ABSTRACT: With the advent of biochemical and microbial stool analysis panels, an increasing number of physicians are seeking a clearer understanding of the relationship between the ecology of the digestive tract and local and systemic factors affecting health and disease. Dysbiosis is a state of living with intestinal flora that has harmful effects. It can be described as being due to either putrefaction, fermentation, deficiency, or sensitization. A number of inflammatory diseases within the bowel or involving skin and connective tissue have been reported in association with dysbiosis. This article details the relationships, causes and treatment options for dysbiotic related conditions.
Recognition that intestinal flora have a major impact on human health first developed with the birth of microbiology in the late nineteenth century. It is generally accepted that our relationship with indigenous gut flora is “Eu-symbiotic,” meaning a state of living together that is beneficial. Metchinkoff popularized the idea of “Dys-symbiosis, or Dysbiosis,” a state of living with intestinal flora thathas harmful effects. He postulated that toxic amines produced by bacterial putrefaction of food were the cause of degenerative diseases, and that ingestion of fermented foods containing Lactobacilli could prolong life by decreasing gut putrefaction(1). Although Metchnikoff’s ideas have been largely ignored in the United States, they have influenced four generations of European physicians. The notion that dysbiotic relationships with gut microflora may influence the development of inflammatory diseases and cancer has received considerable experimental support over the past two decades, but the mechanisms involved are far more diverse than Metchnikoff imagined.
The stool of healthy human beings consuming a Western diet contains 24 x 105¡ bacteria/gram. Twenty species comprise 75% of the total number of colonies; non-spore forming anaerobes predominate over aerobes by a ratio of 5000:1(2). Organisms cultured from mucosal surfaces are significantly different from those found in stool and vary among different parts of the gastrointestinal tract. The bacterial concentration in the stomach and small intestine is several orders of magnitude less than in the colon. The major mucosal organisms there are coccobacilli(1) and streptococci(3). The predominant organisms cultured from gastric and duodenal aspirates, are yeasts and Lactobacilli(2), living in the lumen. In the colon, the presence of these organisms is overshadowed by spirochetes and fusfform bacteria on the mucosal surface and anaerobic rods like Eubacterium, Bacteroides and Bifidobacterium in the lumen. Benefits and adverse effects of the normal gut microflora are listed in Table 1 & 2 and have been described elsewhere(4).
Materials and Methods
lntestinal dysbiosis should be considered as a mechanism promoting disease in all patients with chronic gastrointestinal, inflammatory or autoimmune disorders, food allergy and intolerance, breast and colon cancer, and unexplained fatigue, malnutrition or neuropsychiatric symptoms.
The most useful test for this condition is a Comprehensive Digestive Stool
Analysis (CDSA) which includes:
a) biochemical measurements of digestion/maldigestion (fecal chymotrypsin,
fecal triglycerides, meat and vegetable fibers, pH), intestinal absorption/
malabsorption (long chain fatty acids, fecal cholesterol, and total short
chain fatty acids)
b) metabolic markers of intestinal metabolism
c) identification of the bacterial microflora, including friendly, pathogenic
and imbalanced flora
d) detection of abnormal gut mycology
The authors have developed a Gut Dysbiosis Score (Table 3) to make the
CDSA more useful.
Interpretation of Gut Dysbiosis Score (Refers to Table 3)
Excess meat or vegetable fibers or triglycerides (one point each) suggest mal-
digestion. This is a common effect of bacterial overgrowth but can also con-
tribute to its cause.
Excess cholesterol or fatty acids (one point each) is indicative of malabsorp-
tion; bacterial overgrowth produces this by interfering with micelle forma-
Low concentrations of butyrate or SCFA (two points each) indicate insuffi-
cient anaerobic fermentation of soluble fiber. This may result from a low fiber
diet deficiency of Bifidobacteria.
High concentrations of butyrate or SCFA (two points each) is indicative of
increased anaerobic fermentation.
Alkaline stool pH (two points) often accompanies a low butyrate. When it is
associated with a normal butyrate it signifies increased ammonia production,
reflecting a diet high in meat or excessive urease activity of intestinal bacte-
ria. Bacterial cultures can provide more direct evidence of dysbiosis. The
most common finding is:
A lack of Lactobacillus or of E.Coli on stool culture (3 points each) High
levels of uncommon or atypical Enterobacteriaceae or of Klebsiella, Proteus
or Pseudomonas, may reflect small bowel overgrowth of these organisms
(score 1 point for each.)
