Additional file 2: Table S1. of Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses

Additional file 2: Table S1A. of Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns

Francesca De Filippis (437252)
Nicoletta Pellegrini (826113)
Luca Laghi (654884)
Marco Gobbetti (468669)
Danilo Ercolini (437255)

October 2016

Prevotella oligotypes representative sequences and BLASTn top hit. Table S1B. Bacteroides oligotypes...

Additional file 13: of Uncovering complex microbiome activities via metatranscriptomics during 24âhours of oral biofilm assembly and maturation

Anna Edlund (178072)
Youngik Yang (3155094)
Shibu Yooseph (38227)
Xuesong He (292081)
Wenyuan Shi (180327)
Jeffrey McLean (6059507)

December 2018

Table S11. Ratio estimates of metatranscriptome (MT) and metagenome (MG) read mapping results for in...

Additional file 2: Table S1. of Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism

Elias Broman (3336183)
Johanna SjĂśstedt (4346059)
Jarone Pinhassi (249839)
Mark Dopson (481575)

August 2017

A full list of reads for the various sequencing programs including before and after merging reads, q...

Additional file 1: Figure S1. of Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses

Deepak Kumaresan (4728573)
Jason Stephenson (4728579)
Andrew Doxey (3401237)
Hina Bandukwala (4728570)
Elliot Brooks (4728567)
Alexandra Hillebrand-Voiculescu (3285864)
Andrew Whiteley (3579434)
J Colin Murrell (4728576)

January 2018

Microbial mat floating in the lake room (A) and air bell 2 (B; seen from below). (TIFF 4369Â kb

Additional file 1: Table S1. of Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle

Surajit De Mandal (3920090)
Raghunath Chatterjee (90538)
Nachimuthu Kumar (3512213)

April 2017

List of the genes codes for enzymes involved in carbohydrate degradation identified using PICRUSt. T...

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 Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination

E. Gonzalez (4991489)
F. Pitre (4991495)
A. PagĂŠ (4991522)
J. Marleau (4991507)
W. Guidi Nissim (4991504)
M. St-Arnaud (4991501)
M. Labrecque (4991498)
S. Joly (4991510)
E. Yergeau (4991516)
N. Brereton (4991513)

March 2018

Unknown sequence challenge, upregulated DE Basidiomycota blastn and additional transcriptomic method...

Additional file 1: of Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome

Promi Das (5043527)
Parizad Babaei (6457256)
Jens Nielsen (10549)

March 2019

Table S1. Statistical information on comparison of vitamin gene abundances between different countri...

Additional file 1: of Rock substrate rather than black stain alterations drives microbial community structure in the passage of Lascaux Cave

Lise Alonso (6056708)
Charline Creuzé-des-Châtelliers (6056711)
Théo Trabac (6056714)
Audrey Dubost (697898)
Yvan Moënne-Loccoz (3244134)
Thomas Pommier (158571)

December 2018

Figure S2. Bacterial and micro-eukaryotic abundances according to time (along with mean temperature ...

Additional file 2: of Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome

Promi Das (5043527)
Parizad Babaei (6457256)
Jens Nielsen (10549)

March 2019

Figure S1. Circular plot with links representing the prevalence of vitamin metabolism among differen...

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 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 2: of Profiling microbial strains in urban environments using metagenomic sequencing data

Moreno Zolfo (4176529)
Francesco Asnicar (5198411)
Paolo Manghi (5198408)
Edoardo Pasolli (3155043)
Adrian Tett (642012)
Nicola Segata (103809)

May 2018

Table S1. MetaPhlAn2 output table on the whole MetaSub dataset. Values represent the relative abunda...

Additional file 2: Table 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

Additional information for samples, metagenomic bins, and metagenome-assembled genomes in our study....

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 2: Table S1A. of Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns

Francesca De Filippis (437252)
Nicoletta Pellegrini (826113)
Luca Laghi (654884)
Marco Gobbetti (468669)
Danilo Ercolini (437255)

October 2016

Prevotella oligotypes representative sequences and BLASTn top hit. Table S1B. Bacteroides oligotypes...

Additional file 13: of Uncovering complex microbiome activities via metatranscriptomics during 24âhours of oral biofilm assembly and maturation

Anna Edlund (178072)
Youngik Yang (3155094)
Shibu Yooseph (38227)
Xuesong He (292081)
Wenyuan Shi (180327)
Jeffrey McLean (6059507)

December 2018

Table S11. Ratio estimates of metatranscriptome (MT) and metagenome (MG) read mapping results for in...

