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Gut microbiota modulation: Probiotics, antibiotics or fecal microbiota


transplantation?

Article  in  Internal and Emergency Medicine · March 2014


DOI: 10.1007/s11739-014-1069-4 · Source: PubMed

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Intern Emerg Med (2014) 9:365–373
DOI 10.1007/s11739-014-1069-4

IM - REVIEW

Gut microbiota modulation: probiotics, antibiotics or fecal


microbiota transplantation?
Giovanni Cammarota • Gianluca Ianiro •

Stefano Bibbò • Antonio Gasbarrini

Received: 25 February 2014 / Accepted: 10 March 2014 / Published online: 25 March 2014
Ó SIMI 2014

Abstract Gut microbiota is known to have a relevant role Moreover, fecal microbiota transplantation has shown
in our health, and is also related to both gastrointestinal and promising results, but stronger proofs are needed. Consid-
extradigestive diseases. Therefore, restoring the alteration erable efforts are needed to increase our knowledge in the
of gut microbiota represents an outstanding clinical target field of gut microbiota, especially with regard to the future
for the treatment of gut microbiota-related diseases. The use in its modulation for therapeutic purposes.
modulation of gut microbiota is perhaps an ancestral, innate
concept for human beings. At this time, the restoration of Keywords Gut microbiota  Gut microbiota modulation 
gut microbiota impairment is a well-established concept in Antibiotics  Probiotics  Fecal microbiota transplantation
mainstream medicine, and several therapeutic approaches
have been developed in this regard. Antibiotics, prebiotics
and probiotics are the best known and commercially Gut microbiota in health and disease
available options to overcome gastrointestinal dysbiosis.
Fecal microbiota transplantation is an old procedure that has An enormous number of microbes colonize our body, both
recently become popular again. It has shown a clear effec- inside and out. They number from 10 trillion to 100 trillion
tiveness in the treatment of C. difficile infection, and now cells, outnumbering human eukaryotic cells at least by
represents a cutting-edge option for the restoration of gut tenfold. Most of them reside in our intestine, forming the
microbiota. Nevertheless, such weapons should be used so-called ‘‘human gut microbiota’’ [1]. Gut microbiota and
with caution. Antibiotics can indeed harm and alter gut its whole genome (called microbiome) provides humans
microbiota composition. Probiotics, instead, are not at all with genetic and metabolic features that they did not
the same thing, and thinking in terms of different strains is develop by themselves. Gut microbiota and host act,
probably the only way to improve clinical outcomes. therefore, in a symbiotic manner, constituting essentially a
complex ‘‘super-organism’’ [2].
Most microbes, especially anaerobes, cannot be cultured
through standard microbiological tools. Such technical
limitations have encumbered our understanding of gut
G. Cammarota  G. Ianiro  S. Bibbò  A. Gasbarrini
School of Medicine and Surgery, Catholic University, microbiota. The development of new, culture-independent
Rome, Italy techniques for the study of intestinal microbes, such as
high-throughput DNA sequencing and other metagenomics
G. Cammarota  G. Ianiro  S. Bibbò  A. Gasbarrini
technologies, has enhanced our knowledge in the field of
Division of Internal Medicine and Gastroenterology,
Department of Medical Sciences, A. Gemelli University gut microbiota [3]. Many initiatives have been established,
Hospital, Rome, Italy and are still ongoing, both in the United States (Human
Microbiome Project) [2] and in Europe (MetaHIT Con-
G. Cammarota (&)
sortium) [4], which attempt to characterize microbes of our
A. Gemelli University Hospital,
Largo A. Gemelli 8, 00168 Rome, Italy body and their genomes, and to assess their role in human
e-mail: gcammarota@rm.unicatt.it health and disease.

