nature publishing group

REVIEWS FROM THE ACG ANNUAL MEETING

177

American Journal of Gastroenterology Lecture: Intestinal

Microbiota and the Role of Fecal Microbiota Transplant
(FMT) in Treatment of C. difficile Infection
Lawrence J. Brandt, MD, MACG1

The vital roles that intestinal flora, now called microbiota, have in maintaining our health are being increasingly
appreciated. Starting with birth, exposure to the outside world begins the life-long intimate association our microbiota
will have with our diet and environment, and initiates determination of the post-natal structural and functional
maturation of the gut. Moreover, vital interactions of the microbiota with our metabolic activities, as well as with the
immunological apparatus that constitutes our major defense system against foreign antigens continues throughout
life. A perturbed intestinal microbiome has been associated with an increasing number of gastrointestinal and
non-gastrointestinal diseases including Clostridium difficile infection (CDI). It has become recognized that fecal
microbiota transplantation (FMT) can correct the dysbiosis that characterizes chronic CDI, and effect a seemingly
safe, relatively inexpensive, and rapidly effective cure in the vast majority of patients so treated. In addition, FMT has
been used to treat an array of other gastrointestinal and non-gastrointestinal disorders, although experience in these
other non-CDI diseases is in its infancy. More work needs to be done with FMT to ensure its safety and optimal route
of administration. There is a conceptual sea change that is developing in our view of bacteria from their role only as
pathogens to that of being critical to health maintenance in a changing world. Future studies are certain to narrow the
spectrum of organisms that need to be given to patients to cure disease. FMT is but the first step in this journey.
Am J Gastroenterol 2013; 108:177185; doi:10.1038/ajg.2012.450; published online 15 January 2013

INTRODUCTION
Although the concept that our intestinal microbiota has an
important role in maintaining our health is relatively new, the
subject of fecal transplantation has been around for millennia.
Its first mention in the literature was during the 4th century,
when Ge Hong described the use of human fecal suspension by
mouth for food poisoning or severe diarrhea (1). In the 16th
century, Li Shizhen detailed a variety of fecal preparations called
yellow soup to be given for diarrhea, abdominal pain, vomiting, and constipation (1). I will discuss the modern history
of fecal transplantation later, but we can be sure that future
history will reveal high-quality scientific studies into the nature,
awesome complexity, and therapeutic powers of our intestinal
microbiome.
The intestinal microbiota

We are witness to a paradigm shift in the way the microbial flora

that dwell within our inner recesses are viewed. No longer is it
simply that the host is good and the bacteria that live therein
bad, but the vital roles our intestinal flora, now called microbiota, have in maintaining health are being increasingly appreciated. Results of the Human Microbiome Project launched

by the National Institutes of Health in 2007 along with related

ventures such as the MetaHit (Metagenomics of the Human
Intestinal tract) consortium, which involves 13 research centers
from 8 countries, are now beginning to be published and will
revolutionize knowledge of our microbes and our bodies (2).
For example, although we knew the human body is inhabited by a vast number of microorganisms including bacteria,
archea (single-celled prokaryotic microorganisms separately
classified from bacteria), viruses, fungi, and even parasites, all
of which normally live in peaceful coexistence with us, their
hosts, we soon learned that only 520% of the intestinal microbiota can be cultured and that culture can reliably distinguish
among bacterial phylogenetic groups, but not down to speciesor strain-level (2,3). New approaches to study our microbiota
were developed using culture-independent techniques including bacterial 16S ribosomal RNA gene sequencing and DNA
fingerprinting methods, such as terminal restriction fragment
length polymorphisms. A new vocabulary was even developed
to help detail the meta family techniques used to evaluate
the microbiomic functional capacity including metagenomics
(study of genes collected and sequenced from the environment),
metabolomics (study of metabolites that are end-products of

1
Montefiore Medical Center, Bronx, New York, USA. Correspondence: Lawrence J. Brandt, MD, MACG, Montefiore Medical Center, 111 East 210th Street, Bronx,
New York 10467, USA. E-mail: lbrandt@montefiore.org
Received 29 August 2012; accepted 6 December 2012

2013 by the American College of Gastroenterology

The American Journal of GASTROENTEROLOGY

REVIEW

see related editorial on page x

REVIEW

178

Brandt

cellular processes), metaproteomics (study of all proteins in an

environment), and metatranscriptomics (study of all RNA molecules produced in a population of cells). Microbial communities differed remarkably at each of the 15 (male) to 18 (female)
Human Microbiome Project-sampled body sites (nasal passages, oropharynx, skin, stool, and vagina) and the diversity of
each habitats signature microbes varied widely among healthy
individuals, with further variation not just dependent upon
ethnicity and host genetics, but also on ones diet and environment (2). Stool, representing the distal bowel, showed relatively
high intra- and inter-subject diversity. The majority of our
microbiota is anaerobic, and although more than 50 bacterial
phyla have been described, only four constitute the majority of
mammalian intestinal microbiota (Bacteroidetes, Firmicutes,
Actinobacteria, and Proteobacteria) and only two predominate
in our intestinal tract: the Bacteroidetes and the Firmicutes;
most of the Firmicutes phyla are members of the Clostridia class
(4). It is estimated that about 4,000 bacterial species reside in
our gastrointestinal tract, and that the human microbiota contains as many as 1014 bacterial cells, a number that is 10 times
greater than the number of human cells in our body (5). Per
gram of contents, there is a marked and progressive distal
increase in the number of bacteria: 101 in the stomach, 103 in
the duodenum, 104 in the jejunum, 107 in the ileum, and 1012
in the colon. This longitudinal heterogeneity of the microbiota
population has a predominance of Firmicutes and Proteobacteria (notably Helicobacter pylori in the stomach), Firmicutes
and Actinobacteria in the small intestine and a prevalence of
Bacteroidetes and the Lachnospirae family of Firmicutes in the
colon; of note, bacteria account for 60% of the dry weight of
feces. The microbiota within the intestinal lumen differs significantly from that dwelling in close proximity to or within
the intestinal epithelium (6). Therefore, fecal micro-organisms
cannot be used as a surrogate for all communities of the bowel
microflora. Moreover, luminal microbial communities and
surface adherent/associated populations are distinct and fulfill
different roles, only some of which I will mention briefly.
Our intestine becomes colonized with micro-organisms during
or shortly after birth and the intestinal microbiota of infants delivered by cesarean section differs from that of vaginally-delivered
infants (7,8). The gastrointestinal tract of the newborn is still sterile
after caesarian section and its microbiota is initiated with feeding;
in breast-fed infants Bifidobacteria predominate with minor representation from lactobacilli and streptococci, whereas in formulafed infants, similar amounts of Bacteroides and Bifidobacteria are
found with minor representation from Staphylococci, Escherichia
coli, and Clostridia (8). The first colonization of the intestine is a
profound immunological exposure and early maternal inoculation, as occurs with vaginal delivery, likely has an important role in
subsequent immune reactions and our susceptibility or resistance
to certain diseases. Indeed, this initial exposure heralds the continuing intimate roles our microbiota will have with our diet and
environment, and initiates the vital interactions of the microbiota
with our metabolic activities, as well as with the immunological
apparatus that constitutes our major defense system against forThe American Journal of GASTROENTEROLOGY

