Principal components analysis of unweighted (A) and weighted (B) UniFrac distances for sequences derived from the CloVR pipeline for each of the replicate Hackberry Bay (HB) and Lake Caillou (LC) stomach (S) and gut microbiomes (G).

Associating microbiome composition with environmental covariates using generalized UniFrac distances

Jun Chen
Kyle Bittinger
Emily S. Charlson
Christian Hoffmann
James Lewis
Gary D. Wu
Ronald G. Collman
Frederic D. Bushman
Hongzhe Li

January 2012

Motivation: The human microbiome plays an important role in human disease and health. Identification...

Associating microbiome composition with environmental covariates using generalized UniFrac distances

Jun Chen
Kyle Bittinger
Emily S. Charlson
Christian Hoffmann
James Lewis
Gary D. Wu
Ronald G. Collman
Frederic D. Bushman
Hongzhe Li

January 2012

Motivation: The human microbiome plays an important role in human disease and health. Identification...

Principal component analyses (PCA) of the microbiota profiles and Principal Coordinate of Analyses (PcoA) plot of the weighted and unweighted UniFrac average distance per site and DNA extraction method.

Giske Biesbroek (104538)
Elisabeth A. M. Sanders (104551)
Guus Roeselers (178815)
Xinhui Wang (126681)
Martien P. M. Caspers (179975)
Krzysztof Trzciński (4391362)
Debby Bogaert (23222)
Bart J. F. Keijser (143225)

March 2012

a. Principal component analyses (PCA) of the microbiota profiles of the nares and nasophar...

Cluster analysis based on UniFrac distances for sequences derived from the CloVR pipeline for each of the replicate Hackberry Bay (HB) and Lake Caillou (LC) stomach (S) and gut microbiomes (G).

Gary M. King (113107)
Craig Judd (113111)
Cheryl R. Kuske (113115)
Conor Smith (113119)

December 2012

Cluster analysis based on UniFrac distances for sequences derived from the CloVR pipeline for eac...

Principal component analysis (PCA) with weighted UniFrac distance analysis of the microbiomes from the four animal populations.

Liang Ming (280713)
Li Yi (167757)
Siriguleng (3841750)
Surong Hasi (3841744)
Jing He (58446)
Le Hai (3841741)
Zhaoxia Wang (470659)
Fucheng Guo (3841747)
Xiangyu Qiao (3841753)
Jirimutu (3841738)

March 2017

Principal component analysis (PCA) with weighted UniFrac distance analysis of the microbiomes fro...

Principal coordinate analysis of unweighted UniFrac distances representing phylogenetic clustering of gut and environmental microbiome constituents in samples from households in western Kenya.

Emily Mosites (543355)
Matt Sammons (3713101)
Elkanah Otiang (709575)
Alexander Eng (3713107)
Cecilia Noecker (3713095)
Ohad Manor (396214)
Sarah Hilton (3713098)
Samuel M. Thumbi (525095)
Clayton Onyango (3713092)
Gemina Garland-Lewis (3713089)
Douglas R. Call (140388)
M. Kariuki Njenga (310301)
Judith N. Wasserheit (3713104)
Jennifer A. Zambriski (340591)
Judd L. Walson (122434)
Guy H. Palmer (305017)
Joel Montgomery (3508901)
Elhanan Borenstein (68815)
Richard Omore (2636782)
Peter M. Rabinowitz (305294)

February 2017

Principal coordinate analysis of unweighted UniFrac distances representing phylogenetic clusterin...

Principal component analysis.

Joshua D. Sackett (4966972)
Desiree C. Huerta (4966975)
Brittany R. Kruger (4926280)
Scott D. Hamilton-Brehm (4926274)
Duane P. Moser (396349)

March 2018

Principal component analysis ordinations of a) pairwise abundance-unweighted UniFrac distances an...

UPGMA analysis clustering analysis based on UniFrac distance matrix.

Yu Zuo (4643950)
Wenfang Xie (4662691)
Yue Pang (168110)
Tiesong Li (4039253)
Qingwei Li (168118)
Yingying Li (50341)

December 2017

(A) UPGMA tree based on unweighted unifrac distance matrix; (B) UPGMA tree based on weighted unif...

Principal Component Analysis (PCoA) generated among groups at genus level using Weighted UniFrac metric (a measure of differences in bacterial community structure).

Aránzazu Portillo (4578847)
Ana M. Palomar (6482669)
María de Toro (676611)
Sonia Santibáñez (6482672)
Paula Santibáñez (3536945)
José A. Oteo (5651539)

March 2019

Principal Component Analysis (PCoA) generated among groups at genus level using Weighted UniFrac met...

