The Structure and Function of the Human Small Intestinal Microbiota: Current Understanding and Future Directions

Abstract

There is limited information about the small intestinal microbiota, an ecosystem that is relevant to many physiologic mechanisms and pathologic states. Here, we highlight human and animal studies to advance understanding of microbe-influenced human conditions, and the fundamental distinctions of this population relative to the large intestine. Despite growing literature characterizing the fecal microbiome and its association with health and disease, few studies have analyzed the microbiome of the small intestine. Here, we examine what is known about the human small intestinal microbiota in terms of community structure and functional properties. We examine temporal dynamics of select bacterial populations in the small intestine, and the effects of dietary carbohydrates and fats on shaping these populations. We then evaluate dysbiosis in the small intestine in several human disease models, including small intestinal bacterial overgrowth, short-bowel syndrome, pouchitis, environmental enteric dysfunction, and irritable bowel syndrome. What is clear is that the bacterial biology, and mechanisms of bacteria-induced pathophysiology, are enormously broad and elegant in the small intestine. Studying the small intestinal microbiota is challenged by rapidly fluctuating environmental conditions in these intestinal segments, as well as the complexity of sample collection and bioinformatic analysis. Because the functionality of the digestive tract is determined primarily by the small intestine, efforts must be made to better characterize this unique and important microbial ecosystem.

Duodenal microbiome in patients with or without Helicobacter pylori infection

“…Currently, there is a paucity of information on the composition of small intestinal microbiota due to relative inaccessibility and potential contamination during sampling 55 . These results expand previous knowledge on duodenal microbiome describing its composition in subjects from an Ecuadorian population with high prevalence of H pylori infection that have undergone upper gastro‐duodenal endoscopy after overnight fasting.…”

In Vitro Digestion and Fermentation by Human Fecal Microbiota of Polysaccharides from Flaxseed

“…Here, the interaction between FSP and small intestinal microbiota was not considered. However, it is well known that the small intestine microbiota can also degrade and ferment diet-derived simple carbohydrates into organic acids, aldehydes, alcohols, and gases [ 26 ]. In vitro digestion is used to study the changes of FSP in the gastrointestinal juice, but it is difficult to study the effect of small intestinal microbiota on FSP.…”

The Link between Oral and Gut Microbiota in Inflammatory Bowel Disease and a Synopsis of Potential Salivary Biomarkers

“…Studies show increased inflammatory responses due to oral cavity diseases that cause pernicious shifts in bacterial colony composition in both the oral cavity and the intestines. Interestingly, the oral-gut connection in inflammation and IBD pathogenesis has recently been explored in an article published by Kitamoto et al [49]. In this article, oral-originating inflammatory Th17 cells and oral pathobiont bacterial species present in periodontitis mouse models were able to ectopically colonize and translocate to the intestines causing IBD [49].…”