International Journal of Systematic and Evolutionary Microbiology
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Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species Modern bacterial taxonomy is based on a polyphasic approach that combines phenotypic and genotypic characteristics, including 16S rRNA sequence similarity. However, the 95 % (for genus) and 98.7 % (for species) sequence similarity thresholds that are currently recommended to classify bacterial isolates were defined by comparison of a limited number of bacterial species, and may not apply to many genera that contain human-associated species. For each of 158 bacterial genera containing human-associated species, we computed pairwise sequence similarities between all species that have names with standing in nomenclature and then analysed the results, considering as abnormal any similarity value lower than 95 % or greater than 98.7 %. Many of the current bacterial species with validly published names do not respect the 95 and 98.7 % thresholds, with 57.1 % of species exhibiting 16S rRNA gene sequence similarity rates ≥98.7 %, and 60.1 % of genera containing species exhibiting a 16S rRNA gene sequence similarity rate <95 %. In only 17 of the 158 genera studied (10.8 %), all species respected the 95 and 98.7 % thresholds. As we need powerful and reliable taxonomical tools, and as potential new tools such as pan-genomics have not yet been fully evaluated for taxonomic purposes, we propose to use as thresholds, genus by genus, the minimum and maximum similarity values observed among species.
International Journal of Systematic and Evolutionary Microbiology - Tập 65 Số Pt_6 - Trang 1929-1934 - 2015
Acaricomes phytoseiuli gen. nov., sp. nov., isolated from the predatory mite Phytoseiulus persimilis A Gram-positive, rod-shaped, non-spore-forming bacterium, strain CSCT , was isolated from diseased, surface-sterilized specimens of the predatory mite Phytoseiulus persimilis Athias-Henriot and subjected to polyphasic taxonomic analysis. Comparative analysis of the 16S rRNA gene sequence revealed that the strain was a new member of the family Micrococcaceae . Nearest phylogenetic neighbours were determined as Renibacterium salmoninarum (94·0 %), Arthrobacter globiformis (94·8 %) and Arthrobacter russicus (94·6 %). Although the predominant fatty acids (anteiso C15 : 0 ), cell-wall sugars (galactose, glucose) and polar lipids (diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol) are in accordance with those of members of the genus Arthrobacter , strain CSCT can be distinguished from members of the genus Arthrobacter by biochemical tests, the absence of a rod–coccus life cycle and the occurrence of the partially saturated menaquinone MK-10(H2 ) as the predominant menaquinone. The DNA G+C content is 57·7 mol%. On the basis of morphological, chemotaxonomic and phylogenetic differences from other species of the Micrococcaceae , a novel genus and species are proposed, Acaricomes phytoseiuli gen. nov., sp. nov. The type strain is CSCT (=DSM 14247T =CCUG 49701T ).
International Journal of Systematic and Evolutionary Microbiology - Tập 56 Số 2 - Trang 465-469 - 2006
Desulfonatronobacter acidivorans gen. nov., sp. nov. and Desulfobulbus alkaliphilus sp. nov., haloalkaliphilic heterotrophic sulfate-reducing bacteria from soda lakes Two types of heterotrophic sulfate-reducing bacteria (SRB) were isolated from anoxic sediments of hypersaline soda lakes in Kulunda Steppe (Altai, Russia). The isolates used propionate as an energy and carbon source. Strain APT2T was enriched and isolated with thiosulfate as the electron acceptor. Strains APS1T and ASS1 were isolated with sulfate. Strain APT2T was a short rod and motile with a single subpolar flagellum, while strains APS1T and ASS1 were lemon-shaped oval rods and motile with a single polar flagellum and thin flagella-like filaments. Strain APT2T grew by complete oxidation of C3 –C8 fatty acids with thiosulfate or sulfate as the electron acceptor, while strains APS1T and ASS1 were much less versatile and utilized only propionate and pyruvate as the electron donor and carbon source with sulfate or sulfite as the electron acceptor. Furthermore, strains APS1T and ASS1 oxidized propionate incompletely to form acetate. All of the isolates were moderately halophilic and obligately alkaliphilic. Phylogenetic analysis based on 16S rRNA gene sequences placed the isolates in the orderDesulfobacterales Deltaproteobacteria T belonged to the familyDesulfobacteraceae Desulfosalsimonas propionicica T . Strains APS1T and ASS1 were closely related to each other and clustered with the genusDesulfobulbus Desulfobulbaceae Desulfonatronobacter acidivorans gen. nov., sp. nov. (type strain of the type species APT2T = DSM 24257T = UNIQEM U853T ) andDesulfobulbus alkaliphilus sp. nov. (type strain APS1T = DSM 24258T = UNIQEM U900T ).
