Search

We analyzed the microbial community that developed after 4 years of testing different soil-crop management systems in the savannah–forest transition zone of Eastern Ghana where management systems can rapidly alter stored soil carbon as well as soil fertility. The agricultural managements were: (i) the local practice of fallow regrowth of native elephant grass (Pennisetum purpureum) followed by biomass burning before planting maize in the spring, (ii) the same practice but without burning and the maize receiving mineral nitrogen fertilizer, (iii) a winter crop of a legume, pigeon pea (Cajanus cajan), followed by maize, (iv) vegetation free winter period (bare fallow) followed by maize, and (v) unmanaged elephant grass-shrub vegetation. The mean soil organic carbon (SOC) contents of the soils after 4 years were: 1.29, 1.67, 1.54, 0.80 and 1.34%, respectively, differences that should affect resources for the microbial community.From about 290,000 sequences obtained by pyrosequencing the SSU rRNA gene, canonical correspondence analysis showed that SOC was the most important factor that explained differences in microbial community structure among treatments. This analysis as well as phylogenetic ecological network construction indicated that members of the Acidobacteria GP4 and GP6 were more abundant in soils with relatively high SOC whereas Acidobacteria GP1, GP7, and Actinobacteria were more prevalent in soil with lower SOC. Burning of winter fallow vegetation led to an increase in Bacillales, especially those belonging to spore-forming genera. Of the managements, pigeon-pea cultivation during the winter period promoted a higher microbial diversity and also sequestered more SOC, presumably improving soil structure, fertility, and resiliency.

Sequencing-based interrogation of gut microbiota is a valuable approach for detecting microbes associated with colorectal cancer (CRC); however, such studies are often confounded by the effect of bowel preparation. In this study, we evaluated the viability of identifying CRC-associated mucosal bacteria through centimeter-scale profiling of the microbiota in tumors and adjacent noncancerous tissue from eleven patients who underwent colonic resection without preoperative bowel preparation. High-throughput 16S rRNA gene sequencing revealed that differences between on- and off-tumor microbiota varied considerably among patients. For some patients, phylotypes affiliated with genera previously implicated in colorectal carcinogenesis, as well as genera with less well-understood roles in CRC, were enriched in tumor tissue, whereas for other patients, on- and off-tumor microbiota were very similar. Notably, the enrichment of phylotypes in tumor-associated mucosa was highly localized and no longer apparent even a few centimeters away from the tumor. Through short-term liquid culturing and metagenomics, we further generated more than one- hundred metagenome-assembled genomes, several representing bacteria that were enriched in on-tumor samples. This is one of the first studies to analyze largely unperturbed mucosal microbiota in tissue samples from the resected colons of unprepped CRC patients. Future studies with larger cohorts are expected to clarify the causes and consequences of the observed variability in the emergence of tumor-localized microbiota among patients. [ABSTRACT FROM AUTHOR]

The effect of danglings ends and surface-promixal tails of gene targets on probe-target duplex formation is evaluated by using an oligonucleotide microarray containing 18-mer probes corresponding to the 16S rRNA genes of 10 waterborne pathogens and a number of synthetic and PCR-applied gene targets. The study has highlighted the requirement of a careful target preparation and evaluation of signal intensities for diagnostic arrays by using 16S rRNA and other gene targets because of the potential for target interaction with a complex background.

Nanoliter-volume BioTrove OpenArray platform was used for examining the capacity of quantitative PCR (QPCR) for highly parallel diagnostics of human pathogens. Findings reveal a high correlation between the predicted and experimental threshold cycle.

The development and validation of an in situ-synthesized virulence and marker genes (VMG) biochip for detection of microbial pathogens is reported. The biochip can detect bacterial pathogens when parallel and specific detection is required.

