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Diop A, El Karkouri K, Raoult D, Fournier PE. Genome sequence-based criteria for demarcation and definition of species in the genus Rickettsia. Int J Syst Evol Microbiol 2020; 70:1738-1750. [DOI: 10.1099/ijsem.0.003963] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Over recent years, genomic information has increasingly been used for prokaryotic species definition and classification. Genome sequence-based alternatives to the gold standard DNA–DNA hybridization (DDH) relatedness have been developed, notably average nucleotide identity (ANI), which is one of the most useful measurements for species delineation in the genomic era. However, the strictly intracellar lifestyle, the few measurable phenotypic properties and the low level of genetic heterogeneity made the current standard genomic criteria for bacterial species definition inapplicable to
Rickettsia
species. We evaluated a range of whole genome sequence (WGS)-based taxonomic parameters to develop guidelines for the classification of
Rickettsia
isolates at genus and species levels. By comparing the degree of similarity of 74 WGSs from 31
Rickettsia
species and 61 WGSs from members of three closely related genera also belonging to the order
Rickettsiales
(
Orientia
, 11 genomes;
Ehrlichia
, 22 genomes; and
Anaplasma
, 28 genomes) using digital DDH (dDDh) and ANI by orthology (OrthoANI) parameters, we demonstrated that WGS-based taxonomic information, which is easy to obtain and use, can serve for reliable classification of isolates within the
Rickettsia
genus and species. To be classified as a member of the genus
Rickettsia
, a bacterial isolate should exhibit OrthoANI values with any
Rickettsia
species with a validly published name of ≥83.63 %. To be classified as a new
Rickettsia
species, an isolate should not exhibit more than any of the following degrees of genomic relatedness levels with the most closely related species: >92.30 and >99.19 % for the dDDH and OrthoANI values, respectively. When applied to four rickettsial isolates of uncertain status, the above-described thresholds enabled their classification as new species in one case. Thus, we propose WGS-based guidelines to efficiently delineate
Rickettsia
species, with OrthoANI and dDDH being the most accurate for classification at the genus and species levels, respectively.
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Affiliation(s)
- Awa Diop
- Institut Hospitalo-universitaire Méditerranée Infection, Marseille, France
- UMR VITROME, Aix-Marseille University, Institut pour la Recherche et le Développement, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Khalid El Karkouri
- Institut Hospitalo-universitaire Méditerranée Infection, Marseille, France
- UMR VITROME, Aix-Marseille University, Institut pour la Recherche et le Développement, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Didier Raoult
- UMR MEPHI, Aix-Marseille University, Institut pour la Recherche et le Développement, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Institut Hospitalo-universitaire Méditerranée Infection, Marseille, France
| | - Pierre-Edouard Fournier
- Institut Hospitalo-universitaire Méditerranée Infection, Marseille, France
- UMR VITROME, Aix-Marseille University, Institut pour la Recherche et le Développement, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
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152
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Gorillibacterium timonense sp. nov., isolated from an obese patient. Arch Microbiol 2020; 202:1223-1229. [PMID: 32103285 DOI: 10.1007/s00203-020-01834-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/28/2019] [Accepted: 02/11/2020] [Indexed: 01/15/2023]
Abstract
A Gram-negative and facultative anaerobic bacterium, designated strain SN4T, was isolated from the stool sample of an obese Amazonian patient. The new isolate was characterized by the taxonogenomics approach. The strain SN4T was beige-colored, circular and not haemolytic. Cells are rod shaped and motile with several flagella. Strain SN4T grows optimally at pH 7 and can survive in the presence of a saline concentration of up to 75 g/l NaCl. The 16S ribosomal RNA gene sequence analysis of the novel strain SN4T showed 95.28% similarity in nucleotide sequence with Gorillibacterium massiliense G5T, the phylogenetically closest neighbor and the type species of this genus. Anteiso-C15:0, iso-C15:0 and C16:0 were found as the major components in the cellular fatty acid analysis of this isolate. The genomic draft of strain SN4T is 5,263,742 bp long with 53.33% of G+C content. The differences in physiological, biochemical characteristics and phylogenetic and genomic data make it possible to clearly distinguish the strain SN4T from G. massiliense G5T. Based on the taxonogenomic description and the phenotypic and biochemical characteristics of this bacterium presented in this article, we propose the SN4T strain (= CSUR P2011 = DSM 100,698) as a new species, Gorillibacterium timonense sp. nov.
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153
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Ou YJ, Ren QQ, Fang ST, Wu JG, Jiang YX, Chen YR, Zhong Y, Wang DD, Zhang GX. Complete Genome Insights into Lactococcus petauri CF11 Isolated from a Healthy Human Gut Using Second- and Third-Generation Sequencing. Front Genet 2020; 11:119. [PMID: 32174973 PMCID: PMC7054480 DOI: 10.3389/fgene.2020.00119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 01/31/2020] [Indexed: 12/31/2022] Open
Abstract
Lactococcus petauri CF11 was originally isolated from the gut of healthy humans. To determine the underlying molecular and genetic mechanisms of the probiotic potential of CF11, we performed complete genome sequencing, annotation, and comparative genome analysis. The complete genome of L. petauri CF11 comprised of 1,997,720 bp, with a DNA G+C content of 38.21 mol% containing 1982 protein coding genes and 16 rRNA operons. We found that 1206 genes (56.05%) were assigned a putative function using the gene ontology (GO) resource. The gene products of CF11 were primarily concentrated in molecular function and biological processes, such as catalysis, binding, metabolism, and cellular processes. Furthermore, 1,365 (68.87%) genes were assigned an illative function using COGs. CF11 proteins were associated with carbohydrate transport and metabolism, and amino acid transport and metabolism. This indicates that CF11 bacteria can perform active energy exchange. We classified 1,111 (56.05%) genes into six KEGG functional categories; fructose-bisphosphate aldolase and the phosphoenol pyruvate:phosphotransferase system (PTS), which are necessary in producing short-chain fatty acids (SCFAs), were excited in the carbohydrate metabolic pathway. This suggests that L. petauri CF11 produces SCFAs via glycolysis. The genomic island revealed that some regions contain fragments of antibiotic resistance and bacteriostatic genes. In addition, ANI analysis showed that L. petauri CF11 had the closest relationship with L. petauri 159469T, with an average nucleotide consistency of 98.03%. Taken together, the present study offers further insights into the functional and potential role of L. petauri CF11 in health care.
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Affiliation(s)
- Yun-Jing Ou
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Qiao-Qiao Ren
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Shu-Ting Fang
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Ji-Guo Wu
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yun-Xia Jiang
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yi-Ran Chen
- Department of Water Hygiene, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Yi Zhong
- Department of Water Hygiene, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - De-Dong Wang
- Department of Water Hygiene, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Guo-Xia Zhang
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
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154
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Ay H, Nouioui I, Klenk HP, Cetin D, Igual JM, Sahin N, Isik K. Genome-based classification of Micromonospora craterilacus sp. nov., a novel actinobacterium isolated from Nemrut Lake. Antonie Van Leeuwenhoek 2020; 113:791-801. [PMID: 32060815 DOI: 10.1007/s10482-020-01390-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 01/28/2020] [Indexed: 11/28/2022]
Abstract
A novel actinobacterial strain, designated NA12T, was isolated from coastal sediment sample of Nemrut Lake, a crater lake in eastern Anatolia, Turkey. The taxonomic position of the strain was established using a polyphasic approach. Cultural and chemotaxonomic characteristics of the strain were consistent with its classification within the family Micromonosporaceae. The 16S rRNA gene sequence analysis of strain NA12T showed that the strain closely related to M. radicis AZ1-13T, M. zingiberis PLAI 1-1T, M. craniella LHW63014T and M. endophytica 202201T with pairwise sequence identity values ranging from 99.4 to 99.3%. Digital DNA-DNA hybridization values between strain NA12T and the closely related type strains were ranged from 41.0 to 18.3% while the average nucleotide identity values were between 87.3 and 86.5%, which are well below the designed cut-off points of 70 and 95%, respectively. The G + C content of genomic DNA was 71.5%. Whole-cell hydrolysates of strain NA12T contained 3-hydroxydiaminopimelic acid and meso-diaminopimelic acid. Cell-wall sugars were composed of arabinose, fucose, glucose, mannose, rhamnose and xylose. The polar lipid profile contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, glycophospholipid, amino-phospholipid and two unidentified phospholipids. The predominant menaquinones were MK-9(H6) and MK-9(H4). Major fatty acids were iso-C16:0 and C17:1ω8c. Based upon the consensus of phenotypic and phylogenetic analyses as well as whole genome comparisons, strain NA12T (DSM 100982T = KCTC 39647T) is proposed to represent the type strain of a novel species, Micromonospora craterilacus sp. nov.
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Affiliation(s)
- Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, Samsun, Turkey.
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Demet Cetin
- Division of Science Education, Department of Mathematics and Science Education, Gazi Faculty of Education, Gazi University, 06500, Ankara, Turkey
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiologia de Salamanca, Consejo Superior de Investigaciones Cientificas (IRNASA-CSIC), Salamanca, Spain
| | - Nevzat Sahin
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, Samsun, Turkey
| | - Kamil Isik
- Department of Biology, Faculty of Science and Arts, Ondokuz Mayis University, Samsun, Turkey
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155
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Sun QL, Sun YL, Sun YY, Luan ZD, Lian C. Marinobacter fonticola sp. nov., isolated from deep sea cold seep sediment. Int J Syst Evol Microbiol 2020; 70:1172-1177. [DOI: 10.1099/ijsem.0.003895] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Qing-lei Sun
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, PR China
| | - Yan-ling Sun
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, PR China
| | - Yuan-yuan Sun
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, PR China
| | - Zhen-dong Luan
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China
| | - Chao Lian
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China
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156
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Ming H, Zhao ZL, Ji WL, Ding CL, Cheng LJ, Niu MM, Li M, Yi BF, Xia TT, Nie GX. Thermus thermamylovorans sp. nov., isolated from a hot spring. Int J Syst Evol Microbiol 2020; 70:1729-1737. [PMID: 31967954 DOI: 10.1099/ijsem.0.003965] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermophilic bacterium, designated CFH 72773T was isolated from the enrichment of a Jinze hot spring sample which was collected from Dientan town, Tengchong county, Yunnan province, south-western PR China. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and non-sporulating. The taxonomic position of the strain was investigated by using a polyphasic approach. Growth occurred at 37-75 °C, pH 6.0-8.0 and with 0-2.0 % (w/v) NaCl. Comparison of the 16S rRNA gene sequences indicated the strain represented a member of the genus Thermus and showed close relationships to the type strains Thermus caliditerrae YIM 77925T (96.3 % similarity) and Thermus igniterrae RF-4T (96.2 % similarity). The whole genome of CFH 72773T consisted of 2.25 Mbp and the DNA G+C content was 69.5 mol%. A total of 2262 genes, including a variety of enzymes for chemolithotrophy and anerobic respiration, were predicted. The strain had a unique negative oxidase activity and could hydrolyze starch at high temperature. Furthermore, various genes related to methane, sulfur, fumarate and nitrate metabolism were found, all these indicated that it is worth studying the novel strain. The predominant menaquinone is MK-8. The predominant cellular fatty acids included iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0. The major polar lipids were comprised of aminophospholipid, glycolipid and two phospholipids. On the basis of low ANI values, different phenotypic and chemotaxonomic characters and phylogenetic analysis, we made a proposal that strain CFH 72773T represents a novel member of the genus Thermus, for which the name Thermus thermamylovorans sp. nov. is proposed. The type strain is CFH 72773T (=CCTCC AB2018244T=KCTC 43129T).
