What do we know about the gut microbiota
Bearing in mind the limitations above, the GI tract is often seen as a two phylum system (the
Firmicutes and Bacteroidetes) although it should be noted that members of at least 10 different
phyla can also have important functional contributions. We are also very bacteria-centric when
we look at the gut microbiota; only a handful of papers have looked at the viral component (or
virome) and micro-eukaiyotes (protozoa and fungi). When the gut microbiota of relatively large
cohorts of individuals (eg, more than 100) is analysed, it can be seen that the ratio of the
Firmicutes:Bacteroidetes is not the same in all individuals. Currently we do not know the
significance of being at either end of this continuum, especially as a large shift in the relative
abundance of a group of organisms translates to a modest change in bacterial numbers. Yet there
is evidence that depletion of a single species, for example, Faecalibacterium prausnitzii,
belonging to the Firmicutes phylum, has been associated with IBD. But in the scientific literature,
we see counterarguments for any involvement of this species in IBD. This disparity highlights the
current status of understanding. We know that the gut microbiota is essential to the proper
function and development of the host but we are unsure which are keystone species and
whether the microbiota's function is more important than any individual member of the
community. But this is too simplistic a view. In several cases, strain differences within a species
can be the difference between being a pathogen/pathobiont and being a probiotic: for example,
Escherichia coli is associated with IBD and colorectal cancer (CRC) yet an E. coli strain is used as a
probiotic.