Cell-associated bacteria in the human lung microbiome

Abstract Background Recent studies have revealed that bronchoalveolar lavage (BAL) fluid contains previously unappreciated communities of bacteria. In vitro and in vivo studies have shown that host inflammatory signals prompt bacteria to disperse from cell-associated biofilms and adopt a virulent free-living phenotype. The proportion of the lung microbiota that is cell-associated is unknown. Results Forty-six BAL specimens were obtained from lung transplant recipients and divided into two aliquots: ‘whole BAL’ and ‘acellular BAL,’ the latter processed with a low-speed, short-duration centrifugation step. Both aliquots were analyzed via bacterial 16S rRNA gene pyrosequencing. The BAL specimens represented a wide spectrum of lung health, ranging from healthy and asymptomatic to acutely infected. Bacterial signal was detected in 52% of acellular BAL aliquots, fewer than were detected in whole BAL (96%, p ≤ 0.0001). Detection of bacteria in acellular BAL was associated with indices of acute infection [BAL neutrophilia, high total bacterial (16S) DNA, low community diversity, p < 0.01 for all] and, independently, with low relative abundance of specific taxonomic groups (p < 0.05). When whole and acellular aliquots from the same bronchoscopy were directly compared, acellular BAL contained fewer bacterial species (p < 0.05); whole and acellular BAL similarity was positively associated with evidence of infection and negatively associated with relative abundance of several prominent taxa (p < 0.001). Acellular BAL contained decreased relative abundance of Prevotella spp. (p < 0.05) and Pseudomonas fluorescens (p < 0.05). Conclusions We present a novel methodological and analytical approach to the localization of lung microbiota and show that prominent members of the lung microbiome are cell-associated, potentially via biofilms, cell adhesion, or intracellularity.http://deepblue.lib.umich.edu/bitstream/2027.42/111056/1/40168_2014_Article_75.pd

The role of Gr‐1+ cells and tumour necrosis factor‐α signalling during Clostridium difficile colitis in mice

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/110845/1/imm12425.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/110845/2/imm12425-sup-0001-FigS1-2.pd

Significance of the microbiome in obstructive lung disease

The composition of the lung microbiome contributes to both health and disease, including obstructive lung disease. Because it has been estimated that over 70% of the bacterial species on body surfaces cannot be cultured by currently available techniques, traditional culture techniques are no longer the gold standard for microbial investigation. Advanced techniques that identify bacterial sequences, including the 16S ribosomal RNA gene, have provided new insights into the depth and breadth of microbiota present both in the diseased and normal lung. In asthma, the composition of the microbiome of the lung and gut during early childhood development may play a key role in the development of asthma, while specific airway microbiota are associated with chronic asthma in adults. Early bacterial stimulation appears to reduce asthma susceptibility by helping the immune system develop lifelong tolerance to innocuous antigens. By contrast, perturbations in the microbiome from antibiotic use may increase the risk for asthma development. In chronic obstructive pulmonary disease, bacterial colonisation has been associated with a chronic bronchitic phenotype, increased risk of exacerbations, and accelerated loss of lung function. In cystic fibrosis, studies utilising culture-independent methods have identified associations between decreased bacterial community diversity and reduced lung function; colonisation with Pseudomonas aeruginosa has been associated with the presence of certain CFTR mutations. Genomic analysis of the lung microbiome is a young field, but has the potential to define the relationship between lung microbiome composition and disease course. Whether we can manipulate bacterial communities to improve clinical outcomes remains to be seen

Analysis of the Lung Microbiome in the “Healthy” Smoker and in COPD

Although culture-independent techniques have shown that the lungs are not sterile, little is known about the lung microbiome in chronic obstructive pulmonary disease (COPD). We used pyrosequencing of 16S amplicons to analyze the lung microbiome in two ways: first, using bronchoalveolar lavage (BAL) to sample the distal bronchi and air-spaces; and second, by examining multiple discrete tissue sites in the lungs of six subjects removed at the time of transplantation. We performed BAL on three never-smokers (NS) with normal spirometry, seven smokers with normal spirometry (“heathy smokers”, HS), and four subjects with COPD (CS). Bacterial 16 s sequences were found in all subjects, without significant quantitative differences between groups. Both taxonomy-based and taxonomy-independent approaches disclosed heterogeneity in the bacterial communities between HS subjects that was similar to that seen in healthy NS and two mild COPD patients. The moderate and severe COPD patients had very limited community diversity, which was also noted in 28% of the healthy subjects. Both approaches revealed extensive membership overlap between the bacterial communities of the three study groups. No genera were common within a group but unique across groups. Our data suggests the existence of a core pulmonary bacterial microbiome that includes Pseudomonas, Streptococcus, Prevotella, Fusobacterium, Haemophilus, Veillonella, and Porphyromonas. Most strikingly, there were significant micro-anatomic differences in bacterial communities within the same lung of subjects with advanced COPD. These studies are further demonstration of the pulmonary microbiome and highlight global and micro-anatomic changes in these bacterial communities in severe COPD patients

Comparative genomics of Pseudomonas fluorescens subclade III strains from human lungs

