{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T13:11:26Z","timestamp":1788959486667,"version":"build-2803163510"},"reference-count":72,"publisher":"American Society for Microbiology","issue":"9","license":[{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R21AI190856"],"award-info":[{"award-number":["R21AI190856"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mBio"],"published-print":{"date-parts":[[2026,9,9]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Understanding bacterial gene expression in natural environments remains challenging because most regulatory networks are inferred from\n                      <jats:italic toggle=\"yes\">in vitro<\/jats:italic>\n                      models that poorly capture\n                      <jats:italic toggle=\"yes\">in situ<\/jats:italic>\n                      environmental conditions. Here, we present NEMO (\n                      <jats:underline>ne<\/jats:underline>\n                      twork transcriptomics of\n                      <jats:underline>m<\/jats:underline>\n                      icrobes in native envir\n                      <jats:underline>o<\/jats:underline>\n                      nments), a generalizable pangenome-based metatranscriptomic framework for extracting microbial transcriptional programs from metatranscriptomes generated from natural samples. We applied NEMO to\n                      <jats:italic toggle=\"yes\">Staphylococcus aureus<\/jats:italic>\n                      metatranscriptomes from human chronic wounds and cystic fibrosis sputum, revealing infection-associated transcriptional states that diverged markedly from\n                      <jats:italic toggle=\"yes\">in vitro<\/jats:italic>\n                      growth conditions. Notably, small RNAs (sRNAs) were key drivers of the transcriptional divergence between human infection-derived and\n                      <jats:italic toggle=\"yes\">in vitro<\/jats:italic>\n                      transcriptomes. Among these, we identify\n                      <jats:italic toggle=\"yes\">rsaX20<\/jats:italic>\n                      as a previously uncharacterized, zinc-responsive sRNA that also encodes a small peptide. Meta-analysis of more than 2,000 publicly available\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      RNA-seq data sets showed that\n                      <jats:italic toggle=\"yes\">rsaX20<\/jats:italic>\n                      is induced under zinc limitation and host-associated stress and is co-regulated with known metal-responsive sRNAs. Genetic, transcriptomic, and proteomic analyses demonstrated that\n                      <jats:italic toggle=\"yes\">rsaX20<\/jats:italic>\n                      is repressed by the zinc regulator Zur and functions as a dual-purpose sRNA\/small open reading frame, with the RNA and peptide exerting distinct, sometimes opposing, effects on target proteins. Together, these findings establish NEMO as a broadly applicable framework for interrogating microbial gene regulation directly from native metatranscriptomes and identify\n                      <jats:italic toggle=\"yes\">rsaX20<\/jats:italic>\n                      as a key regulator of zinc homeostasis during chronic human\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      infection.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Most knowledge of bacterial gene regulation comes from laboratory cultures, yet pathogens behave very differently inside the human body. We introduce NEMO, a pangenome-based framework that enables direct analysis of microbial gene expression from natural infection samples. Applying NEMO to human\n                      <jats:italic toggle=\"yes\">Staphylococcus aureus<\/jats:italic>\n                      infections revealed transcriptional programs that differ substantially from standard\n                      <jats:italic toggle=\"yes\">in vitro<\/jats:italic>\n                      models and highlighted small regulatory RNAs as major drivers of this divergence. Using this approach, we discovered\n                      <jats:italic toggle=\"yes\">rsaX20<\/jats:italic>\n                      , a previously uncharacterized zinc-responsive regulatory RNA that also encodes a small peptide with distinct biological functions. These findings demonstrate the power of studying microbes in their native environments and uncover a key regulator of zinc homeostasis during chronic human infection.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/mbio.00637-26","type":"journal-article","created":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T13:00:30Z","timestamp":1786107630000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Discovery of\n                    <i>Staphylococcus aureus<\/i>\n                    small RNAs highly expressed during human chronic infection"],"prefix":"10.1128","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7530-6803","authenticated-orcid":true,"given":"Paul","family":"Briaud","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01zkghx44","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Biological Sciences, Georgia Institute of 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