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

Why do women get more migraines?

August 14, 2018
Research published today reveals a potential mechanism for migraine causation which could explain why women get more migraines than men. The study, in Frontiers in Molecular Biosciences, suggests that sex hormones affect ...

Link between common 'harmless' virus and cardiovascular damage

August 13, 2018
Researchers from Brighton and Sussex Medical School (BSMS) have found an unexpectedly close link between a herpes virus and the occurrence of immune cells damaging cardiovascular tissue.

Rotavirus vaccine cuts infant diarrhoea deaths by a third in Malawi

August 11, 2018
A major new study has shown that rotavirus vaccination reduced infant diarrhoea deaths by 34% in rural Malawi, a region with high levels of child deaths.

Experts highlight Ebola vaccine progress and suggest next steps

August 11, 2018
Despite promising advances, important scientific questions remain unanswered in the effort to develop a safe and effective Ebola vaccine, according to members of an international Ebola research consortium. In a Viewpoint ...

Ebola virus experts discover powerful, new approach for future therapeutics

August 9, 2018
A one-two punch of powerful antibodies may be the best way to stop Ebola virus, reports an international team of scientists in the journal Cell. Their findings suggest new therapies should disable Ebola virus's infection ...

Changes in gut microbiome in only one subset of helminth-infected patients

August 9, 2018
Over the last decade, it's become clearer than ever that bacteria in the human gut— collectively termed the microbiome—play a key role in health and disease. Now, researchers reporting in PLOS Neglected Tropical Diseases ...

0 comments

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.