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.
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.
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.
ABSTRACT
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.
ABSTRACT
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 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.
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.
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.
► Automated empirical modeling approach for analysis of high-throughput microarrays ► Identification of non-specific microarray signals using a new parameter (Td-w/Tm) ► Method does not rely on comparison of perfect match and mismatch dissociations. ► Evaluated three datasets with the new parameter
Danglingends and surface-proximal tails of gene targets influence probe-targetduplex formation and affect the signal intensity of probes ondiagnostic microarrays. This phenomenon was evaluated using ...anoligonucleotide microarray containing 18-mer probes corresponding tothe 16S rRNA genes of 10 waterborne pathogens and a number of syntheticand PCR-amplified gene targets. Signal intensities for Klenow/randomprimer-labeled 16S rRNA gene targets were dissimilar from those for45-mer synthetic targets for nearly 73% of the probes tested.Klenow/random primer-labeled targets resulted in an interaction with acomplex mixture of 16S rRNA genes (used as the background) 3.7 timeshigher than the interaction of 45-mer targets with the same mixture. A7-base-long dangling end sequence with perfect homology to anothersingle-stranded background DNA sequence was sufficient to produce across-hybridization signal that was as strong as the signal obtained bythe probe-target duplex itself. Gibbs free energy between the targetand a well-defined background was found to be a better indicator ofhybridization signal intensity than the sequence or length of thedangling end alone. The dangling end (Gibbs free energy of -7.6kcal/mol) was found to be significantly more prone to target-backgroundinteraction than the surface-proximal tail (Gibbs free energy of-64.5 kcal/mol). This study underlines the need for carefultarget preparation and evaluation of signal intensities for diagnosticarrays using 16S rRNA and other gene targets due to the potential fortarget interaction with a complexbackground.
Abstract Gut microbiota is associated with antitumor efficacy of immune checkpoint blockade therapies, yet the mechanism is not largely understood. Here, we show that a novel bacterial strain of ...Ruminococcaceae isolated from the feces of patients who respond to PD-1 (programmed cell death 1) blockade efficiently primes/activates tumor-specific CD8+ T cells through effective stimulation/maturation of CD103+ dendritic cells (DCs) during migration from the gut to the tumor microenvironment (TME). The administration of this bacteria strain with PD-1 blockade significantly inhibited tumor growth, even when adding them to fecal transplantation of non-responder patients in animal models. Mechanistically, the bacterial strain promoted the IRF8-driven differentiation of CD103+ DCs by stimulating multiple Toll-like receptors and the accumulation of these DCs in tumors and tumor-draining lymph nodes. These CD103+ DCs prolonged engagement with cognate antigen-specific CD8+ T cells, which induced the activation of CD8+ T cells specific for a wide variety of tumor antigens and fostered their PD-1 expression through enhanced T-cell activation signals with NFATc1 nuclear translocation, thereby leading to abundant PD-1+CD8+ T cells, a key effector cell population in PD-1 blockade, with a broader T-cell receptor repertoire in the TME. Our findings with novel single bacterium isolated from feces of responder patients demonstrate the mode of action by gut microbiota to augment antitumor immunity. Citation Format: Nina Yi-Tzu Lin, Shota Fukuoka, Daisuke Motooka, Yuko Shigeno, Takuma Irie, Dieter M. Tourlousse, Kazutoshi Murotomi, Yuji Sekiguchi, Hideyuki Tamaki, Mariko Shindo, Takahiro Tsuji, Hiroaki Wake, Koichi Goto, Toshihiko Doi, Kohei Shitara, Keisuke Watanabe, Yuka Maeda, Shota Nakamura, Yoshimi Benno, Hiroyoshi Nishikawa, Shohei Koyama. The mechanism of gut microbiome-mediated immune activation on the clinical efficacy of PD-1 blocking treatment in solid tumors abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6686.
PDF
