{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T13:11:22Z","timestamp":1764162682716,"version":"3.46.0"},"reference-count":93,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T00:00:00Z","timestamp":1764115200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T00:00:00Z","timestamp":1764115200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100011929","name":"Foundation for Food and Agriculture Research","doi-asserted-by":"publisher","award":["2018-0020-08"],"award-info":[{"award-number":["2018-0020-08"]}],"id":[{"id":"10.13039\/100011929","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Jeff and Tricia Raikes Foundation; Don Dillon Foundation; Nebraska Research Initiative"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Commun Biol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    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\n                    <jats:italic>Pv<\/jats:italic>\n                    05 had impacts on the abundance of several\n                    <jats:italic>Lachnospiraceae<\/jats:italic>\n                    and\n                    <jats:italic>Ruminococcaceae<\/jats:italic>\n                    . 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.\n                  <\/jats:p>","DOI":"10.1038\/s42003-025-09089-2","type":"journal-article","created":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T12:15:15Z","timestamp":1764159315000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genetic variation and historical breeding patterns in common bean (Phaseolus vulgaris L.) affect fermentation patterns by the human gut microbiome"],"prefix":"10.1038","volume":"8","author":[{"given":"Mallory J.","family":"Suhr Van Haute","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qinnan","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nate","family":"Korth","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mary M.","family":"Happ","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Car Reen","family":"Kok","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chenyong","family":"Miao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2723-7249","authenticated-orcid":false,"given":"Jennifer L.","family":"Clarke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kelsey","family":"Karnik","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kent M.","family":"Eskridge","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlos A.","family":"Urrea","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6324-9389","authenticated-orcid":false,"given":"David L.","family":"Hyten","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6739-5527","authenticated-orcid":false,"given":"James C.","family":"Schnable","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1333-6318","authenticated-orcid":false,"given":"Devin J.","family":"Rose","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6330-0252","authenticated-orcid":false,"given":"Andrew K.","family":"Benson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,11,26]]},"reference":[{"key":"9089_CR1","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1038\/nrg1877","volume":"7","author":"TG Whitham","year":"2006","unstructured":"Whitham, T. G. et al. A framework for community and ecosystem genetics: From genes to ecosystems. Nat. Rev. Genet 7, 510\u2013523 (2006).","journal-title":"Nat. Rev. Genet"},{"key":"9089_CR2","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1086\/284513","volume":"127","author":"AE Weis","year":"1986","unstructured":"Weis, A. E. & Abrahamson, W. G. Evolution of host-plant manipulation by gall makers: ecological and genetic factors in the solidago-eurosta system. Am. Nat. 127, 681\u2013695 (1986).","journal-title":"Am. Nat."},{"key":"9089_CR3","doi-asserted-by":"publisher","first-page":"3904","DOI":"10.1073\/pnas.071061998","volume":"98","author":"SD Peacor","year":"2001","unstructured":"Peacor, S. D. & Werner, E. E. The contribution of trait-mediated indirect effects to the net effects of a predator. Proc. Natl. Acad. Sci. USA 98, 3904\u20133908 (2001).