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Commichaux S, Luan T, Muralidharan HS, Pop M. Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes. PLoS Comput Biol 2024; 20:e1012343. [PMID: 39102435 DOI: 10.1371/journal.pcbi.1012343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 07/22/2024] [Indexed: 08/07/2024] Open
Abstract
For decades, the 16S rRNA gene has been used to taxonomically classify prokaryotic species and to taxonomically profile microbial communities. However, the 16S rRNA gene has been criticized for being too conserved to differentiate between distinct species. We argue that the inability to differentiate between species is not a unique feature of the 16S rRNA gene. Rather, we observe the gradual loss of species-level resolution for other nearly-universal prokaryotic marker genes as the number of gene sequences increases in reference databases. This trend was strongly correlated with how represented a taxonomic group was in the database and indicates that, at the gene-level, the boundaries between many species might be fuzzy. Through our study, we argue that any approach that relies on a single marker to distinguish bacterial taxa is fraught even if some markers appear to be discriminative in current databases.
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Affiliation(s)
- Seth Commichaux
- Center for Food Safety and Nutrition, Food and Drug Administration, Laurel, Maryland, United States of America
| | - Tu Luan
- Department of Computer Science, University of Maryland, College Park, Maryland, United States of America
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Harihara Subrahmaniam Muralidharan
- Department of Computer Science, University of Maryland, College Park, Maryland, United States of America
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Mihai Pop
- Department of Computer Science, University of Maryland, College Park, Maryland, United States of America
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
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Das L, Kujur RRA, Debnath T, Das SK. Phylogeny and genomic analysis of Shewanella cutis sp. nov., isolated from freshwater pufferfish. Folia Microbiol (Praha) 2024; 69:723-731. [PMID: 37996658 DOI: 10.1007/s12223-023-01111-6] [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: 02/22/2023] [Accepted: 10/30/2023] [Indexed: 11/25/2023]
Abstract
Three closely related, aerobic, Gram-stain-negative, motile, rod-shaped bacterial strains (PS-2T, PS-17, and PS-19) were isolated from the skin of freshwater pufferfish (Tetraodon cutcutia). Colonies are pinkish-colored. The optimum growth occurred at 28-30 °C, and the pH was 6.5-7. The major cellular fatty acids were C16:1 ω7c, iso-C15.0, C17:1 ω8c, C18:1 ω7c, and C16:0. The predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, and amino lipids. The genome size of strain PS-2T is 4.8 Mbp, and the G + C content was 46.0%. The major fraction of genes were associated with biological processes (45.64%), followed by molecular function (29.86%) and cellular components (24.49%). The unique genes identified in strain PS-2T secreted cyanophycinase, UDP-N-acetylglucosamine 2-epimerase, methyltransferase, kynureninase, ADA regulatory protein, biphenyl degradation, thermostable carboxypeptidase 1, tetrathionate respiration, etc. In addition, alanine and glutamate racemases were present. The 16S rRNA gene sequences shared 98.83-99.24% similarity with the closely related type strains of Shewanella. The ANI and AAI of strain PS-2T with reference type strains of the genus Shewanella were below 95-96%, and the corresponding dDDH values were below 70%. A phylogenetic tree based on 16S rRNA gene sequences and genome-wide core genes revealed that strain PS-2T clustered with Shewanella oneidensis LMG 19005T in both phylogenetic trees. Based on the polyphasic analysis, the new isolates (PS-2T, PS-17, and PS-19) represent a novel species of Shewanella, for which Shewanella cutis sp. nov. is proposed. The type strain is PS-2T (= TBRC 15838T = NBRC 115342T).
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Affiliation(s)
- Lipika Das
- Department of Biotechnology, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, India
| | - Ritu Rani Archana Kujur
- Department of Biotechnology, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, India
| | - Tanmoy Debnath
- Department of Biotechnology, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, India
| | - Subrata K Das
- Department of Biotechnology, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, India.
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Zayulina KS, Podosokorskaya OA, Klyukina AA, Panova TV, Novikov AA, Kublanov IV, Bonch-Osmolovskaya EA, Elcheninov AG. A Novel Species of the Genus Thermanaerothrix Isolated from a Kamchatka Hot Spring Possesses Hydrolytic Capabilities. Curr Microbiol 2024; 81:293. [PMID: 39090416 DOI: 10.1007/s00284-024-03815-5] [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: 01/09/2024] [Accepted: 07/20/2024] [Indexed: 08/04/2024]
Abstract
Hot springs are inhabited by specific microbial communities which are reservoirs of novel taxa. In this work strain 4228-RoLT was isolated from the Solnechny hot spring, Uzon Caldera, Kamchatka. Cells of the strain 4228-RoLT were Gram-negative rods forming multicellular filaments. The strain grew optimally at 60 °C and pH 7.0 and fermented various organic compounds including polysaccharides (microcrystalline cellulose, xylan, chitin, starch, dextrin, dextran, beta-glucan, galactomannan, glucomannan, mannan). Major fatty acids were iso-C17:0, C16:0, C18:0, C20:0, iso-C19:0, anteiso-C17:0 and C22:0. Genome of the strain was of 3.25 Mbp with GC content of 54.2%. Based on the whole genome comparisons and phylogenomic analysis the new isolate was affiliated to a novel species of Thermanaerothrix genus within Anaerolineae class of phylum Chloroflexota, for which the name T. solaris sp. nov. was proposed with 4228-RoLT (= VKM B-3776 T = UQM 41594 T = BIM B-2058 T) as the type strain. 114 CAZymes including 43 glycoside hydrolases were found to be encoded in the genome of strain 4228-RoLT. Cell-bound and extracellular enzymes of strain 4228-RoLT were active against starch, dextran, mannan, xylan and various kinds of celluloses, with the highest activity against beta-glucan. Altogether, growth experiments, enzymatic activities determination and genomic analysis suggested that T. solaris strain 4228-RoLT could serve as a source of glycosidases suitable for plant biomass hydrolysis.
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Affiliation(s)
- Kseniya S Zayulina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 60-Let Oktyabrya Prospect, 7, Bld. 2, 119071, Moscow, Russia
| | - Olga A Podosokorskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 60-Let Oktyabrya Prospect, 7, Bld. 2, 119071, Moscow, Russia
| | - Alexandra A Klyukina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 60-Let Oktyabrya Prospect, 7, Bld. 2, 119071, Moscow, Russia
| | - Tatiana V Panova
- Faculty of Chemistry, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991, Moscow, Russia
| | - Andrei A Novikov
- Gubkin Russian State University of Oil and Gas, Leninskiy Prospect 65, 119991, Moscow, Russia
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 60-Let Oktyabrya Prospect, 7, Bld. 2, 119071, Moscow, Russia
| | - Elizaveta A Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 60-Let Oktyabrya Prospect, 7, Bld. 2, 119071, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991, Moscow, Russia
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 60-Let Oktyabrya Prospect, 7, Bld. 2, 119071, Moscow, Russia.
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Litti Y, Elcheninov A, Botchkova E, Chernyh N, Merkel A, Vishnyakova A, Popova N, Zhang Y, Safonov A. Metagenomic evidence of a novel anammox community in a cold aquifer with high nitrogen pollution. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 365:121629. [PMID: 38944958 DOI: 10.1016/j.jenvman.2024.121629] [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: 01/10/2024] [Revised: 06/06/2024] [Accepted: 06/26/2024] [Indexed: 07/02/2024]
Abstract
The process of anaerobic ammonium oxidation by nitrite (anammox) is a globally essential part of N cycle. To date, 8 Candidatus genera and more than 22 species of anammox bacteria have been discovered in various anthropogenic and natural habitats, including nitrogen-polluted aquifers. In this work, anammox bacteria were detected for the first time in the groundwater ecosystem with high anthropogenic nitrogen pollution (up to 1760 mg NO3--N/L and 280 mg NH4+-N/L) and low year-round temperature (7-8 °C) in the zone of a uranium sludge repository. Further metagenomic analysis resulted in retrieval of metagenome-assembled genomes of 4 distinct anammox bacteria: a new genus named Ca. Frigussubterria, new species in Ca. Kuenenia, and two strains of a new species in Ca. Scalindua. Analysis of the genomes revealed essential genes involved in anammox metabolism. Both strains of Ca. Scalindua chemeplantae had a high copy number of genes encoding the cold shock proteins CspA/B, which can also function as an antifreeze protein (CspB). Ca. Kuenenia glazoviensis and Ca. Frigussubterria udmurtiae were abundant in less N-polluted site, while Ca. Scalindua chemeplantae inhabited both sites. Genes for urea utilization, reduction of insoluble Fe2O3 or MnO2, assimilatory sulfate reduction, reactive oxygen detoxification, nitrate reduction to ammonium, and putatively arsenate respiration were found. These findings enrich knowledge of the functional and phylogenetic diversity of anammox bacteria and improve understanding of the nitrogen cycle in polluted aquifers.
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Affiliation(s)
- Yuriy Litti
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312, Moscow, Russia.
| | - Alexander Elcheninov
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312, Moscow, Russia.
| | - Ekaterina Botchkova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312, Moscow, Russia.
| | - Nikolay Chernyh
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312, Moscow, Russia.
| | - Alexander Merkel
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312, Moscow, Russia.
| | - Anastasia Vishnyakova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312, Moscow, Russia.
| | - Nadezhda Popova
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, 31, bld.4, Leninsky Prospect, 119071, Moscow, Russia.
| | - Yaobin Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.
| | - Alexey Safonov
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, 31, bld.4, Leninsky Prospect, 119071, Moscow, Russia.
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Dutta S, Kothari S, Singh D, Ghosh S, Narayan Sarangi A, Sanjita Behera S, Prajapati S, Kumar Sinha P, Prusty A, Tripathy S. Novel oceanic cyanobacterium isolated from Bangaram island with profound acid neutralizing ability is proposed as Leptolyngbya iicbica sp. nov. strain LK. Mol Phylogenet Evol 2024; 197:108092. [PMID: 38723790 DOI: 10.1016/j.ympev.2024.108092] [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: 11/10/2023] [Revised: 02/16/2024] [Accepted: 05/04/2024] [Indexed: 05/19/2024]
Abstract
An acid-neutralizing, filamentous, non-heterocytous, marine cyanobacterium named 'LK' has been isolated from the seashore of Bangaram Island, an atoll of Lakshadweep, India, and is described here as a novel species. LK has been characterized using morphological, ecological, and genomic features. Based on 16S rRNA, whole-genome sequencing, and marker gene-based analysis, LK has been identified as a new species. LK clustered with Leptolyngbya-like strains belonging to the LPP group but diverged from Leptolyngbya sensu stricto, indicating the polyphyletic nature of the Leptolyngbya genus. Leptolyngbya sp. SIOISBB and Halomicronema sp. CCY15110 were identified as LK's two closest phylogenetic neighbors in various phylogenetic studies. The analysis of 16S rRNA, ITS secondary structures, and genome relatedness indices such as AAI, ANI, and gANI strongly support LK as a novel species of the Leptolyngbya genus. The mechanism behind acid neutralization in LK has been delineated, attributing it to a surface phenomenon most likely due to the presence of salts of calcium, magnesium, sodium, and potassium. We name LK as Leptolyngbya iicbica strain LK which is a novel species with prominent acidic pH-neutralizing properties.
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Affiliation(s)
- Subhajeet Dutta
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shreya Kothari
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Deeksha Singh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Samrat Ghosh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Aditya Narayan Sarangi
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Smruti Sanjita Behera
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Molecular Genetics Division, CSIR Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Satish Prajapati
- Advanced Materials and Chemical Characterisation Division (AMCCD), CSIR-Central Glass & Ceramic Research Institute (CGCRI), Kolkata 700 032, West Bengal, India
| | - Prasanta Kumar Sinha
- Advanced Materials and Chemical Characterisation Division (AMCCD), CSIR-Central Glass & Ceramic Research Institute (CGCRI), Kolkata 700 032, West Bengal, India
| | - Asharani Prusty
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sucheta Tripathy
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Kang T, Choi YJ, Kim J, Park HJ, Jang WJ. Whole genome sequence and comparative genomic analysis of novel Rickettsia koreansis strain CNH17-7 isolated from human. Eur J Clin Microbiol Infect Dis 2024:10.1007/s10096-024-04876-x. [PMID: 39031268 DOI: 10.1007/s10096-024-04876-x] [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: 04/19/2024] [Accepted: 06/15/2024] [Indexed: 07/22/2024]
Abstract
PURPOSE To determine the genomic feature of novel spotted fever-causing Rickettsia koreansis strain CNH17-7, which is different from R. japonica that is a causative agent for Japanese spotted fever (JSF), and to perform its comparative genomic analysis. METHODS Whole genome sequencing (WGS) was performed on R. koreansis strain CNH17-7 by using the Illumina Miseq system. After WGS, assembly and annotation were done by SPAdes. Then, its genomic features were compared with 19 different Rickettsia species. Based on the average nucleotide identity (ANI) value, an unweighted pair group method with an arithmetic mean (UPGMA) dendrogram was generated. Following the dendrogram analysis, pan-and core-genome analysis was performed. Then additional comparative analyses with two genetically closest Rickettsia species were conducted based on gene repertoire. RESULTS R. koreansis strain CNH17-7 has a chromosome consisting of 1,392,633 bp with GC content of 32.4%. The ANI-derived UPGMA showed that R. koreansis strain CNH17-7 is genetically close to R. japonica YH and R. heilongjiangensis 054 but is distinctively differentiated. The ANI value of R. koreansis strain CNH17-7 to R. japonica YH and R. heilongjiangensis 054 are 98.14% and 98.04% respectively, indicating R. koreansis strain CNH17-7 is sufficient to be classified as a new species. Other than ANI, R. koreansis strain CNH17-7 also contains novel CDS and its COG functional category proportion which is distinct compared to R. japonica YH and R. heilongjiangensis 054. CONCLUSION We have revealed genomic features of the novel R. koreansis strain CNH17-7. Hence, we propose R. koreansis strain CNH17-7 as new Rickettsia species.
