Analysis of bacterial bowel communities of ibd patients: what has it revealed?

Analysis of Bacterial Bowel Communities of IBD Patients: Harry Sokol, MD,* Christophe Lay, PhD,† Philippe Seksik, MD, PhD,* and Gerald W. Tannock, PhD‡ the tissue, it is probably best for the present to consider it a Abstract: The bacterial community, in whole or in part,
pathogen and for its presence to be termed an infection.7 The resident in the bowel of humans is considered to fuel the terminal ileum and the large bowel are hospitable places for chronic immune inflammatory conditions characteristic of microbial proliferation because bowel motility is slower, and Crohn’s disease and ulcerative colitis. Chronic or recurrentpouchitis in ulcerative colitis patients is responsive to antibi- microbial communities (mostly bacterial species) reside in otic therapy, indicating that bacteria are the etiological these sites. The surfaces of undigested plant fragments in the agents. Microbiological investigations of the bacterial com- digesta have adherent bacterial associates that are involved in munities in stool or of biopsy-associated bacteria have so far the breakdown of complex carbohydrate molecules, just as failed to reveal conclusively the existence of pathogens or occurs in the rumen of sheep and cows.8 The microbiota of bacterial communities of consistently altered composition in feces represents the microbiology of the distal large bowel IBD patients relative to control subjects. Confounding factors and does not necessarily apply to other regions, even of the need to be eliminated from future studies by using better- colon, and certainly not of the terminal ileum.
defined patient populations of newly diagnosed and untreated The existence of a discrete bacterial community asso- individuals and by improved sampling procedures.
ciated with the mucosal surface of the human bowel has been (Inflamm Bowel Dis 2008;14:858 – 867) postulated by researchers who have drawn on knowledge ofthe distribution of bacteria in the proximal colon of mice.9 Key Words: bowel bacteria, microbiota, microbial communities,
Accurate definition of the mucosa-associated community re- commensals, inflammatory bowel diseases, Crohn’s disease, ulcer-ative colitis, pouchitis mains difficult because mucosal biopsy specimens must becollected: an invasive procedure that is ill-defined in terms ofcollection procedure from study to study. Prior to colonos- The remnants of microbial cells, particularly bacterial copy and biopsy the patient is purged to remove bowel DNA, can be detected along the entire length of the contents. The effect of this preparative treatment on the gastrointestinal tract.1–5 This does not mean, however, that composition of the bowel community has been little investi- bacterial communities colonize all regions of the gut. Not all gated.10 Further, the bowel is not completely decontaminated parts of the gut are suitable for microbial persistence: the acid by this procedure and a fecal fluid continues to be present in secreted in the stomach and the swift flow of contents in the the bowel and to bathe mucosal surfaces. Therefore, it is not duodenum and jejunum ensure that the more proximal re- clear what is being sampled: the mucosal surface contami- gions contain only transient microbial cells in the healthy nated with luminal bacteria or true mucosal inhabitants.11 human host.6 Helicobacter pylori associates with the epithe- Additionally, the extent of contamination of the colonoscope lial surface of the gastric and duodenal mucosa, but since the with bacteria from the fecal fluid has never been determined.
presence of this organism is associated with inflammation of Therefore, reports about the mucosa-associated communityof humans must be treated with caution. At the least, thesestudies have relieved the previous focus on the fecal bacterial Received for publication December 13, 2007; Accepted December 17, community: they now seek to define the microbiology of From the *Gastroenterology and Nutrition Unit, Saint-Antoine Hospital, Feces, and therefore by inference distal large bowel APHP, Paris, France, †Institute of Microelectronics, A*STAR (Agency for contents, contain about 1011 bacterial cells per gram (wet Science, Technology and Research), Singapore, ‡Department of Microbiol- weight) and bacterial cells comprise about 50% of fecal ogy and Immunology, University of Otago, Dunedin, New Zealand.
Reprints: G. W. Tannock, Department of Microbiology and Immunology, mass.12 Four bacterial phyla are represented (Firmicutes, University of Otago, PO Box 56, Dunedin, New Zealand Bacteroidetes, Actinobacteria, and Proteobacteria) and 3 phy- (e-mail: [email protected]).
logenetically broad groups, each containing many genera and Copyright 2008 Crohn’s & Colitis Foundation of America, Inc.
species, are numerically dominant in the feces of healthy DOI 10.1002/ibd.20392Published online 14 February 2008 in Wiley InterScience (www.interscience.
humans (clostridial cluster XIVa [Clostridium coccoides group], clostridial cluster IV [Clostridium leptum subgroup], Inflamm Bowel Dis ● Volume 14, Number 6, June 2008 Inflamm Bowel Dis ● Volume 14, Number 6, June 2008 Bacterial Bowel Communities of IBD Patients Bacteroides-Prevotella group).13,14 Bacteria dominate the as-yet-unidentified factors associated with the pouch con- bowel community but fungi and Archaea may also be resi- tents. Empirical success in the treatment of pouchitis with dent, comprising less than 0.05% and 1% of the total inhab- antibiotics points, however, to bacteria or bacterial products itants, respectively.15,16 Much of the information pertaining to as the likely factors with which the immune system reacts.31 the residents of the bowel has been generated through theapplication of nucleic acid-based methodologies, most of BOWEL COMMENSALS AND CD: FECAL ANALYSES
which target the nucleotide base sequence of small ribosomal A variety of molecular methods have been used to subunit RNA (16S rRNA in the case of bacteria), which analyze the composition of the fecal community of IBD provides a cornerstone of microbial taxonomy. An earlier patients relative to controls. The phylogenetic composition of estimate of the number of bacterial species that might be the fecal community has notable temporal stability in healthy resident in the human large bowel was based on bacteriolog- humans considered individually. In CD patients, however, ical culture. Four hundred species seemed a likely number by temporal instability of the fecal microbiota has been reported.
extrapolation from what had already been cultured.17,18 Nu- Seksik et al32 showed that the dominant members of the fecal cleic acid-based methods of detection suggest that about 50% microbiota varied markedly between remission and flare.
of the bacterial cells seen microscopically in feces cannot yet Scanlan et al33 showed that there was less temporal stability be cultured in the laboratory, even when accounting for the of the dominant fecal microbiota in CD patients compared fact that some of them are dead.19,20 “Operational taxonomic with controls, even in those who stayed in remission until the units” (OTU; molecular species) never encountered in cul- end of the study. A decrease in the number of OTU (reduced ture-based bacteriology are detectable by molecular analyti- biodiversity) has also been reported in relation to the fecal cal methods. Estimates of biodiversity now seem to contin- community of CD patients. The main observation was that ually inflate but pollution of databanks with chimeric and fewer types of Firmicutes (43 in controls versus 13 in CD) other inaccurate sequences mean that about 5% of sequences were detected. Clostridial cluster IV (Clostridium leptum are unreliable.21,22 Curiously, therefore, despite the applica- subgroup) formed a smaller proportion of the fecal commu- tion of state-of-the-art technology, we still do not really nity in CD patients than in controls. Bacteroides and clos- know, in any accurate detail, the composition of the bowel tridial cluster XIVa populations were not different between groups. This outcome has been replicated in other studies.
