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ORIGINAL ARTICLE

Normal ora: diversity and functions


Lynne V. McFarland

From the Department of Medicinal Chemistry, University of Washington, and Biocodex, Inc. Seattle, WA,
USA

Correspondence to: Lynne V. McFarland, Ph.D., Biocodex, Inc., 1910 Fairview Avenue E, Suite # 208, Seattle,
WA 98102, USA. Fax: 206-323-2968; E-mail: lvmcfarl@u.washington.edu

Microbial Ecology in Health and Disease 2000; 12: 193 207

Recent research into the therapeutic use of living organisms has focused attention on the impact of various disruptive factors (antibiotics,
surgery, immunosuppression) and their impact on the hosts normal ora. This review covers what is meant by normal ora, how the
microecology differs by the niche in the body, type of diet, age and health status. In addition, the functions and tools used to investigate
normal ora will be explored. The functions of the normal ora include digestion of substrates, production of vitamins, stimulation of
cell maturation, stimulation of the immune system, aid in intestinal transit and colonization resistance. A variety of factors can disrupt
the normal ora including age, diet, stress, illness and exposure to antibiotics. Research involving microecologic populations is difcult
due to the challenge of unraveling the complex dynamics within a usually inaccessible niche, but progress is being made.

INTRODUCTION predominant types of ora present within body niches and


In the past, the role that microorganisms played in the shared functional traits.
normal functioning of the body was not appreciated. In The adult human body contains 101 4 cells, of which only
the early 1900s when Dr. Metchnikoff was credited with 10% compose the body proper and 90% are accounted for
the discovery of the importance of intestinal ora, other by members of the microora (8). The predominating
physicians felt that the colon was totally unnecessary and types of species in humans differ according to the body
often surgically removed them from their patients (1). The niche (oral cavity, skin, vagina, stomach, ileum, colon or
colon was described as a poisonous cess-pit infecting the urinary tract), as shown in Fig. 1 (3, 9 13). Normal ora
body with rheumatism, tuberculosis, cancer and other found in the oral cavity has been found to vary by the area
diseases. Today, we know that normal ora is a dynamic sampled (tooth enamel, tongue, gingivital surface, saliva)
and complex mixture of microbes that have diverse func- and the state of periodontal health (14, 15). The oral cavity
tions including digestion of essential nutrients, maturation contains a wide mixture of microbes, which are mainly
of intestinal physiology, stimulation of immune system, anaerobic bacteria. Gagliardi et al. sampled normal ora
systemic effects on blood lipids and the inhibition of in the healthy esophagus during upper endoscopy proce-
harmful bacteria. Current research techniques allow better dures in 30 patients and the predominant ora was found
evaluation of the specic bacterial and fungal microbes to be Streptococcus viridans (16). Lactobacilli and alpha-
within various body sites. This paper revisits some popular hemolytic Streptococcus species are frequently isolated on
conceptions about normal ora and updates them with tonsils of healthy children (15, 17). Lactobacillus species
regard to recent scientic ndings. that have the ability to adhere to mannose-containing
receptors, such as L. plantarum, have a distinct advantage
in surviving in the oral cavity (18). Results from different
WHAT IS NORMAL FLORA? studies proling predominant ora may be difcult to
Although the term normal ora is commonly used, it is compare as subject age, sampling techniques (washing of
really a misnomer. Microbial ora has spatial and tempo- the surface, aspirates or biopsies), diet, sampled location
ral complexity that differs by individual, body niche, age, and microbiological assay techniques may produce signi-
geographic location, health status, diet and type of host (2, cantly different results. Fewer bacteria exist in the stomach
3). Even within the same individual, the composition of (usually below 103 :g due to acidic lumen). Helicobacter
the microbial ora can vary according to changes in diet, pylori has been found in patients with peptic ulcers and
stress, sexual behavior, medication, hormonal changes and gastric neoplasia, but is also found in 60% of healthy
other host-related factors (3 7). With this caveat in mind, hosts, which casts suspicion that this microbe is always a
the eld of normal ora can be examined for common cause for gastric disease (19 21). The concentration of

Taylor & Francis 2000. ISSN 0891-060 X Microbial Ecology in Health and Disease
194 L. V. McFarland

microbes increases as progression is made down the intesti- Vaginal ora has been shown to change over the menstrual
nal tract: small intestine ( 104 : ml contents), to 106 107 : cycle (4), sexual activity and hygiene habits (7, 24), and use
ml at the ileocecal region and 1011 101 2 :g in the colon. of intravaginal microbicides (such as nonoxynol-4) (25).
The intestinal microora consists of 1011 organisms:gram However, studies show most healthy women (52 78%)
of feces with over 500 different species, ranging in concen- have transient changes in vaginal ora (4, 7, 24). Some
trations from 102 1011 :ml luminal contents (22). Although more recent prospective studies have shown only a minor-
the variety of organisms is complex, generally there are ity (22 26%) of healthy women had a lactobacilli-predom-
more anaerobic microbes than aerobes (9). The develop- inant ora (5, 24). Thus, the characterization of vaginal
ment of new techniques and genetic probes has allowed ora is open to debate and requires additional prospective
better characterization of the types of organisms that studies in well-dened populations of healthy women.
comprise the normal intestinal ora. Franks et al. devel- The process of the development of normal ora starts at
oped six 16S rRNA-targeted oligonucleotide probes that birth. It is thought that colonization begins during parturi-
can detect at least 66% of the anaerobic fecal ora in tion when the neonates intestine is seeded with mostly
humans (23). When these probes were used to characterize Gram-positive facultative anaerobes from the vaginal mi-
the ora in nine healthy human volunteers, Bacteroides croora during delivery (22, 26, 27). Whether the vaginal
species accounted for 20% of the total fecal population, ora in the last trimester is similar to vaginal ora when
Clostridium coccides and Eubacterium rectale accounted the woman is not pregnant is not known. However, Kar-
for 29%, Gram-positive bacteria accounted for 12% and voven et al. documented that the vaginal ora collected
Bidobacterium species accounted for 3% of the fecal ora. from mothers after delivery was the same as ora found in
These probes may prove very valuable in the characteriza- the stools of neonates (27). Neonates born by caesarian
tion of the microecologic proles, but more research is section usually acquire their rst microbes from the envi-
needed (as discussed later). ronment of the hospital nursery (26). Neonates are quickly
Previous studies have reported that ora in the healthy colonized by facultative anaerobes (E. coli and Streptococ-
vagina is typically a mixture of aerobic Lactobacillus spe- cus), reaching concentrations of 108 to 1010 :g feces within
cies, including L. jensenii, L. acidophilus or L. rhamnosus 1 2 days (9, 26). Previous studies reported that anaerobic
(9). Two strains of lactobacilli (L. crispatus and L. jensenii ) ora do not become established until the second month of
protect vaginal surfaces by producing H2 O2 , which inhibits life (9). The hypothesis for this observation was that when
the colonization of pathogenic anaerobes and mycoplas- the newly seeded facultative microbes grew and produced
mas associated with bacterial vaginosis, Neisseria gonor- a more anaerobic environment, this established an anaero-
rhoeae or other sexually transmitted diseases (5, 13). bic environment suitable for anaerobes (9). However, these

Fig. 1. Predominant ora in different


niches of the human body. Compiled
from references: (3), (9 13).
Normal ora description 195

Table I FUNCTIONS OF THE NORMAL FLORA


Microbial-associated characteristics (MAC) relating to different Digestion
functions of the normal intestinal microecology
The functions of the normal ora have been called mi-
1. Digestion of metabolizable substrates croora-associated characteristics (MAC) by several re-
2. Colonization resistance searchers (22, 36 38). These MAC (Table I) include
3. Production of vitamins
digestion of metabolizable substrates, colonization resis-
4. Development of attachment sites
5. Induces development of the immune system tance, vitamin production, mucosal cell development, im-
6. Production of exogenous enzymes mune system stimulation and intestinal transit regulation
7. Stimulation of intestinal transit (36 49). An important role of the intestinal ora is the
8. Maturation and turn-over of intestinal cells digestion of metabolizable substrates. A major source of
nutrients is the upper intestinal tract and the available
Compiled from references: (22), (36 49). substrates may include dietary bers, starches, oligosac-
charides, sugars, some lipids and proteins. Another source
conclusions were based on standard culturing techniques
of nutrients is within the colon itself and includes endoge-
(9, 28, 29). Harmsen et al. compared newer techniques
nous mucins, sloughed epithelial and enterocyte tissues,
(FISH, 16S rRNA probes) with culturing techniques and
bacterial debris, bile acids and cholesterol. The types of
found high counts were found by culturing only after 8 9
metabolizable substrates are key in determining the type
days, but FISH detected anaerobes by the second day (30).
of ora present in the colon. The main products of bacte-
In addition, another study indicated that neonates can
rial digestion of non-absorbed dietary carbohydrates are
acquire strict anaerobes, such as C. difcile, within the rst
short chain fatty acids (SCFAs). The SCFAs produced in
2 days of stay on a neonatal ward (31). Therefore, the
the largest quantities by the normal ora include acetic,
theory that colonization of the neonatal intestine by anaer-
propionic and butyric acids (50). Acetic and propionic
obes is dependent upon facultative bacteria producing an
acids are rapidly absorbed and are a major source of
anaerobic environment may be erroneous.
energy, in addition to stimulating salt and water absorp-
The type of diet largely inuences the types of ora in
tion (22, 51). Butyric acid has several functions including
pre-weaning infants. Several studies have reported that
the maintenance of the integrity of the colonic epithelial
infants who are breast-fed have higher concentrations of
bidobacteria as compared to formula-fed infants (28, 29, layer, as a chief energy source for these cells and regulat-
32, 33). Breast milk contains low protein content and high ing cell growth and differentiation (22, 51). Treem et al.
levels of oligosaccharides and glycoproteins, which are studied fecal SCFA in patients with Inammatory Bowel
considered to be growth factors for bidobacteria (26). Disease (IBD) (52). Fecal homogenates from 10 patients
Formula-fed infants have a more complex microbiota con- with IBD and 10 age-matched controls were compared as
sisting of Bidobacterium, Bacteroides, Clostridium and to the ability of the fecal homogenat e to produce SCFA.
Streptococcus species (22, 28). However, other researchers Patients with IBD produced less total SCFA, less acetate
have not found a signicant difference in breast-fed and acid and less propionic acid. Since normal ora is respon-
formula-fed infants (34). sible for the production of SCFA, this study may indi-
Historically, the characterization of neonatal fecal ora rectly link normal ora disruption with IBD. However,
has relied on culturing techniques, which are not able to Treem et al. did not characterize the ora responsible, nor
detect non-culturable species and may not be able to compare the microbial proles of patients with IBD and
distinguish different microbial populations. More recent controls. In some rare instances, the role for a member of
techniques using 16S rRNA probes, which are able to the normal ora has been identied for a specic func-
amplify the bacterial genes and are followed by sequence tion. Oxalobacter formigenes is a normal anaerobe in the
analysis, are more sensitive than the traditional culturing colon responsible for regulating the breakdown of oxalic
techniques (23). Harmsen et al. used 16S rRNA probes acid and it has been demonstrated that patients with
and conrmed previous ndings that breast-fed infants recurrent calcium oxalate kidney stone formation prob-
have predominant populations of bidobacteria in their lems do not harbor this useful bacterium (53). Normal
stools and formula-fed neonates had a more complex ora are also involved in the conversion of primary bile
mixture of organisms (32). By 2 years of age, children have salts. The identication of the genes encoding conjugated
a similar complexity and range of microbes as adults (35). bile salt hydrolases has been identied in a strain of L.
Differences in breast-fed and formula-fed microbial pro- johnsonii (54). Usually the role for a specic member of
les found by different studies may be due to sampling the normal ora is not limited to one function, rather the
techniques, time of collection, assay method, hospital prac- role is usually to interact with other members of the ora
tices or by the buffering capacity of different formulas for more complex functions (such as colonization resis-
(34). tance).
196 L. V. McFarland

