Value of recN sequences for species identification and as a phylogenetic marker within the family “Leuconostocaceae”

The genera Leuconostoc, Oenococcus, and Weissella (family “Leuconostocaceae”) constitute a group of lactic acid bacteria of great interest in food microbiology. From the taxonomic point of view, they are considered phylogenetically coherent according to their 16S rRNA gene sequences and other macromolecules. These three genera were the focus of the present study; specifically, the resolution and discriminatory power of recN (encoding a DNA repair and genetic recombination protein) as a molecular marker at the species level were investigated. For this purpose, partial sequences (about 1200 nt) were obtained from 23 type strains and from several additional strains following direct amplification of recN and subsequent sequencing. Phylogeny was evaluated according to different treeing methods (neighbor joining, maximum likelihood, and maximum parsimony) and the inclusion of variability filters. The results showed that recN, used either alone or in combination with 16S rRNA data, can serve as a phylogenetic marker as well as a tool for species identification.[Int Microbiol 2008; 11(1): 33-39

Bacillota y otros exabruptos

A comienzos de año hubo bastante revuelo mediático en torno a la validación de algunos nombres de filo (Oren y Garrity, 2021) conforme a un cambio reciente (Oren et al., 2021a) en el código de nomenclatura procariota. No faltaron ni siquiera algunos memes como los que reproducimos aquí. En una disciplina como la nomenclatura biológica esto es algo tan infrecuente que conviene aprovecharlo para hacer pedagogía, explicando todos los hechos clave y todos los actores. También desmentir errores: las redes sociales aportan mucha rapidez, pero también menos rigor que otras formas de comunicación

Value of recN sequences for species identification and as a phylogenetic marker within the family “Leuconostocaceae”

The genera Leuconostoc, Oenococcus, and Weissella (family “Leuconostocaceae”) constitute a group of lactic acid bacteria of great interest in food microbiology. From the taxonomic point of view, they are considered phylogenetically coherent according to their 16S rRNA gene sequences and other macromolecules. These three genera were the focus of the present study; specifically, the resolution and discriminatory power of recN (encoding a DNA repair and genetic recombination protein) as a molecular marker at the species level were investigated. For this purpose, partial sequences (about 1200 nt) were obtained from 23 type strains and from several additional strains following direct amplification of recN and subsequent sequencing. Phylogeny was evaluated according to different treeing methods (neighbor joining, maximum likelihood, and maximum parsimony) and the inclusion of variability filters. The results showed that recN, used either alone or in combination with 16S rRNA data, can serve as a phylogenetic marker as well as a tool for species identification.Macian Rovira, M. Carmen, [email protected] ; Garay Auban, Esperanza, [email protected]

Revisiting the genus Photobacterium: taxonomy, ecology and pathogenesis

The genus Photobacterium, one of the eight genera included in the family Vibrionaceae, contains 27 species with valid names and it has received attention because of the bioluminescence and pathogenesis mechanisms that some of its species exhibit. However, the taxonomy and phylogeny of this genus are not completely elucidated; for example, P. logei and P. fischeri are now considered members of the genus Aliivibrio, and previously were included in the genus Vibrio. In addition, P. damselae subsp. piscicida was formed as a new combination for former Vibrio damsela and Pasteurella piscicida. Moreover, P. damselae subsp. damselae is an earlier heterotypic synonym of P. histaminum. To avoid these incovenences draft and complete genomic sequences of members of Photobacterium are increasingly becoming available and their use is now routine for many research laboratories to address diverse goals: species delineation with overall genomic indexes, phylogenetic analyses, comparative genomics, and phenotypic inference. The habitats and isolation source of the Photobacterium species include seawater, sea sediments, saline lake waters, and a variety of marine organisms with which the photobacteria establish different relationships, from symbiosis to pathogenic interactions. Several species of this genus contain bioluminescent strains in symbiosis with marine fish and cephalopods; in addition, other species enhance its growth at pressures above 1 atmosphere, by means of several high-pressure adaptation mechanisms and for this, they may be considered as piezophilic (former barophilic) bacteria. Until now, only P. jeanii, P. rosenbergii, P. sanctipauli, and the two subspecies of P. damselae have been reported as responsible agents of several pathologies on animal hosts, such as corals, sponges, fish and homeothermic animals. In this review we have revised and updated the taxonomy, ecology and pathogenicity of several members of this genus. [Int Microbiol 20(1): 1-10 (2017)]Keywords: Photobacterium · taxonomy · symbiosis · pathogenesis · virulence factor