Crohn’s disease (CD) and ulcerative colitis (UC) are Hence, Scanlan et al33 reported that they failed to detect chronic immune inflammatory conditions of the alimentary members of clostridial cluster IV in 27% of CD fecal samples tract referred to collectively as inflammatory bowel diseases (polymerase chain reaction, PCR) but all control samples (IBD). CD lesions can occur even in upper regions of the tract contained these bacteria (P Ͻ 0.0001). Taken together, these but are usually located where there are microbial residents results showed a quantitative and a qualitative (biodiversity) (ileum and colon), whereas UC is limited to the large bowel.
reduction in representation of the Firmicutes phylum, and Experimental animal models of colitis do not mimic exactly particularly clostridial cluster IV members in the feces of CD CD or UC but can be used to examine the role of specific patients. This phylogenetic group contains several butyrate- bacteria in the etiology of enterocolitis in general terms. The producing bacteria, such as Faecalibacterium prausnit- results of this work provide the best evidence that bacteria zii.34–36 Butyrate and other short chain fatty acids are be- resident in the bowel of the animals have an essential role in lieved to be important sources of energy for colonic epithelial the pathogenesis of colitis because, when maintained germ- cells and may have immunomodulator and antiinflammatory free, the animals do not develop disease.23 Current interest properties.37–39 Hence, the decrease in butyrate-producing therefore focuses on the bowel community as the source of bacteria in the colon might have a detrimental effect on the antigens that fuel the chronic inflammation seen in IBD.
colonic epithelium. There seems to be little agreement as to Chronic or recurrent pouchitis is the most common differences in fecal populations of lactobacilli and bifidobac- cause of troublesome, long-term functional disturbance for teria, sometimes regarded as “beneficial” bacteria, between patients with pouches created by ileo-anal anastomosis fol- lowing removal of the large bowel to cure UC.24 Pelvic Quantitative differences in enterobacterial populations pouches show varying degrees of chronic mucosal inflamma- have been reported. Giaffer et al41 reported that patients with tion and other alterations described as “colonic phenotype active CD had significantly larger Escherichia coli fecal change.”25–27 In some patients, however, acute inflammation populations than did patients with quiescent disease or nor- and clinical pouchitis develop by a process that possibly mal controls. In a further study, they showed that enteroad- parallels UC.28 Pouchitis is less common in pouches formed herent E. coli were frequently associated with CD.42 Simi- in patients because of familial adenomatous polyposis (FAP) larly, Seksik et al32 detected enterobacteria in all samples than in patients with UC.29,30 It appears, therefore, that the from CD patients but in none of the samples from controls.
dysfunctional immune system of UC patients reacts with Conflicting data are available with respect to members Inflamm Bowel Dis ● Volume 14, Number 6, June 2008 of the Bacteroidetes phylum. In some studies a decrease in difference in the microbiology of affected and unaffected the Bacteroides group32 or in the B. fragilis subgroup33 was mucosa. One study has contradicted these results,62 but in that reported, whereas other authors have reported an increase in report the authors pooled all inflamed and noninflamed bi- the B. fragilis subgroup, particularly in B. vulgatus and re- opsy data and then made comparisons regardless of the sub- lated species.44,45 The relative biodiversity of the B. fragilis ject, gut location, or disease (CD as well as UC).
subgroup may be reduced,33,46 although the Bacteroidetes As in fecal studies reviewed above, members of the phylum biodiversity seemed to be conserved.46 Firmicutes have been reported to be less prevalent in CDpatients. Two studies using clone library analysis retrieved BOWEL COMMENSALS AND CD: MUCOSAL
fewer sequences from the Firmicutes,52,63 particularly from SURFACE ANALYSIS
the Lachnospiraceae subgroup.63 Among this subgroup, Fae- The preparation of mucosal specimens (biopsies) has calibacterium prausnitzii seems to be lacking in CD patients.
differed from one study to another: samples have sometimes Martinez-Medina et al61 compared the biopsy-associated bac- been washed (with different buffers) or not, and the fixative teria of 19 CD patients with mildly active disease and 15 used to prepare specimens has varied. These differences in controls; F. prausnitzii was found in 13 of 15 controls sample preparation, and the analytical methods used in their (86.7%), whereas the prevalence in CD patients was 52.6% analysis, doubtless influence the outcome of assays and help (P ϭ 0.035). Frank et al63 also reported that F. prausnitzii to explain the variation in results reported from laboratory to laboratory. There is a consensus, however, that larger num- Outcomes of analyses with respect to members of the bers of bacteria are associated with bowel biopsies collected phylum Bacteroidetes have differed. Some authors have from CD patients compared to controls.47–51 This increased noted an increase in the prevalence of this phylum,50–52 while concentration seems to concern anaerobes as well as faculta- others report a decrease.63 On the other hand, a pediatric tive bacteria52,53 and may be due to a disruption in antibac- study detected a decrease in the concentration of B. vulga- terial barrier function.54 The ileal expression of alpha-de- tus.47 It is difficult to reach a consensus view about this from fensins (HD-5 and HD-6) is diminished in ileal CD,5,6 while the literature. The concentration of enterobacteria may be beta-defensin (HBD-2 and HBD-3) expression is weakly increased50,61,64 and may be phenotypically different than induced in colonic CD compared to UC.7,8 This relative commensal E. coli. Darfeuille-Michaud et al65 isolated E. coli defensin deficiency could also allow intestinal microbes to from resected chronic ileal lesions and from neoterminal invade the mucosa, as reported in some studies48,51 or, more ileum (with and without CD recurrence) after surgery. Many rarely, to permit colonization of intestinal crypts.51,59 How- of the isolates from diseased ileum adhered to Caco-2 cells.
ever, other authors did not observe bacteria directly attached Those authors confirmed, in a subsequent study, that an to the epithelial cells or intracellular bacteria.49,59 It is notable adherent-invasive type of E. coli (AIEC; reference strain that the biopsy specimens were not fixed in the same manner LF82) was specifically associated with ileal mucosa in some in these studies (some samples were fixed in nonaqueous CD patients.66 Kotlowski et al64 studied rectocolonic biopsies Carnoy solution,51 whereas others were fixed in 4% buffered from IBD patients and healthy subjects by generating elec- formalin48,49,59), perhaps indicating the importance of sample trophoretic fingerprints. DNA fragments unique to patients originated from E. coli. Culture-based studies detected larger As in fecal microbiota analysis, a reduction in the numbers of enterobacteria associated with IBD patient biop- biodiversity of biopsy-associated bacteria has been reported sies compared to controls. Moreover, the abundance of the in CD patients. Ott et al60 used an electrophoretic method to “B2ϩD” E. coli groups was significantly greater in patients detect biopsy-associated bacterial collections of 26 active CD than in controls. Genotypic characteristics such as serine patients, and 46 controls (31 noninflammatory controls and protease autotransporters (a unique class of transporters 15 inflammatory controls composed of undetermined colitis, found in the Enterobacteriaceae that have been implicated in infectious colitis, and radiation colitis). They found a reduc- virulence), as well as possible adhesins have been detected in tion in biodiversity that was indicated by a decrease in the these E. coli strains.64 Other bacterial species which, although number of bands and of weighted diversity indices in elec- not bowel commensals, have been investigated in relation to CD (Listeria and Mycoplasma)67,68 but a role for these bac- The patchy distribution of the intestinal tract lesions in teria in the pathogenesis of IBD has not been confirmed.