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Affiliation(s)
- Taeuk Kang
- Department of Microbiology, Konkuk University School of Medicine, College of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
- Research Institute of Medical Science, Konkuk University School of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Yeon-Joo Choi
- Department of Microbiology, Konkuk University School of Medicine, College of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
- Research Institute of Medical Science, Konkuk University School of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Jeoungyeon Kim
- Department of Microbiology, Konkuk University School of Medicine, College of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
- Research Institute of Medical Science, Konkuk University School of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Hye-Jin Park
- Department of Microbiology, Konkuk University School of Medicine, College of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
- Research Institute of Medical Science, Konkuk University School of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Won-Jong Jang
- Department of Microbiology, Konkuk University School of Medicine, College of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea.
- Research Institute of Medical Science, Konkuk University School of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea.
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Zhao J, Both JP, Rodriguez-R LM, Konstantinidis KT. GSearch: ultra-fast and scalable genome search by combining K-mer hashing with hierarchical navigable small world graphs. Nucleic Acids Res 2024:gkae609. [PMID: 39011878 DOI: 10.1093/nar/gkae609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/17/2024] Open
Abstract
Genome search and/or classification typically involves finding the best-match database (reference) genomes and has become increasingly challenging due to the growing number of available database genomes and the fact that traditional methods do not scale well with large databases. By combining k-mer hashing-based probabilistic data structures (i.e. ProbMinHash, SuperMinHash, Densified MinHash and SetSketch) to estimate genomic distance, with a graph based nearest neighbor search algorithm (Hierarchical Navigable Small World Graphs, or HNSW), we created a new data structure and developed an associated computer program, GSearch, that is orders of magnitude faster than alternative tools while maintaining high accuracy and low memory usage. For example, GSearch can search 8000 query genomes against all available microbial or viral genomes for their best matches (n = ∼318 000 or ∼3 000 000, respectively) within a few minutes on a personal laptop, using ∼6 GB of memory (2.5 GB via SetSketch). Notably, GSearch has an O(log(N)) time complexity and will scale well with billions of genomes based on a database splitting strategy. Further, GSearch implements a three-step search strategy depending on the degree of novelty of the query genomes to maximize specificity and sensitivity. Therefore, GSearch solves a major bottleneck of microbiome studies that require genome search and/or classification.
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Affiliation(s)
- Jianshu Zhao
- Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Luis M Rodriguez-R
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
- Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Konstantinos T Konstantinidis
- Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
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Behrendt U, Burghard V, Wende S, Ulrich K, Wolf J, Neumann-Schaal M, Ulrich A. Schauerella fraxinea gen. nov., sp. nov., a bacterial species that colonises ash trees tolerant to dieback caused by Hymenoscyphus fraxineus. Syst Appl Microbiol 2024; 47:126516. [PMID: 38772267 DOI: 10.1016/j.syapm.2024.126516] [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: 01/31/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/23/2024]
Abstract
The tolerance of ash trees against the pathogen Hymenoscyphus fraxineus seems to be associated with the occurrence of specific microbial taxa on leaves. A group of bacterial isolates, primarily identified on tolerant trees, was investigated with regard to their taxonomic classification and their potential to suppress the ash dieback pathogen. Examination of OGRI values revealed a separate species position. A phylogenomic analysis, based on orthologous and marker genes, indicated a separate genus position along with the species Achromobacter aestuarii. Furthermore, analysis of the ratio of average nucleotide identities and genome alignment fractions demonstrated genomic dissimilarities typically observed for inter-genera comparisons within this family. As a result of these investigations, the strains are considered to represent a separate species within a new genus, for which the name Schauerella fraxinea gen. nov., sp. nov. is proposed, with the type strain B3P038T (=LMG 33092 T = DSM 115926 T). Additionally, a reclassification of the species Achromobacter aestuarii as Schauerella aestuarii comb. nov. is proposed. In a co-cultivation assay, the strains were able to inhibit the growth of a H. fraxineus strain. Accordingly, a functional analysis of the genome of S. fraxinea B3P038T revealed genes mediating the production of antifungal substances. This potential, combined with the prevalent presence in the phyllosphere of tolerant ash trees, makes this group interesting for an inoculation experiment with the aim of controlling the pathogen in an integrative approach. For future field trials, a strain-specific qPCR system was developed to establish an efficient method for monitoring the inoculation success.
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Affiliation(s)
- Undine Behrendt
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
| | - Valentin Burghard
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
| | - Sonja Wende
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
| | - Kristina Ulrich
- Johann Heinrich Von Thünen Institute, Institute of Forest Genetics, Eberswalder Chaussee 3a, 15377 Waldsieversdorf, Germany.
| | - Jacqueline Wolf
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
| | - Meina Neumann-Schaal
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
| | - Andreas Ulrich
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
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9
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Kobayashi H, Tanizawa Y, Sakamoto M, Ohkuma M, Tohno M. Lacrimispora brassicae sp. nov. isolated from fermented cabbage, and proposal of Clostridium indicum Gundawar et al. 2019 and Clostridium methoxybenzovorans Mechichi et al. 1999 as heterotypic synonyms of Lacrimispora amygdalina (Parshina et al. 2003) Haas and Blanchard 2020 and Lacrimispora indolis (McClung and McCoy 1957) Haas and Blanchard 2020, respectively. Int J Syst Evol Microbiol 2024; 74. [PMID: 39016536 DOI: 10.1099/ijsem.0.006456] [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: 07/18/2024] Open
Abstract
A Gram-stain-negative, endospore-forming, rod-shaped, indole-producing bacterial strain, designated YZC6T, was isolated from fermented cabbage. Strain YZC6T grew at 10-37 °C, pH 5.5-8.5, and with up to 2 % (w/v) NaCl. The major cellular fatty acids were C16 : 0 and C18 : 1 cis 11 dimethyl acetal. Phylogenetic analysis of the 16S rRNA gene revealed that strain YZC6T belonged to the genus Lacrimispora and was closely related to Lacrimispora aerotolerans DSM 5434T (98.3 % sequence similarity), Lacrimispora saccharolytica WM1T (98.1 %), and Lacrimispora algidixylanolytica SPL73T (98.1 %). The average nucleotide identity based on blast (below 87.8 %) and digital DNA-DNA hybridization (below 36.1 %) values between the novel isolate and its corresponding relatives showed that strain YZC6T could be readily distinguished from its closely related species. Based on genotypic, phenotypic, and chemotaxonomic data, a novel Lacrimispora species, Lacrimispora brassicae sp. nov., was proposed, with YZC6T as the type strain (=MAFF 212518T=JCM 32810T=DSM 112100T). This study also proposed Clostridium indicum Gundawar et al. 2019 as a later heterotypic synonym of Lacrimispora amygdalina (Parshina et al. 2003) Haas and Blanchard 2020 and Clostridium methoxybenzovorans Mechichi et al. 1999 as a later heterotypic synonym of Lacrimispora indolis (McClung and McCpy 1957) Haas and Blanchard 2020.
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Affiliation(s)
- Hisami Kobayashi
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masanori Tohno
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
- Innovative Animal Production System, University of Tsukuba, 305-8571 Tsukuba, Japan
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10
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Videau P, Shlafstein MD, Oline DK, Givan SA, Chapman LF, Strangman WK, Hahnke RL, Saw JH, Ushijima B. Genome-based taxonomic analysis of the genus Pseudoalteromonas reveals heterotypic synonyms. Environ Microbiol 2024; 26:e16672. [PMID: 39040020 DOI: 10.1111/1462-2920.16672] [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: 11/02/2023] [Accepted: 05/31/2024] [Indexed: 07/24/2024]
Abstract
The Pseudoalteromonas genus comprises members that have been demonstrated to play significant ecological roles and produce enzymes, natural products, and activities that are beneficial to the environment and economy. A comprehensive evaluation of the genus revealed that the genomes of several Pseudoalteromonas species are highly similar to each other, exceeding species cutoff values. This evaluation involved determining and comparing the average nucleotide identity, in silico DNA-DNA hybridization, average amino acid identity, and the difference in G + C% between Pseudoalteromonas type strains with publicly available genomes. The genome of the Pseudoalteromonas elyakovii type strain was further assessed through additional sequencing and genomic comparisons to historical sequences. These findings suggest that six Pseudoalteromonas species, namely P. mariniglutinosa, P. donghaensis, P. maricaloris, P. elyakovii, P. profundi, and P. issachenkonii, should be reclassified as later heterotypic synonyms of the following validly published species: P. haloplanktis, P. lipolytica, P. flavipulchra, P. distincta, P. gelatinilytica, and P. tetraodonis. Furthermore, two names without valid standing, 'P. telluritireducens' and 'P. spiralis', should be associated with the validly published Pseudoalteromonas species P. agarivorans and P. tetraodonis, respectively.
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Affiliation(s)
- Patrick Videau
- Department of Biology, Southern Oregon University, Ashland, Oregon, USA
| | | | - David K Oline
- Department of Biology, Southern Oregon University, Ashland, Oregon, USA
| | - Scott A Givan
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Linda Fleet Chapman
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - Wendy K Strangman
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Richard L Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jimmy H Saw
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina, USA
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11
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Park Y, Min J, Kim B, Park W. Pedobacter faecalis sp. nov., isolated from the faeces of eland, Taurotragus oryx. Int J Syst Evol Microbiol 2024; 74. [PMID: 39016544 DOI: 10.1099/ijsem.0.006454] [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: 07/18/2024] Open
Abstract
Strain ELA7T, a novel Gram-negative, non-motile bacterium with a white pigment and rod-shaped morphology, was isolated from the faeces of an eland at Seoul Grand Park, a zoo in the Republic of Korea. The novel bacterial strain grew optimally in R2A medium under the following conditions: 0 % (w/v) NaCl, pH 8.0, and 34 °C. Based on phylogenetic analyses using 16S rRNA gene sequencing, strain ELA7T was found to have the closest relatedness to Pedobacter ginsengisoli Gsoil 104T (97.8 %), P. frigoris RP-3-15T (97.2 %), P. humi THG S15-2T (97.0 %), P. seoulensis THG-G12T (97.0 %), and P. foliorum LMG 31463T (96.9 %). The genome size and genomic DNA G+C content of strain ELA7T were 3.63 Mbp and 46.5 %, respectively. A whole genome-level comparison of strain ELA7T with P. ginsengisoli Gsoil 104T, P. frigoris RP-3-15T, P. africanus DSM 12126T, and P. psychroterrae RP-1-14T revealed average nucleotide identity values of 72.0, 71.8, 71.9, and 71.6 %, respectively. The major fatty acids were summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and MK-7 was the predominant respiratory quinone. The major polar lipids of strain ELA7T were phosphatidylethanolamine, sphingolipid, unidentified aminolipid, unidentified phosphoglycolipid, unidentified glycolipid, and eight unidentified lipids. Considering our chemotaxonomic, genotypic, and phenotypic findings, strain ELA7T (=KACC 23137T=JCM 36003T) is identified as representing a novel species within the genus Pedobacter, for which the name Pedobacter faecalis sp. nov. is proposed.
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Affiliation(s)
- Yerim Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Jihyeon Min
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Bitnara Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
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12
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Sánchez-Castro I, Viver T, Martínez-Rodríguez P, Bustos-Caparros E, Ruiz-Fresneda MÁ, Mena-Sanabria MT, Jiménez-García I, Bosch-Estévez G, Descostes M, Merroun ML. Acidovorax bellezanensis sp. nov., a novel bacterium from uranium mill tailings repository sites with selenium bioremediation capabilities. Heliyon 2024; 10:e33171. [PMID: 39005906 PMCID: PMC11239578 DOI: 10.1016/j.heliyon.2024.e33171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 07/16/2024] Open
Abstract
A Gram-stain-negative bacterial strain designated Be4T, belonging to the genus Acidovorax, was isolated from mining porewaters sampled in uranium mill tailings repository sites, located in Bellezane, near Bessines-sur-Gartempe (Limousin, France). Cells were facultative anaerobic, rod-shaped, non-endospore-forming and motile with flagella. The mean cell size was 1.25-1.31 μm long and 0.70-0.73 μm wide. Colonies were light yellow, opaque, circular, convex with smooth margins, and 1-2 mm in diameter. Growth occurs at 4-37 °C and between pH 5.5-9.0. It differed from its phylogenetically related strains by phenotypic and physiological characteristics such as growth at 4 °C, presence of acid phosphatase, naphthol-AS-BI-phosphohydrolase and β-glucosidase enzymatic activities, and fermentation of l-xylose and esculin. The major fatty acids were C16:0, C16:1 ω7c/C16:1 ω6c, C17:0 cyclo and C18:1 ω7c. Phylogenetic analysis based on 16S rRNA and 938 core genes, confirmed its placement within the genus Acidovorax as a novel species. Strain Be4T showed highest 16S rRNA sequence similarity to Acidovorax antarcticus (98.2 %), Acidovorax radicis (97.9 %), Acidovorax temperans (97.8 %) and Acidovorax facilis (97.7 %). The genome of strain Be4T is 5,041,667 bp size with a DNA G + C content of 65.15 %. By automatic annotation numerous sequences involved in the interaction with metals/metalloids including some genes related to Se uptake and selenite resistance were detected in its genome. The average nucleotide identity (ANI) values calculated from whole genome sequences between strain Be4T and the most closely related strains A. radicis and A. facilis were below the threshold value of 95 %. Thus, the data from the phylogenetic, physiological, biochemical, and genomic analyses clearly indicates that strain Be4T represents a novel species with the suggested name Acidovorax bellezanensis sp. nov. The type strain is Acidovorax bellezanensis Be4T (=DSM116209T = CECT30865T). This novel species, due to its unique isolation source, genomic analysis, and preliminary laboratory tests where it was able to reduce toxic Se(IV) to less harmful Se(0) in the form of nanoparticles, holds great potential for further investigation in bioremediation, particularly concerning Se.
