Large-scale evaluation of experimentally determined DNA G+C contents with whole genome sequences of prokaryotes

Description of Ornithinimicrobium cryptoxanthini sp. nov., a Novel Actinomycete Producing β-cryptoxanthin Isolated from the Tongtian River Sediments

Two novel Gram-stain-positive, aerobic, non-motile, and yellow-pigmented, irregular rod-shaped bacteria (JY.X269 and JY.X270^T) were isolated from the near-surface sediments of river in Qinghai Province, P. R. China (32°37'13″N, 96°05'37″E) in July 2019. Both strains were shown to grow at 15-35 °C and pH 7.0-10.0, and in the presence of 0-6.0% (w/v) NaCl. The 16S rRNA gene sequence analysis showed that the isolates were closely related to Ornithinimicrobium cavernae CFH 30183 ^T (98.6-98.8% 16S rRNA gene sequence similarity), O. ciconiae H23M54^T (98.5-98.6%) and O. murale 01-Gi-040^T (98.3-98.5%). The phylogenetic and phylogenomic trees based on the 16S rRNA gene and 537 core gene sequences, respectively, revealed that the two strains formed a distinct cluster with the above three species. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between our two isolates (JY.X269 and JY.X270^T) and other Ornithinimicrobium species were within the ranges of 19.0-23.9% and 70.8-80.4%, respectively, all below the respective recommended 70.0% and 95-96% cutoff point. Furthermore, the major cellular fatty acids (> 10.0%) of strains JY.X269 and JY.X270^T were iso-C_15:0, iso-C_16:0, and summed feature 9. Strain JY.X270^T contained MK-8(H₄) and ornithine as the predominant menaquinone and diagnostic diamino acid component within the cell wall teichoic acids. β-cryptoxanthin (C₄₀H₅₆O) can be extracted from strain JY.X270^T, and its content is 6.3 µg/ml. Based on results from the phylogenetic, chemotaxonomic, and phenotypic analyses, the two strains could be classified as a novel species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium cryptoxanthini sp. nov. is proposed (type strain JY.X270^T = CGMCC 1.19147^T = JCM 34882^T).

Unification of Abyssicoccus albus Jiang et al. 2016 and Auricoccus indicus Prakash et al. 2017 and the status of the genus Auricoccus Prakash et al. 2017

Based on the high phylogenetic relatedness of Auricoccus indicus Prakash et al. 2017 and Abyssicoccus albus Jiang et al. 2016, it is proposed to unite them with retaining the latter name as having nomenclatural priority. As the result of the species unification, the genus Auricoccus name is proposed to consider as illegitimate in the boundaries determined by Rule 51a of the International Code of Nomenclature of Prokaryotes.

Emendation of circumscriptions of taxa in the Lists of Changes in Taxonomic Opinion

In the past 3 years, a large number of emendations of circumscriptions of species, subspecies and higher taxa were published outside the International Journal of Systematic and Evolutionary Microbiology (IJSEM) that only marginally modify the earlier circumscription and may not meet the requirements of Rule 35 of the International Code of Nomenclature of Prokaryotes. Thus far, these emendations were included in the Lists of Changes in Taxonomic Opinion in the IJSEM. The list editors propose to list in the future only meaningful emendations that in their opinion significantly modify the diagnostic characters or the circumscription of taxa.

Minimal standards for the description of new genera and species of rhizobia and agrobacteria

Herein the members of the Subcommittee on Taxonomy of Rhizobia and Agrobacteria of the International Committee on Systematics of Prokaryotes review recent developments in rhizobial and agrobacterial taxonomy and propose updated minimal standards for the description of new species (and genera) in these groups. The essential requirements (minimal standards) for description of a new species are (1) a genome sequence of at least the proposed type strain and (2) evidence for differentiation from other species based on genome sequence comparisons. It is also recommended that (3) genetic variation within the species is documented with sequence data from several clearly different strains and (4) phenotypic features are described, and their variation documented with data from a relevant set of representative strains. Furthermore, it is encouraged that information is provided on (5) nodulation or pathogenicity phenotypes, as appropriate, with relevant gene sequences. These guidelines supplement the current rules of general bacterial taxonomy, which require (6) a name that conforms to the International Code of Nomenclature of Prokaryotes, (7) validation of the name by publication either directly in the International Journal of Systematic and Evolutionary Microbiology or in a validation list when published elsewhere, and (8) deposition of the type strain in two international culture collections in separate countries.

