Modeling metabolism of the human gut microbiome

Abstract

The human gut microbiome plays an important part in human health. The complexity of the microbiome makes it difficult to determine the detailed metabolic functions and cross-talk occurs between the individual species. In silico systems biology studies of the microbiome can help to identify metabolite exchanges among gut microbes. Constraint-based reconstruction and analysis methods use biochemically accurate genome-scale metabolic networks of microorganisms to simulate metabolism between species in a given microbiome and help generate novel hypotheses on microbial interactions. Here, we review metabolic modeling studies that have investigated metabolic functions of the gut microbiome.

Meta‐Omics‐ and Metabolic Modeling‐Assisted Deciphering of Human Microbiota Metabolism

“…The first attempt at fully automated GEM reconstruction was made back in 2006. An algorithm, capable of curating meaningful GEMs from annotated genomes and other available information without human intervention (e.g., ModelSEED, KBase, PathwayTools), has evaded the grasp of developers . Steps towards automation have been successfully taken, with many reconstruction processes having been adopted in semi‐automatic approaches …”

“…Second, the use of metabolic modeling serves as an efficient way to elucidate the systemic interconnected activity of all the enzymes found within and beyond the same microbial species, giving rise to a complex set of metabolic pathways . To achieve this, the constraint‐based reconstruction and analysis (COBRA) approach on genome‐scale metabolic reconstructions has been developed and applied to study the systems metabolic interactions in the human microbiota and predict the effect of their perturbations on human health caused by dysbiosis or therapeutic interventions …”

A multifaceted approach to harness probiotics as antagonists on plant based foods, for enhanced benefits to be reaped at a global level

“…However, the large gamut of diversity seen in the world of microbes obviously makes the task increasingly difficult. The research on gut microbiota has progressed in terms of gene technology . It is observed that, despite having highly divergent gut microbiota composition, functional gene profiles are similar in different individuals .…”

“…Tracking of microbes, like tracking animals in zoological investigations, will help to understand such microecological forces. A molecular technique with the acronym COBRA (Constraint Based Reconstruction Analysis) enables microbial interactions with other microbes and with the host to be determined . A multitude of ecological processes governing plant‐microbe interactions provide information on how plant exudates interact with the plant microbiome .…”

“…The ecology of the microflora on exudates of the intact fruit has not received much attention; this is an important aspect when microbes on the phyllosphere are expected to protect and extend shelf‐life of fruits. A better knowledge of mechanisms of action governing gene expression will provide opportunities to progress and to maximize their efficacy in affecting the health of the host . Multiple approaches and genetic tools will be necessary for an in‐depth understanding of the genetics of the microbiome .…”