CD in normal-looking mucosa, side-by-side with deep ulcer- Mycobacterium avium subspecies paratuberculosis (MAP) ations, encouraged investigators to search for a localized has long been suspected to be involved in CD pathogenesis.
detection of possible “pathogens.” Three studies using 16S MAP was isolated by culture from the bowel of 6 of 7 (86%) rRNA gene clone libraries to catalog the composition of the CD patients in the United States,69 detected by IS900 in situ bacterial collections and 3 other studies using electrophoretic hybridization with fixed gut tissue from 27 of 33 (82%) CD methods1,32,52,53,61 did not find any statistically significant patients in Italy,70 detected by nested PCR IS900 with a Inflamm Bowel Dis ● Volume 14, Number 6, June 2008 Bacterial Bowel Communities of IBD Patients TABLE 1. Summary of Bacteriological Observations in CD
Increased concentration of total bacteria Increased concentration of total and facultative anaerobes Bacterial invasion of the mucosa and presence of No difference between injured and healthy ileo-colonic Firmicutes (particularly C. leptum group) decreased quantitatively and in biodiversity Decreased concentration of Faecalibacterium prausnitzii Increased concentration of the pathogenic E. coli B2ϩD aReferences related to fecal microbiota.
bReferences related to mucosa-associated bacteria.
MAM, mucosa-associated microbes; AIEC, adherent, invasive E. coli; MAP, Mycobacterium avium subspecies pseudotuberculosis.
significantly higher rate in CD patients than in controls in otrexate, 6-mercaptopurine, 5-amino-salicylic acid, and sul- United Kingdom71 and in the USA (40% of the CD patients fapyridine have been recently shown to inhibit MAP growth with granulomas, none of 22 non-IBD controls).72 Ryan et in vitro,81,82 it is difficult to resolve the beneficial effects of al73 detected MAP by nested PCR in 40% of the CD granu- TNF␣ blockade, which is known to cause disseminated tu- lomas (and in none of the 12 granulomatous disease controls), berculosis, but which has not been associated with MAP and Hulten et al72 detected MAP in macrophages and myo- infection in CD patients. Finally, MAP was not detected in fibroblasts. Naser et al74 detected viable MAP in peripheral CD patients in a large-scale 16S rRNA gene library study blood cells in a higher proportion of individuals with CD than (more than 15,000 small subunit ribosomal RNA genes ana- in controls. Several trials have tested the efficacy of antimy- cobacterial therapy in CD, but most of them are open to A summary of investigations relating to CD is provided criticism because of inappropriate use of antibiotics (use of ethambutol or isoniazid,75,76 which are not effective againstMAP complex infection; use of single instead of combined BOWEL COMMENSALS AND ULCERATIVE COLITIS:
antibiotic treatment77), open label design,77–79 or concomitant FECAL ANALYSES
steroid therapy.75,77,78 A recently published Australian trial There are relatively few studies of the fecal microbiota avoided these biases.80 This large placebo-controlled, double- of UC patients and it is difficult to make sense of the outcome blinded, randomized trial evaluated the efficacy of 2-year of disparate studies. Clustering of UC patients’ profiles has combination therapy with clarithromycin, rifabutin, and clo- been reported and, as in CD investigations, the composition fazimine in maintaining clinical remission following cortico- of the fecal microbiota of UC patients may be less biodiverse steroid withdrawal. The proportion of patients who relapsed (reduction in representation of Firmicutes phylum) than in the at 1, 2, and 3 years was not significantly different between the case of controls,83,84 perhaps containing an increased propor- group under an antibiotics regimen and the placebo group.
tion of bacteria not normally present in feces.43 Total Lacto- The trend observed at 1 year (39% of relapse in the antibiotic bacillus numbers have been reported to be reduced in fecal group versus 56% in the placebo group, P ϭ 0.054) was samples from patients with active UC when compared to attributed by the authors to the broad spectrum activity of those in remission (6 patients in each group).85 antibiotics against luminal organisms as induction therapy.
In a study utilizing culture methods, enteroadherent E. The authors concluded that these results did not support a coli were associated frequently with samples from UC pa- pathogenic role for MAP in CD. Moreover, although meth- tients as well as CD patients.42 Moreover, E. coli has been Inflamm Bowel Dis ● Volume 14, Number 6, June 2008 TABLE 2. Summary of Bacteriological Observations in UC
Increased concentration of total bacteria Increased concentration of total anaerobes Bacterial invasion of the mucosa and presence of bacteria No difference between injured and healthy colonic Difference between injured and healthy colonic Firmicutes (particularly C. coccoides group) Increased concentration of the pathogenic E. coli B2ϩD Enteroadherent E. coli associated with UC Increased concentration of “active” E. coli aReferences related to fecal microbiota.
bReferences related to mucosa-associated microbiota.
MAM, mucosa-associated microbes; SRB, sulfate-reducing bacteria.
