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Appendix 1
Appendix 1—key resources table
Reagent type
(species) or resource
Designation
Source or reference
Identifiers
Genetic reagent
(Drosophila
melanogaster)
Canton-Special
EHIME-Fly Drosophila Stocks of Ehime
University
E-10002
Genetic reagent (D.
melanogaster)
Cg-GAL4
Asha et al., 2003 (doi: 10.1093/
genetics/163.1.203)
Strain, strain
background
(Saccharomyces
cerevisiae)
BY4741
NBRP-Yeast
Strain, strain
background
(Lactiplantibacillus
plantarum)
WJL
Kim et al., 2021 (doi: 10.1038/s41586-
021-03522-2)
Strain, strain
background
(Lactiplantibacillus
plantarum)
LactoBCAA
Kim et al., 2021 (doi: 10.1038/s41586-
021-03522-2)
Sequence-based
reagent
ITS3
White et al., 1990
PCR primers
GCATCGATGAAGAACGCAGC
Sequence-based
reagent
ITS4
White et al., 1990
PCR primers
TCCTCCGCTTATTGATATGC
Sequence-based
reagent
341 F
Hugerth et al., 2014 (doi: 10.1128/
AEM.01403-14)
PCR primers
CCTACGGGNGGCWGCAG
Sequence-based
reagent
805R
Hugerth et al., 2014 (doi: 10.1128/
AEM.01403-14)
PCR primers
GACTACHVGGGTATCTAATCC
Sequence-based
reagent
518F
https://www.macrogen-japan.co.jp/cap_
seq_0104.php
PCR primers
CCAGCAGCCGCGGTAATACG
Sequence-based
reagent
NL1
Chandler et al., 2012 (doi: 10.1128/
AEM.01741-12)
PCR primers
GCATATCAATAAGCGGAGGAAAAG
Sequence-based
reagent
NL4
Chandler et al., 2012 (doi: 10.1128/
AEM.01741-12)
PCR primers
GGTCCGTGTTTCAAGACGG
Sequence-based
reagent
27F
Chandler et al., 2011 (doi: 10.1371/
journal.pgen.1002272)
PCR primers
AGAGTTTGATCCTGGCTCAG
Sequence-based
reagent
1492R
Chandler et al., 2011 (doi: 10.1371/
journal.pgen.1002272)
PCR primers
GGTTACCTTGTTACGACTT
QIAamp DNA
Commercial assay or kit Stool Mini Kit
QIAGEN
Cat# 51504
THUNDERBIRD
Commercial assay or kit SYBR qPCR Mix
TOYOBO
Cat# QPS-201
Commercial assay or kit InstaGene Matrix
Bio-Rad
Cat# 7326030
Commercial assay or kit KOD FX
TOYOBO
Cat# KFX-101
BY23849
Wizard SV Gel and
PCR Clean-Up
Commercial assay or kit System
Promega
Cat# A9282
QIAGEN
Genomic-tip 20G
Commercial assay or kit kit
Cat# 10223
QIAGEN
Additional information
Appendix 1 Continued on next page
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Appendix 1 Continued
Reagent type
(species) or resource
Designation
Source or reference
Identifiers
QIAseq FX DNA
Commercial assay or kit Library Kit
QIAGEN
Cat# 180477
Rapid Barcoding
Commercial assay or kit Kit
ONT
Cat# SQK-RBK004
Commercial assay or kit RNeasy mini kit
QIAGEN
Cat# 74104
NEBNext Ultra II
Directional RNA
Library Prep Kit for
Commercial assay or kit Illumina
NEB
Cat# E7760
Biomasher II
Commercial assay or kit homogenizer kit
NIP
Cat# 320103
Chemical compound,
drug
MRS Broth
Merck Millipore
Cat# 110661
Chemical compound,
drug
YPD medium
Clontech
Cat# 630409
Chemical compound,
drug
Potato Dextrose
Broth
Sigma-Aldrich
Cat# P6685-250G
Chemical compound,
drug
Propionic acid
Nacalai Tesque
