Additional file 16: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Additional file 1: of Host genetic variation impacts microbiome composition across human body sites

Ran Blekhman (87226)
Julia Goodrich (3454907)
Katherine Huang (66477)
Qi Sun (127)
Robert Bukowski (424557)
Jordana Bell (667256)
Timothy Spector (348486)
Alon Keinan (153034)
Ruth Ley (3454904)
Dirk Gevers (50883)
Andrew Clark (377028)

September 2015

This is a PDF document containing Supplementary Figures S1 through S19. (PDF 12238 kb

Additional file 5: Table S4. of A diet change from dry food to beef induces reversible changes on the faecal microbiota in healthy, adult client-owned dogs

Kristin Herstad (4054888)
Karina Gajardo (1614955)
Anne Bakke (4054885)
Lars Moe (279381)
Jane Ludvigsen (4054882)
Knut Rudi (74721)
Ida Rud (533224)
Monika Sekelja (3703276)
Ellen Skancke (3429347)

May 2017

Relative abundance of genera in the different diet periods. (L6 table generated with QIIME). (XLSX 4...

Additional file 2: of Dietary probiotics have different effects on the composition of fecal microbiota in farmed raccoon dog (Nyctereutes procyonoides) and silver fox (Vulpes vulpes fulva)

Yongjia Peng (6738020)
Qiumei Shi (6738023)
Yujie Wang (308942)
Fan Zhang (46132)
Zhixin Ji (733291)
Jin Zhang (53297)

May 2019

Table S2. The alpha diversity indices of fecal microbiota of animals subjected to probiotic treatmen...

Additional file 6: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Coelho (5119181)
Jens Kultima (5119178)
Paul Costea (5119172)
Coralie Fournier (5119166)
Yuanlong Pan (447697)
Gail Czarnecki-Maulden (5119175)
Matthew Hayward (2174484)
Sofia Forslund (5119169)
Thomas Schmidt (168952)
Patrick Descombes (16839)
Janet Jackson (849342)
Qinghong Li (5003339)
Peer Bork (438)

April 2018

Table S6. Nutritional content of the 3 diets used in this study. Values shown refer to percentage (%...

Additional file 7: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Coelho (5119181)
Jens Kultima (5119178)
Paul Costea (5119172)
Coralie Fournier (5119166)
Yuanlong Pan (447697)
Gail Czarnecki-Maulden (5119175)
Matthew Hayward (2174484)
Sofia Forslund (5119169)
Thomas Schmidt (168952)
Patrick Descombes (16839)
Janet Jackson (849342)
Qinghong Li (5003339)
Peer Bork (438)

April 2018

Figure S1. Gene accumulation curve for dog, pig, mouse, and human gut microbiomes. (PDF 1676Â kb

Additional file 8: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Coelho (5119181)
Jens Kultima (5119178)
Paul Costea (5119172)
Coralie Fournier (5119166)
Yuanlong Pan (447697)
Gail Czarnecki-Maulden (5119175)
Matthew Hayward (2174484)
Sofia Forslund (5119169)
Thomas Schmidt (168952)
Patrick Descombes (16839)
Janet Jackson (849342)
Qinghong Li (5003339)
Peer Bork (438)

April 2018

Figure S2. (a) Distance between samples from multiple hosts (and from two separate human cohorts as ...

Additional file 14: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Coelho (5119181)
Jens Kultima (5119178)
Paul Costea (5119172)
Coralie Fournier (5119166)
Yuanlong Pan (447697)
Gail Czarnecki-Maulden (5119175)
Matthew Hayward (2174484)
Sofia Forslund (5119169)
Thomas Schmidt (168952)
Patrick Descombes (16839)
Janet Jackson (849342)
Qinghong Li (5003339)
Peer Bork (438)

April 2018

Figure S8. (a) Firmicutes:Bacteroidetes ratio at the end of the Base feeding period (no significant ...

Additional file 9: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Coelho (5119181)
Jens Kultima (5119178)
Paul Costea (5119172)
Coralie Fournier (5119166)
Yuanlong Pan (447697)
Gail Czarnecki-Maulden (5119175)
Matthew Hayward (2174484)
Sofia Forslund (5119169)
Thomas Schmidt (168952)
Patrick Descombes (16839)
Janet Jackson (849342)
Qinghong Li (5003339)
Peer Bork (438)

April 2018

Figure S3. Mapping rates of human reads to the gut gene catalogs of the four mammalian hosts conside...