shown to be more prevalent and metabolically active in the bacilli and members of clostridial cluster IV were reduced in microbiota of UC patients compared to controls.84 prevalence when ulcerated and nonulcerated tissues were Sulfate-reducing bacteria are bowel bacteria that pro- compared (average similarity: 59.9 Ϯ 26.1% and 79.2 duce hydrogen sulfide,86 which could inhibit butyrate oxida- tion and result in colonic lesions. It has been proposed, The clostridial cluster XIVa (Clostridium coccoides therefore, that in UC butyrate oxidation could be dis- group) population associated with the mucosa may have turbed.87–89 Short chain fatty acid enemas have been used reduced prevalence in UC patients.51 Rectal biopsies studied with limited success to treat refractory distal colitis.90–91 by Mylonaki et al93 showed that the epithelium-associated Pitcher et al92 showed that the microbiota of active UC counts of bifidobacteria in active and quiescent UC patients patients contained a higher concentration of sulfate-reducing were lower than in controls. Variations in the Bacteroidetes bacteria than UC patients in remission phase. Moreover, in phylum have been reported. Both increased detection50,51 and the same study 5-ASA inhibited sulfide production in a dose- reduced detection relative to controls have been reported.63 dependent manner in vitro, and stool of UC patients not Conte et al47 reported a lower occurrence of B. vulgatus in administered these drugs had a higher fecal sulfide concen- UC patients compared to controls. Finally, according to a number of authors, enterobacteria are more commonly asso-ciated with UC mucosa,50,64,93 particularly E. coli from BOWEL COMMENSALS AND ULCERATIVE COLITIS:
“B2ϩD” groups, than in healthy subjects.64 BIOPSY ANALYSES
Studies relating to UC patients are summarized in Table As in the case of CD, UC patients were reported to have 2 and a comparison with the outcomes of CD investigations higher concentrations of bacteria,48–51 particularly anaer- obes,50 associated with mucosal samples compared to con-trols. In some studies, bacterial cells were observed micro- MICROBIOLOGY OF POUCHITIS: CULTURE-
scopically in the mucosa or within crypts.48,51,93 Ott et al60 DEPENDENT APPROACH
reported a decrease in biodiversity that was comparable tothat of CD patients. In general, the mucosa-associated bacte- Luminal Microbiota
rial collection did not seem to differ between inflamed and Ruseler-van Embden et al98 analyzed the bacterial com- noninflamed tissues in UC patients,1,94,95 although Zhang et position of the ileal reservoir from patients that had under- al95 revealed differences in subdominant populations. Lacto- gone a restorative proctocolectomy either for ulcerative co- Inflamm Bowel Dis ● Volume 14, Number 6, June 2008 Bacterial Bowel Communities of IBD Patients TABLE 3. Comparisons Between UC and CD Gut Microbiota
Increased concentration of total bacteria C. leptum group and particularly F. Bifidobacteria and lactobacilli decreased Enteroadherent E. coli associated with Increased concentration of “active” E. Increased concentration of the pathogenic aReferences related to CD microbiota.
bReferences related to UC microbiota.
MAM, mucosa-associated microbes; AIEC, adherent, invasive E. coli; MAP, Mycobacterium avium subspecies pseudotuberculosis; SRB, sulfate-reducingbacteria.
litis (n ϭ 12) or familial adenomatous polyposis (n ϭ 2). The pouches of UC patients. Ohge et al100 have also shown an study was carried out at least 1 year after the surgery and 5 association between sulfate-reducing bacteria and pouches.
patients were diagnosed with pouchitis. Two fecal samples Sulfate-reducing bacteria were detected in higher numbers in were collected from each subject of the pouch control group active pouchitis patients (n ϭ 8) in comparison to patients (n ϭ 9) with an interval of at least 2 months. Plate counts without a history of pouchitis (n ϭ 8), patients with past showed large differences in the anaerobic bacterial composi- episode(s) of pouchitis (n ϭ 18), patients having an ongoing tion between 2 samples taken at different times, suggesting antibiotic treatment for pouch inflammation (n ϭ 11), and that the noninflamed pouch has a bacterial community of familial adenomatous polyposis patients (n ϭ 5). The authors unstable composition. Compared to the control group, pou- observed that this particular group of bacteria was sensitive to chitis patients showed an increased number of aerobes, de- antibiotic treatment (metronidazole or ciprofloxacin).
creased ratio of anaerobes to aerobes, less bifidobacteria and Gosselink et al101 monitored the fecal microbiota of lactobacilli, and a large number of Clostridium perfringens.
patients diagnosed with UC and having undergone a pouch Duffy et al99 compared the pouch bacterial content construction (n ϭ 13). The aim of this study was to compare from UC patients (n ϭ 10) and familial adenomatous polyp- the effect of 2 antibiotics, metronidazole and ciprofloxacin, osis (n ϭ 7). None of the patients had had a previous episode on the fecal microbiota at different times. The bacteriological of pouch inflammation. Plate enumerations did not indicate content of the pouch was analyzed at the beginning of an significant differences between the 2 groups of patients re- inflammatory episode before antibiotic treatment, during garding lactobacilli, Clostridium perfringens, Bacteroides, treatment with ciprofloxacin or metronidazole, and during and Bifidobacterium groups. Enterococci and coliforms were pouchitis-free periods. In the absence of inflammation the also similar in numbers between both groups. However, vi- pouch microbiota was characterized by the presence of lac- able sulfate-reducing bacteria were exclusively detected in tobacilli and large numbers of anaerobes. During pouchitis Inflamm Bowel Dis ● Volume 14, Number 6, June 2008 episodes there was a decrease of anaerobes, increase of aer- clone libraries. Using ␥-Proteobacteria/Enterobacteriaceae obic bacteria, lower numbers of lactobacilli, higher numbers group-specific primers, slight differences in terms of phylo- of Clostridium perfringens, and hemolytic strains of E. coli typic composition were observed between the placebo and (in half of the patients) were observed. Administration of VSL#3 groups. Enterobacter species and E. coli were mainly metronidazole eradicated the anaerobic microbiota including identified. Lactobacillus and Bifidobacterium clone libraries C. perfringens. Treatment with ciprofloxacin inhibited not generated from the VSL#3 group displayed a diverse spec- only the growth of C. perfringens but also that of coliforms, trum of species in comparison with the 2 other experimental including hemolytic strains of E. coli. However, ciprofloxacin groups (pretreatment remission [n ϭ 15] and placebo group did not significantly affect the anaerobic microbiota.
[n ϭ 5]). Some of these species were those included in theprobiotic preparation. Analysis of the mucosa-associated mi- Mucosa-Associated Bacteria
crobiota using an electrophoretic fingerprinting technique Using an ex vivo lymphocyte stimulation assay, Bell et showed that VSL#3 therapy increased the bacterial diversity al102 demonstrated the presence of proinflammatory sub- in comparison with pretreatment remission and placebo ad- stances in pouchitis-derived bacterial sonicates. Biopsy sam- ples taken from healthy pouch and pouchitis patients (UC Bacterial colonization of the pouch mucosa was mon- patients) were smeared on agar plates. Bacterial sonicates itored during the first year after pouch construction in 2 UC were prepared from a pool of colonies grown under aerobic patients.106 Neither of the patients had pouchitis during the and anaerobic conditions. Sonicates were also prepared from study. Biopsy samples from the pouches were taken at the strictly anaerobic bacteria grown on agar plates containing time of pouch construction, at closure of the ileostomy, and at metronidazole. Using lymphocyte proliferation as an indica- routine clinical examinations at 1, 3, and 12 months after tor of inflammation, the authors showed that sonicates of ileostomy closure. A variety of molecular analyses were bacteria from pouchitis samples produced an intense stimu- applied to monitor, identify, and characterize the develop- lation of the mononuclear cells. On the contrary, in sonicates ment of the bacterial microbiota in the newly formed pouch.
