Establishment of Molecular Biological Method for Identification of Bacteria by 16S rDNA and gyrB Gene

[Objectives]The paper was to establish a molecular biological method for identification of bacterial strains.[Methods]The thalli of standard bacterial strains existing in the laboratory were collected and genomic DNA was extracted for amplification of 16S rDNA and gyrB gene.The 16S rDNA and gyrB gene sequences were obtained after sequencing.Sequences were aligned and analyzed via EzBioCloud and NCBI database,and phylogenetic trees were constructed to determine the species relationship of strains.Meantime,they were compared with known strains.[Results]This method could identify 5 standard strains accurately to the species level.The 16S rDNA and gyrB gene sequences were aligned and analyzed in EzBioCloud database and NCBI database.The strain with the max score was consistent with the known strain.And the query cover and ident were both above 99%.[Conclusions]The established molecular biological method for identification of bacterial strains by 16S rDNA and gyrB gene has good accuracy,which effectively solves the problem that the laboratory identification of bacteria relies on traditional methods and the accuracy can not be guaranteed,and further improves the identification ability of laboratory bacterial strains.

Comprehensive characterization of indoor airborne bacterial profile

This is the first detailed characterization of the airborne bacterial profiles in indoor environments. Two restaurants were selected for this study. Fifteen genera of bacteria were isolated from each restaurant and identified by three different bacterial identification systems including MIDI, Biolog and Riboprinter. The dominant bacteria of both restaurants were Gram-positive bacteria in which Micrococcus and Bacillus species were the most abundant. Most bacteria identified were representative species of skin and respiratory tract of human, and soil. Although the bacterial levels in these two restaurants were below the limit of the Hong Kong Indoor Air Quality Objective （HKIAQO） Level 1 standard （i.e., 〈 500 cfu/m^3）, the majority of these bacteria were opportunistic pathogens. These results suggested that the identity of airborne bacteria should also be included in the IAQ to ensure there is a safety guideline for the public.

A VIBRIO ANGUILLARUM STRAIN ASSOCIATED WITH SKIN ULCER ON CULTURED FLOUNDER, PARALICHTHYS OLIVACEUS

The characteristics of a bacterium strain M3, isolated from cultured flounder Paralichthys olivaceus with remarkable external sign of skin ulcer during an epizootic outbreak, indicated that the bacterium belonged to the species Vibrio anguillarum . Challenge by I.M. (intramuscular injection), bath, and oral administration with M3 showed that it was highly pathogenic for Paralichthys olivacues . The LD 50 dose was 5.144×10 3 CFU/ per fish infection by I.M. injection. Recovered inoculated bacteria from the surviving fish revealed that the asymptomatic carriers could be a latent contagious source. Study of the effect of bacterial culture CFS (cell free supernatant) showed that the exotoxins produced by M3 play an important role in its pathogenicity for flounder. The resistance of M3 to 36 out of 41 antibiotics indicated that the bacterial disease outbreak was mainly attributable to the frequent and excessive use of antimicrobial agents; and that vaccination would be an effective precaution against bacterial disease.

Gram-Positive Bacteria Associated with Rice in China and Their Antagonists Against the Pathogens of Sheath Blight and Bakanae Disease in Rice

It is necessary to understand the bacterial populations associated with rice so as to provide more information and natural resources for effective management of major diseases in rice. A survey on screening and identification of gram-positive bacteria was conducted during 1998 2004. Seven hundred and fifty-six rice samples were collected from Zhejiang, Jiangsu, Fujian and Yunnan Provinces, China. Over 1000 bacterial isolates were isolated and tested for colony morphology, pathogenicity, and some characteristics of bacteriology including Gram staining, fluorescent pigment on Kings medium B and microscopic observation for endospore. Together with five standard reference strains, 74 representative gram-positive bacterial isolates were confirmed by Biolog and gas chromatographic analysis of fatty acid methyl esters. Five bacterial species of Bacillus and other three genera were identified and isolates from Bacillus sublitis and Bacillus megaterium, exhibited the most effective inhibition against the pathogens of sheath blight and bakanae disease of rice. A few isolates from Bacillus pumilus and Bacillus megaterium showed weak virulent on rice together with some virulent isolates, risk should be considered when isolates from these species were screened for biocontrol agents.

BioCluster:Tool for Identification and Clustering of Enterobacteriaceae Based on Biochemical Data

Presumptive identifcation of different Enterobaeteriaeeae species is routinely achieved based on biochemical properties. Traditional practice includes manual comparison of each biochem- ical property of the unknown sample with known reference samples and inference of its identity based on the maximum similarity pattern with the known samples. This process is labor- intensive, time-consuming, error-prone, and subjective. Therefore, automation of sorting and sim- ilarity in calculation would be advantageous. Here we present a MATLAB-based graphical user interface （GUI） tool named BioCluster. This tool was designed for automated clustering and iden- tification of Enterobacteriaceae based on biochemical test results. In this tool, we used two types of algorithms, i.e., traditional hierarchical clustering （HC） and the Improved Hierarchical Clustering （IHC）, a modified algorithm that was developed specifically for the clustering and identification of within this species. IHC takes into account the variability in result of 1-47 biochemical tests family. This tool also provides different options to optimize the clus- tering in a user-friendly way. Using computer-generated synthetic data and some real data, we have demonstrated that BioCluster has high accuracy in clustering and identifying enterobacterial species based on biochemical test data. This tool can be freely downloaded at http：//microbialgen.du.ac.bd/ biocluster/.