PMC7494187_01
Genome atlas diagrams of 
Bacteroides
 spp. PHL2737 (QAWD00000000) from this study compare to other 
B. fragilis
. 
B. fragilis
 strain NCTC 9343 was used as a reference sequence. A lack of colour represents the absence of genes in the genome of the corresponding strain at that position. Phylogenetic analysis of single nucleotide variation (SNV) of PHL2737. Core-genome SNV-based phylogenetic tree of 
Bacteroides
 genomospecies PHL2737 (accession no. QAWD00000000.1) and closely related GenBank isolates. SNV were called using smalt 0.7.4. 
B. fragilis
 strain 638R was used as a reference. The meta-alignment of informative core SNV positions was used to create a maximum likelihood phylogenetic tree using mega 6 on 28 233 core high-quality SNVs. Maximum likelihood phylogeny indicates the presence of two clusters separated by >25 000 SNVs. One cluster contains four GenBank isolates, with 8-107 SNV differences within each other and >3000 SNVs to reference. The second cluster contains GenBank isolate JANI01000001.1 and clinical isolate PHL2737 with only 8 SNV differences.
acmi-2-111-g001.jpg
PMC7494187_01_acmi-2-111-g001.jpg
F1
The genome atlas plot shows high similarities between PHL2737 and UW isolate 1 compared reference  B. fragilis  strains (Fig. 1). The meta-alignment of informative core SNV positions was used to create a maximum likelihood (ML) phylogenetic tree using mega 6 (Fig. 1b).
Linear schematic representation of region containing the nimE gene and surrounding ORFs in plasmid 1.
acmi-2-111-g002.jpg
PMC7494187_01_acmi-2-111-g002.jpg
F2
The nimE gene on the PHL2737 strain was found on one of the plasmids (Fig. 2). Using rast, we were able to locate nimE and the associated upstream insertion sequence IS5-like element (ISBf6 family transposase) on the largest plasmid (plasmid 1) (Fig. 2).