Colonization resistance the gut. In germ-free mice, S. exneri is present at 109 :g,
Colonization resistance is the rst line of defense against but if the mice are pre-colonized with a mixture of anaero-
bic bacteria, S. exneri is held to 105 :g and when E. coli
invasion by exogenous, pathogeni c organisms or indige-
was added to the mixture, the levels dropped to 103 :g (59).
nous opportunistic organisms and the normal ora is
Romond et al. showed that bidobacteria, given to gnoto-
responsible for this formidable task (8, 55). Even though
biotic mice, prevented the colonization by E. coli (60).
the focus here is the intestinal tract, it should be remem-
The role of colonization resistance has been well studied
bered that colonization resistance plays an important role
in the case of the resistance to C. difcile. C. difcile
at other body sites (oral, skin, vagina, etc.). Colonization
readily colonizes neonatal animals and human babies at
resistance is a dynamic phenomenon that may differ dra-
the time when there is scarce ora established, but is
matically by microbial species, type of host, diet and other
cleared from the intestines once a more mature microecol-
host factors. Colonization resistance has been found to be
ogy develops (55). In the adult host, colonization resis-
an extremely effective natural barrier against such patho-
tance adequately prevents infection by C. difcile unless
gens as C. difcile, Salmonella, Shigella, Pseudomonas, the microbial barrier is disrupted (61). Once the ora is
pathogenic E. coli strains, Candida albicans and others (8, disrupted, C. difcile colonizes the intestines, produces two
56 58). major toxins and may cause overt disease including di-
Autochthonous ora (indigenous species that normally arrhea, colitis, pseudomembranou s colitis or toxic mega-
inhabit a given ecologic niche) may become disrupted and colon (62, 63). If protective ora is seeded back into the
allochthonous species (not normally present) are then able intestines (either by fecal infusion of normal stools or
to colonize the site. Colonization with allochthonous bac- selected biotherapeutic organisms), colonization of C.
teria may or may not result in disease, as the colonizing difcile may be prevented and the disease does not develop
organism may not be a pathogenic species. Early evidence (64).
for colonization resistance arose from the observation that, The mechanism of colonization resistance is dynamic
in germ-free animals (animals with no ora), animals were and complex (Table II). Bacteria comprising the normal
extremely sensitive to colonization with pathogens and ora are capable of producing substances and antimicro-
subsequently developed disease at higher rates than ani- bial peptides that are inhibitory against colonizing bacteria
mals with intestinal ora (57). This increased susceptibility (40, 65). Bacteriocins are a group of anti-bacterial proteins
could be corrected if fecal ora or mixtures of bacteria and produced by intestinal ora that have a broad inhibitory
yeasts were administered (38). Germ-free animals and ani- spectrum including many Gram-positive and Gram-nega-
mals that have been given certain antibiotics are able to be tive bacteria. Lactobacilli bacteria have been shown to
colonized by exogenous bacteria at doses 1000 to 100 000 produce a bacteriocin called reuterin, which is inhibitory in
fold less than in animals with normal ora present (11). vitro for Salmonella, Shigella, Clostridium and Listeria
Freter and Abrams found the concentration of Shigella species (66). Although an intriguing in vitro nding, it has
exneri depends upon the degree of normal ora present in not been shown that these bacteriocins reach concentra-
tions inhibitory to pathogens in the intestinal lumen, thus
Table II the clinical signicance of bacteriocins is not known.
Mechanisms of action for colonization resistance Normal ora may also produce other metabolic end-
products that are inhibitory to other microbes. Most nota-
Mechanism Factor Factors active ble is hydrogen peroxide (H2 O2 ) produced under anaerobic
against
conditions by several strains of normal ora (66). The
Production of Bacteriocins Salmonella, presence of H2 O2 results in peroxidation of lipid mem-
inhibitory Shigella branes, increased bacterial membrane permeability, de-
substances struction of bacterial nuclear acids in bacterial strains that
Toxic metabolic Hydrogen peroxide Chlamydia, do not possess catalase. The vaginal tract is usually pre-
endproducts Gardnerella
dominantly colonized with lactobacilli (Fig. 1) and H2 O2
Adverse microenvi- Acidic endproducts, S. aureus, E. coli
roments short chain fatty producing Lactobacillus strains have been found in 75% of
acids vagina samples from healthy women. Vaginal colonization
Nutrient or sub- Monomeric glucose Clostridium with Lactobacillus strains that produce H2 O2 has been
strate depletion difcile shown to be protective of infections caused by Chlamydia
Attachment Non-toxigenic enterotoxigenic
trachomatis, Gardnerella vaginalis, Ureaplasma urealyticum
interference strains of E. coli E. coli
Immune system Secretory IgA rotavirus, and the development of bacterial vaginosis (13). In women
stimulation C. difcile with bacterial vaginosis, these strains of H2 O2 producing
lactobacilli are absent and, instead, high concentrations of
Compiled from references: (11), (13), (41), (55), (59), (60), (63), Gardnerella vaginalis and anaerobes are present (66). An-
(67), (68), (75), (80). other protective mechanism is the production of a low pH
Normal ora description 197

environment, which may be inhibitory for certain patho- Survival in various body niches necessitates the attach-
gens. The production of acids as an end product of ment to receptor sites, especially in the colonic lumen
carbohydrate metabolism is common in many species of where peristalsis sweeps unattached microbes and undi-
the normal ora and is inhibitory against Gram-positive gested debris away. Competition for attachment sites is a
and Gram-negative bacteria. Several pathogens, including successful mechanism to inhibit colonization of pathogenic
Staphylococcus aureus, Salmonella, E. coli, and Bacillus microbes. Colonization with non-enterotoxin producing E.
cereus, are inhibited by acids produced by normal ora coli has been reported to prevent the subsequent infection
such as lactobacilli and bidobacteria. A common end with enterotoxin strains of E. coli in several mouse and pig
product of microbial fermentation is short chain fatty animal models (40). Fuller reviews several studies in ani-
acids (SCFA). The presence of these SCFA have been mals showing positive interference with attachment of
shown to be inhibitory to nonindigenous bacteria (40). normal ora when an non-indigenous microbe is ingested
Rolfe showed in a hamster model of C. difcile disease (71). A variety of host factors are also involved with
that SCFA levels inhibited C. difcile growth (40). As colonization resistance including secretory IgA levels, peri-
newborn hamsters age, they start to produce high levels of staltic movement , production of mucus, epithelial or ente-
acetic, butyric and propionic acids by day 16 19. Growth rocyte turnover (40).
of C. difcile was signicantly reduced when levels of these An area of intense research is to determine which mem-
SCFA increased (40). If normal ora are disrupted, de- ber or members of the numerous species of microbes
creased levels of SCFA result and pathogenic microbes present in the intestine are responsible for colonization
may take advantage of this decrease and reproduce to resistance. Most studies support the role of anaerobic ora
levels that induce disease. To date however, the identica- as the major microbes responsible for colonization resis-
tance (11, 56). Hazenberg et al. found a mixture of human
tion of which specic SCFA or mixtures of SCFAs are
anaerobic ora restored colonization resistance against P.
responsible for the inhibition of pathogens has not been
aeruginosa in the germ-free mice model (57). Giuliano et
demonstrated.
al. showed cefoxitin increased the numbers of fecal enter-
Competition for nutrients may be another mechanism
obacteriaceae, enterococci and yeasts in human volunteers
for colonization resistance. As it is extremely difcult to
(72). The increase in all three groups of these aerobic
assess the levels of specic nutrients in the interior of the
organisms may be due to the suppression of selected
colon, most of the research on nutrient depletion has been
anaerobic bacteria by cefoxitin. Leonard et al. reported
done using continuous ow culture techniques. Wilson et
that ceftriaxone decreased anaerobic ora in mice and
al. inoculated normal ora from a mouse into a continu-
human volunteers and colonization resistance was also
ous ow culture and found one or more of the ora
depressed in ceftriaxone treated animals (73). Clindamycin
competed more successfully for monomeric glucose, N-
is effective against anaerobes and has been shown to
acetylglucosamine and sialic acid, resulting in signicantly
impair colonization resistance (58). Some antibiotics that
reduced levels of C. difcile (67). Sweeney et al. found that
are effective against anaerobes, but are only present at low
even small numbers of an ingested E. coli strain F-18 could levels in the gut (tinidazole, cephradine), do not impair
supplant established ora, as this strain utilized an avail- colonization resistance (58). Specic members of the nor-
able nutrient (gluconate) more efciently than the other mal ora have also been studied including Bidobacteria
microbes present in the system (68). However, continuous longum, peptostreptococci and Clostridium cocleatum.
ow cultures are extremely dependent on culturing and Romond et al. tested Bidobacterium longum in germ-free
incubation parameters and the applicability of these results mice model (60). Pre-colonization of germ-free mice with
is unclear. E. coli delayed colonization by B. longum for one month,
Normal ora may also produce extracellular enzymes compared to a colonization time of only 24 hours in the
that are inhibitory or interfere with pathogen attachment. totally germ-free animals. Herias et al. observed that pep-
A yeast (Saccharomyces boulardii ) has been shown to tostreptococci reduced translocation of E. coli in germ-free
produce a protease that destroys toxin A and toxin B rat model by priming the immune system (74). Boureau et
receptor sites in rabbit ileal models for C. difcile disease al. showed that a normal member of the mouse intestinal
(69). The toxins of C. difcile act by inactivating Rho ora, C. cocleatum, inhibited the growth of pathogenic C.
proteins that keep the cytoskeleton of the intestinal entero- difcile (75). C. cocleatum was found to produce a variety
cyte intact, thereby distorting the cellular morphology of glycosidases that attacked intestinal oligosaccharides.
leading to uid loss and diarrhea (70). Rho proteins are As the peptide core of the mucin layer in the intestine is
also involved in yeast budding processes (reproduction), protected by oligosaccharides, this bacteria may interfere
thus this yeast may produce the protease to protect itself with the attachment of C. difcile but further study is
against soil Clostridia that may produce similar toxins to needed. Bourlioux et al. found a Ruminococcus species that
C. difcile, but in the human, the protease may coinciden- prevented C. perfringens colonization in a gnotobiotic
tally protect the host against infection with C. difcile. animal model (76). Although these studies have identied
198 L. V. McFarland

