Paraliobacillus zengyii sp. nov., a slightly halophilic and extremely halotolerant bacterium isolated from Tibetan antelope faeces

Whole-genome sequencing of Paracoccus species isolated from the healthy human eye and description of Paracoccus shanxieyensis sp. nov

Currently, the genus Paracoccus comprises 76 recognized species. Members of Paracoccus are mostly isolated from environmental, animal, and plant sources. This report describes and proposes a novel species of Paracoccus isolated from clinical specimens of the human ocular surface. We isolated two aerobic, Gram-stain-negative, non-spore-forming, coccoid or short rod-shaped, and non-motile strains (designated DK398^T and DK608) from conjunctival sac swabs of two healthy volunteers. The results showed that the strains grew best under the conditions of 28°C, pH 7.0, and 1.0 % (w/v) NaCl. Sequence analysis based on the 16S rRNA gene showed that strains DK398^T and DK608 were members of Paracoccus, most similar to Paracoccus laeviglucosivorans 43P^T (98.54 and 98.62 %), Paracoccus litorisediminis GHD-05^T (98.34 and 98.41 %), and Paracoccus limmosus NB88^T (98.21 and 98.29 %). Phenotypic analysis showed that DK398^T and DK608 were positive for catalase and oxidase, negative for producing N-acetyl-β-glucosaminic acid, arginine dihydrolase, and β-glucuronidase but positive for leucine arylamidase. The predominant isoprenoid quinone was Q-10, and the major polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and an unidentified glycolipid. The major fatty acids (>10%) were summed feature 8 (C_18 : 1 ω7c and/or C_18 : 1 ω6c) and C_16 : 0. The meso-diaminopimelic acid was found in the cell wall peptidoglycan of DK398^T. The major cell wall sugars were ribose and galactose. Based on the results of phylogenetic analyses, low (<83.22%) average nucleotide identity, digital DNA-DNA hybridization (<26.0%), chemotaxonomic analysis, and physiological properties, strain DK398^T represents a novel species of the genus Paracoccus, for which the name Paracoccus shanxieyensis sp. nov. is proposed. The type strain is DK398^T (=CGMCC 1.17227^T=JCM 33719^T).

Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Nondomestic Animals Described in 2018 to 2021

Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.

Phenotypic and genomic characteristics of Brevibacterium zhoupengii sp. nov., a novel halotolerant actinomycete isolated from bat feces

Two strictly aerobic, Gram-staining-positive, non-spore-forming, regular rod-shaped (approximately 0.7 × 1.9 mm) bacteria (HY170^T and HY001) were isolated from bat feces collected from Chongzuo city, Guangxi province (22°20′54″N, 106°49′20″E, July 2011) and Chuxiong Yi Autonomous Prefecture, Yunnan province (25°09′10″N, 102°04′39″E, October 2013) of South China, respectively. Optimal growth is obtained at 25–28°C (range, 4–32°C) on BHI-5% sheep blood plate with pH 7.5 (range, 5.0–10.0) in the presence of 0.5–1.0% NaCl (w/v) (range, 0–15% NaCl [w/v]). The phylogenetic and phylogenomic trees based respectively on the 16S rRNA gene and 845 core gene sequences revealed that the two strains formed a distinct lineage within the genus Brevibacterium, most closely related to B. aurantiacum NCDO 739^T (16S rRNA similarity, both 98.5%; dDDH, 46.7–46.8%; ANI, 91.9–92.1%). Strain HY170^T contained MK-8(H₂), diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG), galactose and ribose as the predominant menaquinone, major polar lipids, and main sugars in the cell wall teichoic acids, respectively. The meso-diaminopimelic acid (meso-DAP) was the diagnostic diamino acid of the peptidoglycan found in strain HY170^T. Anteiso-C_15:0 and anteiso-C_17:0 were the major fatty acids (> 10%) of strains HY170^T and HY001, with anteiso-C_17:1A predominant in strain HY170^T but absent in strain HY001. Mining the genomes revealed the presence of secondary metabolite biosynthesis gene clusters encoding for non-alpha poly-amino acids (NAPAA), ectoine, siderophore, and terpene. Based on results from the phylogenetic, chemotaxonomic and phenotypic analyses, the two strains could be classified as a novel species of the genus Brevibacterium, for which the name Brevibacterium zhoupengii sp. nov. is proposed (type strain HY170^T = CGMCC 1.18600^T = JCM 34230^T).

