1
|
Prathaban M, Prathiviraj R, Ravichandran M, Natarajan SD, Sobanaa M, Hari Krishna Kumar S, Chandrasekar V, Selvin J. Isoptericola haloaureus sp. nov., a dimorphic actinobacterium isolated from mangrove sediments of southeast India, implicating biosaline agricultural significance through nitrogen fixation and salt tolerance genes. Antonie Van Leeuwenhoek 2024; 117:89. [PMID: 38861000 DOI: 10.1007/s10482-024-01985-7] [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: 01/29/2024] [Accepted: 05/25/2024] [Indexed: 06/12/2024]
Abstract
Strain MP-1014T, an obligate halophilic actinobacterium, was isolated from the mangrove soil of Thandavarayancholanganpettai, Tamil Nadu, India. A polyphasic approach was utilized to explore its phylogenetic position completely. The isolate was Gram-positive, filamentous, non-motile, and coccoid in older cultures. Ideal growth conditions were seen at 30 °C and pH 7.0, with 5% NaCl (W/V), and the DNA G + C content was 73.3%. The phylogenic analysis of this strain based upon 16S rRNA gene sequence revealed 97-99.8% similarity to the recognized species of the genus Isoptericola. Strain MP-1014T exhibits the highest similarity to I. sediminis JC619T (99.7%), I. chiayiensis KCTC19740T (98.9%), and subsequently to I. halotolerans KCTC19646T (98.6%), when compared with other members within the Isoptericola genus (< 98%). ANI scores of strain MP-1014T are 86.4%, 84.2%, and 81.5% and dDDH values are 59.7%, 53.6%, and 34.8% with I. sediminis JC619T, I. chiayiensis KCTC19740T and I. halotolerans KCTC19646T respectively. The major polar lipids of the strain MP-1014T were phosphatidylinositol, phosphatidylglycerol, diphosphotidylglycerol, two unknown phospholipids, and glycolipids. The predominant respiratory menaquinones were MK9 (H4) and MK9 (H2). The major fatty acids were anteiso-C15:0, anteiso-C17:0, iso-C14:0, C15:0, and C16:0. Also, initial genome analysis of the organism suggests it as a biostimulant for enhancing agriculture in saline environments. Based on phenotypic and genetic distinctiveness, the strain MP-1014 T represents the novel species of the genus Isoptericola assigned Isoptericola haloaureus sp. nov., is addressed by the strain MP-1014 T, given its phenotypic, phylogenetic, and hereditary uniqueness. The type strain is MP-1014T [(NCBI = OP672482.1 = GCA_036689775.1) ATCC = BAA 2646T; DSMZ = 29325T; MTCC = 13246T].
Collapse
Affiliation(s)
- Munisamy Prathaban
- Department of Microbiology, Pondicherry University, Puducherry, 605014, India.
| | | | - Mythili Ravichandran
- Department of Microbiology, Vivekanandha Arts and Science College for Women, Sankagiri, Tamil Nadu, India
| | - Sharmila Devi Natarajan
- School of Biosciences, Mar Athanasios College for Advanced Studies, Thiruvalla, Kerala, India
| | - Murugesan Sobanaa
- Department of Microbiology, Pondicherry University, Puducherry, 605014, India
| | | | | | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Puducherry, 605014, India
| |
Collapse
|
2
|
Liou JS, Zhang WL, Hsu LW, Chen CC, Wang YT, Mori K, Hidaka K, Hamada M, Huang L, Watanabe K, Huang CH. Faecalibacterium taiwanense sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2024; 74. [PMID: 38848117 DOI: 10.1099/ijsem.0.006413] [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: 06/09/2024] Open
Abstract
Two Gram-stain-negative, straight rods, non-motile, asporogenous, catalase-negative and obligately anaerobic butyrate-producing strains, HLW78T and CYL33, were isolated from faecal samples of two healthy Taiwanese adults. Phylogenetic analyses of 16S rRNA and DNA mismatch repair protein MutL (mutL) gene sequences revealed that these two novel strains belonged to the genus Faecalibacterium. On the basis of 16S rRNA and mutL gene sequence similarities, the type strains Faecalibacterium butyricigenerans AF52-21T(98.3-98.1 % and 79.0-79.5 % similarity), Faecalibacterium duncaniae A2-165T(97.8-97.9 % and 70.9-80.1 %), Faecalibacterium hattorii APC922/41-1T(97.1-97.3 % and 80.3-80.5 %), Faecalibacterium longum CM04-06T(97.8-98.0% and 78.3 %) and Faecalibacterium prausnitzii ATCC 27768T(97.3-97.4 % and 82.7-82.9 %) were the closest neighbours to the novel strains HLW78T and CYL33. Strains HLW78T and CYL33 had 99.4 % both the 16S rRNA and mutL gene sequence similarities, 97.9 % average nucleotide identity (ANI), 96.3 % average amino acid identity (AAI), and 80.5 % digital DNA-DNA hybridization (dDDH) values, indicating that these two strains are members of the same species. Phylogenomic tree analysis indicated that strains HLW78T and CYL33 formed an independent robust cluster together with F. prausnitzii ATCC 27768T. The ANI, AAI and dDDH values between strain HLW78T and its closest neighbours were below the species delineation thresholds of 77.6-85.1 %, 71.4-85.2 % and 28.3-30.9 %, respectively. The two novel strains could be differentiated from the type strains of their closest Faecalibacterium species based on their cellular fatty acid compositions, which contained C18 : 1 ω7c and lacked C15 : 0 and C17 : 1 ω6c, respectively. Phenotypic, chemotaxonomic and genotypic test results demonstrated that the two novel strains HLW78T and CYL33 represented a single, novel species within the genus Faecalibacterium, for which the name Faecalibacterium taiwanense sp. nov. is proposed. The type strain is HLW78T (=BCRC 81397T=NBRC 116372T).
Collapse
Affiliation(s)
- Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Wei-Ling Zhang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Li-Wen Hsu
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
| | - Yu-Ting Wang
- Division of Research and Analysis, Food and Drug Administration, Ministry of Health and Welfare, Taipei 11561, Taiwan, ROC
| | - Koji Mori
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Kohei Hidaka
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan University, No. 50, Lane 155, Sec 3, Keelung Rd., Taipei 10673, Taiwan, ROC
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| |
Collapse
|
3
|
Rivera Ortuña FN, Guevara-Luna J, Yan J, Lopez Amezcua E, Arroyo-Herrera I, Li Y, Vásquez-Murrieta MS, Rojas Arellano D, Wang ET. Rhizobium hidalgonense and Rhizobium redzepovicii as faba bean (Vicia faba L.) microsymbionts in Mexican soils. Arch Microbiol 2024; 206:281. [PMID: 38805057 DOI: 10.1007/s00203-024-03989-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024]
Abstract
As a legume crop widely cultured in the world, faba bean (Vicia faba L.) forms root nodules with diverse Rhizobium species in different regions. However, the symbionts associated with this plant in Mexico have not been studied. To investigate the diversity and species/symbiovar affiliations of rhizobia associated with faba bean in Mexico, rhizobia were isolated from this plant grown in two Mexican sites in the present study. Based upon the analysis of recA gene phylogeny, two genotypes were distinguished among a total of 35 isolates, and they were identified as Rhizobium hidalgonense and Rhizobium redzepovicii, respectively, by the whole genomic sequence analysis. Both the species harbored identical nod gene cluster and the same phylogenetic positions of nodC and nifH. So, all of them were identified into the symbiovar viciae. As a minor group, R. hidalgonense was only isolated from slightly acid soil and R. redzepovicii was the dominant group in both the acid and neutral soils. In addition, several genes related to resistance to metals (zinc, copper etc.) and metalloids (arsenic) were detected in genomes of the reference isolates, which might offer them some adaptation benefits. As conclusion, the community composition of faba bean rhizobia in Mexico was different from those reported in other regions. Furthermore, our study identified sv. viciae as the second symbiovar in the species R. redzepovicii. These results added novel evidence about the co-evolution, diversification and biogeographic patterns of rhizobia in association with their host legumes in distinct geographic regions.
Collapse
Affiliation(s)
- Flor N Rivera Ortuña
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México
| | - Joseph Guevara-Luna
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México
| | - Jun Yan
- National Observation Station of Hailun Agro-Ecology System, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Eloisa Lopez Amezcua
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México
| | - Ivan Arroyo-Herrera
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México
| | - Yan Li
- College of Life Science, Yantai University, Shandong Province, Yantai City, 264005, China
| | - Maria Soledad Vásquez-Murrieta
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México
| | - Danae Rojas Arellano
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de Mexico, México.
| |
Collapse
|
4
|
Rey-Velasco X, Lucena T, Belda A, Gasol JM, Sánchez O, Arahal DR, Pujalte MJ. Genomic and phenotypic characterization of 26 novel marine bacterial strains with relevant biogeochemical roles and widespread presence across the global ocean. Front Microbiol 2024; 15:1407904. [PMID: 38863746 PMCID: PMC11165706 DOI: 10.3389/fmicb.2024.1407904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 04/29/2024] [Indexed: 06/13/2024] Open
Abstract
Prokaryotes dominate global oceans and shape biogeochemical cycles, yet most taxa remain uncultured and uncharacterized as of today. Here we present the characterization of 26 novel marine bacterial strains from a large isolate collection obtained from Blanes Bay (NW Mediterranean) microcosm experiments made in the four seasons. Morphological, cultural, biochemical, physiological, nutritional, genomic, and phylogenomic analyses were used to characterize and phylogenetically place the novel isolates. The strains represent 23 novel bacterial species and six novel genera: three novel species pertaining to class Alphaproteobacteria (families Rhodobacteraceae and Sphingomonadaceae), six novel species and three new genera from class Gammaproteobacteria (families Algiphilaceae, Salinispheraceae, and Alteromonadaceae), 13 novel species and three novel genera from class Bacteroidia (family Flavobacteriaceae), and one new species from class Rhodothermia (family Rubricoccaceae). The bacteria described here have potentially relevant roles in the cycles of carbon (e.g., carbon fixation or energy production via proteorhodopsin), nitrogen (e.g., denitrification or use of urea), sulfur (oxidation of sulfur compounds), phosphorus (acquisition and use of different forms of phosphorus and remodeling of membrane phospholipids), and hydrogen (oxidation of hydrogen to obtain energy). We mapped the genomes of the presented strains to the Tara Oceans metagenomes to reveal that these strains were globally distributed, with those of the family Flavobacteriaceae being the most widespread and abundant, while Rhodothermia being the rarest and most localized. While molecular-only approaches are also important, our study stresses the importance of culturing as a powerful tool to further understand the functioning of marine bacterial communities.
Collapse
Affiliation(s)
| | - Teresa Lucena
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
| | - Ana Belda
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
| | - Josep M. Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalunya, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - David R. Arahal
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
| | - María J. Pujalte
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
| |
Collapse
|
5
|
Ali NS, Thakur S, Ye M, Monteil-Rivera F, Pan Y, Qin W, Yang TC. Uncovering the lignin-degrading potential of Serratia quinivorans AORB19: insights from genomic analyses and alkaline lignin degradation. BMC Microbiol 2024; 24:181. [PMID: 38789935 PMCID: PMC11127350 DOI: 10.1186/s12866-024-03331-3] [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: 12/04/2023] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Lignin is an intricate phenolic polymer found in plant cell walls that has tremendous potential for being converted into value-added products with the possibility of significantly increasing the economics of bio-refineries. Although lignin in nature is bio-degradable, its biocatalytic conversion is challenging due to its stable complex structure and recalcitrance. In this context, an understanding of strain's genomics, enzymes, and degradation pathways can provide a solution for breaking down lignin to unlock the full potential of lignin as a dominant valuable bioresource. A gammaproteobacterial strain AORB19 has been isolated previously from decomposed wood based on its high laccase production. This work then focused on the detailed genomic and functional characterization of this strain based on whole genome sequencing, the identification of lignin degradation products, and the strain's laccase production capabilities on various agro-industrial residues. RESULTS Lignin degrading bacterial strain AORB19 was identified as Serratia quinivorans based on whole genome sequencing and core genome phylogeny. The strain comprised a total of 123 annotated CAZyme genes, including ten cellulases, four hemicellulases, five predicted carbohydrate esterase genes, and eight lignin-degrading enzyme genes. Strain AORB19 was also found to possess genes associated with metabolic pathways such as the β-ketoadipate, gentisate, anthranilate, homogentisic, and phenylacetate CoA pathways. LC-UV analysis demonstrated the presence of p-hydroxybenzaldehyde and vanillin in the culture media which constitutes potent biosignatures indicating the strain's capability to degrade lignin. Finally, the study evaluated the laccase production of Serratia AORB19 grown with various industrial raw materials, with the highest activity detected on flax seed meal (257.71 U/L), followed by pea hull (230.11 U/L), canola meal (209.56 U/L), okara (187.67 U/L), and barley malt sprouts (169.27 U/L). CONCLUSIONS The whole genome analysis of Serratia quinivorans AORB19, elucidated a repertoire of genes, pathways and enzymes vital for lignin degradation that widens the understanding of ligninolytic metabolism among bacterial lignin degraders. The LC-UV analysis of the lignin degradation products coupled with the ability of S. quinivorans AORB19 to produce laccase on diverse agro-industrial residues underscores its versatility and its potential to contribute to the economic viability of bio-refineries.
Collapse
Affiliation(s)
- Nadia Sufdar Ali
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Ottawa, ON, Canada
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada
| | - Subarna Thakur
- Department of Bioinformatics, University of North Bengal, Siliguri, India
| | - Mengwei Ye
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Fanny Monteil-Rivera
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Youlian Pan
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Wensheng Qin
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada.
| | - Trent Chunzhong Yang
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Ottawa, ON, Canada.
