Gut Flora
rpautrey2
Escherichia coli, one of the many species of bacteria present in the
human gut.The gut flora are the microorganisms that normally live in
the digestive tract and can perform a number of useful functions for
their hosts. Though widely known as the "intestinal microflora", this
is technically a misnomer since the word root "flora" pertains to
plants and biota refers to microbial life such as bacteria other than
plants. Thus the more appropriate term "intestinal microbiota" is
coming into use, though its use has not eclipsed the entrenched use
and recognition of "flora" with regard to intestinal bacteria, and for
the time being, both terms are being used in different textbooks.
The average human body, consisting of about 1013 (10,000,000,000,000
or about ten trillion) cells, has about ten times that number of
microorganisms in the gut.[1][2][3][4]
Bacteria make up most of the flora in the colon[5] and 60% of the mass
of feces.[2] Somewhere between 300[2] and 1000 different species live
in the gut,[3] with most estimates at about 500.[6][4] However, it is
probable that 99% of the bacteria come from about 30 or 40 species.[7]
Fungi and protozoa also make up a part of the gut flora, but little is
known about their activities.
Research suggests that the relationship between gut flora[8] and
humans is not merely commensal (a non-harmful coexistence), but rather
is a mutualistic, symbiotic relationship.[3] Though people can survive
with no gut flora,[4] the microorganisms perform a host of useful
functions, such as fermenting unused energy substrates, training the
immune system, preventing growth of harmful species,[2] regulating the
development of the gut, producing vitamins for the host (such as
biotin and vitamin K), and producing hormones to direct the host to
store fats. However, in certain conditions, some species are thought
to be capable of causing disease by causing infection or increasing
cancer risk for the host.[2][5]
Contents
1 Localization
2 Types
3 Acquisition of gut flora in human infants
4 Functions
4.1 Carbohydrate fermentation and absorption
4.2 Trophic effects
4.3 Repression of pathogenic microbial growth
4.4 Immunity
4.5 Preventing allergy
4.6 Preventing inflammatory bowel disease
5 Alterations in balance
5.1 Effects of antibiotic use
5.2 Probiotics & Prebiotics
6 Role in disease
6.1 Cancer
6.2 Translocation
6.3 Inflammatory bowel disease
6.4 Colitis
6.5 Obesity
7 Sources and notes
Localization
The colon has the greatest numbers of bacteria and the most different
species, and the activity of these bacteria make the colon the most
metabolically active organ in the body.[6] Most of the bacteria in the
small intestine are Gram-positive, while those in the colon are mostly
Gram-negative.[9] The first part of the colon is mostly responsible
for fermenting carbohydrates,[7][6][2] while the latter part mostly
breaks down proteins and amino acids.[6][2] Bacterial growth is rapid
in the cecum and ascending colon, which has a low pH, and slow in the
descending colon, which has an almost neutral pH.[2] The body
maintains the proper balance and locations of species by altering pH,
the activity of the immune system, and peristalsis.[5]
Over 99% of the bacteria in the gut are anaerobes,[7][2][5][3][10] but
in the cecum, aerobic bacteria reach high densities.[2]
Types
Candida albicans, a dimorphic fungus which grows as a yeast in the
gut.Not all the species in the gut have been identified[2][3] because
some cannot be cultured,[7][3][11] so DNA isolation and identification
is difficult.[12] Populations of species vary widely among different
individuals but stay fairly constant within an individual over time.
[2]. An effort to better describe the microflora of the gut and other
body locations has been initiated; see Human microbiome project.
Most bacteria come from the genera Bacteroides, Clostridium,
Fusobacterium,[7][2][10] Eubacterium, Ruminococcus, Peptococcus,
Peptostreptococcus, and Bifidobacterium.[2][7] Other genera such as
Escherichia and Lactobacillus are present to a lesser extent.[2]
Species from the genus Bacteroides alone constitute about 30% of all
bacteria in the gut, suggesting that that genus is especially
important in the functioning of the host.[3]
The currently known genera of fungi of the gut flora include Candida,
Saccharomyces, Aspergillus, and Penicillium.
Acquisition of gut flora in human infants
Breastfeeding is one mode by which infants acquire gut flora.The
gastrointestinal tract of a normal fetus is sterile. During birth and
rapidly thereafter, bacteria from the mother and the surrounding
environment colonize the infant's gut. Immediately after vaginal
delivery, babies have bacterial strains in the upper gastrointestinal
tract derived from the mothers’ feces.[13] Infants born by caesarean
section may also be exposed to their mothers’ microflora, but the main
exposure is from the surroundings.[14] After birth, environmental,
oral and cutaneous bacteria are readily transferred from the mother to
the infant through suckling, kissing, and caressing. All infants are
initially colonized by large numbers of E. coli and streptococci.
