Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping

Area of Science:

• Microbiome research
• Bioinformatics
• Microbial ecology

Background:

• Sterile swabs are common for microbiome sample collection.
• Room-temperature storage can lead to bacterial overgrowth, confusing results.
• Existing preservation methods have limitations and cannot be applied retrospectively.

Purpose of the Study:

• To identify bacterial taxa that grow during room-temperature storage.
• To develop a computational method to correct microbiome data affected by storage conditions.
• To validate the method's effectiveness on real-world datasets.

Main Methods:

• Meta-analysis of microbiome sample storage studies.
• Development and application of the Deblur technique to identify blooming taxa sequences.
• Analysis of American Gut Project (AGP) samples using the Deblur method.

Main Results:

• Consistent identification of specific bacterial taxa, notably Gammaproteobacteria, that bloom at room temperature.
• Deblur effectively identifies and removes sequences from blooming taxa, reducing false positives.
• AGP samples analyzed with Deblur show results consistent with preserved samples.

Conclusions:

• Removing sequences from a few fast-growing taxa is sufficient to correct microbiome profiles.
• The Deblur technique enables accurate microbiome analysis from room-temperature-stored samples.
• This method is crucial for large-scale citizen science and remote fieldwork microbiome studies.