Paraliobacillus salinarum sp. nov., isolated from saline soil in Yingkou, China

A novel Gram-stain-positive, facultatively aerobic, slightly halophilic, endospore-forming bacterium, designated G6-18^T, was isolated from saline soil collected in Yingkou, Liaoning, PR China. Cells of strain G6-18^T grew at 10-37 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 8.0) and in the presence of 2-15 % (w/v) NaCl (optimum, 5 %). The strain could be clearly distinguished from the related species of the genus Paraliobacillus by its phylogenetic position and biochemical characteristics. It presented MK-7 as the major quinone and the dominant cellular fatty acids were iso-C_16 : 0, anteiso-C_15 : 0, C_16 : 0 and iso-C_14 : 0. The polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol as the major components. The G+C content of strain G6-18^T genome was 35.3 mol%. 16S rRNA analysis showed that strain G6-18^T had the highest similarity to Paraliobacillus ryukyuensis DSM 15140^T, reaching 97.0 %, followed by Paraliobacillus quinghaiensis CGMCC 1.6333^T with a value of 96.3 %. The average nucleotide identity values between strain G6-18^T and Paraliobacillus ryukyuensis DSM 15140^T, Paraliobacillus sedimins KCTC 33762^T, Paraliobacillus quinghaiensis CGMCC 1.6333^T and Paraliobacillus zengyii DSM 107811^T were 74.3, 72.0, 73.2 and 72.8 %, respectively, and the digital DNA-DNA hybridization values between strain G6-18^T and the neighbouring strains were 15.6, 13.8, 14.2 and 14.2 %, respectively. Based on phenotypic, chemotaxonomic and phylogenetic inferences, strain G6-18^T represents a novel species of the genus Paraliobacillus, for which the name Paraliobacillus salinarum sp. nov. (=CGMCC 1.12058^T=DSM 25428^T) is proposed.

Georgenia faecalis sp. nov. isolated from the faeces of Tibetan antelope

Two aerobic, Gram-stain-positive, non-motile, non-sporulating coccoid strains, designated ZLJ0423^T and ZLJ0321, were isolated from the faeces of Tibetan antelope (Pantholops hodgsonii). Their optimal temperature, NaCl concentration and pH for growth were 28°C, 0.5% (w/v) NaCl and pH 7.5, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains ZLJ0423^T and ZLJ0321 were very similar to each other (99.8%) and had a sequence similarity of 97.0% with Georgenia satyanarayanai NBRC 107612^T and Georgenia subflava CGMCC 1.12782^T. Phylogenomic analysis based on 688 core genes indicated that these strains formed a clade with G. satyanarayanai NBRC 107612^T and Georgenia wutianyii Z294. The predominant cellular fatty acids were anteiso-C_15:0, anteiso-C_15:1A and C_16:0. The major menaquinone was MK-8(H₄). The cell-wall amino acids consisted of alanine, lysine, glycine and aspartic acid, with lysine as the diagnostic diamino acid. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and two unidentified lipids formed the polar lipid profile. The DNA G + C content of both isolates was 73.9 mol%. The digital DNA-DNA hybridization value between strains ZLJ0423^T and ZLJ0321 was 91.2%, but their values with closely related species and other available type strains of the genus Georgenia were lower than the 70% threshold. On the basis of polyphasic taxonomic data, strains ZLJ0423^T and ZLJ0321 represent a novel species within the genus Georgenia, for which the name Georgenia faecalis sp. nov. is proposed. The type strain is ZLJ0423^T (= CGMCC 1.13681^T = JCM 33470^T).

Luteimonas yindakuii sp. nov. isolated from the leaves of Dandelion (Taraxacum officinale) on the Qinghai-Tibetan Plateau

Two strains (S-1072^T and 1626) of Gram-stain-negative, oxidase- and catalase-positive, aerobic, rod-shaped, motile bacteria with a single polar flagellum, were isolated from the leaves of Dandelion (Taraxacum officinale) on the Qinghai-Tibet Plateau of China. The cells grew optimally at 28 °C, pH 7.0 and with 0.5 % (w/v) NaCl on brain-heart infusion agar. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains S-1072^T and 1626 belong to the genus Luteimonas, sharing the highest similarity with Luteimonas arsenica CCTCC AB 2014326^T (97.0 %), Luteimonas terricola CGMCC 1.8985^T (96.9 %) and Luteimonas aestuarii KCTC 22048^T (96.6 %). The phylogenomic tree indicated that strains S-1072^T and 1626 were most closely related to Luteimonas abyssi CGMCC 1.12611^T. The biochemical characteristics revealed that strains S-1072^T and 1626 could neither produce trypsin nor produce acid from d-glucose, N-acetylglucosamine and maltose, distinguishing them from four closest relatives. The DNA G+C contents of strains S-1072^T and 1626 were 69.2 and 69.3 mol% respectively. The digital DNA-DNA hybridization values of our isolates with their four closely related species were below the 70 % threshold. The predominant menaquinone was Q-8 (98.7 %) and the major polar lipids included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids (>10 %) were iso-C_15 : 0, iso-C_16 : 0 and summed feature 9 (10-methyl C_16 : 0 and/or iso-C_17 : 1 ω9c). Based on the data obtained, strains S-1072^T and 1626 should be classified as a novel species of the genus Luteimonas, for which the name Luteimonas yindakuii sp. nov. is proposed. The type strain is S-1072^T (=CGMCC 1.13927^T=JCM 33487^T).

