Additional file 1: of Intestinal microbial communities associated with acute enteric infections and disease recovery

Additional file 3: Figure S2. of Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease

Sahil Khanna (4028093)
Yoshiki Vazquez-Baeza (4028090)
Antonio González (18841)
Sophie Weiss (3811390)
Bradley Schmidt (4028096)
David Muñiz-Pedrogo (4028114)
John Rainey (4028084)
Patricia Kammer (4028102)
Heidi Nelson (674930)
Michael Sadowsky (3403913)
Alexander Khoruts (846836)
Stefan Farrugia (4028081)
Rob Knight (11635)
Darrell Pardi (4028087)
Purna Kashyap (3460319)

May 2017

(A) Meta-analysis showing changes in unweighted UniFrac-based beta diversity in a published cohort i...

Additional file 6: of The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms

Brandon Brooks (3170784)
Matthew Olm (5431706)
Brian Firek (627650)
Robyn Baker (627651)
David Geller-McGrath (5431709)
Sophia Reimer (5431703)
Karina Soenjoyo (5431712)
Jennifer Yip (5166962)
Dylan Dahan (5228936)
Brian Thomas (3179601)
Michael Morowitz (3608423)
Jillian Banfield (4238992)

June 2018

Fecal sample community composition. Plotted in each panel is the community composition of each infan...

Additional file 22: of The human jejunum has an endogenous microbiota that differs from those in the oral cavity and colon

Olof Sundin (3145059)
Antonio Mendoza-Ladd (4254088)
Mingtao Zeng (4254085)
Diana Diaz-ArĂŠvalo (4254133)
Elisa Morales (4254091)
B. Fagan (4254094)
Javier OrdoĂąez (4254130)
Philip Velez (4254073)
Nishaal Antony (4254076)
Richard McCallum (4254079)

July 2017

Relative Abundance of 26 Major Genera in the Jejunum of Individual Subjects by 16S Metagenomic Analy...

Additional file 2: of Intestinal microbial communities associated with acute enteric infections and disease recovery

Pallavi Singh (416686)
Tracy Teal (2792575)
Terence Marsh (2480470)
James Tiedje (228498)
Rebekah Mosci (3436736)
Katherine Jernigan (3436745)
Angela Zell (3436748)
Duane Newton (3436733)
Hossein Salimnia (3436739)
Paul Lephart (37479)
Daniel Sundin (3436751)
Walid Khalife (3436754)
Robert Britton (218572)
James Rudrik (3436742)
Shannon Manning (3436730)

September 2015

The richness and diversity estimates for intestinal communities from patients with enteric infection...

Additional file 2: of A comparative study of the gut microbiota in immune-mediated inflammatory diseasesâdoes a common dysbiosis exist?

Jessica Forbes (6085007)
Chih-yu Chen (4730856)
Natalie Knox (427655)
Ruth-Ann Marrie (6085010)
Hani El-Gabalawy (56079)
Teresa Kievit (4126681)
Michelle Alfa (6085013)
Charles Bernstein (3525584)
Gary Domselaar (6085016)

December 2018

Comparison of Gram positive only microbiota versus total microbiota. (XLSX 120 kb

Additional file 2: of Genetic diversity of Escherichia coli in gut microbiota of patients with Crohnâs disease discovered using metagenomic and genomic analyses

Alexander Tyakht (2131003)
Alexander Manolov (4259773)
Alexandra Kanygina (3455015)
Dmitry Ischenko (2145547)
Boris Kovarsky (4519954)
Anna Popenko (2131006)
Alexander Pavlenko (4519966)
Anna Elizarova (5940068)
Daria Rakitina (104963)
Julia Baikova (4259746)
Valentina Ladygina (2131024)
Elena Kostryukova (3455012)
Irina Karpova (3606446)
Tatyana Semashko (6158534)
Andrei Larin (4259758)
Tatyana Grigoryeva (6158537)
Mariya Sinyagina (6158540)
Sergei Malanin (4259740)
Petr Shcherbakov (4519969)
Anastasiya Kharitonova (6158543)
Igor Khalif (4259752)
Marina Shapina (4259755)
Igor Maev (4259779)
Dmitriy Andreev (6158546)
Elena Belousova (116565)
Yulia Buzunova (6158549)
Dmitry Alexeev (1535380)
Vadim Govorun (2131033)

December 2018

Results of subspecies-level analysis of E. coli and other microbes in the metagenomes using ConStrai...