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"9089_CR4","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1038\/nature23292","volume":"548","author":"KR Foster","year":"2017","unstructured":"Foster, K. R., Schluter, J., Coyte, K. Z. & Rakoff-Nahoum, S. The evolution of the host microbiome as an ecosystem on a leash. Nature 548, 43\u201351 (2017).","journal-title":"Nature"},{"key":"9089_CR5","doi-asserted-by":"publisher","first-page":"838","DOI":"10.1038\/s43016-021-00406-6","volume":"2","author":"BK Singh","year":"2021","unstructured":"Singh, B. K. et al. Enhancing science-policy interfaces for food systems transformation. Nat. Food 2, 838\u2013842 (2021).","journal-title":"Nat. Food"},{"key":"9089_CR6","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1007\/s11816-012-0216-5","volume":"6","author":"GS Khush","year":"2012","unstructured":"Khush, G. S., Lee, S., Cho, J., Il & Jeon, J. S. Biofortification of crops for reducing malnutrition. Plant Biotechnol. Rep. 6, 195\u2013202 (2012).","journal-title":"Plant Biotechnol. Rep."},{"key":"9089_CR7","doi-asserted-by":"publisher","first-page":"837","DOI":"10.1016\/j.cell.2006.02.017","volume":"124","author":"RE Ley","year":"2006","unstructured":"Ley, R. E., Peterson, D. A. & Gordon, J. I. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124, 837\u2013848 (2006).","journal-title":"Cell"},{"key":"9089_CR8","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1038\/nm.4517","volume":"24","author":"JA Gilbert","year":"2018","unstructured":"Gilbert, J. A. et al. Current understanding of the human microbiome. Nat. Med. 24, 392\u2013400 (2018).","journal-title":"Nat. Med."},{"key":"9089_CR9","doi-asserted-by":"publisher","first-page":"6528","DOI":"10.1038\/ncomms7528","volume":"6","author":"Q Feng","year":"2015","unstructured":"Feng, Q. et al. Gut microbiome development along the colorectal adenoma-carcinoma sequence. Nat. Commun. 6, 6528\u20136528 (2015).","journal-title":"Nat. Commun."},{"key":"9089_CR10","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1038\/nature11450","volume":"490","author":"J Qin","year":"2012","unstructured":"Qin, J. et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490, 55\u201360 (2012).","journal-title":"Nature"},{"key":"9089_CR11","doi-asserted-by":"publisher","first-page":"11070","DOI":"10.1073\/pnas.0504978102","volume":"102","author":"RE Ley","year":"2005","unstructured":"Ley, R. E. et al. Obesity alters gut microbial ecology. Proc. Natl. Acad. Sci. USA 102, 11070\u201311075 (2005).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"9089_CR12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s12328-017-0813-5","volume":"11","author":"A Nishida","year":"2017","unstructured":"Nishida, A. et al. Gut microbiota in the pathogenesis of inflammatory bowel disease. Clin. J. Gastroenterol. 11, 1\u201310 (2017).","journal-title":"Clin. J. Gastroenterol."},{"key":"9089_CR13","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1038\/nature12820","volume":"505","author":"LA David","year":"2013","unstructured":"David, L. A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559\u2013563 (2013).","journal-title":"Nature"},{"key":"9089_CR14","doi-asserted-by":"publisher","first-page":"6ra14","DOI":"10.1126\/scitranslmed.3000322","volume":"1","author":"PJ Turnbaugh","year":"2009","unstructured":"Turnbaugh, P. J. et al. The effect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice. Sci. Transl. Med. 1, 6ra14 (2009).","journal-title":"Sci. Transl. Med."},{"key":"9089_CR15","doi-asserted-by":"publisher","first-page":"3528","DOI":"10.3390\/molecules25153528","volume":"25","author":"M Alc\u00e1zar-Valle","year":"2020","unstructured":"Alc\u00e1zar-Valle, M. et al. Bioactive compounds, antioxidant activity, and antinutritional content of legumes: A comparison between four Phaseolus species. Molecules 25, 3528 (2020).","journal-title":"Molecules"},{"key":"9089_CR16","doi-asserted-by":"publisher","first-page":"1360","DOI":"10.3390\/molecules22081360","volume":"22","author":"C Ch\u00e1vez-Mendoza","year":"2017","unstructured":"Ch\u00e1vez-Mendoza, C. & S\u00e1nchez, E. Bioactive compounds from Mexican varieties of the common bean (Phaseolus vulgaris): implications for health. Molecules 22, 1360 (2017).","journal-title":"Molecules"},{"key":"9089_CR17","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1080\/19476337.2015.1063548","volume":"14","author":"SE Su\u00e1rez-Mart\u00ednez","year":"2016","unstructured":"Su\u00e1rez-Mart\u00ednez, S. E. et al. Bean seeds: leading nutraceutical source for human health. CyTA - J. Food 14, 131\u2013137 (2016).","journal-title":"CyTA - J. Food"},{"key":"9089_CR18","doi-asserted-by":"publisher","first-page":"9311","DOI":"10.1080\/10408398.2023.2212063","volume":"64","author":"Y Zhang","year":"2024","unstructured":"Zhang, Y. et al. Health benefits of saponins and its mechanisms: perspectives from absorption, metabolism, and interaction with gut. Crit. Rev. Food Sci. Nutr. 64, 9311\u20139332 (2024).","journal-title":"Crit. Rev. Food Sci. Nutr."