Genome Blast Distance Phylogeny Research Articles

Comparative Genomic and Functional Analyses for Insights into Pantoea agglomerans Strains Adaptability in Diverse Ecological Niches.

Pantoea agglomerans inhabit diverse ecological niches, ranging from epiphytes and endophytes in plants, body of animals, and occasionally in the human system. This multifaceted bacterium contributes substantially to plant growth promotion, stress resilience, and biocontrol but can also act as a pathogen to its host. The genetic determinants underlying these diverse functions remain largely unfathomed and to uncover this phenomenon,nineteenstrains ofPantoea agglomeranswere selected and analyzed. Genome-to-Genome Distance Calculator (GGDC) which uses the Genome Blast Distance Phylogeny (GBDP) technique to calculate digital DDH values.Phylogenetic analysis via Genome-to-Genome distance, Average Nucleotide Identity, and Amino Acid Identity calculation revealed that all strains belonged to the genusPantoea. However, strain 33.1 had a lower value than the threshold for the same species delineation. Bacterial Pan Genome Analysis (BPGA) Pipeline and MinPath analysis revealed genetic traits associated with environmental resilience, such as oxidative stress, UV radiation, temperature extremes, and metabolism of distinct host-specific carbohydrates. Protein-protein interactome analysis illustrated osmotic stress proteins closely linked with core proteins, while heavy metal tolerance, nitrogen metabolism, and Type III and VI secretion systems proteins generally associated with pathogenicity formed a separate network, indicating strain-specific characteristics. These findings shed new light on the intricate genetic architecture ofPantoea agglomerans, revealing its adaptability to inhabit diverse niches and thrive in varied environments.

Proposal for reclassification of the species Hungatella xylanolytica as Lacrimispora xylanisolvens nom. nov. and transfer of the genus Hungatella to the family Lachnospiraceae.

Hungatella xylanolytica X5-1T is an anaerobic, xylan-fermenting bacterium first isolated from methane-producing cattle manure. Initially identified as Bacteroides xylanolyticus, this species was later reclassified as H. xylanolytica in 2019. Although this reclassification found support through Genome blast Distance Phylogeny analysis which placed H. xylanolytica X5-1T into the same clade as Hungatella effluvii DSM 24995T, it was contradicted by 16S rRNA gene phylogenetic analysis, which associated it with a set of misnamed Clostridium species later reassigned into the genus Lacrimispora. To ascertain its taxonomic position, comparative analyses were performed to re-examine the relationship between H. xylanolytica X5-1T and all species of the genera Hungatella and Lacrimispora. The ranges of 16S rRNA gene sequence similarity, average amino acid identity, and percentage of conserved protein prediction values were higher between H. xylanolytica X5-1T and species of the genus Lacrimispora than Hungatella. In addition, H. xylanolytica X5-1T was found to harbour genes and pathways conserved and exclusive to species within the genus Lacrimispora but not Hungatella. Essentially, in both the 16S rRNA gene phylogenetic tree and the core-genome phylogenomic tree, H. xylanolytica X5-1T clustered into the same clade as species of the genus Lacrimispora, distinct from species of the genus Hungatella. It is thus clear that H. xylanolytica X5-1T represents a species within the genus Lacrimispora, which we propose to reclassify as Lacrimispora xylanisolvens nom. nov. Finally, based on the results from the phylogenetic and comparative analyses, the genus Hungatella was transferred to the family Lachnospiraceae.

Apirhabdus apintestini gen. nov., sp. nov., a member of a novel genus of the family Enterobacteriaceae, isolated from the gut of the western honey bee Apis mellifera.