Additional file 1: of Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites

Alessio Tovaglieri (5039909)
Alexandra Sontheimer-Phelps (6486695)
Annelies Geirnaert (579263)
Rachelle Prantil-Baun (6486698)
Diogo Camacho (6486701)
David Chou (427894)
Sasan Jalili-Firoozinezhad (6486704)
TomĂĄs Wouters (6486707)
Magdalena Kasendra (706294)
Michael Super (1641175)
Mark Cartwright (1436668)
Camilla Richmond (6486710)
David Breault (3441422)
Christophe Lacroix (35954)
Donald Ingber (6486713)

March 2019

Figure S1. Analysis of relative abundance of PolyFermS commensal bacteria phyla. Relative abundance ...

RESEARCH Open Access Intestinal microbial communities associated with acute enteric infections and disease recovery

Pallavi Singh
Tracy K. Teal
Terence L. Marsh
James M. Tiedje
Rebekah Mosci
Katherine Jernigan
Angela Zell
Duane W. Newton
Hossein Salimnia
Paul Lephart
Daniel Sundin
Walid Khalife
Robert A. Britton
James T. Rudrik
Shannon D. Manning

August 2016

Background: The intestinal microbiome represents a complex network of microbes that are important fo...

Additional file 2: of Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites

Alessio Tovaglieri (5039909)
Alexandra Sontheimer-Phelps (6486695)
Annelies Geirnaert (579263)
Rachelle Prantil-Baun (6486698)
Diogo Camacho (6486701)
David Chou (427894)
Sasan Jalili-Firoozinezhad (6486704)
TomĂĄs Wouters (6486707)
Magdalena Kasendra (706294)
Michael Super (1641175)
Mark Cartwright (1436668)
Camilla Richmond (6486710)
David Breault (3441422)
Christophe Lacroix (35954)
Donald Ingber (6486713)

March 2019

Figure S2. Analysis of relative abundance of PolyFermS commensal bacteria genera. Relative abundance...

Additional file 2: 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 S1. Diversity and abundance distribution of bacterial families in culture-independent or cult...

Additional file 1: of Bloom and bust: intestinal microbiota dynamics in response to hospital exposures and Clostridium difficile colonization or infection

Caroline Vincent (3470177)
Mark Miller (134024)
Thaddeus Edens (3470171)
Sudeep Mehrotra (3470180)
Ken Dewar (220208)
Amee Manges (3470174)

March 2016

Table S1. Significant associations between medication use and intestinal microbiota genera (univaria...

Additional file 1: of Ecology of bacteria in the human gastrointestinal tract—identification of keystone and foundation taxa

Pål Trosvik (74715)
Eric Muinck (3507722)

October 2015

The additional file accompanying this article contains Figures S1–20 and Table S1. (DOCX 753 kb

Additional file 1: Table S1. of Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia

Bruce Rosa (3509876)
Taniawati Supali (161356)
Lincoln Gankpala (4427038)
Yenny Djuardi (236892)
Erliyani Sartono (161341)
Yanjiao Zhou (158268)
Kerstin Fischer (131647)
John Martin (1716)
Rahul Tyagi (743823)
Fatorma Bolay (4896925)
Peter Fischer (482447)
Maria Yazdanbakhsh (90295)
Makedonka Mitreva (27680)

February 2018

Metadata and read counts per taxa for the 98 16S samples from Liberia. (XLSX 595Â kb

Additional file 1 of Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa

Xin Fang (134979)
Jonathan Monk (3548066)
Nathan Mih (3146436)
Bin Du (138774)
Anand Sastry (5369741)
Erol Kavvas (3465563)
Yara Seif (4908814)
Larry Smarr (379158)
Bernhard Palsson (450761)

June 2018

Table S1: Metadata of 110 strains. Table S2: Genes associated with mucus degradation. Table S3: Meta...

