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

Microbial culture collections play a crucial role in the collection, maintenance, and distribution of quality-assured living microbial strains, along with their associated phenotypic and omics data. To enhance the find-able, accessible, interoperable, and re-usable (FAIR) data utilization of microbial resources, the World Data Center for Microorganisms (WDCM) has developed the Global Catalogue of Microorganisms (GCM) and the Global Catalogue of Type Strains (gcType). These platforms provide interactive interfaces for cataloging the holdings of collections, along with detailed annotations of type strain genomes and curated metadata, including ecosystems, growth conditions, and collection locations. The system maximizes the scientific impact of microbial resources and culture collections through an integrated data mining tool that links strain- and species-related information from various public resources. Currently, the GCM and gcType include 574 422 strains from 154 culture collections across 51 countries and regions, along with 25 980 genomes from type species. Additionally, 2 702 655 articles and 103 337 patents are integrated with these microbial resources. The system supports microbial taxonomic research and provides evidence for implementing the Nagoya Protocol in the field of microbial resources and their digital sequence information (DSI). Access is freely available at gcm.wdcm.org and gctype.wdcm.org.

Comparative genome analysis of the genus Marivirga and proposal of two novel marine species: Marivirga arenosa sp. nov., and Marivirga salinae sp. nov.

BACKGROUND: The phylum Bacteroidota represents a significant proportion of heterotrophic bacteria found in marine ecosystems. Members of the phylum Bacteroidota are actively involved in the degradation of biopolymers such as polysaccharides and proteins. Bacteroidota genomes exhibit a significant enrichment of various enzymes, including carbohydrate-active enzymes (CAZymes), carboxypeptidases, esterases, isomerases, peptidases, phosphatases, and sulfatases. The genus Marivirga, a member of the family Marivirgaceae within the phylum Bacteroidota, comprises six documented species. During a microbial diversity study, three novel Marivirga strains (BKB1-2 T, ABR2-2, and BDSF4-3 T) were isolated from the West Sea, Republic of Korea. RESULTS: To explore the taxonomic status and genomic characteristics of the novel isolates, we employed a polyphasic taxonomic approach, which included phylogenetic, chemotaxonomic and comprehensive genome analysis. The three isolates were Gram-stain-negative, aerobic, rod-shaped, moderately halophilic, and had a gliding motility. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among the two isolates, BKB1-2 T and BDSF4-3 T, and the six reference strains were 70.5-76.5% for ANI and 18.1-25.7% for dDDH. Interestingly, the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the strains harbor genes for a comprehensive pathway for dissimilatory nitrate reduction to ammonium (DNRA), as well as other nitrogen pathways for the reduction of nitrite, nitric oxide, and nitrous oxide. Additionally, the antiSMASH analysis indicated that the strains contained three to eight biosynthetic gene clusters (BGCs) associated with the synthesis of secondary metabolites. Furthermore, the strains carried a high number of CAZyme ranging from 53 to 152, which was also demonstrated by an in vitro analysis of degradation of the polysaccharide cellulose, chitin, laminarin, starch, and xylan. Additionally, all the strains carried genes for the metabolism of heavy metals, and exhibited tolerance to heavy metals, with minimum inhibitory concentrations (MICs) in millimoles (mM) in ranges of Co2+ (3-6), Cu2+ (0.2-0.4), Ni2+ (3-5), Zn2+ (2-4), Mn2+ (20-50), and Hg2+ (0.3). CONCLUSIONS: Based on polyphasic taxonomic approach, the three isolated strains represent two novel species names Marivirga arenosa sp. nov. (BKB1-2 T = KCTC 82989 T = InaCC B1618T), and Marivirga salinae sp. nov. (BDSF4-3 T = KCTC 82973 T = InaCC B1619T).

Methylacidiphilum caldifontis gen. nov., sp. nov., a thermoacidophilic methane-oxidizing bacterium from an acidic geothermal environment, and descriptions of the family Methylacidiphilaceae fam. nov. and order Methylacidiphilales ord. nov.

