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Colony behaviour and metatranscriptomics

ResearchBlogging.orgMost places which contain bacteria tend to contain lots of them. In the environment (i.e outside human bodies) bacteria often live in large colonies which can make it difficult to explore their reactions to changing conditions. In the lab, with just one bacteria, information about responses can be obtained by transcriptomics; looking at how the transcriptome changes as the environment does.

The transcriptome is the set of all the mRNA within the cell. Unlike the genome, which is the all DNA present within the cell, the transcriptome only reveals those genes which are being turned into proteins. This therefore acts as an indication of the changes in protein production within the cell.

My MSPaint skills are improving.

For large bacterial colonies however, individual transcriptomic studies aren't much use for finding out the state of the whole colony. Each bacteria within the colony will not only be reacting slightly differently, but will also be experiencing different conditions within the colony depending on where it is within the colony. It's often best, therefore to treat the entire colony as one 'cell' and carry out transcriptome studies on the whole lot. This is metatranscriptomics.

Nowadays one of the easiest ways to carry this out is by isolating the RNA and getting it all directly sequenced by Pyrosequencing (which saves the trouble of making microarrays). As well as giving information about the changes within a colony due to environmental factors, it can also show the changes in protein production at different stages in the colony lifecycle such as at the beginning and end of an algal bloom. The integration of new third-generation sequencing methods into this process will make it faster and hopefully allow isolation of the rarer, less abundant transcripts to find more subtle changes in gene expression.

This has important implications for things like oceanic cyanobacteria which are involved in carbon sequestration in the oceans. Understanding how changes such as increases in ocean acidity (or decreases in salinity) affects their growth and ability to remove carbon from the atmosphere could have important implications for global warming, and how it can be dealt with.

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Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, & Joint I (2008). Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PloS one, 3 (8) PMID: 18725995

3 comments:

Lucas Brouwers said...

The frightening and exciting thing about metatranscriptomics (and meagenomics) is that it confronts us with the huge gaps in our knowledge.. 91% of the transcripts they identified in this study were unknown/novel. There's a whole lot of work to do before we can fully understand complex microbial communities :).

Lab Rat said...

Metatranscriptomics also reveals just how many bacteria there seem to be that simply can't be cultured in labs. It looks like there's a lot of novel bacteria creating these transcripts that can't be isolated and grown up back in the lab.

Lucas Brouwers said...

I just remembered a nice post by Iddo Friedberg on the gap between data and information, and the need for bioinformaticians to join forces with experimentalists to close it:
http://bytesizebio.net/index.php/2010/06/08/computational-bridge-to-experiments/