Category Archives: Microbiome Research

Patient, Family, Caregiver January Symposium Broadcasts During March On C. diff. Spores and More Live Program









SAVE THE DATES to listen in to the leading topic expert presentations

shared on January 15, 2021, at the Patient, Family, Caregiver Symposium:

Beginning Tuesday, March 9 from 1:00 p.m. – 2:00 p.m. EST following through on

March 16,  March 23, and  March 30.

A Symposium specifically developed for Patients Diagnosed With a C. diff. Infection, Being Treated For a Clostridioides diffiicile infection, Recovering From a Clostridioides difficile Infection and Recurrences with Family Members and Caregivers.

The Patient & Family C. diff. Symposium was a gathering of healthcare professionals, keynote speakers, health advocates, practitioners, educators, thought leaders, and patients who are transforming the patient experience and changing the way people experience
C. diff. infections worldwide.

Unlike other conferences on this topic, patients will share their C. diff. infection journeys, providing a real-world perspective on patient experience. Our attendees will learn more from this virtual-online symposium and gain knowledge on important topics that will better aid their care and recovery through tools and strategies delivered by keynote speakers.  

The Symposium followed the C Diff Foundation Mission statement –   Educating and Advocating for the prevention, treatments, clinical trials, diagnostics, and environmental safety of Clostridioides difficile
(C. diff.) infections worldwide.

Keynote speakers presented up-to-date data to expand on the existing knowledge and provide important information focused on, yet not limited to,  a Clostridioides difficile infection (also known as C. diff., C. difficile, CDAD, CDI) ……

  • Prevention
  • Treatments
  • Diagnostics
  • Research
  • Environmental Safety
  • Clinical trials and studies


  • Introduction to Microbiome Research and Studies
  • Infection Prevention
  • Fecal Microbiota Restoration and Transplants
  • Antibiotic Stewardship

We hope you enjoy the broadcasts!


Program Chair:  Paul Feuerstadt, MD, FACG

Barbara McGovern, MD     “Treatment of recurrent C. difficile infection with                                                                                        SER-109, an investigational microbiome drug.”

Paul Feuerstadt, MD          ” C. diff. Overview – What is a C. diff. Infection?”

Sahil Khanna, MD               “C. diff. Treatments + FMT Overview. “




Simon Cutting, Ph. D.         “Bacillus, and C. diff.  Spore Overview. “

Teena Chopra, MD                ” Introduction to Infection Prevention.”

Doe Kley, RN, MPH              “C. diff. Transitioning from Hospital to Home. “

Courtney Jones                    ” Microbiome, Microbiota, and Gut Health.”

Denise Cardo, MD                “Everyone Has a Role in Antibiotic Awareness.”

Larry Kociolek, MD              “C. diff. Infections in Pediatrics.”

Kathy Bischoff                        “My C. diff.  Journey.”

Renata Johnson                      “My C. diff. Journey.”

Paul Feuerstadt, MD      &    Barbara McGovern, MD


This Symposium was hosted by the C Diff Foundation and

Sponsored by Seres Therapeutics  

CDI and Recurrence; Microbiome – Based Therapy Publication

















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Cornell Researchers Develop Tool To Create Maps Of the Locations and Identify Different Microbial Species Including Those That Make Up the Gut Microbiome

Cornell researchers developed an imaging tool to create intricate spatial maps of the locations and identities of hundreds of different microbial species, such as those that make up the gut microbiome. The tool will help scientists understand how complex communities of microorganisms interact with each other and also their environment, which is to say, us.


The team’s paper, “Highly Multiplexed Spatial Mapping of Microbial Communities,” published Dec. 2 in Nature. The paper’s lead author is doctoral student Hao Shi, M.Eng. ’18.


“There are communities of bacteria that live in our bodies and play an important role in human health and biology, and there’s a rich diversity of these microbes. We know this from technologies such as DNA sequencing that create lists of the bacterial species that are present in a community,” said Iwijn De Vlaminck, the Robert N. Noyce Assistant Professor in Life Science and Technology in the Meinig School of Biomedical Engineering, and the paper’s senior author.

“However, there are very limited tools to understand the spatial interactions between these microbes, and those are quite clearly important to understand the metabolism of these communities, and also how these microbes interact with their host,” he said.

De Vlaminck and Shi set out to create their imaging method by using a two-step process called high phylogenetic resolution microbiome mapping by fluorescence in situ hybridization (HiPR-FISH). They collaborated with the labs of co-authors Warren Zipfel, associate professor of biomedical engineering, and Ilana Brito, assistant professor and the Mong Family Sesquicentennial Faculty Fellow in Biomedical Engineering, to incorporate additional imaging and microbiome expertise.

