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; Audax Z.P. Mabulla; Ivan Emil Mwikarago; Yvonne Ayerki Nartey; Le Thanh Tu Nguyen; Charles A. Onyekwere; Lewis R. Roberts; B. Jesse Shapiro; Tommi Vatanen; Laurie E. Comstock; Eric J. Alm; Peter C. Dedon

doi:10.1038/s41467-026-68412-5

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
, Audax Z.P. Mabulla
, Ivan Emil Mwikarago
, Yvonne Ayerki Nartey
, Le Thanh Tu Nguyen
, Charles A. Onyekwere
, Lewis R. Roberts
, B. Jesse Shapiro
, Tommi Vatanen
, Laurie E. Comstock
, Eric J. Alm

Peter C. Dedon

Massachusetts Institute of Technology
CODOMAX INC.
The University of Chicago
Kiel University
Broad Institute
MGH Institute of Health Professions
University of Rwanda
The United States Pharmacopeial Convention
Community Options
Université du Québec à Chicoutimi
CHU de Quebec Research Center Laval University
Finnish Environment Institute
University of Dar es Salaam
Division of Human Medicine and Device Registration
University of Cape Coast Ghana
Lagos State University
Mayo Clinic Rochester, MN
McGill University
McGill Centre for Microbiome Research
University of Helsinki
University of Helsinki
University of Auckland
Singapore-MIT Alliance for Research and Technology

Research output: Contribution to journal › Article › peer-review

1 Citation (Scopus)

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.

Original language	English
Article number	1717
Journal	Nature Communications
Volume	17
Issue number	1
DOIs	https://doi.org/10.1038/s41467-026-68412-5
Publication status	Published - Dec 2026
Externally published	Yes

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Yuan, Y., DeMott, M. S., Byrne, S. R., Flores, K., Poyet, M., Groussin, M., Berdy, B., Bahunde, J. R., Girard, C., Lehtimäki, J., Mabulla, A. Z. P., Mwikarago, I. E., Nartey, Y. A., Nguyen, L. T. T., Onyekwere, C. A., Roberts, L. R., Shapiro, B. J., Vatanen, T., Comstock, L. E., ... Dedon, P. C. (2026). Phosphorothioate DNA modification by BREX type 4 systems in the human gut microbiome. Nature Communications, 17(1), Article 1717. https://doi.org/10.1038/s41467-026-68412-5

@article{bc1842cd217a40d4a3d67b7a40775237,

title = "Phosphorothioate DNA modification by BREX type 4 systems in the human gut microbiome",

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.",

author = "Yifeng Yuan and DeMott, \{Michael S.\} and Byrne, \{Shane R.\} and Katia Flores and Mathilde Poyet and Mathieu Groussin and Brittany Berdy and Bahunde, \{John Rusine\} and Catherine Girard and Jenni Lehtim{\"a}ki and Mabulla, \{Audax Z.P.\} and Mwikarago, \{Ivan Emil\} and Nartey, \{Yvonne Ayerki\} and Nguyen, \{Le Thanh Tu\} and Onyekwere, \{Charles A.\} and Roberts, \{Lewis R.\} and Shapiro, \{B. Jesse\} and Tommi Vatanen and Comstock, \{Laurie E.\} and Alm, \{Eric J.\} and Dedon, \{Peter C.\}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2026.",

year = "2026",

month = dec,

doi = "10.1038/s41467-026-68412-5",

language = "English",

volume = "17",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Research",

number = "1",

}

Yuan, Y, DeMott, MS, Byrne, SR, Flores, K, Poyet, M, Groussin, M, Berdy, B, Bahunde, JR, Girard, C, Lehtimäki, J, Mabulla, AZP, Mwikarago, IE, Nartey, YA, Nguyen, LTT, Onyekwere, CA, Roberts, LR, Shapiro, BJ, Vatanen, T, Comstock, LE, Alm, EJ & Dedon, PC 2026, 'Phosphorothioate DNA modification by BREX type 4 systems in the human gut microbiome', Nature Communications, vol. 17, no. 1, 1717. https://doi.org/10.1038/s41467-026-68412-5

TY - JOUR

T1 - Phosphorothioate DNA modification by BREX type 4 systems in the human gut microbiome

AU - Yuan, Yifeng

AU - DeMott, Michael S.

AU - Byrne, Shane R.

AU - Flores, Katia

AU - Poyet, Mathilde

AU - Groussin, Mathieu

AU - Berdy, Brittany

AU - Bahunde, John Rusine

AU - Girard, Catherine

AU - Lehtimäki, Jenni

AU - Mabulla, Audax Z.P.

AU - Mwikarago, Ivan Emil

AU - Nartey, Yvonne Ayerki

AU - Nguyen, Le Thanh Tu

AU - Onyekwere, Charles A.

AU - Roberts, Lewis R.

AU - Shapiro, B. Jesse

AU - Vatanen, Tommi

AU - Comstock, Laurie E.

AU - Alm, Eric J.

AU - Dedon, Peter C.

PY - 2026/12

Y1 - 2026/12

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/105030393899

U2 - 10.1038/s41467-026-68412-5

DO - 10.1038/s41467-026-68412-5

M3 - Article

C2 - 41571653

AN - SCOPUS:105030393899

SN - 2041-1723

VL - 17

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 1717

ER -

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

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