Additional file 2: of Bloom and bust: intestinal microbiota dynamics in response to hospital exposures and Clostridium difficile colonization or infection

Caroline Vincent (3470177)
Mark Miller (134024)
Thaddeus Edens (3470171)
Sudeep Mehrotra (3470180)
Ken Dewar (220208)
Amee Manges (3470174)

March 2016

Table S2. Significant associations between medication use and intestinal microbiota families (univar...

Additional file 3: Figure S2. of Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease

Sahil Khanna (4028093)
Yoshiki Vazquez-Baeza (4028090)
Antonio González (18841)
Sophie Weiss (3811390)
Bradley Schmidt (4028096)
David Muñiz-Pedrogo (4028114)
John Rainey (4028084)
Patricia Kammer (4028102)
Heidi Nelson (674930)
Michael Sadowsky (3403913)
Alexander Khoruts (846836)
Stefan Farrugia (4028081)
Rob Knight (11635)
Darrell Pardi (4028087)
Purna Kashyap (3460319)

May 2017

(A) Meta-analysis showing changes in unweighted UniFrac-based beta diversity in a published cohort i...

Additional file 6: of The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms

Brandon Brooks (3170784)
Matthew Olm (5431706)
Brian Firek (627650)
Robyn Baker (627651)
David Geller-McGrath (5431709)
Sophia Reimer (5431703)
Karina Soenjoyo (5431712)
Jennifer Yip (5166962)
Dylan Dahan (5228936)
Brian Thomas (3179601)
Michael Morowitz (3608423)
Jillian Banfield (4238992)

June 2018

Fecal sample community composition. Plotted in each panel is the community composition of each infan...

Additional file 22: of The human jejunum has an endogenous microbiota that differs from those in the oral cavity and colon

Olof Sundin (3145059)
Antonio Mendoza-Ladd (4254088)
Mingtao Zeng (4254085)
Diana Diaz-ArĂŠvalo (4254133)
Elisa Morales (4254091)
B. Fagan (4254094)
Javier OrdoĂąez (4254130)
Philip Velez (4254073)
Nishaal Antony (4254076)
Richard McCallum (4254079)

July 2017

Relative Abundance of 26 Major Genera in the Jejunum of Individual Subjects by 16S Metagenomic Analy...

Additional file 2: of Intestinal microbial communities associated with acute enteric infections and disease recovery

Pallavi Singh (416686)
Tracy Teal (2792575)
Terence Marsh (2480470)
James Tiedje (228498)
Rebekah Mosci (3436736)
Katherine Jernigan (3436745)
Angela Zell (3436748)
Duane Newton (3436733)
Hossein Salimnia (3436739)
Paul Lephart (37479)
Daniel Sundin (3436751)
Walid Khalife (3436754)
Robert Britton (218572)
James Rudrik (3436742)
Shannon Manning (3436730)

September 2015

The richness and diversity estimates for intestinal communities from patients with enteric infection...

Additional file 2: of A comparative study of the gut microbiota in immune-mediated inflammatory diseasesâdoes a common dysbiosis exist?