Strain IT6T, a thermoacidophilic and facultative methane-oxidizing bacterium, was isolated from a mud-water mixture collected from Pisciarelli hot spring in Pozzuoli, Italy. The novel strain is white when grown in liquid or solid media and forms Gram-negative rod-shaped, non-flagellated, non-motile cells. It conserves energy by aerobically oxidizing methane and hydrogen while deriving carbon from carbon dioxide fixation. Strain IT6T had three complete pmoCAB operons encoding particulate methane monooxygenase and genes encoding group 1d and 3b [NiFe] hydrogenases. Simple carbon-carbon substrates such as ethanol, 2-propanol, acetone, acetol and propane-1,2-diol were used as alternative electron donors and carbon sources. Optimal growth occurred at 50-55°C and between pH 2.0-3.0. The major fatty acids were C18 : 0, C15 : 0 anteiso, C14 : 0 iso, C16 : 0 and C14 : 0, and the main polar lipids were phosphatidylethanolamine, aminophospholipid, phosphatidylglycerol, diphosphatidylglycerol, some unidentified phospholipids and glycolipids, and other unknown polar lipids. Strain IT6T has a genome size of 2.19 Mbp and a G+C content of 40.70 mol%. Relative evolutionary divergence using 120 conserved single-copy marker genes (bac120) and phylogenetic analyses based on bac120 and 16S rRNA gene sequences showed that strain IT6T is affiliated with members of the proposed order 'Methylacidiphilales' of the class Verrucomicrobiia in the phylum Verrucomicrobiota. It shared a 16S rRNA gene sequence identity of >96 % with cultivated isolates in the genus 'Methylacidiphilum' of the family 'Methylacidiphilaceae', which are thermoacidophilic methane-oxidizing bacteria. 'Methylacidiphilum sp.' Phi (100 %), 'Methylacidiphilum infernorum' V4 (99.02 %) and 'Methylacidiphilum sp.' RTK17.1 (99.02 %) were its closest relatives. Its physiological and genomic properties were consistent with those of other isolated 'Methylacidiphilum' species. Based on these results, we propose the name Methylacidiphilum caldifontis gen. nov., sp. nov. to accommodate strain IT6T (=KCTC 92103T=JCM 39288T). We also formally propose that the names Methylacidiphilaceae fam. nov. and Methylacidiphilales ord. nov. to accommodate the genus Methylacidiphilum gen. nov.

gcType: a high-quality type strain genome database for microbial phylogenetic and functional research.

Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data and methods. As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced by the GCM 10K project which are preserved in global culture collections with a valid published status. Additionally, the information provided through gcType includes >12 000 publicly available type strain genome sequences from GenBank incorporated using quality control criteria and standard data annotation pipelines to form a high-quality reference database. This database integrates type strain sequences with their phenotypic information to facilitate phenotypic and genotypic analyses. Multiple formats of cross-genome searches and interactive interfaces have allowed extensive exploration of the database's resources. In this study, we describe web-based data analysis pipelines for genomic analyses and genome-based taxonomy, which could serve as a one-stop platform for the identification of prokaryotic species. The number of type strain genomes that are published will continue to increase as the GCM 10K project increases its collaboration with culture collections worldwide. Data of this project is shared with the International Nucleotide Sequence Database Collaboration. Access to gcType is free at http://gctype.wdcm.org/.

Streptococcus ruminicola sp. nov., new species of the Streptococcus bovis/Streptococcus equinus complex (SBSEC) isolated from the rumen of Korean domestic ruminants.

A total of three Gram-positive, and oxidase and catalase-negative facultative anaerobic non-motile bacteria were isolated from the rumen fluid of cows and goats and these strains were designated CNU_G2T, CNU_77-61, and CNU_G3. They grew at 20-45 °C, pH 6.5-7, and 0-6.5% NaCl (w/v). The G + C contents (%) of the three isolates were 37.9, 37.8 and 37.8, respectively. Phylogenomic analysis indicated that these strains were distinct from other Streptococcus species. The average nucleotide identity between the isolates and the closest strain S. infantarius subsp. infantarius ATCC BAA-102T was 94.0-94.5%, while the digital DNA-DNA hybridization (dDDH) values between the isolates and the aforementioned related strain were 58.2-61.4%, respectively. Fatty acid analysis revealed higher proportions of C16:0 (> 28%) in all three isolates, while the proportion of C18:0 was higher in CNU_G2T (25.8%); however, it was less than 12% in all the representing strains used in the study. The C14:0 composition of strains CNU_77-61 (22.1%) and CNU_G3 (24.1%) was higher than that of type strains of CNU_G2T (8.1%). Based on the morphological, biochemical, and molecular phylogenetic features of the three novel isolates, they represent a novel species of the genus Streptococcus, for which we propose as Streptococcus ruminicola sp. nov. The type strain is CNU_G2T (= KCTC 43308T = GDMCC 1.2785T).

