Computational profiling of the gut-brain axis: microflora dysbiosis insights to neurological disorders

Brief Bioinform. 2019 May 21;20(3):825-841. doi: 10.1093/bib/bbx154.


Almost 2500 years after Hippocrates' observations on health and its direct association to the gastrointestinal tract, a paradigm shift has recently occurred, making the gut and its symbionts (bacteria, fungi, archaea and viruses) a point of convergence for studies. It is nowadays well established that the gut microflora's compositional diversity regulates via its genes (the microbiome) the host's health and provides preliminary insights into disease progression and regulation. The microbiome's involvement is evident in immunological and physiological studies that link changes in its biodiversity to its contributions to the host's phenotype but also in neurological investigations, substantiating the aptly named gut-brain axis. The definitive mechanisms of this last bidirectional interaction will be our main focus because it presents researchers with a new conundrum. In this review, we prospect current literature for computational analysis methodologies that accommodate the need for better understanding of the microbiome-gut-brain interactions and neurological disorder onset and progression, through cross-disciplinary systems biology applications. We will present bioinformatics tools used in exploring these synergies that help build and interpret microbial 16S ribosomal RNA data sets, produced by shotgun and high-throughput sequencing of healthy and neurological disorder samples stored in biological databases. These approaches provide alternative means for researchers to form hypotheses to their inquests faster, cheaper and swith precision. The goal of these studies relies on the integration of combined metagenomics and metabolomics assessments. An accurate characterization of the microbiome and its functionality can support new diagnostic, prognostic and therapeutic strategies for neurological disorders, customized for each individual host.

Keywords: computational metagenomics; gut–brain axis; microbiome; microflora; neurological disorders; precision medicine.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Brain / metabolism*
  • Computational Biology / methods*
  • Dysbiosis*
  • Gastrointestinal Microbiome*
  • Humans
  • Metagenomics
  • Nervous System Diseases / microbiology*