extracted from bacteria cultured from noninflamed pouches, Instability of the pouch bacterial community was indicated, cell proliferation was minimal. Moreover, when bacterial but most of the bacteria were affiliated with clostridial cluster sonicates were prepared from pouchitis colonies grown on XIVa, clostridial cluster IV, Bacteroides, and Enterobacteri- metronidazole-supplemented medium the proliferation effect aceae groups. Clones similar to clostridial cluster I (C. per- was abolished, suggesting inhibition of the growth of proin- fringens group) were also present in all samples from both flammatory bacteria. Although a bacterial etiology for pou- chitis was supported by this work, it was not possible to In the study of Komanduri et al,107 mucosa-associated pinpoint a particular bacterial species or group of bacteria bacteria in pouchitis was investigated. Twenty UC patients responsible for the proinflammatory effect.
having undergone proctocolectomy and ileal pouch-analanastomosis were enrolled in the study. Biopsy specimens MICROBIOLOGY OF POUCHITIS: CULTURE-
were taken from 5 patients with active pouchitis and 15 INDEPENDENT APPROACH
patients presenting without signs of pouch inflammation. A A beneficial effect of administration of the probiotic fingerprinting technique showed mucosa-associated micro- VSL#3 following antibiotic treatment has been demonstrat- biota patterns unique to each individual. Moreover, specific bacterial amplicons were unique to active pouchitis mucosa: 103,104 VSL#3 contains 300 billion viable lyophilized bac- teria per gram, comprising lactobacilli, bifidobacteria, and clostridial cluster XIVa, Enterobacteriacae, and streptococci were associated with control pouches. Streptococci were ab- randomized, placebo-controlled trial to study the impact of VSL#3 on the dominant mucosa-associated bacteria fromchronic pouchitis patients in remission induced by antibiotics.
Biopsy specimens collected from 15 patients before and after Microbiological analysis of bowel samples from IBD a period of 2 months therapy (10 received VSL#3 and 5 patients is plagued with sampling and technical problems. To placebo) were examined using microscopy and PCR-based the forefront are the remoteness of the fecal community from approaches. The authors observed that the mucosal micro- the sites of inflammation in the bowel, variables associated biota was mainly detected within the epithelium and nearly with the collection of biopsies from bowels that have already all bacteria were affiliated with the Enterobacteriaceae been altered by preparative measures necessary for colonos- group. Compared to the placebo group, an increase in Enter- copy, recruiting matched patients and controls in sufficient obacteriaceae within the mucosa during VSL#3 therapy was numbers to guarantee appropriate statistical power for stud- observed. Investigation at the molecular species level was ies, reliance on single samplings of patients and controls, carried out with the construction of taxonomic group-specific previous or concurrent therapeutic drugs administered to pa- Inflamm Bowel Dis ● Volume 14, Number 6, June 2008 Bacterial Bowel Communities of IBD Patients tients, and a relatively broad spectrum of “normal micro- colonoscopy on post-procedure intestinal microbiota composition. Gut. biota” compositions even in healthy humans. Technical prob- 11. Bibiloni R, Tandon P, Vargas-Voracka F, et al. Differential clustering lems include the noncultivability of a large proportion of the of bowel biopsy-associated bacterial profiles of specimens collected in bowel bacterial community, analytical reliance on a polluted Mexico and Canada: what do these profiles represent? J Med Micro- databank of 16S rRNA gene sequences, relatively shallow 12. Suau A, Bonnet R, Sutren M, et al. Direct analysis of genes encoding phylogenetic analyses due to the nature of the available 16S rRNA from complex communities reveals many novel molecular analytical tools, and PCR bias, which results in preferential species within the human gut. Appl Environ Microbiol. 1999;65:4799 – amplification of 16S rRNA gene sequences from some bac- 13. Franks AH, Harmsen HJM, Raangs GC, et al. Variations of bacterial populations in human feces measured by fluorescent in situ hybridiza- Particular strains of E. coli may be associated with tion with group-specific 16S rRNA-targeted oligonucleotide probes.
disease in a subset of CD patients and biodiversity of the Appl Environ Microbiol. 1998;64:3336 –3345.
14. Lay C, Rigottier-Gois L, Holmstrom K, et al. Colonic microbiota bowel microbiota may be reduced in IBD, especially in CD signatures across five northern European countries. Appl Environ Mi- patients. Little information that can aid clinicians in the crobiol. 2005;71:4153– 4155.
treatment of IBD has been produced, however, from phylo- 15. Miller TL, Wolin MJ. Stability of Methanobacter smithii populations in the microbial flora excreted from the human large bowel. Appl Environ genetic analyses. Thus, microbiologists must feel disappoint- Microbiol. 1983;45:317–318.
ment at their lack of achievement so far. There is much 16. Simon GL, Gorbach SL. Intestinal flora in health and disease. Gastro- disagreement between research groups as to the results of enterology. 1984;86:174 –193.
17. Finegold SM, Attebury R, Sutter VL. Effect of diet on human fecal various studies, probably as a result of the confounding flora: comparison of Japanese and American diets. Am J Clin Nutr. New approaches need to be applied to the study of the 18. Moore WEC, Holdeman LV. Special problems associated with the isolation and identification of intestinal bacteria in fecal flora studies.
bowel bacteria in relation to IBD. Screening the functions of Am J Clin Nutr. 1974;27:1450 –1455.
the microbiota using metagenomic libraries may be useful, as 19. Ben-Amor K, Heilig H, Smidt H, et al. Genetic diversity of viable, may the application of new micromolecular analytical meth- injured, and dead fecal bacteria assessed by fluorescence-activated cellsorting and 16S rRNA gene analysis. Appl Environ Microbiol. 2005; ods.108–111 Nevertheless, the main improvements in the qual- ity of microbiological investigations of IBD patients will rely 20. Tannock GW, Munro K, Harmsen HJM, et al. Analysis of the fecal on the more careful selection of patients (perhaps aided by microflora of human subjects consuming a probiotic product containingLactobacillus rhamnosus DR20. Appl Environ Microbiol. 2000;66:2578– human genotyping), the recruitment of newly diagnosed and untreated patients, and greater attention to the way in which 21. Ashelford KE, Chuzhanova NA, Fry JC, et al. At least 1 in 20 16S specimens to be used in microbiological investigations are rRNA sequence records currently held in public repositories is esti-mated to contain substantial anomalies. Appl Environ Microbiol. 2005; collected. More thoughtful planning of studies are thus needed in order to improve microbiological studies in IBD.
22. Ashelford KE, Chuzhanova NA, Fry JC, et al. New screening software shows that most recent large 16S rRNA gene clone libraries contain REFERENCES
chimeras. Appl Environ Microbiol. 2006;72:5734 –5741.
23. Sartor RB. Microbial influences in inflammatory bowel disease: role in 1. Bibiloni R, Mangold M, Madsen KL, et al. The bacteriology of biopsies pathogenesis and clinical implications. Amsterdam: Elsevier Publish- differs between newly diagnosed, untreated, Crohn’s disease and ul- cerative colitis patients. J Med Microbiol. 2006;55:1141–1149.
