Additional file 2: Table S1. of Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage

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 3: Table S2. of Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling

Jennifer Lau (784600)
Fiona Whelan (689631)
Isiri Herath (3550367)
Christine Lee (587571)
Stephen Collins (2243821)
Premysl Bercik (3545897)
Michael Surette (3476609)

July 2016

Classification of Lachnospiraceae isolates cultured from Donor HV7 and IBS4 fecal samples. (XLSX 38 ...

Additional file 1: of Genomic and metagenomic insights into the microbial community of a thermal spring

Renato Pedron (6258248)
Alfonso Esposito (3322911)
Irene Bianconi (108469)
Edoardo Pasolli (3155043)
Adrian Tett (642012)
Francesco Asnicar (5198411)
Mario Cristofolini (6258251)
Nicola Segata (103809)
Olivier Jousson (281189)

January 2019

Table S1. Assembly statistics and taxonomy for each genome sequenced. (XLSX 18Â kb

Additional file 3: Figure S2. of Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage

Lysiane Duniere (3811201)
Shanwei Xu (1791094)
Jin Long (2967804)
Chijioke Elekwachi (3811198)
Yuxi Wang (450170)
Kelly Turkington (3811204)
Robert Forster (3811207)
Tim McAllister (151974)

March 2017

PCo analysis. Principal coordinates analysis for bacterial (left) and fungal (right) communities acc...

Additional file 2: Table S1. of The nasopharyngeal microbiota of beef cattle before and after transport to a feedlot

Devin Holman (3855493)
Edouard Timsit (3855484)
Samat Amat (3855490)
D. Abbott (3601166)
Andre Buret (3855487)
Trevor Alexander (3708487)

March 2017

Multiplex primers used for the identification of bovine respiratory disease-associated bacteria. (DO...

Additional file 1: of MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions

Carrine Blank (3426413)
Hong Cui (209000)
Lisa Moore (16482)
Ramona Walls (510157)

April 2016

Supplemental Figures (Figures S1-S6) and Tables (Tables S1 and S2). (DOCX 1785Â kb

Additional file 1: of Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination

E. Gonzalez (4991489)
F. Pitre (4991495)
A. PagĂŠ (4991522)
J. Marleau (4991507)
W. Guidi Nissim (4991504)
M. St-Arnaud (4991501)
M. Labrecque (4991498)
S. Joly (4991510)
E. Yergeau (4991516)
N. Brereton (4991513)

March 2018

Unknown sequence challenge, upregulated DE Basidiomycota blastn and additional transcriptomic method...

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: Table S1. of Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

Sonny Lee (4004606)
Stacy Kahn (4004612)
Tom Delmont (4004609)
Alon Shaiber (4004600)
Ăzcan Esen (4004603)
Nathaniel Hubert (4004594)
Hilary Morrison (4004597)
Dionysios Antonopoulos (180809)
David Rubin (2741101)
A. Eren (3420008)

May 2017

Additional information for samples, metagenomic bins, and metagenome-assembled genomes in our study....

Additional file 1: of Gene content dissimilarity for subclassification of highly similar microbial strains

Qichao Tu (201296)
Lu Lin (201289)

August 2016

This file contains the supplementary table and figures for this paper, including Table S1, Figure S1...

Additional file 1: Table S1. of Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences

Marzia Miletto (478876)
Steven Lindow (3480884)

December 2015

OTU table.Â Genus-level taxonomic composition of bacterial communities associated with indoor air an...

Additional file 3: of Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration

Jacquelynn Benjamino (550289)
Stephen Lincoln (3721795)
Ranjan Srivastava (454582)
Joerg Graf (229951)

May 2018

Complete taxonomy table. Rarified (18,000 sequences) taxonomy table used in this study. (XLSX 219Â k...

Additional file 2: of Laboratory colonization stabilizes the naturally dynamic microbiome composition of field collected Dermacentor andersoni ticks

Cory Gall (4493161)
Glen Scoles (3448283)
Krisztian Magori (211754)
Kathleen Mason (4493164)
Kelly Brayton (3523091)

October 2017

R scripts for microbiome analysis. R was used to import sample data, build a data matrix, and the ph...

Additional file 3: of Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes

Suzanne Kosina (3469994)
Annette Greiner (1890286)
Rebecca Lau (3664084)
Stefan Jenkins (3690490)
Richard Baran (1898434)
Benjamin Bowen (740647)
Trent Northen (3569411)

November 2018

Table S1. microbial isolates, Table S2. LCMS parameters, Table S3. metabolite identifications, Table...

Additional file 2: Table S1A. of Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns

Francesca De Filippis (437252)
Nicoletta Pellegrini (826113)
Luca Laghi (654884)
Marco Gobbetti (468669)
Danilo Ercolini (437255)

October 2016

Prevotella oligotypes representative sequences and BLASTn top hit. Table S1B. Bacteroides oligotypes...

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 3: Table S2. of Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling

Jennifer Lau (784600)
Fiona Whelan (689631)
Isiri Herath (3550367)
Christine Lee (587571)
Stephen Collins (2243821)
Premysl Bercik (3545897)
Michael Surette (3476609)

July 2016

Classification of Lachnospiraceae isolates cultured from Donor HV7 and IBS4 fecal samples. (XLSX 38 ...

