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

BACKGROUND: Acinetobacter baumannii has a greater clinical impact and exhibits higher antimicrobial resistance rates than the non-baumannii Acinetobacter species. Therefore, the correct identification of Acinetobacter species is clinically important. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has recently become the method of choice for identifying bacterial species. The purpose of this study was to evaluate the ability of MALDI-TOF MS (Bruker Daltonics GmbH, Germany) in combination with an improved database to identify various Acinetobacter species. METHODS: A total of 729 Acinetobacter clinical isolates were investigated, including 447 A. baumannii, 146 A. nosocomialis, 78 A. pittii, 18 A. ursingii, 9 A. bereziniae, 9 A. soli, 4 A. johnsonii, 4 A. radioresistens, 3 A. gyllenbergii, 3 A. haemolyticus, 2 A. lwoffii, 2 A. junii, 2 A. venetianus, and 2 A. genomospecies 14TU. After 212 isolates were tested with the default Bruker database, the profiles of 63 additional Acinetobacter strains were added to the default database, and 517 isolates from 32 hospitals were assayed for validation. All strains in this study were confirmed by rpoB sequencing. RESULTS: The addition of the 63 Acinetobacter strains' profiles to the default Bruker database increased the overall concordance rate between MALDI-TOF MS and rpoB sequencing from 69.8% (148/212) to 100.0% (517/517). Moreover, after library modification, all previously mismatched 64 Acinetobacter strains were correctly identified. CONCLUSIONS: MALDI-TOF MS enables the prompt and accurate identification of clinically significant Acinetobacter species when used with the improved database.
Acinetobacter Infections/*microbiology/pathology ; Acinetobacter baumannii/*chemistry/classification/isolation & purification ; Bacterial Proteins/chemistry/genetics/metabolism ; Databases, Factual ; Humans ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

OBJECTIVETo evaluate the effect of water pollution with dexamethasone on intestinal flora in mice.

METHODSTwenty Balb/c mice were randomly divided into control group and low-, moderate- and high-dose dexamethasone groups. The mice in dexamethasone groups were exposed to dexamethasone sodium phosphate in drinking water at doses of 0.035, 0.225, and 2.25 ng for 36 days. The changes in behaviors, fur condition, and feces of the mice were observed daily. All the mice were sacrificed at 36 days and the tissues in the ileocecal region was collected for denaturant gradient gel electrophoresis (DGGE) of 16S rDNA V6 variable regions of microbes and sequence analysis with BLAST.

RESULTSThe mice in the 3 dexamethasone groups all showed aggressive behaviors. Cluster analysis of DGGE graph showed relatively stable floras in the ileocecal region in all the mice, but principal component analysis identified differences in the dominating flora among the groups. Diversity analysis of the flora revealed significantly increased amount and types of bacteria in the intestinal flora in all the 3 dexamethasone groups (P<0.05 or 0.01) compared with the control group. Sequence analysis of 16S rDNA V6 regions showed 15 common bacterial species and 2 differential species between the dexamethasone groups and the control group with changes in the type and proportion of the dominating bacterium in the dexamethasone groups. Lactobacillus colonization was detected in the control group but not in moderate- and high-dose dexamethasone groups, and Shigella species were found in the latter two groups.

CONCLUSIONSWater contamination with dexamethasone can affect the nervous system of mice, cause changes in the types and amounts of intestinal bacteria and the dominating bacteria, and inhibit the colonization of probiotics in the intestinal floras to increase the risk of invasion by intestinal pathogenic bacteria.

Animals ; Bacteria ; classification ; Dexamethasone ; pharmacology ; Drinking Water ; chemistry ; Feces ; Gastrointestinal Microbiome ; drug effects ; Lactobacillus ; isolation & purification ; Mice ; Mice, Inbred BALB C ; Probiotics ; RNA, Bacterial ; genetics ; RNA, Ribosomal, 16S ; genetics ; Shigella ; isolation & purification