},{"key":"9089_CR19","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1016\/j.foodres.2014.12.003","volume":"76","author":"MR Moreno-Jim\u00e9nez","year":"2015","unstructured":"Moreno-Jim\u00e9nez, M. R. et al. Phenolic composition changes of processed common beans: their antioxidant and anti-inflammatory effects in intestinal cancer cells. Food Res. Int. 76, 79\u201385 (2015).","journal-title":"Food Res. Int"},{"key":"9089_CR20","doi-asserted-by":"publisher","first-page":"1497","DOI":"10.1016\/j.foodchem.2013.04.010","volume":"141","author":"D Guajardo-Flores","year":"2013","unstructured":"Guajardo-Flores, D., Serna-Sald\u00edvar, S. O. & Guti\u00e9rrez-Uribe, J. A. Evaluation of the antioxidant and antiproliferative activities of extracted saponins and flavonols from germinated black beans (Phaseolus vulgaris L.). Food Chem. 141, 1497\u20131503 (2013).","journal-title":"Food Chem."},{"key":"9089_CR21","doi-asserted-by":"publisher","first-page":"974","DOI":"10.1016\/j.foodchem.2011.05.057","volume":"129","author":"B Xu","year":"2011","unstructured":"Xu, B. & Chang, S. K. C. Reduction of antiproliferative capacities, cell-based antioxidant capacities and phytochemical contents of common beans and soybeans upon thermal processing. Food Chem. 129, 974\u2013981 (2011).","journal-title":"Food Chem."},{"key":"9089_CR22","doi-asserted-by":"publisher","first-page":"167","DOI":"10.3390\/app11010167","volume":"11","author":"Z Shi","year":"2021","unstructured":"Shi, Z., Zhang, X., Zhu, Y., Yao, Y. & Ren, G. Natural extracts from white common bean (Phaseolus vulgaris L.) inhibit 3T3-L1 adipocytes differentiation. Appl Sci. 11, 167 (2021).","journal-title":"Appl Sci."},{"key":"9089_CR23","doi-asserted-by":"publisher","first-page":"824","DOI":"10.1080\/09637486.2017.1418845","volume":"69","author":"MN Ombra","year":"2018","unstructured":"Ombra, M. N. et al. Alpha-amylase, \u03b1-glucosidase and lipase inhibiting activities of polyphenol-rich extracts from six common bean cultivars of Southern Italy, before and after cooking. Int J. Food Sci. Nutr. 69, 824\u2013834 (2018).","journal-title":"Int J. Food Sci. Nutr."},{"key":"9089_CR24","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1016\/j.numecd.2019.07.020","volume":"30","author":"MJC Gomes","year":"2020","unstructured":"Gomes, M. J. C. et al. Common bean protein hydrolysate modulates lipid metabolism and prevents endothelial dysfunction in BALB\/c mice fed an atherogenic diet. Nutr. Metab. Cardiovasc Dis. 30, 141\u2013150 (2020).","journal-title":"Nutr. Metab. Cardiovasc Dis."},{"key":"9089_CR25","doi-asserted-by":"publisher","first-page":"43","DOI":"10.3892\/etm.2014.2040","volume":"9","author":"JY Wang","year":"2015","unstructured":"Wang, J. Y. et al. Extracts of black bean peel and pomegranate peel ameliorate oxidative stress-induced hyperglycemia in mice. Exp. Ther. Med. 9, 43\u201348 (2015).","journal-title":"Exp. Ther. Med."},{"key":"9089_CR26","doi-asserted-by":"publisher","first-page":"886","DOI":"10.1017\/S0007114514001536","volume":"112","author":"RA Chavez-Santoscoy","year":"2014","unstructured":"Chavez-Santoscoy, R. A. et al. Flavonoids and saponins extracted from black bean (Phaseolus vulgaris L.) seed coats modulate lipid metabolism and biliary cholesterol secretion in C57BL\/6 mice. Br. J. Nutr. 112, 886\u2013899 (2014).","journal-title":"Br. J. Nutr."},{"key":"9089_CR27","doi-asserted-by":"publisher","first-page":"1275","DOI":"10.1002\/ptr.3425","volume":"25","author":"M Rondanelli","year":"2011","unstructured":"Rondanelli, M., Giacosa, A., Orsini, F., Opizzi, A. & Villani, S. Appetite control and glycaemia reduction in overweight subjects treated with a combination of two highly standardized extracts from Phaseolus vulgaris and Cynara scolymus. Phytother. Res. 25, 1275\u20131282 (2011).","journal-title":"Phytother. Res"},{"key":"9089_CR28","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0059985","volume":"8","author":"A Nilsson","year":"2013","unstructured":"Nilsson, A., Johansson, E., Ekstr\u00f6m, L. & Bj\u00f6rck, I. Effects