24. Sandborn WJ. Pouchitis following ileal pouch-anal anastomosis: 2. Bik EM, Eckburg PB, Gill SR, et al. Molecular analysis of the bacterial definition, pathogenesis, and treatment. Gastroenterology. 1994;107: microbiota in the human stomach. Proc Natl Acad Sci U S A. 2006; 25. Fruin AB, El-Zammer O, Stucchi AF, et al. Colonic metaplasia in the 3. Eckburg PB, Bik EK, Bernsteinet CN, et al. Diversity of the human ileal pouch is associated with inflammation and is not the result of intestinal microbial flora. Science 2005;308:1635–1638.
long-term adaptation. J Gastrointest Surg. 2003;7:246 –253.
4. Hayashi H, Takahashi R, Nishi T, et al. Molecular analysis of jejunal, 26. Thompson-Fawcett MW, Marcus VA, Redston M, et al. Risk of dys- ileal, caecal and recto-sigmoidal human colonic microbiota using 16S plasia in long-term ileal pouches and pouches with chronic pouchitis.
rRNA gene libraries and terminal restriction fragment length polymor- Gastroenterology. 2001;121:275–281.
phism. J Med Microbiol. 2005;54:1093–1101.
27. Thompson-Fawcett MW, Marcus VA, Redston M, et al. Adenomatous 5. Wang M, Ahrne S, Jeppsson B, et al. Comparison of bacterial diversity polyps develop commonly in the ileal pouch of patients with familial along the human intestinal tract by direct cloning and sequencing of adenomatous polyposis. Dis Colon Rectum 2001;44:347–353.
16S rRNA genes. FEMS Microbiol Ecol. 2005;54:219 –231.
28. Thompson-Fawcett MW. Pouchitis and pouch dysfunction. In: Satsangi 6. Savage DC. Microbial ecology of the gastrointestinal tract. Annu Rev J, Sutherland L, eds. Inflammatory Bowel Diseases. Amsterdam: Microbiol. 1977;31:107–133.
7. Lee A. Helicobacter pylori: opportunistic member of the normal mi- 29. Achkar JP, Al-Haddad M, Lashner B, et al. Differentiating risk factors croflora or agent of communicable disease? In: Tannock GW, ed.
for acute and chronic pouchitis. Clin Gastroenterol Hepatol. 2005;3: Medical Importance of the Normal Microflora. London: Kluwer Aca- 30. Ambroze WL, Dozois RR, Pemberton JH, et al. Familial adenomatous 8. Macfarlane S, Macfarlane GT. Composition and metabolic activities of polyposis: results following ileal pouch-anal anastomosis and ileorect- bacterial biofilms colonizing food residues in the human gut. Appl ostomy. Dis Colon Rectum. 1992;35:12–15.
Environ Microbiol. 2006;72:6204 – 6211.
31. Madden MV, McIntyre AS, Nicholls RJ. Double-blind crossover trial 9. Savage DC, Dubos R, Schaedler RW. The gastrointestinal epithelium of metronidazole versus placebo in chronic unremitting pouchitis. Dig and its autochthonous bacterial flora. J Exp Med. 1968;127:67–76.
Dis Sci. 1994;39:1193–1196.
10. Mai V, Greenwald B, Morris JG, et al. Effect of bowel preparation and 32. Seksik P, Rigottier-Gois L, Gramet G, et al. Alterations of the dominant Inflamm Bowel Dis ● Volume 14, Number 6, June 2008 faecal bacterial groups in patients with Crohn’s disease of the colon.
55. Wehkamp J, Harder J, Weichenthal M, et al. NOD2 (CARD15) muta- tions in Crohn’s disease are associated with diminished mucosal alpha- 33. Scanlan PD, Shanahan F, O’Mahony C, et al. Culture-independent defensin expression. Gut. 2004;53:1658 –1664.
analyses of temporal variation of the dominant fecal microbiota and 56. Wehkamp J, Salzman NH, Porter E, et al. Reduced Paneth cell alpha- targeted bacterial subgroups in Crohn’s disease. J Clin Microbiol. defensins in ileal Crohn’s disease. Proc Natl Acad Sci U S A. 2005; 34. Suau A, Bonnet R, Sutren M, et al. Direct analysis of genes encoding 57. Fahlgren A, Hammarstrom S, Danielsson A, et al. beta-Defensin-3 and 16S rRNA from complex communities reveals many novel molecular -4 in intestinal epithelial cells display increased mRNA expression in species within the human gut. Appl Environ Microbiol. 1999;65:4799 – ulcerative colitis. Clin Exp Immunol. 2004;137:379 –385.
58. Wehkamp J, Harder J, Weichenthal M, et al. Inducible and constitutive 35. Barcenilla A, Pryde SE, Martin JC, et al. Phylogenetic relationships of beta-defensins are differentially expressed in Crohn’s disease and ul- butyrate-producing bacteria from the human gut. Appl Environ Micro- cerative colitis. Inflamm Bowel Dis. 2003;9:215–223.
59. Vasquez N, Mangin I, Lepage P, et al. Patchy distribution of mucosal 36. Suau A, Rochet V, Sghir A, et al. Fusobacterium prausnitzii and lesions in ileal Crohn’s disease is not linked to differences in the related species represent a dominant group within the human fecal dominant mucosa-associated bacteria: a study using fluorescence in situ flora. Syst Appl Microbiol. 2001;24:139 –145.
hybridization and temporal temperature gradient gel electrophoresis.
37. Bohmig GA, Krieger PM, Saemann MD, et al. n-Butyrate downregu- Inflamm Bowel Dis. 2007;13:684 – 692.
lates the stimulatory function of peripheral blood-derived antigen- 60. Ott SJ, Musfeldt M, Wenderoth DF, et al. Reduction in diversity of the presenting cells: a potential mechanism for modulating T-cell re- colonic mucosa associated bacterial microflora in patients with active sponses by short-chain fatty acids. Immunology. 1997;92:234 –243.
inflammatory bowel disease. Gut. 2004;53:685– 693.
38. Klampfer L, Huang J, Sasazuki T, et al. Inhibition of interferon gamma 61. Martinez-Medina M, Aldeguer X, Gonzalez-Huix F, et al. Abnormal signaling by the short chain fatty acid butyrate. Mol Cancer Res. microbiota composition in the ileocolonic mucosa of Crohn’s disease patients as revealed by polymerase chain reaction-denaturing gradient 39. Segain JP, Raingeard de la Bletiere D, Bourreille A, et al. Butyrate gel electrophoresis. Inflamm Bowel Dis. 2006;12:1136 –1145.
inhibits inflammatory responses through NFkappaB inhibition: impli- 62. Sepehri S, Kotlowski R, Bernstein CN, et al. Microbial diversity of cations for Crohn’s disease. Gut. 2000;47:397– 403.
inflamed and noninflamed gut biopsy tissues in inflammatory bowel 40. Favier C, Neut C, Mizon C, et al. Fecal beta-D-galactosidase produc- disease. Inflamm Bowel Dis. 2007;13:675– 683.
tion and bifidobacteria are decreased in Crohn’s disease. Dig Dis Sci. 63. Frank DN, St Amand AL, Feldman RA, et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflam- 41. Giaffer MH, Holdsworth CD, Duerden BI. The assessment of faecal matory bowel diseases. Proc Natl Acad Sci U S A. 2007;104:13780 – flora in patients with inflammatory bowel disease by a simplified bacteriological technique. J Med Microbiol. 1991;35:238 –243.
