misosoup: A metabolic modeling tool for identifying minimal microbial communities reveals pervasive cross–feeding–driven niche expansion

misosoup: A metabolic modeling tool for identifying minimal microbial communities provides valuable insights into microbial ecology and biotechnological applications | bioRxiv /* */ /* */ <!-- <!-- /*! * yepnope1.5.4 * (c) WTFPL, GPLv2 */ (function(a,b,c){function d(a){return"[object Function]"==o.call(a)}function e(a){return"string"==typeof a}function f(){}function g(a){return!a||"loaded"==a||"complete"==a||"uninitialized"==a}function h(){var a=p.shift();q=1,a?a.t?m(function(){("c"==a.t?B.injectCss:B.injectJs)(a.s,0,a.a,a.x,a.e,1)},0):(a(),h()):q=0}function i(a,c,d,e,f,i,j){function k(b){if(!o&&g(l.readyState)&&(u.r=o=1,!q&&h(),l.onload=l.onreadystatechange=null,b)){"img"!=a&&m(function(){t.removeChild(l)},50);for(var d in y[c])y[c].hasOwnProperty(d)&&y[c][d].onload()}}var j=j||B.errorTimeout,l=b.createElement(a),o=0,r=0,u={t:d,s:c,e:f,a:i,x:j};1===y[c]&&(r=1,y[c]=[]),"object"==a?l.data=c:(l.src=c,l.type=a),l.width=l.height="0",l.onerror=l.onload=l.onreadystatechange=function(){k.call(this,r)},p.splice(e,0,u),"img"!=a&&(r||2===y[c]?(t.insertBefore(l,s?null:n),m(k,j)):y[c].push(l))}function j(a,b,c,d,f){return q=0,b=b||"j",e(a)?i("c"==b?v:u,a,b,this.i++,c,d,f):(p.splice(this.i++,0,a),1==p.length&&h()),this}function k(){var a=B;return a.loader={load:j,i:0},a}var l=b.documentElement,m=a.setTimeout,n=b.getElementsByTagName("script")[0],o={}.toString,p=[],q=0,r="MozAppearance"in l.style,s=r&&!!b.createRange().compareNode,t=s?l:n.parentNode,l=a.opera&&"[object Opera]"==o.call(a.opera),l=!!b.attachEvent&&!l,u=r?"object":l?"script":"img",v=l?"script":u,w=Array.isArray||function(a){return"[object Array]"==o.call(a)},x=[],y={},z={timeout:function(a,b){return b.length&&(a.timeout=b[0]),a}},A,B;B=function(a){function b(a){var a=a.split("!"),b=x.length,c=a.pop(),d=a.length,c={url:c,origUrl:c,prefixes:a},e,f,g;for(f=0;f<d;f++)g=a[f].split("="),(e=z[g.shift()])&&(c=e(c,g));for(f=0;f<b;f++)c=x[f](c);return c}function g(a,e,f,g,h){var i=b(a),j=i.autoCallback;i.url.split(".").pop().split("?").shift(),i.bypass||(e&&(e=d(e)?e:e[a]||e[g]||e[a.split("/").pop().split("?")[0]]),i.instead?i.instead(a,e,f,g,h):(y[i.url]?i.noexec=!0:y[i.url]=1,f.load(i.url,i.forceCSS||!i.forceJS&&"css"==i.url.split(".").pop().split("?").shift()?"c":c,i.noexec,i.attrs,i.timeout),(d(e)||d(j))&&f.load(function(){k(),e&&e(i.origUrl,h,g),j&&j(i.origUrl,h,g),y[i.url]=2})))}function h(a,b){function c(a,c){if(a){if(e(a))c||(j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}),g(a,j,b,0,h);else if(Object(a)===a)for(n in m=function(){var b=0,c;for(c in a)a.hasOwnProperty(c)&&b++;return b}(),a)a.hasOwnProperty(n)&&(!c&&!--m&&(d(j)?j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}:j[n]=function(a){return function(){var b=[].slice.call(arguments);a&&a.apply(this,b),l()}}(k[n])),g(a[n],j,b,n,h))}else!c&&l()}var h=!!a.test,i=a.load||a.both,j=a.callback||f,k=j,l=a.complete||f,m,n;c(h?a.yep:a.nope,!!i),i&&c(i)}var i,j,l=this.yepnope.loader;if(e(a))g(a,0,l,0);else if(w(a))for(i=0;i (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0];var j=d.createElement(s);var dl=l!='dataLayer'?'&l='+l:'';j.src='//www.googletagmanager.com/gtm.js?id='+i+dl;j.type='text/javascript';j.async=true;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-M677548'); Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search New Results misosoup: A metabolic modeling tool for identifying minimal microbial communities provides valuable insights into microbial ecology and biotechnological applications View ORCID Profile Nicolas Ochsner , View ORCID Profile Magdalena San Román , Adrián Jiménez-Fernández , View ORCID Profile Sebastian Bonhoeffer , View ORCID Profile Alberto Pascual-García doi: https://doi.org/10.1101/2025.08.07.669121 Nicolas Ochsner 1 ETH-Zurich; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Nicolas Ochsner Magdalena San Román 2 Spanish National Research Council Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Magdalena San Román Adrián Jiménez-Fernández 2 Spanish National Research Council Find this author on Google Scholar Find this author on PubMed Search for this author on this site Sebastian Bonhoeffer 1 ETH-Zurich; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Sebastian