Interactive functional networks in microbiota

Abstract

Humans are not autonomous entities. We are all living in a complex environment, interacting not only with our peers, but as true holobionts we are also very much in interaction with our coexisting microbial ecosystems living on and especially within us, in the intestine. Intestinal microorganisms, often collectively referred to as intestinal microbiota, contribute significantly to our daily energy uptake by breaking down complex carbohydrates into simple sugars, which are fermented to short-chain fatty acids and subsequently absorbed by human cells. They also have an impact on our immune system, by suppressing or enhancing the growth of malevolent and beneficial microbes. Our lifestyle can have a large influence on this ecosystem. What and how much we consume can tip the ecological balance in the intestine. A "western diet" containing mainly processed food will have a different effect on our health than a balanced diet fortified with pre-and probiotics. In recent years, new technologies have emerged, which made a more detailed understanding of microbial communities and ecosystems feasible. This includes progress in the sequencing of PCR-amplified phylogenetic marker genes as well as the collective microbial metagenome and metatranscriptome, allowing us to determine with an increasing level of detail, which microbial species are in the microbiota, understand what these microorganisms do and how they respond to changes in lifestyle and diet. These new technologies also include the use of synthetic and in vitro systems, which allow us to study the impact of substrates and addition of specific microbes to microbial communities at a high level of detail, and enable us to gather quantitative data for modelling purposes. Here we will review the current state of microbiome research, summarizing the computational methodologies in this area, and highlighting possible outcomes for personalized nutrition and medicine. [301]). The researchers in the microbiome field need to be aware that this hype can also happen to the microbiome [302, 303]. Current microbiome research aims to overcome some of these challenges. Obesity research is likely to contribute in the close future to a better understanding of the underlying mechanisms, and the 4P medicine might partially become achievable in not too distant future, leading to better health and combating epidemics like obesity. Chapter 3: Genomic and functional analysis of Romboutsia ilealis CRIB T reveals adaptation to the small intestine.