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Affiliation(s)
- Hong Ming
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, PR China
| | - Zhuo-Li Zhao
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Wei-Li Ji
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, PR China
| | - Chen-Long Ding
- Suqian Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Suqian, 223800, PR China
| | - Li-Jiao Cheng
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Ming-Ming Niu
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Meng Li
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, PR China
| | - Bing-Fang Yi
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Ting-Ting Xia
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, PR China
| | - Guo-Xing Nie
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
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157
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Fernández-Bravo A, Figueras MJ. An Update on the Genus Aeromonas: Taxonomy, Epidemiology, and Pathogenicity. Microorganisms 2020; 8:microorganisms8010129. [PMID: 31963469 PMCID: PMC7022790 DOI: 10.3390/microorganisms8010129] [Citation(s) in RCA: 246] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
The genus Aeromonas belongs to the Aeromonadaceae family and comprises a group of Gram-negative bacteria widely distributed in aquatic environments, with some species able to cause disease in humans, fish, and other aquatic animals. However, bacteria of this genus are isolated from many other habitats, environments, and food products. The taxonomy of this genus is complex when phenotypic identification methods are used because such methods might not correctly identify all the species. On the other hand, molecular methods have proven very reliable, such as using the sequences of concatenated housekeeping genes like gyrB and rpoD or comparing the genomes with the type strains using a genomic index, such as the average nucleotide identity (ANI) or in silico DNA–DNA hybridization (isDDH). So far, 36 species have been described in the genus Aeromonas of which at least 19 are considered emerging pathogens to humans, causing a broad spectrum of infections. Having said that, when classifying 1852 strains that have been reported in various recent clinical cases, 95.4% were identified as only four species: Aeromonas caviae (37.26%), Aeromonas dhakensis (23.49%), Aeromonas veronii (21.54%), and Aeromonas hydrophila (13.07%). Since aeromonads were first associated with human disease, gastroenteritis, bacteremia, and wound infections have dominated. The literature shows that the pathogenic potential of Aeromonas is considered multifactorial and the presence of several virulence factors allows these bacteria to adhere, invade, and destroy the host cells, overcoming the immune host response. Based on current information about the ecology, epidemiology, and pathogenicity of the genus Aeromonas, we should assume that the infections these bacteria produce will remain a great health problem in the future. The ubiquitous distribution of these bacteria and the increasing elderly population, to whom these bacteria are an opportunistic pathogen, will facilitate this problem. In addition, using data from outbreak studies, it has been recognized that in cases of diarrhea, the infective dose of Aeromonas is relatively low. These poorly known bacteria should therefore be considered similarly as enteropathogens like Salmonella and Campylobacter.
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158
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Jagielski T, Borówka P, Bakuła Z, Lach J, Marciniak B, Brzostek A, Dziadek J, Dziurzyński M, Pennings L, van Ingen J, Žolnir-Dovč M, Strapagiel D. Genomic Insights Into the Mycobacterium kansasii Complex: An Update. Front Microbiol 2020; 10:2918. [PMID: 32010067 PMCID: PMC6974680 DOI: 10.3389/fmicb.2019.02918] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/04/2019] [Indexed: 12/31/2022] Open
Abstract
Only very recently, has it been proposed that the hitherto existing Mycobacterium kansasii subtypes (I-VI) should be elevated, each, to a species rank. Consequently, the former M. kansasii subtypes have been denominated as Mycobacterium kansasii (former type I), Mycobacterium persicum (II), Mycobacterium pseudokansasii (III), Mycobacterium innocens (V), and Mycobacterium attenuatum (VI). The present work extends the recently published findings by using a three-pronged computational strategy, based on the alignment fraction-average nucleotide identity, genome-to-genome distance, and core-genome phylogeny, yet essentially independent and much larger sample, and thus delivers a more refined and complete picture of the M. kansasii complex. Furthermore, five canonical taxonomic markers were used, i.e., 16S rRNA, hsp65, rpoB, and tuf genes, as well as the 16S-23S rRNA intergenic spacer region (ITS). The three major methods produced highly concordant results, corroborating the view that each M. kansasii subtype does represent a distinct species. This work not only consolidates the position of five of the currently erected species, but also provides a description of the sixth one, i.e., Mycobacterium ostraviense sp. nov. to replace the former subtype IV. By showing a close genetic relatedness, a monophyletic origin, and overlapping phenotypes, our findings support the recognition of the M. kansasii complex (MKC), accommodating all M. kansasii-derived species and Mycobacterium gastri. None of the most commonly used taxonomic markers was shown to accurately distinguish all the MKC species. Likewise, no species-specific phenotypic characteristics were found allowing for species differentiation within the complex, except the non-photochromogenicity of M. gastri. To distinguish, most reliably, between the MKC species, and between M. kansasii and M. persicum in particular, whole-genome-based approaches should be applied. In the absence of clear differences in the distribution of the virulence-associated region of difference 1 genes among the M. kansasii-derived species, the pathogenic potential of each of these species can only be speculatively assessed based on their prevalence among the clinically relevant population. Large-scale molecular epidemiological studies are needed to provide a better understanding of the clinical significance and pathobiology of the MKC species. The results of the in vitro drug susceptibility profiling emphasize the priority of rifampicin administration in the treatment of MKC-induced infections, while undermining the use of ethambutol, due to a high resistance to this drug.
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Affiliation(s)
- Tomasz Jagielski
- Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Paulina Borówka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Zofia Bakuła
- Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Jakub Lach
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- BBMRI.pl Consortium, Wroclaw, Poland
| | - Błażej Marciniak
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- BBMRI.pl Consortium, Wroclaw, Poland
| | - Anna Brzostek
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Mikołaj Dziurzyński
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Lian Pennings
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Manca Žolnir-Dovč
- Laboratory for Mycobacteria, University Clinic of Respiratory and Allergic Diseases, Golnik, Slovenia
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- BBMRI.pl Consortium, Wroclaw, Poland
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159
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Description of the novel planctomycetal genus Bremerella, containing Bremerella volcania sp. nov., isolated from an active volcanic site, and reclassification of Blastopirellula cremea as Bremerella cremea comb. nov. Antonie van Leeuwenhoek 2020; 113:1823-1837. [DOI: 10.1007/s10482-019-01378-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/12/2019] [Indexed: 02/07/2023]
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160
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Navarro-Torre S, Carro L, Rodríguez-Llorente ID, Pajuelo E, Caviedes MÁ, Igual JM, Klenk HP, Montero-Calasanz MDC. Halomonas radicis sp. nov., isolated from Arthrocnemum macrostachyum growing in the Odiel marshes(Spain) and emended descriptions of Halomonas xinjiangensis and Halomonas zincidurans. Int J Syst Evol Microbiol 2020; 70:220-227. [DOI: 10.1099/ijsem.0.003742] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Salvadora Navarro-Torre
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Calle Profesor García González, 2, 41012 Sevilla, Spain
| | - Lorena Carro
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Ignacio D. Rodríguez-Llorente
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Calle Profesor García González, 2, 41012 Sevilla, Spain
| | - Eloísa Pajuelo
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Calle Profesor García González, 2, 41012 Sevilla, Spain
| | - Miguel Ángel Caviedes
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Calle Profesor García González, 2, 41012 Sevilla, Spain
| | - José M. Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences (SNES), Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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161
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Zhao ZL, Ming H, Ding CL, Ji WL, Cheng LJ, Niu MM, Zhang YM, Zhang LY, Meng XL, Nie GX. Azospirillum thermophilum sp. nov., isolated from a hot spring. Int J Syst Evol Microbiol 2020; 70:550-554. [DOI: 10.1099/ijsem.0.003788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Zhuo-li Zhao
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Hong Ming
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, PR China
| | - Chen-Long Ding
- Suqian Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Suqian, 223800, PR China
| | - Wei-Li Ji
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, PR China
| | - Li-Jiao Cheng
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Ming-ming Niu
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Yan-min Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Ling-Yu Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Xiao-Lin Meng
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Guo-Xing Nie
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
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162
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Ming H, Cheng LJ, Ding CL, Niu MM, Zhao ZL, Ji WL, Zhang LY, Zhang YM, Meng XL, Nie GX. Paracoccus luteus sp. nov., isolated from the intestine of grass carp. Int J Syst Evol Microbiol 2020; 70:543-549. [DOI: 10.1099/ijsem.0.003790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hong Ming
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, PR China
| | - Li-Jiao Cheng
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Chen-Long Ding
- Suqian Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Suqian, 223800, PR China
| | - Ming-Ming Niu
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Zhuo-Li Zhao
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Wei-Li Ji
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, PR China
| | - Ling-Yu Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Yan-min Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Xiao-Lin Meng
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Guo-Xing Nie
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
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163
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Modestobacter excelsi sp. nov., a novel actinobacterium isolated from a high altitude Atacama Desert soil. Syst Appl Microbiol 2019; 43:126051. [PMID: 31892483 DOI: 10.1016/j.syapm.2019.126051] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 12/10/2019] [Accepted: 12/16/2019] [Indexed: 11/20/2022]
Abstract
A polyphasic study was undertaken to establish the taxonomic status of three Modestobacter strains isolated from a high altitude Atacama Desert soil. The isolates, strains 1G6T, 1G14 and 1G50, showed chemotaxonomic and morphological properties characteristic of members of the genus Modestobacter. The peptidoglycan contained meso-diaminopimelic acid, the whole cell sugars were glucose and ribose (diagnostic sugars) and arabinose, the predominant menaquinone was MK-9(H4), polar lipid patterns contained diphosphatidylglycerol, glycophosphatidylinositol, phosphatidylethanolamine (diagnostic component), phosphatidylglycerol and phosphatidylinositol while whole cellular fatty acid profiles consisted of complex mixtures of saturated, unsaturated iso- and anteiso-components. The isolates were shown to have different BOX-PCR fingerprint and physiological profiles. They formed a distinct phyletic line in Modestobacter 16S rRNA gene trees, were most closely related to the type strain of Modestobacter italicus (99.9 % similarity) but were distinguished from this and other closely related Modestobacter type strains using a combination of phenotypic properties. Average nucleotide identity and digital DNA:DNA hybridization similarities between the draft genome sequences of isolate 1G6T and M. italicus BC 501T were 90.9 % and 42.3 %, respectively, indicating that they belong to different species. Based on these phenotypic and genotypic data it is proposed that the isolates be assigned to a novel species in the genus Modestobacter, namely as Modestobacter excelsi with isolate 1G6T (=DSM 107535T =PCM 3004T) as the type strain. Analysis of the whole genome sequence of M. excelsi 1G6T (genome size of 5.26 Mb) showed the presence of genes and gene clusters that encode for properties that are in tune with its adaptation to extreme environmental conditions that prevail in the Atacama Desert biome.
