The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities

Microbiome

Table 2 Random forest classification models of season

Season
Out-of-bag estimate of error rate: 8.94%
Confusion matrix	Autumn	Spring	Summer	Winter	Class error (%)
Autumn	53	1	5	1	11.7
Spring	0	54	1	1	3.6
Summer	9	0	63	0	12.5
Winter	2	2	0	54	6.9
Most important genera in sample classification
Family:genera	Autumn	Spring	Summer	Winter	MDA
Moraxellaceae:Psychrobacter	0.026	0.039	0.040	0.069	0.043
Microbacteriaceae:Cryobacterium	0.022	0.057	0.011	0.004	0.022
Flavobacteriaceae:Flavobacterium	0.009	0.012	0.021	0.040	0.020
Nocardioidaceae:Nocardioides	0.020	0.024	0.011	0.013	0.016
Flavobacteriaceae:Gillisia	0.024	0.003	0.002	0.014	0.010
Chitinophagaceae:Ferruginibacter	0.009	0.012	0.007	0.009	0.009
Gaiellaceae:Gaiella	0.000	0.011	0.002	0.018	0.008
Ilumatobacteraceae:CL500-29_marine_group	0.001	0.015	0.003	0.012	0.007
Burkholderiaceae:Polaromonas	0.008	0.015	0.001	0.002	0.006
Rubritaleaceae:Luteolibacter	0.000	0.018	0.003	0.004	0.006
Sphingomonadaceae:Qipengyuania	0.001	0.001	0.009	0.010	0.005
Clostridiaceae_1:Clostridium_sensu_stricto_13	0.000	0.016	0.001	0.006	0.005
Xanthomonadaceae:Thermomonas	0.001	0.006	0.003	0.012	0.005
Chthoniobacteraceae:Candidatus_Udaeobacter	0.001	0.009	0.002	0.009	0.005
Staphylococcaceae:Staphylococcus	0.012	0.007	0.002	0.000	0.005
Microbacteriaceae:Galbitalea	0.003	0.017	0.000	0.001	0.005
Pseudoalteromonadaceae:Pseudoalteromonas	0.003	0.000	0.010	0.004	0.005
Phormidiaceae:Tychonema_CCAP_1459:11B	0.001	0.000	0.006	0.011	0.004
Ilumatobacteraceae:Ilumatobacter	0.001	0.006	0.002	0.009	0.004
Demequinaceae:Demequina	0.000	0.010	0.002	0.004	0.004

Confusion matrices show the classification of samples and the associated class error. The mean decrease in model accuracy (MDA; from removing the genus in question) and mean Z-scores are given for the 20 most important genera for classifying samples

ISSN: 2049-2618