- BioWise Technologies Inc, Ottawa, Canada.
| |
Collapse
|
6
|
Suh MK, Jin JS, Do HE, Kim JS, Eom MK, Kim HS, Lee JS. Adlercreutzia faecimuris sp. nov., producing propionate and acetate isolated from mouse feces. Antonie Van Leeuwenhoek 2024; 117:80. [PMID: 38772982 DOI: 10.1007/s10482-024-01980-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/15/2024] [Indexed: 05/23/2024]
Abstract
A novel strictly anaerobic bacterium, strain JBNU-10 T, was isolated from BALB/c mouse feces. Cells of the strain JBNU-10 T were Gram-stain positive, non-motile and rod-shaped. Optimum growth occurred at 37℃, with 1% (w/v) NaCl and at pH 7. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain JBNU-10 T belonged to the genus Adlercreutzia and were closely related to Adlercreutzia muris WCA-131-CoC-2 T (95.90%). The genome sequencing of strain JBNU-10 T revealed a genome size of 2,790,983 bp, a DNA G + C content of 69.4 mol%. It contains a total of 2,266 CDSs, 5 rRNA genes and 49 tRNA genes. According to the data obtained strain JBNU-10 T shared ANI value below 77.6- 67.7%, dDDH value below 23.8% with the closely type species. Strain JBNU-10 T possessed iso-C16:0 DMA, C18:1 CIS 9 FAME, and C18:0 DMA as the major fatty acids and had DMMK-6. The major end products of fermentation is propionate and acetate. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain JBNU-10 T represent a novel species of the genus Adlercreutzia. The type strain is JBNU-10 T (= KCTC 25028 T = CCUG 75610 T).
Collapse
Affiliation(s)
- Min Kuk Suh
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-Gil, Jeongeup-Si, Jeollabuk-Do, 56212, South Korea
- Department of Lifestyle Medicine, Jeonbuk National University, 79 Gobong-Ro, Iksan-Si, Jeollabuk-Do, 54596, Republic of Korea
| | - Jong-Sik Jin
- Department of Oriental Medicine Resources, Jeonbuk National University, 79 Gobong-Ro, Iksan-Si, 54596, Jeollabuk-Do, Republic of Korea
| | - Hyo Eun Do
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-Gil, Jeongeup-Si, Jeollabuk-Do, 56212, South Korea
- Department of Oriental Medicine Resources, Jeonbuk National University, 79 Gobong-Ro, Iksan-Si, 54596, Jeollabuk-Do, Republic of Korea
| | - Ji-Sun Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-Gil, Jeongeup-Si, Jeollabuk-Do, 56212, South Korea
| | - Mi Kyung Eom
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-Gil, Jeongeup-Si, Jeollabuk-Do, 56212, South Korea
| | - Han Sol Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-Gil, Jeongeup-Si, Jeollabuk-Do, 56212, South Korea
- Department of Lifestyle Medicine, Jeonbuk National University, 79 Gobong-Ro, Iksan-Si, Jeollabuk-Do, 54596, Republic of Korea
| | - Jung- Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-Gil, Jeongeup-Si, Jeollabuk-Do, 56212, South Korea.
- University of Science and Technology (UST), 217 Gajeong-Ro, Yuseong-Gu, Daejeon, 34113, Republic of Korea.
| |
Collapse
|
7
|
Xie CJ, Yao L, Tang R, Han S, Yang S, Alwathnani H, Rensing C, Liu GH, Zhou SG. Azotosporobacter soli gen. nov., sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil. Antonie Van Leeuwenhoek 2024; 117:79. [PMID: 38755437 DOI: 10.1007/s10482-024-01978-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024]
Abstract
A nitrogen-fixing strain designated SG130T was isolated from paddy soil in Fujian Province, China. Strain SG130T was Gram-staining-negative, rod-shaped, and strictly anaerobic. Strain SG130T showed the highest 16S rRNA gene sequence similarities with the type strains Dendrosporobacter quercicolus DSM 1736T (91.7%), Anaeroarcus burkinensis DSM 6283T (91.0%) and Anaerospora hongkongensis HKU 15T (90.9%). Furthermore, the phylogenetic and phylogenomic analysis also suggested strain SG130T clustered with members of the family Sporomusaceae and was distinguished from other genera within this family. Growth of strain SG130T was observed at 25-45 °C (optimum 30 °C), pH 6.0-9.5 (optimum 7.0) and 0-1% (w/v) NaCl (optimum 0.1%). The quinones were Q-8 and Q-9. The polar lipids were phosphatidylserine (PS), phosphatidylethanolamine (PE), glycolipid (GL), phospholipid (PL) and an unidentified lipid (UL). The major fatty acids (> 10%) were iso-C13:0 3OH (26.6%), iso-C17:1 (15.6%) and iso-C15:1 F (11.4%). The genomic DNA G + C content was 50.7%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG130T and the most closely related type strain D. quercicolus DSM 1736T (ANI 68.0% and dDDH 20.3%) were both below the cut-off level for species delineation. The average amino acid identity (AAI) between strain SG130T and the most closely related type strain D. quercicolus DSM 1736T was 63.2%, which was below the cut-off value for bacterial genus delineation (65%). Strain SG130T possessed core genes (nifHDK) involved in nitrogen fixation, and nitrogenase activity (106.38 μmol C2H4 g-1 protein h-1) was examined using the acetylene reduction assay. Based on the above results, strain SG130T is confirmed to represent a novel genus of the family Sporomusaceae, for which the name Azotosporobacter soli gen. nov., sp. nov. is proposed. The type strain is SG130T (= GDMCC 1.3312T = JCM 35641T).
Collapse
Affiliation(s)
- Cheng-Jie Xie
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, People's Republic of China
| | - Ling Yao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, People's Republic of China
| | - Rong Tang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou City, Guangdong Province, 510006, People's Republic of China
| | - Shuang Han
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, People's Republic of China
| | - Shang Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, People's Republic of China
| | - Hend Alwathnani
- Department of Botany and Microbiology, King Saud University, Riyadh, Saudi Arabia
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, People's Republic of China
| | - Guo-Hong Liu
- Institute of Resources, Environment and Soil Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou City, Fujian Province, 350003, People's Republic of China.
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, People's Republic of China.
| |
Collapse
|
8
|
Jiang CS, Li CY, Gu CT. The Type Strain of Bifidobacterium indicum Scardovi and Trovatelli 1969 (Approved Lists 1980) is ATCC 25912, not DSM 20214, and Rejection to Reclassify Bifidobacterium coryneforme as Bifidobacterium indicum. Curr Microbiol 2024; 81:168. [PMID: 38733376 DOI: 10.1007/s00284-024-03712-x] [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: 01/27/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024]
Abstract
In 2018, Nouioui et al. proposed that Bifidobacterium coryneforme was a later synonym of Bifidobacterium indicum on the basis of the digital DNA-DNA hybridization (dDDH) value (85.0%) between B. coryneforme LMG 18911T and B. indicum LMG 11587T. However, in the study of Scardovi et al. (1970), the type strains of B. indicum and B. coryneforme only exhibited 60% DNA-DNA hybridization value. In the present study, the genomes of B. coryneforme CGMCC 1.2279T, B. coryneforme JCM 5819T, B. indicum JCM 1302T, B. indicum CGMCC 1.2275T, B. indicum DSM 20214T, B. indicum LMG 27437T, B. indicum ATCC 25912T, B. indicum KCTC 3230T, B. indicum CCUG 34985T, were sequenced, and the taxonomic relationship between B. coryneforme and B. indicum was re-evaluated. On the basis of the results presented here, (i) ATCC 25912 and DSM 20214 deposited by Vittorio Scardovi are two different strains; (ii) the type strain of B. indicum is ATCC 25912T (= JCM 1302T = LMG 27437T = CGMCC 1.2275T = KCTC 3230T), and not DSM 20214 (= BCRC 14674 = CCUG 34985 = LMG 11587); (iii) B. coryneforme and B. indicum represent two different species of the genus Bifidobacterium; (iv) strain DSM 20214 (= BCRC 14674 = CCUG 34985 = LMG 11587) belongs to B. coryneforme.
Collapse
Affiliation(s)
- Cheng-Shan Jiang
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Chun Yan Li
- College of Food Science, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Chun Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, People's Republic of China.
| |
Collapse
|
9
|
Kitikhun S, Charoenyingcharoen P, Siriarchawatana P, Likhitrattanapisal S, Nilsakha T, Chanpet A, Jeennor S, Yukphan P, Ingsriswang S. Rhodoferax potami sp. nov. and Rhodoferax mekongensis sp. nov., isolated from the Mekong River in Thailand. Int J Syst Evol Microbiol 2024; 74. [PMID: 38700930 DOI: 10.1099/ijsem.0.006351] [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: 05/05/2024] Open
Abstract
Four newly discovered Gram-stain-negative bacteria, designated as BL00010T, BL00058, D8-11T and BL00200, were isolated from water samples collected at three hydrological monitoring stations (namely Chiang Saen, Chiang Khan and Nong Khai) located along the Mekong River in Thailand. An investigation encompassing phenotypic, chemotaxonomic and genomic traits was conducted. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that all four isolates represented members of the genus Rhodoferax. These isolates were closely related to Rhodoferax bucti KCTC 62564T with a similarity of 99.59%. The major fatty acids of the four novel isolates included C16:0 and C16:1ω7c and/or C16 : 1ω6c, whereas the major respiratory quinone was identified as ubiquinone Q-8. In addition, phosphatidylethanolamine was identified as a major polar lipid in these bacteria. The genomes of BL00010T, BL00058, D8-11T and BL00200 were similar in size (3.88-4.01 Mbp) and DNA G+C contents (59.5, 59.3, 59.5 and 59.3 mol%, respectively). In contrast to R. bucti KCTC 62564T and Rhodoferax aquaticus KCTC 32394T, the newly discovered species possessed several genes involved in nitrite and nitrile metabolism, which may be related to their unique adaptation to nitrile-rich environments. From the results of the pairwise analysis of average nucleotide identity of the whole genome and digital DNA-DNA hybridisation, it was evident that BL00010T and D8-11T represented two novel species, for which we propose the nomenclature Rhodoferax potami sp. nov., with the type strain BL00010T (TBRC 17198T = NBRC 116413T), and Rhodoferax mekongensis sp. nov., with the type strain D8-11T (TBRC 17307T = NBRC 116415T).
Collapse
Affiliation(s)
- Supattra Kitikhun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Piyanat Charoenyingcharoen
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Paopit Siriarchawatana
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Somsak Likhitrattanapisal
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Thanyakorn Nilsakha
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Amonwan Chanpet
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Sukanya Jeennor
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Pattaraporn Yukphan
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Supawadee Ingsriswang
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| |
Collapse
|
10
|
van Lill M, Venter SN, Muema EK, Palmer M, Chan WY, Beukes CW, Steenkamp ET. SeqCode facilitates naming of South African rhizobia left in limbo. Syst Appl Microbiol 2024; 47:126504. [PMID: 38593622 DOI: 10.1016/j.syapm.2024.126504] [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: 01/29/2024] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
South Africa is well-known for the diversity of its legumes and their nitrogen-fixing bacterial symbionts. However, in contrast to their plant partners, remarkably few of these microbes (collectively referred to as rhizobia) from South Africa have been characterised and formally described. This is because the rules of the International Code of Nomenclature of Prokaryotes (ICNP) are at odds with South Africa's National Environmental Management: Biodiversity Act and its associated regulations. The ICNP requires that a culture of the proposed type strain for a novel bacterial species be deposited in two international culture collections and be made available upon request without restrictions, which is not possible under South Africa's current national regulations. Here, we describe seven new Mesorhizobium species obtained from root nodules of Vachellia karroo, an iconic tree legume distributed across various biomes in southern Africa. For this purpose, 18 rhizobial isolates were delineated into putative species using genealogical concordance, after which their plausibility was explored with phenotypic characters and average genome relatedness. For naming these new species, we employed the rules of the recently published Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode), which utilizes genome sequences as nomenclatural types. The work presented in this study thus provides an illustrative example of how the SeqCode allows for a standardised approach for naming cultivated organisms for which the deposition of a type strain in international culture collections is currently problematic.
Collapse
Affiliation(s)
- Melandré van Lill
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Esther K Muema
- Department of Soil Science, Faculty of AgriSciences, Stellenbosch University, South Africa
| | - Marike Palmer
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | | | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| |
Collapse
|
11
|
Liu FL, Abdugheni R, Ran CG, Zhou N, Liu SJ. Eubacterium album sp. nov., a butyrate-producing bacterium isolated from faeces of a healthy human. Int J Syst Evol Microbiol 2024; 74. [PMID: 38739685 DOI: 10.1099/ijsem.0.006380] [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: 05/16/2024] Open
Abstract
An oval to rod-shaped, Gram-stain-positive, strictly anaerobic bacterium, designated LFL-14T, was isolated from the faeces of a healthy Chinese woman. Cells of the strain were non-spore-forming, grew optimally at 37 °C (growth range 30-45 °C) and pH 7.0 (growth range 6.0-9.0) under anaerobic conditions in the liquid modified Gifu anaerobic medium (mGAM). The result of 16S rRNA gene-based analysis indicated that LFL-14T shared an identity of 94.7 0% with Eubacterium ventriosum ATCC 27560T, indicating LFL-14T represented a novel taxon. The results of genome-based analysis revealed that the average nucleotide identity (ANI), the digital DNA-DNA hybridisation (dDDH) and average amino acid identity (AAI) between LFL-14T and its phylogenetically closest neighbour, Eubacterium ventriosum ATCC 27560T, were 77.0 %, 24.6 and 70.9 %, respectively, indicating that LFL-14T represents a novel species of the genus Eubacterium. The genome size of LFL-14T was 2.92 Mbp and the DNA G+C content was 33.14 mol%. We analysed the distribution of the genome of LFL-14T in cohorts of healthy individuals, type 2 diabetes patients (T2D) and patients with non-alcoholic fatty liver disease (NAFLD). We found that its abundance was higher in the T2D cohort, but it had a low average abundance of less than 0.2 % in all three cohorts. The percentages of frequency of occurrence in the T2D, healthy and NAFLD cohorts were 48.87 %, 16.72 % and 13.10 % respectively. The major cellular fatty acids of LFL-14T were C16 : 0 (34.4 %), C17 : 0 2-OH (21.4 %) and C14 : 0 (11.7 %). Additionally, the strain contained diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE), as well as unidentified phospholipids and unidentified glycolipids. The glucose fermentation products of LFL-14T were acetate and butyrate. In summary, On the basis of its chemotaxonomic, phenotypic, phylogenetic and phylogenomic properties, strain LFL-14T (= CGMCC 1.18005T = KCTC 25580T) is identified as representing a novel species of the genus Eubacterium, for which the name Eubacterium album sp. nov. is proposed.
