Evidence map›Paper›PMID 41298788›Full record

ArticleCommunications biology2025

Genetic variation and historical breeding patterns in common bean (Phaseolus vulgaris L.) affect fermentation patterns by the human gut microbiome.

Mallory J Suhr Van Haute, Qinnan Yang, Nate Korth, Mary M Happ, Car Reen Kok, Chenyong Miao, Jennifer L Clarke, Kelsey Karnik, Kent M Eskridge, Carlos A Urrea and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Communications biology, 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

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Mallory J Suhr Van HauteDepartment of Food Science and Technology, University of Nebraska, Lincoln, NE, USA.
Qinnan YangDepartment of Food Science and Technology, University of Nebraska, Lincoln, NE, USA.
Nate KorthNebraska Food for Health Center, University of Nebraska, Lincoln, NE, USA.
Mary M HappDepartment of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA.
Car Reen KokNebraska Food for Health Center, University of Nebraska, Lincoln, NE, USA.
Chenyong MiaoDepartment of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA.
Jennifer L ClarkeDepartment of Food Science and Technology, University of Nebraska, Lincoln, NE, USA.ORCID http://orcid.org/0000-0002-2723-7249
Kelsey KarnikDepartment of Statistics, University of Nebraska, Lincoln, NE, USA.
Kent M EskridgeDepartment of Statistics, University of Nebraska, Lincoln, NE, USA.
Carlos A UrreaDepartment of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA.
David L HytenNebraska Food for Health Center, University of Nebraska, Lincoln, NE, USA.ORCID http://orcid.org/0000-0001-6324-9389
James C SchnableNebraska Food for Health Center, University of Nebraska, Lincoln, NE, USA.ORCID http://orcid.org/0000-0001-6739-5527
Devin J RoseDepartment of Food Science and Technology, University of Nebraska, Lincoln, NE, USA. drose3@unl.edu.ORCID http://orcid.org/0000-0002-1333-6318
Andrew K BensonDepartment of Food Science and Technology, University of Nebraska, Lincoln, NE, USA. abenson1@unl.edu.ORCID http://orcid.org/0000-0001-6330-0252

Funding

Foundation for Food and Agriculture Research (FFAR) 2018-0020-08
6 · The paper itself

Abstract

Common beans, which contain diverse bioactive molecules, have not been systematically studied for their variation in how they affect the human gut microbiome. We measured taxonomic shifts and metabolite production of three human gut microbiomes cultured with 299 common bean cultivars under conditions that mimic the nutrient availability of the human colon. Common bean population structure (landrace and market class) had significant effects on microbiota diversity, composition, and metabolite production. Genome-wide association analysis identified seven multiple effect loci (MEL) where genetic variation in the common bean genome affected the microbiome. One MEL on chromosome Pv05 had impacts on the abundance of several Lachnospiraceae and Ruminococcaceae. Molecular complementation experiments suggested that variation in the biosynthesis of saponins at this MEL was the mechanism driving the variability in microbiota composition and function. This study provides innovative understanding of how genetics of common beans affects the human gut microbiome and potentially human health.

Indexed as

FermentationGastrointestinal MicrobiomeGenetic VariationPhaseolusPlant BreedingGenome-Wide Association StudyHumans

Identifiers

PMID41298788
PMCPMC12657933

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Registered trials

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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.