Table 3.

Changes in the microbiome during exacerbation detected by traditional cultures and 16S pyrosequencing. Only the increases above 20 % are detailed in the pyrosequencing data

Patients	Standard culture positive	16S pyrosequencing abundance increase >20 %	16S pyrosequencing additional relevant information
Colonised patients
1	P. aeruginosa	↑ Moraxella	PPM not identified by culture
2	H. influenzae	↑Haemophilus	No additional information
3	P. aeruginosa	Only changed <20 %	Colonising P. aeruginosa
4	H. influenzae	↑Haemophilus	No additional information
5	Negative	↑Pseudomonas	PPM not identified by culture
Non-PA-colonised patients
1	H. parainfluenzae	↑Haemophilus	No additional information
2	H. influenzae	↑Moraxella	No additional information
	M. catarrhalis
3	H. influenzae	↑Haemophilus	No additional information
4	S. pneumoniae	Only changed <20 %	Colonising S. pneumoniae
5	Negative	↑Moraxella	PPM not identified by culture
6	S. pneumoniae	↑Streptococcus	No additional information
7	S. maltophilia	↑Achromobacter	PPM not identified by culture
	Alcaligenes spp.
8	Negative	↑Streptococcus	PPM not identified by culture