Disclosing the effects of pea-derived proteins on the human gut microbiota

Abstract

Aim: Plant-derived proteins have emerged as promising alternatives to animal-based proteins, offering not only environmental and nutritional benefits to the human host but also potential effects on the gut microbiota. Yellow pea (Pisum sativum) represents an attractive source due to its balanced amino acid composition and suitability for food applications. This preliminary study was designed to evaluate the effects of two commercial pea-derived protein preparations - a wet-extracted protein isolate (PPI) and a dry-fractionated protein concentrate (PPC) - on the human gut microbiota using a dual in vitro approach.

Methods: We combined monoculture assays on selected representative intestinal bacterial strains with in vitro cultivation models of stabilized microbial communities derived from human fecal samples.

Results: Monoculture experiments revealed selective growth responses in certain taxa, such as Bacteroides thetaiotaomicron and Bifidobacterium spp. Moreover, in silico genomic predictions of amino acid biosynthesis and proteolytic capabilities further supported these findings, highlighting functional differences among the tested strains. Furthermore, analysis based on stabilized microbial communities revealed moderate shifts in microbial richness and composition. Notably, PPC was associated with greater variation in taxonomic profiles across samples. Both protein ingredients exhibited similar directional effects on specific taxa, including increases in the load of Bifidobacterium longum and Faecalibacterium duncaniae, and decreases in members of Bacteroides, Parabacteroides, and Phocaeicola.

Conclusion: These findings indicate that pea-derived proteins, especially when used as concentrates, exert selective pressure on gut microbial communities.

Keywords

Microbiota / yellow pea / pea protein / monoculture

References

[1] Zhang X,Shen A.Legumes as an alternative protein source in plant-based foods: applications, challenges, and strategies.Curr Res Food Sci2024;9:100876 PMCID:PMC11491897

[2] Aghababaei F,Pignitter M.A comprehensive review of processing, functionality, and potential applications of lentil proteins in the food industry.Adv Colloid Interface Sci2024;333:103280

[3] Lisciani S,Le Donne C.Legumes and common beans in sustainable diets: nutritional quality, environmental benefits, spread and use in food preparations.Front Nutr2024;11:1385232 PMCID:PMC11104268

[4] Pelgrom PJ,Boom RM.Dry fractionation for production of functional pea protein concentrates.Food Res Int2013;53:232-9

[5] Zhao H,Wu Z,Xu C.Comparison of wheat, soybean, rice, and pea protein properties for effective applications in food products.J Food Biochem2020;44:e13157

[6] Eze CR,Adewale P,Ngadi M.Advances in legume protein extraction technologies: a review.Innov Food Sci Emerg Technol2022;82:103199

[7] Clemente A.Beneficial effects of legumes in gut health.Curr Opin Food Sci2017;14:32-6

[8] Ferreira H,Carneiro TJ.Impact of a legumes diet on the human gut microbiome articulated with fecal and plasma metabolomes: a pilot study.Clin Nutr ESPEN2024;63:332-45

[9] Wu X,Volchanskaya VSB.A legume-enriched diet improves metabolic health in prediabetes mediated through gut microbiome: a randomized controlled trial.Nat Commun2025;16:942 PMCID:PMC11754483

[10] Singh RK,Yan D.Influence of diet on the gut microbiome and implications for human health.J Transl Med2017;15:73 PMCID:PMC5385025

[11] Özdemir A.Dietary legumes and gut microbiome: a comprehensive review.Crit Rev Food Sci Nutr2025;65:5956-70

[12] Alessandri G,Mancabelli L.Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium.NPJ Biofilms Microbiomes2022;8:88 PMCID:PMC9622858

[13] Vandeputte D,D’hoe K.Quantitative microbiome profiling links gut community variation to microbial load.Nature2017;551:507-11

[14] Rawlings ND,Bateman A.MEROPS: the peptidase database.Nucleic Acids Res2010;38:D227-33 PMCID:PMC2808883

[15] Teufel F,Johansen AR.SignalP 6.0 predicts all five types of signal peptides using protein language models.Nat Biotechnol2022;40:1023-5 PMCID:PMC9287161

[16] Mancabelli L,De Biase R.Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation.mSystems2024;9:e0129423 PMCID:PMC11019788

[17] Li L,Ning Z.An in vitro model maintaining taxon-specific functional activities of the gut microbiome.Nat Commun2019;10:4146 PMCID:PMC6742639

[18] Milani C,Fontana F.METAnnotatorX2: a comprehensive tool for deep and shallow metagenomic data set analyses.mSystems2021;6:101128msystems0058321

[19] Caporaso JG,Stombaugh J.QIIME allows analysis of high-throughput community sequencing data.Nat Methods2010;7:335-6 PMCID:PMC3156573

