Disease-specific loss of microbial cross-feeding interactions in the human gut

VR Marcelino; C Welsh; C Diener; EL Gulliver; EL Rutten; RB Young; EM Giles; SM Gibbons; C Greening; SC Forster

Journal article

Disease-specific loss of microbial cross-feeding interactions in the human gut

VR Marcelino, C Welsh, C Diener, EL Gulliver, EL Rutten, RB Young, EM Giles, SM Gibbons, C Greening, SC Forster

Nature Communications | Published : 2023

DOI: 10.1038/s41467-023-42112-w

Download PDF

Abstract

Many gut microorganisms critical to human health rely on nutrients produced by each other for survival; however, these cross-feeding interactions are still challenging to quantify and remain poorly characterized. Here, we introduce a Metabolite Exchange Score (MES) to quantify those interactions. Using metabolic models of prokaryotic metagenome-assembled genomes from over 1600 individuals, MES allows us to identify and rank metabolic interactions that are significantly affected by a loss of cross-feeding partners in 10 out of 11 diseases. When applied to a Crohn’s disease case-control study, our approach identifies a lack of species with the ability to consume hydrogen sulfide as the main di..

View full abstract

University of Melbourne Researchers

Vanessa Rossetto Marcelino Author

Related Projects (2)

BACTERIAL COMMUNITIES IN METROPOLITAN, RURAL AND INDIGENOUS AUSTRALIANS

This project aims to apply recently developed culturing methods to archive and phenotype bacterial species found in the human gut in a repre..

Innate Mucosal Sensing & Shaping Of The Human Microbiome

Grants

Awarded by National Institute of Diabetes and Digestive and Kidney Diseases

Funding Acknowledgements

This work was supported by the Australian Research Council (DP190101504) and the Australian National Health and Medical Research Council (APP1181105 and APP1186371). V.R.M. is supported by an Australian Research Council DECRA Fellowship (DE220100965), C.G. is supported by an National Health & Medical Research Council EL2 Fellowship (APP1178715), and S.C.F. is supported by a CSL Centenary Fellowship. S.M.G. and C.D. were supported by the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health (R01DK133468). The authors acknowledge the Monash eResearch Centre for access to computational resources and expertise and the support of the Victorian Government's Operational Infrastructure Support Program. We thank Dr Paul Harrison and Dr Jamie Gearing for statistical and bioinformatics advice, and Dr Lucas Schiffer for help with curatedMetagenomicData. We also thank the stool donors and researchers who made their metadata publicly available and the reviewers of this manuscript for their constructive feedback. Open access charges funded by the Hudson Institute of Medical Research.