Evidence map›Paper›PMID 40828023›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2025

Synergistic action of specialized metabolites from divergent biosynthesis in the human oral microbiome.

McKenna Loop Yao, Nicholas A Zill, Colin Charles Barber, Yongle Du, Peijun Lin, Rui Zhai, Eunice Yoon, Dunya Al Marzooqi, Wenjun Zhang

Erratum issuedAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Synergistic action of specialized metabolites from divergent biosynthesis in the human oral microbiome.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors.

McKenna Loop Yao *Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720.ORCID 0009-0008-8310-0635
Nicholas A Zill *Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720.
Colin Charles Barber *Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720.
Yongle DuDepartment of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720.
Peijun LinCollege of Computing, Data Science, and Society, University of California Berkeley, Berkeley, CA 94720.
Rui ZhaiDepartment of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720.
Eunice YoonDepartment of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720.
Dunya Al MarzooqiDepartment of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720.
Wenjun ZhangDepartment of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720.ORCID 0000-0001-9348-972X

Funding

National Metabolomics Data Repository - nextgen Metabolomics WorkbenchU2CDK119886 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SUBRAMANIAM, SHANKAR · 2018 to 2021
$12.7M
Biomedical Data Commons Workbench (BDCW)OT2OD030544 · OD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SUBRAMANIAM, SHANKAR · 2020 to 2024
$3.2M
Bioactive natural product discovery from human oral microbesR01DE032732 · NIDCR · UNIVERSITY OF CALIFORNIA BERKELEY · PI Wenjun Zhang · 2024 to 2026
$1.1M
GPU Computing Cluster for Transformative Public Health driven Molecular ScienceS10OD034382 · OD · UNIVERSITY OF CALIFORNIA BERKELEY · PI DURKIN, KATHLEEN A · 2023 to 2023
$491k
HHS | NIH | National Institute of Dental and Craniofacial Research (NIDR) R01DE032732NIDCR NIH HHS R01 DE032732NIDDK NIH HHS U2C DK119886NIH HHS OT2 OD030544NIH HHS S10 OD034382NSF | NSF Graduate Research Fellowship Program (GRFP) DGE2146752
6 · The paper itself

Abstract

Despite extensive efforts, our understanding of the virulence factors contributing to oral biofilm formation-a hallmark of dental caries-remains incomplete. We present evidence that the specialized metabolism of the oral microbiome is a critical yet underexplored factor in oral biofilm formation. Through microbiome analysis, we identified a hybrid nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) encoding biosynthetic gene cluster that correlates with dental caries and is widely represented in oral pathogens, including

Indexed as

MicrobiotaMouthStreptococcus mutansBacterial ProteinsBiofilmsDental CariesHumansMultigene FamilyPeptide SynthasesPolyketide SynthasesBacterial Proteinsnon-ribosomal peptide synthasePeptide SynthasesPolyketide Synthasesdental cariesnatural productsoral microbiomeStreptococcus mutans

Identifiers

PMID40828023
PMCPMC12403116

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.