Assessing Gut Microbial Diversity from Feces and Rectal Mucosa

Abstract

Gut microbiota is the most complex bacterial community in the human body and its study may give important clues to the etiology of different intestinal diseases. Most studies carried out so far have used fecal samples, assuming that these samples have a similar distribution to the communities present throughout the colon. The present study was designed to test this assumption by comparing samples from the rectal mucosa and feces of nine healthy volunteers by sequencing libraries of 16S rRNA genes. At the family taxonomic level, where rarefaction curves indicate that the observed number of taxa is close to the expected one, we observe under different statistical analyses that fecal and mucosal samples cluster separately. The same is found at the level of species considering phylogenetic information. Consequently, it cannot be stated that both samples from a given individual are of similar composition. We believe that the evidence in support of this statement is strong and that it would not change by increasing the number of individuals and/or performing massive sequencing. We do not expect clinicians to stop using feces for research, but we think it is important to caution them on their potential lack of representativeness with respect to the bacterial biofilm on the rectal mucosa.

Molecular analysis of the luminal- and mucosal-associated intestinal microbiota in diarrhea-predominant irritable bowel syndrome

“…The majority of studies that characterized the intestinal microbiota in IBS patients investigated mixed populations of IBS patients (4,42,45) or focused on a single intestinal niche (4,15,16,22,23,25,42,45,46). Recent reports demonstrating compositional and diversity differences between intestinal luminal-and mucosal-associated microbiota in humans highlight the importance of characterizing enteric microorganisms in both niches when investigating the role of the microbiota in intestinal diseases (11,29). Only two studies have investigated the intestinal microbiota of luminal and mucosal niches in patients with IBS (6,9).…”

Gut Bacterial Diversity of the House Sparrow (Passer domesticus) Inferred by 16S rRNA Sequence Analysis

“…We believe that our capacity to make a better description of the gut bacterial communities of birds is related to the fact that we sampled the whole intestine, instead of using only fecal matter or cloacal swabs like in previous studies [15,39,58,71]. In humans, for instance, it has been shown that the bacterial composition obtained from gut biopsies and fecal samples from the same individuals can vary enormously [15].…”

“…We believe that our capacity to make a better description of the gut bacterial communities of birds is related to the fact that we sampled the whole intestine, instead of using only fecal matter or cloacal swabs like in previous studies [15,39,58,71]. In humans, for instance, it has been shown that the bacterial composition obtained from gut biopsies and fecal samples from the same individuals can vary enormously [15]. Because to sample the whole gut is technically complex, and/or requires sacrificing organisms, the use of fecal matter and cloacal swabs is the most common technique used to describe intestinal bacteria diversity in vertebrates [59,74,77].…”

“…The difficulty, and ethical implications related to sampling the different intestinal sections has resulted in the frequent use of fecal matter as an indicator of the intestinal microbiota. However, gut bacteria are poorly represented in fecal matter [15,59,71,77], limiting the information that fecal material provides on the bacteria present in the gut mucosa [15,59,77], and does not allow for a description of changes in bacterial communities along the different sections of the gut. It can be assumed that microbiota changes along the intestinal tract because of the biochemical and morphological differences that can be found in the different sections of vertebrate intestines [41,59].…”

Uso da biblioteca genômica RNAr 16S como ferramenta para o estudo da microbiota fecal humana

“…Este fenômeno é conhecido como "resistência à colonização", "interferência microbiana" ou "efeito barreira" (GARRETT et al, 2010;VRIEZE et al, 2010;DAVID et al, 2005 As análises moleculares de comunidades complexas foram primeiramente empregadas em estudos ambientais analisando de forma abrangente como os ecossistemas respondem às perturbações ambientais (Rondon, et al, 2000;BRITSCHGI e GIOVANNONI,1991;GIL et al, 2006 Análises filogenéticas baseadas em PCR e construção de biblioteca genômica de RNAr 16S têm sido utilizadas para caracterizar a microbiota de fezes humana (HAYASHI et al, 2003;HAYASHI et al, 2005). Os diferentes estudos da microbiota intestinal utilizando o método de amplificação do gene RNAr 16S disponíveis na literatura mostram uma grande diversidade e variedade dos componentes bacterianos desta microbiota (LI et al, 2012;DURBAN et al, 2011;REHMAN et al, 2010;WALKER et al, 2011;SHEN et al, 2010;LIN et al, 2013).…”