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

Over the past decade or so, dramatic developments in our ability to experimentally determine the content and function of genomes have taken place. In particular, next-generation sequencing technologies are now inspiring a new understanding of bacterial transcriptomes on a global scale. In bacterial cells, whole-transcriptome studies have not received attention, owing to the general view that bacterial genomes are simple. However, several recent RNA sequencing results are revealing unexpected levels of complexity in bacterial transcriptomes, indicating that the transcribed regions of genomes are much larger and complex than previously anticipated. In particular, these data show a wide array of small RNAs, antisense RNAs, and alternative transcripts. Here, we review how current transcriptomics are now revolutionizing our understanding of the complexity and regulation of bacterial transcriptomes.
Genome ; Genome, Bacterial ; Hypogonadism ; Mitochondrial Diseases ; Ophthalmoplegia ; RNA ; RNA, Antisense ; RNA, Satellite ; Sequence Analysis, RNA ; Transcription Initiation Site ; Transcriptome

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: High PM concentration is the main feature of increasing haze in developing states, but information on its microbial composition remains very limited. This study aimed to determine the composition of microbiota in PM in Guangzhou, a city located in the tropics in China. Methods: In Guangzhou, from March 5 to 10 , 2016, PM was collected in middle volume air samplers for 23 h daily. The 16S rDNA V4 region of the PM sample extracted DNA was investigated using high-throughput sequence. Results: Among the Guangzhou samples, , , , , and were the dominant microbiota accounting for more than 90% of the total microbiota, and was the dominant gram-negative bacteria, accounting for 21.30%-23.57%. We examined the difference in bacterial distribution of PM between Beijing and Guangzhou at the genus level; was found in both studies, but was only detected in Guangzhou. Conclusion In conclusion, the diversity and specificity of microbial components in Guangzhou PM were studied, which may provide a basis for future pathogenicity research in the tropics.
Air Microbiology ; Air Pollutants ; analysis ; Bacteria ; classification ; isolation & purification ; China ; Cities ; Environmental Monitoring ; Microbiota ; Particle Size ; Particulate Matter ; analysis ; RNA, Bacterial ; analysis ; RNA, Ribosomal, 16S ; analysis

BACKGROUNDThe catheter related infection caused by Staphylococcus epidermidis biofilm is increasing and difficult to treat by antimicrobial chemotherapy. The properties of biofilms that give rise to antibiotic resistance are only partially understood. This study aimed to elucidate the penetration of erythromycin through Staphylococcus epidermidis biofilm.

METHODSThe penetration ratio of erythromycin through Staphylococcus epidermidis biofilms of 1457, 1457-msrA, and wild isolate S68 was detected by biofilm penetration model at different time points according to the standard regression curve. The RNA/DNA ratio and the cell density within the biofilms were observed by confocal laser microscope and transmission electromicroscope, respectively.

RESULTSThe penetration ratios of erythromycin through the biofilms of 1457, 1457-msrA, and S68 after cultivation for 36 hours were 0.93, 0.55 and 0.4, respectively. The erythromycin penetration ratio through 1457 biofilm (0.58 after 8 hours) was higher than that through the other two (0.499 and 0.31 after 24 hours). Lower growth rate of the cells in biofilm was shown, with reduction of RNA/DNA proportion observed by confocal laser microscope through acridine orange stain. Compared with the control group observed by transmission electrmicroscope, the cell density of biofilm air face was lower than that of agar face, with more cell debris.

CONCLUSIONSErythromycin could penetrate to the Staphylococcus epidermidis biofilm, but could not kill the cells thoroughly. The lower growth rate of the cells within biofilm could help decreasing the erythromycin susceptibility.

Acridine Orange ; Anti-Bacterial Agents ; pharmacokinetics ; Biofilms ; DNA, Bacterial ; analysis ; Erythromycin ; pharmacokinetics ; pharmacology ; Microscopy, Electron, Transmission ; RNA, Bacterial ; analysis ; Staphylococcus epidermidis ; drug effects ; metabolism

We had three cases of Moraxella osloensis meningitis. The species identification was impossible by conventional and commercial phenotypic tests. However, we could identify the species using the 16S rRNA gene sequencing. Determination of clinical significance was difficult in one patient. All three patients recovered by appropriate antimicrobial therapy.
Adolescent ; Aged, 80 and over ; Anti-Bacterial Agents/therapeutic use ; *Bacterial Typing Techniques ; Child, Preschool ; Female ; Humans ; Male ; Meningitis, Bacterial/drug therapy/*microbiology ; Moraxella/*pathogenicity ; Moraxellaceae Infections/drug therapy/*microbiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis

Segniliparus species is a novel genus that is reported to be the new emerging respiratory pathogens. Here, we report a very rare case of S. rugosus pulmonary infection in an immunocompetent patient with non-cystic fibrosis. The organism was identified by 16S rRNA gene sequencing. The patient was successfully treated with antibiotics.
Anti-Bacterial Agents ; Fibrosis* ; Genes, rRNA ; Humans ; Nontuberculous Mycobacteria ; Respiratory Tract Infections ; Sequence Analysis, RNA

Air Conditioning ; Humans ; Legionella pneumophila ; isolation & purification ; RNA, Bacterial ; analysis ; Water Microbiology

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

OBJECTIVETo explore the feasibility of using gene chip method to identify pathogens in blood cultures.

METHODSClinical blood samples were obtained and cultured using an automated blood culture system. A gene chip diagnostic kit was used to detect the pathogenic bacteria in these blood cultures following the procedures of target gene extraction and amplification, hybridization and result analysis. The conventional method was also used to isolate and identify the bacteria from the clinical blood cultures, and the results of the two methods were compared.

RESULTSIn the 86 clinical blood samples, 74 were positive and 12 negative according to the conventional method, while 48 were positive and 38 negative as found by the gene chip method, showing significant differences in the results (P<0.05). The two methods only had a concordance rate of 69.77%.

CONCLUSIONThe gene chip diagnostic kit has low concordance rate with the conventional method for detecting pathogens in clinical blood cultures and awaits further improvement.

Bacteria ; genetics ; growth & development ; isolation & purification ; Bacterial Typing Techniques ; methods ; Blood ; microbiology ; DNA, Bacterial ; analysis ; genetics ; isolation & purification ; Humans ; Oligonucleotide Array Sequence Analysis ; methods ; RNA, Ribosomal, 16S ; genetics