Description of Maribellus sediminis sp. nov., a marine nitrogen-fixing bacterium isolated from sediment of cordgrass and mangrove

Two marine bacterial strains designated Y2-1-60^T and GM1-28 were isolated from sediments of cordgrass and mangrove along the Luoyang estuary in Quanzhou Bay, China, respectively. Both strains were Gram-staining-negative, straight rod-shaped, non-flagellum, facultatively anaerobic, nitrogen-fixing, and did not contain carotenoid pigment. Catalase activities were found to be weak positive and oxidase activities negative. The 16S rRNA gene sequences of the two strains were identical and had maximum similarity of 98.0% with Maribellus luteus XSD2^T, and of <94.5% with other species. ANI value (96.9%) and DDH estimate (71.5%) between the two strains supported that they belonged to the same species. ANI value and DDH estimate between the two strains and M. luteus XSD2^T was 74.3% and 19.4%, respectively, indicating that they represent a novel species. Phylogenetic analysis based on 16S rRNA gene and phylogenomic analysis indicated that strains Y2-1-60^T and GM1-28 formed a monophyletic branch within the genus Maribellus. The respiratory quinone was menaquinone MK-7. The major fatty acid (>10%) consisted of iso-C_15:0, and iso-C_17:0 3-OH. The polar lipids consisted of phosphatidylethanolamine and several unidentified lipids. The genomic G + C contents were 41.9–42.0 mol%. Gene annotation revealed that strains Y2-1-60^T and GM1-28 contained a set of nif gene cluster (nifHDKENB) responsible for nitrogen fixation. Based on the above characteristics, strains Y2-1-60^T and GM1-28 represent a novel species within the genus Maribellus. Thus, Maribellus sediminis sp. nov. is proposed with type strain Y2-1-60^T (=MCCC 1K04285^T = KCTC 72884^T), isolated from cordgrass sediment and strain GM1-28 (=MCCC 1K04384 = KCTC 72880), isolated from mangrove sediment.     

Alteromonas flava sp. nov. and Alteromonas facilis sp. nov., two novel copper tolerating bacteria isolated from a sea cucumber culture pond in China

Two bacterial strains, P0211^T and P0213^T, were isolated from a sea cucumber culture pond in China. The strains were able to resist high copper levels. These two strains were characterized at the phenotypic, chemotaxonomic, and genomic level. They were completely different colors, but the 16S rRNA genes showed 99.30% similarity. Phylogenetic analysis based on the sequences of the 16S rRNA gene and five housekeeping genes (dnaK, sucC, rpoB, gyrB, and rpoD) supported the inclusion of these strains within the genus Alteromonas, and the two isolated strains formed a group separated from the closest species Alteromonas aestuariivivens KCTC 52655^T. Genomic analyses, including average nucleotide identity (ANIb and ANIm), DNA–DNA hybridization (DDH), and the percentage of conserved proteins (POCP), clearly separated strains P0211^T and P0213^T from the other species within the genus Alteromonas with values below the thresholds for species delineation. The chemotaxonomic features (including fatty acid and polar lipid analysis) of strains P0211^T and P0213^T also confirmed their differentiation from the related taxa.The results demonstrated that strains P0211^T and P0213^T represented two novel species in the genus Alteromonas, for which we propose the names Alteromonas flava sp. nov., type strain P0211^T (= KCTC 62078^T = MCCC 1H00242^T), and Alteromonas facilis sp. nov., type strain P0213^T (= KCTC 62079^T = MCCC 1H00243^T).     

