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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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2
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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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3
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Lu DC, Wang FQ, Amann RI, Teeling H, Du ZJ. Epiphytic common core bacteria in the microbiomes of co-located green (Ulva), brown (Saccharina) and red (Grateloupia, Gelidium) macroalgae. MICROBIOME 2023; 11:126. [PMID: 37264413 PMCID: PMC10233909 DOI: 10.1186/s40168-023-01559-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/27/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Macroalgal epiphytic microbial communities constitute a rich resource for novel enzymes and compounds, but studies so far largely focused on tag-based microbial diversity analyses or limited metagenome sequencing of single macroalgal species. RESULTS We sampled epiphytic bacteria from specimens of Ulva sp. (green algae), Saccharina sp. (brown algae), Grateloupia sp. and Gelidium sp. (both red algae) together with seawater and sediment controls from a coastal reef in Weihai, China, during all seasons. Using 16S rRNA amplicon sequencing, we identified 14 core genera (consistently present on all macroalgae), and 14 dominant genera (consistently present on three of the macroalgae). Core genera represented ~ 0.7% of all genera, yet accounted for on average 51.1% of the bacterial abundances. Plate cultivation from all samples yielded 5,527 strains (macroalgae: 4,426) representing 1,235 species (685 potentially novel). Sequencing of selected strains yielded 820 non-redundant draft genomes (506 potentially novel), and sequencing of 23 sampled metagenomes yielded 1,619 metagenome-assembled genomes (MAGs), representing further 1,183 non-redundant genomes. 230 isolates and 153 genomes were obtained from the 28 core/dominant genera. We analyzed the genomic potential of phycosphere bacteria to degrade algal polysaccharides and to produce bioactive secondary metabolites. We predicted 4,451 polysaccharide utilization loci (PULs) and 8,810 biosynthetic gene clusters (BGCs). These were particularly prevalent in core/dominant genera. CONCLUSIONS Our metabolic annotations and analyses of MAGs and genomes provide new insights into novel species of phycosphere bacteria and their ecological niches for an improved understanding of the macroalgal phycosphere microbiome. Video Abstract.
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Affiliation(s)
- De-Chen Lu
- Marine College, Shandong University, No. 180, Wenhua Xilu, Weihai, Shandong Province 264209 China
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, 28359 Germany
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Feng-Qing Wang
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, 28359 Germany
| | - Rudolf I. Amann
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, 28359 Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, 28359 Germany
| | - Zong-Jun Du
- Marine College, Shandong University, No. 180, Wenhua Xilu, Weihai, Shandong Province 264209 China
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
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4
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Rosolen RR, Horta MAC, de Azevedo PHC, da Silva CC, Sforca DA, Goldman GH, de Souza AP. Whole-genome sequencing and comparative genomic analysis of potential biotechnological strains of Trichoderma harzianum, Trichoderma atroviride, and Trichoderma reesei. Mol Genet Genomics 2023; 298:735-754. [PMID: 37017807 DOI: 10.1007/s00438-023-02013-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/24/2023] [Indexed: 04/06/2023]
Abstract
Trichoderma atroviride and Trichoderma harzianum are widely used as commercial biocontrol agents against plant diseases. Recently, T. harzianum IOC-3844 (Th3844) and T. harzianum CBMAI-0179 (Th0179) demonstrated great potential in the enzymatic conversion of lignocellulose into fermentable sugars. Herein, we performed whole-genome sequencing and assembly of the Th3844 and Th0179 strains. To assess the genetic diversity within the genus Trichoderma, the results of both strains were compared with strains of T. atroviride CBMAI-00020 (Ta0020) and T. reesei CBMAI-0711 (Tr0711). The sequencing coverage value of all genomes evaluated in this study was higher than that of previously reported genomes for the same species of Trichoderma. The resulting assembly revealed total lengths of 40 Mb (Th3844), 39 Mb (Th0179), 36 Mb (Ta0020), and 32 Mb (Tr0711). A genome-wide phylogenetic analysis provided details on the relationships of the newly sequenced species with other Trichoderma species. Structural variants revealed genomic rearrangements among Th3844, Th0179, Ta0020, and Tr0711 relative to the T. reesei QM6a reference genome and showed the functional effects of such variants. In conclusion, the findings presented herein allow the visualization of genetic diversity in the evaluated strains and offer opportunities to explore such fungal genomes in future biotechnological and industrial applications.
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Affiliation(s)
- Rafaela Rossi Rosolen
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, SP, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, UNICAMP, Campinas, SP, Brazil
| | - Maria Augusta Crivelente Horta
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, SP, Brazil
- Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Paulo Henrique Campiteli de Azevedo
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, SP, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, UNICAMP, Campinas, SP, Brazil
| | - Carla Cristina da Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, SP, Brazil
| | - Danilo Augusto Sforca
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, SP, Brazil
| | - Gustavo Henrique Goldman
- Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, SP, Brazil.
- Department of Plant Biology, Institute of Biology, UNICAMP, Cidade Universitária Zeferino Vaz, Rua Monteiro Lobato, Campinas, SP, Brazil.
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5
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Complete Genome Sequence of Vulcanisaeta souniana Strain IC-059, a Hyperthermophilic Archaeon Isolated from Hot Spring Water in Japan. Microbiol Resour Announc 2023; 12:e0108022. [PMID: 36598242 PMCID: PMC9872577 DOI: 10.1128/mra.01080-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Vulcanisaeta souniana strain IC-059T (=JCM 11219T) is an anaerobic hyperthermophilic archaeon isolated from a Japanese hot spring field. Here, we report the complete genome sequence (2.43 Mbp) of this strain using a hybrid approach with Illumina short-read sequencing and Nanopore long-read sequencing.
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6
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Corynebacterium antarcticum sp. nov., Corynebacterium marambiense sp. nov., Corynebacterium meridianum sp. nov., and Corynebacterium pygosceleis sp. nov., isolated from Adélie penguins (Pygoscelis adeliae). Syst Appl Microbiol 2023; 46:126390. [PMID: 36566621 DOI: 10.1016/j.syapm.2022.126390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
A taxonomic study was conducted on 16 bacterial strains isolated from wild Adélie penguins (Pygoscelis adeliae) from Seymour (Marambio) Island and James Ross Island. An initial screening by repetitive sequence-based PCR fingerprinting divided the strains studied into four coherent groups. Phylogenetic analysis based on 16S rRNA gene sequences assigned all groups to the genus Corynebacterium and showed that Corynebacterium glyciniphilum and Corynebacterium terpenotabidum were the closest species with 16S rRNA gene sequence similarities between 95.4 % and 96.5 %. Further examination of the strains studied with ribotyping, MALDI-TOF mass spectrometry, comprehensive biotyping and calculation of average nucleotide identity and digital DNA-DNA hybridisation values confirmed the separation of the four groups from each other and from the other Corynebacterium species. Chemotaxonomically, the four strains P5828T, P5850T, P6136T, P7210T representing the studied groups were characterised by C16:0 and C18:1ω9c as the major fatty acids, by the presence of meso-diaminopimelic acid in the peptidoglycan, the presence of corynemycolic acids and a quinone system with the predominant menaquinone MK-9(H2). The results of this study show that the strains studied represent four new species of the genus Corynebacterium, for which the names Corynebacterium antarcticum sp. nov. (type strain P5850T = CCM 8835T = LMG 30620T), Corynebacterium marambiense sp. nov. (type strain P5828T = CCM 8864T = LMG 31626T), Corynebacterium meridianum sp. nov. (type strain P6136T = CCM 8863T = LMG 31628T) and Corynebacterium pygosceleis sp. nov. (type strain P7210T = CCM 8836T = LMG 30621T) are proposed.