Collapse
Affiliation(s)
- Feng-Lan Liu
- College of Life Sciences, Hebei University, Baoding, 071000, PR China
| | - Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China
| | - Cong-Guo Ran
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
- University of the Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
- University of the Chinese Academy of Sciences, Beijing, 100049, PR China
| |
Collapse
|
12
|
Hilliard MA, Sela DA. Transmission and Persistence of Infant Gut-Associated Bifidobacteria. Microorganisms 2024; 12:879. [PMID: 38792709 PMCID: PMC11124121 DOI: 10.3390/microorganisms12050879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Bifidobacterium infantis are the primary colonizers of the infant gut, yet scientific research addressing the transmission of the genus Bifidobacterium to infants remains incomplete. This review examines microbial reservoirs of infant-type Bifidobacterium that potentially contribute to infant gut colonization. Accordingly, strain inheritance from mother to infant via the fecal-oral route is likely contingent on the bifidobacterial strain and phenotype, whereas transmission via the vaginal microbiota may be restricted to Bifidobacterium breve. Additional reservoirs include breastmilk, horizontal transfer from the environment, and potentially in utero transfer. Given that diet is a strong predictor of Bifidobacterium colonization in early life and the absence of Bifidobacterium is observed regardless of breastfeeding, it is likely that additional factors are responsible for bifidobacterial colonization early in life.
Collapse
Affiliation(s)
- Margaret A. Hilliard
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA;
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - David A. Sela
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA;
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
- Department of Nutrition, University of Massachusetts, Amherst, MA 01003, USA
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
- Department of Microbiology & Physiological Systems and Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
| |
Collapse
|
13
|
Wang YT, Lin YC, Hsieh YH, Lin YT, Hamada M, Chen CC, Liou JS, Lee AY, Zhang WL, Chen YT, Huang CH. Staphylococcus hsinchuensis sp. nov., Isolated from Soymilk. Pathogens 2024; 13:343. [PMID: 38668298 PMCID: PMC11055063 DOI: 10.3390/pathogens13040343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 04/29/2024] Open
Abstract
A novel coagulase-negative Staphylococcus strain (H164T) was isolated from soymilk in Taiwan. Comparative sequence analysis of the 16S rRNA gene revealed that the H164T strain is a member of the genus Staphylococcus. We used multilocus sequence analysis (MLSA) and phylogenomic analyses to demonstrate that the novel strain was closely related to Staphylococcus gallinarum, Staphylococcus nepalensis, Staphylococcus cohnii, and Staphylococcus urealyuticus. The average nucleotide identity and digital DNA-DNA hybridization values between H164T and its closest relatives were <95% and <70%, respectively. The H164T strain could also be distinguished from its closest relatives by the fermentation of d-fructose, d-maltose, d-trehalose, and d-mannitol, as well as by the activities of α-glucosidase and alkaline phosphatase. The major cellular fatty acids were C15:0 iso and C15:0 anteiso, and the predominant menaquinones were MK-7 and MK-8, respectively. The major cellular fatty acids and predominant menaquinones were C15:0 iso and C15:0 anteiso and MK-7 and MK-8, respectively. In conclusion, this strain represents a novel species, named Staphylococcus hsinchuensis sp. nov., with the type strain H164T (=BCRC 81404T = NBRC 116174T).
Collapse
Affiliation(s)
- Yu-Ting Wang
- Division of Research and Analysis, Food and Drug Administration, Ministry of Health and Welfare, Taipei 115021, Taiwan;
| | - Yu-Chun Lin
- Taiwan Livestock Research Institute, Ministry of Agriculture, Tainan 71246, Taiwan; (Y.-C.L.)
- Fisheries Research Institute, Ministry of Agriculture, Keelung 202008, Taiwan
| | - Yi-Huei Hsieh
- Taiwan Livestock Research Institute, Ministry of Agriculture, Tainan 71246, Taiwan; (Y.-C.L.)
| | - Yu-Tzu Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 404328, Taiwan;
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu 292-0818, Chiba, Japan
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Jong-Shian Liou
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan (A.-Y.L.)
| | - Ai-Yun Lee
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan (A.-Y.L.)
| | - Wei-Ling Zhang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan (A.-Y.L.)
| | - Yung-Tsung Chen
- Department of Food Science, National Taiwan Ocean University, Keelung 202301, Taiwan;
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan (A.-Y.L.)
| |
Collapse
|
14
|
Ali F. Patterns of Change in Nucleotide Diversity Over Gene Length. Genome Biol Evol 2024; 16:evae078. [PMID: 38608148 DOI: 10.1093/gbe/evae078] [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: 07/18/2023] [Revised: 03/26/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Nucleotide diversity at a site is influenced by the relative strengths of neutral and selective population genetic processes. Therefore, attempts to estimate Effective population size based on the diversity of synonymous sites demand a better understanding of their selective constraints. The nucleotide diversity of a gene was previously found to correlate with its length. In this work, I measure nucleotide diversity at synonymous sites and uncover a pattern of low diversity towards the translation initiation site of a gene. The degree of reduction in diversity at the translation initiation site and the length of this region of reduced diversity can be quantified as "Effect Size" and "Effect Length" respectively, using parameters of an asymptotic regression model. Estimates of Effect Length across bacteria covaried with recombination rates as well as with a multitude of translation-associated traits such as the avoidance of mRNA secondary structure around translation initiation site, the number of rRNAs, and relative codon usage of ribosomal genes. Evolutionary simulations under purifying selection reproduce the observed patterns and diversity-length correlation and highlight that selective constraints on the 5'-region of a gene may be more extensive than previously believed. These results have implications for the estimation of effective population size, and relative mutation rates, and for genome scans of genes under positive selection based on "silent-site" diversity.
Collapse
Affiliation(s)
- Farhan Ali
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
| |
Collapse
|
15
|
Lara AC, Kotrbová L, Keller M, Nouioui I, Neumann-Schaal M, Mast Y, Chroňáková A. Lentzea sokolovensis sp. nov., Lentzea kristufekii sp. nov. and Lentzea miocenica sp. nov., rare actinobacteria from Miocene lacustrine sediment of the Sokolov Coal Basin, Czech Republic. Int J Syst Evol Microbiol 2024; 74. [PMID: 38630118 DOI: 10.1099/ijsem.0.006335] [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: 04/19/2024] Open
Abstract
The taxonomic position of three actinobacterial strains, BCCO 10_0061T, BCCO 10_0798T, and BCCO 10_0856T, recovered from bare soil in the Sokolov Coal Basin, Czech Republic, was established using a polyphasic approach. The multilocus sequence analysis based on 100 single-copy genes positioned BCCO 10_0061T in the same cluster as Lentzea waywayandensis, strain BCCO 10_0798T in the same cluster as Lentzea flaviverrucosa, Lentzea californiensis, Lentzea violacea, and Lentzea albidocapillata, and strain BCCO 10_0856T clustered together with Lentzea kentuckyensis and Lentzea alba. Morphological and chemotaxonomic characteristics of these strains support their assignment to the genus Lentzea. In all three strains, MK-9(H4) accounted for more than 80 % of the isoprenoid quinone. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The whole-cell sugars were rhamnose, ribose, mannose, glucose, and galactose. The major fatty acids (>10 %) were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, and C16 : 0. The polar lipids were diphosphatidylglycerol, methyl-phosphatidylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol. The genomic DNA G+C content of strains (mol%) was 68.8 for BCCO 10_0061T, 69.2 for BCCO 10_0798T, and 68.5 for BCCO 10_0856T. The combination of digital DNA-DNA hybridization results, average nucleotide identity values and phenotypic characteristics of BCCO 10_0061T, BCCO 10_0798T, and BCCO 10_0856T distinguishes them from their closely related strains. Bioinformatic analysis of the genome sequences of the strains revealed several biosynthetic gene clusters (BGCs) with identities >50 % to already known clusters, including BGCs for geosmin, coelichelin, ε-poly-l-lysine, and erythromycin-like BGCs. Most of the identified BGCs showed low similarity to known BGCs (<50 %) suggesting their genetic potential for the biosynthesis of novel secondary metabolites. Based on the above results, each strain represents a novel species of the genus Lentzea, for which we propose the name Lentzea sokolovensis sp. nov. for BCCO 10_0061T (=DSM 116175T), Lentzea kristufekii sp. nov. for BCCO 10_0798T (=DSM 116176T), and Lentzea miocenica sp. nov. for BCCO 10_0856T (=DSM 116177T).
Collapse
Affiliation(s)
- Ana Catalina Lara
- Biology Centre Czech Academy of Sciences, Institute of Soil Biology and BiogeochemistryNaSádkách 7, 37005 České Budějovice, Czech Republic
- University of Chemistry, and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Technická 5, 16628 Prague, Czech Republic
| | - Lucie Kotrbová
- Biology Centre Czech Academy of Sciences, Institute of Soil Biology and BiogeochemistryNaSádkách 7, 37005 České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Moritz Keller
- Biology Centre Czech Academy of Sciences, Institute of Soil Biology and BiogeochemistryNaSádkách 7, 37005 České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Imen Nouioui
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Yvonne Mast
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Alica Chroňáková
- Biology Centre Czech Academy of Sciences, Institute of Soil Biology and BiogeochemistryNaSádkách 7, 37005 České Budějovice, Czech Republic
| |
Collapse
|
16
|
Yang H, Jo H, Kim SH, Yun CS, Park SH, Park DS. Veillonella faecalis sp. nov., a propionic acid-producing bacterium isolated from the faeces of an infant. Antonie Van Leeuwenhoek 2024; 117:50. [PMID: 38472420 DOI: 10.1007/s10482-024-01951-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/16/2024] [Indexed: 03/14/2024]
Abstract
A strictly anaerobic, Gram-stain-negative, catalase-negative, cocci-shaped, and propionate-producing bacterial strain, named Ds1651T was isolated from the fecal sample collected from a South Korean infant. Through a comparison of 16S rRNA gene sequences, it was revealed that Ds1651T had the highest phylogenetic affinity with Veillonella nakazawae KCTC 25297 T (99.86%), followed by Veillonella infantium KCTC 25370 T (99.80%), and Veillonella dispar KCTC 25309 T (99.73%) in the family Veillonellaceae. Average nucleotide identity values between Ds1651T and three reference species were 95.48% for Veillonella nakazawae KCTC 25297 T, 94.46% for Veillonella infantium KCTC 25370 T, and 92.81% for Veillonella dispar KCTC 25309 T. The G + C content of Ds1651T was 38.58 mol%. Major fermentation end-products were acetic and propionic acids in Trypticase peptone glucose yeast extract broth with 1% (v/v) sodium lactate. The predominant cellular fatty acids that account for more than 10% were summed in Feature 8 (C17:1 ω8c and/or C17:2) and C13:0. Based on the findings from phylogenetic, genomic, phenotypic, and chemotaxonomic studies, we propose that the type strain Ds1651T (= KCTC 25477 T = GDMCC 1.3707 T) represents a novel bacterial species within the genus Veillonella, with the proposed name Veillonella faecalis sp. nov.
Collapse
Affiliation(s)
- Haneol Yang
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-Gil, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea
- Department of Biology, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Hana Jo
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-Gil, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea
| | - Seung Hyun Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-Gil, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea
| | - Chan-Seok Yun
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-Gil, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-Gil, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea.
| | - Doo-Sang Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-Gil, Jeongeup-Si, Jeollabuk-Do, 56212, Republic of Korea.
| |
Collapse
|
17
|
Qi G, Hao L, Xin T, Gan Y, Lou Q, Xu W, Song J. Analysis of Whole-Genome facilitates rapid and precise identification of fungal species. Front Microbiol 2024; 15:1336143. [PMID: 38500585 PMCID: PMC10946254 DOI: 10.3389/fmicb.2024.1336143] [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: 11/10/2023] [Accepted: 02/13/2024] [Indexed: 03/20/2024] Open
Abstract
Fungal identification is a cornerstone of fungal research, yet traditional molecular methods struggle with rapid and accurate onsite identification, especially for closely related species. To tackle this challenge, we introduce a universal identification method called Analysis of whole GEnome (AGE). AGE includes two key steps: bioinformatics analysis and experimental practice. Bioinformatics analysis screens candidate target sequences named Targets within the genome of the fungal species and determines specific Targets by comparing them with the genomes of other species. Then, experimental practice using sequencing or non-sequencing technologies would confirm the results of bioinformatics analysis. Accordingly, AGE obtained more than 1,000,000 qualified Targets for each of the 13 fungal species within the phyla Ascomycota and Basidiomycota. Next, the sequencing and genome editing system validated the ultra-specific performance of the specific Targets; especially noteworthy is the first-time demonstration of the identification potential of sequences from unannotated genomic regions. Furthermore, by combining rapid isothermal amplification and phosphorothioate-modified primers with the option of an instrument-free visual fluorescence method, AGE can achieve qualitative species identification within 30 min using a single-tube test. More importantly, AGE holds significant potential for identifying closely related species and differentiating traditional Chinese medicines from their adulterants, especially in the precise detection of contaminants. In summary, AGE opens the door for the development of whole-genome-based fungal species identification while also providing guidance for its application in plant and animal kingdoms.
Collapse
Affiliation(s)
- Guihong Qi
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lijun Hao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tianyi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yutong Gan
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qian Lou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Wenjie Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, China
| |
Collapse
|
18
|
Riesco R, Trujillo ME. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2024; 74. [PMID: 38512750 DOI: 10.1099/ijsem.0.006300] [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: 03/23/2024] Open
Abstract
The field of microbial taxonomy is dynamic, aiming to provide a stable and contemporary classification system for prokaryotes. Traditionally, reliance on phenotypic characteristics limited the comprehensive understanding of microbial diversity and evolution. The introduction of molecular techniques, particularly DNA sequencing and genomics, has transformed our perception of prokaryotic diversity. In the past two decades, advancements in genome sequencing have transitioned from traditional methods to a genome-based taxonomic framework, not only to define species, but also higher taxonomic ranks. As technology and databases rapidly expand, maintaining updated standards is crucial. This work seeks to revise the 2018 guidelines for applying genome sequencing data in microbial taxonomy, adapting minimal standards and recommendations to reflect technological progress during this period.
