Additional file 2: Table S1. of Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

Additional file 6: of Gut microbes contribute to variation in solid organ transplant outcomes in mice

Christine McIntosh (5280299)
Luqiu Chen (5280302)
Alon Shaiber (4004600)
A. Eren (3420008)
Maria-Luisa Alegre (367356)

May 2018

Fecal microbiota ASVs in Jax and Tac mice before and after cohousing. Tables providing percent relat...

Additional file 2: Table S2. of A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses

Thomas Weinmaier (124598)
Alexander Probst (3407996)
Myron Duc (3561614)
Doina Ciobanu (2648437)
Jan-Fang Cheng (48619)
Natalia Ivanova (8850)
Thomas Rattei (13991)
Parag Vaishampayan (783948)

December 2015

An Excel table comparing taxonomic annotations to Mahnert et al. [26]. (XLSX 56 kb

Additional file 7: of Gut microbes contribute to variation in solid organ transplant outcomes in mice

Christine McIntosh (5280299)
Luqiu Chen (5280302)
Alon Shaiber (4004600)
A. Eren (3420008)
Maria-Luisa Alegre (367356)

May 2018

Fecal microbiota ASVs in Jax and Tac mice before and after FMT. Tables providing percent relative ab...

Additional file 3: Figure S1. of Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

Sonny Lee (4004606)
Stacy Kahn (4004612)
Tom Delmont (4004609)
Alon Shaiber (4004600)
Ăzcan Esen (4004603)
Nathaniel Hubert (4004594)
Hilary Morrison (4004597)
Dionysios Antonopoulos (180809)
David Rubin (2741101)
A. Eren (3420008)

May 2017

The distribution of all 444 donor bins across samples. Yellow markings represent the 92 MAGs. (PNG 7...

Additional file 1: of Mining, analyzing, and integrating viral signals from metagenomic data

Tingting Zheng (400620)
Jun Li (6494)
Yueqiong Ni (691206)
Kang Kang (120256)
Maria-Anna Misiakou (6486560)
Lejla Imamovic (180270)
Billy Chow (6486563)
Anne Rode (6486566)
Peter Bytzer (5752637)
Morten Sommer (3453896)
Gianni Panagiotou (87405)

March 2019

Table S1. Sample information of human gut microbial metagenomic data and matched phageomes used in t...

Additional file 1: of Changes in microbiota composition, bile and fatty acid metabolism, in successful faecal microbiota transplantation for Clostridioides difficile infection

Jillian Brown (3028008)
Burkhardt Flemer (503386)
Susan Joyce (5696426)
Akbar Zulquernain (5696429)
Donal Sheehan (5696432)
Fergus Shanahan (297960)
Paul OâToole (3461318)

August 2018

Table S1. Primer sequences used in this study. Table S2. Bile acids identified by UPLC-MS analysis. ...

Additional file 1:Table S1. of Towards microbiome transplant as a therapy for periodontitis: an exploratory study of periodontitis microbial signature contrasted by oral health, caries and edentulism

Alex Pozhitkov (17008)
Brian Leroux (3537572)
Timothy Randolph (3537569)
Thomas Beikler (478796)
Thomas Flemmig (3537578)
Peter Noble (3537575)

October 2015

Number of sequences obtained from each condition and sample. Table S2. Comparison of oral microbial ...

Additional file 1: of Long-term colonisation with donor bacteriophages following successful faecal microbial transplantation

L. Draper (6067163)
F. Ryan (6067166)
M. Smith (4798743)
J. Jalanka (6067169)
E. Mattila (6067172)
P. Arkkila (6067175)
R. Ross (3461291)
R. Satokari (6067178)
C. Hill (667956)

December 2018

Table S1. Metadata and sample timeline for donors and recipients. Donor and patient demographics are...

Additional file 3: of Changes in microbiota composition, bile and fatty acid metabolism, in successful faecal microbiota transplantation for Clostridioides difficile infection

Jillian Brown (3028008)
Burkhardt Flemer (503386)
Susan Joyce (5696426)
Akbar Zulquernain (5696429)
Donal Sheehan (5696432)
Fergus Shanahan (297960)
Paul OâToole (3461318)

August 2018

Table S7. Genes associated with archaeal metabolism obtained from shotgun metagenomic sequencing (XL...

