Saccharothrix luteola sp. nov., a novel cellulose-degrading actinobacterium isolated from soil and emended description of the genus Saccharothrix

A novel cellulose-degrading actinobacterium, designated strain NEAU-S10^T, was isolated from soil collected from Chifeng, Inner Mongolia Autonomous Region, PR China, and characterized using a polyphasic approach. Pairwise similarity of the 16S rRNA gene sequence showed that strain NEAU-S10^T was a representative of Saccharothrix and was closely related to Saccharothrix carnea NEAU-yn17^T (99.2 %), Saccharothrix saharensis SA152^T (99.0 %), Saccharothrix texasensis DSM 44231^T (98.5 %) and Saccharothrix xinjiangensis NBRC 101911^T (98.5 %). Physiological and chemotaxonomic characteristics of the strain further supported its affiliation to the genus Saccharothrix. The whole-cell sugars contained galactose, ribose and mannose. The polar lipids contained diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The predominant menaquinones were MK-9(H₀), MK-9(H₂), MK-9(H₄) and MK-10(H₄). The major fatty acids were iso-C_16 : 0, C_16 : 0, anteiso-C_17 : 0, iso-C_15 : 0 and iso-C_17 : 0. The genomic DNA G+C content was 71.8 mol%. The levels of digital DNA-DNA hybridization between isolate and S. carnea NEAU-yn17^T, S. saharensis SA152^T and S. texasensis DSM 44231^T were 40.1 % (37.6-42.6 %), 38.soap8 % (36.3-41.3 %) and 44.8 % (42.2-47.3 %) and the ANI values between them were determined to be 90.2, 89.8 and 91.7 %, the results indicated that strain NEAU-S10^T could be distinguished from its reference strains. The assembled genome sequence of strain NEAU-S10^T was found to be 10 305 394 bp long. The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) revealed 8 994 protein-coding genes. Genomic analysis and Congo red staining test indicated that strain NEAU-S10^T had the potential to degrade cellulose. The genomic and phenotypic results indicate that strain NEAU-S10^T represents a novel species of the genus Saccharothrix, for which the name Saccharothrix luteola sp. nov. is proposed, with NEAU-S10^T (=CCTCC AA 2020037^T=JCM 34800^T) as the type strain.

Streptococcus oriscaviae sp. nov. Infection Associated with Guinea Pigs

Pet bite-related infections are commonly caused by the pet's oral flora transmitted to the animal handlers through the bite wounds. In this study, we isolated a streptococcus, HKU75T, in pure culture from the purulent discharge collected from a guinea pig bite wound in a previously healthy young patient. HKU75T was alpha-hemolytic on sheep blood agar and agglutinated with Lancefield group D and group G antisera. API 20 STREP showed that the most likely identity for HKU75T was S. suis I with 85.4% confidence while Vitek 2 showed that HKU75T was unidentifiable. MALDI-TOF MS identified HKU75T as Streptococcus suis (score of 1.86 only). 16S rRNA gene sequencing showed that HKU75T was most closely related to S. parasuis (98.3% nucleotide identity), whereas partial groEL and rpoB gene sequencing showed that it was most closely related to S. suis (81.8% and 89.8% nucleotide identity respectively). Whole genome sequencing and intergenomic distance determined by ANI revealed that there was <85% identity between the genome of HKU75T and those of all other known Streptococcus species. Genome classification using concatenated sequences of 92 bacterial core genes showed that HKU75T belonged to the Suis group. groEL gene sequences identical to that of HKU75T could be directly amplified from the oral cavities of the two guinea pigs owned by the patient. HKU75T is a novel Streptococcus species, which we propose to be named S. oriscaviae. The oral cavity of guinea pigs is presumably a reservoir of S. oriscaviae. Some of the reported S. suis strains isolated from clinical specimens may be S. oriscaviae. IMPORTANCE We reported the discovery of a novel Streptococcus species, propose to be named Streptococcus oriscaviae, from the pus collected from a guinea pig bite wound in a healthy young patient. The bacterium was initially misidentified as S. suis/S. parasuis by biochemical tests, mass spectrometry. and housekeeping genes sequencing. Its novelty was confirmed by whole genome sequencing. Comparative genomic studies showed that S. oriscaviae belongs to the Suis group. S. oriscaviae sequences were detected in the oral cavities of the two guinea pigs owned by the patient, suggesting that the oral cavity of guinea pigs could be a reservoir of S. oriscaviae. Some of the reported S. suis strains may be S. oriscaviae. Further studies are warranted to refine our knowledge on this novel Streptococcus species.

Soil Collected in the Great Smoky Mountains National Park Yielded a Novel Listeria sensu stricto Species, L. swaminathanii

Soil samples collected in the Great Smoky Mountains National Park yielded a Listeria isolate that could not be classified to the species level. Whole-genome sequence-based average nucleotide identity BLAST and in silico DNA-DNA Hybridization analyses confirmed this isolate to be a novel Listeria sensu stricto species with the highest similarity to L. marthii (ANI = 93.9%, isDDH = 55.9%). Additional whole-genome-based analysis using the Genome Taxonomy Database Toolkit further supported delineation as a novel Listeria sensu stricto species, as this tool failed to assign a species identification. Phenotypic and genotypic characterization results indicate that this species is nonpathogenic. Specifically, the novel Listeria species described here is phenotypically (i) nonhemolytic and (ii) negative for phosphatidylinositol-specific phospholipase C activity; the draft genome lacks all virulence genes found in the Listeria pathogenicity islands 1, 2, 3, and 4 as well as the internalin genes inlA and inlB. While the type strain contains an apparently intact catalase gene (kat), this strain is phenotypically catalase-negative (an unusual characteristic for Listeria sensu stricto species). Additional analyses identified a nonsynonymous mutation in a conserved codon of kat that is likely linked to the catalase-negative phenotype. Rapid species identification systems, including two biochemical and one matrix-assisted laser desorption/ionization, misidentified this novel species as either L. monocytogenes, L. innocua, or L. marthii. We propose the name L. swaminathanii, and the type strain is FSL L7-0020T (=ATCC TSD-239T). IMPORTANCEL. swaminathanii is a novel sensu stricto species that originated from a US National Park and it will be the first Listeria identified to date without official standing in the nomenclature. Validation was impeded by the National Park's requirements for strain access, ultimately deemed too restrictive by the International Committee on Systematics of Prokaryotes. However, lack of valid status should not detract from the significance of adding a novel species to the Listeria sensu stricto clade. Notably, detection of non-monocytogenes sensu stricto species in a food processing environment indicate conditions that could facilitate the presence of the pathogen L. monocytogenes. If isolated, our data show a potential for L. swaminathanii to be misidentified as another sensu stricto, notably L. monocytogenes. Therefore, developers of Listeria spp. detection and identification methods, who historically only include validly published species in their validation studies, should include L. swaminathanii to ensure accurate results.

The Retrospective on Atypical Brucella Species Leads to Novel Definitions

The genus Brucella currently comprises twelve species of facultative intracellular bacteria with variable zoonotic potential. Six of them have been considered as classical, causing brucellosis in terrestrial mammalian hosts, with two species originated from marine mammals. In the past fifteen years, field research as well as improved pathogen detection and typing have allowed the identification of four new species, namely Brucella microti, Brucella inopinata, Brucella papionis, Brucella vulpis, and of numerous strains, isolated from a wide range of hosts, including for the first time cold-blooded animals. While their genome sequences are still highly similar to those of classical strains, some of them are characterized by atypical phenotypes such as higher growth rate, increased resistance to acid stress, motility, and lethality in the murine infection model. In our review, we provide an overview of state-of-the-art knowledge about these novel Brucella sp., with emphasis on their phylogenetic positions in the genus, their metabolic characteristics, acid stress resistance mechanisms, and their behavior in well-established in cellulo and in vivo infection models. Comparison of phylogenetic classification and phenotypical properties between classical and novel Brucella species and strains finally lead us to propose a more adapted terminology, distinguishing between core and non-core, and typical versus atypical brucellae, respectively.

Pseudomonas uvaldensis sp. nov., a bacterial pathogen causing onion bulb rot

A Gram-stain-negative, aerobic and non-spore-forming bacterial strain, designated 20TX0172^T, was isolated from a rotting onion bulb in Texas, USA. The results of phylogenetic analysis based on the 16S rRNA sequence indicated that the novel strain represented a member of the genus Pseudomonas and had the greatest sequence similarities with Pseudomonas kilonensis 520-20^T (99.3 %), Pseudomonas corrugata CFBP 2431^T (99.2 %), and Pseudomonas viciae 11K1^T (99.2 %) but the 16S rRNA phylogenetic tree displayed a monophyletic clade with Pseudomonas mediterranea CFBP 5447^T. In the phylogenetic trees based on sequences of four housekeeping genes (gap1, gltA, gyrB and rpoD), the novel strain formed a separate branch, indicating that the strain was distinct phylogenetically from known species of the genus Pseudomonas. The genome-sequence-derived average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the novel isolate and P. mediterranea DSM 16733^T were 86.7 and 32.7 %, respectively. These values were below the accepted species cutoff threshold of 96 % ANI and 70 % dDDH, affirming that the strain represented a novel species. The genome size of the novel species was 5.98 Mbp with a DNA G+C content of 60.8 mol%. On the basis of phenotypic and genotypic characteristics, strain 20TX0172^T represents a novel species of the genus Pseudomonas. The name Pseudomonas uvaldensis sp. nov. is proposed. The type strain is 20TX0172^T (=NCIMB 15426^T=CIP 112022^T).

Comamonas fluminis sp. nov., isolated from the Han River, Republic of Korea

A Gram-stain-negative, aerobic and motile bacterial strain, designated CJ34^T, was isolated from Han River water in the Republic of Korea. Strain CJ34^T grew optimally on tryptic soy agar at 30 °C and pH 7.0 in the absence of NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequence showed that strain CJ34^T belonged to the genus Comamonas within the family Comamonadaceae and was most closely related to Comamonas testosteroni ATCC 11996^T and Comamonas thiooxydans DSM 17888^T (both 98.63 % similarity). The average nucleotide identity values between strain CJ34^T and two closely related type strains C. testosteroni ATCC 11996^T and C. thiooxydans DSM 17888^T were 82.77 and 82.73 %, respectively. The major isoprenoid quinone of strain CJ34^T was ubiquinone Q-8. The major cellular fatty acids of strain CJ34^T were C_16 : 0, C_16 : 1  ω6c and/or C_16 : 1  ω7c and C_18 : 1  ω6c and/or C_18 : 1  ω7c. The predominant polar lipids of strain CJ34^T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. Whole genome sequencing revealed that strain CJ34^T had a genome of 4.9 Mbp and the G+C content of the genomic DNA was 59.73 mol%. On the basis of the results of this polyphasic taxonomy study, strain CJ34^T represents a novel species in the genus Comamonas, for which the name Comamonas fluminis sp. nov. is proposed. The type strain is CJ34^T (=KACC 22237^T=JCM 34454^T).