The goal of this study was to develop and validate a novel fosmid-clone-based metagenome isotope array approach - termed the community isotope array ( CIArray) - for sensitive detection and identification of microorganisms assimilating a radiolabeled substrate within complex microbial communities. More specifically, a sample-specific CIArray was used to identify anoxic phenol-degrading microorganisms in activated sludge treating synthetic coke-oven wastewater in a single-sludge predenitrification-nitrification process. Hybridization of the CIArray with DNA from the 14C-phenol-amended sample indicated that bacteria assimilating 14C-atoms, presumably directly from phenol, under nitrate-reducing conditions were abundant in the reactor, and taxonomic assignment of the fosmid clone end sequences suggested that they belonged to the Gammaproteobacteria. The specificity of the CIArray was validated by quantification of fosmid-clone-specific DNA in density-resolved DNA fractions from samples incubated with 13C-phenol, which verified that all CIArray-positive probes stemmed from microorganisms that assimilated isotopically labeled carbon. This also demonstrated that the CIArray was more sensitive than DNA- SIP, as the former enabled positive detection at a phenol concentration that failed to yield a 'heavy' DNA fraction. Finally, two operational taxonomic units distantly related to marine Gammaproteobacteria were identified to account for more than half of 16S r RNA gene clones in the 'heavy' DNA library, corroborating the CIArray-based identification. [ABSTRACT FROM AUTHOR]

A review of the literature published in 2008 is presented on topics related to occurrence and detection of fecal indicators and pathogens. This review is divided into three major sections: occurrence, persistence, and transport of fecal indicators and pathogens, detection methods, and microbial source tracking. The first section is subdivided into persistence and transport of fecal indicators, microbiological quality of recreational beaches, occurrence of fecal indicator and pathogens in shellfish, alternative fecal indicators, and fecal indicators and pathogens in groundwater, watersheds, and wetlands. The second section describes the studies related to endpoint PCR and reverse transcription PCR, real-time PCR and real-time reverse transcription PCR, loop mediated isothermal amplification, microarrays, immunoassay-based detection schemes, labelindependent detection schemes, and sample concentration. The third section covers genotypic and phenotypic microbial source tracking methods. [ABSTRACT FROM AUTHOR]

The article focuses on the issues with environmental occurrence and transport of fecal indicators and pathogens, method's development and application for their detection as well as the source that tracks for their detection. It is being noted that the fecal indicator bacteria (FIB) are bacteria that are commensal in animal intestines, which are shed by feces. Accordingly, their presence in the ecosystem is assumed to indicate that there is a presence of fecal matter and therefore the potential presence of pathogens of intestinal origin. Hence, the author implies that interpretation of the detection of conventional FIB in the environment is sometimes straightforward, though not all the time.

Certain symptoms associated with mild sickness and lethargy have not been categorized as definitive diseases. Confirming such symptoms in captive monkeys (Macaca fascicularis, known as cynomolgus monkeys) can be difficult; however, it is possible to observe and analyze their feces. In this study, we investigated the relationship between stool state and various omics data by considering objective and quantitative values of stool water content as a phenotype for analysis. By examining the food intake of the monkeys and assessing their stool, urine, and plasma, we attempted to obtain a comprehensive understanding of the health status of individual monkeys and correlate it with the stool condition. Our metabolomics data strongly suggested that many lipid-related metabolites were correlated with the stool water content. The lipidomic analysis revealed the involvement of saturated and oxidized fatty acids, metallomics revealed the contribution of selenium (a bio-essential trace element), and intestinal microbiota analysis revealed the association of several bacterial species with the stool water content. Based on our results, we hypothesize that the redox imbalance causes minor health problems. However, it is not possible to make a definite conclusion using multi-omics alone, and other hypotheses could be proposed. [ABSTRACT FROM AUTHOR]

Parallel detection approaches are of interest to many researchers interested in identifying multiple water and foodborne pathogens simultaneously. Availability and cost-effectiveness are two key factors determining the usefulness of such approaches for laboratories with limited resources. In this study, we developed and validated a high-density microarray for simultaneous screening of 14 bacterial pathogens using an approach that employs gold labeling with silver enhancement (GLS) protocol. In total, 8887 probes (50-mer) were designed using an in-house database of virulence and marker genes (VMGs), and synthesized in quadruplicate on glass slides using an in-situ synthesis technology. Target VMG amplicons were obtained using multiplex polymerase chain reaction (PCR), labeled with biotin, and hybridized to the microarray. The signals generated after gold deposition and silver enhancement, were quantified using a flatbed scanner having 2-μm resolution. Data analysis indicated that reliable presence/absence calls could be made, if: i) over four probes were used per gene, ii) the signal-to-noise ratio (SNR) cutoff was greater than or equal to two, and iii) the positive fraction (PF), i.e. , number of probes with SNR ≥ 2 for a given VMG was greater than 0.75. Hybridization of the array with blind samples resulted in 100% correct calls, and no false positive. Because amplicons were obtained by multiplex PCR, sensitivity of this method is similar to PCR. This assay is an inexpensive and reliable technique for high throughput screening of multiple pathogens. [ABSTRACT FROM AUTHOR]

