With new DNA sequencing techniques, we can sequence almost any kind of samples with microbes in and get a good idea of the structure and composition of the microbial communities. That is nothing new. How can we use the data and take advantage of the sequencing techniques and new analyzing techniques? Can we go further than that to get more insights into microbial functions, interactions, and others aspects of the community?
Million dollar question even though NGS is less than a million dollar! With the insight into the sequences of microbes present in any environment the possibilities are immense. On application scenario the sequences of genes which are into enzyme (or any other biomolecule) production can be analyzed in relation to the environment of the organism and similar conditions can be developed for better utilization of those enzymes, similarly the understanding the interaction of microorganisms on molecular level can help us in engineering out environment in a better way. I can say the sky is the limit even though the way goes through soil or water or even inside a protista.
I think the best implementation of this technique is in personalised medicine to deal with various kinds of diseases.
It is possible to make a network from the sequencing data and study bacterial interactions among different bacteria in the community. For example, analyze the association / correlation between different bacterial components in the communities across the time (succession) or with different treatments. It is significant to find out the keystone species, the species that positively/negatively associate with the majority of other bacteria in the changing community. The keystone species might regulate/determine the structure of the community, help us explain how the community response to the treatment and why the community change in this way. Based on the identification of keystone species, it is possible to develop some bio-control agents or probiotics to treat the unblalanced community such as environment contamination or gut infection.
If you wish to understand the real microbial dynamics at different stages you need to be sure that all DNA that you're sequencing belongs to live cells. A very interesting approach is sample pre treatment with PMA. You can visit ( www.geniul.com) for more information and examples. Best Regards
Even though we currently can get plenty information on both organismal and functional structure of the whole microbial community, the disadvantage of a microbial community study with high-throughput DNA sequencing techniques (metagenomics) is that
(1) it is hard to identify and characterize the genome of any individual bacterial species in the metagenome technically;
(2) if you find any individuals interesting, you can not pick out and do further research
Therefore, the combination between single-cell technique and metagenomics will provider more insights into detailed functions of individual bacteria and bacterial intercations within and between community.
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