Dear Colleague, There are many molecular methods are available to characterize the bacteria includes 16S rRNA sequence analysis, cellular G+C content analysis, Fatty acid methyl esters analysis and DNA-DNA Hybridization. But there are limitation to identify the bacteria at the Species level, so if need to characterize the bacteria upto species level better you go for polyphasic analysis (which includes all above mentioned molecular methods).....

For ex. Virulent genes are identified by virluent gene markers (primers) in microbes, like that all specific character has specific gene you have to identify the gene of your interest and need to design primers

You want to study the function using molecular tools. There are so many information available now a day as a large number of whole genome sequences have been done for microbes. Just design primers and hit your target genes..good luck.

Dear Aparna,

We can identify specific character of gene can be expressed by EST-marker.Now a days using certain (eg. expression sequence taq )marker with help of specific primer we can amplify our gene of interest.

Hi. characterization depend on the type of bacteria you are studying. point out the specific characters all ready available for such bacteria. then point out what type of characters u can target and go for genomic or proteomic analysis of such characters.

you can identify by Sequence analysis of 16s rRNA gene of bacteria, then go for Phylogenetic tree analysis.

if you are identifying bacteria then specie level 16srRNA analysis and for strain level AFLP is done in common, but now a days more precise is to do fattyacid analysis. but if you are going for some specific character for example indole acetic acid gene in bacteria then ofcouruse you have to go for gene specific primers.

16s rRNA analysis

By using gene specific markers: Internal transcribed spacers (ITS), ISSR, ITS-RFLP etc.

16S rDNA sequencing will certainly be useful to precisely identify your isolates. For further characterization (typing) techniques, it depends on the degree of discrimination and the amount and kind of information you need for your bacterial species. PCR detection and PCR-RFLP of specific genes are useful to predict particular traits such as antibiotic resistance or production of a toxin. RFLP analysis of these products will provide low discriminatory power but let you envisage some degree of variability in your population. Multiplex PCR of repeated sequences such as variable number tandem repeat analysis (MLVA) are more discriminatory and more representative of the whole genome sequence variations, since repeated sequences may be interspersed all along the genome. Multilocus sequence typing has a higher discriminatory power, . It is based on sequencing 7 to 9 housekeeeping genes, it is portable (sequence information may be handled in text files) and databases useful for global epidemiology analysis are available (look for pubmlst or mlst.net web pages), which allow to compare your data with world wide databases. Macrorestriction analysis of the whole genome in pulse field gel electrophoresis (PFGE) is highly discriminatory and is recomended by CDC for outbreak analysis. AFLP is also a highly discriminatory approach. Besides, particular molecular typing techniques may be available for particular pathogens. These techniques are based on particular features of gene or genome structure. Examples of these are spoligotyping for Mycobaterium tuberculosis or spa-typing for Staphylococcus aureus. A useful paper for you to have a wide view on bacterial typing techniques is that of Foxman et al. 2005. Choosing an appropriate typing technique for epidemiological studies. Epidemiologic Perspectives and Innovations 2:10 doi:10.1186/1742-5573-2-10. It is freely available Open Access journal from BioMedCentral. Hope you find this information useful.

You can also use its sequence primer

Internal tendam sequence primers are use for bacterial characterization. There many references on it

16S rRNA sequencing

In addition to ITS one can use gene specific primers in PCR for identification

pcr - blast

Molecular techniques that could be useful could be: DGGE, RFPL, PCR, Sequencing coupled with comparisons of results of previous studies can give you some more information about the characteristics of your microorganism.

Rep-pcr, box pcr, eric pcr

Dear sekhar,

there are many ways to characterized bacteria by molecular methods like

1- for identification and taxonomy use polyphasic methods (RAPD,16S rRNA, MLSA Housekeeping genes, DNA-DNA hybridization, RFLP and AFLP)

2-for any specific gene you can designed specific primers like antibiotics and pyrolidine

3- for specific region used ITS Primers

4- for secondary metabolite use specific prime like for phenazine and other lipopeptides.

be happy.

16S rDNA sequencing, MLST (housekeeping genes depending on the genus), MALDI-TOF, Ribotyping, rep-PCR and DNA-DNA hybridization. What is enough depends on the discriminatory power of each test for the particular organism in question. Sometimes full length 16S sequencing and MLST is good enough for characterization.

For publication purpose there are useful information and guidelines in the IJSEM and Antonie van Leeuwenhoek journals.

Bacteria can be identified by 16S rRNA gene sequencing method. It involves amplification of 16S rRNA gene and sequencing of the PCR product

The most used method is the partial sequencing of 16S that gives you the opportunity for species identification. You can also use the partial sequencing of several other genes depending on the availability of the publicly deposited sequences (e.g. gyrB, rpoD, rpoB for the fluorescent pseudomonads).

Dear Colleague, There are many molecular methods are available to characterize the bacteria includes 16S rRNA sequence analysis, cellular G+C content analysis, Fatty acid methyl esters analysis and DNA-DNA Hybridization. But there are limitation to identify the bacteria at the Species level, so if need to characterize the bacteria upto species level better you go for polyphasic analysis (which includes all above mentioned molecular methods).....

You can use the Rep and Box seq for molecular characterization

Identification of genes say for antibiotic production might reveal genetic characterization of a microbe up to Genus level. In order to elucidate species level genetic characterization, I think, one could target 16S rRNA sequences.