Total Score-7 points or more is always associated with clinical dysbiosis;
5-6 is probable dysbiosis; 3-4 is borderline. There are rare cases in which a
score less than 3 occurs in a dysbiotic stool. These cases are usually under
treatment at the time the stool is obtained. In severe cases abnormal blood
tests may be found. There may be erythrocyte macrocytosis, low circulating
vitamin B12 or hypoalbuminemia. Urinary excretion of essential amino acids
may also be low, signifying impaired assimilation of dietary protein.
Based on available research and clinical data, we now believe that
there are four patterns of intestinal dysbiosis: putrefaction, fermenta-
tion, deficiency, and sensitization.
This is the classic Western degenerative disease pattern advanced by
Metchnikoff. Putrefaction dysbiosis results from diets high in fat and
animal flesh and low in insoluble fiber. This type of diet produces an
increased concentration of Bacteroides sp. and a decreased concentra-
tion of Bifidobacteria sp. in stool. It increases bile flow and induces
bacterial urease activity(1). The alterations in bacterial population
dynamics which result from this diet are not measured directly by the
[Comprehensive Digestive Stool Analysis (CDSA)]. The changes occur
primarily among anaerobes, but the effects are measured in an in-
crease in stool pH (partly caused by elevated ammonia production)
and in bile or urobilinogen and possibly by a decrease in short chain
fatty acids, especially in butyrate. Epidemiologic and experimental
data implicate this type of dysbiosis in the pathogenesis of colon can-
cer and breast cancer(6). A putrefaction dysbiosis is accompanied by
an increase in fecal concentrations of various bacterial enzymes
which metabolize bile acids to tumor promotors and deconjugate ex-
creted estrogens, raising the plasma estrogen level(6). Putrefaction
dysbiosis is corrected by decreasing dietary fat and flesh, increasing
fiber consumption and feeding Bifidobacteria and Lactobacillus prep-
Most adverse effects of the indigenous gut flora are caused by the
intense metabolic activity of luminal organisms. The following are
associated with Putrefaction dysbiosis:
1. The enzyme urease, found in Bacteroides, Proteus and Klebsiella
species, and induced in those organisms by a diet high in meat, hy-
drolyzes urea to ammonia, raising stool pH. A relatively high stool
pH is associated with a higher prevalence of colon cancer(7).
2. Bacterial decarboxylation of amino acids yields vasoactive and
neurotoxic amines, including histamine, octopamine, tyramine and
tryptamine; these are absorbed through the portal circulation and
deaminated in the liver. In severe cirrhosis they reach the systemic
circulation and contribute to the encephalopathy and hypotension of
3. Bacterial tryptophanase degrades tryptophan to carcinogenic phe-
nols, and, like urease, is induced by a high meat diet(8).
4. Bacterial enzymes like beta-glucuronidase hydrolyze conjugated es-
trogens and bile acids. Hepatic conjugation and biliary excretion is an
important mechanism for regulating estrogen levels in the body. Bacte-
rial deconjugation increases the enterohepatic recirculation of estrogen.
A Western diet increases the level of deconjugating enzymes in stool,
lowers estrogen levels in stool and raises estrogen levels in blood and
urine, possibly contributing to the development of breast cancer(6).
5. Beta-glucuronidase and other hydrolytic bacterial enzymes also
deconjugate bile acids.
Deconjugated bile acids are toxic to the colonic epithelium and
cause diarrhea. They or their metabolites appear to be carcinogenic
and are thought to contribute to the development of colon cancer(6,9)
and to ulcerative colitis(10). Gut bacteria also reduce primary bile
acids like cholate and chenodeoxycholate to secondary bile acids like
deoxycholate (DCA) and lithocholate. The secondary bile acids are ab-
sorbed less efficiently than primary bile acids and are more likely to
contribute to colon carcinogenesis. The prevalence of colon cancer is
proportional to stool concentration of DCA.