Flavobacterium endoglycinae sp. nov., an endophytic bacterium isolated from soybean (Glycine max L. cv. Gwangan) stems

A Gram-stain-negative, facultatively anaerobic, motile by gliding, rod-shaped, oxidase- and catalase-positive bacterial strain, designated BB8T, was isolated from the stems of a Korean soybean cultivar (Glycine max L. cv. Gwangan). The strain produced a yellow pigment on tryptic soy agar. Growth of strain BB8T occurred at pH 5.0-8.0 (optimum, pH 7.0), at 10-35 °C (optimum, 25-30 °C) and in the presence of 0-1 % (w/v) NaCl (optimum, 0.5%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BB8T formed a lineage within the genus Flavobacterium and was most closely related to Flavobacterium artemisiae SYP-B1015T (96.9 % 16S rRNA gene sequence similarity) and Flavobacterium ustbae T13T (96.8%). The complete genome sequence of strain BB8T was 5 513 159 bp long with a G+C content of 34.1 mol%. The major fatty acids (>10 %) of strain BB8T were iso-C15 : 0 (21 %), summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c, 20.3%) and iso-C16 : 0 3-OH (13.7%). The predominant polar lipids were phosphatidylethanolamine and unidentified aminolipids, and the major respiratory quinone was menaquinone-6. Based on these phenotypic, genotypic and chemotaxonomic characteristics, strain BB8T is considered to represent a novel species of the genus Flavobacterium, for which the name Flavobacterium endoglycinae sp. nov. is proposed. The type strain is BB8T (=KCTC 82167T=CCTCC AB 2020070T).

Endophytic Colletotrichum Species from Aquatic Plants in Southwest China

Colletotrichum species are plant pathogens, saprobes, and endophytes in many economically important hosts. Many studies have investigated the diversity and pathogenicity of Colletotrichum species in common ornamentals, fruits, and vegetables. However, Colletotrichum species occurring in aquatic plants are not well known. During the investigation of the diversity of endophytic fungi in aquatic plants in southwest China, 66 Colletotrichum isolates were obtained from aquatic plants there, and 26 of them were selected for sequencing and analyses of actin (ACT), chitin synthase (CHS-1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the internal transcribed spacer (ITS) region, and β-tubulin (TUB2) genomic regions. Based on morphological characterization and multi-locus phylogenetic analyses, 13 Colletotrichum species were recognized, namely, C. baiyuense sp. nov., C. casaense sp. nov., C. demersi sp. nov., C. dianense sp. nov., C. fructicola, C. garzense sp. nov., C. jiangxiense, C. karstii, C. philoxeroidis sp. nov., C. spicati sp. nov., C. tengchongense sp. nov., C. vulgaris sp. nov., C. wuxuhaiense sp. nov. Two species complexes, the C. boninense species complex and C. gloeosporioides species complex, were found to be associated with aquatic plants. Pathogenicity tests revealed a broad diversity in pathogenicity and aggressiveness among the eight new Colletotrichum species.

Expanding the Burkholderia pseudomallei Complex with the Addition of Two Novel Species: Burkholderia mayonis sp. nov. and Burkholderia savannae sp. nov

Distinct Burkholderia strains were isolated from soil samples collected in tropical northern Australia (Northern Territory and the Torres Strait Islands, Queensland). Phylogenetic analysis of 16S rRNA and whole genome sequences revealed these strains were distinct from previously described Burkholderia species and assigned them to two novel clades within the B. pseudomallei complex (Bpc). Because average nucleotide identity and digital DNA-DNA hybridization calculations are consistent with these clades representing distinct species, we propose the names Burkholderia mayonis sp. nov. and Burkholderia savannae sp. nov. Strains assigned to B. mayonis sp. nov. include type strain BDU6T (=TSD-80; LMG 29941; ASM152374v2) and BDU8. Strains assigned to B. savannae sp. nov. include type strain MSMB266T (=TSD-82; LMG 29940; ASM152444v2), MSMB852, BDU18, and BDU19. Comparative genomics revealed unique coding regions for both putative species, including clusters of orthologous genes associated with phage. Type strains of both B. mayonis sp. nov. and B. savannae sp. nov. yielded biochemical profiles distinct from each other and from other species in the Bpc, and profiles also varied among strains within B. mayonis sp. nov. and B. savannae sp. nov. Matrix-assisted laser desorption ionization time-of-flight (MLST) analysis revealed a B. savannae sp. nov. cluster separate from other species, whereas B. mayonis sp. nov. strains did not form a distinct cluster. Neither B. mayonis sp. nov. nor B. savannae sp. nov. caused mortality in mice when delivered via the subcutaneous route. The addition of B. mayonis sp. nov. and B. savannae sp. nov. results in a total of eight species currently within the Bpc. IMPORTANCEBurkholderia species can be important sources of novel natural products, and new species are of interest to diverse scientific disciplines. Although many Burkholderia species are saprophytic, Burkholderia pseudomallei is the causative agent of the disease melioidosis. Understanding the genomics and virulence of the closest relatives to B. pseudomallei, i.e., the other species within the B. pseudomallei complex (Bpc), is important for identifying robust diagnostic targets specific to B. pseudomallei and for understanding the evolution of virulence in B. pseudomallei. Two proposed novel species, B. mayonis sp. nov. and B. savannae sp. nov., were isolated from soil samples collected from multiple locations in northern Australia. The two proposed species belong to the Bpc but are phylogenetically distinct from all other members of this complex. The addition of B. mayonis sp. nov. and B. savannae sp. nov. results in a total of eight species within this significant complex of bacteria that are available for future studies.

Co-circulation of a Novel Dromedary Camel Parainfluenza Virus 3 and Middle East Respiratory Syndrome Coronavirus in a Dromedary Herd With Respiratory Tract Infections

Since the emergence of Middle East Respiratory Syndrome (MERS) in 2012, there have been a surge in the discovery and evolutionary studies of viruses in dromedaries. Here, we investigated a herd of nine dromedary calves from Umm Al Quwain, the United Arab Emirates that developed respiratory signs. Viral culture of the nasal swabs from the nine calves on Vero cells showed two different types of cytopathic effects (CPEs), suggesting the presence of two different viruses. Three samples showed typical CPEs of Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) in Vero cells, which was confirmed by partial RdRp gene sequencing. Complete genome sequencing of the three MERS-CoV strains showed that they belonged to clade B3, most closely related to another dromedary MERS-CoV isolate previously detected in Dubai. They also showed evidence of recombination between lineages B4 and B5 in ORF1ab. Another three samples showed non-typical CPEs of MERS-CoV with cell rounding, progressive degeneration, and detachment. Electron microscopy revealed spherical viral particles with peplomers and diameter of about 170nm. High-throughput sequencing and metagenomic analysis showed that the genome organization (3'-N-P-M-F-HN-L-5') was typical of paramyxovirus. They possessed typical genome features similar to other viruses of the genus Respirovirus, including a conserved motif ³²³FAPGNYALSYAM³³⁶ in the N protein, RNA editing sites 5'-⁷¹⁷AAAAAAGGG⁷²⁵-3', and 5'-¹⁰³⁸AGAAGAAAGAAAGG¹⁰⁵¹-3' (mRNA sense) in the P gene with multiple polypeptides coding capacity, a nuclear localization signal sequence ²⁴⁵KVGRMYSVEYCKQKIEK²⁶¹ in the M protein, a conserved sialic acid binding motif ²⁵²NRKSCS²⁵⁷ in the HN protein, conserved lengths of the leader (55nt) and trailer (51nt) sequences, total coding percentages (92.6–93.4%), gene-start (AGGANNAAAG), gene-end (NANNANNAAAAA), and trinucleotide intergenic sequences (CTT, mRNA sense). Phylogenetic analysis of their complete genomes showed that they were most closely related to bovine parainfluenza virus 3 (PIV3) genotype C strains. In the phylogenetic tree constructed using the complete L protein, the branch length between dromedary camel PIV3 (DcPIV3) and the nearest node is 0.04, which is >0.03, the definition used for species demarcation in the family Paramyxoviridae. Therefore, we show that DcPIV3 is a novel species of the genus Respirovirus that co-circulated with MERS-CoV in a dromedary herd in the Middle East.

Enterococcus innesii sp. nov., isolated from the wax moth Galleria mellonella

Four bacterial strains were isolated from two different colony sources of the wax moth Galleria mellonella. They were characterized by a polyphasic approach including 16S rRNA gene sequence analysis, core-genome analysis, average nucleotide identity (ANI) analysis, digital DNA-DNA hybridization (dDDH), determination of G+C content, screening of antibiotic resistance genes, and various phenotypic analyses. Initial analysis of 16S rRNA gene sequence identities indicated that strain GAL7^T was potentially very closely related to Enterococcus casseliflavus and Enterococcus gallinarum, having 99.5-99.9 % sequence similarity. However, further analysis of whole genome sequences revealed a genome size of 3.69 Mb, DNA G+C content of 42.35 mol%, and low dDDH and ANI values between the genomes of strain GAL7^T and closest phylogenetic relative E. casseliflavus NBRC 100478^T of 59.0 and 94.5 %, respectively, indicating identification of a putative new Enterococcus species. In addition, all novel strains encoded the atypical vancomycin-resistance gene vanC-4. Results of phylogenomic, physiological and phenotypic characterization confirmed that strain GAL7^T represented a novel species within the genus Enterococcus, for which the name Enterococcus innesii sp. nov. is proposed. The type strain is GAL7^T (=DSM 112306^T=NCTC 14608^T).

Prevotella illustrans sp. nov., derived from human oropharyngeal abscess puncture fluid

An obligately anaerobic strain, designated as A2931^T, was isolated from oropharyngeal abscess puncture fluid of a patient sampled during routine care at a hospital and further characterized both phenotypically, biochemically and genotypically. This Gram-negative rod-shaped bacterium was moderately saccharolytic and proteolytic. Phylogenetic analyses of full-length 16S rRNA gene and whole-genome sequences revealed it to be best placed in the genus Prevotella, but to be only comparatively distantly related to recognized species, with the closest relationship to Prevotella baroniae (average nucleotide identity and digital DNA-DNA hybridization values both well below the generally accepted thresholds). Strain A2931^T had a genomic DNA G+C content of 47.7 mol%. Its most abundant cellular long-chain fatty acids were anteiso-C_15 : 0, iso-C_15 : 0 and C_16 : 0. Taken together, this polyphasic data suggests strain A2931^T to represent a novel species within the genus Prevotella, for which the name Prevotella illustrans sp. nov. is proposed. The type strain is A2931^T (=DSM 108028^T=CCOS 1232^T=CCUG 72806^T). Interestingly, we found strain A2931^T to correspond to the oral taxon Prevotella HMT-820 in the Human Oral Microbiome Database, as supported by overall genome relatedness index analyses >99 %. Thus, our work not only closes one of the gaps of knowledge about hitherto unnamed species isolated from humans, but also will facilitate identification of this taxon both in the clinical microbiology context and in research alike.

