Mapping the Segmental Microbiomes in the Human Small Bowel in Comparison with Stool: A REIMAGINE Study

Abstract

Background Most gut microbiome studies have been performed using stool samples. However, the small intestine is of central importance to digestion, nutrient absorption, and immune function, and characterizing its microbial populations is essential for elucidating their roles in human health and disease. Aims To characterize the microbial populations of different small intestinal segments and contrast these to the stool microbiome. Methods Male and female subjects undergoing esophagogastroduodenoscopy without colon preparation were prospectively recruited. Luminal aspirates were obtained from the duodenum, jejunum, and farthest distance reached. A subset also provided stool samples. 16S rRNA sequencing was performed and analyses were carried out using CLC Genomics Workbench. Results 16S rRNA sequencing identified differences in more than 2000 operational taxonomic units between the small intestinal and stool microbiomes. Firmicutes and Proteobacteria were the most abundant phyla in the small intestine, and Bacteroidetes were less abundant. In the small intestine, phylum Firmicutes was primarily represented by lactic acid bacteria, including families Streptococcaceae, Lactobacillaceae, and Carnobacteriaceae, and Proteobacteria was represented by families Neisseriaceae, Pasteurellaceae, and Enterobacteriaceae. The duodenal and FD microbial signatures were markedly different from each other, but there were overlaps between duodenal and jejunal and between jejunal and FD microbial signatures. In stool, Firmicutes were represented by families Ruminococcaceae, Lachnospiraceae, Christensenellaceae, and Proteobacteria by class Deltaproteobacteria. Conclusions The small bowel microbiome is markedly different from that in stool and also varies between segments. These findings may be important in determining how compositional changes in small intestinal microbiota contribute to human disease states.

Resolving the Paradox of Colon Cancer Through the Integration of Genetics, Immunology, and the Microbiota

“…This is due to a number of factors such as harsh environment for bacterial communities, a shorter transit time, an increased influx of digestive enzymes of antimicrobial peptides and bile acids, and an intermittent food substrate delivery (121,122). Although the taxonomic classification has been inconsistent across studies, several reports show the predominance of two major phyla, i.e., Firmicutes and Proteobacteria (121,123,124), followed by others (Bacteroidetes, Fusobacteria, Verrucomicrobia, Actinobacteria) residing in the human small intestine (124). At the genus level, several genera are commonly found in the small intestine, such as Lactobacillus, Clostridium, Staphylococcus, Streptococcus, and Bacteroides (124)(125)(126)(127).…”

“…Fecal profiling of the microbial populations is investigated most frequently because the sampling of feces is non-invasive and convenient for patients compared to performing an invasive biopsy or collecting luminal content of ilea or colons (130). However, there is increasing evidence that the observed microbial composition in feces is different from the content of mucosal samples of the GI tract (123,(131)(132)(133)(134)(135). Bacteroidetes and Firmicutes are the main phyla in the healthy human stool samples followed by other phyla such as Actinobacteria, Proteobacteria, Synergistetes, and Verrucomicrobia (123,134,(136)(137)(138)(139)(140)(141)(142).…”

“…However, there is increasing evidence that the observed microbial composition in feces is different from the content of mucosal samples of the GI tract (123,(131)(132)(133)(134)(135). Bacteroidetes and Firmicutes are the main phyla in the healthy human stool samples followed by other phyla such as Actinobacteria, Proteobacteria, Synergistetes, and Verrucomicrobia (123,134,(136)(137)(138)(139)(140)(141)(142). At the genus level, Bacteroides is the most abundant genus (136,140,141) followed by Faecalibacterium, Bifidobacterium, Lachnospira, Roseburia, Subdoligranulum, Collinsella, Ruminococcus, Prevotella, Alistipes, and Akkermansia (123,132,(136)(137)(138)(139)(140)(141)(142).…”

High-Fat Diets Led to OTU-Level Shifts in Fecal Samples of Healthy Adult Dogs

“…We chose to study fecal microbiota as a proxy for gut microbiota as fecal samples make non-invasive periodic measurements possible. One major limitation of using fecal samples is the fact that fecal samples are more representative of the digesta in the lower gut and might not adequately represent important host-microbial interactions specific to different regions of the GI tract (Leite et al, 2020 ). In addition, 16S rRNA gene amplicon datasets offer only limited information about functional roles of members of these microbial communities.…”

Breath Test or Duodenal Aspirate for Small Intestinal Bacterial Overgrowth: Still No Breath of Fresh Air

“…Diagnostic accuracy studies usually require comparison between a test of interest compared with an index or reference 'gold standard' test, which is not possible when a gold standard for SIBO remains lacking [2]. Furthermore, as with other findings accrued in the growing literature addressing the structure and function of the gut microbiome, the bacterial count may be less important than changes in relative abundance and frequency of specific bacterial phyla, changes that may prove important in human health but the significance of which remains poorly understood [11,12]. Finally, the authors used a nonstandard definition for a positive duodenal aspirate which required a higher bacterial count (> 10 5 colony forming units/mL) compared with the more recent North American Consensus (> 10 3 colony forming units/ mL) [6].…”