Markus Göker’s research while affiliated with Leibniz Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH and other places

... Mycobacteroides abscessus (Ng and Ngeow 2020;Val-Calvo and Vázquez-Boland 2023;Oren and Göker 2024) is a rapidly growing NTM of clinical relevance. It causes broncho-pulmonary infections and chronic pulmonary diseases, in immunocompromised individuals (Davidson et al. 2018). ...

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Unlocking the Mycobacteroides abscessus pan-genome using computational tools: insights into evolutionary dynamics and lifestyle

... 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]. ...

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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. ...

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

... It is worth noting that recently the taxonomy of the family Halomonadaceae has been rearranged and several bacterial species within the genus Halomonas have been reclassified to new genera as proposed by de la Haba et al. (2023) and then validated in list n o . 216 by Oren and Göker (2024). For example, H. venusta and H. titanicae have been moved to the genus Vreelandella. ...

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Biodegradation of untreated plasticizers-free linear low-density polyethylene films by marine bacteria

... Names for two divisions named by Gibbons and Murray in 1978-Firmacutes and Gracilicutes-are recorded in the 1980 Approved Lists of Bacterial Names. However, responses to a recent request for opinion have clarified that this does not grant them standing in nomenclature [22,23]. In fact, the absence of the rank of phylum from the Code (until recently, see below) means that none of the phylum names generated over recent decades have any standing, however widely used. ...

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The dynamic history of prokaryotic phyla: discovery, diversity and division

... 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. ...

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

... A maximum-likelihood tree, employing Bac120 marker sets from genome taxonomy database (GTDB), revealed that KSB1 forms a monophyletic clade within the FCB superphylum [4], and clearly separated from other phyla ( Figure S1A). Phylogenetic tree based on 16S rRNA gene further supports the classification of KSB1 as a distinct phylum taxon in the domain Bacteria under the kingdom Psuedomonadati [5] ( Figure S1B). ...

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Metagenomic analysis sheds light on the mixotrophic lifestyle of bacterial phylum Zhuqueibacterota

... For taxonomists in countries such as India, South Africa and Brazil, deposition of type strains in international collections is a major problem as the access regulations linked to the protection of biological material in these countries place restrictions on sharing the cultures (Tindall, 2020;Da Silva et al., 2023;van Lill et al., 2024). For uncultured taxa known mainly from their genetic sequences, the ICNP suggests that the provisional status of Candidatus (Oren, 2021;Arahal et al., 2024) be used when naming these organisms. However, numerous researchers have expressed dissatisfaction with the current status of Candidatus names, mostly around the lack of standing in nomenclature and therefore priority and lack of formal regulations Murray et al., 2020). ...

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Options and considerations for validation of prokaryotic names under the SeqCode

... However, soon after the proposal was published on 11 April 2023, the valid publications of two new prokaryotic species Gramella oceanisediminis and Gramella crocea within the genus Gramella were made respectively on 5 May 2023 by Yang et al. [17] and 1 December 2023 on the Validation List no. 214 [18]. The nomenclatural problem for Gramella oceanisediminis Yang et al. 2023 and Gramella crocea Zhang et al., 2023 was not solved in the proposal previously made by Deshmukh and Oren [16] due to temporal proximity and also no reclassification of Gramella oceanisediminis to the newly established genus Christiangramia was made later in the notification list [19]. ...

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Proposal of Sphingobacterium allocomposti nom. nov., Mycobacterium chelonae subsp. bovistauri nom. nov. and Lactobacillus delbrueckii subsp. allosunkii nom. nov. as new names with replacement specific or subspecific epithets, respectively, for three illegitimate prokaryotic names Sphingobacterium composti Yoo et al. 2007, Mycobacterium chelonae subsp. bovis Kim et al. 2017 and Lactobacillus delbrueckii subsp. sunkii Kudo et al. 2012; proposal of Christiangramia oceanisediminis comb. nov. and...

... The usage of eponyms can have negative consequences, because even if it honors related scientists, it lacks equality and human diversity representation (Heard & Mlynarek 2023;Guedes et al., 2023). There is a gender bias in the eponyms, so that most of them refer to men, with women being underrepresented (Vendetti 2022;Freese et al., 2023). This also occurs, as we have seen, in Kinorhyncha. ...

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Kinomenclature: An analysis of scientific names of mud dragons (Kinorhyncha)