UniFrac principal coordinates analysis (PCoA) displaying correlations among the bacterial communities of the 4 groups.

Phillip R. Myer (747607)
Timothy P. L. Smith (186111)
James E. Wells (747608)
Larry A. Kuehn (487359)
Harvey C. Freetly (487365)

June 2015

A) Weighted PCoA analyzed from rarefied subsets of 25,000 sequences from each sample. B) Unweight...

Cluster analysis based on unweighted (A) and weighted (B) UniFrac distances obtained for C. virginica microbiomes (HB-S, HB-G, LC-S, LC-G as above; this study) and microbiome compositions derived from 16S rRNA gene clone libraries (accession numbers in parenthesis) of an herbivorous coral reef surgeon fish, Acanthurus nigrificans (gut sequences FJ653927–FJ65392774 [68]); the carnivorous mitten crab, Eriocheir sinensis (gut sequences DQ856498–DQ856562 [69]); a detritivorous/phytophagus polychaete, Neanthes glandicincta (gut sequences FJ618851–FJ618896 [70]); the macroalgae-consumng gastropod small abalone, Haliotis diversicolor (gut sequences GU070680–GU070693 [41]); and the filter-feeding Sydney rock oyster, Saccostrea glomerata (digestive gland sequences FM995169–FM995191 [33]).

Gary M. King (113107)
Craig Judd (113111)
Cheryl R. Kuske (113115)
Conor Smith (113119)

December 2012

All sequences were aligned with the NAST Aligner; a BioNJ tree was used as input for UniFrac. Wei...

Principal coordinate analysis (PCoA) based on weighted-UniFrac analysis of bacterial populations associated with P. monodon intestines from the wild-caught group (WC1, WC2, and WC3) and the domesticated group (DB1, DB2 and DB3).

Wanilada Rungrassamee (399945)
Amornpan Klanchui (107611)
Sawarot Maibunkaew (399947)
Sage Chaiyapechara (399946)
Pikul Jiravanichpaisal (218252)
Nitsara Karoonuthaisiri (107618)

March 2014

Principal coordinate analysis (PCoA) based on weighted-UniFrac analysis of bacterial populations ...

PCoA plot based on UniFrac distances of the gut microbial communities established in the luminal and mucosal phases for the ascending, transverse and descending regions over time.

LinShu Liu (2701012)
Jenni Firrman (5523710)
Ceylan Tanes (4007951)
Kyle Bittinger (137003)
Audrey Thomas-Gahring (5523713)
Gary D. Wu (142852)
Pieter Van den Abbeele (1898065)
Peggy M. Tomasula (5523716)

July 2018

After calculating the axes, the samples are faceted into their corresponding regions. The dashed ...

Principal Coordinates Analysis of weighted UniFrac distances for 16S rRNA gene sequence data.

Paola Piombino (512534)
Alessandro Genovese (512535)
Silvia Esposito (266725)
Luigi Moio (512536)
Pier Paolo Cutolo (512537)
Angela Chambery (471340)
Valeria Severino (471334)
Elisabetta Moneta (512538)
Daniel P. Smith (208490)
Sarah M. Owens (512539)
Jack A. Gilbert (53472)
Danilo Ercolini (437255)

January 2014

The distribution shows distances within and across normal-weight (N, red ▪) and obese (O, blu •) ...

Associating microbiome composition with environmental covariates using generalized UniFrac distances

Jun Chen
Kyle Bittinger
Emily S. Charlson
Christian Hoffmann
James Lewis
Gary D. Wu
Ronald G. Collman
Frederic D. Bushman
Hongzhe Li

November 2015

Motivation: The human microbiome plays an important role in human disease and health. Identification...

Associating microbiome composition with environmental covariates using generalized UniFrac distances

Jun Chen
Kyle Bittinger
Emily S. Charlson
Christian Hoffmann
James Lewis
Gary D. Wu
Ronald G. Collman
Frederic D. Bushman
Hongzhe Li

January 2012

Motivation: The human microbiome plays an important role in human disease and health. Identification...

Associating microbiome composition with environmental covariates using generalized UniFrac distances

Jun Chen
Kyle Bittinger
Emily S. Charlson
Christian Hoffmann
James Lewis
Gary D. Wu
Ronald G. Collman
Frederic D. Bushman
Hongzhe Li

January 2012

Motivation: The human microbiome plays an important role in human disease and health. Identification...