Additional file 2: Table S1. of Extending colonic mucosal microbiome analysisâassessment of colonic lavage as a proxy for endoscopic colonic biopsies

Euan Watt (3444731)
Matthew Gemmell (3444737)
Susan Berry (653826)
Mark Glaire (3444728)
Freda Farquharson (3299991)
Petra Louis (526555)
Graeme Murray (368267)
Emad El-Omar (229332)
Georgina Hold (3444734)

November 2016

Sequencing depth of colonic lavage and biopsy samples from study cohort. (DOC 76 kb

Additional file 2: of Reproducible protocols for metagenomic analysis of human faecal phageomes

Andrey N. Shkoporov (5078096)
Feargal J. Ryan (5078093)
Lorraine A. Draper (270459)
Amanda Forde (5078099)
Stephen R. Stockdale (766129)
Karen M. Daly (270469)
Siobhan A. McDonnell (5078084)
James A. Nolan (5078090)
Thomas D.S. Sutton (5078087)
Marion Dalmasso (187925)
Angela McCann (404345)
R. Paul Ross (152753)
Colin Hill (73239)

April 2018

Table S2. Description of faecal samples used in the study and summary of nucleic acid extraction and...

Additional file 1: of Genomic and metagenomic insights into the microbial community of a thermal spring

Renato Pedron (6258248)
Alfonso Esposito (3322911)
Irene Bianconi (108469)
Edoardo Pasolli (3155043)
Adrian Tett (642012)
Francesco Asnicar (5198411)
Mario Cristofolini (6258251)
Nicola Segata (103809)
Olivier Jousson (281189)

January 2019

Table S1. Assembly statistics and taxonomy for each genome sequenced. (XLSX 18Â kb

Additional file 2: of Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative

Jun Wang (5906)
Alexander Kurilshikov (503648)
Djawad Radjabzadeh (5350877)
Williams Turpin (320798)
Kenneth Croitoru (494127)
Marc Bonder (3404252)
Matthew Jackson (2553886)
Carolina Medina-Gomez (152852)
Fabian Frost (5350874)
Georg Homuth (110202)
Malte RĂźhlemann (5350868)
David Hughes (47111)
Han-na Kim (5350871)
Tim Spector (153290)
Jordana Bell (667256)
Claire Steves (5144204)
Nicolas Timpson (5350880)
Andre Franke (77511)
Cisca Wijmenga (32954)
Katie Meyer (3744941)
Tim Kacprowski (793348)
Lude Franke (102406)
Andrew Paterson (267459)
Jeroen Raes (6041)
Robert Kraaij (418732)
Alexandra Zhernakova (102388)

June 2018

Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative Ack...

Additional file 1: of Design and application of a novel two-amplicon approach for defining eukaryotic microbiota

Ana Popovic (1881349)
Celine Bourdon (2741548)
Pauline Wang (3567824)
David Guttman (3524483)
Wieger Voskuijl (2741554)
Michael Grigg (437179)
Robert Bandsma (2741539)
John Parkinson (4087)

December 2018

Table S1. Accuracy of taxonomic assignments of 18S and 28S rRNA variable genetic regions. Related to...

Additional file 2: of Metagenomic and metatranscriptomic analysis of human prostate microbiota from patients with prostate cancer

Ye Feng (196094)
Varune Ramnarine (6374825)
Robert Bell (5218055)
Stanislav Volik (44573)
Elai Davicioni (425648)
Vanessa Hayes (5305292)
Shancheng Ren (121352)
Colin Collins (44574)

February 2019

The number of raw and normalized reads for each taxonomic unit for both metagenome and metatranscrip...

Additional file 6: of Gut microbes contribute to variation in solid organ transplant outcomes in mice

Christine McIntosh (5280299)
Luqiu Chen (5280302)
Alon Shaiber (4004600)
A. Eren (3420008)
Maria-Luisa Alegre (367356)

May 2018

Fecal microbiota ASVs in Jax and Tac mice before and after cohousing. Tables providing percent relat...

