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. Author manuscript; available in PMC: 2021 Jun 24.
Published in final edited form as: Curr Biol. 2021 May 27;31(12):2603–2618.e9. doi: 10.1016/j.cub.2021.04.046

Key Resources Table

REAGENT or RESOURCE SOURCE IDENTIFIER
Bacterial Strains
Escherichia coli OP50 Caenorhabditis Genetics Center OP50
Ochrobactrum pituitosum BH3 Buck Samuel 68 BH3
Acinetobacter sp. BIGb0102 Buck Samuel 16 BIGb0102
Leucobacter sp. BIGb0106 Buck Samuel 16 BIGb0106
Leucobacter sp. BIGb0117 Buck Samuel 16 BIGb0117
Ramlibacter sp. BIGb0124 Buck Samuel 16 BIGb0124
Raoultella sp. BIGb0138 Buck Samuel 16 BIGb0138
Stenotrophomonas sp. BIGb0145 Buck Samuel 16 BIGb0145
Citrobacter sp. BIGb0149 Buck Samuel 16 BIGb0149
Yersinia sp. BIGb0156 Buck Samuel 16 BIGb0156
Limnohabitans sp. BIGb0172 Buck Samuel 16 BIGb0172
Chryseobacterium sp. BIGb0186 Buck Samuel 16 BIGb0186
Citrobacter sp. BIGb0188 Buck Samuel 16 BIGb0188
Erwinia sp. BIGb0193 Buck Samuel 16 BIGb0193
Acinetobacter sp. BIGb0196 Buck Samuel 16 BIGb0196
Citrobacter sp. BIGb0211 Buck Samuel 16 BIGb0211
Chryseobacterium sp. BIGb0215 Buck Samuel 16 BIGb0215
Stenotrophomonas sp. BIGb0219 Buck Samuel 16 BIGb0219
Lactococcus sp. BIGb0220 Buck Samuel 16 BIGb0220
Yersinia sp. BIGb0236 Buck Samuel 16 BIGb0236
Myroides sp. BIGb0244 Buck Samuel 16 BIGb0244
Citrobacter sp. BIGb0267 Buck Samuel 16 BIGb0267
Pseudomonas sp. BIGb0272 Buck Samuel 16 BIGb0272
Pseudomonas sp. BIGb0273 Buck Samuel 16 BIGb0273
Enterobacter sp. BIGb0359 Buck Samuel 16 BIGb0359
Enterobacter sp. BIGb0383 Buck Samuel 16 BIGb0383
Erwinia sp. BIGb0393 Buck Samuel 16 BIGb0393
Raoultella sp. BIGb0399 Buck Samuel 16 BIGb0399
Pseudomonas sp. BIGb0404 Buck Samuel 16 BIGb0404
Pseudomonas sp. BIGb0408 Buck Samuel 16 BIGb0408
Erwinia sp. BIGb0435 Buck Samuel 16 BIGb0435
Pseudomonas sp. BIGb0470 Buck Samuel 16 BIGb0470
Pseudomonas sp. BIGb0473 Buck Samuel 16 BIGb0473
Pseudomonas sp. BIGb0477 Buck Samuel 16 BIGb0477
Providencia sp. BIGb0506 Buck Samuel 16 BIGb0506
Pseudomonas sp. BIGb0525 Buck Samuel 16 BIGb0525
Buttiauxella sp. BIGb0552 Buck Samuel 16 BIGb0552
Gluconobacter sp. BIGb0611 Buck Samuel 16 BIGb0611
Enterobacter sp. JUb101 Marie-Anne Félix 16 JUb101
Providencia sp. JUb102 Marie-Anne Félix 16 JUb102
Arthrobacter sp. JUb115 Marie-Anne Félix 16 JUb115
Leucobacter sp. JUb18 Marie-Anne Félix 16 JUb18
Stenotrophomonas sp. JUb19 Marie-Anne Félix 16 JUb19
Sphingobacterium sp. JUb20 Marie-Anne Félix 16 JUb20
Stenotrophomonas sp. JUb23 Marie-Anne Félix 16 JUb23
Pseudomonas sp. JUb28 Marie-Anne Félix 16 JUb28
Enterobacter sp. JUb30 Marie-Anne Félix 16 JUb30
Curtobacterium sp. JUb34 Marie-Anne Félix 16 JUb34
Providencia sp. JUb39 Marie-Anne Félix 16 JUb39