potential candidates for species which may be responsible on mucin required 5 weeks before it was restored to
for colonization resistance; it is more likely that a complex pre-antibiotic levels, which may indicate the length of time
mixture of many microbes is responsible. that it takes for normal ora to recover from antibiotic
A note of caution must be exercised with these animal exposure. The most abundant intestinal species (Bac-
studies, as the behavior of microbial species has been teroides) does not possess the glycosidases necessary for
found to differ depending upon which animal is studied mucin degradation and only 1% of normal ora species
(including human). Wong et al. evaluated the mouse as a can degrade mucin. Hoskins et al. identied ve strains of
model for studying microbial ecology interactions that mucin oligosaccharide chain-degrading bacteria from
may occur in humans (77). Human strains fed to mice healthy humans, of which three were Ruminococcus strains
usually survived, with the exception of Bacillus and Lacto- and two were Bidobacterium strains (83). Mucin-degrad-
bacillus species. They also found that in the mouse, human ing bacteria represent a distinct subset of normal ora with
organisms only produced 25% of the expected organic a specic function.
acids, which may suggest a change in metabolism when
human strains colonize the mouse. Resistance to a chal- Stimulation of the immune system
lenge strain (Salmonella ) was preserved, indicating that the Normal ora also induces the maturation of the gut-asso-
strains maintain their ability to produce colonization resis- ciated lymphoid system (GALT). The intestinal ora pro-
tance (77). vides an array of antigenic stimulants to the GALT cells,
affecting both local and systemic levels (22). Gnotobiotic
Production of vitamins mice have been shown to have fewer intraepithelial
Intestinal ora are also involved in the production of lymphocytes, plasma cells and Peyers patches than mice
vitamins including panthothenic acid (B5), biotin (vitamin with intact intestinal ora (78). When gnotobiotic mice are
H), pyridoxine (vitamin B6) and menaquinone (Vitamin immunized, the only local immune response is secretory
K2) (66, 78, 79). Without the intestinal ora, these vita- IgA, however, mice with intact intestinal ora also respond
mins would not be produced or in some cases, not broken with IgM and IgG (40, 41). Intestinal ora may also be
down into an absorbable form. Intestinal ora can usually involved in the development of tolerance to antigens (42).
provide the daily minimum requirement for many of the Herias et al. gave germ-free rats E. coli alone or a mixture
vitamins in humans. Microbes that are added to foods of E. coli, Lactobacillus acidophilus and a strain of an
(such as fermented diary products) may also increase the obligate anaerobe (Peptostreptococcus) and observed two
dietary levels of these vitamins (66). Vitamins B12, niacin, effects (74). The peptostreptococci reduced translocation
riboavin and thiamin are also made by intestinal ora, rates of E. coli and increased serum anti-E. coli antibodies.
but are not absorbed in the colon. The value of micro- It may be that peptostreptococci act as an immune system
bially supplemented foods is that the Vitamin B12 is primer to other bacterial antigens, thereby leading to a
ingested and it can be absorbed in the small intestine and decrease in translocation. Further evidence that normal
utilized. ora may act as an immune primer was found in a study
using BALB:c mice. Pulverer et al. found that normal ora
Attachment releases low molecular weight substances that interact with
Attachment to the intestinal mucosa is an important sur- MALT (mucosa associated lymphoid tissue) and these
vival trait for organisms in the intestinal tract. The pres- substances appear to be essential for an adequate immune
ence of intestinal ora has been shown to stimulate the response (43). Antibiotic decontamination in a mouse
production of epithelial glycoconjugates, which may be model resulted in a decreased immune response. Thus,
receptors for some pathogenic bacteria (22). Umesaki et al. normal ora may have an important role as an immune
documented that the presence of a strict anaerobe, B. system primer.
thetaiotaomicron and a segmented lamentous bacterium
were associated with fucosylated glycoconjugates in the Intestinal transit
small intestinal tract (80). Colonic mucins are a class of The presence of intestinal ora has been shown to stimu-
high molecular weight glycoproteins, which are secreted by late peristalsis or otherwise involve the enteric nervous
the mucosa and exocrine glands. Mucin is present in the system (44, 45, 78). In gnotobiotic mice models, the small
lumen and functions as a lubricant, a modulator of water intestine has thinner walls and is smaller than in mice with
and electrolyte absorption, may aid in attachment of mi- intestinal ora (78). Husebye et al. studied germ-free rats
crobes and protects the mucosa from injury (81). A large (who have enlarged caeca) and found a slower progress of
number of oligosaccharide side-chains of mucin glyco- chyme through the intestinal tract when compared to rats
proteins aids in the stability of the mucin layer. Carlstedt- with a normal microbiota (46). He found that the mecha-
Duke et al. found antibiotics including bacitracin, nism may be through the enteric nervous system, rather
clindamycin and vancomycin resulted in altered mucin than stimulating motility by a direct action on intestinal
degradation in healthy human volunteers (82). The effect smooth muscle. This may explain why colonic bacteria are
Normal ora description 199

Table III
Geographical differences in intestinal microora in humans

Microorganisms or groups of English:mixed Western Ugandan vegetaria n Americans: Japanese:vege- Japanese:mixed


microorganisms diet (London) diet (in London) mixed Western tarian diet Western diet
diet

Total anaerobes 10.1 9.3 10.2 9.9 11.5


Total aerobes 8.0 8.2 7.5 9.49.8 9.6
Facultative anaerobes 7.2 4.8
Enterococci 5.7 7.0 5.5 8.4 8.4
Bacteroides 9.7 8.2 9.8 10.1 11.1
Bidobacteria 9.9 9.3 10.0 8.2 9.5
Lactobacilli 6.0 7.2 7.3 5.7 4.0
Clostridia 4.45.0 4.04.6 4.4 5.19.7 9.5
Yeasts 1.3 3.1

Indicates a signicant difference between groups as reported in the original publication (Adapted from reference 3).

able to inuence transit through the small intestine in ora in the elderly, but whether this variation is due to age
gnotobiotic mice. Pothoulakis et al. found that one intesti- or medical exposures, or due to illnesses was unclear (87,
nal response to C. difcile involved events relating to the 88).
neural cascade (84). The role of normal ora on the enteric
nervous system requires further study and may have Geography
promise for therapeutic intervention by medications that There are numerous studies which report differences in
inhibit the neural response. normal ora depending upon geographical location. Benno
et al. compared the fecal ora in elderly Japanese living in
Colonic physiology and maturation rural areas or urban centers (89). On the whole, the diversity
It has been shown that the presence of intestinal ora and counts of fecal ora were similar. Urban Japanese were
stimulates the maturation and turnover rates in colonic found to have signicantly less Bidobacterium adolescentis,
epithelial cells. The surface layer of the mucosa in the but signicantly more total anaerobic bacteria, bacilli and
intestines is replaced every 2 3 days, which allows basal Clostridium spp. than rural Japanese. Benno et al. at-
stem cells to migrate up the crypt, presenting differentiated tributed these slight changes to a different diet (high ber)
mature cells that are involved in nutrient absorption and in the rural population, but did not support this hypothesis
mucin secretion. In germ-free mice (gnotobiotic), the rate of with data on dietary patterns. Sepp et al. also cultured
cell turnover was found to be signicantly slower than mice neonates at 1 week born in Estonia and Sweden (90).
with established microora (78, 80). Bry et al. also found Estonian neonates had signicantly higher counts of
that normal ora induced enterocyte cell turnover (85). staphylococci (coagulase negative), enterococci and enter-
obacteri compared to Swedish neonates. Different feeding
habits and differences in antibiotic use in these two coun-
FACTORS THAT INFLUENCE NORMAL FLORA
tries was proposed to explain these differences, but further
Age study is needed.
Early infancy (B 2 years old) is a time of ux in the As shown in Table III, the composition of normal ora
composition of the normal intestinal ora, as this is the time reported in geographical populations are not due to genetic
that the microecology is becoming established. The diet in differences as originally thought, but to differences in diet
pre-weaned babies is largely inuenced by the diet (breast (3). For example, when intestinal ora is compared for
or formula fed) as previously discussed. Mitsuoka et al. English people living in London and eating a mixed western
characterized the Lactobacillus ora in four age ranges: diet against Ugandans living in London and eating vegetar-
infants B 7 months, children 4 6 years, adults 20 64 years ian diets, the English had more bdobacteria and bac-
and elderly 65 86 years old (86). Infants were found to teroides but less enterococci, lactobacilli and yeasts than
usually be colonized by three types of resident lactobacilli, Ugandans. Vegetarian diets are associated with fewer
and in the older ages both number of different species and anaerobes and higher counts of facultative and aerobic
transient nature increased. Normal ora in older adults may microbes (3). Generally, one individual has a fairly constant
also differ from younger adults. Postmenopausal women prole of microbes that they can consider as normal ora
have been found to have increased numbers of fungi, unless the person is exposed to antibiotics or other factors
clostridia and lactobacilli compared to women who are that disrupt the ora, but inter-individual differences of
pre-menopausal (3). Other studies have shown variation of normal ora may vary considerably.
200 L. V. McFarland

