International Journal of Systematic and Evolutionary Microbiology

The alphaproteobacterial order Hyphomicrobiales consists of 38 families comprising 155 validly published genera as of June 2023. The order Hyphomicrobiales was first described in 1957 and underwent important revisions in 2020. However, several inconsistencies in the taxonomy of this order remain, and there is a need for a consistent framework for defining families within the order. We propose a common genome-based framework for defining families within the order Hyphomicrobiales, suggesting that families represent monophyletic groups in core-genome phylogenies that share pairwise average amino acid identity values above [~]75% when calculated from a core set of 59 proteins. Applying this framework, we propose the formation of four new families and to reassign the genera Salaquimonas, Rhodoblastus, and Rhodoligotrophos into Salaquimonadaceae fam. nov., Rhodoblastaceae fam. nov., and Rhodoligotrophaceae fam. nov., respectively, and the genera Albibacter, Chenggangzhangella, Hansschlegelia, and Methylopila into Methylopilaceae fam. nov.. We further propose to unify the families Bartonellaceae, Brucellaceae, Phyllobacteriaceae, and Notoacmeibacteraceae as Bartonellaceae; the families Segnochrobactraceae and Pseudoxanthobacteraceae as Segnochrobactraceae; the families Lichenihabitantaceae and Lichenibacteriaceae as Lichenihabitantaceae; and the families Breoghaniaceae and Stappiaceae as Stappiaceae. Lastly, we propose to reassign several genera to existing families. Specifically, we propose to reassign the genus Pseudohoeflea to the family Rhizobiaceae; the genera Oricola, Roseitalea, and Oceaniradius to the family Ahrensiaceae; the genus Limoniibacter to the emended family Bartonellaceae; the genus Faunimonas to the family Afifellaceae; and the genus Pseudochelatococcus to the family Chelatococcaceae. Our data also support the recent proposal to reassign the genus Prosthecomicrobium to the family Kaistiaceae.

Strains of two novel Corynebacterium species were cultured from samples of human nostrils and skin collected in the United States and Botswana. These strains demonstrated growth on Columbia Colistin-Nalidixic Acid agar with 5% sheep blood and in liquid media (brain heart infusion and tryptic soy broth) supplemented with Tween 80, a source of the fatty acid oleic acid. Cells were Gram-positive, non-spore-forming, non-motile bacilli that showed catalase but not oxidase activity. Major fatty acids in both of these species were 18:1 {omega}9c (oleic acid), 16:0 (palmitic acid), and 18:0 (stearic acid). Analysis of the 16S ribosomal RNA gene sequences identified these strains as belonging to the genus Corynebacterium (family Corynebacteriaceae). Whole-genome sequencing revealed that these strains formed distinct branches on a phylogenomic tree, with C. tuberculostearicum being the closest relative but with average nucleotide identities of < 95% relative to all previously described species. These results indicate that these strains represent novel species of Corynebacterium, for which we propose the names Corynebacterium hallux sp. nov., with the type strain CTNIH22T (=ATCC TSD-435T=DSM 117774T), and Corynebacterium nasorum sp. nov., with the type strain KPL3804T (=ATCC TSD-439T=DSM 117767T). We also describe the characteristics of two strains isolated from human nasal passages that are members of the recently named species Corynebacterium yonathiae. RepositoriesThe sequencing files supporting the conclusions of this study are available in the Sequence Read Archive (PRJNA804245, PRJNA854648, PRJNA842433). The partial 16S ribosomal RNA gene sequences from PCR amplification and Sanger sequencing are available in GenBank for Corynebacterium hallux sp. nov. CTNIH22T (accession number: PQ252679) and Corynebacterium nasorum sp. nov. KPL3804T (accession number: PQ149068). The annotated genomic sequences for the strains characterized in this study have been deposited in GenBank with the following accession numbers: C. hallux sp. nov. CTNIH22T (GCF_032821755.1), C. nasorum sp. nov. KPL3804T (GCF_037908315.1), C. nasorum sp. nov. MSK185 (GCF_030229765.1), C. yonathiae KPL2619 (GCF_037908465.1), and C. yonathiae MSK136 (GCF_022288805.2).

