Metaproteomic assessment of gut microbial and host functional perturbations in Helicobacter pylori -infected patients subjected to an antimicrobial protocol

Abstract

The impact of therapeutic interventions on the human gut microbiota (GM) is a clinical issue of paramount interest given the strong interconnection between microbial dynamics and human health. Orally administered antibiotics are known to reduce GM biomass and modify GM taxonomic profile. However, the impact of antimicrobial therapies on GM functions and biochemical pathways has scarcely been studied. Here, we characterized the fecal metaproteome of 10 Helicobacter pylori -infected patients before (T0) and after 10 days (T1) of a successful quadruple therapy (bismuth, tetracycline, metronidazole, and rabeprazole) and 30 days after therapy cessation (T2), to investigate how GM and host functions change during the eradication and healing processes. At T1, the abundance ratio between microbial and host proteins was reversed compared with that at T0 and T2. Several pathobionts (including Klebsiella , Proteus , Enterococcus , Muribaculum , and Enterocloster ) were increased at T1. Therapy reshaped the relative contributions of the functions required to produce acetate, propionate, and butyrate. Proteins related to the uptake and processing of complex glycans were increased. Microbial cross-feeding with sialic acid, fucose, and rhamnose was enhanced, whereas hydrogen sulfide production was reduced. Finally, microbial proteins involved in antibiotic resistance and inflammation were more abundant after therapy. Moreover, a reduction in host proteins with known roles in inflammation and H. pylori -mediated carcinogenesis was observed. In conclusion, our results support the use of metaproteomics to monitor drug-induced remodeling of GM and host functions, opening the way for investigating new antimicrobial therapies aimed at preserving gut environmental homeostasis.

Benchmarking low- and high-throughput protein cleanup and digestion methods for human fecal metaproteomics

“…The stool samples used in this study were collected after a successful treatment for eradication of H. pylori infection. Although antibiotic therapies are known to cause profound alterations in the gut microbiota both in terms of total biomass and taxonomic composition, an almost complete reversal of these changes 30 days after the end of the therapy was demonstrated in a previous analysis of the fecal metaproteome in ten subjects belonging to the same cohort of this study ( 40 ). Based on these considerations, we anticipated that the samples analyzed in this study were not substantially different from those that can be obtained from healthy subjects.…”