Chryseobacterium sp. JUb44 Marie-Anne Félix 16 JUb44
Neorhizobium sp. JUb45 Marie-Anne Félix 16 JUb45
Pseudomonas sp. JUb52 Marie-Anne Félix 16 JUb52
Yersinia sp. JUb53 Marie-Anne Félix 16 JUb53
Raoultella sp. JUb54 Marie-Anne Félix 16 JUb54
Sphingobacterium sp. JUb56 Marie-Anne Félix 16 JUb56
Limnohabitans sp. JUb58 Marie-Anne Félix 16 JUb58
Curtobacterium sp. JUb65 Marie-Anne Félix 16 JUb65
Enterobacter sp. JUb66 Marie-Anne Félix 16 JUb66
Sphingobacterium sp. JUb78 Marie-Anne Félix 16 JUb78
Delftia sp. JUb8 Marie-Anne Félix 16 JUb8
Rhodococcus sp. JUb83 Marie-Anne Félix 16 JUb83
Pseudomonas sp. JUb85 Marie-Anne Félix 16 JUb85
Acinetobacter sp. JUb89 Marie-Anne Félix 16 JUb89
Pseudomonas sp. JUb96 Marie-Anne Félix 16 JUb96
Experimental Models: Organisms/Strains
C. elegans: Natural isolate: AB1 Caenorhabditis Genetics Center 18 AB1
C. elegans: Natural isolate: AB3 Caenorhabditis Genetics Center 18 AB3
C. elegans: Natural isolate: CB4853 Caenorhabditis Genetics Center 18 CB4853
C. elegans: Natural isolate: CB4854 Caenorhabditis Genetics Center 18 CB4854
C. elegans: Natural isolate: CB4856 Caenorhabditis Genetics Center 18 CB4856
C. elegans: Natural isolate: ED3017 Caenorhabditis Genetics Center 18 ED3017
C. elegans: Natural isolate: ED3021 Caenorhabditis Genetics Center 18 ED3021
C. elegans: Natural isolate: ED3040 Caenorhabditis Genetics Center 18 ED3040
C. elegans: Natural isolate: ED3042 Caenorhabditis Genetics Center 18 ED3042
C. elegans: Natural isolate: ED3052 Caenorhabditis Genetics Center 18 ED3052
C. elegans: Natural isolate: ED3072 Caenorhabditis Genetics Center 18 ED3072
C. elegans: Natural isolate: GXW0001 Caenorhabditis Genetics Center 18 GXW0001
C. elegans: Natural isolate: JU1088 Caenorhabditis Genetics Center 18 JU1088
C. elegans: Natural isolate: JU1171 Caenorhabditis Genetics Center 18 JU1171
C. elegans: Natural isolate: JU1218 Caenorhabditis Genetics Center 18 JU1218
C. elegans: Natural isolate: JU1400 Caenorhabditis Genetics Center 18 JU1400
C. elegans: Natural isolate: JU1401 Caenorhabditis Genetics Center 18 JU1401
C. elegans: Natural isolate: JU1652 Caenorhabditis Genetics Center 18 JU1652
C. elegans: Natural isolate: JU258 Caenorhabditis Genetics Center 18 JU258
C. elegans: Natural isolate: JU263 Caenorhabditis Genetics Center 18 JU263
C. elegans: Natural isolate: JU300 Caenorhabditis Genetics Center 18 JU300
C. elegans: Natural isolate: JU312 Caenorhabditis Genetics Center 18 JU312
C. elegans: Natural isolate: JU322 Caenorhabditis Genetics Center 18 JU322
C. elegans: Natural isolate: JU323 Caenorhabditis Genetics Center 18 JU323
C. elegans: Natural isolate: JU360 Caenorhabditis Genetics Center 18 JU360