A Gram-negative, motile, rod-shaped bacterial strain, CA-0114T, was isolated from the midgut of a western honey bee, Apis mellifera. The isolate exhibited ≤96.43 % 16S rRNA gene sequence identity (1540 bp) to members of the families Enterobacteriaceae and Erwiniaceae. Phylogenetic trees based on genome blast distance phylogeny and concatenated protein sequences encoded by conserved genes atpD, fusA, gyrB, infB, leuS, pyrG and rpoB separated the isolate from other genera forming a distinct lineage in the Enterobacteriaceae. In both trees, the closest relatives were Tenebrionicola larvae YMB-R21T and Tenebrionibacter intestinalis BIT-L3T, which were isolated previously from Tenebrio molitor L., a plastic-eating mealworm. Digital DNA-DNA hybridization, orthologous average nucleotide identity and average amino acid identity values between strain CA-0114T and the closest related members within the Enterobacteriaceae were ≤23.1, 75.45 and 76.04 %, respectively. The complete genome of strain CA-0114T was 4 451669 bp with a G+C content of 52.12 mol%. Notably, the apparent inability of strain CA-0114T to ferment d-glucose, inositol and l-rhamnose in the API 20E system is unique among closely related members of the Enterobacteriaceae. Based on the results obtained through genotypic and phenotypic analysis, we propose that strain CA-0114T represents a novel species and genus within the family Enterobacteriaceae, for which we propose the name Apirhabdus apintestini gen. nov., sp. nov. (type strain CA-0114T=ATCC TSD-396T=DSM 116385T).

Complete genome sequences of twelve strains of Leptospira interrogans isolated from humans in Sri Lanka.

Leptospirosis, a major zoonotic disease caused by pathogenic Leptospira spp. is recognized globally as an emerging zoonotic disease. Whole-genome sequencing reveals hidden messages about Leptospira's pathogenesis. We used Single Molecule Real-Time (SMRT) sequencing to obtain complete genome sequences of twelve L. interrogans isolates from febrile patients from Sri Lanka for a comparative whole genome sequencing study. The sequence data generated 12 genomes with a coverage greater than X600 with sizes ranging from 4.62Mb to 5.16Mb, and a G+C content ranging from 35.00% to 35.42%. The total number of coding sequences predicted by the NCBI (National Center for Biotechnology Information) genome assembly platform ranged from 3845 to 4621 for the twelve strains. Leptospira serogroup with similar-sized LPS biosynthetic loci that belonged to the same clade had a close relationship in the phylogenetic analysis. Nonetheless, variations in the genes encoding sugar biosynthesis were found in the serovar determinant region (rfb locus). Type I and Type III CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) systems were found in all of the strains. Genome BLAST Distance Phylogeny of these sequences allowed for detailed genomic strain typing. These findings may help us better understand the pathogenesis, develop a tools for early diagnosis, comparative genomic analysis and evolution of Leptospira.

Whole Genome Sequence Analysis of Cupriavidus necator C39, a Multiple Heavy Metal(loid) and Antibiotic Resistant Bacterium Isolated from a Gold/Copper Mine.

Here a multiple heavy metal and antibiotic resistant bacterium Cupriavidus necator C39 (C. necator C39) was isolated from a Gold-Copper mine in Zijin, Fujian, China. C. necator C39 was able to tolerate intermediate concentrations of heavy metal(loid)s in Tris Minimal (TMM) Medium (Cu(II) 2 mM, Zn(II) 2 mM, Ni(II) 0.2 mM, Au(III) 70 μM and As(III) 2.5 mM). In addition, high resistance to multiple antibiotics was experimentally observed. Moreover, strain C39 was able to grow on TMM medium containing aromatic compounds such as benzoate, phenol, indole, p-hydroxybenzoic acid or phloroglucinol anhydrous as the sole carbon sources. The complete genome of this strain revealed 2 circular chromosomes and 1 plasmid, and showed the closest type strain is C. necator N-1T based on Genome BLAST Distance Phylogeny. The arsenic-resistance (ars) cluster GST-arsR-arsICBR-yciI and a scattered gene encoding the putative arsenite efflux pump ArsB were identified on the genome of strain C39, which thereby may provide the bacterium a robust capability for arsenic resistance. Genes encoding multidrug resistance efflux pump may confer high antibiotic resistance to strain C39. Key genes encoding functions in degradation pathways of benzene compounds, including benzoate, phenol, benzamide, catechol, 3- or 4-fluorobenzoate, 3- or 4-hydroxybenzoate and 3,4-dihydroxybenzoate, indicated its potential for degrading those benzene compounds.

