Salinibacterium hongtaonis sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau

Salinibacterium soli sp. nov., isolated from lakeside soil

A Gram-stain-positive, rod-shaped, non-spore-forming and non-motile bacterium, designated strain WY-16T. Growth was observed at 20-42 °C (optimum, 30 °C), pH 6-9 (optimum, pH 7) and salinity of 0-3 % (w/v; optimum, 1 %). Phylogenetic analysis based on genome sequences indicated that WY-16T was affiliated to the family Microbacteriaceae and most closely related to Salinibacterium xinjiangense and Salinibacterium amurskyense. The average nucleotide identity values between strain WY-16T and S. xinjiangense and S. amurskyense were 74.7 and 72.5 %, respectively. The digital DNA-DNA hybridization values between strain WY-16T and S. xinjiangense and S. amurskyense were 19.6 and 18.6 %, respectively. The predominant fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C16 : 0 10-methyl. The major menaquinones were MK-12, MK-13, MK-14 and MK-15. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified glycolipid and one unidentified phospholipid. The cell-wall peptidoglycan contained 2,4-diaminobutyric acid as the diamino acid and ribose, rhamnose, glucose and galactose were the major cell-wall sugars. Based on phenotypic, genotypic and phylogenetic evidence, strain WY-16T represents a novel species in the genus Salinibacterium, for which the name Salinibacterium soli sp. nov. is proposed. The type strain is WY-16T (=GDMCC 1.4011T=JCM 36421T).

Nocardioides bizhenqiangii sp. nov. and Nocardioides renjunii sp. nov., isolated from soil and faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau

Two novel strain pairs (HM61T/HM23 and S-34T/S-58) were isolated from soil and the faeces of Tibetan antelope (Pantholops hodgsonii) collected at the Qinghai-Tibet Plateau of PR China. All four new isolates were aerobic, non-motile, Gram-stain-positive, catalase-positive, oxidase-negative, and short rod-shaped bacteria. The results of phylogenetic analysis based on the full-length 16S rRNA genes and 283 core genomic genes indicated that the four strains were separated into two independent branches belonging to the genus Nocardioides. Strains HM61T and HM23 were most closely related to Nocardioides pelophilus THG T63T (98.58 and 98.65 % 16S rRNA gene sequence similarity). Strains S-34T and S-58 were most closely related to Nocardioides okcheonensis MMS20-HV4-12T (98.89 and 98.89 % 16S rRNA gene sequence similarity). The G+C contents of the genomic DNA of strains HM61T and S-34T were 70.6 and 72.5 mol%, respectively. Strains HM61T, S-34T and the type strains of closely related species in the analysis had average nucleotide identity values of 75.4-90.5 % as well as digital DNA-DNA hybridization values between 20.1 and 40.8 %, which clearly indicated that the four isolates represent two novel species within the genus Nocardioides. The chemotaxonomic characteristics of strains HM61T and S-34T were consistent with the genus Nocardioides. The major fatty acids of all four strains were iso-C16 : 0, C17 : 1  ω8c or C18 : 1  ω9c. For strains HM61T and S-34T, MK-8(H4) was the predominant respiratory quinone, ll-2,6-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan, and the polar lipids profiles were composed of diphosphatidylglycerol and phosphatidylglycerol. Based on phylogenetic, phenotypic, and chemotaxonomic data, we propose that strains HM61T and S-34T represent two novel species of the genus Nocardioides, respectively, with the names Nocardioides bizhenqiangii sp. nov. and Nocardioides renjunii sp. nov. The type strains are HM61T (=GDMCC 4.343T=JCM 36399T) and S-34T (=CGMCC 4.7664T=JCM 33792T).

Antiquaquibacter oligotrophicus gen. nov., sp. nov., a novel oligotrophic bacterium from groundwater

In this study, a Gram-stain-positive, non-motile, oxidase- and catalase-negative, rod-shaped, bacterial strain (SG_E_30_P1T) that formed light yellow colonies was isolated from a groundwater sample of Sztaravoda spring, Hungary. Based on 16S rRNA phylogenetic and phylogenomic analyses, the strain was found to form a distinct linage within the family Microbacteriaceae. Its closest relatives in terms of near full-length 16S rRNA gene sequences are Salinibacterium hongtaonis MH299814 (97.72 % sequence similarity) and Leifsonia psychrotolerans GQ406810 (97.57 %). The novel strain grows optimally at 20-28 °C, at neutral pH and in the presence of NaCl (1-2 w/v%). Strain SG_E_30_P1T contains MK-7 and B-type peptidoglycan with diaminobutyrate as the diagnostic amino acid. The major cellular fatty acids are anteiso-C15 : 0, iso-C16 : 0 and iso-C14 : 0, and the polar lipid profile is composed of diphosphatidylglycerol and phosphatidylglycerol, as well as an unidentified aminoglycolipid, aminophospholipid and some unidentified phospholipids. The assembled draft genome is a contig with a total length of 2 897 968 bp and a DNA G+C content of 65.5 mol%. Amino acid identity values with it closest relatives with sequenced genomes of <62.54 %, as well as other genome distance results, indicate that this bacterium represents a novel genus within the family Microbacteriaceae. We suggest that SG_E_30_P1T (=DSM 111415T=NCAIM B.02656T) represents the type strain of a novel genus and species for which the name Antiquaquibacter oligotrophicus gen. nov., sp. nov. is proposed.