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Affiliation(s)
- Iván Sánchez-Castro
- Departamento de Microbiología, Campus de Fuentenueva, Universidad de Granada, 18071, Granada, Spain
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Pablo Martínez-Rodríguez
- Departamento de Microbiología, Campus de Fuentenueva, Universidad de Granada, 18071, Granada, Spain
| | - Esteban Bustos-Caparros
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | | | | | - Ignacio Jiménez-García
- Departamento de Microbiología, Campus de Fuentenueva, Universidad de Granada, 18071, Granada, Spain
| | - Germán Bosch-Estévez
- Departamento de Microbiología, Campus de Fuentenueva, Universidad de Granada, 18071, Granada, Spain
| | - Michael Descostes
- Environmental R&D Department, Orano Mining, Chatillon, 92320, France
- Centre de Géosciences, MINES Paris, PSL University, 35 rue St Honoré, 77300, Fontainebleau, France
| | - Mohamed Larbi Merroun
- Departamento de Microbiología, Campus de Fuentenueva, Universidad de Granada, 18071, Granada, Spain
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13
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Zhang H, Tang M, Li D, Xu M, Ao Y, Lin L. Applications and advances in molecular diagnostics: revolutionizing non-tuberculous mycobacteria species and subspecies identification. Front Public Health 2024; 12:1410672. [PMID: 38962772 PMCID: PMC11220129 DOI: 10.3389/fpubh.2024.1410672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/10/2024] [Indexed: 07/05/2024] Open
Abstract
Non-tuberculous mycobacteria (NTM) infections pose a significant public health challenge worldwide, affecting individuals across a wide spectrum of immune statuses. Recent epidemiological studies indicate rising incidence rates in both immunocompromised and immunocompetent populations, underscoring the need for enhanced diagnostic and therapeutic approaches. NTM infections often present with symptoms similar to those of tuberculosis, yet with less specificity, increasing the risk of misdiagnosis and potentially adverse outcomes for patients. Consequently, rapid and accurate identification of the pathogen is crucial for precise diagnosis and treatment. Traditional detection methods, notably microbiological culture, are hampered by lengthy incubation periods and a limited capacity to differentiate closely related NTM subtypes, thereby delaying diagnosis and the initiation of targeted therapies. Emerging diagnostic technologies offer new possibilities for the swift detection and accurate identification of NTM infections, playing a critical role in early diagnosis and providing more accurate and comprehensive information. This review delineates the current molecular methodologies for NTM species and subspecies identification. We critically assess the limitations and challenges inherent in these technologies for diagnosing NTM and explore potential future directions for their advancement. It aims to provide valuable insights into advancing the application of molecular diagnostic techniques in NTM infection identification.
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Affiliation(s)
- Haiyang Zhang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Maoting Tang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Deyuan Li
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Min Xu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Yusen Ao
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Liangkang Lin
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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14
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Deb S, Wild MA, LeClair T, Shah DH. Discovery of novel treponemes associated with pododermatitis in elk ( Cervus canadensis). Appl Environ Microbiol 2024; 90:e0010524. [PMID: 38742897 PMCID: PMC11218636 DOI: 10.1128/aem.00105-24] [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: 01/17/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
Pododermatitis, also known as treponeme-associated hoof disease (TAHD), presents a significant challenge to elk (Cervus canadensis) populations in the northwestern USA, with Treponema spp. consistently implicated in the lesion development. However, identifying species-specific Treponema strains from these lesions is hindered by its culture recalcitrance and limited genomic information. This study utilized shotgun sequencing, in silico genome reconstruction, and comparative genomics as a culture-independent approach to identify metagenome-assembled Treponema genomes (MATGs) from skin scraping samples collected from captive elk experimentally challenged with TAHD. The genomic analysis revealed 10 new MATGs, with 6 representing novel genomospecies associated with pododermatitis in elk and 4 corresponding to previously identified species-Treponema pedis and Treponema phagedenis. Importantly, genomic signatures of novel genomospecies identified in this study were consistently detected in biopsy samples of free-ranging elk diagnosed with TAHD, indicating a potential etiologic association. Comparative metabolic profiling of the MATGs against other Treponema genomes showed a distinct metabolic profile, suggesting potential host adaptation or geographic uniqueness of these newly identified genomospecies. The discovery of novel Treponema genomospecies enhances our understanding of the pathogenesis of pododermatitis and lays the foundation for the development of improved molecular surveillance tools to monitor and manage the disease in free-ranging elk.IMPORTANCETreponema spp. play an important role in the development of pododermatitis in free-ranging elk; however, the species-specific detection of Treponema from pododermatitis lesions is challenging due to culture recalcitrance and limited genomic information. The study utilized shotgun sequencing and in silico genome reconstruction to identify novel Treponema genomospecies from elk with pododermatitis. The discovery of the novel Treponema species opens new avenues to develop molecular diagnostic and epidemiologic tools for the surveillance of pododermatitis in elk. These findings significantly enhance our understanding of the genomic landscape of the Treponemataceae consortium while offering valuable insights into the etiology and pathogenesis of emerging pododermatitis in elk populations.
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Affiliation(s)
- Sushanta Deb
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Margaret A. Wild
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Thomas LeClair
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Devendra H. Shah
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
- School of Veterinary Medicine, Texas Tech University, Amarillo, Texas, USA
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15
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Stoll DA, Grimmler C, Hetzer B, Masoura A, Kulling SE, Huch M. Bosea rubneri sp. nov. Isolated from Organically Grown Allium cepa. Curr Microbiol 2024; 81:212. [PMID: 38839619 PMCID: PMC11153308 DOI: 10.1007/s00284-024-03717-6] [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: 11/30/2023] [Accepted: 04/25/2024] [Indexed: 06/07/2024]
Abstract
Strain ZW T0_25T was isolated from an onion sample (Allium cepa var. Hytech F1) within a storage trial and proofed to be a novel, aerobic, Gram-stain negative, rod-shaped bacterial strain. Analyses of the 16S rRNA gene sequence and of the whole draft genome sequences, i.e., digital DNA-DNA hybridization (dDDH), Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) showed that this strain represents a new species of the genus Bosea. The genome size of strain ZW T0_25T is 6.19 Mbp, and the GC content is 66.9%. As whole cell sugars, rhamnose, ribose and glucose were identified. Ubiquinone Q-10 is the major respiratory quinone with 97.8%. Polar lipids in strain ZW T0_25T are composed of one phosphatidylethanolamine, one phosphatidylglycerol, one aminophospholipid, two aminolipids, one glycolipid and two phospholipids whereas the fatty acid profile predominantly consists of C18:1 w7c (63.3%), C16:1 w7c (19.5%) and C16:0 (7.1%). Phenotypic traits were tested in the wet lab as well as predicted in silico from genome data. Therefore, according to this polyphasic approach, the new name Bosea rubneri sp. nov. with the type strain ZW T0_25T (= DSM 116094 T = LMG 33093 T) is proposed.
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Affiliation(s)
- Dominic A Stoll
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany
| | - Christina Grimmler
- Department of Safety and Quality of Meat, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, E.-C.-Baumann-Straße 20, 95326, Kulmbach, Germany
| | - Birgit Hetzer
- Department of Food Technology and Bioprocess Engineering, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany
| | - Alexandra Masoura
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany
| | - Sabine E Kulling
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany
| | - Melanie Huch
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany.
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16
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Zhang HX, Li CY, Gu CT. Lacticaseibacillus salsurivasis sp. nov. and Companilactobacillus muriivasis sp. nov., Isolated from Traditional Chinese Pickle. Curr Microbiol 2024; 81:203. [PMID: 38831185 DOI: 10.1007/s00284-024-03738-1] [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: 12/02/2023] [Accepted: 05/11/2024] [Indexed: 06/05/2024]
Abstract
Three Gram-stain-positive bacterial strains were isolated from traditional Chinese pickle and characterized using a polyphasic taxonomic approach. Results of 16S rRNA gene sequence analysis indicated that strain 74-4T was most closely related to the type strains of Lacticaseibacillus suibinensis and Lacticaseibacillus suilingensis, having 99.9% and 100% 16S rRNA gene sequence similarities, respectively, and that strains 419-1.2T and 262-4 were most closely related to the type strains of Companilactobacillus heilongjiangensis, Companilactobacillus nantensis, Companilactobacillus huachuanensis, and Companilactobacillus nuruki, having 98.5-99.7% 16S rRNA gene sequence similarities. The phylogenomic trees indicated that strain 74-4T was related to the type strains of L. suibinensis and L. suilingensis, and that strains 419-1.2T and 262-4 were related to the type strains of C. heilongjiangensis, C. nantensis, C. huachuanensis, and Companilactobacillus zhachilii. The ANI and dDDH values between strain 74-4T and type strains of phylogenetically related species were less than 92.7% and 49.9%, respectively. The ANI and dDDH values between strains 419-1.2T and 262-4 and type strains of phylogenetically related species were less than 93.4% and 51.7%, respectively. Based upon the data of polyphasic characterization obtained in the present study, two novel species, Lacticaseibacillus salsurivasis sp. nov. and Companilactobacillus muriivasis sp. nov., are proposed and the type strains are 74-4T (= JCM 35890T = CCTCC AB 2022414T) and 419-1.2T (= JCM 35891T = CCTCC AB 2022413T), respectively.
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Affiliation(s)
- Hong Xia Zhang
- 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.
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17
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Min J, Son Y, Park Y, Park W. Niabella defluvii sp. nov., isolated from influent water of a wastewater treatment plant. Int J Syst Evol Microbiol 2024; 74. [PMID: 38885037 DOI: 10.1099/ijsem.0.006425] [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: 06/18/2024] Open
Abstract
Strain I65T (=KACC 22647T=JCM 35315T), a novel Gram-stain-negative, strictly aerobic, non-motile, non-spore-forming, rod-shaped, and orange-pigmented bacterium was isolated from influent water of a wastewater treatment system after treatment with several antibiotics, such as meropenem, gentamicin, and macrolide. The newly identified bacterial strain I65T exhibits significant multi-drug and heavy metal resistance characteristics. Strain I65T was grown in Reasoner's 2A medium [0 %-2 % (w/v) NaCl (optimum, 0 %), pH 5.0-10.0 (optimum, pH 7.0), and 20-45°C (optimum, 30 °C)]. Phylogenetic analysis based on 16S rRNA gene sequencing confirmed that strain I65T was closely related to Niabella yanshanensis CCBAU 05354T (99.56 % sequence similarity), Niabella hibiscisoli THG-DN5.5T (97.51 %), and Niabella ginsengisoli GR10-1T (97.09 %). Further analysis of the whole-genome sequence confirmed that the digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between strain I65T and N. yanshanensis CCBAU 05354T were 23.4, 80.7, and 85.0 %, respectively, suggesting that strain I65T is distinct from N. yanshanensis. The genome size of strain I65T was 6.1 Mbp, as assessed using the Oxford Nanopore platform, and its genomic DNA G+C content was 43.0 mol%. The major fatty acids of strain I65T were iso-C15 : 0 and iso-C15 : 1 G, and the major respiratory quinone was MK-7. Moreover, the major polar lipid of strain I65T was phosphatidylethanolamine. Based on genotypic, chemotaxonomic, and phenotype data, strain I65T represents a novel species belonging to the genus Niabella, for which the name Niabella defluvii sp. nov. is proposed. The type strain is I65T (=KACC 22647T=JCM 35315T).
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Affiliation(s)
- Jihyeon Min
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Yongjun Son
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Yerim Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
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18
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Jung HK, Kim DG, Zin H, Park J, Jung H, Kim YO, Kong HJ, Kim JW, Kim YS. Paenibacillus hexagrammi sp. nov., a novel bacterium isolated from the gut content of Hexagrammos agrammus. Int J Syst Evol Microbiol 2024; 74. [PMID: 38869487 DOI: 10.1099/ijsem.0.006419] [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: 06/14/2024] Open
Abstract
A Gram-stain-positive, aerobic bacterium, designated as YPD9-1T, was isolated from the gut contents of a spotty belly greenling, Hexagrammos agrammus, collected near Dokdo island, South Korea. The rod-shaped cells were oxidase-positive, and catalase-negative. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C16 : 0, iso-C16 : 0 and iso-C17: 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unidentified lipids. The DNA G+C content was 47.6 mol% and the predominant respiratory quinone was menaquinone MK-7. The 16S rRNA gene sequence of YPD9-1T showed low sequence similarities to species of the genus Paenibacillus, Paenibacillus pocheonensis Gsoil 1138T (97.21 % of sequence similarity), Paenibacillus aestuarii CJ25T (97.12 %) and Paenibacillus allorhizoplanae JJ-42T (96.89 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that YPD9-1T formed a distinct branch among other species of the genus Paenibacillus. The digital DNA-DNA hybridisation, average nucleotide identity, and average amino acid identity values between YPD9-1T and the related species were in the ranges of 15.3-16.2 %, 74.1-78.4 %, and 71.1-71.9 %, respectively, which are below the species cutoff values. On the basis of the results of the polyphasic analysis, we conclude that strain YPD9-1T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus hexagrammi sp. nov. is proposed. The type strain of Paenibacillus hexagrammi is YPD9-1T (=KCTC 43424T =LMG 32988T).
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Affiliation(s)
- Hyun-Kyoung Jung
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Dong-Gyun Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Hyunwoo Zin
- Food Safety and Processing Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Jungwook Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Hyejung Jung
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Hee Jeong Kong
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Ju-Won Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Young-Sam Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
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Zhang Y, Quensen J, Chen B, Li H, Tiedje J, Sun W, Qian X. Paenalcaligenes faecalis sp. nov., a novel species of the family Alcaligenaceae isolated from chicken faeces. Int J Syst Evol Microbiol 2024; 74. [PMID: 38896454 DOI: 10.1099/ijsem.0.006429] [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: 06/21/2024] Open
Abstract
A Gram-negative, motile, rod-shaped aerobic and alkalogenic bacterium, designated as strain YLCF04T, was isolated from chicken faeces. Its growth was optimal at 28 °C (range, 10-40 °C), pH 8 (range, pH 6-9) and in 1 % (w/v) NaCl (range, 0-10 %). It was classified to the genus Paenalcaligenes and was most closely related to Paenalcaligenes hominis CCUG 53761AT (97.5 % similarity) based on 16S rRNA gene sequence analysis. Average nucleotide identity and digital DNA-DNA hybridization values between YLCF04T and P. hominis CCUG 53761AT were 76.3 and 18.2 %, respectively. Strain YLCF04T has a genome size of 2.7 Mb with DNA G+C content of 46.3 mol%. Based on its phylogenetic, genomic, phenotypic and biochemical characteristics, strain YLCF04T represents a novel species of the genus Paenalcaligenes, for which the name Paenalcaligenes faecalis sp. nov. is proposed. The type strain is YLCF04T (=CCTCC AB 2022359T= KCTC 92789T).
