Microbial genomic taxonomy

Salibaculum halophilum gen. nov., sp. nov. and Salibaculum griseiflavum sp. nov., in the family Rhodobacteraceae

Two Gram-stain-negative, moderately halophilic, non-motile, rod-shaped, pale yellow, and aerobic strains, designated WDS1C4^T and WDS4C29^T, were isolated from a marine solar saltern in Weihai, Shandong Province, PR China. Growth of strain WDS1C4^T occurred at 10-45 °C (optimum, 37 °C), with 4-16 % (w/v) NaCl (optimum, 8 %) and at pH 6.5-9.0 (optimum, pH 7.5). Growth of strain WDS4C29^T occurred at 10-45 °C (optimum, 40 °C), with 2-18 % (w/v) NaCl (optimum, 6 %) and at pH 6.5-9.0 (optimum, pH 7.5). Q-10 was the sole respiratory quinone of the two strains. The major polar lipids of strains WDS1C4^T and WDS4C29^T were phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The major cellular fatty acid in strains WDS1C4^T and WDS4C29^T was C_18 : 1  ω7c, and the genomic DNA G+C contents of strains WDS1C4^T and WDS4C29^T were 67.6 and 63.3 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains WDS1C4^T and WDS4C29^T were members of the family Rhodobacteraceae and showed 94.3 and 95.3 % similarities to their closest relative, Celeribacter indicus, respectively. The similarity between WDS1C4^T and WDS4C29^T was 97.3 %. Differential phenotypic and genotypic characteristics of the two isolates from recognized genera showed that the two strains should be classified as representing two novel species in a new genus for which the names Salibaculum halophilum gen. nov., sp. nov. (type species, type strain WDS1C4^T=MCCC 1H00179^T=KCTC 52542^T) and Salibaculum griseiflavum sp. nov. (WDS4C29^T=MCCC 1H00175^T=KCTC 52541^T) are proposed.

Molecular Analysis of Bacterial Isolates From Necrotic Wheat Leaf Lesions Caused by Xanthomonas translucens, and Description of Three Putative Novel Species, Sphingomonas albertensis sp. nov., Pseudomonas triticumensis sp. nov. and Pseudomonas foliumensis sp. nov

Xanthomonas translucens is the etiological agent of the wheat bacterial leaf streak (BLS) disease. The isolation of this pathogen is usually based on the Wilbrink's-boric acid-cephalexin semi-selective medium which eliminates 90% of other bacteria, some of which might be novel species. In our study, a general purpose nutrient agar was used to isolate 49 bacterial strains including X. translucens from necrotic wheat leaf tissues. Maximum likelihood cluster analysis of 16S rRNA sequences grouped the strains into 10 distinct genera. Pseudomonas (32.7%) and Pantoea (28.6%) were the dominant genera while Xanthomonas, Clavibacter and Curtobacterium had 8.2%, each. Erwinia and Sphingomonas had two strains, each. BLAST and phylogenetic analyses of multilocus sequence analysis (MLSA) of specific housekeeping genes taxonomically assigned all the strains to validly described bacterial species, except three strains (10L4B, 12L4D and 32L3A) of Pseudomonas and two (23L3C and 15L3B) of Sphingomonas. Strains 10L4B and12L4D had Pseudomonas caspiana as their closest known type strain while strain 32L3A was closest to Pseudomonas asturiensis. Sphingomonas sp. strains 23L3C and 15L3B were closest to S. faeni based on MLSA analysis. Our data on MLSA, whole genome-based cluster analysis, DNA-DNA hybridization and average nucleotide identity, matrix-assisted laser desorption/ionization-time-of-flight, chemotaxonomy and phenotype affirmed that these 5 strains constitute three novel lineages and are taxonomically described in this study. We propose the names, Sphingomonas albertensis sp. nov. (type strain 23L3C^T = DOAB 1063^T = CECT 30248^T = LMG 32139^T), Pseudomonas triticumensis sp. nov. (type strain 32L3A^T = DOAB 1067^T = CECT 30249^T = LMG 32140^T) and Pseudomonas foliumensis sp. nov. (type strain 10L4B^T = DOAB 1069^T = CECT 30250^T = LMG 32142^T). Comparative genomics of these novel species, relative to their closest type strains, revealed unique repertoires of core secretion systems and secondary metabolites/antibiotics. Also, the detection of CRISPR-Cas systems in the genomes of these novel species suggests an acquired mechanism for resistance against foreign mobile genetic elements. The results presented here revealed a cohabitation, within the BLS lesions, of diverse bacterial species, including novel lineages.

Metagenome Assembled Genome of a Novel Verrucomicrobial Methanotroph From Pantelleria Island

Verrucomicrobial methanotrophs are a group of aerobic bacteria isolated from volcanic environments. They are acidophiles, characterized by the presence of a particulate methane monooxygenase (pMMO) and a XoxF-type methanol dehydrogenase (MDH). Metagenomic analysis of DNA extracted from the soil of Favara Grande, a geothermal area on Pantelleria Island, Italy, revealed the presence of two verrucomicrobial Metagenome Assembled Genomes (MAGs). One of these MAGs did not phylogenetically classify within any existing genus. After extensive analysis of the MAG, we propose the name of "Candidatus Methylacidithermus pantelleriae" PQ17 gen. nov. sp. nov. The MAG consisted of 2,466,655 bp, 71 contigs and 3,127 predicted coding sequences. Completeness was found at 98.6% and contamination at 1.3%. Genes encoding the pMMO and XoxF-MDH were identified. Inorganic carbon fixation might use the Calvin-Benson-Bassham cycle since all genes were identified. The serine and ribulose monophosphate pathways were incomplete. The detoxification of formaldehyde could follow the tetrahydrofolate pathway. Furthermore, "Ca. Methylacidithermus pantelleriae" might be capable of nitric oxide reduction but genes for dissimilatory nitrate reduction and nitrogen fixation were not identified. Unlike other verrucomicrobial methanotrophs, genes encoding for enzymes involved in hydrogen oxidation could not be found. In conclusion, the discovery of this new MAG expands the diversity and metabolism of verrucomicrobial methanotrophs.

Cysteiniphilum marinum sp. nov., isolated from coastal seawater

Six aerobic Gram-negative bacteria were isolated from seawater in Guangdong Province, P.R. China. Cells were observed to be Gram-negative, aerobic, non-motile and non-spore forming. Growth of the designated type strain 19X3-30^T occurred at a temperature range of 14-37 °C (optimum, 28 °C), a pH range of 6.0-8.0 (optimum, pH 7) and up to 7.5% NaCl (optimum, 1.5%; w/v), and was enhanced by CO₂ and L-cysteine supplementation. The major polar lipids identified in strain 19X3-30^T were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The principal cellular fatty acids profile showed the presence of anteiso-C_15:0, anteiso-C_17:0 and C_18:0 (> 8% of total fatty acids), and the respiratory quinone was ubiquinone 8 (UQ-8). According to the analysis of 16S rRNA gene sequences, these strains represented a novel species within the family Fastidiosibacteraceae, sharing maximum similarities with Cysteiniphilum litorale DSM 101832^T (96.6%) and Cysteiniphilum halobium DSM 103992^T (95.3%). Phylogenetic dendrograms based on 16S rRNA gene and protein marker genes from the genomic sequences both indicated that the strains formed a monophyletic lineage closely linked to the genus Cysteiniphilum, which was also supported by the UPGMA dendrogram based on the MALDI-TOF MS profile. The genomic DNA G + C contents of six strains ranged from 38.0% to 38.1%. Based on different taxonomic genomic metrics, phylogeny and phenotypic features, we propose that the strains warrant the assignment to a novel species, for which the name Cysteiniphilum marinum sp. nov. is proposed. The type strain is 19X3-30^T (= KCTC 82154^T = CGMCC 1.18585^T).

