Aharon Oren’s research while affiliated with Hebrew University of Jerusalem and other places

... This study reports the isolation of a novel Rhodococcus species that is closely related to R. equi, with potential implications in the identification of this pathogen and in studies on its ecology, epidemiology and environmental distribution. Here we use the name R. equi instead of the synonym Prescottella equi (Magnusson 1923) Sangal et al. 2022 [9], and the circumscription of the genus Rhodococcus Zopf 1891 as emended by Val-Calvo and Vázquez-Boland 2023 [10]. This emendation was based on a recent study that examined the Mycobacteriales taxonomy using a network analysis-aided, context-uniform phylogenomic approach for non-subjective genus demarcation [11]. ...

Reference:

Rhodococcus parequi sp. nov., a new species isolated from equine farm soil closely related to the pathogen Rhodococcus equi

... The highest relative abundance of Salinibacter was observed in the Italian and Vietnamese freshly harvested halite STP and VS8 brine (69.2% and 91.3%, respectively). It is well-know that Salinibacter uses the "salt-in" strategy known from the archaeal Halobacteriota and is a major component of hypersaline aquatic ecosystems worldwide ( [77] for further references). In contrast, to the ubiquitous Salinibacter, the gammaproteobacterium Halovibrio was exclusive to brine and predominated in the Hai Lý samples, comprising 45.8% and 38.75% of the community, respectively. ...

Reference:

Unique Features of Extremely Halophilic Microbiota Inhabiting Solar Saltworks Fields of Vietnam

... enshiensis' [4], but the name was still not validly published under the ICNP since Sinirhodobacter was validly published later (in 2018) and has no priority over Paenirhodobacter (in 2014). Meanwhile, the genus Sedimentimonas was proposed with one species in 2022, neighboured with the genus Sinirhodobacter in phylogenomic trees, and validly published very recently [22]. ...

Reference:

Description of Rhodobacter flavimaris sp. nov. and proposal of the genera Paenirhodobacter, Sedimentimonas, and Sinirhodobacter as synonyms of Rhodobacter

... One of the most important resources in culture collections is type strains. The taxonomy of prokaryotes has evolved from phenotype-based classification to polyphasic methods, ultimately leading to genome-based taxonomic approaches [3] . Since 2018, genome sequence data have been required by the International Journal of Systematic and Evolutionary Microbiology (IJSEM) when publishing a new species. ...

Reference:

GCM and gcType in 2024: comprehensive resources for microbial strains and genomic data

... To determine the phylogenetic position and relationships of PAM 2766 T , we generated a core-genome phylogeny using all available genome assemblies for the type strains of each species of the genus Rhodococcus (as emended by Val-Calvo and Vázquez-Boland 2023 [11,39]) with status name "correct" in the LPSN repository (https://lpsn.dsmz.de/genus/rhodococcus, accessed January 2024) ( Table S1). ...

Reference:

Rhodococcus parequi sp. nov., a new species isolated from equine farm soil closely related to the pathogen Rhodococcus equi

... Specifically, we found that the variation in several key species known to be affected by epilepsy or other CNS disease states were particularly modified in a time x treatment group interaction effect, including Akkermansiaceae, Lachnospiraceae, Lactobacillaceae, and Erysipelotrichaceae ( Figure 5A and Table S1). Further, proportional distribution of all species in each treatment group exhibited marked shifts over time ( Figure 5B); the gut microbiome of SAL pre-treated animals was predominantly made up of Bacillota (Firmicutes) 19 and Bacteroidota, across all . CC-BY-NC-ND 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. ...

Reference:

Intestinal Dysbiosis Alters Acute Seizure Burden and Antiseizure Medicine Activity in the Theiler's Virus Model of Encephalitis

... 5) [20]. The phylogenomic analysis was performed based on the Genome Taxonomy Database (GTDB) as described previously [21], and Halorutilus salinus F3-133 T was selected as the outgroup. ...

Reference:

Genome-Based Classification of ‘Haloarcula aidinensis’ and Description of Three Novel Halophilic Archaea Isolated from an Inland Saline Lake, Coastal Saline Soil, and a Marine Solar Saltern

... However, this proposal overlooked the fact that, according to the International Code of Nomenclature of Prokaryotes [7], Flagellimonas should have been used. Subsequently, a new publication was issued to resolve the matter [8]. Currently, Flagellimonas contains 42 validly published species with Flagellimonas eckloniae as the type species (https://lpsn.dsmz.de/genus/flagellimonas). ...

Reference:

Flagellimonas halotolerans sp. nov., a novel bacterium isolated from the South China Sea

... Originally, the order was affiliated with the phylum Euryarchaeota [2]. However, an updated phylogenetic reconstruction from Genome Taxonomy Database (GTDB) firmly placed these organisms as a separate phylum, namely Thermoplasmatota [8,9]. According to this classification, the phylum Thermoplasmatota comprises classes 'Ca. ...

Reference:

Oxyplasma meridianum gen. nov., sp. nov., an extremely acidophilic organotrophic member of the order Thermoplasmatales

... For the case presented here, although Proteus Müller, 1786 was replaced and is no longer available nowadays in zoological nomenclature [11], it should be noted that Rule 51b(4) of the ICNP [5,6] makes no reference to the status of protozoan names under the zoological code and, therefore, the current wording does not require that only valid or available names be taken into consideration with regards establishing whether names are homonyms [19,20]. In this way, due to the homonymy between the prokaryotic generic name Proteus Hauser 1885 (Approved Lists 1980) and the protozoan genus name Proteus Müller, 1786, the name Proteus Hauser 1885 (Approved Lists 1980), which was validly published before 31 December 2000 and has standing today, should be considered illegitimate and in need of replacement according to Rules 51b(4) and 54 of the ICNP [5,6]. ...

Reference:

Request for an Opinion: conservation of the illegitimate prokaryotic generic name Proteus Hauser 1885 (Approved Lists 1980)