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7
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Whitman WB, Chuvochina M, Hedlund BP, Hugenholtz P, Konstantinidis KT, Murray AE, Palmer M, Parks DH, Probst AJ, Reysenbach AL, Rodriguez-R LM, Rossello-Mora R, Sutcliffe I, Venter SN. Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type. Syst Appl Microbiol 2022; 45:126305. [PMID: 36049255 PMCID: PMC9489671 DOI: 10.1016/j.syapm.2022.126305] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 11/15/2022]
Abstract
Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.
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Affiliation(s)
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | | | - Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Donovan H Parks
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology and Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | | | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innrain 15 / 01-05, Innsbruck 6020, Austria
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (CSIC-UIB), Esporles, Illes Balears, Spain
| | - Iain Sutcliffe
- Faculty of Health & Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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8
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Phylogenomic Analyses and Molecular Signatures Elucidating the Evolutionary Relationships amongst the Chlorobia and Ignavibacteria Species: Robust Demarcation of Two Family-Level Clades within the Order Chlorobiales and Proposal for the Family Chloroherpetonaceae fam. nov. Microorganisms 2022; 10:microorganisms10071312. [PMID: 35889031 PMCID: PMC9318685 DOI: 10.3390/microorganisms10071312] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/23/2022] [Accepted: 06/25/2022] [Indexed: 02/04/2023] Open
Abstract
Evolutionary relationships amongst Chlorobia and Ignavibacteria species/strains were examined using phylogenomic and comparative analyses of genome sequences. In a phylogenomic tree based on 282 conserved proteins, the named Chlorobia species formed a monophyletic clade containing two distinct subclades. One clade, encompassing the genera Chlorobaculum, Chlorobium, Pelodictyon, and Prosthecochloris, corresponds to the family Chlorobiaceae, whereas another clade, harboring Chloroherpeton thalassium, Candidatus Thermochlorobacter aerophilum, Candidatus Thermochlorobacteriaceae bacterium GBChlB, and Chlorobium sp. 445, is now proposed as a new family (Chloroherpetonaceae fam. nov). In parallel, our comparative genomic analyses have identified 47 conserved signature indels (CSIs) in diverse proteins that are exclusively present in members of the class Chlorobia or its two families, providing reliable means for identification. Two known Ignavibacteria species in our phylogenomic tree are found to group within a larger clade containing several Candidatus species and uncultured Chlorobi strains. A CSI in the SecY protein is uniquely shared by the species/strains from this “larger Ignavibacteria clade”. Two additional CSIs, which are commonly shared by Chlorobia species and the “larger Ignavibacteria clade”, support a specific relationship between these two groups. The newly identified molecular markers provide novel tools for genetic and biochemical studies and identification of these organisms.
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9
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Švec P, Králová S, Staňková E, Holochová P, Sedlář K, Koudelková S, Krsek D, Grzesiak J, Šedo O, Váczi P, Urvashi, Gupta V, Sood U, Lal R, Korpole S, Sedláček I. Pedobacter fastidiosus sp. nov., isolated from glacial habitats of maritime Antarctica. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005309] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains P8930T and 478 were isolated from Antarctic glaciers located on James Ross Island and King George Island, respectively. They comprised Gram-stain-negative short rod-shaped cells forming pink pigmented colonies and exhibited identical 16S rRNA gene sequences and highly similar MALDI TOF mass spectra, and hence were assigned as representatives of the same species. Phylogenetic analysis based on 16S rRNA gene sequences assigned both isolates to the genus
Pedobacter
and showed
Pedobacter frigidisoli
and
Pedobacter terrae
to be their closest phylogenetic neighbours, with 97.4 and 97.2 % 16S rRNA gene sequence similarities, respectively. These low similarity values were below the threshold similarity value of 98.7%, confirming the delineation of a new bacterial species. Further genomic characterization included whole-genome sequencing accompanied by average nucleotide identity (ANI) and digital DNA–DNA hybridization calculations, and characterization of the genome features. The ANI values between P8930T and
P. frigidisoli
RP-3-11T and
P. terrae
DSM 17933T were 79.7 and 77.6 %, respectively, and the value between
P. frigidisoli
RP-3-11T and
P. terrae
DSM 17933T was 77.7 %, clearly demonstrating the phylogenetic distance and the novelty of strain P8930T. Further characterization included analysis of cellular fatty acids, quinones and polar lipids, and comprehensive biotyping. All the obtained results proved the separation of strains P8930T and 478 from the other validly named
Pedobacter
species, and confirmed that they represent a new species for which the name Pedobacter fastidiosus sp. nov. is proposed. The type strain is P8930T (=CCM 8938T=LMG 32098T).