Collapse
Affiliation(s)
- Raúl Riesco
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
| |
Collapse
|
19
|
Li K, Luo X, Fan R, Ding Z, Zheng S, Chen Z. Chitiniphilus purpureus sp. nov., a novel chitin-degrading bacterium isolated from crawfish pond sediment. Int J Syst Evol Microbiol 2024; 74. [PMID: 38381513 DOI: 10.1099/ijsem.0.006245] [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: 02/22/2024] Open
Abstract
A novel Gram-stain-negative, curved rod-shaped, motile and chitin-degrading strain, designated CD1T, was isolated from crawfish pond sediment in Caidian District (30° 58' N 114° 03' E), Wuhan City, Hubei Province, PR China. Growth of this strain was observed at 15-40°C (optimum between 28 and 30 °C), at pH 7.0-9.0 (optimum between pH 7.0 and 8.0) and with 0-1 % (w/v) NaCl (optimum at 0 %). With respect to the 16S rRNA gene sequences, strain CD1T had the highest similarity (96.91-97.25 %) to four type strains of the genera 'Chitinolyticbacter' and Chitiniphilus within the family Chitinibacteraceae. The phylogenetic trees based on genome sequences and 16S rRNA gene sequences indicated that strain CD1T was close to members of these two genera, in particular to the genus Chitiniphilus. The genomic DNA G+C content of strain CD1T was 64.8 mol%. The average nucleotide identity and the Genome-to-Genome Distance Calculator results showed low relatedness (below 95 and 70 %, respectively) between strain CD1T and the closely related type strains. Ubiquinone-8 was the predominant quinone. The major cellular fatty acids were C10 : 0, C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The polar lipid profile was composed of a mixture of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unidentified lipids, two unidentified phospholipids, two unidentified aminolipids and an unidentified aminoglycolipid. On the basis of the evidences presented in this study, strain CD1T represents a novel species of the genus Chitiniphilus, for which the name Chitiniphilus purpureus sp. nov. is proposed, with strain CD1T (=CCTCC AB 2022395T=KCTC 92850T) as the type strain.
Collapse
Affiliation(s)
- Kaiyang Li
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xiong Luo
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Rongrong Fan
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Zhuoran Ding
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Shixue Zheng
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Zhengjun Chen
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| |
Collapse
|
20
|
Kim SB, Kim KH, Park JS. Parendozoicomonas callyspongiae sp. nov. Isolated from a Marine Sponge, Callyspongia elongate, and Reclassification of Sansalvadorimonas verongulae as Parendozoicomonas verongulae comb. nov. Curr Microbiol 2024; 81:85. [PMID: 38300357 DOI: 10.1007/s00284-023-03585-6] [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: 05/21/2023] [Accepted: 12/08/2023] [Indexed: 02/02/2024]
Abstract
A strictly aerobic Gram-negative bacterium, designated 2012CJ34-2T, was isolated from marine sponge to Chuja-do in Jeju-island, Republic of Korea and taxonomically characterized. Cells were catalase- and oxidase-positive, and non-motile rods (without flagella). Growth was observed at 15-42 °C (optimum, 30 °C), pH 6-9 (optimum, pH 7), and in the presence of 0.5-10% (w/v) NaCl (optimum, 2-3%). The major cellular fatty acid and respiratory quinones were identified summed feature 3 (C16:1 ω7c/C16:1 ω6c), and Q-8 and Q-9, respectively. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid, two unidentified phospholipids, and three unidentified lipids. The DNA G+C content was 48.0 mol%. Phylogenetic analyses based on 16S rRNA gene and whole genome sequences showed that strain 2012CJ34-2T formed a clade with Parendozoicomonas haliclonae S-B4-1UT and Sansalvadorimonas verongulae LMG 29871T within the family Endozoicomodaceae. Genome relatedness values, including dDDH, ANI and AF, and AAI and POCP, among strain 2012CJ34-2T, P. haliclonae S-B4-1UT, and S. verongulae LMG 29871T were within the range of the bacterial genus cut-off values. Based on the phylogenetic, chemotaxonomic, and genomic analyses, strain 2012CJ34-2T represents a novel bacterial species of the family Endozoicomodaceae, for which the name Parendozoicomonas callyspongiae sp. nov. is proposed. The type strain is 2012CJ34-2T (= KACC 22641T = LMG 32581T). Additionally, we proposed the reclassification of Sansalvadorimonas verongulae of the family Hahellaceae as Parendozoicomonas verongulae of the family Endozoicomonadaceae.
Collapse
Affiliation(s)
- Soo-Bin Kim
- Department of Biological Sciences and Biotechnology, Hannam University Jeonmin-dong, Yuseong-gu, Daejeon, 34430, Republic of Korea
| | - Kyung Hyun Kim
- Department of Biological Sciences and Biotechnology, Hannam University Jeonmin-dong, Yuseong-gu, Daejeon, 34430, Republic of Korea
| | - Jin-Sook Park
- Department of Biological Sciences and Biotechnology, Hannam University Jeonmin-dong, Yuseong-gu, Daejeon, 34430, Republic of Korea.
| |
Collapse
|
21
|
Suman J, Sredlova K, Fraraccio S, Jerabkova M, Strejcek M, Kabickova H, Cajthaml T, Uhlik O. Transformation of hydroxylated polychlorinated biphenyls by bacterial 2-hydroxybiphenyl 3-monooxygenase. CHEMOSPHERE 2024; 349:140909. [PMID: 38070605 DOI: 10.1016/j.chemosphere.2023.140909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/18/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
Monohydroxylated PCBs (OH-PCBs) are an (eco)toxicologically significant group of compounds, as they arise from the oxidation of polychlorinated biphenyls (PCBs) and, at the same time, may exert even more severe toxic effects than their parent PCB molecules. Despite having been widely detected in environmental samples, plants, and animals, information on the fate of OH-PCBs in the environment is scarce, including on the enzymatic machinery behind their degradation. To date, only a few bacterial taxa capable of OH-PCB transformation have been reported. In this study, we aimed to obtain a deeper insight into the transformation of OH-PCBs in soil bacteria and isolated a Pseudomonas sp. strain P1B16 based on its ability to use o-phenylphenol (2-PP) which, when exposed to the Delor 103-derived OH-PCB mixture, depleted a wide spectrum of mono-, di, and trichlorinated OH-PCBs. In the P1B16 genome, a region designated as hbp was identified, which bears a set of putative genes involved in the transformation of OH-PCBs, namely hbpA encoding for a putative flavin-dependent 2-hydroxybiphenyl monooxygenase, hbpC (2,3-dihydroxybiphenyl-1,2-dioxygenase), hbpD (2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase), and the transcriptional activator-encoding gene hbpR. The hbpA coding sequence was heterologously expressed, purified, and its substrate specificity was investigated towards the Delor 103-derived OH-PCB mixture, individual OH-PCBs, and multiple (chlorinated) phenolics. Apart from 2-PP and 2-chlorophenol, HbpA was also demonstrated to transform a range of OH-PCBs, including a 3-hydroxy-2,2',4',5,5'-pentachlorobiphenyl. Importantly, this is the first direct evidence of HbpA homologs being involved in the degradation of OH-PCBs. Moreover, using a P1B16-based biosensor strain, the specific induction of hbp genes by 2-PP, 3-phenylphenol, 4-phenylphenol, and the OH-PCB mixture was demonstrated. This study provides direct evidence on the specific enzymatic machinery responsible for the transformation of OH-PCBs in bacteria, with many implications in ecotoxicology, environmental restoration, and microbial ecology in habitats burdened with PCB contamination.
Collapse
Affiliation(s)
- Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic.
| | - Kamila Sredlova
- Institute for Environmental Studies, Faculty of Science, Charles University, Benatska 2, 128 01, Prague 2, Czech Republic; Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
| | - Serena Fraraccio
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic
| | - Martina Jerabkova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic
| | - Hana Kabickova
- Military Health Institute, Ministry of Defence of the Czech Republic, U Vojenske Nemocnice 1200, 169 02, Prague, Czech Republic
| | - Tomas Cajthaml
- Institute for Environmental Studies, Faculty of Science, Charles University, Benatska 2, 128 01, Prague 2, Czech Republic; Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic.
| |
Collapse
|
22
|
An P, Yang C, Li W, Zhao D, Xiang H. The Isolation and Characterization of a Novel Psychrotolerant Cellulolytic Bacterium, Microbacterium sp. QXD-8 T. Microorganisms 2024; 12:303. [PMID: 38399707 PMCID: PMC10892437 DOI: 10.3390/microorganisms12020303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/29/2023] [Accepted: 01/08/2024] [Indexed: 02/25/2024] Open
Abstract
Cellulolytic microorganisms play a crucial role in agricultural waste disposal. Strain QXD-8T was isolated from soil in northern China. Similarity analyses of the 16S rRNA gene, as well as the 120 conserved genes in the whole-genome sequence, indicate that it represents a novel species within the genus Microbacterium. The Microbacterium sp. QXD-8T was able to grow on the CAM plate with sodium carboxymethyl cellulose as a carbon source at 15 °C, forming a transparent hydrolysis circle after Congo red staining, even though the optimal temperature for the growth and cellulose degradation of strain QXD-8T was 28 °C. In the liquid medium, it effectively degraded cellulose and produced reducing sugars. Functional annotation revealed the presence of encoding genes for the GH5, GH6, and GH10 enzyme families with endoglucanase activity, as well as the GH1, GH3, GH39, and GH116 enzyme families with β-glucosidase activity. Additionally, two proteins in the GH6 family, one in the GH10, and two of nine proteins in the GH3 were predicted to contain a signal peptide and transmembrane region, suggesting their potential for extracellularly degrade cellulose. Based on the physiological features of the type strain QXD-8T, we propose the name Microbacterium psychrotolerans for this novel species. This study expands the diversity of psychrotolerant cellulolytic bacteria and provides a potential microbial resource for straw returning in high-latitude areas at low temperatures.
Collapse
Affiliation(s)
- Peng An
- College of Life Science, Sichuan Normal University, Chengdu 610101, China; (P.A.); (W.L.)
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Changjialian Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- College of Life Science, Sichuan Normal University, Chengdu 610101, China; (P.A.); (W.L.)
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
23
|
Miyazaki U, Mizutani D, Hashimoto Y, Tame A, Sawayama S, Miyazaki J, Takai K, Nakagawa S. Helicovermis profundi gen. nov., sp. nov., a novel mesophilic, asporogenous bacterium within the Clostridia isolated from a deep-sea hydrothermal vent chimney. Antonie Van Leeuwenhoek 2024; 117:24. [PMID: 38217723 DOI: 10.1007/s10482-023-01919-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/12/2023] [Indexed: 01/15/2024]
Abstract
A novel mesophilic bacterial strain, designated S502T, was isolated from a deep-sea hydrothermal vent at Suiyo Seamount, Japan. Cells were Gram-positive, asporogenous, motile, and curved rods, measuring 1.6-5.6 µm in length. The strain was an obligate anaerobe that grew fermentatively on complex substrates such as yeast extract and Bacto peptone. Elemental sulfur stimulated the growth of the strain, and was reduced to hydrogen sulfide. The strain grew within a temperature range of 10-23 °C (optimum at 20 °C), pH range of 4.8-8.3 (optimum at 7.4), and a NaCl concentration range of 1.0-4.0% (w/v) (optimum at 3.0%, w/v). Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the class Clostridia, with Fusibacter paucivorans strain SEBR 4211T (91.1% sequence identity) being its closest relative. The total size of the genome of the strain was 3.12 Mbp, and a G + C content was 28.2 mol%. The highest values for average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) value of strain S502T with relatives were 67.5% (with Marinisporobacter balticus strain 59.4MT), 51.5% (with M. balticus strain 59.4MT), and 40.9% (with Alkaliphilus serpentinus strain LacTT), respectively. Based on a combination of phylogenetic, genomic, and phenotypic characteristics, we propose strain S502T to represent a novel genus and species, Helicovermis profundi gen. nov., sp. nov., with the type strain S502T (= DSM 112048T = JCM 39167T).
Collapse
Affiliation(s)
- Urara Miyazaki
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Daiki Mizutani
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Yurina Hashimoto
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Akihiro Tame
- Depertment of Marine and Earth Sciences, Marine Works Japan Ltd, 3-54-1 Oppamahigashi, Yokosuka, 237-0063, Japan
- General Affairs Department, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Junichi Miyazaki
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan
| | - Ken Takai
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-Cho, Okazaki, 444-8787, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan.
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan.
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-Cho, Okazaki, 444-8787, Japan.
| |
Collapse
|
24
|
Schwarzerova J, Zeman M, Babak V, Jureckova K, Nykrynova M, Varga M, Weckwerth W, Dolejska M, Provaznik V, Rychlik I, Cejkova D. Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis. Microbiol Spectr 2024; 12:e0196423. [PMID: 38099617 PMCID: PMC10782964 DOI: 10.1128/spectrum.01964-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 10/31/2023] [Indexed: 01/13/2024] Open
Abstract
Horizontal gene transfer (HGT) is a key driver in the evolution of bacterial genomes. The acquisition of genes mediated by HGT may enable bacteria to adapt to ever-changing environmental conditions. Long-term application of antibiotics in intensive agriculture is associated with the dissemination of antibiotic resistance genes among bacteria with the consequences causing public health concern. Commensal farm-animal-associated gut microbiota are considered the reservoir of the resistance genes. Therefore, in this study, we identified known and not-yet characterized mobilized genes originating from chicken and porcine fecal samples using our innovative pipeline followed by network analysis to provide appropriate visualization to support proper interpretation.
