Differential co-expression networks of the gut microbiota are associated with depression and anxiety treatment resistance among psychiatric inpatients

Dominique S. Thompson, Chenlian Fu, Tanmay Gandhi, J. Christopher Fowler, B. Christopher Frueh, Benjamin L. Weinstein, Joseph Petrosino, Julia K. Hadden, Marianne Carlson, Cristian Coarfa, Alok Madan

Research output: Contribution to journalReview articlepeer-review

8 Scopus citations


Background: Comorbid anxiety and depression are common and are associated with greater disease burden than either alone. Our recent efforts have identified an association between gut microbiota dysfunction and severity of anxiety and depression. In this follow-up, we applied Differential Co-Expression Analysis (DiffCoEx) to identify potential gut microbiota biomarker(s) candidates of treatment resistance among psychiatric inpatients. Methods: In a sample of convenience, 100 psychiatric inpatients provided clinical data at admission and discharge; fecal samples were collected early during the hospitalization. Whole genome shotgun sequencing methods were used to process samples. DiffCoEx was used to identify clusters of microbial features significantly different based on treatment resistance status. Once overlapping features were identified, a knowledge-mining tool was used to review the literature using a list of microbial species/pathways and a select number of medical subject headlines (MeSH) terms relevant for depression, anxiety, and brain-gut-axis dysregulation. Network analysis used overlapping features to identify microbial interactions that could impact treatment resistance. Results: DiffCoEx analyzed 10,403 bacterial features: 43/44 microbial features associated with depression treatment resistance overlapped with 43/114 microbial features associated with anxiety treatment resistance. Network analysis resulted in 8 biological interactions between 16 bacterial species. Clostridium perfringens evidenced the highest connection strength (0.95). Erysipelotrichaceae bacterium 6_1_45 has been most widely examined, is associated with inflammation and dysbiosis, but has not been associated with depression or anxiety. Conclusion: DiffCoEx potentially identified gut bacteria biomarker candidates of depression and anxiety treatment-resistance. Future efforts in psychiatric microbiology should examine the mechanistic relationship of identified pro-inflammatory species, potentially contributing to a biomarker-based algorithm for treatment resistance.

Original languageEnglish (US)
Article number110638
JournalProgress in Neuro-Psychopharmacology and Biological Psychiatry
StatePublished - Jan 10 2023


  • Anxiety
  • Biomarkers
  • Brain-gut Axis
  • Depression
  • Gastrointestinal microbiome
  • Metagenomics
  • Inpatients
  • Humans
  • Gastrointestinal Microbiome/genetics

ASJC Scopus subject areas

  • Biological Psychiatry
  • Pharmacology


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