Additional file 9: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Brian Fitzgerald
Andrey N. Shkoporov
Thomas D. S. Sutton
Andrei V. Chaplin
Vimalkumar Velayudhan
R. Paul Ross
Colin Hill

December 2018

Abstract Background Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome,...

Additional file 12: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Figure S6. qPCR analysis of prophage induction in strain F. prausnitzii A2–165. qPCR was performed o...

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Fitzgerald, Cormac Brian
Shkoporov, Andrey N.
Sutton, Thomas D. S.
Chaplin, Andrei V.
Velayudhan, Vimalkumar
Ross, R. Paul
Hill, Colin

December 2018

Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to ...

Additional file 6: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Table S3. List of 10,630 protein orthologues encoded by genomes of F. prausnitzii with annotation ac...

Additional file 7: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Figure S4. Composition of F. prausnitzii pan-, core- and accessory genome. A, Pan- and core genome a...

Additional file 10: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Table S5. List of prophage regions found in the F. prausnitzii genomes and their relationships to th...

Additional file 11: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Table S6. Distribution of carbohydrate active enzyme conserved domains in the strains of F. prausnit...

Additional file 5: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Figure S3. De novo orthologous protein groups (nâ=â10,630) encoded in 31âF. prausnitzii genome...

Additional file 2: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Figure S2. BLASTn-based pairwise sequence coverage between available 31 complete and draft genomes o...

Additional file 3: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Table S1. Strains representing other species of the family Ruminococcaceae, used for comparative pur...

Additional file 4: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Table S2. List of 245 orthologous genes in the family Ruminococcaceae used for phylogeny inference. ...

Additional file 8: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Figure S5. Heatmap of gene orthologues differentially abundant between the two F. prausnitzii genomo...

Additional file 1: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Figure S1. Schematic representation of pairwise comparisons of locations of LCBs in genomes of F. pr...

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Brian Fitzgerald (5733284)
Andrey N. Shkoporov (5078096)
Thomas D.S. Sutton (5078087)
Andrei V. Chaplin (783623)
Vimalkumar Velayudhan (126780)
R. Paul Ross (152753)
Colin Hill (73239)

September 2018

R scripts and data tables needed to reproduce figures in the manuscript: Comparative analysis of Fa...

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Brian Fitzgerald (5733284)
Andrey N. Shkoporov (5078096)
Thomas D.S. Sutton (5078087)
Andrei V. Chaplin (783623)
Vimalkumar Velayudhan (126780)
R. Paul Ross (152753)
Colin Hill (73239)

September 2018

R scripts and data tables needed to reproduce figures in the manuscript: Comparative analysis of Fae...

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Brian Fitzgerald
Andrey N. Shkoporov
Thomas D. S. Sutton
Andrei V. Chaplin
Vimalkumar Velayudhan
R. Paul Ross
Colin Hill

December 2018

Abstract Background Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome,...

Additional file 12: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Figure S6. qPCR analysis of prophage induction in strain F. prausnitzii A2–165. qPCR was performed o...

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Fitzgerald, Cormac Brian
Shkoporov, Andrey N.
Sutton, Thomas D. S.
Chaplin, Andrei V.
Velayudhan, Vimalkumar
Ross, R. Paul
Hill, Colin

December 2018

Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to ...

Additional file 6: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Table S3. List of 10,630 protein orthologues encoded by genomes of F. prausnitzii with annotation ac...

Additional file 7: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Figure S4. Composition of F. prausnitzii pan-, core- and accessory genome. A, Pan- and core genome a...

Additional file 10: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Table S5. List of prophage regions found in the F. prausnitzii genomes and their relationships to th...

Additional file 11: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Table S6. Distribution of carbohydrate active enzyme conserved domains in the strains of F. prausnit...

Additional file 5: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Figure S3. De novo orthologous protein groups (nâ=â10,630) encoded in 31âF. prausnitzii genome...

Additional file 2: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Figure S2. BLASTn-based pairwise sequence coverage between available 31 complete and draft genomes o...

Additional file 3: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Table S1. Strains representing other species of the family Ruminococcaceae, used for comparative pur...

Additional file 4: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Table S2. List of 245 orthologous genes in the family Ruminococcaceae used for phylogeny inference. ...

Additional file 8: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Figure S5. Heatmap of gene orthologues differentially abundant between the two F. prausnitzii genomo...

Additional file 1: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Figure S1. Schematic representation of pairwise comparisons of locations of LCBs in genomes of F. pr...

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Brian Fitzgerald (5733284)
Andrey N. Shkoporov (5078096)
Thomas D.S. Sutton (5078087)
Andrei V. Chaplin (783623)
Vimalkumar Velayudhan (126780)
R. Paul Ross (152753)
Colin Hill (73239)

September 2018

R scripts and data tables needed to reproduce figures in the manuscript: Comparative analysis of Fa...

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Brian Fitzgerald (5733284)
Andrey N. Shkoporov (5078096)
Thomas D.S. Sutton (5078087)
Andrei V. Chaplin (783623)
Vimalkumar Velayudhan (126780)
R. Paul Ross (152753)
Colin Hill (73239)

September 2018

R scripts and data tables needed to reproduce figures in the manuscript: Comparative analysis of Fae...

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Brian Fitzgerald
Andrey N. Shkoporov
Thomas D. S. Sutton
Andrei V. Chaplin
Vimalkumar Velayudhan
R. Paul Ross
Colin Hill

December 2018

Abstract Background Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome,...

Additional file 12: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Cormac Fitzgerald (6088049)
Andrey Shkoporov (6088052)
Thomas Sutton (3860260)
Andrei Chaplin (6088055)
Vimalkumar Velayudhan (126780)
R. Ross (3461291)
Colin Hill (73239)

December 2018

Figure S6. qPCR analysis of prophage induction in strain F. prausnitzii A2–165. qPCR was performed o...

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Fitzgerald, Cormac Brian
Shkoporov, Andrey N.
Sutton, Thomas D. S.
Chaplin, Andrei V.
Velayudhan, Vimalkumar
Ross, R. Paul
Hill, Colin

December 2018

Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to ...

Additional file 9: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Abstract

Extracted data

Additional file 9: of Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Abstract

Extracted data

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