A metagenomic insight into our gut's microbiome

Abstract

Advances in sequencing technology and the development of metagenomic and bioinformatics methods have opened up new ways to investigate the 10(14) microorganisms inhabiting the human gut. The gene composition of human gut microbiome in a large and deeply sequenced cohort highlighted an overall non-redundant genome size 150 times larger than the human genome. The in silico predictions based on metagenomic sequencing are now actively followed, compared and challenged using additional 'omics' technologies. Interactions between the microbiota and its host are of key interest in several pathologies and applying meta-omics to describe the human gut microbiome will give a better understanding of this crucial crosstalk at mucosal interfaces. Adding to the growing appreciation of the importance of the microbiome is the discovery that numerous phages, that is, viruses of prokaryotes infecting bacteria (bacteriophages) or archaea with a high host specificity, inhabit the human gut and impact microbial activity. In addition, gene exchanges within the gut microbiota have proved to be more frequent than anticipated. Taken together, these innovative exploratory technologies are expected to unravel new information networks critical for gut homeostasis and human health. Among the challenges faced, the in vivo validation of these networks, together with their integration into the prediction and prognosis of disease, may require further working hypothesis and collaborative efforts.

Modulation of the gut microbiota by prebiotic fibres and bacteriocins

“…Various gut bacteria overlap functionally and they ensure that crucial functions are present in the gut (e.g. the bacterial housekeeping functions involved in metabolic pathways and the putative gut-specific functions involved in adhesion to host proteins), which contributes to robustness in the gut ecosystem [32]. …”

Fusobacterium nucleatum associates with stages of colorectal neoplasia development, colorectal cancer and disease outcome

“…The human intestine is estimated to be colonized by more than 1000 bacterial phylotypes, which are thought to play important roles in nutrition and immune status, as well as many disease processes [4][5][6]. An altered presence of specific micro-organisms has been associated with a number of diseases of the gastro intestinal tract (GIT), such as inflammatory bowel disease (IBD) [7], irritable bowel syndrome (IBS, #14) [8,9] and CRC [10][11][12].…”

Crucial role of plasmacytoid dendritic cells in the development of acute colitis through the regulation of intestinal inflammation

“…[12][13][14] The intestine is the largest compartment of the immune system that is lined by a single layer of epithelium harboring commensal bacteria. 15,16 The gut microbiota contains 10 14 microorganisms, including at least 10 3 different species. 15,16 The intestinal immune system has to balance protective immune responses to potentially pathogenic microorganisms with nonresponsiveness to commensal bacteria and dietary Ags to maintain immune homeostasis in this environment.…”

“…15,16 The gut microbiota contains 10 14 microorganisms, including at least 10 3 different species. 15,16 The intestinal immune system has to balance protective immune responses to potentially pathogenic microorganisms with nonresponsiveness to commensal bacteria and dietary Ags to maintain immune homeostasis in this environment. 17,18 Breakdown of intestinal homeostasis can result in inflammatory bowel diseases (IBDs), represented by Crohn disease (CD) and ulcerative colitis (UC) in humans.…”