Jessica Forbes (6085007)
Chih-yu Chen (4730856)
Natalie Knox (427655)
Ruth-Ann Marrie (6085010)
Hani El-Gabalawy (56079)
Teresa Kievit (4126681)
Michelle Alfa (6085013)
Charles Bernstein (3525584)
Gary Domselaar (6085016)

December 2018

Comparison of Gram positive only microbiota versus total microbiota. (XLSX 120 kb

Additional file 2: of Genetic diversity of Escherichia coli in gut microbiota of patients with Crohnâs disease discovered using metagenomic and genomic analyses

Alexander Tyakht (2131003)
Alexander Manolov (4259773)
Alexandra Kanygina (3455015)
Dmitry Ischenko (2145547)
Boris Kovarsky (4519954)
Anna Popenko (2131006)
Alexander Pavlenko (4519966)
Anna Elizarova (5940068)
Daria Rakitina (104963)
Julia Baikova (4259746)
Valentina Ladygina (2131024)
Elena Kostryukova (3455012)
Irina Karpova (3606446)
Tatyana Semashko (6158534)
Andrei Larin (4259758)
Tatyana Grigoryeva (6158537)
Mariya Sinyagina (6158540)
Sergei Malanin (4259740)
Petr Shcherbakov (4519969)
Anastasiya Kharitonova (6158543)
Igor Khalif (4259752)
Marina Shapina (4259755)
Igor Maev (4259779)
Dmitriy Andreev (6158546)
Elena Belousova (116565)
Yulia Buzunova (6158549)
Dmitry Alexeev (1535380)
Vadim Govorun (2131033)

December 2018

Results of subspecies-level analysis of E. coli and other microbes in the metagenomes using ConStrai...

Additional file 1: of Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites

Alessio Tovaglieri (5039909)
Alexandra Sontheimer-Phelps (6486695)
Annelies Geirnaert (579263)
Rachelle Prantil-Baun (6486698)
Diogo Camacho (6486701)
David Chou (427894)
Sasan Jalili-Firoozinezhad (6486704)
TomĂĄs Wouters (6486707)
Magdalena Kasendra (706294)
Michael Super (1641175)
Mark Cartwright (1436668)
Camilla Richmond (6486710)
David Breault (3441422)
Christophe Lacroix (35954)
Donald Ingber (6486713)

March 2019

Figure S1. Analysis of relative abundance of PolyFermS commensal bacteria phyla. Relative abundance ...

RESEARCH Open Access Intestinal microbial communities associated with acute enteric infections and disease recovery

Pallavi Singh
Tracy K. Teal
Terence L. Marsh
James M. Tiedje
Rebekah Mosci
Katherine Jernigan
Angela Zell
Duane W. Newton
Hossein Salimnia
Paul Lephart
Daniel Sundin
Walid Khalife
Robert A. Britton
James T. Rudrik
Shannon D. Manning

August 2016

Background: The intestinal microbiome represents a complex network of microbes that are important fo...

Additional file 2: of Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites

Alessio Tovaglieri (5039909)
Alexandra Sontheimer-Phelps (6486695)
Annelies Geirnaert (579263)
Rachelle Prantil-Baun (6486698)
Diogo Camacho (6486701)
David Chou (427894)
Sasan Jalili-Firoozinezhad (6486704)
TomĂĄs Wouters (6486707)
Magdalena Kasendra (706294)
Michael Super (1641175)
Mark Cartwright (1436668)
Camilla Richmond (6486710)
David Breault (3441422)
Christophe Lacroix (35954)
Donald Ingber (6486713)

March 2019

Figure S2. Analysis of relative abundance of PolyFermS commensal bacteria genera. Relative abundance...

Additional file 2: 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 S1. Diversity and abundance distribution of bacterial families in culture-independent or cult...

Additional file 1: of Bloom and bust: intestinal microbiota dynamics in response to hospital exposures and Clostridium difficile colonization or infection

Caroline Vincent (3470177)
Mark Miller (134024)
Thaddeus Edens (3470171)
Sudeep Mehrotra (3470180)
Ken Dewar (220208)
Amee Manges (3470174)

March 2016

Table S1. Significant associations between medication use and intestinal microbiota genera (univaria...

