- Volume 73, Issue 2, 2023

Novel Corynebacterium strains, 3BT and 7BT, were isolated from the oral cavities of young chicks of yellow-eyed penguins (hoiho), Megadyptes antipodes. A polyphasic taxonomic characterization of these strains revealed chemotaxonomic, biochemical and morphological features that are consistent with those of the genus Corynebacterium . The 16S rRNA gene sequence similarity values between the strains and their closest phylogenetic neighbour, Corynebacterium ciconiae CCUG 47525T were 99.07 %, values that are in line with their phylogenomic positions within the evolutionary radiation of the genus Corynebacterium . Digital DNA–DNA hybridization values and average nucleotide identities between the genome sequences of the two strains and related Corynebacterium species were well below the defined threshold values (70 and 95–96 %, respectively) for prokaryotic species delineation. The genome size of these strains varied between 2.45–2.46 Mb with G+C content 62.7–62.9 mol%. Strains 3BT and 7BT were Gram-stain positive bacilli that were able to grow in presence of 0–10 % (w/v) NaCl and at temperature ranging between 20–37 °C. The major fatty acids (>15 %) were C16 : 0 and C18 : 1  ω9c, and the mycolic acid profile included 32–36 carbon atoms. We propose that these strains represent a novel species, Corynebacterium megadyptis sp. nov. with 3BT (=DSM 111184T=NZRM 4755T) as the type strain. Phylogenomically, strains 3BT and 7BT belong to two lineages with subtle differences in MALDI-TOF spectra, chemotaxonomic profiles and phenotypic properties. The fatty acid profile of strain 3BT contains C18 : 0 as a predominant type (>15 %), which is a minor component in strain 7BT. Strain 7BT can oxidize N-acetyl-d-glucosamine, l-serine, α-hydroxy-butyric acid, l-malic acid, l-glutamic acid, bromo-succinic acid and l-lactic acid, characteristics not observed in strain 3BT. Therefore, we propose that these strains represent two subspecies, namely Corynebacterium megadyptis subsp. megadyptis subsp. nov. (type strain, 3BT=DSM 111184T=NZRM 4755T) and Corynebacterium megadyptis subsp. dunedinense subsp. nov. (type strain, 7BT=DSM 111183T=NZRM 4756T).

A novel actinobacterium, designated HIs16-36T, was isolated from the rhizosphere of a mangrove on Ishigaki Island, Okinawa, Japan, and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain HIs16-36T was closely related to the members of the genus Arthrobacter . The highest 16S rRNA gene sequence similarity was observed with Arthrobacter crystallopoietes (98.5 %), followed by Arthrobacter globiformis (97.2 %). The peptidoglycan of strain HIs16-36T was of the A4α type, with lysine as the diagnostic diamino acid. The predominant isoprenoid quinone was MK-9(H2) and the major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two glycolipids. These chemotaxonomic features corresponded to those of the genus Arthrobacter . Meanwhile, the differences in some phenotypic characteristics, along with the results of average nucleotide identity and digital DNA–DNA hybridization analyses, indicated that strain HIs16-36T should be distinguished from the recognized species of the genus Arthrobacter . Therefore, strain HIs16-36T represents a novel species of the genus Arthrobacter , for which the name Arthrobacter mangrovi sp. nov. is proposed. The type strain is HIs16-36T (=NBRC 112813T=TBRC 15750T).

