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The hidden half of nature : the microbial roots of life and health
\"Prepare to set aside what you think you know about yourself and microbes. Good health--for people and for plants--depends on Earth's smallest creatures. [This book] tells the story of our tangled relationship with microbes and their potential to revolutionize agriculture and medicine, from garden to gut\"--Dust jacket flap.
BOOK
186 Anaerobic Versus Aerobically Prepared Fecal Microbiota Transplantation Capsules: A Pilot Comparative Cohort Analysis Using a Novel Sequencing Approach
INTRODUCTION:Fecal microbiota transplantation (FMT) capsules have emerged as a therapeutic option for recurrent C.difficile infection (rCDI). Standard FMT capsules are prepared under aerobic conditions; however, anaerobic processing limits oxygen's impact on healthy anaerobic microbes, may enhance microbial community viability, improve engraftment, and may in turn increase efficacy. Thus, we compared the engraftment profiles of FMT capsules prepared by aerobic (AER) versus an anaerobic process (ANA) in rCDI patients. We applied a novel DNA-sequencing method (PMA-seq) to differentiate living and dead microbes.METHODS:We conducted a prospective cohort study of rCDI patients (3 or more confirmed episodes within 1 year) eligible for standard of care FMT. Subjects were enrolled sequentially to receive either a single administration of 30 capsules of standard AER or ANA. 3 healthy donors were use and stool donation was split; half prepared under anaerobic and half under aerobic conditions. This technique was used to address donor and stool specific confounding effects. All measures were taken to manage oxygen exposure, otherwise the split stool samples were treated identically. ANA preparations occurred inside an anaerobic chamber. Patients were assessed, and stool samples collected at 72 hours, 10 days, 4 weeks and 8 weeks post-FMT. Gut microbial communities were profiled via shotgun metagenomic and 16S sequencing. Additionally, PMA-seq, a novel species-specific live-dead assay was conducted. Pre and post treatment microbiome engraftment outcomes were analyzed. Assessment for clinical cure was done at week 8 [testing via (GDH/EIA)].RESULTS:A total of 10 recurrent CDI patients were enrolled (5 AER and 5 ANA). Relevant characteristics were similar between the AER [mean age: 73 (SD = 15.9), mean recurrence 3.4] and ANA groups [mean age: 67.1 years (SD = 18.7), mean recurrence 3.0]. Overall, gut microbial community outcomes from ANA and AER, including alpha diversity, beta diversity and relative abundances, did not vary substantially by 16S, shotgun metagenomic sequencing or PMA-seq (Figures 1 and 2). Clinical cure at week 8 for AER and ANA was 100% (5/5 in each group). Both formulations were safe and well-tolerated.CONCLUSION:To our knowledge, this is the first study to compare aerobically versus anaerobically prepared FMT capsules, including assessment of live and dead specific-microbial profiles. This pilot study suggested there were no significant differences in engraftment profiles in rCDI.
Journal Article
The 6 Ds of Fecal Microbiota Transplantation
A practical handbook on fecal microbiota transplantation (FMT) for physicians, nurses, physician assistants, students, residents, and fellows,
The 6 Ds of Fecal Microbiota Transplantation: A Primer from Decision to Discharge and Beyond
provides a clinical framework to understand and administer this treatment as safely and effectively as possible.
FMT has emerged as a promising treatment for C. difficile infection (CDI), and there is a major need for educational resources on the topic. Drs. Jessica Allegretti, Zain Kassam, and their expert contributors are leaders in the field and have collectively cared for thousands of patients suffering from recurrent CDI who have benefitted from FMT.
This guide provides practical tools, clinical pearls, and answers to frequently asked questions. Beginning with introductory information on the microbiome and exploring the history of FMT,
The 6 Ds of Fecal Microbiota Transplantation
outlines a step-by-step checklist for administering FMT:
Decision: Who is the right CDI patient to receive FMT? What clinical questions should you ask patients in your FMT clinical assessment?
Donor: How do you select and screen a donor for FMT?
Discussion: What are the risks, benefits, and alternatives that need to be discussed with patients?
Delivery: What is the best delivery method for FMT-colonoscopy, nasogastric tube, enema, or capsules?
