Table 1.

List of non-human taxa identified in the Syltholm pitch, including the 40 most abundant oral bacterial taxa, viruses, and eukaryotes. Bacteria in the red complex are denoted with an asterisk. Depth (DoC) and breadth of coverage (>1x) were calculated using BEDTools⁷². Deamination rates at the 5’ ends of DNA fragments were estimated using mapDamage 2.0.9⁵⁹. -Δ% refers to the negative difference proportion introduced by Hübler et al⁷⁹. (see Supplementary Note 5).

Species	Reads	Fragment length (bp)	DoC	SD DoC	>1x (%)	C-T 5′(%)	−Δ%
Bacteria
Neisseria subflava	308,732	56	7.5	6.2	83.7	14.5	0.9
Rothia mucilaginosa	296,610	52	6.9	5.6	82.3	14.0	0.9
Streptococcus pneumoniae	176,782	57	4.7	6.3	65.7	13.8	0.9
Neisseria cinerea	153,683	58	4.9	5.1	71.7	15.1	1.0
Lautropia mirabilis	117,040	53	2.0	1.9	71.9	13.0	1.0
Neisseria meningitidis	100,540	51	2.3	4.3	42.4	14.9	0.9
Aggregatibacter segnis	95,670	58	2.8	2.8	73.3	14.5	0.9
Neisseria elongata	68,407	54	1.6	1.9	67.6	15.1	0.9
Prevotella intermedia	65,324	56	1.2	1.4	55.0	16.2	0.9
Streptococcus sp. ChDC B345	52,614	61	1.6	2.7	50.3	13.8	0.9
Streptococcus sp. 431	43,787	59	1.2	1.9	47.5	13.6	0.8
Aggregatibacter aphrophilus	43,231	56	1.1	1.6	50.4	15.0	0.8
Streptococcus pseudopneumoniae	38,832	61	1.1	2.4	34.9	14.4	0.9
Capnocytophaga leadbetteri	36,461	59	0.9	1.1	49.8	14.0	0.8
Corynebacterium matruchotii	36,070	52	0.7	0.9	44.0	13.0	1.0
Gemella morbillorum	32,284	63	1.2	1.5	56.4	16.3	1.0
Streptococcus viridans	27,840	60	0.8	1.5	36.5	14.5	1.0
Neisseria gonorrhoeae	27,704	53	0.7	2.0	21.3	15.0	1.0
Neisseria sicca	27,290	57	0.6	1.4	22.5	13.7	0.9
Fusobacterium nucleatum	26,783	64	0.8	1.1	47.8	14.1	0.9
Prevotella fusca	26,295	57	0.5	0.7	34.6	15.7	1.0
Kingella kingae	25,811	55	0.7	1.0	44.2	14.4	1.0
Ottowia sp. 894	25,425	52	0.5	0.7	34.6	14.4	1.0
Streptococcus sp. NPS 308	24,937	59	0.8	1.4	37.5	14.3	0.8
Actinomyces oris	24,029	52	0.4	0.7	29.8	12.7	1.0
Streptococcus australis	23,777	60	0.7	1.3	31.5	13.8	1.0
P. propionicum	22,864	50	0.3	0.6	26.8	13.2	0.9
Haemophilus sp. 036	19,707	62	0.7	1.5	28.4	14.5	1.0
Porphyromonas gingivalis*	17,651	55	0.4	0.7	32.2	17.2	1.0
Capnocytophaga gingivalis	16,734	58	0.3	0.6	27.1	15.0	1.0
Neisseria polysaccharea	14,442	57	0.4	1.4	15.0	15.8	1.0
Tannerella forsythia*	14,187	55	0.2	0.5	19.8	15.3	1.0
Streptococcus sp. A12	13,232	59	0.4	0.9	24.9	14.6	0.9
Capnocytophaga sputigena	12,587	58	0.2	0.5	19.9	14.7	0.9
Neisseria lactamica	11,971	56	0.3	1.0	14.2	14.2	0.8
Treponema denticola*	11,379	59	0.2	0.5	19.5	14.0	0.8
Rothia dentocariosa	10,944	54	0.2	0.5	20.0	13.6	1.0
Tannerella sp. HOT-286	10,397	53	0.2	0.5	15.7	14.0	1.0
Actinomyces meyeri	10,105	51	0.3	0.5	21.3	14.0	1.0
Filifactor alocis	9,948	61	0.3	0.6	25.6	15.0	1.0
Viruses
Epstein-Barr virus	593	51	0.2	0.4	13.3	17.8	1.0
Eukaryotes
Anas platyrhynchos	55,986	51	<0.1	0.05	0.2	15.6	1.0
Corylus avellana	8,615	55	<0.1	0.04	0.1	19.7	1.0
Betula pendula	3,291	54	<0.1	0.02	<0.1	16.1	1.0