Back to Search Start Over

Natural and after colon washing fecal samples: the two sides of the coin for investigating the human gut microbiome

Authors :
Elisabetta Piancone
Bruno Fosso
Marinella Marzano
Mariangela De Robertis
Elisabetta Notario
Annarita Oranger
Caterina Manzari
Silvia Bruno
Grazia Visci
Giuseppe Defazio
Anna Maria D’Erchia
Ermes Filomena
Dominga Maio
Martina Minelli
Ilaria Vergallo
Mauro Minelli
Graziano Pesole
Source :
Scientific Reports. 12
Publication Year :
2022
Publisher :
Springer Science and Business Media LLC, 2022.

Abstract

To date several studies address the important role of gut microbiome and its interplay with the human host in the health and disease status. However, the selection of a universal sampling matrix representative of the microbial biodiversity associated with the gastrointestinal (GI) tract, is still challenging. Here we present a study in which, through a deep metabarcoding analysis of the 16S rRNA gene, we compared two sampling matrices, feces (F) and colon washing feces (CWF), in order to evaluate their relative effectiveness and accuracy in representing the complexity of the human gut microbiome. A cohort of 30 volunteers was recruited and paired F and CWF samples were collected from each subject. Alpha diversity analysis confirmed a slightly higher biodiversity of CWF compared to F matched samples. Likewise, beta diversity analysis proved that paired F and CWF microbiomes were quite similar in the same individual, but remarkable inter-individual variability occurred among the microbiomes of all participants. Taxonomic analysis in matched samples was carried out to investigate the intra and inter individual/s variability. Firmicutes, Bacteroidota, Proteobacteria and Actinobacteriota were the main phyla in both F and CWF samples. At genus level, Bacteirodetes was the most abundant in F and CWF samples, followed by Faecalibacterium, Blautia and Escherichia-Shigella. Our study highlights an inter-individual variability greater than intra-individual variability for paired F and CWF samples. Indeed, an overall higher similarity was observed across matched F and CWF samples, suggesting, as expected, a remarkable overlap between the microbiomes inferred using the matched F and CWF samples. Notably, absolute quantification of total 16S rDNA by droplet digital PCR (ddPCR) revealed comparable overall microbial load between paired F and CWF samples. We report here the first comparative study on fecal and colon washing fecal samples for investigating the human gut microbiome and show that both types of samples may be used equally for the study of the gut microbiome. The presented results suggest that the combined use of both types of sampling matrices could represent a suitable choice to obtain a more complete overview of the human gut microbiota for addressing different biological and clinical questions.

Details

ISSN :
20452322
Volume :
12
Database :
OpenAIRE
Journal :
Scientific Reports
Accession number :
edsair.doi.dedup.....c307d932479350ac8c92dcfc98c982e8
Full Text :
https://doi.org/10.1038/s41598-022-20888-z