eign antigens. (Figures 1 and 2). We know that reduced microbial

stimulation during infancy results in slowed postnatal maturation
of the immune system and delayed development of an optimal
balance between TH1 and TH2-like immunity (9). During the first
year of life, the total number of IgA-, IgG- and IgM-secreting cells
is lower in infants born by vaginal delivery than in those born by
cesarean section, possibly reflecting excessive antigen exposure
across the vulnerable intestine (7).
The numbers and types of our intestinal microbiota increase
over the first year of life to assume a relatively stable adult pattern
at the phylum level, but continue to evolve at the species level with
subsequent dietary and environmental exposures, including antimicrobial therapies (3). In one study, diet inventories of 98 individuals were correlated with participants fecal enterotypes to show
that the Bacteroides enterotype was highly associated with animal
protein, a variety of amino acids, and saturated fats (western diet),
whereas the Prevotella enterotype was associated with low values
for these groups but high values for carbohydrates and simple sugars (agrarian diet). Moreover, microbiome composition changed
within 24 h of dietary alteration (10).
Intestinal microbiota has important roles in the post-natal structural and functional maturation of the gut. Germ-free animals
have, for example, enlarged ceca; increased enterochromaffin cell
area; a reduced intestinal surface area with narrower villi resulting
from reduced cell regeneration and prolonged cell cycle time, and
a smaller villous capillary network; hypotonic and hyporesponsive
mesenteric vasculature; impaired lymphoid organs; impaired peristalsis; and abnormal cholesterol and bile acid metabolism (3). It
has been shown, for example, that Bacteroides thetaiotaomicron
can induce angiogenesis (11); influence enteric nerve function,
and, therefore, possibly peristalsis (12); and also modulate intestinal glycocalyx structure (13). Various microbiota, including
B.thetaiotaomicron and Lactobacilli, are also involved in maintaining intestinal barrier integrity through maintenance of cell-to-cell
junctions and promotion of epithelial repair after injury (1).
The areas in which microbiota have a major influence are legion,
growing, and far beyond the scope of this general overview. One
such area is mucosal immunity with influence on immunocytes,
gut-associated lymphoid tissue, Peyers patches, IgA-producing
plasma cells, immunoglobulin secretion, and pattern recognition
receptors including toll-like and NOD-like receptors. As a specific
example, the deficiency of CD4 + T-cells in germ-free mice can
be completely reversed by mono-contamination with Bacteroides
fragilis or administration of its polysaccharide capsular antigen (14).
The gastrointestinal tract needs to coexist with the dense carpet of bacteria that overlies its mucosa without inducing excessive immune reaction, and the intestinal microbiota mediates
such antigenic tolerance. As examples, intestinal dendritic cells
are conditioned to a tolerogenic phenotype by intestinal epithelial cells that are stimulated by Lactobacillus spp and certain E.
coli strains (15); B. thetaiotaomicron prevents activation of the
proinflammatory transcription factor NFk (16); and Aeromonas
or Pseudomonas promote intestinal alkaline phosphatase, which
dephosphorylates and inactivates the lipopolysaccharide found
in the outer membrane of Gram-negative bacteria thus protecting
VOLUME 108 | FEBRUARY 2013 www.amjgastro.com

Intestinal Microbiota and Fecal Microbiota Transplant for C. difficile

179

Vitamin A

REVIEW

6 SFB
2 Microbiota

1 Diet
3 Unmodified
dietary
components

5 Dietary
components
modified by
microbiota
(acetate)

4 Microbial
signals
(MAMPs)

?
GPR43

Other
metabolite
sensors?

Inflammasome
ASC
ProIL-1
IL-1

TLRs
MyD88
NF-B

Metabolic signals

Immunologically
active nutrients
and metabolites?

