REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological Samples
Apis mellifera	AIST (National institute of advanced sciences), Japan	N/A
Apis mellifera	University of Tokyo, Japan	N/A
Apis cerana	Chiba (local beekeeper), Japan	N/A
Apis cerana	Hodogaya (local beekeeper), Japan	N/A
Apis cerana	NIES (National intitute for environmental studies), Japan	N/A
Chemicals, Peptides, and Recombinant Proteins
Tryptic Soy Agar	BD Difco	236950
Columbia blood agar base	Oxoid	CM0331
Sheep blood defibrinated	Oxoid	SR0051E
MRS agar (DE MAN, ROGOSA, SHARPE)	Oxoid	CM0361
BHI agar (Brain Heart Infusion)	BD Difco	11708872
Glucose	Sigma	G7021
Fructose	Sigma	F2543
L-cysteine	Fluka	30120
Bacto Tryptone	BD Difco	211705
Yeast extract	Oxoid	LP0021
Cellobiose	Sigma	22160
Vitamin K	Sigma	V3501
FeSO4	Sigma	F8633
CaCl2	Sigma	746495
MgSO4	Sigma	63140
NaHCO3	Sigma	S6297
NaCl	Acros	207790010
Hematin	Sigma	H-3281
Histidine	Sigma	53319
Na2HPO4	Applichem	A2530
NaH2PO4	Sigma	71504
Ethanol	Wako	Cat#057-00451
NaCl	Wako	Cat#191-01665
KCl	Wako	Cat#163-03545
Na2HPO4	Wako	Cat#194-02875
KH2PO4	Wako	Cat#169-04245
UltraPure™ DNase/RNase-free distilled water	Invitrogen	Cat#10977023
1.0mm glass beads	TOMY	Cat#GB-10
0.1mm zirconia/silica beads	TOMY	Cat#ZSB-01
Ethylenediamine-N,N,N’,N’-tetraacetic acid, disodium salt, dihydrate	DOJINDO	Cat#N001
Proteinase K	Wako	Cat#160-14001
Proteinase K	TaKaRa	Cat#U0506A
2-Mercaptoethanol	Wako	Cat#133-06864
Trizma® base Primary Standard and Buffer, ≥ 99.9% (titration), crystalline	Sigma-Aldrich	Cat#T1503
HCl	Wako	Cat#080-01066
Hexadecyltrimethylammonium Bromide (synonym of CTAB)	Wako	Cat#036-021-02
Phenol/Chloroform/Isoamyl alcohol (25:24:1)	nacalai-tesque	Cat#25970-14
Phenol/Chloroform/Isoamyl alcohol (25:24:1)	NIPPON GENE	Cat#311-90151
Chloroform	Wako	Cat#038-02606
NaOAc	NIPPON GENE	Cat#316-90081
Glycogen	Wako	Cat#079-00832
RNase A (17,500U)	QIAGEN	Cat#19101
T-Vector pMD-20	TaKaRa	Cat#3270
TB Green premix Ex TaqII (Tli RNaseH Plus)	TaKaRa	Cat#RR820S
ROX reference dye II	TaKaRa	Cat#RR820S
Critical Commercial Assays
NexteraXT DNA Library Preparation kit (96 samples)	Illumina	Cat#FC-131-1096
Deposited Data
Raw sequence reds for metagenomes have been deposited on the NCBI Sequence Read Archive	This paper	PRJNA598094
Code used for bioinformatic analysis	This paper	http://doi.org/10.5281/zenodo.3747314
Oligonucleotides
Primers for V3-V4 region of 16S rRNA	[70]	N/A
Primers for actin gene, A. mellifera	See STAR Methods section	N/A
Primers for actin gene, A. cerana	See STAR Methods section	N/A
Software and Algorithms
QuantStudio Design & Analysis Software v1.4 (Firmware version 1.3.0)	Applied Biosystems	N/A
EZR	[71]	http://www.jichi.ac.jp/saitama-sct/SaitamaHP.files/statmed.html
Perl v.5.26.1	[72]	https://www.perl.org
BioPerl v.1.7.5	[73]	https://bioperl.org
Bash v. 4.4 23	https://www.gnu.org/software/bash	https://www.gnu.org/software/bash
R version 3.5.0	R Development Core Team, 2008	https://www.r-project.org
BLAST+ version 2.2.31	[74]	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+
FastQC v.0.11.4	[75]	http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Trimmomatic 0.35	[76]	http://www.usadellab.org/cms/?page=trimmomatic
fastANI v.1.3	[30]	https://github.com/ParBLiSS/FastANI
Orthofinder v.2.3.5	[77]	https://github.com/davidemms/OrthoFinder
mafft v.7.312	[78]	https://mafft.cbrc.jp/alignment/software/
RAxML v.8.1.24	[79]	https://github.com/stamatak/standard-RAxML
FigTree	[80]	https://github.com/rambaut/figtree/releases
SPAdes v.3.10.1	[81]	http://cab.spbu.ru/software/spades/
bwa v.0.7.15-r1142-dirty	[82]	https://sourceforge.net/projects/bio-bwa
Samtools v.1.9	[83]	https://github.com/samtools/samtools
Picard tools v.2.7.1	[84]	https://broadinstitute.github.io/picard/
Prodigal v.2.6.3	[85]	https://github.com/hyattpd/Prodigal
Freebayes v.1.0.2	[86]	https://github.com/ekg/freebayes
GNU parallel 20180422	[87]	http://www.gnu.org/software/parallel
Vcflib v.41	[88]	https://github.com/vcflib/vcflib
CD-HIT v.4.7	[89]	https://github.com/weizhongli/cdhit
eggnog v.5.0	[90]	http://eggnogdb.embl.de/#/app/home
eggNOG-mapper v. 1.0.3	[91]	https://github.com/eggnogdb/eggnog-mapper
HMMER 3.1b2	http:/hmmer.org	http:/hmmer.org
dbCan2 v.8	[38]	http://bcb.unl.edu/dbCAN2/
Other
Tweezer No. 5-Dumoxel BIOLOGIE	Dumont	N/A
Micro SmashTM MS-100 bead-beater	TOMY	N/A
QuantStudio 3 Real-Time PCR Instrument (96-well, 0.2mL Block)	Applied Biosystems	Cat#A28132