Additional file 3: of Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family

Additional file 3: Table S2. of Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses

Daniel Penselin (3362783)
Martin Münsterkötter (13742)
Susanne Kirsten (3362777)
Marius Felder (21057)
Stefan Taudien (47210)
Matthias Platzer (11284)
Kevin Ashelford (254162)
Konrad Paskiewicz (3529364)
Richard Harrison (824846)
David Hughes (47111)
Thomas Wolf (136760)
Ekaterina Shelest (615653)
Jenny Graap (3362765)
Jan Hoffmann (323101)
Claudia Wenzel (3362756)
Nadine Wöltje (3529370)
Kevin King (70030)
Bruce Fitt (3529367)
Ulrich Güldener (13741)
Anna Avrova (3362771)
Wolfgang Knogge (3362762)

November 2016

(A) Core meiotic recombination machinery genes. (B) Genes involved in sexual reproduction in the asp...

Additional file 1: of Hybridization capture reveals microbial diversity missed using current profiling methods

Cyrielle Gasc (801732)
Pierre Peyret (241634)

March 2018

Figure S1. Schematic representation of the hybridization capture method. Figure S2. Mock community p...

Additional file 1: Table S1. of Use of multilocus sequence typing to infer genetic diversity and population structure of Lactobacillus plantarum isolates from different sources

Haiyan Xu (148626)
Wenjun Liu (162986)
Wenyi Zhang (127372)
Jie Yu (150626)
Yuqin Song (690119)
Bilige Menhe (3448532)
Heping Zhang (29038)
Zhihong Sun (401173)

October 2015

Allelic profiles of analyzed L. plantarum strains. Table S2. Bacterial isolates used in this study. ...

Additional file 1: of Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family

Ilias Lagkouvardos (753901)
Till Lesker (5590802)
Thomas Hitch (4792731)
Eric GĂĄlvez (6381071)
Nathiana Smit (6381074)
Klaus Neuhaus (134143)
Jun Wang (5906)
John Baines (2632834)
Birte Abt (158167)
BĂ¤rbel Stecher (6381077)
JĂśrg Overmann (3919514)
Till Strowig (86289)
Thomas Clavel (374686)

February 2019

Table S1. Table of all KEGG Orthologies across S24-7 family members and other Bacteroidales spp. (XL...

Additional file 4: of Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family

Ilias Lagkouvardos (753901)
Till Lesker (5590802)
Thomas Hitch (4792731)
Eric GĂĄlvez (6381071)
Nathiana Smit (6381074)
Klaus Neuhaus (134143)
Jun Wang (5906)
John Baines (2632834)
Birte Abt (158167)
BĂ¤rbel Stecher (6381077)
JĂśrg Overmann (3919514)
Till Strowig (86289)
Thomas Clavel (374686)

February 2019

Figure S2. Extended phylogenomic tree as described in Fig.Â 4 and the corresponding methods. Accessi...

Additional file 2: of Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family

Ilias Lagkouvardos (753901)
Till Lesker (5590802)
Thomas Hitch (4792731)
Eric Gálvez (6381089)
Nathiana Smit (6381074)
Klaus Neuhaus (134143)
Jun Wang (5906)
John Baines (2632834)
Birte Abt (158167)
Bärbel Stecher (78807)
Jörg Overmann (140902)
Till Strowig (86289)
Thomas Clavel (374686)

February 2019

Figure S1. KEGG-based analysis of S24-7 functions. A heatmap of differential completeness of KEGG mo...

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...

Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family.

Lagkouvardos, Ilias
Lesker, Till R
Hitch, Thomas C A
Gálvez, Eric J C
Smit, Nathiana
Neuhaus, Klaus
Wang, Jun
Baines, John F
Abt, Birte
Stecher, Bärbel
Overmann, Jörg
Strowig, Till
Clavel, Thomas

February 2019

Bacteria within family S24-7 (phylum Bacteroidetes) are dominant in the mouse gut microbiota and det...

Additional file 3: Table S3. 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

Bacterial genes predicted to encode select symbiotic activities. Description: Table of all genes ide...

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 12: Table S5. 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

CAZy categories with significantly different abundance in âCa. Homeothermaceaeâ in comparison wi...

