131: Cryptic plasmid pBI143: a small element with outsized presence in the human gut

Fogarty EC et al., Cell (187:1206–1222, February 29, 2024) - This episode summarizes Fogarty et al. 2024, which characterizes pBI143, a 2.7 kb cryptic plasmid that is highly prevalent and abundant across industrialized human gut metagenomes. The team combines large-scale metagenomics, isolate experiments, structural analyses, qPCR assays, and gnotobiotic mouse work to map pBI143’s distribution, transmission, host range, evolutionary constraints, and responses to stress. Key terms: pBI143, cryptic plasmid, human gut microbiome, plasmid prevalence, IBD.

Study Highlights:
pBI143 is a ubiquitous, highly abundant 2.7 kb cryptic plasmid detected in the majority of gut metagenomes from industrialized populations and is estimated to be ~14 times more numerous than crAssphage by copy number. It is typically monoclonal within individuals, often vertically transmitted from mother to infant, and can transfer among Bacteroidales species. Population variation is concentrated at specific sites under strong purifying selection and localized amino-acid changes cluster near MobA DNA-binding regions. pBI143 copy number increases during oxidative stress in culture and is higher in metagenomes from individuals with IBD, and it can occasionally acquire additional cargo genes.

Conclusion:
pBI143 is a highly successful human-gut-restricted cryptic plasmid that behaves largely as a monoclonal, transmissible genetic element under purifying selection, with potential uses as a sensitive human fecal marker and as an indicator of microbial stress in the gut.

Music:
Enjoy the music based on this article at the end of the episode.

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

First author:
Fogarty EC

Journal:
Cell (187:1206–1222, February 29, 2024)

DOI:
10.1016/j.cell.2024.01.039

Reference:
Fogarty EC, Schechter MS, Lolans K, Sheahan ML, Veseli I, Moore RM, et al. A cryptic plasmid is among the most numerous genetic elements in the human gut. Cell. 2024;187:1206–1222. https://doi.org/10.1016/j.cell.2024.01.039

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

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Episode link: https://basebybase.com/episodes/pbi143-the-human-guts-hidden-heavyweight

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-09-08.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited transcript sections describing pBI143 biology (size, mobA/repA), global prevalence and host range, monoclonality and maternal transmission, horizontal transfer experiments, structural/variational analyses, oxidative stress response, cargo acquisition, and clinical/environmental implications.
- transcript topics: pBI143 basic features (size, mobA and repA); global prevalence and host range in Bacteroidales; monoclonality, priority effects, and maternal transmission; horizontal transfer between Bacteroidales species (transfer assays); mutational landscape and AlphaFold-based structure mapping; oxidative stress response and copy-number dynamics

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 6
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- pBI143 is ~2,747 bp with two annotated genes, mobA and repA
- Three versions of pBI143 exist with high overall identity; repA varies among versions
- pBI143 is highly prevalent in industrialized populations (roughly 73% across 4,516 gut metagenomes; up to 92% in Japan and 86% in the USA)
- pBI143 makes up approximately 0.1%–3.5% of metagenomic reads in carriers (with high coverage in carriers)
- pBI143 is largely monoclonal within individuals and is vertically transmitted from mother to infant via priority effects
- pBI143 can transfer between Bacteroidales species (demonstrated via conjugation experiments)

QC result: Pass.