Within a few days, bacterial numbers reach 108 to 1010 per gram of
feces.[14][15] During the first week of life, these bacteria create a
reducing environment favorable for the subsequent bacterial succession
of strict anaerobic species mainly belonging to the genera
Bifidobacterium, Bacteroides, Clostridium, and Ruminococcus.[16]
Breast-fed babies become dominated by bifidobacteria, possibly due to
the contents of bifidobacterial growth factors in breast milk.[17] In
contrast, the microflora of formula-fed infants is more diverse with
high numbers of Enterobacteriaceae, enterococci, bifidobacteria,
Bacteroides, and clostridia.[18][19] After the introduction of solid
food and weaning, the microflora of breast-fed infants becomes similar
to that of formula-fed infants. By the second year of life the fecal
microflora resembles that of adults.
Functions
Bacteria in the gut fulfills a host of useful functions for humans,
including digestion of unutilized energy substrates;[20] stimulating
cell growth; repressing the growth of harmful microorganisms; training
the immune system to respond only to pathogens; and defending against
some diseases.[2][3][21]
Carbohydrate fermentation and absorption
Without gut flora, the human body would be unable to utilize some of
the undigested carbohydrates it consumes, because some types of gut
flora have enzymes that human cells lack for breaking down certain
polysaccharides.[3] Rodents raised in a sterile environment and
lacking in gut flora need to eat 30% more calories just to remain the
same weight as their normal counterparts.[3] Carbohydrates that humans
cannot digest without bacterial help include certain starches; fiber;
oligosaccharides and sugars that the body failed to digest and
absorb[6][2][7] like lactose and sugar alcohols, mucus produced by the
gut, and proteins.[6]
Bacteria turn carbohydrates they ferment into short chain fatty acids,
or SCFAs.[6][5][7] These materials can be used by host cells,
providing a major source of useful energy and nutrients for humans.[6]
They increase the gut's absorption of water, reduce counts of damaging
bacteria, increase growth of human gut cells,[5] and are also used for
the growth of indigenous bacteria.[2] The SCFAs are produced by a form
of fermentation called saccharolytic fermentation[6] and include
acetic acid, propionic acid, and butyric acid.[6][5][7] Gases and
organic acids like lactic acid are also produced by saccahrolytic
fermentation.[7] Acetic acid is used by muscle, propionic acid helps
the liver produce ATP, and butyric acid provides energy to gut cells
and may prevent cancer.[6]
Another, less favorable type of fermentation, proteolytic
fermentation, breaks down proteins like enzymes, dead host and
bacterial cells, and collagen and elastin found in food, and can
produce toxins and carcinogens in addition to SCFAs. Thus a diet lower
in protein lowers exposure to toxins.[2][5]
Evidence also suggests that bacteria enhance the absorption and
storage of lipids.[3] Bacteria also produce and help the body absorb
needed vitamins like vitamin K. In addition, the SCFAs they produce
help the body absorb nutrients such as calcium, magnesium, and iron.
[2]
Trophic effects
Another benefit of SCFAs is that they increase growth of intestinal
epithelial cells and control their proliferation and differentiation.
[2] They may also cause lymphoid tissue near the gut to grow.
Bacterial cells also alter intestinal growth by changing the
expression of cell surface proteins such as sodium/glucose
transporters.[3] In addition, changes they make to cells may prevent
injury to the gut mucosa from occurring.[21]
Repression of pathogenic microbial growth
C. difficile colonies on a blood agar plate. The overgrowth of C.
difficile in the gut can be harmful to the host.Another important role
of helpful gut flora is that they prevent species that would harm the
host from colonizing the gut, an activity termed the "barrier effect".
Yeasts and harmful bacterial species such as Clostridium difficile
(the overgrowth of which can cause pseudomembranous colitis) are
unable to grow too much due to competition from helpful gut flora
species, thus animals without gut flora are infected very easily. The
barrier effect protects humans from both invading species and species
normally present in the gut at low numbers, whose growth is usually
inhibited by the gut flora.[2]
Helpful bacteria prevent the growth of pathogenic species by competing
for nutrition and attachment sites to the epithelium of the colon.
Symbiotic bacteria are more at home in this ecological niche and are
thus more successful in the competition. The indigenous bacteria send
chemical signals to the host about the amount of nutrients they need,
and the host provides only that much, so harmful bacteria are starved
out. Indigenous gut flora also produce bacteriocins, substances which
kill harmful microbes and the levels of which can be regulated by
enzymes produced by the host.[2]
The process of fermentation, since it produces fatty acids, also
serves to lower the pH in the colon, preventing the proliferation of
harmful species of bacteria and facilitating that of helpful species.
