Additional file 1: of Draft genome sequence of Fermentimonas caenicola strain SIT8, isolated from the human gut

Additional file 2: of Fatty acid profiles and desaturase-encoding genes are different in thermo- and psychrotolerant strains of the Bacillus cereus Group

Sara Diomandé (3518057)
Marie-Hélène Guinebretière (75240)
Benoit De Sarrau (3518054)
Christophe Nguyen-the (3518051)
Véronique Broussolle (3518060)
Julien Brillard (75238)

July 2015

Fatty acid (FA) composition of B. cereus sl strains belonging to the 7 phylogenetic groups. This fil...

Additional file 6: of Comparative genomics reveals structural and functional features specific to the genome of a foodborne Escherichia coli O157:H7

Vijay Sharma (651200)
Suryatej Akavaram (6441005)
Robert Schaut (6441008)
Darrell Bayles (3468284)

March 2019

Table S1. Bacterial strains with their corresponding accession numbers used in the study. (DOCX 29 k...

Additional file 1: Table S1. of Complete genome sequence of Paenibacillus yonginensis DCY84T, a novel plant Symbiont that promotes growth via induced systemic resistance

Yeon-Ju Kim (622784)
Johan Sukweenadhi (4513249)
Ji Seok (4513240)
Chang Kang (4355239)
Eul-Su Choi (4513246)
Sathiyamoorthy Subramaniyam (2614864)
Deok Yang (4513243)

October 2017

Genome comparison of strain DCY84T and closest Paenibacillus strains. Table S2. COGs analysis of dir...

Draft genome sequence of Fermentimonas caenicola strain SIT8, isolated from the human gut

Beye, Mamadou
Bakour, Sofiane
Traore, Sory Ibrahima
Rathored, Jaishriram
Labas, Noemie
Raoult, Didier
Fournier, Pierre-Edouard

January 2018

International audienceWe report the properties of a draft genome sequence of the bacterium Fermentim...

Additional file 1: of Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3

Shahid Manzoor (614814)
Bettina MĂźller (3413231)
Adnan Niazi (3413234)
Anna SchnĂźrer (3413237)
Erik Bongcam-Rudloff (168047)

November 2015

Table S1. Associated MIGS record for Syntrophaceticus schinkii strain Sp3. (DOCX 111Â kb

Additional file 2: Table S1. of High-quality-draft genome sequence of the fermenting bacterium Anaerobium acetethylicum type strain GluBS11T (DSM 29698)

Yogita Patil (3760093)
Nicolai MĂźller (3760102)
Bernhard Schink (382427)
William Whitman (3426341)
Marcel Huntemann (34103)
Alicia Clum (111778)
Manoj Pillay (3333165)
Krishnaveni Palaniappan (3333150)
Neha Varghese (146576)
Natalia Mikhailova (224155)
Dimitrios Stamatis (3760096)
T. Reddy (3433427)
Chris Daum (2815984)
Nicole Shapiro (3333144)
Natalia Ivanova (8850)
Nikos Kyrpides (8859)
Tanja Woyke (111784)
Madan Junghare (3760099)

February 2017

IMG annotated functions of selected putative key enzymes involved in the metabolic pathways identifi...

Additional file 1: Table S1. of Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains

Silvia Arboleya (4340116)
Francesca Bottacini (133911)
Mary OâConnell-Motherway (4745418)
C. Ryan (3402638)
R. Ross (3461291)
Douwe van Sinderen (62590)
Catherine Stanton (223943)

January 2018

Bifidobacterium longum genomes publicly available used for different analysis along the study. Table...

Additional file 1: Table S1. of Draft genome sequence of Cellulomonas carbonis T26T and comparative analysis of six Cellulomonas genomes

Weiping Zhuang (2311159)
Shengzhe Zhang (810634)
Xian Xia (398501)
Gejiao Wang (115157)

November 2015

Putative CAZy family and locus_tag number in the six cellulomonas genomes. Table S2. Putative cellul...

Additional file 2: of Genome mining for natural product biosynthetic gene clusters in the Subsection V cyanobacteria

Melinda Micallef (3573422)
Paul DâAgostino (3573425)
Deepti Sharma (802056)
Rajesh Viswanathan (1455286)
Michelle Moffitt (3573419)

September 2015

W. intricata UH strain HT-29-1 and H. welwitschii UH strain IC-52-3 102 housekeeping genes, COGs. (X...

Additional file 1: of Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: implications for in vivo dominance of the vaginal microbiota

Charlotte Veer (6529292)
Rosanne Hertzberger (6529295)
Sylvia Bruisten (438918)
Hanne Tytgat (6529298)
Jorne Swanenburg (6529301)
Alie Kat Angelino-Bart (6529304)
Frank Schuren (126104)
Douwe Molenaar (37991)
Gregor Reid (163342)
Henry Vries (6529307)
Remco Kort (2446096)

March 2019

Biofilm formation, auto-aggregation, carbohydrate degradation, organic acid production, and antimicr...

