The intestinal microbiota impacts nutritional immunity and resistance to Acinetobacter baumannii pneumonia
Contributed by Eric P. Skaar; received November 26, 2025; accepted March 20, 2026; reviewed by Alison K. Criss and Amanda G. Oglesby
Significance
Antibiotics are routinely administered to critically ill hospital patients to treat infection. However, antibiotic treatment is often associated with subsequent healthcare-associated infections, including pneumonias caused by the emerging nosocomial pathogen Acinetobacter baumannii. Here, we show that broad-spectrum antibiotic administration disrupts the intestinal microbiota and suppresses the expression of pulmonary phagocyte pathways that sequester nutrient metals in the lung. This loss of microbiota-dependent nutritional immunity enhances A. baumannii dissemination, resulting in more severe disease. Restoring a healthy microbiota reinstates control of systemic infection, revealing a gut–lung connection that influences susceptibility to this pathogen. These findings identify a mechanism by which antibiotic exposure exacerbates A. baumannii pneumonia severity and highlight the potential of microbiota-targeted strategies to prevent healthcare-associated infections with this pathogen.
Abstract
Broad-spectrum antibiotics are frequently administered to intensive care unit patients as part of empiric care. This treatment has been associated with subsequent infections by the emerging nosocomial pathogen Acinetobacter baumannii; however, the mechanisms underlying this linkage remain unclear. Here, we observe an association between antibiotic treatment and microbiota disruption that precedes A. baumannii infection in a hospitalized patient cohort and demonstrate in a murine model that broad-spectrum antibiotic administration drives susceptibility to intranasal infection with this pathogen. Reconstitution of the intestinal microbiota by fecal microbiota transplant restores control of A. baumannii bloodstream dissemination, implicating microbiota dysbiosis as a key driver of pulmonary disease. Using single-cell RNA sequencing, we determine that antibiotic pretreatment reduces the abundance of transcripts related to phagocyte effector functions in the lung, including nutritional immunity pathways that restrict pathogen access to essential nutrient metals. Depletion studies identify neutrophils and inflammatory monocytes as central mediators of microbiota-dependent protection, and loss of the nutritional immunity components lipocalin-2 or calprotectin abrogates the effects of antibiotics on infected mice, demonstrating a causal relationship between microbiota dysbiosis and impaired phagocyte-mediated nutritional immunity. Together, these findings provide a mechanism for the increased severity of A. baumannii pneumonia following antibiotic exposure and highlight the intestinal microbiota as a potential therapeutic target to prevent nosocomial infections with this and other healthcare-associated pathogens.
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Data, Materials, and Software Availability
Specific parameter settings, a complete collection of all package versions, and code for all steps of the analysis is available at https://github.com/SucreLab/LungAcinetobacterAntibiotics (105). Raw sequencing files associated with 16S rRNA gene sequencing and metagenomic sequencing have been uploaded to the NCBI sequence read archive (SRA) with the following accessions: 16S rRNA gene sequencing: NCBI BioProject PRJNA1363572 (106); metagenomic sequencing from human donors: NCBI BioProjects PRJNA1134172 (107), PRJNA845905 (108), and PRJNA838648 (109). Raw sequencing files associated with scRNA-seq data have been uploaded to the Gene Expression Omnibus under the accession GSE313334 (110). All other data are included in the manuscript and/or supporting information.
Acknowledgments
We thank members of the Skaar Laboratory for critical feedback during the assembly of this manuscript. We thank the VUMC Digital Histology Shared Resource (DHSR) for imaging of RNA FISH staining. This work was supported by the following NIH grants: R01 AI101171 and R01 AI138581 to E.P.S., K22 AI166265 to E.R.G., R01 HL168556 and K08 HL143051 to J.M.S.S., R35 GM146969 to S.H.L., R35 GM138369 to J.P.Z., and R01 DK131104 and 1R01 AI168302 to M.X.B. T32 HL094296 supported E.R.G., T32 GM150375 supported T.H.B., T32 ES007028 supported N.G.S., and T32 GM008554 supported K.A.T. R01 AI138581, R01 AG078803, and U54 DK134302 supported F.A.M. and R.v.d.P. Additional funding was provided by the Advanced Research Projects Agency for Health agreement 1AY2AX000077 to E.P.S., by the Ernest W. Goodpasture professorship to E.P.S., and by the Francis Family Foundation to J.M.S.S. and N.M.N. M.X.B. is a Howard Hughes Medical Institute Freeman Hrabowski Scholar and received additional funding from the Pew Charitable Trusts (2022-A-19568) and the Burroughs Wellcome Fund (022792). N.G.S. was supported by the Howard Hughes Medical Institute Gilliam Fellowship (GT15104) and V.M.R.R. was supported by the Howard Hughes Medical Institute as a HHMI Hanna-Gray Fellow. We acknowledge the use of Claude Sonnet 4.6 and Grammarly for minor proofreading and editing support.
