Evidence map›Paper›PMID 41571653›Full record

ArticleNature communications2026

Phosphorothioate DNA modification by BREX type 4 systems in the human gut microbiome.

Yifeng Yuan, Michael S DeMott, Shane R Byrne, Katia Flores, Mathilde Poyet, Mathieu Groussin, Brittany Berdy, John Rusine Bahunde, Catherine Girard, Jenni Lehtimäki and 11 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Review
  5. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

21 authors.

Yifeng YuanDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Michael S DeMottDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-8575-7277
Shane R ByrneDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Katia FloresDepartment of Microbiology, Duchossois Family Institute, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0009-0006-4410-1462
Mathilde PoyetDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-6905-9017
Mathieu GroussinDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-0942-7217
Brittany BerdyBroad Institute of MIT and Harvard, Cambridge, MA, USA.
John Rusine BahundeGlobal Microbiome Conservancy, Kiel University, Kiel, Germany.
Catherine GirardGlobal Microbiome Conservancy, Kiel University, Kiel, Germany.
Jenni LehtimäkiGlobal Microbiome Conservancy, Kiel University, Kiel, Germany.
Audax Z P MabullaGlobal Microbiome Conservancy, Kiel University, Kiel, Germany.
Ivan Emil MwikaragoGlobal Microbiome Conservancy, Kiel University, Kiel, Germany.
Yvonne Ayerki NarteyGlobal Microbiome Conservancy, Kiel University, Kiel, Germany.
Le Thanh Tu NguyenDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-7012-1121
Charles A OnyekwereGlobal Microbiome Conservancy, Kiel University, Kiel, Germany.
Lewis R RobertsGlobal Microbiome Conservancy, Kiel University, Kiel, Germany.ORCID http://orcid.org/0000-0001-7885-8574
B Jesse ShapiroGlobal Microbiome Conservancy, Kiel University, Kiel, Germany.ORCID http://orcid.org/0000-0001-6819-8699
Tommi VatanenGlobal Microbiome Conservancy, Kiel University, Kiel, Germany.ORCID http://orcid.org/0000-0003-0949-1291
Laurie E ComstockDepartment of Microbiology, Duchossois Family Institute, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0009-0002-6368-8351
Eric J AlmDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Peter C DedonDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. pcdedon@mit.edu.ORCID http://orcid.org/0000-0003-0011-3067

Funding

Secreted antimicrobial proteins of the intestinal BacteriodalesR01AI093771 · NIAID · UNIVERSITY OF CHICAGO · PI LAURIE E COMSTOCK · 2012 to 2026
$5.1M
U.S. Department of Health & Human Services | National Institutes of Health (NIH) R01AI093771U.S. Department of Health & Human Services | National Institutes of Health (NIH) T32-ES007020
6 · The paper itself

Abstract

Among dozens of microbial DNA modifications regulating gene expression and host defense, phosphorothioation (PT) is the only known backbone modification, with sulfur inserted at a non-bridging oxygen by dnd and ssp gene families. Here we explored the distribution of PT genes in 13,663 human gut microbiome genomes, finding that 6.3% possessed dnd or ssp genes predominantly in Bacillota, Bacteroidota, and Pseudomonadota. This analysis revealed several previously undescribed PT synthesis systems, including type 4 Bacteriophage Exclusion (BREX) type 4 brx genes, which we genetically validated in Bacteroides salyersiae. Mass spectrometric analysis of DNA from 226 gut microbiome isolates possessing dnd, ssp, and brx genes revealed 8 PT dinucleotide settings confirmed in 10 consensus sequences by PT-specific DNA sequencing. Genomic analysis showed PT enrichment in rRNA genes and depletion at gene boundaries. These results illustrate the power of the microbiome for discovering prokaryotic epigenetics and the widespread distribution of oxidation-sensitive PTs in gut microbes.

Indexed as

DNA, BacterialMicrobiotaBacteroidesHumansPhosphatesDNA, BacterialPhosphates

Identifiers

PMID41571653
PMCPMC12914056

What OpenQuestion holds

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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.