Pathogenic gram-negatives that produce 16S ribosomal RNA methyltransferases (16S RMTases) have already been distributed all over the world. To investigate the predominance of aminoglycoside resistance associated with 16S RMTases in Korea, we collected a total of 222 amikacin resistant Gram-negative clinical isolates from patient specimens between 1999 and 2015 from three hospital banks across Korea. ArmA and rmtB were the predominant 16S RMTase genes responsible for aminoglycoside-resistant isolates circulating in Korean community settings although only one rmtA-producing isolate was detected in 2006.
Amikacin ; Humans ; Korea* ; Methyltransferases ; RNA, Ribosomal, 16S

Forensic microorganism is one of the hotspots of forensic science research. Due to its conservatism and specificity, the 16S rRNA gene is found to be an ideal marker for forensic identification. With the rapid development of high throughput sequencing technology, the research on microorganisms has been gradually applied to many fields such as environment and health care. In the field of forensic science, the results of forensic microbiology research, represented by 16S rRNA gene sequencing, are also gradually applied to forensic practice, such as biological samples identification, individual identification, postmortem interval estimation, and regional inference, which not only provide clues for the investigation of cases but also complement and assist traditional methods. This paper describes the research methods and related sequencing technologies of 16S rRNA gene sequencing, summarizes its research progress, and discusses the application value and potential of 16S rRNA in forensic science.
Forensic Sciences/trends* ; RNA, Ribosomal, 16S ; Sequence Analysis, RNA

BACKGROUND: Recently, the rate of infections with non-tuberculous mycobacteria (NTM) has been increasing in Korea. Precise identification of NTM is critical to determination of the pathogen and to target treatment of NTM patients. METHODS: Sixty-eight unclassified mycobacteria isolates by rpoB PCR-RFLP assay (PRA) collected in 2008 were analyzed by National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) search after sequencing of 16S rRNA, hsp65, rpoB genes. RESULTS: Nineteen strains of 68 isolates were specified as species after sequencing analysis of 3 gene types. We found 3 M. lentifulavum, 5 M. arupense, 4 M. triviale, 4 M. parascrofulaceum, and one M. obuense. One M. tuberculosis and another M. peregrinum were mutated at the Msp I recognition site needed for rpoB PRA. The remaining 49 isolates did not coincide with identical species at the 3 kinds genes. CONCLUSION: Sequencing analysis of 16S rRNA, hsp65, rpoB was useful for identification of NTM unclassified by rpoB PRA.
Biotechnology ; Korea ; Nontuberculous Mycobacteria ; RNA, Ribosomal, 16S ; Tuberculosis

We describe the laboratory identification of Leptotrichia species from clinical isolates collected over a six-year period. Five isolates from blood cultures were identified as Leptotrichia species. Gram stain showed large, fusiform, gram-negative or -variable bacilli. Identification based on biochemical testing was unsuccessful; however, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry proved to be a useful tool for identifying Leptotrichia species to the genus level. Species level identification was successfully achieved by using 16S ribosomal RNA gene sequencing.
Bacteremia* ; Humans ; Leptotrichia* ; Mass Spectrometry ; RNA, Ribosomal, 16S

Microbiome is a novel research field related with a variety of chronic inflamatory diseases. Technically, there are two major approaches to analysis of microbiome: metataxonome by sequencing the 16S rRNA variable tags, and metagenome by shot-gun sequencing of the total microbial (mainly bacterial) genome mixture. The 16S rRNA sequencing analyses pipeline includes sequence quality control, diversity analyses, taxonomy and statistics; metagenome analyses further includes gene annotation and functional analyses. With the development of the sequencing techniques, the cost of sequencing will decrease, and big data analyses will become the central task. Data standardization, accumulation, modeling and disease prediction are crucial for future exploit of these data. Meanwhile, the information property in these data, and the functional verification with culture-dependent and culture-independent experiments remain the focus in future research. Studies of human microbiome will bring a better understanding of the relations between the human body and the microbiome, especially in the context of disease diagnosis and therapy, which promise rich research opportunities.
Bacteria ; classification ; Humans ; Metagenome ; Microbiota ; RNA, Ribosomal, 16S

We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequence analysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-related species are abundant compared to those in genome-based phylogeny. This phenomenon makes the demarcation of genera within many families ambiguous in the 16S rRNA-based taxonomy. In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes using the CVTree method, which is based on whole-genome information. And many such genera, which are polyphyletic in 16S rRNA-based trees, are well resolved as monophyletic clusters by CVTree. We believe that with genome sequencing of prokaryotes becoming a commonplace, genome-based phylogeny is doomed to play a definitive role in the construction of a natural and objective taxonomy.
Genome ; Genomics ; Phylogeny ; RNA, Ribosomal, 16S ; genetics ; Sequence Analysis, DNA

