lcuthber/CelticFire: SYSTEMIC CULTURE AND SEQUENCE OF AIRWAY COMMENSAL BACTERIA, RELATED TO AIRWAY MUCOSAL GENOMICS
Creators
- 1. Imperial College London
- 2. Max-Delbrück-Center for molecular biology
Description
This GitHub contains all analytical code for the paper, "Systemic culture and sequence of airway commensal bacteria, related to airway mucosal genomics" Contributors include: @jonathanishhorowicz @sofia-forslund @TillBirkner @Theda-sys @michaelolanipekun
ABSTRACT Microbial communities at the airway mucosal barrier are conserved and highly ordered, reflecting co-evolution with human host factors. Freed of selection to digest nutrients, the airway microbiome underpins cognate management of mucosal immunity and pathogen resistance. We show here the initial results of systematic culture and whole-genome sequencing of the thoracic airway bacteria, identifying 52 novel species amongst 126 organisms that constitute 75% of commensals typically present in heathy individuals. Clinically relevant genes encode antimicrobial synthesis, adhesion and biofilm formation, immune modulation, iron utilisation, nitrous oxide (NO) metabolism and sphingolipid signalling. Using whole-genome content we identify dysbiotic features that may influence asthma and chronic obstructive pulmonary disease. We match isolate gene content to transcripts and metabolites expressed late in airway epithelial differentiation, identifying pathways to sustain host interactions with microbiota. Our results provide a systematic basis for decrypting interactions between commensals, pathogens, and mucosa in lung diseases of global significance.
Files
lcuthber/CelticFire-CelticFire.V1.zip
Files
(52.6 MB)
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Additional details
Related works
- Is supplement to
- Software: https://github.com/lcuthber/CelticFire/tree/CelticFire.V1 (URL)