Aureibaculum algae sp. nov. isolated from the Pacific red alga Ahnfeltia tobuchiensis.

A Gram stain-negative, aerobic, rod-shaped, motile by gliding and yellow-orange-pigmented bacterium, designated strain 10Alg 115T, was isolated from the red alga Ahnfeltia tobuchiensis. The phylogenetic analysis based on 16S rRNA gene sequences placed the novel strain within the family Flavobacteriaceae, phylum Bacteroidetes. The nearest neighbor of the new isolate was Aureibaculum marinum KCTC 62204T with sequence similarity of 98.1%. The average nucleotide similarity and digital DNA-DNA hybridization values between the novel strain and Aureibaculum marinum KCTC 62204T were 80% and 22.3%, respectively. The prevalent fatty acids of strain 10Alg 115T were iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH, iso-C16:0 3-OH and C15:0. The polar lipid profile consisted of phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids. The DNA G + C content of the type strain calculated from the whole-genome sequence was 32.2 mol%. A combination of the genotypic and phenotypic data showed that the algal isolate represents a novel species of the of genus Aureibaculum, for which the name Aureibaculum algae sp. nov. is proposed. The type strain is 10Alg 115T (= KCTC 62086T = KMM 6764T).

Algicella marina gen. nov., sp. nov., a novel marine bacterium isolated from a Pacific red alga.

A novel Gram-staining negative, strictly aerobic, rod-shaped, and non-motile bacterium, designated strain 9Alg 56T, was isolated from the red alga Tichocarpus crinitus. The phylogenetic analysis based on 16S rRNA gene sequences placed the novel strain within the family Rhodobacteraceae, the order Rhodobacterales, the class Alphaproteobacteria, the phylum Pseudomonadota. The nearest neighbors of the new strain were Pontivivens insulae KCTC 42458T, Oceanibium sediminis KCTC 62076T, Halovulum dunhuangense YYQ-30T and Monaibacterium marinum C7T with 16S rRNA gene sequence similarity of 94.7, 94.4%, 93.1 and 92.7%, respectively. The AAI/ANI/dDDH values between 9Alg 56T and the five species of the closest genera (Pontivivens, Oceanibium, Halovulum, Monaibacterium, and 'Oceanomicrobium') were 58.63-63.91%/ 75.91-77.37%/ 19.3-20.4%. The prevalent fatty acids of strain 9Alg 56T were C18:1 ω7c, C18:0 and C14:0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidic acid, phosphatidylcholine, and two unidentified lipids. The DNA G+C content of strain 9Alg 56T was 61.5 mol%. A combination of the genotypic and phenotypic data showed that the algal isolate represents a novel genus and species, for which the name Algicella marina gen. nov., sp. nov. is proposed. The type strain is 9Alg 56T (= KCTC 72005T = KMM 6775T).

Flavobacterium litorale sp. nov., isolated from red alga.

