COVID-19 virus increases risk for other infections by disrupting normal mix of gut bacteria

COVID-19 virus increases risk for other infections by disrupting normal mix of gut bacteria
SARS-CoV-2 infection causes gut microbiome alterations in mice. K18-hACE2 mice were infected intranasally with 0 or 104 PFU of SARS-CoV-2. Fecal samples for microbiome analyses were collected daily from day 0 (before infection) until sacrifice; mice were sacrificed on days 5–7. Results show pooled data from three independent experiments with n = 3–5 mice per group. a Timelines of fecal microbiota composition measured by 16S rRNA gene sequencing. Bars represent the composition of the 15 most abundant bacterial families per sample for each day, blocks of samples correspond to an individual mouse’s time course from day 0 to day 6, as exemplified for the first mouse. b α-diversity (inverse Simpson index) per infection group in the beginning (tstart, n = 13 each for control and infected) and at the end (tend, n = 13 each for control and infected) of the experiment (n.s.: non-significant, **: p < 0.01, one-tailed, paired t-test; boxplots show median and quartile ranges). Comparison between infected and non-infected mouse microbiomes at the end of the experiment. c Principal coordinate plot of bacterial compositions in samples collected prior to infection (tstart, top) and at sacrifice (tend, bottom) of the experiment (Bray Curtis dissimilarity). d log10-relative family abundances at the final time point; boxplots show median and quartile ranges, whiskers extend to 1.5 times max- and min- quartile values, n.s.: not significant; *: p value < 0.05; **: p value < 0.01; ***: p value < 0.001; two-sided Wilcoxon rank-sum tests (n = 13 each for control and infected). e Analysis of microbiome composition trajectories in infected mice. Regression coefficients of the estimated changes in family abundances per day in mice infected with 104 PFU were obtained from linear mixed effects models with varying effects per mouse and per cage (only significant coefficient results shown, abbreviations and colors as per the bacterial family legend; Red: separate, analogous analysis for phylum Proteobacteria trajectories). Credit: Nature Communications (2022). DOI: 10.1038/s41467-022-33395-6

Infection with the pandemic virus, SARS-CoV-2, can reduce the number of bacterial species in a patient's gut, with the lesser diversity creating space for dangerous microbes to thrive, a new study finds.

The study builds on the realization that widespread use of antibiotics to fight infections with in recent decades, by killing off species most vulnerable to available drugs, has left in place more species that are resistant to antibiotics. In addition, disruptions in gut bacterial ratios have previously been linked to more severe COVID-19.

However, researchers say, it has remained unclear until now which came first, the coronavirus disrupting the or an already weakened gut making the body more vulnerable to the virus. The new study appears to favor the former explanation. The new investigation also revealed that antibiotic-resistant species can escape into the bloodstream, putting patients at greater risk for life-threatening secondary infections.

Led by researchers at NYU Grossman School of Medicine, the investigation involved 96 men and women hospitalized with COVID-19 in 2020 in New York City and in New Haven, Conn. Results showed that the majority of patients had low gut microbiome diversity, with a full quarter dominated by a single type of bacteria. At the same time, populations of several microbes known to include antibiotic-resistant species increased, possible due to widespread antibiotic use early in the pandemic.

These found in the gut were also observed to have migrated into the bloodstream in 20% of patients. The study authors note that further research is needed to uncover why this group was at higher risk for a secondary infection while others remained protected.

"Our findings suggest that coronavirus infection directly interferes with the healthy balance of microbes in the gut, further endangering patients in the process," says study co-senior author and microbiologist Ken Cadwell, Ph.D. "Now that we have uncovered the source of this bacterial imbalance, physicians can better identify those coronavirus patients most at risk of a secondary bloodstream infection," adds Cadwell.

The new study is the first to show that the alone, and not the initial use of antibiotics to treat the disease as others experts had thought, damages the gut microbiome, says Cadwell, also a professor in the Departments of Microbiology and Medicine at NYU Langone Health. He adds the study is also provides the first evidence that the very same bacteria in the gut are also entering the blood stream of patients, causing dangerous infections.

The report is publishing online Nov. 1 in the journal Nature Communications.

For the investigation, researchers first infected dozens of mice with the coronavirus and analyzed the makeup of bacterial species in their stool samples. This step allowed them to untangle whether the coronavirus could directly disrupt the microbiome independently of hospitalization and treatment.

Next, they collected stool samples and blood tests from COVID-19 patients at NYU Langone Health and Yale University hospitals to assess gut microbe composition and presence of secondary infection. If any bacteria group made up a majority of the bacteria living in the gut, they were considered dominant.

"Our results highlight how the gut microbiome and different parts of the body's are closely interconnected," says study senior author Jonas Schluter, Ph.D., an assistant professor in the Department of Microbiology at NYU Langone and a member of its Institute for Systems Genetics. "An infection in one can lead to major disruptions in the other."

Schluter cautions that since the patients received different kinds of treatments for their illness, the investigation could not entirely account for all factors that may have contributed to the disruption of their microbiome and worsen their disease.

According to Schluter, the study team next plans to examine why certain microbial species are more likely to escape the gut during COVID-19. The researchers say they also intend to explore how different microbes interact, which may contribute to this migration into the bloodstream.

More information: Lucie Bernard-Raichon et al, Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia, Nature Communications (2022). DOI: 10.1038/s41467-022-33395-6

Journal information: Nature Communications

Provided by NYU Langone Health
Citation: COVID-19 virus increases risk for other infections by disrupting normal mix of gut bacteria (2022, November 1) retrieved 3 December 2023 from
This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only.

Explore further

Protecting the microbiome essential to fighting antibiotic-resistant bacteria


Feedback to editors