Miltoncostaea marina gen. nov. sp. nov., and Miltoncostaea oceani sp. nov., a novel deep branching phylogenetic lineage within the class Thermoleophilia isolated from marine environments,and proposal of Miltoncostaeaceae fam. nov. and Miltoncostaeales ord. nov

Two novel marine actinobacteria, designated as SCSIO 60955^T and SCSIO 61214^T, were isolated from deep-sea sediment samples collected from the South China Sea. The cells of these organisms stained Gram-negative and were rod shaped. These strains were aerobic, and catalase- and oxidase-positive. Optimal growth occurred at 28 °C and pH 7 over 14 days of cultivation. Both strains possessed phospholipids and phosphoglycolipids. The main menaquinone was MK-7. The major fatty acid was C_16:0. The peptidoglycan structure was type A1γ′ (meso-Dpm). Analysis of genome sequences revealed that the genome size of SCSIO 60955^T was 3.37 Mbp with G + C content of 76.1%, while the genome size of SCSIO 61214^T was 3.67 Mbp with a G + C content of 74.8%. The ANI and 16S rRNA gene analysis results showed that the pairwise similarities between the two strains were 73.4% and 97.7% and that with other recognized Thermoleophilia species were less than 69.1% and 87.8%, respectively. Phylogenetic analysis of the 16S rRNA gene sequences showed that strains SCSIO 60955^T and SCSIO 61214^T were separately clustered together and formed a well-separated phylogenetic branch distinct from their most related neighbor Gaiella occulta. Based on the data presented here, these two strains are proposed to represent two novel species of a novel genus, for which the name Miltoncostaea marina gen. nov., sp. nov., with the type strain SCSIO 60955^T (=DSM 110281^T =CGMCC 1.18757^T), and Miltoncostaea oceani sp. nov., with the type strain SCSIO 61214^T (=KCTC 49527^T =CGMCC 1.18758^T) are proposed. We also propose that these organisms represent a novel family named Miltoncostaeaceae fam. nov. of a novel order Miltoncostaeales ord. nov.     

Geomesophilobacter sediminis gen. nov., sp. nov., Geomonas propionica sp. nov. and Geomonas anaerohicana sp. nov., three novel members in the family Geobacterecace isolated from river sediment and paddy soil

Bacteria in the family Geobacteraceae have been proven to fill important niches in a diversity of anaerobic environments and global biogeochemical processes. Here, three bacterial strains in this family, designated Red875^T, Red259^T, and Red421^T were isolated from river sediment and paddy soils in Japan. All of them are Gram-staining-negative, strictly anaerobic, motile, flagellum-harboring cells that form red colonies on agar plates and are capable of utilizing Fe(III)-NTA, Fe(III) citrate, ferrihydrite, MnO₂, fumarate, and nitrate as electron acceptors with acetate, propionate, pyruvate, and glucose as electron donors. Phylogenetic analysis based on the 16S rRNA gene and 92 concatenated core proteins sequences revealed that strains Red259^T and Red421^T clustered with the type strains of Geomonas species, whereas strain Red875^T formed an independent lineage within the family Geobacteraceae. Genome comparison based on  average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values clearly distinguished these three strains from other Geobacteraceae members, with lower values than the thresholds for species delineation. Moreover, strain Red875^T also shared low average amino acid identity (AAI) and percentage of conserved proteins (POCP) values with the type species of the family Geobacteraceae. Based on these physiological, chemotaxonomic, and phylogenetic distinctions, we propose that strain Red875^T (=NBRC 114290^T = MCCC 1K04407^T) represents a novel genus in the family Geobacteraceae, namely, Geomesophilobacter sediminis gen. nov., sp. nov., and strains Red259^T (=NBRC 114288^T = MCCC 1K05016^T) and Red421^T (=NBRC 114289^T = MCCC 1K06216^T) represent two novel independent species in the genus Geomonas, namely, Geomonas propionica sp. nov. and Geomonas anaerohicana sp. nov., respectively.     

Description of Aestuariivivens marinum sp. nov., Aestuariivivens sediminis sp. nov. and Aestuariivivens sediminicola sp. nov., three new species isolated from the upper layer of tidal flat sediment

