Cross-Sectional and Longitudinal Comparisons of the Predominant Fecal Microbiota Compositions of a Group of Pediatric Patients with Cystic Fibrosis and Their Healthy Siblings

Abstract

Although only poorly documented, it can be assumed that intensive antibiotic treatments of chronic lung infections in patients with cystic fibrosis (CF) also affect the diversity and metabolic functioning of the gastrointestinal microbiota and potentially lead to a state of dysbiosis. A better knowledge of the differences in gut microbiota composition and stability between patients with CF and healthy subjects could lead to optimization of current antibiotic therapies and/or development of add-on therapies. Using conventional culturing and population fingerprinting by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA amplicons, we compared the predominant fecal microbiota of 21 patients with CF and 24 healthy siblings in a cross-sectional study. General medium counts, as well as counts on media specific for lactic acid bacteria, clostridia, Bifidobacterium spp., Veillonella spp., and Bacteroides-Prevotella spp., were consistently higher in sibling samples than in CF samples, whereas the reverse was found for enterobacterial counts. DGGE fingerprinting uncovered large intersubject variations in both study groups. On the other hand, the cross-sectional data indicated that the predominant fecal microbiota of patients and siblings had comparable species richness. In addition, a longitudinal study was performed on 7 or 8 consecutive samples collected over a 2-year period from two patients and their respective siblings. For these samples, DGGE profiling indicated an overall trend toward lower temporal stability and lower species richness in the predominant fecal CF microbiota. The observed compositional and dynamic perturbations provide the first evidence of a general dysbiosis in children with CF compared to their siblings.

The microbial diversity of an industrially produced lambic beer shares members of a traditionally produced one and reveals a core microbiota for lambic beer fermentation

“…Total DNA solutions were diluted to an OD 260 of 1. Amplification of about 200 bp of the V3 region of the 16S rRNA genes with the F357 (with a GC clamp) and R518 primers, followed by denaturing gradient gel electrophoresis (DGGE) analysis, and processing of the resulting fingerprints was performed as described previously (Duytschaever et al, 2011), except that DGGE gels were run for 960 min instead of 990 min. For the amplification of about 200 bp of the D1 region of the LSUrRNA genes of eukaryotic microorganisms, NL1 (with GC clamp) and LS2 primers were used, as previously reported by Cocolin et al (2000).…”

Gut dysbiosis in cystic fibrosis

“…However, CF-related gut dysbiosis has only recently been subjected to detailed investigation. Using DGGE and culture-based methods, Duytschaever and colleagues [6] showed that children with CF have a quantitatively and qualitatively different faecal microbiota from their healthy siblings. We conducted a pilot study using culture-independent stool microbiome profiling and found evidence consistent with these results, strengthening the case for more targeted exploration of the gut microbiota in CF.…”

Linking Microbial Community Structure to Function in Representative Simulated Systems

“…This approach allows for the study of microorganisms in their natural environmental settings and has produced a wealth of data on microbial communities in the human microbiome (6)(7)(8)(9)(10) and in aquatic systems (11)(12)(13)(14). However, there is no realistic capacity to control parameters within in vivo systems.…”