Discharge and follow-up: What is the ideal post-FMT care? How should you council patients following FMT?
Discovery: What are the most promising emerging clinical applications for FMT? What is the evidence for FMT in obesity, autism, irritable bowel syndrome, inflammatory bowel disease, antibiotic resistant bacteria, and liver disease?
Arming healthcare professionals with the ability to answer questions from patients regarding FMT and the microbiome,
The 6 Ds of Fecal Microbiota Transplantation
provides a pragmatic guide for this exciting treatment.
eBook
P590 Vaginal microbiota and douching cessation: a crossover pilot study
BackgroundObservational studies have demonstrated a dose-dependent association between vaginal douching and bacterial vaginosis. We sought to estimate the effect of douching cessation on the vaginal microbiota in a pilot crossover study.MethodsThirty-two women self-collected vaginal swabs twice-weekly (n=950) during a douching observational phase (“D”, 4 weeks), followed by douching cessation (“DC”, 12 weeks). Vaginal microbiota were characterized by 16S rRNA gene sequencing (V3-V4) and clustered into community state types (CSTs). A conditional logistic regression model, adjusted for menstruation and sexual behaviors, allowed each woman to serve as her own control. Wilcoxon signed-rank tests were used to evaluate paired changes in microbiota between phases. Broad-range qPCR assays provided estimates of bacterial absolute abundance per swab. A piecewise linear mixed effects model was used to assess differences in rates of change in bacterial absolute abundance before and after douching.ResultsThere was not a statistically significant change in the odds of Lactobacillus-dominated CSTs comparing DC to D (aOR 0.54, 95% CI: 0.27–1.11). There were no significant changes for four individual Lactobacillus spp. and no meaningful changes in other taxa investigated. The rates of change in bacterial absolute abundance was not significantly different in samples collected 3 days before and after douching (p=0.46). Women who had a Lactobacillus-dominated CST at baseline experienced shifts to low-Lactobacillus CST in DC, and vice versa for women who had a low-Lactobacillus CST at baseline (interaction on entry CST, p-value <0.02), however, these findings were driven by changes occurring in the final weeks.ConclusionIn this pilot study, douching cessation was not associated with major changes in vaginal microbiota. Shifts in Lactobacillus-dominance may represent regression to the mean as the shifts occurred late in DC, giving ample time for fluctuations. Disparate findings between this study and prior analyses using Nugent score may be related to low-Lactobacillus CSTs receiving low/intermediate Nugent scores.DisclosureNo significant relationships.
Journal Article
P364 Gardnerella vaginalis clade distribution is associated with behaviours and Nugent score in women who have sex with women
Background Gardnerella vaginalis (GV) can be detected in women with BV and without BV. Identification of four genetically distinct GV-clades (defined using clade-specific genetic markers) led to the hypothesis that there may be both pathogenic and commensal GV-clades. We conducted a study investigating the distribution and behavioural associations of GV-clades in a cohort of women-who-have-sex-with-women (WSW).MethodsWomen self-collected vaginal swabs and completed behavioural questionnaires 3-monthly for 24 months or until incident BV(Nugent Score[NS]=7–10). qPCR assays were used to detect GV and the four GV-clades. Multinomial logistic regression assessed factors associated with number of GV-clades. Generalized estimating equations population-averaged models assessed factors associated with each GV-clade. Models accounted for repeated measures.Results369 specimens from 101 women were analysed. GV was detected in 181 specimens, and most GV-positive specimens had multiple clades present (n=119/181, 66%). Detection of multiple GV-clades was associated with smoking (adjusted relative risk ratio [RRR]:2.52; 95%CI:1.25,5.07), increased lifetime female sex partners (FSP; adjRRR:2.43; 95%CI:1.09,5.38), and a NS=4-6 (intermediate microbiota) or NS=7-10 (Nugent BV) relative to no clades. GV4 was the most prevalent clade (n=136/369; 37%; 95% CI: 32,42%), followed by GV1 (n=116/369; 31%; 95% CI: 27,36%) and GV2 (n=76/369; 21%; 95% CI: 17,25%). GV3 was uncommon (n=17/369; 5%; 95% CI:3,7%). GV1 was associated with a NS=7–10 (adjusted odds ratio[AOR]:3.87; 95%CI:1.75,8.56), smoking (AOR:2.74; 95%CI:1.28,5.87) and report of any sexual partners (AOR:3.41; 95%CI:1.18,9.86). GV2 was associated with NS=4–6 (AOR:3.28; 95%CI:1.00,10.77), sharing of sex-toys (AOR:2.30; 95%CI:1.05,5.04) and recent male sex partners (AOR:6.58; 95%CI:2.02,21.40). GV4 presence was associated with increased lifetime FSPs (AOR:3.17; 95%CI:1.25,5.07).ConclusionGV1 and presence of multiple GV-clades was associated with Nugent BV in WSW, whereas GV2 was associated with intermediate microbiota. Individual GV-clades were associated with a range of differing sexual behaviours in adjusted analyses. These associations are of uncertain importance, but do provide support for exchange of GV-clades between sexual partners.DisclosureNo significant relationships.
