Evidence map›Paper›PMID 41345083›Full record

ArticleNature communications2025

Spatial proximity dictates bacterial competition and expansion in microbial communities.

Emrah Şimşek, César A Villalobos, Kinshuk Sahu, Zhengqing Zhou, Nan Luo, Dongheon Lee, Helena R Ma, Deverick J Anderson, Charlotte T Lee, Lingchong You

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Emrah ŞimşekDepartment of Biomedical Engineering, Duke University, Durham, NC, USA. esimsek@ufl.edu.ORCID http://orcid.org/0000-0003-4550-7158
César A Villalobos *Department of Biomedical Engineering, Duke University, Durham, NC, USA.
Kinshuk Sahu *Department of Biomedical Engineering, Duke University, Durham, NC, USA.
Zhengqing ZhouDepartment of Biomedical Engineering, Duke University, Durham, NC, USA.
Nan LuoDepartment of Biomedical Engineering, Duke University, Durham, NC, USA.ORCID http://orcid.org/0000-0002-4363-6637
Dongheon LeeDepartment of Biomedical Engineering, Duke University, Durham, NC, USA.
Helena R MaDepartment of Biomedical Engineering, Duke University, Durham, NC, USA.ORCID http://orcid.org/0000-0003-3659-7948
Deverick J AndersonDivision of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA.
Charlotte T LeeCenter for Quantitative Biodesign, Duke University, Durham, NC, USA.ORCID http://orcid.org/0000-0002-5863-735X
Lingchong YouDepartment of Biomedical Engineering, Duke University, Durham, NC, USA. you@duke.edu.ORCID http://orcid.org/0000-0003-3725-4007

Funding

Post-antibiotic effect and design of optimal antibiotic dosing protocolsR01GM098642 · NIGMS · DUKE UNIVERSITY · PI YOU, LINGCHONG · 2011 to 2025
$3.6M
National Science Foundation (NSF) EEC-2133504National Science Foundation (NSF) MCB-1937259NIGMS NIH HHS R01 GM098642United States Department of Defense | Defense Advanced Research Projects Agency (DARPA) 2501-203-2015861United States Department of Defense | United States Navy | Office of Naval Research (ONR) N00014-20-1-2121
6 · The paper itself

Abstract

In microbial communities, bacteria can inhibit or facilitate each other by altering their shared environment. Most studies of these interactions have focused on well-mixed environments, leaving spatial effects underexplored. Here, we show that in an antibiotic-treated community, bacterial spread depends on a facilitation mechanism that only emerges in spatial settings. The facilitating species enables the community's range expansion but is then suppressed to a minority, making it a hidden initiator of the expansion. Focusing on two pathogens, immotile Klebsiella pneumoniae and motile Pseudomonas aeruginosa, we found that both tolerate a β-lactam antibiotic, with Pseudomonas being more resilient and dominating in well-mixed cultures. During range expansion, however, the antibiotic inhibits Pseudomonas' ability to spread unless it is near Klebsiella-which creates a clear zone by degrading the antibiotic, at the expense of its own growth. As Pseudomonas spreads, it competitively suppresses Klebsiella. Our modeling and experimental analyses reveal that this facilitation operates at a millimeter scale. We also observed similar facilitation by a Bacillus species isolated from a hospital sink, in both pairwise and eight-member bacterial communities with its co-isolates. These findings suggest that spatially explicit experiments are essential to understand certain facilitation mechanisms and have implications for surface-associated microbial communities like biofilms and for polymicrobial infections involving drug-degrading immotile and drug-tolerant motile bacteria.

Indexed as

Klebsiella pneumoniaeMicrobial InteractionsMicrobiotaPseudomonas aeruginosaAnti-Bacterial AgentsBacillusBacteriaBiofilmsAnti-Bacterial Agents

Identifiers

PMID41345083
PMCPMC12678808

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
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.