Table 3.

Identification of differentially expressed functional traits from the KEGG and COG databases with a fold change >1 in unassembled metatranscriptome libraries of suppressive samples compared to non-suppressive samples.

KEGG (K) and COG/NOGa identifiers	log2 FCb	log2 CPMc	P-value	FDRd	Category 1	Category 2	Gene	Most common bacterial taxa
NOG08625	−1.989	7.629	0.001	0.042	Poorly characterized	Function unknown	Hypothetical protein	Arthrobacter
COG1621	−1.584	8.880	0.002	0.049	Metabolism	Carbohydrate transport and metabolism	Glycosidase	Arthrobacter, Nocardiodes
NOG122331	−1.437	8.478	0.001	0.041	Poorly characterized	Function unknown	Hypothetical protein	Arthrobacter, Nocardiodes
K02077	−1.298	8.306	0.001	0.044	Structural complex/Transporters	Environmental information processing and ABC transporters, prokaryotic type	ABC transporter substrate-binding protein	Arthrobacter
K03343	−1.292	7.637	0.001	0.044	Metabolism	Amino acid metabolism	Putrescine oxidase	Arthrobacter
COG0340	−1.243	7.936	0.000	0.020	Metabolism	Coenzyme transport and metabolism	Biotin-(acetyl-CoA carboxylase) ligase	Arthrobacter
K06191	−1.162	7.482	0.000	0.022	Unclassified		Glutaredoxin	Arthrobacter
NOG06580	−1.007	7.782	0.001	0.042	Poorly characterized	Function unknown	Hypothetical protein	Arthrobacter, Nocardiodes
K02074	−1.004	7.481	0.000	0.042	Structural complex/Transporters	Environmental information processing and ABC transporters, prokaryotic type	ABC transporter ATP-binding protein	Arthrobacter
COG1319	1.004	7.444	0.001	0.048	Metabolism	Energy production and conversion	Molybdopterin dehydrogenase; carbon-monoxide dehydrogenase	Mix of species
COG2719	1.017	7.345	0.001	0.037	Poorly characterized	Function unknown	Stage V sporulation protein SpoVR	Mix of species
COG2718	1.044	7.241	0.000	0.034	Poorly characterized	Function unknown	Sporulation protein YhbH	Sporangium, Oscillochloris
COG3903	1.062	7.162	0.002	0.049	Poorly characterized	General function prediction only	XRE family transcriptional regulator	Mix of species
K06281	1.107	8.007	0.001	0.048	Metabolism	Xenobiotics biodegradation and metabolism	Hydrogenase, [Ni-Fe]-hydrogenase large subunit	Mix of species
COG3383	1.116	7.573	0.001	0.042	Poorly characterized	General function prediction only	Formate dehydrogenase subunit alpha	Mix of species
COG3696	1.208	8.884	0.000	0.007	Metabolism	Inorganic ion transport and metabolism	Acriflavin restistance protein	Mix of species
NOG14710	1.232	9.627	0.000	0.020	Poorly characterized	Function unknown	Zinc binding protein	Mix of species
COG1459	1.306	6.671	0.002	0.049	Cellular processes and signaling	Intracellular trafficking, secretion, and vesicular transport	Type II secretion, protein F	Mix of species
COG2805	1.414	7.388	0.001	0.042	Cellular processes and signaling	Intracellular trafficking, secretion, and vesicular transport	Twitching motility protein PilT	Mix of species
COG4796	1.519	6.585	0.002	0.049	Cellular processes and signaling	Intracellular trafficking, secretion, and vesicular transport	Type IV pilus secretin PilQ	Mix of species
K06282	1.581	8.756	0.000	0.015	Metabolism	Xenobiotics Biodegradation and Metabolism	Hydrogenase small subunit	Mix of species
COG3059	1.740	7.005	0.000	0.034	Poorly characterized	Function unknown	Inner membrane protein	Mix of species
K11903	1.788	9.943	0.001	0.044	Environmental Information Processing	Membrane Transport	Type VI secretion system secreted protein Hcp	Pseudomonas
K12549	2.050	6.628	0.000	0.026	Unclassified		Surface adhesion protein lapA	Pseudomonas
NOG243551	2.847	8.564	0.002	0.049	Poorly characterized	General function prediction only	General stress protein csbD	Flavobacterium

^aNon-supervised Orthologous Group (NOG).

^bFold change. A negative FC means the functional trait is more abundant in the non-suppressive sample.

^cCount per million.

^dFalse discovery rate.