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366 Intern Emerg Med (2014) 9:365–373

Nevertheless, gut microbiota composition is not yet homeostasis. Healing the alteration of gut microbiota,
completely defined. Bacteria are certainly the most repre- therefore, represents an outstanding clinical target for the
sented micro-organisms, reaching more than 1 kg of treatment of gut microbiota-related diseases.
weight and more than 1,100 species. Bacteroidetes and
Firmicutes usually are the predominant phyla in adult
people, whereas Actinobacteria, or Proteobacteria are less Available possibility to modulate gut microbiota
common [4, 5]. The human microbiota also contains ar-
chaea, viruses (mainly bacteriophage), fungi and other The modulation of gut microbiota is perhaps an ancestral,
Eukarya (as Blastocystis and Amoebozoa), [5]. innate concept for human individuals. As recently descri-
Three main enterotypes, with different metabolic traits, bed by Leach [23], the Hadzabe people, a hunter-gatherer
have been recently identified [6]. They are distinguished by tribe of Tanzania, often eat the raw intestines of hunted
their relative abundance of one of the following three preys, and also use the animal’s stomach, full of its
genera: Bacteroides (prevalent in enterotype 1); Prevotella microbial matter, as hand cleanser; such a behavior helps to
(more represented in enterotype 2); Ruminococcus (more increase the diversity of gut microbes among tribe mem-
abundant in enterotype 3). The presence of a specific en- bers. Since a decreased bacterial diversity has been found
terotype may depend on a particular long-term dietary in several diseases, including IBD [24], IBS [25], obesity
pattern: animal-based diets, rich in fat and protein, support and metabolic diseases [26, 27] and asthma [28], such a
the development of enterotypes 1 and 3, while a high custom by the Hadzabe tribe can be considered a primitive
carbohydrate diet favors the growth of enterotype 2 [7]. kind of therapeutic modulation of gut microbiota.
Moreover, short-term dietary modifications have been
proven to alter the human gut microbiota [8]. The rapidity Antibiotics
of our microbiota in switching between different functional
profiles may be an evolutionary trick that humans have Antibiotics are the cornerstone of the treatment of infec-
acquired over time. tious disease [29]. However, bacterial resistance to antibi-
At birth, the human gut is sterile, and is rapidly colo- otics has increased over time, and keeps on rising [30]. The
nized by the maternal microbiota; both route of delivery quintessence of this phenomenon is represented by the
and type of feeding influencing its composition [9]. Both growing difficulty in eradicating H. pylori infection [31]
environmental and genetic factors [10] contribute to the because of the rise in antibiotic resistance.
development of a ‘‘core native microbiome,’’ which The improvement in our knowledge of gut microbiota
achieves stability during early life, and is maintained over reveals that antibiotics behave in a two-edged manner
time in the absence of major alterations [11]. toward our intestinal microbes [32]; simultaneously, anti-
In health, gut microbiota plays a relevant role within our biotics demolish both pathogenic bacteria and healthy ones.
body, being involved in many functional processes essen- Moreover, absorbable antibiotics, even if administered for
tial for our homeostasis, such as the control of several an extra-intestinal disease, attack the microbial flora any-
metabolic pathways, the metabolism of nutrients, and is way, because of their widespread, systemic diffusion
also xenobiotic, the production of vitamins and micronu- within our body. Such a phenomenon leads to the impair-
trients, the development and maturation of mucosal and ment of gut microbiota with a consequent increase in
systemic immunity, the regulation of gastrointestinal susceptibility to its associated diseases. This pathophysio-
motility, and the maintenance of intestinal epithelium logical mechanism is well recognized as being the trigger
barrier integrity [12]. for C. difficile infection [33], but is also involved in the
Qualitative or quantitative impairment of gut microbiota pathogenesis of other enteric infections [34] or in the
composition causes the loss of such a homeostasis, leading intestinal outgrowth of fungi. [35] Moreover, it appears to
to the development of a disease state. also influence the development of other diseases, such as
Several illnesses are known to be influenced by the obesity [36].
imbalance of gut microbiota. They include: inflammatory In addition, gut microbiota disruption caused by anti-
bowel disease (IBD,) [13], irritable bowel syndrome (IBS,) biotic therapy may lead to the development of antibiotic
and other functional diseases of the gastrointestinal tract resistance [37]. Antibiotics have indeed been shown to
[14], gastroenteric infections [15], colorectal cancer [16], provoke the enrichment of phage-encoded genes that con-
liver diseases [17, 18], and also non gastrointestinal dis- fer resistance via disparate mechanisms both to the
eases such as obesity and the metabolic syndrome [19, 20], administered antimicrobial, as well as to other unrelated
autism [21], and allergic diseases [22]. However, just as the antibiotics [38]. Therefore, the relationship between anti-
impairment of gut microbiota can lead to a pathological biotics and gut microbiota is truly complex, and should be
condition, so its manipulation can restore the prior state of investigated carefully to identify the correct application of