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 7: of The gut microbiota drives the impact of bile acids and fat source in diet on mouse metabolism

Sarah Just (2632813)
Stanislas Mondot (5590778)
Josef Ecker (2053336)
Katrin Wegner (5590781)
Eva Rath (170714)
Laura Gau (5590787)
Theresa Streidl (5590790)
Genevieve Hery-Arnaud (5590796)
Sinah Schmidt (5590799)
Till Lesker (5590802)
Valentin Bieth (5590805)
Andreas Dunkel (1466371)
Till Strowig (86289)
Thomas Hofmann (77425)
Dirk Haller (374692)
Gerhard Liebisch (78400)
Philippe GĂŠrard (5590808)
Sascha Rohn (441006)
Patricia Lepage (522347)
Thomas Clavel (374686)

August 2018

Table S2. List of microbial genes differentially expressed in the cecum of mice fed high-fat diets s...

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 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 Genomic insights into the evolution of hybrid isoprenoid biosynthetic gene clusters in the MAR4 marine streptomycete clade

Kelley Gallagher (3466736)
Paul Jensen (48036)

November 2015

Table S1. Genome sequences used in this study. Table S2. ABBA PTases used as query sequences. Table ...

Additional file 2: of Fatty acid profiles and desaturase-encoding genes are different in thermo- and psychrotolerant strains of the Bacillus cereus Group

Sara Diomandé (3518057)
Marie-Hélène Guinebretière (75240)
Benoit De Sarrau (3518054)
Christophe Nguyen-the (3518051)
Véronique Broussolle (3518060)
Julien Brillard (75238)

July 2015

Fatty acid (FA) composition of B. cereus sl strains belonging to the 7 phylogenetic groups. This fil...

Additional file 6: of Comparative genomics reveals structural and functional features specific to the genome of a foodborne Escherichia coli O157:H7

Vijay Sharma (651200)
Suryatej Akavaram (6441005)
Robert Schaut (6441008)
Darrell Bayles (3468284)

March 2019

Table S1. Bacterial strains with their corresponding accession numbers used in the study. (DOCX 29 k...

Additional file 1: Table S1. of Complete genome sequence of Paenibacillus yonginensis DCY84T, a novel plant Symbiont that promotes growth via induced systemic resistance

Yeon-Ju Kim (622784)
Johan Sukweenadhi (4513249)
Ji Seok (4513240)
Chang Kang (4355239)
Eul-Su Choi (4513246)
Sathiyamoorthy Subramaniyam (2614864)
Deok Yang (4513243)

October 2017

Genome comparison of strain DCY84T and closest Paenibacillus strains. Table S2. COGs analysis of dir...

Draft genome sequence of Fermentimonas caenicola strain SIT8, isolated from the human gut

Beye, Mamadou
Bakour, Sofiane
Traore, Sory Ibrahima
Rathored, Jaishriram
Labas, Noemie
Raoult, Didier
Fournier, Pierre-Edouard

January 2018

International audienceWe report the properties of a draft genome sequence of the bacterium Fermentim...

Additional file 1: of Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3

Shahid Manzoor (614814)
Bettina MĂźller (3413231)
Adnan Niazi (3413234)
Anna SchnĂźrer (3413237)
Erik Bongcam-Rudloff (168047)

November 2015

Table S1. Associated MIGS record for Syntrophaceticus schinkii strain Sp3. (DOCX 111Â kb

Additional file 2: Table S1. of High-quality-draft genome sequence of the fermenting bacterium Anaerobium acetethylicum type strain GluBS11T (DSM 29698)

Yogita Patil (3760093)
Nicolai MĂźller (3760102)
Bernhard Schink (382427)
William Whitman (3426341)
Marcel Huntemann (34103)
Alicia Clum (111778)
Manoj Pillay (3333165)
Krishnaveni Palaniappan (3333150)
Neha Varghese (146576)
Natalia Mikhailova (224155)
Dimitrios Stamatis (3760096)
T. Reddy (3433427)
Chris Daum (2815984)
Nicole Shapiro (3333144)
Natalia Ivanova (8850)
Nikos Kyrpides (8859)
Tanja Woyke (111784)
Madan Junghare (3760099)

February 2017

IMG annotated functions of selected putative key enzymes involved in the metabolic pathways identifi...