Additional file 3: of Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host

Zhen Zeng (238754)
Yating Fu (5772047)
Dongyang Guo (5772050)
Yuxuan Wu (382359)
Olugbenga Ajayi (5772053)
Qingfa Wu (6499)

September 2018

Clusters of orthologous genes (COG) functional classification of the Cardinium cSfur genome (gene ho...

Additional file 1: of The overlapping continuum of host range among strains in the Pseudomonas syringae complex

Cindy Morris (449679)
Jay Lamichhane (6210977)
Ivan Nikolić (6210989)
Slaviša Stanković (2822078)
Benoit Moury (3294669)

January 2019

Figure S1. Host range relative to phylogenetic context of strains of Pseudomonas syringae (upper fig...

Additional file 1: of Bacterial diversity obtained by culturable approaches in the gut of Glossina pallidipes population from a non sleeping sickness focus in Tanzania: preliminary results

Imna Malele (333829)
Hamis Nyingilili (6006071)
Eugen Lyaruu (6006074)
Marc Tauzin (6006077)
B. Bernard Ollivier (6006080)
Jean-Luc Cayol (6006083)
Marie-Laure Fardeau (6006086)
Anne Geiger (208651)

November 2018

Maximum-likelihood phylogenetic tree based on the comparative analysis of 16S rRNA gene sequences. P...

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 3: Table S2. of Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses

Daniel Penselin (3362783)
Martin Münsterkötter (13742)
Susanne Kirsten (3362777)
Marius Felder (21057)
Stefan Taudien (47210)
Matthias Platzer (11284)
Kevin Ashelford (254162)
Konrad Paskiewicz (3529364)
Richard Harrison (824846)
David Hughes (47111)
Thomas Wolf (136760)
Ekaterina Shelest (615653)
Jenny Graap (3362765)
Jan Hoffmann (323101)
Claudia Wenzel (3362756)
Nadine Wöltje (3529370)
Kevin King (70030)
Bruce Fitt (3529367)
Ulrich Güldener (13741)
Anna Avrova (3362771)
Wolfgang Knogge (3362762)

November 2016

(A) Core meiotic recombination machinery genes. (B) Genes involved in sexual reproduction in the asp...

Additional file 1: of Hybridization capture reveals microbial diversity missed using current profiling methods

Cyrielle Gasc (801732)
Pierre Peyret (241634)

March 2018

Figure S1. Schematic representation of the hybridization capture method. Figure S2. Mock community p...

Additional file 1: Table S1. of Use of multilocus sequence typing to infer genetic diversity and population structure of Lactobacillus plantarum isolates from different sources

Haiyan Xu (148626)
Wenjun Liu (162986)
Wenyi Zhang (127372)
Jie Yu (150626)
Yuqin Song (690119)
Bilige Menhe (3448532)
Heping Zhang (29038)
Zhihong Sun (401173)

October 2015

Allelic profiles of analyzed L. plantarum strains. Table S2. Bacterial isolates used in this study. ...

Additional file 1: of Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family

Ilias Lagkouvardos (753901)
Till Lesker (5590802)
Thomas Hitch (4792731)
Eric GĂĄlvez (6381071)
Nathiana Smit (6381074)
Klaus Neuhaus (134143)
Jun Wang (5906)
John Baines (2632834)
Birte Abt (158167)
BĂ¤rbel Stecher (6381077)
JĂśrg Overmann (3919514)
Till Strowig (86289)
Thomas Clavel (374686)

February 2019

Table S1. Table of all KEGG Orthologies across S24-7 family members and other Bacteroidales spp. (XL...

Additional file 4: of Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family

Ilias Lagkouvardos (753901)
Till Lesker (5590802)
Thomas Hitch (4792731)
Eric GĂĄlvez (6381071)
Nathiana Smit (6381074)
Klaus Neuhaus (134143)
Jun Wang (5906)
John Baines (2632834)
Birte Abt (158167)
BĂ¤rbel Stecher (6381077)
JĂśrg Overmann (3919514)
Till Strowig (86289)
Thomas Clavel (374686)

February 2019

Figure S2. Extended phylogenomic tree as described in Fig.Â 4 and the corresponding methods. Accessi...