The comparison of differences in normal ora for di- Stress


verse geographi c populations is complicated (and may be Stress is frequently cited as a major inuence on intestinal
completely obscured) by vast differences in diet, culturing
function, but the evidence for its impact on normal ora is
techniques, degree of sophisticated technology and differ-
limited. A frequently quoted reference to document the
ent study populations. What is needed are studies which
impact that daily stress has on normal ora may be
follow similar populations (same age range and sex), using
misleading (99). This study was done with postoperative
identical microbiologic techniques and thoroughly docu-
patients, so that the disruption of the normal ora may
menting dietary constituents, in order to compare differ-
have been due to antibiotics or medications associated
ences seen in normal ora of different countries.
with the surgery itself and not due to stress (99). Studies
Diet linking stress and the Irritable Bowel Syndrome (IBS)
often do not provide data on normal ora (100). Bochkov
Diet has been shown to change the ora in several animal
et al. studied the fecal ora of cosmonauts during training
studies, but there is little direct evidence from human
and space ight and concluded that stress affected the
studies other than studies with calcium, sugars or ber
ability of the normal ora to mount effective colonization
manipulation (40). Dietary calcium precipitates cytotoxic
resistance (101). Stress may decrease hydrochloric acid
substances such as bile acids resulting in less cytolysis. A
production in the stomach allowing for the growth of
decreased luminal cytotoxicity may help to reinforce en-
dogenous ora. Bouvee-Oudenhoven et al. found when coliforms and bacteroides (102). There is no direct evi-
calcium supplemented diets were given to rats Salmonella dence that stress causes a signicant shift in normal ora
enteritidis colonization was reduced as was translocation populations.
(91). Fructo-oligosaccharides (FOS), found in bananas,
onions, asparagus and artichokes, are fermented mostly by Antibiotics
Bidobacterium species. Increased ingestion of FOS at
The effect of antibiotics on intestinal ora has been well
doses of 4 g:d was found to increase levels of bidobacte-
studied, mainly because of the frequent occurrence of
ria in the intestines in human volunteers, but resulted in
disease associated with antibiotic use. Antibiotics are often
excessive atus at doses over 20 g:day (92, 93). Budding-
used to treat a specic illness without considering how the
ton et al. also studied dietary fructo-oligosaccharides in 12
antibiotic will impact the normal ora (11). A common use
healthy volunteers (39). FOS was found to increase num-
of antibiotics is to decontaminate the intestines in prepara-
bers of total anaerobes and bidobacteria in this small
tion for intestinal surgery. As it was observed that the
study. Sucrose was found to increase Bacteroides species
etiology of some post-surgical infections was of intestinal
and inulin was found to increase mostly bidobacteria
origin, it was thought that decontaminating the intestines
(92). Different types of ber have found to result in altered
with antibiotics might reduce the risk. However logical this
levels of bidobacteria, lactobacilli and fungi in rats and
tactic appeared it has not been productive, largely due to
pigs (94 96). Some types of fermentable bers may sup-
underestimating both the protective role of normal colonic
port the growth of normal ora, yielding SCFA and
decreased colonic pH, which can act to inhibit the growth ora and the profound disruptive impact of broad-spec-
of certain pathogens , such as C. difcile (95, 97). Tea trum antibiotics. Tetteroo et al. studied selective gut de-
polyphenols given to pigs resulted in increased levels of contamination and found patients experienced rebound
lactobacilli and decreased levels of bacteroides (98). colonization with potentially pathogenic organisms after
Evidence that diet inuences normal ora in adults is surgery (103). Of 135 patients studied, 20 patients had
sparse, but numerous studies have been done in young rebound colonization with a nosocomial aerobic pathogen.
infants. Previous studies have shown that breast-fed in- Lingnau et al. studied 357 patients with trauma who had
fants have been found to harbor mostly bidobacteria. In topical and gut decontamination using two mixtures of
contrast, formula-fed infants are colonized with a wider antibiotics and compared them to trauma patients who
variety of species, namely enterobacteria, bacteroides and were not given mixtures of antibiotics (104). Treatment
clostridia (40). A recent study by Heavey and Rowland with the antibiotics did reduce colonic bacteria, but had no
reported that high levels of bidobacteria were seen in impact on the incidence of expected post-surgical infec-
infants fed formula, but only for formulas that had a low tions (pneumonia, sepsis or organ failure). Unfortunately,
buffering capacity (34). Rubaltelli et al. studied the effect the identication of the inhibited microbes was not per-
of an adapted formula (high maltose) on the intestinal formed. A follow-up study showed that gut decontamina-
colonization of bidobacteria compared to breast-fed in- tion did result in higher rates of oxacillin-resistant
fants (33). Breast-fed babies were again found to have Staphylococcus aureus (105). Terg et al. studied four differ-
more bidobacteria (48%) than formula-fed (15%) infants, ent dose regimens for ciprooxacin in 29 patients with
even as early as the fourth day of life. Unfortunately, cirrhosis (106) but found no statistical differences by dose.
controlled studies that document how well-dened diets Most studies of antibiotics and their impact on ora
can change normal ora have not been done. have been directed at either the antibiotics potential to kill
Normal ora description 201

pathogenic bacteria (and not normal ora) or the inuence treatment with either three of these antibiotics resulted in
antibiotics have on the development of antibiotic resis- increased numbers of C. albicans in the feces. Unfortu-
tance. However, there are a few studies on the impact nately, he did not study other types of normal ora. Van
antibiotics have on normal ora. A summary of antibiotics de Leur et al. suggested that before giving neutropenic
by the impact on the normal ora is given in Table IV. patients ciprooxacin to decontaminate the colon and
Thijm et al. studied mice treated with ampicillin or epicillin reduce disease, the effect of low dose ciprooxacin should
or cephradine and observed the rates in which resistant be studied when the ora has been disturbed (by another
strains of E. coli colonized as the measure of colonization antibiotic) in healthy subjects (113). Therefore, he then
resistance (107). Both penicillins resulted in a loss of treated ve healthy volunteers with ciprooxacin for 20
colonization resistance to E. coli. Oral treatment with days and then ciprooxacin combined with clindamycin
cephradine did not inuence normal ora or effect colo- for 14 days. Fecal samples were analyzed for Gram-nega-
nization resistance. No direct measures on specic strains tive bacilli, enterococci, yeasts and antibiotic levels. Not
of normal ora were done. surprisingly, the addition of a second antibiotic was found
Most of the studies of normal ora and antibiotics have to dramatically increase the acquisition of Gram-negative
been done using healthy volunteers. Barza et al. studied 20 bacilli. When low-dose ciprooxacin was used alone, no
healthy subjects, of whom 16 were given 4 antibiotics increases in Gram-negative bacilli were noted. Edlund et
intravenously and 4 were given no antibiotics (108). Only al. studied 20 healthy human volunteers who received
those subjects exposed to antibiotics (7:16) were later cefuroxime axetil (500 mg:d for 1 week) and ten of those
found to be colonized with Gram-negative bacilli. Van who additionally received vancomycin (500 mg:d) for the
Nispen et al. studied trovaoxacin on the effect on normal following 7 days (114). Cefuroxime resulted in rapid de-
fecal ora in 19 healthy male subjects (109). In comparison crease of anaerobic Bidobacterium and Lactobacillus spe-
with the seven men who received placebo, the 12 who cies, but increased the numbers of three species of
received trovaloxacin had signicantly reduced rates of Enterococcus. Vancomycin resulted in a rapid decline of
enterobacteriaceae, but there were no differences in Gram- Enterococcus faecium, E. faecalis and E. durans, Bac-
positive cocci, anaerobes or yeast populations. Vollaard et teroides and Clostridium species and a signicant increase
al. studied the effect of amoxycillin, erythromycin and in vancomycin-resistant Enterococcus gallinarum and E.
roxithromycin on the colonization resistance in healthy casseliavus. Van der Auwera et al. also documented that
volunteers (110). Amoxycillin decreased colonization resis- 64% of human volunteers given vancomycin carried van-
tance (evidenced by increased numbers of enterobacteri- comycin-resistant enterococci as part of their intestinal
aceae and yeasts). Vollaard followed this study with ora (115).
another in 6 healthy volunteers when he dened impair- These studies show clearly that antibiotics may disrupt
ment of colonization resistance by signicant increase in normal intestinal ora and may predispose patients to
the numbers of fecal yeasts, Gram-negative bacteria or by disease from opportunistic pathogens. Recovery of the
increased colonization by a challenge strain (111). colonization resistance brought on by antibiotic exposure
Thomakos et al. studied the effect of cefamandole, ce- may take weeks to months. Hashimoto et al. exposed rats
furoxime and cefoxitin on Candida albicans colonization in to 6 days of broad-spectrum antibiotics and found that, by
28 surgical patients (112). Thomakos found that 10 days the seventh day, fecal anaerobic levels decreased, bile acids