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Affiliation(s)
- Pavel Švec
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavla Holochová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Karel Sedlář
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technická 12, 616 00 Brno, Czech Republic
| | - Sylva Koudelková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Daniel Krsek
- NRL for Diagnostic Electron Microscopy of Infectious Agents, The National Institute of Public Health, Šrobárova 49/48 100 00 Prague 10, Czech Republic
| | - Jakub Grzesiak
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Ondrej Šedo
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Peter Váczi
- Department of Experimental Biology, Division of Experimental Plant Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Urvashi
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160 036, India
| | - Vipin Gupta
- Ministry of Environment Forest & Climate Change, Integrated Regional Office, Dehradun, 248001, India
| | - Utkarsh Sood
- The Energy and Resources Institute, Lodhi Road New Delhi-110003, India
| | - Rup Lal
- The Energy and Resources Institute, Lodhi Road New Delhi-110003, India
| | - Suresh Korpole
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160 036, India
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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10
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Bello S, Rudra B, Gupta RS. Phylogenomic and comparative genomic analyses of Leuconostocaceae species: identification of molecular signatures specific for the genera Leuconostoc, Fructobacillus and Oenococcus and proposal for a novel genus Periweissella gen. nov. Int J Syst Evol Microbiol 2022; 72. [PMID: 35320068 PMCID: PMC9558574 DOI: 10.1099/ijsem.0.005284] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The genera Convivina, Fructobacillus, Leuconostoc, Oenococcus and Weissella, which formed the family Leuconostocaceae, have recently been merged within the family Lactobacillaceae. Using genome sequences for 47 of the 52 named species from these genera, we report here comprehensive phylogenomic and comparative analyses on protein sequences from these species using multiple approaches. In a phylogenomic tree based on concatenated sequences of 498 core proteins from these five genera, and in a 16S rRNA gene tree, members of the genera Fructobacillus, Leuconostoc and Oenococcus formed distinct strongly supported clades. In contrast, Weissella species grouped into two distinct unrelated clades designated as the ‘Weissella main clade’ and ‘Weissella clade 2’. The presence of these clades is also seen in a matrix of pairwise average amino acid identity based on core protein sequences. In parallel, comparative genomic studies on protein sequences from Leuconostocaceae genomes have identified 46 conserved signature indels (CSIs) in diverse proteins that are unique characteristics of the different observed species clades. Of these identified CSIs, five, five and 13 CSIs are uniquely present in members of the genera Fructobacillus, Leuconostoc and Oenococcus, respectively. We also report here six and five CSIs that are exclusively present in the species from the Weissella main clade and Weissella clade 2, respectively, providing independent evidence supporting their distinctness from each other. The remaining 12 identified CSIs are commonly shared by some or all of the species from the genera Convivina, Fructobacillus and Leuconostoc, clarifying their interrelationships. The identified CSIs provide novel and reliable means for the identification/circumscription of members of the genera Fructobacillus, Leuconostoc and Oenococcus as well as the two Weissella species clades in molecular terms. Based on the strong phylogenetic and molecular evidence presented here, we propose that the genus Weissella be limited to only the species from the Weissella main clade, whereas the species forming Weissella clade 2 should be transferred to a new genus Periweissella gen. nov.
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Affiliation(s)
- Sarah Bello
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| | - Bashudev Rudra
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
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11
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Constructing a Defined Starter for Multispecies Vinegar Fermentation via Evaluating the Vitality and Dominance of Functional Microbes in Autochthonous Starter. Appl Environ Microbiol 2021; 88:e0217521. [PMID: 34818103 DOI: 10.1128/aem.02175-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mature vinegar culture has usually been used as a type of autochthonous starter for rapidly initiate initiating the next batch of acetic acid fermentation (AAF) and maintaining the batch-to-batch uniformity of AAF in the production of traditional cereal vinegar. However, the vitality and dominance of functional microbes in autochthonous starters remain unclear, which hinders further improvement of fermentation yield and production. Here, based on metagenomic (MG), metatranscriptomic (MT), and 16S rRNA gene sequencings, 11 bacterial operational taxonomic units (OTUs) with significant metabolic activity (MT/MG ratio >1) and dominance (relative abundance >1%) were targeted in the autochthonous vinegar starter, all of which were assigned to 4 species (Acetobacter pasteurianus, Lactobacillus acetotolerans, L. helveticus, Acetilactobacillus jinshanensis). Then, we evaluated the successions and interactions of these 11 bacterial OTUs at different AAF stages. Last, a defined starter was constructed with 4 core species isolated from the autochthonous starter (A. pasteurianus, L. acetotolerans, L. helveticus, Ac. jinshanensis). The defined starter culture could rapidly initiate the AAF in a sterile or unsterilized environment and similar dynamics of metabolites (ethanol, titratable acidity, acetic acid, lactic acid, and volatile compounds) and environmental indexes (temperature, pH) of fermentation were observed as compared with that of autochthonous starter (P > 0.05). This work provides a method to construct a defined microbiota from a complex system while preserving its metabolic function. IMPORTANCE Complex microorganisms are beneficial to the flavor formation in natural food fermentation, but they also pose challenges to the mass production of standardized products. It is attractive to construct a defined starter to rapidly initiate fermentation process and significantly improve fermentation yield. This study provides a comprehensive understanding of vital and dominant species in the autochthonous vinegar starter via multi-omics, and designs a defined microbial community for the efficient fermentation of cereal vinegar.
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Yukphan P, Charoenyingcharoen P, Kingcha Y, Likhitrattanapisal S, Muangham S, Tanasupawat S, Yamada Y. Acetobacter garciniae sp. nov., an acetic acid bacterium isolated from fermented mangosteen peel in Thailand. Int J Syst Evol Microbiol 2021; 71. [PMID: 34662265 DOI: 10.1099/ijsem.0.005052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two isolates, MS16-SU-2T and MS18-SU-3, obtained from fermented mangosteen peel in vinegar were suggested to constitute a new species assignable to the genus Acetobacter based on the results of 16S rRNA gene sequencing. The two isolates showed the highest sequence similarity (98.58%) to Acetobacter tropicalis NBRC 16470T and Acetobacter senegalensis LMG 23690T. However, the calculated similarity values were lower than the threshold for species demarcation. The phylogenetic analysis showed that the branches of the two isolates were separated from other Acetobacter species, and the two isolates constituted a new species in the genus Acetobacter. The genomic DNA of isolate MS16-SU-2T was sequenced. The assembled genome of the isolate was analysed, and the results showed that the highest average nucleotide identity value of 75.9 % was with Acetobacter papayae JCM 25143T and the highest digital DNA-DNA hybridization value of 25.1 % was with Acetobacter fallax LMG 1636T, which were lower than the cutoff values for species delineation. The phylogenetic tree based on the genome sequences showed that the lineage of isolate MS16-SU-2T was most closely related to A. papayae JCM 25143T and Acetobacter suratthaniensis TBRC 1719T, but separated from the branches of these two species. In addition, the two isolates could be distinguished from the type strains of closely related species by their phenotypic characteristics and MALDI-TOF profiles. Therefore, the two isolates, MS16-SU-2T (=TBRC 12339T=LMG 32243T) and MS18-SU-3 (=TBRC 12305), can be assigned to an independent species within the genus Acetobacter, and the name of Acetobacter garciniae sp. nov. is proposed for the two isolates.
