Additional file 2: of Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

Additional file 5: of Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana

Matthew Hansen (445716)
Meagan Rubel (6249047)
Aubrey Bailey (520161)
Alessia Ranciaro (6249053)
Simon Thompson (3411839)
Michael Campbell (562588)
William Beggs (168608)
Jaanki Dave (6249065)
Gaonyadiwe Mokone (6249071)
Sununguko Mpoloka (6249074)
Thomas Nyambo (6249080)
Christian Abnet (3703321)
Stephen Chanock (23589)
Frederic Bushman (3286380)
Sarah Tishkoff (6249089)

January 2019

Contains the genetic similarity values, where each row corresponds to a pair of individuals. (GZ 47 ...

Additional file 5: Table S3. of Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis

Lena Hersemann (3618917)
Daniel Wibberg (839038)
Jochen Blom (104512)
Alexander Goesmann (11354)
Franco Widmer (3171993)
Frank-Jörg Vorhölter (86202)
Roland Kölliker (3474368)

January 2017

Type VI secretion system homologues identified in Xtg2 and their corresponding COG numbers (E-value ...

Additional file 1: of Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites

Alessio Tovaglieri (5039909)
Alexandra Sontheimer-Phelps (6486695)
Annelies Geirnaert (579263)
Rachelle Prantil-Baun (6486698)
Diogo Camacho (6486701)
David Chou (427894)
Sasan Jalili-Firoozinezhad (6486704)
TomĂĄs Wouters (6486707)
Magdalena Kasendra (706294)
Michael Super (1641175)
Mark Cartwright (1436668)
Camilla Richmond (6486710)
David Breault (3441422)
Christophe Lacroix (35954)
Donald Ingber (6486713)

March 2019

Figure S1. Analysis of relative abundance of PolyFermS commensal bacteria phyla. Relative abundance ...

Additional file 1: of Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

Michael Coyne (3514196)
Kevin Roelofs (2213431)
Laurie Comstock (3514190)

January 2016

Proteins encoded by each of the 205 genomes that match the profile HMMs for Tss, Tag, TetR, Rhs, PAA...

Additional file 3: of Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

Michael Coyne (3514196)
Kevin Roelofs (2213431)
Laurie Comstock (3514190)

January 2016

Identification of putative effector and immunity proteins by comparison to those identified in Zhang...

Additional file 4: of Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

Michael Coyne (3514196)
Kevin Roelofs (2213431)
Laurie Comstock (3514190)

January 2016

Alignment of the ICE from the Bacteroidales CL02T12 strains against contigs of strains harboring GA1...

Additional file 5: of Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

Michael Coyne (3514196)
Kevin Roelofs (2213431)
Laurie Comstock (3514190)

January 2016

Alignment of contigs harboring GA2 T6SS loci with the B. fragilis CL05T00C05 contig bearing the GA2 ...

Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

Coyne, Michael J.
Roelofs, Kevin G.
Comstock, Laurie E.

February 2016

Background: Type VI secretion systems (T6SSs) are contact-dependent antagonistic systems employed by...

Additional file 2: Table S2. of Comparison of Xenorhabdus bovienii bacterial strain genomes reveals diversity in symbiotic functions

Kristen Murfin (3533495)
Amy Whooley (3533498)
Jonathan Klassen (1300188)
Heidi Goodrich-Blair (81292)

November 2015

Secretion system genes. Description: Table of all genes identified encoding the complete secretion s...

Additional file 6: Table S3. of Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals

Kate Ormerod (3443333)
David Wood (435499)
Nancy Lachner (3443339)
Shaan Gellatly (3443345)
Joshua Daly (171086)
Jeremy Parsons (1874845)
Cristiana DalâMolin (3443348)
Robin Palfreyman (3443336)
Lars Nielsen (664146)
Matthew Cooper (94332)
Mark Morrison (159827)
Philip Hansbro (707776)
Philip Hugenholtz (13833)

July 2016

Cell wall associated PFAMs identified in âCa. Homeothermaceaeâ genomes. (XLSX 13 kb

Additional file 6: of Competitive lottery-based assembly of selected clades in the human gut microbiome

Adrian Verster (5875283)
Elhanan Borenstein (68815)

October 2018

Figure S5. Distribution of within-group abundances for higher-level taxonomic groups. Details are as...

Additional file 3: of Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages

Lucy Cheng (4901179)
Laura Marinelli (4901185)
NoĂŤl Grosset (4901173)
Sorel Fitz-Gibbon (3251946)
Charles Bowman (4901176)
Brian Dang (4901188)
Daniel Russell (2094130)
Deborah Jacobs-Sera (199566)
Baochen Shi (16761)
Matteo Pellegrini (2078)
Jeff Miller (4901182)
Michel Gautier (492401)
Graham Hatfull (3402956)
Robert Modlin (4535785)

March 2018

Figure S2. Genome organization of phage E6. See Additional file 2: Figure S1 for details. (PDF 161Â ...

