Review: Tools for the tract: understanding the functionality of the gastrointestinal tract

Abstract

The human gastrointestinal tract comprises a series of complex and dynamic organs ranging from the stomach to the distal colon, which harbor immense microbial assemblages that are known to be vital for human health. Until recently, most of the details concerning our gut microbiota remained obscure. Over the past several years, however, a number of crucial technological and conceptual innovations have been introduced to shed more light on the composition and functionality of human gut microbiota. Recently developed high throughput approaches, including next-generation sequencing technologies and phylogenetic microarrays targeting ribosomal RNA gene sequences, allow for comprehensive analysis of the diversity and dynamics of the gut microbiota composition. Nevertheless, most of the microbes especially in the human large intestine still remain uncultured, and the in situ functions of distinct groups of the gut microbiota are therefore largely unknown, but pivotal to the understanding of their role in human physiology. Apart from functional and metagenomics approaches, stable isotope probing is a promising tool to link the metabolic activity and diversity of microbial communities, including yet uncultured microbes, in a complex environment. Advancements in current stable isotope probing approaches integrated with the application of high-throughput diagnostic microarray-based phylogenetic profiling and metabolic flux analysis should facilitate the understanding of human microbial ecology and will enable the development of innovative strategies to treat or prevent intestinal diseases of as yet unknown etiology.

Duodenal-Mucosal Bacteria Associated with Celiac Disease in Children

“…Previous data also suggest that only 12% of the total species richness was detected by applying both molecular and cultivationbased approaches (50). Remarkably, with both approaches, Firmicutes represented the most abundant group, Proteobacteria were relatively poorly detected by molecular approaches, and Bacteroidetes were less abundant when they were assessed with cultivation-based approaches than with molecular techniques (49)(50)(51).…”

“…Culture-independent studies indicate that the members of the normal human gut microbiota mainly belong to two phyla, Firmicutes and Bacteroidetes, with a smaller number of bacteria belonging to the Proteobacteria and Actinobacteria, although these conclusions are mainly based on analyses of the fecal microbiota composition (45,49). Previous data also suggest that only 12% of the total species richness was detected by applying both molecular and cultivationbased approaches (50). Remarkably, with both approaches, Firmicutes represented the most abundant group, Proteobacteria were relatively poorly detected by molecular approaches, and Bacteroidetes were less abundant when they were assessed with cultivation-based approaches than with molecular techniques (49)(50)(51).…”

Intestinal microbiology in early life: specific prebiotics can have similar functionalities as human-milk oligosaccharides

“…Recent investigations have not always confirmed the bifidogenic effect of human milk (39,47). However, these controversial observations may result from technical challenges, because the DNA sequencing tools not properly detect Bifidobacterium species and may require further optimization (48).…”

Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis

“…Hence, considerable interest has focused on studying the intestinal microbiota, and over the years more than 1000 different microbial phylotypes have been reported to inhabit the human intestinal tract (Rajilić-Stojanović et al, 2007), providing an overwhelming catalogue of metabolic functions to their host, as was recently shown by metagenome analysis of over 100 individuals (Qin et al, 2010). To better understand the composition and functionality of this complex microbial ecosystem, a number of methodologies have been developed (Zoetendal et al, 2008), among which in vitro model systems have been introduced to bypass obvious restrictions with respect to the accessibility of the intestine for frequent sampling (Egert et al, 2006;Kovatcheva-Datchary et al, 2009b). Currently available models of the large intestine range from simple batch fermentation systems to more or less sophisticated, well-controlled, single-and multi-vessel continuous bioreactor systems (for a recent overview and discussion of the different models, see Macfarlane & Macfarlane, 2007).…”