The pH may also enhance the excretion of carcinogens.[6]
Immunity
Gut flora have a continuous and dynamic effect on the host's gut and
systemic immune systems. The bacteria are key in promoting the early
development of the gut's mucosal immune system both in terms of its
physical components and function and continue to play a role later in
life in its operation. The bacteria stimulate the lymphoid tissue
associated with the gut mucosa to produce antibodies to pathogens. The
immune system recognizes and fights harmful bacteria, but leaves the
helpful species alone, a tolerance developed in infancy.[2][11][4][5]
As soon as an infant is born, bacteria begin colonizing its digestive
tract. The first bacteria to settle in are able to affect the immune
response, making it more favorable to their own survival and less so
to competing species; thus the first bacteria to colonize the gut are
important in determining the person's lifelong gut flora makeup.
However, there is a shift at the time of weaning from predominantly
facultative aerobic species such as Streptococci and Escherichia coli
to mostly obligate anaerobic species.[2][3]
Recent findings have shown that gut bacteria play a role in the
expression of Toll-like receptors (TLRs) in the intestines, molecules
that help the host repair damage due to injury. TLRs cause parts of
the immune system to repair injury caused for example by radiation.[3]
[21]
Bacteria can influence the phenomenon known as oral tolerance, in
which the immune system is less sensitive to an antigen (including
those produced by gut bacteria) once it has been ingested. This
tolerance, mediated in part by the gastrointestinal immune system and
in part by the liver, can reduce an overreactive immune response like
those found in allergies and auto-immune disease.[22]
Some species of gut flora, such as some of those in the Bacteroides
genus, are able to change their surface receptors to mimic those of
host cells in order to evade immune response. Bacteria with neutral
and harmful effects on the host can also use these types of
strategies. The host immune system has also adapted to this activity,
preventing overgrowth of harmful species.[2][4]
Preventing allergy
Bacteria are also implicated in preventing allergies,[1] an
overreaction of the immune system to non-harmful antigens. Studies on
the gut flora of infants and young children have shown that those who
have or later develop allergies have different compositions of gut
flora from those without allergies, with higher chances of having the
harmful species C difficile and S aureus and lower prevalence of
Bacteroides and Bifidobacteria.[1] One explanation is that since
helpful gut flora stimulate the immune system and "train" it to
respond properly to antigens, a lack of these bacteria in early life
leads to an inadequately trained immune system which overreacts to
antigens.[1] On the other hand, the differences in flora could be a
result, not a cause, of the allergies.[1]
Preventing inflammatory bowel disease
Another indicator that bacteria help train the immune system is the
epidemiology of Inflammatory Bowel Disease, or IBD, such as Crohn's
Disease (CD). Some authors suggest that SCFAs prevent IBD. In
addition, some forms of bacteria can prevent inflammation.[23] The
incidence and prevalence of IBD is high in industrialized countries
with a high standard of living and low in less economically developed
countries, having increased in developed countries throughout the
twentieth century. The disease is also linked to good hygiene in
youth; lack of breastfeeding; and consumption of large amounts of
sucrose and animal fat.[23] Its incidence is inversely linked with
poor sanitation during the first years of life and consumption of
fruits, vegetables, and unprocessed foods.[23] Also, the use of
antibiotics, which kill native gut flora and harmful infectious
pathogens alike, especially during childhood, is associated with
inflammatory bowel disease.[20] On the other hand, using probiotics,
bacteria consumed as part of the diet that impart health benefits
(aside from just nutrition), helps treat IBD.