of a brown beans evening meal on metabolic risk markers and appetite regulating hormones at a subsequent standardized breakfast: A randomized cross-over study. PLoS One 8, e59985 (2013).","journal-title":"PLoS One"},{"key":"9089_CR29","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1016\/j.foodres.2017.07.018","volume":"100","author":"I Luzardo-Ocampo","year":"2017","unstructured":"Luzardo-Ocampo, I. et al. Bioaccessibility and antioxidant activity of free phenolic compounds and oligosaccharides from corn (Zea mays L.) and common bean (Phaseolus vulgaris L.) chips during in vitro gastrointestinal digestion and simulated colonic fermentation. Food Res. Int. 100, 304\u2013311 (2017).","journal-title":"Food Res. Int."},{"key":"9089_CR30","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1089\/109662004322984734","volume":"7","author":"J Shi","year":"2004","unstructured":"Shi, J. et al. Saponins from edible legumes: Chemistry, processing, and health benefits. J. Med Food 7, 67\u201378 (2004).","journal-title":"J. Med Food"},{"key":"9089_CR31","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1089\/jmf.2005.8.281","volume":"8","author":"BA Graf","year":"2005","unstructured":"Graf, B. A., Milbury, P. E. & Blumberg, J. B. Flavonols, flavones, flavanones, and human health: Epidemiological evidence. J. Med. Food 8, 281\u2013290 (2005).","journal-title":"J. Med. Food"},{"key":"9089_CR32","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1093\/ajcn\/87.1.162","volume":"87","author":"R Villegas","year":"2008","unstructured":"Villegas, R. et al. Legume and soy food intake and the incidence of type 2 diabetes in the Shanghai Women\u2019s Health Study. Am. J. Clin. Nutr. 87, 162\u2013167 (2008).","journal-title":"Am. J. Clin. Nutr."},{"key":"9089_CR33","doi-asserted-by":"publisher","first-page":"1189","DOI":"10.3390\/molecules13051189","volume":"13","author":"GY Tang","year":"2008","unstructured":"Tang, G. Y., Li, X. J. & Zhang, H. Y. Antidiabetic components contained in vegetables and legumes. Molecules 13, 1189\u20131194 (2008).","journal-title":"Molecules"},{"key":"9089_CR34","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1007\/s00394-010-0115-x","volume":"50","author":"HHM Hermsdorff","year":"2011","unstructured":"Hermsdorff, H. H. M., Zulet, M. \u00c1, Abete, I. & Mart\u00ednez, J. A. A legume-based hypocaloric diet reduces proinflammatory status and improves metabolic features in overweight\/obese subjects. Eur. J. Nutr. 50, 61\u201369 (2011).","journal-title":"Eur. J. Nutr."},{"key":"9089_CR35","doi-asserted-by":"publisher","first-page":"S52","DOI":"10.1017\/S0007114512000761","volume":"108","author":"AM Hutchins","year":"2012","unstructured":"Hutchins, A. M., Winham, D. M. & Thompson, S. V. Phaseolus beans: Impact on glycaemic response and chronic disease risk in human subjects. Br. J. Nutr. 108, S52\u2013S65 (2012).","journal-title":"Br. J. Nutr."},{"key":"9089_CR36","doi-asserted-by":"publisher","first-page":"S273","DOI":"10.1079\/BJN2002717","volume":"88","author":"JC Mathers","year":"2002","unstructured":"Mathers, J. C. Pulses and carcinogenesis: Potential for the prevention of colon, breast and other cancers. Br. J. Nutr. 88, S273\u2013S279 (2002).","journal-title":"Br. J. Nutr."},{"key":"9089_CR37","doi-asserted-by":"publisher","first-page":"979","DOI":"10.1007\/s00122-008-0955-4","volume":"118","author":"M Kwak","year":"2009","unstructured":"Kwak, M. & Gepts, P. Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae). Theor. Appl. Genet 118, 979\u2013992 (2009).","journal-title":"Theor. Appl. Genet"},{"key":"9089_CR38","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0211342","volume":"14","author":"T Gioia","year":"2019","unstructured":"Gioia, T., Logozzo, G., Marzario, S., Zeuli, P. S. & Gepts, P. Evolution of SSR diversity from wild types to U.S. advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris). PLoS One 14, e0211342 (2019).","journal-title":"PLoS One"},{"key":"9089_CR39","first-page":"1","volume":"13","author":"Q Yang","year":"2022","unstructured":"Yang, Q. et al. Genetic analysis of seed traits in Sorghum bicolor that affect the human gut microbiome. Nat. Commun. 13, 1\u201315 (2022).","journal-title":"Nat. Commun."