Progressive Post-Acute Gut Microbiome Disruption Following SARS-CoV-2 Infection in Mice
- 1Division of Pulmonary Medicine, Department of Medicine, Faculty of Medicine & Dentistry, and Alberta Respiratory Centre, University of Alberta, Edmonton, Albert
Abstract
SARS-CoV-2 infection is increasingly recognized to produce long-lasting physiological disturbances that extend beyond the acute phase. The gut microbiome has emerged as a potential contributor to post-infection outcomes, yet the longitudinal progression of microbial disruption following infection remains poorly defined. Here, we used a mouse model of SARS-CoV-2 infection to characterize gut microbiome dynamics at 7 (late acute phase), 14 (early recovery), and 21 (post-COVID condition, PCC) days post-infection (dpi). Viral RNA was detected in the lungs through 21 dpi. Longitudinal microbiome profiling revealed a two-phase restructuring marked by early shifts in Bacillota and Bacteroidota abundance, followed by pronounced post-acute dysbiosis characterized by reduced diversity, expansion of Bacillota, and near-complete loss of Bacteroidota. Functional pathway predictions showed progressive metabolic remodeling, including disruptions in nucleotide turnover, fermentation, and vitamin-related pathways. Together, these findings demonstrate that SARS-CoV-2 infection drives progressive and sustained alterations in gut microbial composition and function after the transition from acute infection through recovery into PCC.
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BibTeX
@misc{mannnuttel2026progressive,
title = {{Progressive Post-Acute Gut Microbiome Disruption Following SARS-CoV-2 Infection in Mice}},
author = {R. Mann-Nuttel and N. S. Ogando and M. Armbruster and S. Mandal and D. Ospondpant and M. Elaish and T. C. Hobman and C. Power and P. Forsythe},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.16.751817},
url = {https://www.biorxiv.org/content/10.64898/2026.09.16.751817v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Progressive Post-Acute Gut Microbiome Disruption Following SARS-CoV-2 Infection in Mice
AU - R. Mann-Nuttel
AU - N. S. Ogando
AU - M. Armbruster
AU - S. Mandal
AU - D. Ospondpant
AU - M. Elaish
AU - T. C. Hobman
AU - C. Power
AU - P. Forsythe
PY - 2026
DA - 2026/09/16
PB - bioRxiv
DO - 10.64898/2026.09.16.751817
UR - https://www.biorxiv.org/content/10.64898/2026.09.16.751817v1
AB - SARS-CoV-2 infection is increasingly recognized to produce long-lasting physiological disturbances that extend beyond the acute phase. The gut microbiome has emerged as a potential contributor to post-infection outcomes, yet the longitudinal progression of microbial disruption following infection remains poorly defined. Here, we used a mouse model of SARS-CoV-2 infection to characterize gut microbiome dynamics at 7 (late acute phase), 14 (early recovery), and 21 (post-COVID condition, PCC) days post-infection (dpi). Viral RNA was detected in the lungs through 21 dpi. Longitudinal microbiome profiling revealed a two-phase restructuring marked by early shifts in Bacillota and Bacteroidota abundance, followed by pronounced post-acute dysbiosis characterized by reduced diversity, expansion of Bacillota, and near-complete loss of Bacteroidota. Functional pathway predictions showed progressive metabolic remodeling, including disruptions in nucleotide turnover, fermentation, and vitamin-related pathways. Together, these findings demonstrate that SARS-CoV-2 infection drives progressive and sustained alterations in gut microbial composition and function after the transition from acute infection through recovery into PCC.
ER -