Collapse
Affiliation(s)
- Jana Schwarzerova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Michal Zeman
- Veterinary Research Institute, Brno, Czech Republic
| | | | - Katerina Jureckova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Marketa Nykrynova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Margaret Varga
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Monika Dolejska
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Brno, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Valentine Provaznik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
- Department of Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Ivan Rychlik
- Veterinary Research Institute, Brno, Czech Republic
| | - Darina Cejkova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| |
Collapse
|
25
|
Suh MK, Kim JS, Eom MK, Kim HS, Do HE, Shin YK, Lee JS. Jatrophihabitans cynanchi sp. nov., isolated from rhizosphere soil of Cynanchum wilfordii. Antonie Van Leeuwenhoek 2024; 117:19. [PMID: 38189847 DOI: 10.1007/s10482-023-01902-4] [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: 03/16/2023] [Accepted: 11/17/2023] [Indexed: 01/09/2024]
Abstract
A novel actinobacterial strain, SB3-54T was isolated from rhizosphere soil of Cynanchum wilfodill, Jaecheon, Chungcheongbuk-do, Republic of Korea. Cells of strain SB3-54T were Gram-stain-positive, aerobic, rod-shaped, and flagellated which formed pale yellow colonies on Reasoner's 2A (R2A) agar. Growth occurred at 15-30 °C (optimum 25 °C), pH 5-8 (optimum pH 7), and 0-2.5% NaCl (optimum 0%). Phylogenetic and phylogenomic analyses showed that strain SB3-54T formed a separate lineage in the genus Jatrophihabitans with Jatrophihabitans telluris N237T. Strain SB3-54T was positive for catalase activity. Genomic analysis showed that SB3-54T has plant-beneficial function contributing (referred to as PBFC) genes such as root colonization and plant protection from oxidative stress. Furthermore, genome of SB3-54T contained gene clusters related to cytokinin biosynthesis, auxin response, tryptophan biosynthesis, siderophore biosynthesis and bacterial toxin-antitoxin systems. Strain SB3-54T contained iso-C16:0 as the major fatty acid and MK-9(H4) and MK-9(H6) as the predominant quinones. The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan. The major polar lipids were diphosphatidylglycerol, phosphatidylinositol polymannosides, two unidentified aminoglycophospholipids and three unidentified phospholipids. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain SB3-54T represents a novel species of the genus Jatrophihabitans. The type strain is SB3-54T (= KCTC 49134T = NBRC 114108T).
Collapse
Affiliation(s)
- Min Kuk Suh
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, South Korea
- Department of Lifestyle Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do, 54596, Republic of Korea
| | - Ji-Sun Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, South Korea
| | - Mi Kyung Eom
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, South Korea
| | - Han Sol Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, South Korea
- Department of Lifestyle Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do, 54596, Republic of Korea
| | - Hyo Eun Do
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, South Korea
- Department of Oriental Medicine Resources, Jeonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do, 54596, Republic of Korea
| | - Yong Kook Shin
- Semyung University, 65 Semyung-ro, Jecheon-si, Chungcheongbuk-do, 27136, Republic of Korea
| | - Jung- Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, South Korea.
- University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
| |
Collapse
|
26
|
Liu X, Liu X, Deng Z, He X, Jiang Y. Xanthomonas chitinilytica sp. nov., a novel chitinolytic bacterium isolated from a microbial fermentation bed material. Antonie Van Leeuwenhoek 2024; 117:17. [PMID: 38189878 DOI: 10.1007/s10482-023-01904-2] [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: 09/03/2023] [Accepted: 10/27/2023] [Indexed: 01/09/2024]
Abstract
A Gram-stain-negative bacterium, H13-6T, was isolated from a microbial fermentation bed material collected from a pig farm located in Yan'an, Shaanxi, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain H13-6T was affiliated with the genus Xanthomonas and showed highest similarity to strain Xanthomonas maliensis M97T (98.38%), Xanthomonas prunicola CFBP 8353T (98.26%) and Xanthomonas oryzae ATCC 35933T (98.11%). The pairwise ortho Average Nucleotide Identity values and the digital DNA-DNA hybridization values between strain H13-6T and the other Xanthomonas species were all below their respective cut-offs. Two genes encoding for chitinase were found and the strain showed a strong chitin-degrading activity. The major fatty acids were Iso-C15:0 (55.9%), Antesio-C15:0 (7.4%) and Iso-C11:0 (5.5%) and the major polar lipids were diphosphatidylglycerol, phosphatidyglycerol and phosphatidylethanolamine. Based on the phenotypic properties and phylogenetic distinctiveness, Xanthomonas chitinilytica was proposed as a novel species of the genus Xanthomonas, with strain H13-6T (= CGMCC 1.61317T = NBRC 115641T) as type strain.
Collapse
Affiliation(s)
- Xiaodong Liu
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
- Shaanxi Key Laboratory of Chinese Jujube, Yan'an University, Yan'an, 716000, Shaanxi, China
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, China
| | - Xin Liu
- Research and Development Department, Shandong Xianglong Pharmaceutical Research Institute Co., Ltd, Yantai, 264003, China
| | - Zhenshan Deng
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
- Shaanxi Key Laboratory of Chinese Jujube, Yan'an University, Yan'an, 716000, Shaanxi, China
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, China
| | - Xiaolong He
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
- Shaanxi Key Laboratory of Chinese Jujube, Yan'an University, Yan'an, 716000, Shaanxi, China
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, China
| | - Yingying Jiang
- College of Life Sciences, Yan'an University, Yan'an, 716000, China.
- Shaanxi Key Laboratory of Chinese Jujube, Yan'an University, Yan'an, 716000, Shaanxi, China.
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, China.
| |
Collapse
|
27
|
Choi DG, Baek JH, Han DM, Khan SA, Jeon CO. Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions. BMC Genomics 2024; 25:28. [PMID: 38172677 PMCID: PMC10765913 DOI: 10.1186/s12864-023-09945-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Enterococcus faecium and E. lactis are phylogenetically closely related lactic acid bacteria that are ubiquitous in nature and are known to be beneficial or pathogenic. Despite their considerable industrial and clinical importance, comprehensive studies on their evolutionary relationships and genomic, metabolic, and pathogenic traits are still lacking. Therefore, we conducted comparative pangenome analyses using all available dereplicated genomes of these species. RESULTS E. faecium was divided into two subclades: subclade I, comprising strains derived from humans, animals, and food, and the more recent phylogenetic subclade II, consisting exclusively of human-derived strains. In contrast, E. lactis strains, isolated from diverse sources including foods, humans, animals, and the environment, did not display distinct clustering based on their isolation sources. Despite having similar metabolic features, noticeable genomic differences were observed between E. faecium subclades I and II, as well as E. lactis. Notably, E. faecium subclade II strains exhibited significantly larger genome sizes and higher gene counts compared to both E. faecium subclade I and E. lactis strains. Furthermore, they carried a higher abundance of antibiotic resistance, virulence, bacteriocin, and mobile element genes. Phylogenetic analysis of antibiotic resistance and virulence genes suggests that E. faecium subclade II strains likely acquired these genes through horizontal gene transfer, facilitating their effective adaptation in response to antibiotic use in humans. CONCLUSIONS Our study offers valuable insights into the adaptive evolution of E. faecium strains, enabling their survival as pathogens in the human environment through horizontal gene acquisitions.
Collapse
Affiliation(s)
- Dae Gyu Choi
- Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, 06974, Seoul, Republic of Korea
| | - Ju Hye Baek
- Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, 06974, Seoul, Republic of Korea
| | - Dong Min Han
- Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, 06974, Seoul, Republic of Korea
| | - Shehzad Abid Khan
- Atta‑ur‑Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000, Islamabad, Pakistan
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, 06974, Seoul, Republic of Korea.
| |
Collapse
|
28
|
Zhernakova DV, Wang D, Liu L, Andreu-Sánchez S, Zhang Y, Ruiz-Moreno AJ, Peng H, Plomp N, Del Castillo-Izquierdo Á, Gacesa R, Lopera-Maya EA, Temba GS, Kullaya VI, van Leeuwen SS, Xavier RJ, de Mast Q, Joosten LAB, Riksen NP, Rutten JHW, Netea MG, Sanna S, Wijmenga C, Weersma RK, Zhernakova A, Harmsen HJM, Fu J. Host genetic regulation of human gut microbial structural variation. Nature 2024; 625:813-821. [PMID: 38172637 PMCID: PMC10808065 DOI: 10.1038/s41586-023-06893-w] [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: 12/22/2022] [Accepted: 11/23/2023] [Indexed: 01/05/2024]
Abstract
Although the impact of host genetics on gut microbial diversity and the abundance of specific taxa is well established1-6, little is known about how host genetics regulates the genetic diversity of gut microorganisms. Here we conducted a meta-analysis of associations between human genetic variation and gut microbial structural variation in 9,015 individuals from four Dutch cohorts. Strikingly, the presence rate of a structural variation segment in Faecalibacterium prausnitzii that harbours an N-acetylgalactosamine (GalNAc) utilization gene cluster is higher in individuals who secrete the type A oligosaccharide antigen terminating in GalNAc, a feature that is jointly determined by human ABO and FUT2 genotypes, and we could replicate this association in a Tanzanian cohort. In vitro experiments demonstrated that GalNAc can be used as the sole carbohydrate source for F. prausnitzii strains that carry the GalNAc-metabolizing pathway. Further in silico and in vitro studies demonstrated that other ABO-associated species can also utilize GalNAc, particularly Collinsella aerofaciens. The GalNAc utilization genes are also associated with the host's cardiometabolic health, particularly in individuals with mucosal A-antigen. Together, the findings of our study demonstrate that genetic associations across the human genome and bacterial metagenome can provide functional insights into the reciprocal host-microbiome relationship.
Collapse
Affiliation(s)
- Daria V Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Daoming Wang
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
| | - Lei Liu
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | - Sergio Andreu-Sánchez
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
| | - Yue Zhang
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
| | - Angel J Ruiz-Moreno
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
| | - Haoran Peng
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Niels Plomp
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
| | - Ángela Del Castillo-Izquierdo
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | - Ranko Gacesa
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
| | - Esteban A Lopera-Maya
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Godfrey S Temba
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Vesla I Kullaya
- Department of Medical Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Center, Moshi, Tanzania
| | - Sander S van Leeuwen
- University of Groningen, University Medical Center Groningen, Department of Laboratory Medicine, Groningen, The Netherlands
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Quirijn de Mast
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Genetics, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Niels P Riksen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joost H W Rutten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
- Human Genomics Laboratory, Craiova University of Medicine and Pharmacy, Craiova, Romania
| | - Serena Sanna
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- Institute for Genetic and Biomedical Research, National Research Council, Cagliari, Italy
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Rinse K Weersma
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Hermie J M Harmsen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands.
| | - Jingyuan Fu
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands.
| |
Collapse
|
29
|
Sato K, Ikagawa Y, Niwa R, Nishioka H, Horie M, Iwahashi H. Genome Sequencing Unveils Nomadic Traits of Lactiplantibacillus plantarum in Japanese Post-Fermented Tea. Curr Microbiol 2023; 81:52. [PMID: 38155273 DOI: 10.1007/s00284-023-03566-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023]
Abstract
Post-fermented tea production involving microbial fermentation is limited to a few regions, such as Southeast Asia and Japan, with Japan's Shikoku island being particularly prominent. Lactiplantibacillus plantarum was the dominant species found in tea leaves after anaerobic fermentation of Awa-bancha in Miyoshi City, Tokushima, and Ishizuchi-kurocha in Ehime. Although the draft genome of L. plantarum from Japanese post-fermented tea has been previously reported, its genetic diversity requires further exploration. In this study, whole-genome sequencing was conducted on four L. plantarum strains isolated from Japanese post-fermented tea using nanopore sequencing. These isolates were then compared with other sources to examine their genetic diversity revealing that L. plantarum isolated from Japanese post-fermented tea contained several highly variable gene regions associated with sugar metabolism and transportation. However, no source-specific genes or clusters were identified within accessory or core gene regions. This study indicates that L. plantarum possesses high genetic diversity and that the unique environment of Japanese post-fermented tea does not appear to exert selective pressure on L. plantarum growth.
Collapse
Affiliation(s)
- Kyoka Sato
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, Gifu, 501-1193, Japan.
| | - Yuichiro Ikagawa
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, Gifu, 501-1193, Japan
| | - Ryo Niwa
- Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Hiroki Nishioka
- Food and Biotechnology Division, Tokushima Prefectural Industrial Technology Center, Tokushima, 770-8021, Japan
| | - Masanori Horie
- Health and Medical Research Institute (HMRI), National Institute of Advanced Industrial Science and Technology (AIST), Kagawa, 761-0395, Japan
| | - Hitoshi Iwahashi
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, Gifu, 501-1193, Japan.
| |
Collapse
|
30
|
Wen Y, Zhang B, Zhang G, Wu M, Chen X, Chen T, Liu G, Zhang W. Comparative genomics reveals environmental adaptability and antimicrobial activity of a novel Streptomyces isolated from soil under black Gobi rocks. Antonie Van Leeuwenhoek 2023; 116:1407-1419. [PMID: 37847451 DOI: 10.1007/s10482-023-01882-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
A novel Streptomyces strain, designated 3_2T, was isolated from soil under the black Gobi rock sample of Northwest China. The taxonomic position of this strain was revealed by a polyphasic approach. Comparative analysis of the 16S rRNA gene sequences indicated that 3_2T was closely related to the members of the genus Streptomyces, with the highest similarity to Streptomyces rimosus subsp. rimosus CGMCC 4.1438 (99.17%), Streptomyces sioyaensis DSM 40032 (98.97%). Strain 3_2T can grow in media up to 13% NaCl. The genomic DNA G + C content of strain 3_2T was 69.9%. We obtained the genomes of 22 Streptomyces strains similar to strain 3_2T, compared the average nucleotide similarity, dDDH and average amino acid identity, and found that the genomic similarity of the new isolate 3_2T to all strains was below the threshold for interspecies classification. Chemotaxonomic data revealed that strain 3_2T possessed MK-9 (H6) and MK-9 (H8) as the major menaquinones. The cell wall contained LL-diaminopimelic acid (LL-DAP) and the whole-cell sugars were ribose and glucose. The major fatty acid methyl esters were iso-C16:0 (23.6%) and anteiso-C15:0 (10.4%). The fermentation products of strain 3_2T were inhibitory to Staphylococcus aureus and Bacillus thuringiensi. The genome of 3_2T was further predicted using anti-smash and the strain was found to encode the production of 41 secondary metabolites, and these gene clusters may be key to the good inhibitory activity exhibited by the strain. Genomic analysis revealed that strain 3_2T can encode genes that produce a variety of genes in response to environmental stresses, including cold shock, detoxification, heat shock, osmotic stress, oxidative stress, and these genes may play a key role in the harsh environment in which the strain can survive. Therefore, this strain represents a novel Streptomyces species, for which the name Streptomyces halobius sp. nov. is proposed. The type strain is 3_2T (= JCM 34935T = GDMCC 4.217T).
