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. Author manuscript; available in PMC: 2014 Feb 28.
Published in final edited form as: J Cyst Fibros. 2012 Aug 28;12(2):154–164. doi: 10.1016/j.jcf.2012.07.009

TABLE 1.

Results summary for all viromes, microbiomes, and metatranscriptomes.

Metagenomes Metatranscriptomes
Patient
ID		 Time
Point		 Date of
Collection		 Health
Status		 Microbial Viral Microbial
% Microbial sequences
(Number of
microbial sequences)		 % Viral sequencesa
VLPs Observedb 		% non-rRNA sequences
(Number of
non-rRNA sequences)
CF1 A 09/02/2010 Stable N/Af N/Af 10.7%
d (738)
B 10/18/2010 Stable N/Af N/Af 30.3%d
(41,789)
C 11/12/2010 On
Treatment		 N/Af N/Af 30.6%d
(38,532)
D 02/11/2011 Exacerbation 9%
(14,691)		 31.99%
Yes		 N/Af
F 03/14/2011 Post
Treatment		 79%
(40,825)		 6.07%
No		 31.6%e
(7,971)
CF2 A 11/10/2010 On
Treatment		 N/Af N/Af 87.6%d
(68,976)
CF3 B 11/10/2010 On
Treatment		 N/Af N/Af 89.6%d
(93,375)
CF4 A 01/22/2011 Exacerbation 2%
(3,834)		 0.90%c
No		 86.8% d
(59,394)
B 02/01/2011 Post
Treatment		 0.2%
(405)		 6.77%
No		 99.1 %e
(32,446)
C 03/20/2011 Stable 23%
(41,636)		 1.93%
No		 95.1%e
(34,411)
CF5 A 10/07/2011 Exacerbation 2%
(1,034)		 3.00%
Yes		 N/Af
B 10/21/2011 Post
Treatment		 1%
(247)		 3.78%
Yes		 N/Af
a

Based on tBLASTx against viral genome database (threshold of 40% identity over at least 60% of the query sequence).

b

Observation by epifluorescence microscopy of the viral fraction collected following cesium chloride density gradient centrifugation.

c

Sample collected by filtration through 0.45 μm filter without cesium chloride density gradient ultracentrifugation.

d

Following rRNA depletion by the Ambion kits.

e

Following rRNA depletion by the Ribo-Zero™ (Epidemiology) kit.

f

Sample not available.