Table 1.

Number of sequences assigned and unassigned in the MEGAN analysis.

Daphnia species/dataset	Assigned to cellular organisms	Assigned to Bacteria without Firmicutes1	Not assigned2	Sequences without hits
D. pulex	38,249	25,868	97,852	120,355
D. pulicaria	99,178	25,604	966,027	23,469
D. magna GS 20	3,028	2,560	16,007	26
D. magna GS FLX	4,781	4,285	21,535	12

¹ The Firmicutes were excluded, because the D. magna datasets contained a bacterial parasite belonging into this taxon. For each dataset, the sum of columns 2, 4, and 5 is less than the total number of sequences analyzed (Table 2) due to the few sequences assigned to other NCBI taxonomy categories such as "Other" and "Unclassified".

² The unassigned sequences are sequences without hits above the defined thresholds (See Materials and Methods). They may be A) sequences that do not have homologs in the current NCBI-nt database, B) sequences that evolved so strongly that their homologs are disguised by bit scores below our threshold or C) sequences that are assigned to species to which no other sequences is assigned (min-support threshold = 2).