Table 2 Bacterial noon/night ratios of transcripts cell⁻¹ for genes indicative of metabolite consumption.

From: Diel investments in metabolite production and consumption in a model microbial system

	Compound	Gene locus tag	Gene name	Protein function	Noon/Night transcript ratio	Reference
Amide	Urea	SPO1707	urtD	ABC transporter, ATP-binding protein	43.0	[25]
		SPO1708	urtC	ABC transporter, permease	37.7
		SPO1709	urtB	ABC transporter, permease	34.6
		SPO1710	urtA	ABC transporter, substrate binding	0.8 (n.s.)
Amine	TMAO	SPO1548	tmoX	ABC transporter, periplasmic binding	38.0	[53]
		SPO1550	tmoV	ABC transporter, permease protein	41.2
		SPO1549	tmoW	ABC transporter, ATP binding	43.1
Amine	TMA	SPO1551	tmm	TMA monooxygenase	42.6	[25]
Amino acid derivative	Betaine	SPO3186	opuD	Glycine-betaine transporter	1.6 (n.s.)	[25]
Amino Acid	Leucine	SPO2793	ivD	isovaleryl-CoA dehydrogenase	2.6
		SPO2789	mccA	methylcrotonyl-CoA carboxylase, alpha subunit	3.1
		SPO2790	mccB	methylcrotonyl-CoA carboxylase, beta subunit	3.4
		SPO0390		glutamate/leucine/phenylalanine/valine dehydrogenase	1.2 (n.s.)
Amino acid derivative	Ectoine/ 5-hydroxyectoine	SPO1146	uehB	TRAP transporter, small integral membrane protein	48.4	[31]
		SPO1147	uehA	TRAP transporter, large integral membrane protein	29.7
		SPO1145	uehC	TRAP transporter, periplasmic binding	36.7
Amino Acid	Proline	SPO1031		hypothetical protein	21.2
		SPO2441		ABC transporter, periplasmic betaine/proline-binding	16.4
		SPOA0231		ABC transporter, periplasmic substrate-binding	43.3
Choline	Choline	SPO1087	betT	Choline transporter	0.9 (n.s.)	[75]
Glycerol derivative	SN-glycerol-3-phosphate	SPO0238	ugpE	ABC transporter, permease	4.3	[25]
		SPO0239	ugpA	ABC transporter, permease	3.3
		SPO0237	upgC	ABC transporter, ATP-binding	3.5
		SPO0240	ugpB	ABC transporter, periplasmic substrate-binding protein	1.3 (n.s.)
Nuceloside	Xanthine	SPO0654	xdhA	Xanthine dehydrogenase, A subunit	33.4	[76]
		SPO0653	xdhB	Xanthine dehydrogenase, B subunit	33.0
		SPO0652	xdhC	Xanthine dehydrogenase accessory factor	25.8
Nucleoside	Uridine	SPO2470	iunH	inosine-uridine preferring nucleoside hydrolase	9.9
Organic Acid	Acetate	SPO1813	acs	acetyl-coenzyme A synthetase	0.9 (n.s.)
		SPO0325	phbB	acetoacetyl-CoA reductase	1.9
		SPO0326	phbA	acetyl-CoA acetyltransferase	1.1 (n.s.)
Organic acid	Glycolate	SPO3478	glcD	glycolate oxidase, GlcD subunit	18.6	[25]
		SPO3479	glcE	glycolate oxidase, GlcE subunit	19.9
		SPO3480	glcF	glycolate oxidase, iron-sulfur subunit	21.6
Phosphonate	Phosphonate	SPO0780	phnC	ABC transporter, ATP-binding	32.4
		SPO0781	phnD	ABC transporter, periplasmic phosphonate-binding	18.6
		SPO0782	phnE-1	ABC transporter, permease	38.3
		SPO0783	phnE-2	ABC transporter, permease	35.6
Polyamine	Putrescine	SPO3469	potF	ABC transporter, periplasmic putrescine-binding	1.2	[55]
		SPO3466	potI	ABC transporter, permease	2.5
		SPO3467	potH	ABC transporter, permease	2.6
		SPO3468	potG	ABC transporter, ATP-binding	2.1
Polyamine	Spermidine	SPOA0381		ABC transporter, periplasmic substrate-binding protein	22.7	[55]
		SPOA0383		ABC transporter, permease protein	53.4
		SPOA0384		ABC transporter, permease protein	42.7
		SPOA0382		ABC transporter, ATP-binding protein	29.2
Sugar	Ribose	SPOA0253		ABC transporter, periplasmic substrate-binding	30.9	[47]
		SPOA0254	rbsC-1	ABC transporter, permease	54.9
		SPOA0256		ABC transporter, periplasmic substrate-binding protein	21.4
		SPOA0257	rbsC-2	ABC transporter, permease	50.4
		SPOA0258	rbsA	ABC transporter, ATP-binding	55.7
Sugar	Glucose	SPO0861	xylF	ABC transporter, periplasmic substrate-binding	2.7 (n.s.)	[47]
		SPO0862	xylH	ABC transporter, permease	6.2
		SPO0863	xylG	ABC transporter, ATP-binding	4.2
Sulfur compound	Choline-O-sulfate	SPO1083	betC	Choline sulfatase	15.1	[75]
Sulfur compound	Cysteate	SPO2658		ABC transporter, periplasmic substrate-binding	22.4	[41]
		SPO2659		ABC transporter, permease	38.3
		SPO2660		ABC transporter, permease	28.0
		SPO2661		ABC transporter, ATP-binding	32.7
Sulfur compound	Dihydroxypropane-sulfonate (DHPS)	SPO0591	hpsK	TRAP transporter	13.0	[77]
		SPO0592	hpsL	TRAP transporter	32.3
		SPO0593	hpsM	TRAP transporter	24.5
Sulfur compound	Dimethylsulfonio-propionate (DMSP)	SPO1913	dmdA	DMSP demethylase	15.0	[41]
		SPO0453	dddW	DMSP lyase	30.7
		SPO1703	dddD	DMSP lyase	41.3
		SPO2299	dddP	DMSP lyase	31.4
		SPO1596	dddQ	DMSP lyase	19.2
Sulfur compound	Isethionate	SPO2358	iseK	TRAP transporter, periplasmic	30.0	[41]
		SPO2357	iseL	TRAP transporter, small permease	13.2
		SPO2356	iseM	TRAP transporter, DctM	38.2
Sulfur compound	N-acetyltaurine	SPO0660	naaA	ABC transporter, periplasmic substrate-binding	54.3	[41]
		SPO0661	naaB	ABC transporter, permease	32.3
		SPO0662	naaB'	ABC transporter, permease	42.7
		SPO0663	naaC	ABC transporter, ATP-binding	58.2
		SPO0664	naaC'	ABC transporter, ATP-binding	28.2
Sulfur compound	Taurine	SPO0674	tauA	ABC transporter, periplasmic substrate-binding	1.8 (n.s.)	[41]
		SPO0675	tauB	ABC transporter, ATP-binding	3.7
		SPO0676	tauC	ABC transporter, permease	3.1

Bold font indicates the compounds appearing in both the endometabolite and bacterial gene expression datasets.
n.s., not statistically significant (DeSeq2, adjusted p > 0.05).

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Table 2 Bacterial noon/night ratios of transcripts cell⁻¹ for genes indicative of metabolite consumption.

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