Evidence map›Paper›PMID 29056429›Full record

ArticleCell host & microbe2017

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung.

Neha Garg, Mingxun Wang, Embriette Hyde, Ricardo R da Silva, Alexey V Melnik, Ivan Protsyuk, Amina Bouslimani, Yan Wei Lim, Richard Wong, Greg Humphrey and 10 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell host & microbe, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.

0numbers the graph read from it
0cells of the map it votes in
75citing 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

75 citing papers in PubMed.

  1. Review
  2. Article
  3. Review
  4. Article
  5. Review
  6. Review
  7. Article
  8. Review
  9. Review
  10. Metabolomic Analysis of Polymicrobial Wound Infections and an Associated Adhesive Bandage.Journal of the American Society for Mass Spectrometry · 2023
    Article
  11. Article
  12. Article
  13. The biogeography of infection revisited.Nature reviews. Microbiology · 2022
    Review
  14. Review
  15. Article
  16. Article
  17. Review
  18. Chemical Cartography Approaches to Study Trypanosomatid Infection.Journal of visualized experiments : JoVE · 2022
    Article
  19. Review
  20. Article

15 more citing papers are in PubMed but not listed here.

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

20 authors.

Neha GargCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
Mingxun WangDepartment of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
Embriette HydeDepartment of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
Ricardo R da SilvaCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
Alexey V MelnikCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
Ivan ProtsyukStructural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
Amina BouslimaniCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
Yan Wei LimBiology Department, San Diego State University, San Diego, CA, USA.
Richard WongDepartment of Pathology, University of California, San Diego Health, San Diego, CA 92103, USA.
Greg HumphreyDepartment of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
Gail AckermannDepartment of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
Timothy SpiveyDepartment of Radiology, University of California, San Diego Health, San Diego, CA 92103, USA.
Sharon S BrouhaDepartment of Radiology, University of California, San Diego Health, San Diego, CA 92103, USA.
Nuno BandeiraDepartment of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
Grace Y LinDepartment of Pathology, University of California, San Diego Health, San Diego, CA 92103, USA.
Forest RohwerBiology Department, San Diego State University, San Diego, CA, USA.
Douglas J ConradDepartment of Medicine, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: dconrad@ucsd.edu.
Theodore AlexandrovCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany. Electronic address: theodore.alexandrov@embl.de.
Rob KnightDepartment of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: rknight@ucsd.edu.
Pieter C DorresteinCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: pdorrestein@ucsd.edu.

Funding

SAN DIEGO CLINICAL AND TRANSLATIONAL RESEARCH INSTITUTEUL1RR031980 · NCRR · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI FIRESTEIN, GARY S · 2010 to 2011
$14.0M
TrainingP41GM103484 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PEVZNER, PAVEL A · 2012 to 2018
$8.7M
Ecology of Cystic Fibrosis: Administrative SupplementR01GM095384 · NIGMS · SAN DIEGO STATE UNIVERSITY · PI ROHWER, FOREST L · 2011 to 2014
$1.9M
Reuse of Public Metabolomics DataR03CA211211 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DORRESTEIN, PIETER C · 2016 to 2016
$155k
NCI NIH HHS R03 CA211211NCRR NIH HHS UL1 RR031980NIGMS NIH HHS P41 GM103484NIGMS NIH HHS R01 GM095384
6 · The paper itself

Abstract

Our understanding of the spatial variation in the chemical and microbial makeup of an entire human organ remains limited, in part due to the size and heterogeneity of human organs and the complexity of the associated metabolome and microbiome. To address this challenge, we developed a workflow to enable the cartography of metabolomic and microbiome data onto a three-dimensional (3D) organ reconstruction built off radiological images. This enabled the direct visualization of the microbial and chemical makeup of a human lung from a cystic fibrosis patient. We detected host-derived molecules, microbial metabolites, medications, and region-specific metabolism of medications and placed it in the context of microbial distributions in the lung. Our tool further created browsable maps of a 3D microbiome/metabolome reconstruction map on a radiological image of a human lung and forms an interactive resource for the scientific community.

Indexed as

AdultBase SequenceBiodiversityCystic FibrosisDNA, BacterialHumansImaging, Three-DimensionalLungLung DiseasesMaleMass SpectrometryMetabolomeMetabolomicsMicrobiotaRNA, Ribosomal, 16SRNA, Ribosomal, 18SDNA, BacterialRNA, Ribosomal, 16SRNA, Ribosomal, 18SXenobioticscartographycystic fibrosismass spectrometrymetabolomicsmicrobiomemolecular networking

Identifiers

PMID29056429
PMCPMC6267898

What OpenQuestion holds

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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 OpenQuestion graph.