Characterization and genome analysis of Vibrio phage vB_VhaP_PG11, representing a new viral genus

Vibrio is a kind of common gram-negative bacteria, which is widely distributed in marine and estuarine environments. In the study, a novel marine phage vB_VhaP_PG11, infecting Vibrio hangzhouensis, was isolated from the offshore waters of Qingdao, China. vB_VhaP_PG11 is a double-stranded DNA phage. The whole genome proteomic tree shows that vB_VhaP_PG11 phage is related to two Vibrio phages, Vibrio phage 1.238.A._10N.261.52.F10 and Vibrio phage 1.245.O._10N.261.54.C7, but with low homology. Their amino acids identity with vB_VhaP_PG11 is 42.77 and 41.49% respectively. The prediction results of genome-blast distance phylogeny (GBDP) and the analysis gene-sharing network indicate that vB_VhaP_PG11 belongs to a new genus in Schitoviridae, named Qingschitovirus. The study of Vibrio phage vB_VhaP_PG11 provides basic information contributing to a better understanding of interactions between Vibrio phages and their hosts and helps analyze unknown viral sequences in the metagenomic database.

Streptomyces pacificus sp. nov., a novel spongiicolazolicin-producing actinomycete isolated from a coastal sediment.

A polyphasic approach was used to determine the taxonomic position of a marine actinomycete, designated isolate CWH03T, which we previously reported to produce new linear azole-containing peptides spongiicolazolicins A and B. Strain CWH03T is mesophilic, neutrophilic, and halotolerant streptomycete that forms spiral spore chains on aerial mycelium. Comparative 16S rRNA gene sequencing showed that CWH03T was most closely related to Streptomyces tirandamycinicus HNM0039T (99.7%), Streptomyces spongiicola HNM0071T (99.4%), 'Streptomyces marianii' ICN19T (99.1%) and Streptomyces wuyuanensis CGMCC4.7042T (99.0%). The phylogenetic tree prepared using the 16S rRNA gene, as well as the phylogenomic tree using the genome BLAST distance phylogeny method and 81 core housekeeping genes, respectively, showed that the closest relative of strain CWH03T was S. spongiicola HNM0071T. The average nucleotide identity and digital DNA-DNA hybridization values between strains CWH03T and S. spongiicola HNM0071T were 91.46% and 44.2%, respectively, which were below the thresholds of 96% and 70% for prokaryotic conspecific assignation. The G+C content of the genomic DNA of strain CWH03T was 72.3%. Whole-cell hydrolysates of strain CWH03T contained LL-diaminopimelic acid. The predominant menaquinone was MK-9(H8) (88.3%), and the major fatty acids were iso-C16:0 (28.4%), anteiso-C15:0 (15.0%) and iso-C15:0 (12.9%). The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. Based on data obtained from phenotypic, phylogenetic, genomic, and chemotaxonomic analyses, strain CWH03T represents a novel species of the genus Streptomyces, for which the proposed name is Streptomyces pacificus sp. nov. The type strain is CWH03T ( = NBRC 114659T = TBRC 15780T).

Strains of Bradyrhizobium barranii sp. nov. associated with legumes native to Canada are symbionts of soybeans and belong to different subspecies (subsp. barranii subsp. nov. and subsp. apii subsp. nov.) and symbiovars (sv. glycinearum and sv. septentrionale).

Four bacterial strains isolated from root nodules of soybean plants that had been inoculated with root-zone soils of legumes native to Canada were previously identified as a novel Bradyrhizobium lineage consisting of symbiovars (sv.) glycinearum and septentrionale. Our purpose was to verify the taxonomic status of these strains using phylogenetic, genomic and phenotypic analyses. Multiple phylogenetic analyses including analysis of 51 full-length ribosome protein subunit (rps) gene sequences confirmed placement of the novel strains in a highly supported lineage distinct from named Bradyrhizobium species with B. japonicum USDA 6T as the closest relative. The results of genomic and phylogenomic analyses based on digital DNA–DNA hybridization and genome blast distance phylogeny showed that novel strains in comparisons with type strains of closest relatives were below the established threshold (70 %) for species delineation. Moreover, the novel strains were divided into two subspecies clusters based on the established threshold of 79 %. The genomes of strains 144S4T, 323S2, 1S5 and 38S5T have sizes of 11 399 526, 11 474 152, 10580853 and 10 530 141 bp with DNA G+C contents of 63.1, 63.0, 63.4 and 63.3 mol%, respectively. These strains possess symbiosis islands harbouring key nodulation, nitrogen-fixation and type III secretion system genes as well as abundant insertion sequences and between two and four putative plasmids. Strains 144S4T and 323S2 (sv. glycinearum) are effective with regard to nitrogen fixation in symbiotic association with soybeans whereas strains 1S5 and 38S5T (sv. septentrionale) are ineffective. Data for morphological, physiological and symbiotic characteristics complement the sequence-based results. The data presented here support the description of a new species and two new subspecies for which the names Bradyrhizobium barranii sp. nov. subsp. barranii subsp. nov. (sv. glycinearum) and Bradyrhizobium barranii sp. nov. subsp. apii subsp. nov. (sv. septentrionale) are proposed with strain 144S4T (=LMG 31552T=HAMBI 3722T) as the species type strain and type strain of subsp. barranii subsp. nov., and strain 38S5T (=LMG 31556T=HAMBI 3721T) as the type strain of subsp. apii subsp. nov.

