Additional file 3: of Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue

Additional file 10: Figure S9. of Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease

Stewart, Christopher J.
Embleton, Nicholas D.
Marrs, Emma C L
Smith, Daniel P.
Nelson, Andrew
Abdulkadir, Bashir
Skeath, Tom
Petrosino, Joseph F.
Perry, John D.
Berrington, Janet E.
Cummings, Stephen P.
Embleton, Nicholas
Teesside University
National Horizons Centre
Teesside University

January 2016

Pulse field gel electrophoresis (PFGE) of two E. coli isolates from NEC patients and 4 E. coli isola...

Additional file 10: Figure S9. of Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease

Stewart, Christopher J.
Embleton, Nicholas D.
Marrs, Emma C L
Smith, Daniel P.
Nelson, Andrew
Abdulkadir, Bashir
Skeath, Tom
Petrosino, Joseph F.
Perry, John D.
Berrington, Janet E.
Cummings, Stephen P.
Embleton, Nicholas
Teesside University
National Horizons Centre
Teesside University

January 2016

Pulse field gel electrophoresis (PFGE) of two E. coli isolates from NEC patients and 4 E. coli isola...

Additional file 3: 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

Comparison of relative peak area of metabolite picked up by the PCLâ>â0.7. (DOCX 229 kb

Additional file 4: of Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue

Christopher Stewart (3608402)
Roxana Fatemizadeh (6423359)
Pamela Parsons (6423362)
Christopher Lamb (6423365)
Deborah Shady (6423368)
Joseph Petrosino (39790)
Amy Hair (6423371)

March 2019

Table S2. Relative abundance of significant genera as determined by MaAsLin analysis, per section of...

Additional file 5: of Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue

Christopher Stewart (3608402)
Roxana Fatemizadeh (6423359)
Pamela Parsons (6423362)
Christopher Lamb (6423365)
Deborah Shady (6423368)
Joseph Petrosino (39790)
Amy Hair (6423371)

March 2019

Figure S3. Stacked bar plot of dominant phyla. Marginal and representative sections from each infant...

Additional file 2: of Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue

Christopher Stewart (3608402)
Roxana Fatemizadeh (6423359)
Pamela Parsons (6423362)
Christopher Lamb (6423365)
Deborah Shady (6423368)
Joseph Petrosino (39790)
Amy Hair (6423371)

March 2019

Figure S2. Stacked bar plot of dominant genera. Marginal and representative sections from each infan...

Additional file 1: of Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue

Christopher Stewart (3608402)
Roxana Fatemizadeh (6423359)
Pamela Parsons (6423362)
Christopher Lamb (6423365)
Deborah Shady (6423368)
Joseph Petrosino (39790)
Amy Hair (6423371)

March 2019

Figure S1. Comparison of resulting microbiota profiles following DNA extraction with either xylene o...

Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue

Christopher J. Stewart
Roxana Fatemizadeh
Pamela Parsons
Christopher A. Lamb
Deborah A. Shady
Joseph F. Petrosino
Amy B. Hair

March 2019

Abstract Background Necrotising enterocolitis (NEC) is a common cause of death in preterm infants an...

Additional file 2: of Gut microbiota of preterm infants supplemented with probiotics: sub-study of the ProPrems trial

Erica Plummer (5961608)
Dieter Bulach (368712)
Gerald Murray (4876939)
Susan Jacobs (5961611)
Sepehr Tabrizi (3638359)
Suzanne Garland (398522)

November 2018

Heatmap of bacterial abundance in all study specimens. Each vertical line represents the bacterial c...

Additional file 8: Table S3. of Extending colonic mucosal microbiome analysisâassessment of colonic lavage as a proxy for endoscopic colonic biopsies

Euan Watt (3444731)
Matthew Gemmell (3444737)
Susan Berry (653826)
Mark Glaire (3444728)
Freda Farquharson (3299991)
Petra Louis (526555)
Graeme Murray (368267)
Emad El-Omar (229332)
Georgina Hold (3444734)

November 2016

Top 50 OTUs found to be similarly abundant between biopsy and colonic lavage samples. (DOC 64 kb

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 8: of Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis

Mohan Pammi (3822313)
Julia Cope (103124)
Phillip Tarr (3416615)
Barbara Warner (3822322)
Ardythe Morrow (3822325)
Volker Mai (288569)
Katherine Gregory (3608483)
J. Kroll (3427700)
Valerie McMurtry (3822319)
Michael Ferris (347884)
Lars Engstrand (48331)
Helene Lilja (3822316)
Emily Hollister (3548546)
James Versalovic (158351)
Josef Neu (200821)

March 2017

Comparison of microbiota profiles in NEC and control infants subgrouped by diet. Observed species (o...

