New manuscript: The bacterial density of clinical rectal swabs is highly variable, correlates with sequencing contamination, and predicts patient risk of extraintestinal infection

Just published in Microbiome: a new study from our group, led by Rishi Chanderraj, studying the methodological, biological, and clinical importance of bacterial density in rectal swabs obtained from hospitalized patients.

Imagine comparing two cities (say, Chicago and Ann Arbor), limiting your comparison to relative demographics (age, gender, race), and ignoring that one is >20 times the population size of the other. We do this all the time with gut microbiome studies: we compare community composition and diversity, and don’t bother to measure and report bacterial density.

In this new study, we quantified the bacterial density in rectal swabs collected from 118 hospitalized patients. We found that bacterial density matters methodologically (it correlates with background contamination in low-biomass swabs), biologically (it correlates with the relative abundance of bacteriocin-producing taxa, and clinically (it is predictably influenced by antibiotic exposure and is predictive of extra-intestinal infections in this at-risk population).

Population density is a fundamental ecologic features of communities (both microbial and otherwise). We should stop overlooking it in microbiome studies.

Manuscript: The bacterial density of clinical rectal swabs is highly variable, correlates with sequencing contamination, and predicts patient risk of extraintestinal infection (Microbiome)

Rishi Chanderraj