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

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 5: of Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana

Matthew Hansen (445716)
Meagan Rubel (6249047)
Aubrey Bailey (520161)
Alessia Ranciaro (6249053)
Simon Thompson (3411839)
Michael Campbell (562588)
William Beggs (168608)
Jaanki Dave (6249065)
Gaonyadiwe Mokone (6249071)
Sununguko Mpoloka (6249074)
Thomas Nyambo (6249080)
Christian Abnet (3703321)
Stephen Chanock (23589)
Frederic Bushman (3286380)
Sarah Tishkoff (6249089)

January 2019

Contains the genetic similarity values, where each row corresponds to a pair of individuals. (GZ 47 ...

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 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 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 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 16: 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 S10. Prevalence change split by experimental cohorts (cf. Fig.Â 3a). (PDF 42Â kb

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 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 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 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...

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 5: of Skin and gut microbiomes of a wild mammal respond to different environmental cues

Anton Lavrinienko (5699762)
Eugene Tukalenko (5699765)
Tapio Mappes (208603)
Phillip Watts (541434)

November 2018

Correlations (Spearman’s correlation analysis) between the SK microbiome alpha diversity estimates (...

Network-based gut microbiome analysis in dogs

Elisa Scarsella (9249364)
Aashish Jha (13874363)
Misa Sandri (3802945)
Bruno Stefanon (803057)

September 2022

A growing number of studies in the last decade described the microbial populations in different nich...

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 5: of Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana

Matthew Hansen (445716)
Meagan Rubel (6249047)
Aubrey Bailey (520161)
Alessia Ranciaro (6249053)
Simon Thompson (3411839)
Michael Campbell (562588)
William Beggs (168608)
Jaanki Dave (6249065)
Gaonyadiwe Mokone (6249071)
Sununguko Mpoloka (6249074)
Thomas Nyambo (6249080)
Christian Abnet (3703321)
Stephen Chanock (23589)
Frederic Bushman (3286380)
Sarah Tishkoff (6249089)

January 2019

Contains the genetic similarity values, where each row corresponds to a pair of individuals. (GZ 47 ...

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 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 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 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 16: 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 S10. Prevalence change split by experimental cohorts (cf. Fig.Â 3a). (PDF 42Â kb

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 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 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 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...

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 5: of Skin and gut microbiomes of a wild mammal respond to different environmental cues

Anton Lavrinienko (5699762)
Eugene Tukalenko (5699765)
Tapio Mappes (208603)
Phillip Watts (541434)

November 2018

Correlations (Spearman’s correlation analysis) between the SK microbiome alpha diversity estimates (...

Network-based gut microbiome analysis in dogs

Elisa Scarsella (9249364)
Aashish Jha (13874363)
Misa Sandri (3802945)
Bruno Stefanon (803057)

September 2022

A growing number of studies in the last decade described the microbial populations in different nich...

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 5: of Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana

Matthew Hansen (445716)
Meagan Rubel (6249047)
Aubrey Bailey (520161)
Alessia Ranciaro (6249053)
Simon Thompson (3411839)
Michael Campbell (562588)
William Beggs (168608)
Jaanki Dave (6249065)
Gaonyadiwe Mokone (6249071)
Sununguko Mpoloka (6249074)
Thomas Nyambo (6249080)
Christian Abnet (3703321)
Stephen Chanock (23589)
Frederic Bushman (3286380)
Sarah Tishkoff (6249089)

January 2019

Contains the genetic similarity values, where each row corresponds to a pair of individuals. (GZ 47 ...

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

Abstract

Extracted data

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

Abstract

Extracted data

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