Journal: Microbiology Spectrum

Article Title: Comparative Genomic Analysis of Fusobacterium necrophorum Provides Insights into Conserved Virulence Genes

doi: 10.1128/spectrum.00297-22

Figure Lengend Snippet: (A) Gene content cladogram of genus Fusobacterium. The unweighted pair group method with arithmetic means (UPGMA) cladogram was constructed based on the dissimilarities among core gene sequence analyses using a UBCG set in 167 Fusobacterium strains. Leptotrichia buccalis DSM 1135 and Cetobacterium somerae ATCC BAA-474 (red font) were used as outgroups. Each colored strip denotes a different Fusobacterium species, as defined in the legend. Gene support index values are given at branching points. (B) Phylogenetic tree of Fusobacterium necrophorum species. Maximum-likelihood phylogenetic tree based on UBCG sequences of 41 RefSeq and five F. necrophorum test strains (bold). The clades are distinctly defined for each subspecies. The blue branch represents the clade for F. necrophorum subsp. necrophorum , and the red branch represents the clade for F. necrophorum subsp. funduliforme . strains BL and FDAARGOS 565 in the red boxes fall into the clade of F. necrophorum subsp. necrophorum , indicating that they are most likely F. necrophorum subsp. necrophorum . Bar, 0.01substitution per nucleotide position. (C) Heat map of ANI of whole-genome comparison of 46 (41 RefSeq sequences and five test strains) F. necrophorum strains. The row and column labels in the heat map correspond to the pairwise alignment of 46 F. necrophorum species. Cells in the heat map correspond to 95% identity and 70% coverage or greater. The identity match ranges from green to yellow to red as identity matches drop to 94.5%. F. necrophorum subsp. necrophorum and F. necrophorum subsp. funduliforme form each group represented in two distinct green blocks in the heat map and clustered together into separate clades in the phylogenetic tree. KG35 had a comparatively small ANI value, with the lowest-identity matches (some values were <95%), as indicated in the red grid. Strains are represented by their acronym and are provided in a supplementary material S1, see Data set S1.

Article Snippet: The Fusobacterium phylogenic topology published by McGuire et al. is comparable to the phylogeny in our study , although F. necrophorum strain D12 was shown to be in closer relation to F. gonidiaformans ATCC 25563.

Techniques: Construct, Sequencing, Stripping Membranes, Comparison

Journal: Microbiology Spectrum

Article Title: Comparative Genomic Analysis of Fusobacterium necrophorum Provides Insights into Conserved Virulence Genes

doi: 10.1128/spectrum.00297-22

Figure Lengend Snippet: Predicted subspecies of publicly available reference sequences of Fusobacterium necrophorum based on phylogenetic analysis

Article Snippet: The Fusobacterium phylogenic topology published by McGuire et al. is comparable to the phylogeny in our study , although F. necrophorum strain D12 was shown to be in closer relation to F. gonidiaformans ATCC 25563.

Techniques: Isolation

Journal: Microbiology Spectrum

Article Title: Comparative Genomic Analysis of Fusobacterium necrophorum Provides Insights into Conserved Virulence Genes

doi: 10.1128/spectrum.00297-22

Figure Lengend Snippet: (A) Pangenome alignment of Fusobacterium species. Pangenome analysis was performed using Roary. Pangenome analysis of Fusobacterium (genus level [part 1]) and F. necrophorum (species level [part 2]). The gene matrix shows the presence (blue blocks) and absence (gray areas) of core and accessory genes. In the matrix, genomes are shown as rows and gene clusters as columns. The dendrogram is based on the phylogenetic relatedness of the core genes and accessory gene clusters. (B) F. necrophorum population structure cladogram. The maximum-likelihood tree was constructed based on the pangenome analysis with 826 core genes and calculated based on the GTR+I+G4 model and 100 bootstrap replicates for 46 F. necrophorum strains. The right side of the cladogram includes three color-coded columns representing GC content, source, and genome size of the isolates. The cladogram forms distinct clades of F. necrophorum subsp. funduliforme , F. necrophorum subsp. necrophorum , and F. necrophorum not identified to the subspecies level. (C) F. necrophorum subsp. necrophorum - and F. necrophorum subsp. funduliforme -specific genes. Genes specific to F. necrophorum subsp. necrophorum and F. necrophorum subsp. funduliforme were separated by functional annotation. In the grid, color represents the presence and the absence of color shows the absence of genes. A total of 40 subspecies-specific genes with different biological functions were identified through the UniProt-based search. Nineteen hypothetical genes identified are shown in yellow.