Table IV
Inuence of antibiotics on normal ora from human volunteer studies

Antibiotic tested Daily dose Number of volunteers Effect Reference

Clindamycin 800 mg bid 10 anaerobes (136)


Erythromycin 500, 1000 mg, tid 12 anaerobes, (137)
aerobic GNB,
No effect on enterococci or GPB
Ciprooxacin 50, 100, 200 mg 10 No signicant effect by dose (138)
bid
Cefoxitin, cefoxitin or cefamandole na 28 in yeasts (112)
Ciprooxacin 20 mg 5 GNB (113)
Ciprooxacin (and clindamycin) (300mg) 5 Cipro resistant GNB
Trovaoxacin 200 mg bid 12 E. coli (109)

in surgical patients.
Abbreviations: GNBGram-negative bacilli, GPBGram-positive bacilli, nadata not available, bid twice a day, tid three times
a day.
202 L. V. McFarland

decreased and the cecum enlarged in size (116). After required, but these assays still cannot identify unknown
antibiotics were stopped, fecal microbes recovered to their species if there is no known biomarker. Corthier et al. also
initial counts within a week, but the restoration of bile used luciferase gene biosensors to detect Lactococcus lactis
acid and cholesterol metabolism did not return to baseline (124). Serotyping and plasma proles have been helpful to
until 3 weeks later. Unfortunately, no other measures of differentiate different strains of similar bacterial and fun-
colonization resistance were made. Larson and Borriello gal species. The most practical use for these techniques
found that the susceptibility to C. difcile in hamsters may be in the tracking of outbreaks. However, these
exposed to clindamycin was prolonged (74 days) compared techniques cannot quantitate levels of different microbes
to a relatively short period of susceptibility (2 days) if the nor provide any functional measurements.
hamsters were given ampicillin (117). Although many an-
tibiotics have their activity tested against pathogenic or- 16 S ribosomal RNA typing
ganisms or on selected populations of normal ora, few Cumulative databases allow placement of unknown species
studies have measured their impact directly on coloniza- using 16S ribosomal RNA ngerprint techniques (125).
tion resistance. This technique is applicable for both culturable and non-
culturable microbes and is becoming increasing popular as
TOOLS AND MODELS a research tool. Use of polymerase chain reaction tech-
Selective culture techniques nologies are increasing, but it is costly. Dore et al. used
16S rRNA targeted oligonucleotide probe to detect and
Routine biochemical assays can identify specic species quantify Bacteroides species in human fecal samples (126).
and these traditional methods are standard and well- Franks et al. used 16S rRNA-target oligonucleotide probes
known (118). However, the results will only quantitate to quantify predominant groups of anaerobic bacteria in
culturable bacteria and cannot identify unknown types of human fecal samples (23). These probes were able to detect
microbes nor test microbial interactions or protective func- at least two-thirds of the anaerobic fecal ora.
tions. Routine microbiological culturing will underestimate Several researchers report good agreement between 16S
both the number and diversity of ora and in addition, rDNA probe identication and culturing techniques (32,
frozen samples may result in less sensitive results (119). 127, 128). But other researchers have noted DNA probes
can detect more anaerobes than by culturing techniques
Continuous ow cultures
(30, 129). Several advantages of the newer probe tech-
In an attempt to control some of the interactive factors niques are that frozen stools may be used, and non-cul-
present in microecologies within various body sites, re- tivable species may be detected. Standard culturing has
liance upon continuous ow cultures has become estab- advantages of being inexpensive and widely available.
lished. Although the results may depend more on culture When 16S rDNA probes are used to characterize the
specications than the microbial interactions, this tech- species composition of a population, several sources of
nique is popular. Bernhardt et al. studied the growth of C. bias may arise. Bacterial strains may react differently to
albicans using a continuous ow culture (120). This the processing required by this technique. Bacteria will be
method exhibited a colonization resistance effect on C. detected more frequently if they are susceptible to lysing,
albicans. Macfarlane et al. used a three-stage compound amplication and permeability (129).
continuous culture system to study normal ora (121).
Stage 1 models for the proximal colon and Stages 2 and 3 Functioning analysis
model the distal colon. Metabolism, bacterial interactions The above probes all share the disadvantage of not guar-
and changes in the diet and environmental conditions may anteeing that the species identied by the probe may not
be studied using this system. Kontula et al. used SHIME be the microbe responsible for a specic microbial associ-
(simulator of human intestinal microbial ecosystem) to ated function. Also, as colonization resistance results from
study ora changes and observed changes in fatty acids the interactions of many microbes, the above probes do
and gas production and enterococci numbers (122). Con- not measure these interactions. Measuring the function of
tinuous ow cultures have the advantage of being able to the target organ as a whole corrects for this disadvantage.
tightly control various factors (nutrient concentration, Collinder et al. and others have suggested using MACs
types of species, etc.) but whether the results can be (Microora-Associated Characteristics) to study coloniza-
extrapolated to the intact intestinal microecosystem is tion resistance (36 38, 130). MACs include: degradation
uncertain. of mucin, conversion of cholesterol to coprostanol, biliru-
bin to urobilinogens (to study hepatic-intestinal interac-
Serotyping, plasmid proles, antibiotic resistance patterns tions), inactivation of tryptic activity (to study
Monoclonal antibodies have been used to enumerate Bac- pancreatic-intestinal interactions), degradation of b-as-
teriodes species present in human fecal ora samples (123). partylglycine (found in disturbed ora) and production of
These techniques do not require culturing, so less work is SCFA. Several types of indicators of functions can be
Normal ora description 203

measured, including bacterial enzymes and bacterial differ for the distal and proximal segments of the intestine.
metabolite levels. The metabolite levels include NH3 levels Marteau et al. overcame this difculty by sampling jejunal
(breakdown product of protein and urea), phenols and ora directly by using a lumen tube with a proximal
cresols (amino acid catabolism), and the breath hydrogen occluding balloon (135). This allows sampling of the ora
test (118, 131). at the desired location within the intestine. However, this
technique is invasive and not as simple as culturing feces,
Animal models but is well tolerated by subjects. The use of selective media
Gnotobiotic models have been used to test normal ora and polymerase chain reactions (PCR) probes of 16S
and disruptive factors (132, 133). Wilson et al. used gnoto- rDNA have enhanced the detection of fastidious organ-
biotic mice to test the ability of hamster ora for the isms and should provide valuable assistance to future
protection for C. difcile and E. coli (134). Segmented studies of normal ora.
lamentous bacteria restored diffuse GALT in gnotobiotic
animals (80). Bourlioux et al. used gnotobiotic animals to REFERENCES
study colonization resistance to C. perfringens linked to a
1. Gordon R. The alarming history of medicine. New York: St.
Ruminococcus species and colonization resistance to C.
Martins Press, 1993: 164.
difcile linked to mucin interactions (76). 2. Savage DC. Microbial ecology of the gastrointestinal tract.
Mouse models with normal ora are typically used by Annu Rev Microbiol 1977; 31: 107 33.
rst shocking the intestine with a dose of antibiotics, then 3. Salminen S, Isolauri E, Onnela T. Gut ora in normal and
testing with various microbial species. Sweeney et al. disordered states. Chemotherapy 1995; 41: 5 15.
4. Keane FE, Ison CA, Taylor-Robinson D. A longitudinal
shocked mice with streptomycin and then exposed them to
study of the vaginal ora over a menstrual cycle. Int J STD
a human fecal isolate of E. coli F18 (68). He found that E. AIDS 1997; 8: 489 94.
coli F18 occupies a distinct niche in the large intestine 5. Martin HL Jr, Richardson BA, Nyange PM, Lavreys L,
(dened by the presence of gluconate). Animal models Hillier SL, Chohan B, Mandaliya K, Ndinya-Achola JO,
have the advantage of studying ora in situ, but are less Bwayo J, Kreiss J. Vaginal lactobacilli, microbial ora, and
risk of human immunodeciency virus type 1 and sexually
easy to control, can be expensive and the results may not
transmitted disease acquisition. J Infect Dis 1999; 180:
be typical of the human microecosystem. 1863 8.
6. Marshall JC. Gastrointestinal ora and its alterations in
critical illness. Curr Opin Clin Nutr Metab Care 1999; 2:
CONCLUSIONS AND FUTURE CHALLENGES
405 11.
Normal ora is a dynamic ecosystem with a wide variety 7. Priestley CJ, Jones BM, Dhar J, Goodwin L. What is normal
of microbes and functions. These functions provide one of vaginal ora? Genitourin Med 1997; 73: 23 8.
8. Hooper LV, Bry L, Falk PG, Gordon JI. Host-microbial
the more powerful sentinels against infection by oppor-
symbiosis in the mammalian intestine: exploring an internal
tunistic pathogens and enable the body to function ef- ecosystem. BioEssays 1998; 20: 336 43.
ciently. The disruption of normal microecology by a wide 9. Hentges DJ. The anaerobic microora of the human body.
variety of factors may have dire consequences. Coloniza- Clin Infect Dis 1993; 16: S175 80.
tion by multiple bacterial species makes it difcult to 10. Hagiage M. La ora intestinale de lequilibre au desequili-
bre. Paris: Vigot, 1994: 25.
distinguish specic contributions by individual species to
11. Vollaard EJ, Clasener HAL, van Saene HKF, Muller NF.
symbiotic interactions. Most of the indigenous species are Effect on colonization resistance: an important criterion in
obligate anaerobes and are difcult to culture and identify selecting antibiotics. DICP 1990; 24: 60 6.
and quantitate. The development of more precise tools and 12. Reid G, Bruce AW, McGroarty JA, Cheng K-J, Costerton
models will aid our understanding of this complex JW. Is there a role for lactobacilli in prevention of urogenital
and intestinal infections? Clin Microbiol Rev 1990; 3: 335
bionetwork.
44.
The challenge with studies on normal ora is that it 13. Hillier SL. The role of naturally occurring and exogenously
exists as a complex and diverse system that may be supplied lactobacilli in the human vagina. Microbial Ecology
difcult to sample and impossible to identify every micro- in Health and Disease 1998; 10: 193.
bial species. Intestinal normal ora are composed of a 14. Listgarten MA. Structure of the microbial ora associated
with periodontal health and disease in man., A light and
mixture of identiable bacteria, fungi and viruses, but
electron microscopic study. J Periodontol 1976; 47: 1 18.
there are many non-cultivable organisms. For over twenty 15. Stjernquist-Desatnik A, Holst E. Tonsillar microbial ora:
years, it has also been acknowledged that microbiologic comparison of recurrent tonsillitis and normal tonsils. Acta
studies of ora from stool samples may not accurately Otolaryngol 1999; 119: 102 6.
reect the ora or metabolic state inside the intestinal tract 16. Gagliardi D, Makihara S, Corsi PR, Viana A, de T, Wiczer
MV, Nakakubo S, Mimica LM. Microbial ora of the
(2). Microbial ora in the feces represent only those mi-
normal esophagus. Dis Esophagus 1998; 11: 248 50.
crobes who are not attached to mucin or the mucosa and 17. Marushko IuV. The colonization resistance of the tonsils in
have survived intestinal digestion, transit and dehydration healthy and frequently ill children. Lik Sprava 1998; 1:
processes. Metabolic activity and species composition also 115 7.
204 L. V. McFarland