Collapse
Affiliation(s)
- Ying Wen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Binglin Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
| | - Minghui Wu
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Ximing Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
| | - Wei Zhang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
| |
Collapse
|
31
|
Nithimongkolchai N, Hinwan Y, Kaewseekhao B, Chareonsudjai P, Reungsang P, Kraiklang R, Chareonsudjai S, Wonglakorn L, Chetchotisakd P, Sirichoat A, Nithichanon A, Faksri K. MALDI-TOF MS analysis of Burkholderia pseudomallei and closely related species isolated from soils and water in Khon Kaen, Thailand. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105532. [PMID: 37995885 DOI: 10.1016/j.meegid.2023.105532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/10/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023]
Abstract
Melioidosis is caused by Burkholderia pseudomallei (Bp) acquired from the environment. Conventional identification methods for environmental Bp are challenging due to the presence of closely related species. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is accurate for bacterial identification, but has been little used to identify Bp from environmental samples. This study aims to evaluate MALDI-TOF MS for the identification of Bp and closely related species isolated from environmental samples in Thailand using whole-genome sequencing (WGS) as the gold standard, including determining the best sample preparation method for this purpose. We identified Bp (n = 22), Burkholderia spp. (n = 28), and other bacterial species (n = 32) using WGS. MALDI-TOF analysis of all Bp isolates yielded results consistent with WGS. A decision-tree algorithm identified 16 important variable peaks, using the protein extraction method (PEM), demonstrating distinct MALDI-TOF profiles for the three categories (Bp, Burkholderia spp. and "other bacterial species"). Three biomarker peaks (4060, 5196, and 6553 Da) could discriminate Bp from other Burkholderia and closely related species with 100% sensitivity and specificity. Hence, the MALDI-TOF technique has shown its potential as a species discriminatory tool, providing results comparable to WGS for classification and surveillance of environmental Bp.
Collapse
Affiliation(s)
- Nut Nithimongkolchai
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Yothin Hinwan
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Benjawan Kaewseekhao
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Pisit Chareonsudjai
- Department of Environmental Science, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Pipat Reungsang
- College of Computing, Khon Kaen University, Khon Kaen, Thailand
| | - Ratthaphol Kraiklang
- Nutrition for Health Program, Faculty of Public Health, Khon Kaen University, Khon Kaen, Thailand
| | - Sorujsiri Chareonsudjai
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Lumyai Wonglakorn
- Clinical Laboratory Section, Srinagarind Hospital, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | | | - Auttawit Sirichoat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Arnone Nithichanon
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand.
| |
Collapse
|
32
|
Lee JK, Baek JH, Han DM, Lee SH, Kim SY, Jeon CO. Description and Genomic Characteristics of Weissella fermenti sp. nov., Isolated from Kimchi. J Microbiol Biotechnol 2023; 33:1448-1456. [PMID: 37482799 DOI: 10.4014/jmb.2306.06010] [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: 06/07/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/25/2023]
Abstract
A Gram-positive, non-motile, and non-spore-forming lactic acid bacterium, designated as BK2T, was isolated from kimchi, a Korean traditional fermented vegetable food, and the taxonomic characteristics of strain BK2T, along with strain LMG 11983, were analyzed. Both strains optimally grew at 30°C, pH 7.0, and 1.0% NaCl. Cells of both strains were heterofermentative and facultatively anaerobic rods, demonstrating negative reactions for catalase and oxidase. Major fatty acids (>10%) identified in both strains were C18:1 ω9c, C16:0, and summed feature 7 (comprising C19:1 ω6c and/or C19:1 ω7c). The genomic DNA G+C contents of both strains were 44.7 mol%. The 16S rRNA gene sequence similarity (99.9%), average nucleotide identity (ANI; 99.9%), and digital DNA-DNA hybridization (dDDH; 99.7%) value between strains BK2T and LMG 11983 indicated that they are different strains of the same species. Strain BK2T was most closely related to Weissella confusa JCM 1093T and Weissella cibaria LMG 17699T, with 100% and 99.4% 16S rRNA gene sequence similarities, respectively. However, based on the ANI and dDDH values (92.3% and 48.1% with W. confusa, and 78.4% and 23.5% with W. cibaria), it was evident that strain BK2T represents a distinct species separate from W. confusa and W. cibaria. Based on phylogenetic, phenotypic, and chemotaxonomic features, strains BK2T and LMG 11983 represent a novel species of the genus Weissella, for which the name Weissella fermenti sp. nov. is proposed. The type of strain is BK2T (=KACC 22833T=JCM 35750T).
Collapse
Affiliation(s)
- Jae Kyeong Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ju Hye Baek
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dong Min Han
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Se Hee Lee
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - So Young Kim
- Department of Agro-Food Resources, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| |
Collapse
|
33
|
Tian R, Imanian B. VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution. MICROBIOME 2023; 11:247. [PMID: 37936197 PMCID: PMC10631056 DOI: 10.1186/s40168-023-01705-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/18/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND Phylogenomic analysis has become an inseparable part of studies of bacterial diversity and evolution, and many different bacterial core genes have been collated and used for phylogenomic tree reconstruction. However, these genes have been selected based on their presence and single-copy ratio in all bacterial genomes, leaving out the gene's 'phylogenetic fidelity' unexamined. RESULTS From 30,522 complete genomes covering 11,262 species, we examined 148 bacterial core genes that have been previously used for phylogenomic analysis. In addition to the gene presence and single-copy rations, we evaluated the gene's phylogenetic fidelity by comparing each gene's phylogeny with its corresponding 16S rRNA gene tree. Out of the 148 bacterial genes, 20 validated bacterial core genes (VBCG) were selected as the core gene set with the highest bacterial phylogenetic fidelity. Compared to the larger gene set, the 20-gene core set resulted in more species having all genes present and fewer species with missing data, thereby enhancing the accuracy of phylogenomic analysis. Using Escherichia coli strains as examples of prominent bacterial foodborne pathogens, we demonstrated that the 20 VBCG produced phylogenies with higher fidelity and resolution at species and strain levels while 16S rRNA gene tree alone could not. CONCLUSION The 20 validated core gene set improves the fidelity and speed of phylogenomic analysis. Among other uses, this tool improves our ability to explore the evolution, typing and tracking of bacterial strains, such as human pathogens. We have developed a Python pipeline and a desktop graphic app (available on GitHub) for users to perform phylogenomic analysis with high fidelity and resolution. Video Abstract.
Collapse
Affiliation(s)
- Renmao Tian
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, 60501, USA
| | - Behzad Imanian
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, 60501, USA.
- Food Science and Nutrition Department, Illinois Institute of Technology, Chicago, IL, 60616, USA.
| |
Collapse
|
34
|
Tambong JT, Xu R, Fleitas MC, Wang L, Hubbard K, Kutcher R. Phylogenomic Insights on the Xanthomonas translucens Complex, and Development of a TaqMan Real-Time Assay for Specific Detection of pv. translucens on Barley. PHYTOPATHOLOGY 2023; 113:2091-2102. [PMID: 37097305 DOI: 10.1094/phyto-01-23-0022-sa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The reemergence and spread of Xanthomonas translucens, the causal agent of bacterial leaf streak in cereal crops and wilt in turfgrass and forage species, is a concern to growers in the United States and Canada. The pathogen is seedborne and listed as an A2 quarantine organism by EPPO, making it a major constraint to international trade and exchange of germplasm. The pathovar concept of the X. translucens group is confusing due to overlapping of plant host ranges and specificity. Here, comparative genomics, phylogenomics, and 81 up-to-date bacterial core gene set (ubcg2) were used to assign the pathovars of X. translucens into three genetically and taxonomically distinct clusters. The study also showed that whole genome-based digital DNA-DNA hybridization unambiguously can differentiate the pvs. translucens and undulosa. Orthologous gene and proteome matrix analyses suggest that the cluster consisting of graminis, poae, arrhenatheri, phlei, and phleipratensis is very divergent. Whole-genome data were exploited to develop the first pathovar-specific TaqMan real-time PCR tool for detection of pv. translucens on barley. Specificity of the TaqMan assay was validated using 62 Xanthomonas and non-Xanthomonas strains as well as growth chamber-inoculated and naturally infected barley leaves. Sensitivity levels of 0.1 pg (purified DNA) and 23 CFUs per reaction (direct culture) compared favorably with other previously reported real-time PCR assays. The phylogenomics data reported here suggest that the clusters could constitute novel taxonomic units or new species. Finally, the pathovar-specific diagnostic tool will have significant benefits to growers and facilitate international exchange of barley germplasm and trade.
Collapse
Affiliation(s)
- James T Tambong
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
| | - Renlin Xu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Maria Constanza Fleitas
- Department of Plant Sciences & Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Lipu Wang
- Department of Plant Sciences & Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Keith Hubbard
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Randy Kutcher
- Department of Plant Sciences & Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| |
Collapse
|
35
|
Yun JU, Jung HS, Jung MJ, Song HS, Kim YB, Kim Y, Kim JG, Roh SW, Lee SH, Lee JS, Whon TW. Cutibacterium equinum sp. nov., isolated from horse faeces. Int J Syst Evol Microbiol 2023; 73. [PMID: 37910171 DOI: 10.1099/ijsem.0.006099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Strain CBA3108T is a Gram-positive, non-spore-forming, obligately anaerobic bacterium isolated from horse faecal samples obtained in Jeju Island, Republic of Korea. The cells of CBA3108T are non-motile short rods that have been assessed as catalase-positive and oxidase-negative. Growth of the strain occurs under the following conditions: 25-45 °C (optimum, 35 °C); pH 6-9 (optimum, pH 6); and in the presence of 0-6 % (w/v) NaCl (optimum, 2%). Major fatty acids in the strain include C15 : 0 iso and C15 : 0 iso DMA, while major polar lipids include phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. Based on phylogenetic analysis using 16S rRNA gene sequences, strain CBA3108T forms a phyletic lineage distinct from other closely related species within the genus Cutibacterium. It was found to be most closely related to Cutibacterium avidum ATCC 25577T (98.27 % 16S rRNA gene sequence similarity) and other strains within the genus (≤98.0 %). The genomic DNA G+C content of strain CBA3108T was 63.2 mol%. The in silico DNA-DNA hybridization values of strain CBA3108T with C. avidum ATCC 25577T, C. porci WCA-380-WT-3AT and C. acnes subsp. acnes DSM 1897T were 33.6, 21.7 and 22.7 %, respectively. Its phenotypic, chemotaxonomic and molecular properties support the hypothesis that strain CBA3108T represents a novel species in the genus Cutibacterium, for which we propose the name Cutibacterium equinum sp. nov. The type strain is CBA3108T (=KACC 22889T=JCM 35966T).
Collapse
Affiliation(s)
- Jeong Ui Yun
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
- Department of Life Science, Chosun University, Gwangju 61452, Republic of Korea
| | - Hye Su Jung
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
- Biobank, Institut Pasteur Korea, Seongnam, 13488, Republic of Korea
| | - Mi-Ja Jung
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Hye Seon Song
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Yeon Bee Kim
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Yujin Kim
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Joon-Gyu Kim
- Department of Equine Science, Cheju Halla University, Jeju, 63092, Republic of Korea
| | - Seong Woon Roh
- Microbiome Research Team, LISCure Biosciences Inc., Seongnam 13486, Republic of Korea
| | - Se Hee Lee
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Jun Sik Lee
- Department of Life Science, Chosun University, Gwangju 61452, Republic of Korea
| | - Tae Woong Whon
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| |
Collapse
|
36
|
Moon YL, Kim KH, Park JS. Muricauda myxillae sp. nov., isolated from a marine sponge ( Myxilla rosacea), and reclassification of Flagellimonas hymeniacidonis as Muricauda symbiotica nom. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37982333 DOI: 10.1099/ijsem.0.006040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023] Open
Abstract
A Gram-stain-negative, aerobic and non-motile rods strain, designated as strain 2012CJ39-3T, was isolated from a marine sponge, Myxilla rosacea, collected on Chuja Island, Republic of Korea. Optimal growth of strain 2012CJ39-3T was observed at 25 °C, pH 7.0 and in the presence of 2.0-3.0 % (w/v) NaCl. Strain 2012CJ39-3T contained menaquinone-6 as the respiratory quinone, iso-C15 : 1 G, iso-C15 : 0, and iso-C17 : 0 3-OH as the predominant fatty acids, and phosphatidylethanolamine, an unidentified phospholipid, an unidentified glycolipid, three unidentified aminolipids and nine unidentified lipids as major polar lipids. The genomic DNA G+C content was 38.4 mol%. Results of phylogenetic analyses based on the 16S rRNA gene and whole-genome sequences revealed that strain 2012CJ39-3T formed a distinct phyletic lineage in the genus Muricauda. Strain 2012CJ39-3T was most closely related to Flagellimonas hymeniacidonis 176CP5-101T, Muricauda spongiicola 2012CJ35-5T, Muricauda algicola AsT0115T, Muricauda flava DSM 22638T and Muricauda parva SW169T with 96.5, 96.4, 96.3, 95.8 and 95.6 % 16S rRNA gene sequence similarity, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between strain 2012CJ39-3T and M. spongiicola 2012CJ35-5T, F. hymeniacidonis 176CP5-101T, M. algicola AsT0115T, M. flava DSM 22638T and M. parva SW169T were 75.6, 74.2, 78.6, 75.3 and 74.8 % and 27.4, 19.9, 36.3, 24.2 and 18.9 %, respectively. Based on these results, strain 2012CJ39-3T represents a novel species of the genus Muricauda, for which the name Muricauda myxillae sp. nov. is proposed. The type strain is 2012CJ39-3T (=KACC 22644T= LMG 32582T). In addition, Flagellimonas hymeniacidonis is reclassified as Muricauda symbiotica nom. nov.