Journal Article
Inflammatory Bowel Diseases and Gut Microbiota
Inflammatory bowel disease (IBD) is an inflammatory disease of the gastrointestinal tract, the incidence of which has rapidly increased worldwide, especially in developing and Western countries. Recent research has suggested that genetic factors, the environment, microbiota, and immune responses are involved in the pathogenesis; however, the underlying causes of IBD are unclear. Recently, gut microbiota dysbiosis, especially a decrease in the abundance and diversity of specific genera, has been suggested as a trigger for IBD-initiating events. Improving the gut microbiota and identifying the specific bacterial species in IBD are essential for understanding the pathogenesis and treatment of IBD and autoimmune diseases. Here, we review the different aspects of the role played by gut microbiota in the pathogenesis of IBD and provide a theoretical basis for modulating gut microbiota through probiotics, fecal microbiota transplantation, and microbial metabolites.
Journal Article
O-012 The Intestinal Wound Regeneration Modulates Mucosal Microenvironment to Stimulate Expansion of a Local Pro-restitutive Microbiota
Ulcerative colitis and Crohn's disease frequently cause epithelial damage in the intestine, leading to gut inflammation accompanied by areas of ulceration. The regeneration of damaged mucosa as well as the restoration of intestinal homeostasis involve induced and coordinated proliferation and migration of intestinal epithelial cells. Commensal bacterial colonization of the intestine is essential for normal intestinal development, renewal, and repair. N-formyl peptide receptors (FPRs) are widely expressed pattern recognition receptors that can specifically bind and induce responses to host-derived and bacterial peptides and small molecules during repair of mucosal injury in a redox dependent manner. However, little is known about the host-microbiota crosstalk mediated by FPRs during repair of gut mucosal injuries. Herein, purpose of this study is to exploit the mechanism of mucosal healing promoted by a consortium of gut microbiota that preferentially colonizes ulcerated mucosa undergoing resealing.MethodsThe regeneration of injured epithelial was studied using defined mechanical wounds inflicted in the mouse distal colon by employing a miniature endoscope and forceps. Microbiota studies were performed by high throughput sequencing of the V4 region of 16s rRNA gene of the bacteria harvested from mucosal wounds undergoing different stages of regenerative events.ResultsThe high throughput sequencing analysis of bacterial 16s rDNA determined rapid, reversible spatiotemporal alterations in the composition and diversity of microbiota in the wound microenvironment. Our data demonstrated that these ecological changes are dependent on FPR1/NOX2-mediated local tissue hypoxia, depletion of muc2 mucin, and compensatory effect of the over expression of HIF1-regulated MUC3 mucin. Our data show that these events of mucosal regeneration enrich a dominant member of this wound-associated consortium, Akkermansia muciniphila, which is associated with the pro-restitutive function. A. muciniphila, an anaerobic, mucinophilic commensal bacterium, enhanced proliferation and migration of enterocytes adjacent to the colonic wound beds in a process involving FPR1/NOX1 dependent redox signaling.ConclusionsThese findings highlight a novel role of FPR1 to promote changes in the wound microenvironment to such extent that enriches a specific mucosa-associated bacterium to enhance enterocyte migration and proliferation in an FPR1-mediated and redox-dependent fashion.
Journal Article