Salinibacterium sedimenticola sp. nov., Isolated from Tidal Flat Sediment

An actinobacterium, designated as SYSU T00001^T, was isolated from a tidal flat sediment sample from Guangdong province, China. Cells were Gram-stain-positive, aerobic, motile and short rod-shaped. Colonies on marine agar 2216 were smooth, yellow-pigmented, and circular with low convexity. The isolate was able to grow at the temperature range 4-37 °C (optimum 30 °C), at pH 4.0-10.0 (optimum 7.0) and in the presence of 0-10% (w/v) NaCl. The major menaquinones were MK-11 and MK-10. The cell wall contained alanine, glutamic acid, lysine and ornithine. The major fatty acids were C_19:0 cyclo ω8c (35.7%) and anteiso C_15:0 (26.0%). The polar lipids consisted of one diphosphatidyl glycerol, one unidentified glycolipid and one unknown lipid. Whole genome sequencing of strain SYSU T00001^T revealed 2,837,702 bp with a DNA G + C content of 67.8%. Phylogenetic analyses clearly demonstrated that strain SYSU T00001^T belonged to the genus Salinibacterium, and the highest 16S rRNA gene similarity to Salinibacterium hongtaonis 194^T (97.8%). The ANI and dDDH values of strain SYSU T00001^T relative to Salinibacterium hongtaonis 194^T were 74.5% and 19.5%, respectively. According to our data, strain SYSU T00001^T represents a novel species of the genus Salinibacterium, for which the name Salinibacterium sedimenticola sp. nov. is proposed, the type strain is SYSU T00001^T (= GDMCC 1.3283^T = KCTC 49758^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.

First report on antibiotic resistance and antimicrobial activity of bacterial isolates from 13,000-year old cave ice core

Despite the unique physiology and metabolic pathways of microbiomes from cold environments providing key evolutionary insights and promising leads for discovering new bioactive compounds, cultivable bacteria entrapped in perennial ice from caves remained a largely unexplored life system. In this context, we obtained and characterized bacterial strains from 13,000-years old ice core of Scarisoara Ice Cave, providing first isolates from perennial ice accumulated in caves since Late Glacial, and first culture-based evidences of bacterial resistome and antimicrobial compounds production. The 68 bacterial isolates belonged to 4 phyla, 34 genera and 56 species, with 17 strains representing putative new taxa. The Gram-negative cave bacteria (Proteobacteria and Bacteroidetes) were more resistant to the great majority of antibiotic classes than the Gram-positive ones (Actinobacteria, Firmicutes). More than 50% of the strains exhibited high resistance to 17 classes of antibiotics. Some of the isolates inhibited the growth of clinically important Gram-positive and Gram-negative resistant strains and revealed metabolic features with applicative potential. The current report on bacterial strains from millennia-old cave ice revealed promising candidates for studying the evolution of environmental resistome and for obtaining new active biomolecules for fighting the antibiotics crisis, and valuable cold-active biocatalysts.

Aeromicrobium chenweiae sp. nov. and Aeromicrobium yanjiei sp. nov., isolated from Tibetan antelope (Pantholops hodgsonii) and plateau pika (Ochotona curzoniae), respectively

