Monday, January 26, 2015

The iChip: A tool for high-throughput microbial culturing

It is commonly accepted that only ~1% of naturally occurring microbes are culturable using standard culturing techniques.  Until recently, culturing microbes has been the only way to investigate their presence and effects on various environments (i.e. human gut, soil, plant roots, oceans, etc).  Metagenomics, sequencing DNA from a pool of microbes, has broadened our understanding of microbial communities by circumventing the need for culturing.  However, culturing remains an important aspect of investigating microbial communities particularly for environments where the microbial diversity is so great that generating complete genome sequences via metagenomics is impractical (i.e. soil).

In 2010, a study from the Epstein and Lewis groups (Nichols et al., 2010) describes a new technology which can increase culturing success from ~1% to nearly 50%!  This technology, the isolation chip or iChip, contains 384 chambers.  A single microbial cell is deposited in each chamber.  Then a semi-permeable membrane is used to cover all the chambers and the iChip is placed into the environment from which the microbes originate.  The membrane allows cells access to nutrients and growth factors found in its natural environment.

The iChip has been successfully used to study novel secondary metabolites (Lewis et al., 2010) and discover novel antibiotics (Ling et al., 2015Lewis, 2013).  However, a possible reason why high-throughput culturing techniques have not gained much traction is the emphasis on metagenomic applications and studies which do not suffer from culturing bias.  High-throughput culturing and metagenomic sequencing each have a unique set of strengths and weaknesses.  Perhaps more thought should be put into designing methods using a combination of high-throughput culturing and metagenomic sequencing to leverage both sets of strengths and mitigate their weaknesses.  

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