Abstract
The human intestine hosts a complex bacterial community that plays a major role in nutrition and in maintaining human health. A functional metagenomic approach was used to explore the prebiotic breakdown potential of human gut bacteria, including non-cultivated ones. Two metagenomic libraries, constructed from ileum mucosa and fecal microbiota, were screened for hydrolytic activities on the prebiotic carbohydrates inulin, fructo-oligosaccharides, xylo-oligosaccharides, galacto-oligosaccharides and lactulose. The DNA inserts of 17 clones, selected from the 167 hits that were identified, were pyrosequenced in-depth, yielding in total 407, 420 bp of metagenomic DNA. From these sequences, we discovered novel prebiotic degradation pathways containing carbohydrate transporters and hydrolysing enzymes, for which we provided the first experimental proof of function. Twenty of these proteins are encoded by genes that are also present in the gut metagenome of at least 100 subjects, whatever are their ages or their geographical origin. The sequence taxonomic assignment indicated that still unknown bacteria, for which neither culture conditions nor genome sequence are available, possess the enzymatic machinery to hydrolyse the prebiotic carbohydrates tested. The results expand the vision on how prebiotics are metabolized along the intestine, and open new perspectives for the design of functional foods.
Highlights
The human gut hosts a complex microorganism community that is dominated by bacterial phylotypes belonging to Firmicutes, Bacteroidetes and Actinobacteria
Prebiotics are defined as food ingredients that fit to the three following criteria: 1) resistance to gastric acidity, to hydrolysis by mammalian enzymes, and to gastrointestinal absorption; 2) fermentation by intestinal microbiota; and 3) selective stimulation of the growth and/or activity of those intestinal bacteria that contribute to health and well-being [14], in particular bifidobacteria
E. coli was chosen as the recombinant host because it was previously shown to allow expression of genes belonging to bacteria that are distantly related from a taxonomical point of view, like Bifidobacteria [44]
Summary
The human gut hosts a complex microorganism community that is dominated by bacterial phylotypes belonging to Firmicutes, Bacteroidetes and Actinobacteria. Prebiotics are defined as food ingredients that fit to the three following criteria: 1) resistance to gastric acidity, to hydrolysis by mammalian enzymes, and to gastrointestinal absorption; 2) fermentation by intestinal microbiota; and 3) selective stimulation of the growth and/or activity of those intestinal bacteria that contribute to health and well-being [14], in particular bifidobacteria For this last reason, the world market for prebiotics has grown rapidly in the last three decades [15], focusing on the production of compounds with established prebiotic effects (inulin, fructo-oligosaccharides, galacto-oligosaccharides and lactulose), as well as development and commercialization of other dietary carbohydrates, like resistant starch [16], xylo-oligosaccharides [17], gluco-oligosaccharides [18,19], polydextrose [20], lactosucrose [21], pectinderived [22] or soybean oligosaccharides [23]
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