Additional file 7: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

Additional file 2: of Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant

Dagmara Sirová (5130959)
Jiří Bárta (547462)
Karel Šimek (176502)
Thomas Posch (444623)
Jiří Pech (6093119)
James Stone (3432734)
Jakub Borovec (2663791)
Lubomír Adamec (6093122)
Jaroslav Vrba (6093125)

December 2018

Table S5. a Prokaryotic OTUs distribution in samples. b Methanotropic OTUs distribution in samples (...

Additional file 11: 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

Results of similarity calculation for OTU-based family and genus-level classification. (DOCX 15.1 kb

Additional file 7: Table S3. of Temporal dynamics in microbial soil communities at anthrax carcass sites

Karoline Valseth (4470688)
Camilla NesbĂ¸ (4470682)
W. Easterday (4470679)
Wendy Turner (4470673)
Jaran Olsen (4470685)
Nils Stenseth (4470676)
Thomas Haverkamp (4470691)

September 2017

Comparison of taxonomic classification with four different methods: MetaBIT, Metaxa2, MEGAN, and Kra...

Additional file 5: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

Aaron Walsh (4978487)
Fiona Crispie (166390)
Orla O’Sullivan (166383)
Laura Finnegan (4978490)
Marcus Claesson (3421388)
Paul Cotter (802473)

March 2018

Figure S3. Species detected ≥ 2.5% relative abundance in kefir samples using each species classifier...

Additional file 9: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

Aaron Walsh (4978487)
Fiona Crispie (166390)
Orla OâSullivan (3406223)
Laura Finnegan (4978490)
Marcus Claesson (3421388)
Paul Cotter (802473)

March 2018

Figure S6. Dissimilarity plot based on the relative abundances of the 865 level-4 enzyme commission ...

Additional file 10: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

Aaron Walsh (4978487)
Fiona Crispie (166390)
Orla OâSullivan (3406223)
Laura Finnegan (4978490)
Marcus Claesson (3421388)
Paul Cotter (802473)

March 2018

Table S4. Statistical differences in alpha diversity at different sequencing depths. (XLSX 10Â kb

Additional file 2: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

Aaron Walsh (4978487)
Fiona Crispie (166390)
Orla OâSullivan (3406223)
Laura Finnegan (4978490)
Marcus Claesson (3421388)
Paul Cotter (802473)

March 2018

Figure S2. False positives detected using each species classifier with the total number of reads fro...

Additional file 13: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

Aaron Walsh (4978487)
Fiona Crispie (166390)
Orla OâSullivan (3406223)
Laura Finnegan (4978490)
Marcus Claesson (3421388)
Paul Cotter (802473)

March 2018

Figure S8. SUPER-FOCUS level 2 subsystems which were significantly altered at different sequencing d...

Additional file 11: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

Aaron Walsh (4978487)
Fiona Crispie (166390)
Orla OâSullivan (3406223)
Laura Finnegan (4978490)
Marcus Claesson (3421388)
Paul Cotter (802473)

March 2018

Table S5. Statistical differences in the relative abundances of enzyme commission (EC) level-4 categ...

Additional file 7: of Phylogenetic approaches to microbial community classification

Jie Ning (3420689)
Robert Beiko (3245190)

October 2015

Taxonomic composition of samples. The relative abundance of each group in subgingival and supragingi...

Additional file 1: 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

Table S1. PERMANOVA analysis used to assess microbial community structure differences. Table S2. Med...

Additional file 4: of Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant

Dagmara Sirová (5130959)
Jiří Bárta (547462)
Karel Šimek (176502)
Thomas Posch (444623)
Jiří Pech (6093119)
James Stone (3432734)
Jakub Borovec (2663791)
Lubomír Adamec (6093122)
Jaroslav Vrba (6093125)

December 2018

Table S7. Summary of selected protein families (Pfam) based on rpstblastx algorithm. (PDF 410 kb

Additional file 13: 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

Example of similarity calculation (results of calculation in the yellow area of Additional file 12)....

Additional file 14: 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

Relative abundance of intestinal microbiome (species level classification of OTUs). (XLSX 2182 kb

Additional file 11: of Phylogenetic approaches to microbial community classification

Jie Ning (3420689)
Robert Beiko (3245190)

October 2015

The predictions on all samples: (a) SVM vs random forests, (b) SVM vs SourceTracker. The values on x...

Additional file 2: of Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant

Dagmara Sirová (5130959)
Jiří Bárta (547462)
Karel Šimek (176502)
Thomas Posch (444623)
Jiří Pech (6093119)
James Stone (3432734)
Jakub Borovec (2663791)
Lubomír Adamec (6093122)
Jaroslav Vrba (6093125)

December 2018

Table S5. a Prokaryotic OTUs distribution in samples. b Methanotropic OTUs distribution in samples (...

