{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T18:58:57Z","timestamp":1785437937907,"version":"3.56.0"},"reference-count":50,"publisher":"American Society for Microbiology","issue":"7","license":[{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1019093"],"award-info":[{"award-number":["OPP1019093"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                      is one of the leading pathogens causing diarrhea in children globally. Stool culture remains the standard for diagnosing\n                      <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                      infections; however, quantitative PCR (qPCR) offers greater sensitivity. In this study, we evaluated the fecal microbiomes of 27 diarrheal children with and without\n                      <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                      identified by culture and quantitative PCR, respectively, aiming to characterize the fecal microbiome profiles of children with\n                      <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                      diarrhea and to explore the differences in microbiome and the mechanisms associated with the culturability of\n                      <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                      . Our results showed that\n                      <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                      qPCR positive cases were characterized by a significantly higher abundance of\n                      <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                      and other\n                      <jats:italic toggle=\"yes\">Proteobacteria<\/jats:italic>\n                      , alongside a lower abundance of the probiotic genus\n                      <jats:italic toggle=\"yes\">Bifidobacterium<\/jats:italic>\n                      . This profile was associated with specific virulence factors (VFGs) and antimicrobial resistance genes (ARGs), indicating a unique pathogenic module related to\n                      <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                      infection. While no significant difference in\n                      <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                      abundance was found between the\n                      <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                      culture positive and culture negative groups, genera\n                      <jats:italic toggle=\"yes\">Bifidobacterium<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">Ligilactobacillus<\/jats:italic>\n                      were enriched in the culture positive group. Interestingly, the culture positive group also possessed a higher abundance of virulence factors associated with pathogenicity, likely resulting from the higher copy number of pINV plasmid. The fecal metagenomic analyses from diarrheal children suggested a potentially distinct intestinal microbial profile associated with\n                      <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                      infection and a possible correlation between increased pathogenicity and the\n                      <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                      culturability. These findings might contribute to a more comprehensive understanding of\n                      <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                      pathogenicity and improving diagnostic methods for\n                      <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                      .\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        Diarrhea represents the fifth leading cause of mortality among children under the age of five, with\n                        <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                        representing the second most common pathogen responsible for diarrhea-related mortality. In the current study, we employed metagenomics to comprehensively characterize the fecal microbiome profiles of children infected with\n                        <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                        and to investigate the factors affecting\n                        <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                        culturability. We identified a distinct intestinal microbial profile associated with\n                        <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                        -infected diarrheal children, observed a correlation between increased pathogenicity and the\n                        <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                        culturability, and also proposed some potential factors that might promote the\n                        <jats:italic toggle=\"yes\">in vitro<\/jats:italic>\n                        growth of\n                        <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                        strains. These findings might provide evidence for improving diagnostic methods for\n                        <jats:italic toggle=\"yes\">Shigella<\/jats:italic>\n                        .\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.00573-25","type":"journal-article","created":{"date-parts":[[2025,6,11]],"date-time":"2025-06-11T08:39:26Z","timestamp":1749631166000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":3,"title":["Fecal microbiome profiling of children with\n                    <i>Shigella<\/i>\n                    diarrhea from low- and middle-income countries"],"prefix":"10.1128","volume":"13","author":[{"given":"Yeshun","family":"Fan","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/021cj6z65","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Public Health, Qingdao University","place":["Qingdao, 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