Nine bacterial strains designated MT3-5-12^T, MT3-5-27, MTV1-9, S-DT1-15^T, S-DT1-34, MTV5-3^T, MTV4-17, MTV5-12 and MTV5-13 were isolated from the upper layer (1–5 cm in depth) of tidal flat sediment in Quanzhou Bay, China. The 16S rRNA gene of these strains shared maximum sequence similarities with Aestuariivivens insulae KCTC 42350^T of 94.9–97.1%. Phylogenetic analyses based on 16S rRNA gene sequences and 120 conserved concatenated proteins placed these strains in three novel phylogenetic clades affiliated to the genus Aestuariivivens of the family Flavobacteriaceae. Strains MT3-5-12^T, MT3-5-27 and MTV1-9 were phylogenetically close to A. insulae KCTC 42350^T. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strains MT3-5-12^Tand MTV1-9 and A. insulae KCTC 42350^T were estimated to be 78.5-78.7% and 22.5%, respectively. Strains S-DT1-15^T and S-DT1-34 formed a distinctly separated clade from A. insulae KCTC 42350^T. The ANI and dDDH values between strains S-DT1-15^T and S-DT1-34 and A. insulae KCTC 42350^T were 76.3–76.4% and 20.4–20.5%, respectively. The other four strains MTV5-3^T, MTV4-17, MTV5-12 and MTV5-13, formed a third novel clade, distinctly separated from A. insulae KCTC 42350^T. The ANI and dDDH values between strains MTV5-3^T and MTV4-17 and A. insulae KCTC 42350^T were 74.7% and 19.1–19.2%, respectively. The phylogenetic analyses and whole genomic comparisons, combined with phenotypic and chemotaxonomic features, strongly supported the nine strains could be classified as three novel species within the genus Aestuariivivens, for which the names Aestuariivivens marinum sp. nov. MT3-5-12^T, Aestuariivivens sediminis sp. nov. S-DT1-15^T, and Aestuariivivens sediminicola sp. nov. MTV5-3^T are proposed.     

Genomic insight into Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. isolated from farmed rainbow trout in Turkey

Four strains, designated as C-2, C-17^T, C-39^T and Ch-15, were isolated from farmed rainbow trout samples showing clinical signs during an investigation for a fish-health screening study. The pairwise 16S rRNA gene sequence analysis showed that strain C-17^T shared the highest identity level of 98.1 % with the type strain of Chryseobacterium piscium LMG 23089^T while strains C-2, C-39^T and Ch-15 were closely related to Chryseobacterium balustinum DSM 16775^T with an identity level of 99.3 %. A polyphasic approach involving phenotypic, chemotaxonomic and genome-based analyses was employed to determine the taxonomic provenance of the strains. The overall genome relatedness indices including dDDH and ANI analyses confirmed that strains C-2, C-17^T, C-39^T and Ch-15 formed two novel species within the genus Chryseobacterium. Chemotaxonomic analyses showed that strains C-17^T and C-39^T have typical characteristics of the genus Chryseobacterium by having phosphatidylethanolamine in their polar lipid profile, MK-6 as only isoprenoid quinone and the presence of iso-C_15:0 as major fatty acid. The genome size and G + C content of the strains ranged between 4.4 and 5.0 Mb and 33.5 – 33.6 %, respectively. Comprehensive genome analyses revealed that the strains have antimicrobial resistance genes, prophages and horizontally acquired genes in addition to secondary metabolite-coding gene clusters. In conclusion, based on the polyphasic analyses conducted on the present study, strains C-17^T and C-39^T are representatives of two novel species within the genus Chryseobacterium, for which the names Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. with the type strains C-17^T (=JCM 34190^T = KCTC 82250^T) and C-39^T (=JCM 34191^T = KCTC 822251^T), respectively, are proposed.     

Characterization of two novel pentose-fermenting and GABA-producing species: Levilactobacillus tujiorum sp. nov. and Secundilactobacillus angelensis sp. nov. Isolated from a solid-state fermented zha-chili