Three new Curtobacterium species from healthy tissues of agricultural crop plants in the United States are reported. They are Curtobacterium glycinis sp. nov. from soybean in Missouri, Curtobacterium gossypii from cotton in Puerto Rico and corn in Missouri, and Curtobacterium oryzae sp. nov. from rice in Texas.

Five novel species from healthy plants and other substrates are described. These are Paenibacillus glycinicola sp. nov. from Glycine max in Iowa, United States; Paenibacillus triticicola sp. nov. from Triticum aestivum in Australia, Allium cepa in Texas, garden soil in Wisconsin, cows milk in New York state, Panicum virgatum in Michigan, sweet sorghum in Nebraska, and Zea mays in Ohio; Pseudescherichia oryzae sp. nov. from Oryza sativa in Arkansas; Pseudomonas gossypii sp. nov. from a healthy Bos taurus in Kansas, Capsicum annuum from Arizona, Gossypium hirsutum in New Mexico, Oklahoma, and Texas, and Zea mays from Arkansas; and Tardiphaga zeae sp. nov. from Zea mays in Iowa. No pathogenic strains are known for any of the novel species.

Recently Hordt et al. 2020 proposed to merge Ochrobactrum and Brucella genera based on up to date phylogenomic evidence and overall genomic divergence among Brucella-Ochrobactrum clade. This led to the description of the new combinations Brucella ciceri comb. nov., basonym: Ochrobactrum ciceri Imran et al. 2010 and Brucella intermedia comb. nov., basonym: Ochrobactrum intermedium Velasco et al. 1998. However, the type species for Brucella ciceri DSM 22292T and Brucella intermedia LMG 3301T show whole-genome coherence at the species level (ANI = 98.21 %, Mash D = 0.0154006, dDDH relatedness >70%), suggesting that may belong to the same genomospecies. Also, both taxa formed a single clade in the phylogenomic tree based on single-copy gene sequences. Previously reported phenotypic data offer a context where both taxa are highly related supporting this synonymy. Therefore, Brucella ciceri should be reclassified as later heterotypic synonyms of Brucella intermedia, which has priority. The species description is consequently amended.

Streptomycetaceae is one of the oldest families within phylum Actinobacteria and it is large and diverse in terms of number of described taxa. The members of the family are known for their ability to produce medically important secondary metabolites and antibiotics. In this study, strains showing low 16S rRNA gene similarity (&lt;97.3 %) with other members of Streptomycetaceae were identified and subjected to phylogenomic analysis using 33 orthologous gene clusters (OGC) for accurate taxonomic reassignment resulted in identification of eight distinct and deeply branching clades, further average amino acid identity (AAI) analysis showed lower AAI values or AAI within the range of 60-80 % which was previously observed in related but different genera of bacteria. The whole genome phylogeny based on concatenated core genes and AAI analyses supported the claim that those phylogenetically distinct members may be assigned to 8 novel genera namely Actinoacidiphila, Actinomesophilus, Charcoactinospora, Curviacidiphilus, Kafeoacidiphilus, Mangroviactinospora, Peterkaempfera, and Streptantibioticus. In addition, based on the core genome phylogeny and 16S rRNA tree topology and distinct chemotaxonomic and physiological properties, the sequence belonged to Streptomyces thermoautotrophicus was assigned to a novel genera Charcoactinospora which is placed under novel family Charcoactinosporaceae. Lastly, a clade comprising of strains that showed high 16S rRNA gene similarity (100 %) with similar tree topology in phylogenetic trees was subjected to overall genome related indices analyses such as digital DNA – DNA hybridization, and average nucleotide identity that supported the claim that Streptomyces asterosporus is a later heterotypic synonym of Streptomyces calvus.Competing Interest StatementThe authors have declared no competing interest.AbbreviationsOGCOrthologous gene clusterAAIaverage amino acid identitydDDHdigital DNA-DNA hybridizationANIaverage nucleotide identityView Full Text

