{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T13:28:40Z","timestamp":1787059720337,"version":"build-2736575974"},"reference-count":48,"publisher":"American Society for Microbiology","issue":"8","license":[{"start":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T00:00:00Z","timestamp":1787011200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T00:00:00Z","timestamp":1787011200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100019180","name":"HORIZON EUROPE European Research Council","doi-asserted-by":"publisher","award":["101087042"],"award-info":[{"award-number":["101087042"]}],"id":[{"id":"10.13039\/100019180","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000199","name":"U.S. Department of Agriculture","doi-asserted-by":"publisher","award":["2024-67019-42477"],"award-info":[{"award-number":["2024-67019-42477"]}],"id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSystems"],"published-print":{"date-parts":[[2026,8,18]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Quantifying the abundance and activity of bacteria within populations and communities is fundamental to systems microbiology and microbiome research. Yet direct microscopic cell counting remains low throughput, labor-intensive, and prone to user variability, leading many researchers to rely on indirect proxies such as optical density or multicopy marker-gene quantification. These indirect approaches do not distinguish between active and inactive cells and can obscure ecological interpretation. Here, we introduce\n                      <jats:underline>m<\/jats:underline>\n                      icrobial\n                      <jats:underline>a<\/jats:underline>\n                      ctivity and\n                      <jats:underline>t<\/jats:underline>\n                      otal cell quantification via\n                      <jats:underline>r<\/jats:underline>\n                      apid\n                      <jats:underline>i<\/jats:underline>\n                      maging and e\n                      <jats:underline>x<\/jats:underline>\n                      traction (MATRIX), an efficient workflow that integrates sample extraction, fluorescence staining, microscopy and automated image analysis, and Bayesian statistical inference to quantify total and redox-active cells and derive single-cell measurements for environmental bacterial populations and communities. We demonstrate its reproducibility and versatility using both cultured isolates and high-diversity soil communities. The resulting quantitative, phenotypic data sets provide rapid, direct measurements of bacterial population and community size and activity, enabling well-powered analyses that strengthen mechanistic insight into microbial responses and improve the ecological grounding of microbiome studies.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Microbiome studies commonly rely on relative abundance data, which cannot distinguish whether compositional shifts reflect true population growth, declines in total community size, or both. Without explicit measurements of population and community sizes, the mechanistic interpretation of microbiome dynamics remains incomplete. Here, we present a rapid, throughput workflow,\n                      <jats:underline>m<\/jats:underline>\n                      icrobial\n                      <jats:underline>a<\/jats:underline>\n                      ctivity and\n                      <jats:underline>t<\/jats:underline>\n                      otal cell quantification via\n                      <jats:underline>r<\/jats:underline>\n                      apid\n                      <jats:underline>i<\/jats:underline>\n                      maging and e\n                      <jats:underline>x<\/jats:underline>\n                      traction (MATRIX), that quantifies both total and redox\u2011active bacterial cells from environmental samples. By integrating single\u2011cell phenotypes with community\u2011level metrics, this approach anchors microbiome data sets in direct ecological accounting rather than proxies. These measurements can clarify whether the observed changes in community structure represent shifts in abundance, activity, or both, improving inference about microbial responses to stress or environmental change. MATRIX offers an efficient way to incorporate quantitative ecology into systems microbiology and microbiome studies and to strengthen the link between microbial cellular physiology, community dynamics, and ecosystem function.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/msystems.00308-26","type":"journal-article","created":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T13:03:30Z","timestamp":1784120610000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["MATRIX: rapid quantification of total and active microbial cells with single-cell phenotypes for environmental microbiomes"],"prefix":"10.1128","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0411-9335","authenticated-orcid":true,"given":"Milena","family":"Gonzalo","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/029brtt94","id-type":"ROR","asserted-by":"publisher"}],"name":"LEM, UMR 5557, UMR 1418, Universit\u00e9 Lyon 1, CNRS, INRAE","place":["Villeurbanne, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3121-715X","authenticated-orcid":false,"given":"Xipeng","family":"Liu","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/029brtt94","id-type":"ROR","asserted-by":"publisher"}],"name":"LEM, UMR 5557, UMR 1418, Universit\u00e9 Lyon 