Second Annual MIT-OpenBiome Translational Microbiome Workshop

December 9, 2016

Sponsored by the MIT Center for Microbiome Informatics and Therapeutics

Location: The Broad Institute of MIT and Harvard, Yellowstone Room, 7 Cambridge Center, Cambridge, MA 02142


Part I: Welcome and Keynote

1:30 PM: Meet and Greet (snacks provided)

2:00 PM: Welcome! 

Eric Alm, PhD, MIT, and Mark Smith, PhD, OpenBiome

2:10 PM: Keynote Addresses

John Bartlett, MD, Johns Hopkins, and Jeremiah Faith, MD, Mt. Sinai


Part II: Interactive Speaker Presentations and Group Problem-Solving Sessions

Problem-solving sessions will be 40 minutes long and will focus on specific issues and questions in the microbiome space. These sessions will each be led on an expert in that particular area, who will deliver a 10-15 minute presentation and then lead a group discussion. During each time slot, four talks will be given in parallel. Each speaker will speak twice. The talks are organized into themes vital to translation of research into effective therapies. You may choose to attend any talk during each session -- the schedule has been designed to maximize choice.

3:00 - 3:45 PM:

Foyer: Regulating the Microbiome (Carolyn Edelstein, OpenBiome)

How does the FDA approach the use of human-derived microbes in medicine? This discussion will walk through the (short) history of federal regulation of microbiota therapies and consider how to design a policy approach to optimize the impact of this new field on public health. 

Yellowstone Room: SporeSeq (Sean Kearney, MIT)

Over 50% of the organisms in human GI tracts carry genes necessary for entry into a super-resistant, dormant endospore state. SporeSeq enables culture-free identification of organisms present as endospores, providing a new way to study the microorganisms living in the human GI tract.

Monadnock Room: Clinical Education and Safety (Majdi Osman, OpenBiome)

Presenting case vignettes to highlight the critical importance of good clinical practice, education and safety monitoring in FMT.

Katahdin Room: FMT in Irritable Bowel Syndrome (1) (Olga Aroniadis, Montefiore Medical Center)

The main goals of this session are: (1) To highlight the challenges encountered designing clinical trials that assess the role of FMT for the treatment of IBS, specific focus on patient selection, measurement of clinical efficacy and assessment of adverse events in this highly heterogeneous patient population. (2) To discuss the obstacles faced assessing changes in the gut microbiota among IBS patients undergoing FMT who may be using complimentary and alternative treatment modalities. 


3:45-4:30 PM:

Foyer: Intellectual Property and the Microbiome (Stephen Altieri, Morgan, Lewis & Bockus LLP)

Intellectual property is often a cornerstone of a biotech company’s value.  The microbiome area brings with it interesting challenges and opportunities for intellectual property protection, driven by technical and legal considerations.  The IP session will involve a discussion of these points.

Yellowstone Room: The Microbial Metacommunity Standard (Sonia Timberlake, Finch Therapeutics)

The Microbial Metacommunity Standard can be used for estimating aliquoting, sequencing, plate, and inter-run variance, as well as across-plate or across-run standardization. It also addresses the Standards Matter Challenge: identifying important extraction protocol and sequencing variables.

Monadnock Room: Malnutrition and Tropical Disease (Majdi Osman, OpenBiome)

This session will provide an overview of the evidence on the microbiome in malnutrition and tropical diseases. Potential applications of FMT will also be explored.

Katahdin Room: FMT in Irritable Bowel Syndrome (2) (Olga Aroniadis, Montefiore Medical Center)



Foyer: Host-Microbe Evolution (1) (Mathieu Groussin, MIT)

Economic globalization is bringing western lifestyles to populations with traditional lifestyles around the world, at the expense of the biodiversity of their gut microbiome, which could experience irreversible losses of important commensal microbes that are intimately linked to human health. The WeAreMicrobiome Initiative aims to globally collect, understand and conserve the human gut microbial heritage in a library that will serve as a safeguard of our pan-microbiome’s biodiversity. It also aims to investigate the evolutionary processes shaping gut microbiomes, with a focus on major events of human history, such as migrations from Africa or the Neolithic transition.

Yellowstone Room: Modeling Host-Microbe Interactions (1) (Georg Gerber, Brigham and Women's Hospital)

In this session we will discuss challenges and opportunities in computational modeling of host-microbiome interactions, including topics such as: key scientific questions that can be addressed through these models, relevant types of computational models, data sources and their limitations, and experimental designs to yield maximal information.

Monadnock Room: Multidrug Resistant Organisms and the Microbiome (Marina Santiago, Finch Therapeutics)

Antibiotic resistance bacterial infections are a global public health threat. This talk will discuss the relationship between multi-drug-resistant organism acquisition and the human microbiome as well as how we might be able to use microbiome remediation to prevent antibiotic resistant infections. 

Katahdin Room: FMT in Inflammatory Bowel Disease (1) (Zain Kassam, OpenBiome)

What do we know and where are we going? This session will explore the current landscape of FMT for IBD trials and the trajectory of the field.


5:15-6:00 PM:

Foyer: Host-Microbe Evolution (2) (Mathieu Groussin, MIT)

Yellowstone Room: Modeling Host-Microbe Interactions (2) (Georg Gerber, Brigham and Women's Hospital)

Monadnock Room: Pre-Treatment Antibiotics (Shrish Budree, OpenBiome)

Studies investigating the efficacy of FMT in the management of ulcerative colitis (UC) have been promising. However, experts agree that the administration of antibiotics prior to the FMT may improve FMT related outcomes in UC. The mechanism underlying improved FMT outcomes following a course of antibiotics include clearance of the dysbiotic microbial community within the intestinal tract which enhances colonization and engraftment of the new microbial community administered via FMT from a healthy donor. The aim of this session is to explore this topic in further detail.

Katahdin Room: FMT in Inflammatory Bowel Disease (2) (Zain Kassam, OpenBiome)


Part III: Continuing Collaborations

6:00 PM into the future

Following the conclusion of the workshop, all attendees are invited to attend a reception to be held at OpenBiome's holiday party, held at 200 Inner Belt Road. Transportation will be provided. All participants are encouraged to follow-up on new ideas and relationships developed at the workshop to move from discussion into action!