18. Ahrne S, Nobaek A, Jeppsson B, Adlerberth I, Wold AE, 34. Heavey PM, Rowland IR. The gut microora of the devel-
Molin G. The normal Lactobacillus ora of healthy human oping infant: microbiology and metabolism. Microbial Ecol-
rectal and oral mucosa. J Appl Microbiol 1998; 86: 88 94. ogy in Health and Disease 1999; 11: 75 83.
19. Smith VC, Genta RM. Role of Helicobacter pylori gastritis 35. Ducluzeau R. Development, balance and role of the micro-
in gastric atrophy, intestinal metaplasia, and gastric neo- bial ora of the newborn. Annales Pediatriques (Paris) 1993;
plasia. Microsc Res Tech 2000; 48: 313 20. 40: 13 22.
20. Quartero AO, Numans ME, de Melker RA, de Wit NJ. 36. Norin KE, Gustafsson BE, Lindblad BS, Midtvedt T. The
In-practice evaluation of whole-blood Helicobacter pylori establishment of some microora associated biochemical
test: its usefulness in detecting peptic ulcer disease. Br J Gen characteristics in feces from children during the rst years of
Pract 2000; 50: 13 6. life. Acta Paediatr Scand 1985; 74: 207 12.
21. Parente F, Cucino C, Bollani S, Imbesi V, Maconi G, 37. Midtvedt AC, Carlstedt-Duke B, Norin KE, Saxerholt H,
Bonetto S, Vago L, Porro GB. Focal gastric inammatory Midtvedt T. Development of ve metabolic activities associ-
inltrates in inammatory bowel diseases: prevalence, im- ated with the intestinal microora of health infants. J Pediatr
munohistochemical characteristics, and diagnostic role. Am Gastroenterol Nutr 1988; 7: 559 67.
J Gastroenterol 2000; 95: 705 11. 38. Gustafsson A, Berstad A, Lund-Tonnesen S, Midtvedt T,
22. Salminen S, Bouley C, Boutron-Ruault M-C, Cummings JH, Norin E. The effect of faecal enema on ve microora-asso-
Franck A, Gibson GR, Isolauri E, Moreau M-C, Roberfroid ciated characteristics in patients with antibiotic-associated
M, Rowland I. Functional food science and gastrointestinal diarrhoea. Scand J Gastroenterol 1999; 34: 580 6.
physiology and function. Br J Nutr 1998; 80: S147 71. 39. Buddington RK, Williams CH, Chen SC, Witherly SA.
23. Franks AH, Harmsen HJM, Raangs GC, Jansen GJ, Schut Dietary supplement of neosugar alters the fecal ora and
F, Welling GW. Variations of bacterial populations in hu- decreases activities of some reductive enzymes in human
man feces measured by uorescent in situ hybridization with subjects. Am J Clin Nutr 1996; 63: 709 16.
group-specic 16S rRNA-targeted oligonucleotide probes. 40. Rolfe RD. Colonization resistance. In: Mackie RI, White
Appl Environ Microbiol 1998; 64: 3336 45. BA, Isaacson RE, eds. Gastrointestinal microbiology, vol 2.
24. Schwebke JR, Richey CM, Weiss HL. Correlation of behav- New York: Chapman & Hall, Inc., 1997: 501 36.
41. Moreau MC, Bisetti N, Dubuquoy C. Immunomodulating
iors with microbiological changes in vaginal ora. J Infect
properties of a strain of Bidobacterium used as probiotic on
Dis 1999; 180: 1632 6.
the faecal and cellular intestinal IgA anti-rotavirus responses
25. Rosenstein IJ, Stafford MK, Kitchen VS, Ward H, Weber
in mice. In: Functional Foods Proceedings. Royal Society of
JN, Taylor-Robinson D. Effect on normal vaginal ora of
Chemistry, 1998.
three intravaginal microbicidal agents potentially active
42. Moreau M, Gaboriau-Routhiau V. The absence of gut ora,
against human immunodeciency virus type 1. J Infect Dis
the doses of antigen ingested and aging affect the long-term
1998; 177: 1386 90.
peripheral tolerance induced by ovalbumin feeding in mice.
26. Collins MD, Gibson GR. Probiotics, prebiotics and synbi-
Research Immunology 1996; 147: 49 59.
otics: approaches for modulating the microbial ecology of
43. Pulverer G, Ko HL, Beuth J. Microora-associated defense
the gut. Am J Clin Nutr ; : S 1999; 69: 1052S 7.
stimulating factors. Scand J Gastroenterol 1997; 32: 107 11.
27. Karvonen AV, Vesikari T, Casas IA. Lactobacillus and
44. Guandalini S. Enteric nervous system: intestinal absorption
Lactobacillus reuteri: mother-child vinculum at birth and
and secretion. J Pediatr Gastroenterol Nutr 1997; 25: S5 6.
during early age of infants. Microbial Ecology in Health and
45. Midtvedt T. Gastro-intestinal motility. In: Heidt PJ, Rusch
Disease. 1998; 10: 204.
V, Van der Waaij D, eds. Old Herborn University Seminar
28. Benno Y, Sawada K, Mitsuoka T. The intestinal microora Monograph, Vol 9. Herborn-Dill: Inst Microecology &
of infants: composition of fecal ora in breast-fed and Biochem, 1997: 1 7.
bottle-fed infants. Microbiol Immunol 1984; 28: 975 86. 46. Husebye E. The stimulatory inuence of the intestinal mi-
29. Bezirtzoglou E, Romond C. Effect of the feeding practices croora on gastro-intestinal motility and myoelectric activity
on the establishment of bacterial interactions in the intestine of small intestine. In: Heidt PJ, Rusch V, Van der Waaij D,
of the newborn delivered by cesarian section. J Perinat Med eds. Old Herborn University Seminar Monograph, Vol 9.
1989; 17: 139 43. Herborn-Dill: Inst Microecology & Biochem, 1997: 41 52.
30. Harmsen HJ, Gibson GR, Elfferich P, Raangs GC, Wilde- 47. Conway PL. Microbial ecology of the human large intestine.
boer-Veloo AC, Argaiz A, Roberfroid MB, Welling GW. In: Gibson GR, Macfarlane GT, eds. Human colonic bacte-
Comparison of viable cell counts and uorescence in situ ria: role in nutrition, physiology, and pathology. Boca Ra-
hybridization using specic rRNA-based probes for the ton, FL: CRC Press, 1995: 1 24.
quantication of human fecal bacteria. FEMS Microbiol 48. Buts J-P, Bernasconi P, Vaerman J-P, Dive C. Stimulation
Lett 2000; 183: 125 9. of secretory IgA and secretory component of immunoglobu-
31. McFarland LV, Surawicz CM, Greenberg RN, Bowen KE, lins in small intestine of rats treated with Saccharomyces
Melcher SA, Mulligan ME. Possible role of cross-transmis- boulardii. Dig Dis Sci 1990; 36: 251 6.
sion between neonates and mothers with recurrent Clostrid- 49. Buts J-P, de Keyser N, de Raedemaeker L. Saccharomyces
ium difcile infections. AJIC Am J Infect Control 1999; 27: boulardii enhances rat intestinal enzyme expression by endo-
301 3. luminal release of polyamines. Pediatr Res 1994; 36: 522 7.
32. Harmsen HJM, Wildeboer-Veloo ACM, Raangs GC, Wa- 50. Cummings JH. Short chain fatty acids. In: Gibson GR,
gendorp AA, Klijn N, Bindels JG, Welling GW. Analysis of Macfarlane GT, eds. Human colonic bacteria: role in nutri-
intestinal ora development in breast-fed and formula-fed tion, physiology, and pathology. Boca Raton, FL: CRC
infants by using molecular identication and detection meth- Press, 1995: 101 30.
ods. J Pediatr Gastroenterol Nutr 2000; 30: 61 7. 51. Clausen MR, Bonnen H, Tvede M, Mortensen PB. Colonic
33. Rubaltelli FF, Biadaioli R, Pecile P, Nicoletti P. Intestinal fermentation to short-chain fatty acids is decreased in antibi-
ora in breast- and bottle-fed infants. J Perinat Med 1998; otic-associated diarrhea. Gastroenterology 1991; 101: 1497
26: 186 91. 504.
Normal ora description 205