Principal component analyses (PCA) of the microbiota profiles and Principal Coordinate of Analyses (PcoA) plot of the weighted and unweighted UniFrac average distance per site and DNA extraction method.

Giske Biesbroek (104538)
Elisabeth A. M. Sanders (104551)
Guus Roeselers (178815)
Xinhui Wang (126681)
Martien P. M. Caspers (179975)
Krzysztof Trzciński (4391362)
Debby Bogaert (23222)
Bart J. F. Keijser (143225)

March 2012

a. Principal component analyses (PCA) of the microbiota profiles of the nares and nasophar...

Cluster analysis based on UniFrac distances for sequences derived from the CloVR pipeline for each of the replicate Hackberry Bay (HB) and Lake Caillou (LC) stomach (S) and gut microbiomes (G).

Gary M. King (113107)
Craig Judd (113111)
Cheryl R. Kuske (113115)
Conor Smith (113119)

December 2012

Cluster analysis based on UniFrac distances for sequences derived from the CloVR pipeline for eac...

Principal component analysis (PCA) with weighted UniFrac distance analysis of the microbiomes from the four animal populations.

Liang Ming (280713)
Li Yi (167757)
Siriguleng (3841750)
Surong Hasi (3841744)
Jing He (58446)
Le Hai (3841741)
Zhaoxia Wang (470659)
Fucheng Guo (3841747)
Xiangyu Qiao (3841753)
Jirimutu (3841738)

March 2017

Principal component analysis (PCA) with weighted UniFrac distance analysis of the microbiomes fro...

Principal coordinate analysis of unweighted UniFrac distances representing phylogenetic clustering of gut and environmental microbiome constituents in samples from households in western Kenya.

Emily Mosites (543355)
Matt Sammons (3713101)
Elkanah Otiang (709575)
Alexander Eng (3713107)
Cecilia Noecker (3713095)
Ohad Manor (396214)
Sarah Hilton (3713098)
Samuel M. Thumbi (525095)
Clayton Onyango (3713092)
Gemina Garland-Lewis (3713089)
Douglas R. Call (140388)
M. Kariuki Njenga (310301)
Judith N. Wasserheit (3713104)
Jennifer A. Zambriski (340591)
Judd L. Walson (122434)
Guy H. Palmer (305017)
Joel Montgomery (3508901)
Elhanan Borenstein (68815)
Richard Omore (2636782)
Peter M. Rabinowitz (305294)

February 2017

Principal coordinate analysis of unweighted UniFrac distances representing phylogenetic clusterin...

Principal component analysis.

Joshua D. Sackett (4966972)
Desiree C. Huerta (4966975)
Brittany R. Kruger (4926280)
Scott D. Hamilton-Brehm (4926274)
Duane P. Moser (396349)

March 2018

Principal component analysis ordinations of a) pairwise abundance-unweighted UniFrac distances an...

UPGMA analysis clustering analysis based on UniFrac distance matrix.

Yu Zuo (4643950)
Wenfang Xie (4662691)
Yue Pang (168110)
Tiesong Li (4039253)
Qingwei Li (168118)
Yingying Li (50341)

December 2017

(A) UPGMA tree based on unweighted unifrac distance matrix; (B) UPGMA tree based on weighted unif...

Principal Component Analysis (PCoA) generated among groups at genus level using Weighted UniFrac metric (a measure of differences in bacterial community structure).

Aránzazu Portillo (4578847)
Ana M. Palomar (6482669)
María de Toro (676611)
Sonia Santibáñez (6482672)
Paula Santibáñez (3536945)
José A. Oteo (5651539)

March 2019

Principal Component Analysis (PCoA) generated among groups at genus level using Weighted UniFrac met...

UniFrac principal coordinates analysis (PCoA) displaying correlations among the bacterial communities of the 4 groups.

Phillip R. Myer (747607)
Timothy P. L. Smith (186111)
James E. Wells (747608)
Larry A. Kuehn (487359)
Harvey C. Freetly (487365)

June 2015

A) Weighted PCoA analyzed from rarefied subsets of 25,000 sequences from each sample. B) Unweight...

Cluster analysis based on unweighted (A) and weighted (B) UniFrac distances obtained for C. virginica microbiomes (HB-S, HB-G, LC-S, LC-G as above; this study) and microbiome compositions derived from 16S rRNA gene clone libraries (accession numbers in parenthesis) of an herbivorous coral reef surgeon fish, Acanthurus nigrificans (gut sequences FJ653927–FJ65392774 [68]); the carnivorous mitten crab, Eriocheir sinensis (gut sequences DQ856498–DQ856562 [69]); a detritivorous/phytophagus polychaete, Neanthes glandicincta (gut sequences FJ618851–FJ618896 [70]); the macroalgae-consumng gastropod small abalone, Haliotis diversicolor (gut sequences GU070680–GU070693 [41]); and the filter-feeding Sydney rock oyster, Saccostrea glomerata (digestive gland sequences FM995169–FM995191 [33]).