Revisiting the genus Photobacterium: taxonomy, ecology and pathogenesis

The genus Photobacterium, one of the eight genera included in the family Vibrionaceae, contains 27 species with valid names and it has received attention because of the bioluminescence and pathogenesis mechanisms that some of its species exhibit. However, the taxonomy and phylogeny of this genus are not completely elucidated; for example, P. logei and P. fischeri are now considered members of the genus Aliivibrio, and previously were included in the genus Vibrio. In addition, P. damselae subsp. piscicida was formed as a new combination for former Vibrio damsela and Pasteurella piscicida. Moreover, P. damselae subsp. damselae is an earlier heterotypic synonym of P. histaminum. To avoid these incovenences draft and complete genomic sequences of members of Photobacterium are increasingly becoming available and their use is now routine for many research laboratories to address diverse goals: species delineation with overall genomic indexes, phylogenetic analyses, comparative genomics, and phenotypic inference. The habitats and isolation source of the Photobacterium species include seawater, sea sediments, saline lake waters, and a variety of marine organisms with which the photobacteria establish different relationships, from symbiosis to pathogenic interactions. Several species of this genus contain bioluminescent strains in symbiosis with marine fish and cephalopods; in addition, other species enhance its growth at pressures above 1 atmosphere, by means of several high-pressure adaptation mechanisms and for this, they may be considered as piezophilic (former barophilic) bacteria. Until now, only P. jeanii, P. rosenbergii, P. sanctipauli, and the two subspecies of P. damselae have been reported as responsible agents of several pathologies on animal hosts, such as corals, sponges, fish and homeothermic animals. In this review we have revised and updated the taxonomy, ecology and pathogenicity of several members of this genus

Proposals to revise the statutes of the International Committee on Systematics of Prokaryotes

The International Committee on Systematics of Prokaryotes serves to administer the rules of prokaryotic nomenclature via the International Code of Nomenclature of Prokaryotes, ensures the publication of the International Journal of Sys-tematic and Evolutionary Microbiology, and works to represent the interests of the microbiological disciplines regarding prokaryotic nomenclature. The functions and mechanisms of operation of the International Committee on Systematics of Prokaryotes (ICSP) are defined in its Statutes, which were last revised in 2019. As members of the 2020–2023 and the 2023–2026 ICSP Executive Board and the Judicial Commission, we propose here some further revisions to help improve the clarity and functionality of the Statutes.info:eu-repo/semantics/publishedVersio

Chryseobacterium potabilaquae sp. nov., Chryseobacterium aquaeductus sp. nov. and Chryseobacterium fistulae sp. nov., from drinking water systems

A polyphasic taxonomic study was conducted on three strains isolated from drinking water systems that had previously been deposited as Chryseobacterium species at the Spanish Type Culture Collection in order to complete their classification. Strains CECT 9293T, CECT 9390T and CECT 9393T were isolated from sites in Barcelona, Spain, in the framework of a project aimed at generating the first MALDI-TOF database specific for bacteria present in water for human consumption. Their partial 16S rRNA sequences showed that their closest relatives among the type strains of Chryseobacterium exhibited 98 % similarity or less, supporting their taxonomic novelty. At the same time, comparison between them revealed that strains CECT 9293T and CECT 9393T could perhaps be related at the species level as they shared 99.5 % similarity. However, whole genome sequencing was performed and the subsequent calculation of relatedness indices, average nucleotide identity and estimated DNA-DNA hybridization, ruled out that possibility and confirmed instead that each of the strains should be considered a separate species in the genus Chryseobacterium. Having clarified their status, we also performed phylogenomic analyses and searched for possible environmental or non-type material sequences that could be related to any of them at the species level. In parallel, the strains were characterized phenotypically and compared to their closest relatives to determine diagnostic traits to support their formal proposal. The proposed species are Chryseobacterium potabilaquae sp. nov. with the type strain CECT 9293T (=LMG 32084T), Chryseobacterium aquaeductus sp. nov. with the type strain CECT 9390T (=LMG 32085T) and Chryseobacterium fistulae sp. nov. with the type strain CECT 9393T (=LMG 32086T)

Public discussion on a proposed revision of the International Code of Nomenclature of Prokaryotes

The Editorial Board for the International Code of Nomenclature of Prokaryotes (ICNP) has compiled proposed revisions of the ICNP. As outlined previously (Oren et al., Int J Syst Evol Microbiol 2021;71:004598; https://doi.org/10.1099/ijsem.0.004598) and to comply with Articles 13(b)(4) and 4(d) of the statutes of the International Committee on Systematics of Prokaryotes, a public discussion of the document will start on 1 July 2021, to last for 6 months. Here, we present the procedure for this discussion

Emendation of Rules 5b, 8, 15 and 22 of the International Code of Nomenclature of Prokaryotes to include the rank of phylum

Following the International Committee on Systematics of Prokaryotes electronic discussion and vote on proposals to include the rank of phylum in the rules of the International Code of Nomenclature of Prokaryotes, we here announce the results of the ballot. We also present draft versions of the emended Rules 5b, 8, 15 and 22, based on the outcome of the ballot, to be included in the proposal for the preparation of a new revision of the International Code of Nomenclature of Prokaryotes

Proposals to emend Rules 8, 15, 22, 25a, 30(3)(b), 30(4), 34a, and Appendix 7 of the International Code of Nomenclature of Prokaryotes

To complete the ongoing revision of the International Code of Nomenclature of Prokaryotes, we here propose emendation of Rules 8, 15, 22, 25a, 30(3)(b), 30(4), 34a and Appendix 7. These proposed emendations deal with: the nomenclatural type of taxa above genus; the suitability of names published in supplementary material or in papers published on e-print servers for effective publication; the number of culture collection designations to be included in an effective publication of a name of a species or subspecies to qualify for validation of the name; the kinds of restrictions that may be attached to deposits of type strains; and the question whether elevation of a subspecies to the rank of species or lowering of a species to the rank of subspecies establish new combinations. Some of these emendations change the meaning of the Code while others are mere textual clarifications