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Affiliation(s)
- Yiran Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - John Quensen
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Bo Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Hailong Li
- Xi'an Environmental Monitoring Station, Xi'an, Shaanxi, 710119, PR China
| | - James Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Wei Sun
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Xun Qian
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling,Shaanxi, 712100, PR China
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Mu W, Liu H, Guo B, Wang K, Hu J, Song J, Li X, Wei S, Liu A, Liu H. Paracoccus benzoatiresistens sp. nov., a benzoate resistance and selenite reduction bacterium isolated from wetland. Antonie Van Leeuwenhoek 2024; 117:81. [PMID: 38777900 DOI: 10.1007/s10482-024-01969-7] [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: 02/10/2024] [Accepted: 04/13/2024] [Indexed: 05/25/2024]
Abstract
A Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive, pale orange, rod-shaped strain EF6T, was isolated from a natural wetland reserve in Hebei province, China. The strain grew at 25-37 °C (optimum, 30 °C), pH 5-9 (optimum, pH 7), and in the presence of 1.0-4.0% (w/v) NaCl (optimum, 2%). A phylogenetic analysis based on 16S rRNA gene sequence revealed that strain EF6T belongs to the genus Paracoccus, and the closest members were Paracoccus shandongensis wg2T with 98.1% similarity, Paracoccus fontiphilus MVW-1 T (97.9%), Paracoccus everestensis S8-55 T (97.7%), Paracoccus subflavus GY0581T (97.6%), Paracoccus sediminis CMB17T (97.3%), Paracoccus caeni MJ17T (97.0%), and Paracoccus angustae E6T (97.0%). The genome size of strain EF6T was 4.88 Mb, and the DNA G + C content was 65.3%. The digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between strain EF6T and the reference strains were all below the threshold limit for species delineation (< 32.8%, < 88.0%, and < 86.7%, respectively). The major fatty acids (≥ 5.0%) were summed feature 8 (86.3%, C18:1 ω6c and/or C18:1 ω7c) and C18:1 (5.0%) and the only isoprenoid quinone was Q-10. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids, five unidentified phospholipids, and an unidentified aminolipid. Strain EF6T displays notable resistance to benzoate and selenite, with higher tolerance levels (25 g/L for benzoate and 150 mM for selenite) compared to the closely related species. Genomic analysis identified six benzoate resistance genes (acdA, pcaF, fadA, pcaC, purB, and catA) and twenty selenite resistance and reduction-related genes (iscR, ssuB, ssuD, selA, selD and so on). Additionally, EF6T possesses unique genes (catA, ssuB, and ssuC) absent in the closely related species for benzoate and selenite resistance. Its robust resistance to benzoate and selenite, coupled with its genomic makeup, make EF6T a promising candidate for the remediation of both organic and inorganic pollutants. It is worth noting that the specific resistance phenotypes described above were not reported in other novel species in Paracoccus. Based on the results of biochemical, physiological, phylogenetic, and chemotaxonomic analyses, combined with comparisons of the 16S rRNA gene sequence and the whole genome sequence, strain EF6T is considered to represent a novel species of the genus Paracoccus within the family Rhodobacteraceae, for which the name Paracoccus benzoatiresistens sp. nov. is proposed. The type strain is EF6T (= GDMCC 1.3400 T = JCM 35642 T = MCCC 1K08702T).
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Affiliation(s)
- Weidong Mu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Haoran Liu
- College of Life Sciences, Shandong Agricultural University, Taian, 271018, People's Republic of China
| | - Bai Guo
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Kaiyue Wang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Jinhua Hu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Jianjun Song
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Xiuyun Li
- Shandong Provincial Maternal and Child Health Care Hospital, Jinan, 250014, People's Republic of China
| | - Shuzhen Wei
- Center for Wetland Conservation and Research, Hengshui University, Hengshui, 053000, People's Republic of China.
- Collaborative Innovation Center for Wetland Conservation and Green Development of Hebei Province, Hengshui, 053000, People's Republic of China.
- Hebei Key Laboratory of Wetland Ecology and Conservation, Hengshui, 053000, People's Republic of China.
| | - Aijv Liu
- Collaborative Innovation Center for Wetland Conservation and Green Development of Hebei Province, Hengshui, 053000, People's Republic of China
- School of Resources and Environmental Engineering, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Hongliang Liu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China.
- Collaborative Innovation Center for Wetland Conservation and Green Development of Hebei Province, Hengshui, 053000, People's Republic of China.
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Kim M, Cha IT, Lee KE, Park SJ. Chryseobacterium gotjawalense sp. nov. Isolated from Soil in the Volcanic Forest Gotjawal, Jeju Island. Curr Microbiol 2024; 81:187. [PMID: 38777886 DOI: 10.1007/s00284-024-03711-y] [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: 12/18/2023] [Accepted: 04/21/2024] [Indexed: 05/25/2024]
Abstract
Strain wdc7T, a rod-shaped bacterium, was isolated from soil in the Gotjawal Forest on Jeju Island, South Korea. Strain wdc7T was Gram stain-negative, facultatively anaerobic, catalase- and oxidase positive, yellow pigmented, and non-flagellated. It grew at 4-37 °C and pH 5.0-8.0 in 0-3% (w/v) NaCl. 16S rRNA gene sequencing analysis revealed that strain wdc7T belonged to the genus Chryseobacterium and was most closely related to Chryseobacterium salivictor NBC 122T, with a sequence similarity of 98.51%. Menaquinone 6 was the sole respiratory quinone, and C15:0 anteiso, C15:0 iso, and summed feature 9 were the major fatty acids. The genome length was 3.30 Mbp, with a 37% G + C content. Average amino acid identity, average nucleotide identity, and digital DNA-DNA relatedness between strain wdc7T and C. salivictor NBC 122T were 93.52%, 92.80%, and 49.7%, respectively. Digital genomic and polyphasic analyses showed that strain wdc7T likely represented a new species of the genus Chryseobacterium. We proposed the name Chryseobacterium gotjawalense sp. nov., with wdc7T (= KCTC 92440T = JCM 35602T) as the type strain.
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Affiliation(s)
- Minji Kim
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, South Korea
| | - In-Tae Cha
- Climate Change and Environmental Biology Research Division, National Institute of Biological Resource, Incheon, 22689, South Korea
| | - Ki-Eun Lee
- Species Diversity Research Division, National Institute of Biological Resource, Incheon, 22689, South Korea
| | - Soo-Je Park
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, South Korea.
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Zhang L, Lin TY, Liu WT, Ling F. Toward Characterizing Environmental Sources of Non-tuberculous Mycobacteria (NTM) at the Species Level: A Tutorial Review of NTM Phylogeny and Phylogenetic Classification. ACS ENVIRONMENTAL AU 2024; 4:127-141. [PMID: 38765059 PMCID: PMC11100324 DOI: 10.1021/acsenvironau.3c00074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 05/21/2024]
Abstract
Nontuberculous mycobacteria (NTM) are any mycobacteria that do not cause tuberculosis or leprosy. While the majority of NTM are harmless and some of them are considered probiotic, a growing number of people are being diagnosed with NTM infections. Therefore, their detection in the environment is of interest to clinicians, environmental microbiologists, and water quality researchers alike. This review provides a tutorial on the foundational approaches for taxonomic classifications, with a focus on the phylogenetic relationships among NTM revealed by the 16S rRNA gene, rpoB gene, and hsp65 gene, and by genome-based approaches. Recent updates on the Mycobacterium genus taxonomy are also provided. A synthesis on the habitats of 189 mycobacterial species in a genome-based taxonomy framework was performed, with attention paid to environmental sources (e.g., drinking water, aquatic environments, and soil). The 16S rRNA gene-based classification accuracy for various regions was evaluated (V3, V3-V4, V3-V5, V4, V4-V5, and V1-V9), revealing overall excellent genus-level classification (up to 100% accuracy) yet only modest performance (up to 63.5% accuracy) at the species level. Future research quantifying NTM species in water systems, determining the effects of water treatment and plumbing conditions on their variations, developing high throughput species-level characterization tools for use in the environment, and incorporating the characterization of functions in a phylogenetic framework will likely fill critical knowledge gaps. We believe this tutorial will be useful for researchers new to the field of molecular or genome-based taxonomic profiling of environmental microbiomes. Experts may also find this review useful in terms of the selected key findings of the past 30 years, recent updates on phylogenomic analyses, as well as a synthesis of the ecology of NTM in a phylogenetic framework.
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Affiliation(s)
- Lin Zhang
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tzu-Yu Lin
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Wen-Tso Liu
- Department
of Civil and Environmental Engineering, University of Illinois, Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Fangqiong Ling
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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23
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Goris T, Braune A. Genomics and physiology of Catenibacillus, human gut bacteria capable of polyphenol C-deglycosylation and flavonoid degradation. Microb Genom 2024; 10:001245. [PMID: 38785231 PMCID: PMC11170127 DOI: 10.1099/mgen.0.001245] [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: 10/30/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024] Open
Abstract
The genus Catenibacillus (family Lachnospiraceae, phylum Bacillota) includes only one cultivated species so far, Catenibacillus scindens, isolated from human faeces and capable of deglycosylating dietary polyphenols and degrading flavonoid aglycones. Another human intestinal Catenibacillus strain not taxonomically resolved at that time was recently genome-sequenced. We analysed the genome of this novel isolate, designated Catenibacillus decagia, and showed its ability to deglycosylate C-coupled flavone and xanthone glucosides and O-coupled flavonoid glycosides. Most of the resulting aglycones were further degraded to the corresponding phenolic acids. Including the recently sequenced genome of C. scindens and ten faecal metagenome-assembled genomes assigned to the genus Catenibacillus, we performed a comparative genome analysis and searched for genes encoding potential C-glycosidases and other polyphenol-converting enzymes. According to genome data and physiological characterization, the core metabolism of Catenibacillus strains is based on a fermentative lifestyle with butyrate production and hydrogen evolution. Both C. scindens and C. decagia encode a flavonoid O-glycosidase, a flavone reductase, a flavanone/flavanonol-cleaving reductase and a phloretin hydrolase. Several gene clusters encode enzymes similar to those of the flavonoid C-deglycosylation system of Dorea strain PUE (DgpBC), while separately located genes encode putative polyphenol-glucoside oxidases (DgpA) required for C-deglycosylation. The diversity of dgpA and dgpBC gene clusters might explain the broad C-glycoside substrate spectrum of C. scindens and C. decagia. The other Catenibacillus genomes encode only a few potential flavonoid-converting enzymes. Our results indicate that several Catenibacillus species are well-equipped to deglycosylate and degrade dietary plant polyphenols and might inhabit a corresponding, specific niche in the gut.
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Affiliation(s)
- Tobias Goris
- Research Group Intestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany
| | - Annett Braune
- Research Group Intestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany
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24
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Sorokin DY, Elcheninov AG, Bale NJ, Sininghe Damsté J, Kublanov IV. Natronosalvus hydrolyticus sp. nov., a beta-1,3-glucan utilizing natronoarchaeon from hypersaline soda lakes. Syst Appl Microbiol 2024; 47:126514. [PMID: 38735274 DOI: 10.1016/j.syapm.2024.126514] [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: 03/05/2024] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024]
Abstract
Use of curldlan, an insoluble β-1,3-glucan, as an enrichment substrate under aerobic conditions resulted in the selection from hypersaline soda lakes of a single natronarchaeon, strain AArc-curdl1. This organism is an obligately aerobic saccharolytic, possessing a poorly explored (in Archaea) potential to utilize beta-1-3 glucans, being only a second example of a haloarchaeon with this ability known in pure culture. The main phenotypic property of the isolate is the ability to grow with insoluble β-1,3-backboned glucans, i.e. curdlan and pachyman. Furthermore, the strain utilized starch family α-glucans, beta-fructan inulin and a limited spectrum of sugars. The major ether-bound membrane polar phospholipids included PGP-Me and PG. The glyco- and sulfolipids were absent. The major respiratory menaquinone is MK-8:8. According to phylogenomic analysis, AArc-curdl1 represents a separate species in the recently described genus Natronosalvus within the family Natrialbaceae. The closest related species is Natronosalvus amylolyticus (ANI, AAI and DDH values of 90.2, 91.6 and 44 %, respectively). On the basis of its unique physiological properties and phylogenomic distance, strain AArc-curdl1T is classified as a novel species Natronosalvus hydrolyticus sp. nov. (=JCM 34865 = UQM 41566).
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia; Department of Biotechnology, Delft University of Technology, Delft, the Netherlands.
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nicole J Bale
- NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Texel, the Netherlands
| | - Jaap Sininghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Texel, the Netherlands
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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Kim S, Heo J, Choi H, Lee D, Kwon SW, Kim Y. Sphingobacterium oryzagri sp. nov., isolated from rice paddy soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 38713185 DOI: 10.1099/ijsem.0.006371] [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: 05/08/2024] Open
Abstract
An aerobic, Gram-stain-negative and short rod-shaped bacterial strain, designated M6-31T, was isolated from rice paddy soil sampled in Miryang, Republic of Korea. Growth was observed at 4-35 °C (optimum, 28 °C), pH 6.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 0-4 % (w/v) NaCl (optimum, 0 % w/v). Phylogenetic analysis based on 16S rRNA gene sequences grouped strain M6-31T with Sphingobacterium bambusae IBFC2009T, Sphingobacterium griseoflavum SCU-B140T and Sphingobacterium solani MLS-26-JM13-11T in the same clade, with the 16S rRNA gene sequence similarities ranging from 95.8 to 96.6 %. A genome-based phylogenetic tree reconstructed by using all publicly available Sphingobacterium genomes placed strain M6-31T with S. bambusae KACC 22910T, 'Sphingobacterium deserti' ACCC 05744T, S. griseoflavum CGMCC 1.12966T and Sphingobacterium paludis CGMCC 1.12801T. Orthologous average nucleotide identity and digital DNA-DNA hybridization values between strain M6-31T and its closely related strains were lower than 74.6 and 22.0 %, respectively. The respiratory quinone was menaquinone-7, and the major polar lipid was phosphatidylethanolamine. The major fatty acids (>10 %) were C15 : 0 iso, C17 : 0 iso 3OH and summed feature 3. The phenotypic, chemotaxonomic and genotypic data obtained in this study showed that strain M6-31T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium oryzagri sp. nov. (type strain M6-31T=KACC 22765T=JCM 35893T) is proposed.