Lactobacilli are dominant in zha-chili. This study provides a taxonomic characterization of five bacterial strains isolated from zha-chili in China. The cells were Gram-positive, facultative anaerobic, non-spore-forming, flagella-free, catalase-negative, heterofermentative, pentose-fermenting, and gamma-aminobutyric acid (GABA)-producing rods. For HBUAS51241^T, HBUAS51329, and HBUAS51416, C_16:0, C_18:1 ω9c and C_19:0 iso were the predominant cellular fatty acids; diphosphatidylglycerol (DPG), phosphatidylglycerol (DP), glycolipids (GL), and glycolipids (AL) were the major phospholipids. While for HBUAS51383^T and HBUAS58055, C_16:0, C_18:1 ω9c, C_19:0 cyclo ω8c were the predominant cellular fatty acids; DPG, DP, GL, and AL were the major phospholipids. Strains HBUAS51241^T, HBUAS51329, and HBUAS51416 showed 98.1–99.1% 16S rRNA gene sequence similarity, 80.2–81.4% ANI, 87.7–90.0% AAI, and 23.8–32.8% digital DDH to their closest related type strains Levilactobacillus hammesii DSM 16381^T, Levilactobacillus parabrevis ATCC 53295^T, and Levilactobacillus fuyuanensis 244-4^T. Strains HBUAS51383^T and HBUAS58055 showed 98.7–99.5% 16S rRNA gene sequence similarity, 75.4–81.4% ANI, 75.5–89.1% AAI, and 19.7–24.0% digital DDH to their closest related type strains Secundilactobacillus silagincola IWT5^T, Secundilactobacillus silagei JCM 19001^T, Secundilactobacillus pentosiphilus IWT25^T, Secundilactobacillus mixtipabuli IWT30^T, Secundilactobacillus odoratitofui DSM 19909^T, and Secundilactobacillus similis DSM 23365^T. The central carbon metabolism pathways for the five strains were summarizeded. Based on the phenotypic, chemotaxonomic, and genomic data, we propose two novel species Levilactobacillus tujiorum sp. nov. whose type strain is HBUAS51241^T (=GDMCC 1.3022^T = JCM 35241^T), and Secundilactobacillus angelensis sp. nov. whose type strain is HBUAS51383^T (=GDMCC 1.3021^T = JCM 35209^T).     

Acetobacter oryzifermentans sp. nov., isolated from Korean traditional vinegar and reclassification of the type strains of Acetobacter pasteurianus subsp. ascendens (Henneberg 1898) and Acetobacter pasteurianus subsp. paradoxus (Frateur 1950) as Acetobacter ascendens sp. nov., comb. nov.

Twelve Acetobacter pasteurianus-related strains with publicly available genomes in GenBank shared high 16S rRNA gene sequence similarity (>99.59%), but average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) values and multilocus sequence- and genome-based relatedness analyses suggested that they were divided into four different phylogenetic lineages. Relatedness analyses based on multilocus sequences, 1,194 core genes and whole-cell MALDI-TOF profiles supported that strains LMG 1590^T and LMG 1591 (previously classified as the type strains of A. pasteurianus subsp. ascendens and paradoxus, respectively) and strain SLV-7^T do not belong to A. pasteurianus. Strain SLV-7^T, isolated from Korean traditional vinegar, shared low ANI (<91.0%) and in silico DDH (44.2%) values with all other Acetobacter type strains analyzed in this study, indicating that strain SLV-7^T represents a new Acetobacter species. The phenotypic and chemotaxonomic analyses confirmed these results and therefore a new species named Acetobacter oryzifermentans sp. nov. is proposed with SLV-7^T (= KACC 19301^T = JCM 31096^T) as the type strain. Strains LMG 1590^T and LMG 1591 shared high ANI (99.4%) and in silico DDH (96.0%) values between them, but shared low ANI (<92.3%) and in silico DDH (<49.0%) values with other type strains analyzed in this study, indicating that strains LMG 1590^T and LMG 1591 should be reclassified into a new single species that should be named Acetobacter ascendens sp. nov., comb. nov., with LMD 51.1^T (= LMG 1590^T = NCCB 51001^T) as its type strain.     

