Evidence map›Paper›PMID 30059804›Full record

ReviewCurrent opinion in microbiology2018

Are microbiome studies ready for hypothesis-driven research?

Anupriya Tripathi, Clarisse Marotz, Antonio Gonzalez, Yoshiki Vázquez-Baeza, Se Jin Song, Amina Bouslimani, Daniel McDonald, Qiyun Zhu, Jon G Sanders, Larry Smarr and 2 more

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Current opinion in microbiology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing 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

12 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Gut dysbiosis: Ecological causes and causative effects on human disease.Proceedings of the National Academy of Sciences of the United States of America · 2023
    Article
  5. Discovering functional small molecules in the gut microbiome.Current opinion in chemical biology · 2023
    Review
  6. The fecal bacterial microbiota of healthy and sick newborn foals.Journal of veterinary internal medicine · 2023
    Article
  7. Review
  8. Review
  9. How gut microbiome interactions affect nutritional traits ofThe Journal of experimental biology · 2020
    Article
  10. Review
  11. Article
  12. Article
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

12 authors.

Anupriya TripathiDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Clarisse MarotzDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Antonio GonzalezDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Yoshiki Vázquez-BaezaDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Se Jin SongDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Amina BouslimaniSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Daniel McDonaldDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Qiyun ZhuDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Jon G SandersDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Larry SmarrDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA; California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, CA, USA.
Pieter C DorresteinDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Rob KnightDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. Electronic address: robknight@ucsd.edu.

Funding

Epidemiology of the gut microbiome, prediabetes and diabetes in LatinosR01MD011389 · NIMHD · ALBERT EINSTEIN COLLEGE OF MEDICINE, INC · PI BURK, ROBERT D, KAPLAN, ROBERT C · 2016 to 2020
$4.3M
Integrated analysis of CVD risk in HIV: gut microbiota, immune function and metabolitesR01HL140976 · NHLBI · ALBERT EINSTEIN COLLEGE OF MEDICINE, INC · PI KAPLAN, ROBERT C, KNIGHT, ROB · 2018 to 2021
$3.3M
New Tools for Understanding the Composition and Dynamics of Microbial CommunitiesR01HG004872 · NHGRI · UNIVERSITY OF COLORADO · PI KNIGHT, ROB · 2008 to 2012
$1.8M
NHGRI NIH HHS R01 HG004872NHLBI NIH HHS R01 HL140976NIMHD NIH HHS R01 MD011389
6 · The paper itself

Abstract

Hypothesis-driven research has led to many scientific advances, but hypotheses cannot be tested in isolation: rather, they require a framework of aggregated scientific knowledge to allow questions to be posed meaningfully. This framework is largely still lacking in microbiome studies, and the only way to create it is by discovery-driven, tool-driven, and standards-driven research projects. Here we illustrate these issues using several such non-hypothesis-driven projects from our own laboratories, including spatial mapping, the American Gut Project, the Earth Microbiome Project (which is an umbrella project integrating many smaller hypothesis-driven projects), and the knowledgebase-driven tools GNPS and Qiita. We argue that an investment of community resources in infrastructure tasks, and in the controls and standards that underpin them, will greatly enhance the investment in hypothesis-driven research programs.

Indexed as

MicrobiotaAnimalsBiomedical ResearchHumans

Identifiers

PMID30059804
PMCPMC6153026

What OpenQuestion holds

Textmetadata
LicenceTDM
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.