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Affiliation(s)
- Seunghwan Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Hyorim Choi
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
- Department of Biotechnology, Jeonbuk National University, Iksan 55496, Republic of Korea
| | - Daseul Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Yiseul Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
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St John E, Reysenbach AL. Genomic comparison of deep-sea hydrothermal genera related to Aeropyrum, Thermodiscus and Caldisphaera, and proposed emended description of the family Acidilobaceae. Syst Appl Microbiol 2024; 47:126507. [PMID: 38703419 DOI: 10.1016/j.syapm.2024.126507] [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: 12/15/2023] [Revised: 03/02/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024]
Abstract
Deep-sea hydrothermal vents host archaeal and bacterial thermophilic communities, including taxonomically and functionally diverse Thermoproteota. Despite their prevalence in high-temperature submarine communities, Thermoproteota are chronically under-represented in genomic databases and issues have emerged regarding their nomenclature, particularly within the Aeropyrum-Thermodiscus-Caldisphaera. To resolve some of these problems, we identified 47 metagenome-assembled genomes (MAGs) within this clade, from 20 previously published deep-sea hydrothermal vent and submarine volcano metagenomes, and 24 MAGs from public databases. Using phylogenomic analysis, Genome Taxonomy Database Toolkit (GTDB-Tk) taxonomic assessment, 16S rRNA gene phylogeny, average amino acid identity (AAI) and functional gene patterns, we re-evaluated of the taxonomy of the Aeropyrum-Thermodiscus-Caldisphaera. At least nine genus-level clades were identified with two or more MAGs. In accordance with SeqCode requirements and recommendations, we propose names for three novel genera, viz. Tiamatella incendiivivens, Hestiella acidicharens and Calypsonella navitae. A fourth genus was also identified related to Thermodiscus maritimus, for which no available sequenced genome exists. We propose the novel species Thermodiscus eudorianus to describe our high-quality Thermodiscus MAG, which represents the type genome for the genus. All three novel genera and T. eudorianus are likely anaerobic heterotrophs, capable of fermenting protein-rich carbon sources, while some Tiamatella, Calypsonella and T. eudorianus may also reduce polysulfides, thiosulfate, sulfur and/or selenite, and the likely acidophile, Hestiella, may reduce nitrate and/or perchlorate. Based on phylogenomic evidence, we also propose the family Acidilobaceae be amended to include Caldisphaera, Aeropyrum, Thermodiscus and Stetteria and the novel genera described here.
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Affiliation(s)
- Emily St John
- Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA.
| | - Anna-Louise Reysenbach
- Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA.
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27
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Choi H, Choi Y, Kim S, Kim Y, Naito H, Yamada T, Hamada M, Kim N, Lee Y, Heo J. Microbacterium horticulturae sp. nov., a novel actinobacterium isolated from flowerpot soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 38743475 DOI: 10.1099/ijsem.0.006384] [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
Strain CJN36-1NT, a Gram-stain-positive, non-flagellated, strictly aerobic and short rod-shaped bacterium, was isolated from flowerpot soil sampled in the Jeonju region of the Republic of Korea. Based on 16S rRNA gene sequences and the resulting phylogenetic tree, the strain belonged to the genus Microbacterium. Strain CJN36-1NT contained a chromosome of 3.6 Mbp with a G+C content of 68.5 mol%. The strain grew at 10-37 °C (optimally at 28 °C), at pH 5.0-8.0 (optimally at pH 8.0), and in the presence of 0-7 % NaCl (w/v; optimally with 0 % NaCl). Digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values between strain CJN36-1NT and its closest related species, Microbacterium protaetiae DFW100M-13T, were 82.0, 81.2, and 23.2 %, respectively. We propose naming this novel species Microbacterium horticulturae sp. nov., with CJN36-1NT (=KACC 23027T=NBRC 116065T) as the type strain.
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Affiliation(s)
- Hyorim Choi
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
- Division of Biotechnology, Jeonbuk National University, Jeollabuk-do, Republic of Korea
| | - Yunhee Choi
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Seunghwan Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Yiseul Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Hanako Naito
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomomi Yamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriyuki Hamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - NamJung Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Yonghoon Lee
- Division of Biotechnology, Jeonbuk National University, Jeollabuk-do, Republic of Korea
| | - Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
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Li Y, Guo T, Sun L, Wang ET, Young JPW, Tian CF. Phylogenomic analyses and reclassification of the Mesorhizobium complex: proposal for 9 novel genera and reclassification of 15 species. BMC Genomics 2024; 25:419. [PMID: 38684951 PMCID: PMC11057113 DOI: 10.1186/s12864-024-10333-y] [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: 01/31/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUD The genus Mesorhizobium is shown by phylogenomics to be paraphyletic and forms part of a complex that includes the genera Aminobacter, Aquamicrobium, Pseudaminobacter and Tianweitania. The relationships for type strains belong to these genera need to be carefully re-evaluated. RESULTS The relationships of Mesorhizobium complex are evaluated based on phylogenomic analyses and overall genome relatedness indices (OGRIs) of 61 type strains. According to the maximum likelihood phylogenetic tree based on concatenated sequences of 539 core proteins and the tree constructed using the bac120 bacterial marker set from Genome Taxonomy Database, 65 type strains were grouped into 9 clusters. Moreover, 10 subclusters were identified based on the OGRIs including average nucleotide identity (ANI), average amino acid identity (AAI) and core-proteome average amino acid identity (cAAI), with AAI and cAAI showing a clear intra- and inter-(sub)cluster gaps of 77.40-80.91% and 83.98-86.16%, respectively. Combined with the phylogenetic trees and OGRIs, the type strains were reclassified into 15 genera. This list includes five defined genera Mesorhizobium, Aquamicrobium, Pseudaminobacter, Aminobacterand Tianweitania, among which 40/41 Mesorhizobium species and one Aminobacter species are canonical legume microsymbionts. The other nine (sub)clusters are classified as novel genera. Cluster III, comprising symbiotic M. alhagi and M. camelthorni, is classified as Allomesorhizobium gen. nov. Cluster VI harbored a single symbiotic species M. albiziae and is classified as Neomesorhizobium gen. nov. The remaining seven non-symbiotic members were proposed as: Neoaquamicrobium gen. nov., Manganibacter gen. nov., Ollibium gen. nov., Terribium gen. nov., Kumtagia gen. nov., Borborobacter gen. nov., Aerobium gen. nov.. Furthermore, the genus Corticibacterium is restored and two species in Subcluster IX-1 are reclassified as the member of this genus. CONCLUSION The Mesorhizobium complex are classified into 15 genera based on phylogenomic analyses and OGRIs of 65 type strains. This study resolved previously non-monophyletic genera in the Mesorhizobium complex.
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Affiliation(s)
- Yan Li
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Jiaodong Microbial Resource Center of Yantai University, College of Life Sciences, Yantai University, Yantai, 264005, Shandong, China.
| | - Tingyan Guo
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Jiaodong Microbial Resource Center of Yantai University, College of Life Sciences, Yantai University, Yantai, 264005, Shandong, China
| | - Liqin Sun
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Jiaodong Microbial Resource Center of Yantai University, College of Life Sciences, Yantai University, Yantai, 264005, Shandong, China
| | - En-Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, 11340, México
| | - J Peter W Young
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Chang-Fu Tian
- State Key Laboratory of Plant Environmental Resilience, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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Khomyakova MA, Merkel AY, Novikov AA, Slobodkin AI. Peloplasma aerotolerans gen. nov., sp. nov., a Novel Anaerobic Free-Living Mollicute Isolated from a Terrestrial Mud Volcano. Life (Basel) 2024; 14:563. [PMID: 38792585 PMCID: PMC11122141 DOI: 10.3390/life14050563] [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: 03/27/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
A novel aerotolerant anaerobic bacterium (strain M4AhT) was isolated from a terrestrial mud volcano (Taman Peninsula, Russia). Cells were small, cell-wall-less, non-motile cocci, 0.32-0.65 μm in diameter. The isolate was a mesophilic, neutrophilic chemoorganoheterotroph, growing on carbohydrates (D-glucose, D-trehalose, D-ribose, D-mannose, D-xylose, D-maltose, D-lactose, D-cellobiose, D-galactose, D-fructose, and D-sucrose), proteinaceous compounds (yeast extract, tryptone), and pyruvate. Strain M4AhT tolerated 2% oxygen in the gas phase, was catalase-positive, and showed sustainable growth under microaerobic conditions. The dominant cellular fatty acids of strain M4AhT were C16:0 and C18:0. The G+C content of the genomic DNA was 32.42%. The closest phylogenetic relative of strain M4AhT was Mariniplasma anaerobium from the family Acholeplasmataceae (order Acholeplasmatales, class Mollicutes). Based on the polyphasic characterization of the isolate, strain M4AhT is considered to represent a novel species of a new genus, for which the name Peloplasma aerotolerans gen. nov., sp. nov. is proposed. The type strain of Peloplasma aerotolerans is M4AhT (=DSM 112561T = VKM B-3485T = UQM 41475T). This is the first representative of the order Acholeplasmatales, isolated from a mud volcano.
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Affiliation(s)
- Maria A. Khomyakova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071 Moscow, Russia
| | - Alexander Y. Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071 Moscow, Russia
| | - Andrei A. Novikov
- Department of Physical and Colloid Chemistry, Gubkin University, Leninskiy Prospect, 65/1, 119991 Moscow, Russia
| | - Alexander I. Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071 Moscow, Russia
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Serra Moncadas L, Hofer C, Bulzu PA, Pernthaler J, Andrei AS. Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis. Nat Commun 2024; 15:3421. [PMID: 38653968 PMCID: PMC11039613 DOI: 10.1038/s41467-024-47767-7] [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: 07/18/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
The emergence of bacterial species is rooted in their inherent potential for continuous evolution and adaptation to an ever-changing ecological landscape. The adaptive capacity of most species frequently resides within the repertoire of genes encoding the secreted proteome (SP), as it serves as a primary interface used to regulate survival/reproduction strategies. Here, by applying evolutionary genomics approaches to metagenomics data, we show that abundant freshwater bacteria exhibit biphasic adaptation states linked to the eco-evolutionary processes governing their genome sizes. While species with average to large genomes adhere to the dominant paradigm of evolution through niche adaptation by reducing the evolutionary pressure on their SPs (via the augmentation of functionally redundant genes that buffer mutational fitness loss) and increasing the phylogenetic distance of recombination events, most of the genome-reduced species exhibit a nonconforming state. In contrast, their SPs reflect a combination of low functional redundancy and high selection pressure, resulting in significantly higher levels of conservation and invariance. Our findings indicate that although niche adaptation is the principal mechanism driving speciation, freshwater genome-reduced bacteria often experience extended periods of adaptive stasis. Understanding the adaptive state of microbial species will lead to a better comprehension of their spatiotemporal dynamics, biogeography, and resilience to global change.
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Affiliation(s)
- Lucas Serra Moncadas
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Cyrill Hofer
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Paul-Adrian Bulzu
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Adrian-Stefan Andrei
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland.
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Hassani Y, Aboudharam G, Drancourt M, Grine G. The discovery of Candidatus Nanopusillus phoceensis sheds light on the diversity of the microbiota nanoarchaea. iScience 2024; 27:109488. [PMID: 38595798 PMCID: PMC11001627 DOI: 10.1016/j.isci.2024.109488] [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: 08/11/2023] [Revised: 12/11/2023] [Accepted: 03/08/2024] [Indexed: 04/11/2024] Open
Abstract
To further assess the spectrum of nanoarchaea in human microbiota, we prospectively searched for nanoarchaea in 110 leftover stool specimens, using the complementary approaches of PCR-sequencing screening, fluorescent in situ hybridization, scanning electron microscopy and metagenomics. These investigations yielded a nanoarchaea, Candidatus Nanopusillus phoceensis sp. nov., detected in stool samples by specific PCR-based assays. Microscopic observations indicated its close contact with the archaea Methanobrevibacter smithii. Genomic sequencing revealed 607,775-bp contig with 24.5% G + C content encoding 30 tRNAs, 3 rRNA genes, and 1,403 coding DNA sequences, of which 719 were assigned to clusters of orthologous groups. Ca. Nanopusillus phoceensis is only the second nanoarchaea to be detected in humans, expanding our knowledge of the repertoire of nanoarchaea associated with the human microbiota and encouraging further research to explore the repertoire of this emerging group of nanomicrobes in clinical samples.
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Affiliation(s)
- Yasmine Hassani
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Gerard Aboudharam
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France
- Ecole de Médecine Dentaire, Aix-Marseille Université, 13005 Marseille, France
| | - Michel Drancourt
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Ghiles Grine
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France
- Ecole de Médecine Dentaire, Aix-Marseille Université, 13005 Marseille, France
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Bao R, Guo H, Liang Y, Tang K, Feng F, Meng J. Terrihabitans rhizophilus sp. nov., isolated from the rhizosphere soil of plant in temperate semi-arid steppe. Antonie Van Leeuwenhoek 2024; 117:67. [PMID: 38607451 DOI: 10.1007/s10482-024-01966-w] [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: 01/11/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
A bacterial strain PJ23T was isolated from the rhizosphere soil of Elymus dahuricus Turcz. sampled from a temperate semi-arid steppe in the northern of Inner Mongolia Autonomous Region, China. The strain is Gram-stain-negative, aerobic, light-pink, short rod-shaped, and non-spore-forming. Cell growth could be observed at 4-29℃ (optimal at 24℃), pH 6.0-8.6 (optimal at 8.0) and in the presence of 0-5.0% (w/v) NaCl (optimal at 2.5%). The major cellular fatty acids of strain PJ23T were Summed feature 8 (C18:1 ω6c and/or C18:1 ω7c) (39.42%) and C16:0 (9.60%). The polar lipids were phosphatidylcholine, two unidentified glycolipids, one unidentified aminophospholipid, and two other unidentified polar lipids. The major respiratory quinone was ubiquinone-10. Phylogeny analysis based on 16S rRNA gene sequences retrieved from the genomes showed that, the strain was closely related to the species Terrihabitans soli IZ6T and Flaviflagellibacter deserti SYSU D60017T, with the sequence similarities of 96.79% and 96.15%, respectively. The G + C content was 65.23 mol% calculated on draft genome sequencing. Between the strains PJ23T and Terrihabitans soli IZ6T, the average nucleotide identity (ANI), amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) was 73.39%,71.12% and 15.7%, these values were lower than the proposed and generally accepted species boundaries of ANI, AAI and dDDH, respectively. Based on phenotypic, chemotaxonomic, and phylogenetic characteristics, strain PJ23T represents a novel species of Terrihabitans, for which the name Terrihabitans rhizophilus sp. nov. is proposed. The type strain is PJ23T (= KCTC 92977 T = CGMCC 1.61577 T).
