New Technique Reveals Vast Array of Gut Bacteria

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New research completed at the Stanford University School of Medicine reveals that the number and diversity of bacteria inhabiting the human colon is simply mind-blowing. This ecosystem is around ten times more diverse than has ever been suggested by prior research.

This new information makes the statistics pretty staggering – in terms of numbers, the human colon is one of the most diverse ecosystems on earth, and certainly one of the most densely populated of microbial communities. For every single cell in your body, there are approximately ten micro-organisms making their home inside your digestive tract.

Previously it was thought that around five hundred different species of bacteria were commonly resident within the human colon. However, determining accurate numbers has been difficult due to the fact that there are enormous number disparities between species of abundant and species of less common bacteria that typically reside in the gut. Those rare species have been difficult to isolate and identify within the laboratory.

The problem has been made even more difficult by the fact that while some of these species can grow in vitro, others simply die when removed from their native habitat (less than 40% of bacterial species in the human distal gut have ever been cultivated in a laboratory). Because of these issues, estimates of numbers and diversity of gut microflora have been extremely disparate.

A newly-developed gene sequencing technology called pyrosequencing (which works by detecting light emitted during DNA synthesis) has revealed that the previous figure of around five hundred species is way off the mark. The Stanford researchers found more than 5,600 different species of bacteria in the colons of their human test subjects. The results are largely thanks to the use of pyrosequencing, a technique which allowed the researchers to check for a much larger number of different bacterial species, and also allowed for the detection of rarer species which had previously evaded identification.

Another advantage of the technology is that it is now much easier to assess the effects of drugs – in particular antibiotics – on the composition of human colon microflora.


Dethlefsen L, Huse S, Sogin ML, Relman DA (2008) The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing. PLoS Biol 6(11): e280 doi:10.1371/journal.pbio.0060280

O’Day K (2008) Gut Reaction: Pyrosequencing Provides the Poop on Distal Gut Bacteria. PLoS Biol 6(11): e295 doi:10.1371/journal.pbio.0060295