A novel Gram-stain-negative, thin-rod-shaped, aerobic, non-motile and yellow-pigmented marine bacterium (designated strain 2012CJ35-5T) was isolated from a marine sponge Callyspongia elongata sampled in Jeju-do, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 2012CJ35-5T belonged to the family Flavobacteriaceae , and was most closely related to Muricauda olearia KCCM 90075T (96.3 %), Muricauda alvinocaridis JCM 33425T (95.7 %), Muricauda flava KCTC 22665T (95.6 %), Muricauda koreensis KCTC 52351T (95.6 %) and Muricauda eckloniae KCTC 22266T (94.9 %). Average nucleotide identity, amino acid identities and digital DNA–DNA hybridization between strain 2012CJ35-5T and the closest related strain were 72.6, 73.6 and 17.3 % respectively, indicating that strain 2012CJ35-5T represents a novel species of the genus Muricauda . The genome size of strain 2012CJ35-5T is 3.8 Mbp and the G+C content is 43.9 mol%. Strain 2012CJ35-5T contained menaquinone 6 as the major respiratory quinone and phosphatidylethanolamine, four unidentified aminophospholipids and five unidentified lipids as major polar lipids. The fatty acids were mainly (>15 %) defined as C15 : 0 iso (31.7 %), C15 : 1 iso G (29.2 %) and C17 : 0 iso 3OH (18.0 %). Strain 2012CJ35-5T could be distinguished from the other members of the genus Muricauda by a number of chemotaxonomic and phenotypic characteristics. Based on the results of polyphasic taxonomic analysis, strain 2012CJ35-5T (=KACC 22643T=LMG 32584T) represents a novel species within the genus Muricauda , for which the name Muricauda spongiicola sp. nov. is proposed.

A Gram-stain-negative or -positive, strictly anaerobic, non-spore-forming and pleomorphic bacterium (designated 14-104T) was isolated from the saliva sample of a patient with oral squamous cell carcinoma. It was an acid-tolerant neutralophilic mesophile, growing at between 20 and 40 °C (with optimum growth at 30 °C) and pH between pH 3.0 and 7.0 (with optimum growth at pH 6.0–7.0). It contained anteiso-C15 : 0 and C15 : 0 as the major fatty acids. The genome size of strain 14-104T was 2.98 Mbp, and the G+C content was 39.6 mol%. It shared <87 % 16S rRNA sequence similarity, <71 % orthologous average nucleotide identity, <76 % average amino acid identity and <68 %% of conserved proteins with its closest relative, Phocaeicola abscessus CCUG 55929T. Reconstruction of phylogenetic and phylogenomic trees revealed that strain 14-104T and P. abscessus CCUG 55929T were clustered as a distinct clade without any other terminal node. The phylogenetic and phylogenomic analyses along with physiological and chemotaxonomic data indicated that strain 14-104T represents a novel species in the genus Phocaeicola , for which the name Phocaeicola oris sp. nov. is proposed. The type strain is 14-104T (=BCRC 81305T= NBRC 115041T).

A rod-shaped, non-motile, Gram-negative bacterium, strain RS28T, was isolated from rice straw used as material for periphyton growth. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain RS28T was affiliated with the genus Mucilaginibacter and had the highest sequence similarity to Mucilaginibacter ginkgonis HMF7856T (96.47 %) and Mucilaginibacter polytrichastri DSM 26907T (96.12 %). Strain RS28T was found to grow at pH 5.5–8.0, 17–40 °C and in the presence of 0–1.5 % (w/v) NaCl. Strain RS28T contained summed feature 3 (comprising C16 : 1  ω7c and/or C16 : 1  ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids (> 10.0 %). The major polar lipids were phosphatidylethanolamine, two unidentified phospholipids, two unidentified aminophospholipids, three unidentified aminolipids and one unidentified lipid. The respiratory quinone was menaquinone 7. The genomic DNA G+C content was 44.7 mol%. Strain RS28T possessed six putative secondary metabolite gene clusters involved in the synthesis of resorcinol, NRPS-like, terpene, lassopeptide, T3PKS and arylpolyene. On the basis of the phenotypic, chemotaxonomic, and phylogenetic characteristics, strain RS28T represents a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter straminoryzae sp. nov. is proposed. The type strain is RS28T (=KCTC 92039T=LMG 32424T).

