The flora of the major body systems

The oral cavity and the gastrointestinal tract

The mouth and the gastro intestinal tract are collectively, the most heavily colonized portions of the human body, but
bacterial population density varies dramatically from one portion to another. The stomach, for example, has a very
low resident population while the number of organisms in stool in the large intestine may contain in excess of 1 x
1011 bacterial cells per gram.

The normal flora of the mouth

Due to its accessibility and its association with dental caries, there is probably no area of the body in which the
normal flora has been so intensively investigated. Within the mouth there are a number of regions, which support
quite different microbial populations. The gums, cheeks, hard and soft pallet, the gingival crevices between the teeth
and the gums and the teeth themselves each offer unique niches for the colonization of bacteria.

Much of the colonized surface of the oral cavity consists of the oral mucosa, which sheds epithelial cells which are
constantly replaced.

Teeth introduce an entirely novel niche for the development of biofilm communities. The enamel surface of teeth
represents the only non-cellular, non-shedding surface in the body in a region with a normal flora.

The gingival crevice is the space between the teeth and the gums. This space is constantly bathed by the flow of
gingival crevicularfluid which also results in a lower oxygen concentration than the gingival surface itself. This
relatively high flow rate and low redox potential affect the microbial population. Sixteen SRNA studies suggest that
only about half ot the species inhabiting the gingival crevice have been cultured. Among the more common species
represented are nonpathogenic spirochetes of the genus Treponema, Actinomycete spp., Eubacterium spp.,
Haemophilus spp., Neisseria spp., Viellonella spp. Prevotella spp., and Fusobacterium spp.

Counterintuitively, the mouth is predominantly an anaerobic environment. The regions between the lips and gums,
crevicular spaces between gums and teeth the spaces between the papillae of the tongue all have a very low redox
potential and consequently harbor microorganisms that are predominantly facultative and anaerobic. In addition, the
deep crypts (up to 1.8 mm) that lie between the papillae provide additional anaerobic niches for colonization. The
constant influx of food materials makes the tongue a nutritional smorgasbord for microbes, and consequently the
tongue has one of the highest microbial population densities of any place in the human body (10 7 to 109 cfu/cm2).

The resident flora of the tongue includes streptococci, Viellionella spp., and Actinomyces spp. Gram negative
anaerobic rods are also found in abundance. Interestingly, the tongue also harbors the Porphyromonas,
Provedencia, and actinomycete species collectively responsible for periodontal disease and thus may serve as a
reservoir for this condition.

Most of the volatile gasses including hydrogen sulfide, methyl mercaptan, amines, indol and short chain fatty acids
responsible for halitosis are produced by the bacteria inhabiting the uppersurface of the tongue. These compounds
are produced by a consortium of oral microorganisms including, Porphyromonasgingivalis, Prevatellaintermedia,
Treponemadenticola, Tannerellaforsythensis, Por. endodontais and Eubacteria species.

No entirely effective treatment for halitosis has been found, but regular brushing and flossing of the teeth, scraping of
the tongue to remove microorganisms, along with the use of mouthwashes containing broad-spectrum antiseptics
(e.g. alcohol, methylparaben, hexetidine, benzalkonium chloride) and oxidizing agents (e.g. Hydrogen peroxide) have
been somewhat successful.

The gastro intestinal tract consists of the mouth, the esophagus, the stomach the small and large intestine. In addition
there are accessory glands and organs that such as the liver, the gall bladder and the pancreas that connect with and
add materials to the large intestine. These organs, and their connecting ducts, though usually sterile may,
occasionally, be subject to invasion by biofilm forming organisms. If one considers the human body topologically as a
donut, the GI tract is the hole. The function of this system is the ingestion and processing of food and its digestion,
absorption and elimination. The mouth and oral cavity function in manipulation of food, determining its sensory
suitability for ingestion, and preliminary processing (mastication, combining food with saliva containing
enzymes). The esophagus delivers the preprocessed food to the stomach and prevents (under normal conditions)
regurgitation. The stomach with its extensive production of hydrochloric acid has been for generations considered
sterile. More recently the investigations of Marshall (1980) have shown that some humans carry populations
of Helicobacter pylori, an acid tolerant Gram negativespiral-shaped bacterium which, on occasion, can cause peptic
ulcers and less commonly stomach cancer.

