Table 7.

Respiratory microbiome composition at the phylum level of patients with severe pneumococcal pneumonia.

Patient	SPN-1		SPN-2		SPN-3		SPN-4		SPN-5		SPN-6		SPN-7		SPN-8		SPN-9		SPN-10		SPN-11		SPN-12		Mean
Concomitant viral pathogen	None		RSV		None		Influenza AH1		hMPV		None		None		None		Influenza AH1		Influenza AH1		Influenza AH1		None
Phylum	Readsa	%b	Reads	%	Reads	%	Reads	%	Reads	%	Reads	%	Count	%	Count	%	Count	%	Count	%	Count	%	Count	%	%
Actinobacteria	516	0.8	2859	4.0	4621	14.4	223	0.2	857	0.5	1335	3.0	9737	12.6	681	0.2	11	0.0	14	0.1			347	0.5	3.0
Bacteroidetes			19,260	26.9	3429	10.7			877	0.5	490	1.1	12,830	16.6			1834	1.3	1197	9.8			27	0.0	5.6
Chloroflexi													251	0.3											0.0
Crenarchaeota					321	1.0																			0.1
Cyanobacteria					3196	10.0	109	0.1			98	0.2	794	1.0											0.9
Deinococcus-Thermus					10	0.0					314	0.7													0.1
Firmicutes	67,114	99.2	43,870	61.3	9175	28.6	10,061	9.1	181,097	97.2	37,247	83.9	18,844	24.3	34,156	10.9	133,249	97.1	10,888	89.3	1447	3.2	22,453	33.4	53.1
Fusobacteria			3011	4.2	40	0.1			20	0.0			858	1.1	28	0.0	229	0.2							0.5
Gemmatimonadetes													65	0.1											0.0
Proteobacteria	43	0.1	2618	3.7	11,309	35.2	100,208	90.6	3414	1.8	4925	11.1	32,574	42.0	278,693	88.9	1891	1.4	96	0.8	43,143	96.8	44,491	66.1	36.5
Spirochaetes													1,114	1.4											0.1
Synergistetes													237	0.3											0.0
Tenericutes													159	0.2											0.0
Verrucomicrobia													35	0.0											0.0
Total	67,673	100	71,618	100	32,101	100	110,601	100	186,265	100	44,409	100	77,498	100	313,558	100	137,214	100	12,195	100	44,590	100	67,318	100	100

^aReads count.

^bPercentage of reads.

^cMean of reads.