PURPOSE: Identifying microbial communities with 16S ribosomal RNA (rRNA) gene sequencing is a popular approach in microbiome studies, and various software tools and data resources have been developed for microbial analysis. Our aim in this study is investigating various available software tools and reference sequence databases to compare their performance in differentiating subject samples and negative controls. METHODS: We collected 4 negative control samples using various acquisition protocols, and 2 respiratory samples were acquired from a healthy subject also with different acquisition protocols. Quantitative methods were used to compare the results of taxonomy compositions of these 6 samples by varying the configuration of analysis software tools and reference databases. RESULTS: The results of taxonomy assignments showed relatively little difference, regardless of pipeline configurations and reference databases. Nevertheless, the effect on the discrepancy was larger using different software configurations than using different reference databases. In recognizing different samples, the 4 negative controls were clearly separable from the 2 subject samples. Additionally, there is a tendency to differentiate samples from different acquisition protocols. CONCLUSION: Our results suggest little difference in microbial compositions between different software tools and reference databases, but certain configurations can improve the separability of samples. Changing software tools shows a greater impact on results than changing reference databases; thus, it is necessary to utilize appropriate configurations based on the objectives of studies.
Classification ; Computational Biology ; Healthy Volunteers ; Metagenome ; Microbiota ; RNA, Ribosomal, 16S

The 16S rRNA gene is the most commonly used molecular marker for identifying microorganisms. It is used in sequencing technology, including the first-generation, the second-generation, and the third-generation sequencing technology. A large number of studies on the 16S rRNA gene have contributed to a deeper understanding of oral microbial diversity. In the healthy oral cavity, there is microbial diversity in time and space. With the occurrence or development of oral diseases such as caries, periodontal disease, or halitosis, the microbial diversity will be changed.
High-Throughput Nucleotide Sequencing ; Mouth ; RNA, Ribosomal, 16S ; genetics

The marine genus Marinobacterium was first identified in 1997, and a total of 18 species have been characterized so far, 10 of which have published whole-genome sequencing data. This article summarizes the characteristics of Marinobacterium genus and analyzes the genome sequencing data related to the carbon source utilization, polyhydroxyalkanoate metabolism, and aromatic compounds degradation. The Marinobacterium species possess the complete glycolysis pathway and tricarboxylic acid cycle, yet lack genes involved in xylose utilization. All strains of the Marinobacterium genus contain the genes encoding for the typeⅠand type Ⅲ polyhydroxyalkanoate synthases, suggesting that the genus may have ability of polyhydroxyalkanoate accumulation. The Marinobacterium species contain the degradation pathways of aromatic compounds. Benzene, phenol and benzoic acid can be degraded into catechol via different enzymes, subsequently catechol is converted to 3-ketoadipate through the ortho-cleavage pathway. Alternatively, catechol can be degraded into pyruvate and acetyl-CoA. The analysis of genome sequencing data of the Marinobacterium genus provides in-depth understanding of the metabolic characteristics, indicating that the genus may have certain applications in the synthesis of polyhydroxyalkanoate and the removal of marine aromatic compounds.
Alteromonadaceae ; DNA, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA

Microorganisms are the dominant players driving the degradation and transformation of chloramphenicol (CAP) in the environment. However, little bacterial strains are able to efficiently degrade and mineralize CAP, and the CAP degrading pathways mediated by oxidative reactions remain unclear. In this study, a highly efficient CAP-degrading microbial consortium, which mainly consists of Rhodococcus (relative abundance >70%), was obtained through an enrichment process using CAP-contaminated activated sludge as the inoculum. A bacterial strain CAP-2 capable of efficiently degrading CAP was isolated from the consortium and identified as Rhodococcus sp. by 16S rRNA gene analysis. Strain CAP-2 can efficiently degrade CAP under different nutrient conditions. Based on the biotransformation characteristics of the detected metabolite p-nitrobenzoic acid and the reported metabolites p-nitrobenzaldehyde and protocatechuate by strain CAP-2, a new oxidative pathway for the degradation of CAP was proposed. The side chain of CAP was oxidized and broken to generate p-nitrobenzaldehyde, which was further oxidized to p-nitrobenzoic acid. Strain CAP-2 can be used to further study the molecular mechanism of CAP catabolism, and has the potential to be used in in situ bioremediation of CAP-contaminated environment.
Biodegradation, Environmental ; Chloramphenicol ; RNA, Ribosomal, 16S/genetics* ; Rhodococcus/genetics* ; Sewage