1
|
Wu M, Xu Y, Dai M, Li W, Zhang C, Li X, Sun B. Butyriproducens baijiuensis BJN0003: a potential new member of the family Oscillospiraceae isolated from Chinese Baijiu. 3 Biotech 2023; 13:205. [PMID: 37223001 PMCID: PMC10200727 DOI: 10.1007/s13205-023-03624-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/10/2023] [Indexed: 05/25/2023] Open
Abstract
Acid-producing bacteria are one kind of crucial species for Baijiu fermentation. The strain BJN0003 with the ability of producing butyric acid was isolated from the cellar mud of Baijiu, and the 16S rRNA gene sequence similarity was 94.2% to its most closely related type species Caproicibacterium lactiferaments JNU-WLY1368T, less than the threshold value of 94.5% for distinguishing genera. Furthermore, the genome of BJN0003 showed a length of 2,458,513 bp and a DNA G + C content of 43.3% through high throughput sequence. BJN0003 exhibited whole-genome average nucleotide identity value of 68.9% to the most closely related species, while the whole-genome digital DNA-DNA hybridization value was only 23.1%, which were both below the delineation thresholds of species. These results indicated BJN0003 could represent a potential novel species of a new genus of the family Oscillospiraceae, and was proposed the name as Butyriproducens baijiuensis. In addition, gene annotation and metabolic analysis showed that BJN0003 harbored the metabolic pathway of converting glucose to butyric acid. The discovery of the new species provided bacterial resource for Baijiu production and the revealing of genetic characteristics would promote the investigation of acid synthesis during Baijiu manufacturing process. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03624-w.
Collapse
Affiliation(s)
- Mengqin Wu
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commerce, Beijing Technology and Business University, No. 33, Fucheng Road, Haidian District, Beijing, 100048 China
| | - Youqiang Xu
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commerce, Beijing Technology and Business University, No. 33, Fucheng Road, Haidian District, Beijing, 100048 China
| | - Mengqi Dai
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commerce, Beijing Technology and Business University, No. 33, Fucheng Road, Haidian District, Beijing, 100048 China
| | - Weiwei Li
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commerce, Beijing Technology and Business University, No. 33, Fucheng Road, Haidian District, Beijing, 100048 China
| | - Chengnan Zhang
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commerce, Beijing Technology and Business University, No. 33, Fucheng Road, Haidian District, Beijing, 100048 China
| | - Xiuting Li
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commerce, Beijing Technology and Business University, No. 33, Fucheng Road, Haidian District, Beijing, 100048 China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, No. 33, Fucheng Road, Haidian District, Beijing, 100048 China
| | - Baoguo Sun
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commerce, Beijing Technology and Business University, No. 33, Fucheng Road, Haidian District, Beijing, 100048 China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, No. 33, Fucheng Road, Haidian District, Beijing, 100048 China
| |
Collapse
|
2
|
Kato H, Su L, Tanaka A, Katsu H, Ohtsubo Y, Otsuka S, Senoo K, Nagata Y. Genome evolution related to γ-hexachlorocyclohexane metabolic function in the soil microbial population. Biosci Biotechnol Biochem 2022; 86:800-809. [PMID: 35298590 DOI: 10.1093/bbb/zbac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/12/2022] [Indexed: 11/12/2022]
Abstract
γ-Hexachlorocyclohexane (γ-HCH)-degrading strain, Sphingobium sp. TA15, was newly isolated from an experimental field soil from which the archetypal γ-HCH-degrading strain, S. japonicum UT26, was isolated previously. Comparison of the complete genome sequences of these 2 strains revealed that TA15 shares the same basic genome backbone with UT26, but also has the variable regions that are presumed to have changed either from UT26 or from a putative common ancestor. Organization and localization of lin genes of TA15 were different from those of UT26. It was inferred that transposition of IS6100 had played a crucial role in these genome rearrangements. The accumulation of toxic dead-end products in TA15 was lower than in UT26, suggesting that TA15 utilizes γ-HCH more effectively than UT26. These results suggested that genome evolution related to the γ-HCH metabolic function in the soil microbial population is ongoing.