Author contributions
E.R.G., N.M.N., J.M.S.S., and E.P.S. designed research; E.R.G., N.M.N., T.H.B., N.G.S., S.L.D., K.A.T., and V.M.R.R. performed research; F.A.M. and R.v.d.P. contributed new reagents/analytic tools; E.R.G., N.M.N., T.H.B., N.G.S., F.A.M., T.S.Y., C.J.L., M.X.B., R.v.d.P., J.P.Z., S.H.L., and J.M.S.S. analyzed data; and E.R.G. and E.P.S. wrote the paper.
Competing interests
The authors declare no competing interest.
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Copyright © 2026 the Author(s). Published by PNAS. This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).
Data, Materials, and Software Availability
Specific parameter settings, a complete collection of all package versions, and code for all steps of the analysis is available at https://github.com/SucreLab/LungAcinetobacterAntibiotics (105). Raw sequencing files associated with 16S rRNA gene sequencing and metagenomic sequencing have been uploaded to the NCBI sequence read archive (SRA) with the following accessions: 16S rRNA gene sequencing: NCBI BioProject PRJNA1363572 (106); metagenomic sequencing from human donors: NCBI BioProjects PRJNA1134172 (107), PRJNA845905 (108), and PRJNA838648 (109). Raw sequencing files associated with scRNA-seq data have been uploaded to the Gene Expression Omnibus under the accession GSE313334 (110). All other data are included in the manuscript and/or supporting information.
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Received: November 26, 2025
Accepted: March 20, 2026
Published online: April 21, 2026
Published in issue: April 28, 2026
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Acknowledgments
We thank members of the Skaar Laboratory for critical feedback during the assembly of this manuscript. We thank the VUMC Digital Histology Shared Resource (DHSR) for imaging of RNA FISH staining. This work was supported by the following NIH grants: R01 AI101171 and R01 AI138581 to E.P.S., K22 AI166265 to E.R.G., R01 HL168556 and K08 HL143051 to J.M.S.S., R35 GM146969 to S.H.L., R35 GM138369 to J.P.Z., and R01 DK131104 and 1R01 AI168302 to M.X.B. T32 HL094296 supported E.R.G., T32 GM150375 supported T.H.B., T32 ES007028 supported N.G.S., and T32 GM008554 supported K.A.T. R01 AI138581, R01 AG078803, and U54 DK134302 supported F.A.M. and R.v.d.P. Additional funding was provided by the Advanced Research Projects Agency for Health agreement 1AY2AX000077 to E.P.S., by the Ernest W. Goodpasture professorship to E.P.S., and by the Francis Family Foundation to J.M.S.S. and N.M.N. M.X.B. is a Howard Hughes Medical Institute Freeman Hrabowski Scholar and received additional funding from the Pew Charitable Trusts (2022-A-19568) and the Burroughs Wellcome Fund (022792). N.G.S. was supported by the Howard Hughes Medical Institute Gilliam Fellowship (GT15104) and V.M.R.R. was supported by the Howard Hughes Medical Institute as a HHMI Hanna-Gray Fellow. We acknowledge the use of Claude Sonnet 4.6 and Grammarly for minor proofreading and editing support.
Author contributions
E.R.G., N.M.N., J.M.S.S., and E.P.S. designed research; E.R.G., N.M.N., T.H.B., N.G.S., S.L.D., K.A.T., and V.M.R.R. performed research; F.A.M. and R.v.d.P. contributed new reagents/analytic tools; E.R.G., N.M.N., T.H.B., N.G.S., F.A.M., T.S.Y., C.J.L., M.X.B., R.v.d.P., J.P.Z., S.H.L., and J.M.S.S. analyzed data; and E.R.G. and E.P.S. wrote the paper.
Competing interests
The authors declare no competing interest.
Notes
Reviewers: A.K.C., University of Virginia; and A.G.O., University of Maryland Baltimore.
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The intestinal microbiota impacts nutritional immunity and resistance to Acinetobacter baumannii pneumonia, Proc. Natl. Acad. Sci. U.S.A.
123 (17) e2534432123,
https://doi.org/10.1073/pnas.2534432123
(2026).
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