A phylogenetic study of Anoxybacillus, Geobacillus and Parageobacillus was performed using publicly available whole genome sequences. A total of 113 genomes were selected for phylogenomic metrics including calculation of Average Nucleotide Identity (ANI) and Average Amino acid Identity (AAI), and a maximum likelihood tree was built from alignment of a set of 662 orthologous core genes. The combined results from the core gene tree and ANI and AAI dendrograms show that the genomes split into two main clades, clade I containing all Geobacillus, all Parageobacillus and some species of Anoxybacillus, and clade II, containing the majority of Anoxybacillus species. Clade I is further partitioned into three clades, consisting separately of Geobacillus, Parageobacillus, and a third clade which we suggest should be elevated to a new genus Quasigeobacillus gen. nov. Two species of Anoxybacillus showed inconsistent positioning among the trees produced by differing methods and could not be clearly resolved into any of the three existing genera or the new genus. This research shows the importance of considering closely related genera together when studying phylogeny or assigning genomic affinities.

The Pectobacteriaceae family comprises plant pathogens able to provoke diverse diseases, including plant maceration due to the production of pectinases disrupting the plant cell wall. To better understand their natural diversity, a survey of pectinolytic bacteria was performed in lakes of the French region La Camargue near the Mediterranean Sea. Sixteen atypical pectinolytic isolates were obtained from brackish water of three lakes. The genome of six isolates was sequenced; their size is around 4.8 to 5.0 Mb, including a plasmid of 59 to 61 kb; their G+C values range from 49.1 to 49.3 mol%. Phylogenetic analyses indicated that the novel strains formed a new clade of Pectobacteriaceae, separate from previously described genera of this family. These analyses suggested also that Acerihabitans does not belong to Pectobacteriaceae and should be reclassified in the Bruguierivoracaceae family, while Symbiopectobacterium could be a true Pectobacteriaceae member. Based on phenotypic, genomic and phylogenetic characteristics, we propose the creation of a new genus with the name Prodigiosinella gen. nov. Both the phenotypic and phylogenetic analyses separated the strains into two distinct subgroups. However, the DNA-DNA relatedness values revealed a close relationship between the two groups, supporting their appurtenance to the same species. Thus, it is proposed to classify them as two subspecies of Prodigiosinella aquatilis sp. nov., for which we propose the name Prodigiosinella aquatilis subsp. aquatilis ssp. nov. (LS101T = CFBP 8826T = LMG 32072T) and Prodigiosinella aquatilis subsp. natabilis ssp. nov. (CE70T = CFBP 9054T = LMG 32867T).

We present the description of the new species, Rhodococcus (Prescottella) parequi, found during phylogenomic investigations of a global collection of strains identified as Rhodococcus (Prescottella) equi. Strain PAM 2766 was isolated from horse-breeding farm soil in Normandy, France, and was indistinguishable from R. equi based on the usual identification tests. Whole-genome phylogenetic analyses located PAM 2766 in the same Rhodococcus sublineage as R. equi, together with Rhodococcus agglutinans, Rhodococcus defluvii, Rhodococcus soli, Rhodococcus subtropicus, Rhodococcus spongiicola and Rhodococcus xishaensis. PAM 2766 is most closely related to, but sufficiently distinct from R. equi DSM 20307T to be considered as a separate species. Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) values are 88.60% and 92.35, respectively, well below the species cutoff. The PAM 2766 draft genome is [~]5.3 Mb in size with 68.98% G+C mol content. PAM 2766T is aerobic, non-motile, and produces smooth creamy to buff-coloured colonies very similar to those of R. equi. It phenotypically differs from the latter by the ability to grow at 5{degrees}C, a strongly positive urease test at 24 h, and specificities in the carbon and nitrogen source utilization profile as determined by phenotype microarray screens. Our data indicate that PAM 2766 belongs to a novel species, for which the name Rhodococcus parequi sp. nov. is proposed. R. parequi was avirulent in macrophage infection assays and is assumed to be non-pathogenic. The type strain is PAM 2766T (=CETC 30995T = NCTC 14987T).