Not all bacterial enzyme activity is harmful to the host. Fermenta-
tion of soluble flber by Bifidobacteria sp. yields SCFA. Recent interest
has focused on the beneficial role of short-chain fatty acids like buty-
rate in nourishing healthy colonic mucosal cells. Butyrate has been
shown to induce differentiation of neoplastic cells(l1), decreased ab-
sorption of ammonia from the intestine(1), decreased inflammation in
ulcerative colitis(12) and, following absorption, decreased cholesterol
synthesis in the liver(7). Butyrate lowers the stool pH. A relatively
low stool pH is associated with protection against colon cancer(S). The
principal source of colonic butyrate is fermentation of soluble fiber by
colonic anaerobes. Thus, putrefaction dysbiosis results from the inter-
play of bacteria and diet in their effects on health and disease.
This is a condition of carbohydrate intolerance induced by overgrowth
of endogenous bacteria in the stomach, small intestine and cecum.
The causes and effects of small bowel bacterial overgrowth have been
Bacterial overgrowth is promoted by gastric hypochlorhydria, by
stasis due to abnormal motility, strictures, fistulae and surgical blind
loops, by immune deficiency or by malnutrition( 13). Small bowel
parasitosis may also predispose to bacterial overgrowth(4). Some of
the damage resulting from small bowel bacterial overgrowth is pro-
duced by the action of bacterial proteases which degrade pancreatic
and intestinal brush border enzymes causing pancreatic insufficiency,
mucosal damage and malabsorption. In more severe cases the intesti-
nal villi are blunted and broadened and mononuclear cells infiltrate
the lamina propria. Increased fecal nitrogen leads to hypoalbumine-
mia. Bacterial consumption of cobalamin lowers blood levels of vita-
min B12. Bile salt dehydroxylation impairs micelle formation(10).
Endotoxemia resulting from bacterial overgrowth contributes to hep-
atic damage in experimental animals(14).
Gastric bacterial overgrowth increases the risk of systemic infec-
tion. Gastric bacteria convert dietary nitrates to nitrites and nitro-
samines; hence, the increased risk of gastric cancer in individuals
with hypochlorhydria( 15) . Some bacterial infections of the small
bowel increase passive intestinal permeability(16).
Carbohydrate intolerance may be the only symptom of bacterial
overgrowth, making it indistinguishable from intestinal candidosis;
in either case dietary sugars can be fermented to produce endogenous
ethanol(17,18). Chronic exposure of the small bowel to ethanol may
itself impair intestinal permeability(19). Another product of bacterial
fermentation of sugar is D-lactic acid. Although D-lactic acidosis is
usually a complication of short-bowel syndrome or of jejuno-ileal by-
pass surgery (colonic bacteria being the source of acidosis), elevated
levels of D-lactate were found in blood samples of 1.12% of randomly
selected hospitalized patients with no history of gastro-intestinal sur-
gery or disease(20). Small bowel fermentation is a likely cause of
D-lactic acidosis in these patients. British physicians working with
the gut-fermentation syndrome as described by Hunisett et al(18)
have tentatively concluded, based on treatment results, that the ma-
jority of cases are due to yeast overgrowth and about 20% are bacte-
rial in origin. The symptoms include abdominal distension, carbohy-
drate intolerance, fatigue and impaired cognitive function.
Exposure to antibiotics or a diet depleted of soluble fiber may create
an absolute deficiency of normal fecal flora, including Bifidobacteria,
Lactobacillus and E. Coli. Direct evidence of this condition is seen on
stool culture when concentrations of Lactobacillus or E. Coli are re-
duced. Low fecal short chain fatty acids provide presumptive evi-
dence. This condition has been described in patients with irritable
bowel syndrome and food intolerance (see below). Deficiency and pu-
trefaction dysbiosis are complementary conditions which often occur
together and have the same treatment.
Aggravation of abnormal immune responses to components of the
normal indigenous intestinal microflora may contribute to the patho-
genesis of inflammatory bowel disease, spondyloarthropathies, other
connective tissue disease and skin disorders like psoriasis or acne.