Parvimonas parva sp. nov., derived from a human genito-urinary lesion

A strain of obligately anaerobically growing Gram-positive cocci was isolated from a human genito-urinary sample and characterized by a polyphasic approach. Analyses of 16S rRNA gene and whole-genome sequences of this strain S3374^T indicated that it belonged to the genus Parvimonas. Overall genome relatedness index calculations confirmed it to be phylogenetically distinct from Parvimonas micra (NCTC 11808^T) as its most closely related species with standing in nomenclature, with average nucleotide identity and genome-to-genome distance values of 85.8 and 30.2 %, respectively. Biochemically, strain S3374^T was strongly proteolytic and can be differentiated from P. micra (DSM 20468^T) by absence of phosphatase activity. The DNA G+C content of strain S3374^T was 28.6 mol%. Based on the phenotypical, biochemical and genetic findings, strain S3374^T is considered to represent a novel species within the genus Parvimonas, for which the name Parvimonas parva sp. nov. is proposed. The type strain is S3374^T (=DSM 110786^T=CCOS 1934^T=CCUG 74294^T). This description adds strain S3374^T as a second species to the genus Parvimonas which has so far been monotypic. While the type strain of this genus, P. micra, has a long standing in nomenclature and its role in human health and disease has been studied to some extent, this description of the proposed novel species represented by strain S3374^T will allow microbiologists worldwide to identify isolates of P. parva sp. nov., a prerequisite for further investigation of its relevance in the clinical context and beyond.

Corynebacterium zhongnanshanii sp. nov. isolated from trachea of Marmota himalayana, Corynebacterium lujinxingii sp. nov. and Corynebacterium wankanglinii sp. nov. from human faeces

Six novel facultatively anaerobic, Gram-stain-positive, rod-shaped, non-haemolytic bacteria (zg-320^T/zg-336, zg-917^T/zg-910 and zg-913^T/zg-915) isolated from animal tissues and human faeces were found to belong to the genus Corynebacterium based on the phylogenetic analyses of 16S rRNA gene and 262 core genes set. Based on the greatest degree of 16S rRNA similarity, zg-320^T/zg-336 had the highest 16S rRNA gene similarity to Corynebacterium falsenii DSM 44353^T (97.51 %), zg-917^T/zg-910 to Corynebacterium coyleae DSM 44184^T (98.68 %), and zg-913^T/zg-915 to Corynebacterium afermentans subsp. lipophilum CIP 103500^T (98.79 %). The three novel type strains had a relatively high DNA G+C content (61.2-64.4 mol%), low DNA relatedness and ANI values with their respective neighbours: 23.5/72.7 %, 25.0/72.3%and 22.6/73.1 % (zg-320^T vs. Corynebacterium auriscanis CIP 106629^T, Corynebacterium resistens DSM 45100^T and Corynebacterium suicordis DSM 45110^T); 24.4/82.3% and 23.7/81.3 % (zg-917^T vs. C. coyleae DSM 44184^T and Corynebacterium jeddahense JCB^T); 26.8/83.7% and 27.7/84.4 % (zg-913^T vs. Corynebacterium mucifaciens ATCC 700355^T and C. afermentans subsp. lipophilum CCUG 32105^T). The three novel species had C_16 : 0, C_18 : 0, C_18 : 1  ω9c and C_18 : 0 ante/C_18 : 2  ω6,9c as the major cellular fatty acids; MK-8(H₂) in strain zg-917^T and MK-9(H₂) in strains zg-320^T and zg-913^T were found to be the major respiratory quinones. For the three novel species, the detected major polar lipids included diphosphatidylglycerol, phosphatidyl inositol mannoside, phosphatidylglycerol and phosphatidylinositol, the cell-wall peptidoglycan was based on meso-DAP, and the whole-cell sugars mainly included ribose, arabinose and galactose. The three novel species grew optimally at 35-37 °C, 0.5 % (w/v) NaCl and pH 7.0-8.0; notably, they were tolerant of 10.5 % (w/v) NaCl. Based on the results of these comprehensive analyses, three novel species in the genus Corynebacterium are proposed, aptly named Corynebacterium zhongnanshanii sp. nov. (zg-320^T = GDMCC 1.1719^T = JCM 34106^T), Corynebacterium lujinxingii sp. nov. (zg-917^T = GDMCC 1.1707^T = JCM 34094^T) and Corynebacterium wankanglinii sp. nov. (zg-913^T = GDMCC 1.1706^T = JCM 34398^T).

Hepatic phaeohyphomycosis due to a novel dematiaceous fungus, Pleurostoma hongkongense sp. nov., and importance of antifungal susceptibility testing

Pleurostoma species are wood-inhabiting fungi and emerging opportunistic pathogens causing phaeohyphomycosis. In this study, we isolated a dematiaceous fungus, HKU44T, from the subhepatic abscess pus and drain fluids of a liver transplant recipient with post-transplant biliary and hepatico-jejunostomy bypass strictures. Histology of the abscess wall biopsy showed abundant fungal hyphae. The patient survived after a second liver transplant and antifungal therapy. On SDA, HKU44T grew initially as white powdery colonies which turned beige upon maturation. Hyphae were septate and hyaline. Phialides were monophialidic and laterally located, generally closely associated to a cluster of conidia which were usually reniform. Phylogenetic analyses showed that HKU44T is most closely related to, but distinct from, Pleurostoma ootheca and Pleurostoma repens. These suggested that HKU44T is a novel Pleurostoma species, for which the name Pleurostoma hongkongense sp. nov. is proposed. Antifungal susceptibility testing showed that Pleurostoma species possessed high MICs/MECs for fluconazole, 5-flucytosine and the echinocandins; whereas they exhibited a high strain-to-strain variability to the susceptibilities to the other triazoles. As for amphotericin B, ∼65% of the Pleurostoma strains had low MICs (≤1 µg/mL). DNA sequencing should be performed to accurately identify fungi with Pleurostoma/Phialophora-like morphologies, so is antifungal susceptibility testing for patients with Pleurostoma infections.

Dyadobacter sandarakinus sp. nov., isolated from Arctic tundra soil, and emended descriptions of Dyadobacter alkalitolerans, Dyadobacter koreensis and Dyadobacter psychrophilus

Strain Q3-56^T, isolated from Arctic tundra soil, was found to be a Gram-stain-negative, yellow-pigmented, oxidase- and catalase-positive, non-motile, non-spore-forming, rod-shaped and aerobic bacterium. Strain Q3-56^T grew optimally at pH 7.0 and 28 °C. The strain could tolerate up to 1 % (w/v) NaCl with optimum growth in the absence of NaCl. The strain was not sensitive to oxacillin and ceftazidime. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Q3-56^T belonged to the genus Dyadobacter. Strain Q3-56^T showed the highest sequence similarities to Dyadobacter luticola T17^T (96.58 %), Dyadobacter ginsengisoli Gsoil 043^T (96.50 %), Dyadobacter flavalbus NS28^T (96.43 %) and Dyadobacter bucti QTA69^T (96.43 %). The predominant respiratory isoprenoid quinone was identified as MK-7, The polar lipid profile of strain Q3-56^T was found to contain one phosphatidylethanolamine, three unidentified aminolipids, three unidentified lipids and one unidentified phospholipid. The G+C content of the genomic DNA was determined to be 49.1 mol%. The main fatty acids were summed feature 3 (comprising C_16 : 1  ω7c/C_16 : 1  ω6c), iso-C_15 : 0, C_16 : 1  ω5c and iso-C_16 : 1 3-OH. On the basis of the evidence presented in this study, a novel species of the genus Dyadobacter, Dyadobacter sandarakinus sp. nov., is proposed, with the type strain Q3-56^T (=CCTCC AB 2019271^T=KCTC 72739^T). Emended descriptions of Dyadobacter alkalitolerans, Dyadobacter koreensis and Dyadobacter psychrophilus are also provided.

Phylogenetic analyses and morphological characters reveal two new species of Ganoderma from Yunnan province, China

Ganodermadianzhongense sp. nov. and G.esculentum sp. nov. are proposed as two new species based on both phenotypic and genotypic evidences. Ganodermadianzhongense is characterized by the stipitate basidiomata, laccate and oxblood red pileus, gray white pore surface, duplex context and broadly ellipsoid basidiospores (9.0-12.5 × 6.5-9.0 μm) with coarse interwall pillars. Ganodermaesculentum is characterized by its basidiomata with slender stipe, white pore surface, homogeneous pileus context, and slightly truncate, narrow basidiospores (8.0-12.5 × 5.0-8.0 µm). Phylogenetic analyses were carried out based on the internal transcribed spacer (ITS), translation elongation factor 1-α (TEF1-α) and the second subunit of RNA polymerase II (RPB2) sequence data. The illustrations and descriptions for the new taxa are provided.

Sphingobacterium micropteri sp. nov. and Sphingobacterium litopenaei sp. nov., isolated from aquaculture water

Two novel bacterial strains, designated as DN00404^T and DN04309^T, were isolated from aquaculture water and characterized by using a polyphasic taxonomic approach. Cells of strains DN00404^T and DN04309^T were Gram-stain-negative, aerobic, non-motile, oxidase-positive and catalase-positive. Cells of DN00404^T were short rod-shaped and those of DN04309^T were long rod-shaped. Strain DN00404^T was found to grow at 15-37 °C (optimum, 25-30 °C), at pH 6.0-11.0 (optimum, pH 7.5) and in 0-2.0 % (w/v) NaCl (optimum, 1.0 %). Strain DN04309^T was found to grow at 15-45 °C (optimum, 20-37 °C), at pH 5.5-11.0 (optimum, 7.5) and in 0-4.0 % (w/v) NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that the two strains belonged to the genus Sphingobacterium and were distinct from all known species of this genus. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains and between each of the two strains and related type strains of this genus were well below the recognized thresholds of 95.0-96.0 % ANI and 70.0 % dDDH for species delineation. The genomic DNA G+C contents of strains DN00404^T and DN04309^T were 41.6 and 36.0 mol%, respectively. The respiratory quinone in both strains was identified as MK-7, and their major fatty acids were iso-C_15 : 0 and summed feature 3 (C_16 : 1  ω6c and/or C_16 : 1  ω7c), which were similar to those of other species of this genus. The two major fatty acids C_16 : 0 and iso-C_17 : 0 3-OH were also found in strain DN00404^T. Based on genotypic and phenotypic characteristics, two novel species of the genus Sphingobacterium are proposed: Sphingobacterium micropteri sp. nov. with DN00404^T (=GDMCC 1.1865^T=KACC 21924^T) as the type strain and Sphingobacterium litopenaei sp. nov. with DN04309^T (=GDMCC 1.1984^T=KCTC 82348^T) as the type strain.

