Food Industry Research and Development Institute

A novel mesophilic, hydrogenotrophic methanogen, strain CWC-01T, 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-01T are rod-shaped, measuring 0.4-0.5 µm in width and 1.0-2.0 µm in length. Strain CWC-01T 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-01T is most closely related to Methanobacterium petrolearium Mic5c12T, with 96.63% identity. Genome size of strain CWC-01T 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-01T is 44.15 mol%. Based on these phenotypic, phylogenetic and genomic analyses, we propose that strain CWC-01T represents a novel species in genus Methanobacterium, for which the name Methanobacterium aridiramus sp. nov. is proposed. The type strain is CWC-01T (=BCRC AR10053T=NBRC 113991T).

ABSTRACT \\Levels of progesterone, an endogenous female hormone, increase after ovulation; progesterone is crucial in the luteal phase to maintain successful pregnancy and prevent early miscarriage. Both endogenous and exogenous progesterone are recycled between the liver and gut; thus, the gut microbiota regulate host progesterone levels by inhibiting enterohepatic progesterone circulation. Our data indicated Clostridium innocuum as a major species involved in gut progesterone metabolism in women with infertility. C. innocuum converts progesterone into the neurosteroid epipregnanolone (with negligible progestogenic activity). We purified and characterized the corresponding enzyme, namely NADPH-dependent 5β-dihydroprogesterone reductase, which is highly oxygen sensitive and whose corresponding genes are prevalent in C. innocuum. Moreover, C. innocuum–administered female C57BL/6 mice (aged 7 weeks) exhibited decreased plasma progesterone levels (~35%). Clostridium-specific antibiotics (metronidazole) restored low plasma progesterone levels in these mice. Furthermore, prolonged C. innocuum administration (12 weeks) arrested ovarian follicular development in female mice. Cytological and histological analyses indicated that C. innocuum may cause luteal phase insufficiency and affect menstrual regularity. Our findings suggest C. innocuum as a causal factor of progesterone resistance in women taking progesterone.

Abstract The development of electronic networks promotes economic growth and international trade flows. Because of the short life cycle of electrical and electronic equipment, considerable electronic waste (e‐waste) is generated. We identified the determinants of e‐waste trade, focusing on ASEAN+6 countries and their trading partners for the years 2000 to 2018. The empirical results regarding trade value and trade weight revealed that electronic networks significantly promoted the import of e‐waste into ASEAN+6 countries. The results were robust to using different measures of electronic networks and different estimation methods.

Streptococcus spp. are important opportunistic pathogen of bacteremia in both immunocompetent and immunosuppressed patients. A streptococcal strain, designated ST2T, was isolated from the blood specimen of a bacteremic patient. Comparative analyses of 16S rRNA, rpoB and groEL gene sequences demonstrated that the novel strain ST2T is a member of the genus Streptococcus. Based on of 16S rRNA gene sequence similarities, the type strains of Streptococcus (S.) parasanguinis (99.2%), S. ilei (98.8%), S. oralis subsp. oralis (97.6%), S. australis (97.5%) and S. sanguinis (97.5%) were the closest neighbours to strain ST2T. The housekeeping gene sequences (rpoB and groEL) similarities of strain ST2T to these closely related type strains were 80.4-97.4%, respectively. The complete draft genome of strain ST2T consisted of 2,155,906bp with a G + C content of 42.0%. Strain ST2T has an average nucleotide identity (ANI) value of 94.1 and 81.3% with S. parasanguinis ATCC 15912T and S. ilei I-G2T, respectively. The highest in silico DNA-DNA hybridization value with respect to the closest species S. parasanguinis was 55.6%, below the species cut-off of 70% hybridization. The primary cellular fatty acids of strain ST2T were C16:0, C18:1 ω9c, C18:0 and C14:0. Based on biochemical criteria and molecular genetic evidence, it is proposed that strain ST2T be assigned to a new species of the genus Streptococcus as Streptococcus taoyuanensis sp. nov. The type strain of Streptococcus taoyuanensis is ST2T (=NBRC 115928T = BCRC 81374T) as the type strain.

Two Gram-stain-negative, straight rods, non-motile, asporogenous, catalase-negative and obligately anaerobic butyrate-producing strains, HLW78T 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 AF52-21T(98.3–98.1 % and 79.0–79.5 % similarity), Faecalibacterium duncaniae A2-165T(97.8–97.9 % and 70.9–80.1 %), Faecalibacterium hattorii APC922/41-1T(97.1–97.3 % and 80.3–80.5 %), Faecalibacterium longum CM04-06T(97.8–98.0% and 78.3 %) and Faecalibacterium prausnitzii ATCC 27768T(97.3–97.4 % and 82.7–82.9 %) were the closest neighbours to the novel strains HLW78T and CYL33. Strains HLW78T 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 HLW78T and CYL33 formed an independent robust cluster together with F. prausnitzii ATCC 27768T. The ANI, AAI and dDDH values between strain HLW78T 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 C18 : 1 ω7c and lacked C15 : 0 and C17 : 1 ω6c, respectively. Phenotypic, chemotaxonomic and genotypic test results demonstrated that the two novel strains HLW78T 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 HLW78T (=BCRC 81397T=NBRC 116372T).

Trichoderma spp. are widely distributed worldwide. Members of Trichoderma have been shown to play a significant role in the biocontrol of plant disease, as well as the industrial production of enzymes and antibiotics, and as a mycoparasite of edible fungi. In this study, a new species, Trichoderma orarium, is introduced and illustrated. This new species was isolated from coastal soil in Northeastern Taiwan and identified based on morphological characteristics and multi-gene sequence analyses of three loci (ITS, tef1, and rpb2). The phylogenetic analyses revealed that T. orarium belongs to the Harzianum clade. Distinctions between the new species and its close relatives are discussed in detail.

The CRISPR-Cas system has been widely used for genome editing due to its convenience, simplicity and flexibility. Using a plasmid-carrying Cas protein and crRNA or sgRNA expression cassettes is an efficient strategy in the CRISPR-Cas genome editing system. However, the plasmid remains in the cells after genome editing. Development of general plasmid-curing strategies is necessary. Based on our previous CRISPR-Cpf1 genome-editing system in Saccharomyces cerevisiae, the crRNA, designed for the replication origin of the CRISPR-Cpf1 plasmid, and the ssDNA, as a template for homologous recombination, were introduced for plasmid curing. The efficiency of the plasmid curing was 96 ± 4%. In addition, we further simplified the plasmid curing system by transforming only one crRNA into S. cerevisiae, and the curing efficiency was about 70%. In summary, we have developed a CRISPR-mediated plasmid-curing system. The RNA-only plasmid curing system is fast and easy. This plasmid curing strategy can be applied in broad hosts by designing crRNA specific for the replication origin of the plasmid. The plasmid curing system via CRISPR-Cas editing technology can be applied to produce traceless products without foreign genes and to perform iterative processes in multiple rounds of genome editing.