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164
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Abou Abdallah R, Okdah L, Bou Khalil J, Anani H, Fournier PE, Raoult D, Bittar F. Draft genome and description of Chryseobacterium phocaeense sp. nov.: a new bacterial species isolated from the sputum of a cystic fibrosis patient. Arch Microbiol 2019; 201:1361-1368. [DOI: 10.1007/s00203-019-01704-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/21/2019] [Accepted: 07/10/2019] [Indexed: 11/28/2022]
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165
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Genomic repertoire of Mameliella alba Ep20 associated with Symbiodinium from the endemic coral Mussismilia braziliensis. Symbiosis 2019. [DOI: 10.1007/s13199-019-00655-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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166
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Tarhriz V, Nouioui I, Spröer C, Verbarg S, Ebrahimi V, Cortés-Albayay C, Schumann P, Hejazi MA, Klenk HP, Hejazi MS. Pseudomonas khazarica sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from Khazar Sea sediments. Antonie van Leeuwenhoek 2019; 113:521-532. [PMID: 31768782 DOI: 10.1007/s10482-019-01361-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 11/14/2019] [Indexed: 11/26/2022]
Abstract
A novel Gram-negative, aerobic, motile and rod-shaped bacterium with the potential to biodegrade polycyclic aromatic hydrocarbons, was isolated from Khazar (Caspian) Sea. Strain TBZ2T grows in the absence of NaCl and tolerates up to 8.5% NaCl. Growth occurred at pH 3.0-10.0 (optimum, pH 6.0-7.0) and 10-45 °C (optimum, 30 °C). The major fatty acids are C18:1ω7C, C16:1ω7C/ C15:0 iso 2-OH, C16:0, C12:0, C10:0 3-OH, C12:0 3-OH. The major polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and the predominant respiratory quinone is ubiquinone Q-9. The 16S rRNA gene sequence analysis showed that strain TBZ2T is a member of the genus Pseudomonas with the highest similarity to P. oleovorans subsp. oleovorans DSM 1045T (98.83%), P. mendocina NBRC 14162T (98.63%), P. oleovorans subsp. lubricantis RS1T (98.61%) and P. alcaliphila JCM 10630T (98.49%) based on EzBioCloud server. Phylogenetic analyses using housekeeping genes (16S rRNA, rpoD, gyrB and rpoB) and genome sequences demonstrated that the strain TBZ2T formed a distinct branch closely related to the type strains of P. mendocina and P. guguanensis. Digital DNA-DNA hybridisation and average nucleotide identity values between strain TBZ2T and its closest relatives, P. mendocina NBRC 14162T (25.3%, 81.5%) and P. guguanensis JCM 18146T (26.8%, 79.0%), rate well below the designed threshold for assigning prokaryotic strains to the same species. On the basis of phenotypic, chemotaxonomic, genomic and phylogenetic results, it is recommended that strain TBZ2T is a novel species of the genus Pseudomonas, for which the name Pseudomonas khazarica sp. nov., is proposed. The type strain is TBZ2T (= LMG 29674T = KCTC 52410T).
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Affiliation(s)
- Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Brunswick, Germany
| | - Susanne Verbarg
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Brunswick, Germany
| | - Vida Ebrahimi
- Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Carlos Cortés-Albayay
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Brunswick, Germany
| | - Mohammad Amin Hejazi
- Branch for the Northwest and West Region, Agriculture Biotechnology Research Institute of Iran (ABRII), Tabriz, Iran
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK.
| | - Mohammad Saeid Hejazi
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.
- Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
- School of Advanced Biomedical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
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167
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Anaerophilus nitritogenes gen. nov., sp. nov., isolated from salt lake sediment in Xinjiang Province, China. Antonie van Leeuwenhoek 2019; 113:417-425. [PMID: 31713080 DOI: 10.1007/s10482-019-01351-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/18/2019] [Indexed: 10/25/2022]
Abstract
An obligately anaerobic, nitrate-reducing bacterial strain (MJB2T) was isolated from sediments of saline in Xinjiang province of China. Cells were Gram-stain-positive rods and motile by means of flagella and formed endospores. The novel strain MJB2T was able to grow at 15-37 °C (optimum 28-30 °C), pH 5.8-9.4 (optimum 7.8) and with 1.0-7.0% NaCl (optimum 5.0-6.0%, w/v). Sulfate, sulfite, thiosulfate, elemental sulfur, nitrite and Fe(III) were not used as terminal electron acceptors. Oxidase and catalase reactions were positive. H2S was producted from L-cystine. Complex substrates such as beef extract, peptone and yeast extract can be used as sole energy sources. The DNA G+C content was 29.4 mol%. The major cellular fatty acids (> 10%) were C14:0, C16:1 cis 7 and C16:1 cis 9. The main polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, three unidentified amino lipids, one unidentified amino glycolipid, two unidentified glycolipid, one unidentified aminophospholipid and two unidentified lipids. No respiratory quinones were detected. According to phylogenetic analysis based on 16S rRNA gene sequences, strain MJB2T was affiliated to the family Clostridiaceae (order Clostridiales) with highest 16S rRNA gene sequence similarity of 95.3% to Crassaminicella profunda Ra1766HT. Strain MJB2T exhibited 74.9% ANI values to C. profunda Ra1766HT. In silico DNA-DNA relatedness value between strain MJB2T and C. profunda Ra1766HT was 19.5%. The distinct biochemical, chemotaxonomic and phylogenetic differences from the previously described taxa supported that strain MJB2T represents a novel species of a new genus, for which the name Anaerophilus nitritogenes gen. nov., sp. nov. is proposed. The type strain is MJB2T (=KCTC 15800T=MCCC 1K03631T).
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168
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Nouioui I, Sangal V, Cortés-Albayay C, Jando M, Igual JM, Klenk HP, Zhang YQ, Goodfellow M. Mycolicibacterium stellerae sp. nov., a rapidly growing scotochromogenic strain isolated from Stellera chamaejasme. Int J Syst Evol Microbiol 2019; 69:3465-3471. [PMID: 31460855 DOI: 10.1099/ijsem.0.003644] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
A polyphasic study was undertaken to establish the taxonomic provenance of a rapidly growing Mycolicibacterium strain, CECT 8783T, recovered from the plant Stellera chamaejasme L. in Yunnan Province, China. Phylogenetic analyses based upon 16S rRNA and whole-genome sequences showed that the strain formed a distinct branch within the evolutionary radiation of the genus Mycolicibacterium. The strain was most closely related to Mycolicibacterium moriokaense DSM 44221T with 98.4 % 16S rRNA gene sequence similarity, but was distinguished readily from this taxon by a combination of chemotaxonomic and phenotypic features and by low average nucleotide identity and digital DNA-DNA hybridization values of 79.5 and 21.1 %, respectively. Consequently, the strain is considered, to represent a novel species of Mycolicibacterium for which the name Mycolicibacterium stellerae sp. nov is proposed; the type strain is I10A-01893T (=CECT 8783T=KCTC 19843T=DSM 45590T).
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Carlos Cortés-Albayay
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Marlen Jando
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - José Mariano Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Tiantanxili Road, Beijing 100050, PR China
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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169
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Carro L, Golinska P, Nouioui I, Bull AT, Igual JM, Andrews BA, Klenk HP, Goodfellow M. Micromonospora acroterricola sp. nov., a novel actinobacterium isolated from a high altitude Atacama Desert soil. Int J Syst Evol Microbiol 2019; 69:3426-3436. [PMID: 31395106 DOI: 10.1099/ijsem.0.003634] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Micromonospora strain, designated 5R2A7T, isolated from a high altitude Atacama Desert soil was examined by using a polyphasic approach. Strain 5R2A7T was found to have morphological, chemotaxonomic and cultural characteristics typical of members of the genus Micromonospora. The cell wall contains meso- and hydroxy-diaminopimelic acid, the major whole-cell sugars are glucose, ribose and xylose, the predominant menaquinones MK-10(H4), MK-10(H6), MK-10(H8) and MK-9(H6), the major polar lipids diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and an unknown glycolipid, and the predominant cellular fatty acids iso-C16 : 0, iso-C15 : 0 and 10-methyl C17 : 0. The digital genomic DNA G+C content is 72.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain 5R2A7T was closely related to Micromonospora coriariae DSM 44875T (99.8 %) and Micromonospora cremea CR30T (99.7 %), and was separated readily from the latter, its closest phylogenetic neighbour, based on gyrB and multilocus sequence data, by low average nucleotide identity (92.59 %) and in silico DNA-DNA relatedness (51.7 %) values calculated from draft genome assemblies and by a range of chemotaxonomic and phenotypic properties. Consequently, strain 5R2A7T is considered to represent a novel species of Micromonospora for which the name Micromonospora acroterricola sp. nov. is proposed. The type strain is 5R2A7T (=LMG 30755T=CECT 9656T).