Paenihalocynthiibacter styelae gen. nov., sp. nov., isolated from stalked sea squirt Styela clava

A Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterial strain, MYP1-1^T, was isolated from the intestine of a stalked sea squirt (Styela clava) of the South Sea in the Republic of Korea. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain MYP1-1^T clustered with the type strains of Halocynthiibacter species and Pseudohalocynthiibacter aestuariivivens. Strain MYP1-1^T exhibited 16S rRNA gene sequence similarity values of 97.0-97.6 % to the type strains of Halocynthiibacter namhaensis, Halocynthiibacter arcticus and P. aestuariivivens. The phylogenetic tree based on genomic sequences showed that strain MYP1-1^T formed a distinct branch separating it from the type strains of two Halocynthiibacter species and P. aestuariivivens and other taxa. The DNA G+C content of strain MYP1-1^T from its genomic sequence was 55.0 mol%. Strain MYP1-1^T contained Q-10 as the predominant ubiquinone and C_18 : 1  ω7c as the major fatty acid. The major polar lipids of strain MYP1-1^T were phosphatidylcholine, phosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. The differences in fatty acid and polar lipid profiles and other differential phenotypic properties made it reasonable to distinguish strain MYP1-1^T from the genera Halocynthiibacter and Pseudohalocynthiibacter. On the basis of the polyphasic taxonomic investigations, we conclude that strain MYP1-1^T constitutes a new genus and species within the class Alphaproteobacteria, for which the name Paenihalocynthiibacter styelae gen. nov., sp. nov. is proposed. The type strain is MYP1-1^T (=KCTC 82143^T=NBRC 114355^T).

Chryseobacterium endalhagicum sp. nov., isolated from seed of leguminous plant

A Gram-stain-negative, yellow-pigmented bacterium, designated as L7^T, was isolated from seeds of Alhagi sparsifolia Shap., a leguminous plant that grows in northwest PR China. Strain L7^T was found to be non-flagellated, non-spore forming rods which can grow at 10–37 °C, pH 6.0–8.5 and in 0–3 % (v/w) NaCl concentration. The 16S rRNA gene sequence analysis showed that strain L7^T belongs to the genus Chryseobacterium with sequence similarities to Chryseobacterium vietnamense GIMN1.005^T (98.1%), C. bernardetii NCCTC13530^T (98.0%), C. vrystaatense LMG 22846^T (97.9%), C. nakagawai NCTC13529^T (97.7%), C. shigense DSM 17126^T (97.6%) and C. rhizosphaerae RSB3-1^T (97.5%). The average nucleotide identity of strain L7^T to 31 reference strains were 78.6–85.6 %, lower than the species delineation threshold of 95 %. MK-6 was the only respiratory quinone of L7^T and major fatty acids were iso-C_15 : 0, iso-C_17 : 0 3-OH, C_16 : 1 ω7c and/or C_16 : 1 ω6c, isoC_17 : 1 ω9c and/or C_16 : 0 10-methyl. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminophospholipids, two unidentified aminolipids, three unidentified glycolipids and two unidentified lipids. The G+C content of the genome was 38.58 mol%. On the basis of polyphasic taxonomy analyses in this study, strain L7^T is considered to represent a novel species in the genus Chryseobacterium, for which the name Chryseobacterium endalhagicum sp. nov. is proposed. The type strain is L7^T (=MCCC 1K05687^T=JCM 34506^T)

Flagellatimonas centrodinii gen. nov., sp. nov., a novel member of the family Nevskiaceae isolated from toxin-producing dinoflagellate Centrodinium punctatum

A Gram-stain-negative, aerobic, rod-shaped strain (R2A-3^T) was isolated from the toxin-producing dinoflagellate Centrodinium punctatum and identified as a novel genus and new species based on a polyphasic taxonomic approach. The optimum conditions for growth of the strain were at 25 °C, pH 8.0 and in the presence of 3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA genes and 92 core genes sets revealed that strain R2A-3^T belongs to the family Nevskiaceae in the class Gammaproteobacteria and represented an independent taxon separated from other genera. The 16S rRNA gene of strain R2A-3^T showed the highest sequence similarity to Polycyclovorans algicola TG408^T (95.2%), Fontimonas thermophila HA-01^T (94.1%) and Sinimarinibacterium flocculans NH6-24^T (93.2%), and less than 92.8 % similarity to other genera in the family Nevskiaceae. The genome length of strain R2A-3^T was 3608892 bp with 65.2 mol% G+C content. Summed feature 8 (comprising C_18 : 1  ω7c and/or C_18 : 1  ω6c) was the major fatty acid (>10 %). Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were detected as the major polar lipids. The major respiratory quinone was ubiquinone-8. According to its phylogenetic, phenotypic, chemotaxonomic and genomic features, strain R2A-3^T represents a new species in the new genus of the family Nevskiaceae. It is recommended to name it Flagellatimonas centrodinii gen. nov., sp. nov. The type strain is R2A-3^T (=KCTC 82469^T=GDMCC 1.2523^T).

Identification and Antifungal Mechanism of a Novel Actinobacterium Streptomyces huiliensis sp. nov. Against Fusarium oxysporum f. sp. cubense Tropical Race 4 of Banana

Banana is an important fruit crop. Fusarium wilt caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) seriously threatens the global banana industry. It is difficult to control the disease spread using chemical measures. In addition, commercial resistant cultivars are also lacking. Biological control is considered as a promising strategy using antagonistic microbes. Actinomycetes, especially Streptomyces, are potential sources of producing novel bioactive secondary metabolites. Here, strain SCA2-4 T with strong antifungal activity against Foc TR4 was isolated from the rhizospheric soil of Opuntia stricta in a dry hot valley. The morphological, physiological and chemotaxonomic characteristics of the strain were consistent with the genus Streptomyces. Based on the homology alignment and phylogenetic trees of 16S rRNA gene, the taxonomic status of strain SCA2-4 T exhibited a paradoxical result and low bootstrap value using different algorithms in the MEGA software. It prompted us to further discriminate this strain from the closely related species by the multilocus sequence analysis (MLSA) using five house-keeping gene alleles (atpD, gyrB, recA, rpoB, and trpB). The MLSA trees calculated by three algorithms demonstrated that strain SCA2-4 T formed a distinct clade with Streptomyces mobaraensis NBRC 13819 T . The MLSA distance was above 0.007 of the species cut-off. Average nucleotide identity (ANI) values between strain SCA2-4 T genome and two standard strain genomes were below 95-96% of the novel species threshold. Strain SCA2-4 T was assigned to a novel species of the genus Streptomyces and named as Streptomyces huiliensis sp. nov. The sequenced complete genome of SCA2-4 T encoded 51 putative biosynthetic gene clusters of secondary metabolites. Genome alignment revealed that ten gene clusters were involved in the biosynthesis of antimicrobial metabolites. It was supported that strain SCA2-4 T showed strong antifungal activities against the pathogens of banana fungal diseases. Extracts abstracted from the culture filtrate of strain SCA2-4 T seriously destroyed cell structure of Foc TR4 and inhibited mycelial growth and spore germination. These results implied that strain SCA2-4 T could be a promising candidate for biological control of banana Fusarium wilt.

Coniochaeta elegans sp. nov., Coniochaeta montana sp. nov. and Coniochaeta nivea sp. nov., three new species of endophytes with distinctive morphology and functional traits

A growing interest in fungi that occur within symptom-less plants and lichens (endophytes) has uncovered previously uncharacterized species in diverse biomes worldwide. In many temperate and boreal forests, endophytic Coniochaeta (Sacc.) Cooke (Coniochaetaceae, Coniochaetales, Sordariomycetes, Ascomycota) are commonly isolated on standard media, but rarely are characterized. We examined 26 isolates of Coniochaeta housed at the Gilbertson Mycological Herbarium. The isolates were collected from healthy photosynthetic tissues of conifers, angiosperms, mosses and lichens in Canada, Sweden and the United States. Their barcode sequences (nuclear ribosomal internal transcribed spacer and 5.8S; ITS rDNA) were ≤97% similar to any documented species available through GenBank. Phylogenetic analyses based on two loci (ITS rDNA and translation elongation factor 1-alpha) indicated that two isolates represented Coniochaeta cymbiformispora, broadening the ecological niche and geographic range of a species known previously from burned soil in Japan. The remaining 24 endophytes represented three previously undescribed species that we characterize here: Coniochaeta elegans sp. nov., Coniochaeta montana sp. nov. and Coniochaeta nivea sp. nov. Each has a wide host range, including lichens, bryophytes and vascular plants. C. elegans sp. nov. and C. nivea sp. nov. have wide geographic ranges. C. montana sp. nov. occurs in the Madrean biome of Arizona (USA), where it is sympatric with the other species described here. All three species display protease, chitinase and cellulase activity in vitro. Overall, this study provides insight into the ecological and evolutionary diversity of Coniochaeta and suggests that these strains may be amenable for studies of traits relevant to a horizontally transmitted, symbiotic lifestyle.

Novel Cyclovirus Species in Dogs with Hemorrhagic Gastroenteritis

Nested PCRs with circovirus/cyclovirus pan-rep (replicase gene) primers detected eukaryotic circular Rep-encoding single-stranded DNA (CRESS DNA) viruses in three (samples CN9E, CN16E and CN34) of 18 canine parvovirus-2-positive fecal samples from household dogs with hemorrhagic gastroenteritis on the Caribbean island of Nevis. The complete genomes of CRESS DNA virus CN9E, CN16E and CN34 were determined by inverse nested PCRs. Based on (i) genome organization, (ii) location of the putative origin of replication, (iii) pairwise genome-wide sequence identities, (iv) the presence of conserved motifs in the putative replication-associated protein (Rep) and the arginine-rich region in the amino terminus of the putative capsid protein (Cp) and (v) a phylogenetic analysis, CN9E, CN16E and CN34 were classified as cycloviruses. Canine-associated cycloviruses CN16E and CN34 were closely related to each other and shared low genome-wide nucleotide (59.642–59.704%), deduced Rep (35.018–35.379%) and Cp (26.601%) amino acid sequence identities with CN9E. All the three canine-associated cycloviruses shared < 80% genome-wide pairwise nucleotide sequence identities with cycloviruses from other animals/environmental samples, constituting two novel species (CN9E and CN16E/34) within the genus Cyclovirus. Considering the feeding habits of dogs, we could not determine whether the cycloviruses were of dietary origin or infected the host. Interestingly, the CN9E putative Rep-encoding open reading frame was found to use the invertebrate mitochondrial genetic code with an alternative initiation codon (ATA) for translation, corroborating the hypothesis that cycloviruses are actually arthropod-infecting viruses. To our knowledge, this is the first report on the detection and complete genome analysis of cycloviruses from domestic dogs.

