Question

Say you were to isolate and sequence the genomic information of microbes within a sample, how would you make use of this information to inform what type of growth medium to grow your microbes on? And, what other methods could you sue in order to learn more about the microbes present in your sample?

Answer 1

soil consists of many different microorganisms. It is a consortium of microbes, which need to be isolated, identified and characterized. Identification of bacteria at species level can be done by identifying specific biochemical reactions that they do, or by comparing them from the other relevant strain at genetic level.

The genome sequence generated is used to compare variations among strains and there by identify the strain of the bacterium.

Isolation of microorganisms starts with dilution of the sample. serial dilution of the sample is done and the diluted sample is poured into several petri plates having the basic medium- nutrient agar. The 10000 times diluted sample usually gives isolated colonies of the microorganisms. From this diluted sample, one mL of sample is added to petri plates and then organisms are allowed to grow. within 24 hours growth of colonies would be observed.

The isolated colonies are subcultured and then again left for 24h to grow. This would result in pure colonies that can be grown in nutrient broth to get good amount of bacterial sample for conducting various test.

The samples are first subjected to staining - this is for morphological observation of the microbes using methylene blue or saffranine. . This is followed by diffrential staining using Grams Iodine method, or acid fast staining etc.

IMViC test are conducted for further characterization which come under biochemical characterizations. These include- Indole test, Methyl red test, Voges-Proskauer test, catalase test. Apart from these oxidase test, Kilger- Iron agar test, Simmons citrate test, protease test etc are carried out.

The results are compared with standards. These are then grown in differential media for further conclusion of bacteria.

It may so happen that differentiation of strains would be difficult. In such situations the individual can use the saved results of their experiment conducted till genome sequencing.

The unidentified sample is taken, the microbes genome is isolated, subjected to restriction digestion and then sequenced.

This can be subjected to pair wise sequence alignment using bioinformatics tools and conclusion can be drawn