64. Kotlowski R, Bernstein CN, Sepehri S, et al. High prevalence of 42. Giaffer MH, Holdsworth CD, Duerden BI. Virulence properties of Escherichia coli belonging to the B2ϩD phylogenetic group in inflam- Escherichia coli strains isolated from patients with inflammatory bowel matory bowel disease. Gut. 2007;56:669 – 675.
disease. Gut. 1992;33:646 – 650.
65. Darfeuille-Michaud A, Neut C, Barnich N, et al. Presence of adherent 43. Sokol H, Seksik P, Rigottier-Gois L, et al. Specificities of the fecal Escherichia coli strains in ileal mucosa of patients with Crohn’s dis- microbiota in inflammatory bowel disease. Inflamm Bowel Dis. 2006;12:106 –111.
ease. Gastroenterology. 1998;115:1405–1413.
44. Mangin I, Bonnet R, Seksik P, et al. Molecular inventory of faecal 66. Darfeuille-Michaud A, Boudeau J, Bulois P, et al. High prevalence of microflora in patients with Crohn’s disease. FEMS Microbiol Ecol. adherent-invasive Escherichia coli associated with ileal mucosa in Crohn’s disease. Gastroenterology. 2004;127:412– 421.
45. Ruseler-van Embden JG, Both-Patoir HC. Anaerobic gram-negative 67. Chen W, Li D, Paulus B, et al. Detection of Listeria monocytogenes by faecal flora in patients with Crohn’s disease and healthy subjects.
polymerase chain reaction in intestinal mucosal biopsies from patients Antonie Van Leeuwenhoek. 1983;49:125–132.
with inflammatory bowel disease and controls. J Gastroenterol Hepa- 46. Manichanh C, Rigottier-Gois L, Bonnaud E, et al. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic ap- 68. Huijsdens XW, Linskens RK, Taspinar H, et al. Listeria monocyto- proach. Gut. 2006;55:205–211.
genes and inflammatory bowel disease: detection of Listeria species in 47. Conte MP, Schippa S, Zamboni I, et al. Gut-associated bacterial mi- intestinal mucosal biopsies by real-time PCR. Scand J Gastroenterol. crobiota in paediatric patients with inflammatory bowel disease. Gut. 69. Schwartz D, Shafran I, Romero C, et al. Use of short-term culture for 48. Kleessen B, Kroesen AJ, Buhr HJ, et al. Mucosal and invading bacteria identification of Mycobacterium avium subsp. paratuberculosis in tis- in patients with inflammatory bowel disease compared with controls.
sue from Crohn’s disease patients. Clin Microbiol Infect. 2000;6:303– Scand J Gastroenterol. 2002;37:1034 –1041.
49. Schultsz C, Van Den Berg FM, Ten Kate FW, et al. The intestinal 70. Sechi LA, Mura M, Tanda F, et al. Identification of Mycobacterium mucus layer from patients with inflammatory bowel disease harbors avium subsp. paratuberculosis in biopsy specimens from patients with high numbers of bacteria compared with controls. Gastroenterology. Crohn’s disease identified by in situ hybridization. J Clin Microbiol. 50. Swidsinski A, Ladhoff A, Pernthaler A, et al. Mucosal flora in inflam- 71. Bull TJ, McMinn EJ, Sidi-Boumedine K, et al. Detection and verifi- matory bowel disease. Gastroenterology. 2002;122:44 –54.
cation of Mycobacterium avium subsp. paratuberculosis in fresh ileo- 51. Swidsinski A, Weber J, Loening-Baucke V, et al. Spatial organization colonic mucosal biopsy specimens from individuals with and without and composition of the mucosal flora in patients with inflammatory Crohn’s disease. J Clin Microbiol. 2003;41:2915–2923.
bowel disease. J Clin Microbiol. 2005;43:3380 –3389.
72. Hulten K, El-Zimaity HM, Karttunen TJ, et al. Detection of Mycobac- 52. Gophna U, Sommerfeld K, Gophna S, et al. Differences between terium avium subspecies paratuberculosis in Crohn’s disease tissues by tissue-associated intestinal microfloras of patients with Crohn’s disease in situ hybridization. Am J Gastroenterol. 2001;96:1529 –1535.
and ulcerative colitis. J Clin Microbiol. 2006;44:4136 – 4141.
73. Ryan P, Kelly RG, Lee G, et al. Bacterial DNA within granulomas of 53. Prindiville T, Cantrell M, Wilson KH. Ribosomal DNA sequence patients with Crohn’s disease— detection by laser capture microdissec- analysis of mucosa-associated bacteria in Crohn’s disease. Inflamm tion and PCR. Am J Gastroenterol. 2004;99:1539 –1543.
Bowel Dis. 2004;10:824 – 833.
74. Naser SA, Ghobrial G, Romero C, et al. Culture of Mycobacterium 54. Wehkamp J, Schmid M, Stange EF. Defensins and other antimicrobial avium subspecies paratuberculosis from the blood of patients with peptides in inflammatory bowel disease. Curr Opin Gastroenterol. Crohn’s disease. Lancet. 2004;364:1039 –1044.
75. Goodgame RW, Kimball K, Akram S, et al. Randomized controlled Inflamm Bowel Dis ● Volume 14, Number 6, June 2008 Bacterial Bowel Communities of IBD Patients trial of clarithromycin and ethambutol in the treatment of Crohn’s 94. Sokol H, Lepage P, Seksik P, et al. Molecular comparison of dominant disease. Aliment Pharmacol Ther. 2001;15:1861–1866.
microbiota associated with injured versus healthy mucosa in ulcerative 76. Thomas GA, Swift GL, Green JT, et al. Controlled trial of antituber- colitis. Gut. 2007;56:152–154.
culous chemotherapy in Crohn’s disease: a five year follow up study.
