hello Stephanie Greige
1. For whole microbial community analysis you can use the methods: DNA-DNA reassociation, G+C fractionation, whole genome sequencing, metagenomics, metaproteomic, proteogenomic, and metatranscriptomic.
2. For partial community analysis you can use methods as you mentioned:
a. Genetic fingerprinting techniques such as ARDRA, SSCP, T-RFLP, DGGE, RISA, LH-PCR, RAPD.
b. Clone library method
c. Q- PCR (real-time PCR)
d. FISH, dot-blot hybridization
e. Microbial lipid analysis
f. DNA microarrays
g. Microautoradiography and isotope array
h. Microautoradiography and isotope array
i. CARD-FISH, Raman-FISH, NanoSIMS
Check them out and find the suitable methods for your samples.
Hope it would help
Goodluck :)
I would suggest more than one (16S) gene metagenome analysis. Look at Keshri J, Mishra A, Jha B. Microbial population index and community structure in saline–alkaline soil using gene targeted metagenomics. Microbiological research. 2013 Mar 30;168(3):165-73. Article Microbial population index and community structure in saline...
Hello Wiwiek Harsonowati
Thank you for your answer and ideas.
Will definitely check these methods,
Regards
Alex Ignatov thank you for your suggestion
will read this paper right away
If you do not intend to identify individual microbial species, rather want to study, what type of microbes present, you may try controlled culture/selective culture by altering the culture media. Now, following the exact same time protocol, checking the bacterial concentration of each type. Similar to isolating bacteria from soil. Therefore, before even going into the extensive tests, with the aid of microscopy you will get a rough idea of what "type" /class of bacteria are there. This might be a screening phase for your study.
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