Centers and Institutes
Published February 29, 2024 | Version v1
Journal article Open

A cryptic plasmid is among the most numerous genetic elements in the human gut

Creators

  • 1. University of Chicago
  • 2. University of Delaware
  • 3. Columbia University
  • 4. Toyota Technological Institute at Chicago
  • 5. ETH Zurich
  • 6. University of Wisconsin-Milwaukee
  • 7. University of Washington

Description

Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing features. However, many bacteria carry "cryptic" plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes and is 14 times as numerous as crAssphage, currently established as the most abundant extrachromosomal genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales, and although it does not appear to impact bacterial host fitness in vivo, it can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an alternative approach to track human colonic inflammatory states.

Data availability

All molecular data used in this study are publicly available via the NCBI Sequence Read Archive, and Table S1 reports the accession numbers for all genomes and metagenomes.

Original code accompanying this paper, anvi'o data products that describe metagenomic read recruitment results, and sequences for pBI143 versions and bioinformatics workflows is available at https://merenlab.org/data/pBI143.

Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

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Additional details

Identifiers

DOI
10.1016/j.cell.2024.01.039
Other
oai:uchicago.tind.io:11321

Funding

University of Chicago
International Student Fellowship
NIGMS
R35 GM133420
University of Chicago
National Science Foundation
Graduate Research Fellowship
Swiss National Science Foundation
NCCR Microbiomes
NIDDK
RC2 DK122394
University of Chicago
start-up funds

UChicago Information

Division(s)
Biological Sciences Division, Pritzker School of Molecular Engineering
Department(s)
Biochemistry and Molecular Biology, Biophysical Sciences, Medicine, Microbiology
Center(s) or Institute(s)
Duchossois Family Institute, Marine Biological Laboratory