Two new Polyangium species,P. aurulentum sp. nov. and P. jinanense sp. nov., isolated from a soil sample

Polyangium belongs to Polyangiaceae family of Myxococcales, a taxonomic group well-known for their extraordinary social lifestyle and diverse novel gene clusters of secondary metabolites. A yellow-golden strain, designated SDU3-1^T, and two rose pink strains, designated SDU13 and SDU14^T, were isolated from a soil sample. These three strains were aerobic, mesophilic, not salt-tolerant and were able to prey on living microorganisms. SDU13 and SDU14^T formed solitary sporangioles under starvation conditions, while SDU3-1^T had no fruiting body structures. They showed 95.9–97.0% (SDU3-1^T) or 98.7–98.9% (SDU13 and SDU14^T) 16S rRNA gene similarity with the type strains of Polyangium, but were phylogenetically separate from them based on the 16S rRNA gene and genome sequences. Their genomes were 12.3 Mbp (SDU3-1^T), 13.9 Mbp (SDU13) and 13.8 Mbp (SDU14^T) with the G + C content range of 68.3–69.4 mol%. The average nucleotide identity and DNA-DNA hybridization analyses of genomes further indicated that these three strains belonged to two new species in Polyangium. Their major fatty acids were C_18:1ω9c, C_16:0 and C_18:0. The polyphasic taxonomic characterization suggest that the three strains represent two novel species in the genus Polyangium, for which the names Polyangium aurulentum sp. nov. and Polyangium jinanense sp. nov. are proposed, and the type strains are SDU3-1^T (=CGMCC 1.16875^T = KCTC 72136^T) and SDU14^T (=CCTCC AB 2021123^T = KCTC 82625^T), respectively.     

Description and genomic characterization of Nocardioides bruguierae sp. nov., isolated from Bruguiera gymnorhiza

Strains BSK12Z-3^T and BSK12Z-4, two Gram-stain-positive, aerobic, non-spore-forming strains, were isolated from Shankou Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. The diagnostic diamino acid in the cell-wall peptidoglycan of strain BSK12Z-3^T was LL-diaminopimelic acid and MK-8(H₄) was the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phospholipid (PL). The major fatty acids was iso-C_16:0. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the two strains fell within the genus Nocardioides, appearing most closely related to Nocardioides ginkgobilobae KCTC 39594^T (97.5–97.6 % sequence similarity) and Nocardioides marinus DSM 18248^T (97.4–97.6 %). Genome-based phylogenetic analysis confirmed that strains BSK12Z-3^T and BSK12Z-4 formed a distinct phylogenetic cluster within the genus Nocardioides. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strains BSK12Z-3^T, BSK12Z-4 with their most related species N. marinus DSM18248^T were within the ranges of 77.2–77.3 % and 21.3–21.4 %, respectively, clearly indicated that strains BSK12Z-3^T, BSK12Z-4 represented novel species. Strains BSK12Z-3^T and BSK12Z-4 exhibited 99.9 % 16S rRNA gene sequence similarity. The ANI and dDDH values between the two strains were 97.8 % and 81.1 %, respectively, suggesting that they belong to the same species. However, DNA fingerprinting discriminated that they were not from one clonal origin. Based on phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizatons, strains BSK12Z-3^T and BSK12Z-4 could be classified as a novel species of the genus Nocardioides, for which the name Nocardioides bruguierae sp. nov., is proposed. The type strain is BSK12Z-3^T (=CGMCC 4.7709^T = JCM 34554^T).     

Thaumasiovibrio occultus gen. nov. sp. nov. and Thaumasiovibrio subtropicus sp. nov. within the family Vibrionaceae,isolated from coral reef seawater off Ishigaki Island,Japan

Two phylogenetically distinct Vibrionaceae strains C4II189^T and C4V358^T isolated from reef seawater off Ishigaki Island, Japan, in 2014 were studied with advanced genome-based taxonomy approaches. All aspects of phylogenetic (16S rRNA phylogeny, MLSA), phenotypic and genetic (ANI, DDH, AAI, and the number of core genes) cohesions between the two identified species were high enough to propose them as members of a new genus within the family Vibrionaceae. Consequently, an eighth genus Thaumasiovibrio gen. nov. is proposed that contains two new species Thaumasiovibrio occultus sp. nov. strain C4II189^T (=DSM 101554^T = JCM 31629^T) (type species) and Thaumasiovibrio subtropicus sp. nov. strain C4V358^T (=DSM 101555^T = JCM 31630^T). Thaumasiovibrio species were phylogenetically distinct from the other Vibrionaceae species based on pyrH gene sequences. The combination of catalase negative, sensitivity to vibriostatic agent O/129, and green colony formation on TCBS for the phylogenetically affiliated strains was the diagnostic features for the current tentative identification of this genus.     

