Microbial ecology of the cystic fibrosis lung*
Haemophilus influenzae
Staphylococcus aureus
Pseudomonas aeruginosa
Burkholderia cepacia complex (BCC)
Venn diagram showing reported coinfections of the CF airways. (NB: coinfection does not necessarily imply direct interaction between species.)A, Aspergillus spp.; AV, adenovirus;AX, A. xylosoxidans; BP, bacteriophage; C, Candida spp.; Ent, enterobacteria; IPV, influenza and/or parainfluenza virus; K, Klebsiella spp.;
M, mycoplasma; MA, Mycobacterium abscessus; N, Neisseria spp.; OF, oropharyngeal flora; RSV,respiratory syncytial virus; SM, S. maltophilia.
From Wikipedia: Metagenomics
"Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. Traditional microbiology and microbial genome sequencing rely upon cultivated clonal cultures. This relatively new field of genetic research enables studies of organisms that are not easily cultured in a laboratory as well as studies of organisms in their natural environment.[1]
Early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods.[2] Recent studies use "shotgun" Sanger sequencing or massively parallel pyrosequencing to get (mostly) unbiased samples of all genes from all members of sampled communities.[3]"
From:Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals*
"We obtained sequences from sputum DNA viral communities in 5 individuals with cystic fibrosis (CF) and 5 individuals without the disease. Overall, diversity of viruses in the airways was low, with an average richness of 175 distinct viral genotypes. The majority of viral diversity was uncharacterized.
CF phage communities were highly similar to each other, whereas Non-CF individuals had more distinct phage communities, which may reflect organisms in inhaled air.
CF eukaryotic viral communities were dominated by a few viruses, including human herpesviruses and retroviruses.
From:
Deciphering the role of phage in the cystic fibrosis airway*
"There was a striking difference in metabolic functions encoded by phage in CF versus Non-CF individuals.Regardless of which viral taxa were present,CF-associated phage shared a common core metabolism that reflected the disease state and aberrant airway physiology".
From:
Mathematical Modeling of Cystic Fibrosis Ecology*
"A complete mathematical model of CF would need equations that follow the concentrations of all different kinds of bacterial and phage species in each compartment"
See QUORUM SENSING*