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Intern Emerg Med (2014) 9:365–373 367

antibiotics for gut microbiota-related diseases, and to completely meet such a definition [48]. Two bacterial
improve disease outcomes. genera, respectively, Lactobacilli and Bifidobacteria, are
the main target of prebiotics [50], even if other strains have
Probiotics and prebiotics also been proven to benefit of prebiotic properties [51].
Proposed mechanisms of the action of prebiotics include
According to the 2001 FAO/WHO definition, probiotics an increase in the production of short-chain fatty acids
are ‘‘live micro-organisms, which when administered in (SCFA) or a decrease of intestinal pH [52]. To date, defi-
adequate amounts confer a health benefit on the host’’ [39]. nite evidence of the effectiveness of prebiotics for the
The rationale for the use of probiotics for the treatment of treatment of gut microbiota-related diseases is lacking, and
gut microbiota-related disease is the restoration of intesti- adequate trials have not yet been performed.
nal homeostasis by beneficial microbes. Most probiotics
consist of Lactobacilli and Bifidobacteria, but also yeasts Fecal microbiota transplantation (FMT)
such as Saccharomyces boulardii have been used with
good outcomes [40]. Suggested mechanisms of action FMT, also known as ‘‘fecal infusion’’ or ‘‘fecal bacterio-
include the inhibition of microbial adherence and translo- therapy’’, refers to the introduction of a liquid filtrate of
cation, the establishment of a restrictive luminal environ- stools from a healthy donor into the gastrointestinal tract of
ment (e.g., through, modification of the luminal pH), the a patient for the treatment of specific diseases. The
production of peptides with antibacterial properties (such administration of feces for therapeutic purposes was first
as bacteriocins), or the induction of an host immune described more than 1,500 years ago by Ge Hong [53].
response (such as expression of human defensins) [41]. In Afterward, in the sixteenth century, Li Shizhen treated
clinical practice, probiotics have been used for the treat- several gastrointestinal symptoms, such as diarrhea, con-
ment of many diseases, even without solid evidence. [42]. stipation, vomiting or pain, by fecal products. The trans-
Assessing the effectiveness of probiotics in a specific dis- plantation of enteric bacteria (later called transfaunation)
ease can be difficult, mainly because of the large hetero- was applied also in veterinary science, for the cure of
geneity among different studies in terms of administered animals unable to ruminate, as described by the Italian
strains, dosage, length of treatment, and administration anatomist Fabricius Acquapendente in the seventeenth
methods [43]. century [54]. The consumption of camel stools has been
In addition, considering all probiotics the same thing, described both by German soldiers during World War II, as
without taking into account strain specificity, impairs an well as by Bedouins as a treatment for dysentery [55].
adequate understanding of their real therapeutic potential. FMT came to the attention of mainstream medical sci-
Several lines of evidence, both in vitro models as well as ence only in the late 50’s: in 1958, Eiseman, a surgeon
in vivo human studies, support the variability in actions from Colorado, successfully treated four patients with
and outcomes among different strains [44, 45]. Further pseudomembranous colitis using fecal enemas [56]. The
trials should, therefore, involve probiotics not as such, but efficacy of FMT against C. difficile infection was later also
with a strain-specific approach [46]. confirmed. Early attempts, however, even if almost always
Prebiotics were defined for the first time in 1995 by successful, were described in occasional case series and
Gibson and Roberfroid [47] as ‘‘non-digestible food anecdotally carried out in a totally empirical way.
ingredients that beneficially affect the host by selectively Both the rising epidemic of C. difficile infection and the
stimulating the growth or activity of one of a limited growing scientific interest toward the gut microbiota have
number of bacterial species already present in the colon, recently led to the renewal of FMT. Recently, a profound
thus improving host health.’’ To include other fields that change in the epidemiology of C. difficile infection has
may profit by prebiotic action [48], this definition has been occurred, with a rise in its frequency, severity, and mor-
renewed by Roberfroid in 2007: ‘‘A prebiotic is a selec- tality [57]. Both the refractoriness of the infection to
tively fermented ingredient that allows specific changes, standard therapy as well as its probability of recurrence
both in the composition or activity in the gastrointestinal have also increased [58], representing an important clinical
microflora that confer benefits upon host well-being and issue. Positive results shown by FMT in the eradication of
health’’ [49, 50]. To be classified as a prebiotic, a food recurrent C. difficile infections have encouraged the use of
ingredient needs to fulfill the following criteria: resistance this procedure worldwide, especially in Western Countries.
to gastric acid secretion and to hydrolysis by digestive Well-designed studies, both large case series [59] and
enzymes; absorption in the upper gastrointestinal tract and randomized controlled trials [60], have been conducted to
fermentation by the intestinal gut microbiota; and stimu- assess its effectiveness.
lation of the growth or activity of beneficial microbes. At In addition, the recent advancement in our understand-
present, only inulin and trans-galacto-oligosaccharides ing of gut microbiota has given a solid pathophysiological