International Journal of Systematic and Evolutionary Microbiology - Tập 62 Số Pt_9 - Trang 2107-2113 - 2012
Methanosarcina spelaei sp. nov., a methanogenic archaeon isolated from a floating biofilm of a subsurface sulphurous lake A novel methanogenic archaeon, strain MC-15T , was isolated from a floating biofilm on a sulphurous subsurface lake in Movile Cave (Mangalia, Romania). Cells were non-motile sarcina-like cocci with a diameter of 2–4 µm, occurring in aggregates. The strain was able to grow autotrophically on H2 /CO2 . Additionally, acetate, methanol, monomethylamine, dimethylamine and trimethylamine were utilized, but not formate or dimethyl sulfide. Trypticase peptone and yeast extract were not required for growth. Optimal growth was observed at 33 °C, pH 6.5 and a salt concentration of 0.05 M NaCl. The predominant membrane lipids of MC-15T were archaeol and hydroxyarchaeol phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol as well as hydroxyarchaeol phosphatidylserine and archaeol glycosaminyl phosphatidylinositol. The closely related species,Methanosarcina vacuolata Methanosarcina horonobensis ,T . The 16S rRNA gene sequence of strain MC-15T was similar to those ofMethanosarcina vacuolata T (sequence similarity 99.3 %),Methanosarcina horonobensis T (98.8 %),Methanosarcina barkeri T (98.7 %) andMethanosarcina siciliae T (98.4 %). DNA–DNA hybridization revealed 43.3 % relatedness between strain MC-15T andMethanosarcina vacuolata T . The G+C content of the genomic DNA was 39.0 mol%. Based on physiological, phenotypic and genotypic differences, strain MC-15T represents a novel species of the genusMethanosarcina Methanosarcina spelaei sp. nov. is proposed. The type strain is MC-15T ( = DSM 26047T = JCM 18469T ).
International Journal of Systematic and Evolutionary Microbiology - Tập 64 Số Pt_10 - Trang 3478-3484 - 2014
Desulfobulbus japonicus sp. nov., a novel Gram-negative propionate-oxidizing, sulfate-reducing bacterium isolated from an estuarine sediment in Japan Two strictly anaerobic, mesophilic, sulfate-reducing bacterial strains, Pro1T and Pro16, were isolated from an estuarine sediment in the Sea of Japan of the Japanese islands and were characterized by phenotypic and phylogenetic methods. Strains Pro1T and Pro16 had almost the same physiological and chemotaxonomic characteristics. Cells of both strains were Gram-negative, motile, non-spore-forming rods. Catalase activity was not detected. The optimum NaCl concentration for growth was 3.0 % (w/v). The optimum temperature for growth was 35 °C and the optimum pH was 6.7. Both strains used formate, propionate, pyruvate, lactate, fumarate, malate, ethanol, propanol, butanol, glycerol, alanine, glucose, fructose and H2 as electron donors for sulfate reduction and did not use acetate, butyrate, succinate, methanol, glycine, serine, aspartate, glutamate, cellobiose or sucrose. Organic electron donors were incompletely oxidized mainly to acetate. Both strains also used thiosulfate as an electron acceptor. Without electron acceptors, both strains fermented pyruvate and lactate. The genomic DNA G+C contents of strains Pro1T and Pro16 were 48.6 and 46.0 mol%, respectively. The major respiratory quinone of both strains was menaquinone MK-5(H2 ). Major cellular fatty acids of both strains were C15 : 0 , C16 : 0 , C17 : 1
ω 6 and C18 : 1
ω 7. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the class Deltaproteobacteria . The closest recognized relative of strains Pro1T and Pro16 was Desulfobulbus mediterraneus with sequence similarities of 95.2 and 94.8 %, respectively. Based on phylogenetic, physiological and chemotaxonomic characteristics, strains Pro1T and Pro16 represent a novel species of the genus Desulfobulbus , for which the name Desulfobulbus japonicus is proposed. The type strain is Pro1T (=JCM 14043T =DSM 18378T ) and strain Pro16 (=JCM 14044=DSM 18379) is a reference strain.
