Table 1.

All mutations present in E. faecium TX1330 at the final timepoint.

Replicate	Gene/predicted function	Type	AA change	Frequency (%)
1	RpoC	Non-synonymous snp	H419R	38.2
1	RpoC	Non-synonymous snp	S926T	21.1
1	RpoC	Non-synonymous snp	L800V	14.8
1	Hypothetical protein in capsule synthesis locus	Non-synonymous snp	M29I	30
1	yqwD2	Non-synonymous snp	P58L	37.6
1	yqwD2	Non-synonymous snp	P58H	19.2
2	Malonate decarboxylase beta subunit/malonate decarboxylase gamma subunit CDS	Non-synonymous snp	G148V	45.5
2	Predicted hydrolase of the HAD superfamily CDS	Nonsense	S191stop	33.3
2	murA – UDP-N-acetylglucosamine 1-carboxyvinyltransferase	Non-synonymous snp	G20C	40
2	yqwD2	Non-synonymous snp	P58H	100
3	RpoC	Non-synonymous snp	H419R	79.2
3	yqwD2	Non-synonymous snp	K89N	72.2
3	hydrolase, haloacid dehalogenase-like family CDS	Nonsense	E68stop	50
4	yqwD2	Non-synonymous snp	P58H	92.5

All bacterial mutations are from timepoint 16 of coevolution replicates. No mutations were seen in the host controls. Locus tags for each gene can be found in Supplementary Table S1.