Vagococcus bubulae sp. nov., isolated from ground beef, and Vagococcus vulneris sp. nov., isolated from a human foot wound

Two unusual catalase-negative, Gram-stain-positive, Vagococcus-like isolates that were referred to the CDC Streptococcus Laboratory for identification are described. Strain SS1994^T was isolated from ground beef and strain SS1995^T was isolated from a human foot wound. Comparative 16S rRNA gene sequence analysis of isolates SS1994^T and SS1995^T against Vagococcus type strain sequences supported their inclusion in the genus Vagococcus. Strain SS1994^T showed high sequence similarity (>97.0 %) to the two most recently proposed species, Vagococcus martis (99.2 %) and Vagococcus teuberi (99.0 %) followed by Vagococcus penaei (98.8 %), strain SS1995^T (98.6 %), Vagococcus carniphilus (98.0 %), Vagococcus acidifermentans (98.0 %) and Vagococcus fluvialis (97.9 %). The 16S rRNA gene sequence of strain SS1995^T was most similar to V. penaei (99.1 %), followed by SS1994^T (98.6 %), V. martis (98.4 %), V. teuberi (98.1 %), V. acidifermentans (97.8 %), and both V. carniphilus and V. fluvialis (97.5 %). A polyphasic taxonomic study using conventional biochemical and the rapid ID 32 STREP system, MALDI-TOF MS, cell fatty acid analysis, pairwise sequence comparisons of the 16S rRNA, rpoA, rpoB, pheS and groL genes, and comparative core and whole genome sequence analyses revealed that strains SS1994^T and SS1995^T were two novel Vagococcus species. The novel taxonomic status of the two isolates was confirmed with core genome phylogeny, average nucleotide identity <84 % and in silico DNA-DNA hybridization <28 % to any other Vagococcus species. The names Vagococcusbubulae SS1994^T=(CCUG 70831^T=LMG 30164^T) and Vagococcusvulneris SS1995^T=(CCUG 70832^T=LMG 30165^T) are proposed.

Effect of CT manifestations of cholesteatoma on MMP-2, MMP-9 and IL-6 in the serum of patients

Effect of CT manifestations of cholesteatomatous otitis media on matrix metalloproteinase-2 (MMP-2), matrix metalloproteinase-9 (MMP-9) and interleukin-6 (IL-6) in the serum of patients was investigated. A total of 176 patients with cholesteatomatous otitis media were enrolled as the study group and 181 patients with simple otitis media were enrolled as the control group. Patients were admitted to the Changxing People's Hospital from January 2010 to December 2016. The patients in the study group were classified according to the 64-row spiral CT diagnosis. The expression levels of MMP-2, MMP-9 and IL-6 in the serum of the selected patients were detected by ELISA. MMP-2, MMP-9 and IL-6 expression levels in the study group were higher than those in the control group (P<0.05). MMP-2, MMP-9 and IL-6 expression levels in the serum of the patients with injured ossicular chain were significantly higher than those in the serum of patients with injured malleus or incus (P<0.05), and significantly higher than those in the serum of patients with intact ossicular chain (P<0.05). The levels of MMP-2, MMP-9 and IL-6 in the serum of the patients whose malleus or incus was injured were higher than those in the serum of the patients with intact ossicular chain (P<0.05). There was an obvious positive correlation between the injury degree of different sclerotins in CT manifestations of the patients in the study group and MMP-2, MMP-9, and IL-6 (P<0.05). The high expression levels of MMP-2, MMP-9 and IL-6 in the serum of patients with cholesteatomatous otitis media were positively correlated with the injury degree of ossicle, which may be a sign of poor prognosis of cholesteatomatous otitis media.

The endosphere of the salt marsh plant Halimione portulacoides is a diversity hotspot for the genus Salinicola: description of five novel species Salinicola halimionae sp. nov., Salinicola aestuarinus sp. nov., Salinicola endophyticus sp. nov., Salinicola halophyticus sp. nov. and Salinicola lusitanus sp. nov