},{"key":"9089_CR40","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2023.2178799","volume":"15","author":"Q Yang","year":"2023","unstructured":"Yang, Q. et al. The waxy mutation in sorghum and other cereal grains reshapes the gut microbiome by reducing levels of multiple beneficial species. Gut Microbes 15, 2178799 (2023).","journal-title":"Gut Microbes"},{"key":"9089_CR41","doi-asserted-by":"crossref","unstructured":"Korth, N. et al. Genomic co-localization of variation affecting agronomic and human gut microbiome traits in a meta-analysis of diverse sorghum. G3 14, (2024).","DOI":"10.1093\/g3journal\/jkae145"},{"key":"9089_CR42","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.921456","volume":"13","author":"N Korth","year":"2022","unstructured":"Korth, N. et al. The unique seed protein composition of quality protein popcorn promotes growth of beneficial bacteria from the human gut microbiome. Front Microbiol 13, 921456 (2022).","journal-title":"Front Microbiol"},{"key":"9089_CR43","doi-asserted-by":"publisher","first-page":"707","DOI":"10.1038\/ng.3008","volume":"46","author":"J Schmutz","year":"2014","unstructured":"Schmutz, J. et al. A reference genome for common bean and genome-wide analysis of dual domestications. Nat. Genet 46, 707\u2013713 (2014).","journal-title":"Nat. Genet"},{"key":"9089_CR44","doi-asserted-by":"publisher","first-page":"10816","DOI":"10.3389\/fpls.2011.00025","volume":"2","author":"S Sawai","year":"2011","unstructured":"Sawai, S. & Saito, K. Triterpenoid biosynthesis and engineering in plants. Front Plant Sci. 2, 10816 (2011).","journal-title":"Front Plant Sci."},{"key":"9089_CR45","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1007\/BF02887079","volume":"45","author":"SP Singh","year":"1991","unstructured":"Singh, S. P., Gepts, P. & Debouck, D. G. Races of common bean (Phaseolus vulgaris, Fabaceae). Econ. Bot. 45, 379\u2013396 (1991).","journal-title":"Econ. Bot."},{"key":"9089_CR46","doi-asserted-by":"publisher","first-page":"854","DOI":"10.2135\/cropsci2001.413854x","volume":"41","author":"S Beebe","year":"2001","unstructured":"Beebe, S., Rengifo, J., Gaitan, E., Duque, M. C. & Tohme, J. Diversity and origin of Andean landraces of common bean. Crop Sci. 41, 854\u2013862 (2001).","journal-title":"Crop Sci."},{"key":"9089_CR47","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1007\/s00122-007-0644-8","volume":"116","author":"MW Blair","year":"2007","unstructured":"Blair, M. W., D\u00edaz, J. M., Hidalgo, R., D\u00edaz, L. M. & Duque, M. C. Microsatellite characterization of Andean races of common bean (Phaseolus vulgaris L.). Theor. Appl Genet 116, 29\u201343 (2007).","journal-title":"Theor. Appl Genet"},{"key":"9089_CR48","doi-asserted-by":"publisher","first-page":"627","DOI":"10.3390\/d5030627","volume":"5","author":"A Biddle","year":"2013","unstructured":"Biddle, A., Stewart, L., Blanchard, J. & Leschine, S. Untangling the genetic basis of fibrolytic specialization by Lachnospiraceae and Ruminococcaceae in diverse gut communities. Diversity (Basel) 5, 627\u2013640 (2013).","journal-title":"Diversity (Basel)"},{"key":"9089_CR49","doi-asserted-by":"publisher","first-page":"16731","DOI":"10.1073\/pnas.0804812105","volume":"105","author":"H Sokol","year":"2008","unstructured":"Sokol, H. et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc. Natl. Acad. Sci. USA 105, 16731\u201316736 (2008).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"9089_CR50","doi-asserted-by":"publisher","first-page":"3710","DOI":"10.1158\/0008-5472.CAN-23-0605","volume":"83","author":"Y Gao","year":"2023","unstructured":"Gao, Y. et al. Faecalibacterium prausnitzii abrogates intestinal toxicity and promotes tumor immunity to increase the efficacy of dual CTLA4 and PD-1 checkpoint blockade. Cancer Res. 83, 3710\u20133725 (2023).","journal-title":"Cancer Res"},{"key":"9089_CR51","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1016\/j.jep.2004.05.016","volume":"94","author":"SG Sparg","year":"2004","unstructured":"Sparg, S. G., Light, M. E. & Van Staden, J. Biological activities and distribution of plant saponins. J. Ethnopharmacol. 94, 219\u2013243 (2004).","journal-title":"J. Ethnopharmacol."},{"key":"9089_CR52","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1016\/j.livsci.2016.04.021","volume":"189","author":"JL Guil-Guerrero","year":"2016","unstructured":"Guil-Guerrero, J. L. et al. Antimicrobial activity of plant-food by-products: a review focusing on the tropics. Livest. Sci. 189, 32\u201349 (2016).","journal-title":"Livest. Sci."