Enterococcus faecium

The Development of Probiotic-Containing Functional Foods 31
Lozupone and Knight 52 introduced a new method called UniFrac for computing
differences between microbial communities based on phylogenetic information.
UniFrac is applied to published 16S rRNA gene libraries and measures the phylogenetic
distance between sets of taxa in a phylogenetic tree. Ley et al. 53 used the Uni-
Frac method to test the effects of kinship and genotype on diversity. The 16S rRNA
sequences from cecal microbiota of genetically obese ob/ob mice, lean ob/+ mice,
and wild-type siblings, and their ob/+ mothers, all fed on the same polysacchariderich
diet were analyzed. The results revealed that regardless of their ob genotype, the
mothers and their offspring shared cecal microbiotas with similar community membership.
Obesity was associated with a shift in the relevant abundance of the specific
taxa present, such that there was an increased ratio of Firmicutes to Bacteroidetes in
obese mice compared to lean mice.
The influence of intestinal bacteria on human health can be considered harmful,
beneficial, or neutral. Bifidobacterium and Lactobacillus species are beneficial
microorganisms and can contribute to digestion, immune stimulation, and inhibition
of pathogens. Bacteroides, Escherichia, Clostridium, and Proteus species are
examples of potentially harmful bacteria found in the GIT, as they are capable of
producing harmful substances including amines, indole, hydrogen sulfide, and phenols
from food components. 14 Harmful bacteria in the intestine have been linked
to a number of clinical disorders such as cancer, inflammatory disease, ulcerative
colitis, and also an increase in the host’s susceptibility to infection by enteropathogens
such as Salmonella, Campylobacter, Escherichia, and Listeria. It is important
that the correct balance of bacteria be maintained in order to allow the intestine to
operate optimally. 13 In order to understand the interaction of the microbiota with
the host, as well as microbe-microbe interactions in the intestine, there is an urgent
need for genome sequences of commensals. The number of beneficial food-related
microorganisms for which genome sequence data are available is increasing, 54 and
additional genome statistics have been published by Klaenhammer et al. 55
One approach to sequencing genomes of commensals is the construction of
metagenomic libraries, consisting of large, cloned DNA fragments in the absence of
culturing. 56 A human gut microbiome initiative has been proposed that will deliver
deep draft whole genome sequences for 100 species representing the bacterial divisions
found in our distal gut. 57 A number of studies have used gnotobiotics (animals
raised under germfree conditions) for colonizing at varying points in their life cycle
by a single microbe, or complex collections of microbes. The development of communities
has been investigated, and the impact determined that different members
have on community function and host biology. 58 Although these models have been
available for 50 yr, genomic and powerful computational tools for assessing diversity
in our gut microbiota, the gene content of the microbiome, and the metabolome
encrypted by this collection of microbial genes have only been developed in the last
5 yr. 53,59,60,61 Examples of model organisms include: Mus musculus (common mouse),
as the mouse and human microbiota are similar at the division level, with Firmicutes
and Bacteroidetes dominating, 53 and zebrafish, as they are transparent until adulthood,
allowing visualization of microbes in their native gut habitats in real time. 58
In a recent reciprocal transplantation experiment where the gut microbiota of a common
mouse was introduced into a germ-free zebrafish, and vice versa, the recipient