The lung tissue microbiota of mild and moderate chronic obstructive pulmonary disease

Microbiome

Table 2 Sequencing yield

Subject	Site	Raw sequences	Trimmed^a	Full data set sequences^b
1	Oral	1,221,461	1,200,471	1,179,919
1	Nasal	894,311	875,853	730,412
1	Bronchial	720,011	697,567	8380
1	Lung tissue	1,995,525	1,917,602	5978
2	Oral	1,756,838	1,718,429	1,682,345
2	Nasal	940,535	916,270	26,571
2	Bronchial	2,268,600	2,130,104	2811
2	Lung tissue	1,965,320	1,849,877	4270
3	Oral	2,011,911	1,973,158	1,907,839
3	Nasal	1,181,978	1,155,811	818,142
3	Bronchial	1,649,122	1,599,897	10,906
3	Lung tissue	1,649,943	1,573,465	4104
4	Oral	720,179	709,279	697,399
4	Nasal	825,382	795,668	342,890
4	Bronchial	1,031,715	404,201	1050
4	Lung tissue	1,065,648	113,879	1068
5	Oral	593,186	581,011	574,101
5	Nasal	602,148	591,781	562,469
5	Bronchial	997,054	232,540	582
5	Lung tissue	716,643	83,992	684
6	Oral	483,289	470,953	463,259
6	Nasal	619,329	365,827	253,711
6	Bronchial	945,424	9583	691
6	Lung tissue	828,782	18,768	563
7	Oral	899,992	885,538	868,523
7	Nasal	624,109	571,341	378,236
7	Bronchial	671,694	56,354	859
7	Lung tissue	781,672	39,506	931
8	Oral	658,356	646,638	638,699
8	Nasal	582,451	451,154	439,653
8	Bronchial	1,063,865	297,224	1103
8	Lung tissue	10,670	1307	35 ^c
9	Oral	808,428	798,595	789,718
9	Nasal	1,054,717	304,938	264,946
9	Bronchial	1,286,746	275,686	2161
9	Lung tissue	653,161	87,316	1998
Control	1	19,266	274	115
Control	2	79,459	1956	820
Control	3	22,596	232	103
Control	4	24,344	188	75
Control	5	21,875	348	134
Control	6	23,358	254	111
			Total count^d	12,667,009
			Median^d	18,739
			Mean^d	351,861

^aNumber of sequences that passed trimming steps
^bNumber of sequences that passed trimming, OTU clustering, singleton removal, and removal of taxa not assigned to the 16S rRNA gene. Corresponds to the “Full data set” as noted in Fig. 1
^cSample 8-lung tissue was omitted from the analysis due to poor sequencing yield
^dFor samples only, not including control samples

ISSN: 2049-2618