Improving prediction accuracy of Crohn's disease based on repeated fecal sampling

November 21, 2017 by Deborah Jude, University of California - San Diego
Credit: CC0 Public Domain

Researchers at the University of California San Diego Center for Microbiome Innovation (CMI) have found that sampling the gut microbiome over time can provide insights that are not available with a single time point. The findings could help doctors and researchers more accurately determine if a patient has Crohn's disease. The findings were published as a letter in Gut on October 21, 2017.

Researchers say the idea for the work came from a recently published study on the instability of the gut microbiomes of patients with Crohn's . "It is difficult to get a useful picture by collecting one fecal sample, and this property is likely what hinders our ability to do so," said lead author on the study and researcher in Center director Rob Knight's lab Yoshiki Vázquez-Baeza.

According to Vázquez-Baeza, we all have ever-changing microbiomes, but people with Crohn's Disease appear to have microbiomes that change much more frequently. He and his team wondered, could sampling the over time provide a new way to classify the disease? Furthermore, could a machine-learning model use this increased variability as a 'tell-tale' to discriminate between affected and unaffected subjects?

In order to investigate these questions, the researchers collected stool samples daily from a total of 31 people. According to Knight , also a professor in the Departments of Pediatrics and Computer Science and Engineering at UC San Diego, the researchers believe this is the most densely sampled longitudinal study of Crohn's disease.

Following sample collection, the created a computational model to gain insights from the data. When multiple fecal samples per subject were used, the model was able to predict whether someone had Crohn's disease better even than biopsy samples, which are more expensive and inconvenient to collect.

The methodology was repeated and the results replicated in a second cohort. According to Vazquez-Baeza, the results highlight the importance of treating Crohn's Disease as a volatile, time-varying condition, even during clinical remission.

What's next? "Testing this in a larger cohort would be a wonderful next step," said Vázquez-Baeza. "We're hoping to see whether this is robust to fairly heterogeneous populations, and if the features themselves are consistent."

Explore further: Count your blessings: Quantitative microbiome profiling

More information: Yoshiki Vázquez-Baeza et al. Guiding longitudinal sampling in IBD cohorts, Gut (2017). DOI: 10.1136/gutjnl-2017-315352

Related Stories

Count your blessings: Quantitative microbiome profiling

November 16, 2017
A broad range of metabolic and inflammatory diseases is associated with alterations in gut microbiota composition and metabolic potential. Until now, sequencing-based gut microbiota research has described such dysbiotic states ...

Engineering the gut microbiome with 'good' bacteria may help treat Crohn's disease

November 15, 2017
Penn Medicine researchers have singled out a bacterial enzyme behind an imbalance in the gut microbiome linked to Crohn's disease. The new study, published online this week in Science Translational Medicine, suggests that ...

Microbiomes more in flux in patients with inflammatory bowel disease

February 13, 2017
Patients with inflammatory bowel disease are more likely to see dramatic shifts in the make-up of the community of microbes in their gut than healthy people, according to the results of a study published online Feb. 13 in ...

Fecal analyses may lead to noninvasive diagnostics for inflammatory bowel disease

February 5, 2016
New research indicates that analyses of vapors from fecal samples can identify volatile metabolites indicative of different types of inflammatory bowel disease, including Crohn's disease and ulcerative colitis.

Liquid nutrition may benefit children with Crohn's disease

August 23, 2017
An analysis of published studies indicates that exclusive enteral nutrition (EEN)—when individuals receive only liquid nutrition—may be an effective treatment for children with Crohn's disease. The findings are published ...

Recommended for you

Reconstructing Zika's spread

May 24, 2018
The urgent threat from Zika virus, which dominated news headlines in the spring and summer of 2016, has passed for now. But research into how Zika and other mosquito-borne infections spread and cause epidemics is still very ...

Molecular network boosts drug resistance and virulence in hospital-acquired bacterium

May 24, 2018
In response to antibiotics, a gene regulation network found in the bacterium Acinetobacter baumannii acts to boost both virulence and antibiotic resistance. Edward Geisinger of Tufts University School of Medicine and colleagues ...

Past use of disinfectants and PPE for Ebola could inform future outbreaks

May 24, 2018
Data from the 2014 Ebola virus outbreak at two Sierra Leone facilities reveal daily usage rates for disinfectant and personal protective equipment, informing future outbreaks, according to a study published May 24, 2018 in ...

Tick bite protection: New CDC study adds to the promise of permethrin-treated clothing

May 24, 2018
The case for permethrin-treated clothing to prevent tick bites keeps getting stronger.

Early lactate measurements appear to improve results for septic patients

May 24, 2018
On October 1, 2015, the United States Centers for Medicare and Medicaid Services (CMS) issued a bundle of recommendations defining optimal treatment of patients suffering from sepsis, a life-threatening response to infection ...

Dengue: Investigating antibodies to identify at-risk individuals

May 23, 2018
Using an original mathematical and statistical analysis method, a team of scientists from the Institut Pasteur partnered with researchers from the United States and Thailand to analyze a Thai cohort that has long been a focus ...


Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.