Abstract Background While the taxonomy and genomics of environmental strains from the P. fluorescens species-complex has been reported, little is known about P. fluorescens strains from clinical samples. In this report, we provide the first genomic analysis of P. fluorescens strains in which human vs. environmental isolates are compared. Results Seven P. fluorescens strains were isolated from respiratory samples from cystic fibrosis (CF) patients. The clinical strains could grow at a higher temperature (>34 °C) than has been reported for environmental strains. Draft genomes were generated for all of the clinical strains, and multi-locus sequence analysis placed them within subclade III of the P. fluorescens species-complex. All strains encoded type- II, −III, −IV, and -VI secretion systems, as well as the widespread colonization island (WCI). This is the first description of a WCI in P. fluorescens strains. All strains also encoded a complete I2/PfiT locus and showed evidence of horizontal gene transfer. The clinical strains were found to differ from the environmental strains in the number of genes involved in metal resistance, which may be a possible adaptation to chronic antibiotic exposure in the CF lung. Conclusions This is the largest comparative genomics analysis of P. fluorescens subclade III strains to date and includes the first clinical isolates. At a global level, the clinical P. fluorescens subclade III strains were largely indistinguishable from environmental P. fluorescens subclade III strains, supporting the idea that identifying strains as ‘environmental’ vs ‘clinical’ is not a phenotypic trait. Rather, strains within P. fluorescens subclade III will colonize and persist in any niche that provides the requirements necessary for growth.http://deepblue.lib.umich.edu/bitstream/2027.42/116129/1/12864_2015_Article_2261.pd

Characterization of prostaglandin formation pathways and long -chain fatty acid utilization in the pathogenic fungus <italic>Cryptococcus neoformans</italic>.

The pathogenic fungus Cyptococcus neoformans has been shown to produce bioactive fatty acids called prostaglandins which are immunomodulatory in vitro. However, how prostaglandins are made in this system is unknown because none of the enzymes thought to be required for prostaglandin synthesis appear to exist in C. neoformans. Little is known about the effect of long-chain fatty acids, precursors for prostaglandins, on C. neoformans. The objective of this project was two-fold: (1) to characterize the enzyme(s) critical for the first step in prostaglandin synthesis in C. neoformans and (2) to characterize the effect of long-chain fatty acids on the growth and development of C. neoformans. Prostaglandins were generated in cryptococcal lysates, extracted into ethyl acetate, purified using reverse-phase HPLC and measured using a prostaglandin screening assay. Cryptococcal prostaglandins were chemically and antigenic similar to commercially available prostaglandins based on solvent solubility, HPLC elution times, and EIA reactivity. However, cyclooxygenase inhibitors had no effect on prostaglandin production. Genomic analysis also could not find an enzyme homologous to either a cyclooxygenase or lipoxygenase. The polyphenolic inhibitors reveratrol, nordihydroguaiaretic acid (NDGA) and caffeic acid proved effective at inhibiting cryptococcal prostaglandin synthesis. This led to an investigation of the diphenol oxidase (laccase) CNLAC1. Removal of CNLAC1 by antibody depletion or deletion of the gene resulted in a loss of prostaglandin synthetic activity. These results demonstrate that CNLAC1 is critical for prostaglandin production in C. neoformans. To address the role of fatty acids, C. neoformans were grown in culture with the long-chain polyunsaturated fatty acids (PUFA) arachidonic, linolenic, linoleic or oleic acid at 37&deg;C or 25&deg;C with or without resveratrol. The presence of linoleic acid shut down growth at 25&deg;C. The addition of resveratrol resulted in a growth of chains which, over time, developed into hyphal C. neoformans. The addition of nutrients to long-term hyphal masses resulted in a shift from a hyphal form to a mycelial (mold-like) form and production of new C. neoformans yeast cells. These findings demonstrate that the PUFA environment in which C. neoformans is grown can drive morphologic changes in the fungus, including yeast-to-hyphal transformation.Ph.D.BiochemistryBiological SciencesMicrobiologyPure SciencesUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/125353/2/3192630.pd

Production of Eicosanoids and Other Oxylipins by Pathogenic Eukaryotic Microbes

Oxylipins are oxygenated metabolites of fatty acids. Eicosanoids are a subset of oxylipins and include the prostaglandins and leukotrienes, which are potent regulators of host immune responses. Host cells are one source of eicosanoids and oxylipins during infection; however, another potential source of eicosanoids is the pathogen itself. A broad range of pathogenic fungi, protozoa, and helminths produce eicosanoids and other oxylipins by novel synthesis pathways. Why do these organisms produce oxylipins? Accumulating data suggest that phase change and differentiation in these organisms are controlled by oxylipins, including prostaglandins and lipoxygenase products. The precise role of pathogen-derived eicosanoids in pathogenesis remains to be determined, but the potential link between pathogen eicosanoids and the development of TH2 responses in the host is intriguing. Mammalian prostaglandins and leukotrienes have been studied extensively, and these molecules can modulate Th1 versus Th2 immune responses, chemokine production, phagocytosis, lymphocyte proliferation, and leukocyte chemotaxis. Thus, eicosanoids and oxylipins (host or microbe) may be mediators of a direct host-pathogen “cross-talk” that promotes chronic infection and hypersensitivity disease, common features of infection by eukaryotic pathogens

Boletín de Segovia: Número 124 - 1840 octubre 15

Copia digital. Madrid : Ministerio de Cultura. Subdirección General de Coordinación Bibliotecaria, 200

Additional file 4: Table S4. of Comparative genomics of Pseudomonas fluorescens subclade III strains from human lungs

Secondary metabolite genes and reference organism for BLAST. Each gene involved in the production of the secondary metabolites analyzed in Table 3 is listed in the left column. The source organism of each gene’s nucleotide sequence used for the blast search is in the middle column. The NCBI ID for each source organism is the right column. (PDF 54 kb