1, CNRS, INRAE","place":["Villeurbanne, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0244-0192","authenticated-orcid":false,"given":"Yann S.","family":"Dufour","sequence":"additional","affiliation":[{"name":"DatInsights","place":["Lyon, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7189-3067","authenticated-orcid":true,"given":"Ashley","family":"Shade","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/029brtt94","id-type":"ROR","asserted-by":"publisher"}],"name":"LEM, UMR 5557, UMR 1418, Universit\u00e9 Lyon 1, CNRS, INRAE","place":["Villeurbanne, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2018.08.005"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00051-12"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2021.627910"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2020.00403"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-025-01165-5"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.00984-25"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1009113"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0420-9"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1038\/s43705-023-00266-0"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00248-020-01586-7"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.65.10.4475-4483.1999"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1010220"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-019-0212-7"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23821-6"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2504"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1128\/mmbr.00354-25"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.3390\/molecules25214949"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00435-19"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01166-10"},{"key":"e_1_3_4_21_2","volume-title":"QUANTOM Tx microbial cell counter user manual","author":"LOGOS biosystems","year":"2021","unstructured":"LOGOS biosystems. 2021. QUANTOM Tx microbial cell counter user manual. Aligned Genetics, Inc."},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1128\/mra.01133-23"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-018-0276-6"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2017.1"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1094\/MPMI-07-10-0148"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1002\/elsc.201600030"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00374-021-01600-1"},{"key":"e_1_3_4_28_2","unstructured":"The R Foundation. 2026. R: the R project for statistical computing. Available from: https:\/\/www.r-project.org"},{"key":"e_1_3_4_29_2","doi-asserted-by":"crossref","unstructured":"B\u00fcrkner PC. 2021. Bayesian item response modeling in R with brms and Stan","DOI":"10.18637\/jss.v100.i05"},{"key":"e_1_3_4_30_2","unstructured":"Stan Development Team. 2000. RStan: the R interface to Stan"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.soilbio.2016.12.026"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2024.102558"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.mi.39.100185.001541"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2012.02817.x"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1093\/jambio\/lxaf168"},{"key":"e_1_3_4_36_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.soilbio.2021.108178"},{"key":"e_1_3_4_37_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02646-18"},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.soilbio.2011.06.019"},{"key":"e_1_3_4_39_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02776-19"},{"key":"e_1_3_4_40_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00336510"},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00248-002-2028-6"},{"key":"e_1_3_4_42_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02710-13"},{"key":"e_1_3_4_43_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2008.32"},{"key":"e_1_3_4_44_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6941.2001.tb00801.x"},{"key":"e_1_3_4_45_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijms24076841"},{"key":"e_1_3_4_46_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.58.6.1801-1808.1992"},{"key":"e_1_3_4_47_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-9-590"},{"key":"e_1_3_4_48_2","doi-asserted-by":"publisher","DOI":"10.1002\/elsc.201500149"},{"key":"e_1_3_4_49_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2022.102263"}],"container-title":["mSystems"],"original-title":[],"contributor":[{"given":"Canan","family":"Karakoc","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"reviewer"}]}],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msystems.00308-26","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msystems.00308-26","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T13:02:23Z","timestamp":1787058143000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/msystems.00308-26"}},"subtitle":[],"editor":[{"given":"Ariane L.","family":"Peralta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,8,18]]},"references-count":48,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2026,8,18]]}},"alternative-id":["10.1128\/msystems.00308-26"],"URL":"https:\/\/doi.org\/10.1128\/msystems.00308-26","relation":{},"ISSN":["2379-5077"],"issn-type":[{"value":"2379-5077","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,18]]},"assertion":[{"value":"2026-03-13","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-06-22","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-07-15","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00308-26"}}