Additional file 2: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Coelho (5119181)
Jens Kultima (5119178)
Paul Costea (5119172)
Coralie Fournier (5119166)
Yuanlong Pan (447697)
Gail Czarnecki-Maulden (5119175)
Matthew Hayward (2174484)
Sofia Forslund (5119169)
Thomas Schmidt (168952)
Patrick Descombes (16839)
Janet Jackson (849342)
Qinghong Li (5003339)
Peer Bork (438)

April 2018

Table S2. Basic statistics of the metagenomics data: number of base pairs and reads per sample. (XLS...

Additional file 12: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Coelho (5119181)
Jens Kultima (5119178)
Paul Costea (5119172)
Coralie Fournier (5119166)
Yuanlong Pan (447697)
Gail Czarnecki-Maulden (5119175)
Matthew Hayward (2174484)
Sofia Forslund (5119169)
Thomas Schmidt (168952)
Patrick Descombes (16839)
Janet Jackson (849342)
Qinghong Li (5003339)
Peer Bork (438)

April 2018

Figure S6. Distance boxplots of the samples in the 3 diets using Bray-Curtis divergence on log-norma...

Additional file 5: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Coelho (5119181)
Jens Kultima (5119178)
Paul Costea (5119172)
Coralie Fournier (5119166)
Yuanlong Pan (447697)
Gail Czarnecki-Maulden (5119175)
Matthew Hayward (2174484)
Sofia Forslund (5119169)
Thomas Schmidt (168952)
Patrick Descombes (16839)
Janet Jackson (849342)
Qinghong Li (5003339)
Peer Bork (438)

April 2018

Table S5. Spearman correlation and SparCC-derived p value for all nodes in the co-abundance correlat...

Dog gut gene catalog. Supplemental data for "Similarity of the dog and human gut microbiomes in gene content and response to diet"

Coelho, Luis Pedro
Kultima, Jens Roat
Costea, Paul Igor
Fournier, Coralie
Pan, Yuanlong
Czarnecki-Maulden, Gail
Hayward, Matthew Robert
Forslund, Sofia K.
Schmidt, Thomas Sebastian Benedikt
Descombes, Patrick
Jackson, Janet R
Li, Qinghong
Bork, Peer

April 2018

Gene catalogue for the dog gut microbiome including FASTA file of nucleotide sequences (including...

Additional file 13: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Coelho (5119181)
Jens Kultima (5119178)
Paul Costea (5119172)
Coralie Fournier (5119166)
Yuanlong Pan (447697)
Gail Czarnecki-Maulden (5119175)
Matthew Hayward (2174484)
Sofia Forslund (5119169)
Thomas Schmidt (168952)
Patrick Descombes (16839)
Janet Jackson (849342)
Qinghong Li (5003339)
Peer Bork (438)

April 2018

Figure S7. (a) left: Principal coordinate analysis using weighted Unifrac distance [37]; right: corr...

Coelho, L.P.
Kultima, J.R.
Costea, P.I.
Fournier, C.
Pan, Y.
Czarnecki-Maulden, G.
Hayward, M.R.
Forslund, S.K.
Schmidt, T.S.B.
Descombes, P.
Jackson, J.R.
Li, Q.
Bork, P.

April 2018

Background: Gut microbes influence their hosts in many ways, in particular by modulating the impact ...

Additional file 2 of Comparison of 16S and whole genome dog microbiomes using machine learning

Scott Lewis (646389)
Andrea Nash (4616053)
Qinghong Li (5003339)
Tae-Hyuk Ahn (11310361)

August 2021

Additional file 2: Supplemental Figure S1: A. The increased detection rate in WGS data compared to 1...

Additional file 1: of Host genetic variation impacts microbiome composition across human body sites

Ran Blekhman (87226)
Julia Goodrich (3454907)
Katherine Huang (66477)
Qi Sun (127)
Robert Bukowski (424557)
Jordana Bell (667256)
Timothy Spector (348486)
Alon Keinan (153034)
Ruth Ley (3454904)
Dirk Gevers (50883)
Andrew Clark (377028)

September 2015

This is a PDF document containing Supplementary Figures S1 through S19. (PDF 12238 kb

Additional file 5: Table S4. of A diet change from dry food to beef induces reversible changes on the faecal microbiota in healthy, adult client-owned dogs

Kristin Herstad (4054888)
Karina Gajardo (1614955)
Anne Bakke (4054885)
Lars Moe (279381)
Jane Ludvigsen (4054882)
Knut Rudi (74721)
Ida Rud (533224)
Monika Sekelja (3703276)
Ellen Skancke (3429347)

May 2017

Relative abundance of genera in the different diet periods. (L6 table generated with QIIME). (XLSX 4...