A robust phylogenetic framework for members of the order Legionellales and its main genera (Legionella, Aquicella, Coxiella and Rickettsiella) based on phylogenomic analyses and identification of molecular markers demarcating different clades

The order Legionellales contains several clinically important microorganisms. Although members of this order are well-studied for their pathogenesis, there is a paucity of reliable characteristics distinguishing members of this order and its constituent genera. Genome sequences are now available for 73 Legionellales species encompassing ≈90% of known members from different genera. With the aim of understanding evolutionary relationships and identifying reliable molecular characteristics that are specific for this order and its constituent genera, detailed phylogenetic and comparative analyses were conducted on the protein sequences from these genomes. A phylogenomic tree was constructed based on 393 single copy proteins that are commonly shared by the members of this order to delineate the evolutionary relationships among its members. In parallel, comparative analyses were performed on protein sequences from Legionellales genomes to identify novel molecular markers consisting of conserved signature indels (CSIs) that are specific for different clades and genera. In the phylogenomic tree and in an amino acid identity matrix based on core proteins, members of the genera Aquicella, Coxiella, Legionella and Rickettsiella formed distinct clades confirming their monophyly. In these studies, Diplorickettsia massiliensis exhibited a close relationship to members of the genus Rickettsiella. The results of our comparative genomic analyses have identified 59 highly specific molecular markers consisting of CSIs in diverse proteins that are uniquely shared by different members of this order. Four of these CSIs are specific for all Legionellales species, except the two deeper-branching "Candidatus Berkiella" species, providing means for identifying members of this order in molecular terms. Twenty four, 7 and 6 CSIs are uniquely shared by members of the genera Legionella, Coxiella and Aquicella, respectively, identifying these groups in molecular terms. The descriptions of these three genera are emended to include information for their novel molecular characteristics. We also describe 12 CSIs that are uniquely shared by D. massiliensis and different members of the genus Rickettsiella. Based on these results, we are proposing an integration of the genus Diplorickettsia with Rickettsiella. Three other CSIs suggest that members of the genera Coxiella and Rickettsiella shared a common ancestor exclusive of other Legionellales. The described molecular markers, due to their exclusivity for the indicated taxa/genera, provide important means for the identification of these clinically important microorganisms and for discovering novel properties unique to them.

Genome sequence of Vibrio fluvialis 362.3 isolated from coral Mussismilia braziliensis reveals genes related to marine environment adaptation

Vibrio fluvialis is a halophilic bacterium frequently found in estuarine and coastal waters environments. The strain 362.3 was isolated from Mussismilia braziliensis coral of Abrolhos Bank. In this study, to gain insights into the marine adaptation in V. fluvialis, we sequenced the genome of 362.3 strain, which comprised 4,607,294 bp with a G + C content of 50.2%. In silico analysis showed that V. fluvialis 362.2 encodes genes related to chitin catabolic pathway, iron metabolism, osmotic stress and membrane transport.

Description of Paenibacillus dokdonensis sp. nov., a new bacterium isolated from soil

Two strains isolated from soil samples were designated as YH-JAE5^T and YH-JAE2. The isolates were facultative anaerobic, Gram-stain-variable, motile, rod-shaped bacteria. Phylogenetic analysis indicated that the isolates belonged to the genus Paenibacillus, but the 16S rRNA gene sequence similarities were <98 % when compared with other species within the genus. Analysis of rpoB gene revealed the isolates formed a sub-cluster with P. chibensis. The only menaquinone identified was MK-7. The two isolates contained meso-diaminopimelic acid within their cell wall peptidoglycan. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phospholipid, aminophospholipids, and lipids. The major fatty acids were C_15 : 0 anteiso and C_15 : 0 iso. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between isolate YH-JAE5^T and the most closely related reference strain (Paenibacillus chibensis KCTC 3758^T) were 81.7, 84.8 and 23.4 %, respectively. The G+C content of the genomic DNA was 47.4 mol%. Thus, the polyphasic data revealed that YH-JAE2 (=KCTC 43239=JCM 34435) and YH-JAE5^T (=KCTC 43059=JCM 33533) represent a new species. The name Paenibacillus dokdonensis sp. nov. is proposed.

Companilactobacillus pabuli sp. nov., a lactic acid bacterium isolated from animal feed

A Gram-positive, facultative anaerobic, catalase-negative, non-motile, non-spore-forming and rod-shaped lactic acid bacterium strain, denoted as NFFJ11^T and isolated from total mixed fermentation feed in the Republic of Korea, was characterized through polyphasic approaches, including sequence analyses of the 16S rRNA gene and housekeeping genes (rpoA and pheS), determination of average nucleotide identity and in silico DNA-DNA hybridization, fatty acid methyl ester analysis, and phenotypic characterization. Phylogenetic analyses based on 16S rRNA, rpoA and pheS gene sequences revealed that strain NFFJ11^T belonged to the genus Companilactobacillus. The 16S rRNA gene sequence of strain NFFJ11^T exhibited high similarity to Companilactobacillus formosensis S215^T (99.66 %), Companilactobacillus farciminis Rv4 na^T (99.53 %), Companilactobacillus crustorum LMG 23699^T (99.19 %), Companilactobacillus futsaii YM 0097^T (99.06 %), Companilactobacillus zhachilii HBUAS52074^T (98.86 %) and Companilactobacillus heilongiiangensis S4-3^T (98.66 %). However, average nucleotide identity and in silico DNA-DNA hybridization values for these type strains were in the range of 79.90-92.93 % and 23.80-49.30 %, respectively, which offer evidence that strain NFFJ11^T belongs to a novel species of the genus Companilactobacillus. The cell-wall peptidoglycan type was A4α (l-Lys-d-Asp) and the G+C content of the genomic DNA was 35.7 mol%. The main fatty acids of strain NFFJ11^T were C_18 : 1  ω9c (43.3 %), C_16 : 0 (20.1 %) and summed feature 7 (18.3 %; comprising any combination of C_19 : 1  ω7c, C_19 : 1  ω6c and C_19 : 0 cyclo ω10c). Through polyphasic taxonomic analysis, it was observed that strain NFFJ11^T represents a novel species belonging to the genus Companilactobacillus, for which the name Companilactobacillus pabuli sp. nov. is proposed. The type strain is NFFJ11^T (= KACC 21771^T= JCM 34088^T).

Bruguierivorax albus gen. nov. sp. nov. Isolated from Mangrove Sediment and Proposal of Bruguierivoracaceae fam. nov

A novel Gram-negative, motile, aerobic rod-shaped bacterium designated BGMRC 2031^T was isolated from mangrove sediment collected from Guangxi Province, China. Optimal growth occurred at 28 °C and pH 7.0-8.0 in the presence of 1% (w/v) NaCl. Alignment based on 16S rRNA gene sequences indicated that strain BGMRC 2031^T is most closely related to Sodalis praecaptivus HS1^T (95.6%, sequence similarity), followed by Biostraticola tofi DSM 19580^T (95.5%), Sodalis glossinidius DSM 16929^T (95.4%), and Brenneria goodwinii FRB141^T (94.9%) sequence similarity. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BGMRC 2031^T formed a distinct branch in a robust cluster and revealed that strain BGMRC 2031^T, genera Biostraticola and Sodalis, formed a novel family-level clade in the order Enterobacterales. The novel strain showed an average nucleotide similarity of 74.7%, 74.2%, and 73.1% for S. praecaptivus HS1^T, S. glossinidius DSM 16929^T, and B. tofi DSM 19580^T, respectively. The genomes of the BGMRC 2031^T shared the presence of a riboflavin synthesis gene cluster. The menaquinones of strain BGMRC 2031^T were MK-8 and Q-8, which were similar to those of genus Biostraticola. The major fatty acids (> 10%) were C_16:0 (19.9%), summed feature 2 (iso-C_16:1 and/or C_14:0 3-OH, 18.10%), summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c, 15.3%), C_12:0 (13.9%), C_17:0 cyclo (11.4%), and C_14:0 (10.4%). The main polar lipids were phosphatidyl methylethanolamine, phosphatidyl glycerol, diphosphatidyl glycerol, phosphatidyl inositol, one unidentified phospholipid, and one unknown polar lipid. The G+C content of strain BGMRC 2031^T was 55.4%. Strain BGMRC 2031^T could extend the mean lifespan and maximum lifespan of Caenorhabditis elegans by 4.5% and 12.5%, respectively. Overall, the results of this study indicate that BGMRC 2031^T is a novel species in a new genus, for which the name Bruguierivorax albus gen. nov. sp. nov. is proposed, and the type of strain is designated as BGMRC 2031^T (= NBRC 111907^T = KCTC 52119^T). In addition, a novel family, Bruguierivoracaceae fam. nov., is proposed to accommodate the genera Bruguierivorax, Biostraticola, and Sodalis.