Paracoccus liaowanqingii sp. nov., isolated from Tibetan antelope (Pantholops hodgsonii)

Two strains, designated 2251^T and 3058, that were aerobic, Gram-stain-negative, non-motile, coccoid or short rod-shaped bacilli, have recently been isolated from Tibetan antelopes on the Qinghai-Tibet Plateau. The results of phylogenetic analyses of 16S rRNA gene sequences indicated that strains 2251^T and 3058 represent a new species within the genus Paracoccus and are most similar to 'Paracoccus gahaiensis' CUG00006^T (98.9 and 99.3 %), Paracoccus nototheniae I-41R45^T (98.3 and 98.7 %) and Paracoccus hibiscisoli THG-T2.31^T (97.6 and 97.8 %). Results of genomic sequence-based phylogenomic analysis agreed with those from 16S rRNA gene sequence analysis. Optimal growth was achieved at pH 7.0-7.5 and 28 °C with marine medium. Cells contained C_18 : 1 ω7c as the major cellular fatty acid and ubiquinone-10 as the predominant menaquinone. The polar lipids comprised phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phospholipid, glycolipid and an unidentified lipid. The cell-wall peptidoglycan amino acids were meso-2,6-diaminopimelic acid, alanine and glutamic acid; the major cell-wall sugar was galactose. The G+C content of strain 2251^T was 66.5 mol%. Both strains (2251^T and 3058) had DNA-DNA relatedness values less than 50 % with all available genomes of the genus Paracoccus in the ncbi database. Differential genotypic inferences, together with phenotypic and biochemical characteristics, demonstrated that strains 2251^T and 3058 should be classified as a novel species of the genus Paracoccus, for which the name Paracoccus liaowanqingii sp. nov. is suggested. The type strain is 2251^T (=CGMCC 1.16490^T=DSM 106269^T).

Apibacter raozihei sp. nov. isolated from bat feces of Hipposideros and Taphozous spp

Strains HY041^T and HY039 were oxidase- and Gram-stain-negative, catalase-positive, rod-shaped, non-motile, and facultatively anaerobic bacteria. They were isolated from the feces of bats of the Hipposideros and Taphozous spp. collected from Chongqing City and Guangxi province (PR China), respectively. Phylogenetic analysis based on the 16S rRNA gene and 463 core genes indicated that HY041^T and HY039 represent members of the genus Apibacter, forming a clade with Apibacter adventoris wkB301^T (95.2 % 16S rRNA gene sequence similarity) and Apibacter mensalis R-53146^T (94.0 %). In silico DNA-DNA hybridization (isDDH) and average nucleotide identity (ANI) values of our isolates with the most closely related species were lower than the 70 % and 95-96 % threshold, respectively, in contrast to values above these two thresholds (isDDH value: 89.1 %; ANI value: 98.5 %) between strains HY041^T and HY039. The novel isolates could grow on nutrient and MacConkey agar. HY041^T and HY039 could produce β-galactosidase and N-acetyl-β-glucosaminidase, and utilize d-adonitol, d-mannose, gentiobiose, glucose and salicin. The major fatty acids (>10.0 %) of HY041^T were iso-C_17 : 0 3OH, iso-C_15 : 0, C_16 : 0, summed feature 9 (C_16 : 0 10-methyl and/or iso-C_17 : 1ω9c) and C_16 : 0 3OH. Polar lipids included phosphatidylethanolamine, glycolipid, two unidentified aminolipids and four unidentified lipids. Menaquinone 6 (MK-6) was the sole respiratory quinone. On the basis of all analyses so far, strains HY041^T and HY039 represent a novel species of the genus Apibacter, for which the name Apibacter raozihei sp. nov. is proposed. The type strain is HY041^T (=CGMCC 1.16567^T=JCM 33423^T) with a genomic DNA G+C content of 32.2 mol%.