By Beatrice Marg-Haufe

It is becoming increasingly clear that at least some medical conditions previously ascribed only to genetic and biochemical changes in the brain, including neurodegenerative diseases and psychiatric disorders, are linked to alterations in the gut microbiome. Metagenomic research is underway using next-gen sequencing (NGS) and microarrays to characterize the healthy gut microbiome and to identify and quantify aberrations in the types and levels of microbes inhabiting the intestines of patient populations at various stages of disease.

More than a feeling - the brain-gut axis.

More than a feeling - the brain-gut axis.

The brain-gut axis

The gut microbiome helps to maintain digestive health. But when the microbial composition of the gut goes out of whack – a new bacterium that does not belong takes up residence, for example, one species flourishes while another declines in number, or an antibiotic-induced tsunami virtually wipes out microbial life in the gut – the effects on the body's immune system and delicate homeostasis can cause problems far beyond the intestines.

A rapidly expanding body of scientific literature describes advances in techniques to analyze the metagenome. Current research is largely focusing on characterizing the gut microbiome. A growing number of examples relate to neurologic, chronic inflammatory, and psychiatric disorders.

Sequencing the human gut microbiome

Recently, a paper published in Scientific Reports presented data showing that the microbiome of patients with the autoimmune disorder multiple sclerosis (MS) differs from that of their healthy peers.1 Chen et al. profiled gut microbial populations using hypervariable tag sequencing of the V3-V5 region of the 16S ribosomal RNA gene. They reported an increased abundance of some microbes, such as Pseudomonas, and a decreased abundance of others in the gut microbiomes of patients with relapsing remitting MS. Furthermore, "patients with active disease showed decreased species richness compared to patients in remission and controls," which the researchers suggest "points toward an important role of gut microbiota in disease exacerbation."

Chronic fatigue syndrome (CFS, or myalgic encephalomyelitis) is another example. Not only are gastrointestinal disturbances common among individuals who suffer from CFS, but new research indicates that the gut microbiome of these patients shows decreased diversity and an altered microbial composition. Giloteaux used deep sequencing of bacterial 16S rRNA from stool samples to compare the gut microbiomes of healthy individuals and patients with CFS.2 In addition to reporting overall reduced diversity among the CFS group, the researchers found increases in specific microbial species typically described as being pro-inflammatory and reduced levels of species often described as being anti-inflammatory. These alterations in the gut microbiota could have a role in the inflammatory symptoms of CFS.

Evidence links brain to gut


Annadora Bruce-Keller and colleagues have published metagenomic sequencing data from a study in mice to support a link between neurologic dysfunction -- and psychiatric and cognitive disorders including depression, anxiety, and dementia - and gut dysbiosis.3 A gut microbiome profile characteristic of obesity (induced in non-obese mice) led to increased brain inflammation, disrupted cerebrovascular homeostasis, and neurobehavioral changes. Based on these findings the researchers concluded that "dietary and/or pharmacologic manipulation of gut microbiota could attenuate the neurologic complications of obesity."


Kelly and coauthors reviewed the emerging links between the gut microbiome and the central nervous system, focusing mainly on the role a "leaky gut" plays in stress-related psychiatric disorders and the potential to develop psychobiotic therapeutics.4 A healthy balance of microbes in the gut appear to help maintain intestinal barrier function. When regulation of intestinal permeability goes awry and the gut becomes leaky, the increased potential for chronic low-grade inflammation could contribute to or underlie stress-related conditions such as depression.

Accelerating microbial sequencing

Much of the time and effort required to identify and quantify the bacteria in a fecal sample for the purpose of profiling and monitoring an individual's gut microbiome is devoted to sample prep and the creation of sequencing-ready libraries. The availability of ready-to-use kits, such as the Nextera® XT DNA Library Preparation Kit from Illumina, and automated protocols that facilitate sample multiplexing and greatly increased throughput are accelerating genomic workflows.

Download the application note on automated Nextera® XT DNA library preparation. 



  1. Chen J, Chia N, Kalari KR, et al. Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls. Sci Reports 2016; doi:10.1038/srep28484
  2. Giloteaux L, Goodrich JK, Walters WW, et al. Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome. Microbiome 2016; 4:30.
  3. Bruce-Keller AJ, Salbaum, JM, Luo M, et al. Obese-type gut microbiota induce neurobehavioral changes in the absence of obesity. Biol Psychiatry 2014; 77(7):607-615.
  4. Kelly JR, Kennedy PJ, Cryan JF, et al. Breaking down the barriers: The gut microbiome, intestinal permeability and stress-related psychiatric disorders. Front Cell Neurosci 2015; doi:10.3389/fncel.2015.00392.

About the author

Dr Beatrice Marg-Haufe

Dr Beatrice Marg-Haufe

Dr. Beatrice Marg-Haufe is a product manager at Tecan Switzerland with over 10 years of experience in assay development and product management. She studied biochemistry at the University of Bielefeld, Germany, and at Harvard Medical School, USA. She focused on cancer research during her PhD in Biochemistry at the MPI, Munich, Germany. She joined Tecan in 2009 focusing on applications for the agriculture and genomics market.