Classical innate signals

Antigen-presenting cell
T cell

T cell

Antigen-presenting cell

mTOR
Promotes TH1, TH2, TH17 cell
differentiation; inhibits Treg cell
differentiation

TLRs
Inflammasomes

RAR-RXR
Promotes intestinal T-cell homing;
promotes TH2 and Treg cell
differentiation
VDR-RXR
Promotes Treg cell differentiation;
inhibits TH1 and TH17 cell
differentiation
AHR
Promotes TH17 and Treg cell
differentiation

mTOR
Modulates DC function and
differentiation
RAR-RXR and VDR-RXR
AHR
Modulates DC differentiation
PKR
Regulates inflammatory
responses
GPR120
Inhibits inflammatory responses
in macrophages

LXR and PPAR

Control T-cell differentination
Figure 1. Inter-relationships of nutrients, immune responses and the microbiome. Ingested nutrients (1) influence our microbiota (2) which, in turn,
changes the nutritional value of the consumed food. (3) Absorbed dietary components interact with a variety of immune cells (e.g., omega 3-fatty acids).
(4) Microbial signals in the form of Microbe Associated Molecular Patterns (MAMPs) also modify local mucosal immune responses through innate
signaling pathways, e.g., the inflammasome or Toll-like receptors (TLRs). (5) Additionally, microbe-modified dietary components (e.g., acetate produced
from fermentation of polysaccharides) provide signals by which the immune system can monitor the metabolic activities of the microbiota. (6) An example
of micronutrients directly modifying intestinal microbial ecology is vitamin A, which can modify the representation of segmented filamentous bacterium
(SFB) in the mouse gut microbiota; SFB induce differentiation of Th17 cells. From Kau et al. (54).

against septic shock (17). Our commensal bacteria, their structural

components and their metabolic products can induce expression and
activation of antimicrobial proteins to protect against pathogens and
to prevent overgrowth of the commensals themselves (3). For example,
B. thetaiotaomicron colonization of germ-free mice induces
Paneth cells to express matrilysin, a matrix metalloproteinase that acti 2013 by the American College of Gastroenterology

vates defensins. Even the mere presence of microbiota in the gastrointestinal tract, especially Gram-positive anaerobes, serves as a deterrent
to pathogen colonization; as an example, Lactobacilli and Bifidobacteria prevent Listeria infection of cultured epithelial cells (18).
As mentioned above, our intestinal microbiota is related to
the type of food we eat, but it also is very much involved with
The American Journal of GASTROENTEROLOGY

180

Brandt

REVIEW

Bifidobacterium spp.
Clostridium spp.

Bacteroidetes
B. fragilis (PSA)

Gm-PG
Gm-LPS

SCFA
metabolism

Conjugation of
linoleic acid

Cellular immunity
Lymphoid organogenesis
Mucosal immunity

IgA

Nutrition

Xenobiotics metabolism
Drug disposition

Lipid
metabolism

Behavior

SCFAs

AMPs

Immunocompetence
Tolerance

Lap
activation

DC tolerization

Lactobacillus spp.

E. coli

NFKB
inactivation

Normalization of
HPA stress response

B. thetaiotaomicron

B. infantis

Peristalsis
Glycosylation

Barrier
maintenance

Oxalate
excretion

O. fomigenes

Angiogenesis

GIT surface maturation

GIT functional maturation

Figure 2. Some examples of the effects of intestinal microbiota and host physiology. The intestinal microbiota can affect many aspects of normal host
development and function. Members of the microbiota, with their various components or products of metabolism are shown in red. Microbial effects
on the host are shown in green. Affected host phenotypes are shown in blue. AMP, antimicrobial peptides; DC, dendritic cells; Gm, Gram negative;
HPA, hypothalamus-pituitary adrenal; Iap, intestinal alkaline phosphatase; PG, peptidoglycan; PSA, polysaccharide. From Sekirov et al. (3).

appetite regulation, energy utilization, digestion and absorption

of ingested nutrients, and drug metabolism. Bacterial metabolism of dietary fiber to short chain fatty acids, and conversion of
indigestible polysaccharides to absorbable monosaccharides are
well known examples of such interaction. B. thetaiotaomicron, as
another example, has been shown to upregulate expression of pancreatic co-lipase and an intestinal Na + /glucose co-transporter (12).
Awareness of the interplay between these complex metabolic functions and the intestinal microbiome sets the stage to study whether
manipulation of the microbiome can be used to understand and
treat conditions of obesity and underweight (19). Inter-individual
and inter-population differences in intestinal microbiomes with
their attendant varied metabolic profiles may explain the different toxicities of commonly used therapeutics in varied geographic/
cultural populations and set the stage for the development of
personalized medicine-based on ones intestinal microbiome
profile (20).
Clostridium difficile infection and fecal microbiota
transplantation (FMT): introduction

A perturbed intestinal microbiome has been associated with an

increasing number of gastrointestinal and non-gastrointestinal
diseases which brings us to C. difficile infection (CDI) and fecal
The American Journal of GASTROENTEROLOGY

microbiota transplantation (FMT). Fecal microbiota transplant is

the term used when stool is taken from a healthy individual and
instilled into a sick person to cure a certain disease. As the exact
agent or agents that effect cure is currently unknown, the term
fecal microbiota transplant (FMT) presently is preferred to fecal
bacterial transplantation, or fecal bacteriotherapy; stool transplant is an accurate but unaesthetic term (21).
Ive already reviewed the very early history of FMT, but FMT
also has been used for centuries in veterinary medicine per rectum
to treat horses with diarrhea or per os as rumen transfaunation to
treat a variety of illness in cattle. Its first clinical use in the English
language dates back to a 1958 case series of four patients with
pseudomembranous enterocolitis, three of whom were critically
ill. C. difficile had not yet been recognized as a cause of pseudomembranous colitis and Micrococcus pyogenes (hemolytic,
coagulase-positive Staphylococcus aureus) was cultured from each
patients stool. Fecal enemas were administered as an adjunct to
antibiotic treatment and all four patients had dramatic resolution of symptoms within 2448 h of FMT (22); the first use
of FMT for confirmed recurrent CDI was reported in 1983 by
Schwan et al. (23), in a 65-year-old woman who thereafter had
prompt and complete normalization of bowel function. Up until
1989, retention enemas had been the most common technique
VOLUME 108 | FEBRUARY 2013 www.amjgastro.com

for FMT, however, alternative methods of fecal infusion subsequently were developed including nasogastric duodenal tube in
1991 (24), colonoscopy in 2000 (25), and self-administered enemas in 2010 (26). In 2011, a review was reported of 325 cases of
FMT performed worldwide, ~75% of which had been administered by colonoscopy or retention enema, and 25% by nasogastric
or nasoduodenal tube, or by EGD (27,28). Worldwide mean cure
rates to date are consistently around 91% (28) and FMT is effective even in patients with the C. difficile NAP1/BI/027 strain (29).
Route does seem to influence results, however, and when FMT
is done via upper tract endoscopy, nasogastric, or nasoduodenal
tube, resolution rates are in the range of 7679% (28,30). Regardless of route, FMT appears to be safe, with no adverse effects or
complications directly attributed to the procedure yet published
(21,31).
CDI and FMT: pathophysiology and rationale