A Gram-stain-negative and rod-shaped bacterial strain (WSW3-B6T) was isolated from red alga collected from the West Sea, Republic of Korea. Cells of strain WSW3-B6T were non-motile, aerobic and produced slightly yellow and mucoid colonies on marine agar. The strain grew optimally at 23-30 °C, with 0.5-4 % NaCl (w/v) and at pH 6.5-8.5. A phylogenetic analysis of the 16S rRNA gene revealed that strain WSW3-B6T belongs to the genus Flavobacterium within the family Flavobacteriaceae, having the highest sequence similarity to Flavobacterium arcticum SM1502T (96.7%), followed by Flavobacterium salilacus subsp. altitudinum LaA7.5T (96.2%) and Flavobacterium salilacus subsp. salilacus SaA2.12T (96.2%). The complete sequence of a circular chromosome of strain WSW3-B6T determined by combination of Oxford Nanopore and Illumina platforms comprised a total 2 725 095 bp with G+C content of 37.1 mol%. A comparative analysis based on the whole genome also showed the distinctiveness of strain WSW3-B6T. The average nucleotide identity (ANI) values between strain WSW3-B6T and the closest strains F. arcticum SM1502T, F. salilacus subsp. altitudinum LaA7.5T and F. salilacus subsp. salilacus SaA2.12T were 78.3, 77.8 and 77.7 %, respectively, while the digital DNA-DNA hybridization (dDDH) values between strain WSW3-B6T and the above closely related strains were 21.0, 20.4 and 20.3 %, respectively. Both the ANI and dDDH values supported the creation of a new species in the genus Flavobacterium. The major fatty acids (>10 %) were iso-C15 : 0 (19.3 %), C16 : 0 (14.0 %), iso-C17 : 0 3-OH (13.1 %) and C18 : 0 (10.7 %). The polar lipids of strain WSW3-B6T included phosphatidylethanolamine, three unidentified aminolipids and three unidentified lipids. Moreover, MK-6 was the only respiratory quinone. A comparison of the phylogenetic distinctiveness and the unique phenotypic and chemotaxonomic characteristics among strain WSW3-B6T and closely related type strains supported that strain WSW3-B6T (=KCTC 82708T=GDMCC 1.2627T) represents a novel species of the genus Flavobacterium, for which the name Flavobacterium litorale sp. nov. is proposed.

Cellulosimicrobium protaetiae sp. nov., isolated from the gut of the larva of Protaetia brevitarsis seulensis.

A Gram-stain-positive, non-spore-forming, yellow-pigmented, non-motile, non-flagellated, facultative anaerobic and rod-shaped bacterial strain, designated BI34T, was isolated from the gut of the larva of Protaetia brevitarsis seulensis. Strain BI34T grew at 15-40 °C (optimum, 37 °C), at pH 6.5-9.0 (optimum, pH 7.5) and in the presence of 0-7 % (w/v) NaCl (optimum, 2 %). Based on the results of 16S rRNA gene sequence analysis, strain BI34T belonged to the phylum Actinobacteria and was closely related to Cellulosimicrobium funkei NBRC 104118T (99.3 %), Cellulosimicrobium cellulans NBRC 15516T (99.1 %), Cellulosimicrobium composti BIT-GX5T (99.0 %), Cellulosimicrobium fucosivorans SE3T (99.0 %), Cellulosimicrobium marinum NBRC 110994T (98.4 %) and Cellulosimicrobium terreum DS-61T (97.0 %). The genome to genome relatedness of the average nucleotide identity (ANI) and the digital DNA-DNA hybridization (dDDH) values calculated by the Genome-to-Genome Distance Calculator between strain BI34T and its related species mentioned above were lower than the threshold of 95 and 70 % for speciation, respectively. The predominant menaquinone of strain BI34T contained MK-9(H4), and the major fatty acids were anteiso-C15 : 0, C16 : 0 and anteiso-C17 : 0. Strain BI34T had diphosphatidylglycerol and phosphatidylglycerol as major polar lipids. The whole-cell sugars were galactose, glucose and ribose, and the cell-wall peptidoglycan contained lysine, alanine, aspartic acid and glutamic acid. The DNA G+C content of strain BI34T was 73.8 mol%. The difference in physiological and biochemical characteristics and the below-threshold values of genome-to-genome relatedness indicate that strain BI34T represents a novel species in the genus Cellulosimicrobium, for which the name Cellulosimicrobium protaetiae sp. nov. is proposed. The type strain is BI34T (=KCTC 49302T=NBRC 114073T).

Vibrio ostreae sp. nov., a novel gut bacterium isolated from a Yellow Sea oyster.