To locate the microbial communities, the researchers designed oligonucleotide probes that target specific bacteria cells based on the presence of a signature gene sequence, 16S ribosomal RNA, and they made another group of probes that label the cells with fluorophores. Then the team used confocal microscopy to light up the fluorescent markers with lasers, and they used machine learning and custom software to decode the fluorescence spectra and interpret the images, resulting in an efficient and cost-effective technology with single-cell resolution.

The researchers created the palette for their spatial maps with a mixture of 10 basic colors that could “paint” a total of 1,023 possible color combinations of E. coli, each fluorescently labeled with a unique binary barcode.

“The imaging itself leads to very beautiful, rich images with all bacterial cells in different colors,” De Vlaminck said. “But to allow the quantitative understanding of microbe interactions, the distances between cells, cluster sizes and so on, you need to be able to interpret these in an automated way by a computer so that you can convert this image into a digitized representation of the community.”

The team applied their technology to two different systems: the gut microbiome in mice and the human oral plaque microbiome. In the case of the , they were able to demonstrate how the spatial associations between different bacteria are disrupted by antibiotic treatment.

Spatial mapping could be an important tool for studying and possibly treating a range of diseases in which bacteria are a major culprit, such as inflammatory bowel disease, colorectal cancer, and infection.

“We’d like to dig deeper into the biology of systems where microbiomes play important roles and try to understand how these kinds of spatial dynamics change when you have a disease in progression,” Shi said. “We want to see if that offers any clues and therapeutic insights that we can harness to help people.”

Gut Microbes Raise the Bar In Treating C. difficile Infections

Seres’s success with an industrially made bacterial mix in phase 3 trials against Clostridium difficile infection promises an alternative to fecal microbial transplantation in clinical practice.

The August announcement of positive data from Seres Therapeutics’ phase 3 trial to prevent recurrent Clostridium difficile infections renewed hopes that purified, defined mixtures of bacteria can treat such infections as effectively as — and presumably more safely than — fecal microbial transplantation (FMT). Several other companies have now also shown favorable late-stage trial data in ‘C. diff.’ using customized stool-derived cocktails. Along with Seres, they are teeing up clinical studies of these compounds in a variety of diseases.

……..Two other companies, Rebiotix, and Vedanta Biosciences are pursuing microbe-based drugs to stop C. diff infection recurrences, and both are in late-stage development. Rebiotix is running a pivotal phase 3 study of its commercially prepared FMT in enema form. Vedanta Biosciences is expecting a readout of its phase 2 trial of VE303, which, unlike the other three drug candidates, is a defined consortium of eight types of cultured, clonal commensal bacteria strains.






Microbial Cocktails Raise Bar For C. diff. Treatments

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Clinical Trial Study Moving Closer to Having Safe and Effective Products to Restore the Gut Microbiome for Patients with Recurrent C. difficile Infections.

Sahil Khanna, M.B.B.S.

A new study published online in the journal ClinicalInfectious Diseases looked at the use of a non-frozen capsule of microbiome restoration therapy for treating patients with recurrent C. difficile infection.

“Patients with C. difficile are typically managed with antibiotics or fecal transplantation for recurrent C. difficile,” says the study’s author, Sahil Khanna, M.B.B.S., a gastroenterologist at Mayo Clinic. Dr. Khanna says fecal transplantation has been demonstrated to have high success rates by restoring the gut microbiome of patients.  However, he says there are several challenges with fecal transplantation including standardization of the product, keeping it frozen, and mitigating the risk of infectious disease transmission during the procedure. 

To help reduce the risks, Dr. Khanna and his team studied a transplantation method using a non-frozen capsule instead of whole stool transplantation. An initial dose-finding, the investigator-initiated study looked at the efficacy of different doses of fecal matter and the safety of performing microbiome restoration therapy using an oral product, RBX7455 developed by Rebiotix, Inc. The team found no concerns related to safety.

“Our study has several implications,” says Dr. Khanna. “We think that products like capsules may be able to replace fecal transplantation that is currently done via a colonoscopy. We also think that products that are non-frozen may allow for repeat dosing and for patient-administered self-treatment at home. The good news is that we are  moving closer to having safe and effective products to restore the gut microbiome for patients with recurrent C. difficile.”

Dr. Khanna says that larger clinical trials and blinded, placebo-controlled trials are the next step in moving this potential treatment from research into practice.


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