Wei-Ling Zhang

A microbial community study using a culture-dependent method was conducted on dehydrated sludge collected from a steel factory’s wastewater treatment plant. One isolate, designated QWL-01^T, was a strictly anaerobic, Gram-stain-negative, non-motile, non-spore-forming bacterium with coccoid cells measuring 0.6–0.9 μm in diameter. The growth of strain QWL-01^T was observed at 4–40 °C (optimum at 28–35 °C), pH 5.5–8.0 (optimum at pH 7.1), and a range of 0–3% NaCl (optimum at 0.5%). An analysis of the Biolog AN plate revealed positive carbon source utilization only for palatinose, α-ketovaleric acid, and pyruvic acid. The predominant fatty acids were iso-C_13:0 (17.0%), C_16:0 dimethyl acetal (12.0%), and anteiso-C_13:0 (9.2%). A 16S rRNA gene sequence analysis through BLASTN demonstrated that the nearest phylogenetic neighbors of the novel strain were Youngiibacter multivorans DSM 6139^T (93.82%) and Proteiniclasticum ruminis JCM 14817^T (93.75%). The genome size of strain QWL-01^T was 3.69 Mbp, with a G+C content of 50.8 mol%. Comparing strain QWL-01^T with closely related species of genera Proteiniclasticum and Youngiibacter, the digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), and average amino acid identity (AAI) values ranged from 26.60% to 36.80%, 65.89% to 68.30%, and 49.27% to 51.58%, respectively. Based on phenotypic, physiological, phylogenetic, and genomic relatedness evidence, strain QWL-01^T represents a novel genus in the family Clostridiaceae, for which the name Anaerococcoides asporogena gen. nov. sp. nov. is proposed. Strain QWL-01^T (=BCRC 81396^T = CICC 25258^T = NBRC 117088^T) is the type strain of the proposed novel species.

Here, we report the complete genome sequence of Oscillospiraceae bacterium MB24-C1 (= BCRC 81428), isolated from sewage sludge of the Sanming Steel wastewater treatment plant, China. The genome comprises 2,952,321 bp with a GC content of 48.1% and was used for further species delineation and comparative genomic analyses.

Here, we report the complete genome sequence of Bacteroidales bacterium strain MB20-C3-3 (=BCRC 81427) isolated from sewage sludge. The genome is 2,379,874 bp in length with a guanine and cytosine content of 40.0%. The genome of strain MB20-C3-3 was used for further species delineation and comparative genomic analyses.

Here, we report the complete genome sequence of Oscillospiraceae bacterium MB08-C2-2 (=BCRC 81394), isolated from feces of black soldier fly ( Hermetia illucens ) larvae, comprising 3,292,498 bp, a GC content of 49.67%, and identification of a 72,574 bp plasmid for further species delineation and comparative genomic analysis.

The gut microbiota of Tenebrio molitor has attracted attention for its potential in solving plastic waste problems. Here, we report the complete genome sequence of Propionimicrobium sp. PCR01-08-3, isolated from the feces of Tenebrio molitor larvae. The genome of strain PCR01-08-3 was selected for further species delineation and comparative genomic analysis.

A novel mesophilic, hydrogenotrophic methanogen, strain CWC-01^T, was isolated from the sediment sample of the piston core collected at station 3 at Good Weather Ridge area offshore southwestern Taiwan from ORI-902A cruise in 2009. Cells of strain CWC-01^T are rod-shaped, measuring 0.4–0.5 µm in width and 1.0–2.0 µm in length. Strain CWC-01^T utilizes formate and H₂/CO₂ to produce methane, but not secondary alcohol, methanol, ethanol, methylamines or acetate as catabolic substrates. The optimal growth conditions are 37 °C, 0.043 M NaCl and pH 6.3. Growth effectors tests indicate tryptone, but not acetate and yeast extract, could stimulate the growth of strain CWC-01. Phylogenetic analysis of 16S rRNA gene reveals that strain CWC-01^T is most closely related to Methanobacterium petrolearium Mic5c12^T, with 96.63% identity. Genome size of strain CWC-01^T is 1.98 Mb and it is the smallest genome size of genus. The genomic DNA G+C content obtained from the genome sequence of strain CWC-01^T is 44.15 mol%. Based on these phenotypic, phylogenetic and genomic analyses, we propose that strain CWC-01^T represents a novel species in genus Methanobacterium, for which the name Methanobacterium aridiramus sp. nov. is proposed. The type strain is CWC-01^T (=BCRC AR10053^T=NBRC 113991^T).