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368 Intern Emerg Med (2014) 9:365–373

background to FMT. Accounting our microbial flora as a gastric acid secretion, and a lower route may be preferable
bodily organ [61] let the interpretation of FMT change [72, 73]. A combined approach of delivery has not yet been
from being considered a mere injection of feces to attempted [74], and may perhaps become an option in the
becoming a true organ transplantation. Such a conceptual future.
transition has led FMT to being used in the treatment of Donor selection is certainly easier for FMT than for
several diseases associated with the disruption of gut other organ transplants, since there is no need of immu-
microbiota, such as inflammatory bowel disease (IBD) [62] nological matching of donor and recipient. Nevertheless,
and the metabolic syndrome [63]. an accurate evaluation is necessary to avoid disease
FMT may be more effective than probiotics in the res- transmission to the recipient, and unfortunately, the trans-
toration of altered gut microbiota, since a fecal infusion fer of unknown pathogens is not completely avoidable [75].
overcomes the intrinsic quantitative gap of probiotics (oral Usually, to overcome the repulsion of the patient toward
probiotic doses are usually more than three orders of receiving an infusion of feces (the so-called yuck factor,)
magnitude lower than the 100 trillion native micro-organ- donors are usually friends or family members, both related
isms of the large bowel). In addition, the administration of and unrelated. The administration of feces derived from
fecal flora establishes a durable alteration of the recipient’s related donors appears to achieve slightly higher resolution
gut microbiota [64], while probiotics are able to colonize rates than stools from unrelated ones (respectively, 93
the gut lumen only for a temporary period [65]. versus 84 % resolution rates) for the treatment of C. diffi-
FMT can be performed through various routes: naso- cile infection, as observed through systematic review by
gastric or nasojejunal tube, upper endoscopy, retention Gough et al.. Donor gender, instead, does not influence
enema, as well as colonoscopy [66]. In early usage, eradication rates [76].
retention enemas were the preferred mode of delivery [67]. Initially, the medical history of potential donors is col-
In a recent systematic review of studies using FMT for the lected, usually by clinical questionnaire. The following
treatment of recurrente C. difficile infection, Cammarota clinical characteristics have been proposed: [67] as abso-
et al. [68] report that the lower gastrointestinal route lute contraindications to the donation of feces for the
(colonoscopy, enema) leads to the achievement of higher treatment of C. difficile infection: known human immu-
eradication rates than upper delivery (gastroscopy, naso- nodeficiency virus (HIV), hepatitis B or C infections;
gastric or nasojejunal tube) (81–86 versus 84–93 %, known exposure to HIV or viral hepatitis (within the pre-
respectively). vious 12 months); high-risk sexual behaviors; use of illicit
In theory, among different lower gastrointestinal routes, drugs; tattoos or body piercing performed within 6 months;
colonoscopy appears to be a more reliable route than incarceration or history of incarceration; known current
retention enemata for the treatment of C. difficile infection, communicable disease (e.g., upper respiratory tract infec-
since it can reach the whole colon (while enemas only tion); risk factors for variant Creutzfeldt–Jakob disease;
ascend to the left colon), and colonoscopy can also assess travel (within the last 6 months) to areas of the world
the features of the disease: such as its extent and severity where diarrheal illnesses are endemic or with high risk of
[69, 70]. traveler’s diarrhea; history of IBD, IBS and other func-
Nevertheless, low invasiveness and costs of the retention tional diseases; history of gastrointestinal malignancy or
enema approach and its proven efficacy even when self- known polyposis; use of antibiotics within the preceding
administered, [71] make it extremely competitive for a 3 months, immunosuppressant, chemotherapeutic drugs;
routine use. and recent consumption of a potential allergen for the
Probably the optimal route of administration does not recipient. The following features are deemed as relative
exist absolutely, and any of the therapeutic routes should contraindications: history of major gastrointestinal surgery;
be chosen depending on the features and the location of the the metabolic syndrome, autoimmune diseases, atopic
disease, as shown by the successful results obtained in the diseases, and chronic pain syndromes [67].
treatment of metabolic diseases by duodenal administration After completion of the questionnaire, potential donors
of feces [62]. undergo serum and stool testing. Donor serum testing
Further discoveries of the therapeutic chances of FMT, includes screening for HIV, Hepatitis A Virus, Hepatitis B
and its systematic application to several gut microbiota- Virus, Hepatitis C Virus and syphilis, while donor stool
associated diseases will make the specific administration testing consists of stool culture for common enteric
route an important issue. The growth of many beneficial pathogens, C. difficile toxin, Giardia antigens, Cryptospo-
bacteria is indeed influenced by their specific transfer ridium antigens, Helicobacter pylori antigens, helminths,
through the gastrointestinal tract. Many spore-forming ova and parasites.
Firmicutes require transit through the upper gastrointestinal This protocol has been applied with success for donor
tract to work effectively. Bacteroidetes can be injured by selection in the management of C. difficile infection by