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Affiliation(s)
- Lorena Carro
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.,Departamento de Microbiología y Genética, Edificio Departamental, Lab. 214, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Patrycja Golinska
- Department of Microbiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, 87 100 Torun, Poland
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Alan T Bull
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Jose Mariano Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Barbara A Andrews
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB) University of Chile, Santiago, Chile
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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170
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Hu M, Zhai Y, Zhang Y, Han X, Fang W, Fang Z, Xiao Y. Marinomonas flavescens sp. nov., isolated from seawater adjacent to Fildes Peninsula, Antarctica. Int J Syst Evol Microbiol 2019; 69:3414-3419. [DOI: 10.1099/ijsem.0.003631] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Miaomiao Hu
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, PR China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui 230601, PR China
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, PR China
| | - Yanwu Zhai
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, PR China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui 230601, PR China
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, PR China
| | - Yanfeng Zhang
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, PR China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui 230601, PR China
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, PR China
| | - Xiaoyan Han
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, PR China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui 230601, PR China
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, PR China
| | - Wei Fang
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, PR China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui 230601, PR China
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, PR China
| | - Zemin Fang
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui 230601, PR China
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, PR China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, PR China
| | - Yazhong Xiao
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, PR China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui 230601, PR China
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, PR China
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171
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Bellali S, Naud S, Ndongo S, Lo C, Anani H, Raoult D, Lagier JC. Corynebacterium pacaense sp. nov., Alistipes megaguti sp. nov., Alistipes provencensis sp. nov., 3 new bacteria isolated from fresh human stool specimens. New Microbes New Infect 2019; 32:100593. [PMID: 31641510 PMCID: PMC6796624 DOI: 10.1016/j.nmni.2019.100593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/06/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022] Open
Abstract
Here we describe the basic characteristics of Corynebacterium pacaense strain Marseille-P2417T (= CSUR P2417), Alistipes megaguti strain Marseille-P5997T (= CSUR P5997) and Alistipes provencensis strain Marseille-P2431T (= CSUR P2431 = DSM 102308). The phenotypic criteria, the 16S ribosomal RNA sequencing and MALDI-TOF MS spectra analysis were used to identify and characterize these new bacteria species, which were isolated from fresh human stool specimens.
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Affiliation(s)
- S. Bellali
- Aix-Marseille Université, IRD, MEPHI, Marseille, France
- IHU–Méditerranée Infection, Marseille, France
| | - S. Naud
- Aix-Marseille Université, IRD, MEPHI, Marseille, France
- IHU–Méditerranée Infection, Marseille, France
| | - S. Ndongo
- Aix-Marseille Université, IRD, MEPHI, Marseille, France
- IHU–Méditerranée Infection, Marseille, France
| | - C.I. Lo
- IHU–Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - H. Anani
- IHU–Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, IRD, MEPHI, Marseille, France
- IHU–Méditerranée Infection, Marseille, France
| | - J.-C. Lagier
- Aix-Marseille Université, IRD, MEPHI, Marseille, France
- IHU–Méditerranée Infection, Marseille, France
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172
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Li L, Zhang D, Tang WZ, Lin HW, Lu YH. Geodermatophilus marinus sp. nov., isolated from the marine sponge Leucetta chagosensis. Int J Syst Evol Microbiol 2019; 69:2966-2971. [PMID: 31418670 DOI: 10.1099/ijsem.0.003478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
A novel actinobacterium, designated LHW52908T, was isolated from a marine sponge, Leucettachagosensis, collected in the South China Sea. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain LHW52908T was member of the family Geodermatophilaceae, with highest similarities to Geodermatophilus obscurus DSM 43160T (97.7 %), Geodermatophilus siccatus CF6T (97.6 %) and Geodermatophiluschilensis B12T (97.5 %). Multilocus sequence analysis confirmed that the strain should be a member of genus Geodermatophilus. Chemotaxonomic characteristics confirmed the genus-level affiliation of strain LHW52908T. Based on phylogenetic data, average nucleotide identity and digital DNA-DNA hybridization results, strain LHW52908T could be distinguished from its closest neighbours, representing a novel species of the genus Geodermatophilus, for which the name Geodermatophilusmarinus sp. nov. is proposed, with the type strain LHW52908T (=DSM 106570T=CCTCC AA 2018014T).
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Affiliation(s)
- Lei Li
- Marine Drugs Research Center, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PR China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Die Zhang
- College of Biological and Environmental Engineering, Changsha University, Changsha 410022, PR China
| | - Wei-Zhuo Tang
- College of Biological and Environmental Engineering, Changsha University, Changsha 410022, PR China
- Marine Drugs Research Center, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PR China
| | - Hou-Wen Lin
- Marine Drugs Research Center, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PR China
| | - Yan-Hua Lu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China
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173
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Li GD, Jiang Y, Li YL, Chen X, Zhang K, Shen R, Han L, Huang XS, Jiang CL. Flavobacterium macacae sp. nov., isolated from Macaca mulatta faeces. Int J Syst Evol Microbiol 2019; 70:51-57. [PMID: 31584868 DOI: 10.1099/ijsem.0.003708] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A yellow, Gram-stain-negative, aerobic, non-gliding, non-spore-forming, rod-shaped strain, designated YIM 102600T, was isolated from the faeces of Macaca mulatta dwelling in the Yunnan Wild Animal Park, Yunnan Province, South-West PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 102600T was a member of the genus Flavobacterium, and closely related to Flavobacterium qiangtangense F3T (96.9 % similarity) and Flavobacterium noncentrifugens R-HLS-17T (96.0 % similarity). Phylogenetic trees showed that strain YIM 102600T formed a clade with F. qiangtangense F3T and F. noncentrifugens R-HLS-17T. Growth occurred at 4-30 °C (optimum, 28 °C), pH 7.0-8.0 (pH 7.5) and NaCl concentration 0-2 % (w/v; 0-1 %, w/v). The major fatty acids were iso-C15:0 and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c). The predominant polar lipid was phosphatidylethanolamine and the sole respiratory quinone was menaquinone-6. The DNA G+C content was 36.4 mol%. The calculated digital DNA-DNA hybridization values between strain YIM 102600T and other species of Flavobacterium ranged from 70.0 to 75.0 % and average nucleotide identity values were in a range between 13.7 to 23.5 %. Based above the consensus of phenotypic and phylogenetic analyses as well as whole genome comparisons, strain YIM 102600T (=KCTC 52099T=CCTCC AB 201632T) is proposed to represent type strain of a novel species, Flavobacterium macacae sp. nov.
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Affiliation(s)
- Gui-Ding Li
- Institute of Microbial Pharmaceuticals, College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning 110819, PR China.,Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 2# North Cuihu Road, Kunming, Yunnan 650091, PR China
| | - Yi Jiang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 2# North Cuihu Road, Kunming, Yunnan 650091, PR China
| | - You-Long Li
- Yunnan Wild Animal Park, Fengyuan Road, Panlong District, Kunming, Yunnan 650224, PR China
| | - Xiu Chen
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 2# North Cuihu Road, Kunming, Yunnan 650091, PR China
| | - Kun Zhang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 2# North Cuihu Road, Kunming, Yunnan 650091, PR China
| | - Rui Shen
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 2# North Cuihu Road, Kunming, Yunnan 650091, PR China
| | - Li Han
- Institute of Microbial Pharmaceuticals, College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning 110819, PR China
| | - Xue-Shi Huang
- Institute of Microbial Pharmaceuticals, College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning 110819, PR China
| | - Cheng-Lin Jiang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 2# North Cuihu Road, Kunming, Yunnan 650091, PR China
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174
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Zhang JX, Ming H, Zhao ZL, Ji WL, Chang XL, Zhang LY, Cheng LJ, Meng XL, Li WJ, Nie GX. Nocardia yunnanensis sp. nov., an actinomycete isolated from a soil sample. Int J Syst Evol Microbiol 2019; 69:3116-3120. [DOI: 10.1099/ijsem.0.003600] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jian-Xin Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Hong Ming
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, PR China
| | - Zhuo-Li Zhao
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Wei-Li Ji
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, PR China
| | - Xu-Lu Chang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Ling-Yu Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Li-Jiao Cheng
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Xiao-Lin Meng
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Guo-Xing Nie
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
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175
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García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol 2019; 10:2083. [PMID: 31608019 PMCID: PMC6767994 DOI: 10.3389/fmicb.2019.02083] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/23/2019] [Indexed: 11/25/2022] Open
Abstract
Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Richard L. Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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176
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Halobellus captivus sp. nov., an extremely halophilic archaeon isolated from a subterranean salt mine. Antonie van Leeuwenhoek 2019; 113:221-231. [PMID: 31535337 DOI: 10.1007/s10482-019-01332-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/12/2019] [Indexed: 10/26/2022]
Abstract
An extremely halophilic archaeon, strain ZY21T, was isolated from a subterranean rock salt sample in Yunnan, China. Colonies of strain ZY21T on nutrient-rich agar plates are orange, wet and transparent. Cells are pleomorphic, motile, Gram-stain negative and lyse in distilled water. Cells can grow at 20-55 °C (optimum 42 °C), in the presence of 15-30% (w/v) NaCl (optimum 18-20%) and at pH 6.0-9.5 (optimum 7.5). Mg2+ is required for growth (optimum 0.3 M). The major polar lipids of strain ZY21T are phosphatidylglycerol, phosphatidylglycerol sulfate and phosphatidylglycerol phosphate methyl ester, sulfated mannosyl-glucosyl-glycerol diether-1 and seven unidentified glycolipids. Sequence similarity searches with the 16S rRNA gene and rpoB' gene showed that strain ZY21T is closely related to Halobellus rufus CBA1103T (sequence similarities: 97.5% for 16S rRNA gene and 93.3% for rpoB' gene). The DNA G+C content of strain ZY21T was determined to be 63.0 mol% based on the draft genome sequence. Genome-based sequence similarity analysis showed that the values of the ANI, AAI, and DDH were far below the boundary for delineation of new species. Phenotypic, chemotaxonomic characteristics and phylogenetic properties suggest that strain ZY21T represents a novel species in the genus Halobellus, for which the name Halobellus captivus sp. nov. is proposed. The type strain is ZY21T (= CGMCC 1.16343T = NBRC 113439T).