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Affiliation(s)
- Runze Bao
- Laboratory of Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Science, Inner Mongolia Agricultural University, Huhhot, 010018, PR, China
| | - Huiling Guo
- Laboratory of Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Science, Inner Mongolia Agricultural University, Huhhot, 010018, PR, China
| | - Yungang Liang
- Laboratory of Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Science, Inner Mongolia Agricultural University, Huhhot, 010018, PR, China
| | - Kai Tang
- Laboratory of Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Science, Inner Mongolia Agricultural University, Huhhot, 010018, PR, China
| | - Fuying Feng
- Laboratory of Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Science, Inner Mongolia Agricultural University, Huhhot, 010018, PR, China
| | - Jianyu Meng
- Laboratory of Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Science, Inner Mongolia Agricultural University, Huhhot, 010018, PR, China.
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Garry M, Farasin J, Drevillon L, Quaiser A, Bouchez C, Le Borgne T, Coffinet S, Dufresne A. Ferriphaselus amnicola strain GF-20, a new iron- and thiosulfate-oxidizing bacterium isolated from a hard rock aquifer. FEMS Microbiol Ecol 2024; 100:fiae047. [PMID: 38573825 PMCID: PMC11044966 DOI: 10.1093/femsec/fiae047] [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: 11/01/2023] [Revised: 02/18/2024] [Accepted: 04/03/2024] [Indexed: 04/06/2024] Open
Abstract
Ferriphaselus amnicola GF-20 is the first Fe-oxidizing bacterium isolated from the continental subsurface. It was isolated from groundwater circulating at 20 m depth in the fractured-rock catchment observatory of Guidel-Ploemeur (France). Strain GF-20 is a neutrophilic, iron- and thiosulfate-oxidizer and grows autotrophically. The strain shows a preference for low oxygen concentrations, which suggests an adaptation to the limiting oxygen conditions of the subsurface. It produces extracellular stalks and dreads when grown with Fe(II) but does not secrete any structure when grown with thiosulfate. Phylogenetic analyses and genome comparisons revealed that strain GF-20 is affiliated with the species F. amnicola and is strikingly similar to F. amnicola strain OYT1, which was isolated from a groundwater seep in Japan. Based on the phenotypic and phylogenetic characteristics, we propose that GF-20 represents a new strain within the species F. amnicola.
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Affiliation(s)
- Mélissa Garry
- Géosciences Rennes, CNRS, Univ Rennes, UMR 6118, Rennes, France
- OSUR, Univ Rennes, UMS 3343, Rennes, France
| | | | - Laetitia Drevillon
- Ecobio—Ecosystèmes, Biodiversité, Evolution, CNRS, Univ Rennes, UMR 6553, Rennes, France
| | - Achim Quaiser
- Ecobio—Ecosystèmes, Biodiversité, Evolution, CNRS, Univ Rennes, UMR 6553, Rennes, France
| | - Camille Bouchez
- Géosciences Rennes, CNRS, Univ Rennes, UMR 6118, Rennes, France
| | | | - Sarah Coffinet
- Ecobio—Ecosystèmes, Biodiversité, Evolution, CNRS, Univ Rennes, UMR 6553, Rennes, France
| | - Alexis Dufresne
- Ecobio—Ecosystèmes, Biodiversité, Evolution, CNRS, Univ Rennes, UMR 6553, Rennes, France
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Lu H, Chen L, Huang L. Arcicella gelida sp. nov. and Arcicella lustrica sp. nov., isolated from streams in China and re-examining the taxonomic status of all the genera within the families Spirosomataceae and Cytophagaceae. Int J Syst Evol Microbiol 2024; 74. [PMID: 38629951 DOI: 10.1099/ijsem.0.006345] [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
Three Gram-stain-negative, aerobic, rod-shaped, non-motile strains (DC2WT, DC25WT, and LKC2W) were isolated from streams in China. Comparisons based on the 16S rRNA gene sequences showed that these three strains share 16S rRNA gene sequence similarity values over 97.0 % with the species of genus Arcicella. There was confusion due to the fact that all species of genera Flectobacillus, Aquirufa, and Sandaracinomonas show 16S rRNA gene sequence similarity of over 90.0 % to the above three strains, but the genus Flectobacillus belongs to the family Spirosomataceae and the genera Aquirufa and Sandaracinomonas belong to the family Cytophagaceae. Observing the phylogenetic trees, strains DC2WT, DC25WT, and LKC2W cluster closely with the species of genus Arcicella, but some species within the families Spirosomataceae and Cytophagaceae are not monophyletic. The phylogenomic tree also showed a confused phylogenetic relationships among these non-monophyletic species. Combining the phylogenetic relationships and average nucleotide identity values, the current taxonomic status of all the genera within the families Spirosomataceae and Cytophagaceae were re-examined. The genera 'Chryseosolibacter', 'Dawidia', and Chryseotalea should belong to the new family Chryseotaleaceae fam. nov., the genera Arcicella, Flectobacillus, Pseudarcicella, Aquirufa, and Sandaracinomonas should belong to the new family Flectobacillaceae fam. nov., the genera Fluviimonas, Taeseokella, Arcticibacterium, Emticicia, Jiulongibacter, Marinilongibacter, Lacihabitans, and Leadbetterella should belong to the new family Leadbetterellaceae fam. nov., the genus Litoribacter should be reassigned to the family Cyclobacteriaceae, and the genera Arundinibacter and Tellurirhabdus should be reassigned to the family Spirosomataceae. Strains DC2WT and DC25WT are reported to represent two novel species of the genus Arcicella, for which the names Arcicella gelida sp. nov. (type strain DC2WT=GDMCC 1.3209T=KCTC 92559T) and Arcicella lustrica sp. nov. (type strain DC25WT=GDMCC 1.3210T=KCTC 92557T) are proposed.
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Affiliation(s)
- Huibin Lu
- Yunnan Key Laboratory of Plateau Geographical Process and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, PR China
| | - Li Chen
- Yunnan Key Laboratory of Plateau Geographical Process and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, PR China
| | - Linpei Huang
- Yunnan Key Laboratory of Plateau Geographical Process and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, PR China
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He W, Wang HC, Wang L, Xue HP, Li YF, Zhang AH, Zhang DF. Ruegeria marisflavi sp. nov. and Ruegeria aquimaris sp. nov., isolated from seawater of the Yellow Sea. Int J Syst Evol Microbiol 2024; 74. [PMID: 38568051 DOI: 10.1099/ijsem.0.006323] [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: 04/05/2024] Open
Abstract
Two novel Gram-stain-negative, aerobic, non-motile and rod-shaped bacteria, designated as WL0004T and XHP0148T, were isolated from seawater samples collected from the coastal areas of Nantong and Lianyungang, PR China, respectively. Both strains were found to grow at 10-42 °C (optimum, 37 °C) and with 2.0-5.0 % (w/v) NaCl (optimum, 3.0 %). Strain WL0004T grew at pH 6.0-9.0 (optimum, pH 7.0-8.0), while XHP0148T grew at pH 6.0-10.0 (optimum, pH 7.0-8.0). The major cellular fatty acids (>10 %) of both strains included summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). In addition, strain WL0004T contained 11-methyl C18 : 1 ω7c and strain XHP0148T contained C12 : 0 3-OH. The respiratory quinone of both strains was ubiquinone-10. The G+C content of genomic DNA of strains WL0004T and XHP0148T were 62.5 and 63.0 mol%, respectively. Strains WL0004T and XHP0148T showed the highest 16S rRNA gene sequence similarity to Ruegeria pomeroyi DSS-3T (99.4 and 99.0 %, respectively), and the 16S rRNA gene-based phylogenetic analysis indicated that the two strains were closely related to members of the genus Ruegeria. The average nucleotide identity and digital DNA-DNA hybridization values among the two strains and type strains of the genus Ruegeria were all below 95 and 70 %, respectively, and the phylogenetic tree reconstructed from the bac120 gene set indicated that the two strains are distinct from each other and the members of the genus Ruegeria. Based on this phenotypic and genotypic characterization, strains WL0004T (=MCCC 1K07523T=JCM 35565T=GDMCC 1.3083T) and XHP0148T (=MCCC 1K07543T=JCM 35569T=GDMCC 1.3089T) should be recognized as representing two novel species of the genus Ruegeria and the names Ruegeria marisflavi sp. nov. and Ruegeria aquimaris sp. nov. are proposed, respectively.
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Affiliation(s)
- Wei He
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, PR China
| | - Hong-Chuan Wang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, PR China
| | - Lu Wang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, PR China
| | - Hua-Peng Xue
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, PR China
| | - Yong-Fu Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, PR China
| | - Ai Hua Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, PR China
| | - Dao-Feng Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, PR China
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Park Y, Min J, Kim W, Park W. Kaistella rhinocerotis sp. nov., isolated from the faeces of rhinoceros and reclassification of Chryseobacterium faecale as Kaistella faecalis comb. nov. Int J Syst Evol Microbiol 2024; 74. [PMID: 38602466 DOI: 10.1099/ijsem.0.006338] [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: 04/12/2024] Open
Abstract
Strain Ran72T, a novel Gram-stain-negative, obligately aerobic, non-motile, and rod-shaped bacterium, was isolated from the faeces of the rhinoceros species Ceratotherium simum. The novel bacterial strain grew optimally in Reasoner's 2A medium under the following conditions: 0 % (w/v) NaCl, pH 7.5, and 30 °C. Based on phylogenetic analysis using 16S rRNA gene sequencing, strain Ran72T was found to be most closely related to Chryseobacterium faecale F4T (98.4 %), Kaistella soli DKR-2T (98.0 %), and Kaistella haifensis H38T (97.4 %). A comprehensive genome-level comparison between strain Ran72T with C. faecale F4T, K. soli DKR-2T, and K. haifensis H38T revealed average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values of ≤74.9, ≤19.3, and ≤78.7 %, respectively. The major fatty acids were anteiso-C15 : 0 (22.3 %), with MK-6 being the predominant respiratory quinone. The major polar lipids of strain Ran72T were phosphatidylethanolamine, four unidentified aminolipids, and two unidentified lipids. Based on our chemotaxonomic, genotypic, and phenotype characterizations, strain Ran72T was identified as representing a novel species in the genus Kaistella, for which the name Kaistella rhinocerotis sp. nov. is proposed, with the type strain Ran72T (=KACC 23136T=JCM 36038T). Based on the outcomes of our phylogenomic study, Chryseobacterium faecale should be reclassified under the genus Kaistella as Kaistella faecalis comb. nov.
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Affiliation(s)
- Yerim Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Jihyeon Min
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Wonjae Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
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Lee HJ, Whang KS. Falsiroseomonas oryziterrae sp. nov., and Falsiroseomonas oryzae sp. nov., isolated from rice paddy soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 38634861 DOI: 10.1099/ijsem.0.006349] [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
Three Gram-stain-negative, aerobic, non-motile and coccobacilli-shaped bacterial strains, designated as NPKOSM-4T, NPKOSM-8 and MO-31T, were isolated from rice paddy soil. They had 96.5-100 % 16S rRNA gene sequence similarity to each other, and strains NPKOSM-4T and NPKOSM-8 showed 100 % 16S rRNA gene sequence similarity, confirming that they were the same species. Comparative analysis of 16S rRNA genes with closely related type strains showed that three isolates were most closely related to Falsiroseomonas terricola EM0302T (96.1-97.8 %), Falsiroseomonas wooponensis WW53T (95.51-96.3 %) and Falsiroseomonas bella CQN31T (96.0-96.5 %), respectively. The genomes of strains NPKOSM-4T and MO-31T consisted of 4 632 875 and 6 455 771 bps, respectively, with 72.0 and 72.1 mol% G+C content. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between strains NPKOSM-4T and MO-31T and type strains of Falsiroseomonas species were lower than the cut-offs (≥95 % for ANI, ≥95-96 % for AAI and ≥ 70 % for dDDH) required to define a bacterial species. The major fatty acids of strains NPKOSM-4T, NPKOSM-8 and MO-31T were C18 : 1 ω7c and C18 : 1 2-OH (<10 %) and the predominant quinone was Q-10. The polar lipids of strain NPKOSM-4T were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified aminophospholipid and three unidentified aminolipids. The polar lipid profiles of strain MO-31T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified aminolipid and three unidentified lipids. Based on their distinctive phenotypic, phylogenetic, and chemotaxonomic characteristics, strains NPKOSM-4T, NPKOSM-8 and MO-31T are considered to represent two novel species of the genus Falsiroseomonas, for which the names Falsiroseomonas oryziterrae sp. nov. [to accommodate strains NPKOSM-4T (= KACC 22135T=JCM 34745T), NPKOSM-8 (=KACC 22134=JCM 34746)] and Falsiroseomonas oryzae sp. nov. [to accommodate strain MO-31T (= KACC 22465T=JCM 35532T)] are proposed.
