REAGENT OR RESOURCE	SOURCE	IDENTIFIER
Bacterial strains
Lactobacillus rhamnosus GG	ATCC	Cat# 53103
Lactobacillus acidophilus	ATCC	Cat# 4356
Lactobacillus bulgaricus LB-87	Custom Probiotic Inc	Cat# CP-2016
Lactobacillus casei LC-11	Custom Probiotic Inc	Cat# CP-2012
Lactobacillus salivarius LS-33	Custom Probiotic Inc	Cat# CP-2010
Bacteroides thetaiotaomicron	ATCC	Cat# 29148
Bacteroides fragilis	ATCC	Cat# 25285
Eubacterium rectale	ATCC	Cat# 33656
E. coli Top10	Invitrogen	Cat# C404006
E. coli BL21 (DE3)	Invitrogen	Cat# C600003
Plasmids and primers
pET28b-MBP-TEV	Addgene	Cat# 69929
pET28b-MBP-TEV-Msp1	This study	N/A
pET28b-MBP-TEV-Msp2	This study	N/A
pET28b-MBP-TEV-Msp3	This study	N/A
Primers see Table S5	N/A	N/A
Chemicals, Peptides, and Recombinant Proteins
MRS broth	Hardy Diagnostics	Cat# C5931
BHI broth	Hardy Diagnostics	Cat# C5141
Lemon fruits	Sam’s Club	Cat#127308
Kanamycin	Sigma	Cat# K1876
RNAprotect Bacteria Reagent	Qiagen	Cat# 76506
Porcine bile extract	Sigma	Cat# B8631
Ni-NTA Agarose	Qiagen	Cat# 30210
IRDye 800cw streptavidin	VWR	Cat# 102673-342
Dynabeads™ M-270 Streptavidin	Invitrogen	Cat# 65305
Tskgel G5000PW column	VWR	Cat# 100368-036
SuperScrip III First-Strand Synthesis System	Invitrogen	Cat#18080051
RNase-free DNase І	NEB	Cat# M0303S
TEV protease	Sigma	Cat# T4455
Nuclease P1	NEB	Cat# M0660S
CIP	NEB	Cat# M0525S
Critical Commercial Assays
RNeasy Mini Kit	Qiagen	Cat# 74104
miRNeasy Mini Kit	Qiagen	Cat# 217004
RiboPure RNA Purification Kit, bacteria	Invitrogen	Cat# AM1925
QuantiTect SYBR Green PCR Kits	Qiagen	Cat# 204143
PKH26 Fluorescent Cell Linker Kit	Sigma	Cat# PKH26GL
GeneArt Seamless Cloning and Assembly Kit	Invitrogen	cat# A14606
HiScribe T7 Quick High Yield RNA Synthesis Kit	NEB	Cat# E2050S
QIAamp DNA Stool Mini Kits	Qiagen	Cat# 51504
Experimental Models: Organisms/Strains Mouse
C57BL/6	Jackson Laboratory Stock	Cat# 000664
Deposited data
Sequenced data reported in this paper is stored at Sequence Read Archive (SRA): Accession code for Deposited Data: PRJNA722680
Software and algorithms
Prism (GraphPad Software)	GraphPad	https://www.graphpad.com
BioEdit	BioEdit	https://www.bioedit.com
Sequence manipulation suite	(Stothard, 2000)	https://www.bioinformatics.org/sms2