The responsible bacterial components include endotoxins, which can
activate the alternative complement pathway and antigens, some of
which may cross react with mammalian antigens. Treatment studies
in ankylosing spondylitis and inflammatory bowel disease suggest
that sensitization may complement fermentation excess and that sim-
ilar treatments may benefit both conditions.
Clinical research has implicated bacterial dysbiosis in a number of
diseases of inflammation within the bowel or involving skin or con-
nective tissue. The published associations are reviewed below:
Ionescu and his colleagues have studied fecal and duodenal flora in
patients with atopic eczema and found evidence of small bowel dys-
biosis and subtle malabsorption phenomena in the majority(21,22).
Treatment with antibiotics or with a natural antibiotic derived from
grapefruit seeds, produced major improvement in the gastro-intesti-
nal symptoms of eczema patients and moderate improvement in se-
verity of eczema(23). One advantage in the use of grapefruit seed ex-
tract over conventional antibiotics lies in its anti-fungal activity. This
agent adds a second therapeutic dimension and eliminates the possi-
bility of secondary candidosis. The minimum effective dose of grape-
fruit seed extract for bacterial dysbiosis is 600 mg a day.
Irritable Bowel Syndrome
Hunter and his colleagues have studied patients with the irritable
bowel syndrome in whom diarrhea, cramps and specific food intol-
erances are major symptoms(24). They have found abnormal fecal
flora to be a consistent finding, with a decrease in the ratio of anaer-
obes to aerobes, apparently due to a deficiency of anaerobic flora
(25,26). Previous exposure to antibiotics, metronidazole in particular,
was associated with the development of this disorder(27).
Inflammatory Bowel Disease
Two decades ago, exaggerated immunologic responses to components
of the normal fecal flora were proposed as possible mechanisms in the
etiology of inflammatory bowel disease(28). Little progress has been
made in confirming or disproving this theory, although bacterial
overgrowth of the jejunum has been found in 30% of patients hospi-
talized for Crohn’s disease, in which it contributes to diarrhea and
The demonstration of increased intestinal permeability in patients
with active Crohn’s disease and in healthy first degree relatives sug-
gests the existence of a pre-existing abnormality that allows an exag-
gerated immune response to normal gut contents to occur(30).
It is interesting to note that elemental diets can induce remission
in Crohn’s disease as effectively as prednisone. The chief bacteriologic
effect of elemental diets is to lower the concentration of Lactobacilli
in stool drastically without altering levels of other bacteria(31). It is
well-known that many patients with Crohn’s disease can be brought
into remission with metronidazole, tetracycline and other antibiotics.
In ulcerative colitis, colonic damage from toxic metabolites of bile
acids has been suggested(9). Alpha-tocopherylquinone, a vitamin E
derivative that antagonizes vitamin K dependent bacterial enzymes
reversed ulcerative colitis dramatically in one subject(32).
Drawing on much broader experience with inflammatory bowel dis-
ease, Gottschall has proposed that gut dysbiosis plays the major
etiologic role, with small and large bowel fermentation being a key
component. She has used a specific carbohydrate diet restricted in
disaccharide sugars and devoid of cereal grains to alter gut flora(33).
Some will undoubtedly argue that Gottschall’s success is due to food
allergen elimination, but the time course of patients’ responses is
more consistent with the authors’ contention that a gradual alter-
ation of gut flora content is the mechanism.
McCann has pioneered a dramatic, experimental treatment for in-
flammatory bowel disease which has induced a rapid remission in 16
out of 20 patients with ulcerative colitis. A two-day course of multi-
ple-broad spectrum antibiotics to “decontaminate” the gut is followed
by administration of defined strains of E. coli, and Lactobacillus ac-
idophillus to produce a “reflorastation” of the colon(34).