Article Snippet: The Fusobacterium phylogenic topology published by McGuire et al. is comparable to the phylogeny in our study , although F. necrophorum strain D12 was shown to be in closer relation to F. gonidiaformans ATCC 25563.

Techniques: Construct, Functional Assay

Journal: Microbiology Spectrum

Article Title: Comparative Genomic Analysis of Fusobacterium necrophorum Provides Insights into Conserved Virulence Genes

doi: 10.1128/spectrum.00297-22

Figure Lengend Snippet: (A) Virulence genes detected in Fusobacterium necrophorum . The heat map shows the percent sequence identity of 13 potential virulence genes compared to the 46 genes in the custom database. The names of F. necrophorum strains are shown on the right, and the virulence genes are below the heat map. Blue indicates ≤40%, white indicates 40 to 50%, and red indicates >50 to 100% sequence identity. Virulence gene acronyms are defined at the bottom. (B) ARGs detected in Fusobacterium. The gene matrix shows the presence and absence of genes detected in each Fusobacterium genome (indicated on the left) using ABRicate. Black indicates the presence and white indicates the absence of antimicrobial resistance genes shown at the tops of the columns. aadA1 , aminoglycoside; bla OXA-85, beta-lactam; catA , catA13 , catA15 , chloramphenicol; erm (B), macrolide; lnu (C), lincosamide; lsa (C), ABC efflux/lincomycin, clindamycin, tiamulin; lsa (E), pleuromutilin, lincosamide, streptogramin A; msr (D), macrolide; mupB , mupirocin; qacC , quaternary ammonium compound; tet (32), tet (C), tet (M), tet (O), tet (T), tetA (P), tetracycline; vat (B), streptogramin.

Article Snippet: The Fusobacterium phylogenic topology published by McGuire et al. is comparable to the phylogeny in our study , although F. necrophorum strain D12 was shown to be in closer relation to F. gonidiaformans ATCC 25563.

Techniques: Sequencing

Journal: Microbiology Spectrum

Article Title: Comparative Genomic Analysis of Fusobacterium necrophorum Provides Insights into Conserved Virulence Genes

doi: 10.1128/spectrum.00297-22

Figure Lengend Snippet: (A) ClonalFrameML analysis of recombination in F. necrophorum based on 46 genomes mapped to F. necrophorum assembly genomes. In the recombination plot, white vertical bars indicate reconstructed substitutions and dark blue horizontal bars indicate recombination events for each branch of the maximum-likelihood tree. The strain names are on the left, and the sizes and gene positions of the recombination events are shown across the alignment. (B) Phylogenetic tree constructed based on ClonalFrameML analysis of recombination in 46 F. necrophorum genomes, five tests and 41 reference strains. Three distinct clades are formed, with the red and yellow branches representing clade I and III, specific to F. necrophorum subsp. funduliforme , and the blue branch representing clade II, specific to F. necrophorum subsp. necrophorum (clade IIa), with F. necrophorum strains not identified to the subspecies level. Strain KG35 had the longest branch, which indicates significant recombination events. Test strains are in bold. The scale bar represents the length of the branch corresponding to the number of changes per site.

Article Snippet: The Fusobacterium phylogenic topology published by McGuire et al. is comparable to the phylogeny in our study , although F. necrophorum strain D12 was shown to be in closer relation to F. gonidiaformans ATCC 25563.

Techniques: Construct