Chromobacterium alticapitis sp. nov. and Chromobacterium sinusclupearum sp. nov. isolated from wild cranberry bogs in the Cape Cod National Seashore, USA.

Two non-pigmented strains in the genus Chromobacterium, MWU14-2602T and MWU13-2610T, were isolated from wild cranberry bogs in the Cape Cod National Seashore, USA. The isolates were characterized by genomic and phenotypic analyses, the results of which indicated that they represent two novel species. Based on total genome sequences, the closest relatives were in the Chromobacterium amazonense group, which includes the recently described Chromobacterium paludis. Whole genome sequences were compared by genome blast distance phylogeny, digital DNA-DNA hybridization and average nucleotide identity analyses with each other and with the type strains of their nearest species. MWU14-2602T and MWU13-2610T fell well below the accepted cutoff values for species relatedness, clearly indicating that they represent novel species. Although little is known about these organisms in situ, under laboratory conditions, MWU13-2610T produced a modest amount of HCN and was strongly positive for exoprotease activity, whereas MWU14-2602T did not produce HCN or exoproteases. The predominant fatty acids for both isolates were summed C16 : 1ω7cis/C16 : 1ω6cis. Both isolates produced siderophores and pyomelanin pigment on rich media, and neither was haemolytic on sheep blood agar. We propose the names Chromobacterium alticapitis sp. nov. (type strain MWU14-2602T=ATCC TSD 260T=CCOS 1979T) and Chromobacterium sinusclupearum sp. nov. (type strain MWU13-2610T=ATCC TSD-259T=CCOS 1981T) for these taxa.

Campylobacter bilis sp. nov., isolated from chickens with spotty liver disease.

A novel species of Campylobacter was isolated from bile samples of chickens with spotty liver disease in Australia, making it the second novel species isolated from chickens with the disease, after Campylobacter hepaticus was isolated and described in 2016. Six independently derived isolates were obtained. They were Gram-stain-negative, microaerobic, catalase-positive, oxidase-positive and urease-negative. Unlike most other species of the genus Campylobacter, more than half of the tested strains of this novel species hydrolysed hippurate and most of them could not reduce nitrate. Distinct from C. hepaticus, many of the isolates were sensitive to 2,3,5-triphenyltetrazolium chloride (0.04%) and metronidazole (4 mg ml-1), and all strains were sensitive to nalidixic acid. Phylogenetic analysis using 16S rRNA and hsp60 gene sequences demonstrated that the strains formed a robust clade that was clearly distinct from recognized Campylobacter species. Whole genome sequence analysis of the strains showed that the average nucleotide identity and the genome blast distance phylogeny values compared to other Campylobacter species were less than 86 and 66%, respectively, which are below the cut-off values generally recognized for isolates of the same species. The genome of the novel species has a DNA G+C content of 30.6 mol%, while that of C. hepaticus is 27.9 mol%. Electron microscopy showed that the cells were spiral-shaped, with bipolar unsheathed flagella. The protein spectra generated from matrix-assisted laser desorption/ionization time of flight analysis demonstrated that they are different from the most closely related Campylobacter species. These data indicate that the isolates belong to a novel Campylobacter species, for which the name Campylobacter bilis sp. nov. is proposed. The type strain is VicNov18T (=ATCC TSD-231T=NCTC 14611T).

Streptomyces silvae sp. nov., isolated from forest soil.

