Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021

A number of factors, including microbiome analyses and the increased utilization of whole-genome sequencing in the clinical microbiology laboratory, has contributed to the explosion of novel prokaryotic species discovery, as well as bacterial taxonomy revision. This review attempts to summarize such changes relative to human clinical specimens that occurred in 2020 and 2021, per primary publication in the International Journal of Systematic and Evolutionary Microbiology or acceptance on Validation Lists published by the International Journal of Systematic and Evolutionary Microbiology. Of particular significance among valid and effectively published taxa within the past 2 years were novel Corynebacterium spp., coagulase-positive staphylococci, Pandoraea spp., and members of family Yersiniaceae. Noteworthy taxonomic revisions include those within the Bacillus and Lactobacillus genera, family Staphylococcaceae (including unifications of subspecies designations to species level taxa), Elizabethkingia spp., and former members of Clostridium spp. and Bacteroides spp. Revisions within the Brucella genus have the potential to cause deleterious effects unless the relevance of such changes is properly communicated by microbiologists to stakeholders in clinical practice, infection prevention, and public health.

Gordonibacter faecihominis is a later heterotypic synonym of Gordonibacter urolithinfaciens

In this study, the phylogenetic position of Gordonibacter faecihominis and Gordonibacter urolithinfaciens was investigated using phenotypic and molecular (rep-PCR, ARDRA, 16S rRNA gene sequencing and whole-genome sequencing) methods. Our results show that Gordonibacter faecihominis cannot be distinguished from Gordonibacter urolithinfaciens on the basis of the results of this polyphasic approach. Therefore, it is proposed that the two species Gordonibacter faecihominis and Gordonibacter urolithinfaciens belong to the same species.

Proposal to emend Rules 50a and 50b of the International Code of Nomenclature of Prokaryotes

Rules 50a and 50b of the International Code of Nomenclature of Prokaryotes respectively regulate the elevation of a subspecies to the rank of a species and the lowering of a species to the rank of subspecies. The Code does not indicate that the resulting new names must be considered new combinations, as the cases described in Rules 50a and 50b are not covered by Rule 34a. Based on the rules of the Code, new combination events are applicable only at the identical rank, and therefore new combination events and new species/subspecies events are mutually exclusive. In spite of this there have been at least 44 cases in which the new names were described as comb. nov. during elevation in rank from subspecies to species and at least 30 such cases during lowering in rank from species to subspecies. To prevent confusion in the future we propose adding notes to Rules 50a and 50b to clarify the issue.

What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015

Technological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by the International Journal of Systematic and Evolutionary Microbiology Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by the Journal of Clinical Microbiology on a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015.

Complete genome sequence of Methanoculleus bourgensis strain MAB1, the syntrophic partner of mesophilic acetate-oxidising bacteria (SAOB)

Methanoculleus bourgensis strain MAB1 has been identified as the hydrogenotrophic partner of mesophilic acetate-oxidising bacteria, a syntrophic relationship operating close to the thermodynamic equilibrium and of considerable importance in ammonia-rich engineered biogas processes. Methanoculleus bourgensis strain MAB1 belongs to the order Methanomicrobiales, family Methanomicrobiaceae, within the phylum Euryarchaeota. The genome shows a total size of 2,859,299 bp encoding 3450 predicted protein-encoding genes, of which only 1472 (43 %) have been assigned tentative functions. The genome encodes further 44 tRNA genes and three rRNA genes (5S, 16S and 23S rRNA). This study presents assembling and annotation features as well as genomic traits related to ammonia tolerance and methanogenesis.