Legionella septentrionalis sp. nov., isolated from aquatic environments in the northern PR China

Four strains (km711^T, km714, km542 and km524), representing a novel Legionella species, were isolated from aquatic environments in northern PR China. Cells were Gram-stain-negative, rod-shaped, microaerobic, motile and growth depended on l-cysteine. They grew at 25‒42 °C (optimum, 35‒37 °C) and could tolerate up to 1.5 % (w/v) NaCl (optimum, 0.5 %). The major fatty acids (>5 %) of the type strain km711^T were C_17 : 0 anteiso, C_15 : 0 anteiso, iso-C_16 : 0 and C_16 : 1  ω7c and/or iso-C_15 : 0 2OH. The pairwise comparison values were <96.1 % for 16S rRNA gene sequences, 23.3‒28.7 % interspecies variation for mip gene sequences, <93.6 % average nucleotide identity and <72.8 % average amino acid identity between these four strains and related type strains within the genus Legionella. The phylogenetic tree based on the four concatenated genes (16S rRNA, mip, rpoB and rnpB) and protein-concatamer tree based on concatenation of 21 protein markers both revealed that these four strains formed a separate phylogenetic branch cluster within the genus Legionella. The results of phenotypic and genotypic features suggest that these four strains represent a novel species of the genus Legionella, for which the name Legionella septentrionalis sp. nov. is proposed (type strain km711^T=KCTC 15655^T=NBRC 113219^T).

Genome-based classification of Acidihalobacter prosperus F5 (=DSM 105917=JCM 32255) as Acidihalobacter yilgarnensis sp. nov

The genus Acidihalobacter has three validated species, Acidihalobacter ferrooxydans, Acidihalobacter prosperus and Acidihalobacter aeolinanus, all of which were isolated from Vulcano island, Italy. They are obligately chemolithotrophic, aerobic, acidophilic and halophilic in nature and use either ferrous iron or reduced sulphur as electron donors. Recently, a novel strain was isolated from an acidic, saline drain in the Yilgarn region of Western Australia. Strain F5T has an absolute requirement for sodium chloride (>5 mM) and is osmophilic, growing in elevated concentrations (>1 M) of magnesium sulphate. A defining feature of its physiology is its ability to catalyse the oxidative dissolution of the most abundant copper mineral, chalcopyrite, suggesting a potential role in biomining. Originally categorized as a strain of A. prosperus, 16S rRNA gene phylogeny and multiprotein phylogenies derived from clusters of orthologous proteins (COGS) of ribosomal protein families and universal protein families unambiguously demonstrate that strain F5T forms a well-supported separate branch as a sister clade to A. prosperus and is clearly distinguishable from A. ferrooxydans DSM 14175T and A. aeolinanus DSM14174T. Results of comparisons between strain F5T and the other Acidihalobacter species, using genome-based average nucleotide identity, average amino acid identity, correlation indices of tetra-nucleotide signatures (Tetra) and genome-to-genome distance (digital DNA-DNA hybridization), support the contention that strain F5T represents a novel species of the genus Acidihalobacter. It is proposed that strain F5T should be formally reclassified as Acidihalobacter yilgarnenesis F5T (=DSM 105917T=JCM 32255T).

LINbase: a web server for genome-based identification of prokaryotes as members of crowdsourced taxa

High throughput DNA sequencing in combination with efficient algorithms could provide the basis for a highly resolved, genome phylogeny-based and digital prokaryotic taxonomy. However, current taxonomic practice continues to rely on cumbersome journal publications for the description of new species, which still constitute the smallest taxonomic units. In response, we introduce LINbase, a web server that allows users to genomically circumscribe any group of prokaryotes with measurable DNA similarity and that uses the individual isolate as smallest unit. Since LINbase leverages the concept of Life Identification Numbers (LINs), which are codes assigned to individual genomes based on reciprocal average nucleotide identity, we refer to groups circumscribed in LINbase as LINgroups. Users can associate with each LINgroup a name, a short description, and a URL to a peer-reviewed publication. As soon as a LINgroup is circumscribed, any user can immediately identify query genomes as members and submit comments about the LINgroup. Most genomes currently in LINbase were imported from GenBank, but users can upload their own genome sequences as well. In conclusion, LINbase combines the resolution of LINs with the power of crowdsourcing in support of a highly resolved, genome phylogeny-based digital taxonomy. LINbase is available at http://www.LINbase.org.

Phylogenomic analyses of the Staphylococcaceae family suggest the reclassification of five species within the genus Staphylococcus as heterotypic synonyms, the promotion of five subspecies to novel species, the taxonomic reassignment of five Staphylococcus species to Mammaliicoccus gen. nov., and the formal assignment of Nosocomiicoccus to the family Staphylococcaceae

Phylogenetic analyses based on 16S rRNA gene sequences of members of the family Staphylococcaceae showed the presence of para- and polyphyletic genera. This finding prompted a thorough investigation into the taxonomy of the Staphylococcaceae family by analysing their core genome phylogeny complemented with genome-based indices such as digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity. The resulting data suggested the following proposals: Auricoccus indicus was reduced in taxonomic rank as a later heterotypic synonym of Abyssicoccus albus ; Staphylococcus petrasii subsp. jettensis as a later heterotypic synonym of Staphylococcus petrasii subsp. petrasii ; the unification of Staphylococcus aureus subsp. anaerobius and Staphylococcus aureus subsp. aureus as Staphylococcus aureus ; the unification of Staphylococcus carnosus subsp. utilis and Staphylococcus carnosus subsp. carnosus as Staphylococcus carnosus ; the unification of Staphylococcus saprophyticus subsp. bovis and Staphylococcus saprophyticus subsp. saprophyticus as Staphylococcus saprophyticus ; Staphylococcus succinis subsp. casei as the novel species Staphylococcus casei; Staphylococcus schleiferi subsp. coagulans as the novel species Staphylococcus coagulans; Staphylococcus petrasii subsp. croceilyticus as the novel species Staphylococcus croceilyticus; Staphylococcus petrasii subsp. pragensis as the novel species Staphylococcus pragensis; Staphylococcus cohnii subsp. urealyticus as the novel species Staphylococcus urealyticus; the reassignment of Staphylococcus sciuri , Staphylococcus fleurettii , Staphylococcus lentus , Staphylococcus stepanovicii and Staphylococcus vitulinus to the novel genus Mammaliicoccus with Mammaliicoccus sciuri as the type species; and the formal assignment of Nosocomiicoccus as a member of the family Staphylococcaceae .

Unlocking the Genomic Taxonomy of the Prochlorococcus Collective

Prochlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC. Novel genomic data for the PC prompted us to revisit this group, applying the current methods used in genomic taxonomy. As a result, we were able to distinguish the five genera: Prochlorococcus, Eurycolium, Prolificoccus, Thaumococcus, and Riococcus. The novel genera have distinct genomic and ecological attributes.