Gary M. King (113107)
Craig Judd (113111)
Cheryl R. Kuske (113115)
Conor Smith (113119)

December 2012

All sequences were aligned with the NAST Aligner; a BioNJ tree was used as input for UniFrac. Wei...

Principal coordinate analysis (PCoA) based on weighted-UniFrac analysis of bacterial populations associated with P. monodon intestines from the wild-caught group (WC1, WC2, and WC3) and the domesticated group (DB1, DB2 and DB3).

Wanilada Rungrassamee (399945)
Amornpan Klanchui (107611)
Sawarot Maibunkaew (399947)
Sage Chaiyapechara (399946)
Pikul Jiravanichpaisal (218252)
Nitsara Karoonuthaisiri (107618)

March 2014

Principal coordinate analysis (PCoA) based on weighted-UniFrac analysis of bacterial populations ...

PCoA plot based on UniFrac distances of the gut microbial communities established in the luminal and mucosal phases for the ascending, transverse and descending regions over time.

LinShu Liu (2701012)
Jenni Firrman (5523710)
Ceylan Tanes (4007951)
Kyle Bittinger (137003)
Audrey Thomas-Gahring (5523713)
Gary D. Wu (142852)
Pieter Van den Abbeele (1898065)
Peggy M. Tomasula (5523716)

July 2018

After calculating the axes, the samples are faceted into their corresponding regions. The dashed ...

Principal Coordinates Analysis of weighted UniFrac distances for 16S rRNA gene sequence data.

Paola Piombino (512534)
Alessandro Genovese (512535)
Silvia Esposito (266725)
Luigi Moio (512536)
Pier Paolo Cutolo (512537)
Angela Chambery (471340)
Valeria Severino (471334)
Elisabetta Moneta (512538)
Daniel P. Smith (208490)
Sarah M. Owens (512539)
Jack A. Gilbert (53472)
Danilo Ercolini (437255)

January 2014

The distribution shows distances within and across normal-weight (N, red ▪) and obese (O, blu •) ...

Associating microbiome composition with environmental covariates using generalized UniFrac distances

Jun Chen
Kyle Bittinger
Emily S. Charlson
Christian Hoffmann
James Lewis
Gary D. Wu
Ronald G. Collman
Frederic D. Bushman
Hongzhe Li

November 2015

Motivation: The human microbiome plays an important role in human disease and health. Identification...

Associating microbiome composition with environmental covariates using generalized UniFrac distances

Jun Chen
Kyle Bittinger
Emily S. Charlson
Christian Hoffmann
James Lewis
Gary D. Wu
Ronald G. Collman
Frederic D. Bushman
Hongzhe Li

January 2012

Motivation: The human microbiome plays an important role in human disease and health. Identification...

Associating microbiome composition with environmental covariates using generalized UniFrac distances

Jun Chen
Kyle Bittinger
Emily S. Charlson
Christian Hoffmann
James Lewis
Gary D. Wu
Ronald G. Collman
Frederic D. Bushman
Hongzhe Li

January 2012

Motivation: The human microbiome plays an important role in human disease and health. Identification...

Principal component analyses (PCA) of the microbiota profiles and Principal Coordinate of Analyses (PcoA) plot of the weighted and unweighted UniFrac average distance per site and DNA extraction method.

Giske Biesbroek (104538)
Elisabeth A. M. Sanders (104551)
Guus Roeselers (178815)
Xinhui Wang (126681)
Martien P. M. Caspers (179975)
Krzysztof Trzciński (4391362)
Debby Bogaert (23222)
Bart J. F. Keijser (143225)

March 2012

a. Principal component analyses (PCA) of the microbiota profiles of the nares and nasophar...

Principal components analysis of unweighted (A) and weighted (B) UniFrac distances for sequences derived from the CloVR pipeline for each of the replicate Hackberry Bay (HB) and Lake Caillou (LC) stomach (S) and gut microbiomes (G).

Abstract

Extracted data

Principal components analysis of unweighted (A) and weighted (B) UniFrac distances for sequences derived from the CloVR pipeline for each of the replicate Hackberry Bay (HB) and Lake Caillou (LC) stomach (S) and gut microbiomes (G).

Abstract

Extracted data

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