Additional file 2: Table S2. of A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses

Thomas Weinmaier (124598)
Alexander Probst (3407996)
Myron Duc (3561614)
Doina Ciobanu (2648437)
Jan-Fang Cheng (48619)
Natalia Ivanova (8850)
Thomas Rattei (13991)
Parag Vaishampayan (783948)

December 2015

An Excel table comparing taxonomic annotations to Mahnert et al. [26]. (XLSX 56 kb

Additional file 7: of Gut microbes contribute to variation in solid organ transplant outcomes in mice

Christine McIntosh (5280299)
Luqiu Chen (5280302)
Alon Shaiber (4004600)
A. Eren (3420008)
Maria-Luisa Alegre (367356)

May 2018

Fecal microbiota ASVs in Jax and Tac mice before and after FMT. Tables providing percent relative ab...

Additional file 3: Figure S1. of Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

Sonny Lee (4004606)
Stacy Kahn (4004612)
Tom Delmont (4004609)
Alon Shaiber (4004600)
Ăzcan Esen (4004603)
Nathaniel Hubert (4004594)
Hilary Morrison (4004597)
Dionysios Antonopoulos (180809)
David Rubin (2741101)
A. Eren (3420008)

May 2017

The distribution of all 444 donor bins across samples. Yellow markings represent the 92 MAGs. (PNG 7...

Additional file 1: of Mining, analyzing, and integrating viral signals from metagenomic data

Tingting Zheng (400620)
Jun Li (6494)
Yueqiong Ni (691206)
Kang Kang (120256)
Maria-Anna Misiakou (6486560)
Lejla Imamovic (180270)
Billy Chow (6486563)
Anne Rode (6486566)
Peter Bytzer (5752637)
Morten Sommer (3453896)
Gianni Panagiotou (87405)

March 2019

Table S1. Sample information of human gut microbial metagenomic data and matched phageomes used in t...

Additional file 1: of Changes in microbiota composition, bile and fatty acid metabolism, in successful faecal microbiota transplantation for Clostridioides difficile infection

Jillian Brown (3028008)
Burkhardt Flemer (503386)
Susan Joyce (5696426)
Akbar Zulquernain (5696429)
Donal Sheehan (5696432)
Fergus Shanahan (297960)
Paul OâToole (3461318)

August 2018

Table S1. Primer sequences used in this study. Table S2. Bile acids identified by UPLC-MS analysis. ...

Additional file 1:Table S1. of Towards microbiome transplant as a therapy for periodontitis: an exploratory study of periodontitis microbial signature contrasted by oral health, caries and edentulism

Alex Pozhitkov (17008)
Brian Leroux (3537572)
Timothy Randolph (3537569)
Thomas Beikler (478796)
Thomas Flemmig (3537578)
Peter Noble (3537575)

October 2015

Number of sequences obtained from each condition and sample. Table S2. Comparison of oral microbial ...

Additional file 1: of Long-term colonisation with donor bacteriophages following successful faecal microbial transplantation

L. Draper (6067163)
F. Ryan (6067166)
M. Smith (4798743)
J. Jalanka (6067169)
E. Mattila (6067172)
P. Arkkila (6067175)
R. Ross (3461291)
R. Satokari (6067178)
C. Hill (667956)

December 2018

Table S1. Metadata and sample timeline for donors and recipients. Donor and patient demographics are...

Additional file 3: of Changes in microbiota composition, bile and fatty acid metabolism, in successful faecal microbiota transplantation for Clostridioides difficile infection

Jillian Brown (3028008)
Burkhardt Flemer (503386)
Susan Joyce (5696426)
Akbar Zulquernain (5696429)
Donal Sheehan (5696432)
Fergus Shanahan (297960)
Paul OâToole (3461318)

August 2018

Table S7. Genes associated with archaeal metabolism obtained from shotgun metagenomic sequencing (XL...

Additional file 2: Table S1. of Extending colonic mucosal microbiome analysisâassessment of colonic lavage as a proxy for endoscopic colonic biopsies

Euan Watt (3444731)
Matthew Gemmell (3444737)
Susan Berry (653826)
Mark Glaire (3444728)
Freda Farquharson (3299991)
Petra Louis (526555)
Graeme Murray (368267)
Emad El-Omar (229332)
Georgina Hold (3444734)

November 2016

Sequencing depth of colonic lavage and biopsy samples from study cohort. (DOC 76 kb

Additional file 2: of Reproducible protocols for metagenomic analysis of human faecal phageomes

Andrey N. Shkoporov (5078096)
Feargal J. Ryan (5078093)
Lorraine A. Draper (270459)
Amanda Forde (5078099)
Stephen R. Stockdale (766129)
Karen M. Daly (270469)
Siobhan A. McDonnell (5078084)
James A. Nolan (5078090)
Thomas D.S. Sutton (5078087)
Marion Dalmasso (187925)
Angela McCann (404345)
R. Paul Ross (152753)
Colin Hill (73239)

April 2018

Table S2. Description of faecal samples used in the study and summary of nucleic acid extraction and...