A bacterial strain, named For3T, was isolated from forest soil sampled in Champenoux, France. Based on its 16S rRNA gene sequence, the strain was affiliated to the family Streptomycetaceae and, more specifically, to the genus Streptomyces . The strain had 99.93% 16S rRNA gene sequence similarity to its closest relative strains Streptomyces pratensis ATCC 33331T, Streptomyces anulatus ATCC 27416T, Streptomyces setonii NRRL ISP-5322T and Kitasatospora papulosa NRRL B-16504T. The phylogenomic tree using the genome blast distance phylogeny method showed that the closest relative strain was Streptomyces atroolivaceus NRRL ISP-5137T and that For3T represents a new branch among the Streptomyces . Genome relatedness indexes revealed that the average nucleotide identity and digital DNA–DNA hybridization values between For3T and its closest phylogenomic relative ( S. atroolivaceus NRRL ISP-5137T) were 88.39 and 39.2 %, respectively. The G+C content of the genome was 71.4 mol% and its size was 7.96 Mb with 7492 protein-coding genes. Strain For3T harboured complete metabolic pathways absent in the closest relative strains such as cellulose biosynthesis, glycogen degradation I, glucosylglycerate biosynthesis I. Anteiso-C15:0, iso-C15:0, anteiso-C17:0 and MK-9(H4)/MK-9(H6) were the predominant cellular fatty acids and respiratory quinones, respectively. Phenotypic and genomic data supported the assignment of strain For3T to a novel species Streptomyces silvae sp. nov., within the genus Streptomyces , for which the type strain is For3T (=CIP 111908T=LMG 32186T).

Taxonomic note on the family Pseudonocardiaceae based on phylogenomic analysis and descriptions of Allosaccharopolyspora gen. nov. and Halosaccharopolyspora gen. nov.

The taxonomic positions of members within the family Pseudonocardiaceae were assessed based on phylogenomic trees reconstructed using core-proteome and genome blast distance phylogeny approaches. The closely clustered genome sequences from the type strains of validly published names within the family Pseudonocardiaceae were analysed using overall genome-related indices based on average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values. The family Pseudonocardiaceae consists of the type genus Pseudonocardia, as well as the genera Actinoalloteichus, Actinocrispum, Actinokineospora, Actinomycetospora, Actinophytocola, Actinopolyspora, Actinorectispora, Actinosynnema, Allokutzneria, Allosaccharopolyspora gen. nov., Amycolatopsis, Bounagaea, Crossiella, Gandjariella, Goodfellowiella, Haloactinomyces, Haloechinothrix, Halopolyspora, Halosaccharopolyspora gen. nov., Herbihabitans, Kibdelosporangium, Kutzneria, Labedaea, Lentzea, Longimycelium, Prauserella, Saccharomonospora, Saccharopolyspora, Saccharothrix, Salinifilum, Sciscionella, Streptoalloteichus, Tamaricihabitans, Thermocrispum, Thermotunica and Umezawaea. The G+C contents of the Pseudonocardiaceae genomes ranged from 66.2 to 74.6 mol% and genome sizes ranged from 3.69 to 12.28 Mbp. Based on the results of phylogenomic analysis, the names Allosaccharopolyspora coralli comb. nov., Halosaccharopolyspora lacisalsi comb. nov. and Actinoalloteichus caeruleus comb. nov. are proposed. This study revealed that Actinokineospora mzabensis is a heterotypic synonym of Actinokineospora spheciospongiae, Lentzea deserti is a heterotypic synonym of Lentzea atacamensis, Prauserella endophytica is a heterotypic synonym of Prauserella coralliicola, and Prauserella flava and Prauserella sediminis are heterotypic synonyms of Prauserella salsuginis. This study addresses the nomenclature conundrums of Actinoalloteichus cyanogriseus and Streptomyces caeruleus as well as Micropolyspora internatus and Saccharomonospora viridis.

Complete Genome Sequencing of Leptospira interrogans Isolates from Malaysia Reveals Massive Genome Rearrangement but High Conservation of Virulence-Associated Genes.