52. Treem WR, Ahsan N, Kastoff G, Hyams JS. Fecal short- 73. Leonard F, Andremont A, Leclerq B, Labia R, Tancrede C.
chain fatty acids in patients with diarrhea-predominant irri- Use of b-lactamase-producing anaerobes to prevent ceftriax-
table bowel syndrome: in vitro studies of carbohydrate one from degrading intestinal resistance to colonization. J
fermentation. J Pediatr Gastroenterol Nutr 1996; 23: 280 6. Infect Dis 1989; 160: 274 80.
53. Sidhu H, Holmes RP, Allison MJ, Peck AB. Direct quanti- 74. Herias MV, Midtvedt T, Hanson LA, Wold AE. Increased
cation of the enteric bacterium Oxalobacter formigenes in antibody production against gut-colonizing Escherichia coli
human fecal samples by quantitative competitive-template in the presence of the anaerobic bacterium Peptostreptococ-
PCR. J Clin Microbiol 1999; 37: 1503 9. cus. Scand J Immunol 1998; 48: 277 82.
54. Elkins CA, Savage DC. Identication of genes coding conju- 75. Boureau H, Decre D, Carlier JP, Guichet C, Bourlioux P.
gated bile salt hydrolase and transport in Lactobacillus john- Identication of a Clostridium cocleatum strain involved in
sonii 100-100. J Bacteriol 1998; 80: 4344 9. an anti-Clostridium difcile barrier effect and determination
55. Wilson KH. The microecology of Clostridium difcile. Clin of its mucin-degrading enzymes. Res Microbiol 1993; 144:
Infect Dis 1993; 16: S214 8. 405 10.
56. Apperloo-Renkema HZ, van der Waaij BD, van der Waaij 76. Bourlioux P. What is currently known about the molecular
D. Determination of colonization resistance of the digestive mechanisms of colonisation resistance. Anaerobe 1997; 3:
tract by biotyping of Enterobacteriaceae. Epidemiol Infect 179 84.
1990; 105: 355 61. 77. Wong WC, Hentges DJ, Dougherty SH. Adequacy of the
57. Hazenberg MP, Bakker M, Verschoor-Burggraaf A. Effects human faecal microbiota associated mouse as a model for
of the human intestinal ora on germ-free mice. J Appl studying the ecology of the human intestinal tract. Microbial
Bacteriol 1981; 50: 95 106. Ecology in Health and Disease 1996; 9: 187 98.
58. Nord CE, Kager L. The normal ora of the gastrointestinal 78. Rolfe RD. Interactions among microorganisms of the indige-
tract. Neth J Med 1984; 27: 249 52. nous intestinal ora and their inuence on the host. Rev
59. Freter R, Abrams GD. Function of various intestinal bacte- Infect Dis 1984; 6: S73 9.
ria in converting germfree mice to the normal state. Infect 79. Silverman H, Romano J, Elmer G. The vitamin book. New
Immun 1972; 6: 119 26. York: Bantam Books, 1999.
60. Romond MB, Haddou Z, Mielcareck C, Romond C. 80. Umesaki Y, Okada Y, Matsumoto S, Imaoka A, Setoyama
Bidobacteria and human health: regulatory effect of indige- H. Segmented lamentous bacteria are indigenous intestinal
bacteria that activate intraepithelial lymphocytes and induce
nous bidobacteria on Escherichia coli intestinal coloniza-
MHC class II molecules and fucosyl asialo GM1 glycolipids
tion. Anaerobe 1997; 3: 131 6.
on the small intestinal epithelial cells in the ex-germ-free
61. McFarland LV. Epidemiology, risk factors and treatments
mouse. Microbiol Immunol 1995; 39: 555 62.
for antibiotic-associated diarrhea. Dig Dis 1998; 16: 292
81. Kindon H, Pothoulakis C, Thim L, Lynch-Devaney K,
307.
Podolsky DK. Trefoil peptide protection of intestinal epithe-
62. Borriello SP. Pathogenesis of Clostridium difcile infection. J
lial barrier function: cooperative interaction with mucin
Antimicrob Chemother 1998; 41: 13 9.
glycoprotein. Gastroenterology 1995; 109: 516 23.
63. Guerrant RL, Steiner TS, Lima AAM, Bobak DA. How
82. Carlstedt-Duke B, Hoverstad T, Lingaas E, Norin KE,
intestinal bacteria cause disease. J Infect Dis 1999; 179:
Saxerholt H, Steinbakk M, Midtvedt T. Inuence of antibi-
S331 7.
otics on intestinal mucin in healthy subjects. Eur J Clin
64. Fekety R. Guidelines for the diagnosis and management of
Microbiol 1986; 5: 634 8.
Clostridium difcile-associated diarrhea and colitis. Am J
83. Hoskins LC, Agustines M, McKee WB, Boulding ET, Kri-
Gastroenterol 1997; 92: 739 50. aris M, Niedermeyer G. Mucin degradation in human colon
65. Boman HG. Gut microora. ASM News 2000; 66: 57. ecosystems. J Clin Invest 1985; 75: 944 53.
66. Naidu AS, Bidlack WR, Clemens RA. Probiotic spectra of 84. Pothoulakis C, Castagliuolo I, LaMont JT. Nerves and
lactic acid bacteria (LAB). Critical Reviews in Food Science intestinal mast cells modulate responses to enterotoxins.
and Nutrition 1999; 38: 13 126. News Physiol Sci 1998; 13: 58 63.
67. Wilson KH, Perini F. Role of competition for nutrients in 85. Bry L, Falk PG, Midvedt T, Gordon J. A model for
suppression of Clostridium difcile by the colonic microora. host-microbial interactions in an open mammalian ecosys-
Infect Immun 1988; 56: 2610 4. tem. Science 1996; 273: 1380 3.
68. Sweeney NJ, Klemm P, McCormick BA, MollerNielsen E, 86. Mitsuoka T, Hayakawa K, Kimura N. Die faekalora bei
Utley M, Schembri MA, Laux DC, Cohen PS. The Es - menschen. III. Mitteilung: die zusammensetzung der lakto-
cherichia coli K-12 gntP gene allows E. coli F-18 to occupy bazillenora der verschiedenen altersgruppen. Zentralbl Bak-
a distinct nutritional niche in the streptomycin-treated mouse teriol Orig A 1975; 232: 499 511.
large intestine. Infect Immun 1996; 64: 3497 503. 87. Valenti WM, Trudell RG, Bentley ND. Factors predisposing
69. Castagliuolo I, Riegler MF, Valenick L, LaMont JT, to oropharyngeal colonization with gram-negative bacilli in
Pothoulakis C. Saccharomyces boulardii protease inhibits the the aged. N Engl J Med 1978; 298: 1108 11.
effects of Clostridium difcile toxins A and B in human 88. McFarland LV, Surawicz CM, Stamm WE. Risk factors for
colonic mucosa. Infect Immun 1999; 67: 302 7. Clostridium difcile carriage and C. difcile -associated di-
70. Just I, Fritz G, Aktories K, Giry M, Popoff MR, Boquet P, arrhea in a cohort of hospitalized patients. J Infect Dis 1990;
Hegenbarth S, von Eichel-Streiber C. Clostridium difcile 162: 678 84.
toxin B acts on the GTP-binding protein Rho. Journal of 89. Benno Y, Endo K, Mizutani T, Namba Y, Komori T,
Biological Chemistry 1994; 269: 10706 12. Mitsuoka T. Comparison of fecal microblora of elderly
71. Fuller R. Probiotics 2. Applications and practical aspects. persons in rural and urban areas of Japan. Appl Environ
London: Chapman & Hall. 1997: 21. Microbiol 1989; 55: 1100 5.
72. Giuliano M, Barza M, Jacobus NV, Gorbach SL. Effects of 90. Sepp E, Loivukene K, Koljalg S, Naaber P, Mikelsaar M,
broad-spectrum parenteral antibiotics on composition of Bjorksten B. Comparison of intestinal microora of Esto-
intestinal microora of humans. Antimicrob Agents nian and Swedish neonates. Microbial Ecology in Health
Chemother 1987; 31: 202 6. and Disease 1998; 10: 203.
206 L. V. McFarland