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Intern Emerg Med (2014) 9:365–373 369

Table 1 Fully published reports on FMT treatment


First author Year Indication Study design No. of patients

Eiseman 1958 Pseudomembranous colitis Case series 4


Cutolo 1959 Pseudomembranous colitis Case report 1
Collins 1960 Pseudomembranous colitis Case series 4
Fenton 1974 Pseudomembranous colitis Case report 1
Bowden 1981 Pseudomembranous colitis Case series 16
Schwan 1984 C. difficile infection Case report 1
Tvede 1989 C. difficile infection Case series 6
Bennet 1989 IBD Case report 1
Borody 1989 IBS and IBD Case series 55
Flotterod 1991 C. difficile infection Case report 1
Andrews 1992 Chronic constipation Case report 1
Paterson 1994 C. difficile infection Case series 7
Harkonen 1996 Pseudomembranous colitis Case report 1
Lund- Tønnesen 1998 C. difficile infection Case series 18
Gustafsson 1998 C. difficile infection Case series 9
Persky 2000 C. difficile infection Case report 1
Aas 2003 C. difficile infectiona Case series 18
Borody 2003 IBD Case series 6
Jorup-Ronstrom 2006 C. difficile infection Case series 5
Nieuwdrop 2008 C. difficile infection Case series 7
You 2008 C. difficile infection Case report 1
Hellermans 2009 C. difficile infection Case report 1
MacConnachie 2009 C. difficile infection Case series 15
Garborg 2010 C. difficile infection Case series 40
Grehan 2010 C. difficile infectiona Open-label trial 10
Khoruts 2010 C. difficile infection Case report 1
Rohlke 2010 C. difficile infection Case series 19
Russell 2010 C. difficile infection Case report 1
Silverman 2010 C. difficile infection Case series 7
Yoon 2010 C. difficile infection Case series 12
Kelly 2011 C. difficile infection Case series 26
Polak 2011 C. difficile infection Case series 15
Brandt 2012 C. difficile infection Multicenter long-term follow-up study 77
Hamilton 2012 C. difficile infection Open-label trial 43
Jorup-Ronstrom 2012 C. difficile infection Case series 32
Kahn 2012 C. difficile infection Case report 1
Mattila 2012 C. difficile infection Case series 70
Nagy 2012 C. difficile infection Case report 1
Neeman 2012 C. difficile infection Case report 1
Rubin 2012 C. difficile infection Case series 74
Trubiano 2012 C. difficile infection Case report 1
Vrieze 2012 Metabolic syndrome Randomized controlled trial 18
Zainah 2012 C. difficile infectiona Case report 1
Angelberger 2013 IBD Open-label trial 5
Broecker 2013 C. difficile infection Case report 1
De Leon 2013 C. difficile infectiona Case report 1
Emanuelsson 2013 C. difficile infection Case series 31
Kleger 2013 C. difficile infection Case report 1