A Gram-stain-negative, oxidase- and catalase-positive, facultative anaerobic motile bacterium, designated strain OG9-811T, was isolated from the gut of an oyster collected in the Yellow Sea, Republic of Korea. The strain grew at 10-37 °C, pH 6.0-9.0 and with 0.5-10% (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain OG9-811T affiliated with the genus Vibrio, with the highest sequence similarity of 98.2% to Vibrio coralliilyticus ATCC BAA-450T followed by Vibrio variabilis R-40492T (98.0 %), Vibrio hepatarius LMG 20362T (97.7 %) and Vibrio neptunius LMG 20536T (97.6 %); other relatives were Vibrio tritonius JCM 16456T (97.4 %), Vibrio fluvialis NBRC 103150T (97.0 %) and Vibrio furnissii CIP 102972T (97.0 %). The complete genome of strain OG9-811T comprised two chromosomes of a total 4 807 684 bp and the G+C content was 50.2 %. Results of analysis based on the whole genome sequence showed the distinctiveness of strain OG9-811T. The average nucleotide identity (ANI) values between strain OG9-811T and the closest strains V. coralliilyticus ATCC BAA-450T, V. variabilis R-40492T, V. hepatarius LMG 20362T, V. neptunius KCTC 12702T , V. tritonius JCM 16456T, V. fluvialis ATCC 33809T and V. furnissi CIP 102972T were 73.0, 72.6, 73.3, 73.0, 72.7, 78.5 and 77.8 %, respectively, while the digital DNA-DNA hybridization values between strain OG9-811T and the above closely related strains were 20.8, 21.2, 20.8, 21.7, 20.7, 23.2 and 22.4 %, respectively. The major fatty acids of strain OG9-811T were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω6c and/or C18:1 ω7c) and C16:0. The polar lipids contained phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Strain OG9-811T contained Q-8 as a quinone. On the basis of polyphasic taxonomic characteristics, strain OG9-811T is considered to represent a novel species, for which the name Vibrio ostreae sp. nov. is proposed. The type strain is OG9-811T (=KCTC 72623T=GDMCC 1.2610T).

Halorubrum salinarum sp. nov., an extremely halophilic archaeon isolated from a saturated brine pond of a saltern.

A novel extremely halophilic archaeon, strain RHB-CT, was isolated from a saturated brine pond of a solar saltern in Bolinao, Pangasinan, Philippines. Colonies were orange-red-pigmented, smooth, convex and round on a solid modified growth medium containing 25 % (w/v) of total salts. Cells of strain RHB-CT on the solid modified growth medium were ovoid-shaped (0.89-2.66 µm long), while the cells in a liquid modified growth medium were rod-shaped (1.53-5.65 µm long and 0.45-1.03 µm wide). The strain was Gram-stain-negative, motile and strictly aerobic. Strain RHB-CT grew with NaCl concentrations ranging from 10 to 30 % (w/v; optimum, 20-25 %), at pH 6.5-8.5 (optimum, pH 7.0-7.5) and at 20-55 °C (optimum, 40-45 °C). Furthermore, the strain grew even in the absence of Mg2+; however, when supplemented with Mg2+, growth was observed optimally at 0.2-0.4 M Mg2+. The 16S rRNA gene phylogeny inferred that the strain is a member of the genus Halorubrum and was related to Halorubrum xinjiangense CGMCC 1.3527T (99.0 %), Halorubrum sodomense DSM 3755T (98.8 %), Halorubrum coriense Ch2T (98.8 %), Halorubrum trapanicum NRC 34021T (98.4 %) and Halorubrum distributum JCM 9100T (98.1 %). The rpoB' gene sequences also showed that strain RHB-CT is related to Hrr. xinjiangense JCM 12388T (97.1 %), Hrr. distributum JCM 9100T (97.1 %), Hrr. coriense JCM 9275T (96.5 %), Hrr. californiense JCM 14715T (96.5 %), Hrr. trapanicum JCM 10477T (96.3%), Hrr. sodomense JCM 8880T (96.2%) and Hrr. tebenquichense DSM 14210T (95.6 %). The DNA G+C content of strain RHB-CT was 68.7 mol% (genome). Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain RHB-CT and the closely related species of Halorubrum were below 40 and 90 %, respectively, which are far below the thresholds to delineate a new species. The polar lipids of strain RHB-CT were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulphate and sulfated mannosyl glycosyl diether. Based on dDDH and ANI values, and the significant morphological and physiological differences from known taxa, it is hereby suggested that strain RHB-CT represents a novel species of the genus Halorubrum, for which the name Halorubrum salinarum sp. nov. is proposed. The type strain is RHB-CT (=KCTC 4274T=CMS 2103T).

