Table 1 In silico taxonomic coverage for published 18S V4 primer sets

		Off-target groups		Eukaryotic endosymbiont groups		Specific examples
	n =	20,197	381,535	4229	15,265	198	23
Primer ID	Primer sets	Archaea	Bacteria	Helminths	Protozoa	Plasmodium	Giardia
Bates¹⁰⁶	515 f/1119r	0	0	80.4	95.9	94.8	0
Bower^a ¹⁰⁷	18SEUK581F/18SEUK1134R	46.2^a	8.2^a	0.4	82.4	0	72.7
Bradley³⁷	TAReuk454FWD1/V4r	0	0	48.9	67.1	97.9	0
C-S¹⁰⁸/Brate 2¹⁰⁹	3NDf/V4_euk_R2	0	0	50.8	22.8	0	0
C-S¹⁰⁸/Brate 1¹⁰⁹	3NDf/V4_euk_R1	0	0	5.8	21.1	0	0
C-S¹⁰⁸/Geisen¹¹⁰	3NDf/1132mod	0.3	0	80.7	94.2	0	0
Comeau¹¹¹	E572F/E1009R	0	0	65.3	44.5	0	0
DeMone^b¹¹²	18SV4_F/_R/Giardia_R	0	0	86.4	62.3	0	100
Hadziavdic 566⁷³	F-566/R-1200	0	0	76.4	81	99.6	0
Hadziavdic 574⁷³	F-574/R-952	0	0	48.3	62.9	61.3	0
Hugerth 574^a¹¹³	574/1132	12.5^a	0	80	94.2	0	0
Hugerth 616¹¹³	616/1132	3.3	0.2	93.1	75.8	0	45.5
Hugerth 563^a¹¹³	563/1132	47.9^a	72^a	96.1	96.4	0	100
Krogsgaard^b³²	G3F1/R1/G4F3/R3/G6F1/R1	0	0	78.5	67	94.8	0
Machida¹¹⁴	18S#1/18S#2RC	0	0	78.1	45.2	97.9	0
Sikder^a¹¹⁵	MMSF/MMSR	17.5^a	0	79.3	42.7	0	0
Stoeck¹¹⁶	TAReuk454F1/R3	0	0	49.1	78.4	97.9	0
Wood¹¹⁷	Nem18SlongF/Nem18SlongR	0	0	32.2	25.2	2.6	0
Zhan¹¹⁸	Uni18S/R	0	0	72.8	64	0	0

Bold font denotes target organisms. See Supplementary Table 1 for full primer names and sequences.
Numbers shown are % coverage allowing for 1 mismatch with a 2-base pair 3′ window using the SILVA 138.1 SSU rRNA NR Ref database.
n, number of total eligible accessions.
^aRemoved from further analysis due to high prokaryotic complementarity.
^bMultiple primer sets were combined for analysis.

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