},{"key":"9089_CR53","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1016\/j.foodchem.2012.03.020","volume":"134","author":"D Guajardo-Flores","year":"2012","unstructured":"Guajardo-Flores, D., Garc\u00eda-Pati\u00f1o, M., Serna-Guerrero, D., Guti\u00e9rrez-Uribe, J. A. & Serna-Sald\u00edvar, S. O. Characterization and quantification of saponins and flavonoids in sprouts, seed coats and cotyledons of germinated black beans. Food Chem. 134, 1312\u20131319 (2012).","journal-title":"Food Chem."},{"key":"9089_CR54","doi-asserted-by":"publisher","first-page":"416","DOI":"10.1007\/s11130-013-0384-7","volume":"68","author":"RA Ch\u00e1vez-Santoscoy","year":"2013","unstructured":"Ch\u00e1vez-Santoscoy, R. A., Guti\u00e9rrez-Uribe, J. A. & Serna-Sald\u00edvar, S. O. Effect of flavonoids and saponins extracted from black bean (Phaseolus vulgaris L.) seed coats as cholesterol micelle disruptors. Plant Foods Hum. Nutr. 68, 416\u2013423 (2013).","journal-title":"Plant Foods Hum. Nutr."},{"key":"9089_CR55","doi-asserted-by":"publisher","DOI":"10.1016\/j.lwt.2019.108673","volume":"117","author":"SRM Coelho","year":"2020","unstructured":"Coelho, S. R. M. et al. NMR and LC-MS assessment of compound variability of common bean (Phaseolus vulgaris) stored under controlled atmosphere. LWT\u2014Food Sci. Technol. 117, 108673 (2020).","journal-title":"LWT\u2014Food Sci. Technol."},{"key":"9089_CR56","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1016\/j.foodchem.2006.08.005","volume":"103","author":"EA Shimelis","year":"2007","unstructured":"Shimelis, E. A. & Rakshit, S. K. Effect of processing on antinutrients and in vitro protein digestibility of kidney bean (Phaseolus vulgaris L.) varieties grown in East Africa. Food Chem. 103, 161\u2013172 (2007).","journal-title":"Food Chem."},{"key":"9089_CR57","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1016\/j.foodchem.2017.04.161","volume":"233","author":"B Singh","year":"2017","unstructured":"Singh, B., Singh, J. P., Singh, N. & Kaur, A. Saponins in pulses and their health promoting activities: A review. Food Chem. 233, 540\u2013549 (2017).","journal-title":"Food Chem."},{"key":"9089_CR58","doi-asserted-by":"publisher","first-page":"1941","DOI":"10.1080\/87559129.2023.2245026","volume":"40","author":"Q Bai","year":"2024","unstructured":"Bai, Q. et al. Influence of processing methods on phytochemical composition of different varieties of beans (phaseolus vulgaris). Food Rev. Int. 40, 1941\u20131979 (2024).","journal-title":"Food Rev. Int."},{"key":"9089_CR59","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1016\/j.jfoodeng.2008.12.035","volume":"93","author":"J Shi","year":"2009","unstructured":"Shi, J. et al. Kinetic study of saponins B stability in navy beans under different processing conditions. J. Food Eng. 93, 59\u201365 (2009).","journal-title":"J. Food Eng."},{"key":"9089_CR60","doi-asserted-by":"publisher","DOI":"10.1002\/leg3.88","volume":"3","author":"OA S\u00e1nchez-Vel\u00e1zquez","year":"2021","unstructured":"S\u00e1nchez-Vel\u00e1zquez, O. A. et al. Impact of processing on the in vitro protein quality, bioactive compounds, and antioxidant potential of 10 selected pulses. Legume Sci. 3, e88 (2021).","journal-title":"Legume Sci."},{"key":"9089_CR61","doi-asserted-by":"publisher","DOI":"10.1016\/j.foodchem.2021.129718","volume":"356","author":"JAC Bento","year":"2021","unstructured":"Bento, J. A. C. et al. Chemical profile of colorful bean (Phaseolus vulgaris L) flours: Changes influenced by the cooking method. Food Chem. 356, 129718 (2021).","journal-title":"Food Chem."},{"key":"9089_CR62","doi-asserted-by":"publisher","DOI":"10.1016\/j.jff.2023.105513","volume":"104","author":"N Nina","year":"2023","unstructured":"Nina, N. et al. Chemical profile and bioactivity of Chilean bean landraces (Phaseolus vulgaris L. J. Funct. Foods 104, 105513 (2023).","journal-title":"J. Funct. Foods"},{"key":"9089_CR63","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1042\/ETLS20170045","volume":"1","author":"JAK McDonald","year":"2017","unstructured":"McDonald, J. A. K. In vitro models of the human microbiota and microbiome. Emerg. Top. Life Sci. 1, 373\u2013384 (2017).","journal-title":"Emerg. Top. Life Sci."