Metallococcus carri gen. nov., sp. nov., a novel member of the family Dermacoccaceae isolated from an automotive air conditioning system.

Strain designated DB0510T was isolated from an automobile evaporator core collected in Korea. Cells are gram-stain-positive, aerobic, and coccoid. The strain grew at 15-45 â„ƒ, pH 5.0-8.5 and 0-8.0% (w/v) NaCl. Growth occurs on R2A, trypticase soy agar, Luria-Bertani agar, and nutrient agar. Phylogenetic analysis showed that the strain belongs to the family Dermacoccaceae and strain DB0510T was distinctly separated from validly named genera of this family. Signature nucleotides in 16S rRNA gene sequence revealed that the strain contained the Dermacoccaceae family-specific 16S rRNA signature nucleotides patterns. The major fatty acids were C17:0 and C17:1 cis-9. The only menaquinone was MK-8 (H4). The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, and two unidentified lipids. The diagnostic cell-wall amino acid at position 3 of the peptide subunit was found to be lysine. The cell-wall peptidoglycan contained alanine, aspartic acid, glutamic acid, glycine, lysine, and serine and thus the peptidoglycan type was concluded to be of A4α type with Lys-Gly-Ser-Asp interpeptide bridge. The genome size was 3.49 Mbp and G + C content of the genome DNA was 69.4 mol%. On the basis of the phenotypic, genomic, and chemotaxonomic characteristics, strain DB0510T is considered to represent a novel genus and species within the family Dermacoccaceae, for which the name Metallococcus carri gen. nov., sp. nov. is proposed. The type strain of Metallococcus carri is DB0510T (= KACC 19663 T = NBRC 113349 T).

Lactococcus kimchii sp. nov., a new lactic acid bacterium isolated from kimchi.

A coccus strain designated S-13T was isolated from commercial baechu-kimchi in Korea. Comparison of the 16S rRNA gene sequence indicated that strain S-13T had the highest similarity to Lactococcus taiwanensis 0905C15T (97.9 %), Lactococcus lactis subsp. tructae L105T (97.6 %), Lactococcus lactis subsp. cremoris NCDO 607T (97.5 %), Lactococcus lactis subsp. hordniae NBRC 100931T (97.2 %), and Lactococcus lactis subsp. lactis JCM 5805T (97.2 %). The detailed phylogenetic analyses based on the 16S rRNA, rpoB and recA genes indicated that S-13T was separated from the other species and subspecies in the genus Lactococcus. The DNA-DNA relatedness between S-13T and closely related type strains, such as L. taiwanensis 0905C15T, L. lactis subsp. tructae L105T, L. lactis subsp. cremoris NCDO 607T, L. lactis subsp. hordniae NBRC 100931T, and L. lactis subsp. lactis JCM 5805T was 25.6, 20.4, 25.1, 20.2 and 21.7 %, respectively. The major fatty acids were C16 : 0, cyclo-C19 : 0ω8c and C 14 : 0. The DNA G+C content of S-13T was 39.4 mol%. From the results of the phenotypic characteristics and chemotaxonomic analysis, it was concluded that strain S-13T represents a novel species in the genus Lactococcus for which the name Lactococcus kimchii sp. nov. (=KCTC 21096T=NBRC 113348T) is proposed.

Complete genome sequence of Bacillus ciccensis 5L6T, a new species isolated from maize (Zea mays L.) seeds with anti-fungal activity.

Maize is a crop grown worldwide. Bacillus ciccensis 5L6T was isolated from maize (Zea mays L., Jingke968) seeds and was a new species of Bacillus with potential anti-fungal activity. The complete genome of 5L6T was sequenced and assembled with a length of 5,207,802 bp and a GC content of 37.42%. The proteins responsible for anti-fungal activity and the potential beneficial interaction with maize of 5L6Twere annotated and reported here. The complete genome sequence of the new species B. ciccensis 5L6T will promote its biological application.

Flavobacterium ustbae sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia.