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177
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Fall N, Lo C, Fournier PE, Sokhna C, Raoult D, Fenollar F, Lagier JC. Arcanobacterium ihumii sp. nov., Varibaculum vaginae sp. nov. and Tessaracoccus timonensis sp. nov., isolated from vaginal swabs from healthy Senegalese women. New Microbes New Infect 2019; 31:100585. [PMID: 31367386 PMCID: PMC6656688 DOI: 10.1016/j.nmni.2019.100585] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/19/2019] [Accepted: 06/26/2019] [Indexed: 12/22/2022] Open
Abstract
Culturomics studies the microbial variety of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. This study identifies three putative new bacterial species: Arcanobacterium ihumii sp. nov. strain Marseille-P5647T, Varibaculum vaginae sp. nov. strain Marseille-P5644T and Tessaracoccus timonensis sp. nov. strain Marseille-P5995T, which we describe according to the concept of taxonogenomics.
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Affiliation(s)
- N.S. Fall
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - P.-E. Fournier
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C. Sokhna
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - F. Fenollar
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - J.-C. Lagier
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
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178
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Thorell K, Meier-Kolthoff JP, Sjöling Å, Martín-Rodríguez AJ. Whole-Genome Sequencing Redefines Shewanella Taxonomy. Front Microbiol 2019; 10:1861. [PMID: 31555221 PMCID: PMC6722870 DOI: 10.3389/fmicb.2019.01861] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/29/2019] [Indexed: 12/30/2022] Open
Abstract
The genus Shewanella encompasses a diverse group of Gram negative, primarily aquatic bacteria with a remarkable ecological relevance, an outstanding set of metabolic features and an emergent clinical importance. The rapid expansion of the genus over the 2000 s has prompted questions on the real taxonomic position of some isolates and species. Recent work by us and others identified inconsistencies in the existing species classification. In this study we aimed to clarify such issues across the entire genus, making use of the genomic information publicly available worldwide. Phylogenomic analyses, including comparisons based on genome-wide identity indexes (digital DNA-DNA hybridization and Average Nucleotide Identity) combined with core and accessory genome content evaluation suggested that the taxonomic position of 64 of the 131 analyzed strains should be revisited. Based on the genomic information currently available, emended descriptions for some Shewanella species are proposed. Our study establishes for the first time a whole-genome based phylogeny for Shewanella spp. including a classification at the subspecific level.
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Affiliation(s)
- Kaisa Thorell
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jan P Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Brunswick, Germany
| | - Åsa Sjöling
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alberto J Martín-Rodríguez
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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179
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Sun S, Chen F, Xu Y, Liu J, Chen S. Halorubrum amylolyticum sp. nov., a novel halophilic archaeon isolated from a salt mine. Antonie van Leeuwenhoek 2019; 112:1849-1861. [PMID: 31401696 DOI: 10.1007/s10482-019-01313-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/31/2019] [Indexed: 01/24/2023]
Abstract
A pleomorphic and non-motile halophilic archaeon forming light-red pigmented colonies, strain ZC67T, was isolated from the Yuanyongjing Salt Mine, Yunnan, China. Based on similarity search and phylogenetic analysis of the 16S rRNA gene sequence, strain ZC67T belongs to the genus Halorubrum and is closely related to the species of Halorubrum (Hrr.) saccharovorum JCM 8865T, Hrr. persicum C49T, Hrr. halophilum B8T, Hrr. lipolyticum 9-3T, Hrr. salsamenti Y69T and Hrr. depositum Y78T with 16S rRNA gene sequence similarities of 99.0%, 98.7%, 98.5%, 98.4%, 98.1% and 97.7%, respectively. The values of average nucleotide identity (ANI) and average amino-acid identity (AAI) between strain ZC67T and its close relatives were less than 90.5% and 89.3%, respectively. In silico DNA-DNA hybridization (DDH) analysis showed that DNA-DNA relatedness between strain ZC67T and its relatives is less than 45%. Values of ANI, AAI and in silico DDH were clearly below the thresholds used for the delineation of a new species. The major polar lipids of strain ZC67T were similar to other neutrophilic members in the genus Halorubrum containing phosphatidylglycerol, phosphatidylglycerolphosphate methyl ester, phosphatidylglycerol sulfate and sulfated mannosyl-glucosyl-glycerol diether-1. The DNA G+C content was determined to be 66.3 mol% (based on the draft genome). Combined with other diagnostic characteristics, e.g. phenotypic and chemotaxonomic differences, strain ZC67T is concluded to represent a novel species in the genus Halorubrum, for which the name Halorubrum amylolyticum sp. nov. is proposed. The type strain is ZC67T (=CGMCC 1.15718T = JCM 31850T).
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Affiliation(s)
- Siqi Sun
- College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu, 241000, Anhui, People's Republic of China
| | - Feilong Chen
- College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu, 241000, Anhui, People's Republic of China
| | - Yao Xu
- College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu, 241000, Anhui, People's Republic of China
| | - Jingwen Liu
- College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu, 241000, Anhui, People's Republic of China
| | - Shaoxing Chen
- College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu, 241000, Anhui, People's Republic of China. .,College of Life Sciences, Honghe University, No.1 Xuefu Road, Mengzi, 661100, Yunnan, People's Republic of China.
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180
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Barbeyron T, Zonta E, Le Panse S, Duchaud E, Michel G. Alteromonas fortis sp. nov., a non-flagellated bacterium specialized in the degradation of iota-carrageenan, and emended description of the genus Alteromonas. Int J Syst Evol Microbiol 2019; 69:2514-2521. [DOI: 10.1099/ijsem.0.003533] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tristan Barbeyron
- 1CNRS / Sorbonne Université, UMR 8227 Integrative Biology of Marine Models (LBI2M), research group of Marine Glycobiology, Station Biologique de Roscoff (SBR), 29680 Roscoff, Brittany, France
| | - Erwann Zonta
- 1CNRS / Sorbonne Université, UMR 8227 Integrative Biology of Marine Models (LBI2M), research group of Marine Glycobiology, Station Biologique de Roscoff (SBR), 29680 Roscoff, Brittany, France
| | - Sophie Le Panse
- 2CNRS / Sorbonne Université, FR 2424 Research and training in marine biology, Merimage platform, Station Biologique de Roscoff (SBR), 29680 Roscoff, Brittany, France
| | - Eric Duchaud
- 3INRA VIM-UR0892 Molecular Immunology and Virology, research group of Infection and Immunity of Fish, Research Center of Jouy-en-Josas, F-78352 Jouy-en-Josas, Ile-de-France, France
| | - Gurvan Michel
- 1CNRS / Sorbonne Université, UMR 8227 Integrative Biology of Marine Models (LBI2M), research group of Marine Glycobiology, Station Biologique de Roscoff (SBR), 29680 Roscoff, Brittany, France
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181
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Cortés-Albayay C, Dorador C, Schumann P, Andrews B, Asenjo J, Nouioui I. Streptomyces huasconensis sp. nov., an haloalkalitolerant actinobacterium isolated from a high altitude saline wetland at the Chilean Altiplano. Int J Syst Evol Microbiol 2019; 69:2315-2322. [DOI: 10.1099/ijsem.0.003468] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Carlos Cortés-Albayay
- 1School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle upon Tyne NE1 7RU, UK
- 2Centre for Biotechnology and Bioengineering, University of Chile, Beauchef 851, Santiago, Chile
| | - Cristina Dorador
- 3Laboratory of Microbial Complexity and Functional Ecology, Departamento de Biotecnología, Facultad de Ciencias del Mary Recursos Biológicos and Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Chile
| | - Peter Schumann
- 4Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany
| | - Barbara Andrews
- 2Centre for Biotechnology and Bioengineering, University of Chile, Beauchef 851, Santiago, Chile
| | - Juan Asenjo
- 2Centre for Biotechnology and Bioengineering, University of Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- 1School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle upon Tyne NE1 7RU, UK
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182
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Komaki H, Tamura T. Reclassification of Streptomyces rimosus subsp. paromomycinus as Streptomyces paromomycinus sp. nov. Int J Syst Evol Microbiol 2019; 69:2577-2583. [PMID: 31225792 DOI: 10.1099/ijsem.0.003545] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptomyces rimosus is currently composed of two subspecies: Streptomyces rimosus subsp. rimosus and Streptomyces rimosus subsp. paromomycinus. The 16S rRNA gene similarity between type strains of these two subspecies is 99.03 %, whereas that between S. rimosus subsp. paromomycinus and Streptomyces chrestomyceticusis 100 %. To assess the taxonomic status of S. rimosus subsp. paromomycinus, genome sequencing was performed on the type strains of S. rimosus subsp. paromomycinus and S. chrestomyceticus. Digital DNA-DNA hybridization values between S. rimosus subsp. paromomycinus NBRC 15454T and S. rimosus subsp. rimosus ATCC 10970T and between S. rimosus subsp. paromomycinus NBRC 15454T and S. chrestomyceticus NBRC 13444T were 35.4 and 59.9 %, respectively, which are less than the thresholds for bacterial species delineation and indicate that S. rimosus subsp. paromomycinus is not S. rimosus, but an independent species different from S. rimosus and S. chrestomyceticus. In addition, phenotypic data also support that S. rimosus subsp. paromomycinus is distinct from S. chrestomyceticus. Therefore, S. rimosus subsp. paromomycinus should be reclassified as a novel species, for which we propose the name Streptomyces paromomycinus sp. nov. The type strain is NBRC 15454T (=ATCC 14827T=DSM 41429T=JCM 4541T=JCM 4871T=NRRL 2455T=VKM Ac-605T).
