REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
L. plantarum: LpNIZO2877	Martino et al., 2015a	LKHZ01000000
L. plantarum: LpWJL	Martino et al., 2015a, Martino et al., 2015b	LKLZ00000000
L. plantarum: FlyG2.1.8	This paper	PEBE00000000
L. plantarum: FlyG3.1.8	This paper	PEGI00000000
L. plantarum: FlyG7.1.6	This paper	PEGJ00000000
L. plantarum: FlyG8.1.1	This paper	PEGK00000000
L. plantarum: FlyG8.1.2	This paper	PEGL00000000
L. plantarum: FlyG9.1.4	This paper	PEGM00000000
L. plantarum: FlyG10.1.5	This paper	PEGN00000000
L. plantarum: FlyG10.1.9	This paper	PEGO00000000
L. plantarum: FlyG11.1.2	This paper	PEGP00000000
L. plantarum: FlyG11.1.6	This paper	PEGQ00000000
L. plantarum: FlyG20.1.4	This paper	PEGR00000000
L. plantarum: FlyG2.1.8Rev	This paper	N/A
L. plantarum: FlyG9.2.5	This paper	PEGS00000000
L. plantarum: FlyG11.2.6	This paper	PEGT00000000
L. plantarum: FlyG20.2.6	This paper	PEGU00000000
L. plantarum: DietG20.1.2	This paper	PEGV00000000
L. plantarum: DietG20.2.2	This paper	PEGW00000000
E. coli E135	Zhang et al., 2012	N/A
Chemicals, Peptides, and Recombinant Proteins
Inactivated Dried Yeast	Bio Springer	Springaline BA95/0-PW
Cornmeal	Westhove	Farigel maize H1
Agar	VWR	#20768.361
Methylparaben Sodium Salt	MERCK	#106756
Propionic Acid	Sigma-Aldrich	P1386
Man, Rogosa and Sharpe (MRS) Broth Medium	Difco	#288130
Man, Rogosa and Sharpe (MRS) Agar Medium	Difco	#288210
N-Acetyl Glutamine	Sigma-Aldrich	A9125-25G
PBS	Dutscher	NA.25
Glycerol	Sigma-Aldrich	G5516
SuperScript™ II Reverse Transcriptase	Invitrogen, Thermofisher Scientific	18064014
SYBR GreenER™ qPCR SuperMix Universal	Invitrogen, Thermofisher Scientific	1176202K
Rifampicin	Sigma-Aldrich	R3501
Chloramphenicol	Sigma-Aldrich	C0378
Erythromycin	Sigma-Aldrich	E1300000
Ampicillin	Sigma-Aldrich	A9393
Glycine	Sigma-Aldrich	67419
Sucrose	Sigma-Aldrich	S7903
Magnesium chloride	Sigma-Aldrich	M8266
Critical Commercial Assays
NucleoSpin RNA Isolation Kit	Macherey-Nagel	740955.240C
UltraClean Microbial DNA Isolation Kit	MOBIO Laboratories, Inc.	12224-250
Ion Xpress™ Plus Fragment Library Kit	Ion Torrent	4471269
Gibson Assembly Master Mix	NEB	E2611S
T4 Polynucleotide Kinase	NEB	M0201S
T4 DNA Ligase	NEB	M0202S
Deposited Data
Metabolomic Dataset of Diet	This paper	Table S3
L. plantarum FlyG2.1.8 genome	This paper	PEBE00000000
L. plantarum FlyG3.1.8 genome	This paper	PEGI00000000
L. plantarum FlyG7.1.6 genome	This paper	PEGJ00000000
L. plantarum FlyG8.1.1 genome	This paper	PEGK00000000
L. plantarum FlyG8.1.2 genome	This paper	PEGL00000000
L. plantarum FlyG9.1.4 genome	This paper	PEGM00000000
L. plantarum FlyG10.1.5 genome	This paper	PEGN00000000
L. plantarum FlyG10.1.9 genome	This paper	PEGO00000000
L. plantarum FlyG11.1.2 genome	This paper	PEGP00000000
L. plantarum FlyG11.1.6 genome	This paper	PEGQ00000000
L. plantarum FlyG20.1.4 genome	This paper	PEGR00000000
L. plantarum FlyG9.2.5 genome	This paper	PEGS00000000
L. plantarum FlyG11.2.6 genome	This paper	PEGT00000000
L. plantarum FlyG20.2.6 genome	This paper	PEGU00000000
L. plantarum DietG20.1.2 genome	This paper	PEGV00000000
L. plantarum DietG20.2.2 genome	This paper	PEGW00000000
Experimental Models: Organisms/Strains
D.melanogaster: y,w (reference strain for this work)		N/A
Oligonucleotides
Primer: 16S_UniF: GTGSTGCAYGGYTGTCGTCA	Packey et al., 2013	N/A
Primer: 16S_UniR: ACGTCRTCCMCACCTTCCTC	Packey et al., 2013	N/A
Primers for SNP verification, see Table S4	This paper	N/A
Primers for competition tests, see Table S4	This paper	N/A
Primers for engineering L. plantarum with CRISPR-Cas9, see Table S6	This paper	N/A
Recombinant DNA
Plasmids used to engineer L. plantarum with CRISPR-Cas9, see Table S5	This paper	N/A
pJP005		CB651
pMSP3545		Addgene 46888
pCas9	Jiang et al., 2013	Addgene 42876
Software and Algorithms
ImageJ	NIH Image	https://imagej.net/ImageJ
Leica application suite (LAS)	Leica	N/A
Scan 1200 Automatic HD colony counter and Software	Intersciences	Ref. 437 000
Breseq	Deatherage and Barrick, 2014	http://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing
R Studio	RStudio Team, 2015	https://www.rstudio.com/
PROVEAN	Choi et al., 2012	http://provean.jcvi.org
Geneious	Kearse et al., 2012	https://www.geneious.com
Gibson assembly	Choi et al., 2012	http://provean.jcvi.org