Genomic Characterization of a Novel Alphacoronavirus Isolated from Bats, Korea, 2020

Coronavirus, an important zoonotic disease, raises concerns of future pandemics. The bat is considered a source of noticeable viruses resulting in human and livestock infections, especially the coronavirus. Therefore, surveillance and genetic analysis of coronaviruses in bats are essential in order to prevent the risk of future diseases. In this study, the genome of HCQD-2020, a novel alphacoronavirus detected in a bat (Eptesicus serotinus), was assembled and described using next-generation sequencing and bioinformatics analysis. The comparison of the whole-genome sequence and the conserved amino acid sequence of replicated proteins revealed that the new strain was distantly related with other known species in the Alphacoronavirus genus. Phylogenetic construction indicated that this strain formed a separated branch with other species, suggesting a new species of Alphacoronavirus. Additionally, in silico prediction also revealed the risk of cross-species infection of this strain, especially in the order Artiodactyla. In summary, this study provided the genetic characteristics of a possible new species belonging to Alphacoronavirus.

Pseudooceanicola endophyticus sp. nov., a novel endophytic bacterium isolated from bark Aegiceras corniculatum

A Gram-stain-negative, aerobic, short-rod-shaped bacterium, designated strain CBS1P-1^T, was isolated from a surface-sterilized bark of Aegiceras corniculatum. Growth of strain CBS1P-1^T was observed with between 0 and 12.0 % (w/v) NaCl (optimally with 5.0 %) and at between pH 6.0-9.0. It grew at temperatures between 25-37 °C (optimum, 30 °C). Chemotaxonomic analysis showed that ubiquinone-10 was the respiratory quinone. The lipids comprised diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid, an unidentified phospholipid and an unidentified aminolipid. The major fatty acids of strain CBS1P-1^T were C_18 : 1  ω7c, C_16 : 0 and C_19 : 0 cyclo ω8c. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CBS1P-1^T was most related to Pseudooceanicola antarcticus CGMCC 1.12662^T with a sequence similarity of 96.5 %. The average nucleotide identity and digital DNA-DNA hybridization values between strain CBS1P-1^T and P. antarcticus 1.12662^T were 77.5 and 21.1 %, respectively. The G+C content of the genomic DNA was 67.3 mol%. Based on phylogenetic, chemotaxonomic and phenotypic data, strain CBS1P-1^T is considered to represent a novel species of the genus Pseudooceanicola, for which the name Pseudooceanicola endophyticus is proposed. The type strain is CBS1P-1^T (=KCTC 62836^T=CGMCC 1.13743^T).

Actinomyces capricornis sp. nov., isolated from the oral cavity of a Japanese serow

A novel Gram-positive, facultatively anaerobic, rod-shaped, nonspore forming, nonmotile organism was isolated from a Japanese serow oral cavity. Designated strain MAS-1^T , it is most closely related to Actinomyces bowdenii DSM 15435^T , with which it shares 98.07% sequence homology in the 16S ribosomal RNA gene. The primarily detected cellular fatty acids in strain MAS-1^T were C_16:0 and C_18:1 w9c. The predominant respiratory quinone was MK-9 (H₄ ). The major polar lipids were phosphatidylcholines, phosphatidylinositols, and glycophospholipids. The genomic DNA GC content of the isolate was 71.3 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between MAS-1^T and its related species were 23.5%-39.5% and 82.11%-91.01%, respectively, which were below the threshold (70% and 95%, respectively) for species delineation, indicating that strain MAS-1^T represents a novel species. Strain MAS-1^T can be differentiated from A. bowdenii by their reactions to naphthol-AS-BI-phosphohydrolase, α-galactosidase, β-galactosidase, and N-acetyl-β-glucosaminidase, as well as differing acid production from glycogen. Based on the results of genotypic, phenotypic, and biochemical analyses, herein it is proposed that the identified bacteria can be classified as a novel species, Actinomyces capricornis sp. nov., strain MAS-1^T (=JCM 34236^T  = DSM 111732^T ).

Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species

A novel species within the genus Eikenella is described, based on the phenotypical, biochemical and genetic characterization of a strain of a facultatively anaerobic, Gram-negative rod-shaped bacterium. Strain S3360^T was isolated from the throat swab of a patient sampled during routine care at a hospital. Phylogenetic analyses (full-length 16S rRNA gene and whole-genome sequences) placed the strain in the genus Eikenella, separate from all recognized species but with the closest relationship to Eikenella longinqua (NML 02-A-017^T). Eikenella is one of the genera in the HACEK group known to be responsible for rare cases of endocarditis in humans. Until the recent descriptions of Eikenella exigua, Eikenella halliae and Eikenella longinqua, Eikenella corrodens had been the only validly published species in this genus since its description as Bacteroides corrodens in 1958. Unlike these species, strain S3360^T is able to metabolize carbohydrates (glucose). The average nucleotide identities of strain S3360^T with E. longinqua (NML 02-A-017^T) and E. corrodens (NCTC 10596^T), the type species of the genus, were 90.5 and 84.7 %, respectively, and the corresponding genome-to-genome distance values were 41.3 and 29.0 %, respectively. The DNA G+C content of strain S3360^T was 58.4 mol%. Based on the phenotypical, biochemical and genetic findings, strain S3360^T is considered to represent a novel species within the genus Eikenella, for which the name Eikenella glucosivorans sp. nov. is proposed. The type strain is S3360^T (DSM 110714^T=CCOS 1935^T=CCUG 74293^T). In addition, an emendation of the genus Eikenella is proposed to include species which are saccharolytic.

Massilia puerhi sp. nov., isolated from soil of Pu-erh tea cellar

A Gram-reaction-negative, yellow-pigmented, non-spore-forming rod, aerobic, motile bacterium, designated SJY3^T, was isolated from soil samples collected from a Pu-erh tea cellar in Bolian Pu-erh tea estate Co. Ltd. in Pu'er city, Yunnan, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Massilia. The closest phylogenetic relative was Massilia arenae CICC 24458^T (99.5 %), followed by M. timonae CCUG45783^T (97.9 %), M. oculi CCUG43427A^T (97.8 %), and M. aurea DSM 18055^T (97.8 %). The major fatty acids were C_16 : 0 and C_16 : 1  ω7c and/or C_16 : 1  ω6c. The major respiratory quinone was ubiquinone Q-8 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Genome sequencing revealed a genome size of 5.97 M bp and a G+C content of 65.4 mol%. Pairwise determined whole genome average nucleotide identity (gANI) values and digital DNA-DNA hybridization (dDDH) values were all below the threshold. Although the 16S rRNA gene similarity of stain SJY3^T and Massilia arenae CICC 24458^T was more than 99 %, the gANI, dDDH values and genomic tree clearly indicated that they were not of the same species. In summary, strain SJY3^T represents a new species, for which we propose the name Massilia puerhi sp. nov. with the type strain SJY3^T (=CGMCC 1.17158^T=KCTC 82193^T).

Sphingomonas aliaeris sp. nov., a new species isolated from pork steak packed under modified atmosphere

Species belonging to the genus Sphingomonas have been isolated from environments such as soil, water and plant tissues. Many strains are known for their capability of degrading aromatic molecules and producing extracellular polymers. A Gram-stain-negative, strictly aerobic, motile, red-pigmented, oxidase-negative, catalase-positive, rod-shaped strain, designated DH-S5^T, has been isolated from pork steak packed under CO₂-enriched modified atmosphere. Cell diameters were 1.5×0.9 µm. Growth optima were at 30 °C and at pH 6.0. Phylogenetic analyses based on both complete 16S rRNA gene sequence and whole-genome sequence data revealed that strain DH-S5^T belongs to the genus Sphingomonas, being closely related to Sphingomonas alpina DSM 22537^T (97.4 % gene sequence similarity), followed by Sphingomonas qilianensis X1^T (97.4 %) and Sphingomonas hylomeconis GZJT-2^T (97.3 %). The DNA G+C content was 64.4 mol%. The digital DNA-DNA hybridization value between the isolate strain and S. alpina DSM 22537^T was 21.0 % with an average nucleotide identity value of 77.03 %. Strain DH-S5^T contained Q-10 as the ubiquinone and major fatty acids were C_18 : 1 cis 11 (39.3 %) and C_16 : 1 cis 9 (12.5 %), as well as C_16 : 0 (12.1 %) and C_14 : 0 2-OH (11.4 %). As for polar lipids, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, dimethylphosphatidylethanolamine and sphingoglycolipid could be detected, alongside traces of monomethylphosphatidylethanolamine. Based on its phenotypic, chemotaxonomic and phylogenetic characteristics, strain DH-S5^T (=DSM 110829^T=LMG 31606^T) is classified as a representative of the genus Sphingomonas, for which the name Sphingomonas aliaeris sp. nov. is proposed.

Detection and Complete Genome Analysis of Circoviruses and Cycloviruses in the Small Indian Mongoose (Urva auropunctata): Identification of Novel Species

Fecal samples from 76 of 83 apparently healthy small Indian mongooses (Urva auropunctata) were PCR positive with circovirus/cyclovirus pan-rep (replicase gene) primers. In this case, 30 samples yielded high quality partial rep sequences (~400 bp), of which 26 sequences shared maximum homology with cycloviruses from an arthropod, bats, humans or a sheep. Three sequences exhibited maximum identities with a bat circovirus, whilst a single sequence could not be assigned to either genus. Using inverse nested PCRs, the complete genomes of mongoose associated circoviruses (Mon-1, -29 and -66) and cycloviruses (Mon-20, -24, -32, -58, -60 and -62) were determined. Mon-1, -20, -24, -29, -32 and -66 shared <80% maximum genome-wide pairwise nucleotide sequence identities with circoviruses/cycloviruses from other animals/sources, and were assigned to novel circovirus, or cyclovirus species. Mon-58, -60 and -62 shared maximum pairwise identities of 79.90–80.20% with human and bat cycloviruses, which were borderline to the cut-off identity value for assigning novel cycloviral species. Despite high genetic diversity, the mongoose associated circoviruses/cycloviruses retained the various features that are conserved among members of the family Circoviridae, such as presence of the putative origin of replication (ori) in the 5′-intergenic region, conserved motifs in the putative replication-associated protein and an arginine rich region in the amino terminus of the putative capsid protein. Since only fecal samples were tested, and mongooses are polyphagous predators, we could not determine whether the mongoose associated circoviruses/cycloviruses were of dietary origin, or actually infected the host. To our knowledge, this is the first report on detection and complete genome analysis of circoviruses/cycloviruses in the small Indian mongoose, warranting further studies in other species of mongooses.