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Affiliation(s)
- Pattaraporn Yukphan
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | - Piyanat Charoenyingcharoen
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | - Yutthana Kingcha
- Food Biotechnology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | - Somsak Likhitrattanapisal
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | - Supattra Muangham
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand.,Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, 254 Phayathai Road, Wangmai, Pathumwan, Bangkok 10330, Thailand
| | - Yuzo Yamada
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand.,Japan International Cooperation Agency (JICA Senior Overseas Volunteer), Shibuya-ku, Tokyo 151-8558, Japan.,Laboratory of Applied Microbiology (Professor Emeritus), Department of Applied Biological Chemistry, Faculty of Agriculture, Shizuoka University, Suruga-ku, Shizuoka 422-8529, Japan
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Chen S, Rudra B, Gupta RS. Phylogenomics and molecular signatures support division of the order Neisseriales into emended families Neisseriaceae and Chromobacteriaceae and three new families Aquaspirillaceae fam. nov., Chitinibacteraceae fam. nov., and Leeiaceae fam. nov. Syst Appl Microbiol 2021; 44:126251. [PMID: 34600238 DOI: 10.1016/j.syapm.2021.126251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/22/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
The order Neisseriales contains 37 genera harboring 122 species with validly published names, which are placed into two families, Neisseriaceae and Chromobacteriaceae. Genome sequences are now available for 35 of the 37 Neisseriales genera for reliably determining their evolutionary relationships and taxonomy. We report here comprehensive phylogenomic and comparative analyses on protein sequences from 110 Neisseriales genomes plus 3 Chitinimonas genomes using multiple approaches. In a phylogenomic tree based on 596 core proteins, Neisseriales species formed 5 strongly supported clades. In addition to the clades for Neisseriaceae and Chromobacteriaceae families, three novel species clades designated as the "Chitinibacteraceae", "Aquaspirillaceae", and "Leeiaceae" were observed. The genus Chitinimonas grouped reliably with members of the "Chitinibacteraceae" clade. The major clades within the order Neisseriales can also be distinguished based on average amino acid identity analysis. In parallel, our comparative genomic studies have identified 30 conserved signature indels (CSIs) that are specific for members of the order Neisseriales or its five main clades. One of these CSIs is uniquely shared by all Neisseriales, whereas 8, 4, 9, 3 and 5 CSIs are distinctive characteristics of the Neisseriaceae, Chromobacteriaceae, "Chitinibacteraceae", "Aquaspirillaceae" and "Leeiaceae" clades, respectively. Based on the strong phylogenetic and molecular evidence presented here, we are proposing that the three newly identified clades should be recognized as novel families (Chitinibacteraceae fam. nov., Aquaspirillaceae fam. nov. and Leeiaceae fam. nov.) within the order Neisseriales. In addition, we are also emending descriptions of the families Neisseriaceae and Chromobacteriaceae regarding their constituent genera and other distinguishing characteristics.
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Affiliation(s)
- Shu Chen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Bashudev Rudra
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.
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Kajitani R, Yoshimura D, Ogura Y, Gotoh Y, Hayashi T, Itoh T. Platanus_B: an accurate de novo assembler for bacterial genomes using an iterative error-removal process. DNA Res 2021; 27:5870828. [PMID: 32658266 PMCID: PMC7433917 DOI: 10.1093/dnares/dsaa014] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/07/2020] [Indexed: 11/14/2022] Open
Abstract
De novo assembly of short DNA reads remains an essential technology, especially for large-scale projects and high-resolution variant analyses in epidemiology. However, the existing tools often lack sufficient accuracy required to compare closely related strains. To facilitate such studies on bacterial genomes, we developed Platanus_B, a de novo assembler that employs iterations of multiple error-removal algorithms. The benchmarks demonstrated the superior accuracy and high contiguity of Platanus_B, in addition to its ability to enhance the hybrid assembly of both short and nanopore long reads. Although the hybrid strategies for short and long reads were effective in achieving near full-length genomes, we found that short-read-only assemblies generated with Platanus_B were sufficient to obtain ≥90% of exact coding sequences in most cases. In addition, while nanopore long-read-only assemblies lacked fine-scale accuracies, inclusion of short reads was effective in improving the accuracies. Platanus_B can, therefore, be used for comprehensive genomic surveillances of bacterial pathogens and high-resolution phylogenomic analyses of a wide range of bacteria.
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Affiliation(s)
- Rei Kajitani
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Dai Yoshimura
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan.,Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
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15
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Shi W, Sun Q, Fan G, Hideaki S, Moriya O, Itoh T, Zhou Y, Cai M, Kim SG, Lee JS, Sedlacek I, Arahal DR, Lucena T, Kawasaki H, Evtushenko L, Weir BS, Alexander S, Dénes D, Tanasupawat S, Eurwilaichitr L, Ingsriswang S, Gomez-Gil B, Hazbón MH, Riojas MA, Suwannachart C, Yao S, Vandamme P, Peng F, Chen Z, Liu D, Sun X, Zhang X, Zhou Y, Meng Z, Wu L, Ma J. gcType: a high-quality type strain genome database for microbial phylogenetic and functional research. Nucleic Acids Res 2021; 49:D694-D705. [PMID: 33119759 PMCID: PMC7778895 DOI: 10.1093/nar/gkaa957] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/06/2020] [Accepted: 10/28/2020] [Indexed: 02/07/2023] Open
Abstract
Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data and methods. As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced by the GCM 10K project which are preserved in global culture collections with a valid published status. Additionally, the information provided through gcType includes >12 000 publicly available type strain genome sequences from GenBank incorporated using quality control criteria and standard data annotation pipelines to form a high-quality reference database. This database integrates type strain sequences with their phenotypic information to facilitate phenotypic and genotypic analyses. Multiple formats of cross-genome searches and interactive interfaces have allowed extensive exploration of the database's resources. In this study, we describe web-based data analysis pipelines for genomic analyses and genome-based taxonomy, which could serve as a one-stop platform for the identification of prokaryotic species. The number of type strain genomes that are published will continue to increase as the GCM 10K project increases its collaboration with culture collections worldwide. Data of this project is shared with the International Nucleotide Sequence Database Collaboration. Access to gcType is free at http://gctype.wdcm.org/.