International Journal of Systematic and Evolutionary Microbiology - Tập 57 Số 4 - Trang 849-855 - 2007
Notes on the characterization of prokaryote strains for taxonomic purposes Taxonomy relies on three key elements: characterization, classification and nomenclature. All three elements are dynamic fields, but each step depends on the one which precedes it. Thus, the nomenclature of a group of organisms depends on the way they are classified, and the classification (among other elements) depends on the information gathered as a result of characterization. While nomenclature is governed by the Bacteriological Code, the classification and characterization of prokaryotes is an area that is not formally regulated and one in which numerous changes have taken place in the last 50 years. The purpose of the present article is to outline the key elements in the way that prokaryotes are characterized, with a view to providing an overview of some of the pitfalls commonly encountered in taxonomic papers.
International Journal of Systematic and Evolutionary Microbiology - Tập 60 Số 1 - Trang 249-266 - 2010
Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species Despite recent advances in commercially optimized identification systems, bacterial identification remains a challenging task in many routine microbiological laboratories, especially in situations where taxonomically novel isolates are involved. The 16S rRNA gene has been used extensively for this task when coupled with a well-curated database, such as EzTaxon, containing sequences of type strains of prokaryotic species with validly published names. Although the EzTaxon database has been widely used for routine identification of prokaryotic isolates, sequences from uncultured prokaryotes have not been considered. Here, the next generation database, named EzTaxon-e, is formally introduced. This new database covers not only species within the formal nomenclatural system but also phylotypes that may represent species in nature. In addition to an identification function based on Basic Local Alignment Search Tool (blast ) searches and pairwise global sequence alignments, a new objective method of assessing the degree of completeness in sequencing is proposed. All sequences that are held in the EzTaxon-e database have been subjected to phylogenetic analysis and this has resulted in a complete hierarchical classification system. It is concluded that the EzTaxon-e database provides a useful taxonomic backbone for the identification of cultured and uncultured prokaryotes and offers a valuable means of communication among microbiologists who routinely encounter taxonomically novel isolates. The database and its analytical functions can be found at http://eztaxon-e.ezbiocloud.net/ .
International Journal of Systematic and Evolutionary Microbiology - Tập 62 Số Pt_3 - Trang 716-721 - 2012
Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea The polyphasic approach used today in the taxonomy and systematics of the
Bacteria
and
Archaea
includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the
Bacteria
and
Archaea
coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.
International Journal of Systematic and Evolutionary Microbiology - Tập 64 Số Pt_2 - Trang 316-324 - 2014
Proposal for a new class within the phylum Proteobacteria , Acidithiobacillia classis nov., with the type order Acidithiobacillales , and emended description of the class Gammaproteobacteria The order
Acidithiobacillales
was previously assigned to the class
Gammaproteobacteria
. Recent analyses have indicated that this order actually lies outside all the proteobacterial classes, as a sister group to the combined classes
Betaproteobacteria
and
Gammaproteobacteria
. We now confirm this result with multiprotein phylogenetic analysis of all the available genomes of members of the order
Acidithiobacillales
and representatives of all available bacterial orders, and propose the new proteobacterial class, Acidithiobacillia , with the type order
Acidithiobacillales
, comprising the families
Acidithiobacillaceae
and
Thermithiobacillaceae
with the type genus
Acidithiobacillus
.
International Journal of Systematic and Evolutionary Microbiology - Tập 63 Số Pt_8 - Trang 2901-2906 - 2013
Gene sequences useful for predicting relatedness of whole genomes in bacteria
International Journal of Systematic and Evolutionary Microbiology - Tập 53 Số 6 - Trang 1893-1900 - 2003
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