Burkholderia semiarida sp. nov. and Burkholderia sola sp. nov., two novel B. cepacia complex species causing onion sour skin

Two putative novel Burkholderia cenocepacia lineages found in the semi-arid region of north-east Brazil causing onion sour skin were studied using genomic approaches to determine their taxonomic position. Four strains belonging to one novel lineage (CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171) and one strain (CCRMBC51) belonging to another novel lineage had their whole genome sequenced to carry out taxogenomic analyses. The phylogenomic tree built using the type (strain) genome server (TYGS) clustered the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171 into the same clade, while grouped the strain CCRMBC51 separately. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analysis showed values above 99.21 % and 93.2 %, respectively, among the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171, while ANI and dDDH values between these strains and the strain CCRMBC51 were below 94.49 % and 56.6 %, respectively. All these strains showed ANI and dDDH values below 94.78 % and 58.8 % concerning type strains of the B. cepacia complex (Bcc) species. The phylogenetic maximum likelihood tree constructed based on the multilocus sequence analysis of core genes (cMLSA) clustered the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171 and the strain CCRMBC51 in two exclusive clades, which did not cluster with any known species of the Bcc. Therefore, combined data from TYGS, ANI, dDDH, and cMLSA demonstrated that the strains represent two novel species of the Bcc, which we classified as Burkholderia semiarida sp. nov. and Burkholderia sola sp. nov., and proposed the strains CCRMBC74^T (=IBSBF 3371 ^T = CBAS 905 ^T) and CCRMBC51^T (=IBSBF3370^T = CBAS 904 ^T) as type strains, respectively.     

Neptuniibacter pectenicola sp. nov. and Neptuniibacter marinus sp. nov., two novel species isolated from a Great scallop (Pecten maximus) hatchery in Norway and emended description of the genus Neptuniibacter.

Nine isolates obtained from a great scallop hatchery in Norway were characterized using a polyphasic approach. Strains were Gram-negative, aerobic and motile rods with oxidative metabolism. Phylogenetic analysis based on the sequences of 16S rRNA and rpoB genes showed that these strains formed two different groups associated with members of the genus Neptuniibacter. DNA–DNA hybridization (DDH) and Average Nucleotide Identity (ANI) demonstrated that the isolates constituted two novel species of this genus, which can be phenotypically differentiated from their closest relatives. The names Neptuniibacter marinus sp. nov. and Neptuniibacter pectenicola sp. nov are proposed, with ATR 1.1^T (=CECT 8938^T = DSM 100783^T) and LFT 1.8^T (=CECT 8936^T = DSM 100781^T) as respective type strains.     

Description of Tropicibacter mediterraneus sp. nov. and Tropicibacter litoreus sp. nov.

Four strains (M15∅_3, M17^T, M49 and R37^T) were isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. Together with an older preserved isolate (strain 2OM6) from cultured oysters at Vinaroz, Castellón, Spain, the strains were thoroughly characterized in a polyphasic study and were placed phylogenetically within the Roseobacter clade in the family Rhodobacteraceae. Highest 16S rRNA sequence similarities of the five strains to the types of any established species corresponded to Tropicibacter multivorans (95.8–96.4%), Phaeobacter inhibens (95.9–96.3%) and Phaeobacter gallaeciensis (95.9–96.2%). On the other hand, whole genome (ANI) and protein fingerprinting (MALDI-TOF) data proved: (i) non clonality among the strains, and (ii) the existence of two genospecies, one consisting of strains M15∅_3, M17^T, M49 and 2OM6 and another one consisting of strain R37^T. Phenotypic traits determined allow differentiating both genospecies from each other and from closely related taxa. In view of all data collected we propose to accommodate these isolates in two species as members of the genus Tropicibacter, Tropicibacter mediterraneus sp. nov. (type strain M17^T = CECT 7615^T = KCTC 23058^T) and Tropicibacter litoreus sp. nov. (type strain R37^T = CECT 7639^T = KCTC 23353^T).     

