgaris). Int J Syst Evol Microbiol 2015; 65:3326-3332. [DOI: 10.1099/ijsem.0.000420] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, oxidase- and catalase-negative, rod-shaped, facultatively anaerobic bacterial strain, DCY75T, was isolated from a queen wasp (Vespula vulgaris). Growth occurred at 4–37 °C (optimum, 30 °C), at pH 3.5–8.0 (optimum, pH 5.0–6.0) and with ≤ 7.0 % (w/v) NaCl. Strain DCY75T produced gas during growth on glucose. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DCY75T belonged to the genus Lactobacillus and was closely related to Lactobacillus sanfranciscensis ATCC 27651T and Lactobacillus lindneri DSM 20690T at sequence similarities of 96.7 and 96.4 %, respectively. A comparison of two housekeeping genes, pheS and rpoA, revealed that strain DCT75T was well separated from other species of the genus Lactobacillus. Strain DCY75T produced d- and l-lactic acid isomers in a ratio of 22.5 : 77.5 (v/v). The major fatty acids were summed feature 8 (comprising C18 :
1ω7c and/or C18 : 1ω6c), C16 : 0, C18 : 1ω9c and C18 : 0.The peptidoglycan structure was of the A4α (l-Lys–d-Asp) type. Cell-wall sugars were glucose, galactose and ribose. The DNA G+C content was 35.5 ± 1.3 mol%. Based on phenotypic and genotypic properties, strain DCY75T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus vespulae sp. nov. is proposed. The type strain is DCY75T ( = KCTC 21023T = JCM 19742T).
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Affiliation(s)
- Van-An Hoang
- Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung Hee University Giheung-gu Yongin-si, Gyeonggi-do, Republic of Korea
| | - Yeon-Ju Kim
- Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung Hee University Giheung-gu Yongin-si, Gyeonggi-do, Republic of Korea
| | - Ngoc-Lan Nguyen
- Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung Hee University Giheung-gu Yongin-si, Gyeonggi-do, Republic of Korea
| | - Si-Kwan Kim
- Department of Biomedical Chemistry, Institute of Biomedical & Health Science, College of Biomedical & Health Science, Konkuk University, Chungju-si 380-701, Republic of Korea
| | - Deok-Chun Yang
- Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung Hee University Giheung-gu Yongin-si, Gyeonggi-do, Republic of Korea
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22
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Tohno M, Kitahara M, Irisawa T, Ohmori H, Masuda T, Ohkuma M, Tajima K. Lactobacillus mixtipabuli sp. nov. isolated from total mixed ration silage. Int J Syst Evol Microbiol 2015; 65:1981-1985. [DOI: 10.1099/ijs.0.000204] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Using a polyphasic taxonomic approach, we investigated three bacterial strains – IWT30T, IWT8 and IWT75 – isolated from total mixed ration silage prepared in Hachimantai, Iwate, Japan. The isolates comprised Gram-stain positive, non-motile, non-spore-forming, catalase-negative, rod-shaped bacteria. Good growth occurred at 15–45 °C and at pH 4.0–7.5. Their major cellular fatty acids were C18:1ω9c and C19:1 cyclo 9,10.The G+C content of genomic DNA of strain IWT30T was 44.6 mol%. Comparative 16S rRNA gene sequence analysis showed that these novel strains belonged to the genus Lactobacillus. These strains shared 100 % 16S rRNA gene sequence similarity and were most closely related to the type strains of Lactobacillus silagei, Lactobacillus odoratitofui, Lactobacillus similis, Lactobacillus collinoides, Lactobacillus paracollinoides and Lactobacillus kimchicus, with sequence similarity values of 99.5, 98.8, 98.7, 97.8, 97.8 and 96.8 %, respectively. The level of DNA–DNA relatedness between these strains and their closest phylogenetic neighbours was less than 30 %. On the basis of additional phylogenetic analysis of pheS and rpoA gene sequences and phenotypic and chemotaxonomic characteristics, we conclude that these three strains represent a novel species of the genus Lactobacillus, for which we propose the name Lactobacillus mixtipabuli sp. nov. The type strain is IWT30T ( = JCM 19805T = DSM 28580T).
