Fecal dysbiosis in infants with cystic fibrosis is associated with early linear growth failure

Abstract

Most infants with cystic fibrosis (CF) have pancreatic exocrine insufficiency that results in nutrient malabsorption and requires oral pancreatic enzyme replacement. Newborn screening for CF has enabled earlier diagnosis, nutritional intervention and enzyme replacement for these infants, allowing most infants with CF to achieve their weight goals by 12 months of age1. Nevertheless, most infants with CF continue to have poor linear growth during their first year of life1. Although this early linear growth failure is associated with worse long-term respiratory function and survival2,3, the determinants of body length in infants with CF have not been defined. Several characteristics of the CF gastrointestinal (GI) tract, including inflammation, maldigestion and malabsorption, may promote intestinal dysbiosis4,5. As GI microbiome activities are known to affect endocrine functions6,7, the intestinal microbiome of infants with CF may also impact growth. We identified an early, progressive fecal dysbiosis that distinguished infants with CF and low length from infants with CF and normal length. This dysbiosis included altered abundances of taxa that perform functions that are important for GI health, nutrient harvest and growth hormone signaling, including decreased abundance of Bacteroidetes and increased abundance of Proteobacteria. Thus, the GI microbiota represent a potential therapeutic target for the correction of low linear growth in infants with CF.

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Fig. 1: Fecal microbial composition is altered in infants with CF compared with controls.
Fig. 2: Development of the fecal microbiome in infants with CF is delayed compared with controls.
Fig. 3: Low-length infants with CF have more extreme dysbiosis than normal-length infants with CF.

Data availability

All metagenomic DNA sequence data required to assess the conclusions of this research are available without restriction from the Sequence Read Archive at the National Center for Biotechnology Information under BioProject accession PRJNA510445.

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Acknowledgements

This project was supported by grants from the National Institutes of Health (R01DK095869, K24HL141669, 5P30DK089507) and the Cystic Fibrosis Foundation (SINGH15R0). E.B. is a Faculty Fellow of the Edmond J. Safra Center for Bioinformatics at Tel Aviv University. We gratefully acknowledge the contributions of the principal investigators (including D. Borowitz, B. Ramsey and D. Gelfond), study site coordinators and participants of the BONUS and Healthy Infants Study.

Author information

L.R.H., S.I.M. and E.B. designed the study. C.E.P., K.R.H., A.T.V. and H.S.H. isolated and sequenced metagenomes of stool samples. C.E.P. performed fecal fat assays. A.E., M.J.B. and E.J.W. performed bioinformatic analyses. A.E. and M.J.B. performed statistical analyses with assistance from B.D.M. and S.L.H. H.S.H., A.E., C.E.P., M.J.B., D.H.L., E.B., S.I.M. and L.R.H. analyzed data and wrote the manuscript.

Correspondence to Elhanan Borenstein or Samuel I. Miller or Lucas R. Hoffman.

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Competing interests

The authors declare no competing interests.

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Peer review information Alison Farrell was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Principal coordinates analysis of the fecal microbiota of infants with CF and controls at month 4.

The structure of the fecal microbiomes of infants in this study at month 4 presented in a multidimensional scaling plot is dominated by the large abundances of B. longum, B. breve and E. coli. One sample is represented for each of 109 infants with CF and 25 controls. Each colored dot represents the microbiota of a different study sample, as indicated.

Extended Data Fig. 2 Phylogenetic plot comparing average microbiota at multiple taxonomic levels at months 4 and 12 for infants with CF and controls.

As indicated in the legend at the lower right, greyscale bars indicate relative abundance, and red or black bars on the outside of the circular graph indicate whether taxa were enriched in infants with CF (black) or controls (red) at month 12.

Extended Data Fig. 3 Mean percent relative abundance of genera in Phylum Proteobacteria in fecal samples from infants with CF and normal length, infants with CF and low length and controls.

Proteobacteria remained relatively high in infants with CF, especially those with low length, owing primarily to replacement with E. coli. In addition, abundances of Klebsiella and Enterobacter remained relatively high. Bar heights represents mean percent relative abundance of Proteobacteria at each timepoint, and the mean relative abundance contribution for selected genera are indicated within each bar.

Extended Data Fig. 4 Average percent relative abundance of different bacterial phyla in fecal samples from infants with CF with normal length, infants with CF with low length and controls.

Phylum-level average microbiota at each collection time point of the control infants (left) compared with normal-length infants with CF (middle) and low-length infants with CF (right).

Extended Data Fig. 5 Fecal microbiota development is significantly delayed in infants with CF relative to controls when omitting infants prescribed any acid suppressors and when models are trained on a sparse set of taxonomic features.

a, Infants prescribed any acid suppressors, including proton pump inhibitors and/or H2 blockers were omitted. b, Models trained on a sparse set of taxonomic features. The distributions of relative microbiota age are shown (x axis), following the approach in Subramanian et al.22 for each subject group (infants with CF or controls) using abundances at all taxonomic levels as the normalized error in a sample’s predicted microbiota age when using a computational model constructed for the other group. For example, negative relative microbiota age indicates delayed development compared with the group used to construct the model. The y axis shows density of samples that mapped to a given relative microbiota age at the indicated timepoints. Colored ratios summarize the fraction of replicate full-feature models that produced a distribution of relative microbiota ages that was significantly negatively (green for CF samples relative to control models) or positively (blue for control samples relative to CF models) different from zero. q < 0.01, one-sided Wilcoxon signed-rank test.

Extended Data Fig. 6 Levels of fecal fat percentage and fecal calprotectin during the first year of life.

Lines above the boxes represent significant differences between time points within a cohort (colored lines) or between cohorts at the same time point (black lines). q ≤ 0.01, two-sided Wilcoxon rank-sum test. The boxplot hinges indicate the first and third quartiles, and the whiskers indicate 1.5 times the IQR above and below.

Extended Data Fig. 7 Fecal microbiota development is significantly delayed in infants with CF with low length relative to infants with CF with normal length at month 12.

The distributions of relative microbiota age (x axis) are shown, following the approach in Subramanian et al.22 for each subject group (infants with CF and low length or infants with CF and normal length) as described in Fig. 2. Colored ratios summarize the fraction of replicate full-feature models that produced a distribution of relative microbiota ages that was significantly negatively (red for CF low-length samples relative to CF normal-length models) or positively (purple for CF normal-length samples relative to CF low-length models) different from zero. q < 0.01, one-sided Wilcoxon signed-rank test.

Extended Data Fig. 8 Prevalence of selected butyrate-producing species with significantly different prevalence between infants with CF compared with controls at month 12.

n = 23 for controls and 152 for infants with CF, q < 0.05, chi-squared test.

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Hayden, H.S., Eng, A., Pope, C.E. et al. Fecal dysbiosis in infants with cystic fibrosis is associated with early linear growth failure. Nat Med 26, 215–221 (2020). https://doi.org/10.1038/s41591-019-0714-x

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