95. Zhang M, Liu B, Zhang Y, et al. Structural shifts of mucosa-associated lactobacilli and Clostridium leptum subgroup in patients with ulcerative 77. Leiper K, Morris AI, Rhodes JM. Open label trial of oral clarithromy- colitis. J Clin Microbiol. 2007;45:496 –500.
cin in active Crohn’s disease. Aliment Pharmacol Ther. 2000;14:801– 96. Seksik P, Lepage P, de la Cochetiere MF, et al. Search for localized dysbiosis in Crohn’s disease ulcerations by temporal temperature gra- 78. Borody TJ, Leis S, Warren EF, et al. Treatment of severe Crohn’s dient gel electrophoresis of 16S rRNA. J Clin Microbiol. 2005;43: disease using antimycobacterial triple therapy—approaching a cure? Dig Liver Dis. 2002;34:29 –38.
97. Lucke K, Miehlke S, Jacobs E, et al. Prevalence of Bacteroides and 79. Shafran I, Kugler L, El-Zaatari FA, et al. Open clinical trial of rifabutin Prevotella spp. in ulcerative colitis. J Med Microbiol. 2006;55:617– and clarithromycin therapy in Crohn’s disease. Dig Liver Dis. 2002; 98. Ruseler-van Embden JG, Schouten WR, van Lieshout LM. Pouchitis: 80. Selby W, Pavli P, Crotty B, et al. Two-year combination antibiotic result of microbial imbalance? Gut. 1994;35:658 – 664.
therapy with clarithromycin, rifabutin, and clofazimine for Crohn’s 99. Duffy M, O’Mahony L, Coffey JC, et al. Sulfate-reducing bacteria disease. Gastroenterology. 2007;132:2313–2319.
colonize pouches formed for ulcerative colitis but not for familial 81. Greenstein RJ, Su L, Haroutunian V, et al. On the action of metho- adenomatous polyposis. Dis Colon Rectum. 2002;45:384 –388.
trexate and 6-mercaptopurine on M. avium subspecies paratuberculo- 100. Ohge H, Furne JK, Springfield J, et al. Association between fecal sis. PLoS ONE. 2007;2:e161.
hydrogen sulfide production and pouchitis. Dis Colon Rectum. 2005; 82. Greenstein RJ, Su L, Shahidi A, et al. On the action of 5-amino- salicylic acid and sulfapyridine on M. avium including subspecies 101. Gosselink MP, Schouten WR, van Lieshout LM, et al. Eradication of paratuberculosis. PLoS ONE. 2007;2:e516.
pathogenic bacteria and restoration of normal pouch flora: comparison 83. Andoh A, Sakata S, Koizumi Y, et al. Terminal restriction fragment of metronidazole and ciprofloxacin in the treatment of pouchitis. Dis length polymorphism analysis of the diversity of fecal microbiota in Colon Rectum. 2004;47:1519 –1525.
patients with ulcerative colitis. Inflamm Bowel Dis. 2007;13:955–962.
102. Bell AJ, Nicholls RJ, Forbes A, et al. Human lymphocyte stimulation 84. Sokol H, Lepage P, Seksik P, et al. Temperature gradient gel electro- with pouchitis flora is greater than with flora from a healthy pouch but phoresis of fecal 16S rRNA reveals active Escherichia coli in the is suppressed by metronidazole. Gut. 2004;53:1801–1805.
microbiota of patients with ulcerative colitis. J Clin Microbiol. 2006; 103. Gionchetti P, Rizzello F, Venturi A, et al. Oral bacteriotherapy as maintenance treatment in patients with chronic pouchitis: a double- 85. Bullock NR, Booth JC, Gibson GR. Comparative composition of blind, placebo-controlled trial. Gastroenterology. 2000;119:305–309.
bacteria in the human intestinal microflora during remission and active 104. Gionchetti P, Rizzello F, Helwig U, et al. Prophylaxis of pouchitis ulcerative colitis. Curr Issues Intest Microbiol. 2004;5:59 – 64.
onset with probiotic therapy: a double-blind, placebo-controlled trial.
86. Gibson GR, Cummings JH, Macfarlane GT, et al. Alternative pathways Gastroenterology. 2003;124:1202–1209.
for hydrogen disposal during fermentation in the human colon. Gut.
105. Kuhbacher T, Ott SJ, Helwig U, et al. Bacterial and fungal microbiota in relation to probiotic therapy (VSL#3) in pouchitis. Gut. 2006;55: 87. Chapman MA, Grahn MF, Boyle MA, et al. Butyrate oxidation is impaired in the colonic mucosa of sufferers of quiescent ulcerative 106. Falk A, Olsson C, Ahrne S, et al. Ileal pelvic pouch microbiota from colitis. Gut. 1994;35:73–76.
two former ulcerative colitis patients, analysed by DNA-based meth- 88. Clausen MR, Mortensen PB. Kinetic studies on colonocyte metabolism ods, were unstable over time and showed the presence of Clostridium of short chain fatty acids and glucose in ulcerative colitis. Gut. 1995; perfringens. Scand J Gastroenterol. 2007;42:973–985.
107. Komanduri S, Gillevet PM, Sikaroodi M, et al. Dysbiosis in pouchitis: 89. Roediger WE. The colonic epithelium in ulcerative colitis: an energy- evidence of unique microfloral patterns in pouch inflammation. Clin deficiency disease? Lancet. 1980;2:712–715.
Gastroenterol Hepatol. 2007;5:352–360.
90. Breuer RI, Soergel KH, Lashner BA, et al. Short chain fatty acid rectal 108. Ottesen EA, Hong JW, Quake SR, et al. Microfluidic digital PCR irrigation for left-sided ulcerative colitis: a randomised, placebo con- enables multigene analysis of individual environmental bacteria. Sci- trolled trial. Gut. 1997;40:485– 491.
91. Cummings JH. Short-chain fatty acid enemas in the treatment of distal 109. Liu WT, Zhu L. Environmental microbiology-on-a-chip and its future ulcerative colitis. Eur J Gastroenterol Hepatol. 1997;9:149 –153.
impacts. Trends Biotechnol. 2005;23:174 –179.
92. Pitcher MC, Beatty ER, Cummings JH. The contribution of sulphate 110. Marcy Y, Ouverney C, Bik EM, et al. Dissecting biological “dark reducing bacteria and 5-aminosalicylic acid to faecal sulphide in pa- matter” with single-cell genetic analysis of rare and uncultivated TM7 tients with ulcerative colitis. Gut. 2000;46:64 –72.
microbes from the human mouth. Proc Natl Acad Sci U S A. 2007; 93. Mylonaki M, Rayment NB, Rampton DS, et al. Molecular character- ization of rectal mucosa-associated bacterial flora in inflammatory 111. Palmer C, Bik EM, Digiulio DB, et al. Development of the human bowel disease. Inflamm Bowel Dis. 2005;11:481– 487.
infant intestinal microbiota. PLoS Biol. 2007;5:e177.


In the U.S., 10% of the male population has some form of erectile dysfunction, although current statistics show that only about 1 in 20 of those suffering from impotence seek medical treatment. Men between the ages of 40 to 70 are the most likely to suffer from erectile dysfunction, with an estimated average of just under half being affected by the condition. Erectile dysfunction – commonly ref

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