Additional file 6: of Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages

Lucy Cheng (4901179)
Laura Marinelli (4901185)
NoĂŤl Grosset (4901173)
Sorel Fitz-Gibbon (3251946)
Charles Bowman (4901176)
Brian Dang (4901188)
Daniel Russell (2094130)
Deborah Jacobs-Sera (199566)
Baochen Shi (16761)
Matteo Pellegrini (2078)
Jeff Miller (4901182)
Michel Gautier (492401)
Graham Hatfull (3402956)
Robert Modlin (4535785)

March 2018

Figure S5. Genome organization of phage B3. See Additional file 2: Figure S1 for details. (PDF 159Â ...

Additional file 2: of Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

Almut Heinken (171782)
Dmitry Ravcheev (6704966)
Federico Baldini (4039547)
Laurent Heirendt (6656426)
Ronan Fleming (4110700)
Ines Thiele (11375)

May 2019

Figure S1. Maximum-likelihood phylogenetic tree for bile salt hydrolase (BSH) proteins and their hom...

Additional file 6: of Culture-enriched human gut microbiomes reveal core and accessory resistance genes

Frédéric Raymond (51256)
Maurice Boissinot (59036)
Amin Ouameur (6561317)
Maxime Déraspe (3480068)
Pier-Luc Plante (604214)
Sewagnouin Kpanou (6561320)
Ève Bérubé (6561323)
Ann Huletsky (2418028)
Paul Roy (6561326)
Marc Ouellette (51263)
Michel Bergeron (6561329)
Jacques Corbeil (51262)

April 2019

Figure S3. Distribution of pathways in culture-independent or culture-enriched microbiomes. Pathways...

Additional file 5: of Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana

Matthew Hansen (445716)
Meagan Rubel (6249047)
Aubrey Bailey (520161)
Alessia Ranciaro (6249053)
Simon Thompson (3411839)
Michael Campbell (562588)
William Beggs (168608)
Jaanki Dave (6249065)
Gaonyadiwe Mokone (6249071)
Sununguko Mpoloka (6249074)
Thomas Nyambo (6249080)
Christian Abnet (3703321)
Stephen Chanock (23589)
Frederic Bushman (3286380)
Sarah Tishkoff (6249089)

January 2019

Contains the genetic similarity values, where each row corresponds to a pair of individuals. (GZ 47 ...

Additional file 5: Table S3. of Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis

Lena Hersemann (3618917)
Daniel Wibberg (839038)
Jochen Blom (104512)
Alexander Goesmann (11354)
Franco Widmer (3171993)
Frank-Jörg Vorhölter (86202)
Roland Kölliker (3474368)

January 2017

Type VI secretion system homologues identified in Xtg2 and their corresponding COG numbers (E-value ...

Additional file 1: of Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites

Alessio Tovaglieri (5039909)
Alexandra Sontheimer-Phelps (6486695)
Annelies Geirnaert (579263)
Rachelle Prantil-Baun (6486698)
Diogo Camacho (6486701)
David Chou (427894)
Sasan Jalili-Firoozinezhad (6486704)
TomĂĄs Wouters (6486707)
Magdalena Kasendra (706294)
Michael Super (1641175)
Mark Cartwright (1436668)
Camilla Richmond (6486710)
David Breault (3441422)
Christophe Lacroix (35954)
Donald Ingber (6486713)

March 2019

Figure S1. Analysis of relative abundance of PolyFermS commensal bacteria phyla. Relative abundance ...

Additional file 1: of Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

Michael Coyne (3514196)
Kevin Roelofs (2213431)
Laurie Comstock (3514190)

January 2016

Proteins encoded by each of the 205 genomes that match the profile HMMs for Tss, Tag, TetR, Rhs, PAA...

Additional file 3: of Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

Michael Coyne (3514196)
Kevin Roelofs (2213431)
Laurie Comstock (3514190)

January 2016

Identification of putative effector and immunity proteins by comparison to those identified in Zhang...

Additional file 4: of Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

Michael Coyne (3514196)
Kevin Roelofs (2213431)
Laurie Comstock (3514190)

January 2016

Alignment of the ICE from the Bacteroidales CL02T12 strains against contigs of strains harboring GA1...

Additional file 5: of Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

Michael Coyne (3514196)
Kevin Roelofs (2213431)
Laurie Comstock (3514190)

January 2016

Alignment of contigs harboring GA2 T6SS loci with the B. fragilis CL05T00C05 contig bearing the GA2 ...

Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

Coyne, Michael J.
Roelofs, Kevin G.
Comstock, Laurie E.

February 2016

Background: Type VI secretion systems (T6SSs) are contact-dependent antagonistic systems employed by...

Additional file 2: Table S2. of Comparison of Xenorhabdus bovienii bacterial strain genomes reveals diversity in symbiotic functions

Kristen Murfin (3533495)
Amy Whooley (3533498)
Jonathan Klassen (1300188)
Heidi Goodrich-Blair (81292)

November 2015

Secretion system genes. Description: Table of all genes identified encoding the complete secretion s...