The point where the microbiologically deadly acidic effusion from the stomach meets the flow of bile from the gall
bladder creates what Costerton describes as a ”microbial nightmare” which keeps the microbial population low in the
upper regions of the small intestine (Costerton 2007 Primer p 123). In the small intestine ingested food is acted upon
by digestive enzymes the product of epithelial glands and is converted to a fluid mass referred to as
chyme. Peristaltic action causes the chyme to pass through the small intestine rapidly with a transit time of only 3 to
5 hours. This rapid passage is viewed as an important defense mechanism in that it makes the colonization of the
intestinal surface difficult. Mucus, the product of epithelial goblet cells covers the intestinal lining to a depth of as
much as 200 µm. This mucus is a viscous gel consisting of water, high molecular weight glycoprpteins called mucins
and oligosaccharides. Some of this mucus adheres rather tightly to the epithelium while the rest is moved along the
axis of flow by peristaltic action and is eventually sloughed off into the luminal mass. The high carbohydrate content
contains many receptor sites for the attachment of bacteria and biofilm forming bacteria are found on the surface and
imbedded as microcolonies and diffuse masses within the mucus sheath. Mucus serves to protect the epithelium
from colonization by bacteria, provides lubrication which facilitates movement of material through the gut and protects
the underlying cells from the action of acid, and digestive enzymes as well as from the possible erosive action of
particles suspended in the luminal mass. Interesting is the healthy individual very few bacteria are found incontact
with the gut epithelium.

In addition to these mucus associated biofilms one should not forget the enormous load of microorganisms attached
to particulate matter in the luminal mass. These organisms secrete enzymes that aid in the digestion of
macromolecules providing nutrient not only for the microorganisms themselves, but also for the host. Wilson
estimates that bacteria in the lower small intestine and large intestine account for as much as 3-9% of the hosts total
energy requirement.

The gut as a biofilm reactor.

Approximately 9 L of liquid material are received by the small intestine from the stomach each day. Peristalsis moves
this mass along at a rapid rate so that the 6 m of the small intestine are traversed in about 3 to 5 hours. About 80%
of this fluid is adsorbed by the epithelial lining of the gut, reducing the volume greatly. As the mass of liquefied food
passes through the small intestine it is acted upon by enzymes of host origin, and the large molecular weight
components are hydrolyzed (digested) into smaller subunits, which are also absorbed by the intestinal
epithelium. Due to the low pH caused by thehigh hydrochloric acid production of the stomach and the high
concentration of bile salts produced by the liver, upper portion of the small intestine is a very harsh environment for
microorganisms, in Bill Costerton’s words, a microbial nightmare (Costerton 2007 Primer p 123). The small intestine
then seems to have the characteristics of a plug flow reactor as described by Characklis and Marshall (1990).

A plug flow reactor is one in which the nutrient is supplied continuously and travels through the reactor in the axial
direction much as water flows through a pipe. In the ideal plug flow reactor there is little or no mixing in the direction
of flow, although there may be mixing at the interface of the bulk fluid mass and the reactor wall. The composition of
the reactor vessel at any point along its length is assumed to remain constant although conditions within any given
bolus change as the mass moves along the axis of flow.

Because the ceacum and the ascending colon are are constantly stirred by peristaltic action, and are continuously
supplied with fresh nutrient they are described by Wilson (2005) as having the characteristics of a continuous culture
system, perhaps a Continuously Stirred Tank Reactor. This “reactor” receives about 1.5 kg of material from the small
intestine daily. The large intestine in contrast seems to be better described as a batch reactor. In contrast to the
ceacum and ascending colon, the transverse and descending colon, little further nutrient input, transit time is long, in
the range of days, and mixing is through due to peristaltic activity. These characteristics more closely resemble the
description of a batch reactor. There is, indeed a slow but constant admixture of new material and loss of material
through the elimination of faeces but these occur so slowly that according to Wilson this portion of the intestine
functions “more like a batch or fed-batch system” (2005).