Arthritis and Ankylosing Spondylitis
Immunologic responses to gut flora have been advanced by several
authors as important factors in the pathogenesis of inflammatory
joint diseases. It is well-known that reactive arthritis can be acti-
vated by intestinal infections with Yersinia, Salmonella and other
enterobacteria(35). In some cases bacterial antigens have been found
in synovial cells(36,37) and may enter the circulation because of the
increased intestinal permeability associated with the intestinal infec-
tion(l5). Increased intestinal permeability and immune responses to
bacterial debris may cause other types of inflammatory joint disease
as well. but there is little evidence of the frequency with which this
occurs(38-40). Several groups have proposed a specific mechanism by
which Klebsiella pneumoniae may provoke ankylosing spondylitis
(41-43). HLA-B27 is expressed on the lymphocytes and synovial cells
of 97% of patients with ankylosing spondylitis. This antigen cross-
reacts with antigens found on Klebsiella pneumoniae and possibly
other enterobacteria. Patients with ankylosing spondylitis have
higher levels of Klebsiella pneumoniae in their stools than controls
and have higher levels of anti-Klebsiella IgA in plasma than do con-
trols. Patients who are HLA-B27 positive but who do not have an-
kylosing spondylitis do not have Klebsiella in their stools or Kleb-
siella antibodies in their plasma.
Molecular mimicry appears to be the mechanism by which intesti-
nal enterobacteria cause ankylosing spondylitis in genetically suscep-
Ebringer has successfully treated ankylosing spondylitis with a low
starch diet similar to Gottschall’s regimen for bowel disease. This diet
lowers the concentration of Klebsiella in stool and decreases the titre
of anti-Klebsiella IgA. He has also proposed that rheumatoid ar-
thritis, which is associated with HLA-DR4, involves a similar molecu-
lar mimicry between HLA-DR4 and Proteus mirabilis, as cross-reac-
tive Proteus antibodies are higher in patients with rheumatoid
arthritis than in controls. Abnormal immune responses to compo-
nents of the normal gut flora represents a form of dysbiosis which
suggests novel treatment for inflammatory diseases.
Diet-Putrefaction dysbiosis is usually managed with a diet high in
both soluble and insoluble fiber and low in saturated fat and animal
protein. Dairy products have a variable effect. Fermented dairy foods
like fresh yogurt are occasionally helpful. These dietary changes
work to lower the concentrations of Bacteroides and increase concen-
trations of lactic acid-producing bacteria (Bifidobacteria, Lactobacil-
lus and lactic acid streptococci) in the colon(44,45). Supplementing
the diet with defined sources of fiber can have variable effects on colo-
nic dysbiosis. Insoluble fiber decreases bacterial concentration and
microbial enzyme activity(46,47). Soluble fiber, on the other hand,
tends to elevate bacterial concentration and enzyme activity at the
same time that it raises the levels of beneficial short chain fatty
acids. This disparity may explain the superior effect of insoluble fiber
in the prevention of colon cancer(48-51). Fructose-containing oligosac-
charides, found in vegetables like onion and asparagus, have been
developed as a food supplement for raising stool levels of Bifidobac-
teria and lower stool pH.(52)
In fermentation dysbiosis, by contrast, starch and soluble fiber may
exacerbate the abnormal gut ecology(3,33). When the upper small
bowel is involved, simple sugars are also contra-indicated. A diet free
of cereal grains and added sugar is generally the most helpful. Fruit,
fat and starchy vegetables are tolerated to variable degree in differ-
ent cases. Oligosaccharides found in some vegetables, carrots in par-
ticular, inhibit the binding of enterobacteria to the intestinal mucosa.
Carrot juice and concentrated carrot oligosaccharides have been used
in Europe for bacterial diarrhea for almost a century(53).
BiotherapiesÑAdministration of bacteria indigenous to the healthy
human colon can reverse relapsing Clostridium difficile infection(54).
Lactobacillus administration has long been used in an attempt to im-
prove gut microbial ecology. Regular ingestion of acidophilus milk
lowers stool concentrations of urease-positive organisms and of bacte-
rial enzymes which may contribute to carcinogenesis(55). Fermented
dairy products and Iyophilized Lactobacillus preparations have been
shown to be useful in treating and preventing salmonellosis, shig-
ellosis, antibiotic-induced diarrhea and in inhibiting tumor growth
(56). Problems with Lactobacilli include the failure of organisms to
adhere to the intestinal mucosa or to survive damage from gastric
acid and bile. The acidophilus sweepstakes has led to the search for
newer and better strains for medical uses(57,58).