Strain LLG6346-3.1T, isolated from the thallus of the brown alga Ericaria zosteroides collected in Mediterranean Sea near Bastia in Corsica, France, was characterized using a polyphasic method. Cells were Gram-stain-negative, strictly aerobic, non-flagellated, motile by gliding, rod-shaped and grew optimally at 30-33 {degrees}C, at pH 8-8.5 and with 4-5 % NaCl. Strain LLG6346-3.1T used the seaweed polysaccharide alginic acid as sole carbon source which was vigorously liquefied. Phylogenetic analyses showed that the bacterium is affiliated to the genus Zobellia (family Flavobacteriaceae, class Flavobacteriia). Strain LLG6346-3.1T exhibited 16S rRNA gene sequence similarity values of 98.5 and 98.3 % to the type strains of Zobellia russellii and Zobellia roscoffensis respectively, and of 97.4-98.2 % to other species of the genus Zobellia. The DNA G+C content of strain LLG6346-3.1T was determined to be 38.28 mol%. Digital DNA-DNA hybridization predictions by the ANI and GGDC methods between strain LLG6346-3.1T and other members of the genus Zobellia showed values of 76-88 %, and below 37 %, respectively. The phenotypic, phylogenetic and genomic analyses show that strain LLG6346-3.1T is distinct from species of the genus Zobellia with validly published names and that it represents a novel species of the genus Zobellia, for which the name Zobellia alginoliquefaciens sp. nov. is proposed. The type strain is LLG6346-3.1T (RCC 7657T = LLG 32918T).

A novel bacterial strain designated ADMK78T was isolated from the saline desert soil. The cells were rod-shaped, Gram-negative, and non-motile. The strain ADMK78T grows best at 28{degrees}C and pH 7.0 and can tolerate up to 2% (w/v) NaCl. Based on 16S rRNA gene phylogeny, the strain ADMK78T belongs to the genus Rhizobium, with the highest similarity to Rhizobium wuzhouense W44T (98.7%) and Rhizobium ipomoeae shin9-1T (97.9%). Core-genes based phylogenetic analysis revealed that the strain ADMK78T forms a distinct branch in between Rhizobium ipomoeae shin9-1T and Rhizobium selenitireducens BAA-1503T. The average nucleotide identity of ADMK78T was less than 82%, to members of the family Rhizobiaceae. The genomic DNA G+C content of strain ADMK78T is 58.6 mol%. The major fatty acids of strain ADMK78T were C18:0 and C18:1 {omega}7c. The strain ADMK78T showed differences in physiological, phenotypic, and protein profiles estimated by MALDI-TOF MS to its closest relatives. Based on the phenotypic, chemotaxonomic properties, and phylogenetic analyses, the strain ADMK78T could be distinguished from the recognized species of the genus Rhizobium. It is suggested to represent a novel species of this genus, for which the name Rhizobium desertarenae sp. nov. is proposed. The type strain is ADMK78T (=MCC 3400T; KACC 21383T; JCM 33657T).

Bradyrhizobia are widespread across the Australian continent, where they are essential to Australian ecosystems by helping legumes to compensate nutrient deficiencies and low fertility of Australian soils. Among the Bradyrhizobium genospecies identified during a survey of Australian native rhizobia communities in 1994-1995, genospecies L appeared to be only distantly related to any Bradyrhizobium lineages known at the time. We take advantage of the recent sequencing of the genome of strain BDV5419, the original strain corresponding to Bradyrhizobium genospecies L, to re-assess this lineage taxonomic status. We characterized further strain BDV5419 based on morpho-physiological traits and determined its phylogenetic relationships with the type strains of the 88 currently known Bradyrhizobium species based on sequence comparisons of SSU rRNA genes and complete genomes. The digital DNA-DNA hybridization relatedness with any type strain was less than 33% and both SSU rRNA gene and genome phylogenies confirmed that this strain does not belong to any formerly described species within the Bradyrhizobium genus. Whereas its position within the lineage encompassing the B. elkanii and B. jicamae supergroups is unresolved in the SSU rDNA phylogeny, strain BDV5419 appears to be one of most basal lineages of the B. elkanii supergroup in the genome comparison. All data thus support the description of the novel species Bradyrhizobium hardenbergiae sp. nov. which type strain is BDV5419T (= CFBP 9111T = LMG 32897T), isolated from a nodule of Hardenbergia violaceae in Black Mountain Nature Reserve, in Canberra, ACT, Australia.