The ability of Leptospirae to persist in environments and animal hosts but to cause clinically highly variable disease in humans has made leptospirosis the most common zoonotic disease. Considering the paucity of data on variation in complete genomes of human pathogenic Leptospirae, we have used a combination of Single Molecule Real-Time (SMRT) and Illumina sequencing to obtain complete genome sequences of six human clinical L. interrogans isolates from Malaysia. All six contained the larger (4.28–4.56 Mb) and smaller (0.34–0.395 Mb) chromosome typical of human pathogenic Leptospirae and 0–7 plasmids. Only 24% of the plasmid sequences could be matched to databases. We identified a chromosomal core genome of 3318 coding sequences and strain-specific accessory genomes of 49–179 coding sequences. These sequences enabled detailed genomic strain typing (Genome BLAST Distance Phylogeny, DNA–DNA hybridization, and multi locus sequence typing) and phylogenetic classification (whole-genome SNP genotyping). Even though there was some shared synteny and collinearity across the six genomes, there was evidence of major genome rearrangement, likely driven by horizontal gene transfer and homologous recombination. Mobile genetic elements were identified in all strains in highly varying numbers, including in the rfb locus, which defines serogroups and contributes to immune escape and pathogenesis. On the other hand, there was high conservation of virulence-associated genes including those relating to sialic acid, alginate, and lipid A biosynthesis. These findings suggest (i) that the antigenic variation, adaption to various host environments, and broad spectrum of virulence of L. interrogans are in part due to a high degree of genomic plasticity and (ii) that human pathogenic strains maintain a core set of genes required for virulence.

Whole Genome Sequencing Based Taxonomic Classification, and Comparative Genomic Analysis of Potentially Human Pathogenic Enterobacter spp. Isolated from Chlorinated Wastewater in the North West Province, South Africa.

Comparative genomics, in particular, pan-genome analysis, provides an in-depth understanding of the genetic variability and dynamics of a bacterial species. Coupled with whole-genome-based taxonomic analysis, these approaches can help to provide comprehensive, detailed insights into a bacterial species. Here, we report whole-genome-based taxonomic classification and comparative genomic analysis of potential human pathogenic Enterobacter hormaechei subsp. hoffmannii isolated from chlorinated wastewater. Genome Blast Distance Phylogeny (GBDP), digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANI) confirmed the identity of the isolates. The algorithm PathogenFinder predicted the isolates to be human pathogens with a probability of greater than 0.78. The potential pathogenic nature of the isolates was supported by the presence of biosynthetic gene clusters (BGCs), aerobactin, and aryl polyenes (APEs), which are known to be associated with pathogenic/virulent strains. Moreover, analysis of the genome sequences of the isolates reflected the presence of an arsenal of virulence factors and antibiotic resistance genes that augment the predictions of the algorithm PathogenFinder. The study comprehensively elucidated the genomic features of pathogenic Enterobacter isolates from wastewaters, highlighting the role of wastewaters in the dissemination of pathogenic microbes, and the need for monitoring the effectiveness of the wastewater treatment process.

Staphylococcus caledonicus sp. nov. and Staphylococcus canis sp. nov. isolated from healthy domestic dogs.

Two strains, H8/1T and H16/1AT, of Gram-stain-positive, coagulase-negative staphylococci were isolated from separate healthy domestic dogs in Scotland. Both strains were genome sequenced and their inferred DNA–DNA hybridisation indicates that H8/1T and H16/1AT represent two novel species of the genus Staphylococcus. On the basis of the results of genome sequence analysis (genome blast distance phylogeny and single nucleotide polymorphism analysis) H8/1T is most closely related to Staphylococcus devriesei and H16/1AT most closely related to Staphylococcus felis. Also, average nucleotide identity distinguished H8/1T and H16/1AT from S. devriesei and S. felis as did minor phenotypic differences. On the basis of these results, it is proposed that H8/1T and H16/1AT represent novel species with the respective names Staphylococcus caledonicus and Staphylococcus canis. The type strain of S. caledonicus is H8/1T (=NCTC 14452T=CCUG 74789T). The type strain of S. canis is H16/1AT (=NCTC 14451T=CCUG 74790T)

Genome analysis reveals that the correct name of type strain Adlercreutzia caecicola DSM 22242T is Parvibacter caecicola Clavel et al. 2013.

