Evidence map›Paper›PMID 33594000›Full record

ArticlemSystems2021

Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus.

St Elmo Wilken, Jonathan M Monk, Patrick A Leggieri, Christopher E Lawson, Thomas S Lankiewicz, Susanna Seppälä, Chris G Daum, Jerry Jenkins, Anna M Lipzen, Stephen J Mondo and 7 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in mSystems, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.

0numbers the graph read from it
0cells of the map it votes in
39citing papers in PubMed
4.2field-weighted citation impact, top 5% of its field
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

39 citing papers in PubMed, 67 citations in OpenAlex.

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  16. NAR genomics and bioinformatics · 2024
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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

17 authors at 4 institutions in 2 countries.

St Elmo WilkenDepartment of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA.
Jonathan M MonkDepartment of Bioengineering, University of California San Diego, San Diego, California, USA.
Patrick A LeggieriDepartment of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA.
Christopher E LawsonJoint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, USA.
Thomas S LankiewiczJoint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, USA.
Susanna SeppäläDepartment of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA.
Chris G DaumUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Jerry JenkinsUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Anna M LipzenUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Stephen J MondoUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Kerrie W BarryUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Igor V GrigorievUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
John K HenskeDepartment of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA.
Michael K TheodorouAgriculture Centre for Sustainable Energy Systems, Animal Production, Department of Agriculture and the Environment, Harper Adams University, Newport, United Kingdom.
Bernhard O PalssonDepartment of Bioengineering, University of California San Diego, San Diego, California, USA.ORCID https://orcid.org/0000-0003-2357-6785
Linda R PetzoldDepartment of Computer Science, University of California Santa Barbara, Santa Barbara, California, USA.
Michelle A O'MalleyDepartment of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA momalley@ucsb.edu.ORCID https://orcid.org/0000-0002-6065-8491
Lawrence Berkeley National Laboratory · USUniversity of California, Santa Barbara · USCentre for Sustainable Energy · GBUniversity of California San Diego · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Anaerobic gut fungi in the phylum Neocallimastigomycota typically inhabit the digestive tracts of large mammalian herbivores, where they play an integral role in the decomposition of raw lignocellulose into its constitutive sugar monomers. However, quantitative tools to study their physiology are lacking, partially due to their complex and unresolved metabolism that includes the largely uncharacterized fungal hydrogenosome. Modern omics approaches combined with metabolic modeling can be used to establish an understanding of gut fungal metabolism and develop targeted engineering strategies to harness their degradation capabilities for lignocellulosic bioprocessing. Here, we introduce a high-quality genome of the anaerobic fungus

Indexed as

13C metabolic flux analysisanaerobesanaerobic fungiflux balance analysisgenome-scale metabolic modelNeocallimastigomycotaNeocallimastix lanatinonmodel fungus

Identifiers

PMID33594000
PMCPMC8561657
OpenAlexW3131545130

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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 Socratic graph.