The rationale for FMT in patients with recurrent CDI lies in

the belief that CDI results when the community of organisms
residing in the gastrointestinal tract is perturbed and that persisting imbalance, or dysbiosis, explains the high CDI recurrence rates of 1020% after initial antibiotic therapy and up to
4065% in patients who are retreated for a second episode (32).
It is believed that reintroduction of normal flora via donor feces
corrects the imbalance, restores both phylogenetic richness and
colonization resistance, and thereby enables recovery of normal
bowel function; this contrasts with the chronic use of antibiotics,
which, in a sense, perpetuates the very condition that lead to the
initial episode of CDI, namely an altered intestinal microbiome.
In an elegant series of experiments, Lawley et al. (33) treated
mice with clindamycin for 7 days and then infected them with
C. difficile (genotype 027/BI) isolated from hospitalized patients.
They showed that the mice went on to develop highly contagious, chronic disease with persistent dysbiosis characterized by:
(1) a simplified microbiota with reduced phylotypic diversity;
(2) opportunistic pathogens (e.g., Klebsiella pneumonia, E. coli,
Proteus mirabilis, Parabacteroides distasonis, and Enterococcus
faecalis all of which have been identified in the microbiota of
humans with chronic CDI (34); (3) upregulated pro-inflammatory genesparticularly those known to promote neutrophil
infiltration; (4) and altered metabolite production, similar
to that which occurs in the human immune response to CDI.
Specifically, they demonstrated a disturbance in fecal short- chain
fatty acids, which are the end-products of intestinal bacterial
metabolism of ingested complex carbohydrates. This disturbance
included a reduction in butyrate and acetate, which are the main
nutrient sources for the colon and an increase in succinate levels;
of note, there was an increase in P. disasonis, which is a succinate
producer. Acetate and butyrate influence a wealth of functions
in the colon; acetate: crypt cell proliferation, motility, blood
flow, adipogenesis, and cellular immunity; butyrate: colonocyte
health, inflammation, intestinal permeability, inflammation,
apoptosis, cell growth and differentiation, and barrier function,
to name but a few (35). Lawley et al. (33) then demonstrated that
vancomycin administration was associated with suppression of
2013 by the American College of Gastroenterology

C. difficile excretion and that upon cessation of treatment relapse

occurred, just as in the human who has recurrent CDI. FMT
using homogenized feces from a healthy mouse and given by
oral gavage, suppressed C. difficile shedding for months. Finally,
these authors reasoned that introduction of a phylogenetically
diverse but limited bacterial mixture might trigger recovery of
the intestinal ecosystem and disrupt the stability of the microbiota of the mice with chronic CDI. Ultimately they fashioned
a mixture of six physiologically diverse species including both
obligate and facultative anaerobes that resolved the CDI. This
series of experiments addresses the major concepts involved in
trying to understand the pathophysiology of the effectiveness of
FMT in treating patients afflicted with chronic, recurrent CDI.
(Figure 3): (1) perturbation of the intestinal microbiota, (2)
colonization and establishment of C. difficile, which allows (3)
persistence of a disturbed intestinal microbiota with (4) altered
intestinal fermentation, and (5) loss of nutrients to the bowel; (6)
FMT induces re-establishment of microbiota diversity and (7)
termination or suppression of C. difficile colonization. It is likely
that the colitis seen with chronic CDI is also associated with
increased colonic permeability that is worsened by the reduction in butyrate and acetate and which then facilitates colonic
protein loss with hypoalbuminemia, and bacterial translocation
with sepsis, especially in cases of severe CDI.
CDI and FMT: how to do it

The potential for transmission of infectious agents is a major

concern, however, and rigorous screening tests are recommended to reduce such risk (21). As an integral part of our protocol for a double-blind randomized controlled trial of FMT for
recurrent CDI (see below), the NIH required that donor stool be
tested for C. difficile toxin, enteric bacterial pathogens (including specifically Listeria monocytogenes, Vibrio cholera and Vibrio
parahemolyticus), parasites such as Giardia (Giardia antigen test)
Cryptosporidium (Cryptosporidium antigen test), and Isospora
(acid-fast stain), and Rotavirus; donor blood must be screened
for hepatitis A (IgM), B (HBsAg, anti-HBc (IgG and IgM), and
anti-HBsAg) and C (HCV antibody) viruses, human immunodeficiency virus (HIV) types 1 and 2, and syphilis. Screening for H.
pylori is also prudent regardless whether FMT is performed via
the upper or lower route. Recipients are tested for HIV 1 and 2,
Hepatitis A, C, and syphilis. This testing is much more rigorous
and extensive than that performed in the community, where most
practitioners just have donor stool screened for enteric pathogens, ova and parasites, and C. difficile toxin. Of course, because
of the ready availability of stool, patients may accept offers of
unscreened stool from well-meaning friends and relatives who
are aware of FMT. I have had several patients who wanted me to
perform FMT on them after self-administration of unscreened
donor stool had failed. This practice of using unscreened stool
is to be eschewed, except perhaps for emergent FMT, when timing may be more critical than long-term safety outcome. As the
perturbing effect of antibiotics on the intestinal microflora can
persist for 3 months or more, donors are excluded if they have
had antibiotics within this time; high-risk sexual behaviors, a
The American Journal of GASTROENTEROLOGY

