Table 4. Predominant species identified in the two analyzed honeys considering the ≥75% sequence identity level based on reads accounting >5% overall reads of the identified organism groups.

Honey	Dataset	Taxid		Scientific name	N. of reads	% of reads†	‰ of readsTOT‡
Orange tree blossom honey	Arthropods	7460		Apis mellifera	41	39.05	0.15
		7176		Culex quinquefasciatus	8	7.62	0.03
		28612		Rhagoletis zephyria	8	7.62	0.03
		7029		Acyrthosiphon pisum	7	6.67	0.03
	Plants	2711		Citrus sinensis	72	11.92	0.27
		29760		Vitis vinifera	51	8.44	0.19
		85681		Citrus clementina	41	6.79	0.15
		3880		Medicago truncatula	37	6.13	0.14
	Fungi	1108849		Penicillium rubens	27	14.52	0.10
		4956		Zygosaccharomyces rouxii	19	10.22	0.07
		500148		Metarhizium brunneum	15	8.06	0.06
	Bacteria	1906742		Microbacterium sp. BH-3-3-3	3,479	17.36	12.86
		2033		Microbacterium testaceum	3,075	15.34	11.37
		148814		Lactobacillus kunkeei	1,989	9.92	7.35
	Viruses	1100043		Apis mellifera filamentous virus	248,133	100.00	917.52
Eucalyptus tree blossom honey	Arthropods	7460		Apis mellifera	1,820	66.50	6.87
		7461		Apis cerana	165	6.03	0.62
		597456		Habropoda laboriosa	162	5.92	0.61
	Plants	71139		Eucalyptus grandis	185	28.20	0.70
		223129		Orobanche rapum-genistae	112	17.07	0.42
		4686		Asparagus officinalis	55	8.38	0.21
	Fungi	4956		Zygosaccharomyces rouxii	456	16.26	1.72
		1365886		Zygosaccharomyces parabailii	282	10.05	1.06
		4896		Schizosaccharomyces pombe	225	8.02	0.85
	Bacteria	148814		Lactobacillus kunkeei	37,752	44.11	142.51
		542		Zymomonas mobilis	11,721	13.70	44.25
	Viruses	1100043		Apis mellifera filamentous virus	172,213	99.97	650.10

^† Data considers as background the specific number of reads representing the five subsets and the honeys, as reported in Table A in S1 File (columns “sequence identity <75%”).

^‡ Data considers as background the total number of annotated reads of that honey, as reported in Table A in S1 File (columns “sequence identity <75%”).