Additional file 2: Table S1. of Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism

Elias Broman (3336183)
Johanna SjĂśstedt (4346059)
Jarone Pinhassi (249839)
Mark Dopson (481575)

August 2017

A full list of reads for the various sequencing programs including before and after merging reads, q...

Additional file 1: Figure S1. of Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses

Deepak Kumaresan (4728573)
Jason Stephenson (4728579)
Andrew Doxey (3401237)
Hina Bandukwala (4728570)
Elliot Brooks (4728567)
Alexandra Hillebrand-Voiculescu (3285864)
Andrew Whiteley (3579434)
J Colin Murrell (4728576)

January 2018

Microbial mat floating in the lake room (A) and air bell 2 (B; seen from below). (TIFF 4369Â kb

Additional file 1: Table S1. of Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle

Surajit De Mandal (3920090)
Raghunath Chatterjee (90538)
Nachimuthu Kumar (3512213)

April 2017

List of the genes codes for enzymes involved in carbohydrate degradation identified using PICRUSt. T...

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 Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination

E. Gonzalez (4991489)
F. Pitre (4991495)
A. PagĂŠ (4991522)
J. Marleau (4991507)
W. Guidi Nissim (4991504)
M. St-Arnaud (4991501)
M. Labrecque (4991498)
S. Joly (4991510)
E. Yergeau (4991516)
N. Brereton (4991513)

March 2018

Unknown sequence challenge, upregulated DE Basidiomycota blastn and additional transcriptomic method...

Additional file 1: of Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome

Promi Das (5043527)
Parizad Babaei (6457256)
Jens Nielsen (10549)

March 2019

Table S1. Statistical information on comparison of vitamin gene abundances between different countri...

Additional file 1: of Rock substrate rather than black stain alterations drives microbial community structure in the passage of Lascaux Cave

Lise Alonso (6056708)
Charline Creuzé-des-Châtelliers (6056711)
Théo Trabac (6056714)
Audrey Dubost (697898)
Yvan Moënne-Loccoz (3244134)
Thomas Pommier (158571)

December 2018

Figure S2. Bacterial and micro-eukaryotic abundances according to time (along with mean temperature ...

Additional file 2: of Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome

Promi Das (5043527)
Parizad Babaei (6457256)
Jens Nielsen (10549)

March 2019

Figure S1. Circular plot with links representing the prevalence of vitamin metabolism among differen...

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 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 2: of Profiling microbial strains in urban environments using metagenomic sequencing data

Moreno Zolfo (4176529)
Francesco Asnicar (5198411)
Paolo Manghi (5198408)
Edoardo Pasolli (3155043)
Adrian Tett (642012)
Nicola Segata (103809)

May 2018

Table S1. MetaPhlAn2 output table on the whole MetaSub dataset. Values represent the relative abunda...

Additional file 2: Table 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

Additional information for samples, metagenomic bins, and metagenome-assembled genomes in our study....

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 2: Table S1A. of Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns

Francesca De Filippis (437252)
Nicoletta Pellegrini (826113)
Luca Laghi (654884)
Marco Gobbetti (468669)
Danilo Ercolini (437255)

October 2016

Prevotella oligotypes representative sequences and BLASTn top hit. Table S1B. Bacteroides oligotypes...

Additional file 13: of Uncovering complex microbiome activities via metatranscriptomics during 24âhours of oral biofilm assembly and maturation

Anna Edlund (178072)
Youngik Yang (3155094)
Shibu Yooseph (38227)
Xuesong He (292081)
Wenyuan Shi (180327)
Jeffrey McLean (6059507)

December 2018

Table S11. Ratio estimates of metatranscriptome (MT) and metagenome (MG) read mapping results for in...

Additional file 2: Table S1. of Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism

Elias Broman (3336183)
Johanna SjĂśstedt (4346059)
Jarone Pinhassi (249839)
Mark Dopson (481575)

August 2017

A full list of reads for the various sequencing programs including before and after merging reads, q...

Additional file 2: Table S1. of Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses

Abstract

Extracted data

Additional file 2: Table S1. of Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses

Abstract

Extracted data

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