Four novel strains (592^T, S592, MF47^T and SMF47) were isolated from Tibetan antelopes (Pantholops hodgsonii) and plateau pikas (Ochotona curzoniae), respectively. The cells were aerobic, non-motile, Gram-stain- and catalase-positive, rod-shaped bacteria. The 16S rRNA gene sequences of the four strains showed highest similarities to Aeromicrobium fastidiosum DSM 10552^T (98.1, 98.6, 98.7 and 98.7 %, respectively), and the phylogenetic analyses based on 16S rRNA gene and genomic sequences indicated that strains 592^T and MF47^T represent two novel species. The four isolates produced acid from l-rhamnose, d-xylose and cellobiose, but were unable to reduce nitrate. The DNA G+C contents of strains 592^T and MF47^T were 70.3 and 69.8 mol%, respectively. The digital DNA-DNA hybridization value between strains 592^T and MF47^T was 32.6 %, lower than the threshold of 70 %, indicating they belong to different species. The four strains' genomes displayed less than 24.6 % DNA-DNA relatedness with all available genomes of the genus Aeromicrobium in the NCBI database, including Aeromicrobium fastidiosum NBRC 14897^T and Aeromicrobium ginsengisoli JCM 14732^T. The major fatty acids of the four strains were C_18 : 1  ω9c and C_18 : 0 10-methyl, and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The predominant respiratory quinones were MK-9(H₄) and MK-8(H₄). The cell-wall peptidoglycan contained ll-diaminopimelic acid. Based on these genotypic, phenotypic and biochemical analyses, it is proposed that the four unidentified bacteria be classified as two novel species, Aeromicrobium chenweiae sp. nov. and Aeromicrobium yanjiei sp. nov. The type strains are 592^T (=CGMCC1.16526^T=DSM 106289^T) and MF47^T (=CGMCC 1.17444^T=JCM 33790^T), respectively.

Microbacterium wangchenii sp. nov., isolated from faeces of Tibetan gazelles (Procapra picticaudata) on the Qinghai-Tibet Plateau

Two strains of Gram-stain-positive, aerobic, non-spore-forming, non-motile, rod-shaped bacteria (designated dk512^T and dk508) were isolated from the faeces of Tibetan gazelle (Procapra picticaudata) collected from the Qinghai-Tibet Plateau, PR China. The 16S rRNA gene sequences of the strains showed the highest identity to Microbacterium saccharophilum K-1^T (98.0 and 97.9 % similarity, respectively). The phylogenetic analysis based on 16S rRNA gene sequences revealed that dk512^T and dk508 were members of the genus Microbacterium, and most closely related to strains Microbacterium mitrae M4-8^T and Microbacterium hatanonis FCC-01^T. The strains grew optimally on brain-heart infusion (BHI) agar with 5.0 % (v/v) sheep blood at 30 °C, pH 7.0 and with 1.0 % (w/v) NaCl. The genome of type strain dk512^T was 3.8 Mb with a G+C content of 70.6 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain dk512^T and previously characterized Microbacterium species were <95 and <70 %, respectively. In strain dk512^T, the detected primary cellular fatty acids were anteiso-C_15 : 0 and anteiso-C_17 : 0, the main respiratory quinones were MK-9 (37.9 %) and MK-10 (35.7 %), and the polar lipids included diphosphatidylglycerol, phosphatidylglycerol and three unidentified glycolipids. The major cell-wall sugars were rhamnose, ribose and galactose. Alanine, glutamic acid, glycine and ornithine were in the cell-wall peptidoglycan. Based on phenotypic data and phylogenetic inference, these two strains represent a novel species of the genus Microbacterium, named here as Microbacterium wangchenii sp. nov, where dk512^T is designated the type strain (=CGMCC 1.16590^T=JCM 33494^T=KCTC 49313^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).

Mumia zhuanghuii sp. nov., isolated from the intestinal contents of plateau pika (Ochotona curzoniae) on the Qinghai-Tibet Plateau

Two Gram-staining-positive, catalase-positive, oxidase-negative, aerobic, non-motile, irregular rod-shaped bacterial strains (Z350^T and Z527) were isolated from intestinal contents of plateau pika (Ochotona curzoniae) from the Qinghai-Tibet Plateau, PR China. Results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain Z350^T belongs to the genus Mumia (family Nocardioidaceae) but clearly differs from the currently recognized species Mumia xiangluensis DSM 101040^T (98.4 % similarity) and Mumia flava DSM 27763^T (97.4 %). Strain Z350^T had a DNA G+C content of 70.7 mol% and shared 80.4 and 76.7 % average nucleotide identity values and 23.4 and 20.6 % in silico DNA-DNA hybridization relatedness with M. xiangluensis DSM 101040^T and M. flava DSM 27763^T, respectively. Further phylogenetic analyses based on 497 core genes indicated that our isolates were members of the genus Mumia but separated from all existing genera within the family Nocardioidaceae. The major cellular fatty acids were C_{18 : 1} ω9c and 10-methyl C_{18 : 0}. The cell wall contained ll-diaminopimelic acid as the diamino acid, and rhamnose, ribose and glucose as whole cell-wall sugars. MK-9(H₄) was detected as the major menaquinone. Polar lipids present were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified phospholipid. Based on distinct differences in the genotypic and phenotypic data from the two Mumia species, a novel species, Mumia zhuanghuii sp. nov., is proposed. The type strain is Z350^T (=CGMCC 4.7464^T=DSM 106288^T).