Collapse
Affiliation(s)
- Hiromi Kato
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Japan
| | - Lijun Su
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Japan
| | - Ayami Tanaka
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Japan
| | - Honami Katsu
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Japan
| | - Yoshiyuki Ohtsubo
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Japan
| | - Shigeto Otsuka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, Japan
| | - Yuji Nagata
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Japan
| |
Collapse
|
3
|
Complete Genome Sequence of Sphingobium xenophagum PH3-15, Isolated from La Roche-Posay Thermal Water Sources. Microbiol Resour Announc 2021; 10:e0070021. [PMID: 34410160 PMCID: PMC8375476 DOI: 10.1128/mra.00700-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report here the complete genome sequence of Sphingobium xenophagum strain PH3-15, which was isolated from La Roche-Posay thermal water sources. The assembled 4.6-Mbp genome consisted of two chromosomes and three plasmids. These data will provide valuable information and important insights into the physiology and metabolism of this Sphingobium organism.
Collapse
|
4
|
Lakra P, Verma H, Talwar C, Singh DN, Singhvi N, Lal R, Gupta V. Genome based reclassification of Deinococcus swuensis as a heterotypic synonym of Deinococcus radiopugnans. Int J Syst Evol Microbiol 2021; 71. [PMID: 34236299 DOI: 10.1099/ijsem.0.004879] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Deinococcus species are widely studied due to their utility in bioremediation of sites contaminated with radioactive elements. In the present study, we re-evaluated the taxonomic placement of two species of the genus Deinococcus namely D. swuensis DY59T and D. radiopugnans ATCC 19172T based on whole genome analyses. The 16S rRNA gene analysis revealed a 99.58% sequence similarity between this species pair that is above the recommended threshold value for species delineation. These two species also clustered together in both the 16S rRNA gene and core genome based phylogenies depicting their close relatedness. Furthermore, more than 98% of genes were shared between D. swuensis DY59T and D. radiopugnans ATCC 19172T. Interestingly, D. swuensis DY59T and D. radiopugnans ATCC 19172T shared high genome similarity in different genomic indices. They displayed an average nucleotide identity value of 97.63%, an average amino acid identity value of 97% and a digital DNA-DNA hybridization value equal to 79.50%, all of which are well above the cut-off for species delineation. Altogether, based on these evidences, D. swuensis DY59T and D. radiopugnans ATCC 19172T constitute a single species. Hence, as per the priority of publication, we propose that Deinococcus swuensis Lee et al. 2015 should be reclassified as a later heterotypic synonym of Deinococcus radiopugnans.
Collapse
Affiliation(s)
- Priya Lakra
- Department of Zoology, University of Delhi, Delhi-110007, India
| | - Helianthous Verma
- Molecular Biology and Genomics Research Laboratory, Ramjas College, University of Delhi, Delhi-110007, India
| | - Chandni Talwar
- Department of Zoology, University of Delhi, Delhi-110007, India
| | | | - Nirjara Singhvi
- Department of Zoology, University of Delhi, Delhi-110007, India
| | - Rup Lal
- The Energy and Resources Institute, Lodhi Road, New Delhi-110003, India
- Present address: 6C, India Habitat Complex, Lodhi Road, New Delhi-110003, India & 101, GH-11, Sector 47, Gurugram, Haryana-122001, India
| | - Vipin Gupta
- PhiXGen Private Limited, Gurugram, Haryana-122001, India
| |
Collapse
|
5
|
Ohta Y, Katsumata M, Kurosawa K, Takaki Y, Nishimura H, Watanabe T, Kasuya KI. Degradation of ester linkages in rice straw components by Sphingobium species recovered from the sea bottom using a non-secretory tannase-family α/β hydrolase. Environ Microbiol 2021; 23:4151-4167. [PMID: 33939871 DOI: 10.1111/1462-2920.15551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 04/27/2021] [Accepted: 04/29/2021] [Indexed: 11/28/2022]
Abstract