A hydrogenotrophic methanoarchaeon, designated strain FWC-SCC4^T, was isolated from cold seep sediment of Four-Way Closure Ridge, offshore southwestern Taiwan. Strain FWC-SCC4^Tutilizes H₂/CO₂ or formate, but not acetate, secondary alcohols, methylamines, methanol or ethanol for growth and methane production. Yeast extract is required for growth. The cell morphology is coccoid, with a diameter of 0.8–1.2 µm, and the cell envelope is composed of S-layer protein with M_r about 137.00 kDa. Cells possess multiple flagella and usually occur singly. Strain FWC-SCC4^T grows at a temperature range of 20–40 °C (optimum 37 °C) and a pH range of 5.4–7.2 (optimum 7.0). The NaCl range for growth is 0–0.86 M (optimum 0.09 M). The result of phylogenetic analysis of 16S rRNA gene sequences indicates that the most closely related species are Methanoplanus limicola M3^T and Methanoplanus endosymbiosus MC1^T, with similarities of 95.95 and 95.63%, respectively. The G+C content of the genomic DNA is 40.3 mol%. The overall genome-relatedness indexes (OGRIs) and concatenated ribosomal protein (RBP) phylogenic analysis indicate that strain FWC-SCC4^T is a novel lineage of Methanomicrobiaceae. In addition to strain FWC-SCC4^T, the differences between Methanomicrobium antiquum MobH^T and Methanomicrobium mobile BP^T demonstrated by comparative analysis of genomic G+C content and phylogenetic analysis with non-type strain genomes are enough to support the establishment of a novel genus. In conclusion, strain FWC-SCC4^T (BCRC AR10058^T= NBRC 114595^T) is proposed as the type strain of Methanochimaera problematica gen. nov., sp. nov., and Methanoeremita antiquus gen. nov., comb. nov. is proposed as the new name for Methanomicrobium antiquum MobH^T (=DSM 21220^T= NBRC 104160^T).

Two Gram-stain-negative, straight rods, non-motile, asporogenous, catalase-negative and obligately anaerobic butyrate-producing strains, HLW78^T and CYL33, were isolated from faecal samples of two healthy Taiwanese adults. Phylogenetic analyses of 16S rRNA and DNA mismatch repair protein MutL (mutL) gene sequences revealed that these two novel strains belonged to the genus Faecalibacterium. On the basis of 16S rRNA and mutL gene sequence similarities, the type strains Faecalibacterium butyricigenerans AF52-21^T(98.3–98.1 % and 79.0–79.5 % similarity), Faecalibacterium duncaniae A2-165^T(97.8–97.9 % and 70.9–80.1 %), Faecalibacterium hattorii APC922/41-1^T(97.1–97.3 % and 80.3–80.5 %), Faecalibacterium longum CM04-06^T(97.8–98.0% and 78.3 %) and Faecalibacterium prausnitzii ATCC 27768^T(97.3–97.4 % and 82.7–82.9 %) were the closest neighbours to the novel strains HLW78^T and CYL33. Strains HLW78^T and CYL33 had 99.4 % both the 16S rRNA and mutL gene sequence similarities, 97.9 % average nucleotide identity (ANI), 96.3 % average amino acid identity (AAI), and 80.5 % digital DNA–DNA hybridization (dDDH) values, indicating that these two strains are members of the same species. Phylogenomic tree analysis indicated that strains HLW78^T and CYL33 formed an independent robust cluster together with F. prausnitzii ATCC 27768^T. The ANI, AAI and dDDH values between strain HLW78^T and its closest neighbours were below the species delineation thresholds of 77.6–85.1 %, 71.4–85.2 % and 28.3–30.9 %, respectively. The two novel strains could be differentiated from the type strains of their closest Faecalibacterium species based on their cellular fatty acid compositions, which contained C_18 : 1  ω7c and lacked C_15 : 0 and C_17 : 1  ω6c, respectively. Phenotypic, chemotaxonomic and genotypic test results demonstrated that the two novel strains HLW78^T and CYL33 represented a single, novel species within the genus Faecalibacterium, for which the name Faecalibacterium taiwanense sp. nov. is proposed. The type strain is HLW78^T (=BCRC 81397^T=NBRC 116372^T).