The strain Adlercreutzia caecicola DSM 22242T (=CCUG 57646T=NR06T) was taxonomically described in 2013 and named as Parvibacter caecicola Clavel et al. 2013. In 2018, the name of the strain DSM 22242T was changed to Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 due to taxonomic investigations of the closely related genera Adlercreutzia, Asaccharobacter and Enterorhabdus within the phylum Actinobacteria. However, the first whole draft genome of strain DSM 22242T was published by our group in 2019. Therefore, the genome was not available within the study of Nouioui et al. (2018). The results of the polyphasic approach within this study, including phenotypic and biochemical analyses and genome-based taxonomic investigations [genome-wide average nucleotide identity (gANI), alignment fraction (AF), average amino acid identity (AAI), percentage of orthologous conserved proteins (POCP) and genome blast distance phylogeny (GBDP) tree], indicated that the proposed change of the name Parvibacter caecicola to Adlercreutzia caecicola was not correct. Therefore, it is proposed that the correct name of Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 strain DSM 22242T is Parvibacter caecicola Clavel et al. 2013.

Genetic characterisation of Campylobacter concisus: Strategies for improved genomospecies discrimination

Although at least two genetically distinct groups, or genomospecies, have been well documented for Campylobacter concisus, no phenotype has yet been identified for their differentiation and thus formal description as separate species. C. concisus has been isolated from a variety of sites in the human body, including saliva and stool samples from both healthy and diarrhoeic individuals. We evaluated the ability of a range of whole genome-based tools to distinguish between the two C. concisus genomospecies (GS) using a collection of 190 C. concisus genomes. Nine genomes from related Campylobacter species were included in some analyses to provide context. Analyses incorporating sequence analysis of multiple ribosomal genes generated similar levels of C. concisus GS discrimination as genome-wide comparisons. The C. concisus genomes formed two groups; GS1 represented by ATCC 33237T and GS2 by CCUG 19995. The two C. concisus GS were separated from the nine genomes of related species. GS1 and GS2 also differed in G+C content with medians of 37.56% and 39.51%, respectively. The groups are consistent with previously established GS and are supported by DNA reassociation results. Average Nucleotide Identity using MUMmer (ANIm) and Genome BLAST Distance Phylogeny generated in silico DNA-DNA hybridisation (isDDH) (against ATCC 33237T and CCUG 19995), plus G+C content provides cluster-independent GS discrimination suitable for routine use. Pan-genomic analysis identified genes specific to GS1 and GS2. WGS data and genomic species identification methods support the existence of two GS within C. concisus. These data provide genome-level metrics for strain identification to genomospecies level.

Chromobacterium paludis sp. nov., a novel bacterium isolated from a Chesapeake Bay marsh.

Two isolates of Gram-reaction-negative, motile, violet-pigmented bacteria were isolated from a small pool in marshland near the mouth of the Nanticoke River in Maryland, USA. The isolates IIBBL 257-1T and IIBBL 257-2 had identical 16S rRNA gene sequences as determined by PCR, and highly similar fatty acid and biochemical profiles. The 16S rRNA gene sequences indicated the isolates belonged to the genus Chromobacterium. Genomic sequencing of IIBBL 257-1T revealed a genome of 4.27 Mb, with a G+C content of 63.6 %. Whole genome comparisons with other members of the Chromobacterium using JSpecies and the genome blast distance phylogeny approach indicated that among described species, IIBBL 257-1T was most closely related to C. amazonense and C. phragmitis. Comparison of the IIBBL 257-1T genome with those of type strains of these species resulted in ANIb and dDDH values of ca. 85 and 30 %, respectively, for both. These results demonstrate that IIBBL 257-1T and IIBBL 257-2 represent a new taxon within the genus Chromobacterium. We propose the name Chromobacterium paludis sp. nov. for this taxon; the type strain is IIBBL 257-1T (=NRRL B-65555T=JCM 33770T).

Salifodinibacter halophilus gen. nov., sp. nov., a halophilic gammaproteobacterium in the family Salinisphaeraceae isolated from a salt mine in the Colombian Andes.