Nanchangia anserum gen. nov., sp. nov., isolated from feces of greater white-fronted geese (Anser albifrons)

Two rod-shaped and Gram-stain-positive bacteria (strains C64^T and C62) were isolated in 2020 from faeces of greater white-fronted geese (Anser albifrons) from Poyang Lake, PR China. Their optimal growth conditions were at 37 °C, pH 7.0 and with 0.5 % (w/v) NaCl. The two isolates showed a highest 16S rRNA gene sequence similarity to Bowdeniella nasicola DSM 19116^T (92.1 %). Phylogenetic/phylogenomic analyses indicated that strains C64^T and C62 clustered independently in the vicinity of the genera Varibaculum, Winkia and Mobiluncus within the family Actinomycetaceae, but could not be classified clearly as members of any of these known genera. The average amino acid identity values between our isolates and available genomes of members of the family Actinomycetaceae were around the genus threshold value (45-65 %). The major cellular fatty acids of the strains were C_18 : 1ω9c and C_16 : 0. The predominant polar lipids were phosphatidylinositol, phosphatidylglycerol, phosphatidylcholine, diacylglycerol, triacylglycerol and cardiolipin. The amino acid composition of peptidoglycan contained alanine, glutamic acid and glycine. The major respiratory menaquinones were MK-8(H₄) and MK-9(H₄). The whole cell sugars included galactose, arabinose and glucose. On the basis of the results of the 16S rRNA gene sequences comparison, whole-genome phylogenomic analysis, phenotypic and chemotaxonomic characteristics, we propose that strains C64^T and C62 represent a novel species belonging to a novel genus within the family Actinomycetaceae, for which the name Nanchangia anserum gen. nov., sp. nov. is proposed. The type strain is Nanchangia anserum C64^T (=CGMCC 1.18410^T=GDMCC 1.1969^T=KCTC 49511^T=KACC 22143^T).

Pseudomonas capsici sp. nov., a plant-pathogenic bacterium isolated from pepper leaf in Georgia, USA

Three phytopathogenic bacterial strains (Pc19-1^T, Pc19-2 and Pc19-3) were isolated from seedlings displaying water-soaked, dark brown-to-black, necrotic lesions on pepper (Capsicum annuum) leaves in Georgia, USA. Upon isolation on King’s medium B, light cream-coloured colonies were observed and a diffusible fluorescent pigment was visible under ultraviolet light. Analysis of their 16S rRNA gene sequences showed that they belonged to the genus Pseudomonas, with the highest similarity to Pseudomonas cichorii ATCC 10857^T (99.7 %). The fatty acid analysis revealed that the majority of the fatty acids were summed feature 3 (C_{16  :  1} ω7c/C_{16  :  1} ω6c), C_{16  :  0} and summed feature 8 (C_{18  :  1} ω7c/C_{18  :  1} ω6c). Phylogenomic analyses based on whole genome sequences demonstrated that the pepper strains belonged to the Pseudomonas syringae complex with P. cichorii as their closest neighbour, and formed a separate monophyletic clade from other species. Between the pepper strains and P. cichorii, the average nucleotide identity values were 91.3 %. Furthermore, the digital DNA–DNA hybridization values of the pepper strains when compared to their closest relatives, including P. cichorii, were 45.2 % or less. In addition, biochemical and physiological features were examined in this study and the results indicate that the pepper strains represent a novel Pseudomonas species. Therefore, we propose a new species Pseudomonas capsici sp. nov., with Pc19-1^T (=CFBP 8884^T=LMG 32209^T) as the type strain. The DNA G+C content of the strain Pc19-1^T is 58.4 mol%.

Faecalibacter rhinopitheci sp. nov., a bacterium isolated from the faeces of Rhinopithecus bieti

A novel Gram-stain-negative strain, WQ 117^T, isolated from the faeces of Rhinopithecus bieti collected at Yunnan Snub-nosed Monkey National Park, Yunnan province, PR China, was subjected to a polyphasic taxonomic study. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate represented a member of the genus Faecalibacter, sharing 97.64 % sequence similarity with the type strain Faecalibacter macacae YIM 102668^T. The G+C content of the genomic DNA of WQ117^T was 30.5 mol%. The predominant isoprenoid quinone was MK-6. The major cellular fatty acids was iso-C_15 : 0. The whole genome average nucleotide identity (gANI) values and the digital DNA-DNA hybridization values between WQ 117^T and YIM 102668^T were 79.66 % and 22.20 %, respectively. Growth occurred at 0-50 °C (optimally at 28-35 °C), pH 7.0-9.0 (optimally at pH 8.0) and with 0-2 % (w/v) NaCl (optimally without NaCl). On the basis of the taxonomic evidence, a novel species, Faecalibacter rhinopitheci sp. nov., is proposed. The type strain is WQ 117^T (=KCTC 82394^T=CCTCC AA 2020027^T).

Population Analysis of Vibrio cholerae in Aquatic Reservoirs Reveals a Novel Sister Species (Vibrio paracholerae sp. nov.) with a History of Association with Humans

Most efforts to understand the biology of Vibrio cholerae have focused on a single group, the pandemic-generating lineage harboring the strains responsible for all known cholera pandemics. Consequently, little is known about the diversity of this species in its native aquatic environment. To understand the differences in the V. cholerae populations inhabiting regions with a history of cholera cases and those lacking such a history, a comparative analysis of population composition was performed. Little overlap was found in lineage compositions between those in Dhaka, Bangladesh (where cholera is endemic), located in the Ganges Delta, and those in Falmouth, MA (no known history of cholera), a small coastal town on the United States east coast. The most striking difference was the presence of a group of related lineages at high abundance in Dhaka, which was completely absent from Falmouth. Phylogenomic analysis revealed that these lineages form a cluster at the base of the phylogeny for the V. cholerae species and were sufficiently differentiated genetically and phenotypically to form a novel species. A retrospective search revealed that strains from this species have been anecdotally found from around the world and were isolated as early as 1916 from a British soldier in Egypt suffering from choleraic diarrhea. In 1935, Gardner and Venkatraman unofficially referred to a member of this group as Vibrio paracholerae. In recognition of this earlier designation, we propose the name Vibrio paracholerae sp. nov. for this bacterium. Genomic analysis suggests a link with human populations for this novel species and substantial interaction with its better-known sister species. IMPORTANCE Cholera continues to remain a major public health threat around the globe. Understanding the ecology, evolution, and environmental adaptation of the causative agent (Vibrio cholerae) and tracking the emergence of novel lineages with pathogenic potential are essential to combat the problem. In this study, we investigated the population dynamics of Vibrio cholerae in an inland locality, which is known as endemic for cholera, and compared them with those of a cholera-free coastal location. We found the consistent presence of the pandemic-generating lineage of V. cholerae in Dhaka, where cholera is endemic, and an exclusive presence of a lineage phylogenetically distinct from other V. cholerae lineages. Our study suggests that this lineage represents a novel species that has pathogenic potential and a human link to its environmental abundance. The possible association with human populations and coexistence and interaction with toxigenic V. cholerae in the natural environment make this potential human pathogen an important subject for future studies.

Morphological and molecular characterization of Quinqueserialis (Digenea: Notocotylidae) species diversity in North America

Estimates of trematode diversity are inaccurate due to unrecognized cryptic species and phenotypic plasticity within species. Integrative taxonomy (genetics, morphology and host use) increases the clarity of species delineation and improves knowledge of parasite biology. In this study, we used this approach to resolve taxonomic issues and test hypotheses of cryptic species in a genus of trematode, Quinqueserialis. Specimens from throughout North America were field collected from hosts and obtained from museums. We found three morphologically distinct groups and successfully sequenced specimens from two of these groups. DNA sequencing at the 28S and CO1 gene regions revealed that two of the three groups were genetically distinct. One genetic group included two morphological clusters demonstrating host-induced phenotypic plasticity within Quinqueserialis quinqueserialis. The other unique genetic group is a novel species, Quinqueserialis kinsellai n. sp., which is described herein. Our study illustrates the importance of integrating multiple sources of evidence when investigating trematode diversity to account for the influence of cryptic species or phenotypic plasticity. However, further sampling is needed to understand Quinqueserialis spp. diversity as some species have no genetic information associated with them.

Leucobacter chromiisoli sp. nov., isolated from chromium-containing chemical plant soil

A Gram-stain-positive, rod-shaped, aerobic, non-motile, non-sporulating bacterial strain, designated CSA1^T, was isolated from chromium-containing soil sampled at a chemical plant. Growth of strain CSA1^T occurred at pH 6-10 (optimum, pH 7), 15-45 °C (optimum, 30 °C) and in the presence of 0.5-6.5 % (w/v) NaCl (optimum, 2 %). The 16S rRNA gene sequence of strain CSA1^T revealed the highest similarity to Leucobacter ruminantium A2^T (97.5 %), Leucobacter tardus K 70/01^T (97.3 %), Leucobacter humi Re6^T (96.6 %), Leucobacter kyeonggiensis F3-P9^T (96.2 %), Leucobacter zeae CC-MF41^T (96.1 %) and Leucobacter weissii S27^T (96.0 %). The draft genome of CSA1^T was approximately 3 350 931 bp in size with a G+C content of 70.6 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among strain CSA1^T and the selected Leucobacter species were 74.0-79.2 % (ANIb), 84.3-87.1 % (ANIm) and 21.5-25.4 % (dDDH), which are below the recommended cutoff values for species delineation. The major fatty acids were anteiso-C_15 : 0, iso-C_16 : 0 and anteiso-C_17 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid. The predominant menaquinones were MK-11, MK-8 and MK-6. The cell-wall amino acids were 2,4-diaminobutyric acid, alanine, glycine, glutamic acid and threonine. From the phenotypic, chemotaxonomic and molecular features, strain CSA1^T was considered to represent a novel species of the genus Leucobacter, for which the name Leucobacter chromiisoli sp. nov. is proposed. The type strain is CSA1^T (=JCM 34359^T=CGMCC 1.18746^T).