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Affiliation(s)
- Masanori Tohno
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Nasushiobara 329-2793, Japan
| | - Maki Kitahara
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Tomohiro Irisawa
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Hideyuki Ohmori
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Tsukuba, Ibaraki, 305-0901, Japan
| | - Takaharu Masuda
- Iwate Agricultural Research Center Animal Industry research Institute, Morioka 028-2711, Japan
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Kiyoshi Tajima
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Tsukuba, Ibaraki, 305-0901, Japan
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23
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Djukic M, Poehlein A, Strauß J, Tann FJ, Leimbach A, Hoppert M, Daniel R. High quality draft genome of Lactobacillus kunkeei EFB6, isolated from a German European foulbrood outbreak of honeybees. Stand Genomic Sci 2015. [PMID: 26203329 PMCID: PMC4511666 DOI: 10.1186/1944-3277-10-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The lactic acid bacterium Lactobacillus kunkeei has been described as an inhabitant of fructose-rich niches. Here we report on the genome sequence of L. kunkeei EFB6, which has been isolated from a honeybee larva infected with European foulbrood. The draft genome comprises 1,566,851 bp and 1,417 predicted protein-encoding genes.
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Affiliation(s)
- Marvin Djukic
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Juliane Strauß
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Fabian Jannik Tann
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Andreas Leimbach
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Michael Hoppert
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
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24
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Recommended minimal standards for description of new taxa of the genera Bifidobacterium, Lactobacillus and related genera. Int J Syst Evol Microbiol 2014; 64:1434-1451. [DOI: 10.1099/ijs.0.060046-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Minimal standards for the description of new cultivable strains that represent novel genera and species belonging to the genera
Bifidobacterium
,
Lactobacillus
and related genera are proposed in accordance with Recommendation 30b of the Bacteriological Code (1990 Revision): the description of novel species should be based on phenotypic, genotypic and ecological characteristics to ensure a rich polyphasic characterization. Concerning genotypic characterization, in addition to DNA G+C content (mol%) data, the description should be based on DNA–DNA hybridization (DDH), 16S rRNA gene sequence similarities and at least two housekeeping gene (e.g. hsp60 and recA) sequence similarities. DDH might not be needed if the 16S rRNA gene sequence similarity to the closest known species is lower than 97 %. This proposal has been endorsed by members of the Subcommittee on the Taxonomy of
Bifidobacterium
,
Lactobacillus
and related organisms of the International Committee on the Systematics of Prokaryotes.
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25
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Boonma P, Spinler JK, Qin X, Jittaprasatsin C, Muzny DM, Doddapaneni H, Gibbs R, Petrosino J, Tumwasorn S, Versalovic J. Draft genome sequences and description of Lactobacillus rhamnosus strains L31, L34, and L35. Stand Genomic Sci 2014; 9:744-54. [PMID: 25197459 PMCID: PMC4148986 DOI: 10.4056/sigs.5048907] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactobacillus rhamnosus is a facultative, lactic acid bacterium in the phylum Firmicutes. Lactobacillus spp. are generally considered beneficial, and specific strains of L. rhamnosus are validated probiotics. We describe the draft genomes of three L. rhamnosus strains (L31, L34, and L35) isolated from the feces of Thai breastfed infants, which exhibit anti-inflammatory properties in vitro. The three genomes range between 2.8 - 2.9 Mb, and contain approximately 2,700 protein coding genes.
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Affiliation(s)
- Prapaporn Boonma
- Interdisciplinary Program of Medical Microbiology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Jennifer K Spinler
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, Texas, USA ; Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Chutima Jittaprasatsin
- Interdisciplinary Program of Medical Microbiology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Richard Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Joe Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA ; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Somying Tumwasorn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - James Versalovic
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, Texas, USA ; Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA ; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
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26
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Tohno M, Kitahara M, Irisawa T, Masuda T, Uegaki R, Ohkuma M, Tajima K. Lactobacillus silagei sp. nov., isolated from orchardgrass silage. Int J Syst Evol Microbiol 2013; 63:4613-4618. [DOI: 10.1099/ijs.0.053124-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-positive, facultatively anaerobic, non-spore-forming and catalase-negative rod-shaped bacterial strain, designated IWT126T, was isolated from orchardgrass (Dactylis glomerata L.) silage preserved in Hachimantai, Iwate, Japan. The isolate showed growth at 15–45 °C, pH 3.5–7.5 and with 4.0 % (w/v) NaCl. The cell wall peptidoglycan did not contain meso-diaminopimelic acid, and the DNA G+C content was 45.6 mol%. The major cellular fatty acids were C16 : 0 and C19 : 1 cyclo 9,10. Based on 16S rRNA gene sequence similarity, strain IWT126T was classified as a member of the genus
Lactobacillus
and was most closely related to
Lactobacillus odoratitofui
YIT 11304T (98.7 %),
Lactobacillus similis
JCM 2765T (98.5 %),
Lactobacillus collinoides
JCM 1123T (97.6 %),
Lactobacillus paracollinoides
DSM 15502T (97.6 %) and
Lactobacillus kimchicus
DCY51T (96.9 %). Based on sequence analysis of the phenylalanyl-tRNA synthase α-subunit (pheS) gene, strain IWT126T was well separated from its phylogenetic neighbours in the genus
Lactobacillus
. Based on physiological, biochemical and genotypic results, as well as low DNA–DNA relatedness to recognized phylogenetic relatives in the genus
Lactobacillus
, classification of strain IWT126T as a representive of a novel species named Lactobacillus silagei sp. nov. is proposed. The type strain is IWT126T ( = JCM 19001T = DSM 27022T).