Two morphologically similar halophilic strains, named USBA 874 and USBA 960T, were isolated from water and sediment samples collected from the Zipaquirá salt mine in the Colombian Andes. Both isolates had non-spore-forming, Gram-stain-negative and motile cells that grew aerobically. The strains grew optimally at 30 °C, pH 7.0 and with 25 % NaCl (w/v). The isolates showed almost identical 16S rRNA gene sequences (99.0 % similarity). The predominant quinones of USBA-960T were Q-8, Q-7 and Q-9. The major cellular fatty acids were C19 : 0 cyclo ω8c, C18 : 0 and C16 : 0. According to 16S rRNA gene sequencing, the closest phylogenetic relatives are Salinisphaera species (similarity between 93.6 and 92.3 %), Abyssibacter profundi OUC007T (88.6 %) and Oceanococcus atlanticus 22II-S10r2T (88.7 %). In addition, the result of genome blast distance phylogeny analysis between strains USBA 874 and USBA 960T, Salinisphaera halophila (YIM 95161T), Salinisphaera shabanensis (E1L3AT), Salinisphaera orenii (MK-B5T) and Salinisphaera japonica (YTM-1T) was 18.5 %. Other in silico species delineation analyses also showed low identity such as ANIb and ANIm values (<69.0 and <84.0 % respectively), TETRA (<0.81) and AAI values (<0.67). Genome sequencing of USBA 960T revealed a genome size of 2.47 Mbp and a G+C content of 59.71 mol%. Phylogenetic analysis of strains USBA 874 and USBA 960T indicated that they formed a different lineage within the family Salinisphaeraceae. Based on phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA-DNA relatedness values, along with identity at whole genome level, it can be concluded that strains USBA 960T and USBA 874 represent a novel genus of the family Salinisphaeraceae and the name Salifodinibacter halophilus gen. nov., sp. nov. is proposed. The type strain is USBA 960T (CMPUJ U095T=CECT 30006T).

Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism.

Comparative analysis of partial gyrB, recA, and gltB gene sequences of 84 Pandoraea reference strains and field isolates revealed several clusters that included no taxonomic reference strains. The gyrB, recA, and gltB phylogenetic trees were used to select 27 strains for whole-genome sequence analysis and for a comparative genomics study that also included 41 publicly available Pandoraea genome sequences. The phylogenomic analyses included a Genome BLAST Distance Phylogeny approach to calculate pairwise digital DNA–DNA hybridization values and their confidence intervals, average nucleotide identity analyses using the OrthoANIu algorithm, and a whole-genome phylogeny reconstruction based on 107 single-copy core genes using bcgTree. These analyses, along with subsequent chemotaxonomic and traditional phenotypic analyses, revealed the presence of 17 novel Pandoraea species among the strains analyzed, and allowed the identification of several unclassified Pandoraea strains reported in the literature. The genus Pandoraea has an open pan genome that includes many orthogroups in the ‘Xenobiotics biodegradation and metabolism’ KEGG pathway, which likely explains the enrichment of these species in polluted soils and participation in the biodegradation of complex organic substances. We propose to formally classify the 17 novel Pandoraea species as P. anapnoica sp. nov. (type strain LMG 31117T = CCUG 73385T), P. anhela sp. nov. (type strain LMG 31108T = CCUG 73386T), P. aquatica sp. nov. (type strain LMG 31011T = CCUG 73384T), P. bronchicola sp. nov. (type strain LMG 20603T = ATCC BAA-110T), P. capi sp. nov. (type strain LMG 20602T = ATCC BAA-109T), P. captiosa sp. nov. (type strain LMG 31118T = CCUG 73387T), P. cepalis sp. nov. (type strain LMG 31106T = CCUG 39680T), P. commovens sp. nov. (type strain LMG 31010T = CCUG 73378T), P. communis sp. nov. (type strain LMG 31110T = CCUG 73383T), P. eparura sp. nov. (type strain LMG 31012T = CCUG 73380T), P. horticolens sp. nov. (type strain LMG 31112T = CCUG 73379T), P. iniqua sp. nov. (type strain LMG 31009T = CCUG 73377T), P. morbifera sp. nov. (type strain LMG 31116T = CCUG 73389T), P. nosoerga sp. nov. (type strain LMG 31109T = CCUG 73390T), P. pneumonica sp. nov. (type strain LMG 31114T = CCUG 73388T), P. soli sp. nov. (type strain LMG 31014T = CCUG 73382T), and P. terrigena sp. nov. (type strain LMG 31013T = CCUG 73381T).