Members of Phytobacter, a recently described genus within the family Enterobacteriaceae, are still frequently misclassified as species of other genera. Here, we present genomic evidence that the taxa "Citrobacter bitternis" and "Kluyvera intestini", as cited in the literature and listed in NCBI databases, are heterotypic synonyms of Phytobacter diazotrophicus. Comparative analyses of 16S rRNA gene phylogeny, core genome phylogeny, average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH) consistently place the type strains of both "C. bitternis" and "K. intestini" within the species P. diazotrophicus. Recognizing these taxa as synonyms will help resolve persistent taxonomic inconsistencies and reduce misidentification in clinical and environmental microbiology.

Six strains of a novel anaerobic bacterial taxa exhibiting bile acid-transforming activity were isolated from fecal samples of clinically healthy cats living in Oakland, California. 16S rRNA sequencing and phylogenetic analysis indicate that strain AB800T belongs to the genus Peptacetobacter, with Peptacetobacter hiranonis strain JCM 10541 (98% coverage, 99.7% identity) as its closest relative. Whole genome sequencing shows an average nucleotide identity (ANI) of less than 96% (95.73% ANI, 90.53% AF) with the closest validly named species being Peptacetobacter hiranonis DGF055142. The size is about 2.58 Mb, containing 2,355 predicted coding sequences and 2,450 annotated genes. Phenotypic characterisation, and comprehensive genomic analysis, including ANI, digital DNA-DNA hybridization (dDDH) and core genome phylogenetic analysis, placing the strain AB800T on a separate branch, supported the classification of a novel species, strain AB800T (DSM 120482 = LMG 34035) with the proposed name Candidatus Peptacetobacter felis sp. nov., derived from "felis" the latin name of cat felis catus. These findings expand our understanding of host-associated bile acid converters and provide promising candidates for probiotic development.

Four novel bacterial species collected from healthy tissues of corn, rice and soybean plants in the United States are described. These include Cellulomonas zeae sp. nov. isolated from corn in Indiana; Lelliottia zeae sp. nov. from corn in Indiana and rice in Arkansas; Paraburkholderia zeae sp. nov. isolated from corn in Iowa; and Sphingomonas zeigerminis sp. nov. from corn in Mississippi and soy in Arkansas. No pathogenic strains are known for any of the novel species based on genome comparisons to assemblies in GenBank.

A strictly anaerobic bacterial strain, F2T, was isolated from an anaerobic bioreactor fermenting source-separated organic waste. Cells of strain F2T are non-spore-forming, rod-shaped (1.5-2.5 x 0.27-0.33 m), and Gram-negative, although they possess a monoderm cell wall architecture. The strain grew at 37 degrees C within a pH range of 5 to 8 and produced short-, branched-, and medium-chain carboxylates as well as ammonium, H2 and CO2, with acetate and propanoate produced or consumed depending on fermentation conditions. The genome consists of a single 2.4 Mbp chromosome with a G+C content of 50.2% and 2,131 predicted genes. Phylogenetic analysis of the 16S rRNA gene against other isolates revealed that strain F2T is most similar to Eubacterium pyruvativorans I-6T (92.06% 16S rRNA identity). Based on further phenotypic, genomic, and phylogenetic analysis, strain F2T represents a novel genus and species within the family Anaerovoracaceae with the proposed name Peptonella octanoica gen. nov. sp. nov. The type strain is F2T (strain accession pending). As a member of this same genus-level clade, we propose reclassifying Eubacterium pyruvativorans as Peptonella pyruvativorans comb. nov. These findings disambiguate Peptonella spp. from the phylogenetically distant and phenotypically distinct Eubacterium limosum ATCC 8486T.

Genus Xanthomonas is primarily comprise phytopathogenic species. In a recent study by carrying out deep phyto-taxonogenomics, we reported that even the genera Xylella, Stenotrophomonas and Pseudoxanthomonas are miss-classified and belong to genus Xanthomonas. Hence to understand the breadth of the genus, we carried out deep phylo-taxonogenomics of the order Xanthomonadales. Such investigation revealed that at least four more genera belong to genus Xanthomonas with prominent being Lysobacter. Further order level deep phylo-taxonogenomics revealed two major families. One being the original family Xanthomonadaceae and other is proposed as Frateuriaceae fam. nov. as synonym of family Rhodanobacteraceae with novel genus Frateuria gen. nov.