Additional file 1: of Genomic and metagenomic insights into the microbial community of a thermal spring

Renato Pedron (6258248)
Alfonso Esposito (3322911)
Irene Bianconi (108469)
Edoardo Pasolli (3155043)
Adrian Tett (642012)
Francesco Asnicar (5198411)
Mario Cristofolini (6258251)
Nicola Segata (103809)
Olivier Jousson (281189)

January 2019

Table S1. Assembly statistics and taxonomy for each genome sequenced. (XLSX 18Â kb

Additional file 3: Figure S2. of Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage

Lysiane Duniere (3811201)
Shanwei Xu (1791094)
Jin Long (2967804)
Chijioke Elekwachi (3811198)
Yuxi Wang (450170)
Kelly Turkington (3811204)
Robert Forster (3811207)
Tim McAllister (151974)

March 2017

PCo analysis. Principal coordinates analysis for bacterial (left) and fungal (right) communities acc...

Additional file 2: Table S1. of The nasopharyngeal microbiota of beef cattle before and after transport to a feedlot

Devin Holman (3855493)
Edouard Timsit (3855484)
Samat Amat (3855490)
D. Abbott (3601166)
Andre Buret (3855487)
Trevor Alexander (3708487)

March 2017

Multiplex primers used for the identification of bovine respiratory disease-associated bacteria. (DO...

Additional file 1: of MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions

Carrine Blank (3426413)
Hong Cui (209000)
Lisa Moore (16482)
Ramona Walls (510157)

April 2016

Supplemental Figures (Figures S1-S6) and Tables (Tables S1 and S2). (DOCX 1785Â kb

Additional file 1: of Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination

E. Gonzalez (4991489)
F. Pitre (4991495)
A. PagĂŠ (4991522)
J. Marleau (4991507)
W. Guidi Nissim (4991504)
M. St-Arnaud (4991501)
M. Labrecque (4991498)
S. Joly (4991510)
E. Yergeau (4991516)
N. Brereton (4991513)

March 2018

Unknown sequence challenge, upregulated DE Basidiomycota blastn and additional transcriptomic method...

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: Table S1. of Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

Sonny Lee (4004606)
Stacy Kahn (4004612)
Tom Delmont (4004609)
Alon Shaiber (4004600)
Ăzcan Esen (4004603)
Nathaniel Hubert (4004594)
Hilary Morrison (4004597)
Dionysios Antonopoulos (180809)
David Rubin (2741101)
A. Eren (3420008)

May 2017

Additional information for samples, metagenomic bins, and metagenome-assembled genomes in our study....

Additional file 1: of Gene content dissimilarity for subclassification of highly similar microbial strains

Qichao Tu (201296)
Lu Lin (201289)

August 2016

This file contains the supplementary table and figures for this paper, including Table S1, Figure S1...

Additional file 1: Table S1. of Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences

Marzia Miletto (478876)
Steven Lindow (3480884)

December 2015

OTU table.Â Genus-level taxonomic composition of bacterial communities associated with indoor air an...

Additional file 3: of Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration

Jacquelynn Benjamino (550289)
Stephen Lincoln (3721795)
Ranjan Srivastava (454582)
Joerg Graf (229951)

May 2018

Complete taxonomy table. Rarified (18,000 sequences) taxonomy table used in this study. (XLSX 219Â k...

Additional file 2: of Laboratory colonization stabilizes the naturally dynamic microbiome composition of field collected Dermacentor andersoni ticks

Cory Gall (4493161)
Glen Scoles (3448283)
Krisztian Magori (211754)
Kathleen Mason (4493164)
Kelly Brayton (3523091)

October 2017

R scripts for microbiome analysis. R was used to import sample data, build a data matrix, and the ph...

Additional file 3: of Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes

Suzanne Kosina (3469994)
Annette Greiner (1890286)
Rebecca Lau (3664084)
Stefan Jenkins (3690490)
Richard Baran (1898434)
Benjamin Bowen (740647)
Trent Northen (3569411)

November 2018

Table S1. microbial isolates, Table S2. LCMS parameters, Table S3. metabolite identifications, Table...

Additional file 2: Table S1A. of Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns

Francesca De Filippis (437252)
Nicoletta Pellegrini (826113)
Luca Laghi (654884)
Marco Gobbetti (468669)
Danilo Ercolini (437255)

October 2016

Prevotella oligotypes representative sequences and BLASTn top hit. Table S1B. Bacteroides oligotypes...

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 3: Table S2. of Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling

Jennifer Lau (784600)
Fiona Whelan (689631)
Isiri Herath (3550367)
Christine Lee (587571)
Stephen Collins (2243821)
Premysl Bercik (3545897)
Michael Surette (3476609)

July 2016

Classification of Lachnospiraceae isolates cultured from Donor HV7 and IBS4 fecal samples. (XLSX 38 ...

Additional file 1: of Genomic and metagenomic insights into the microbial community of a thermal spring

Renato Pedron (6258248)
Alfonso Esposito (3322911)
Irene Bianconi (108469)
Edoardo Pasolli (3155043)
Adrian Tett (642012)
Francesco Asnicar (5198411)
Mario Cristofolini (6258251)
Nicola Segata (103809)
Olivier Jousson (281189)

January 2019

Table S1. Assembly statistics and taxonomy for each genome sequenced. (XLSX 18Â kb

Additional file 2: Table S1. of Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage

Abstract

Extracted data

Additional file 2: Table S1. of Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage

Abstract

Extracted data

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