In microbiota research, whole stool sampling is the conventional approach but can be problematic or infeasible for certain patients. This study aims to validate the use of rectal swabbing as an alternative method for microbiota analysis and determine optimal storage conditions suitable for various clinical settings, including intensive care units. We evaluated different sampling techniques, conservation media and storage temperatures. Our findings indicated that rectal swabs yield microbiota diversity comparable to whole stool samples. Notably, storage conditions significantly impacted microbiota profiles, with increased E. coli and Enterococcus sp. quantifications observed at room temperature. Consequently, we recommend immediate refrigeration of rectal swabs to reliably assess aerobic and total microbiota, particularly for patients requiring urgent care such as antibiotic treatment.

Importance We developed a pragmatic approach to study total and aerobic gut microbiota, applicable in numerous clinical units such as intensive care or emergency units, where whole stool sampling is often impractical. This approach employs ESwab™ devices which are already commonly used in hospital.

The authors have declared no competing interest.

This study did not receive any funding

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

In accordance with APHP (Assistance publique Hopitaux de Paris) ethics regulations and the Declaration of Helsinki, all participants received comprehensive information and provided consent. All individuals were collected thanks to ethical authorization CLEA number 2019-72 obtained by the Comite local de Protection des Personnes des hopitaux universitaires de Paris Seine Saint Denis.

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All data produced in the present study are available upon reasonable request to the authors