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 ...

Additional file 4: of Gut microbiota of preterm infants supplemented with probiotics: sub-study of the ProPrems trial

Erica Plummer (5961608)
Dieter Bulach (368712)
Gerald Murray (4876939)
Susan Jacobs (5961611)
Sepehr Tabrizi (3638359)
Suzanne Garland (398522)

November 2018

Logistic mixed model regression analysis for examining the effect of time from birth on bacterial ge...

Additional file 3: Figure S2. of Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease

Christopher Stewart (3608402)
Nicholas Embleton (3608411)
Emma Marrs (3608408)
Daniel Smith (6120)
Andrew Nelson (209359)
Bashir Abdulkadir (3608405)
Tom Skeath (3608399)
Joseph Petrosino (39790)
John Perry (3608414)
Janet Berrington (3608417)
Stephen Cummings (1943005)

December 2016

Longitudinal development of the core (dashed lines) and satellite (solid lines) communities in each ...

Additional file 10: Figure S9. of Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease

Stewart, Christopher J.
Embleton, Nicholas D.
Marrs, Emma C L
Smith, Daniel P.
Nelson, Andrew
Abdulkadir, Bashir
Skeath, Tom
Petrosino, Joseph F.
Perry, John D.
Berrington, Janet E.
Cummings, Stephen P.
Embleton, Nicholas
Teesside University
National Horizons Centre
Teesside University

January 2016

Pulse field gel electrophoresis (PFGE) of two E. coli isolates from NEC patients and 4 E. coli isola...

Additional file 10: Figure S9. of Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease

Stewart, Christopher J.
Embleton, Nicholas D.
Marrs, Emma C L
Smith, Daniel P.
Nelson, Andrew
Abdulkadir, Bashir
Skeath, Tom
Petrosino, Joseph F.
Perry, John D.
Berrington, Janet E.
Cummings, Stephen P.
Embleton, Nicholas
Teesside University
National Horizons Centre
Teesside University

January 2016

Pulse field gel electrophoresis (PFGE) of two E. coli isolates from NEC patients and 4 E. coli isola...

Additional file 3: 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

Comparison of relative peak area of metabolite picked up by the PCLâ>â0.7. (DOCX 229 kb

Additional file 4: of Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue

Christopher Stewart (3608402)
Roxana Fatemizadeh (6423359)
Pamela Parsons (6423362)
Christopher Lamb (6423365)
Deborah Shady (6423368)
Joseph Petrosino (39790)
Amy Hair (6423371)

March 2019

Table S2. Relative abundance of significant genera as determined by MaAsLin analysis, per section of...

Additional file 5: of Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue

Christopher Stewart (3608402)
Roxana Fatemizadeh (6423359)
Pamela Parsons (6423362)
Christopher Lamb (6423365)
Deborah Shady (6423368)
Joseph Petrosino (39790)
Amy Hair (6423371)

March 2019

Figure S3. Stacked bar plot of dominant phyla. Marginal and representative sections from each infant...

Additional file 2: of Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue

Christopher Stewart (3608402)
Roxana Fatemizadeh (6423359)
Pamela Parsons (6423362)
Christopher Lamb (6423365)
Deborah Shady (6423368)
Joseph Petrosino (39790)
Amy Hair (6423371)

March 2019

Figure S2. Stacked bar plot of dominant genera. Marginal and representative sections from each infan...

Additional file 1: of Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue

Christopher Stewart (3608402)
Roxana Fatemizadeh (6423359)
Pamela Parsons (6423362)
Christopher Lamb (6423365)
Deborah Shady (6423368)
Joseph Petrosino (39790)
Amy Hair (6423371)

March 2019

Figure S1. Comparison of resulting microbiota profiles following DNA extraction with either xylene o...

Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue

Christopher J. Stewart
Roxana Fatemizadeh
Pamela Parsons
Christopher A. Lamb
Deborah A. Shady
Joseph F. Petrosino
Amy B. Hair

March 2019

Abstract Background Necrotising enterocolitis (NEC) is a common cause of death in preterm infants an...

Additional file 2: of Gut microbiota of preterm infants supplemented with probiotics: sub-study of the ProPrems trial

Erica Plummer (5961608)
Dieter Bulach (368712)
Gerald Murray (4876939)
Susan Jacobs (5961611)
Sepehr Tabrizi (3638359)
Suzanne Garland (398522)

November 2018

Heatmap of bacterial abundance in all study specimens. Each vertical line represents the bacterial c...

Additional file 8: Table S3. of Extending colonic mucosal microbiome analysisâassessment of colonic lavage as a proxy for endoscopic colonic biopsies

Euan Watt (3444731)
Matthew Gemmell (3444737)
Susan Berry (653826)
Mark Glaire (3444728)
Freda Farquharson (3299991)
Petra Louis (526555)
Graeme Murray (368267)
Emad El-Omar (229332)
Georgina Hold (3444734)

November 2016

Top 50 OTUs found to be similarly abundant between biopsy and colonic lavage samples. (DOC 64 kb

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 8: of Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis

Mohan Pammi (3822313)
Julia Cope (103124)
Phillip Tarr (3416615)
Barbara Warner (3822322)
Ardythe Morrow (3822325)
Volker Mai (288569)
Katherine Gregory (3608483)
J. Kroll (3427700)
Valerie McMurtry (3822319)
Michael Ferris (347884)
Lars Engstrand (48331)
Helene Lilja (3822316)
Emily Hollister (3548546)
James Versalovic (158351)
Josef Neu (200821)

March 2017

Comparison of microbiota profiles in NEC and control infants subgrouped by diet. Observed species (o...

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 ...

Additional file 4: of Gut microbiota of preterm infants supplemented with probiotics: sub-study of the ProPrems trial

Erica Plummer (5961608)
Dieter Bulach (368712)
Gerald Murray (4876939)
Susan Jacobs (5961611)
Sepehr Tabrizi (3638359)
Suzanne Garland (398522)

November 2018

Logistic mixed model regression analysis for examining the effect of time from birth on bacterial ge...

Additional file 3: Figure S2. of Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease

Christopher Stewart (3608402)
Nicholas Embleton (3608411)
Emma Marrs (3608408)
Daniel Smith (6120)
Andrew Nelson (209359)
Bashir Abdulkadir (3608405)
Tom Skeath (3608399)
Joseph Petrosino (39790)
John Perry (3608414)
Janet Berrington (3608417)
Stephen Cummings (1943005)

December 2016

Longitudinal development of the core (dashed lines) and satellite (solid lines) communities in each ...

Additional file 10: Figure S9. of Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease

Stewart, Christopher J.
Embleton, Nicholas D.
Marrs, Emma C L
Smith, Daniel P.
Nelson, Andrew
Abdulkadir, Bashir
Skeath, Tom
Petrosino, Joseph F.
Perry, John D.
Berrington, Janet E.
Cummings, Stephen P.
Embleton, Nicholas
Teesside University
National Horizons Centre
Teesside University

January 2016

Pulse field gel electrophoresis (PFGE) of two E. coli isolates from NEC patients and 4 E. coli isola...

Additional file 10: Figure S9. of Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease

Stewart, Christopher J.
Embleton, Nicholas D.
Marrs, Emma C L
Smith, Daniel P.
Nelson, Andrew
Abdulkadir, Bashir
Skeath, Tom
Petrosino, Joseph F.
Perry, John D.
Berrington, Janet E.
Cummings, Stephen P.
Embleton, Nicholas
Teesside University
National Horizons Centre
Teesside University

January 2016

Pulse field gel electrophoresis (PFGE) of two E. coli isolates from NEC patients and 4 E. coli isola...

Additional file 3: 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

Comparison of relative peak area of metabolite picked up by the PCLâ>â0.7. (DOCX 229 kb

Additional file 3: of Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue

Abstract

Extracted data

Additional file 3: of Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue

Abstract

Extracted data

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