Additional file 2: of Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family

Ilias Lagkouvardos (753901)
Till Lesker (5590802)
Thomas Hitch (4792731)
Eric Gálvez (6381089)
Nathiana Smit (6381074)
Klaus Neuhaus (134143)
Jun Wang (5906)
John Baines (2632834)
Birte Abt (158167)
Bärbel Stecher (78807)
Jörg Overmann (140902)
Till Strowig (86289)
Thomas Clavel (374686)

February 2019

Figure S1. KEGG-based analysis of S24-7 functions. A heatmap of differential completeness of KEGG mo...

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...

Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family.

Lagkouvardos, Ilias
Lesker, Till R
Hitch, Thomas C A
Gálvez, Eric J C
Smit, Nathiana
Neuhaus, Klaus
Wang, Jun
Baines, John F
Abt, Birte
Stecher, Bärbel
Overmann, Jörg
Strowig, Till
Clavel, Thomas

February 2019

Bacteria within family S24-7 (phylum Bacteroidetes) are dominant in the mouse gut microbiota and det...

Additional file 3: Table S3. 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

Bacterial genes predicted to encode select symbiotic activities. Description: Table of all genes ide...

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 12: Table S5. 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

CAZy categories with significantly different abundance in âCa. Homeothermaceaeâ in comparison wi...

Additional file 3: of Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host

Zhen Zeng (238754)
Yating Fu (5772047)
Dongyang Guo (5772050)
Yuxuan Wu (382359)
Olugbenga Ajayi (5772053)
Qingfa Wu (6499)

September 2018

Clusters of orthologous genes (COG) functional classification of the Cardinium cSfur genome (gene ho...

Additional file 1: of The overlapping continuum of host range among strains in the Pseudomonas syringae complex

Cindy Morris (449679)
Jay Lamichhane (6210977)
Ivan Nikolić (6210989)
Slaviša Stanković (2822078)
Benoit Moury (3294669)

January 2019

Figure S1. Host range relative to phylogenetic context of strains of Pseudomonas syringae (upper fig...

Additional file 1: of Bacterial diversity obtained by culturable approaches in the gut of Glossina pallidipes population from a non sleeping sickness focus in Tanzania: preliminary results

Imna Malele (333829)
Hamis Nyingilili (6006071)
Eugen Lyaruu (6006074)
Marc Tauzin (6006077)
B. Bernard Ollivier (6006080)
Jean-Luc Cayol (6006083)
Marie-Laure Fardeau (6006086)
Anne Geiger (208651)

November 2018

Maximum-likelihood phylogenetic tree based on the comparative analysis of 16S rRNA gene sequences. P...

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 3: Table S2. of Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses

Daniel Penselin (3362783)
Martin Münsterkötter (13742)
Susanne Kirsten (3362777)
Marius Felder (21057)
Stefan Taudien (47210)
Matthias Platzer (11284)
Kevin Ashelford (254162)
Konrad Paskiewicz (3529364)
Richard Harrison (824846)
David Hughes (47111)
Thomas Wolf (136760)
Ekaterina Shelest (615653)
Jenny Graap (3362765)
Jan Hoffmann (323101)
Claudia Wenzel (3362756)
Nadine Wöltje (3529370)
Kevin King (70030)
Bruce Fitt (3529367)
Ulrich Güldener (13741)
Anna Avrova (3362771)
Wolfgang Knogge (3362762)

November 2016

(A) Core meiotic recombination machinery genes. (B) Genes involved in sexual reproduction in the asp...

Additional file 1: of Hybridization capture reveals microbial diversity missed using current profiling methods

Cyrielle Gasc (801732)
Pierre Peyret (241634)

March 2018

Figure S1. Schematic representation of the hybridization capture method. Figure S2. Mock community p...

Additional file 1: Table S1. of Use of multilocus sequence typing to infer genetic diversity and population structure of Lactobacillus plantarum isolates from different sources

Haiyan Xu (148626)
Wenjun Liu (162986)
Wenyi Zhang (127372)
Jie Yu (150626)
Yuqin Song (690119)
Bilige Menhe (3448532)
Heping Zhang (29038)
Zhihong Sun (401173)

October 2015

Allelic profiles of analyzed L. plantarum strains. Table S2. Bacterial isolates used in this study. ...

Additional file 3: of Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family

Abstract

Extracted data

Additional file 3: of Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family

Abstract

Extracted data

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