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Affiliation(s)
- Hyo-Jin Lee
- Institute of Microbial Ecology & Resources, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
- Department of Microbial Biotechnology, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
| | - Kyung-Sook Whang
- Institute of Microbial Ecology & Resources, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
- Department of Microbial Biotechnology, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
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Jung JY, Lee MH, Nam YH, Kang HK, Jeon JH, Kim JS, Kim EJ. Paucibacter sediminis sp. nov., isolated from sediment in a freshwater pond. Int J Syst Evol Microbiol 2024; 74. [PMID: 38656473 DOI: 10.1099/ijsem.0.006312] [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: 04/26/2024] Open
Abstract
A Gram-stain-negative, aerobic, oxidase-positive, weakly catalase-positive, motile by means of a single polar flagellum, rod-shaped bacterium designated as strain S2-9T was isolated from sediment sampled in Wiyang pond, Republic of Korea. Growth of this strain was observed at 10-40 °C (optimum, 35 °C) and pH 5.5-9.5 (optimum, pH 7.0-8.0) and in the presence of 0-0.5 % NaCl in Reasoner's 2A broth. The major fatty acids (>10 %) of strain S2-9T were C16 : 0 and summed feature 3 (comprising a mixture of C16 : 1 ω7c and/or C16 : 1 ω6c). Ubiquinone-8 was detected as the respiratory quinone. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Strain S2-9T showed the highest 16S rRNA gene sequence similarity to Paucibacter oligotrophus CHU3T (98.7 %), followed by 'Paucibacter aquatile' CR182 (98.4 %), all type strains of Pelomonas species (98.1-98.3 %), Mitsuaria chitosanitabida NBRC 102408T (97.9 %), Kinneretia asaccharophila KIN192T (97.8 %), Mitsuaria chitinivorans HWN-4T (97.4 %), and Paucibacter toxinivorans 2C20T (97.4 %). Phylogenetic trees based on the 16S rRNA gene and whole-genome sequences showed that strain S2-9T formed a tight phylogenetic lineage with Paucibacter species (CHU3T, CR182, and 2C20T). Average nucleotide identity and digital DNA-DNA hybridization values between strain S2-9T and Paucibacter strains were 76.6-79.3% and 19.5-21.5 %, respectively. The genomic DNA G+C content of strain S2-9T was 68.3 mol%. Notably, genes responsible for both sulphur oxidation and reduction and denitrification were found in the genome of strain S2-9T, suggesting that strain S2-9T is involved in the nitrogen and sulphur cycles in pond ecosystems. Based on the polyphasic taxonomic results, strain S2-9T represents a novel species of the genus Paucibacter, for which the name Paucibacter sediminis sp. nov. is proposed. The type strain is S2-9T (= KACC 22267T= JCM 34541T).
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Affiliation(s)
- Ji Young Jung
- Biological Resources Research Department, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do 37242, Republic of Korea
| | - Mi Hwa Lee
- Diversity Conservation Research Department, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do 37242, Republic of Korea
| | - Young Ho Nam
- Using Technology Development Department, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do 37242, Republic of Korea
| | - Hye-Kyeong Kang
- Biological Resources Research Department, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do 37242, Republic of Korea
| | - Ju Hyung Jeon
- Biological Resources Research Department, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do 37242, Republic of Korea
| | - Jun Sung Kim
- Biological Resources Research Department, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do 37242, Republic of Korea
| | - Eui Jin Kim
- Using Technology Development Department, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do 37242, Republic of Korea
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Zhang WL, Lai MC, Lin S, Chen WC, Deng YC, Lai SJ, Wu SY, Hung CC, Ding JY, Chen SC. Methanooceanicella nereidis gen. nov., sp. nov., the first oceanic Methanocellaceae methanogen, isolated from potential methane hydrate bearing area offshore southwestern Taiwan. Int J Syst Evol Microbiol 2024; 74. [PMID: 38634834 DOI: 10.1099/ijsem.0.006322] [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
A novel mesophilic, hydrogenotrophic methanogen, strain CWC-04T, was obtained from a sediment sample extracted from a gravity core retrieved at station 22 within the KP-9 area off the southwestern coast of Taiwan during the ORIII-1368 cruise in 2009. Cells of strain CWC-04T were rod-shaped, 1.4-2.9 µm long by 0.5-0.6 µm wide, and occurred singly. Strain CWC-04Tutilized formate, H2/CO2, 2-propanol/CO2 or 2-butanol/CO2 as catabolic substrates. The optimal growth conditions were 42 °C, 0.17 M NaCl and pH 5.35. The genomic DNA G+C content calculated from the genome sequence of strain CWC-04T was 46.19 mol%. Phylogenetic analysis of 16S rRNA gene revealed that strain CWC-04T is affiliated with the genus Methanocella. The 16S rRNA gene sequences similarities within strains Methanocella arvoryzae MRE50T, Methanocella paludicola SANAET and Methanocella conradii HZ254T were 93.7, 93.0 and 91.3 %, respectively. In addition, the optical density of CWC-04T culture dropped abruptly upon entering the late-log growth phase, with virus-like particles (150 nm in diameter) being observed on and around the cells. This observation suggests that strain CWC-04T harbours a lytic virus. Based on these phenotypic, phylogenetic and genomic results, we propose that strain CWC-04T represents a novel species of a novel genus in the family Methanocellaceae, for which the name Methanooceanicella nereidis gen. nov., sp. nov. is proposed. The type strain is CWC-04T (=BCRC AR10050T=NBRC 113165T).
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Affiliation(s)
- Wei-Ling Zhang
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Saulwood Lin
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan, ROC
| | - Wen-Chieh Chen
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Yu-Chen Deng
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Shu-Jung Lai
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung City, Taiwan, ROC
- Research Center for Cancer Biology, China Medical University, Taichung City, Taiwan, ROC
| | - Sue-Yao Wu
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Chuan-Chuan Hung
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Jiun-Yan Ding
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Sheng-Chung Chen
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, PR China
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming, Fujian, PR China
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Williams TJ, Allen MA, Ray AE, Benaud N, Chelliah DS, Albanese D, Donati C, Selbmann L, Coleine C, Ferrari BC. Novel endolithic bacteria of phylum Chloroflexota reveal a myriad of potential survival strategies in the Antarctic desert. Appl Environ Microbiol 2024; 90:e0226423. [PMID: 38372512 PMCID: PMC10952385 DOI: 10.1128/aem.02264-23] [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: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 02/20/2024] Open
Abstract
The ice-free McMurdo Dry Valleys of Antarctica are dominated by nutrient-poor mineral soil and rocky outcrops. The principal habitat for microorganisms is within rocks (endolithic). In this environment, microorganisms are provided with protection against sub-zero temperatures, rapid thermal fluctuations, extreme dryness, and ultraviolet and solar radiation. Endolithic communities include lichen, algae, fungi, and a diverse array of bacteria. Chloroflexota is among the most abundant bacterial phyla present in these communities. Among the Chloroflexota are four novel classes of bacteria, here named Candidatus Spiritibacteria class. nov. (=UBA5177), Candidatus Martimicrobia class. nov. (=UBA4733), Candidatus Tarhunnaeia class. nov. (=UBA6077), and Candidatus Uliximicrobia class. nov. (=UBA2235). We retrieved 17 high-quality metagenome-assembled genomes (MAGs) that represent these four classes. Based on genome predictions, all these bacteria are inferred to be aerobic heterotrophs that encode enzymes for the catabolism of diverse sugars. These and other organic substrates are likely derived from lichen, algae, and fungi, as metabolites (including photosynthate), cell wall components, and extracellular matrix components. The majority of MAGs encode the capacity for trace gas oxidation using high-affinity uptake hydrogenases, which could provide energy and metabolic water required for survival and persistence. Furthermore, some MAGs encode the capacity to couple the energy generated from H2 and CO oxidation to support carbon fixation (atmospheric chemosynthesis). All encode mechanisms for the detoxification and efflux of heavy metals. Certain MAGs encode features that indicate possible interactions with other organisms, such as Tc-type toxin complexes, hemolysins, and macroglobulins.IMPORTANCEThe ice-free McMurdo Dry Valleys of Antarctica are the coldest and most hyperarid desert on Earth. It is, therefore, the closest analog to the surface of the planet Mars. Bacteria and other microorganisms survive by inhabiting airspaces within rocks (endolithic). We identify four novel classes of phylum Chloroflexota, and, based on interrogation of 17 metagenome-assembled genomes, we predict specific metabolic and physiological adaptations that facilitate the survival of these bacteria in this harsh environment-including oxidation of trace gases and the utilization of nutrients (including sugars) derived from lichen, algae, and fungi. We propose that such adaptations allow these endolithic bacteria to eke out an existence in this cold and extremely dry habitat.
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Affiliation(s)
- Timothy J. Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Michelle A. Allen
- School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Angelique E. Ray
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Nicole Benaud
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Devan S. Chelliah
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Davide Albanese
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Claudio Donati
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università, Viterbo, Italy
- Mycological Section, Italian Antarctic National Museum (MNA), Genova, Italy
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università, Viterbo, Italy
| | - Belinda C. Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
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Lee HJ, Hwang JS, Lee EK, Whang KS. Erythrobacter oryzae sp. nov., isolated from rice paddy soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 38441415 DOI: 10.1099/ijsem.0.006287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
Two novel bacterial strains, designated as COR-2T and CR-8, were isolated from paddy soil. These isolates were aerobic, Gram-stain-negative, non-spore-forming, non-motile, rod-shaped, and formed orange-coloured colonies. Phylogenetic analysis based on 16S rRNA gene sequences showed that two strains formed a clear phylogenetic lineage with the genus Erythrobacter. Strains COR-2T and CR-8 showed 99.9 % 16S rRNA gene sequence similarity. Both strains had the highest 16S rRNA gene similarity of 99.1-99.7 % to Erythrobacter colymbi TPW-24T, Erythrobacter donghaensis SW-132T and Erythrobacter tepidarius DSM 10594T, respectively. The genome of strain COR-2T comprised 3 559 918 bp and the genomic DNA G + C content was 67.7 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain COR-2T and its closely related species of the genus Erythrobacter were 79.3-85.5% and 24.1-29.1 %, respectively. The major respiratory quinone was Q-10, while the major fatty acids were C18 : 1 ω7c and C17 : 1 ω6c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two unidentified phospholipids and eight unidentified lipids. Based on phylogenetic and phenotypic considerations, the two strains [COR-2T (type strain; = KACC 22941T=JCM 35529T) and CR-8 (= KACC 22945=JCM 35530)] are considered to represent novel species of the genus Erythrobacter, for which the name Erythrobacter oryzae sp. nov. is proposed.
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Affiliation(s)
- Hyo-Jin Lee
- Institute of Microbial Ecology & Resources, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
- Department of Microbial Biotechnology, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
| | - Ji-Soo Hwang
- Institute of Microbial Ecology & Resources, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
| | - Eun-Kyung Lee
- Institute of Microbial Ecology & Resources, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
- Department of Microbial Biotechnology, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
| | - Kyung-Sook Whang
- Institute of Microbial Ecology & Resources, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
- Department of Microbial Biotechnology, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
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Emsley SA, Loughran RM, Shlafstein MD, Pfannmuller KM, De La Flor YT, Lein CG, Dove NC, Koyack MJ, Oline DK, Hanson TE, Videau P, Saw JH, Ushijima B. Fluctibacter corallii gen. nov., sp. nov., isolated from the coral Montipora capitata on a reef in Kāne'ohe Bay, O'ahu, Hawai'i, reclassification of Aestuariibacter halophilus as Fluctibacter halophilus comb. nov., and Paraglaciecola oceanifecundans as a later heterotypic synonym of Paraglaciecola agarilytica. Antonie Van Leeuwenhoek 2024; 117:45. [PMID: 38424217 DOI: 10.1007/s10482-024-01934-4] [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: 12/31/2023] [Accepted: 01/25/2024] [Indexed: 03/02/2024]
Abstract
Strain AA17T was isolated from an apparently healthy fragment of Montipora capitata coral from the reef surrounding Moku o Lo'e in Kāne'ohe Bay, O'ahu, Hawai'i, USA, and was taxonomically evaluated using a polyphasic approach. Comparison of a partial 16S rRNA gene sequence found that strain AA17T shared the greatest similarity with Aestuariibacter halophilus JC2043T (96.6%), and phylogenies based on 16S rRNA gene sequences grouped strain AA17T with members of the Aliiglaciecola, Aestuariibacter, Lacimicrobium, Marisediminitalea, Planctobacterium, and Saliniradius genera. To more precisely infer the taxonomy of strain AA17T, a phylogenomic analysis was conducted and indicated that strain AA17T formed a monophyletic clade with A. halophilus JC2043T, divergent from Aestuariibacter salexigens JC2042T and other related genera. As a result of monophyly and multiple genomic metrics of genus demarcation, strain AA17T and A. halophilus JC2043T comprise a distinct genus for which the name Fluctibacter gen. nov. is proposed. Based on a polyphasic characterisation and identifying differences in genomic and taxonomic data, strain AA17T represents a novel species, for which the name Fluctibacter corallii sp. nov. is proposed. The type strain is AA17T (= LMG 32603 T = NCTC 14664T). This work also supports the reclassification of A. halophilus as Fluctibacter halophilus comb. nov., which is the type species of the Fluctibacter genus. Genomic analyses also support the reclassification of Paraglaciecola oceanifecundans as a later heterotypic synonym of Paraglaciecola agarilytica.
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Affiliation(s)
- Sarah A Emsley
- Department of Biology, Southern Oregon University, Ashland, OR, USA
| | - Rachel M Loughran
- Microbiology Graduate Program, University of Delaware, Newark, DE, USA
| | | | | | - Yesmarie T De La Flor
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | | | | | - Marc J Koyack
- School of Arts and Sciences, Gwynedd Mercy University, Gwynedd Valley, PA, USA
| | - David K Oline
- Department of Biology, Southern Oregon University, Ashland, OR, USA
| | - Thomas E Hanson
- Microbiology Graduate Program, University of Delaware, Newark, DE, USA
- School of Marine Science and Policy and Delaware Biotechnology Institute, University of Delaware, Delaware, USA
| | - Patrick Videau
- Department of Biology, Southern Oregon University, Ashland, OR, USA
- AgBiome, Research Triangle Park, NC, USA
| | - Jimmy H Saw
- Department of Biological Sciences, The George Washington University, Washington, DC, USA.
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA.
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Victor MP, Kujur RRA, Das L, Das SK. Genome analysis deciphered Chryseobacterium indicum is a distinct species associated with freshwater pufferfish. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 118:105561. [PMID: 38280473 DOI: 10.1016/j.meegid.2024.105561] [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: 12/19/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 01/29/2024]
Abstract
A bacterium, strain PS-8T of the genus Chryseobacterium, was isolated from the skin of freshwater pufferfish (Tetraodon cutcutia). Strain PS-8T is a Gram-negative, aerobic, non-motile, and rod-shaped bacterium. Colonies appear in yellowish-orange colors. The major cellular fatty acids were C15:0 iso, C17:0 iso 3OH, C15:0 iso 3OH, and C11:0 anteiso. The predominant polar lipids were phosphatidylethanolamine and amino lipids. The genome size is 4.83 Mb. The G + C content was 35.6%. The in silico dDDH homology, ANI, and AAI were below the cutoff value, 70% and 95% to 96%, respectively, suggesting that strain PS-8T represents a defined species. The phylogenetic tree based on core and the non-recombinant genes showed the strain PS-8T clustered with Chryseobacterium gambrini DSM 18014T. Genome-wide analysis decodes several virulence factors of the genus Chryseobacterium, including genes for adherence, biofilm and stability, proliferation, resistance to immune response, and host-defense evasion system. The cladogram of the virulence genes showed a phylogenetic relationship among the Chryseobacterium species. Knowledge of the association of Chryseobacterium with freshwater pufferfish adds a new ecological niche to this bacterium.