Cat# 29018-55
Chemical compound,
drug
Cycloheximide
Wako
Cat# 037-20991
Chemical compound,
drug
Ampicillin
Nacalai Tesque
Chemical compound,
drug
Zymolyase-20T
Nacalai Tesque
Cat# 07663-91
Chemical compound,
drug
Leucine
Nacalai Tesque
Cat# 20327-62
Chemical compound,
drug
Isoleucine
Peptide Institute
Cat# 2712
Chemical compound,
drug
Phloxine B
Wako
Cat# 166-02072
Software, algorithm
FLASH
Magoč and Salzberg, 2011 (doi:
10.1093/bioinformatics/btr507)
Software, algorithm
CD-HIT-OTU
Fu et al., 2012 (doi: 10.1093/
bioinformatics/bts565); Li and Godzik,
2006 (doi: 10.1093/bioinformatics/
btl158)
Software, algorithm
QIIME
Caporaso et al., 2010 (doi: 10.1038/
nmeth.f.303)
Software, algorithm
NCBI BLAST
search
Johnson et al., 2008 (doi: 10.1093/nar/
gkn201)
Software, algorithm
RDP sequence
match tool
Cole et al., 2014 (doi: 10.1093/nar/
gkt1244)
Software, algorithm
Platanus_trim
http://platanus.bio.titech.ac.jp/pltanus_
trim
Software, algorithm
GenomeScope
Vurture et al., 2017 (doi: 10.1093/
bioinformatics/btx153)
Software, algorithm
Albacore ver. 2.3.3. ONT
Additional information
Appendix 1 Continued on next page
Mure et al. eLife 2023;12:RP90148. DOI: https://doi.org/10.7554/eLife.90148
31 of 32
Developmental Biology | Microbiology and Infectious Disease
Research article
Appendix 1 Continued
Reagent type
(species) or resource
Designation
Source or reference
Software, algorithm
NanoFilt
De Coster et al., 2018 (doi: 10.1093/
bioinformatics/bty149)
Software, algorithm
Porechop
https://github.com/rrwick/Porechop
Software, algorithm
MaSuRCA v3.2.6
Zimin et al., 2013 (doi: 10.1093/
bioinformatics/btt476)
Software, algorithm
BUSCO
Simão et al., 2015 (doi: 10.1093/
bioinformatics/btv351)
Software, algorithm
GenomeMatcher
Ohtsubo et al., 2008 (doi:
10.1186/1471-2105-9-376)
Software, algorithm
FunGAP
Min et al., 2017 (doi: 10.1093/
bioinformatics/btx353)
Software, algorithm
Hisat2
Kim et al., 2015 (doi: 10.1038/
nmeth.3317)
Software, algorithm
gplots
Warnes et al., 2022 (https://CRAN.R-
project.org/package=gplots)
Software, algorithm
R Development Core Team, 2020
Software, algorithm
Database for
annotation,
visualization
and integrated
discovery (DAVID) Huang et al., 2009 (doi: 10.1038/
Functional
nprot.2008.211); Sherman et al., 2022
Annotation Chart (doi: 10.1093/nar/gkac194)
Software, algorithm
MetaboAnalystR
3.3.0.
Pang et al., 2020 (doi: 10.3390/
metabo10050186)
Other
UltrafreeMC-
PLHCC for
Metabolome
Analysis column
Human Metabolome Technologies
Other
Discovery HS F5-3
column
Sigma-Aldrich
Mure et al. eLife 2023;12:RP90148. DOI: https://doi.org/10.7554/eLife.90148
Identifiers
Additional information
RRID:SCR_001905
Cat# UFC3LCCNB- See 'Preparing samples for LC–MS
HMT
analysis' in Materials and methods
Cat# 567503-U
See 'LC–MS/MS measurement' in
Materials and methods
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