Related Experiment Video

Updated: May 31, 2026

Fecal Microbiota Transplantation via Colonoscopy for Recurrent C. difficile Infection
07:06

Fecal Microbiota Transplantation via Colonoscopy for Recurrent C. difficile Infection

Published on: December 8, 2014

Cohesive modules of engraftment in fecal microbiota transplantation

Armin Rashidi1,2, Samuel S Minot3, Stephanie J Lee1,2

  • 1Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.

Iscience
|May 29, 2026
PubMed

Insights

Researchers identified cohesive modules of engraftment (CME) from fecal microbiota transplantation (FMT) trials. These small, stable microbial communities show promise for developing predictable, next-generation therapeutic microbial consortia.

Area of Science:

  • Microbiology
  • Gastroenterology
  • Systems Biology

Background:

  • Single-strain probiotics have limited efficacy for complex microbiota injuries in dysbiosis.
  • Fecal microbiota transplantation (FMT) can restore gut microbiota but often results in unpredictable community compositions.
  • Oligomicrobial strategies, using small defined consortia, offer a potential middle-ground between single strains and FMT.

Purpose of the Study:

  • To develop a method for identifying stable, engraftable microbial subsets from FMT data.
  • To introduce the concept of cohesive modules of engraftment (CME) as predictable units within the microbiota.
  • To evaluate CMEs as potential building blocks for future therapeutic microbial consortia.

Main Methods:

  • Developed a workflow to identify cohesive modules of engraftment (CME) from fecal microbiota transplantation (FMT) trial datasets.
  • Analyzed data from five FMT trials to identify and characterize CMEs.
  • Investigated potential mechanisms, such as cross-feeding, that maintain CME integrity.

Main Results:

  • >200 highly cohesive CMEs, comprising 2-5 species, were identified across five FMT trials.
  • Evidence suggests that cross-feeding interactions are crucial for maintaining the cohesiveness and integrity of CMEs.
  • CMEs demonstrated predictable compositions post-treatment, indicating modular engraftment.

Conclusions:

  • Cohesive modules of engraftment (CME) represent stable, predictable subsets of the gut microbiota that engraft as units.
  • CMEs, identified through a novel workflow from FMT trials, offer a promising strategy for developing defined microbial therapeutics.
  • The predictable nature of CMEs makes them ideal candidates for future precision microbial consortia development.
Keywords:
bioinformaticsimmunologymicrobiomeprecision medicinesystems biology

More Related Videos

Therapeutic Evaluation of Fecal Microbiota Transplantation in an Interleukin 10-Deficient Mouse Model05:41

Therapeutic Evaluation of Fecal Microbiota Transplantation in an Interleukin 10-Deficient Mouse Model

Published on: April 6, 2022

Related Concept Videos

Microbiota of the Large Intestine01:27

Microbiota of the Large Intestine

The large intestine hosts the most densely populated microbial ecosystem in the human body. This complex community primarily consists of anaerobic bacteria, with Bacillota (formerly Firmicutes) and Bacteroidota (formerly Bacteroidetes) as the predominant groups. The distribution of these microbes varies along different sections of the large intestine, influenced by local environmental factors such as oxygen availability and nutrient composition.The cecum, located at the beginning of the large...
Microbiota of the Urogenital Tract01:28

Microbiota of the Urogenital Tract

The human urogenital system, once thought to be sterile in healthy individuals, is now recognized as a complex microbial habitat. Advancements in molecular sequencing techniques have revealed that even in healthy adults, the kidneys and bladder harbor microbial populations similar to those found in the distal urethra, albeit in much lower abundance. These resident microorganisms, while generally innocuous, can become opportunistic pathogens under conditions that alter the urogenital...
Microbiota Modulation by Antibiotics01:21

Microbiota Modulation by Antibiotics

Antibiotics have revolutionized modern medicine by saving countless lives from bacterial infections. However, their widespread use has inadvertently harmed the delicate balance of the human gut microbiota. The gut microbiota, a complex community of bacteria, archaea, viruses, and fungi, plays a vital role in regulating metabolism, immune responses, and maintaining intestinal health. Antibiotics, especially broad-spectrum types, disrupt this ecosystem by eradicating both harmful and beneficial...
Bacterial Flora of the Large Intestine01:29

Bacterial Flora of the Large Intestine

The gut microbiome is formed by a vast and diverse community of bacteria that colonizes our large intestine. These bacteria start residing in the gut from birth and continue diversifying throughout life, influenced by factors such as diet, lifestyle, and stress. The gut bacterial community also includes bacteria from food and those that enter the colon through the anus.
The normal gut flora of the colon plays a critical role in generating essential vitamins such as vitamins K, B5, and B7.
Microbiota of the Stomach and Small Intestine01:27

Microbiota of the Stomach and Small Intestine

The human gastrointestinal (GI) tract is characterized by distinct physicochemical conditions that shape its microbial communities. Among these, the stomach presents a particularly challenging environment for microbial colonization due to its highly acidic pH, ranging from 1 to 3. This extreme acidity effectively limits microbial density. However, certain acid-tolerant microorganisms are capable of surviving in this niche. Notably, Helicobacter pylori can colonize the gastric mucosa,...
Functions of the Gut Microbiota01:18

Functions of the Gut Microbiota

The gut microbiota includes trillions of microorganisms that colonize the human gastrointestinal tract, including bacteria, archaea, viruses, and fungi. This complex ecosystem plays a critical role in maintaining intestinal and systemic health. Most of these microbes inhabit the large intestine, establishing a relatively stable and diverse community that contributes to gut homeostasis through various metabolic, immunological, and protective mechanisms.Dominant bacterial phyla, such as...