Tzu-Yu Lin

A polyphasic taxonomic approach was employed to characterize a novel bacterium, designated strain CC-YST694^T, isolated from a poultry manure sample in Taiwan. The cells were Gram-stain-negative, aerobic, rod-shaped, non-flagellated, catalase- and oxidase-positive, and capable of growth at 15–45 ℃ (optimum, 30 ℃), at pH 6.0–9.0 (optimum, pH 9.0), and in the presence of 0–9% (w/v) NaCl (optimum, 6%). The genome size was 3.27 Mb, with a genomic DNA G + C content of 62.8%. The primary polyamine was spermidine and predominant respiratory quinone was ubiquinone-10. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, and sphingoglycolipid. The major cellular fatty acids (> 5%) were C_16:0, C_18:1 ω7c 11-methyl, C_14:0 2OH, iso-C_17:0 3OH, and C_18:1 ω6c and/or C_18:1 ω7c. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CC-YST694^T was close to Altererythrobacter fulvus S-54 ^T. The 85.3% OrthoANI, 87.3% AAI, and 28.7% dDDH between strain CC-YST694^T and A. fulvus S-54 ^T were all well below the accepted species delineation thresholds, indicating that strain CC-YST694^T should represent a putative novel species. Moreover, phylogenomic and chemotaxonomic analyses indicated that strain CC-YST694^T and A. fulvus S-54 ^T forms a distinct monophyletic clade that is separate from other genera and thus should be classified as a novel genus. Based on the results of phylogenetic, phylogenomic, genomic relatedness, and chemotaxonomic analyses, strain CC-YST694ᵀ is proposed to represent a novel genus and species within the family Erythrobacteraceae, for which the name Fulverythrobacter ferritrahens gen. nov., sp. nov. is proposed. The type strain is CC-YST694^T (= BCRC 81283 ^T = JCM 34166 ^T).

A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-CFT758^T, isolated from a maize-rice rotation agriculture field in Taiwan. The cells are aerobic, Gram-stain-negative, rod-shaped, positive for catalase and oxidase, and grow at 20–30 °C (optimal 30 ℃), at pH 6.0–8.0 (optimal 8.0), and with 0–4% (w/v) NaCl (optimum, 2–3%). Phylogenetic analysis based on 16S rRNA gene sequencing, the strain CC-CFT758^T belongs to the genus “Aliirhizobium” of the family Rhizobiaceae. The closest known relatives of this strain are “Aliirhizobium wenxiniae” 166^T (with 98.7% similarity), “Aliirhizobium cellulosilyticum” SEMIA 448^T (with 97.9% similarity), and “Aliirhizobium smilacinae” PTYR-5^T (with 97.0% similarity). The genome size was 5.9 Mbp, with a G + C content of 60.6%. Values of digital DNA–DNA hybridization between the strain and closely related species were 29.5% for “Ali. cellulosilyticum”, and 23.9% for “Ali. wenxiniae” and “Ali. smilacinae”. Strain CC-CFT758^T exhibited the highest orthologous average nucleotide identity (OrthoANI) values with members of the genus “Aliirhizobium”, ranging from 80.4 to 81.6% (n = 3). Chemotaxonomical analysis indicated that strain CC-CFT758^T contained C_16:0, C_16:0 3OH, C_19:0 cyclo ω8c, C_14:0 3OH/iso-C_16:1 I, and C_18:2 ω6,9c/ante C_18:0 as dominant fatty acids, and the major polyamines were putrescine and spermidine. The polar lipids comprised diphosphatidylglycerol, phosphatidylcholin, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, seven unidentified aminolipids, three unidentified phospholipids, and two unidentified polar lipids. Strain CC-CFT758^T exhibited distinct phylogenetic, phenotypic, and chemotaxonomic characteristics, as well as unique results in comparative analysis of 16S rRNA gene sequence, OrthoANI, AAI, dDDH, and phylogenomic placement. Therefore, this strain represents a new species of the genus “Aliirhizobium”, for which the name Aliirhizobium terrae sp. nov. is proposed, with the type strain is CC-CFT758^T (= BCRC 81364^T = JCM 35482^T).

Nontuberculous mycobacteria (NTM) are any mycobacteria that do not cause tuberculosis or leprosy. While the majority of NTM are harmless and some of them are considered probiotic, a growing number of people are being diagnosed with NTM infections. Therefore, their detection in the environment is of interest to clinicians, environmental microbiologists, and water quality researchers alike. This review provides a tutorial on the foundational approaches for taxonomic classifications, with a focus on the phylogenetic relationships among NTM revealed by the 16S rRNA gene, rpoB gene, and hsp65 gene, and by genome-based approaches. Recent updates on the Mycobacterium genus taxonomy are also provided. A synthesis on the habitats of 189 mycobacterial species in a genome-based taxonomy framework was performed, with attention paid to environmental sources (e.g., drinking water, aquatic environments, and soil). The 16S rRNA gene-based classification accuracy for various regions was evaluated (V3, V3–V4, V3–V5, V4, V4–V5, and V1–V9), revealing overall excellent genus-level classification (up to 100% accuracy) yet only modest performance (up to 63.5% accuracy) at the species level. Future research quantifying NTM species in water systems, determining the effects of water treatment and plumbing conditions on their variations, developing high throughput species-level characterization tools for use in the environment, and incorporating the characterization of functions in a phylogenetic framework will likely fill critical knowledge gaps. We believe this tutorial will be useful for researchers new to the field of molecular or genome-based taxonomic profiling of environmental microbiomes. Experts may also find this review useful in terms of the selected key findings of the past 30 years, recent updates on phylogenomic analyses, as well as a synthesis of the ecology of NTM in a phylogenetic framework.

A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-YST667^T, isolated from poultry manure sampled in Taiwan. The cells were observed to be aerobic, motile and non-spore-forming rods, displaying positive reactions for oxidase. Optimal growth of CC-YST667^T was observed at 25 °C, pH 8.0 and with 1 % (w/v) NaCl. The polar lipid profile consisted of phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and multiple unidentified polar lipids. The major polyamine was spermidine. The major cellular fatty acids (>5 %) included C_16 : 0, C_17 : 0cyclo, C_19 : 0cyclo ω8c and C_14 : 0 3OH/iso-C_16 : 1 I. On the basis of the results of analysis of 16S rRNA gene sequences, this isolate showed the closest phylogenetic relationship with ‘Neopusillimonas minor’ (with 98.2 % similarity) and Paralcaligenes ureilyticus (with 97.3 % similarity) of the family Alcaligenaceae . The draft genome, (3.3 Mb) with a DNA G+C content of 57.2 mol%, harboured various genes involved in the biodegradation of aromatic hydrocarbons. CC-YST667^T shared highest orthologous average nucleotide identity (OrthoANI) with the type strains of species of of the genera Neopusillimonas (72.4‒77.9 %, n=2), Pusillimonas (72.8‒73.0 %, n=2) and Pollutimonas (71.7‒73.0 %, n=5). On the basis of its distinct phylogenetic, phenotypic and chemotaxonomic traits together with the results of comparative 16S rRNA gene sequencing, OrthoANI, digital DNA–DNA hybridization (DDH) and the phylogenomic placement, strain CC-YST667^T is considered to represent a novel species of the genus Neopusillimonas, for which the name Neopusillimonas aromaticivorans sp. nov. is proposed. The type strain is CC-YST667^T (=BCRC 81321^T =JCM 34761^T).