Infants with cystic fibrosis have altered fecal functional capacities with potential clinical and metabolic consequences

Alexander Eng, Hillary S. Hayden, Christopher E. Pope, Mitchell J. Brittnacher, Anh T. Vo, Eli J. Weiss, Kyle R. Hager, Daniel H. Leung, Sonya L. Heltshe, Daniel Raftery, Samuel I. Miller, Lucas R. Hoffman*, Elhanan Borenstein*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


Background: Infants with cystic fibrosis (CF) suffer from gastrointestinal (GI) complications, including pancreatic insufficiency and intestinal inflammation, which have been associated with impaired nutrition and growth. Recent evidence identified altered fecal microbiota taxonomic compositions in infants with CF relative to healthy infants that were characterized by differences in the abundances of taxa associated with GI health and nutrition. Furthermore, these taxonomic differences were more pronounced in low length infants with CF, suggesting a potential link to linear growth failure. We hypothesized that these differences would entail shifts in the microbiome’s functional capacities that could contribute to inflammation and nutritional failure in infants with CF. Results: To test this hypothesis, we compared fecal microbial metagenomic content between healthy infants and infants with CF, supplemented with an analysis of fecal metabolomes in infants with CF. We identified notable differences in CF fecal microbial functional capacities, including metabolic and environmental response functions, compared to healthy infants that intensified during the first year of life. A machine learning-based longitudinal metagenomic age analysis of healthy and CF fecal metagenomic functional profiles further demonstrated that these differences are characterized by a CF-associated delay in the development of these functional capacities. Moreover, we found metagenomic differences in functions related to metabolism among infants with CF that were associated with diet and antibiotic exposure, and identified several taxa as potential drivers of these functional differences. An integrated metagenomic and metabolomic analysis further revealed that abundances of several fecal GI metabolites important for nutrient absorption, including three bile acids, correlated with specific microbes in infants with CF. Conclusions: Our results highlight several metagenomic and metabolomic factors, including bile acids and other microbial metabolites, that may impact nutrition, growth, and GI health in infants with CF. These factors could serve as promising avenues for novel microbiome-based therapeutics to improve health outcomes in these infants.

Original languageEnglish
Article number247
JournalBMC Microbiology
Issue number1
StatePublished - Dec 2021


FundersFunder number
National Institutes of HealthK24HL141669, 1S10OD021562, R01DK095869
National Institute of Diabetes and Digestive and Kidney DiseasesP30DK089507
Cystic Fibrosis FoundationSINGH15R0


    • Cystic fibrosis
    • Fecal microbiome
    • Infants
    • Metabolomics
    • Metagenomics
    • Nutrition


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