Apilactobacillus nanyangensis sp. nov., Secundilactobacillus hailunensis sp. nov., Secundilactobacillus yichangensis sp. nov., Levilactobacillus andaensis sp. nov., Levilactobacillus wangkuiensis sp. nov., Levilactobacillus lanxiensis sp. nov., Lacticaseibacillus mingshuiensis sp. nov. and Lacticaseibacillus suilingensis sp. nov., isolated from traditional Chinese pickle and the gut of honeybee (Apis mellifera)

Thirteen Gram-stain-positive bacterial strains were isolated from Chinese traditional pickle and the gut of honeybee (Apis mellifera). These strains were characterized using a polyphasic taxonomic approach. The data demonstrated that 12 of the 13 strains represented eight novel species belonging to the genera Apilactobacillus, Secundilactobacillus, Levilactobacillus and Lacticaseibacillus; strains HN36-1^T, 887-11^T, F79-211-2^T, 866-3^T, 6-5(1)^T, 13B17^T, 117-1^T and ZW152^T were designated as the type strains. Based upon the data of polyphasic characterization obtained in the present study, eight novel species, Apilactobacillus nanyangensis sp. nov., Secundilactobacillus hailunensis sp. nov., Secundilactobacillus yichangensis sp. nov., Levilactobacillus andaensis sp. nov., Levilactobacillus wangkuiensis sp. nov., Levilactobacillus lanxiensis sp. nov., Lacticaseibacillus mingshuiensis sp. nov. and Lacticaseibacillus suilingensis sp. nov., are proposed and the type strains are HN36-1^T (=JCM 33867^T=CCTCC AB 2019385^T), 887-11^T (=NCIMB 15201^T=CCM 8950^T=JCM 33864^T=CCTCC AB 2018396^T), F79-211-2^T (=NCIMB 15254^T=JCM 33866^T=CCTCC AB 2019384^T), 866-3^T (=JCM 33863^T=CCTCC AB 2019383^T), 6-5(1)^T (=NCIMB 15229^T=CCM 8977^T=JCM 33564^T=CCTCC AB 2019168^T), 13B17^T (=NCIMB 15230^T=CCM 8979^T=JCM 33565^T=CCTCC AB 2019167^T), 117-1^T (=NCIMB 15232^T=CCM 8980^T=JCM 33567^T) and ZW152^T (=JCM 34363^T=CCTCC AB 2020299^T=LMG 32143^T=CCM 9110^T), respectively.

Pedobacter endophyticus sp. nov., an endophytic bacterium isolated from Carex pumila

An aerobic, Gram-stain-negative, weak-motile, short-rod-shaped bacterial strain, designated JBR3-12^T, was isolated from halophyte Carex pumila plants, and its taxonomic position was investigated by using a polyphasic taxonomic approach. The strain produced a pink pigment on tryptic soy agar and grew optimally at 25 °C, pH 8 and in the presence of 3 % (w/v) NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain JBR3-12^T formed a lineage within the genus Pedobacter and was most closely related to Pedobacter sandarakinus DS-27^T (98.0 %) and Pedobacter agri PB92^T (97.6 %). The DNA G+C content of the genome was 41.3 mol%; the whole genome length was 5 426 070 bp. The major fatty acids of JBR3-12^T were iso-C_15 : 0, summed feature 3 (comprising C_16 : 1  ω6c and/or C_16 : 1  ω7c) and iso-C_17 : 0 3-OH. The predominant polar lipid was phosphatidylethanolamine. The predominant quinone was menaquinone-7. Based on its phenotypic, phylogenetic and genotypic features, strain JBR3-12^T is proposed to represent a novel species of the genus Pedobacter, for which the name is Pedobacter endophyticus sp. nov. The type strain is JBR3-12^T (=KCTC 82363^T=NBRC 114901^T).

Cellulosimicrobium composti sp. nov., a thermophilic bacterium isolated from compost

A Gram-stain-positive, yellow-pigmented, non-motile actinobacterial strain, designated as BIT-GX5^T, was isolated from a sesame husks compost collected in Beijing, PR China. This bacterium was found to be able to grow in the temperature range from 16 to 50 °C and had an optimal growth temperature at 45 °C. Its taxonomic position was analysed using a polyphasic approach. The 16S rRNA gene sequence (1482 bp) of strain BIT-GX5^T was most similar to Cellulosimicrobium funkei ATCC BAA-886^T (99.45%), Cellulosimicrobium cellulans LMG 16121^T (99.17%) and Cellulosimicrobium marinum RS-7-4^T (98.75%). The results of phylogenetic analyses, based on the 16S rRNA gene, concatenated sequences of five housekeeping genes (gyrB, rpoB, recA, atpD and trpB) and genome sequences, placed strain BIT-GX5^T in a separate lineage among the genus Cellulosimicrobium within the family Promicromonosporaceae. The major polar lipids of strain BIT-GX5^T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid and aminolipid. The major isoprenoid quinone was MK-9(H₄), while the cell-wall sugars were galactose, rhamnose, glucose and mannose. The peptidoglycan type was A4α l-Lys-d-Ser-d-Asp. The major fatty acids were anteiso-C_15:0 and iso-C_15: 0, which were similar to other members in the genus Cellulosimicrobium. Results of in silico DNA-DNA hybridization and average nucleotide identity calculations plus physiological and biochemical tests exhibited the genotypic and phenotypic differentiation of strain BIT-GX5^T from the other members of the genus Cellulosimicrobium. Therefore, strain BIT-GX5^T is considered to represent a novel species within the genus Cellulosimicrobium, for which the name Cellulosimicrobium composti sp. nov. is proposed. The type strain is BIT-GX5^T (= CGMCC 1.17687^T = KCTC 49391^T).

Belnapia mucosa sp. nov. and Belnapia arida sp. nov., isolated from desert biocrust

Two novel Gram-staining-negative, aerobic, cocci-shaped, non-motile, non-spore forming, pink-pigmented bacteria designated strains T6^T and T18^T, were isolated from a biocrust (biological soil crust) sample from the vicinity of the Tabernas Desert (Spain). Both strains were catalase-positive and oxidase-negative, and grew under mesophilic, neutrophilic and non-halophilic conditions. According to the 16S rRNA gene sequences, strains T6^T and T18^T showed similarities with Belnapia rosea CGMCC 1.10758^T and Belnapia moabensis CP2C^T (98.11 and 98.55% gene sequence similarity, respectively). The DNA G+C content was 69.80 and 68.96% for strains T6^T and T18^T, respectively; the average nucleotide identity by blast (ANIb) and digital DNA–DNA hybridization (dDDH) values confirmed their adscription to two novel species within the genus Belnapia. The predominant fatty acids were summed feature 8 (C_{18 : 1}ω7c/C_{18 : 1}ω6c), C_{16 : 0}, C_{18 : 1} 2-OH and summed feature 3 (C_{16 : 1}ω7c/C_{16 : 1}ω6c). According to he results of the polyphasic study, strains T6^T and T18^T represent two novel species in the genus Belnapia (which currently includes only three species), for which names Belnapia mucosa sp. nov. (type strain T6^T = CECT 30228^T=DSM 112073^T) and Belnapia arida sp. nov. (type strain T18^T=CECT 30229^T=DSM 112074^T) are proposed, respectively.

Gordonia jinghuaiqii sp. nov. and Gordonia zhaorongruii sp. nov., isolated from Tibetan Plateau wildlife

Four mesophilic and Gram-stain-positive strains (zg-686^T/zg-691 and HY186^T/HY189) isolated from Tibetan Plateau wildlife (PR China) belong to the genus Gordonia according to 16S rRNA gene and genomic sequence-based phylogenetic/genomic results. They have a DNA G+C content range of 67.4-68.3 mol% and low DNA relatedness (19.2-27.6 %) with all available genomes in the genus Gordonia. Strains zg-686^T/zg-691 and HY186^T/HY189 had C_18 : 1ω9c, C_18 : 0 10-methyl, C_16 : 1 ω7c/C_16 : 1ω6c and C_16 : 0 as major cellular fatty acids. The polar lipids detected in strains zg-686^T and HY186^T included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyl inositol mannoside and phosphatidylinositol. The respiratory quinones comprised MK8(H₂) (10.8 %) and MK9(H₂) (89.2 %) for strain zg-686^T, and MK6 (7.7 %), MK8(H₂) (8.4 %), MK8(H₄) (3.1 %) and MK9(H₂) (80.8 %) for strain HY186^T. Optimal growth conditions were pH 7.0, 35-37 °C and 0.5-1.5 % NaCl (w/v) for strains pair zg-686^T/zg-691, and pH 7.0, 28 °C and 1.5 % (w/v) NaCl for strains pair HY186^T/HY189. Based on these genotypic and phenotypic results, these four strains could be classified as two different novel species in the genus Gordonia, for which the names Gordonia jinghuaiqii sp. nov. and Gordonia zhaorongruii sp. nov. are proposed. The type strains are zg-686^T (=GDMCC 1.1715^T =JCM 33890^T) and HY186^T (=CGMCC 4.7607^T =JCM 33466^T), respectively.

Clinical Spectrum, Molecular Characterization, Antifungal Susceptibility Testing of Exophiala spp. From India and Description of a Novel Exophiala Species, E. arunalokei sp. nov

Introduction

Exophiala spp. are important opportunist pathogens causing subcutaneous or even fatal disseminated infections in otherwise both immunosuppressed and healthy individuals but there are no systematic studies on the isolates of Exophiala species from India.

Methods

Twenty-four isolates of Exophiala species were retrieved from the National Culture Collection of Pathogenic Fungi (NCCPF) and identified phenotypically and by molecular methods (ITS region sequencing) followed by antifungal susceptibility testing (AFST) as per CLSI-M38A3 guidelines. A review of the literature of cases from India was performed up to 1^st January 2021 using the Medline and Cochrane database.

Results

E. dermatitidis (n = 8), E. jeanselmei (n = 6), E. spinifera (n = 6), E. mesophila (n = 1), E. oligosperma (n = 1), E. xenobiotica (n = 1) were identified and the sequencing of ITS, β-tubulin and β-actin revealed a novel species, E. arunalokei sp. nov. (n = 1). The ITS sequence phylogram of E. jeanselmei revealed that the majority (83%) formed a separate cluster close to type A while majority (75%) of E. dermatitidis were type B. The MIC50 (mg/L) of amphotericin, itraconazole, voriconazole, micafungin, caspofungin, anidulafungin, and posaconazole, was 1, 0.25, 0.125, 0.12, 0.125, 0.062, and 0.062, respectively. Sixteen more cases were identified on the literature review and a significant association of E. dermatitidis with history of surgical procedures (p = 0.013), invasive disease (p = 0.032) and of E. mesophila with tuberculosis (p = 0.026) was seen.

Conclusion

This, to the best of our knowledge is the first study from India elucidating the molecular and clinical characteristics of Exophiala species and the first Indian report of human infection due to E. xenobiotica and E. arunalokei.

