91
reveal clusters and chains of bacteria and fungi. Another wave of bacteria arrives when
the first teeth appear. The first is Streptococcus sanguis, followed by Streptococcus mutans. By
middle childhood, the diversity inside the mouth surpasses a hundred species, and their
total number is greater than 10 billion.15 Bacteria also settle in the nasal cavities, which are
connected to the mouth via the upper respiratory tract. The bacteria eventually lodge in
the intestinal tract. In the small intestine, incoming microbes engage the infant’s dormant
immune system. Pits on the surface of the Peyer’s patches (aggregated lymphoid tissue
in the ileum) capture passing bacteria, where they are ushered into the underlying lymph
tissue. Interaction on the Peyer’s patches triggers the production of an abundance of
immunoglobulin A (IgA) antibodies. Instead of marking the bacteria for destruction, IgA
clusters across the bacterial surface, preventing the bacteria from attaching to the intestinal
wall. This also leads to the proliferation of T and B cells that will marshal an attack against
these same bacteria should they turn up in the blood or other forbidden areas.16 The small
intestine must provide a platform for nutrient absorption, but at the same time, the epithe-
lium and its associated immune cells must keep out pathogens that escape the inhospitable
environment of the stomach. To satisfy these responsibilities, small intestinal epithelial cells
divide at a rate of 13 to 16 cells every hour.17
When the child reaches adulthood, his or her intestine becomes home to an almost
inconceivable number of microorganisms. The size of the population—up to 100 tril-
lion—far exceeds all other microbial communities associated with the body’s surfaces
and is more than 10 times greater than the total number of our somatic and germ cells
combined.18 (There is a significant variation in both the total number of bacteria and the
composition of the bacterial flora in different body regions.19) Since humans depend on
their microbiome for various essential services, a person should really be considered a
superorganism, consisting of his or her own cells and those of all the commensal bacteria.
Humans are not inherently endowed with a healthy immune or digestive system.
Fortunately, our intestinal tract, which includes our inhabitants (microbiome), provides
us with genetic and metabolic attributes we have not been required to evolve on our
own, including the ability to harvest otherwise inaccessible nutrients and to modify host
immune reactivity.20
Inhabitants
The adult human gastrointestinal (GI) tract contains all three domains of life—bacteria,
archaea and eukaryotes.21 Archaea are a group of prokaryotic and single-celled micro-
organisms, and while similar to bacteria, evolved differently. Archaea were originally
described in extreme environments but have since been found in all habitats including
the digestive tracts of animals such as ruminants, termites and humans.22 Eukaryotes are
organisms whose cells contain a limiting membrane around the nuclear material (the
nucleus). Bacteria living in the human gut achieve the highest cell densities recorded for
any ecosystem.23 The vast majority belong to two divisions, the Bacteroidetes (48%) and
the Firmicutes (51%). Bacteroidetes include a number of Bacteroides genera, which have yet
to be encountered in any environment other than animal GI tracts. Firmicutes include the
genera Clostridium, Lactobacillus, Eubacterium, Ruminoccus and several others. In the first
comprehensive molecular survey of the gut microbiota (normal microflora), 395 bacterial
and one archaeal phylotype (bacteria defined by their ribosomal RNA gene sequence)
were identified.24 Thus, the gut microbiota is a tremendously diverse bioreactor. Eight
divisions with divergent lineages are represented. This diversity is desirable for ecosystem
stability. There appears to be a strong host selection for specific bacteria whose behavior is
beneficial to the host. Cooperative activity by bacteria is required to break down nutrients
and provide the host with energy. Populations of bacteria are remarkably stable within
the human gut, which implies that mechanisms exist to suppress undesirable bacteria and
promote the abundance of those that are needed.25
Probiotics and Microflora
reveal clusters and chains of bacteria and fungi. Another wave of bacteria arrives when
the first teeth appear. The first is Streptococcus sanguis, followed by Streptococcus mutans. By
middle childhood, the diversity inside the mouth surpasses a hundred species, and their
total number is greater than 10 billion.15 Bacteria also settle in the nasal cavities, which are
connected to the mouth via the upper respiratory tract. The bacteria eventually lodge in
the intestinal tract. In the small intestine, incoming microbes engage the infant’s dormant
immune system. Pits on the surface of the Peyer’s patches (aggregated lymphoid tissue
in the ileum) capture passing bacteria, where they are ushered into the underlying lymph
tissue. Interaction on the Peyer’s patches triggers the production of an abundance of
immunoglobulin A (IgA) antibodies. Instead of marking the bacteria for destruction, IgA
clusters across the bacterial surface, preventing the bacteria from attaching to the intestinal
wall. This also leads to the proliferation of T and B cells that will marshal an attack against
these same bacteria should they turn up in the blood or other forbidden areas.16 The small
intestine must provide a platform for nutrient absorption, but at the same time, the epithe-
lium and its associated immune cells must keep out pathogens that escape the inhospitable
environment of the stomach. To satisfy these responsibilities, small intestinal epithelial cells
divide at a rate of 13 to 16 cells every hour.17
When the child reaches adulthood, his or her intestine becomes home to an almost
inconceivable number of microorganisms. The size of the population—up to 100 tril-
lion—far exceeds all other microbial communities associated with the body’s surfaces
and is more than 10 times greater than the total number of our somatic and germ cells
combined.18 (There is a significant variation in both the total number of bacteria and the
composition of the bacterial flora in different body regions.19) Since humans depend on
their microbiome for various essential services, a person should really be considered a
superorganism, consisting of his or her own cells and those of all the commensal bacteria.
Humans are not inherently endowed with a healthy immune or digestive system.
Fortunately, our intestinal tract, which includes our inhabitants (microbiome), provides
us with genetic and metabolic attributes we have not been required to evolve on our
own, including the ability to harvest otherwise inaccessible nutrients and to modify host
immune reactivity.20
Inhabitants
The adult human gastrointestinal (GI) tract contains all three domains of life—bacteria,
archaea and eukaryotes.21 Archaea are a group of prokaryotic and single-celled micro-
organisms, and while similar to bacteria, evolved differently. Archaea were originally
described in extreme environments but have since been found in all habitats including
the digestive tracts of animals such as ruminants, termites and humans.22 Eukaryotes are
organisms whose cells contain a limiting membrane around the nuclear material (the
nucleus). Bacteria living in the human gut achieve the highest cell densities recorded for
any ecosystem.23 The vast majority belong to two divisions, the Bacteroidetes (48%) and
the Firmicutes (51%). Bacteroidetes include a number of Bacteroides genera, which have yet
to be encountered in any environment other than animal GI tracts. Firmicutes include the
genera Clostridium, Lactobacillus, Eubacterium, Ruminoccus and several others. In the first
comprehensive molecular survey of the gut microbiota (normal microflora), 395 bacterial
and one archaeal phylotype (bacteria defined by their ribosomal RNA gene sequence)
were identified.24 Thus, the gut microbiota is a tremendously diverse bioreactor. Eight
divisions with divergent lineages are represented. This diversity is desirable for ecosystem
stability. There appears to be a strong host selection for specific bacteria whose behavior is
beneficial to the host. Cooperative activity by bacteria is required to break down nutrients
and provide the host with energy. Populations of bacteria are remarkably stable within
the human gut, which implies that mechanisms exist to suppress undesirable bacteria and
promote the abundance of those that are needed.25
Probiotics and Microflora