Collapse
Affiliation(s)
- Yea-Lin Moon
- Department of Biological Sciences and Biotechnology, Hannam University Jeonmin-dong, Yuseong-gu, Daejeon 34430, Republic of Korea
| | - Kyung-Hyun Kim
- Department of Biological Sciences and Biotechnology, Hannam University Jeonmin-dong, Yuseong-gu, Daejeon 34430, Republic of Korea
| | - Jin-Sook Park
- Department of Biological Sciences and Biotechnology, Hannam University Jeonmin-dong, Yuseong-gu, Daejeon 34430, Republic of Korea
| |
Collapse
|
37
|
Ravin NV, Smolyakov DD, Markov ND, Beletsky AV, Mardanov AV, Rudenko TS, Grabovich MY. tilS and rpoB: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus Thiothrix. Microorganisms 2023; 11:2521. [PMID: 37894178 PMCID: PMC10609254 DOI: 10.3390/microorganisms11102521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/01/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Currently, the phylogeny of the genus Thiothrix is based on comparative whole genome analysis because of the high homology of the 16S ribosomal RNA gene sequences within the genus. We analyzed the possibility of using various conservative genes as phylogenetic markers for the genus Thiothrix. We found that the levels of similarity of the nucleotide sequences of the tRNA(Ile)-lysidine synthase (tilS) and the β subunit of RNA polymerase (rpoB) genes are in good agreement with the average nucleotide identity (ANI) values between the genomes of various representatives of the genus Thiothrix. The genomes of Thiothrix strains MK1, WS, DNT52, DNT53, and H33 were sequenced. Taxonomic analysis using both whole genomes and the tilS gene consistently showed that MK1 and WS belong to Thiothrix lacustris, while DNT52, DNT53, and H33 belong to Thiothrix subterranea. The tilS gene fragments were subjected to high-throughput sequencing to profile the Thiothrix mat of a sulfidic spring, which revealed the presence of known species of Thiothrix and new species-level phylotypes. Thus, the use of tilS and rpoB as phylogenetic markers will allow for rapid analyses of pure cultures and natural communities for the purpose of phylogenetic identification of representatives of the genus Thiothrix.
Collapse
Affiliation(s)
- Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (A.V.M.)
| | - Dmitry D. Smolyakov
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (N.D.M.); (T.S.R.)
| | - Nikita D. Markov
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (N.D.M.); (T.S.R.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (A.V.M.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (A.V.M.)
| | - Tatyana S. Rudenko
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (N.D.M.); (T.S.R.)
| | - Margarita Yu. Grabovich
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (N.D.M.); (T.S.R.)
| |
Collapse
|
38
|
Kim KH, Kim JM, Jin HM, Hao L, Jeon CO. Alishewanella maricola sp. nov., isolated from seawater of the Yellow Sea. Int J Syst Evol Microbiol 2023; 73. [PMID: 37877986 DOI: 10.1099/ijsem.0.005807] [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: 10/26/2023] Open
Abstract
A Gram-stain-negative and facultative aerobic bacterium, strain 16-MAT, was isolated from seawater of Yellow Sea in South Korea. Cells were catalase- and oxidase-positive and non-motile rods. Growth occurred at 4-37 °C (optimum, 30 °C) and pH 6.0-11.0 (optimum, 8.0), and in the presence of 0-7.0% NaCl (optimum, 3 %). Strain 16-MAT contained ubiquinone-8 as the sole isoprenoid quinone, C16 : 0 and summed feature three as the major fatty acids (>10 %), and phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminophospholipid, and an unidentified polar lipid as the major polar lipids. The genome size and DNA G+C content of strain 16-MAT were 3.69 Mb and 46.0 mol%, respectively. Strain 16-MAT was most closely related to Alishewanella alkalitolerans LNK-7.1T with a 97.9 % 16S rRNA gene sequence similarity. A phylogenomic tree based on whole genome sequences showed that strain 16-MAT formed a phylogenetic lineage within the genus Alishewanella. Based on the phenotypic, chemotaxonomic, and molecular analyses, strain 16-MAT represents a novel species of the genus Alishewanella, for which the name Alishewanella maricola is proposed. The type strain is 16-MAT (=KACC 22238T =JCM 34596T).
Collapse
Affiliation(s)
- Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Biological Sciences and Biotechnology, Hannam University, Daejon 34054, Republic of Korea
| | - Jeong Min Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyun Mi Jin
- Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do 37242, Republic of Korea
| | - Lujiang Hao
- School of Bioengineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, PR China
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| |
Collapse
|
39
|
Kristyanto S, Jung J, Kim JM, Choi BJ, Han DM, Lee SC, Jeon CO. Psychroserpens ponticola sp. nov. and Marinomonas maritima sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2023; 73. [PMID: 37830909 DOI: 10.1099/ijsem.0.006090] [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: 10/14/2023] Open
Abstract
Two Gram-stain-negative, catalase- and oxidase-positive, aerobic non-motile and motile rod bacteria, strains MSW6T and RSW2T, were isolated from surface seawater. Strain MSW6T optimally grew at 20 °C, pH 7.0 and 3 % NaCl, while strain RSW2T optimally grew at 25 °C, pH 7.0-8.0 and 2 % NaCl. Strain MSW6T possessed menaquinone-6 as the major respiratory quinone, and its major fatty acids were iso-C15 : 1 G, iso-C15 : 0 and iso-C15 : 0 3-OH. The major polar lipid identified in strain MSW6T was phosphatidylethanolamine (PE). On the other hand, strain RSW2T had ubiquinone-8 as the predominant respiratory quinone, and its major fatty acids consisted of summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The major polar lipids identified in strain RSW2T were PE and phosphatidylglycerol. As the sole respiratory quinone, strain MSW6T possessed menaquinone-6, while strain RSW2T had ubiquinone-8. The DNA G+C contents of strains MSW6T and RSW2T were 31.9 and 43.4 mol%, respectively. Phylogenetic analyses based on 16S rRNA and core gene sequences showed that strain MSW6T formed a phylogenic lineage with Psychroserpens mesophilus KOPRI 13649T, while strain RSW2T formed a phylogenic lineage with Marinomonas primoryensis KMM 3633T. Strain MSW6T shared 97.9 % 16S rRNA gene sequence similarity and 80.7 % average nucleotide identity (ANI) ith P. mesophilus KOPRI 13649T, and strain RSW2T shared 99.1 % 16S rRNA gene sequence similarity and 93.1 % ANI with M. primoryensis KMM 3633T. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strains MSW6T and RSW2T represent novel species of the genera Psychroserpens and Marinomonas, respectively, for which the names Psychroserpens ponticola sp. nov. and Marinomonas maritima sp. nov. are proposed, respectively. The type strain of P. ponticola is MSW6T (=KACC 22338T=JCM 35022T) and the type strain of M. maritima is RSW2T (=KACC 22716T=JCM 35550T).
Collapse
Affiliation(s)
- Sylvia Kristyanto
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jaejoon Jung
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jeong Min Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Byeong Jun Choi
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dong Min Han
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sung Chul Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| |
Collapse
|
40
|
Kim YS, Hwang EM, Jeong CM, Cha CJ. Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov., Isolated from Freshwater and Soil. J Microbiol 2023; 61:891-901. [PMID: 37851309 DOI: 10.1007/s12275-023-00081-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 10/19/2023]
Abstract
Two novel bacterial strains CJ74T and CJ75T belonging to the genus Flavobacterium were isolated from freshwater of Han River and ginseng soil, South Korea, respectively. Strain CJ74T was Gram-stain-negative, aerobic, rod-shaped, non-motile, and non-flagellated, and did not produce flexirubin-type pigments. Strain CJ75T was Gram-stain-negative, aerobic, rod-shaped, motile by gliding, and non-flagellated, and produced flexirubin-type pigments. Both strains were shown to grow optimally at 30 °C in the absence of NaCl on R2A medium. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ74T and CJ75T belonged to the genus Flavobacterium and were most closely related to Flavobacterium niveum TAPW14T and Flavobacterium foetidum CJ42T with 96.17% and 97.29% 16S rRNA sequence similarities, respectively. Genomic analyses including the reconstruction of phylogenomic tree, average nucleotide identity, and digital DNA-DNA hybridization suggested that they were novel species of the genus Flavobacterium. Both strains contained menaquinone 6 (MK-6) as the primary respiratory quinone and phosphatidylethanolamine as a major polar lipid. The predominant fatty acids of both strains were iso-C15:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). Based on the polyphasic taxonomic study, strains CJ74T and CJ75T represent novel species of the genus Flavobacterium, for which names Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov. are proposed, respectively. The type strains are CJ74T (=KACC 19819T =JCM 32889T) and CJ75T (=KACC 23149T =JCM 36132T).
Collapse
Affiliation(s)
- Yong-Seok Kim
- Department or Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Eun-Mi Hwang
- Department or Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Chang-Myeong Jeong
- Department or Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Chang-Jun Cha
- Department or Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea.
| |
Collapse
|
41
|
Ma T, Xue H, Piao C, Jiang N, Li Y. Genome-based analyses of family Oxalobacteraceae reveal the taxonomic classification. Res Microbiol 2023; 174:104076. [PMID: 37137377 DOI: 10.1016/j.resmic.2023.104076] [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: 12/04/2022] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/05/2023]
Abstract
Family Oxalobacteraceae is known for the indicator of bacterial diversity in the environment and many of which are important beneficial bacteria. Previous studies on the taxonomic structure of family Oxalobacteraceae mostly relied on 16S rRNA gene analysis, or core-genome phylogeny of a limited number of species and resulted in taxonomic confusion within several genera. Developments in sequencing technologies have allowed more genome sequences to be obtained, enabling the revision of family Oxalobacteraceae. Here, we report a comprehensive analysis of phylogenomic trees, concatenated protein and up-to-date bacterial core gene phylogenetic trees, and genomic metrics for genus demarcation on 135 genomes of Oxalobacteraceae species to elucidate their interrelationships. Following this framework for classification of species in family Oxalobacteraceae, all the proposed genera formed monophyletic lineages in the phylogenomic trees and could also be clearly separated from others in the genomic similarity indexes of average amino acid identity, percentage of conserved proteins and core-proteome average amino acid identity.
Collapse
Affiliation(s)
- Tengfei Ma
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China.
| | - Han Xue
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China.
| | - Chungen Piao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China.
| | - Ning Jiang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China.
| | - Yong Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China.
| |
Collapse
|
42
|
Jerabkova M, Smrhova T, Lopez-Echartea E, Dresler J, Suman J, Kapinusova G, Cajthaml T, Skrob Z, Kyclt R, Fagerman J, Strejcek M, Uhlik O. Silvimonas soli sp. nov., a new member of Chromobacteriaceae isolated from soil in Norrbyskär island, Sweden. Int J Syst Evol Microbiol 2023; 73. [PMID: 37768182 DOI: 10.1099/ijsem.0.006048] [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: 09/29/2023] Open
Abstract
A novel bacterial species is described that was isolated from the soil of Norrbyskär island (Sweden). This Gram-negative, facultatively anaerobic and motile rod, designated 17-6T, was classified in the family Chromobacteriaceae, class Betaproteobacteria, and further characterized by a polyphasic approach. Comparative 16S rRNA gene analysis revealed the potential species novelty of the strain, with Silvimonas terrae (98.20 % similarity) and Silvimonas amylolytica (98.13 %) being its closest type strains. The phylogenetic novelty of the isolate at the level of species was confirmed using phylogenetic analyses based on the whole genome: average nucleotide identity values ranged from 79 to 81 %, average amino acid identity values from 75 to 81 % and percentage of conserved proteins values from 69-81 % with the members of genera Silvimonas and Amantichitinum. On the basis of phenotypic, phylogenetic, functional and genotypic analyses, we propose the isolate as the type strain of a novel species within the genus Silvimonas with the designation Silvimonas soli 17-6T (=DSM 115342T=CCM 9308T).
Collapse
Affiliation(s)
- Martina Jerabkova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| | - Tereza Smrhova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| | - Eglantina Lopez-Echartea
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| | - Jiri Dresler
- Military Health Institute, Ministry of Defence of the Czech Republic, Prague, Czechia
| | - Jachym Suman
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| | - Gabriela Kapinusova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| | - Tomas Cajthaml
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Zdena Skrob
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | | | | | - Michal Strejcek
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| |
Collapse
|
43
|
Baek JH, Kristyanto S, Kim JM, Han DM, Quan ZX, Jeon CO. Hoeflea algicola sp. nov. and Hoeflea ulvae sp. nov., isolated from phycosphere of marine algae. Int J Syst Evol Microbiol 2023; 73. [PMID: 37755148 DOI: 10.1099/ijsem.0.006058] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
Two Gram-negative, moderately halophilic, and motile rod bacteria, strains G2-23T and J2-29T, showing catalase- and oxidase-positive activities were isolated from species of the marine algae Chondrus and Ulva, respectively. Both strains optimally grew at 30 °C, pH 7.0 and 2% (w/v) NaCl. Both strains contained ubiquinone-10 as the sole isoprenoid quinone. Strain G2-23T contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c/ω6c) as major cellular fatty acids, and phosphatidylethanolamine (PE), phosphatidyl-N-monomethylethanolamine (PME), phosphatidylglycerol (PG), diphosphatidylglycerol and an unidentified phospholipid (PL) as major polar lipids. Strain J2-29T contained summed feature 8, C18 : 1 ω7c 11-methyl and C16 : 0 as major cellular fatty acids and PE, PME, PG and PL as major polar lipids. The genomic DNA G+C contents of strains G2-23T and J2-29T were 59.5 and 62.2 mol%, respectively. Both strains shared 97.9 % 16S rRNA gene sequence similarity, 79.8 % average nucleotide identity (ANI) and 22.8 % digital DNA-DNA hybridization (dDDH) values, indicating that they represent different species. Phylogenetic and phylogenomic analyses by 16S rRNA gene and genome sequences, respectively, revealed that strains G2-23T and J2-29T formed different phylogenic lineages within the genus Hoeflea. ANI and dDDH values between strains G2-23T and J2-29T and other Hoeflea type strains were less than 79.0 and 22.1% and 80.5 and 23.3 %, respectively, suggesting that they represent novel species of the genus Hoeflea. In summary, based on their phenotypic, chemotaxonomic and molecular properties, strains G2-23T and J2-29T represent two different novel species of the genus Hoeflea, for which the names Hoeflea algicola sp. nov. (G2-23T=KACC 22714T=JCM 35548T) and Hoeflea ulvae sp. nov. (J2-29T=KACC 22715T=JCM 35549T), respectively, are proposed.
