1
|
Yen HC, Wang SC, Chen WM, Lai EM, Kuo CH. Complete genome sequence of Sphingomonas sp. strain R1, a bacterium isolated from tomato ( Solanum lycopersicum). Microbiol Resour Announc 2024:e0024224. [PMID: 38940606 DOI: 10.1128/mra.00242-24] [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: 03/11/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024] Open
Abstract
Sphingomonas sp. strain R1 was isolated from the stem of a tomato plant and exhibited antagonism with Agrobacterium. The complete genome sequence of this bacterium consists of one 3,874,532 bp circular chromosome and two plasmids.
Collapse
Affiliation(s)
- Hsi-Ching Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Si-Chong Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
2
|
Castillo-Ramírez S. On the road to genomically defining bacterial intra-species units. mSystems 2024:e0058424. [PMID: 38940600 DOI: 10.1128/msystems.00584-24] [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: 06/29/2024] Open
Abstract
Over almost three decades, average nucleotide identity (ANI) analysis has been instrumental in operationally defining species in bacteria. However, barely any attention has been paid to soundly defining intra-species units employing ANI analyses until recently. Notably, some very recent publications are good steps forward in that direction. The level of granularity provided by these intra-species units will be relevant to understanding the eco-evolutionary dynamics and transmission of bacterial lineages and mobile genetic elements, antibiotic resistance, and virulence genes. These intra-species units will undoubtedly advance the genomic epidemiology of many bacterial pathogens. In the coming years, we anticipate that many studies will implement ANI-based definitions of different intra-species units, such as strains or sequence types, for many different bacterial species.
Collapse
Affiliation(s)
- Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| |
Collapse
|
3
|
Botero J, Peeters C, De Canck E, Laureys D, Wieme AD, Cleenwerck I, Depoorter E, Praet J, Michez D, Smagghe G, Vandamme P. A comparative genomic analysis of Fructobacillus evanidus sp. nov. from bumble bees. Syst Appl Microbiol 2024; 47:126505. [PMID: 38564984 DOI: 10.1016/j.syapm.2024.126505] [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] [Received: 01/18/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
The increase in studies on bee microbiomes is prompted by concerns over global pollinator declines. Bumble bees host core and non-core microbiota which may contribute to increased lifetime fitness. The presence of Fructobacillus in the gut microbiomes of bumble bee workers, or the replacement of core symbionts with Fructobacillus bacteria, has been considered a marker of dysbiosis. A phylogenomic analysis and functional genomic characterization of the genomes of 21 Fructobacillus isolates from bumble bees demonstrated that they represented four species, i.e. Fructobacillus cardui, Fructobacillus fructosus, Fructobacillus tropaeoli, and the novel species Fructobacillus evanidus sp. nov. Our results confirmed and substantiated the presence of two phylogenetically and functionally distinct Fructobacillus species clades that differ in genome size, percentage G + C content, the number of coding DNA sequences and metabolic characteristics. Clade 1 and clade 2 species differed in amino acid and, to a lesser extent, in carbohydrate metabolism, with F. evanidus and F. tropaeoli genomes featuring a higher number of complete metabolic pathways. While Fructobacillus genomes encoded genes that allow adhesion, biofilm formation, antibacterial activity and detoxification, other bacteria isolated from the bumble bee gut appeared better equipped to co-exist with the bumble bee host. The isolation and identification of multiple Fructobacillus species from several bumble bee gut samples in the present study also argued against a specific partnership between Fructobacillus species and their bumble bee hosts.
Collapse
Affiliation(s)
- Juliana Botero
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Evelien De Canck
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - David Laureys
- Innovation Centre for Brewing & Fermentation, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Anneleen D Wieme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium; BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Ilse Cleenwerck
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium; BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Eliza Depoorter
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Jessy Praet
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Denis Michez
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Place du parc 20, 7000 Mons, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium; BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium.
| |
Collapse
|
4
|
Yang Y, Zhou J. Unveiling the hidden world of microorganisms and their impact on the Earth's ecosystems. MLIFE 2023; 2:339-340. [PMID: 38818265 PMCID: PMC10989080 DOI: 10.1002/mlf2.12100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 06/01/2024]
Affiliation(s)
- Yunfeng Yang
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Tsinghua UniversityShenzhenChina
| | - Jizhong Zhou
- Institute for Environmental GenomicsUniversity of OklahomaNormanOklahomaUSA
- School of Biological SciencesUniversity of OklahomaNormanOklahomaUSA
- School of Civil Engineering and Environmental SciencesUniversity of OklahomaNormanOklahomaUSA
- School of Computer SciencesUniversity of OklahomaNormanOklahomaUSA
- Earth and Environmental SciencesLawrence Berkeley National LaboratoryBerkeleyCalifoniaUSA
| |
Collapse
|