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

Table 3 Generalised linear mixed effect models investigating (a) the infection status of Eimeria spp. (infected vs uninfected) and (b) the effects of Eimeria spp. abundance on the body mass index of house mice from a natural population

	Estimate	SE	t-value	P-value
(a) Eimeria spp. presence effects on body mass index, N = 607, localities = 171
Intercept	0.00252	0.00002	132.173	< 0.001 *
E. ferrisi	−0.00001	0.00003	−0.423	0.672
*E. falciformis*	−0.00012	0.00005	−2.370	0.018 *
E. vermiformis	−0.00012	0.00011	−1.015	0.311
(b) Eimeria spp. infection intensity effects on body mass index, N = 163, localities = 67
Intercept	0.00258	0.00004	62.904	< 0.001 *
*E. ferrisi*	−0.00005	0.00002	−3.132	0.002 *
*E. falciformis*	−0.00011	0.00003	−3.189	0.002 *
E. vermiformis	−0.00025	0.00033	−0.750	0.446

The location where mice were captured is included as a random effect. Abundance is the relative abundance after total sum scaling within each amplicon, and summed across amplicons for each sample
SE, standard error; *Statistically significant

ISSN: 1756-3305