Genomic analysis of facultatively oligotrophic haloarchaea of the genera Halarchaeum, Halorubrum, and Halolamina, isolated from solar salt

Extremely halophilic archaea (haloarchaea) belonging to the phylum Euryarchaeota have been found in high-salinity environments. In this study, Halarchaeum sp. CBA1220, Halorubrum sp. CBA1229, and Halolamina sp. CBA1230, which are facultatively oligotrophic haloarchaea, were isolated from solar salt by culture under oligotrophic culture conditions. The complete genomes of strains CBA1220, CBA1229, and CBA1230 were sequenced and were found to contain 3,175,875, 3,582,278, and 3,465,332 bp, with a G + C content of 68.25, 67.66, and 66.75 mol %, respectively. In total, 60, 36, and 33 carbohydrate-active enzyme genes were determined in the respective strains. The strains harbored various genes encoding stress-tolerance proteins, including universal stress proteins, cold-shock proteins, and rubrerythrin and rubrerythrin-related proteins. The genome data produced in this study will facilitate further research to improve our understanding of other halophilic strains and promote their industrial application.

Pseudokineococcus galaxeicola sp. nov., isolated from mucus of a stony coral

A Gram-stain-positive, aerobic, motile, coccus-shaped bacterium, designated strain SCSIO 13315^T, was isolated from mucus of the coral Galaxea sp. collected from Luhuitou fringing reef (Sanya, Hainan, PR China). Analysis of the 16S rRNA gene sequence showed that strain SCSIO 13315^T exhibits 95.5 % 16S rRNA gene sequence similarity to Pseudokineococcus basanitobsidens SKC1-2^T, 95.8 % to Pseudokineococcus lusitanus T2A-S27^T and 96.4 % to Pseudokineococcus marinus KST3-3^T. Results of phylogenetic analysis suggested that strain SCSIO 13315^T was a member of the genus Pseudokineococcus. The DNA G+C content of strain SCSIO 13315^T was 73.5 %. Chemotaxonomic assessment of strain SCSIO 13315^T showed that the menaquinones were MK-8(H₄) and MK-9(H₂). The main cellular fatty acids were anteiso-C_15 : 0, C_16 : 0 and summed feature 3 (C_16 : 1  ω7c/C_16 : 1  ω6c). The polar lipids present were diphosphatidylglycerol, phosphatidylglycerol, two unknown phospholipids, four unidentified aminolipids and one unidentified lipid. Based on the phylogenetic and phenotypic analysis, it was evident that strain SCSIO 13315^T represents a novel species of the genus Pseudokineococcus, for which the name Pseudokineococcus galaxeicola sp. nov. is proposed. The type strain is SCSIO 13315^T (=NBRC 109944^T=DSM 27812^T).

Vibrio tetraodonis sp. nov.: genomic insights on the secondary metabolites repertoire

Description of a Gram-negative, motile, circular-shaped bacterial strain, designated A511^T obtained from the skin of the pufferfish Sphoeroides spengleri (Family Tetraodontidae), collected in Arraial do Cabo, Brazil. Optimum growth occurs at 20-28 °C in the presence of 3% NaCl. The genome sequence of the novel isolate consisted of 4.36 Mb, 3,976 coding genes and G + C content of 42.5%. Genomic taxonomy analyses based on average amino acid (AAI), genome-to-genome-distance (GGDH) and phylogenetic reconstruction placed A511^T (= CBAS 712^T = CAIM 1939^T) into a new species of the genus Vibrio (Vibrio tetraodonis sp. nov.). The genome of the novel species contains eight genes clusters (~ 183.9 Kbp in total) coding for different types of bioactive compounds that hint to several possible ecological roles in the pufferfish host.

A new genomic taxonomy system for the Synechococcus collective

Cyanobacteria of the genus Synechococcus are major contributors to global primary productivity and are found in a wide range of aquatic ecosystems. This Synechococcus collective (SC) is metabolically diverse, with some lineages thriving in polar and nutrient-rich locations and others in tropical or riverine waters. Although many studies have discussed the ecology and evolution of the SC, there is a paucity of knowledge on its taxonomic structure. Thus, we present a new taxonomic classification framework for the SC based on recent advances in microbial genomic taxonomy. Phylogenomic analyses of 1085 cyanobacterial genomes demonstrate that organisms classified as Synechococcus are polyphyletic at the order rank. The SC is classified into 15 genera, which are placed into five distinct orders within the phylum Cyanobacteria: (i) Synechococcales (Cyanobium, Inmanicoccus, Lacustricoccus gen. Nov., Parasynechococcus, Pseudosynechococcus, Regnicoccus, Synechospongium gen. nov., Synechococcus and Vulcanococcus); (ii) Cyanobacteriales (Limnothrix); (iii) Leptococcales (Brevicoccus and Leptococcus); (iv) Thermosynechococcales (Stenotopis and Thermosynechococcus) and (v) Neosynechococcales (Neosynechococcus). The newly proposed classification is consistent with habitat distribution patterns (seawater, freshwater, brackish and thermal environments) and reflects the ecological and evolutionary relationships of the SC.

Metabacillus sediminilitoris sp. nov., a marine bacterium isolated from a tidal sediment

A Gram-stain-positive, endospore-forming, motile and rod-shaped bacterium, designated as strain DSL-17^T, was isolated from a tidal sediment of the East China Sea and characterized phylogenetically and phenotypically. The strain could grow at 16-47 °C (optimum 37 °C), at pH 6.0-10.0 (optimum 6.0) and with 1-7% (w/v) NaCl (optimum 3 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DSL-17^T was related to members of the genus Metabacillus and shared the highest similarity with Metabacillus litoralis SW-211^T (98.6 %), followed by Metabacillus halosaccharovorans E33^T (97.9 %), Metabacillus crassostreae JSM 100118^T (97.7 %), Metabacillus niabensis 4T19^T (97.7 %) and Metabacillus malikii NCCP-662^T (97.5 %). 16S rRNA gene sequence similarities between strain DSL-17^T and other members of the genus Metabacillus were below 96.6 %. The sole respiratory quinone was MK-7. Strain DSL-17^T had a cell-wall peptidoglycan based on meso-diaminopimelic acid. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), three unidentified glycolipids and six unidentified lipids. The strain had iso-C_15 : 0, anteiso-C_15 : 0, iso-C_14 : 0, C_16 : 0 and iso-C_16 : 0 as major fatty acids. The G+C content of the genomic DNA was 35.7 mol%. The combined genotypic and phenotypic data indicated that strain DSL-17^T represents a novel species of the genus Metabacillus, for which the name Metabacillus sediminilitoris sp. nov. is proposed The type strain is DSL-17^T (=MCCC 1K03777^T=DSM 109843^T).

Description of Komagataeibacter melaceti sp. nov. and Komagataeibacter melomenusus sp. nov. Isolated from Apple Cider Vinegar

Two novel strains AV382 and AV436 were isolated from a submerged industrial bioreactor for production of apple cider vinegar in Kopivnik (Slovenia). Both strains showed very high (≥98.2%) 16S rRNA gene sequence similarities with Komagataeibacter species, but lower 16S-23S rRNA gene internal transcribed spacer (ITS). The highest similarity of the 16S-23S rRNA gene ITS of AV382 was to Komagataeibacter kakiaceti LMG 26206T (91.6%), of AV436 to Komagataeibacter xylinus LMG 1515T (93.9%). The analysis of genome sequences confirmed that AV382 is the most closely related to K. kakiaceti (ANIb 88.2%) and AV436 to K. xylinus (ANIb 91.6%). Genome to genome distance calculations exhibit for both strains ≤47.3% similarity to all type strains of the genus Komagataeibacter. The strain AV382 can be differentiated from its closest relatives K. kakiaceti and Komagataeibacter saccharivorans by its ability to form 2-keto and 5-keto-D-gluconic acids from glucose, incapability to grow in the presence of 30% glucose, formation of C19:0 cyclo ω8c fatty acid and tolerance of up to 5% acetic acid in the presence of ethanol. The strain AV436 can be differentiated from its closest relatives K. xylinus, Komagataeibacter sucrofermentans, and Komagataeibacter nataicola by its ability to form 5-keto-D-gluconic acid, growth on 1-propanol, efficient synthesis of cellulose, and tolerance to up to 5% acetic acid in the presence ethanol. The major fatty acid of both strains is C18:1ω7c. Based on a combination of phenotypic, chemotaxonomic and phylogenetic features, the strains AV382T and AV436T represent novel species of the genus Komagataeibacter, for which the names Komagataeibactermelaceti sp. nov. and Komagataeibacter melomenusus are proposed, respectively. The type strain of Komagataeibacter melaceti is AV382T (= ZIM B1054T = LMG 31303T = CCM 8958T) and of Komagataeibacter melomenusus AV436T (= ZIM B1056T = LMG 31304T = CCM 8959T).

Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia

Turfs are among the major benthic components of reef systems worldwide. The nearly complete genome sequences, basic physiological characteristics, and phylogenomic reconstruction of two phycobiliprotein-rich filamentous cyanobacteria strains isolated from turf assemblages from the Abrolhos Bank (Brazil) are investigated. Both Adonisia turfae CCMR0081^T (= CBAS 745^T) and CCMR0082 contain approximately 8 Mbp in genome size and experiments identified that both strains exhibit chromatic acclimation. Whereas CCMR0081^T exhibits chromatic acclimation type 3 (CA3) regulating both phycocyanin (PC) and phycoerythrin (PE), CCMR0082 strain exhibits chromatic acclimation type 2 (CA2), in correspondence with genes encoding specific photosensors and regulators for PC and PE. Furthermore, a high number and diversity of secondary metabolite synthesis gene clusters were identified in both genomes, and they were able to grow at high temperatures (28 °C, with scant growth at 30 °C). These characteristics provide insights into their widespread distribution in reef systems.

Complete Genome Sequences of Two Marine Biofilm Isolates, Leisingera sp. nov. Strains 201A and 204H, Novel Representatives of the Roseobacter Group

Here, we report the complete-genome assemblies of biofilm isolates 201A and 204H. They possess six and seven plasmids, respectively, with a size ranging from 44 kb to 159 kb. Genomic comparisons place the two strains into one new species belonging to the genus Leisingera as novel representatives of the Roseobacter group.

Francisella salimarina sp. nov., isolated from coastal seawater

Four strains (SYSU SYW-1^T, SYW-2, SYW-3 and XLW-1) were isolated from seawater near the shore in Guangdong Province, China. Cells were Gram-stain-negative, aerobic, non-motile and non-spore-forming. Growth was observed at a temperature range of 16-40 °C (optimum, 32 °C), a pH range of 4-8 (optimum, pH 7) and in the presence of up to 10 % (w/v) NaCl. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified phospholipid. The respiratory quinone was ubiquinone 8 (UQ-8), and the predominant fatty acids were C_18 : 0 3-OH, C_10 : 0, C_14 : 0 and C_18 : 1ω9c. Comparison of 16S rRNA gene and genome sequences confirmed that these strains represented a novel member of the genus Francisella, with less than 98.8 % 16S rRNA gene sequence similarity and less than 95 % genomic average nucleotide identity to recognized Francisella species. The phylogenetic tree based on 16S rRNA gene sequences and the protein-concatamer tree based on a concatenation of 28 protein marker sequences both indicated that the strains clustered with 'Francisella salina' TX07-7308 and 'Francisella marina' E95-16, but formed a distinct lineage group among the other members of the genus Francisella. The DNA G+C contents of the four strains were determined to be 32.9, 32.7, 32.9 and 32.9 %, respectively (genome). On the basis of phenotypic and genotypic features, the strains are considered to represent a novel species of the genus Francisella, for which the name Francisella salimarina sp. nov. is proposed. The type strain is SYSU SYW-1^T (=CGMCC 1.17031^T=NBRC 113781^T).

Proposal for transfer of Defluviimonas alba to the genus Frigidibacter as Frigidibacter mobilis nom. nov

A polyphasic taxonomic study was undertaken to clarify the exact position of the type strain cai42^T of the species Defluviimonas alba Pan et al. 2015. The results of the 16S rRNA gene sequence analysis indicated that the two sequences from cai42^T shared 99.6 and 99.7 % similarity to that of the type strain SP32^T of the species Frigidibacter albus and formed a coherent clade in the phylogenetic tree. Whole genomic comparison between cai42^T and SP32^T yielded a digital DNA-DNA hybridization estimate of 36.3 %, an average nucleotide identity of 88.8 % and an average amino acid identity of 89.8 %, clearly indicating that the two strains should belong to two genospecies of the same genus. The close relationship between the two strains was underpinned by the results of genome-based phylogenetic analysis. Although cai42^T and SP32^T shared similar physiological and biochemical properties, some striking differences, such as mobility, the temperature range for growth and the polar lipid components, could distinguish them as separate species. Therefore, the comparative phenotypic and genotypic analyses supported the incorporation of Defluviimonas alba into the genus Frigidibacter as Frigidibacter mobilis nom. nov. with the type strain cai42^T (=CGMCC 1.12518^T=LMG 27406^T).

Muricauda hadalis sp. nov., a novel piezophile isolated from hadopelagic water of the Mariana Trench and reclassification of Muricauda antarctica as a later heterotypic synonym of Muricauda teanensis

A novel marine Gram-stain-negative, non-motile, aerobic and rod-shaped bacterium, designated as strain MT-229T, was isolated from the deep seawater in the Mariana Trench and characterized phylogenetically and phenotypically. Bacterial optimal growth occurred at 30 °C (ranging 10–40 °C), pH 6 (ranging 3–11) and with 11 % (w/v) NaCl (ranging 0–17 %). Strain MT-229T was a piezophile, growing optimally at 20 MPa (range 0.1–70 MPa). The nearest phylogenetic neighbours were Muricauda antarctica CGMCC 1.2174T and Muricauda taeanensis JCM 17757T with 16S rRNA gene similarity of 98.7 %. The sole respiratory quinone was menaquinone-6 (MK-6). The major polar lipids were phosphatidylethanolamine (PE), two unidentified aminolipids (AL) and ten unidentified lipids. The major fatty acids of strain MT-229T were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The G+C content of the genomic DNA was 45.6 mol%. The combined genotypic and phenotypic data indicated that strain MT-229T represents a novel species of the genus Muricauda , for which the name Muricauda hadalis sp. nov. is proposed, with the type strain MT-229T (=DSM 109894T=MCCC 1K04201T). In addition, the whole-genome-based comparisons revealed that the type strains of Muricauda antarctica and Muricauda teanensis belong to a single species. It is, therefore, proposed that M. antarctica be recognized as a heterotypic synonym of M. teanensis.

Molecular Characterization and Antimicrobial Susceptibilities of Nocardia Species Isolated from the Soil; A Comparison with Species Isolated from Humans

Nocardia species, one of the most predominant Actinobacteria of the soil microbiota, cause infection in humans following traumatic inoculation or inhalation. The identification, typing, phylogenetic relationship and antimicrobial susceptibilities of 38 soil Nocardia strains from Lara State, Venezuela, were studied by 16S rRNA and gyrB (subunit B of topoisomerase II) genes, multilocus sequence analysis (MLSA), whole-genome sequencing (WGS), and microdilution. The results were compared with those for human strains. Just seven Nocardia species with one or two strains each, except for Nocardia cyriacigeorgica with 29, were identified. MLSA confirmed the species assignments made by 16S rRNA and gyrB analyses (89.5% and 71.0% respectively), and grouped each soil strain with its corresponding reference and clinical strains, except for 19 N. cyriacigeorgica strains found at five locations which grouped into a soil-only cluster. The soil strains of N. cyriacigeorgica showed fewer gyrB haplotypes than the examined human strains (13 vs. 17) but did show a larger number of gyrB SNPs (212 vs. 77). Their susceptibilities to antimicrobials were similar except for beta-lactams, fluoroquinolones, minocycline, and clarithromycin, with the soil strains more susceptible to the first three (p ≤ 0.05). WGS was performed on four strains belonging to the soil-only cluster and on two outside it, and the results compared with public N. cyriacigeorgica genomes. The average nucleotide/amino acid identity, in silico genome-to-genome hybridization similarity, and the difference in the genomic GC content, suggest that some strains of the soil-only cluster may belong to a novel subspecies or even a new species (proposed name Nocardia venezuelensis).