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 (T t ). 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 T t 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 T t , and SYTO-81 had the widest range of working concentrations. The optimized protocol detected 10 genome copies of Mycobacterium tuberculosis in less than 10 min, 10 copies of Giardia intestinalis in ~ 20 min, and 10 copies of Staphylococcus aureus or Salmonella enterica in less than 15 min. 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. [ABSTRACT FROM AUTHOR]

Abstract: Non-equilibrium dissociation curves (NEDCs) have the potential to identify non-specific hybridizations on high throughput, diagnostic microarrays. We report a simple method for the identification of non-specific signals by using a new parameter that does not rely on comparison of perfect match and mismatch dissociations. The parameter is the ratio of specific dissociation temperature (Td-w) to theoretical melting temperature (Tm) and can be obtained by automated fitting of a four-parameter, sigmoid, empirical equation to the thousands of curves generated in a typical experiment. The curves fit perfect match NEDCs from an initial experiment with an R2 of 0.998±0.006 and root mean square of 108±91 fluorescent units. Receiver operating characteristic curve analysis showed low temperature hybridization signals (20–48°C) to be as effective as area under the curve as primary data filters. Evaluation of three datasets that target 16S rRNA and functional genes with varying degrees of target sequence similarity showed that filtering out hybridizations with Td-w/Tm <0.78 greatly reduced false positive results. In conclusion, Td-w/Tm successfully screened many non-specific hybridizations that could not be identified using single temperature signal intensities alone, while the empirical modeling allowed a simplified approach to the high throughput analysis of thousands of NEDCs. [Copyright &y& Elsevier]

Development of quantitative PCR (QPCR) assays typically requires extensive screening within and across a given species to ensure specific detection and lucid identification among various pathogenic and nonpathogenic strains and to generate standard curves. To minimize screening requirements, multiple virulence and marker genes (VMGs) were targeted simultaneously to enhance reliability, and a predictive threshold cycle (CT) equation was developed to calculate the number of starting copies based on an experimental CT The empirical equation was developed with Sybr green detection in nanoliter-volume QPCR chambers (OpenArray) and tested with 220 previously unvalidated primer pairs targeting 200 VMGs from 30 pathogens. A high correlation (R² = 0.816) was observed between the predicted and experimental CTs based on the organism's genome size, guanine and cytosine (GC) content, amplicon length, and stability of the primer's 3′ end. The performance of the predictive CT equation was tested using 36 validation samples consisting of pathogenic organisms spiked into genomic DNA extracted from three environmental waters. In addition, the primer success rate was dependent on the GC content of the target organisms and primer sequences. Targeting multiple assays per organism and using the predictive CT equation are expected to reduce the extent of the validation necessary when developing QPCR arrays for a large number of pathogens or other targets. [ABSTRACT FROM AUTHOR]

Abstract: 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 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. [Copyright &y& Elsevier]

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%., Competing Interests: The authors declare no conflict of interest.

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., Competing Interests: The authors declare no conflict of interest.

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., Competing Interests: The authors declare no conflict of interest.