The human gastrointestinal tract is inhabited by various microorganisms, including thousands of bacterial taxa that have yet to be cultured and characterized. In this report, we describe the isolation, cultivation, genotypic and phenotypic characterization and taxonomy of five novel anaerobic bacterial strains that were recovered during the massive cultivation and isolation of gut microbes from human faecal samples. On the basis of the polyphasic taxonomic results, we propose two novel genera and five novel species. They are Acidaminococcus hominis sp. nov. (type strain NSJ-142T=CGMCC 1.17903T=KCTC 25346T), Amedibacillus hominis sp. nov. (type strain NSJ-176T=CGMCC 1.17933T=KCTC 25355T), Lientehia hominis gen. nov. sp. nov. (type strain NSJ-141T=CGMCC 1.17902T=KCTC 25345T), Merdimmobilis hominis gen. nov. sp. nov. (type strain NSJ-153T=CGMCC 1.17915T=KCTC 25350T) and Paraeggerthella hominis sp. nov. (type strain NSJ-152T=CGMCC 1.17914T=KCTC 25349T).

A novel Gram-positive, aerobic, rod-shaped, non-motile, endospore-forming salt-tolerant bacterium strain (80T), was isolated from woodland soil collected near Kanas lake in the Altay region of Xinjiang, PR China. The strain grew at 15−45 °C, pH6.0–9.0 and with 0–14 % (w/v) NaCl. The complete genome size of the novel strain was 4 031 766 bp including a circle chromosome and a circle plasmid. The genomic DNA G+C content was 38.99 mol %. Phylogenetic analysis based on 16S rRNA gene sequence and genome showed that strain 80T has the highest similarity to Radiobacillus deserti TKL69T. However, the novel strain showed an average nucleotide identity value of 78.65 % (lower than 95 %) and a digital DNA–DNA hybridization value of 22.30 % with R. deserti TKL69T based on the genome sequences. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17:0 and C16 : 1 ω7c alcohol. The only respiratory quinone was MK-7. The cell wall peptidoglycan was meso-diaminopimelic acid. Diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid, one unidentified aminophospholipid and two unidentified glycolipids were identified as the major polar lipids. The phylogenetic, phenotypic and chemotaxonomic analyses showed that strain 80T represents a novel species of the genus Radiobacillus and the name Radiobacillus kanasensis sp. nov. is proposed. The type strain is 80T (=GDMCC 1.2844T=JCM 35077T).

Six strains, KI11_D11T, KI4_B1, KI11_C11T, KI16_H9T, KI4_A6T and KI3_B9T, were isolated from insects and flowers on Kangaroo Island, South Australia. On the basis of 16S rRNA gene phylogeny, strains KI11_D11T, KI4_B1, KI11_C11T, KI16_H9T, KI4_A6T were found to be closely related to Fructilactobacillus ixorae Ru20-1T. Due to the lack of a whole genome sequence for this species, whole genome sequencing of Fructilactobacillus ixorae Ru20-1T was undertaken. KI3_B9T was found to be closely related to Fructobacillus tropaeoli F214-1T. Utilizing core gene phylogenetics and whole genome analyses, such as determination of AAI, ANI and dDDH, we propose that these six isolates represent five novel species with the names Fructilactobacillus cliffordii (KI11_D11T= LMG 32130T = NBRC 114988T), Fructilactobacillus hinvesii (KI11_C11T = LMG 32129T = NBRC 114987T), Fructilactobacillus myrtifloralis (KI16_H9T= LMG 32131T = NBRC 114989T) Fructilactobacillus carniphilus (KI4_A6T = LMG 32127T = NBRC 114985T) and Fructobacillus americanaquae (KI3_B9T = LMG 32124T = NBRC 114983T). Chemotaxonomic analyses detected no fructophilic characters for these strains of member of the genus Fructilactobacillus . KI3_B9T was found to be obligately fructophilic, similarly to its phylogenetic neighbours in the genus Fructobacillus . This study represents the first isolation, to our knowledge, of novel species in the family Lactobacillaceae from the Australian wild.