Acinetobacter pakistanensis Abbas et al. 2014 is a later heterotypic synonym of Acinetobacter bohemicus Krizova et al. 2014

Two novel species names, Acinetobacter bohemicus and Acinetobacter pakistanensis, appeared on validation list no. 161 (January 2015) under priority numbers 26 and 28, respectively. As the published data suggested a high similarity of the organisms associated with these names, we aimed to define their taxonomic relationship. The study set included all strains used in the original nomenclatural proposals, i.e. 25 strains of A. bohemicus and one strain of A. pakistanensis. The average nucleotide identity values (95.9 and 96.1 % based on blast and MUMmer, respectively) between the whole-genome sequences of A. bohemicus ANC 3994T and A. pakistanensis KCTC 42081T supported the identity of these type strains at the species level. Based on the genus-wide comparative analyses of the rpoB sequences and whole-cell fingerprints generated by matrix-assisted laser desorption/ionization-time-of-flight MS, A. pakistanensis KCTC 42081T fell within the respective clusters formed by the 25 A. bohemicus strains. The same picture was obtained on the basis of comparative analysis of 16S rRNA gene sequences of KCTC 42081T and three A. bohemicus strains. Finally, the metabolic and physiological features of KCTC 42081T were found to be congruent with those of A. bohemicus. Based on these results, we conclude that Acinetobacter pakistanensis is a later heterotypic synonym of Acinetobacter bohemicus.

Winogradskyella crassostreae sp. nov., isolated from an oyster (Crassostrea gigas)

A Gram-stain-negative, non-flagellated, non-gliding, aerobic and rod-shaped bacterium, designated TYO-19T, was isolated from an oyster collected from the South Sea in South Korea, and was subjected to a taxonomic study using a polyphasic approach. Strain TYO-19T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0  % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain TYO-19T belonged to the genus Winogradskyella, clustering coherently with the type strain of Winogradskyella epiphytica. Strain TYO-19T exhibited a 16S rRNA gene sequence similarity value of 99.7  % to W. epiphytica KMM 3906T and 94.2–96.9  % to the type strains of other species of the genus Winogradskyella. Strain TYO-19T contained MK-6 as the predominant menaquinone and iso-C15[hairsp] :[hairsp] 1 G, iso-C17[hairsp] :[hairsp] 0 3-OH, iso-C15[hairsp] :[hairsp] 0 and anteiso-C15[hairsp] :[hairsp] 0 as the major fatty acids. The major polar lipids detected in strain TYO-19T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content was 39.0 mol% and the mean DNA–DNA relatedness value with the type strain of W. epiphytica was 59 ± 4.3  %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain TYO-19T is separated from recognized species of the genus Winogradskyella. On the basis of the data presented, strain TYO-19T is considered to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella crassostreae sp. nov. is proposed. The type strain is TYO-19T  ( = KCTC 42462T = NBRC 110924T).

Marinobacter nitratireducens sp. nov., a halophilic and lipolytic bacterium isolated from coastal surface sea water

A novel Gram-stain-negative, rod-shaped, motile bacterium, designated strain AK21T, was isolated from coastal surface sea water at Visakhapatnam, India. The strain was positive for oxidase, catalase, lipase, l-proline arylamidase and tyrosine arylamidase activities. The predominant fatty acids were C12:0, C12:0 3-OH, C16:0, C16:1ω9c, C18:1ω9c and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid, two unidentified phospholipids and one unidentified lipid. Q-10 was the predominant respiratory quinone. The DNA G+C content of the strain was 54.6 mol%. 16S rRNA gene sequence analysis indicated that strain AK21T was a member of the genus Marinobacter and was closely related to Marinobacter xestospongiae, with pairwise sequence similarity of 97.2 % to the type strain, with similarity to other members of the genus of 94.0–96.8 %. The mean DNA–DNA relatedness of strain AK21T with M. xestospongiae JCM 17469T was 34.5 %, and relatedness with Marinobacter mobilis JCM 15154T was 40.5 %. Phylogenetic analysis showed that strain AK21T clustered with the type strains of M. xestospongiae and M. mobilis at distances of 2.9 and 2.8 % (97.1 and 97.2 % similarity), respectively. Based on the phenotypic characteristics and on phylogenetic inference, it appears that strain AK21T represents a novel species of the genus Marinobacter, for which the name Marinobacter nitratireducens sp. nov. is proposed. The type strain of Marinobacter nitratireducens is AK21T ( = MTCC 11704T = JCM 18428T).