PURPOSE: The genus Aeromonas is a pathogen that is well known to cause severe clinical illnesses, ranging from gastroenteritis to sepsis. Accurate identification of A. hydrophila, A. caviae, and A. veronii is important for the care of patients. However, species identification remains difficult using conventional methods. The aim of this study was to compare the accuracy of different methods of identifying Aeromonas at the species level: a biochemical method, matrix-assisted laser desorption ionization mass spectrometry-time of flight (MALDI-TOF MS), 16S rRNA sequencing, and housekeeping gene sequencing (gyrB, rpoB). MATERIALS AND METHODS: We analyzed 65 Aeromonas isolates recovered from patients at a university hospital in Korea between 1996 and 2012. The isolates were recovered from frozen states and tested using the following four methods: a conventional biochemical method, 16S rRNA sequencing, housekeeping gene sequencing with phylogenetic analysis, and MALDI-TOF MS. RESULTS: The conventional biochemical method and 16S rRNA sequencing identified Aeromonas at the genus level very accurately, although species level identification was unsatisfactory. MALDI-TOF MS system correctly identified 60 (92.3%) isolates at the species level and an additional four (6.2%) at the genus level. Overall, housekeeping gene sequencing with phylogenetic analysis was found to be the most accurate in identifying Aeromonas at the species level. CONCLUSION: The most accurate method of identification of Aeromonas to species level is by housekeeping gene sequencing, although high cost and technical difficulty hinder its usage in clinical settings. An easy-to-use identification method is needed for clinical laboratories, for which MALDI-TOF MS could be a strong candidate.
Aeromonas/classification/*genetics/isolation & purification ; DNA, Bacterial/genetics ; Genes, Essential/*genetics ; Humans ; Molecular Typing/*methods ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Republic of Korea ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods

No abstract available.
Anti-Bacterial Agents/pharmacology ; DNA, Bacterial/analysis ; Female ; Humans ; Hypertrophy/diagnosis ; Magnetic Resonance Imaging ; Microbial Sensitivity Tests ; Middle Aged ; Mycobacterium/classification/drug effects/*isolation & purification ; Nontuberculous Mycobacteria/classification/drug effects/isolation & purification ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/metabolism ; Real-Time Polymerase Chain Reaction ; Republic of Korea ; Sequence Analysis, RNA ; Sequence Homology, Nucleic Acid ; Tenosynovitis/*diagnosis/microbiology/pathology

No abstract available.
Aged ; Bacterial Proteins/genetics ; Empyema/complications/diagnosis/*microbiology ; Humans ; Immunocompromised Host ; Male ; Nocardia/classification/*genetics/isolation & purification ; Phylogeny ; Pneumonia/complications/diagnosis/*microbiology ; Positron-Emission Tomography ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; Tomography, X-Ray Computed

Sphingobacterium spiritivorum has been rarely isolated from clinical specimens of immunocompromised patients, and there have been no case reports of S. spiritivorum infection in Korea to our knowledge. We report a case of S. spiritivorum bacteremia in a 68-yr-old woman, who was diagnosed with acute myeloid leukemia and subsequently received chemotherapy. One day after chemotherapy ended, her body temperature increased to 38.3degrees C. A gram-negative bacillus was isolated in aerobic blood cultures and identified as S. spiritivorum by an automated biochemical system. A 16S rRNA sequencing analysis confirmed that the isolate was S. spiritivorum. The patient received antibiotic therapy for 11 days but died of septic shock. This is the first reported case of human S. spiritivorum infection in Korea. Although human infection is rare, S. spiritivorum can be a fatal opportunistic pathogen in immunocompromised patients.
Aged ; Anti-Bacterial Agents/therapeutic use ; Bacteremia/*complications/drug therapy/*microbiology ; Bone Marrow Cells/pathology ; Fatal Outcome ; Female ; Humans ; Immunocompromised Host ; Leukemia, Myeloid, Acute/*complications ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Shock, Septic/etiology/microbiology ; Sphingobacterium/classification/genetics/isolation & purification/*physiology

No abstract available.
Anti-Bacterial Agents/therapeutic use ; Aorta/pathology ; Bacteremia/*complications/drug therapy/*microbiology ; Ceftriaxone/therapeutic use ; Female ; Gram-Positive Bacterial Infections/*complications/drug therapy/*pathology ; Hematoma/*complications ; Humans ; *Immunocompromised Host ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Tomography, X-Ray Computed ; Weissella/classification/genetics/isolation & purification/*physiology

OBJECTIVEThe catheter-related infections caused by mechanical ventilation have become a intractable clinical problem, and it is related to the formation of bacterial biofilm (BF) on the surface of the implanted material. The majority of natural biofilms are formed by multiple bacterial species. However, there always only one or limited species were detected on tracheal tubes removed from intubated neonates by using traditional methods including bacterium culture and antigen detection. The aims of this study were to observe the bacterial communities diversity of BF on endotracheal tube (ETT), and discuss the difference between traditional bacterium culture methods and the use of molecular biology techniques on the basis of denatured gradient gel electrophoresis (DGGE), to provide new ideas for clinical prevention, diagnosis and treatment of bacterial infections.