A novel sulphur-reducing bacterium was isolated from a pyrite-forming enrichment culture inoculated with sewage sludge from a wastewater treatment plant. Based on phylogenetic data, strain J.5.4.2-T.3.5.2T could be affiliated with the phylum Synergistota . Among type strains of species with validly published names, the highest 16S rRNA gene sequence identity value was found with Aminiphilus circumscriptus ILE-2T (89.2 %). Cells of the new isolate were Gram-negative, non-spore-forming, straight to slightly curved rods with tapered ends. Motility was conferred by lateral flagella. True branching of cells was frequently observed. The strain had a strictly anaerobic, asaccharolytic, fermentative metabolism with peptides and amino acids as preferred substrates. Sulphur was required as an external electron acceptor during fermentative growth and was reduced to sulphide, whereas it was dispensable during syntrophic growth with a Methanospirillum species. Major fermentation products were acetate and propionate. The cellular fatty acid composition was dominated by unsaturated and branched fatty acids, especially iso-C15 : 0. Its major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and distinct unidentified polar lipids. Respiratory lipoquinones were not detected. Based on the obtained data we propose the novel species and genus Aminithiophilus ramosus, represented by the type strain J.5.4.2-T.3.5.2T (=DSM 107166T=NBRC 114655T) and the novel family Aminithiophilaceae fam. nov. to accommodate the genus Aminithiophilus. In addition, we suggest reclassifying certain members of the Synergistaceae into new families to comply with current standards for the classification of higher taxa. Based on phylogenomic data, the novel families Acetomicrobiaceae fam. nov., Aminiphilaceae fam. nov., Aminobacteriaceae fam. nov., Dethiosulfovibrionaceae fam. nov. and Thermovirgaceae fam. nov. are proposed.

A novel endophytic bacterium, designated strain BGMRC 0089T, was isolated from a surface-sterilized root of Sonneratia apetala. Cells were observed to be Gram-negative, rod-shaped and motile with polar flagella. Strain BGMRC 0089T was found to grow optimally at 28–30 °C, pH 7.0–8.0 and in the presence of 1 % (w/v) NaCl. Strain BGMRC 0089T contained ubiquinone Q-10 and the predominant fatty acid was summed feature 8. The polar lipid profile of strain BGMRC 0089T was found to contain diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine and phosphatidylethanolamine. Based on the results of 16S rRNA gene analysis, this isolate has the closest phylogenetic relationships with Rhizobium lemnae L6-16T (96.5 %) and Allorhizobium oryziradicis N19T (96.4 %). Average nucleotide identity, amino acid identity and digital DNA–DNA hybridization values of the isolate with the type strains of the genera Rhizobium and Allorhizobium were below 84.6, 73.9 and 22.1  %, respectively. Analysis the 4.55 Mb draft genome of strain BGMRC 0089T revealed several plant-associated genes, which may play important roles for the plant in the adaptation to the mangrove habitat. Based on its distinct phylogenetic, phenotypic and chemotaxonomic characteristics, strain BGMRC 0089T is proposed to represent a novel Allorhizobium species, for which the name Allorhizobium sonneratiae sp. nov. is proposed (type strain BGMRC 0089T=DSM 100171T=MCCC 1K04805T).

A Gram-stain-negative, rod-shaped bacterial strain, designated Vibrio floridensis IRLE0018 (=NRRL B-65642=NCTC 14661), was isolated from a cyanobacterial bloom along the Indian River Lagoon (IRL), a large and highly biodiverse estuary in eastern Florida (USA). The results of phylogenetic, biochemical, and phenotypic analyses indicate that this isolate is distinct from species of the genus Vibrio with validly published names and is the closest relative to the emergent human pathogen, Vibrio vulnificus . Here, we present the complete genome sequence of V. floridensis strain IRLE0018 (4 535 135 bp). On the basis of the established average nucleotide identity (ANI) values for the determination of different species (ANI <95 %), strain IRLE0018, with an ANI of approximately 92 % compared with its closest relative, V. vulnificus , represents a novel species within the genus Vibrio . To our knowledge, this represents the first time this species has been described. The results of genomic analyses of V. floridensis IRLE0018 indicate the presence of antibiotic resistance genes and several known virulence factors, however, its pathogenicity profile (e.g. survival in serum, phagocytosis avoidance) reveals limited virulence potential of this species in contrast to V. vulnificus .

