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We analyzed associations between host gene expression and microbiome composition in a cohort of 315 healthy individuals, integrating microarray-based gene expression data from three intestinal sites (ileum, transverse colon, and rectum) and six immune cell types with microbiome sequencing data. Using a hierarchical feature aggregation strategy combining principal component analysis, clustering, and covariate correction, we discovered significant associations primarily related to immunity. While microbial profiles were similar across the three intestinal sites, the transverse colon yielded the most \u201cmicrobiome-host gene expression\u201d associations. Among the immune cell types, CD8+ cells showed the highest number of associations. The first principal component of microbiome composition, reflecting a gradient from commensals (e.g.,\n                      <jats:italic toggle=\"yes\">Ruminococcaceae<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">Christensenellaceae<\/jats:italic>\n                      ) to proinflammatory taxa ([\n                      <jats:italic toggle=\"yes\">Ruminococcus<\/jats:italic>\n                      ]\n                      <jats:italic toggle=\"yes\">gnavus<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">Lachnoclostridium<\/jats:italic>\n                      ), correlated with the expression of TNF-\u03b1-linked genes (\n                      <jats:italic toggle=\"yes\">HMOX1<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">CPI17<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">HSD3B2<\/jats:italic>\n                      , and\n                      <jats:italic toggle=\"yes\">SLC5A1<\/jats:italic>\n                      ). Among individual genera,\n                      <jats:italic toggle=\"yes\">Catenibacterium<\/jats:italic>\n                      abundance was associated with gene expression in both intestinal and immune cells, including negative associations with MRPS21 (related to mitochondrial function) in the transverse colon and with CD8+ gene programs related to T cell differentiation. These findings align with emerging evidence implicating mitochondrial dysfunction in intestinal inflammation. Our results identify multi-level associations between the gut microbiome and host gene expression, suggesting potential mechanisms by which microbiota shape local and systemic immunity and vice versa. The implicated genes and taxa represent candidates for experimental validation to improve understanding of host-microbiome homeostasis and its disruption in disease.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>The gut microbiome and immune system are engaged in a complex interplay throughout human life. While most associative studies focus on case-control comparisons\u2014typically examining patients with conditions such as inflammatory bowel disease or metabolic diseases\u2014less is known about the molecular links between the microbiome and immune system in healthy individuals. In this study of a large cohort of healthy individuals, we addressed this gap by applying multiscale modeling to tackle the high dimensionality of host-microbiome data. We identified multi-level associations between microbiome composition and host gene expression in both intestinal tissues and immune cells. These findings offer a valuable reference for understanding baseline host-microbiome communication and highlight molecular candidates\u2014such as TNF-\u03b1-related genes and mitochondrial pathways\u2014for future experimental validation.<\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.03593-25","type":"journal-article","created":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T13:00:23Z","timestamp":1786366823000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Multi-level aggregation analysis of microbiome composition and host gene expression reveals associations with systemic and local immunity"],"prefix":"10.1128","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1325-3085","authenticated-orcid":false,"given":"Lev 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