Abstract
Current meta-omics developments provide a portal into the functional potential and activity of the intestinal microbiota. The comparative and functional meta-omics approaches have made it possible to get a molecular snap shot of microbial function at a certain time and place. To this end, metagenomics is a DNA-based approach, metatranscriptomics studies the total transcribed RNA, metaproteomics focuses on protein levels and metabolomics describes metabolic profiles. Notably, the metagenomic toolbox is rapidly expanding and has been instrumental in the generation of draft genome sequences of over 1000 human associated microorganisms as well as an astonishing 3.3 million unique microbial genes derived from the intestinal tract of over 100 European adults. Remarkably, it appeared that there are at least 3 clusters of co-occurring microbial species, termed enterotypes, that characterize the intestinal microbiota throughout various continents. The human intestinal microbial metagenome further revealed unique functions carried out in the intestinal environment and provided the basis for newly discovered mechanisms for signaling, vitamin production and glycan, amino-acid and xenobiotic metabolism. The activity and composition of the microbiota is affected by genetic background, age, diet, and health status of the host. In its turn the microbiota composition and activity influence host metabolism and disease development. Exemplified by the differences in microbiota composition and activity between breast- as compared to formula-fed babies, healthy and malnourished infants, elderly and centenarians as compared to youngsters, humans that are either lean or obese and healthy or suffering of inflammatory bowel diseases (IBD). In this review we will focus on our current understanding of the functionality of the human intestinal microbiota based on all available metagenome, metatranscriptome, and metaproteome results
Highlights
The human intestinal microbiota is known to play a key role in several metabolic, nutritional, physiological, and immunological processes, and recent years have seen a rapid development in the techniques for studying this previously overlooked organ (O’Hara and Shanahan, 2006)
Understanding the factors relating to the existence and host interactions of bifidobacteria and linking the functionality of this early intestinal colonizer to specific diets and groups of healthy or diseased individuals may eventually lead to the possibility of guiding the development of the microbiota. This can be achieved with pro- and prebiotic supplemented infant formulas that are aimed at increasing the bacterial diversity and a more optimal bifidobacterial community composition
The results showed that Bacteroidetes, Firmicutes, Actinobacteria, Verrucomicrobia, and Proteobacteria were the dominant groups in the microbiota of the study subjects
Summary
The comparative and functional meta-omics approaches have made it possible to get a molecular snap shot of microbial function at a certain time and place To this end, metagenomics is a DNA-based approach, metatranscriptomics studies the total transcribed RNA, metaproteomics focuses on protein levels and metabolomics describes metabolic profiles. The metagenomic toolbox is rapidly expanding and has been instrumental in the generation of draft genome sequences of over 1000 human associated microorganisms as well as an astonishing 3.3 million unique microbial genes derived from the intestinal tract of over 100 European adults. It appeared that there are at least 3 clusters of co-occurring microbial species, termed enterotypes, that characterize the intestinal microbiota throughout various continents.
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