Ralstonia solanacearum species complex (RSSC) is a genetically diverse group of plant pathogens, yet genomic data from South America remain limited. Here, we characterize 13 RSSC strains isolated from tomato, pepper, and eggplant in northeastern Argentina. Phylogenetic analysis of the egl marker gene assigned these strains to phylotype IIA and suggested two closely related lineages. Complete genomes (5.63-5.76 Mb) were generated for four representative strains, yielding high-quality (99.94% completeness with f_Burkholderiaceae CheckM markers), closed assemblies with canonical bipartite architecture. Phylogenetic analysis of the egl marker, 49 conserved bacterial genes, and average nucleotide identity (ANI) analyses, consistently assigned one lineage to sequevar IIA-50, forming a coherent and monophyletic group. In contrast, although egl analysis suggested the second lineage was related to one sequevar IIA-38 reference strain, genomic analysis did not support this assignment. Further, the genomic analysis revealed significant genomic distance between the genomes for two sequevar 38 representative strains, supporting a conclusion that sequevar 38 itself was not monophyletic and instead appears paraphyletic. These findings highlight limitations of single-locus classification and support genome-informed refinement of RSSC sub-phylotype taxonomy. Outcome statementReports of bacterial wilt disease in Argentina had not yet been published in the international literature although the disease has been long-standing. This study provides complete genome sequences for four Ralstonia solanacearum strains from Northern Argentina and places them within a global phylogenomic framework. The Argentine strains cluster into two closely related phylotype IIA lineages, indicating that bacterial wilt in this regional dataset is associated with genetically similar populations. For clear communication of which strains are present in Northern Argentina, we attempted to classify the lineages to the long-standing sequence variant (sequevar) system for naming R. solanacearum species complex (RSSC) strains. One lineage was confidently assigned to IIA-50 with genomic support that confirmed phylogenetic analysis of the classical genetic marker egl. However, newly available genomes for sequevar reference strains revealed an issue where two distantly related strains are currently recognized as references for sequevars. Overall, these results provide evidence supporting the need for genome-informed refinement of sub-phylotype classification and expand genomic representation of South American RSSC populations. Data summaryComplete genome assemblies and raw reads for INTABV18, INTABV29, INTABV624 and INTABV2657 are deposited to NCBI under the project number PRJNA1407867. The curated dataset of public RSSC genomes is available to users who register a free account on KBase via a KBase narrative (https://narrative.kbase.us/narrative/189849). The narrative described in a living BioRxiv pre-print [1]. Supplemental files such as Figure S1, rectangular versions of all trees (Figure 2 and 3 and S1) and supplementary table S1, S2, S3 and S4 are available on Zenodo at doi.org/10.5281/zenodo.19502890 O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=172 SRC="FIGDIR/small/721750v1_figS1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1ac3168org.highwire.dtl.DTLVardef@1dfd0d6org.highwire.dtl.DTLVardef@107ae42org.highwire.dtl.DTLVardef@141937c_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure S1.C_FLOATNO Maximum-likelihood phylogenetic tree inferred from 471 bp of endoglucanase (egl) gene sequences assigned Argentine strains as phylotype II sequevar 38 and sequevar 50. The tree was constructed using PhyML v3.0 under the GTR nucleotide substitution model with gamma-distributed rate heterogeneity ( = 0.33), as selected by the SMART model selection procedure implemented in PhyML (Lefort et al., 2017). The egl sequences from Argentine strains are highlighted in blue, and their corresponding GenBank accession numbers for both the egl nucleotide sequence and the whole-genome assembly are shown in parentheses. Reference egl sequences representing sequevars IIA-38 (CFBP6801 and CIP120) and IIA-50 (T1-UY and ACH1076) are also shown in bold and marked with yellow circles. A searchable PDF of this tree in rectangular format is available on Zenodo (doi.org/10.5281/zenodo.19502890). C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/721750v1_fig2.gif" ALT="Figure 2"> View larger version (53K): org.highwire.dtl.DTLVardef@39d776org.highwire.dtl.DTLVardef@170bd89org.highwire.dtl.DTLVardef@aba166org.highwire.dtl.DTLVardef@1f156dd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 2.C_FLOATNO Maximum-likelihood phylogenetic tree inferred from 710 bp of endoglucanase (egl) gene sequences assigned Argentine strains as phylotype II sequevar 38 and sequevar 50. The phylogenetic tree was constructed using PhyML v3.0 under the GTR+R nucleotide substitution model, as selected by the SMART model selection procedure (Lefort et al., 2017). egl sequences from four Argentine strains (INTABV18, INTABV29, INTABV624, and INTABV2657) are shown in bold and highlighted in blue. Reference egl sequences representing sequevars IIA-38 (CFBP6801 and CIP120) and IIA-50 (T1-UY and ACH1076) are also shown in bold and marked with yellow circles. Two USA strains identified as IIA-38 (UCD576 and RS124) are shown in bold. A searchable PDF of this tree in rectangular format is available on Zenodo (doi.org/10.5281/zenodo.19502890). C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/721750v1_fig3.gif" ALT="Figure 3"> View larger version (37K): org.highwire.dtl.DTLVardef@17dd372org.highwire.dtl.DTLVardef@1c5156corg.highwire.dtl.DTLVardef@179d9org.highwire.dtl.DTLVardef@e6d529_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 3.C_FLOATNO Approximate maximum-likelihood phylogeny based on a concatenated alignment of 49 conserved genes places four Argentine genomes (INTABV18, INTABV29, INTABV624 and INTABV2657) within the phylotype IIA clade. The tree was constructed using the SpeciesTreeBuilder v0.1.4 application on the KBase platform, incorporating the four Argentine genomes into a reference dataset of 825 genomes representing the known global diversity of the RSSC. The tree was visualized and annotated using iTOL v7.4.2. Argentine genomes are shown in bold and highlighted in blue, and egl reference strains for the sequevar IIA-38 (CIP120 and CFBP6801) and IIA-50 (T1-UY) are shown in bold and marked with yellow circles. Branches with approximate likelihood-ratio support values higher than >70% are colored in blue. A searchable PDF of this tree in rectangular format is available on Zenodo (doi.org/10.5281/zenodo.19502890). C_FIG