Sequencing-based interrogation of gut microbiota is a valuable approach for detecting microbes associated with colorectal cancer (CRC); however, such studies are often confounded by the effect of bowel preparation. In this study, we evaluated the viability of identifying CRC-associated mucosal bacteria through centimeter-scale profiling of the microbiota in tumors and adjacent noncancerous tissue from eleven patients who underwent colonic resection without preoperative bowel preparation. High-throughput 16S rRNA gene sequencing revealed that differences between on- and off-tumor microbiota varied considerably among patients. For some patients, phylotypes affiliated with genera previously implicated in colorectal carcinogenesis, as well as genera with less well-understood roles in CRC, were enriched in tumor tissue, whereas for other patients, on- and off-tumor microbiota were very similar. Notably, the enrichment of phylotypes in tumor-associated mucosa was highly localized and no longer apparent even a few centimeters away from the tumor. Through short-term liquid culturing and metagenomics, we further generated more than one-hundred metagenome-assembled genomes, several representing bacteria that were enriched in on-tumor samples. This is one of the first studies to analyze largely unperturbed mucosal microbiota in tissue samples from the resected colons of unprepped CRC patients. Future studies with larger cohorts are expected to clarify the causes and consequences of the observed variability in the emergence of tumor-localized microbiota among patients., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Fukuoka, Tourlousse, Ohashi, Suzuki, Nakagawa, Ozawa, Ishibe, Endo and Sekiguchi.)

We generated a complete genome sequence of Coprobacter fastidiosus JCM 33896 T 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., Competing Interests: The authors declare no conflict of interest.

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., Competing Interests: The authors declare no conflict of interest.

Standardization and quality assurance of microbiome community analysis by high-throughput DNA sequencing require widely accessible and well-characterized reference materials. Here, we report on newly developed DNA and whole-cell mock communities to serve as control reagents for human gut microbiota measurements by shotgun metagenomics and 16S rRNA gene amplicon sequencing. The mock communities were formulated as near-even blends of up to 20 bacterial species prevalent in the human gut, span a wide range of genomic guanine-cytosine (GC) contents, and include multiple strains with Gram-positive type cell walls. Through a collaborative study, we carefully characterized the mock communities by shotgun metagenomics, using previously developed standardized protocols for DNA extraction and sequencing library construction. Further, we validated fitness of the mock communities for revealing technically meaningful differences among protocols for DNA extraction and metagenome/16S rRNA gene amplicon library construction. Finally, we used the mock communities to reveal varying performance of metagenome-based taxonomic profilers and the impact of trimming and filtering of sequencing reads on observed species profiles. The latter showed that aggressive preprocessing of reads may result in substantial GC-dependent bias and should thus be carefully evaluated to minimize unintended effects on species abundances. Taken together, the mock communities are expected to support a myriad of applications that rely on well-characterized control reagents, ranging from evaluation and optimization of methods to assessment of reproducibility in interlaboratory studies and routine quality control. IMPORTANCE Application of high-throughput DNA sequencing has greatly accelerated human microbiome research and its translation into new therapeutic and diagnostic capabilities. Microbiome community analyses results can, however, vary considerably across studies or laboratories, and establishment of measurement standards to improve accuracy and reproducibility has become a priority. The here-developed mock communities, which are available from the NITE Biological Resource Center (NBRC) at the National Institute of Technology and Evaluation (NITE, Japan), provide well-characterized control reagents that allow users to judge the accuracy of their measurement results. Widespread and consistent adoption of the mock communities will improve reproducibility and comparability of microbiome community analyses, thereby supporting and accelerating human microbiome research and development.

We report a complete genome sequence of Blautia producta JCM 1471 T The genome consists of a single circular chromosome of 6,197,116 bp with a G+C content of 45.7%. The genome was annotated as containing 5 complete sets of rRNA genes, 70 tRNA genes, and 5,516 protein-coding sequences., (Copyright © 2020 Tourlousse et al.)

We report the complete genome sequence of Flavonifractor plautii JCM 32125 T (=VPI 0310 T ). The genome consists of a single circular chromosome of 3,985,392 bp (G+C content, 60.9%) and was predicted to contain 3 complete sets of rRNA genes, 63 tRNA genes, and 3,764 protein-coding sequences., (Copyright © 2020 Tourlousse et al.)

We announce the complete genome sequence of Megamonas funiformis JCM 14723 T (YIT 11815 T ). The genome consists of a circular chromosome (2,522,577 bp, 31.5% G+C content) and a plasmid of 46,189 bp (29.4% G+C content). The genome was predicted to contain 6 rRNA operons, 53 tRNA genes, and 2,440 protein-coding sequences., (Copyright © 2020 Tourlousse et al.)