91. Bouvee-Oudenhoven IM, Termont DS, Weerkamp AH, 109. Van Nispen CHM, Hoepelman AIM, Rozenberg-Arska M,
Faassen-Peters MA, Van der Meer R. Dietary calcium in- Verhoef J, Purkins L, Willavize SA. A double-blind,
hibits the intestinal colonization and translocation of placebo-controlled, parallel group study of oral
Salmonella in rats. Gastroenterology 1997; 113: 550 7. trovaoxacin on bowel microora in healthy male volun-
92. Gibson GR. Dietary modulation of the human gut mi- teers. Am J Surg ; : S 1998; 176: 27S 31.
croora using prebiotics. Br J Nutr 1998; 80: S209 12. 110. Vollaard EJ, Clasener HA, van Griethuysen AJ, Janssen AJ,
93. Bouhnik Y, Vahedi K, Achour L, Attar A, Salfati J, Pochart Sanders-Reijmers AJ. Inuence of amoxycillin, erythromycin
P, Marteau P, Flourie B, Bornet F, Rambaud J-C. Short- and roxithromycin on colonization resistance and on appear-
chain fructo-oligosaccharide administration dose-depen- ance of secondary colonization in healthy volunteers. J An-
dently increases fecal bidobacteria in healthy humans. J timicrob Chemother 1987; 20: 131 8.
Nutr 1999; 129: 113 6. 111. Vollaard EJ, Clasener HA, Janssen AJ. Co-trimoxazole im-
94. Kuda T, Goto H, Yokoyama M, Fujii T. Fermentable pairs colonization resistance in healthy volunteers. J Antimi-
dietary ber in dried products of brown algae and their crob Chemother 1992; 30: 685 91.
effects on cecal microora and levels of plasma lipid in rats.
112. Thomakos N, Maraki S, Liakakos T, Macheras A,
Fisheries Science 1998; 64: 582 8.
Kanavaki S, Marinis E, Sehas M, Margioris AN, Samonis
95. May T, Mackie RI, Fahey GC Jr, Cremin JC, Garleb KA.
G. Effect of cefamandole, cefuroxime and cefoxitin on yeast
Effect of ber source on short-chain fatty acid production
fecal ora of surgical patients. Chemotherapy 1998; 44:
and on the growth and toxin production by Clostridium
324 7.
difcile. Scand J Gastroenterol 1994; 29: 916 22.
113. Van de Leur JJJPM, Vollaard EJ, Janssen AJHM, Doffer-
96. Elmer GW, Martin SW, Horner KL, McFarland LV, Levy
RH. Survival of Saccharomyces boulardii in the rat gas- hoff ASM. Inuence of low dose ciprooxacin on microbial
trointestinal tract and effects of dietary ber. Microbial colonization of the digestive tract on healthy volunteers
Ecology in Health and Disease 1999; 11: 29 34. during normal and during impaired colonization resistance.
97. Ward PB, Young GP. Dynamics of Clostridium difcile Scand J Infect Dis 1997; 29: 297 300.
infection. Control using diet. Adv Exp Med Biol 1997; 412: 114. Edlund C, Barkholt L, Olsson-Liljequist B, Nord CE. Effect
63 75. of vancomycin on intestinal ora of patients who previously
98. Hara H, Orita N, Hatano S, Ichikawa H, Hara Y, Mat- received antimicrobial therapy. Clin Infect Dis 1997; 25:
sumoto N, Kimura Y, Terada A, Mitsuoka T. Effect of tea 729 32.
polyphenols on fecal ora and fecal metabolic products of 115. Van der Auwera P, Pensart N, Korten V, Murray BE,
pigs. J Vet Med Sci 1995; 57: 45 9. Leclercq R. Inuence of oral glycopeptides on the fecal ora
99. Dal Nogare AR, Toews GB, Pierce AK. Increased salivary of human volunteers: selection of highly glycopeptide-resis-
elastase precedes gram-negative bacillary colonization in tant enterococci. J Infect Dis 1996; 173: 1129 36.
postoperative patients. Am Rev Respir Dis 1987; 135: 671 116. Hashimoto S, Igimi H, Uchida K, Satoh T, Benno Y,
5. Takeuchi N. Effects of beta-lactam antibiotics on intestinal
100. Drossman DA, McKee DC, Sandler RS, Mitchell CM, microora and bile acid metabolism in rats. Lipids 1996; 31:
Cramer EM, Lowman BC, Burger AL. Psychosocial factors 601 9.
in the irritable bowel syndrome. A multivariate study of 117. Larson HE, Borriello SP. Quantitative study of antibiotic-in-
patients and nonpatients with irritable bowel syndrome. duced susceptibility to Clostridium difcile enterocecitis in
Gastroenterology 1988; 95: 701 8. hamsters. Antimicrob Agents Chemother 1990; 34: 1348 53.
101. Bochkov IA, Lizko NN, Semina NA, Borunov NL, Lurko 118. Papasouliotis K, Sparkes AH, Gruffydd-Jones TJ, Cripps
LP. Peculiarities of cosmonauts fecal ora. Aviakosm PJ, Harper EJ. Use of the breath hydrogen test to assess the
Ekolog Med 1998; 32: 25 8. effect of age on orocecal transit time and carbohydrate
102. Lidbeck A, Nord CE. Lactobacilli and the normal human assimilation in cats. Am J Vet Res 1998; 59: 1299 302.
anaerobic microora. Clin Infect Dis 1993; 16: S181 7. 119. Bonten MJM, Nathan C, Weinsein RA. Recovery of noso-
103. Tetteroo GW, Wagenvoort JH, Bruining HA. Bacteriology comial fecal ora from frozen stool specimens and rectal
of selective decontamination: efcacy and rebound coloniza- swabs. Comparison of preservatives for epidemiological
tion. J Antimicrob Chemother 1994; 34: 139 48.
studies. Diagn Microbiol Infect Dis 1997; 27: 103 6.
104. Lingnau W, Berger J, Javorsky F, Lejeune P, Mutz N,
120. Bernhardt H, Wellmer A, Zimmermann K, Knoke M.
Benzer H. Selective intestinal decontamination in multiple
Growth of Candida albicans in normal and altered faecal
trauma patients: prospective, controlled trial. J Trauma
ora in the model of continuous ow culture. Mycoses 1995;
1997; 42: 687 94.
38: 265 70.
105. Lingnau W, Berger J, Javorsky F, Fille M, Allerberger F,
121. Macfarlane GT, Macfarlane S, Gibson GR. Validation of a
Benzer H. Changing bacterial ecology during a ve year
three-stage compound continuous culture system for investi-
period of selective intestinal decontamination. J Hosp Infect
1998; 39: 195 206. gating the effect of retention time on the ecology and
106. Terg R, Llano K, Cobas SM, Brotto C, Barrios A, Levi D, metabolism of bacteria in the human colon. Microb Ecol
Wasen W, Bartellini MA. Effects of oral ciprooxacin on 1998; 35: 180 7.
aerobic gram-negative fecal ora in patients with cirrhosis: 122. Kontula P, Jaskari J, Nollet L, De Smet I, von Wright A,
results of short- and long-term administration, with daily Poutanen K, Mattila-Sandholm T. The colonization of a
and weekly dosages. J Hepatol 1998; 29: 437 42. simulator of the human intestinal microbial ecosystem by a
107. Thijm HA, van der Waaij D. The effect of three frequently probiotic strain fed on a fermented oat bran product: effects
applied antibiotics on the colonization resistance of the on the gastrointestinal microbiota. Appl Microbiol Biotech-
digestive tract of mice. J Hyg (Lond) 1979; 82: 397 405. nol 1998; 50: 246 52.
108. Barza M, Giuliano M, Jacobus NV, Gorbach SL. Effect of 123. Corthier G, Muller MC, LHaridon R. Selective enumera-
broad-spectrum parenteral antibiotics on colonization resis- tion of Bacteroides vulgatus and B. distasonis organisms in
tance of intestinal microora of humans. Antimicrob Agents the predominant human fecal ora by using monoclonal
Chemother 1987; 31: 723 7. antibodies. Appl Environ Microbiol 1996; 62: 735 8.
Normal ora description 207

124. Corthier G, Delorme C, Ehrlich SD, Renault P. Use of 131. Goldin BR, Gorbach SL. The effect of milk and lactobacil-
luciferase genes as biosensors to study bacterial physiology lus feeding on human intestinal bacterial enzyme activity.
in the digestive tract. Appl Environ Microbiol 1998; 64: Am J Clin Nutr 1984; 39: 756 61.
2721 2. 132. Onderdonk AB, Cisneros RL, Bartlett JG. Clostridium dif -
125. Bergeron MG, Ouellette M. Preventing antibiotic resistance cile in gnotobiotic mice. Infect Immun 1980; 28: 277 82.
through rapid genotypic identication of bacteria and of 133. Umesaki Y, Sakata T, Yajima T. Abrupt induction of
their antibiotic resistance genes in the clinical microbiology GDP-fucose:asialo GM1 fucosyltransferase in the small in-
laboratory. J Clin Microbiol 1998; 36: 2169 72. testine after conventionalization of germ-free mice. Biochem
126. Dore J, Sghir A, HannequartGramet G, Corthier G, Pochart Biophys Res Commun 1982; 105: 439 43.
P. Design and evaluation of a 16S rRNA-targeted oligonu- 134. Wilson KH, Sheagren JN, Freter R, Weatherbee L, Lyerly
cleotide probe for specic detection and quantitation of D. Gnotobiotic models for study of the microbial ecology of
Clostridium difcile and Escherichia coli. J Infect Dis 1986;
human faecal Bacteroides populations. Systematic and Ap-
153: 547 51.
plied Microbiology 1998; 21: 65 71.
135. Marteau P, Vaerman J-P, Dehennin J-P, Bord S, Brassart D,
127. Langendijk PS, Schut F, Jansen GJ, Raangs GC, Kamphuis
Pochart P, Desjeux J-F, Rambaud J-C. Effects of intrajeju-
GR, Wilkinson MHF, Welling GW. Quantitative uores-
nal perfusion and chronic ingestion of Lactobacillus johnsonii
cence in situ hybridization of Bidobacterium spp. with
strain La1 on serum concentrations and jejunal secretions of
genus-specic 16S rRNA-targeted probes and its application
immunoglobulins and serum proteins in healthy humans.
in fecal samples. Appl Environ Microbiol 1995; 61: 3069 75. Gastroenterol Clin Biol 1997; 21: 293 8.
128. Wilson KH, Blitchington RB. Human colonic biota studied 136. Heimdahl A, Nord CE. Effect of phenoxymethylpenicillin
by ribosomal DNA sequence analysis. Appl Environ Micro- and clindamycin on the oral, throat and faecal microora of
biol 1996; 62: 2273 778. man. Scand J Infect Dis 1979; 11: 233 42.
129. Welling GW, Elfferich P, Raangs GC, Wildeboer-Veloo AC, 137. Kaukoranta-Tolvanen S-S, Renkonen O-V, Gordin A,
Jansen GJ, Degener JE. 16S ribosomal RNA-targeted Tamm L, Mannisto PT. Effect of erythromycin acistrate and
oligonucleotide probes for monitoring of intestinal tract erythromycin stearate on human colonic microora. Scand J
bacteria. Scand J Gastroenterol Suppl 1997; 222: 17 9. Infect Dis 1989; 21: 717 20.
130. Collinder E, Lindholm A, Midtvedt T, Norin E. The useful- 138. Meijer-Severs GJ, van Santen E, de Vries-Hospers HG.
ness of microbial-associated characteristics (MACs) for stud- Low-dose ciprooxacin for selective decontamination of the
ies of microbial intestinal functions in different species. digestive tract in human volunteers. Eur J Clin Microbiol
Microbial Ecology in Health and Disease 1998; 10: 203 4. Infect Dis 1990; 9: 285 7.