181

REVIEW

Intestinal Microbiota and Fecal Microbiota Transplant for C. difficile

182

Brandt

REVIEW

(a) Homeostasis

(d) Expansion of commensals

(b) Antibiotic perturbation

(c) Transient dysbiosis

(h) C.difficile clearance

(e) C.difficile exposure

(g) Disrupting dysbiosis

(f) Persistent dysbiosis

Bacteriotherapy

or FMT

Figure 3. Role of antibiotics and C. difficile in perturbing Intestinal homeostasis and the corrective effect of fecal microbiota transplantation (FMT).
Intestinal homeostasis (a) is characterized by a diverse, stable microbiota. Antibiotic perturbation (bc) kills susceptible bacteria resulting in a less diverse
community structure with loss of colonization resistance. In the absence of opportunistic infection, the microbiota usually recovers its diversity (d) to
re-establish homeostasis and colonization resistance (a). Exposure to C. difficile (e) after antibiotic perturbation (b), however, can lead to persistent
dysbiosis (f). Bacteriotherapy or FMT can disrupt the dysbiosis (g) allowing clearance of C. difficile (h) and re-establishment of intestinal homeostasis (a).
Modified from Lawley et al. (33).

body piercing or tattoo in the previous 3 months or recent incarceration are also exclusions. A history of diarrhea, constipation,
inflammatory bowel disease, colorectal polyps or cancer, irritable bowel syndrome, immunocompromise, morbid obesity,
metabolic syndrome, atopy, and chronic fatigue syndrome are
additional donor exclusions because they conceivably may be
transmittable by inoculation with intestinal microbiota.
One systematic review provided data to suggest that FMT
using stool from a related donor (spouse, or intimate partner),
yields a somewhat higher rate (93.3%) of CDI resolution than
when stool from an unrelated donor (84%) was used (28). More
recent experience with frozen/thawed or fresh fecal preparations
obtained from standard or universal donors, however, gave
excellent results (9092% resolution, 9% recurrence) exceeding
those obtained with patient-selected donors (70% resolution,
30% recurrence), and casting doubt on preference for related or
intimate contacts (36).
So what are the nuts and bolts of FMT? The donor has a relatively simple job: to provide the stool in a timely fashion. This, I
have seen, may cause a level of performance anxiety in some
donors. To facilitate passage and to enable me to work with a
soft stool, I have the donor take a double dose of milk of magnesia before bedtime the night before the procedure. A soft stool
is passed into a clean plastic container. I add non-bacteriostatic
saline to the stool, stir it, shake it, and mix it thoroughly. Others have opted for the blender method and some practitioners
have even had patients bring their own blender. Obviously, if a
The American Journal of GASTROENTEROLOGY

blender is to be used for several patients, its parts would have to

be sterilized before the next procedure. Some authors use milk
as the suspending fluid, others water; saline and milk may give
slightly lower resolution (86.2 and 88.6%, respectively) and recurrence (3.0 and 3.2%, respectively) rates, while water may give
higher resolution (98.5%) and recurrence (7.8%) rates (28). The
amount of stool to use has not been standardized, although those
given to weighing and measuring rather than just eyeballing the
products appearance favor 50 g in 250 cc of diluent. It seems as
if more is better and most FMTers are now using about 300 cc
for colonic FMT and 60 cc for upper tract FMT. An administered
volume of < 200 ml gave a resolution rate of 80% and a relapse
rate of 6.2%, whereas a volume of > 500 ml gave a resolution rate
of 97.3% and a relapse rate of 4.7%. Use of < 50 g of stool was
associated with resolution and relapse rates of 8.2% and 3.8%,
respectively, whereas > 50 g of stool had resolution and relapse
rates of 86.2% and 1.0%, respectively (28). I like to use donor stool
within 8 h of passage although this time limit has never been studied rigorously. Stool should not be frozen and need not, but may,
be refrigerated for travel. After adding my beverage of choice to
the stool and getting it to the proper consistency, I filter the mixture through gauze pads to remove large particulate matter that
may obstruct the colonoscopes channel and then draw the elixir
into 60 cc catheter-tipped syringes. It is recommended that stool
preparation be performed under a hood, because stool is rated as
a Level 2 biohazard, although this recommendation is not practical and this is the safest stool we, as gastroenterologists, will ever
VOLUME 108 | FEBRUARY 2013 www.amjgastro.com

encounter. Recipients should take a large volume colon lavage

before the procedure, regardless of which route is chosen. In cases
of recurrent CDI, I have the patients stop their vancomycin and
other antibiotics 3 days before the procedure if possible; this too
has not been studied against continuing the antibiotics up until or
even after the procedure. I also have the recipient take two loperamide tablets before they leave home or about an hour before the
procedure to help them hold the administered stool for at least
4 h, and preferably 6 h, after FMT. To actually do the transplant,
I perform a colonoscopy and upon reaching the cecum, I remove
the accessory channel cap of the colonoscope, connect a piece of
suction tubing to it, and then administer one syringe-full of stool
suspension after another into the cecum/ascending colon or into
the ileum until the desired amount has been given. I have on many
occasions taken random colon biopsy specimens during insertion
to ascertain histology without adverse effect. After infusion of the
donor stool, I withdraw swiftly, aspirating air only from the distal
left colon, sigmoid and rectum for patient comfort.

study, principal investigators of which are Dr Colleen Kelly

and I, will evaluate FMT in 80 patients with at least three bouts
of CDI, and compare results of blinded FMT, using either donor
or recipient stool for the transplant.
The use of stool for such transplants is but the first step in a
long journey. Stool is the ultimate probiotic but greater knowledge of the intestinal microbiota and its functions will certainly
enable us to administer one or more intestinal micro-organisms

Table 1. Disorders associated with an altered intestinal

microbiome
Gastrointestinal
Cholelithiasis
Colorectal cancer
Hepatic encephalopathy
Idiopathic constipationa