Genomic description and characterization of Nigeribacterium massiliense gen. nov., sp. nov., isolated from the human gut

Strain Marseille-P1302 was isolated from the stool of a 2-year-old Nigerian boy suffering from Kwashiorkor, a form of severe acute malnutrition. The strain grows in aerobic atmosphere and bacterial cells are Gram-positive cocci ranging in diameter from 0.8 to 1 μm. Among species with standing in nomenclature, strain Marseille-P1302 exhibited a highest 16S rRNA sequence similarity of 94.97% with Brevilactibacter flavus strain VG341^T, but was phylogenetically-closest to Brevilactibacter sinopodophylli strains KCTC 33808^T. The draft genome of strain Marseille-P1302 was 2,934,258-bp-long with a 70.38% G + C content, and contained 2704 protein-coding genes and 55 RNAs that included 9 rRNA genes. On the basis of these data, we propose the creation of the new genus Nigeribacterium gen. nov., with strain Marseille-P1302^T (= CSUR P1302 = DSM 29084) being the type strain of the new species Nigeribacterium. massiliense gen. nov., sp. nov.     

Arthrospiribacter ruber gen. nov., sp. nov., a novel bacterium isolated from Arthrospira cultures

Polyphasic analysis of ten isolates of the red-pigmented bacteria isolated from ten Arthrospira cultures originating from different parts of the world is described. The 16S rRNA analysis showed <95 % identity with the known bacteria on public databases, therefore, additional analyses of fatty acids profiles, MALDI-TOF/MS, genome sequencing of the chosen isolate and following phylogenomic analyses were performed. Gram-stain-negative, strictly aerobic rods were positive for catalase, negative for oxidase, proteolytic and urease activity. Major fatty acids were 15 : 0 iso, 17:0 iso 3 OH and 17:1 iso w9c/16:0 10-methyl. The whole phylogenomic analyses revealed that the genomic sequence of newly isolated strain DPMB0001 was most closely related to members of Cyclobacteriaceae family and clearly indicated distinctiveness of newly isolated bacteria. The average nucleotide identity and in silico DNA–DNA hybridisation values were calculated between representative of the novel strains DPMB0001 and its phylogenetically closest species, Indibacter alkaliphilus CCUG57479 (LW1)^T (ANI 69.2 % is DDH 17.2 %) and Mariniradius saccharolyticus AK6^T (ANI 80.02 % isDDH 26.1 %), and were significantly below the established cut-off <94 % (ANI) and <70 % (isDDH) for species and genus delineation.The obtained results showed that the analysed isolates represent novel genus and species, for which names Arthrospiribacter gen nov. and Arthrospiribacter ruber sp. nov. (type strain DPMB0001 = LMG 31078 = PCM 3008) is proposed.     

Description of Aureibaculum luteum sp. nov. and Aureibaculum flavum sp. nov. isolated from Antarctic intertidal sediments