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Affiliation(s)
- Masanori Tohno
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Nasushiobara 329-2793, Japan
| | - Maki Kitahara
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Tomohiro Irisawa
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Takaharu Masuda
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan
- Iwate Agricultural Research Center Animal Industry Research Institute, Morioka 028-2711, Japan
| | - Ryuichi Uegaki
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Nasushiobara 329-2793, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Kiyoshi Tajima
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Tsukuba, Ibaraki 305-0901, Japan
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27
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Tohno M, Kitahara M, Irisawa T, Masuda T, Uegaki R, Ohkuma M, Tajima K. Description of
Lactobacillus
iwatensis sp. nov., isolated from orchardgrass (Dactylis glomerata L.) silage, and
Lactobacillus
backii sp. nov. Int J Syst Evol Microbiol 2013; 63:3854-3860. [DOI: 10.1099/ijs.0.051920-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains, designated IWT246T and IWT248, were isolated from orchardgrass (Dactylis glomerata L.) silage from Iwate prefecture, Japan, and examined for a taxonomic study. Both organisms were rod-shaped, Gram-stain-positive, catalase-negative, facultatively anaerobic and homofermentative. The cell wall did not contain meso-diaminopimelic acid and the major fatty acids were C18 : 1ω9c and C19 cyclo 9,10/:1. Comparative analyses of 16S rRNA, pheS and rpoA gene sequences revealed that these strains were novel and belonged to the genus
Lactobacillus
. Based on 16S rRNA gene sequence similarity, the isolates were most closely related to the type strains of the following members of the genus
Lactobacillus
:
Lactobacillus coryniformis subsp. coryniformis
(96.7 % similarity),
L. coryniformis subsp. torquens
(96.6 %),
L. bifermentans
(95.5 %) and
L. rennini
(94.1 %). However, the 16S rRNA gene sequences of both IWT246T and IWT248 were 99.7 % similar to that of ‘
Lactobacillus
backi’ JCM 18665; this name has not been validly published. Genotypic, phenotypic and chemotaxonomic analyses confirmed that these novel strains occupy a unique taxonomic position. DNA–DNA hybridization experiments demonstrated genotypic separation of the novel isolates from related
Lactobacillus
species. The name
Lactobacillus
iwatensis sp. nov. is proposed for the novel isolates, with strain IWT246T ( = JCM 18838T = DSM 26942T) as the type strain. Our results also suggest that ‘L. backi’ does represent a novel
Lactobacillus
species. The cells did not contain meso-diaminopimelic acid in their cell-wall peptidoglycan and the major fatty acids were C16 : 0, C19 cyclo 9,10/:1 and summed feature 10 (one or more of C18 : 1ω11c, C18 : 1ω9t, C18 : 1ω6t and unknown ECL 17.834). We therefore propose the corrected name
Lactobacillus
backii sp. nov., with the type strain JCM 18665T ( = LMG 23555T = DSM 18080T = L1062T).