Rapid screening of marine bacterial symbionts using MALDI-TOF MS

Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) is a rapid, cost-effective and high-throughput method for bacteria characterization. However, most previous studies focused on clinical isolates. In this study, we evaluated the use of MALDI-TOF MS as a rapid screening tool for marine bacterial symbionts. A set of 255 isolates from different marine sources (corals, sponge, fish and seawater) was analyzed using cell lysates to obtain a rapid grouping. Cluster analysis of mass spectra and 16S rRNA showed 18 groups, including Vibrio, Bacillus, Pseudovibrio, Alteromonas and Ruegeria. MALDI-TOF distance similarity scores ≥ 60% and ≥ 70% correspond to ≥ 98.7% 16S rRNA gene sequence similarity and ≥ 95% pyrH gene sequence similarity, respectively. MALDI-TOF MS is a useful tool for Vibrio species groups' identification.

Endosymbiotic adaptations in three new bacterial species associated with Dictyostelium discoideum: Paraburkholderia agricolaris sp. nov., Paraburkholderia hayleyella sp. nov., and Paraburkholderia bonniea sp. nov

Here we give names to three new species of Paraburkholderia that can remain in symbiosis indefinitely in the spores of a soil dwelling eukaryote, Dictyostelium discoideum. The new species P. agricolaris sp. nov., P. hayleyella sp. nov., and P. bonniea sp. nov. are widespread across the eastern USA and were isolated as internal symbionts of wild-collected D. discoideum. We describe these sp. nov. using several approaches. Evidence that they are each a distinct new species comes from their phylogenetic position, average nucleotide identity, genome-genome distance, carbon usage, reduced length, cooler optimal growth temperature, metabolic tests, and their previously described ability to invade D. discoideum amoebae and form a symbiotic relationship. All three of these new species facilitate the prolonged carriage of food bacteria by D. discoideum, though they themselves are not food. Further studies of the interactions of these three new species with D. discoideum should be fruitful for understanding the ecology and evolution of symbioses.

Genome-based analyses reveal the presence of 12 heterotypic synonyms in the genus Streptomyces and emended descriptions of Streptomyces bottropensis, Streptomyces celluloflavus, Streptomyces fulvissimus, Streptomyces glaucescens, Streptomyces murinus, and Streptomyces variegatus

Phylogenetic analysis based on 16S rRNA gene sequences of the genus Streptomyces showed the presence of six distinguishable clusters, with 100 % sequence similarity values among strains in each cluster; thus they shared almost the same evolutionary distance. This result corroborated well with the outcome of core gene (orthologous gene clusters) based genome phylogeny analysis of 190 genomes including the Streptomyces species in those six clusters. These preeminent results led to an investigation of genome-based indices such as digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) and average amino acid identity (AAI) for the strains in those six clusters. Certain strains recorded genomic indices well above the threshold values (70 %, 95-96 % and >95 % for dDDH, ANI and AAI, respectively) determined for species affiliation, suggesting only one type strain belongs to described species and the other(s) may need to be reduced in taxa to a later heterotypic synonym. To conclude, the results of comprehensive analyses based on phylogenetic and genomic indices suggest that the following six reclassifications are proposed: Streptomyces flavovariabilis as a later heterotypic synonym of Streptomyces variegatus; Streptomyces griseofuscus as a later heterotypic synonym of Streptomyces murinus; Streptomyces kasugaensis as a later heterotypic synonym of Streptomyces celluloflavus; Streptomyces luridiscabiei as a later heterotypic synonym of Streptomyces fulvissimus; Streptomyces pharetrae as a later heterotypic synonym of Streptomyces glaucescens; and Streptomyces stelliscabiei as a later heterotypic synonym of Streptomyces bottropensis.

All ANIs are not created equal: implications for prokaryotic species boundaries and integration of ANIs into polyphasic taxonomy

In prokaryotic taxonomy, a set of criteria is commonly used to delineate species. These criteria are generally based on cohesion at the phylogenetic, phenotypic and genomic levels. One such criterion shown to have promise in the genomic era is average nucleotide identity (ANI), which provides an average measure of similarity across homologous regions shared by a pair of genomes. However, despite the popularity and relative ease of using this metric, ANI has undergone numerous refinements, with variations in genome fragmentation, homologue detection parameters and search algorithms. To test the robustness of a 95-96 % species cut-off range across all the commonly used ANI approaches, seven different methods were used to calculate ANI values for intra- and interspecies datasets representing three classes in the Proteobacteria. As a reference point, these methods were all compared to the widely used blast-based ANI (i.e. ANIb as implemented in JSpecies), and regression analyses were performed to investigate the correlation of these methods to ANIb with more than 130000 individual data points. From these analyses, it was clear that ANI methods did not provide consistent results regarding the conspecificity of isolates. Most of the methods investigated did not correlate perfectly with ANIb, particularly between 90 and 100% identity, which includes the proposed species boundary. There was also a difference in the correlation of methods for the different taxon sets. Our study thus suggests that the specific approach employed needs to be considered when ANI is used to delineate prokaryotic species. We furthermore suggest that one would first need to determine an appropriate cut-off value for a specific taxon set, based on the intraspecific diversity of that group, before conclusions on conspecificity of isolates can be made, and that the resulting species hypotheses be confirmed with analyses based on evolutionary history as part of the polyphasic approach to taxonomy.

Dokdonia sinensis sp. nov., a flavobacterium isolated from surface seawater

A taxonomic study was carried out on strain SH27^T, which was isolated from seawater collected around Xiaoshi Island, PR China. Cells of strain SH27^T were Gram-stain-negative, non-motile, rod-shaped, orange-pigmented and grew at 15-37 °C (optimum, 28 °C), at pH 6.0-8.0 (pH 7.0) and in 1.0-7.0 % (w/v) NaCl (2.0-3.0 %). The isolate was positive for catalase, but negative for nitrate reduction, oxidase, indole production and urease. Carotenoid pigment was produced. Phylogenetic analysis based on the 16S rRNA gene placed strain SH27^T in the genus Dokdonia with the closest relative being Dokdonia donghaensis KCTC 12391^T, exhibiting 96.7 % 16S rRNA gene pairwise similarity. The results of genomic comparisons, including average nucleotide identity and digital DNA-DNA hybridization, showed 72.9 and 19.2 % identity to D. donghaensis KCTC 12391^T, respectively. The major cellular fatty acids were iso-C_15 : 0, iso-C_15 : 1 G and iso-C_17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine and two unidentified lipids. Menaquinone-6 was the only respiratory quinone. The G+C content of the genomic DNA was 32.9 mol%. On the basis of the phenotypic and phylogenetic data, strain SH27^T represents a novel species of the genus Dokdonia, for which the name Dokdonia sinensis sp. nov. is proposed, with the type strain SH27^T (MCCC 1H00358^T=CCTCC AB 2018323^T=KCTC 62962^T).

