PhyloPlus: a Universal Tool for Phylogenetic Interrogation of Metagenomic Communities.

Xinyang Huang, David L Erickson, Jianghong Meng

Abstract read

In one paragraph

Article in mBio, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Xinyang HuangJoint Institute for Food Safety and Applied Nutrition, Center for Food Safety Security Systems, University of Maryland, College Park, Maryland, USA.

David L EricksonJoint Institute for Food Safety and Applied Nutrition, Center for Food Safety Security Systems, University of Maryland, College Park, Maryland, USA.

Jianghong MengJoint Institute for Food Safety and Applied Nutrition, Center for Food Safety Security Systems, University of Maryland, College Park, Maryland, USA.

Funding

Cooperative Agreement to Support the Joint Institute for Food Safety and Applied Nutrition (JIFSAN)U01FD001418 · FDA · UNIV OF MARYLAND, COLLEGE PARK · PI Jianghong Meng · 2005 to 2026

$55.4M

FDA HHS U01 FD001418

6 · The paper itself

Abstract

Phylogeny is a powerful tool that can be incorporated into quantitative descriptions of community diversity, yet its use has been limited largely due to the difficulty in constructing phylogenies which incorporate the wide genomic diversity of microbial communities. Here, we describe the development of a web portal, PhyloPlus, which enables users to generate customized phylogenies that may be applied to any bacterial or archaeal communities. We demonstrate the power of phylogeny by comparing metrics that employ phylogeny with those that do not when applied to data sets from two metagenomic studies (fermented food,

Indexed as

MetagenomeMicrobiotaBacteriaHumansMetagenomicsPhylogenyRNA, Ribosomal, 16SRNA, Ribosomal, 16Sdiversitymetagenomicsmicrobial genomicsmicrobiomephylogeny

Identifiers

PMID36645293

DOI10.1128/mbio.03455-22

PMCPMC9973285

What OpenQuestion holds

Textmetadata

LicenceCC BY

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.