Fecal Swabs vs Rectal Swabs: Are They Interchangeable?

Rectal swabs and stool samples are two common ways to analyze the gut microbiome. Stool samples are considered to represent the luminal gut microbiota while rectal swabs are thought to capture a combination of luminal and mucosal communities. However, are rectal swabs a good proxy for stool samples?

What are the differences in microbial composition between rectal swabs and stool samples?

A study in 2021 has shown differences in microbial composition between rectal swabs and stool, with swabs showing higher alpha diversity. The taxonomic profiles are distinct but more similar to each other compared to mucosal samples. Swabs are enriched in certain genera like Propionibacterium and Prevotella while stool has higher Methanobrevibacter. Overall, swabs seem to capture a mixture of luminal and mucosal microbes.

How consistent is microbiome data between rectal swabs and stool samples?

When analyzing associations between the microbiome and host factors like BMI and antibiotics use, the results are highly consistent between stool and rectal swabs. This indicates that rectal swabs could serve as reasonable proxies for stool, especially when stool collection is difficult. However, swabs do not fully recapitulate the stool microbiome.

What about functional pathways besides taxonomy?

For functional pathways, stool and swabs are again more similar than mucosal samples. But some pathways like peptidoglycan biosynthesis show differences between stool and swabs. So functional profiles are not completely interchangeable.

Can rectal swabs replace mucosal biopsies?

Mucosal samples are distinct in both taxonomy and function from luminal stool and swabs. Also, associations with host factors vary between mucosal and other samples. So rectal swabs cannot fully substitute for mucosal biopsies to study gut mucosa-associated microbes.

So rectal swabs provide microbiome profiles that are relatively consistent with stool samples for both taxonomy and pathways. So swabs can potentially stand in for stool when stool collection is impractical. However, swabs do not replicate all aspects of stool or mucosal samples. The choice of biospecimen can impact study results.

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References

Sun S, Zhu X, Huang X, Murff HJ, Ness RM, Seidner DL, Sorgen AA, Blakley IC, Yu C, Dai Q, Azcarate-Peril MA, Shrubsole MJ, Fodor AA. On the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples. Sci Rep. 2021 Jul 21;11(1):14828. doi: 10.1038/s41598-021-94205-5. PMID: 34290321; PMCID: PMC8295290.