Additional file 2: of Dietary probiotics have different effects on the composition of fecal microbiota in farmed raccoon dog (Nyctereutes procyonoides) and silver fox (Vulpes vulpes fulva)

Yongjia Peng (6738020)
Qiumei Shi (6738023)
Yujie Wang (308942)
Fan Zhang (46132)
Zhixin Ji (733291)
Jin Zhang (53297)

May 2019

Table S2. The alpha diversity indices of fecal microbiota of animals subjected to probiotic treatmen...

Additional file 6: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Coelho (5119181)
Jens Kultima (5119178)
Paul Costea (5119172)
Coralie Fournier (5119166)
Yuanlong Pan (447697)
Gail Czarnecki-Maulden (5119175)
Matthew Hayward (2174484)
Sofia Forslund (5119169)
Thomas Schmidt (168952)
Patrick Descombes (16839)
Janet Jackson (849342)
Qinghong Li (5003339)
Peer Bork (438)

April 2018

Table S6. Nutritional content of the 3 diets used in this study. Values shown refer to percentage (%...

Additional file 7: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Coelho (5119181)
Jens Kultima (5119178)
Paul Costea (5119172)
Coralie Fournier (5119166)
Yuanlong Pan (447697)
Gail Czarnecki-Maulden (5119175)
Matthew Hayward (2174484)
Sofia Forslund (5119169)
Thomas Schmidt (168952)
Patrick Descombes (16839)
Janet Jackson (849342)
Qinghong Li (5003339)
Peer Bork (438)

April 2018

Figure S1. Gene accumulation curve for dog, pig, mouse, and human gut microbiomes. (PDF 1676Â kb

Additional file 8: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Coelho (5119181)
Jens Kultima (5119178)
Paul Costea (5119172)
Coralie Fournier (5119166)
Yuanlong Pan (447697)
Gail Czarnecki-Maulden (5119175)
Matthew Hayward (2174484)
Sofia Forslund (5119169)
Thomas Schmidt (168952)
Patrick Descombes (16839)
Janet Jackson (849342)
Qinghong Li (5003339)
Peer Bork (438)

April 2018

Figure S2. (a) Distance between samples from multiple hosts (and from two separate human cohorts as ...

Additional file 14: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Coelho (5119181)
Jens Kultima (5119178)
Paul Costea (5119172)
Coralie Fournier (5119166)
Yuanlong Pan (447697)
Gail Czarnecki-Maulden (5119175)
Matthew Hayward (2174484)
Sofia Forslund (5119169)
Thomas Schmidt (168952)
Patrick Descombes (16839)
Janet Jackson (849342)
Qinghong Li (5003339)
Peer Bork (438)

April 2018

Figure S8. (a) Firmicutes:Bacteroidetes ratio at the end of the Base feeding period (no significant ...

Additional file 9: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Coelho (5119181)
Jens Kultima (5119178)
Paul Costea (5119172)
Coralie Fournier (5119166)
Yuanlong Pan (447697)
Gail Czarnecki-Maulden (5119175)
Matthew Hayward (2174484)
Sofia Forslund (5119169)
Thomas Schmidt (168952)
Patrick Descombes (16839)
Janet Jackson (849342)
Qinghong Li (5003339)
Peer Bork (438)

April 2018

Figure S3. Mapping rates of human reads to the gut gene catalogs of the four mammalian hosts conside...

Additional file 2: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Coelho (5119181)
Jens Kultima (5119178)
Paul Costea (5119172)
Coralie Fournier (5119166)
Yuanlong Pan (447697)
Gail Czarnecki-Maulden (5119175)
Matthew Hayward (2174484)
Sofia Forslund (5119169)
Thomas Schmidt (168952)
Patrick Descombes (16839)
Janet Jackson (849342)
Qinghong Li (5003339)
Peer Bork (438)

April 2018

Table S2. Basic statistics of the metagenomics data: number of base pairs and reads per sample. (XLS...

Additional file 12: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Coelho (5119181)
Jens Kultima (5119178)
Paul Costea (5119172)
Coralie Fournier (5119166)
Yuanlong Pan (447697)
Gail Czarnecki-Maulden (5119175)
Matthew Hayward (2174484)
Sofia Forslund (5119169)
Thomas Schmidt (168952)
Patrick Descombes (16839)
Janet Jackson (849342)
Qinghong Li (5003339)
Peer Bork (438)

April 2018

Figure S6. Distance boxplots of the samples in the 3 diets using Bray-Curtis divergence on log-norma...