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Affiliation(s)
- Wenyu Shi
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,World Data Center for Microorganisms, Beijing 100101, China
| | - Qinglan Sun
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,World Data Center for Microorganisms, Beijing 100101, China.,China-Thailand Joint Laboratory on Microbial Biotechnology, Beijing 100190, China
| | - Guomei Fan
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,World Data Center for Microorganisms, Beijing 100101, China
| | | | - Ohkuma Moriya
- Japan Collection of Microorganisms (JCM)/ Microbe Divion, RIKEN BioResource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms (JCM)/ Microbe Divion, RIKEN BioResource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan
| | - Yuguang Zhou
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Man Cai
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Song-Gun Kim
- Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Ivo Sedlacek
- Czech Collection of Microorganisms, Masaryk University, Kamenice 5, building A25, 625 00 Brno, Czech Republic
| | - David R Arahal
- Colección Española de Cultivos Tipo (CECT), and Departamento de Microbiología y Ecología, University of Valencia, 46100 Burjassot (Valencia), Spain
| | - Teresa Lucena
- Colección Española de Cultivos Tipo (CECT), and Departamento de Microbiología y Ecología, University of Valencia, 46100 Burjassot (Valencia), Spain
| | - Hiroko Kawasaki
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Lyudmila Evtushenko
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow region 142290, Russia
| | - Bevan S Weir
- Mycology & Bacteriology Systematics, Manaaki Whenua - Landcare Research, Auckland, New Zealand
| | - Sarah Alexander
- National Collection of Type Cultures (NCTC), Public Health England (PHE), UK
| | - Dlauchy Dénes
- National Collection of Agricultural and Industrial Microorganisms, Faculty of Food Science, Szent István University, H-1118, Budapest, Somlói út 14-16, Hungary
| | - Somboon Tanasupawat
- Faculty of Pharmaceutical Sciences, Chulalongkorn University (PCU), Bangkok 10330, Thailand
| | - Lily Eurwilaichitr
- China-Thailand Joint Laboratory on Microbial Biotechnology, Beijing 100190, China.,Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand
| | - Supawadee Ingsriswang
- China-Thailand Joint Laboratory on Microbial Biotechnology, Beijing 100190, China.,Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand
| | - Bruno Gomez-Gil
- CIAD, A.C., Collection of Aquatic Important Microorganisms (CAIM). AP 711 Mazatlán, Sinaloa, Mexico
| | - Manzour H Hazbón
- American Type Culture Collection(ATCC), 10801 University Boulevard, Manassas, VA 20110, USA
| | - Marco A Riojas
- American Type Culture Collection(ATCC), 10801 University Boulevard, Manassas, VA 20110, USA
| | - Chatrudee Suwannachart
- Biodiversity Research Centre, Thailand Institute of Scientific and Technological Research (TISTR), 35 M 3 Technopolis Khlong 5 Khlong Luang Pathum Thani 12120, Thailand
| | - Su Yao
- China Center of Industrial Culture Collection (CICC), Beijing, China
| | - Peter Vandamme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zenghui Chen
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,World Data Center for Microorganisms, Beijing 100101, China
| | - Dongmei Liu
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,World Data Center for Microorganisms, Beijing 100101, China
| | - Xiuqiang Sun
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,World Data Center for Microorganisms, Beijing 100101, China
| | - Xinjiao Zhang
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,World Data Center for Microorganisms, Beijing 100101, China
| | - Yuanchun Zhou
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhen Meng
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Linhuan Wu
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,World Data Center for Microorganisms, Beijing 100101, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Juncai Ma
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,World Data Center for Microorganisms, Beijing 100101, China.,China-Thailand Joint Laboratory on Microbial Biotechnology, Beijing 100190, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Ikenaga M, Kataoka M, Yin X, Murouchi A, Sakai M. Characterization and Distribution of Agar-degrading Steroidobacter agaridevorans sp. nov., Isolated from Rhizosphere Soils. Microbes Environ 2021; 36:ME20136. [PMID: 33716238 PMCID: PMC7966939 DOI: 10.1264/jsme2.me20136] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/30/2021] [Indexed: 11/25/2022] Open
Abstract
The environment of plant rhizosphere soil differs from that of non-rhizosphere soil due to the secretion of mucilage polysaccharides from the roots. This environment is regarded as one of the preferential habitats for agar-degrading bacteria. In a previous study, agar-degrading Steroidobacter agariperforans KA5-BT was isolated from agar-enriched agricultural soil using diffusible metabolites from Rhizobiales bacteria. Based on the hypothesis that similar characteristic bacteria still exist in the rhizosphere, isolation was performed using rhizosphere soils. Agar-degrading SA29-BT and YU21-B were isolated from onion and soybean rhizosphere soils. The 16S rRNA genes of these strains showed ≥98.7% identities with the most closely related strain KA5-BT. However, differences were noted in polysaccharide utilization, and average nucleotide identities were <95-96% against strain KA5-BT, indicating that they are different species from S. agariperforans KA5-BT. To investigate the distribution of bacterial sequences affiliated with novel strains, a primer set was designed and a meta-analysis of the 16S rRNA gene was performed. Sequences were widely distributed in rhizospheres throughout Japan, but varied in plant- and region-dependent manners. Regarding phenotypic characterization, distinguishable features were observed in growth temperatures, pH, and dominant fatty acids. SA29-BT and YU21-B grew at 15-40°C and pH 6.0-12 and contained C16:0 as the dominant cell fatty acid, whereas KA5-BT showed no growth at 40°C and pH 12 and contained a moderate amount of C16:0. Based on these characteristics, SA29-BT (JCM 333368T=KCTC 72223T) and YU21-B (JCM 333367=KCTC 72222) represent novel species in the genus Steroidobacter, for which the name Steroidobacter agaridevorans sp. nov. is proposed.
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Affiliation(s)
- Makoto Ikenaga
- Research Field in Agriculture, Agriculture Fisheries and Veterinary Medicine Area, Kagoshima University, 1–21–24, Korimoto, Kagoshima, 890–0065, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1–21–24, Korimoto, Kagoshima, 890–0065, Japan
| | - Machi Kataoka
- Faculty of Agriculture, Kagoshima University, 1–21–24, Korimoto, Kagoshima, 890–0065, Japan
| | - Xuan Yin
- Faculty of Agriculture, Kagoshima University, 1–21–24, Korimoto, Kagoshima, 890–0065, Japan
| | - Aya Murouchi
- Graduate School of Agriculture, Kagoshima University, 1–21–24, Korimoto, Kagoshima, 890–0065, Japan
| | - Masao Sakai
- Research Field in Agriculture, Agriculture Fisheries and Veterinary Medicine Area, Kagoshima University, 1–21–24, Korimoto, Kagoshima, 890–0065, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1–21–24, Korimoto, Kagoshima, 890–0065, Japan
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17
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Liu N, Song T, Zhang S, Liu H, Zhao X, Shao Y, Li C, Zhang W. Characterization of the Potential Probiotic Vibrio sp. V33 Antagonizing Vibrio Splendidus Based on Iron Competition. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 18:e2259. [PMID: 32884955 PMCID: PMC7461713 DOI: 10.30498/ijb.2019.85192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Background: Vibrio Splendidus Vs is an important aquaculture pathogen that can infect a broad host of marine organisms. In our previous study,
an antagonistic bacterium Vibrio sp. V33 that possessed inhibitory effects on the growth and virulence of a pathogenic isolate V. splendidus Vs was identified. Objectives: Here, we further explored the antagonistic substances and antagonistic effects from the viewpoint of iron competition. Materials and Methods: The main antagonistic substances in the supernatants from Vibrio sp. V33 were identified using the bioassay-guided method.
The response of V. splendidus Vs under the challenge of cell-free supernatant from Vibrio sp. V33 was determined via sodium dodecyl
sulfate-polyacrylamide gel electrophoresis and real-time reverse-transcription PCR. Results: The main antagonistic substances produced by Vibrio sp. V33 have low molecular weights, are water soluble, and are heat-stable substances.
Meanwhile, the iron uptake rate of Vibrio sp. V33 was higher than that of V. splendidus Vs. In the presence of cell-free supernatant
from Vibrio sp. V33, expressions of two functional genes, viuB and asbJ related to ferric uptake processes in V. splendidus Vs,
were up-regulated, whereas furVs coding the ferric uptake repressor was suppressed below 0.5-fold. One gene coding phosphopyruvate
hydratase does not change at mRNA level, but was up-regulated at protein level. Conclusions: Our results suggested that antagonistic effect of Vibrio sp. V33 on the pathogenic isolate V. splendidus Vs was partially due to the stronger
ability of Vibrio sp. V33 to seize iron. This cell-free supernatant from Vibrio sp. V33 created an iron-limited milieu for V. splendidus Vs,
which led to the changed expression profiles of genes that were related to iron uptake in V. splendidus Vs.