Microbial decomposition of allochthonous plant components imported into the aquatic environment is one of the vital steps of the carbon cycle on earth. To expand the knowledge of the biodegradation of complex plant materials in aquatic environments, we recovered a sunken wood from the bottom of Otsuchi Bay, situated in northeastern Japan in 2012. We isolated Sphingobium with high ferulic acid esterase activity. The strain, designated as OW59, grew on various aromatic compounds and sugars, occurring naturally in terrestrial plants. A genomic study of the strain suggested its role in degrading hemicelluloses. We identified a gene encoding a non-secretory tannase-family α/β hydrolase, which exhibited ferulic acid esterase activity. This enzyme shares the consensus catalytic triad (Ser-His-Asp) within the tannase family block X in the ESTHER database. The molecules, which had the same calculated elemental compositions, were produced consistently in both the enzymatic and microbial degradation of rice straw crude extracts. The non-secretory tannase-family α/β hydrolase activity may confer an important phenotypic feature on the strain to accelerate plant biomass degradation. Our study provides insights into the underlying biodegradation process of terrestrial plant polymers in aquatic environments.
Collapse
Affiliation(s)
- Yukari Ohta
- Gunma University Center for Food Science and Wellness, 4-2 Aramaki, Maebashi, Gunma, 371-8510, Japan
| | - Madoka Katsumata
- Gunma University Center for Food Science and Wellness, 4-2 Aramaki, Maebashi, Gunma, 371-8510, Japan
| | - Kanako Kurosawa
- Super-cutting-edge Grand and Advanced Research Program, JAMSTEC, 2-15, Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research Program, JAMSTEC, 2-15, Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Hiroshi Nishimura
- Biomass Conversion, Research Institute for Sustainable Humanosphere, Kyoto University Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Takashi Watanabe
- Biomass Conversion, Research Institute for Sustainable Humanosphere, Kyoto University Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Ken-Ichi Kasuya
- Gunma University Center for Food Science and Wellness, 4-2 Aramaki, Maebashi, Gunma, 371-8510, Japan.,Division of Molecular Science, Faculty of Science and Technology, Gunma University, 1-5-1 Tenjin, Kiryu, Gunma, 376-8515, Japan
| |
Collapse
|
6
|
Feng GD, Wang QB, Zhang XJ, Chen WD, Li JL, Zhu HH. Sphingobium paulinellae and Sphingobium algicola Lee and Jeon 2017 are two later heterotypic synonyms of Sphingobium limneticum Chen et al. 2013 and emended description of the species. Int J Syst Evol Microbiol 2020; 70:1644-1647. [DOI: 10.1099/ijsem.0.003946] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic analysis of the genus
Sphingobium
had shown that the type strains of
Sphingobium paulinellae
,
Sphingobium algicola
and
Sphingobium limneticum
shared a very close relationship between each other. The 16S rRNA gene sequences similarity values between each other ranged from 99.65 to 99.93 %. Whole genome sequencing was performed and genomic relatedness values between each pair of the species were 97.49–100 % (ANI) and 79.3–100 % (dDDH), respectively, all higher than the threshold values of 95–96 % ANI and 70 % dDDH suggested for species discrimination, and implicated that the type strains should belong to the same species of the genus
Sphingobium
. The phenotypic and chemotaxonomic characterizations performed in the original descriptions of
S. paulinellae
and
S. algicola
also supported the same conclusion. Due to priority of publication
Sphingobium paulinellae
and
Sphingobium algicola
Lee and Jeon 2017, should be taken as two later heterotypic synonyms of
Sphingobium limneticum
Chen et al. 2013. Correspondingly, the species description of
Sphingobium limneticum
was emended based on this study.
Collapse
Affiliation(s)
- Guang-Da Feng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Qing-Bai Wang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Xian-Jiao Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Wen-Di Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Jia-Li Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Hong-Hui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| |
Collapse
|