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

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

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

Actinomyces meyeri is rarely isolated in cases of actinomycosis. The identification of A. meyeri had historically been difficult and unreliable. With the recent development of 16S ribosomal RNA (16S rRNA) sequencing, Actinomyces species such as A. meyeri can be isolated much more reliably. A. meyeri often causes disseminated disease, which can be secondary to frequent pulmonary infections. A penicillin-based regimen is the mainstay of A. meyeri treatment, with a prolonged course usually required. Here, we report a case of pulmonary actinomycosis with brain abscess caused by A. meyeri that was initially thought to represent lung cancer with brain metastasis.
Actinomyces* ; Actinomycosis ; Brain Abscess ; Brain* ; Lung Neoplasms ; Lung* ; Neoplasm Metastasis ; RNA ; RNA, Ribosomal, 16S ; Sequence Analysis

OBJECTIVETo investigate the dynamic changes of intestinal 16S rDNA metagenome in healthy infants.

METHODSSeventeen fecal samples were collected at ages of 3 days, 1 month, 6 months and 1 year in 5 infants. Total bacterial DNAs were extracted and submitted high throughout sequencing on the V6 viable region of 16S rDNA. Tags and Operational Taxonomic Units (OTU) were then obtained and analysis of taxonomy, abundance and alpha diversity were performed.

RESULTSIn total 2,190.66 Mbp raw data in 17 samples were produced. The OTU numbers ranged from 36 to 308. The dominate phylum included Proteobacteria, Firmicutes and Bacteroidetes and Actinobacteria. The bacterial families>1% increased from only 2-4 per sample on day 3 to 7 at 1 or 6 months, 10 at 12 months. The average npShannon and Simpson index on day 3, at 1 month, 6 months and 1 year were 1.117, 1.460, 2.088, 2.50 and 0.443, 0.408, 0.229, 0.143 respectively.

CONCLUSIONSInfants' intestines harbor abounding bacterial genomes. Distinct individual differences exist in infants in terms of intestinal bacterial abundance and composition. The abundance and diversity of gut bacteria increase over time.

DNA, Bacterial ; analysis ; Female ; Humans ; Infant ; Intestines ; microbiology ; Male ; Metagenome ; RNA, Ribosomal, 16S ; analysis

Objective To describe the microbiological characteristics of ()CGMCC 12426 and determine and analyze its complete genome sequences.Methods strain CGMCC 12426 genomic DNA sequencing was performed on a single molecule real-time sequencing(SMRT)platform and the annotation was completed in the NCBI Prokaryotic Genomic Annotation Pipeline(pGAP).Results The complete genomic sequences of the released CGMCC 12426 consisted of a 4 138 265-bp circular chromosome and a 74 165-bp plasmid,which resulted in the prediction of 4581 genes including 4222 coding sequences,87 tRNAs,and 30 rRNAs(which included 5S rRNA,16S rRNA,and 23S rRNA).Conclusion The genome sequencing provided a basis for further investigations on the genetic background of and on the metabolic and regulatory mechanisms.
Bacillus subtilis ; genetics ; Genome, Bacterial ; Plasmids ; RNA, Ribosomal, 16S ; genetics ; RNA, Ribosomal, 23S ; genetics ; RNA, Ribosomal, 5S ; genetics ; Sequence Analysis, DNA

This study aimed to investigate bacterial community in an urban drinking water distribution system (DWDS) during an occurrence of colored water. Variation in the bacterial community diversity and structure was observed among the different waters, with the predominance of Proteobacteria. While Verrucomicrobia was also a major phylum group in colored water. Limnobacter was the major genus group in colored water, but Undibacterium predominated in normal tap water. The coexistence of Limnobacter as well as Sediminibacterium and Aquabacterium might contribute to the formation of colored water.
Bacteria ; genetics ; isolation & purification ; Drinking Water ; microbiology ; RNA, Ribosomal, 16S ; genetics ; Water Microbiology ; Water Supply ; analysis

