Table 1 Members of the CeMbio v1.0 collection
Strain NameStrain TaxonomyaStrain Source (Lab of Origin)OTU RankbOTU %OTU Taxonomy
CEent1Enterobacter hormaecheiC. elegans N2 from mesocosm (Shapira)OTU_0112.7%dEnterobacteriaceae
JUb66Lelliottia amnigenarotting apple with wild C. elegans (Félix)OTU_0112.7%dEnterobacteriaceae
MYb10Acinetobacter guillouiaewild C. elegans from compost (Schulenburg)OTU_0211.3%Moraxellaceae; Acinetobacter
JUb134Sphingomonas molluscorumwild C. elegans from rotting plant stem (Félix)OTU_039.4%Sphingomonadaceae; Sphingomonas
JUb19Stenotrophomonas indicatrixrotting pear with wild C. elegans (Félix)OTU_04 / OTU_09c10.6%Xanthomonadaceae; Stenotrophomonas
MYb11Pseudomonas luridawild C. elegans from compost (Schulenburg)OTU_055.4%Pseudomonadaceae; Pseudomonas
MSPm1Pseudomonas berkeleyensisC. elegans N2 from mesocosm (Shapira)OTU_063.6%Pseudomonadaceae
BIGb0172Comamonas pisciswild C. elegans from rotting apple (Samuel)OTU_073.4%Comamonadaceae
BIGb0393Pantoea nemavictuswild C. elegans from rotting plant stem (Samuel)OTU_083.1%Enterobacteriaceae; Erwinia
MYb71Ochrobactrum vermiswild C. elegans from compost (Schulenburg)OTU_102.1%Brucellaceae; Ochrobactrum
BIGb0170Sphingobacterium multivorumwild C. elegans from rotting apple (Samuel)OTU_111.1%Sphingobacteriaceae; Sphingobacterium
JUb44Chryseobacterium scophthalmumrotting apple with wild C. elegans (Félix)OTU_120.8%Weeksellaceae; Chryseobacterium
  • a The phylogenetic identity of each isolate was assigned first using 16S rRNA maximum likelihood analysis; all isolates could be assigned to a genus. Then further phylogenomic analysis was performed on the full length genome compared to their close relative to assign species level taxonomy.

  • b Each strain corresponds to a bacterial core OTU identified to be abundant in the microbiomes of natural C. elegans nematodes. The average relative abundance across previously sampled natural C. elegans is given (Table S2).

  • c OTU_04 and OTU_09 were joined because they both refer to a Stenotrophomonas strain and because for OTU_09 we could not include a separate isolate from our culture collections.

  • d Two Enterobacteriaceae strains (CEent1 and JUb66) were chosen to represent OTU_01 to better reflect the functional differences in this family of bacteria. The strains are ordered according to their OTU rank.