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Field expedient stool collection methods for gut microbiome analysis in deployed military environments
Car Reen Kok1, James B Thissen1, Michele Cerroni2,3,4
1Lawrence Livermore National Laboratory, Livermore, California, USA.
Msphere
|May 15, 2025
Summary
Field-deployable stool sample collection methods are crucial for military microbiome research. Both FTA cards and OMNIgene Gut tubes capture most bacteria, but standardized protocols are needed for accurate microbiome analysis.
Area of Science:
- Microbiome research
- Field-deployable sample collection
- Military health
Background:
- Advancing microbiome research in military health requires field-expedient methods for stool sample collection, storage, and shipment.
- Accurate microbiome evaluation is hindered by unclear biases from preservatives and sampling methods.
- Assessing microbiome signatures linked to travelers' diarrhea susceptibility and gut function recovery is important.
Purpose of the Study:
- To compare microbiome composition using two field-deployable collection methods: Flinters Technology Associates (FTA) cards and OMNIgene (OG) Gut tubes.
- To evaluate potential biases introduced by different collection and storage methods in microbiome measurements.
- To inform the design of standardized fecal microbiome study protocols for field and military deployment settings.
Main Methods:
- Shotgun metagenomic sequencing was performed on paired fecal samples from 49 adult participants.
- Samples were collected using FTA cards and OG tubes before and during international travel.
- Microbiome composition was compared between the two methods, considering asymptomatic individuals and those with travelers' diarrhea.
Main Results:
- OMNIgene Gut tubes yielded higher concentrations of nucleic acid and sequencing libraries.
- A majority of bacterial genera (82.9%) were detected by both methods; method-specific detections were rare and low in abundance.
- Differences in beta diversity were primarily driven by inter-individual variation, followed by collection method and disease state.
- Differential abundance analysis revealed consistent differences, with Corynebacterium higher in FTA samples and Blautia higher in OG samples.
Conclusions:
- Both FTA cards and OG tubes are viable for field-based microbiome studies, capturing most bacterial genera.
- Observed differences in microbiome composition highlight the necessity for consistent, standardized collection protocols within studies.
- Findings provide foundational data to guide the development of robust fecal microbiome study protocols for operational and remote settings.