Rheinheimera sediminis sp. nov., a marine bacterium isolated from coastal sediment

A Gram-stain-negative, aerobic, rod-shaped bacterium, designated strain YQF-1^T, was isolated from coastal sediment in Jiangsu Province (PR China) and characterized phylogenetically and phenotypically. Bacterial optimal growth occurred at 28 °C (range 4-40 °C) and pH 7 (range pH 6-11). Phylogenetic analysis based on 16S rRNA gene sequence indicated that YQF-1^T was related to members of the genus Rheinheimera and shared the highest sequence identities with Rheinheimera mesophila DSM 29723^T (98.5 %), followed by Rheinheimera tangshanensis DSM 19460^T (98.4 %), Rheinheimera tilapiae Ruye-90^T (97.9 %), Rheinheimera soli BD-d46^T (97.9 %), Rheinheimera aquatica GR5^T (97.4 %), Rheinheimera coerulea TAPG2^T (97.3 %) and Rheinheimera texasensis A62-14B^T (97.1 %). The 16S rRNA gene sequence identities between YQF-1^T and other members of the genus Rheinheimera were below 97.0 %. The digital DNA-DNA hybridization value between YQF-1^T and Rheinheimera mesophila DSM 29723^T was 25.1±2.3 %. The average nucleotide identity (ANI) value between YQF-1^T and Rheinheimera mesophila DSM 29723^T was 81.4 %. The major respiratory quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phospholipid, two unidentified aminolipids and three unidentified lipids. The strain had summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c), C_16 : 0, summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), iso-C_15 : 0, and anteiso-C_17 : 1  ω9c as the major fatty acids. The G+C content of the genomic DNA was 46.2 mol%. On the basis of phenotypic, genotypic and phylogenetic evidence, strain YQF-1^T represents a novel species of the genus Rheinheimera, for which the name Rheinheimera sediminis sp. nov. is proposed, with the type strain YQF-1^T (=KCTC 72183^T=MCCC 1K03646^T).

Tessaracoccus antarcticus sp. nov., a rhodopsin-containing bacterium from an Antarctic environment and emended description of the genus Tessaracoccus

A Gram-stain-positive, facultatively anaerobic bacterium, strain JDX10T, was isolated from a soil sample of Fildes Peninsula, Antarctica. Cells of the strain were irregular rod-shaped and non-motile. Cells grew at 4–40 °C (optimum, 28 °C), at pH 6.0–9.0 (optimum, 7.5) and with 0.0–3.0 % (w/v) NaCl (optimum, 1.0 %). According to phylogenetic analysis based on 16S rRNA gene sequences, strain JDX10T was associated with the genus Tessaracoccus , and showed highest similarities to Tessaracoccus rhinocerotis CCTCC AB 2013217T (97.2 %), Tessaracoccus flavescens SST-39T (96.9 %) and Tessaracoccus terricola JCM 32157T (96.9 %). The average nucleotide identity scores of strain JDX10T to T. rhinocerotis CCTCC AB 2013217T and T. bendigoensis JCM 13525T were 74.8 and 73.3 %, respectively and the Genome-to-Genome Distance Calculator scores were 19.2 and 18.7 %, respectively. The major (>10.0 %) cellular fatty acid was anteiso-C15 : 0. The predominant isoprenoid quinone was MK-10(H4). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid. The phylogenetic analysis and physiological and biochemical data showed that strain JDX10T should be classified as representing a novel species in the genus Tessaracoccus , for which the name Tessaracoccus antarcticus sp. nov. is proposed. The type strain is JDX10T (=MCCC 1H00351T=KCTC 49242T).

Marisediminitalea mangrovi gen. nov., sp. nov., isolated from marine mangrove sediment, and reclassification of Aestuariibacter aggregatus as Marisediminitalea aggregata comb. nov

Strain GS-14^T was isolated from a mangrove sediment sample collected at Beilun Estuary National Nature Reserve, Guangxi Province, PR China. Cells were Gram-stain-negative, strictly aerobic and rod-shaped with a polar flagellum. Optimal growth occurred in the presence of 3-6 % (w/v) NaCl, at pH 6-8 and at a temperature of 37 °C. The predominant polar lipids were phosphatidylglycerol and phosphatidylethanolamine. Ubiquinone 8 (Q-8) was the sole respiratory quinone. The major fatty acids (>10 % of the total fatty acids) were summed feature 3 (C_16 : 1ω7c and/or C_16 : 1ω6c) and C_16 : 0. The DNA G+C content was 47.6 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain GS-14^T had the highest sequence similarity to Aestuariibacter aggregatus WH169^T (96.63 %), Aliiglaciecola coringensis AK49^T (96.56 %) and Alteromonas lipolytica JW12^T (96.22 %). In addition, the OrthoANIu value and dDDH values calculated from the genomes of strain GS-14^T and A. aggregatus WH169^T were 79.5 and 21.9 %, respectively. Based on the polyphasic taxonomic results, strain GS-14^T is considered to represent a novel species in a new genus, for which the name Marisediminitalea mangrovi gen. nov., sp. nov. is proposed. The type strain of Marisediminitalea mangrovi is GS-14^T (=KCTC 72401^T=MCCC 1K03622^T). Because Aestuariibacter aggregatus WH169^T clustered with strain GS-14^T in the phylogenetic trees and was clearly separated from the two species within the genus Aestuariibacter, it is reclassified as a member of the genus Marisediminitalea as Marisediminitalea aggregata comb. nov. (type strain WH169^T=CGMCC 1.8995^T=LMG 25283^T). The type species of the genus Marisediminitalea is Marisediminitalea aggregata gen. nov., comb. nov.

Reclassification of Sphingomonas aeria as a later heterotypic synonym of Sphingomonas carotinifaciens based on whole-genome sequence analysis

The 16S rRNA gene sequences of Sphingomonas carotinifaciens L9-754^T and Sphingomonas aeria B093034^T possess 99.71 % sequence similarity. Further studies were undertaken to clarify the taxonomic assignments of these species. Whole-genome comparisons showed that S. aeria B093034^Tand S. carotinifaciens L9-754^T shared 96.9 % average nucleotide identity, 98.4 % average amino acid identity and 76.1 % digital DNA-DNA hybridization values. These values exceeded or approached the recommended species delineation threshold values. Furthermore, a phylogenetic tree based on 41 of the most conserved genes provided additional evidence that S. aeria B093034^T and S. carotinifaciens L9-754^T are very closely related. Based on this evidence we propose the reclassification of S. aeria Xue et al. 2018 as a later heterotypic synonym of S. carotinifaciens Madhaiyan et al. 2017.

Robust Demarcation of the Family Caryophanaceae (Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures

The family Caryophanaceae/Planococcaceae is a taxonomically heterogeneous assemblage of >100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable phylogenetic overlap with other families, primarily Bacillaceae, the evolutionary history of this family, containing the potent mosquitocidal species Lysinibacillus sphaericus, remains incoherent. To develop a reliable phylogenetic and taxonomic framework for the family Caryophanaceae/Planococcaceae and its genera, we report comprehensive phylogenetic and comparative genomic analyses on 124 genome sequences from all available Caryophanaceae/Planococcaceae and representative Bacillaceae species. Phylogenetic trees were constructed based on multiple datasets of proteins including 819 core proteins for this group and 87 conserved Firmicutes proteins. Using the core proteins, pairwise average amino acid identity was also determined. In parallel, comparative analyses on protein sequences from these species have identified 92 unique molecular markers (synapomorphies) consisting of conserved signature indels that are specifically shared by either the entire family Caryophanaceae/Planococcaceae or different monophyletic clades present within this family, enabling their reliable demarcation in molecular terms. Based on multiple lines of investigations, 18 monophyletic clades can be reliably distinguished within the family Caryophanaceae/Planococcaceae based on their phylogenetic affinities and identified molecular signatures. Some of these clades are comprised of species from several polyphyletic genera within this family as well as other families. Based on our results, we are proposing the creation of three novel genera within the family Caryophanaceae/Planococcaceae, namely Metalysinibacillus gen. nov., Metasolibacillus gen. nov., and Metaplanococcus gen. nov., as well as the transfer of 25 misclassified species from the families Caryophanaceae/Planococcaceae and Bacillaceae into these three genera and in Planococcus, Solibacillus, Sporosarcina, and Ureibacillus genera. These amendments establish a coherent taxonomy and evolutionary history for the family Caryophanaceae/Planococcaceae, and the described molecular markers provide novel means for diagnostic, genetic, and biochemical studies. Lastly, we are also proposing a consolidation of the family Planococcaceae within the emended family Caryophanaceae.

