Complete genome sequence of JCM 31256.

We describe a complete genome sequence of JCM 31256. The genome consists of a single circular chromosome with a length of 3,090,452 base pairs and a GC content of 40.8%, and was predicted to contain 3,061 total genes, encoding for 2,907 proteins.

Identification of Mycobacterium abscessus using the peaks of ribosomal protein L29, L30 and hemophore-related protein by MALDI-MS proteotyping.

Mycobacteroides (Mycobacterium) abscessus, which causes a variety of infectious diseases in humans, is becoming detected more frequently in clinical specimens as cases are spreading worldwide. Taxonomically, M. abscessus is composed of three subspecies of M.

Isolation and identification of from blood culture by MALDI-MS.

is a genus of budding yeast that is mainly isolated from environmental samples, and 40 species have been detected. The yeast isolated from human clinical samples usually only contain three species: , and . In this study, we isolated from a blood sample of a six-year-old female with a history of B-cell precursor lymphoblastic leukemia in Japan in 2022.

A large-scale genomically predicted protein mass database enables rapid and broad-spectrum identification of bacterial and archaeal isolates by mass spectrometry.

MALDI-TOF MS-based microbial identification relies on reference spectral libraries, which limits the screening of diverse isolates, including uncultured lineages. We present a new strategy for broad-spectrum identification of bacterial and archaeal isolates by MALDI-TOF MS using a large-scale database of protein masses predicted from nearly 200,000 publicly available genomes. We verify the ability of the database to identify microorganisms at the species level and below, achieving correct identification for > 90% of measured spectra.

Complete genome sequences of strains JCM 36208 and JCM 36209, isolated from the feces of a healthy Japanese male.

Here, we report the complete genome sequences of two 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.

Complete genome sequence of JCM 18676.

We report a complete genome sequence of JCM 18676, 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.

Complete genome sequence of JCM 17040.

We generated a complete genome sequence of the type strain of (JCM 17040 = DSM 14534) 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.

Elucidating colorectal cancer-associated bacteria through profiling of minimally perturbed tissue-associated microbiota.

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.

Complete Genome Sequence of Anaerostipes hadrus JCM 17467.

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%.

Complete Genome Sequence of Coprobacter fastidiosus JCM 33896.

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%.

Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer.

Members of the genus Nitrosomonas are major ammonia oxidizers that catalyse the first step of nitrification in various ecosystems. To date, six subgenus-level clades have been identified. We have previously isolated novel ammonia oxidizers from an additional clade (unclassified cluster 1) of the genus Nitrosomonas.

Characterization and Demonstration of Mock Communities as Control Reagents for Accurate Human Microbiome Community Measurements.

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.

Sulphur metabolism in colon cancer tissues: a case report and literature review.

Sulphur-containing compounds have been linked to colorectal cancer by factors such as the presence of methyl mercaptan in intestinal gas and long-term dietary intake associated with sulphur-metabolizing microbiota. Therefore, this current case report hypothesized that active sulphur metabolism in colorectal cancer results in the formation of sulphur compounds in the intestine and, thus, examined sulphur metabolites possibly associated with sulphur respiration in colon cancer tissues. The patient was a 73-year-old female that underwent laparoscopic right hemicolectomy for ascending colon cancer.

Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements.

Background: Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out to establish standards-based solutions to improve the accuracy and reproducibility of metagenomics-based microbiome profiling of human fecal samples.

Results: In the first phase, we performed a head-to-head comparison of a wide range of protocols for DNA extraction and sequencing library construction using defined mock communities, to identify performant protocols and pinpoint sources of inaccuracy in quantification.

Genomic and Physiological Characteristics of a Novel Nitrite-Oxidizing Strain Isolated From a Drinking Water Treatment Plant.

Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, which is an important process of the biogeochemical nitrogen cycle and is exploited extensively as a biological nitrogen removal process. Members of the genus are often identified as the dominant NOB in a diverse range of natural and artificial environments. Additionally, a number of studies examining the distribution, abundance, and characterization of complete ammonia oxidation (comammox) support the ecological importance of the genus .

Complete Genome Sequence of Blautia producta JCM 1471.

We report a complete genome sequence of JCM 1471 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.

Complete Genome Sequence of Flavonifractor plautii JCM 32125.

We report the complete genome sequence of JCM 32125 (=VPI 0310). 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.

Complete Genome Sequence of Megamonas funiformis JCM 14723.

We announce the complete genome sequence of JCM 14723 (YIT 11815). The genome consists of a circular chromosome (2,522,577 bp, 31.5% G+C content) and a plasmid of 46,189 bp (29.

Complete Genome Sequence of Collinsella aerofaciens JCM 10188.

We report a complete genome sequence of JCM 10188 (=VPI 1003). The genome consists of a circular chromosome (2,428,218 bp with 60.6% G+C content) and two extrachromosomal elements.

Physiological and genomic characterization of a new 'Candidatus Nitrotoga' isolate.

Oxidation of nitrite to nitrate is an important process in the global nitrogen cycle. Recent molecular biology-based studies have revealed that the widespread nitrite-oxidizing bacteria (NOB) belonging to the genus 'Candidatus Nitrotoga' may be highly important for the environment. However, the insufficient availability of pure Nitrotoga cultures has limited our understanding of their physiological and genomic characteristics.

Diversity and geochemical community assembly processes of the living rare biosphere in a sand-and-gravel aquifer ecosystem in the Midwestern United States.

Natural microbial communities consist of a limited number of abundant species and an extraordinarily diverse population of rare species referred to as the rare biosphere. Recent studies have revealed that the rare biosphere is not merely an inactive dormant population but may play substantial functional roles in the ecosystem. However, structure, activity and community assembly processes of the rare biosphere are poorly understood.

Development of certified reference material NMIJ CRM 6205-a for the validation of DNA quantification methods: accurate mass concentrations of 600-bp DNA solutions having artificial sequences.

Two 600-bp DNA solutions (DNA600-G and DNA600-T) were developed as certified reference material, NMIJ CRM 6205-a, for the validation of DNA quantification methods. Both DNA600-G and DNA600-T are ideal as "spike-in control" because these materials have artificial nucleic acid sequences. The certified values were determined as the mass concentration of total DNA (whole DNA materials in sample solution regardless of sequence) at 25 °C by formic acid hydrolysis/liquid chromatography-isotope dilution mass spectrometry (LC-IDMS) and inductively coupled plasma-mass spectrometry (ICP-MS) based on the amount of phosphorus.

Genome Features and Secondary Metabolites Biosynthetic Potential of the Class .

The prevalence of antibiotic resistance and the decrease in novel antibiotic discovery in recent years necessitates the identification of potentially novel microbial resources to produce natural products. , a class of deeply branched bacterial lineage in the ancient phylum , are ubiquitous in terrestrial environments and characterized by their large genome size and complex life cycle. These characteristics indicate as a potential active producer of bioactive compounds.