Additional file 11: 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

Results of similarity calculation for OTU-based family and genus-level classification. (DOCX 15.1 kb

Additional file 7: Table S3. of Temporal dynamics in microbial soil communities at anthrax carcass sites

Karoline Valseth (4470688)
Camilla NesbĂ¸ (4470682)
W. Easterday (4470679)
Wendy Turner (4470673)
Jaran Olsen (4470685)
Nils Stenseth (4470676)
Thomas Haverkamp (4470691)

September 2017

Comparison of taxonomic classification with four different methods: MetaBIT, Metaxa2, MEGAN, and Kra...

Additional file 5: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

Aaron Walsh (4978487)
Fiona Crispie (166390)
Orla O’Sullivan (166383)
Laura Finnegan (4978490)
Marcus Claesson (3421388)
Paul Cotter (802473)

March 2018

Figure S3. Species detected ≥ 2.5% relative abundance in kefir samples using each species classifier...

Additional file 9: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

Aaron Walsh (4978487)
Fiona Crispie (166390)
Orla OâSullivan (3406223)
Laura Finnegan (4978490)
Marcus Claesson (3421388)
Paul Cotter (802473)

March 2018

Figure S6. Dissimilarity plot based on the relative abundances of the 865 level-4 enzyme commission ...

Additional file 10: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

Aaron Walsh (4978487)
Fiona Crispie (166390)
Orla OâSullivan (3406223)
Laura Finnegan (4978490)
Marcus Claesson (3421388)
Paul Cotter (802473)

March 2018

Table S4. Statistical differences in alpha diversity at different sequencing depths. (XLSX 10Â kb

Additional file 2: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

Aaron Walsh (4978487)
Fiona Crispie (166390)
Orla OâSullivan (3406223)
Laura Finnegan (4978490)
Marcus Claesson (3421388)
Paul Cotter (802473)

March 2018

Figure S2. False positives detected using each species classifier with the total number of reads fro...

Additional file 13: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

Aaron Walsh (4978487)
Fiona Crispie (166390)
Orla OâSullivan (3406223)
Laura Finnegan (4978490)
Marcus Claesson (3421388)
Paul Cotter (802473)

March 2018

Figure S8. SUPER-FOCUS level 2 subsystems which were significantly altered at different sequencing d...

Additional file 11: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

Aaron Walsh (4978487)
Fiona Crispie (166390)
Orla OâSullivan (3406223)
Laura Finnegan (4978490)
Marcus Claesson (3421388)
Paul Cotter (802473)

March 2018

Table S5. Statistical differences in the relative abundances of enzyme commission (EC) level-4 categ...

Additional file 7: of Phylogenetic approaches to microbial community classification

Jie Ning (3420689)
Robert Beiko (3245190)

October 2015

Taxonomic composition of samples. The relative abundance of each group in subgingival and supragingi...

Additional file 1: 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

Table S1. PERMANOVA analysis used to assess microbial community structure differences. Table S2. Med...

Additional file 4: of Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant

Dagmara Sirová (5130959)
Jiří Bárta (547462)
Karel Šimek (176502)
Thomas Posch (444623)
Jiří Pech (6093119)
James Stone (3432734)
Jakub Borovec (2663791)
Lubomír Adamec (6093122)
Jaroslav Vrba (6093125)

December 2018

Table S7. Summary of selected protein families (Pfam) based on rpstblastx algorithm. (PDF 410 kb

Additional file 13: 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

Example of similarity calculation (results of calculation in the yellow area of Additional file 12)....

Additional file 14: 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

Relative abundance of intestinal microbiome (species level classification of OTUs). (XLSX 2182 kb

Additional file 11: of Phylogenetic approaches to microbial community classification

Jie Ning (3420689)
Robert Beiko (3245190)

October 2015

The predictions on all samples: (a) SVM vs random forests, (b) SVM vs SourceTracker. The values on x...

Additional file 2: of Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant

Dagmara Sirová (5130959)
Jiří Bárta (547462)
Karel Šimek (176502)
Thomas Posch (444623)
Jiří Pech (6093119)
James Stone (3432734)
Jakub Borovec (2663791)
Lubomír Adamec (6093122)
Jaroslav Vrba (6093125)

December 2018

Table S5. a Prokaryotic OTUs distribution in samples. b Methanotropic OTUs distribution in samples (...

Additional file 11: 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

Results of similarity calculation for OTU-based family and genus-level classification. (DOCX 15.1 kb

Additional file 7: Table S3. of Temporal dynamics in microbial soil communities at anthrax carcass sites

Karoline Valseth (4470688)
Camilla NesbĂ¸ (4470682)
W. Easterday (4470679)
Wendy Turner (4470673)
Jaran Olsen (4470685)
Nils Stenseth (4470676)
Thomas Haverkamp (4470691)

September 2017

Comparison of taxonomic classification with four different methods: MetaBIT, Metaxa2, MEGAN, and Kra...

Additional file 7: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

Abstract

Extracted data

Additional file 7: of Species classifier choice is a key consideration when analysing low-complexity food microbiome data

Abstract

Extracted data

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