Ligustrazine is an important active ingredient of the traditional Chinese medicine Chuanxiong Rhizoma, but its content is a controversial topic. The endophytes of medicinal plants have the ability to produce the same active substances as the host, so this report focused on the endophytic Bacillus subtilis, to study the origin of ligustrazine in Chuanxiong Rhizoma preliminarily by inoculating the isolated endophytic B. subtilis to the Chuanxiong Rhizoma medium for solid state fermentation. Tissue grinding method was used to isolate the endogenetic B. subtilis. The morphological features, conventional physiological and biochemical reactions and 16S rRNA molecular techniques were combined to identify the endogenetic strains. Then, the strains that grew well in the medicinal matrix of Chuanxiong Rhizoma were screened out for further fermentation studies. The solid-state fermentation was performed at 37 °C for 30 d using Chuanxiong Rhizoma fermentation medium (40 g Chuanxiong Rhizoma powder, 100 mL sterile water, 121 °C, sterilization for 25 minutes). UPLC was used to detect the contents of ligustrazine, acetoin in the Chuanxiong Rhizoma fermentation medium and Chuanxiong Rhizoma. All the five strains were Gram-positive and had spores. Phylogenetic analysis of the 16S rRNA sequence showed that the endophytes were B. subtilis. The results of UPLC showed that ligustrazine was detected in the Chuanxiong Rhizoma fermentation medium inoculated with endogenetic B. subtilis LB3, LB3-2-1, LB4, LB5 and LB6-2, while not detected neither in blank Chuanxiong Rhizoma fermentation medium nor in Chuanxiong Rhizoma. This study showed that the endogenetic B. subtilis of Ligusticum chuanxiong Hort. can make use of Chuanxiong Rhizoma fermentation medium to produce ligustrazine. Endogenetic B. subtilis has a certain correlation with the accumulation of ligustrazine in Rhizoma Chuanxiong. We speculate that the ligustrazine may be derived from the catabolism of endogenetic B. subtilis in Ligusticum chuanxiong.
Bacillus subtilis ; Endophytes ; Fermentation ; Ligusticum ; chemistry ; microbiology ; Phylogeny ; Pyrazines ; analysis ; RNA, Ribosomal, 16S ; Rhizome ; chemistry

Metagenomic sequencing provides a powerful tool for microbial research. However, traditional experimental DNA extraction process will inevitably mix with environmental microorganisms which float in the air. It is still unclear whether the mixed environmental microbial DNA will heavily affect the metagenomic results of samples with extremely low microbial content. In this study, we first collected environmental bacteria in the laboratory and quantified the mixed environmental microbial DNA content during DNA extraction based on a qPCR-based quantification assay. We then extracted DNA from pure water in order to determine the mixed microbial taxons during extraction under open environment. At last, we extracted total DNA from a skin sample in a Biosafety cabinet or under open laboratory environment, to assess the impact of the mixed environmental microorganisms on the metagenomic results. Our results showed that DNA extraction under open laboratory environment in Beijing region resulted in 28.9 pg contaminant, which may accout for 30% of total DNA amount from skin samples. Metagenomic analysis revealed that the main incorporated environmental taxons were Cutibacterium acnes and Escherichia coli. Tens of environmental bacteria were foisted in the skin DNA samples, which largely decreased the relative abundance of dominant species and thus deteriorated the result accuracy. Therefore, analyzing microbial composition of samples with extremely low DNA content should better performed under aseptic environment.
DNA ; DNA, Bacterial/genetics* ; Laboratories ; Metagenomics ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA

OBJECTIVES: To study the effect of probiotics combined with applied behavior analysis (ABA) in the treatment of children with autism spectrum disorder (ASD). METHODS: A total of 41 children with ASD who attended the Affiliated Hospital of Jiangsu University from May 2019 to December 2020 were enrolled and randomly divided into an observation group with 21 children and a control group with 20 children. The children in the observation group were given oral probiotics combined with ABA intervention, while those in the control group were given ABA intervention alone. The treatment outcomes were compared between the two groups. Autism Treatment Evaluation Checklist (ATEC) was used to evaluate the severity of behavioral symptoms in both groups before intervention and at 3 months after intervention. The fecal samples were collected to analyze the difference in intestinal flora between the two groups based on 16s rRNA high-throughput sequencing. RESULTS: Before intervention, there was no significant difference in the ATEC score between the observation and control groups ( CONCLUSIONS Probiotics may improve the effect of conventional ABA intervention in children with ASD by regulating intestinal flora.
Applied Behavior Analysis ; Autism Spectrum Disorder/therapy* ; Child ; Humans ; Probiotics ; Prospective Studies ; RNA, Ribosomal, 16S