, 13:8

The association of fecal microbiota and fecal, blood serum and urine metabolites in myalgic encephalomyelitis/chronic fatigue syndrome

  • Christopher W. Armstrong
  • Neil R. McGregor
  • Donald P. Lewis
  • Henry L. Butt
  • Paul R. Gooley
Original Article

DOI: 10.1007/s11306-016-1145-z

Cite this article as:
Armstrong, C.W., McGregor, N.R., Lewis, D.P. et al. Metabolomics (2017) 13: 8. doi:10.1007/s11306-016-1145-z



The human gut microbiota has the ability to modulate host metabolism. Metabolic profiling of the microbiota and the host biofluids may determine associations significant of a host–microbe relationship. Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a long-term disorder of fatigue that is poorly understood, but has been linked to gut problems and altered microbiota.


Find changes in fecal microbiota and metabolites in ME/CFS and determine their association with blood serum and urine metabolites.


A workflow was developed that correlates microbial counts with fecal, blood serum and urine metabolites quantitated by high-throughput 1H NMR spectroscopy. The study consists of thirty-four females with ME/CFS (34.9 ± 1.8 SE years old) and twenty-five non-ME/CFS female (33.0 ± 1.6 SE years old).


The workflow was validated using the non-ME/CFS cohort where fecal short chain fatty acids (SCFA) were associated with serum and urine metabolites indicative of host metabolism changes enacted by SCFA. In the ME/CFS cohort a decrease in fecal lactate and an increase in fecal butyrate, isovalerate and valerate were observed along with an increase in Clostridium spp. and a decrease in Bacteroides spp. These differences were consistent with an increase in microbial fermentation of fiber and amino acids to produce SCFA in the gut of ME/CFS patients. Decreased fecal amino acids positively correlated with substrates of gluconeogenesis and purine synthesis in the serum of ME/CFS patients.


Increased production of SCFA by microbial fermentation in the gut of ME/CFS patients may be associated with deleterious effects on the host energy metabolism.


Myalgic encephalomyelitis/chronic fatigue syndrome Feces Microbiota Short chain fatty acids Energy metabolism Amino acids 



Branched-chain fatty acids


Irritable bowel disease


Myalgic encephalomyelitis/chronic fatigue syndrome


Nuclear overhauser effect spectroscopy


Nuclear magnetic resonance


Principal component analysis


Short chain fatty acids


Total correlated spectroscopy

Funding information

Funder NameGrant NumberFunding Note
Judith Jane Mason and Harold Stannett Williams Memorial Foundation
  • CT9957
  • MAS2015F020

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleAustralia
  2. 2.Faculty of Medicine, Dentistry and Health SciencesUniversity of MelbourneParkvilleAustralia
  3. 3.CFS Discovery, Donvale Medical CentreDonvaleAustralia
  4. 4.Bioscreen (Aust) Pty LtdYarravilleAustralia

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