How Different are the Bacteria in our Gut?

David McCormick

David McCormick

Our bodies are not our own – our intestinal tracts are colonized by an amazing variety of bacterial species – and we’re just now realizing how dramatic their effect on our life truly is.  A quick search shows that researchers are investigating the role of bacteria in processes as diverse as obesity, Crohn’s Disease, immune suppression, blood clotting, and nutritional disorders.  However, a recent talk by Dr. Vincent Denef of the University of California, Berkeley, suggests that we may be going about these investigations in the wrong way.

His argument centers on the fact that two things that look alike may not act alike – and that these small differences can drastically change the ecology of entire systems.  Until the advent of genomic sequencing and PCR, the only way to discover if a bacteria lived somewhere was to try to isolate it and regrow it in your lab.  Unfortunately, only about 0.01% of bacteria can grow under laboratory conditions, so researchers switched to using DNA bar codes – they found a certain DNA sequence served that as a unique “fingerprint” for different species.  Or so they thought.

Dr. Denef has shown that even bacteria with the same fingerprint can have slightly different genomic profiles, and that these different profiles can change the bacterial composition.  To put the idea of small genetic differences leading to large changes in phenotype and ecology, consider that the genomes of humans and chimpanzees are 99.9% similar – but that differing 0.01% makes a world of difference.  Do these types of difference matter in bacteria?  The answer is a resounding yes.  One all-too-common example of small differences within the same species is antibiotic resistance.  Not all strains of Staphylococcus aureus (the bug that causes staph infections) are harmful, and most people’s skin is permanently colonized with these bacteria to no ill effect.  But if you get infected with MRSA – the drug resistant strain – it will lead to a medical emergency.  However, if you compared the normal strain to the resistant stain using the same techniques we use to fingerprint bacteria, they’d come up as the same species.

Antibiotic resistance is the best example in bacteria that affect humans, and right now we just don’t know how common these differences are in the bacteria living in our gut.  They could be common, and they could have drastic effects (imagine if these kinds of differences caused irritable bowel syndrome!) or they could just end up being a scientific curiosity.  But we won’t know until we look.

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