Seven endophytic strains were isolated from the halophyte Halimione portulacoides, collected from Ria de Aveiro, Portugal. To determine their exact taxonomic position, comparative analyses were performed with these strains and closely related type strains of Salinicola species. Genome sequencing and comparison indicated that five of the seven isolated strains comprised distinct and novel species (average nucleotide identity <0.95; in silico DNA-DNA hybridization <70 %; G+C difference >1 %). Multilocus sequence analysis was performed using gyrB, rpoD and 16S rRNA gene sequences from the novel and type strains to determine their phylogenetic positions. The novel strains are facultative anaerobes, mesophilic, facultative alkaliphic and halophilic, test positive for catalase and oxidase activities, for hydrolysis of Tween 20 and phosphate, for production of indole-3-acetic acid, but do not produce H2S. Ubiquinone UQ-9 is present in major amounts in all strains. The major fatty acids include C16 : 0 and the summed feature containing C18 : 1ω7c and/or C18 : 1ω6c. The DNA G+C content ranges from 60.6 to 65.8 mol%. Five strains were confirmed as new species belonging to the genus Salinicola, for which the names Salinicolahalimionae sp. nov. (type strain CPA60^T=CECT 9338^T=LMG 30107^T), Salinicolaaestuarinus sp. nov. (type strain CPA62^T=CECT 9339^T=LMG 30108^T), Salinicolaendophyticus sp. nov. (type strain CPA92^T=CECT 9340^T=LMG 30109^T), Salinicolahalophyticus sp. nov. (type strain CR45^T=CECT 9341^T=LMG 30105^T) and Salinicola lusitanus sp. nov. (type strain CR50^T=CECT 9342^T=LMG 30106^T) are proposed.

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

The recent advent of DNA sequencing technologies facilitates the use of genome sequencing data that provide means for more informative and precise classification and identification of members of the Bacteria and Archaea. Because the current species definition is based on the comparison of genome sequences between type and other strains in a given species, building a genome database with correct taxonomic information is of paramount need to enhance our efforts in exploring prokaryotic diversity and discovering novel species as well as for routine identifications. Here we introduce an integrated database, called EzBioCloud, that holds the taxonomic hierarchy of the Bacteria and Archaea, which is represented by quality-controlled 16S rRNA gene and genome sequences. Whole-genome assemblies in the NCBI Assembly Database were screened for low quality and subjected to a composite identification bioinformatics pipeline that employs gene-based searches followed by the calculation of average nucleotide identity. As a result, the database is made of 61 700 species/phylotypes, including 13 132 with validly published names, and 62 362 whole-genome assemblies that were identified taxonomically at the genus, species and subspecies levels. Genomic properties, such as genome size and DNA G+C content, and the occurrence in human microbiome data were calculated for each genus or higher taxa. This united database of taxonomy, 16S rRNA gene and genome sequences, with accompanying bioinformatics tools, should accelerate genome-based classification and identification of members of the Bacteria and Archaea. The database and related search tools are available at www.ezbiocloud.net/.

The impact of culturomics on taxonomy in clinical microbiology

Over the past decade, new culture methods coupled to genome and metagenome sequencing have enabled the number of isolated bacterial species with standing in nomenclature to rise to more than 15,000 whereas it was only 1791 in 1980. 'Culturomics', a new approach based on the diversification of culture conditions, has enabled the isolation of more than 1000 distinct human-associated bacterial species since 2012, including 247 new species. This strategy was demonstrated to be complementary to metagenome sequencing for the exhaustive study of the human microbiota and its roles in health and diseases. However, by identifying a large number of new bacterial species in a short time, culturomics has highlighted a need for taxonomic approaches adapted to clinical microbiology that would include the use of modern and reproducible tools, including high throughput genomic and proteomic analyses. Herein, we review the development of culturomics and genomics in the clinical microbiology field and their impact on bacterial taxonomy.

Agromyces aureus sp. nov., isolated from the rhizosphere of Salix caprea L. grown in a heavy-metal-contaminated soil

A Gram-reaction-positive, motile, yellow-pigmented and rod-shaped bacterial strain, designated AR33T, was isolated from the rhizosphere of Salix caprea L. growing in a former zinc/lead mining and processing site in Austria. A polyphasic approach was applied to determine its taxonomic position. 16S rRNA gene sequence analysis, and morphological and chemotaxonomic properties showed that strain AR33T belongs to the genus Agromyces. Strain AR33T had peptidoglycan type B2γ and the major menaquinones were MK-11, MK-10 and MK-12. The main branched-chain fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. Strain AR33T showed catalase and oxidase activity and multiple heavy metal resistances to zinc, lead and cadmium. The DNA G+C content was 70.1 mol%. Levels of 16S rRNA gene sequence similarity with closely related recognized species of the genus Agromyces ranged between 98 and 99 %. However, DNA-DNA hybridization between strain AR33T and the type strains of three Agromyces species showed values lower than 42 % relatedness. Therefore, differential phenotypic characteristics together with DNA-DNA relatedness suggested that strain AR33T can be recognized as representing a distinct Agromyces species, for which the name Agromyces aureus sp. nov. is proposed. The type strain is AR33T (=DSM 101731T=LMG 29235T).