Bacterial strain Y-6T, isolated from a landfill site in Yiwu, PR China, was characterized using a polyphasic taxonomy approach. Cells were Gram-stain-negative, aerobic, rod-shaped, motile by means of a single polar flagellum and formed pale beige colonies. Strain Y-6T grew at 4–40 °C (optimal at 30–37 °C), pH 6.5–9.5 (optimal at pH 7.2–8.5) and in the presence of 0.5–10.0 % (w/v) NaCl (optimal at 1.0–3.0 %). Phylogenetic analysis revealed that strain Y-6T was a member of the genus Aliidiomarina and closely related to Aliidiomarina taiwanensis MCCC 1A06493T with a 16S rRNA sequence similarity of 98.2 %. The major cellular fatty acids of the isolate were iso-C15 : 0, C16 : 0, iso-C17 : 0 and summed feature 9 (iso-C17 : 1  ω9c and/or 10-methyl-C16 : 0). Q-8 was the predominant ubiquinone. The major polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminoglycophospholipid, aminophospholipid, phospholipid, three glycolipids and two unknown lipids. The genomic DNA G+C content was 46.6 mol%. The digital DNA–DNA hybridization value between Y-6T and A. taiwanensis MCCC 1A06493T was 18.3 %. Strain Y-6T had an average nucleotide identity value of 74.09 % with A. taiwanensis MCCC 1A06493T. Results from the polyphasic taxonomy study support the conclusion that strain Y-6T represents a novel Aliidiomarina species, for which the name Aliidiomarina quisquiliarum sp.nov. is proposed. The type strain is Y-6T (=MCCC 1K06228T=KCTC 82676T).

Two anaerobic, tetrachloroethene- (PCE-) respiring bacterial isolates, designated strain ACSDCE T and strain ACSTCE, were characterized using a polyphasic approach. Cells were Gram-stain-negative, motile, non-spore-forming and shared a vibrioid- to spirillum-shaped morphology. Optimum growth occurred at 30 °C and 0.1–0.4 % salinity. The pH range for growth was pH 5.5–7.5, with an optimum at pH 7.2. Hydrogen, formate, pyruvate and lactate as electron donors supported respiratory reductive dechlorination of PCE to cis-1,2-dichloroethene (cDCE) in strain ACSDCE T and of PCE to trichloroethene (TCE) in strain ACSTCE. Both strains were able to grow with pyruvate under microaerobic conditions. Nitrate, elemental sulphur, and thiosulphate were alternative electron acceptors. Autotrophic growth was not observed and acetate served as carbon source for both strains. The major cellular fatty acids were C16 : 1  ω7c, C16 : 0, C14 : 0 and C18 : 1  ω7c. Both genomes feature a circular plasmid. Strains ACSDCE T and ACSTCE were previously assigned to the candidate species 'Sulfurospirillum acididehalogenans'. Here, based on key genomic features and pairwise comparisons of whole-genome sequences, including average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity, strains ACSDCE T and ACSTCE, 'Ca. Sulfurospirillum diekertiae' strains SL2-1 and SL2-2, and the unclassified   Sulfurospirillum   sp. strain SPD-1 are grouped into one distinct species separate from previously described   Sulfurospirillum   species. Compared to   Sulfurospirillum multivorans   and   Sulfurospirillum halorespirans  , which dechlorinate PCE to cDCE without substantial TCE accumulation, these five strains produce TCE or cDCE as the end product. In addition, some cellular fatty acids (e.g., C16 : 0 3OH, C17 : 0 iso 3OH, C17 : 0 2OH) were detected in strains ACSDCE T and ACSTCE but not in other   Sulfurospirillum   species. On the basis of phylogenetic, physiological and phenotypic characteristics, 'Ca. Sulfurospirillum acididehalogenans' and 'Ca. Sulfurospirillum diekertiae' are proposed to be merged into one novel species within the genus   Sulfurospirillum  , for which the name   Sulfurospirillum diekertiae   sp. nov. is proposed. The type strain is ACSDCE T (=JCM 33349T= KCTC 15819T=CGMCC 1.5292T).

