January 19, 2022 1:25 PM

Size matters in microbiome studies

The size of a microbiome sample from rectal swabs varies from patient to patient and can predict infection risk.

lab notes general image of stethoscope drawn in blue ink on lined paper
Michigan Medicine

Rectal swabs are used in the clinical setting to sample a patient’s gut microbiome, the population of bacteria that lives inside all of us. And while these swabs are typically analyzed to determine the type of bacteria present and how many of one type of bacteria versus another, these reports do not often report the size of the overall population of bacteria.

A new study from Rishi Chanderraj, M.D., Robert Dickson, M.D., and their collaborators in the Division of Pulmonary and Critical Care Medicine, Infectious Disease and the Department of Computational Medicine and Bioinformatics reveals that the measure of bacterial density matters both from a methodological perspective (i.e., low density samples are prone to contamination) and from a clinical one. Specifically, low bacterial density is associated with the administration of certain antibiotics, increased density with the presence of multiple medical comorbidities, and independently predicts infection risk.

Paper cited: “The bacterial density of clinical rectal swabs is highly variable, correlates with sequencing contamination, and predicts patient risk of extraintestinal infection,” Microbiome. DOI: 10.1186/s40168-021-01190-y