Sulfitobacter aestuariivivens sp. nov., isolated from a tidal flat

A Gram-stain-negative, aerobic, non-flagellated, coccoid, ovoid or rod-shaped bacterial strain, TSTF-M16^T, was isolated from a tidal flat on the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain TSTF-M16^T fell within a clade comprising the type strains of Sulfitobacter species. Strain TSTF-M16^T exhibited 16S rRNA gene sequence similarities of 98.5 and 98.1 % to the type strains of Sulfitobacter mediterraneus and Sulfitobacter sabulilitoris, respectively, and 96.2-97.8 % to the type strains of the other Sulfitobacter species. The average nucleotide identity and digital DNA-DNA hybridization values between the genomic sequences of strain TSTF-M16^T and the type strains of 16 Sulfitobacter species were 70.6-74.2 and 17.9-19.0 %, respectively. The DNA G+C content of strain TSTF-M16^T from genomic sequence data was 59.26 mol%. Strain TSTF-M16^T contained Q-10 as the predominant ubiquinone and C_18 : 1  ω7c as the major fatty acid. The major polar lipids of strain TSTF-M16^T were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. Distinguished phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain TSTF-M16^T is separated from recognized Sulfitobacter species. On the basis of the data presented here, strain TSTF-M16^T is considered to represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter aestuariivivens sp. nov. is proposed. The type strain is TSTF-M16^T (=KACC 21645^T=NBRC 114501^T).

Kordia aestuariivivens sp. nov. and Olleya sediminilitoris sp. nov., isolated from a tidal flat

Two Gram-stain-negative and non-flagellated bacteria, YSTF-M3^T and YSTF-M6^T, were isolated from a tidal flat from Yellow Sea, Republic of Korea, and subjected to a polyphasic taxonomic study. Neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strains YSTF-M3^T and YSTF-M6^T belong to the genera Kordia and Olleya of the family Flavobacteriaceae, respectively. The 16S rRNA gene sequence similarities between strain YSTF-M3^T and the type strains of Kordia species and between strain YSTF-M6^T and the type strains of Olleya species were 94.1-98.4 and 97.3-98.3 %, respectively. The ANI and dDDH values between genomic sequences of strain YSTF-M3^T and the type strains of five Kordia species and between those of strain YSTF-M6^T and the type strains of three Olleya species were in ranges of 77.0-83.2 and 20.7-27.1 % and 79.4-81.5 and 22.3-23.9 %, respectively. The DNA G+C contents of strain YSTF-M3^T and YSTF-M6^T from genomic sequences were 34.1 and 31.1 %, respectively. Both strains contained MK-6 as predominant menaquinone and phosphatidylethanolamine as only major phospholipid identified. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strains YSTF-M3^T and YSTF-M6^T are separated from recognized species of the genera Kordia and Olleya, respectively. On the basis of the data presented, strains YSTF-M3^T (=KACC 21639^T=NBRC 114499^T) and YSTF-M6^T (=KACC 21640^T=NBRC 114500^T) are considered to represent novel species of the genera Kordia and Olleya, respectively, for which the names Kordia aestuariivivens sp. nov. and Olleya sediminilitoris sp. nov. are proposed.

Flavimobilis rhizosphaerae sp. nov., isolated from rhizosphere soil of Spartina alterniflora

A novel Gram-stain positive, facultatively anaerobic, motile, irregularly rod-shaped bacterium, designated GY 10621^T, was isolated from rhizosphere soil of Spartina alterniflora in Beihai City, Guangxi Province, PR China, and characterized using a polyphasic taxonomic approach. GY 10621^T was positive for catalase and oxidase. Growth occurred at 4-42 °C (optimum 30-37 °C), at pH 5.0-9.0 (optimum pH 7.0) and in the presence of 0-5% NaCl (w/v) (optimum 1-3%). The main menaquinones were MK-9 (H₄) (92.2 %) and MK-10 (7.8 %). The major cellular fatty acids were anteiso-C_15 : 0 and C_14 : 0. The peptidoglycan was the type A4α (l-Lys-Ser-d-Glu). The polar lipids included four phosphoglycolipids, four glycolipids, an unidentified lipid and six unidentified phospholipids. The DNA G+C content of the type strain was 71.7 mol%. On the basis of the results of 16S rRNA gene analysis, the type strain of a species with a validly published name with the highest similarity to GY 10621^T was Flavimobilis soli KCTC 13155^T (97.16 %), followed by Sanguibacter suarezii NBRC 16159^T (96.39 %). The calculated results indicated that compared with GY 10621^T, the average nucleotide identity (ANI) values of three strains closely related to GY 10621^T (the two aforementioned type strains and 'S. massiliensis' Marseille-P3815) were 74.18-94.97 %, and the digital DNA-DNA hybridization (dDDH) values were 20.3-60.6 %. The results of 16S rRNA-based and genome-based phylogenetic tree analysis indicated that GY 10621^T should be assigned to the genus Flavimobilis. On the basis of evidence from polyphasic studies, GY 10621^T should be designated as representing a novel species of the genus Flavimobilis, for which the name Flavimobilis rhizosphaerae sp. nov. is proposed. The type strain is GY 10621^T (=CGMCC 1.17411^T=KCTC 49515^T).

Phylogenomic Characterization of a Novel Corynebacterium Species Associated with Fatal Diphtheritic Stomatitis in Endangered Yellow-Eyed Penguins

Yellow-eyed penguins, Megadyptes antipodes, are an endangered species that are endemic to New Zealand. Outbreaks of diphtheritic stomatitis have caused significant mortality for this species, especially among young chicks. In this study, we isolated 16 Corynebacterium sp. isolates from the oral cavities of 2- to 14-day-old chicks at a range of infection stages and sequenced the genomes to understand their virulence mechanisms. Phylogenomic and matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) characterization indicate that these strains belong to a novel Corynebacterium species. A simple multiplex PCR-based diagnostic assay has been developed to identify these strains rapidly and reliably. Similar to other corynebacteria, genomic islands and prophages introduced significant diversity among these strains that has potentially led to minor functional variations between the two lineages. Despite the presence of multiple corynebacterial virulence genes and a spaDEF-type pilus gene cluster among these strains, the survival rate was much higher in Galleria mellonella larvae than in those inoculated with Corynebacterium ulcerans NZRM 818 and Corynebacterium pseudotuberculosis NZRM 3004. Therefore, these strains are opportunistic pathogens causing high mortality among young penguin chicks due to a less-developed immune system.

IMPORTANCE Yellow-eyed penguins, Megadyptes antipodes, are endangered species with a sharp decline in the numbers of breeding pairs over the last 2 decades. Diphtheritic stomatitis, characterized by a thick fibrinopurulent exudate in the oral cavities and symptoms, including inanition and significant weight loss, is responsible for significant mortality among the young chicks. These chicks are treated with antibiotics, amoxicillin-clavulanic acid or enrofloxacin, but do not always recover from the infection. The pathogen causing these infections and the mechanism of pathogenesis are unclear. This study has identified a novel Corynebacterium species to be associated with diphtheritic stomatitis in yellow-eyed penguins with potential virulence genes that are likely involved in pathogenesis. Importantly, a gene encoding an exotoxin, phospholipase D, is present among these strains. The inactivated form of this enzyme could potentially be used as an effective vaccine to protect these penguins from infection.

Lactobacillus nasalidis sp. nov., isolated from the forestomach of a captive proboscis monkey (Nasalis larvatus)

Three strains (YZ01^T, YZ02 and YZ03) of Gram-stain-positive, facultatively anaerobic rods were isolated from the forestomach contents collected from a captive male proboscis monkey (Nasalis larvatus) at Yokohama Zoo in Japan. Phylogenetic analysis of the 16S rRNA gene sequences revealed that these strains belonged to the genus Lactobacillus. Based on the sequence similarity of the 16S rRNA gene, Lactobacillus delbrueckii subsp. indicus JCM 15610^T was the closest phylogenetic neighbour to YZ01^T. Sequence analyses of two partial concatenated housekeeping genes, the RNA polymerase alpha subunit (rpoA) and phenylalanyl-tRNA synthase alpha subunit (pheS) also indicated that the novel strains belonged to the genus Lactobacillus. The average nucleotide identity and digital DNA-DNA hybridization (dDDH) between L. delbrueckii subsp. indicus and YZ01^T were 85.9 and 31.4 %, respectively. The phylogenetic tree based on the whole genomic data of strains YZ01^T, YZ02 and YZ03 suggested that these three strains formed a single monophyletic cluster in the genus Lactobacillus, indicating that it belonged to a new species. The DNA G+C content of strain YZ01^T was 51.6 mol%. The major fatty acids were C_16 : 0 and C_18 : 1 ω9c. Therefore, based on phylogenetic, phenotypic and physiological evidence, strains YZ01^T, YZ02 and YZ03 represent a novel species of the genus Lactobacillus, for which the name Lactobacillus nasalidis sp. nov. is proposed with the type strain YZ01^T (=JCM 33769^T=DSM 110539^T).

Listeria cossartiae sp. nov., Listeria farberi sp. nov., Listeria immobilis sp. nov., Listeria portnoyi sp. nov. and Listeria rustica sp. nov., isolated from agricultural water and natural environments

A total of 27 Listeria isolates that could not be classified to the species level were obtained from soil samples from different locations in the contiguous United States and an agricultural water sample from New York. Whole-genome sequence-based average nucleotide identity blast (ANIb) showed that the 27 isolates form five distinct clusters; for each cluster, all draft genomes showed ANI values of <95 % similarity to each other and any currently described Listeria species, indicating that each cluster represents a novel species. Of the five novel species, three cluster with the Listeria sensu stricto clade and two cluster with sensu lato. One of the novel sensu stricto species, designated L. cossartiae sp. nov., contains two subclusters with an average ANI similarity of 94.9%, which were designated as subspecies. The proposed three novel sensu stricto species (including two subspecies) are Listeria farberi sp. nov. (type strain FSL L7-0091T=CCUG 74668T=LMG 31917T; maximum ANI 91.9 % to L. innocua), Listeria immobilis sp. nov. (type strain FSL L7-1519T=CCUG 74666T=LMG 31920T; maximum ANI 87.4 % to L. ivanovii subsp. londoniensis) and Listeria cossartiae sp. nov. [subsp. cossartiae (type strain FSL L7-1447T=CCUG 74667T=LMG 31919T; maximum ANI 93.4 % to L. marthii) and subsp. cayugensis (type strain FSL L7-0993T=CCUG 74670T=LMG 31918T; maximum ANI 94.7 % to L. marthii). The two proposed novel sensu lato species are Listeria portnoyi sp. nov. (type strain FSL L7-1582T=CCUG 74671T=LMG 31921T; maximum ANI value of 88.9 % to L. cornellensis and 89.2 % to L. newyorkensis) and Listeria rustica sp. nov. (type strain FSL W9-0585T=CCUG 74665T=LMG 31922T; maximum ANI value of 88.7 % to L. cornellensis and 88.9 % to L. newyorkensis). L. immobilis is the first sensu stricto species isolated to date that is non-motile. All five of the novel species are non-haemolytic and negative for phosphatidylinositol-specific phospholipase C activity; the draft genomes lack the virulence genes found in Listeria pathogenicity island 1 (LIPI-1), and the internalin genes inlA and inlB, indicating that they are non-pathogenic.