CAMITAX: Taxon labels for microbial genomes

BACKGROUND

The number of microbial genome sequences is increasing exponentially, especially thanks to recent advances in recovering complete or near-complete genomes from metagenomes and single cells. Assigning reliable taxon labels to genomes is key and often a prerequisite for downstream analyses.

FINDINGS

We introduce CAMITAX, a scalable and reproducible workflow for the taxonomic labelling of microbial genomes recovered from isolates, single cells, and metagenomes. CAMITAX combines genome distance-, 16S ribosomal RNA gene-, and gene homology-based taxonomic assignments with phylogenetic placement. It uses Nextflow to orchestrate reference databases and software containers and thus combines ease of installation and use with computational reproducibility. We evaluated the method on several hundred metagenome-assembled genomes with high-quality taxonomic annotations from the TARA Oceans project, and we show that the ensemble classification method in CAMITAX improved on all individual methods across tested ranks.

CONCLUSIONS

While we initially developed CAMITAX to aid the Critical Assessment of Metagenome Interpretation (CAMI) initiative, it evolved into a comprehensive software package to reliably assign taxon labels to microbial genomes. CAMITAX is available under Apache License 2.0 at https://github.com/CAMI-challenge/CAMITAX.

Enterovibrio baiacu sp. nov

We report here the novel species to encompass the isolate A649^T (=CBAS 716^T = CBRVS P1061^T) obtained from viscera of the healthy pufferfish Sphoeroides spengleri (Family Tetraodontidae). Genomic taxonomy analysis demonstrates that the novel strain A649^T had < 95% average amino acid identity/average nucleotide identity (AAI/ANI) and < 70% similarity of genome-to-genome distance (GGDH) towards its closest neighbors which places A649^T into a new Enterovibrio species (Enterovibrio baiacu sp nov.). In silico phenotyping disclosed several features that may be used to differentiate related Enterovibrio species. The nearly complete genome assembly of strain A649^T consisted of 5.4 Mbp and 4826 coding genes.

Taxonomically Characterized and Validated Bacterial Species Based on 16S rRNA Gene Sequences from India During the Last Decade

Microbial taxonomy dealing with identification and characterization of prokaryotes like bacteria and archaea has always been a major area of research all over the world. Exploring diversity of microbes and description of novel species with different genes and secondary compounds is of utmost importance for better future and sustenance of life. India having an enormous range of ecosystems and diverse species inhabiting these niches is considered to be one of the richest biodiversity regions of the world. During the last decade, with newer methodologies and better technology, the prokaryotic taxonomy from India has extended our inventory of microbial communities in specific niches. However, there still exist some limitations in classifying the microbes from India as compared to that is done world-over. This review enlists the taxonomic description of novel taxa of prokaryotes from India in the past decade. A total of 378 new bacterial species have been classified from different habitats in India in the last ten years and no descriptions of archaeal species is documented till date.

Controversies in bacterial taxonomy: The example of the genus Borrelia

In this paper we survey key issues in bacterial taxonomy and review the literature regarding the recent genus separation proposed for the genus Borrelia. We discuss how information on members of the genus Borrelia is increasing but detailed knowledge on the relevant features is available only for a small subset of species. The data accumulated here show that there is considerable overlap in ecology, clinical aspects and molecular features between clades that argue against splitting of the genus Borrelia.

Taxogenomics and Systematics of the Genus Pantoea

Members of the genus Pantoea are Gram-negative bacteria isolated from various environments. Taxonomic affiliation based on multilocus sequence analysis (MLSA) is used routinely for inferring accurate phylogeny and identification of bacterial species and genera. Partial sequences of five housekeeping genes (fusA, gyrB, leuS, rpoB, and pyrG) were extracted from 206 draft or complete genomes of Pantoea strains publicly available in databases and analyzed together with the representative sequences of the 25 validly published Pantoea type strains to verify and assess their phylogenetic assignations. Of a total of 159 strains assigned to species level, 11.3% of the non-type strains were incorrectly assigned within suitable Pantoea species. The highest proportion of misidentified strains was recorded in Pantoea vagans, 8 out of 15 (53.3%) inaccurate assignations at the species level. One probable reason for this incorrect classification could be the method previously used for strain identification. Forty-seven (22.8%) genome sequences were from strains identified at the genus level only (Pantoea sp.). A combination of MLSA, average nucleotide identities [ANI and MuMmer-based ANI (ANIm)], tetranucleotide usage pattern (TETRA), and genome-based DNA-DNA hybridization (gDDH) data was used to accurately assign 25 of the 47 strains to validly published Pantoea species, while 17 strains could be assigned as putative novel species within the genus Pantoea. Four genomes designed as Pantoea sp. were identified as Mixta calida. Positive and significant correlation coefficients were computed between MLSA and all the indices derived from whole-genome sequences being proposed for species delimitation. gDDH exhibited the best correlation with MLSA while TETRA was the worst. Accurate species-level identification is key to a better understanding of bacterial diversity and evolution. The MLSA scheme used here could be instrumental to determine the correct taxonomic status of new whole-genome sequenced Pantoea strains, especially non-type strains, before depositing into public databases.

Confluentibacter sediminis sp. nov., isolated from the junction between the ocean and a freshwater lake and emended description of the genus Confluentibacter

A novel marine Gram-stain-negative, non-motile, aerobic and rod-shaped bacterium, designated strain DSL-48^T, was isolated from tidal flat sediment sampled from the East China Sea and characterized phylogenetically and phenotypically. Bacterial optimal growth occurred at 35 °C (range, 4-37 °C), pH 6 (pH 5-10) and with 4 % (w/v) NaCl (0-7 %). The nearest phylogenetic neighbour was Confluentibacter citreus KCTC 52638^T with 16S rRNA gene similarity of 97.1 %. The predominant respiratory quinone was menaquinone-6 (MK-6). The major polar lipids were phosphatidylethanolamine, three unidentified aminolipids and four unidentified lipids. The major fatty acids of strain DSL-48^T were iso-C_15 : 0, iso-C_17 : 0 3-OH, anteiso-C_15 : 0, iso-C_15 : 0 3-OH and iso-C_16 : 0 3-OH. The G+C content of the genomic DNA was 33.3 mol%. The combined genotypic and phenotypic data indicated that strain DSL-48^T represents a novel species of the genus Confluentibacter, for which the name Confluentibacter sediminis sp. nov. is proposed, with the type strain DSL-48^T (=KCTC 62648^T=MCCC 1K03537^T).

AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination

We present AAI-profiler, a web server for exploratory analysis and quality control in comparative genomics. AAI-profiler summarizes proteome-wide sequence search results to identify novel species, assess the need for taxonomic reclassification and detect multi-isolate and contaminated samples. AAI-profiler visualises results using a scatterplot that shows the Average Amino-acid Identity (AAI) from the query proteome to all similar species in the sequence database. Taxonomic groups are indicated by colour and marker styles, making outliers easy to spot. AAI-profiler uses SANSparallel to perform high-performance homology searches, making proteome-wide analysis possible. We demonstrate the efficacy of AAI-profiler in the discovery of a close relationship between two bacterial symbionts of an omnivorous pirate bug (Orius) and a thrip (Frankliniella occidentalis), an important pest in agriculture. The symbionts represent novel species within the genus Rosenbergiella so far described only in floral nectar. AAI-profiler is easy to use, the analysis presented only required two mouse clicks and was completed in a few minutes. AAI-profiler is available at http://ekhidna2.biocenter.helsinki.fi/AAI.