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Affiliation(s)
- Masanori Tohno
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Nasushiobara 329-2793, Japan
| | - Maki Kitahara
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Tomohiro Irisawa
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Takaharu Masuda
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan
- Iwate Agricultural Research Center, Animal Industry Research Institute, Morioka 028-2711, Japan
| | - Ryuichi Uegaki
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Nasushiobara 329-2793, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Kiyoshi Tajima
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Tsukuba, Ibaraki 305-0901, Japan
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28
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Tohno M, Kitahara M, Irisawa T, Inoue H, Uegaki R, Ohkuma M, Tajima K. Lactobacillus
oryzae sp. nov., isolated from fermented rice grain (Oryza sativa L. subsp. japonica). Int J Syst Evol Microbiol 2013; 63:2957-2962. [DOI: 10.1099/ijs.0.048918-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of three
Lactobacillus
-like micro-organisms (strains SG293T, SG296 and SG310) isolated from fermented rice grain (Oryza sativa L. subsp. japonica) in Japan was investigated. These heterofermentative lactic acid bacteria were Gram-stain-positive, rod-shaped, facultatively anaerobic, non-motile, non-spore-forming and did not show catalase activity. 16S rRNA gene sequence analysis of strain SG293T revealed that the type strains of
Lactobacillus malefermentans
(98.3 %),
Lactobacillus odoratitofui
(96.2 %),
Lactobacillus similis
(96.1 %),
Lactobacillus kimchicus
(96.1 %),
Lactobacillus paracollinoides
(95.9 %) and
Lactobacillus collinoides
(95.7 %) were the closest neighbours. Additional phylogenetic analysis on the basis of pheS and rpoA gene sequences, as well as biochemical and physiological characteristics, indicated that these three strains were members of the genus
Lactobacillus
and that the novel isolates had a unique taxonomic position. The predominant cellular fatty acids were C18 : 1ω9c and C19 : 1 cyclo 9,10. Because low DNA–DNA hybridization values among the isolates and
Lactobacillus malefermentans
JCM 12497T were observed, it is proposed that these unidentified isolates be classified as a novel species of the genus
Lactobacillus
,
Lactobacillus
oryzae sp. nov. The type strain is SG293T ( = JCM 18671T = DSM 26518T).
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Affiliation(s)
- Masanori Tohno
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Nasushiobara 329-2793, Japan
| | - Maki Kitahara
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Tomohiro Irisawa
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Hidehiko Inoue
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Nasushiobara 329-2793, Japan
| | - Ryuichi Uegaki
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Nasushiobara 329-2793, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Kiyoshi Tajima
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Tsukuba, Ibaraki 305-0901, Japan
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29
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Tohno M, Kitahara M, Uegaki R, Irisawa T, Ohkuma M, Tajima K. Lactobacillus
hokkaidonensis sp. nov., isolated from subarctic timothy grass (Phleum pratense L.) silage. Int J Syst Evol Microbiol 2013; 63:2526-2531. [DOI: 10.1099/ijs.0.047027-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four strains of Gram-positive, non-spore-forming, rod-shaped, catalase-negative and non-motile lactic acid bacteria, LOOC260T, LOOC253, LOOC273 and LOOC279, were isolated from timothy grass (Phleum pratense L.) silage produced in Hokkaido, a subarctic region of Japan. These isolates grew at 4–37 °C, indicating the psychrotolerant nature of these strains. Phylogenetic analysis on the basis of 16S rRNA and pheS gene sequences, as well as biochemical and physiological characteristics, indicated that these four strains were members of the genus
Lactobacillus
. 16S rRNA gene sequence analysis of strain LOOC260T demonstrated that the closest neighbours were the type strains of
Lactobacillus suebicus
(97.7 %),
Lactobacillus oligofermentans
(96.7 %) and
Lactobacillus vaccinostercus
(96.7 %). Strain LOOC260T showed low levels of DNA–DNA association with
Lactobacillus suebicus
JCM 9504T (14.7±3.5 %),
Lactobacillus oligofermentans
JCM 16175T (15.1±4.8 %) and
Lactobacillus vaccinostercus
JCM 1716T (10.7±3.0 %). The cell wall contained meso-diaminopimelic acid and the major fatty acids were C18 : 1ω9c and C19 : 1 cyclo 9,10. On the basis of phenotypic, physiological and phylogenetic evidence, these isolates represent a novel species of the genus
Lactobacillus
, for which the name
Lactobacillus
hokkaidonensis sp. nov. is proposed. The type strain is LOOC260T ( = JCM 18461T = DSM 26202T).
