Amplicon sequencing allows differential quantification of closely related parasite species: an example from rodent Coccidia (Eimeria)

Table 1 The relationship of individual ASV abundance with qPCR-derived Eimeria genome copies/ng while controlling for days post-infection as a random effect

		Estimate	SE	t-value	P-value	F-value	df	P-value
(a)
Standard PCR	Intercept	4.119	0.470	8.756	< 0.001*
	ASV1	8.894	0.840	10.592	< 0.001*	34.665	1	< 0.001*
	ASV2	28.29	4.426	6.391	< 0.001*	4.567	1	< 0.001*
	ASV3	−12.064	26.970	−0.447	0.655	0.200	1	0.655
	ASV4	20.027	59.011	0.339	0.735	0.115	1	0.735
(b)
Microfluidic PCR	Intercept	4.961	0.476	10.412	< 0.001*	–	–	–
	ASV1	6.389	0.785	8.134	< 0.001*	66.169	1	< 0.001*
	ASV2	27.096	5.555	4.878	< 0.001*	23.797	1	< 0.001*

(a) ASVs sequenced from standard amplification, n (samples) = 152, groups (dpi) = 10. (b) ASVs sequenced from microfluidic amplification, n (samples) = 128, groups (dpi) = 10. ASV abundance is the relative abundance after total sum scaling for each amplicon
SE, standard error; *Statistically significant

ISSN: 1756-3305