C. elegans: Natural isolate: JU361 Caenorhabditis Genetics Center 18 JU361
C. elegans: Natural isolate: JU397 Caenorhabditis Genetics Center 18 JU397
C. elegans: Natural isolate: JU533 Caenorhabditis Genetics Center 18 JU533
C. elegans: Natural isolate: JU642 Caenorhabditis Genetics Center 18 JU642
C. elegans: Natural isolate: JU775 Caenorhabditis Genetics Center 18 JU775
C. elegans: Natural isolate: KR314 Caenorhabditis Genetics Center 18 KR314
C. elegans: Natural isolate: LKC34 Caenorhabditis Genetics Center 18 LKC34
C. elegans: Natural isolate: MY1 Caenorhabditis Genetics Center 18 MY1
C. elegans: Natural isolate: MY14 Caenorhabditis Genetics Center 18 MY14
C. elegans: Natural isolate: MY16 Caenorhabditis Genetics Center 18 MY16
C. elegans: Natural isolate: MY2 Caenorhabditis Genetics Center 18 MY2
C. elegans: Natural isolate: PX174 Caenorhabditis Genetics Center 18 PX174
C. elegans: Wild-type: N2 Caenorhabditis Genetics Center N2
daf-2(e1370) Caenorhabditis Genetics Center CB1370 43
daf-16(mgDf50) Caenorhabditis Genetics Center GR1307 69
daf-16(mgDf50);daf-2(e1370) Caenorhabditis Genetics Center HT1890 47
unc-119(ed3);wgIs201 Caenorhabditis Genetics Center OP201 70
daf-16(mgDf50);unc-119(ed3);lpIs14 Caenorhabditis Genetics Center HT1889 47
Chemicals and Commercial Assays
Triton X-100 Sigma-Aldrich Cat#: T8787
Trizol Thermo-Fisher Cat#: 15596026
Garnet beads (1.0 mm) Biospect Cat#: 11079110gar
Silica beads (0.1 mm) Biospect Cat#: 11079101Z
Proteinase K New England Biolabs Cat#: P8107S
Nematode Growth Medium RPI Cat#: N81800–1000.0
Levamisole Fisher Cat#: AC187870100
Carbenicillin Sigma-Aldrich Cat#: C1389
IPTG Sigma-Aldrich Cat#: I6758
MirVANA total RNA kit Thermo-Fisher Cat#: A27828
Miseq (paired-end 250bp) Illumina N.A.
Hiseq4000 (paired-end 150bp) Illumina N.A.
Deposited Data
Code for data analysis Bitbucket https://bitbucket.org/the-samuel-lab/natural-variation/src/master/
Original 16S rRNA amplicon of gut microbiome sequences NCBI Bioproject PRJNA540192 (SAMN13068200–13068238, 13071563–13071602, 16597785–16597833, 16611296–16611371, 17054579–17054627)
Original RNAseq data from wild worms NCBI Bioproject PRJNA540192 (SAMN13050735–13050742)
Software and Algorithms
RStudio GNU Version 1.3.1093
ggplot: Various R Programming Tools for Plotting Data. R package Version 3.3.2
ggbeeswarm R package Version 0.6.1
ggtern R package Version 3.1.0
FASTQC 71 Version 0.11.9
bbmap JGI-DOE N.A.
bbduk JGI-DOE N.A.
kallisto 72 Version 0.45.0
DESeq2 73 Version 1.30.0
WormExp 29 Version 1.0
WormCat 27 N.A.
Worm machine 74 N.A.
CeNDR 53 Version 1.2.9
ImageJ NIH Version 2.0.0
Deblur 75 Version 1.0.2
QIIME 76 Version 1.8.0
Oligonucleotides
primer set (515F/806R) for 16S rRNA 77,78 N.A.