A yellow-pigmented bacterial strain, designated T13T, was isolated from the rhizosphere soil of Alhagi sparsifolia collected from Xinjiang, PR China. Cells were rod-shaped, Gram-stain-negative, aerobic and gliding. Strain T13T grew optimally at 25-30 °C and pH 7.0-8.0 with a NaCl tolerance of 0-2 % on Reasoner's 2A agar. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain T13T belonged to the genus Flavobacterium within the family Flavobacteriaceae and was closely related to Flavobacterium nitrogenifigens KCTC 42884T with a similarity value of 97.4 %. The major polar lipid was phosphatidylethanolamine; the only respiratory quinone was MK-6, and the polyamine profile contained sym-homospermidine as the major polyamine and a trace amount of spermidine. The major fatty acids were iso-C15 : 0, C16 :  1ω7c and summed feature 3 (comprising C16 : 1ω7c or C16 : 1ω6c). The G+C content of the genomic DNA was 34.1 mol%. It is concluded from the phenotypic and genotypic data that strain T13T represents a novel species of the genus Flavobacterium, for which the name Flavobacteriumustbae sp. nov. with the type strain T13T (=KCTC 62874T=ACCC 60126T) is proposed.

Sulfitobacter aestuarii sp. nov., a marine bacterium isolated from a tidal flat of the Yellow Sea.

A novel bacterial strain, designated hydD52T, was isolated from a sample of tidal flat sediment of the Yellow Sea in the Republic of Korea. The cells were motile, rod-shaped and Gram-stain-negative. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain hydD52T was a member of the genus Sulfitobacter and most closely related to Sulfitobacter dubius DSM 16472T (98.0 %), Sulfitobacter indolifex HEL-45T (97.8 %) and Sulfitobacter delicatus DSM 28223T (97.6 %). The major fatty acids (>5 %) of hydD52T were C18 : 1ω7c/C18 : 1ω6c, C16 : 0, C18 : 1ω7c 11-methyl and C19 : 0ω8c. The respiratory quinone of strain hydD52T was ubiquinone-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified amino lipid. The G+C content of this strain was 64.0 mol%. The DNA-DNA relatedness values of hydD52T with the type strains of S. dubius, S. indolifex and S. delicatus were 18.8, 13.1 and 15.7 %, respectively. Based on the results of morphological, physiological and chemotaxonomic characterization, DNA-DNA hybridization relatedness, and 16S rRNA genes analysis, we concluded that strain hydD52T represents a novel species, for which the name Sulfitobacter aestuarii sp. nov. is proposed. The type strain is hydD52T (=KCTC 32982T=TISTR 2562T).

Polaribacter staleyi sp. nov., a polysaccharide-degrading marine bacterium isolated from the red alga Ahnfeltia tobuchiensis.

A Gram-stain-negative, rod-shaped, motile by gliding and yellow-pigmented bacterium, designated strain 10Alg 139T, was isolated from the Pacific red alga Ahnfeltiato buchiensis. The phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain belonged to the genus Polaribacter, a member of the family Flavobacteriaceae, the phylum Bacteroidetes, with highest sequence similarity to Polaribacter butkevichii KMM 3938T (99.3 %) and 93.3-98.6 % to other recognized Polaribacter species. The prevalent fatty acids of strain 10Alg 139T were iso-C15 : 0 3-OH, C15 : 0 3-OH, iso-C15:0, iso-C13 : 0, C15 : 0 and C15 : 1ω6c. The polar lipid profile consisted of the major lipids phosphatidylethanolamine, two unidentified aminolipids and four unidentified lipids. The main respiratory quinone was menaquinone 6. The DNA G+C content of the type strain is 31.8 mol%. The new isolate and the type strains of recognized species of the genus Polaribacter were readily distinguished based on a number of phenotypic characteristics. A combination of the genotypic and phenotypic data showed that the isolate from alga represents a novel species of the genus Polaribacter, for which the name Polaribacterstaleyi sp. nov. is proposed. The type strain is 10Alg 139T (=KCTC 52773T=KMM 6729T).

Aquimarina algiphila sp. nov., a chitin degrading bacterium isolated from the red alga Tichocarpus crinitus.