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Affiliation(s)
- Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Chiba 292-0818, Japan
| | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Chiba 292-0818, Japan
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183
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Cortés-Albayay C, Dorador C, Schumann P, Schniete JK, Herron P, Andrews B, Asenjo J, Nouioui I. Streptomyces altiplanensis sp. nov., an alkalitolerant species isolated from Chilean Altiplano soil, and emended description of Streptomyces chryseus (Krasil'nikov et al. 1965) Pridham 1970. Int J Syst Evol Microbiol 2019; 69:2498-2505. [PMID: 31204968 DOI: 10.1099/ijsem.0.003525] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic approach was used for evaluating the taxonomic status of strain HST21T isolated from Salar de Huasco in the Atacama Desert. The results of 16S rRNA gene and multilocus sequence phylogenetic analyses assigned strain HST21T to the genus Streptomyceswith Streptomyces albidochromogenes DSM 41800Tand Streptomyces flavidovirens DSM 40150T as its nearest neighbours. Digital DNA-DNA hydridization (dDDH) and average nucleotide identity (ANI) values between the genome sequences of strain HST21T and S. albidochromogenes DSM 41800T (35.6 and 88.2 %) and S. flavidovirens DSM 40105T (47.2 and 88.8 %) were below the thresholds of 70 and 95-96 % for prokaryotic conspecific assignation. Phenotypic, chemotaxonomic and genetic results distinguished strain HST21T from its closest neighbours. Strain HST21T is characterized by the presence of ll-diaminopimelic acid in its peptidoglycan layer; glucose and ribose as whole cell sugars; diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, glycophospholipids, unknown lipids and phospholipids as polar lipids; and anteiso-C15 : 0 (21.6 %) and anteiso-C17 : 0 (20.5 %) as major fatty acids (>15 %). Based on these results, strain HST21T merits recognition as a novel species, for which the name Streptomyces altiplanensis sp. nov. is proposed. The type strain is HST21T=DSM 107267T=CECT 9647T. While analysing the phylogenies of strain HST21T, Streptomyces chryseus DSM 40420T and Streptomyces helvaticus DSM 40431T were found to have 100 % 16S rRNA gene sequence similarity with digital DNA-DNA hydridization (dDDH) and average nucleotide identity (ANI) values of 95.3 and 99.4 %, respectively. Therefore, S. helvaticus is considered as a later heterotypic synonym of S. chryseus and, consequently, we emend the description of S. chryseus.
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Affiliation(s)
- Carlos Cortés-Albayay
- School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle upon Tyne NE1 7RU, UK
- Centre for Biotechnology and Bioengineering, University of Chile, Beauchef 851, Santiago, Chile
| | - Cristina Dorador
- Laboratory of Microbial Complexity and Functional Ecology, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos & Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Chile
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany
| | - Jana K Schniete
- Department of Physics, University of Strathclyde, 107 Rottenrow, Glasgow G4 0NG, UK
| | - Paul Herron
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Barbara Andrews
- Centre for Biotechnology and Bioengineering, University of Chile, Beauchef 851, Santiago, Chile
| | - Juan Asenjo
- Centre for Biotechnology and Bioengineering, University of Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle upon Tyne NE1 7RU, UK
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184
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Geng Y, Zhang Y, Tian J, Liu J, Qin K, Huang Y, Wei Z, Peng F. Hymenobacter oligotrophus sp. nov., isolated from a contaminated agar plate. Antonie van Leeuwenhoek 2019; 112:1533-1544. [PMID: 31165292 DOI: 10.1007/s10482-019-01279-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/15/2019] [Indexed: 11/26/2022]
Abstract
A taxonomic study of a Gram-stain negative, rod-shaped, motile, asporogenous, catalase- and oxidase-positive bacterium, sh-6T, forming pink-red colonies, isolated from a contaminated R2A plate in the laboratory was performed. Its optimum growth temperature was determined to be 28 °C in the absence of NaCl on R2A plates. On the basis of 16S rRNA gene sequence analysis, strain sh-6T belongs to the genus Hymenobacter and is closely related to Hymenobacter deserti ZLB-3T (95.05%), Hymenobacter paludis KBP-30T (94.96%), Hymenobacter coalescens WW84T (94.04%), Hymenobacter gummosus ANT-18T (93.38%), Hymenobacter ocellatus Myx2105T (93.70%), Hymenobacter jeollabukensis 1-3-3-8T (93.48%) and Hymenobacter koreensis GYR3077T (93.21%). Comparison of the genome of strain sh-6T and that of H. gummosus ANT-18T gave digital DNA-DNA hybridization and Average Nucleotide Identity values of 20.6% and 78.4%, respectively. The respiratory isoprenoid quinone and polyamine component were identified as MK-7 and sym-homospermidine, respectively. The major cellular fatty acids identified as iso-C15:0, summed feature 4 (iso-C17:1 I/anteiso B), iso-C16:0, iso-C17:0 3-OH and iso-C17:0. The major polar lipid of strain sh-6T determined to be phosphatidylethanolamine. The DNA G+C content was determined to be 60.5 mol%. On the basis of the evidence presented in this study, a novel species of the genus Hymenobacter, Hymenobacter oligotrophus sp. nov., is proposed, with the type strain sh-6T (= CCTCC AB 2016064T = KCTC 62345T).
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Affiliation(s)
- Yingchao Geng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yumin Zhang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jin Tian
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jia Liu
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Kun Qin
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yao Huang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ziyan Wei
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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185
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Amphritea opalescens sp. nov., isolated from sediment adjacent to Fildes Peninsula, Antarctica. Int J Syst Evol Microbiol 2019; 69:1585-1590. [DOI: 10.1099/ijsem.0.003359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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186
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Montero-Calasanz MDC, Yaramis A, Nouioui I, Igual JM, Spröer C, Castro JF, Schumann P, Klenk HP, Urzì C. Modestobacter italicus sp. nov., isolated from Carrara marble quarry and emended descriptions of the genus Modestobacter and the species Modestobacter marinus, Modestobacter multiseptatus, Modestobacter roseus and Modestobacter versicolor. Int J Syst Evol Microbiol 2019; 69:1537-1545. [DOI: 10.1099/ijsem.0.003282] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - Adnan Yaramis
- 1School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Imen Nouioui
- 1School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - José Mariano Igual
- 2Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Cathrin Spröer
- 3Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jean Franco Castro
- 4Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Beauchef 851, Santiago, Chile
| | - Peter Schumann
- 3Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- 1School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Clara Urzì
- 5Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Italy
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187
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Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182. [PMID: 31097708 PMCID: PMC6522516 DOI: 10.1038/s41467-019-10210-3] [Citation(s) in RCA: 1509] [Impact Index Per Article: 301.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 04/29/2019] [Indexed: 02/07/2023] Open
Abstract
Microbial taxonomy is increasingly influenced by genome-based computational methods. Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS, the Type (Strain) Genome Server, a user-friendly high-throughput web server for genome-based prokaryote taxonomy, connected to a large, continuously growing database of genomic, taxonomic and nomenclatural information. It infers genome-scale phylogenies and state-of-the-art estimates for species and subspecies boundaries from user-defined and automatically determined closest type genome sequences. TYGS also provides comprehensive access to nomenclature, synonymy and associated taxonomic literature. Clinically important examples demonstrate how TYGS can yield new insights into microbial classification, such as evidence for a species-level separation of previously proposed subspecies of Salmonella enterica. TYGS is an integrated approach for the classification of microbes that unlocks novel scientific approaches to microbiologists worldwide and is particularly helpful for the rapidly expanding field of genome-based taxonomic descriptions of new genera, species or subspecies.
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Affiliation(s)
- Jan P Meier-Kolthoff
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Braunschweig, Germany.
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Braunschweig, Germany
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188
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Togo A, Diop A, Dubourg G, Khelaifia S, Richez M, Armstrong N, Maraninchi M, Fournier PE, Raoult D, Million M. Anaerotruncus massiliensis sp. nov., a succinate-producing bacterium isolated from human stool from an obese patient after bariatric surgery. New Microbes New Infect 2019; 29:100508. [PMID: 30891246 PMCID: PMC6403417 DOI: 10.1016/j.nmni.2019.01.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 01/15/2019] [Indexed: 12/30/2022] Open
Abstract
A new bacterium, strain AT3T, was isolated by microbial culturomics from a faecal sample from a Frenchman after bariatric surgery. The isolate exhibited 96.6% 16S ribosomal RNA gene nucleotide sequence similarity with Anaerotruncus colihominis strain WAL 14565T = CCUG 45055T = CIP 107754T. Phenotypic and genomic characteristics showed that the new strain represents a novel species, for which the name Anaerotruncus massiliensis sp. nov. is proposed. The type strain is strain AT3T = CSUR P2007T = DSM 100567T.
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Affiliation(s)
- A.H. Togo
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - A. Diop
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, VITROME, France
| | - G. Dubourg
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - S. Khelaifia
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - M. Richez
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - N. Armstrong
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - M. Maraninchi
- Aix-Marseille Université, NORT ‘Nutrition, Obesity and Risk of Thrombosis,’ INSERM1062, INRA1260, Marseille, France
| | | | - D. Raoult
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - M. Million
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
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189
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Flavobacterium viscosus sp. nov. and Flavobacterium tangerina sp. nov., from Primates Feces. Curr Microbiol 2019; 76:818-823. [DOI: 10.1007/s00284-019-01692-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 04/16/2019] [Indexed: 11/26/2022]
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190
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Haloterrigena salifodinae sp. nov., an extremely halophilic archaeon isolated from a subterranean rock salt. Antonie van Leeuwenhoek 2019; 112:1317-1329. [DOI: 10.1007/s10482-019-01264-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/08/2019] [Indexed: 10/27/2022]
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191
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Kämpfer P, Busse HJ, Criscuolo A, Bizet C, Clermont D, McInroy JA, Glaeser SP. Pigmentiphaga humi sp. nov., isolated from soil amended with humic acid. Int J Syst Evol Microbiol 2019; 69:1573-1578. [PMID: 30958260 DOI: 10.1099/ijsem.0.003355] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A slightly beige-pigmented, Gram-stain-negative, rod-shaped bacterium, strain IMT-318T, was isolated from soil in a field located in Malvern, Alabama, USA. Phylogenetic analysis based on the 16S rRNA gene placed the strain within the genus Pigmentiphaga with highest 16S rRNA gene sequence similarity of 98.74 % and 98.67 % to the type strains of Pigmentiphaga kullae and Pigmentiphaga daeguensis, respectively. Sequence similarities to all other species of the genus were below 98.0 %. Results of the chemotaxonomic analysis, however, showed clear similarities to the genus Pigmentiphaga. The main cellular fatty acids of the strain were C16 : 0, C18 : 1 ω7c, C17 : 0 cyclo and C19 : 0 cyclo ω8c. The major quinone was ubiquinone Q-8. The polar lipid profile was composed of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified aminophospholipid. In the polyamine pattern, putrescine and 2-hydroxyputrescine were predominant. The diamino acid of the peptidoglycan was meso-diaminopimelic acid. Based on phylogenetic, chemotaxonomic and phenotypic analyses, we propose a new species of the genus Pigmentiphaga, with the name Pigmentiphaga humi sp. nov. and strain IMT-318T (=LMG 30658T=CIP 111626T=CCM 8859T) as the type strain.
