Abstract
Newborn screening for cystic fibrosis (CF) can identify affected but asymptomatic infants. The selection of omic technique for gut microbiota study is crucial due to both the small amount of feces available and the low microorganism load. Our aims were to compare the agreement between 16S rRNA amplicon sequencing and metaproteomics by a robust statistical analysis, including both presence and abundance of taxa, to describe the sequential establishment of the gut microbiota during the first year of life in a small size sample (8 infants and 28 fecal samples). The taxonomic assignations by the two techniques were similar, whereas certain discrepancies were observed in the abundance detection, mostly the lower predicted relative abundance of Bifidobacterium and the higher predicted relative abundance of certain Firmicutes and Proteobacteria by amplicon sequencing. During the first months of life, the CF gut microbiota is characterized by a significant enrichment of Ruminococcus gnavus, the expression of certain virulent bacterial traits, and the detection of human inflammation-related proteins. Metaproteomics provides information on composition and functionality, as well as data on host-microbiome interactions. Its strength is the identification and quantification of Actinobacteria and certain classes of Firmicutes, but alpha diversity indices are not comparable to those of amplicon sequencing. Both techniques detected an aberrant microbiota in our small cohort of infants with CF during their first year of life, dominated by the enrichment of R. gnavus within a human inflammatory environment.
Original language | English |
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Article number | e01466-22 |
Number of pages | 16 |
Journal | Microbiology spectrum |
Volume | 10 |
Issue number | 6 |
Early online date | 18 Oct 2022 |
DOIs | |
Publication status | Published - Dec 2022 |
Bibliographical note
Funding Information:Editor Joanna B. Goldberg, Emory University School of Medicine Copyright © 2022 Saralegui et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Concepción Gil, conchagil@ucm.es, or Rosa del Campo, rosa.campo@salud.madrid.org. The authors declare a conflict of interest. Rosa del Campo is recipient of a Vertex grant. The remaining authors have no conflict of interest. [This article was published on 18 October 2022 with information missing from Acknowledgments. This information was added in the current version, posted on 15 November 2022.] Received 21 April 2022 Accepted 23 September 2022 Published 18 October 2022
Publisher Copyright:
© 2022 Saralegui et al. T.
Keywords
- amplicon sequencing
- Bland-Altman test
- cystic fibrosis
- gut microbiota establishment
- metaproteomics
- Ruminococcus gnavus
ASJC Scopus subject areas
- Physiology
- Ecology
- General Immunology and Microbiology
- Genetics
- Microbiology (medical)
- Cell Biology
- Infectious Diseases