CDI and FMT: long-term follow-up and safety issues

In the only long-term follow-up of FMT to date, a fivemedical center cross-country joint effort, 77 patients who had
had FMT and were followed for more than 3 months experienced a 91% primary cure rate and a 98% secondary cure rate,
the latter defined as cure enabled by use of antibiotics to which
the patient hadnt responded to before the FMT or by a second
FMT (37). It is interesting that 97% of these patients stated they
would have another FMT were they to develop CDI again and
58% said they would choose to have FMT rather than antibiotics.
It is not unusual for patients to develop some gastrointestinal
complaints or altered bowel habit for several days after FMT,
including absence of bowel movement, abdominal cramping,
gurgling bowel sounds, or increased feelings of gaseousness.
Of the 77 subjects in this study, four developed an autoimmune
disease (rheumatoid arthritis, Sjogren syndrome, idiopathic
thrombocytopenic purpura, and peripheral neuropathy) at some
time after the FMT, although a clear relationship between the
new disease and FMT was not evident. Safety of FMT in immunosuppressed patients needs to be established, although limited
experience to date would suggest immune-compromise is not
of concern. I personally have performed FMT in many patients
who were either on glucocorticoids, immunosuppressive
(6-mercaptopurine, azathioprine), or biological agents (infliximab, adalimumab), or who had diseases or therapies characterized by immunocompromise (kidney transplant, chronic
lymphocytic leukemia, lymphoma, primary immune deficiency,
SchwachmanDiamond syndrome) without ill effect. Nonetheless, safety remains the prime consideration and larger numbers
of observations in controlled circumstances are needed. Controlled trials also are necessary to prove the efficacy of FMT,
and to determine the optimal route of administration among
other variables. Two such randomized, controlled trials are
pending; one that compares conventional vancomycin therapy
alone and with bowel lavage, or with bowel lavage plus FMT
is currently in progress (38). A recently approved NIH-funded
2013 by the American College of Gastroenterology

IBSa
IBDa
Familial Mediterranean Fever
Gastric carcinoma and lymphoma
Recurrent Clostridium difficile infectiona
Non-gastrointestinal
Arthritis
Asthma
Atopy
Autisma
Autoimmune disorders
Chronic fatigue syndromea
Diabetes mellitus and insulin resistancea
Eczema
Fatty liver
Fibromyalgiaa
Hay fever
Hypercholesterolemia
Idiopathic thrombocytopenic purpuraa
Ischemic heart disease
Metabolic syndromea
Mood disorders
Multiple sclerosisa
Myoclonus dystoniaa
Obesity
Oxalic acid kidney stones
Parkinsons diseasea
IBD, inflammatory bowel disease; IBS, irritable bowel syndrome.
a
Indicates some reports on transient or long-term improvement or cure with
fecal microbiota transplant.

The American Journal of GASTROENTEROLOGY

183

REVIEW

Intestinal Microbiota and Fecal Microbiota Transplant for C. difficile

REVIEW

184

Brandt

or genetically refined products derived from stool rather

than stool itself to treat CDI. The next step in this journey
has already been taken with the development of a standardized filtered, frozen preparation of stool for FMT and use of a
universal donor (36).
When should FMT be done?

When should FMT be done for CDI? The clearest indication,

as discussed above, is recurrent or refractory disease, but even
this is not universally accepted and awaits the results of randomized controlled trials; to quote a reviewer of our NIH grant,
however, we all know it works. I believe it also has a role as
first-line treatment for patients with CDI rather than antibiotics because of its rapid effect, minimal risk, relatively low cost
and reestablishment of a balanced colonic microbiota (39). I,
and others, also have used FMT to treat patients with severe CDI
manifest by toxic megacolon or ileus and have seen the patients,
familys, gastroenterologists, and even surgeons relief as the
patients abdominal distention, fever, and white blood cell count
decreased, occasionally within hours of the procedure; in none
of these cases was the patients condition or course of disease
worsened by FMT.
FMT also has been used to treat a variety of other gastrointestinal disorders including ulcerative colitis, Crohns disease,
irritable bowel syndrome, and constipation and there is a growing literature on an altered intestinal microbiome in these disorders (4042) (See Table 1). I now have personal experience with
FMT in 20 patients with UC, 4 with Crohns disease and 20 with
IBS; and in all groups, I have noted remarkable symptomatic
improvement in some individuals. Rigorous studies of FMT in
these areas are also needed to determine who is the optimal candidate, and via what route and how often FMT should be delivered,
among other considerations.
Use of FMT is not confined to gastrointestinal disease and there
is a scattering of studies on the intestinal microbiota or FMT in a
wide range of disorders (see Table 1) including Parkinsons disease (43), fibromyalgia, chronic fatigue syndrome (44), multiple
sclerosis (45), myoclonus dystonia (46), obesity (47) insulin resistance and the metabolic syndrome (48), and childhood regressive autism (49) among others. The beneficial effect of FMT on
non-gastrointestinal disorders was an unanticipated observation
that was initially made in one patient with UC and idiopathic
thrombocytopenic purpura who had remission of both diseases
(50) and in three patients with multiple sclerosis who underwent
FMT for chronic constipation, in whom normal defecation was
achieved and improvement was noted in motor symptoms and
urinary function resulting in a regained ability to walk and removal
of indwelling catheters (45). Of 34 patients with chronic fatigue
syndrome who were reachable 1128 months after FMT, 14 (41%)
reported persistent relief and 12 (35%) showed little or late relief
of their chronic fatigue symptoms (44). In autism, the link with
intestinal microbiota is supported by observations that disease
onset often follows antimicrobial therapy; associated gastrointestinal abnormalities are not uncommon; certain Clostridium spp. are
present at 10-fold higher numbers in stool samples from autistic
The American Journal of GASTROENTEROLOGY

children; and autistic symptoms have sometimes been reduced by

oral vancomycin treatment (3). Although at first glance it appears
as if there is no connection with neuropsychiatric disease and
intestinal flora, studies now have expanded the original concept
of the brain-gut axis and recognize the brain-gut-microbiota axis
(51). Moreover, the increasing recognition of the role that microbiota have in affecting mood and thought is actively being worked
on (52,53).