Additional file 6: Table S3. of Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals

Kate Ormerod (3443333)
David Wood (435499)
Nancy Lachner (3443339)
Shaan Gellatly (3443345)
Joshua Daly (171086)
Jeremy Parsons (1874845)
Cristiana DalâMolin (3443348)
Robin Palfreyman (3443336)
Lars Nielsen (664146)
Matthew Cooper (94332)
Mark Morrison (159827)
Philip Hansbro (707776)
Philip Hugenholtz (13833)

July 2016

Cell wall associated PFAMs identified in âCa. Homeothermaceaeâ genomes. (XLSX 13 kb

Additional file 6: of Competitive lottery-based assembly of selected clades in the human gut microbiome

Adrian Verster (5875283)
Elhanan Borenstein (68815)

October 2018

Figure S5. Distribution of within-group abundances for higher-level taxonomic groups. Details are as...

Additional file 3: of Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages

Lucy Cheng (4901179)
Laura Marinelli (4901185)
NoĂŤl Grosset (4901173)
Sorel Fitz-Gibbon (3251946)
Charles Bowman (4901176)
Brian Dang (4901188)
Daniel Russell (2094130)
Deborah Jacobs-Sera (199566)
Baochen Shi (16761)
Matteo Pellegrini (2078)
Jeff Miller (4901182)
Michel Gautier (492401)
Graham Hatfull (3402956)
Robert Modlin (4535785)

March 2018

Figure S2. Genome organization of phage E6. See Additional file 2: Figure S1 for details. (PDF 161Â ...

Additional file 6: of Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages

Lucy Cheng (4901179)
Laura Marinelli (4901185)
NoĂŤl Grosset (4901173)
Sorel Fitz-Gibbon (3251946)
Charles Bowman (4901176)
Brian Dang (4901188)
Daniel Russell (2094130)
Deborah Jacobs-Sera (199566)
Baochen Shi (16761)
Matteo Pellegrini (2078)
Jeff Miller (4901182)
Michel Gautier (492401)
Graham Hatfull (3402956)
Robert Modlin (4535785)

March 2018

Figure S5. Genome organization of phage B3. See Additional file 2: Figure S1 for details. (PDF 159Â ...

Additional file 2: of Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

Almut Heinken (171782)
Dmitry Ravcheev (6704966)
Federico Baldini (4039547)
Laurent Heirendt (6656426)
Ronan Fleming (4110700)
Ines Thiele (11375)

May 2019

Figure S1. Maximum-likelihood phylogenetic tree for bile salt hydrolase (BSH) proteins and their hom...

Additional file 6: of Culture-enriched human gut microbiomes reveal core and accessory resistance genes

Frédéric Raymond (51256)
Maurice Boissinot (59036)
Amin Ouameur (6561317)
Maxime Déraspe (3480068)
Pier-Luc Plante (604214)
Sewagnouin Kpanou (6561320)
Ève Bérubé (6561323)
Ann Huletsky (2418028)
Paul Roy (6561326)
Marc Ouellette (51263)
Michel Bergeron (6561329)
Jacques Corbeil (51262)

April 2019

Figure S3. Distribution of pathways in culture-independent or culture-enriched microbiomes. Pathways...

Additional file 5: of Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana

Matthew Hansen (445716)
Meagan Rubel (6249047)
Aubrey Bailey (520161)
Alessia Ranciaro (6249053)
Simon Thompson (3411839)
Michael Campbell (562588)
William Beggs (168608)
Jaanki Dave (6249065)
Gaonyadiwe Mokone (6249071)
Sununguko Mpoloka (6249074)
Thomas Nyambo (6249080)
Christian Abnet (3703321)
Stephen Chanock (23589)
Frederic Bushman (3286380)
Sarah Tishkoff (6249089)

January 2019

Contains the genetic similarity values, where each row corresponds to a pair of individuals. (GZ 47 ...

Additional file 5: Table S3. of Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis

Lena Hersemann (3618917)
Daniel Wibberg (839038)
Jochen Blom (104512)
Alexander Goesmann (11354)
Franco Widmer (3171993)
Frank-Jörg Vorhölter (86202)
Roland Kölliker (3474368)

January 2017

Type VI secretion system homologues identified in Xtg2 and their corresponding COG numbers (E-value ...

Additional file 1: of Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites

Alessio Tovaglieri (5039909)
Alexandra Sontheimer-Phelps (6486695)
Annelies Geirnaert (579263)
Rachelle Prantil-Baun (6486698)
Diogo Camacho (6486701)
David Chou (427894)
Sasan Jalili-Firoozinezhad (6486704)
TomĂĄs Wouters (6486707)
Magdalena Kasendra (706294)
Michael Super (1641175)
Mark Cartwright (1436668)
Camilla Richmond (6486710)
David Breault (3441422)
Christophe Lacroix (35954)
Donald Ingber (6486713)

March 2019

Figure S1. Analysis of relative abundance of PolyFermS commensal bacteria phyla. Relative abundance ...

Additional file 2: of Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

Abstract

Extracted data

Additional file 2: of Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

Abstract

Extracted data

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