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Additional file 2: of Knomics-Biota - a system for exploratory analysis of human gut microbiota data

Daria Efimova (5940050)
Alexander Tyakht (2131003)
Anna Popenko (2131006)
Anatoly Vasilyev (5940053)
Ilya Altukhov (3455018)
Nikita Dovidchenko (5940056)
Vera Odintsova (4519951)
Natalya Klimenko (5940059)
Robert Loshkarev (5940062)
Maria Pashkova (5940065)
Anna Elizarova (5940068)
Viktoriya Voroshilova (5940071)
Sergei Slavskii (5940074)
Yury Pekov (5940077)
Ekaterina Filippova (5940080)
Tatiana Shashkova (2145550)
Evgenii Levin (5940083)
Dmitry Alexeev (1535380)

Publication date

November 2018

DOI

10.6084/m9.figshare.7305305.v1

Abstract

Figure S2. Manually curated vitamin biosynthesis pathways used in the analysis. (PDF 1598 kb

Extracted data

Related items

Additional file 2: Table S1. of Modulation of the human gut microbiota by dietary fibres occurs at the species level

Wing Chung (3521765)
Alan Walker (3508322)
Petra Louis (526555)
Julian Parkhill (30393)
Joan Vermeiren (3521771)
Douwina Bosscher (3521768)
Sylvia Duncan (3521762)
Harry Flint (3521759)

January 2016

Proportional abundance of each operational taxonomic unit (OTU; in %) per sample (97 % OTU cut-off)....

Additional file 3: Table S2. of Modulation of the human gut microbiota by dietary fibres occurs at the species level

Wing Chung (3521765)
Alan Walker (3508322)
Petra Louis (526555)
Julian Parkhill (30393)
Joan Vermeiren (3521771)
Douwina Bosscher (3521768)
Sylvia Duncan (3521762)
Harry Flint (3521759)

January 2016

Metastats analysis of the top 38 most abundant operational taxonomic unit (OTUs; those accounting fo...

Additional file 1: of Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis

Yan He (116705)
Wei Wu (27708)
Shan Wu (67551)
Hui-Min Zheng (5784281)
Pan Li (335711)
Hua-Fang Sheng (188412)
Mu-Xuan Chen (5784284)
Zi-Hui Chen (5784287)
Gui-Yuan Ji (5784290)
Zhong-Dai-Xi Zheng (5784293)
Prabhakar Mujagond (5784296)
Xiao-Jiao Chen (3920246)
Zu-Hua Rong (5784299)
Peng Chen (6514)
Li-Yi Lyu (5784302)
Xian Wang (15374)
Jia-Bao Xu (5784305)
Chong-Bin Wu (5784308)
Nan Yu (757123)
Yan-Jun Xu (639271)
Jia Yin (287896)
Jeroen Raes (6041)
Wen-Jun Ma (3543602)
Hong-Wei Zhou (188423)

November 2018

Supplementary Data:Â containsÂ Supplementary Methods and Materials, Supplementary Results, Supplemen...

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 3: 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 S2. Circular plot with links representing the prevalence of vitamin metabolism among differen...

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 6: 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 S5. Boxplot showing total relative abundance of species with biotin biosynthesis (BIO-B) and/...

Additional file 7: 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 S1âTable S10. List of all the KEGG Orthologies (KOs) and Enzyme Commission (EC) numbers that...

Additional file 4: 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 S3. Alluvial plot showing the relationship between the kind of correlation for each vitamin t...

Additional file 5: 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 S4. Heatmap showing the presence and absence of reactions associated with gene annotations of...

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 2: of Taxonomic classification for microbiome analysis, which correlates well with the metabolite milieu of the gut

Yoshihisa Wakita (5984351)
Yumi Shimomura (5984354)
Yusuke Kitada (5984357)
Hiroyuki Yamamoto (31403)
Yoshiaki Ohashi (1775269)
Mitsuharu Matsumoto (181952)

November 2018

Principal component loading of each metabolite for metabolome first principal component (PC1). (XLSX...

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 1: Table S1. of Potential and active functions in the gut microbiota of a healthy human cohort

Alessandro Tanca (494538)
Marcello Abbondio (3706183)
Antonio Palomba (494539)
Cristina Fraumene (374294)
Valeria Manghina (3498188)
Francesco Cucca (145742)
Edoardo Fiorillo (518797)
Sergio Uzzau (186221)

July 2017

Gender, age, and BMI of the human subjects selected for the study. Table S2. Metrics of metagenome a...

Additional file 2: Table S1. of Modulation of the human gut microbiota by dietary fibres occurs at the species level

Wing Chung (3521765)
Alan Walker (3508322)
Petra Louis (526555)
Julian Parkhill (30393)
Joan Vermeiren (3521771)
Douwina Bosscher (3521768)
Sylvia Duncan (3521762)
Harry Flint (3521759)

January 2016

Proportional abundance of each operational taxonomic unit (OTU; in %) per sample (97 % OTU cut-off)....