CONCLUSION
I believe that the intestinal microbiota will be shown to have
important roles in maintaining our health and modulating energy
expenditure, inflammation, and resistance or susceptibility to various disease, some gastrointestinal and some not. Bacteria should
no longer be regarded as just bad guys and we have come a long
way since Hippocrates said, All disease begins in the gut; today
he might instead say Our health is determined by the microbiota in our gut. We are witnessing a paradigm shift in the way
we understand health and treat disease and in its center is our
microbiota.
CONFLICT OF INTEREST

Guarantor of the article: Lawrence J. Brandt, MD, MACG.

Financial support: None.
Potential competing interests: Dr Brandt is on the Speakers
Bureau of Optimer Pharmaceuticals, Inc. and has received a research
grant from Optimer Pharmaceuticals, Inc.
REFERENCES
1. Zhang F, Luo W, Shi Y et al. Should we standardize the 1700-year-old
fecal microbiota transplantation? Am J Gastroenterol 2012; 107:1755.
2. The Human Microbiome Project Consortium.. Structure, function and
diversity of the healthy human microbiome. Nature 2012;486:20714.
3. Sekirov I, Russell SL, Antunes CM, Finlay RB. Gut microbiota in health and
disease. Physiol Rev 2010;90:859904.
4. Eckburg PB, Bik EM, Bernstein CN et al. Diversity of the human intestinal
microbial flora. Science 2005;308:16358.
5. Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces
shaping microbial diversity in the human intestine. Cell 2006;124:83748.
6. Swidsinski A, Loening-Bauke V, Lochs H, Hale LP. Spatial organization
of bacterial flora in normal and inflamed intestine: a fluorescence in situ
hybridization study in mice. World J Gastroenterol 2005;11:113140.
7. Huurre A, Kalliomaki M, Rautava S et al. Mode of delivery: effects on gut
microbiota and humoral immunity. Neonatology 2008;93:23640.
8. Harmsen HJ, Wildeboer-Veloo AC, Raangs GC et al. Analysis of
intestinal flora development in breast-fed and formula-fed infants by using
molecular identification and detection methods. J Pediatr Gastroenterol
Nutr. 2000;30:617.
9. Biasucci G, Rubini M, Riboni S et al. Mode of delivery affects the bacterial
community in the newborn gut. Early Hum Dev 2010;86 (Suppl 1): 135.
10. Wu GD, Chen J, Hoffmann C et al. Linking long-term dietary patterns with
gut microbial enterotypes. Science 2011;334:1058.
11. Stappenback TS, Hooper LV, Gordon JI. Developmental regulation of
intestinal angiogenesis by indigenous microbes via Paneth cells. Proc Natl
Acad Sci USA 2002;99:154515.
12. Hooper LV, Wong MH, Thelin A et al. Molecular analysis of commensal
host-microbial relationships in the intestine. Science 2001;291:8814.
13. Hooper LV, Gordon JI. Commensal host-bacterial relationships in the gut.
Science 2001;292:11158.
14. Mazmanian SK, Lin CH, Tzianabos AO, Kasper DL. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune
system. Cell 2005;122:10718.

VOLUME 108 | FEBRUARY 2013 www.amjgastro.com

15. Zeuthen LH, Fink LN, Frokiner H. Epithelial cells prime the immune
response to an array of gut-derived commensals towards a tolerogenic
phenotype through distinct actions of thymic stromal lymphopoietin and
transforming growth-factor beta. Immunology 2008;123:197208.
16. Kelly D, Campbell JI, King TP et al. Commensal anaerobic gut bacteria
attenuate inflammation by regulating nuclear-cytoplasmic shuttling of
PPAR-gamma and RelA. Nat Immunol 2004;5:10412.
17. Bates JM, Akerland J, Mittge E, Guillemin K. Intestinal alkaline phosphatase
detoxifies lipopolysaccharide and prevents inflammation in zebrafish in
response to the gut microbiota. Cell Host Microbe 2007;2:37182.
18. Corr SC, Gahan CG, Hill C. Impact of selected Lactobacillus and Bifidobacterium species on Listeria monocytogenes infection and the mucosal
immune response. FEMS Immunol Med Microbiol 2007;50:3808.
19. Flint HJ. Obesity and the gut microbiota. J Clin Gastroenterol
2011;45:S12832.
20. Nicholson JK, Holmes E, Wilson ID. Gut microorganisms, mammalian
metabolism, and personalized health care. Nat Rev Microbiol 2005;3:4318.
21. Bakken JS, Borody T, Brandt LJ et al. Fecal Microbiota Transplantation (FMT) Workgroup. Treating Clostridium difficile infection with
fecal microbiota transplantation. Clin Gastroenterol and Hepatol
2011;9:10449.
22. Eiseman B, Silen W, Bascom GS et al. Fecal enema as an adjunct in the
treatment of pseudomembranous enterocolitis. Surgery 1958;44:8549.
23. Schwan A, Sjolin S, Trottestam U et al. Relapsing Clostridium difficile
enterocolitis cured by rectal infusion of homologous faeces. Lancet
1983;2:845.
24. Aas J, Gessert CE, Bakken JS. Recurrent Clostridium difficile colitis: case
series involving 18 patients treated with donor stool administered via a
nasogastric tube. Clin Infect Dis 2003;36:5805.
25. Persky SE, Brandt LJ. Treatment of recurrent Clostridium difficile-associated
diarrhea by administration of donated stool directly through a colonoscope.
Am J Gastroenterol 2000;95:32835.
26. Silverman MS, Davis I, Pillai DR. Success of self-administered home fecal
transplantation for chronic Clostridium difficile infection. Clin Gastroenterol Hepatol 2010;8:4713.
27. Brandt LJ, Reddy S. Fecal microbiota transplantation for recurrent
Clostridium difficile infection. J Clin Gastroenterol 2011;45:S15967.
28. Gough E, Shaikh H, Manges AR. Systematic review of intestinal microbiota
transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile
infection. Clin Infect Dis 2011;53:9941002.
29. Mattila E, Uusitalo-Seppl R, Wuorela M et al. Fecal Transplantation,
through colonoscopy, is effective therapy for recurrent Clostridium difficile
infection. Gastroenterology 2010;142:4906.
30. Rubin TA, Gessert CE, Aas J, Bakken JS. Fecal microbiome transplantation for recurrent Clostridium difficile infection: report on a case series.
Anaerobe; 23 November 2012 pii S10759964(12)00153-9; doi: 10.1016/
j.anaerobe.2012.11.004 (e-pub ahead of print).
31. Borody TJ, Warren EF, Leis SM et al. Bacteriotherapy using fecal flora: toying with human motions. J Clin Gastroenterol 2004;38:47583.
32. McFarland LV, Surawicz CM, Rubin M et al. Recurrent Clostridium difficile
Disease. Epidemiology and Clinical Characteristics. Infect Contr and Hosp
Epidemiol 1999;20:4350.
33. Lawley TD, Clare S, Walker AW et al. Targeted restoration of the intestinal
microbiota with a simple, defined bacteriotherapy resolves relapsing
Clostridium difficile disease in mice. PLoS Pathog 8: e1002995;
doi: 10.1371/journal.ppat.1002995.

