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PICRUSt specifications

Information


Unique identifier OMICS_06549
Name PICRUSt
Alternative name Phylogenetic investigation of communities by reconstruction of unobserved states
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Morgan G. I. Langille

Information


Unique identifier OMICS_06549
Name PICRUSt
Alternative name Phylogenetic investigation of communities by reconstruction of unobserved states
Interface Web user interface
Restrictions to use None
Programming languages Python
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Morgan G. I. Langille

Publications for Phylogenetic investigation of communities by reconstruction of unobserved states

PICRUSt citations

 (497)
call_split

Food Starch Structure Impacts Gut Microbiome Composition

2018
PMCID: 5956147
PMID: 29769378
DOI: 10.1128/mSphere.00086-18
call_split See protocol

[…] tric () in QIIME. Calypso () version 5.2 was used to generate hierarchical clustering, principal-coordinate analysis (PCoA) plots, and microbial network maps. Metagenomic function was predicted using PICRUSt () online Galaxy version by the method of Umu et al. (). Heat maps were generated using Calypso and gplots package in R.The White’s nonparametric t test and Kruskal-Wallis H test were performe […]

library_books

Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer

2018
mSystems
PMCID: 5954203
DOI: 10.1128/mSystems.00205-17

[…] -driven glycan production.It is important to note that our study uses 16S rRNA gene sequencing to characterize microbiome taxonomic composition and computationally predicted pathway composition using PICRUSt v1.0.0 (). Although this method is widely used, metagenomic shotgun sequencing can be more accurate and informative in understanding the functional makeup of a microbial community. Similarly, […]

library_books

Different rearing conditions alter gut microbiota composition and host physiology in Shaoxing ducks

2018
Sci Rep
PMCID: 5943461
PMID: 29743727
DOI: 10.1038/s41598-018-25760-7

[…] To evaluate the functional capabilities of gut microbiome of each luminal section and each rearing conditions, PICRUSt was used to predict the functions of microbial communities. In addition, differentially abundant functional components across different intestinal sections and under different rearing conditio […]

library_books

Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate

2018
Microbiome
PMCID: 5935910
PMID: 29729671
DOI: 10.1186/s40168-018-0468-6

[…] nd a neighbor joining tree [] was constructed using MEGA v7.0.26 []. The phylogeny of OTUs classified to the phylum Fibrobacteres was constructed in the same fashion. Metagenomes were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt 1.1.1) [] after normalizing for 16S rRNA gene copy number. Oligotyping was done using the DADA2 R-package [] w […]

call_split

Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging

2018
Front Microbiol
PMCID: 5943489
PMID: 29774014
DOI: 10.3389/fmicb.2018.00862
call_split See protocol

[…] Se) (Segata et al., ). A heatmap was obtained using R scripts with the clustering distance of “correlation” and clustering method of the “ward.D2” settings. The metagenome content was predicted using PICRUSt (Langille et al., ), and the KEGG pathway was generated. […]

call_split

Small Bowel Transit and Altered Gut Microbiota in Patients With Liver Cirrhosis

2018
Front Physiol
PMCID: 5946013
PMID: 29780327
DOI: 10.3389/fphys.2018.00470
call_split See protocol

[…] sed in LC included Acidaminococcaceae, Porphyromonadaceae, Prevotellaceae, and Bacteroidaceae. Functional composition profiles of the gut metagenomes were predicted from 16S rRNA gene sequences using PICRUSt in the form of level III KEGG database pathways ().All statistical analyzes were performed using R and SPSS 19.0 software. For comparison of continuous variables, the Mann–Whitney U test was u […]

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PICRUSt institution(s)
Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada

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