},{"key":"9089_CR64","doi-asserted-by":"publisher","unstructured":"Moghaddam, S. M. et al. Genome-wide association study identifies candidate loci underlying agronomic traits in a Middle American Diversity Panel of common bean. Plant Genome 9, https:\/\/doi.org\/10.3835\/plantgenome2016.02.0012 (2016).","DOI":"10.3835\/plantgenome2016.02.0012"},{"key":"9089_CR65","unstructured":"Oladzad, A. et al. Single and multi-trait GWAS identify genetic factors associated with production traits in common bean under abiotic stress environments. G3, 1881\u20131892 (2019)."},{"key":"9089_CR66","unstructured":"National Cancer Institute. Diet history questionnaire, Version III. https:\/\/epi.grants.cancer.gov\/dhq3\/ (2025)."},{"key":"9089_CR67","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","volume":"13","author":"BJ Callahan","year":"2016","unstructured":"Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581\u2013583 (2016).","journal-title":"Nat. Methods"},{"key":"9089_CR68","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","volume":"41","author":"C Quast","year":"2013","unstructured":"Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590\u2013D596 (2013).","journal-title":"Nucleic Acids Res."},{"key":"9089_CR69","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0061217","volume":"8","author":"PJ McMurdie","year":"2013","unstructured":"McMurdie, P. J. & Holmes, S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8, e61217 (2013).","journal-title":"PLoS One"},{"key":"9089_CR70","doi-asserted-by":"publisher","first-page":"749","DOI":"10.1016\/j.nutres.2014.08.006","volume":"34","author":"J Yang","year":"2014","unstructured":"Yang, J. & Rose, D. J. Long-term dietary pattern of fecal donor correlates with butyrate production and markers of protein fermentation during in vitro fecal fermentation. Nutr. Res. 34, 749\u2013759 (2014).","journal-title":"Nutr. Res"},{"key":"9089_CR71","doi-asserted-by":"publisher","first-page":"2633","DOI":"10.1093\/bioinformatics\/btm308","volume":"23","author":"PJ Bradbury","year":"2007","unstructured":"Bradbury, P. J. et al. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633\u20132635 (2007).","journal-title":"Bioinformatics"},{"key":"9089_CR72","doi-asserted-by":"crossref","unstructured":"Wickham, H. Ggplot2: Elegant Graphics for Data Analysis. (Springer-Verlag, New York, 2016).","DOI":"10.1007\/978-3-319-24277-4_9"},{"key":"9089_CR73","unstructured":"Karnik, K. Exploring experimental design and multivariate analysis techniques for evaluating community structure of bacteria in microbiome data. (University of Nebraska-Lincoln, 2023)."},{"key":"9089_CR74","doi-asserted-by":"crossref","unstructured":"Johnson, R. & Wichern, D. Applied Multivariate Statistical Analysis. (Prentice Hall, Englewood Cliffs, New Jersey, 1998).","DOI":"10.2307\/2533879"},{"key":"9089_CR75","first-page":"0","volume":"4","author":"R Core","year":"2021","unstructured":"Core, R. Team. R: A language and environment for statistical computing. Version 4, 0 (2021).","journal-title":"Version"},{"key":"9089_CR76","doi-asserted-by":"publisher","first-page":"e0156744","DOI":"10.1371\/journal.pone.0156744","volume":"11","author":"G Covarrubias-Pazaran","year":"2016","unstructured":"Covarrubias-Pazaran, G. Genome-assisted prediction of quantitative traits using the R package sommer. PLoS One 11, e0156744 (2016).","journal-title":"PLoS One"},{"key":"9089_CR77","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1005767","volume":"12","author":"X Liu","year":"2016","unstructured":"Liu, X., Huang, M., Fan, B., Buckler, E. S. & Zhang, Z. Iterative usage of fixed and random effect models for powerful and efficient genome-wide association studies. PLoS Genet 12, e1005767 (2016).","journal-title":"PLoS Genet"},{"key":"9089_CR78","doi-asserted-by":"publisher","first-page":"619","DOI":"10.1016\/j.gpb.2020.10.007","volume":"19","author":"L Yin","year":"2021","unstructured":"Yin, L. et al. rMVP: a memory-efficient, visualization-enhanced, and parallel-accelerated tool for genome-wide association study. Genom., Proteom. Bioinform 19, 619\u2013628 (2021).","journal-title":"Genom., Proteom. Bioinform"},{"key":"9089_CR79","doi-asserted-by":"publisher","first-page":"D1178","DOI":"10.1093\/nar\/gkr944","volume":"40","author":"DM Goodstein","year":"2012","unstructured":"Goodstein, D. M. et al. Phytozome: A comparative platform for green plant genomics. Nucleic Acids Res. 40, D1178\u2013D1186 (2012).","journal-title":"Nucleic Acids Res"},{"key":"9089_CR80","unstructured":"Oksanen J. et al. vegan: Community ecology package. (2024)."