The composition of the gut microbiota is linked to multiple diseases,including Parkin-son's disease(PD).Abundance of bacteria producing short-chain fatty acids(SCFAs)and fecal SCFA concentrations are reduced in PD.SCFAs exert various beneficial functions in humans.In the interventional,monocentric,open-label clinical trial"Effects of Resistant Starch on Bowel Habits,Short Chain Fatty Acids and Gut Microbiota in Parkinson's Disease"(RESISTA-PD;ID:NCT02784145),we aimed at altering fecal SCFAs by an 8-week prebiotic intervention with resistant starch(RS).We enrolled 87 subjects in three study-arms:32 PD patients received RS(PD+RS),30 control subjects received RS,and 25 PD patients received solely dietary instructions.We performed paired-end 100 bp length metagenomic sequencing of fecal samples using the BGISEQ platform at an average of 9.9 GB.RS was well-tolerated.In the PD+RS group,fecal butyrate concentrations increased significantly,and fecal calprotectin concentrations dropped significantly after 8 weeks of RS intervention.Clinically,we observed a reduction in non-motor symptom load in the PD+RS group.The reference-based analysis of metagenomes highlighted stable alpha-diversity and beta-diversity across the three groups,including bacteria producing SCFAs.Reference-free analysis suggested punctual,yet pronounced differences in the metagenomic signature in the PD+RS group.RESISTA-PD highlights that a prebiotic treatment with RS is safe and well-tolerated in PD.The stable alpha-diversity and beta-diversity alongside altered fecal butyrate and calprotectin concentrations call for long-term studies,also investigating whether RS is able to modify the clinical course of PD.

Emerging antibiotic resistance is a major global health threat. The analysis of nucleic acid sequences linked to susceptibility phenotypes facilitates the study of genetic antibiotic resistance determinants to inform molecular diagnostics and drug development. We collected genetic data (11,087 newly-sequenced whole genomes) and culture-based resistance profiles (10,991 out of the 11,087 isolates comprehensively tested against 22 antibiotics in total) of clinical isolates including 18 main species spanning a time period of 30 years. Species and drug specific resistance patterns were observed including increased resistance rates for Acinetobacter baumannii to carbapenems and for Escherichia coli to fluoroquinolones. Species-level pan-genomes were constructed to reflect the genetic repertoire of the respective species, including conserved essential genes and known resistance factors. Integrating phenotypes and genotypes through species-level pan-genomes allowed to infer gene-drug resistance associations using statistical testing. The isolate collection and the analysis results have been integrated into GEAR-base, a resource available for academic research use free of charge at https://gear-base.com.
Acinetobacter baumannii ; genetics ; isolation & purification ; Bacteria ; genetics ; isolation & purification ; Cell Culture Techniques ; methods ; Drug Resistance, Microbial ; genetics ; Escherichia coli ; genetics ; isolation & purification ; Genome, Bacterial ; Genotype ; Humans ; Internet ; Microbial Sensitivity Tests ; Phenotype ; Whole Genome Sequencing