Microbiota and Metabolite Profiling Reveal Specific Alterations in Bacterial Community Structure and Environment in the Cystic Fibrosis Airway during Exacerbation

Abstract

Chronic polymicrobial infections of the lung are the foremost cause of morbidity and mortality in cystic fibrosis (CF) patients. The composition of the microbial flora of the airway alters considerably during infection, particularly during patient exacerbation. An understanding of which organisms are growing, their environment and their behaviour in the airway is of importance for designing antibiotic treatment regimes and for patient prognosis. To this end, we have analysed sputum samples taken from separate cohorts of CF and non-CF subjects for metabolites and in parallel, and we have examined both isolated DNA and RNA for the presence of 16S rRNA genes and transcripts by high-throughput sequencing of amplicon or cDNA libraries. This analysis revealed that although the population size of all dominant orders of bacteria as measured by DNA- and RNA- based methods are similar, greater discrepancies are seen with less prevalent organisms, some of which we associated with CF for the first time. Additionally, we identified a strong relationship between the abundance of specific anaerobes and fluctuations in several metabolites including lactate and putrescine during patient exacerbation. This study has hence identified organisms whose occurrence within the CF microbiome has been hitherto unreported and has revealed potential metabolic biomarkers for exacerbation.

A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation

“…Antibiotic treatment quickly eliminated these bacteria, indicating that the CF microbial community was dynamic through exacerbation events in this patient. Similar signatures of microbial fermentation have been described in other studies , including in exacerbation samples (Twomey et al, 2013), and the anaerobe Gamella was the most discriminate genus between exacerbation and stable samples in a previous microbiome study (Carmody et al, 2013). In light of these results, we propose that the CAM, originally described by Conrad et al (2012), should be focused on microbial physiology.…”

“…Some studies find little change (Fodor et al, 2012;Deschaght et al, 2013;Price et al, 2013), while others are finding fluctuations in anaerobic microbial abundance (Carmody et al, 2013;Deschaght et al, 2013;Twomey et al, 2013;Zemanick et al, 2013). The WinCF system demonstrated that obligate anaerobes are abundant prior to exacerbation and actively fermenting.…”

“…Although metagenomic studies have revealed aspects of the core physiology of CF microbes containing both respiratory and fermentative metabolisms Quinn et al, 2014), little is known about microbial physiology during exacerbation events. Although some studies report that the microbial community changes as exacerbations develop (Carmody et al, 2013;Twomey et al, 2013), others provide evidence for relative stability (Stressmann et al, 2011;Price et al, 2013). A better understanding of the microbial community dynamics and physiology through CFPE is critical to understand how this community contributes to disease flares.…”

Putrescine Reduces Antibiotic-Induced Oxidative Stress as a Mechanism of Modulation of Antibiotic Resistance in Burkholderia cenocepacia

“…For example, the putrescine concentration was reported to be 3 mM in urine (11), whereas it was shown to be up to 0.2 mM in sputum samples from CF patients (39,40). However, it is difficult to predict the local concentration of putrescine and other polyamines in the lung of CF patients, as infection alters the rheology of the mucus and the lung environment (41).…”

“…However, it is difficult to predict the local concentration of putrescine and other polyamines in the lung of CF patients, as infection alters the rheology of the mucus and the lung environment (41). Moreover, putrescine levels increase dramatically (by 10-fold or more) during exacerbations of bacterial infections in CF patients (39,40). Hence, the concentrations used in this study could potentially resemble the physiological situation in certain body compartments.…”