2013 by the American College of Gastroenterology

34. Chang JY, Antonopoulos DA, Kalra A et al. Decreased diversity of the fecal
microbiome in recurrent Clostridium difficile-associated diarrhea. J Infect
Dis 2008;197:4358.
35. Macfarlane GT, Macfarlane S. Fermentation in the human large intestine.
Its physiologic consequences and the potential contribution of probiotics.
J Clin Gastrooenterol 2011;45:S1207.
36. Hamilton MJ, Weingarden AR, Sadowsky MJ et al. Standardized frozen
preparation for transplantation of fecal microbiota for recurrent
Clostridium difficile infection. Am J Gastroenterol 2012;107:7617.
37. Brandt LJ, Aroniadis OC, Mellow M et al. Long-term follow-up of colonoscopic fecal microbiota transplant for recurrent Clostridium difficile
infection. Am J Gastroenterol. 2012;107:107987.
38. van Nood E, Speelman P, Kuiper EJ et al. Struggling with recurrent Clostridium
difficile infections: is donor faeces the solution? Euro Surveill 2009;14:pii:19316.
39. Brandt LJ, Borody TJ, Campbell J. Endoscopic Fecal Microbiota Transplantation: First-Line treatment for severe Clostridium difficile infection.
J Clin Gastroenterol. 2011;45:6557.
40. Sartour RB. Microbial influences in inflammatory bowel diseases.
Gastroenterology 2008;134:57794.
41. Rajiilic-Stojanovic M, Biagi E, Heilig HG et al. Global and deep molecular
analysis of microbiota signatures in fecal samples from patients with
irritable bowel syndrome. Gastroenterology 2011;141:1792801.
42. Quigley E. The enteric microbiota in the pathogenesis and management of
constipation. Best Pract Res Clin Gastroenterol 2011;25:11926.
43. Anathaswamy A. Faecal transplant eases symptoms of Parkinsons.
New Scientist; issue 2796, 19 January 2011.
44. Borody TJ, Nowak A, Torres M et al. Bacteriotherapy in chronic fatigue
syndrome: a retrospective review. Am J Gastroenterol 2012;107 (Suppl 1),
S591592 (A1481).
45. Borody TJ, Leis S, Campbell J et al. Fecal microbiota transplantation (FMT)
in multiple sclerosis (MS) [abstract]. Am J Gastroenterol 2011;106:S352.
46. Borody TJ, Rosen DM, Torres M et al. Myoclonus-dystonia (M-D)
mediated by GI microbiota diarrhoea treatment improves M-D symptoms.
Am J Gastroenterol 2011;106:S352.
47. Turnbaugh PJ, Ley RE, Mahowald MA et al. An obesity-associated
gut microbiome with increased capacity for energy harvest. Nature
2006;444:102731.
48. Vrieze A, van Nood E, Holleman F et al. Transfer of intestinal microbiota
from lean donors increases insulin sensitivity in subjects with metabolic
syndrome. Gastroenterology 2012;143:913916.
49. Finegold SM, Molitors D, Song Y. Gastrointestinal micro flora studies in
late-onset autism. Clin Infect Dis. 2002;35:S616.
50. Borody TJ, Campbell J, Torres M et al. Reversal of idiopathic thrombocytopenic purpura (ITP) with fecal microbiota transplantation (FMT)
[abstract]. Am J Gastroenterol 2011;106:S352.
51. Collins SM, Bercik P. The Relationship between intestinal microbiota and
the central nervous system in normal gastrointestinal function and disease.
Gastroenterology 2009;136:200314.
52. Bravo JA, Forsythe P, Chew MV et al. Ingestion of Lactobacillus strain
regulates emotional behavior and central GABA receptor expression in
a mouse via the vagus nerve. Proc Natl Acad Sci USA 2011;108:160505.
53. Bercik P, Park AJ, Sinclair D et al. The anxiolytic effect of Bifidobacterium
longum NCC3001 involves vagal pathways for gut-brain communication.
Neurogastroenterol Motil 2011;23:11329.
54. Kau AL, Ahern PP, Griffen NW et al. Human nutrition, the gut microbiome,
and immune system: envisioning the future. Nature 2011;474:32736.

The American Journal of GASTROENTEROLOGY

185

REVIEW

Intestinal Microbiota and Fecal Microbiota Transplant for C. difficile