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Affiliation(s)
- Peter Kämpfer
- 1Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Hans-Jürgen Busse
- 2Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, A-1210 Wien, Austria
| | - Alexis Criscuolo
- 3Hub de Bioinformatique et Biostatistique - C3BI, Institut Pasteur, USR 3756, CNRS, Paris (75015), France
| | - Chantal Bizet
- 4Institut Pasteur - CIP - Collection of Institut Pasteur - CRBIP-Centre de Ressources Biologiques, Paris, France
| | - Dominique Clermont
- 5Institut Pasteur - CIP - Collection of Institut Pasteur - Paris, France
| | - John A McInroy
- 6Department of Entomology and Plant Pathology, Auburn University, AL 36849, USA
| | - Stefanie P Glaeser
- 1Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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192
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Kämpfer P, Bizet C, Clermont D, Criscuolo A, Kloepper LN, Duncan MB, McInroy JA, Kloepper JW, Schumann P, Glaeser SP. Filibacter tadaridae sp. nov., isolated from within a guano pile from a colony of Mexican free-tailed bats Tadarida brasiliensis. Int J Syst Evol Microbiol 2019; 69:1438-1442. [PMID: 30893028 DOI: 10.1099/ijsem.0.003334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic bacterium, TB-66T, was isolated from a pile of bat guano in a cave of New Mexico, USA. On the basis of 16S rRNA gene sequence similarity comparisons, strain TB-66Tgrouped together with Filibacter limicola showing a 16S rRNA gene sequence similarity of 98.5 % to the type strain. The quinone system of strain TB-66T consisted predominantly of menaquinone MK-7. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylserine and three unidentified phospholipids. The peptidoglycan type was A4α l-Lys-d-Glu (A11.33). The major fatty acids were C15 : 0 anteiso, C16 : 0, and C16 : 1 ω7c. The G+C content of the genomic DNA was 37.6 (±1.8) mol%. On the basis of the genotypic and phenotypic properties it is clear that strain TB-66T represents a member of the genus Filibacter, but is distinct from the only other species in the genus, Filibacter limicola DSM 13886T. We propose a novel species with the name Filibacter tadaridae sp. nov. The type strain is TB-66T (= CIP 111629T= LMG 30660T= CCM 8866T).
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Affiliation(s)
- Peter Kämpfer
- 1Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Chantal Bizet
- 2Institut Pasteur - CIP - Collection of Institut Pasteur, Paris, France
| | - Dominique Clermont
- 2Institut Pasteur - CIP - Collection of Institut Pasteur, Paris, France
| | - Alexis Criscuolo
- 3Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France
| | - Laura N Kloepper
- 4Department of Biology, Saint Mary's College, Notre Dame, Indiana, USA
| | - Makenzie B Duncan
- 4Department of Biology, Saint Mary's College, Notre Dame, Indiana, USA
| | - John A McInroy
- 5Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | - Joseph W Kloepper
- 5Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | | | - Stefanie P Glaeser
- 1Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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193
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Ramezani M, Nikou MM, Pourmohyadini M, Spröer C, Schumann P, Harirchi S, Aryaefar M, Fazeli SAS, Amoozegar MA, Ventosa A. Planomicrobium iranicum sp. nov., a novel slightly halophilic bacterium isolated from a hypersaline wetland. Int J Syst Evol Microbiol 2019; 69:1433-1437. [PMID: 30860463 DOI: 10.1099/ijsem.0.003332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strain, designated as MX6T was isolated from Meighan wetland, in the centre of Iran. The cells were Gram-stain-positive, motile, coccoid to rod-shaped, oxidase- and catalase-positive. The strain grew optimally at 35 °C, 3 % (w/v) NaCl and pH 7-7.5. A polyphasic taxonomic study was undertaken in order to characterize the strain in detail. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that MX6T represented a member of the phylum Firmicutes, family Planococcaceae, genus Planomicrobium, and showed the highest similarity with Planomicrobium flavidum ISL-41T (98.2 %) and Planomicrobium psychrophilum CMC 53orT (98.0 %). The main polar lipids of MX6T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and seven unidentified phospholipids and its DNA G+C content was 45.5 mol%. Major cellular fatty acids were anteiso-C15 : 0, C16 : 1ω7c alcohol, iso-C14 : 0, iso-C15 : 0 and iso-C16 : 0 and the predominant respiratory quinone was Q-8 (62 %). Experimental DNA-DNA hybridization between MX6T and Planomicrobium flavidum IBRC-M 11047T was 20 %, supporting the differential taxonomic status of MX6T as representing a different taxon. All these data indicate that MX6T represents a novel species of the genus Planomicrobium, for which the name Planomicrobium iranicum sp. nov. is proposed. The type strain is MX6T (=IBRC M 10928T=LMG 28548T).
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Affiliation(s)
- Mohaddaseh Ramezani
- 1Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
| | - Mahdi Moshtaghi Nikou
- 1Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
| | | | - Cathrin Spröer
- 2Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Peter Schumann
- 2Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Shrareh Harirchi
- 1Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
| | - Mahnaz Aryaefar
- 1Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
| | - Seyed Abolhassan Shahzadeh Fazeli
- 1Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran.,3Department of Molecular and Cellular Biology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Mohammad Ali Amoozegar
- 4Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, Extremophiles Laboratory, University of Tehran, Tehran, Iran
| | - Antonio Ventosa
- 5Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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194
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Gonçalves Pessoa RB, de Oliveira WF, Marques DSC, Dos Santos Correia MT, de Carvalho EVMM, Coelho LCBB. The genus Aeromonas: A general approach. Microb Pathog 2019; 130:81-94. [PMID: 30849490 DOI: 10.1016/j.micpath.2019.02.036] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 02/07/2023]
Abstract
The genus Aeromonas comprises more than thirty Gram-negative bacterial species which mostly act as opportunistic microorganisms. These bacteria are distributed naturally in diverse aquatic ecosystems, where they are easily isolated from animals such as fish and crustaceans. A capacity for adaptation also makes Aeromonas able to colonize terrestrial environments and their inhabitants, so these microorganisms can be identified from different sources, such as soils, plants, fruits, vegetables, birds, reptiles, amphibians, among others. Infectious processes usually develop in immunocompromised humans; in fish and other marine animals this process occurs under conditions of stress. Such events are most often associated with incorrect practices in aquaculture. Aeromonas has element diverse ranges, denominated virulence factors, which promote adhesion, colonization and invasion into host cells. These virulence factors, such as membrane components, enzymes and toxins, for example, are differentially expressed among species, making some strains more virulent than others. Due to their diversity, no single virulence factor was considered determinant in the infectious process generated by these microorganisms. Unlike other genera, Aeromonas species are erroneously differentiated by conventional biochemical tests. Therefore, molecular assays are necessary for this purpose. Nevertheless, new means of identification have been considered in order to generate methods that, like molecular tests, can correctly identify these microorganisms. The main objectives of this review are to explain environmental and structural characteristics of the Aeromonas genus and to discuss virulence mechanisms that these bacteria use to infect aquatic organisms and humans, which are important aspects for aquaculture and public health, respectively. In addition, this review aims to clarify new tests for the precise identification of the species of Aeromonas, contributing to the exact and specific diagnosis of infections by these microorganisms and consequently the treatment.
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Affiliation(s)
- Rafael Bastos Gonçalves Pessoa
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, s/n, Cidade Universitária, CEP: 50670-420, Recife, Pernambuco, Brazil
| | - Weslley Felix de Oliveira
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, s/n, Cidade Universitária, CEP: 50670-420, Recife, Pernambuco, Brazil
| | - Diego Santa Clara Marques
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, s/n, Cidade Universitária, CEP: 50670-420, Recife, Pernambuco, Brazil
| | - Maria Tereza Dos Santos Correia
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, s/n, Cidade Universitária, CEP: 50670-420, Recife, Pernambuco, Brazil
| | - Elba Verônica Matoso Maciel de Carvalho
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, s/n, Cidade Universitária, CEP: 50670-420, Recife, Pernambuco, Brazil
| | - Luana Cassandra Breitenbach Barroso Coelho
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, s/n, Cidade Universitária, CEP: 50670-420, Recife, Pernambuco, Brazil.
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195
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Diop A, Diop K, Tomei E, Armstrong N, Bretelle F, Raoult D, Fenollar F, Fournier PE. Collinsella vaginalis sp. nov. strain Marseille-P2666 T, a new member of the Collinsella genus isolated from the genital tract of a patient suffering from bacterial vaginosis. Int J Syst Evol Microbiol 2019; 69:949-956. [PMID: 30806613 DOI: 10.1099/ijsem.0.003221] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A strictly anaerobic, Gram-stain-positive, non motile and non-spore-forming rod-shaped bacterium, strain Marseille-P2666T, was isolated using the culturomics approach from a vaginal sample of a French patient suffering from bacterial vaginosis. Cells were saccharolytic and were negative for catalase, oxidase, urease, nitrate reduction, indole production, hydrolysis of aesculin and gelatin. Strain Marseille-P2666T exhibited 97.04 % 16S rRNA sequence similarity to Collinsella tanakaei type strain YIT 12063T, the phylogenetically closest species with standing in nomenclature. The major fatty acids were C18:1ω9 (38 %), C16 : 0 (24 %) and C18 : 0 (19 %). The G+C content of the genome sequence of strain Marseille-P2666T is 64.6 mol%. On the basis of its phenotypic, phylogenetic and genomic features, strain Marseille-P2666T (=CSUR 2666T=DSM103342T) was classified as type strain of a novel species within the genus Collinsella for which the name Collinsella vaginalis sp. nov. is proposed.