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Affiliation(s)
- Ningning Liu
- School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China
| | - Tongxiang Song
- School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China
| | - Shanshan Zhang
- School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China
| | - Huijie Liu
- School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China
| | - Xuelin Zhao
- School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China
| | - Yina Shao
- School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China
| | - Chenghua Li
- School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China
| | - Weiwei Zhang
- School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China
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Yukphan P, Charoenyingcharoen P, Malimas S, Muramatsu Y, Nakagawa Y, Tanasupawat S, Yamada Y. Gluconobacter aidae sp. nov., an acetic acid bacterium isolated from tropical fruits in Thailand. Int J Syst Evol Microbiol 2020; 70:4351-4357. [PMID: 32584749 DOI: 10.1099/ijsem.0.004292] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Two bacterial strains, isolates AC10T and AC20, which were reported in a previous study on the diversity of acetic acid bacteria in Thailand, were subjected to a taxonomic study. The phylogenetic analysis based on the 16S rRNA gene sequences showed that the two isolates were located closely to the type strains of Gluconobacter oxydans and Gluconobacter roseus. However, the two isolates formed a separate cluster from the type strains of the two species. The genomic DNA of isolate AC10T was sequenced. The assembled genomes of the isolate were analysed for average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH). The results showed that the highest ANI and dDDH values between isolate AC10T and G. oxydans DSM 3503T were 91.15 and 68.2 %, which are lower than the suggested values for species delineation. The genome-based tree was reconstructed and the phylogenetic lineage based on genome sequences showed that the lineage of isolate AC10T was distinct from G. oxydans DSM 3503T and its related species. The two isolates were distinguished from G. oxydans and their relatives by their phenotypic characteristics and MALDI-TOF profiles. Therefore, the two isolates, AC10T (=BCC 15749T=TBRC 11329T=NBRC 103576T) and AC20 (=BCC 15759=TBRC 11330=NBRC 103579), can be assigned to an independent species within the genus Gluconobacter, and the name Gluconobacter aidae sp. nov. is proposed for the two isolates.
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Affiliation(s)
- Pattaraporn Yukphan
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | - Piyanat Charoenyingcharoen
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | - Sukunphat Malimas
- Rungrueng-Fertilizer.co, Ltd. 207/5 Moo1, Nong Ya, Muang Kanchanaburi, Kanchanaburi 71000, Thailand
| | - Yuki Muramatsu
- NITE Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8 Kazusa-Kamatari, Kisarazu 292-0818, Japan
| | - Yasuyoshi Nakagawa
- NITE Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8 Kazusa-Kamatari, Kisarazu 292-0818, Japan
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, 254 Phayathai Road, Wangmai, Pathumwan, Bangkok 10330, Thailand
| | - Yuzo Yamada
- Laboratory of Applied Microbiology (Professor Emeritus), Department of Applied Biological Chemistry, Faculty of Agriculture, Shizuoka University, Suruga-ku, Shizuoka 422-8529, Japan.,Japan International Cooperation Agency (JICA Senior Overseas Volunteer), Shibuya-ku, Tokyo 151-8558, Japan.,Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
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19
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Abstract
Diversity within the fungal kingdom is evident from the wide range of morphologies fungi display as well as the various ecological roles and industrial purposes they serve. Technological advances, particularly in long-read sequencing, coupled with the increasing efficiency and decreasing costs across sequencing platforms have enabled robust characterization of fungal genomes. These sequencing efforts continue to reveal the rampant diversity in fungi at the genome level. Here, we discuss studies that have furthered our understanding of fungal genetic diversity and genomic evolution. These studies revealed the presence of both small-scale and large-scale genomic changes. In fungi, research has recently focused on many small-scale changes, such as how hypermutation and allelic transmission impact genome evolution as well as how and why a few specific genomic regions are more susceptible to rapid evolution than others. High-throughput sequencing of a diverse set of fungal genomes has also illuminated the frequency, mechanisms, and impacts of large-scale changes, which include chromosome structural variation and changes in chromosome number, such as aneuploidy, polyploidy, and the presence of supernumerary chromosomes. The studies discussed herein have provided great insight into how the architecture of the fungal genome varies within species and across the kingdom and how modern fungi may have evolved from the last common fungal ancestor and might also pave the way for understanding how genomic diversity has evolved in all domains of life.
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Affiliation(s)
- Shelby J. Priest
- Department of Molecular Genetics and Microbiology, Duke University Medical Centre, Durham, NC, USA
| | - Vikas Yadav
- Department of Molecular Genetics and Microbiology, Duke University Medical Centre, Durham, NC, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Centre, Durham, NC, USA
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20
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Salvà-Serra F, Jaén-Luchoro D, Jakobsson HE, Gonzales-Siles L, Karlsson R, Busquets A, Gomila M, Bennasar-Figueras A, Russell JE, Fazal MA, Alexander S, Moore ERB. Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies. Sci Rep 2020; 10:11656. [PMID: 32669560 PMCID: PMC7363880 DOI: 10.1038/s41598-020-68249-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/16/2020] [Indexed: 01/23/2023] Open
Abstract
We present the first complete, closed genome sequences of Streptococcus pyogenes strains NCTC 8198T and CCUG 4207T, the type strain of the type species of the genus Streptococcus and an important human pathogen that causes a wide range of infectious diseases. S. pyogenes NCTC 8198T and CCUG 4207T are derived from deposit of the same strain at two different culture collections. NCTC 8198T was sequenced, using a PacBio platform; the genome sequence was assembled de novo, using HGAP. CCUG 4207T was sequenced and a de novo hybrid assembly was generated, using SPAdes, combining Illumina and Oxford Nanopore sequence reads. Both strategies yielded closed genome sequences of 1,914,862 bp, identical in length and sequence identity. Combining short-read Illumina and long-read Oxford Nanopore sequence data circumvented the expected error rate of the nanopore sequencing technology, producing a genome sequence indistinguishable to the one determined with PacBio. Sequence analyses revealed five prophage regions, a CRISPR-Cas system, numerous virulence factors and no relevant antibiotic resistance genes. These two complete genome sequences of the type strain of S. pyogenes will effectively serve as valuable taxonomic and genomic references for infectious disease diagnostics, as well as references for future studies and applications within the genus Streptococcus.
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Affiliation(s)
- Francisco Salvà-Serra
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden.
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden.
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, 413 46, Gothenburg, Sweden.
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 413 46, Gothenburg, Sweden.
- Microbiology, Department of Biology, University of the Balearic Islands, 07122, Palma, Spain.