[20] Bokulich NA,Rideout JR.Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin.Microbiome2018;6:90 PMCID:PMC5956843

[21] Meslé MM,Dlakić M.Bacteroides thetaiotaomicron, a model gastrointestinal tract species, prefers heme as an iron source, yields protoporphyrin IX as a product, and acts as a heme reservoir.Microbiol Spectr2023;11:e0481522 PMCID:PMC10100974

[22] Peng Y.Meet the extended Segatella copri complex.Cell Host Microbe2023;31:1766-9

[23] Arumugam M,Pelletier E.MetaHIT ConsortiumEnterotypes of the human gut microbiome.Nature2011;473:174-80 PMCID:PMC3728647

[24] Lopez-Siles M,Garcia-Gil LJ.Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics.ISME J2017;11:841-52 PMCID:PMC5364359

[25] Huang YJ,Wright C.Faecalibacterium prausnitzii A2-165 metabolizes host- and media-derived chemicals and induces transcriptional changes in colonic epithelium in GuMI human gut microphysiological system.Microbiome Res Rep2024;3:30 PMCID:PMC11480719

[26] Martin AJM,Riquelme E,Garrido D.Microbial interactions and the homeostasis of the gut microbiome: the role of bifidobacterium.Microbiome Res Rep2023;2:17 PMCID:PMC10688804

[27] Louis P.Formation of propionate and butyrate by the human colonic microbiota.Environ Microbiol2017;19:29-41

[28] Li L,Liu B.Factors involved in the abundant dominance of Bifidobacterium longum within the genus in the human gut.Food Biosci2024;61:104638

[29] Cui S,Wang W.Characterization of peptides available to different bifidobacteria.LWT2022;169:113958

[30] Martín R,Huillet E.Faecalibacterium: a bacterial genus with promising human health applications.FEMS Microbiol Rev2023;47:fuad039 PMCID:PMC10410495

[31] Fagundes RR,Saeed A.Inulin-grown Faecalibacterium prausnitzii cross-feeds fructose to the human intestinal epithelium.Gut Microbes2021;13:1993582 PMCID:PMC8604389

[32] Li J,Amend L.A versatile genetic toolbox for Prevotella copri enables studying polysaccharide utilization systems.EMBO J2021;40:e108287 PMCID:PMC8634118

[33] Abdelsalam NA,Aziz RK.The curious case of Prevotella copri.Gut Microbes2023;15:2249152 PMCID:PMC10478744

[34] Amaretti A,Simone M.Profiling of protein degraders in cultures of human gut microbiota.Front Microbiol2019;10:2614 PMCID:PMC6874058

[35] Price MN,Arkin AP.GapMind: automated annotation of amino acid biosynthesis.mSystems2020;5:e00291-20 PMCID:PMC7311316

[36] Bai Z,Jin Y.Comprehensive analysis of 84 Faecalibacterium prausnitzii strains uncovers their genetic diversity, functional characteristics, and potential risks.Front Cell Infect Microbiol2022;12:919701 PMCID:PMC9846645

[37] Panwar D,Fraser ASC,Brumer H.Transcriptional delineation of polysaccharide utilization loci in the human gut commensal Segatella copri DSM18205 and co-culture with exemplar Bacteroides species on dietary plant glycans.Appl Environ Microbiol2025;91:e0175924 PMCID:PMC11784079

[38] Venema K.Experimental models of the gut microbiome.Best Pract Res Clin Gastroenterol2013;27:115-26

[39] Culp EJ.Cross-feeding in the gut microbiome: ecology and mechanisms.Cell Host Microbe2023;31:485-99 PMCID:PMC10125260

[40] Shetty SA,Atashgahi S,Smidt H.Inter-species metabolic interactions in an in-vitro minimal human gut microbiome of core bacteria.NPJ Biofilms Microbiomes2022;8:21 PMCID:PMC8993927

[41] Jia J,Izquierdo-Sandoval D.Exploiting the interactions between plant proteins and gut microbiota to promote intestinal health.Trends Food Sci Tech2024;153:104749

[42] Bartlett A.Dietary protein and the intestinal microbiota: an understudied relationship.iScience2022;25:105313 PMCID:PMC9626677

[43] Blakeley-Ruiz JA,McMillan AS.Dietary protein source alters gut microbiota composition and function.ISME J2025;19:wraf048 PMCID:PMC12066410

[44] Rivière A,Geirnaert A,De Vuyst L.Complementary mechanisms for degradation of inulin-type fructans and arabinoxylan oligosaccharides among bifidobacterial strains suggest bacterial cooperation.Appl Environ Microbiol2018;84:e02893-17 PMCID:PMC5930331