Collapse
Affiliation(s)
- Ju Hye Baek
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sylvia Kristyanto
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jeong Min Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dong Min Han
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Zhe-Xue Quan
- School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| |
Collapse
|
44
|
Park MS, Kang I, Cho JC. Zwartia vadi sp. nov., a Novel Species of the GKS98 Cluster Isolated from a Stream, and the Reclassification of 'Achromobacter Panacis' as Zwartia panacis comb. nov. Microorganisms 2023; 11:2150. [PMID: 37763994 PMCID: PMC10535154 DOI: 10.3390/microorganisms11092150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
A Gram-stain-negative, aerobic, motile by gliding, and rod-shaped bacterium, designated IMCC34845T, was isolated from a freshwater stream in the Republic of Korea. The results of 16S rRNA gene-based phylogenetic analyses showed that strain IMCC34845T was affiliated with the genus Zwartia and was most closely related to 'Achromobacter panacis' DCY105T (100%) and Zwartia hollandica LF4-65T (98.9%). The whole-genome sequence of strain IMCC34845T was 3.2 Mbp in size with a 51.5% DNA G+C content. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain IMCC34845T and 'Achromobacter panacis' KCTC 42751T were 77.7% and 20.7%, respectively, revealing that they are independent species. Moreover, the strains IMCC34845T and KCTC 42751T exhibited ≤ 72.5% ANI and ≤18.5% dDDH values with closely related species Zwartia hollandica LF4-65T, further supporting that the two strains represent each novel species of the genus. The major respiratory quinone of strain IMCC34845T was ubiquinone-8 (Q-8), and the predominant cellular fatty acids were C16:0 (41.3%) and C17:0 cyclo (34.5%). The major polar lipids of the strain were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified phospholipids, and unidentified aminolipids. Based on the phylogenetic, genomic, physiological, and chemotaxonomic characteristics, strain IMCC34845T was considered to represent a novel species within the genus Zwartia, for which the name Zwartia vadi sp. nov. is proposed. The type of strain is IMCC34845T (=KCTC 92920T = NBRC 114902T). Furthermore, based on the taxonomic data, 'Achromobacter panacis' is proposed to be reclassified as Zwartia panacis comb. nov.
Collapse
Affiliation(s)
- Miri S. Park
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea;
- Center for Molecular and Cell Biology, Inha University, Incheon 22212, Republic of Korea
| | - Ilnam Kang
- Center for Molecular and Cell Biology, Inha University, Incheon 22212, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea;
| |
Collapse
|
45
|
Ma T, Xue H, Piao C, Jiang N, Li Y. Phylogenomic reappraisal of the family Rhizobiaceae at the genus and species levels, including the description of Ectorhizobium quercum gen. nov., sp. nov. Front Microbiol 2023; 14:1207256. [PMID: 37601364 PMCID: PMC10434624 DOI: 10.3389/fmicb.2023.1207256] [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: 04/17/2023] [Accepted: 07/12/2023] [Indexed: 08/22/2023] Open
Abstract
The family Rhizobiaceae contains 19 validly described genera including the rhizobia groups, many of which are important nitrogen-fixing bacteria. Early classification of Rhizobiaceae relied heavily on the poorly resolved 16S rRNA genes and resulted in several taxonomic conflicts. Although several recent studies illustrated the taxonomic status of many members in the family Rhizobiaceae, several para- and polyphyletic genera still needed to be elucidated. The rapidly increasing number of genomes in Rhizobiaceae has allowed for a revision of the taxonomic identities of members in Rhizobiaceae. In this study, we performed analyses of genome-based phylogeny and phylogenomic metrics to review the relationships of 155-type strains within the family Rhizobiaceae. The UBCG and concatenated protein phylogenetic trees, constructed based on 92 core genes and concatenated alignment of 170 single-copy orthologous proteins, demonstrated that the taxonomic inconsistencies should be assigned to eight novel genera, and 22 species should be recombined. All these reclassifications were also confirmed by pairwise cpAAI values, which separated genera within the family Rhizobiaceae with a demarcation threshold of ~86%. In addition, along with the phenotypic and chemotaxonomic analyses, a novel strain BDR2-2T belonging to a novel genus of the family Rhizobiaceae was also confirmed, for which the name Ectorhizobium quercum gen. nov., sp. nov. was proposed. The type strain is BDR2-2T (=CFCC 16492T = LMG 31717T).
Collapse
Affiliation(s)
| | | | | | | | - Yong Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, China
| |
Collapse
|
46
|
Kim KH, Han DM, Lee JK, Jeon CO. Alkalicoccobacillus porphyridii sp. nov., isolated from a marine red alga, reclassification of Shouchella plakortidis and Shouchella gibsonii as Alkalicoccobacillus plakortidis comb. nov. and Alkalicoccobacillus gibsonii comb. nov., and emended description of the genus Alkalicoccobacillus Joshi et al. 2022. Int J Syst Evol Microbiol 2023; 73. [PMID: 37610811 DOI: 10.1099/ijsem.0.006019] [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: 08/24/2023] Open
Abstract
A Gram-stain-positive alkali-tolerant and strictly aerobic bacterium, designated strain P16T, was isolated from a marine red alga, Porphyridium cruentum, in the Yellow Sea, Republic of Korea. Cells were motile rods with peritrichous flagella and exhibited catalase and oxidase activities. The optimal growth of strain P16T was observed to occur at 30 °C and pH 8.0 and in the presence of 2.0 % (w/v) NaCl. Menaquinone-7 was identified as the sole respiratory quinone. Strain P16T contained anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major cellular fatty acids and polar lipids, respectively. The G+C content of strain P16T was 40.8 mol%. Strain P16T was most closely related to Shouchella plakortidis P203T, Shouchella gibsonii DSM 8722T and Alkalicoccobacillus murimartini LMG 21005T with 98.1, 98.1 and 98.0 % 16S rRNA gene sequence similarities, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that strain P16T, S, plakortidis, S. gibsonii and A. murimartini formed a single phylogenetic lineage cluster, and genomic relatedness analyses showed that they are different species. Based on phylogenetic, phenotypic, chemotaxonomic and molecular features, strain P16T represents a novel species of the genus Alkalicoccobacillus, for which the name Alkalicoccobacillus porphyridii sp. nov. is proposed. The type strain is P16T (=KACC 19520T=JCM 32931T). In addition, S. plakortidis and S. gibsonii are reclassified as Alkalicoccobacillus plakortidis comb. nov. (type strain P203T=DSM 19153T=NCIMB 14288T) and Alkalicoccobacillus gibsonii comb. nov. (type strain PN-109T=ATCC 700164T=DSM 8722T=KCCM 41407T), respectively.
Collapse
Affiliation(s)
- Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Biological Sciences and Biotechnology, Hannam University, Daejon 34054, Republic of Korea
| | - Dong Min Han
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jae Kyeong Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| |
Collapse
|
47
|
Ali F. Patterns of change in nucleotide diversity over gene length. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548940. [PMID: 37503020 PMCID: PMC10369989 DOI: 10.1101/2023.07.13.548940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Nucleotide diversity at a site is influenced by the relative strengths of neutral and selective population genetic processes. Therefore, attempts to identify sites under positive selection require an understanding of the expected diversity in its absence. The nucleotide diversity of a gene was previously found to correlate with its length. In this work, I measure nucleotide diversity at synonymous sites and uncover a pattern of low diversity towards the translation initiation site (TIS) of a gene. The degree of reduction in diversity at the TIS and the length of this region of reduced diversity can be quantified as "Effect Size" and "Effect Length" respectively, using parameters of an asymptotic regression model. Estimates of Effect Length across bacteria covaried with recombination rates as well as with a multitude of fast-growth adaptations such as the avoidance of mRNA secondary structure around TIS, the number of rRNAs, and relative codon usage of ribosomal genes. Thus, the dependence of nucleotide diversity on gene length is governed by a combination of selective and non-selective processes. These results have implications for the estimation of effective population size and relative mutation rates based on "silent-site" diversity, and for pN/pS-based prediction of genes under selection.
Collapse
Affiliation(s)
- Farhan Ali
- Biodesign Institute, Arizona State University, Tempe, Arizona
| |
Collapse
|
48
|
Na SI, Bailey MJ, Chalita M, Cho JH, Chun J. UACG: Up-to-Date Archaeal Core Genes and Software for Phylogenomic Tree Reconstruction. J Microbiol 2023; 61:683-692. [PMID: 37566173 DOI: 10.1007/s12275-023-00064-2] [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: 05/15/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 08/12/2023]
Abstract
In the post-genomic era, phylogenomics is a powerful and routinely-used tool to discover evolutionary relationships between microorganisms. Inferring phylogenomic trees by concatenating core gene sequences into a supermatrix is the standard method. The previously released up-to-date bacterial core gene (UBCG) tool provides a pipeline to infer phylogenomic trees using single-copy core genes for the Bacteria domain. In this study, we established up-to-date archaeal core gene (UACG), comprising 128 genes suitable for inferring archaeal phylogenomic trees. To test the gene set, we selected the Haloarcula genus and scrutinized its phylogeny. The phylogeny inferred using the UACG tool was consistent with the orthoANIu dendrogram, whereas the 16S rRNA gene phylogeny showed high intragenomic heterogeneity resulting in phylogenetic discrepancies. The software tool using the UACG set is available at https://www.ezbiocloud.net/tools/uacg .
Collapse
Affiliation(s)
- Seong-In Na
- CJ Bioscience, Seoul, 04527, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 00826, Republic of Korea
| | | | | | | | - Jongsik Chun
- CJ Bioscience, Seoul, 04527, Republic of Korea.
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 00826, Republic of Korea.
| |
Collapse
|
49
|
Kouya T, Ishiyama Y, Ohashi S, Kumakubo R, Yamazaki T, Otaki T. Philodulcilactobacillus myokoensis gen. nov., sp. nov., a fructophilic, acidophilic, and agar-phobic lactic acid bacterium isolated from fermented vegetable extracts. PLoS One 2023; 18:e0286677. [PMID: 37342988 DOI: 10.1371/journal.pone.0286677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 05/21/2023] [Indexed: 06/23/2023] Open
Abstract
Lactic acid bacteria are commonly in the fermentation industry and pose potential positive effects on health. In this study, a new lactic acid bacterium was isolated from fermented vegetable extracts in Myoko, Niigata, Japan. This bacterium is fructophilic, acidophilic, and hard to grow on agar medium. The isolate is Gram-stain-positive, non-spore-forming, non-motile, rod-shaped, and catalase-negative. Growth occurred at pH 3.5-5.5, with optimal growth at pH 4.5-5.0. The cells formed colonies on a solid MRS medium with 20% (w/v) sucrose and 0.8% (w/v) gellan gum under anaerobic conditions. The bacterium was able to grow on up to 50% (w/v) sucrose but not on d-glucose. Moreover, 16S rRNA gene sequence analysis revealed that the strain was most closely related to Apilactobacillus ozensis (93.1% sequence similarity). The values of average nucleotide identity, digital DNA-DNA hybridization, average amino acid sequence identity, and amino acid identity of conserved genes were calculated between the isolated strain (type strain is WR16-4T = NBRC 115064T = DSM 112857T) and its phylogenetically closest type strains. The average nucleotide identity values (73.36-78.28%) and DNA-DNA hybridization values (16.3-32.9%) were significantly lower than the threshold values for species boundaries. The average amino acid sequence identity values (53.96-60.88%) were significantly below the threshold boundary of genus demarcation (68%). The amino acid identity of conserved genes values compared to strain WR16-4T were the genera Apilactobacillus, Nicoliella spurrieriana SGEP1_A5T, Acetilactobacillus jinshanensis HSLZ-75T, and Fructilactobacillus were 62.51-63.79%, 62.87%, 62.03%, and 58.00-61.04%, respectively. The 16S rRNA gene and core genome phylogenetic trees suggested that this novel strain was most closely related to the type strain of A. jinshanensis HSLZ-75T. Based on the physiological, morphological, and phenotypical characteristics of strain WR16-4T, we propose its classification as a novel genus, Philodulcilactobacillus myokoensis gen. nov., sp. nov.
Collapse
Affiliation(s)
- Tomoaki Kouya
- Department of Materials Chemistry and Bioengineering, National Institute of Technology, Oyama College, Oyama, Tochigi, Japan
| | | | - Shota Ohashi
- Department of Materials Chemistry and Bioengineering, National Institute of Technology, Oyama College, Oyama, Tochigi, Japan
| | - Ryota Kumakubo
- Department of Materials Chemistry and Bioengineering, National Institute of Technology, Oyama College, Oyama, Tochigi, Japan
| | - Takeshi Yamazaki
- Department of Materials Chemistry and Bioengineering, National Institute of Technology, Oyama College, Oyama, Tochigi, Japan
| | | |
Collapse
|
50
|
Pardo-De la Hoz CJ, Magain N, Piatkowski B, Cornet L, Dal Forno M, Carbone I, Miadlikowska J, Lutzoni F. Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria. Syst Biol 2023; 72:694-712. [PMID: 36827095 DOI: 10.1093/sysbio/syad008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 02/12/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema.].
Collapse
Affiliation(s)
| | - Nicolas Magain
- Evolution and Conservation Biology, InBioS Research Center, Université de Liège, Liège 4000, Belgium
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Luc Cornet
- Evolution and Conservation Biology, InBioS Research Center, Université de Liège, Liège 4000, Belgium
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Brussels, Belgium
| | | | - Ignazio Carbone
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA
| | | | | |
Collapse
|