GC–MS quantification of fecal short-chain fatty acids and spectrophotometric detection of indole: Do rectal swabs produce comparable results as stool samples? - A pilot study

Rationale

The exploration of the gut microbiome and related metabolites holds an exciting future in health science. The challenges associated with fecal sample testing are proper sample collection, sterile transportation, optimal transport conditions, and processing as all these factors could potentially change the microbiome composition, further exacerbated by the patient's customary discomfort regarding feces samples. The study aimed to compare the usage of rectal swabs and stool samples for short-chain fatty acid estimation using gas chromatography–mass spectrometry (GC–MS) and indole estimation using spectrophotometry.

Method

From May 2022 to June 2022, three women were recruited from the Department of Obstetrics and Gynecology (OBG) in a secondary care hospital in coastal Karnataka. During their clinical visit, a rectal swab was collected, and the stool sample was transported to the hospital from the patient's home in sterile containers provided. After the extraction, short-chain fatty acids (acetate, propionate, and butyrate) were quantified using GC–MS. The fecal indole concentration was determined using a hydroxylamine-based assay.

Results

The GC–MS analysis failed to detect the concentrations of short-chain fatty acids in rectal swab samples. Indole concentrations in stool and swab samples were significantly different.

Conclusion

The study's findings do not support the use of rectal swabs to analyze gut metabolites.