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370 Intern Emerg Med (2014) 9:365–373

Table 1 continued
First author Year Indication Study design No. of patients

Kump 2013 IBD Open-label trial 6


Kunde 2013 IBD Open-label trial 10
Gutman 2013 C. difficile infection Case series 2
Lofland 2013 C. difficile infection Case report 1
Quera 2013 C. difficile infectiona Case report 1
Schwartz 2013 C. difficile infection Case series 2
Song 2013 C. difficile infection Open-label trial 14
van Nood 2013 C. difficile infection Randomized controlled trial 42
Weingarden 2013 C. difficile infection Open-label trial 16
Weingarden 2013 C. difficile infection Case series 4
Zhang 2013 IBD Case report 1
IBD inflammatory bowel disease, IBS irritable bowel syndrome
a
Including also patients with IBD and C. difficile superinfection

FMT [77]. However, such an approach seems to be inad- excellent results [68]. Nevertheless, the future application
equate when dealing with other gut microbiota-related of FMT to chronic diseases (such as IBD, IBS, obesity)
diseases, such as IBD, where the composition of the may perhaps require several infusions to achieve success.
donor’s gut microbiota may influence clinical outcomes FMT is a theoretically promising option for several
[74]. New tools for the investigation of gut microbiota diseases, differing from each other by pathophysiology and
composition, such as metagenomics and target gene clinical features. Probably, a unique protocol of stool
sequencing will probably aid in our understanding in this preparation is, therefore, an outdated idea, and in the future
field, and their application for the selection of donors is an every clinical indication will correspond to a different
interesting future prospect. protocol. An up-to-date overview of fully published reports
After donation, stools are processed for being infused. on FMT treatment for both gastrointestinal and extra-
Most data about the stool preparation protocol comes from intestinal diseases is described in Table 1.
studies applying FMT for the treatment of recurrent C. dif-
ficile infection, as reviewed by Gough and colleagues [76].
Even if there is no standardization about the required amount Conclusions
of feces, using less than 50 g has been correlated with
C. difficile relapse rates [76]. Feces are then suspended in a The role of gut microbiota in health and disease was first
diluent, generally saline or water; the use of water appears to hypothesized in 1907 by Metchnikoff and Mitchell [81].
get higher eradication rates than saline (98.5 versus 86 %), More than one century after, our knowledge of gut mic-
but also higher relapse rates. Other diluents, including milk robiota has enormously grown, and our consideration of
or yoghurt, achieve resolution rates of 94 %. The suspension gut microbiota has changed from an amalgam of microbes
is then passed through gauzes or sieve, to eliminate gross to another organ of our body, forming a ‘‘super-organism’’
materials. The filtrate volume is largely heterogeneous with us. Moreover, we have discovered a deep relationship
among studies, ranging between 200 ml or less and 500 ml between gut microbiota and both gastrointestinal and ex-
or more. The use of larger volumes ([500 ml) is positively tradigestive diseases. New technologies such as metage-
associated (although in a nonsignificant manner) with higher nomics have increased our understanding of gut microbiota
resolution rates [76]. composition in health and disease.
In most cases, the transplantation is performed within Such gain in knowledge can potentially change our
6–8 h after the donation [78, 79]. Frozen stools have, therapeutic perspectives: gut modulation can become a
however, shown a comparable efficacy to fresh ones for the therapeutic option. Some tools, such as antibiotics or pro-
treatment of recurrent C. difficile infection [80]. Usually, biotics, are well known, and other, such as FMT, represent
patients undergo a bowel preparation the day before the an intriguing, cutting-edge weapon. However, in the recent
infusion. Many physicians advocate using a PPI if the past scientific community learned that ‘‘all that glitters is
upper route is chosen [74]. no gold.’’ Antibiotics can indeed harm and alter gut mic-
In trials dealing with C. difficile infection, a single robiota composition. Probiotics, instead, are not all the
infusion of feces has usually been administered, with same, and thinking in terms of different strains is probably

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Intern Emerg Med (2014) 9:365–373 371

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