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Affiliation(s)
- Awa Diop
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France
| | - Khoudia Diop
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France
| | - Enora Tomei
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France
| | - Nicholas Armstrong
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France
| | - Florence Bretelle
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France.,Department of Gynecology and Obstetrics, Gynépole, Marseille, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Didier Raoult
- UMR MEPHI, Aix-Marseille University, IRD, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Uuniversitaire Méditerranée Infection, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Florence Fenollar
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France
| | - Pierre-Edouard Fournier
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France
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196
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Chua MJ, Campen RL, Wahl L, Grzymski JJ, Mikucki JA. Genomic and physiological characterization and description of Marinobacter gelidimuriae sp. nov., a psychrophilic, moderate halophile from Blood Falls, an antarctic subglacial brine. FEMS Microbiol Ecol 2019; 94:4850642. [PMID: 29444218 DOI: 10.1093/femsec/fiy021] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 02/08/2018] [Indexed: 11/12/2022] Open
Abstract
Antarctic subice environments are diverse, underexplored microbial habitats. Here, we describe the ecophysiology and annotated genome of a Marinobacter strain isolated from a cold, saline, iron-rich subglacial outflow of the Taylor Glacier, Antarctica. This strain (BF04_CF4) grows fastest at neutral pH (range 6-10), is psychrophilic (range: 0°C-20°C), moderately halophilic (range: 0.8%-15% NaCl) and hosts genes encoding potential low temperature and high salt adaptations. The predicted proteome suggests it utilizes fewer charged amino acids than a mesophilic Marinobacter strain. BF04_CF4 has increased concentrations of membrane unsaturated fatty acids including palmitoleic (33%) and oleic (27.5%) acids that may help maintain cell membrane fluidity at low temperatures. The genome encodes proteins for compatible solute biosynthesis and transport, which are known to be important for growth in saline environments. Physiological verification of predicted metabolic functions demonstrate BF04_CF4 is capable of denitrification and may facilitate iron oxidation. Our data indicate that strain BF04_CF4 represents a new Marinobacter species, Marinobacter gelidimuriae sp. nov., that appears well suited for the subglacial environment it was isolated from. Marinobacter species have been isolated from other cold, saline environments in the McMurdo Dry Valleys and permanently cold environments globally suggesting that this lineage is cosmopolitan and ecologically relevant in icy brines.
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Affiliation(s)
- Michelle J Chua
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Richard L Campen
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Lindsay Wahl
- Department of Environmental Studies, Dartmouth College, Hanover, NH, 03755, USA
| | - Joseph J Grzymski
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, 89512, USA
| | - Jill A Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
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197
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Li L, Xu QH, Wang XT, Lin HW, Lu YH. Actinomadura craniellae sp. nov., isolated from a marine sponge in the South China Sea. Int J Syst Evol Microbiol 2019; 69:1207-1212. [PMID: 30777821 DOI: 10.1099/ijsem.0.003295] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel marine actinomycete, designated LHW63021T, was isolated from a marine sponge, genus Craniella, collected in the South China Sea. A polyphasic approach was applied to characterize the taxonomic position of this strain. The strain was found to have scarce aerial mycelia that differentiated into spore chains. The cell-wall hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid. Glucose, galactose, mannose and madurose were found in the whole-cell hydrolysates. The dominant polar lipids were phosphatidylinositol and diphosphatidylglycerol. MK-9(H6) and MK-9(H8) were the predominant menaquinones. The major fatty acids were iso-C16 : 0, iso-C18 : 0, 10-methyl C17 : 0 and C18 : 1 ω9c. The DNA G+C content based on the draft genome sequence was 72.0 mol%. 16S rRNA gene sequence analysis indicated that strain LHW63021T was a member of the genus Actinomadura and had the highest similarity to Actinomadura echinospora DSM 43163T (97.3 %). Phylogenetic trees supported their close relationship. The average nucleotide identity and digital DNA-DNA hybridization values between the whole genome sequences of strain LHW63021T and A. echinospora DSM 43163T were 79.13 and 23.20 %, respectively. The evidence from the polyphasic study shows that strain LHW63021T represents a novel species of the genus Actinomadura, for which the name Actinomadura craniellae sp. nov. is proposed. The type strain is LHW63021T (=DSM 106125T=CCTCC AA 2018015T).
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Affiliation(s)
- Lei Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China.,Marine Drugs Research Center, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PR China
| | - Qi-Hang Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China.,Marine Drugs Research Center, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PR China
| | - Xiao-Tian Wang
- Shanghai Pinghe Bilingual School, Shanghai 201206, PR China
| | - Hou-Wen Lin
- Marine Drugs Research Center, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PR China
| | - Yan-Hua Lu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China
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198
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Oshkin IY, Kulichevskaya IS, Rijpstra WIC, Sinninghe Damsté JS, Rakitin AL, Ravin NV, Dedysh SN. Granulicella sibirica sp. nov., a psychrotolerant acidobacterium isolated from an organic soil layer in forested tundra, West Siberia. Int J Syst Evol Microbiol 2019; 69:1195-1201. [PMID: 30775959 DOI: 10.1099/ijsem.0.003290] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
An isolate of strictly aerobic, pale-pink pigmented bacteria, strain AF10T, was obtained from an organic soil layer in forested tundra, Nadym region, West Siberia. Cells of strain AF10T were Gram-negative, non-motile rods that produced an amorphous extracellular polysaccharide-like substance and formed large cell aggregates in old cultures. These bacteria were chemoorganotrophic, mildly acidophilic and psychrotolerant, and grew between pH 3.5 and 7.0 (optimum, pH 4.5-5.0) and at temperatures between 2 and 30 °C. The preferred growth substrates were sugars and some polysaccharides. The major fatty acids were iso-C15 : 0, C16 : 0, C16 : 1∆9 c and 13,16-dimethyl octacosanedioic acid. The genome of strain AF10T was 6.14 Mbp in size and encoded a wide repertoire of carbohydrate active enzymes. The genomic DNA G+C content was 59.8 mol%. Phylogenetic analysis indicated that strain AF10T is a member of the genus Granulicella, family Acidobacteriaceae, but displays 94.4-98.0 % 16S rRNA gene sequence similarity to currently described members of this genus. On the basis of phenotypic, chemotaxonomic, phylogenetic and genomic analyses, we propose to classify this bacterium as representing a novel species of the genus Granulicella, Granulicellasibirica sp. nov. Strain AF10T (=DSM 104461T=VKM B-3276T) is the type strain.
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Affiliation(s)
- Igor Y Oshkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Irina S Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - W Irene C Rijpstra
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, 1790 AB Den Burg, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, 1790 AB Den Burg, The Netherlands.,Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht University, Utrecht, The Netherlands
| | - Andrey L Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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199
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Nouioui I, Klenk HP, Igual JM, Gulvik CA, Lasker BA, McQuiston JR. Streptacidiphilus bronchialis sp. nov., a ciprofloxacin-resistant bacterium from a human clinical specimen; reclassification of Streptomyces griseoplanus as Streptacidiphilus griseoplanus comb. nov. and emended description of the genus Streptacidiphilus. Int J Syst Evol Microbiol 2019; 69:1047-1056. [PMID: 30741626 DOI: 10.1099/ijsem.0.003267] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of strain 15-057AT, an acidophilic actinobacterium isolated from the bronchial lavage of an 80-year-old male, was determined using a polyphasic approach incorporating morphological, phenotypic, chemotaxonomic and genomic analyses. Pairwise 16S rRNA gene sequence similarities calculated using the GGDC web server between strain 15-057AT and its closest phylogenetic neighbours, Streptomyces griseoplanus NBRC 12779T and Streptacidiphilus oryzae TH49T, were 99.7 and 97.6 %, respectively. The G+C content of isolate 15-057AT was determined to be 72.6 mol%. DNA-DNA relatedness and average nucleotide identity between isolate 15-057AT and Streptomyces griseoplanus DSM 40009T were 29.2±2.5 % and 85.97 %, respectively. Chemotaxonomic features of isolate 15-057AT were consistent with its assignment within the genus Streptacidiphilus: the whole-cell hydrolysate contained ll-diaminopimelic acid as the diagnostic diamino acid and glucose, mannose and ribose as cell-wall sugars; the major menaquinone was MK9(H8); the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, glycophospholipid, aminoglycophospholipid and an unknown lipid; the major fatty acids were anteiso-C15 : 0 and iso-C16 : 0. Phenotypic and morphological traits distinguished isolate 15-057AT from its closest phylogenetic neighbours. The results of our taxonomic analyses showed that strain 15-057AT represents a novel species within the evolutionary radiation of the genus Streptacidiphilus, for which the name Streptacidiphilus bronchialis sp. nov. is proposed. The type strain is 15-057AT (=DSM 106435T=ATCC BAA-2934T).
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - José Mariano Igual
- Instituto de Recursos Naturales y Agrobiologia de Salamanca, Consejo Superior de Investigaciones Cientificas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Christopher A Gulvik
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Disease, Centers for Diseases Control and Prevention, Atlanta, GA 30333, USA
| | - Brent A Lasker
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Disease, Centers for Diseases Control and Prevention, Atlanta, GA 30333, USA
| | - John R McQuiston
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Disease, Centers for Diseases Control and Prevention, Atlanta, GA 30333, USA
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200
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Meng XL, Ming H, Huang JR, Zhang LY, Cheng LJ, Zhao ZL, Ji WL, Li WJ, Nie GX. Paracoccus halotolerans sp. nov., isolated from a salt lake. Int J Syst Evol Microbiol 2019; 69:523-528. [DOI: 10.1099/ijsem.0.003190] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Xiao-Lin Meng
- 1College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Hong Ming
- 2Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, PR China
| | - Jian-Rong Huang
- 1College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Ling-Yu Zhang
- 1College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Li-Jiao Cheng
- 1College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Zhuo-Li Zhao
- 1College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Wei-Li Ji
- 2Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, PR China
| | - Wen-Jun Li
- 3State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Guo-Xing Nie
- 1College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
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