Bonhoeffer Alberto Pascual-García 2 Spanish National Research Council Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Alberto Pascual-García For correspondence: alberto.pascual.garcia{at}gmail.com Abstract Info/History Metrics Data/Code Preview PDF Abstract Microbial survival and function often depend on metabolic interactions within communities. Therefore, a central question in disentangling microbial organization is determining which minimal groups of species are able to thrive in a given medium--referred to as 'minimal communities'. Answering this question is essential for understanding microbial distribution, enhancing laboratory cultivation, and designing synthetic communities (SynComs). Here, we introduce misosoup, a Python package for identifying minimal communities (MInimal Supplying cOmmunity Search). Through genome-scale constraint-based metabolic modeling, misosoup enables the systematic identification of communities that support microbial growth in environments where individual species fail to survive alone. We validate misosoup against experimentally verified minimal communities, demonstrating its ability to predict known cooperative interactions, cocultures, and consortia with biotechnological potential. We further illustrate the use of misosoup to investigate broad microbial ecology questions by applying it to a set of 60 marine microbes, revealing pervasive cross-feeding-driven niche expansion and showing how the detailed outputs provided by misosoup facilitate research on topics such as the identification of functional groups. In summary, misosoup provides a powerful tool for microbial ecology and community design, with potential applications in both research and biotechnological innovation. Competing Interest Statement The authors have declared no competing interest. Footnotes The manuscript has been updated to include more applications of the software presented, and to tackle some technical issues. Supplementary Materials have been expanded to illustrate modelling limitations. An additional author contributing to new contents was added. https://github.com/sirno/misosoup https://github.com/sirno/niche_expansion_data Funder Information Declared Agencia Estatal de Investigación, https://ror.org/003x0zc53 , RyC2021-032424-I (MICIU/AEI; 10.13039/501100011033/ PRTR, EU) , PID2022-139900NA-I00 (MICIU/AEI; 10.13039/501100011033/ FEDER, EU) , CEX2023-001386-S (MICIU/AEI; 10.13039/501100011033/ FEDER, EU) Spanish National Research Council, https://ror.org/02gfc7t72 , 20232AT031 Simons Foundation , 542381 Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license . View the discussion thread. Back to top Previous Next Posted May 25, 2026. Download PDF Data/Code Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. 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Share misosoup: A metabolic modeling tool for identifying minimal microbial communities provides valuable insights into microbial ecology and biotechnological applications Nicolas Ochsner , Magdalena San Román , Adrián Jiménez-Fernández , Sebastian Bonhoeffer , Alberto Pascual-García bioRxiv 2025.08.07.669121; doi: https://doi.org/10.1101/2025.08.07.669121 Share This Article: Copy Citation Tools misosoup: A metabolic modeling tool for identifying minimal microbial communities provides valuable insights into microbial ecology and biotechnological applications Nicolas Ochsner , Magdalena San Román , Adrián Jiménez-Fernández , Sebastian Bonhoeffer , Alberto Pascual-García bioRxiv 2025.08.07.669121; doi: https://doi.org/10.1101/2025.08.07.669121 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Area Bioinformatics Subject Areas All Articles Animal Behavior and Cognition (7635) Biochemistry (17697) Bioengineering (13895) Bioinformatics (41951) Biophysics (21456) Cancer Biology (18594) Cell Biology (25520) Clinical Trials (138) Developmental Biology (13381) Ecology (19903) Epidemiology (2067) Evolutionary Biology (24323) Genetics (15612) Genomics (22510) Immunology (17738) Microbiology (40401) Molecular Biology (17184) Neuroscience (88622) Paleontology (667) Pathology (2833) Pharmacology and Toxicology (4825) Physiology (7644) Plant Biology (15158) Scientific Communication and Education (2046) Synthetic Biology (4296) Systems Biology (9825) Zoology (2271)