A strictly aerobic, Gram-stain-negative, rod-shaped and motile bacterium, designated strain KMM 296, isolated from the coelomic fluid of mussel Crenomytilus grayanus, was investigated in details due to its ability to produce a highly active alkaline phosphatase of the structural family PhoA. A previous taxonomic study placed the strain to the species Cobetia marina, a member of the family Halomonadaceae of the class Gammaproteobacteria. However, the comprehensive phylogenetic analysis based on 16S rRNA gene sequencing revealed that the strain KMM 296 is most closely related to Cobetia amphilecti NRIC 815T with the 16S rRNA gene sequence similarity of 100%. The mussel isolate grew with 0.5-19% NaCl and at 4 - 42{degrees}C and hydrolysed Tweens 20 and 40, and L-tyrosine. The DNA G+C content was 62.5 mol%. The prevalent fatty acids were C18:1 {omega}7c, C12:0 3-OH, C18:1 {omega}7c, C12:0 and C17:0 cyclo. The polar lipid profile was characterized by the presence of phosphatidylethanolamine, phosphatidylglycerol, phosphatidic acid, and unidentified aminolipid, phospholipid, and lipids. The major respiratory quinone was Q-8. According to phylogenetic evidence and similarity in the chemotaxonomic and genotypic properties of the mussel isolate and its nearest neighbors, the strain KMM 296 represents a member of the species C. amphilecti. A comparative analysis of the type strains genomes of the species C. amphilecti and C. litoralis showed that they belong to a single species. In addition, a high similarity of the genome sequences of C. pacifica NRIC 813T and C. marina LMG 2217T also allows suggesting the affiliation of these two species to one species. Based on the rules of priority, C. litoralis should be reclassified as a later heterotypic synonym of C. amphilecti, and C. pacifica is a later heterotypic synonym of C. marina. The emended descriptions of the species C. amphilecti and C. marina are also proposed.

We report the complete genome sequences of eight Fusobacterium watanabei clinical isolates, ranging from 1.95 to 2.09 Mbp. Analysis against the Genome Taxonomy Database (GTDB) indicates that Fusobacterium watanabei genomes are part of the "Fusobacterium nucleatum_J" group, which also encompasses the previously published FNU strain and Fna C1 isolates.