ABSTRACT
Here, we report the complete genome sequences of two
Ruminococcus torques
strains (JCM 36208 and JCM 36209) that were newly isolated from the feces of a healthy Japanese male. Both genomes ...consist of a single circular chromosome with a length of ~2.8 Mbp and a G+C content of 41.8%.
We report a complete genome sequence of
Butyricimonas faecihominis
JCM 18676
T
, generated by nanopore sequencing. The genome consists of a single circular chromosome of 4,851,806 bp, with a G + C ...content of 42.9%, and was predicted to contain 15 rRNA and 61 tRNA genes and encode for 3,946 proteins.
We generated a complete genome sequence of the type strain of
Blautia luti
(JCM 17040
T
= DSM 14534
T
) by Nanopore sequencing. The genome consists of a circular chromosome of 3,741,599 bp with a G + ...C content of 42.9% and was predicted to contain 3,431 protein-coding sequences.
We report a complete genome sequence of Anaerostipes hadrus JCM 17467
. The genome consists of a circular chromosome of 2,804,089 bp, with a G+C content of 37.3%. The genome was predicted to contain ...21 rRNA genes, 65 tRNA genes, and 2,675 protein-coding sequences.
We report a complete genome sequence of
Anaerostipes hadrus
JCM 17467
T
. The genome consists of a circular chromosome of 2,804,089 bp, with a G+C content of 37.3%. The genome was predicted to ...contain 21 rRNA genes, 65 tRNA genes, and 2,675 protein-coding sequences.
We generated a complete genome sequence of Coprobacter fastidiosus JCM 33896
by nanopore sequencing. The genome consists of a single circular chromosome of 3,444,538 bp with a G+C content of 38.4%. ...Annotation predicted 15 rRNA genes, 67 tRNA genes and 2,662 protein-coding sequences.
We generated a complete genome sequence of Coprobacter fastidiosus JCM 33896T by nanopore sequencing. The genome consists of a single circular chromosome of 3,444,538 bp with a G+C content of 38.4%. ...Annotation predicted 15 rRNA genes, 67 tRNA genes and 2,662 protein-coding sequences.
Inexpensive, portable, and easy-to-use devices for rapid detection of microbial pathogens are needed to ensure safety of water and food. In this study, a disposable polymer microfluidic chip for ...quantitative detection of multiple pathogens using isothermal nucleic acid amplification was developed. The chip contains an array of 15 interconnected reaction wells with dehydrated primers for loop-mediated isothermal amplification (LAMP), and requires only a single pipetting step for dispensing of sample. To improve robustness of loading and amplification, hydrophobic air vents and microvalves were monolithically integrated in the multi-layered structure of the chip using an inexpensive knife plotter. For quantification, LAMP was performed with a highly fluorescent DNA binding dye (SYTO-82) and the reactions monitored in real-time using a low-cost fluorescence imaging system previously developed by our group (Ahmad et al., Biomed. Microdevices 13(5), 929–937). Starting from genomic DNA mixtures, the chip was successfully evaluated for rapid analysis of multiple virulence and marker genes of
Salmonella
,
Campylobacter jejuni
,
Shigella
, and
Vibrio cholerae
, enabling detection and quantification of 10–100 genomes per μl in less than 20 min. It is anticipated that the microfluidic chip, along with the real-time imaging system, may be a key enabling technology for developing inexpensive and portable systems for on-site screening of multiple pathogens relevant to food and water safety.
Loop-mediated isothermal amplification (LAMP) is increasingly used for point-of-care nucleic acid based diagnostics. LAMP can be monitored in real-time by measuring the increase in fluorescence of ...DNA binding dyes. However, there is little information comparing the effect of various fluorescent dyes on signal to noise ratio (SNR) or threshold time (Tt). This information is critical for implementation with field deployable diagnostic tools that require small, low power consumption, robust, and inexpensive optical components with reagent saving low volume reactions. In this study, SNR and Tt during real-time LAMP was evaluated with eleven fluorescent dyes. Of all dyes tested, SYTO-82, SYTO-84, and SYTOX Orange resulted in the shortest Tt, and SYTO-81 had the widest range of working concentrations. The optimized protocol detected 10 genome copies of Mycobacterium tuberculosis in less than 10min, 10 copies of Giardia intestinalis in ~20min, and 10 copies of Staphylococcus aureus or Salmonella enterica in less than 15min. Results demonstrate that reaction efficiency depends on both dye type and concentration and the selected polymerase. The optimized protocol was evaluated in the Gene-Z™ device, a hand-held battery operated platform characterized via simple and low cost optics, and a multiple assay microfluidic chip with micron volume reaction wells. Compared to the more conventional intercalating dye (SYBR Green), reliable amplification was only observed in the Gene-Z™ when using higher concentrations of SYTO-81.
•Eleven DNA dyes were compared for real-time loop-mediated isothermal amplification.•SYTO-81 and SYTO-82 had the highest fluorescence enhancement.•SYTO-81 had the widest range of working concentrations.•These dyes were better suited for detection with simple optical setup (Gene-Z).•Gene-Z was used to detect 10 copies of M. tuberculosis DNA in less than 10min.
► A methanogenic benzene-degrading culture was obtained from lotus field soil. ► The culture degraded benzene to equimolar amounts of methane and carbon dioxide. ► The culture also degraded the ...putative intermediates phenol, toluene and benzoate. ► Phenol moderately inhibited benzene degradation but was not a major intermediate. ► A novel metabolite, 4-hydroxycoumarin, was formed from phenol.
Microbial degradation of benzene under anaerobic conditions plays an important role in remediation of contaminated sites but the microorganisms and metabolic pathways involved remain poorly understood. In this study, we evaluated degradation of benzene by a methanogenic enrichment culture obtained from non-contaminated lotus field soil, alone and in the presence of several putative metabolic intermediates, that is, toluene, benzoate and phenol. Using stable isotope (13C) labeled substrate, benzene was shown to be degraded almost completely to equimolar concentrations of methane and carbon dioxide, without detectable accumulation of extracellular metabolites. Concurrently, toluene, benzoate and phenol were also effectively mineralized, but probably by microorganisms other than the benzene degraders. The latter included Hasda-A, which is putative benzene-degrading deltaproteobacterium present in the culture. While toluene and benzoate did not affect benzene degradation, phenol had a moderate inhibitory effect although it was not a major metabolic intermediate of benzene in our culture. Finally, 4-hydroxycoumarin was detected as a compound formed from phenol but further experiments are required to elucidate its relationship to degradation of phenol.