Additional file 1: of Genomic and metagenomic insights into the microbial community of a thermal spring

Renato Pedron (6258248)
Alfonso Esposito (3322911)
Irene Bianconi (108469)
Edoardo Pasolli (3155043)
Adrian Tett (642012)
Francesco Asnicar (5198411)
Mario Cristofolini (6258251)
Nicola Segata (103809)
Olivier Jousson (281189)

January 2019

Table S1. Assembly statistics and taxonomy for each genome sequenced. (XLSX 18Â kb

Additional file 2: of Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative

Jun Wang (5906)
Alexander Kurilshikov (503648)
Djawad Radjabzadeh (5350877)
Williams Turpin (320798)
Kenneth Croitoru (494127)
Marc Bonder (3404252)
Matthew Jackson (2553886)
Carolina Medina-Gomez (152852)
Fabian Frost (5350874)
Georg Homuth (110202)
Malte RĂźhlemann (5350868)
David Hughes (47111)
Han-na Kim (5350871)
Tim Spector (153290)
Jordana Bell (667256)
Claire Steves (5144204)
Nicolas Timpson (5350880)
Andre Franke (77511)
Cisca Wijmenga (32954)
Katie Meyer (3744941)
Tim Kacprowski (793348)
Lude Franke (102406)
Andrew Paterson (267459)
Jeroen Raes (6041)
Robert Kraaij (418732)
Alexandra Zhernakova (102388)

June 2018

Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative Ack...

Additional file 1: of Design and application of a novel two-amplicon approach for defining eukaryotic microbiota

Ana Popovic (1881349)
Celine Bourdon (2741548)
Pauline Wang (3567824)
David Guttman (3524483)
Wieger Voskuijl (2741554)
Michael Grigg (437179)
Robert Bandsma (2741539)
John Parkinson (4087)

December 2018

Table S1. Accuracy of taxonomic assignments of 18S and 28S rRNA variable genetic regions. Related to...

Additional file 2: of Metagenomic and metatranscriptomic analysis of human prostate microbiota from patients with prostate cancer

Ye Feng (196094)
Varune Ramnarine (6374825)
Robert Bell (5218055)
Stanislav Volik (44573)
Elai Davicioni (425648)
Vanessa Hayes (5305292)
Shancheng Ren (121352)
Colin Collins (44574)

February 2019

The number of raw and normalized reads for each taxonomic unit for both metagenome and metatranscrip...

Additional file 6: of Gut microbes contribute to variation in solid organ transplant outcomes in mice

Christine McIntosh (5280299)
Luqiu Chen (5280302)
Alon Shaiber (4004600)
A. Eren (3420008)
Maria-Luisa Alegre (367356)

May 2018

Fecal microbiota ASVs in Jax and Tac mice before and after cohousing. Tables providing percent relat...

Additional file 2: Table S2. of A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses

Thomas Weinmaier (124598)
Alexander Probst (3407996)
Myron Duc (3561614)
Doina Ciobanu (2648437)
Jan-Fang Cheng (48619)
Natalia Ivanova (8850)
Thomas Rattei (13991)
Parag Vaishampayan (783948)

December 2015

An Excel table comparing taxonomic annotations to Mahnert et al. [26]. (XLSX 56 kb

Additional file 7: of Gut microbes contribute to variation in solid organ transplant outcomes in mice

Christine McIntosh (5280299)
Luqiu Chen (5280302)
Alon Shaiber (4004600)
A. Eren (3420008)
Maria-Luisa Alegre (367356)

May 2018

Fecal microbiota ASVs in Jax and Tac mice before and after FMT. Tables providing percent relative ab...

Additional file 2: Table S1. of Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

Abstract

Extracted data

Additional file 2: Table S1. of Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

Abstract

Extracted data

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