},{"key":"9089_CR81","first-page":"2","volume":"0","author":"A Kassambara","year":"2023","unstructured":"Kassambara, A. rstatix: pipe-friendly framework for basic statistical tests. R. package version 0.7.2 (2023).","journal-title":"R. package version"},{"key":"9089_CR82","unstructured":"Harrell Jr F. Hmisc: Harrell Miscellaneous version 5.1-0 from CRAN. https:\/\/CRAN.R-project.org\/package=Hmisc. (2023)."},{"key":"9089_CR83","unstructured":"Warnes G., Gorjanc G., Leisch F. & Man M. genetics: Population Genetics. R package version 1.3.8.1.3. https:\/\/CRAN.R-project.org\/package=genetics. (2021)."},{"key":"9089_CR84","unstructured":"van den Brand, T. ggh4x: Hacks for \u2018ggplot2\u2019. R package version 0.2.6, <https:\/\/CRAN.R-project.org\/package=ggh4x. (2023)."},{"key":"9089_CR85","unstructured":"Slowikowski, K. ggrepel: Automatically position non-overlapping text labels with \u2018ggplot2\u2019. R package version 0.9.3, https:\/\/CRAN.R-project.org\/package=ggrepel. (2023)."},{"key":"9089_CR86","unstructured":"Wilke, C. W. B. ggtext: Improved Text Rendering Support for \u2018ggplot2\u2019. R package version 0.1.2, https:\/\/CRAN.R-project.org\/package=ggtext. (2022)."},{"key":"9089_CR87","unstructured":"Graves S., Piepho H. & Dorai-Raj S. multcompView: Visualizations of Paired Comparisons. R package version 0.1-9, https:\/\/CRAN.R-project.org\/package=multcompView. (2023)."},{"key":"9089_CR88","doi-asserted-by":"publisher","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","volume":"32","author":"Z Gu","year":"2016","unstructured":"Gu, Z., Eils, R. & Schlesner, M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32, 2847\u20132849 (2016).","journal-title":"Bioinformatics"},{"key":"9089_CR89","doi-asserted-by":"publisher","first-page":"2811","DOI":"10.1093\/bioinformatics\/btu393","volume":"30","author":"Z Gu","year":"2014","unstructured":"Gu, Z., Gu, L., Eils, R., Schlesner, M. & Brors, B. Circlize implements and enhances circular visualization in. R. Bioinforma. 30, 2811\u20132812 (2014).","journal-title":"R. Bioinforma."},{"key":"9089_CR90","unstructured":"Van Haute M. J. S. et al. Genetic variation and historical breeding patterns in common bean (Phaseolus vulgaris L.) affect fermentation patterns by the human gut microbiome: Sequence data. National Center for Biotechnology Information https:\/\/www.ncbi.nlm.nih.gov\/bioproject\/PRJNA1062343\/."},{"key":"9089_CR91","doi-asserted-by":"publisher","unstructured":"Van Haute M. J. S. et al. Genetic variation and historical breeding patterns in common bean (Phaseolus vulgaris L.) affect fermentation patterns by the human gut microbiome: R code used to generate figures and data files needed to run the code. figshare. Dataset https:\/\/doi.org\/10.6084\/m9.figshare.30138733.v1 (2025).","DOI":"10.6084\/m9.figshare.30138733.v1"},{"key":"9089_CR92","doi-asserted-by":"publisher","unstructured":"Van Haute M. J. S. et al. Genetic variation and historical breeding patterns in common bean (Phaseolus vulgaris L.) affect fermentation patterns by the human gut microbiome: Source data for figures. figshare. Dataset https:\/\/doi.org\/10.6084\/m9.figshare.30138844.v1 (2025).","DOI":"10.6084\/m9.figshare.30138844.v1"},{"key":"9089_CR93","unstructured":"Van Haute M. J. S. Genetic analysis in common bean for variation affecting the human gut microbiome. ETD Collection for University of Nebraska-Lincoln AAI28865399, (2021)."}],"container-title":["Communications Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-09089-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-09089-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-09089-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T13:04:44Z","timestamp":1764162284000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-09089-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,26]]},"references-count":93,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["9089"],"URL":"https:\/\/doi.org\/10.1038\/s42003-025-09089-2","relation":{},"ISSN":["2399-3642"],"issn-type":[{"type":"electronic","value":"2399-3642"}],"subject":[],"published":{"date-parts":[[2025,11,26]]},"assertion":[{"value":"5 March 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 October 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 November 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"1690"}}