METHODThirty-five ETTs were obtained from 26 neonates on mechanical ventilator (from October 2012 to March 2013) in Department of Neonatology of Children's Hospital. Among the patients, 18 were boys and 8 girls, and 19 patients were < 37 weeks gestational age and 7 patients ≥ 37 weeks. DGGE profiling of 16S rDNA gene amplicons was used to assess the diversity of the bacterial population by using the software of quantity one. TA Cloning Kit and sequencing were used to investigate the distribution of bacteria and common dominant bacteria in ETT-BF.

RESULTThe mean bands of 35 ETTs cases were 13.8 ± 5.4 from 16S rDNA PCR-DGGE, and the mean Shanon-Wiener indexes was 2.42 ± 0.38. The 16 ETTs were collected in different stages of diseases from the 7 patients. The indwelling days of 6/7 patients' ETTs increased, the Shanon-siener indexes were decreased. Among the 6 cases from different basic illnesses, and there were different Shanon-siener indexes. The result of molecular cloning and sequencing for 24 dominant bands showed that 35 cases (100%) contained Klebsiella SP·, 28 cases (80%) had Pseudomonas SP·, 27 cases (77%) had Streptococcus SP·, and 32 cases (91%) had Uncultured bacterium, while more than 2 bacterial species were found in 34 cases (97%). 28/35 (80%) Klebsiella SP· and 22/27(82%) Streptococcus SP· were accompanied by Pseudomonas SP·. There were 22 positive results of sputum culture from 26 newborns, including 10 strains (45%) of Klebsiella pneumoniae, 2 strains (9%) of Acinetobacter baumannii, Enterobacter cloacae and non-cultured bacterium in each patient (5%), but only one bacterium isolated from every sputum. Eight sputum samples had normal flora only, corresponding to the ETTs on which Klebsiella and other bacterial genuses were found.

CONCLUSIONThe diversity of microbiota in BF on ETT was confirmed. 16S rDNA PCR-DGGE could produce a more complete picture of bacterial community than traditional bacterium culture method. Klebsiella, Pseudomonas and Streptococcus were common dominant bacteria in ETT-BF, and there might be interactions among them in the formation of BF.

Bacteria ; classification ; genetics ; isolation & purification ; Biodiversity ; Biofilms ; Catheter-Related Infections ; microbiology ; DNA, Bacterial ; analysis ; genetics ; Denaturing Gradient Gel Electrophoresis ; Female ; Humans ; Infant, Newborn ; Intubation, Intratracheal ; adverse effects ; Klebsiella ; genetics ; isolation & purification ; Male ; Polymerase Chain Reaction ; Pseudomonas ; genetics ; isolation & purification ; RNA, Ribosomal, 16S ; genetics ; Respiration, Artificial ; adverse effects ; Sputum ; microbiology ; Streptococcus ; genetics ; isolation & purification ; Ventilators, Mechanical ; microbiology

In this study, traditional plate culturing method was used to isolate autotoxin-degrading microbial strains, and which were then identified by 16S rDNA homological analysis and morphological characteristics. Furthermore, the growth and autotoxin-degrading efficiency of them were analyzed by liquid culturing method and GC-MS to illustrate their autotoxin-degradation characteristics. As a result, five bacterial strains having autotoxin-degrading activity were isolated from 6-years ginseng nonrhizospheric soil successfully, and which can growth successfully by taking autotoxins added artificially as carbon source in liquid culturing condition. Results indicated that it was feasible to isolate autotoxin-degrading bacteria from ginseng nonrhizospheric soil, and the isolated bacterial strains can be used to degrade autotoxins in soils once planted Panax ginseng.
Bacteria ; classification ; genetics ; isolation & purification ; metabolism ; DNA, Bacterial ; genetics ; DNA, Ribosomal ; genetics ; Molecular Sequence Data ; Panax ; chemistry ; growth & development ; metabolism ; microbiology ; Phylogeny ; RNA, Ribosomal, 16S ; genetics ; Soil ; chemistry ; Soil Microbiology ; Toxins, Biological ; metabolism