Additional file 1: of Ecology of bacteria in the human gastrointestinal tract—identification of keystone and foundation taxa

Pål Trosvik (74715)
Eric Muinck (3507722)

October 2015

The additional file accompanying this article contains Figures S1–20 and Table S1. (DOCX 753 kb

Additional file 1: Table S1. of Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia

Bruce Rosa (3509876)
Taniawati Supali (161356)
Lincoln Gankpala (4427038)
Yenny Djuardi (236892)
Erliyani Sartono (161341)
Yanjiao Zhou (158268)
Kerstin Fischer (131647)
John Martin (1716)
Rahul Tyagi (743823)
Fatorma Bolay (4896925)
Peter Fischer (482447)
Maria Yazdanbakhsh (90295)
Makedonka Mitreva (27680)

February 2018

Metadata and read counts per taxa for the 98 16S samples from Liberia. (XLSX 595Â kb

Additional file 1 of Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa

Xin Fang (134979)
Jonathan Monk (3548066)
Nathan Mih (3146436)
Bin Du (138774)
Anand Sastry (5369741)
Erol Kavvas (3465563)
Yara Seif (4908814)
Larry Smarr (379158)
Bernhard Palsson (450761)

June 2018

Table S1: Metadata of 110 strains. Table S2: Genes associated with mucus degradation. Table S3: Meta...

Additional file 2: of Bloom and bust: intestinal microbiota dynamics in response to hospital exposures and Clostridium difficile colonization or infection

Caroline Vincent (3470177)
Mark Miller (134024)
Thaddeus Edens (3470171)
Sudeep Mehrotra (3470180)
Ken Dewar (220208)
Amee Manges (3470174)

March 2016

Table S2. Significant associations between medication use and intestinal microbiota families (univar...

Additional file 3: Figure S2. of Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease

Sahil Khanna (4028093)
Yoshiki Vazquez-Baeza (4028090)
Antonio González (18841)
Sophie Weiss (3811390)
Bradley Schmidt (4028096)
David Muñiz-Pedrogo (4028114)
John Rainey (4028084)
Patricia Kammer (4028102)
Heidi Nelson (674930)
Michael Sadowsky (3403913)
Alexander Khoruts (846836)
Stefan Farrugia (4028081)
Rob Knight (11635)
Darrell Pardi (4028087)
Purna Kashyap (3460319)

May 2017

(A) Meta-analysis showing changes in unweighted UniFrac-based beta diversity in a published cohort i...

Additional file 6: of The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms

Brandon Brooks (3170784)
Matthew Olm (5431706)
Brian Firek (627650)
Robyn Baker (627651)
David Geller-McGrath (5431709)
Sophia Reimer (5431703)
Karina Soenjoyo (5431712)
Jennifer Yip (5166962)
Dylan Dahan (5228936)
Brian Thomas (3179601)
Michael Morowitz (3608423)
Jillian Banfield (4238992)

June 2018

Fecal sample community composition. Plotted in each panel is the community composition of each infan...

Additional file 22: of The human jejunum has an endogenous microbiota that differs from those in the oral cavity and colon

Olof Sundin (3145059)
Antonio Mendoza-Ladd (4254088)
Mingtao Zeng (4254085)
Diana Diaz-ArĂŠvalo (4254133)
Elisa Morales (4254091)
B. Fagan (4254094)
Javier OrdoĂąez (4254130)
Philip Velez (4254073)
Nishaal Antony (4254076)
Richard McCallum (4254079)

July 2017

Relative Abundance of 26 Major Genera in the Jejunum of Individual Subjects by 16S Metagenomic Analy...

Additional file 1: of Intestinal microbial communities associated with acute enteric infections and disease recovery

Abstract

Extracted data

Additional file 1: of Intestinal microbial communities associated with acute enteric infections and disease recovery

Abstract

Extracted data

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