Two Gram-stain-negative, aerobic, non-motile, and rod-shaped bacterial strains, designated SM1352^T and A20^T, were isolated from intertidal sediments collected from King George Island, Antarctic. They shared 99.8% 16S rRNA gene sequence similarity with each other and had the highest sequence similarity of 98.1% to type strain of Aureibaculum marinum but?<?93.4% sequence similarity to those of other known bacterial species. The genomes of strains SM1352^T and A20^T consisted of 5,108,092 bp and 4,772,071 bp, respectively, with the G?+?C contents both being 32.0%. They respectively encoded 4360 (including 37 tRNAs and 6 rRNAs) and 4032 (including 36 tRNAs and 5 rRNAs) genes. In the phylogenetic trees based on 16S rRNA gene and single-copy orthologous clusters (OCs), both strains clustered with Aureibaculum marinum and together formed a separate branch within the family Flavobacteriaceae. The ANI and DDH values between the two strains and Aureibaculum marinum BH-SD17^T were all below the thresholds for species delineation. The major cellular fatty acids (>?10%) of the two strains included iso-C_15:0, iso-C_15:1 G, iso-C_17:0 3-OH. Their polar lipids predominantly included phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified aminolipid, and two unidentified lipids. Genomic comparison revealed that both strains possessed much more glycoside hydrolases and sulfatase-rich polysaccharide utilization loci (PULs) than Aureibaculum marinum BH-SD17^T. Based on the above polyphasic evidences, strains SM1352^T and A20^T represent two novel species within the genus Aureibaculum, for which the names Aureibaculum luteum sp. nov. and Aureibaculum flavum sp. nov. are proposed. The type strains are SM1352^T (=?CCTCC AB 2014243 ^T?=?JCM 30335 ^T) and A20^T (=?CCTCC AB 2020370 ^T?=?KCTC 82503 ^T), respectively.

     

Nonlabens marina sp. nov., a novel member of the Flavobacteriaceae isolated from the Pacific Ocean

Two aerobic, Gram-negative, orange pigmented and irregular rod-shaped bacteria, designated S1-05 and S1-08^T, were isolated from seawater from the Pacific Ocean. Phylogenetic analysis based on their 16S rRNA gene sequences revealed that the novel isolates could be affiliated with the genus Nonlabens of the family Flavobacteriaceae. The strains S1-05 and S1-08^T shared 100 % pairwise sequences similarity with each other and showed less than 96.8 % similarity with the cultivated members of the genus Nonlabens. The novel isolates are phenotypically and physiologically different from strains described previously. The strains were found to be non-motile, oxidase positive, catalase positive and hydrolyzed gelatin and aesculin. The G+C contents of the DNA were determined to 41.4 and 41.7 mol% and MK-6 the predominant menaquinone. Anteiso-C15:0 and iso-C15:0 were found to be the major two cellular fatty acids. On the basis of polyphasic taxonomic studies, it was concluded that strains S1-05 and S1-08^T represent a novel species within the genus Nonlabens, for which the name Nonlabens marina sp. nov. is proposed. The type strain of N. marina is S1-08^T (=KCTC 23432^T = NBRC 107738^T).     

Vibrio aestivus sp. nov. and Vibrio quintilis sp. nov., related to Marisflavi and Gazogenes clades,respectively

Two new Vibrio species, Vibrio aestivus and Vibrio quintilis, are described after a polyphasic characterization of strains M22^T, M61 and M62^T, isolated from seawater collected off a beach on the East coast of Spain (Valencia). All three strains are Gram negative, mesophilic, slightly halophilic, fermentative rods. V. aestivus (M22^T = CECT 7558^T = CAIM 1861^T = KCTC 23860^T and M61 = CECT 7559 = CAIM 1862 = KCTC 23861) is oxidase positive, reduces nitrates to nitrites, is negative for Voges Proskauer, arginine dihydrolase and indole and non hydrolytic on most substrates tested. The 16S rRNA gene sequences of M22^T and M61 are most similar to Vibrio marisflavi (97.1–97.2%) but phylogenetic analysis using NJ, MP and ML methods display Vibrio stylophorae (96.2% similarity) as sibling species. The three species form a deep clade in the genus Vibrio. Average Nucleotide Identity (ANI) values, determined as a measure of overall genomic resemblance, confirmed that strains M22^T and M61 are members of the same species, different to V. marisflavi CECT 7928^T.V. quintilis (M62^T = CECT 7734^T = CAIM 1863^T = KCTC 23833^T) is aerogenic, arginine dihydrolase and Voges Proskauer positive, oxidase negative and unable to reduce nitrate, traits shared by most species in the Gazogenes clade. It is unpigmented and does not grow on TCBS Agar. 16S rRNA gene similarities to its nearest species, Vibrio aerogenes and Vibrio mangrovi, are 97.6% and 96.0% respectively. Strain M62^T and V. aerogenes CECT 7868^T display ANI values well below the 95% boundary for genomic species.