The intestinal microbiota
We are witness to a paradigm shift in the way the microbial fl ora
that dwell within our inner recesses are viewed. No longer is it
simply that the host is “ good ” and the bacteria that live therein
“ bad ” , but the vital roles our intestinal fl ora, now called microbiota,
have in maintaining health are being increasingly appreciated.
Results of the Human Microbiome Project launched by the National Institutes of Health in 2007 along with related
ventures such as the MetaHit (Metagenomics of the Human
Intestinal tract) consortium, which involves 13 research centers
from 8 countries, are now beginning to be published and will
revolutionize knowledge of our microbes and our bodies ( 2 ).
For example, although we knew the human body is inhabited
by a vast number of microorganisms including bacteria,
archea (single-celled prokaryotic microorganisms separately
classifi ed from bacteria), viruses, fungi, and even parasites, all
of which normally live in peaceful coexistence with us, their
hosts, we soon learned that only 5 – 20 % of the intestinal microbiota
can be cultured and that culture can reliably distinguish
among bacterial phylogenetic groups, but not down to speciesor
strain-level ( 2,3 ). New approaches to study our microbiota
were developed using culture-independent techniques including
bacterial 16S ribosomal RNA gene sequencing and DNA
fi ngerprinting methods, such as terminal restriction fragment
length polymorphisms. A new vocabulary was even developed
to help detail the “ meta ” family techniques used to evaluate
the microbiomic functional capacity including metagenomics
(study of genes collected and sequenced from the environment),
metabolomics (study of metabolites that are end-products of