Alterations in balance
Effects of antibiotic use
Altering the numbers of gut bacteria, for example by taking broad-
spectrum antibiotics, may affect the host's health and ability to
digest food.[24] People may take the drugs to cure bacterial illnesses
or may unintentionally consume significant amounts of antibiotics by
eating the meat of animals to which they were fed.[24] Antibiotics can
cause antibiotic-associated diarrhea (AAD) by irritating the bowel
directly, changing the levels of gut flora, or allowing pathogenic
bacteria to grow.[7] Another harmful effect of antibiotics is the
increase in numbers of antibiotic-resistant bacteria found after their
use, which, when they invade the host, cause illnesses that are
difficult to treat with antibiotics.[24]
Changing the numbers and species of gut flora can reduce the body's
ability to ferment carbohydrates and metabolize bile acids and may
cause diarrhea. Carbohydrates that are not broken down may absorb too
much water and cause runny stools, or lack of SCFAs produced by gut
flora could cause the diarrhea.[7]
A reduction in levels of native bacterial species also disrupts their
ability to inhibit the growth of harmful species such as C. difficile
and Salmonella kedougou, and these species can get out of hand, though
their overgrowth may be incidental and not be the true cause of
diarrhea.[7][24][2]
Gut flora composition also changes in severe illnesses, due not only
to antibiotic use but also to such factors as ischemia of the gut,
failure to eat, and immune compromise. Negative effects from this have
led to interest in selective digestive tract decontamination (SDD), a
treatment to kill only pathogenic bacteria and allow the
reestablishment of healthy ones.[25]
Probiotics & Prebiotics
Since the lack of gut flora can have such harmful health effects, the
use of probiotics has anti-inflammatory effects in the gut and may be
useful for improving health. Prebiotics are dietary components that
can help foster the growth of microorganisms in the gut, which may
lead to better health.[23]
Role in disease
Bacteria in the digestive tract have pathogenic properties in addition
to their health-inducing ones: they can produce toxins and
carcinogens[5] and have been implicated in such conditions as
multisystem organ failure, sepsis, colon cancer, and IBD.[2] A major
factor in health is the balance of bacterial numbers; if the numbers
grow too high or low, it will result in harm to the host. The host has
enzymes to regulate this balance.[5]
Cancer
Some genera of bacteria, such as Bacteroides and Clostridium, have
been associated with an increase in tumor growth rate, while other
genera like Lactobacillus and Bifidobacteria are known to prevent
tumor formation.[2]
Translocation
Helpful bacteria can be very harmful to the host if they get outside
of the intestinal tract.[3][5][10] Translocation, which occurs when
bacteria leave the gut through its mucosal lining, the border between
the lumen of the gut and the inside of the body,[4][26] can occur in a
number of different diseases.[10][23] It can be caused by too much
growth of bacteria in the small intestine, reduced immunity of the
human, or increased gut lining permeability.[23] The gut can become
more permeable in diseases like cirrhosis, which is damaging due in
part to the activity of gut flora.[27]
If the gut is perforated, bacteria can invade the body, causing a
potentially fatal infection. Aerobic bacteria can make infection by
anaerobes worse by using up all available oxygen and creating an
environment favorable to anaerobes.[10]
[edit] Inflammatory bowel disease
Some suspect that IBD is due to a reduction in immune tolerance and
subsequent overreaction of the host's immune system to harmful or non-
harmful bacteria. IBD may be caused by all of the gut flora together
or some specific types.[20][28]
It has been noted that though Ulcerative Colitis and Crohn's disease
(two types of IBD) probably have genetic components, they are not
inherited in a Mendelian fashion and are thus probably due to a
complex set of factors rather than solely to a gene.[28] Though
neither bacterial colonization nor genetics is sufficient to cause the
disease, bacteria probably play a role in these disorders.[28]
Some suspect that inflammation in IBD is due to increased permeability
of the inner lining of the colon, which may allow bacteria to invade
the tissues and cause an immune reaction that leads prolonged
inflammation.[4][26] Abnormal tight junctions, which are supposed to
prevent permeability, have been found in cells of patients with IBD.
[26] Because of the potentially harmful role of these bacteria,
antibiotics are frequently prescribed to treat Crohn’s disease.[21]
However, inflammation could occur first and cause the increased
intestinal permeability found in diseases such as Crohn's, so the
causative role of bacteria is not clear.[26]
Colitis
It has been suggested that commensal bacteria are responsible for the
development of colitis, since mice raised in a sterile environment do
not get the disease.[29] However, while some bacterial strains such as
C. difficile[23] and even normal gut bacteria cause colitis,[29]
others prevent the disease in mice.[23]
Obesity
It is known from experiments on mice that obese mice lacking leptin, a
lipid metabolism regulator (ob/ob mice), have a distinct gut flora
compared to (normal) lean mice, reflected in a change in the ratio
between bacteria from the divisions bacteroidetes and firmicutes,
which is shifted towards less bacteroidetes and more firmicutes in
obese mice.
The microbes occupying the human gut are also in direct relation to
obesity. A shift in the ratio between bacterial-divisions firmicutes
and bacteroidetes can be observed in lean and obese individuals – in
latter a shift towards firmicutes can be observed. The ratio between
firmicutes and bacteroidetes dynamically reflects the overall weight-
condition of an individual, shifting towards bacteroides if an obese
individual loses weight.
The mutual influence of gut flora composition and weight-condition is
connected to differences in the energy-resorption potential of
different ratios of firmicutes and bacteroidetes, especially in the
digestion of fatty acids and dietary polysaccharides, as shown by
experiments wherein the (caecum) gut flora of obese mice was
transplanted into germ free recipient mice, leading to an increase in
weight despite a decrease in food consumption.[30][31][32][33]
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