Table 1. Reduction and clustering of reads during the quality filtering. Initial number of reads = 924,102, of which 81% were further excluded. The unique BLAST hits give a rough estimation of the diversity.

	Trimmed	De-replication (cd-hit)	Validated by BLAST (Silva)	Second BLAST (our database)	Unique BLAST hits	Aligned, short sequences removed	Chimera removal (uchime) & by eye	Pre-cluster (mothur)	OTUs 96% sim.	Unique BLAST hits	# of sequences
A Acanthamoeba
AEG	29,144	619	555		50	396	377	309	87	28	28,224
HEG	59,094	847	778		52	535	496	398	102	26	56,176
SEG	46,318	855	732		54	239	216	191	84	27	40,916
TOTAL	134,556	2,321	2,065		55	1,170	1,089	898	273	36	125,316
Clustered or removed		98%	11%			43%	7%	18%	70%
B Myxomycetes
AEG	7,392	1,074	971	899	46	892	500	349	100	24	4,763
HEG	13,460	1,221	1,146	1,095	51	1,039	587	387	111	31	9,606
SEG	21,874	1,106	989	897	51	795	353	290	127	31	14,960
TOTAL	42,726	3,401	3,106	2,891	60	2,726	1,440	1,026	338	35	29,329
Clustered or removed		92%	9%	7%		6%	47%	29%	67%