Bifidobacteria are the predominant lactic acid bacteria of the colon
with a concentration that is 1000 times higher than Lactobacilli. Ad-
ministration of Bifidobacterium brevum to humans and animals re-
duces fecal concentrations of Clostridia and Enterobacter species, am-
monia, and toxigenic bacterial enzymes including beta-glucuronidase
and tryptophanase; urinary indican is also lowered(59). Administra-
tion of defined strains of E. coli and Enterococcus for the purpose of
altering gut flora has been popular in Europe, but documentation of
the health effects is scanty.
Bacillus laterosporus, a novel organism classified as non patho-
genic to humans(60), produces unique metabolites with antibiotic,
anti-tumor and immune modulating activity(61-63). This organism
has been available as a food supplement in the United States for
about 5 years. We have found it to be an effective adjunctive treat-
ment for control of symptoms associated with small bowel dysbiosis in
a number of patients.
Of equal interest, and more thoroughly researched, a yeast, Sac-
charomyces boulardii, has been used in Europe for control of non-
specific diarrhea for several decades. Originally isolated from Indo-
chinese leechee nuts, S. boulardii is grown and packaged as a medica-
tion in France, where it is popularly called, “Yeast Against Yeast”.
Controlled studies have demonstrated its effectiveness in preventing
antibiotic associated diarrhea and Clostridium difficile colitis(64,65).
S. boulardii has also been shown to stimulate production of secretory
IgA in rats(66). Immune enhancing therapy of this type may be con-
traindicated in patients suffering from reactive arthritis and other
diseases in which an exaggerated intestinal immune response is
Antibiotic drugs may either cause or help control dysbiosis, depend-
ing upon the drug and the nature of the disorder. Where contamina-
tion of the small bowel by anaerobes is the problem, metronidazole or
tetracyclines may be beneficial. When enterobacterial overgrowth
predominates, ciprofloxacin is usually the drug of choice because it
tends to spare anaerobes. Herbal antibiotics may be preferred because
of their greater margin of safety and the need for prolonged anti-
microbial therapy in bacterial overgrowth syndromes. Citrus seed ex-
tract may be a desirable first line of treatment because of its broad
spectrum of antibacterial, anti-fungal and anti-protozoan effects(23).
The usual dose required is 600 to 1600 mg/day. Animal studies have
shown no toxicity except for intestinal irritation producing diarrhea
at very high doses. The mechanism of action is not known; there is no
evidence of systemic absorption. Bayberry leaf, containing the alka-
loid berberine, appears to be cidal for enterobacteria, yeasts and
amoebae. The control of dysbiotic symptoms usually requires several
grams a day. Artemesia annua has primarily been used for treatment
of protozoan infection(67). The most active ingredient, artemisinin, is
a potent pro-oxidant whose activity is enhanced by polyunsaturated
fats like cod liver oil and antagonized by vitamin E.(68). Artemisinin
is used intravenously in Southeast Asia for the treatment of cerebral
malaria; it has no known side effects except for induction of abortion
when used at high doses in pregnant animals.
The herbal pharmacopeia lists many substances with natural anti-
biotic activity and the potential for herbal treatment of gut dysbiosis
is virtually unlimited. A tannin-rich mixture of herbal concentrates
including extracts of gentiana, sanguinaria and hydrastis has been
marketed under various names. In vitro studies at Great Smokies Di-
agnostic Laboratory have found this mixture to exert more potent ac-
tivity against enterobacteriaceae and Staphylococcus than any of the
common antibiotic drugs tested; its major side effect is nausea pro-
duced by the high tannin content.
Summary and Conclusions
Altered microbial ecology in the gut may produce disease and dys-
function because of the intense metabolic activity and antigenicity of
the bacterial flora. Bacterial enzymes can degrade pancreatic en-
zymes, damage the intestinal brush border, deconjugate and reduce
bile acids and alter the intestinal milieu in numerous ways, some of
which can be easily measured in a properly collected sample of stool.
Bacterial antigens may elicit dysfunctional immune responses which
contribute to autoimmune diseases of the bowel and of connective
tissue. Effective treatment of dysbiosis with diet, antimicrobial sub-
stances and biotherapies must distinguish among patterns of dys-
biosis. The failure of common approaches utilizing fiber and Lacto-
bacilli is a strong indication of small bowel bacterial overgrowth, a
challenging disorder which demands a radically different approach.
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