We report a complete genome sequence of Collinsella aerofaciens JCM 10188 T (=VPI 1003 T ). The genome consists of a circular chromosome (2,428,218 bp with 60.6% G+C content) and two extrachromosomal elements. The genome was predicted to contain 5 sets of rRNA genes, 58 tRNA genes, and 2,079 protein-encoding sequences., (Copyright © 2020 Tourlousse et al.)

We report here a high-quality draft genome sequence of Terrimicrobium sacchariphilum strain NM-5 T , a facultative anaerobic, mesophilic, fermentative bacterium belonging to the class Spartobacteria of the phylum Verrucomicrobia The genome comprises 4,751,807 bp in three contigs and has a G+C content of 60.19%. Annotation predicted 4,175 protein-coding sequences and 54 RNAs., (Copyright © 2017 Qiu et al.)

We report here a high-quality draft genome sequence of Paludibacter jiangxiensis strain NM7 T , a mesophilic, anaerobic, propionate-producing fermentative bacterium within the family Porphyromonadaceae of the phylum Bacteroidetes The genome comprises 3,664,884 bp in four contigs, has a G+C content of 42.92%, and contains 2,949 protein-coding sequences and 62 RNAs., (Copyright © 2017 Qiu et al.)

A novel, strictly anaerobic, short rod-shaped bacterium, designated strain TBC1 T , was isolated from methanogenic granular sludge in a full-scale mesophilic upflow anaerobic sludge blanket reactor treating high-strength starch-based organic wastewater. Cells of this strain were 2-4 µm long and 0.4-0.6 µm wide. They were non-motile and Gram-stain-negative. The optimum growth temperature was 30-37 °C, with a range of 20-40 °C. The optimum pH for growth was around pH 7.0, while growth occurred in a range of pH 6.5-9.0. Strain TBC1 T grew chemo-organotrophically on a narrow range of carbohydrates under anaerobic conditions. Yeast extract was required for its growth. The major fermentative end products from glucose, supplemented with yeast extract, were acetate, malate, propionate, formate and hydrogen. Doubling time under optimal growth conditions was estimated to be 1 day. The DNA G+C content of strain TBC1 T was 49.2 mol% as determined by HPLC. Major cellular fatty acids were C16 : 0, C18 : 0, C16 : 1ω9c and C18 : 1ω9c. Based on its 16S rRNA gene sequence, strain TBC1 T was shown to represent a distinct lineage at the family level in the phylum Bacteroidetes. Among previously described species of this phylum, Mucilaginibacter boryungensis BDR-9 T (Sphingobacteriaceae) displayed the highest sequence similarity (85.9 %) with strain TBC1 T . Phylogenomic analyses using 38-83 single copy marker genes also supported the novelty of strain TBC1 T at the family level. Based on its characteristics, strain TBC1 T (=JCM 30898 T =DSM 100618 T ) is considered to be the type strain of a novel species of a new genus, Lentimicrobium saccharophilum gen. nov., sp. nov. A new family, Lentimicrobiaceae fam. nov., is also proposed encompassing the strain and related environmental 16S rRNA gene clone sequences.

We report a high-quality draft genome sequence of the type strain (TGE-P1(T)) of Thermodesulfovibrio aggregans, an obligately anaerobic, thermophilic, sulfate-reducing bacterium in the phylum Nitrospirae. The genome comprises 2.00 Mb in 16 contigs (3 scaffolds), has a G+C content of 34.5%, and contains 1,998 predicted protein-encoding genes., (Copyright © 2016 Matsuura et al.)

We report here a high-quality draft genome sequence of the type strain (JL) of Tepidanaerobacter syntrophicus, an obligately anaerobic and moderately thermophilic bacterium, which is able to perform syntrophic lactate degradation with hydrogenotrophic methanogens. The genome comprises 2.43 Mb in 9 scaffolds, with a G+C content of 38.6%., (Copyright © 2016 Matsuura et al.)