Additional file 5: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Coelho (5119181)
Jens Kultima (5119178)
Paul Costea (5119172)
Coralie Fournier (5119166)
Yuanlong Pan (447697)
Gail Czarnecki-Maulden (5119175)
Matthew Hayward (2174484)
Sofia Forslund (5119169)
Thomas Schmidt (168952)
Patrick Descombes (16839)
Janet Jackson (849342)
Qinghong Li (5003339)
Peer Bork (438)

April 2018

Table S5. Spearman correlation and SparCC-derived p value for all nodes in the co-abundance correlat...

Dog gut gene catalog. Supplemental data for "Similarity of the dog and human gut microbiomes in gene content and response to diet"

Coelho, Luis Pedro
Kultima, Jens Roat
Costea, Paul Igor
Fournier, Coralie
Pan, Yuanlong
Czarnecki-Maulden, Gail
Hayward, Matthew Robert
Forslund, Sofia K.
Schmidt, Thomas Sebastian Benedikt
Descombes, Patrick
Jackson, Janet R
Li, Qinghong
Bork, Peer

April 2018

Gene catalogue for the dog gut microbiome including FASTA file of nucleotide sequences (including...

Additional file 13: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Luis Coelho (5119181)
Jens Kultima (5119178)
Paul Costea (5119172)
Coralie Fournier (5119166)
Yuanlong Pan (447697)
Gail Czarnecki-Maulden (5119175)
Matthew Hayward (2174484)
Sofia Forslund (5119169)
Thomas Schmidt (168952)
Patrick Descombes (16839)
Janet Jackson (849342)
Qinghong Li (5003339)
Peer Bork (438)

April 2018

Figure S7. (a) left: Principal coordinate analysis using weighted Unifrac distance [37]; right: corr...

Coelho, L.P.
Kultima, J.R.
Costea, P.I.
Fournier, C.
Pan, Y.
Czarnecki-Maulden, G.
Hayward, M.R.
Forslund, S.K.
Schmidt, T.S.B.
Descombes, P.
Jackson, J.R.
Li, Q.
Bork, P.

April 2018

Background: Gut microbes influence their hosts in many ways, in particular by modulating the impact ...

Additional file 2 of Comparison of 16S and whole genome dog microbiomes using machine learning

Scott Lewis (646389)
Andrea Nash (4616053)
Qinghong Li (5003339)
Tae-Hyuk Ahn (11310361)

August 2021

Additional file 2: Supplemental Figure S1: A. The increased detection rate in WGS data compared to 1...

Additional file 1: of Host genetic variation impacts microbiome composition across human body sites

Ran Blekhman (87226)
Julia Goodrich (3454907)
Katherine Huang (66477)
Qi Sun (127)
Robert Bukowski (424557)
Jordana Bell (667256)
Timothy Spector (348486)
Alon Keinan (153034)
Ruth Ley (3454904)
Dirk Gevers (50883)
Andrew Clark (377028)

September 2015

This is a PDF document containing Supplementary Figures S1 through S19. (PDF 12238 kb

Additional file 5: Table S4. of A diet change from dry food to beef induces reversible changes on the faecal microbiota in healthy, adult client-owned dogs

Kristin Herstad (4054888)
Karina Gajardo (1614955)
Anne Bakke (4054885)
Lars Moe (279381)
Jane Ludvigsen (4054882)
Knut Rudi (74721)
Ida Rud (533224)
Monika Sekelja (3703276)
Ellen Skancke (3429347)

May 2017

Relative abundance of genera in the different diet periods. (L6 table generated with QIIME). (XLSX 4...

Additional file 2: of Dietary probiotics have different effects on the composition of fecal microbiota in farmed raccoon dog (Nyctereutes procyonoides) and silver fox (Vulpes vulpes fulva)

Yongjia Peng (6738020)
Qiumei Shi (6738023)
Yujie Wang (308942)
Fan Zhang (46132)
Zhixin Ji (733291)
Jin Zhang (53297)

May 2019

Table S2. The alpha diversity indices of fecal microbiota of animals subjected to probiotic treatmen...

Additional file 16: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Abstract

Extracted data

Additional file 16: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Abstract

Extracted data

Topics

Related items

Topics

Related items