A strictly aerobic, Gram-stain-negative, rod-shaped, motile by gliding and yellow-orange pigmented flavobacterium, designated strain 9Alg 151T, was isolated from the Pacific red alga Tichocarpus crinitus. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain fell into the genus Aquimarina of the family Flavobacteriaceae with a 16S rRNA gene sequence similarity range of 94.2-98.2 % to the recognized species of the genus. Strain 9Alg 151T grew in the presence of 0.5-5 % NaCl and at 5-34 °C, and hydrolysed aesculin, agar, gelatin, starch, Tween 40, DNA and chitin. The predominant fatty acids were iso-C17 : 0 3-OH, iso-C15 : 0, iso-C15 : 1 G, iso-C15 : 0 3-OH, iso-C16 : 0, iso-C17 : 1ω8c and summed feature 3. The polar lipid profile comprised phosphatidylethanolamine, three unidentified aminolipids and three unidentified lipids. The major respiratory quinone was MK-6. The genomic DNA G+C content was 32.6 mol%. On the basis of 16S rRNA gene sequence data, and chemotaxonomic and phenotypic characteristics, strain 9Alg 151T represents a novel species of the genus Aquimarina, for which the name Aquimarina algiphila sp. nov. is proposed. The type strain is 9Alg 151T (=KCTC 23622T=KMM 6462T).

Flavisolibacter metallilatus sp. nov., isolated from an automotive air conditioning system and emended description of the genus Flavisolibacter.

A Gram-stain-negative, aerobic, non-motile, rod-shaped and pale yellow-pigmented bacterium, designated strain TX0661T, was isolated from an automotive air conditioning system collected in the Republic of Korea. 16S rRNA gene sequence analysis showed that the strain TX0661T was grouped with members of the genus Flavisolibacter and the strain had 98.2-95.3 % 16S rRNA gene sequence similarities to the species of the genus Flavisolibacter. DNA-DNA relatedness between TX0661T and Flavisolibacter ginsenosidimutans KCTC 22818T and Flavisolibacter ginsengisoli KCTC 12657T was less than 30 %. The low levels of DNA-DNA relatedness identified strain TX0661T as a novel species in the genus Flavisolibacter. The strain grew at 28-37 °C (optimum, 37 °C), at pH 6.0-7.0 (optimum, pH 6.5) and in the presence of 0-0.5 % (w/v, optimum, 0.5 %) NaCl. It contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH as major fatty acids and MK-7 as the predominant menaquinone. The polar lipid profile revealed that the presence of phosphatidylethanolamine, aminoglycophospholipid, two unidentified aminolipids and two unidentified lipids. The DNA G+C content of the strain was 49.1 mol%. Based on phenotypic, genotypic and chemotaxonomic data, strain TX0661T represents a novel species in the genus Flavisolibacter, for which the name Flavisolibactermetallilatus sp. nov. (=KACC 19145T=KCTC 52779T=NBRC 111784T) is proposed.

Flavisolibacter carri sp. nov., isolated from an automotive air-conditioning system.

A Gram-stain negative, aerobic, non-motile, rod-shaped and yellow bacterium, designated TX0651T, was isolated from an automotive air-conditioning system. Phylogenetically, the strain groups with the members of the genus Flavisolibacter and exhibits high 16S rRNA gene sequence similarities with Flavisolibacter ginsenosidimutans Gsoil 636T (97.4%), Flavisolibacter ginsengiterrae Gsoil 492T (96.3%) and Flavisolibacter ginsengisoli Gsoil 643T (96.2%). DNA-DNA relatedness between TX0651T and F. ginsenosidimutans KCTC 22818T and F. ginsengiterrae KCTC 12656T were determined to be less than 40%. The low levels of DNA-DNA relatedness identifies the strain TX0651T as a novel species in the genus Flavisolibacter. The major cellular fatty acids were identified as iso-C15:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), iso-C15:1 G and iso-C17:0 3-OH. The predominant respiratory quinone was identified as MK-7. The polar lipids were found to be comprised of phosphatidylethanolamine, unidentified amino-glycophospholipids, an unidentified aminophospholipid, an unidentified amino lipid and unidentified lipids. The DNA G+C content of the strain was determined to be 31.2 mol%. On the basis of the phenotypic, genotypic and chemotaxonomic characteristics, strain TX0651T should be classified in a novel species in the genus Flavisolibacter, for which the name Flavisolibacter carri sp. nov. (= KACC 19014T = KCTC 52836T = NBRC 111784T) is proposed.