Acetic acid bacteria (family Acetobacteraceae ) are found in the gut of most insects. Two clades are currently recognized: Commensalibacter–Entomobacter and Bombell a– Oecophyllibacter . The latter group is only found in hymenopteran insects and the described species have been isolated from bees and ants. In this study, two new strains DDB2-T1T (=KACC 21507T=LMG 31759T) and DM15PD (=CCM 9165=DSM 112731=KACC 22353=LMG 32454) were isolated from wasps collected in the Republic of Korea and Germany, respectively. Molecular and phenotypic analysis revealed that the strains are closely related, with 16S rRNA gene sequences showing 100 % identity and genomic average nucleotide identity (ANI) values ≥99 %. The closest related species based on type strain 16S rRNA gene sequences are Swingsia samuiensis , Acetobacter peroxydans , Bombella favorum and Bombella intestini (94.8–94.7% identity), whereas the closest related species based on type strain genome analysis are Saccharibacter floricola and Bombella intestini (ANI values of 68.8 and 68.2 %, respectively). The reconstruction of a phylogenomic tree based on 107 core proteins revealed that the branch leading to DDB2-T1T and DM15PD is localized between Oecophyllibacter and Saccharibacter–Bombella. Further genomic distance metrics such as ANI, percentage of conserved proteins and alignment fraction values were consistent with these strains belonging to a new genus. The key phenotypic characteristics were one MALDI-TOF-MS peak (m/z=4601.9±2.0) and the ability to produce acid from d-arabinose. Based on this polyphasic approach, including phylogenetics, phylogenomics, genome distance calculations, ecology and phenotypic characteristics, we propose to name the novel strains Aristophania vespae gen. nov., sp. nov., with the type strain DDB2-T1T (=KACC 21507T=LMG 31759T).

The bacterial strain In5T was previously isolated from a suppressive potato field in southern Greenland and has been characterized and described as Pseudomonas fluorescens . However, the results of new polyphasic analyses coupled with those of phenotypic, phylogenetic and genomic analyses reported here demonstrate that the affiliation to the species P. fluorescens was incorrect. The strain is Gram-stain-negative, rod-shaped, aerobic and displays growth at 4–28 °C (optimum temperature 20–25 °C) and at pH 5–9 (optimum pH 6–7). Major fatty acids were C16 : 0 (38.2 %), a summed feature consisting of C16 : 1ω6c and/or C16 : 1ω7c) (20.7 %), C17 : 0cyclo ω7c (14.3 %) and a summed feature consisting of C18 : 1ω6c and/or C18 : 1ω7c (11.7 %). The respiratory quinones were determined to be Q9 (95.5 %) and Q8 (4.5 %) and major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was determined to be 59.4 mol%. The results of phylogenetic analysis based on the 16S rRNA gene and multi-locus sequence analysis (MLSA; concatenated 16S rRNA, gyrB, rpoB and rpoD sequences) indicated that In5T was affiliated with the Pseudomonas mandelii subgroup within the genus Pseudomonas . Comparison of the genome sequence of In5T and those of related type strains of species of the genus Pseudomonas revealed an average nucleotide identity (ANI) of 87.7 % or less and digital DNA–DNA hybridization (dDDH) of less than 34.5 % relatedness, respectively. Two more strains, In614 and In655, isolated from the same suppressive soil were included in the genome analysis. The ANI and dDDH of In614 and In655 compared with In5T were ANI: 99.9 and 97.6 and dDDH (GGDC) 99.9 and 79.4, respectively, indicating that In5T, In614 and In655 are representatives of the same species. The results of the phenotypic, phylogenetic and genomic analyses support the hypothesis that strain In5T represents a novel species of the genus Pseudomonas , for which the name Pseudomonas nunensis sp. nov. is proposed. The type strain is In5T(=LMG 32653T=NCIMB 15428T).