TABLE 1

Differences in gene presence/absence for each taxon based on strain origin, sequencing technology, sequence assembler method, culture medium, and study/reference

Taxon and factorVariables (n)R2aP valuea
B. cereus
    Strain originBE-Earth (1), BE-ISS (8), culture-Earth (1),
culture-Shenzhou VIII (2), human (33), soil (11)
0.2030.001
    Culture mediumbB. cereus selective agar (8), brain heart infusion medium (2),
custom medium (6), fastidious broth to blood agar (3),
HEPA filter to R2A agar (3), Luria-Bertani medium (8),
Trypticase soy agar (3)
0.3270.002
    Sequencing
  technology
Illumina (32), 454 (12), combination (10)0.1000.002
    AssemblerA5 (3), ABySS (10), CANU (1), Celera (4),
CLC NGS Cell (2), IDBA-UD (5), combination (5),
Newbler (11), SOAPdenovo (3), SPAdes (8), Velvet (1)
0.3230.001
    Study19 different studies/NCBI references (Table S1)0.4840.001
S. aureus
    Strain originBE-Earth (3), BE-ISS (21), human (24),
human-MRSA (55), soil (2)
0.2330.001
    Culture mediumbBrain heart infusion agar (2), HCH-supplemented liquid medium (1),
Trypticase soy agar (28), Trypticase soy broth (37)
0.2180.001
    Sequencing
  technology
Illumina (32), PacBio (15)0.0270.004
    AssemblerA5 (13), CLC Genomics Workbench (51), PacBio HGAP3 (15),
SeqMan NGen (16), SOAPdenovo (1), SPAdes (8), Velvet (1)
0.3850.001
    Study9 different studies/NCBI references (Table S1)0.4720.001
  • a PERMANOVA results for genome associations with each factor.

  • b Reflects the medium that was used in initial bacterial isolation or that which was used in isolate collection/processing, where available (i.e., not all studies provided culture method details, and some provided only information for how strains were processed rather than initial isolation).