Additional file 1: Table S1. of Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains

Silvia Arboleya (4340116)
Francesca Bottacini (133911)
Mary OâConnell-Motherway (4745418)
C. Ryan (3402638)
R. Ross (3461291)
Douwe van Sinderen (62590)
Catherine Stanton (223943)

January 2018

Bifidobacterium longum genomes publicly available used for different analysis along the study. Table...

Additional file 1: Table S1. of Draft genome sequence of Cellulomonas carbonis T26T and comparative analysis of six Cellulomonas genomes

Weiping Zhuang (2311159)
Shengzhe Zhang (810634)
Xian Xia (398501)
Gejiao Wang (115157)

November 2015

Putative CAZy family and locus_tag number in the six cellulomonas genomes. Table S2. Putative cellul...

Additional file 2: of Genome mining for natural product biosynthetic gene clusters in the Subsection V cyanobacteria

Melinda Micallef (3573422)
Paul DâAgostino (3573425)
Deepti Sharma (802056)
Rajesh Viswanathan (1455286)
Michelle Moffitt (3573419)

September 2015

W. intricata UH strain HT-29-1 and H. welwitschii UH strain IC-52-3 102 housekeeping genes, COGs. (X...

Additional file 1: of Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: implications for in vivo dominance of the vaginal microbiota

Charlotte Veer (6529292)
Rosanne Hertzberger (6529295)
Sylvia Bruisten (438918)
Hanne Tytgat (6529298)
Jorne Swanenburg (6529301)
Alie Kat Angelino-Bart (6529304)
Frank Schuren (126104)
Douwe Molenaar (37991)
Gregor Reid (163342)
Henry Vries (6529307)
Remco Kort (2446096)

March 2019

Biofilm formation, auto-aggregation, carbohydrate degradation, organic acid production, and antimicr...

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 7: of The gut microbiota drives the impact of bile acids and fat source in diet on mouse metabolism

Sarah Just (2632813)
Stanislas Mondot (5590778)
Josef Ecker (2053336)
Katrin Wegner (5590781)
Eva Rath (170714)
Laura Gau (5590787)
Theresa Streidl (5590790)
Genevieve Hery-Arnaud (5590796)
Sinah Schmidt (5590799)
Till Lesker (5590802)
Valentin Bieth (5590805)
Andreas Dunkel (1466371)
Till Strowig (86289)
Thomas Hofmann (77425)
Dirk Haller (374692)
Gerhard Liebisch (78400)
Philippe GĂŠrard (5590808)
Sascha Rohn (441006)
Patricia Lepage (522347)
Thomas Clavel (374686)

August 2018

Table S2. List of microbial genes differentially expressed in the cecum of mice fed high-fat diets s...

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 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 Genomic insights into the evolution of hybrid isoprenoid biosynthetic gene clusters in the MAR4 marine streptomycete clade

Kelley Gallagher (3466736)
Paul Jensen (48036)

November 2015

Table S1. Genome sequences used in this study. Table S2. ABBA PTases used as query sequences. Table ...

Additional file 2: of Fatty acid profiles and desaturase-encoding genes are different in thermo- and psychrotolerant strains of the Bacillus cereus Group

Sara Diomandé (3518057)
Marie-Hélène Guinebretière (75240)
Benoit De Sarrau (3518054)
Christophe Nguyen-the (3518051)
Véronique Broussolle (3518060)
Julien Brillard (75238)

July 2015

Fatty acid (FA) composition of B. cereus sl strains belonging to the 7 phylogenetic groups. This fil...

Additional file 6: of Comparative genomics reveals structural and functional features specific to the genome of a foodborne Escherichia coli O157:H7

Vijay Sharma (651200)
Suryatej Akavaram (6441005)
Robert Schaut (6441008)
Darrell Bayles (3468284)

March 2019

Table S1. Bacterial strains with their corresponding accession numbers used in the study. (DOCX 29 k...

Additional file 1: Table S1. of Complete genome sequence of Paenibacillus yonginensis DCY84T, a novel plant Symbiont that promotes growth via induced systemic resistance

Yeon-Ju Kim (622784)
Johan Sukweenadhi (4513249)
Ji Seok (4513240)
Chang Kang (4355239)
Eul-Su Choi (4513246)
Sathiyamoorthy Subramaniyam (2614864)
Deok Yang (4513243)

October 2017

Genome comparison of strain DCY84T and closest Paenibacillus strains. Table S2. COGs analysis of dir...

Additional file 1: of Draft genome sequence of Fermentimonas caenicola strain SIT8, isolated from the human gut

Abstract

Extracted data

Additional file 1: of Draft genome sequence of Fermentimonas caenicola strain SIT8, isolated from the human gut

Abstract

Extracted data

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