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Affiliation(s)
- Masanori Tohno
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Nasushiobara 329-2793, Japan
| | - Maki Kitahara
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Ryuichi Uegaki
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Nasushiobara 329-2793, Japan
| | - Tomohiro Irisawa
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Kiyoshi Tajima
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Tsukuba, Ibaraki 305-0901, Japan
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30
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Kim J, Kim JY, Kim MS, Roh SW, Bae JW. Lactobacillus kimchiensis sp. nov., isolated from a fermented food. Int J Syst Evol Microbiol 2013; 63:1355-1359. [DOI: 10.1099/ijs.0.037572-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium was isolated from a traditional fermented food, kimchi. The morphology, physiology, biochemical properties and 16S rRNA gene sequence of strain L133T were studied. Strain L133T was Gram-reaction-positive, catalase-negative and homofermentative, with rod-shaped cells that formed cream colonies. Cells grew in the presence of 0–5 % (w/v) NaCl (optimum, 1–2 %), at pH 5.0–9.0 (optimum, pH 7.0–8.0) and at 15–37 °C (optimum, 25 °C). Comparative 16S rRNA gene and pheS sequence analysis of strain L133T indicated that the strain belonged to the genus
Lactobacillus
. The major fatty acids were identified as C18 : 1ω9c, C16 : 0 and C18 : 0, and the cell wall contained peptidoglycan of the l-Lys–d-Asp type. DNA–DNA relatedness values between strain L133T and related species were below 11±0.4 %. The DNA G+C content of strain L133T was 35.7 mol%. Analysis of 16S rRNA gene sequences, as well as physiological and biochemical tests, identified genotypic and phenotypic differences between strain L133T and other species of the genus
Lactobacillus
. Based on these analyses, strain L133T is proposed to be a novel species of the genus
Lactobacillus
, named Lactobacillus kimchiensis. The type strain is L133T ( = KACC 15533T = JCM 17702T = DSM 24716T).
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Affiliation(s)
- Jandi Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Joon Yong Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Min-Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Seong Woon Roh
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
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31
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32
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Zou Y, Liu F, Fang C, Wan D, Yang R, Su Q, Yang R, Zhao J. Lactobacillus shenzhenensis sp. nov., isolated from a fermented dairy beverage. Int J Syst Evol Microbiol 2012; 63:1817-1823. [PMID: 23002044 DOI: 10.1099/ijs.0.041111-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Lactobacillus strains, designated LY-73(T) and LY-30B, were isolated from a dairy beverage, sold in Shenzhen market, China. The two isolates were Gram-positive, non-spore-forming, non-motile, facultatively anaerobic rods that were heterofermentative and did not exhibit catalase activity. Sequencing of the 16S rRNA, pheS and rpoA genes revealed that the two isolates shared 99.5, 99.8 and 99.9 % sequence similarity, which indicates that they belong to the same species. Phylogenetic analysis demonstrated clustering of the two isolates with the genus Lactobacillus. Strain LY-73(T) showed highest 16S rRNA gene sequence similarities with Lactobacillus harbinensis KACC 12409(T) (97.73%), Lactobacillus perolens DSM 12744(T) (96.96 %) and Lactobacillus selangorensis DSM 13344(T) (93.10 %). Comparative analyses of their rpoA and pheS gene sequences indicated that the novel strains were significantly different from other Lactobacillus species. Low DNA-DNA reassociation values (50.5 %) were obtained between strain LY-73(T) and its phylogenetically closest neighbours. The G+C contents of the DNA of the two novel isolates were 56.1 and 56.5 mol%. Straight-chain unsaturated fatty acids C18 : 1ω9c (78.85 and 74.29 %) were the dominant components, and the cell-wall peptidoglycan was of the l-Lys-d-Asp type. Based on phenotypic characteristics, and chemotaxonomic and genotypic data, the novel strains represent a novel species of the genus Lactobacillus, for which the name Lactobacillus shenzhenensis sp. nov. is proposed, with LY-73(T) ( = CCTCC M 2011481(T) = KACC 16878(T)) as the type strain.
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Affiliation(s)
- Yuanqiang Zou
- Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, PR China
| | - Feng Liu
- Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, PR China
| | - Chengxiang Fang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Daiwei Wan
- Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, PR China
| | - Rentao Yang
- Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, PR China
| | - Qingqing Su
- Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, PR China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China.,Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, PR China
| | - Jiao Zhao
- Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, PR China
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