A novel obligately anaerobic bacterium, designated strain TC1 T , was isolated from methanogenic granular sludge in a full-scale mesophilic upflow anaerobic sludge blanket reactor treating high-strength starch-based wastewater. Cells had a multicellular filamentous morphology, stained Gram-negative and were non-motile. The filaments were flexible, generally >100 μm long and 0.3-0.4 μm wide. Growth of the isolate was observed at 25-43 °C (optimum 37 °C) and pH 6.0-8.5 (optimum pH 7.0). Strain TC1 T grew chemo-organotrophically on a range of carbohydrates under anaerobic conditions. Yeast extract was required for growth. The major fermentative end products of glucose, supplemented with yeast extract, were acetate, lactate, succinate, propionate, formate and hydrogen. Co-cultivation with the hydrogenotrophic methanogen Methanospirillum hungatei DSM 864 T enhanced growth of the isolate. The DNA G+C content was determined experimentally to be 42.1 mol%. The major cellular fatty acids were anteiso-C 15 : 0 , iso-C 15 : 0 and iso-C 17 : 0 3-OH. Based on 16S rRNA gene sequence analysis, strain TC1 T belonged to the class Anaerolineae in the phylum Chloroflexi , in which Ornatilinea apprima P3M-1 T was its closest phylogenetic relative (88.3 % nucleotide identity). Phylogenomic analyses using 38 and 83 single-copy marker genes also supported the novelty of strain TC1 T at least at the genus level. Based on phylogenetic, genomic and phenotypic characteristics, we propose that strain TC1 T represents a novel species of a new genus, for which we suggest the name Flexilinea flocculi gen. nov., sp. nov. The type strain of Flexilinea flocculi is strain TC1 T ( = JCM 30897 T  = CGMCC 1.5202 T ).

We report here the draft genome sequence of Bacteroidales strain TBC1, isolated from a methanogenic wastewater treatment system. The draft genome has a size of 4,514,407 bp and a G+C content of 46.7%. The predicted genomic content provides the basis for characterizing the metabolism and ecological strategies of strain TBC1., (Copyright © 2015 Tourlousse et al.)

We generated a high-quality draft genome sequence of Bacteroidales strain 6E, a strict anaerobe newly isolated from Japanese rice paddy field soil. The genome consists of 61 contigs, with a total size of 4,436,542 bp and mean G+C content of 45.4%. Annotation predicted 3,620 protein-coding and 54 RNA genes., (Copyright © 2015 Tourlousse et al.)

We report the draft genome sequence of Anaerolineae bacterium strain TC1, newly isolated from a methanogenic wastewater treatment system. The assembly contains 16 contigs in 3 scaffolds representing 3,510,630 bp in total with a G+C content of 41.35%. The genome is predicted to contain 2,793 protein-coding genes and 56 RNAs., (Copyright © 2015 Matsuura et al.)

Members of the class Anaerolineae in the bacterial phylum Chloroflexi are widespread in a range of ecosystems but remain poorly understood. We present here the draft genome sequences of the type strains of five Anaerolineae species, Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, and Longilinea arvoryzae KOME-1., (Copyright © 2015 Matsuura et al.)

By 2012, point of care (POC) testing will constitute roughly one third of the $59 billion in vitro diagnostics market. The ability to carry out multiplexed genetic testing and wireless connectivity are emerging as key attributes of future POC devices. In this study, an inexpensive, user-friendly and compact device (termed Gene-Z) is presented for rapid quantitative detection of multiple genetic markers with high sensitivity and specificity. Using a disposable valve-less polymer microfluidic chip containing four arrays of 15 reaction wells each with dehydrated primers for isothermal amplification, the Gene-Z enables simultaneous analysis of four samples, each for multiple genetic markers in parallel, requiring only a single pipetting step per sample for dispensing. To drastically reduce the cost and size of the real-time detector necessary for quantification, loop-mediated isothermal amplification (LAMP) was performed with a high concentration of SYTO-81, a non-inhibiting fluorescent DNA binding dye. The Gene-Z is operated using an iPod Touch, which also receives data and carries out automated analysis and reporting via a WiFi interface. This study presents data pertaining to performance of the device including sensitivity and reproducibility using genomic DNA from Escherichia coli and Staphylococcus aureus. Overall, the Gene-Z represents a significant step toward truly inexpensive and compact tools for POC genetic testing.