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Affiliation(s)
- Manish Prakash Victor
- Institute of Life Sciences, Department of Biotechnology, Nalco Square, Bhubaneswar 751023, India
| | - Ritu Rani Archana Kujur
- Institute of Life Sciences, Department of Biotechnology, Nalco Square, Bhubaneswar 751023, India
| | - Lipika Das
- Institute of Life Sciences, Department of Biotechnology, Nalco Square, Bhubaneswar 751023, India
| | - Subrata K Das
- Institute of Life Sciences, Department of Biotechnology, Nalco Square, Bhubaneswar 751023, India.
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Choi H, Kim Y, Kim S, Kwon SW, Lee D, Han BH, Hong SB, Naito H, Yamada T, Hamada M, Heo J. Lacticaseibacillus pabuli sp. nov., isolated from fermented cattle feed. Int J Syst Evol Microbiol 2024; 74. [PMID: 38446021 DOI: 10.1099/ijsem.0.006277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
Strain BSF-3MT is a Gram-stain-positive, non-flagellated, facultative anaerobic and rod-shaped bacterium that was isolated from fermented feed collected at a cattle farm in the Daejeon region of the Republic of Korea. It was studied using polyphasic taxonomic methods. Using 16S rRNA gene sequences and the resulting phylogenetic tree, the strain was primarily identified as a member of the genus Lacticaseibacillus. Strain BSF-3MT contained a chromosome of 2.5 Mbp and a plasmid of 33.4 kbp. The G+C content of genomic DNA was 51.3 mol%. Strain BSF-3MT had the highest ortho-average nucleotide identity value of 73.7 % with Lacticaseibacillus songhuajiangensis 7-19T, its closest relative in the phylogenetic tree based on the 16S rRNA gene sequences and the phylogenomic tree based on up-to-date bacterial core genes. Based on the results of a polyphasic taxonomic study, strain BSF-3MT represents a novel species in the genus Lacticaseibacillus, for which the name Lacticaseibacillus pabuli sp. nov. is proposed. The type strain is BSF-3MT (=KACC 23028T=NBRC 116014T).
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Affiliation(s)
- Hyorim Choi
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
- Division of Biotechnology, Jeonbuk National University, Jeollabuk-do, Republic of Korea
| | - Yiseul Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Seunghwan Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Daseul Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Byeong-Hak Han
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Seung-Beom Hong
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Hanako Naito
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomomi Yamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriyuki Hamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
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León MJ, Sánchez-Porro C, de la Haba RR, Pfeiffer F, Dyall-Smith M, Oksanen HM, Ventosa A. Halobacterium hubeiense sp. nov., a haloarchaeal species isolated from a bore core drilled in Hubei Province, PR China. Int J Syst Evol Microbiol 2024; 74:006296. [PMID: 38512754 PMCID: PMC11004503 DOI: 10.1099/ijsem.0.006296] [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: 08/21/2023] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Eight colonies of live microbes were isolated from an extensively surface-sterilized halite sample which had been retrieved from a depth of 2000 m from a salt mine in the Qianjiang Depression, Hubei Province, PR China. The eight colonies, obtained after 4 weeks of incubation, were named JI20-1T-JI20-8 and JI20-1T was selected as the type strain. The strains have been previously described, including a genomic analysis based on the complete genome for strain JI20-1T and draft genomes for the other strains. In that study, the name Halobacterium hubeiense was suggested, based on the location of the drilling site. Previous phylogenomic analysis showed that strain JI20-1T is most closely related to the Permian isolate Halobacterium noricense from Alpine rock salt. The orthologous average nucleotide identity (orthoANI) and digital DNA-DNA hybridization (dDDH) percentages between the eight strains are 100-99.6 % and 99.8-96.4 %, respectively. The orthoANI and dDDH values of these strains with respect to the type strains of species of the genus Halobacterium are 89.9-78.2 % and 37.3-21.6 %, respectively, supporting their placement in a novel extremely halophilic archaeal species. The phylogenomic tree based on the comparison of sequences of 632 core-orthologous proteins confirmed the novel species status for these haloarchaea. The polar lipid profile includes phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, and sulfated galactosyl mannosyl galactosyl glucosyl diether, a profile compatible with that of Halobacterium noricense. Based on genomic, phenotypic, and chemotaxonomic characterization, we propose strain JI20-1T (=DSM 114402T = HAMBI 3616T) as the type strain of a novel species in the genus Halobacterium, with the name Halobacterium hubeiense sp. nov.
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Affiliation(s)
- María José León
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max-Planck-Institute of Biochemistry, Martinsried, Germany
- Biology II, Ulm University, 89069 Ulm, Germany
| | - Mike Dyall-Smith
- Computational Biology Group, Max-Planck-Institute of Biochemistry, Martinsried, Germany
- Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3052, Australia
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Whitman WB, Chuvochina M, Hedlund BP, Konstantinidis KT, Palmer M, Rodriguez‐R LM, Sutcliffe I, Wang F. Why and how to use the SeqCode. MLIFE 2024; 3:1-13. [PMID: 38827511 PMCID: PMC11139209 DOI: 10.1002/mlf2.12092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/16/2023] [Accepted: 11/01/2023] [Indexed: 06/04/2024]
Abstract
The SeqCode, formally called the Code of Nomenclature of Prokaryotes Described from Sequence Data, is a new code of nomenclature in which genome sequences are the nomenclatural types for the names of prokaryotic species. While similar to the International Code of Nomenclature of Prokaryotes (ICNP) in structure and rules of priority, it does not require the deposition of type strains in international culture collections. Thus, it allows for the formation of permanent names for uncultured prokaryotes whose nearly complete genome sequences have been obtained directly from environmental DNA as well as other prokaryotes that cannot be deposited in culture collections. Because the diversity of uncultured prokaryotes greatly exceeds that of readily culturable prokaryotes, the SeqCode is the only code suitable for naming the majority of prokaryotic species. The start date of the SeqCode was January 1, 2022, and the online Registry (https://seqco.de/) was created to ensure valid publication of names. The SeqCode recognizes all names validly published under the ICNP before 2022. After that date, names validly published under the SeqCode compete with ICNP names for priority. As a result, species can have only one name, either from the SeqCode or ICNP, enabling effective communication and the creation of unified taxonomies of uncultured and cultured prokaryotes. The SeqCode is administered by the SeqCode Committee, which is comprised of the SeqCode Community and elected administrative components. Anyone with an interest in the systematics of prokaryotes is encouraged to join the SeqCode Community and participate in the development of this resource.
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Affiliation(s)
| | - Maria Chuvochina
- School of Chemistry and Molecular Biosciences, Australian Centre for EcogenomicsThe University of QueenslandSt LuciaAustralia
| | | | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Marike Palmer
- Department of MicrobiologyUniversity of ManitobaWinnipegManitobaCanada
- School of Life SciencesUniversity of Nevada Las VegasLas VegasNevadaUSA
| | - Luis M. Rodriguez‐R
- Department of Microbiology and Digital Science Center (DiSC)University of InnsbruckInnsbruckAustria
| | - Iain Sutcliffe
- Faculty of Health & Life SciencesNorthumbria UniversityNewcastle upon TyneUK
| | - Fengping Wang
- School of Oceanography, International Center for Deep Life InvestigationShanghai Jiao Tong UniversityShanghaiChina
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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.
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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
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48
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Zhu L, Wang YC, Li LL, Huang XM, Zhu M, Gao X, Cai J. Psychromicrobium Xiongbiense sp. nov., an Actinobacterium Isolated from Forest Soil. Curr Microbiol 2024; 81:99. [PMID: 38372800 DOI: 10.1007/s00284-024-03629-5] [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: 06/14/2023] [Accepted: 01/30/2024] [Indexed: 02/20/2024]
Abstract
A novel Gram-stain-positive, oval-shaped, and non-flagellated bacterial strain YIM S02556T was isolated from forest soil in Xiongbi Town, Shizong County, Qujing City, Yunnan Province, southwestern China. The strain exhibited high pairwise 16 S rRNA gene sequence similarity with Psychromicrobium lacuslunae (97.3%) and Psychromicrobium silvestre (96.3%). Strain YIM S02556T exhibited an average nucleotide identity (ANI) of 72.5% with P. lacuslunae IHBB 11,108T and 72.8% ANI with P. silvestre AK 20-18T. The digital DNA-DNA hybridization (dDDH) value between strain YIM S02556T and P. lacuslunae IHBB 11,108T was 20.2%, while with P. silvestre AK 20-18T, the dDDH value was 20.8%. Strain YIM S02556T exhibited optimal growth at 28 °C, pH 7.0, without NaCl. Growth occurred within 10-37 ℃, pH 5.0-8.0, and in the presence of up to 5% w/v NaCl concentration. The genome size was 3.1 Mbp with 64.2% G + C content. The predominant menaquinone was MK-8(H4). The major cellular fatty acid was anteiso-C15:0. Based on the polyphasic analysis, strain YIM S02556T (= KCTC 49,805T = CCTCC AB2020166T) represents a novel Psychromicrobium species in which the name Psychromicrobium xiongbiense sp.nov. was proposed.
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Affiliation(s)
- Ling Zhu
- Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, Yunnan, 655011, People's Republic of China
| | - Yu-Chen Wang
- School of Chemistry Biology and Environment, Yuxi Normal University, Yuxi, Yunnan, 653100, People's Republic of China
| | - Le-Le Li
- Department of Medicine, Qujing Vocational and Technical College, Qujing, Yunnan, 655000, People's Republic of China
| | - Xian-Min Huang
- School of Agronomy and Life Sciences, Zhaotong University, Zhaotong, Yunnan, 657000, People's Republic of China
| | - Man Zhu
- Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, Yunnan, 655011, People's Republic of China
| | - Xiu Gao
- Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, Yunnan, 655011, People's Republic of China.
| | - Jian Cai
- Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, Yunnan, 655011, People's Republic of China.
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49
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Fatahi-Bafghi M. Genomic and phylogenomic analysis of Fusobacteriaceae family and proposal to reclassify Fusobacterium naviforme Jungano 1909 into a novel genus as Zandiella naviformis gen. nov., comb. nov. and reclassification of Fusobacterium necrophorum subsp. funduliforme as later heterotypic synonym of Fusobacterium necrophorum subsp. necrophorum and Fusobacterium equinum as later heterotypic synonym of Fusobacterium gonidiaformans. Antonie Van Leeuwenhoek 2024; 117:34. [PMID: 38347234 DOI: 10.1007/s10482-023-01921-1] [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: 06/18/2023] [Accepted: 12/14/2023] [Indexed: 02/15/2024]
Abstract
The family Fusobacteriaceae is a large family within the phylum Fusobacteriota. The reclassification of F. naviforme as Zandiella naviformis gen. nov., comb. nov. is proposed because of the separate and distinct phylogenetic situation on the basis of the results of 16S rRNA gene sequence analysis, the genetic and genomic differences from all other species and subspecies in the Fusobacteriaceae family. The type strain is ATCC 25832; CCUG 50052; NCTC 13121. In phylogenetic trees drawn using complete genome sequences and 16S rRNA gene sequences, F. necrophorum subsp. funduliforme and F. equinum were clades together with F. necrophorum subsp. necrophorum and F. gonidiaformans, respectively. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between themes exceeded the cut-off values for species delineation. Based on these results, F. necrophorum subsp. funduliforme and F. equinum should be reclassified as later heterotypic synonyms of F. necrophorum subsp. necrophorum and F. gonidiaformans, respectively.
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Affiliation(s)
- Mehdi Fatahi-Bafghi
- Research Center for Health Technology Assessment and Medical Informatics, School of Public Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
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50
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Xu Q, Liu B, Wan Y, Jiang X, Chen L, Mao D, Chen G, Cheng D, He J, Shen Q. Paenibacillus lacisoli sp. nov., a mesotrione-degrading strain isolated from lakeside soil. Antonie Van Leeuwenhoek 2024; 117:32. [PMID: 38329631 DOI: 10.1007/s10482-023-01925-x] [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: 09/13/2023] [Accepted: 12/27/2023] [Indexed: 02/09/2024]
Abstract
A Gram-stain-positive, facultatively anaerobic, rod-shaped bacterium, designated JX-17T, was isolated from a soil sample collected in Jiangxi Province, PR China. Growth was observed at 15-48 °C (optimum 37 °C), at pH 5.0-9.0 (optimum pH 7.0) and with 0-6.0% (w/v) NaCl (optimum 1.0%). Strain JX-17T could degrade approximately 50% of 50 mg/L mesotrione within 2 days of incubation, but could not use mesotrione as sole carbon source for growth. Strain JX-17T showed less than 95.3% 16S rRNA gene sequence similarity with type strains of the genus Paenibacillus. In the phylogenetic tree based on 16S rRNA gene and genome sequences, strain JX-17T formed a distinct lineage within the genus Paenibacillus. The ANI values between JX-17T and the most closely related type strains P. lentus CMG1240T and P. farraposensis UY79T were 70.1% and 71.4%, respectively, and the dDDH values between them were 19.0% and 23.3%, respectively. The major cellular fatty acids were anteiso-C15:0, iso-C16:0, anteiso-C17:0 and C16:0, the predominant respiratory quinone was MK-7, the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified glycolipid, an aminophospholipid and a phosphatidylinositol. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid, and the DNA G + C content was 50.1 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic characteristics, strain JX-17T represents a novel species within the genus Paenibacillus, for which the name Paenibacillus lacisoli sp. nov is proposed, with strain JX-17T (= GDMCC 1.3962T = KCTC 43568T) as the type strain.
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Affiliation(s)
- Qimiao Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Bin Liu
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, Jiangxi, China
| | - Yingying Wan
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, Jiangxi, China
| | - Xueting Jiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Le Chen
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210095, People's Republic of China
| | - Dongmei Mao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Gang Chen
- Anhui Neotec Co., Ltd., Huaibei, 235100, Anhui, People's Republic of China
| | - Dan Cheng
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China.
| | - Jian He
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Qirong Shen
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, 210095, Jiangsu, People's Republic of China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
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