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 413 46, Gothenburg, Sweden
| | - Hedvig E Jakobsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 413 46, Gothenburg, Sweden
| | - Lucia Gonzales-Siles
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 413 46, Gothenburg, Sweden
| | - Roger Karlsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 413 46, Gothenburg, Sweden
- Nanoxis Consulting AB, 400 16, Gothenburg, Sweden
| | - Antonio Busquets
- Microbiology, Department of Biology, University of the Balearic Islands, 07122, Palma, Spain
| | - Margarita Gomila
- Microbiology, Department of Biology, University of the Balearic Islands, 07122, Palma, Spain
| | | | - Julie E Russell
- National Collection of Type Cultures (NCTC), Public Health England, London, NW9 5EQ, UK
| | - Mohammed Abbas Fazal
- National Collection of Type Cultures (NCTC), Public Health England, London, NW9 5EQ, UK
| | - Sarah Alexander
- National Collection of Type Cultures (NCTC), Public Health England, London, NW9 5EQ, UK
| | - Edward R B Moore
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 413 46, Gothenburg, Sweden
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21
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Shi W, Qi H, Sun Q, Fan G, Liu S, Wang J, Zhu B, Liu H, Zhao F, Wang X, Hu X, Li W, Liu J, Tian Y, Wu L, Ma J. gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data. Nucleic Acids Res 2020; 47:D637-D648. [PMID: 30365027 PMCID: PMC6324004 DOI: 10.1093/nar/gky1008] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/13/2018] [Indexed: 11/26/2022] Open
Abstract
Meta-omics approaches have been increasingly used to study the structure and function of the microbial communities. A variety of large-scale collaborative projects are being conducted to encompass samples from diverse environments and habitats. This change has resulted in enormous demands for long-term data maintenance and capacity for data analysis. The Global Catalogue of Metagenomics (gcMeta) is a part of the ‘Chinese Academy of Sciences Initiative of Microbiome (CAS-CMI)’, which focuses on studying the human and environmental microbiome, establishing depositories of samples, strains and data, as well as promoting international collaboration. To accommodate and rationally organize massive datasets derived from several thousands of human and environmental microbiome samples, gcMeta features a database management system for archiving and publishing data in a standardized way. Another main feature is the integration of more than ninety web-based data analysis tools and workflows through a Docker platform which enables data analysis by using various operating systems. This platform has been rapidly expanding, and now hosts data from the CAS-CMI and a number of other ongoing research projects. In conclusion, this platform presents a powerful and user-friendly service to support worldwide collaborative efforts in the field of meta-omics research. This platform is freely accessible at https://gcmeta.wdcm.org/.
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Affiliation(s)
- Wenyu Shi
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Heyuan Qi
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qinglan Sun
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guomei Fan
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuangjiang Liu
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing 100101, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases First Attainted Hospital, College of Medicine, Zhejiang University, Hangzhou 310058, China.,Beijing Key Laboratory of Antimicrobial Resistance and Pathogen Genomics, Beijing 100101, China
| | - Hongwei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Science, Beijing 100101, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaochen Wang
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoxuan Hu
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Li
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jia Liu
- Internet of Things Information Technology and Application Laboratory, Computer Network Information Center, Chinese Academy of Sciences. Beijing 100101, China
| | - Ye Tian
- Internet of Things Information Technology and Application Laboratory, Computer Network Information Center, Chinese Academy of Sciences. Beijing 100101, China
| | - Linhuan Wu
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Juncai Ma
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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22
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de Lajudie P, Young JPW. International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 17 July 2019. Int J Syst Evol Microbiol 2020; 70:3563-3571. [DOI: 10.1099/ijsem.0.004157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Minutes of the closed meeting of the ICSP Subcommittee on the Taxonomy of Rhizobia and Agrobacteria held by videoconference on 17 July 2019, and list of recent species.
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23
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Wallace EWJ, Maufrais C, Sales-Lee J, Tuck LR, de Oliveira L, Feuerbach F, Moyrand F, Natarajan P, Madhani HD, Janbon G. Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom. Nucleic Acids Res 2020; 48:2312-2331. [PMID: 32020195 PMCID: PMC7049704 DOI: 10.1093/nar/gkaa060] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 01/13/2020] [Accepted: 01/20/2020] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic protein synthesis generally initiates at a start codon defined by an AUG and its surrounding Kozak sequence context, but the quantitative importance of this context in different species is unclear. We tested this concept in two pathogenic Cryptococcus yeast species by genome-wide mapping of translation and of mRNA 5' and 3' ends. We observed thousands of AUG-initiated upstream open reading frames (uORFs) that are a major contributor to translation repression. uORF use depends on the Kozak sequence context of its start codon, and uORFs with strong contexts promote nonsense-mediated mRNA decay. Transcript leaders in Cryptococcus and other fungi are substantially longer and more AUG-dense than in Saccharomyces. Numerous Cryptococcus mRNAs encode predicted dual-localized proteins, including many aminoacyl-tRNA synthetases, in which a leaky AUG start codon is followed by a strong Kozak context in-frame AUG, separated by mitochondrial-targeting sequence. Analysis of other fungal species shows that such dual-localization is also predicted to be common in the ascomycete mould, Neurospora crassa. Kozak-controlled regulation is correlated with insertions in translational initiation factors in fidelity-determining regions that contact the initiator tRNA. Thus, start codon context is a signal that quantitatively programs both the expression and the structures of proteins in diverse fungi.
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Affiliation(s)
- Edward W J Wallace
- Institute for Cell Biology and SynthSys, School of Biological Sciences, University of Edinburgh, UK
| | - Corinne Maufrais
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
- Institut Pasteur, HUB Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS, F-75015 Paris, France
| | - Jade Sales-Lee
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Laura R Tuck
- Institute for Cell Biology and SynthSys, School of Biological Sciences, University of Edinburgh, UK
| | - Luciana de Oliveira
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
| | - Frank Feuerbach
- Institut Pasteur, Unité Génétique des Interactions Macromoléculaire, Département Génome et Génétique, F-75015 Paris, France
| | - Frédérique Moyrand
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
| | - Prashanthi Natarajan
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Guilhem Janbon
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
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24
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Chen J, O'Leary M, Burbank L, Zheng Z, Deng X. Whole Genome Sequence of Xylella fastidiosa ATCC 35879 T and Detection of Genome Rearrangements Within Subsp. fastidiosa. Curr Microbiol 2020; 77:1858-1863. [PMID: 32179972 DOI: 10.1007/s00284-020-01937-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/24/2020] [Indexed: 10/24/2022]
Abstract
Xylella fastidiosa is a Gram-negative and nutritionally fastidious bacterial pathogen causing Pierce's disease (PD) of grapevine and other plant diseases. X. fastidiosa strain ATCC 35879T which originated from Florida is the designated type strain for the species and for subsp. fastidiosa. In bacterial taxonomy, type strains preserve the characters of the original descriptions. Whole genome sequence of a type strain not only provides a standard reference for bacterial taxonomy, but also facilitates research in other fields such as population diversity and genome evolution. In this study, the whole genome sequence of strain ATCC 35879T was determined using PacBio RSII format. The ATCC 35879T genome has a circular chromosome of 2,565,504 bp with 2,904 predicted protein coding genes and 55 RNA genes, and a circular plasmid of 41,753 bp. The chromosomal sequence of strain ATCC 35879T was compared to that of X. fastidosa subsp. fastidiosa strain M23 from California which causes both PD and almond leaf scorch disease. Genome rearrangements involving a ~ 1,200 K bp region were detected. Genome annotations showed clusters of phage-related genes around the rearrangement junctions, suggesting the likely involvement of phage activities. This is the first report on genome structure variations within strains of X. fastidiosa subsp. fastidiosa.