Additional file 3: Table S2. of Modulation of the human gut microbiota by dietary fibres occurs at the species level

Wing Chung (3521765)
Alan Walker (3508322)
Petra Louis (526555)
Julian Parkhill (30393)
Joan Vermeiren (3521771)
Douwina Bosscher (3521768)
Sylvia Duncan (3521762)
Harry Flint (3521759)

January 2016

Metastats analysis of the top 38 most abundant operational taxonomic unit (OTUs; those accounting fo...

Additional file 1: of Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis

Yan He (116705)
Wei Wu (27708)
Shan Wu (67551)
Hui-Min Zheng (5784281)
Pan Li (335711)
Hua-Fang Sheng (188412)
Mu-Xuan Chen (5784284)
Zi-Hui Chen (5784287)
Gui-Yuan Ji (5784290)
Zhong-Dai-Xi Zheng (5784293)
Prabhakar Mujagond (5784296)
Xiao-Jiao Chen (3920246)
Zu-Hua Rong (5784299)
Peng Chen (6514)
Li-Yi Lyu (5784302)
Xian Wang (15374)
Jia-Bao Xu (5784305)
Chong-Bin Wu (5784308)
Nan Yu (757123)
Yan-Jun Xu (639271)
Jia Yin (287896)
Jeroen Raes (6041)
Wen-Jun Ma (3543602)
Hong-Wei Zhou (188423)

November 2018

Supplementary Data:Â containsÂ Supplementary Methods and Materials, Supplementary Results, Supplemen...

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 3: 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 S2. Circular plot with links representing the prevalence of vitamin metabolism among differen...

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 6: 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 S5. Boxplot showing total relative abundance of species with biotin biosynthesis (BIO-B) and/...

Additional file 7: 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 S1âTable S10. List of all the KEGG Orthologies (KOs) and Enzyme Commission (EC) numbers that...

Additional file 4: 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 S3. Alluvial plot showing the relationship between the kind of correlation for each vitamin t...

Additional file 5: 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 S4. Heatmap showing the presence and absence of reactions associated with gene annotations of...

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 2: of Taxonomic classification for microbiome analysis, which correlates well with the metabolite milieu of the gut

Yoshihisa Wakita (5984351)
Yumi Shimomura (5984354)
Yusuke Kitada (5984357)
Hiroyuki Yamamoto (31403)
Yoshiaki Ohashi (1775269)
Mitsuharu Matsumoto (181952)

November 2018

Principal component loading of each metabolite for metabolome first principal component (PC1). (XLSX...

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 1: Table S1. of Potential and active functions in the gut microbiota of a healthy human cohort

Alessandro Tanca (494538)
Marcello Abbondio (3706183)
Antonio Palomba (494539)
Cristina Fraumene (374294)
Valeria Manghina (3498188)
Francesco Cucca (145742)
Edoardo Fiorillo (518797)
Sergio Uzzau (186221)

July 2017

Gender, age, and BMI of the human subjects selected for the study. Table S2. Metrics of metagenome a...

Additional file 2: Table S1. of Modulation of the human gut microbiota by dietary fibres occurs at the species level

Wing Chung (3521765)
Alan Walker (3508322)
Petra Louis (526555)
Julian Parkhill (30393)
Joan Vermeiren (3521771)
Douwina Bosscher (3521768)
Sylvia Duncan (3521762)
Harry Flint (3521759)

January 2016

Proportional abundance of each operational taxonomic unit (OTU; in %) per sample (97 % OTU cut-off)....

Additional file 3: Table S2. of Modulation of the human gut microbiota by dietary fibres occurs at the species level

Wing Chung (3521765)
Alan Walker (3508322)
Petra Louis (526555)
Julian Parkhill (30393)
Joan Vermeiren (3521771)
Douwina Bosscher (3521768)
Sylvia Duncan (3521762)
Harry Flint (3521759)

January 2016

Metastats analysis of the top 38 most abundant operational taxonomic unit (OTUs; those accounting fo...

Additional file 1: of Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis

Yan He (116705)
Wei Wu (27708)
Shan Wu (67551)
Hui-Min Zheng (5784281)
Pan Li (335711)
Hua-Fang Sheng (188412)
Mu-Xuan Chen (5784284)
Zi-Hui Chen (5784287)
Gui-Yuan Ji (5784290)
Zhong-Dai-Xi Zheng (5784293)
Prabhakar Mujagond (5784296)
Xiao-Jiao Chen (3920246)
Zu-Hua Rong (5784299)
Peng Chen (6514)
Li-Yi Lyu (5784302)
Xian Wang (15374)
Jia-Bao Xu (5784305)
Chong-Bin Wu (5784308)
Nan Yu (757123)
Yan-Jun Xu (639271)
Jia Yin (287896)
Jeroen Raes (6041)
Wen-Jun Ma (3543602)
Hong-Wei Zhou (188423)

November 2018

Supplementary Data:Â containsÂ Supplementary Methods and Materials, Supplementary Results, Supplemen...