Table 6 Respiratory microbiome composition at the phylum level of patients with severe SARS-CoV-2 pneumonia.

Patient	COVID-1		COVID-2		COVID-3		COVID-4		COVID-5		COVID-6		COVID-7		COVID-8		Mean
Phylum	Reads^a	%^b	Reads^a	%^b	Reads^a	%^b	Reads^a	%^b	Reads^a	%^b	Reads^a	%^b	Reads^a	%^b	Reads^a	%^b	%^c
Acidobacteria											322	0.4					0.1
Actinobacteria	14,197	27.6	7619	10.1	12,184	12.5	34,402	28.4	23,529	28.4	18,280	22.8	30,552	31.8	43,955	35.2	24.6
Bacteroidetes	2180	4.2	2340	3.1	16,149	16.6	10,330	8.5	3381	4.1	5029	6.3	3359	3.5	5463	4.4	6.3
Chloroflexi	244	0.5			926	1.0											0.2
Cyanobacteria	279	0.5	1624	2.2	10,191	10.5			212	0.3	6726	8.4	86	0.1	714	0.6	2.8
Deinococcus-Thermus									180	0.2					3584	2.9	0.4
Firmicutes	16,871	32.8	39,784	52.9	30,634	31.5	10,734	8.9	14,763	17.8	10,741	13.4	16,398	17.1	9472	7.6	22.8
Fusobacteria	1689	3.3			10	0.0	1341	1.1	12	0.0			327	0.3			0.6
Gemmatimonadetes			59	0.1	13	0.0											0.0
Lentisphaerae					115	0.1											0.0
Nitrospinae													103	0.1			0.0
Planctomycetes					66	0.1					321	0.4					0.1
Proteobacteria	15,951	31.0	23,342	31.1	26,662	27.5	63,665	52.6	37,939	45.8	38,606	48.2	45,181	47.1	61,581	49.4	41.6
Tenericutes							483	0.4									0.0
Thermotogae			407	0.5	167	0.2			2879	3.5	35	0.0					0.5
Total	51,411	100	75,175	100	97,117	100	120,955	100	82,895	100	80,060	100	96,006	100	124,769	100	100

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