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Affiliation(s)
- J Chen
- Agricultural Research Service, United States Department of Agriculture, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, USA.
| | - M O'Leary
- Agricultural Research Service, United States Department of Agriculture, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, USA
| | - L Burbank
- Agricultural Research Service, United States Department of Agriculture, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, USA
| | - Z Zheng
- Department of Plant Pathology, South China Agricultural University, Guangzhou, People's Republic of China
| | - X Deng
- Department of Plant Pathology, South China Agricultural University, Guangzhou, People's Republic of China
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25
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Meyer A, Saaem I, Silverman A, Varaljay VA, Mickol R, Blum S, Tobias AV, Schwalm ND, Mojadedi W, Onderko E, Bristol C, Liu S, Pratt K, Casini A, Eluere R, Moser F, Drake C, Gupta M, Kelley-Loughnane N, Lucks JP, Akingbade KL, Lux MP, Glaven S, Crookes-Goodson W, Jewett MC, Gordon DB, Voigt CA. Organism Engineering for the Bioproduction of the Triaminotrinitrobenzene (TATB) Precursor Phloroglucinol (PG). ACS Synth Biol 2019; 8:2746-2755. [PMID: 31750651 DOI: 10.1021/acssynbio.9b00393] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Organism engineering requires the selection of an appropriate chassis, editing its genome, combining traits from different source species, and controlling genes with synthetic circuits. When a strain is needed for a new target objective, for example, to produce a chemical-of-need, the best strains, genes, techniques, software, and expertise may be distributed across laboratories. Here, we report a project where we were assigned phloroglucinol (PG) as a target, and then combined unique capabilities across the United States Army, Navy, and Air Force service laboratories with the shared goal of designing an organism to produce this molecule. In addition to the laboratory strain Escherichia coli, organisms were screened from soil and seawater. Putative PG-producing enzymes were mined from a strain bank of bacteria isolated from aircraft and fuel depots. The best enzyme was introduced into the ocean strain Marinobacter atlanticus CP1 with its genome edited to redirect carbon flux from natural fatty acid ester (FAE) production. PG production was also attempted in Bacillus subtilis and Clostridium acetobutylicum. A genetic circuit was constructed in E. coli that responds to PG accumulation, which was then ported to an in vitro paper-based system that could serve as a platform for future low-cost strain screening or for in-field sensing. Collectively, these efforts show how distributed biotechnology laboratories with domain-specific expertise can be marshalled to quickly provide a solution for a targeted organism engineering project, and highlights data and material sharing protocols needed to accelerate future efforts.
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Affiliation(s)
- Adam Meyer
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ishtiaq Saaem
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Adam Silverman
- Center for Synthetic Biology, Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Vanessa A. Varaljay
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Rebecca Mickol
- American Society for Engineering Education, 1818 N Street NW Suite 600, Washington, D.C. 20036, United States
| | - Steven Blum
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Alexander V. Tobias
- U.S. Army Research Laboratory, FCDD-RLS-EB, 2800 Powder Mill Road, Adelphi, Maryland 20783, United States
| | - Nathan D. Schwalm
- U.S. Army Research Laboratory, FCDD-RLS-EB, 2800 Powder Mill Road, Adelphi, Maryland 20783, United States
| | - Wais Mojadedi
- Oak Ridge Associate Universities, P.O.
Box 117, MS-29, Oak Ridge, Tennessee 37831, United States
| | - Elizabeth Onderko
- National Research Council, 500 5th Street NW, Washington, D.C. 20001, United States
| | - Cassandra Bristol
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Shangtao Liu
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
| | - Katelin Pratt
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Arturo Casini
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Raissa Eluere
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Felix Moser
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Carrie Drake
- UES, Inc., 4401 Dayton-Xenia Road, Dayton, Ohio 45432, United States
| | - Maneesh Gupta
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Nancy Kelley-Loughnane
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Julius P. Lucks
- Center for Synthetic Biology, Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Katherine L. Akingbade
- U.S. Army Research Laboratory, FCDD-RLS-EB, 2800 Powder Mill Road, Adelphi, Maryland 20783, United States
| | - Matthew P. Lux
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Sarah Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Wendy Crookes-Goodson
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Michael C. Jewett
- Center for Synthetic Biology, Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - D. Benjamin Gordon
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Christopher A. Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
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26
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Wu L, Ma J. The Global Catalogue of Microorganisms (GCM) 10K type strain sequencing project: providing services to taxonomists for standard genome sequencing and annotation. Int J Syst Evol Microbiol 2019; 69:895-898. [PMID: 30832757 DOI: 10.1099/ijsem.0.003276] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The World Federation of Culture Collections and the World Data Center for Microorganisms (wdcm) initiated an international community-led project to sequence and annotate newly described prokaryotic taxa. This sequencing project aims to cooperate with international culture collections and the International Journal of Systematic and Evolutionary Microbiology and contribute to the expansion of whole genome sequencing databases for type strains. It will provide global microbial taxonomists with free standard genome sequencing and annotation services. Taxonomists are encouraged to contact the wdcm and participant culture collections to submit a type strain sequencing proposal.
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Affiliation(s)
- Linhuan Wu
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- WFCC-MIRCEN World Data Center for microorganisms, WDCM, Beijing 100101, PR China
| | - Juncai Ma
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- WFCC-MIRCEN World Data Center for microorganisms, WDCM, Beijing 100101, PR China
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27
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Draft Genome Sequence of the Type Strain Streptomyces armeniacus ATCC 15676. Microbiol Resour Announc 2018; 7:MRA01107-18. [PMID: 30533638 PMCID: PMC6256661 DOI: 10.1128/mra.01107-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 08/23/2018] [Indexed: 11/20/2022] Open
Abstract
The Streptomyces genus represents a prolific and significant source for secondary metabolite discovery. Here, we report a de novo assembly and draft genome sequence for the type strain Streptomyces armeniacus ATCC 15676. The Streptomyces genus represents a prolific and significant source for secondary metabolite discovery. Here, we report a de novo assembly and draft genome sequence for the type strain Streptomyces armeniacus ATCC 15676.
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