Lower Microbiome Diversity May Indicate Severe COVID Infection

HONOLULU — Patients with severe COVID-19 infection had lower microbiome diversity, indicating a potential biomarker of disease progression and severity, researchers said here.

Stool samples taken from patients who were admitted to the intensive care unit (ICU) with severe COVID showed significant increases Parasutterella, Odoribacter, Staphylococcus, and Sellimonas bacteria, reported Irina Timofte, MD, of UT Southwestern Medical Center in Dallas, during the CHEST annual meeting hosted by the American College of Chest Physicians.

These bacteria have been implicated in gastrointestinal dysbiotic conditions, such as inflammatory bowel disease and irritable bowel syndrome, Timofte noted.

Patients who received mechanical ventilation also had a significantly increased abundance of Staphylococcus and Enterococcus, which can attach to skin and mucous membranes, but can also be aerosolized, she said.

In addition, patients with COVID pneumonia who required supplemental oxygen had significantly lower community biodiversity in both the GI tract and oral cavity.

“We can conclude that changes in the gut microbiome may represent an indicator of disease progression,” Timofte said. “Our study has the potential to identify biomarker-related disease progression.”

She explained that the relationship between respiratory and gut health has long been established, noting that the gut-lung axis is a concept that suggests changes to the gut microbiota can impact immune responses and can therefore influence respiratory conditions, such as asthma and chronic obstructive pulmonary disease.

“This is not new. Manipulating the gut-lung axis was previously proposed as a treatment for lung diseases,” she said. “And previous studies have demonstrated changes in the composition of gut microbiota in COVID-19 patients. Therefore, our study is trying to find the relationship that could be responsible for varying severity of COVID-19.”

Jaime Hook, MD, of the Icahn School of Medicine at Mount Sinai in New York City, told MedPage Today via email that the changes observed in the study, particularly those in the gut and mouth, can leave patients even more vulnerable to additional infections, putting them at further risk.

“These results add new support to the idea that there is a relationship between COVID-19 severity and changes in the microbes that normally live in the body,” noted Hook, who was not involved in the study.

“The results show that people with severe COVID-19 had more S. aureus in the mouth and gut, which is important because when the bacteria are inhaled into the lungs of people with COVID-19 and influenza infection, they can cause a secondary pneumonia that is hard to treat and can be fatal,” she said. “We need to better understand how these secondary pneumonias happen, so that we can develop new and better ways of preventing and treating them.”

For this study, Timofte and team collected stool, oral, and nasal samples from COVID-19 patients admitted at the University of Maryland Medical Center from January to June 2021. The samples were characterized using whole community shotgun metagenomic sequencing on the Illumina NovaSeq 6000 platform. Clinical factors including ICU status, survival, and use of ventilation were correlated with microbiome characteristics.

Timofte noted that the majority of patients had samples taken around the time of admission, and many had subsequent follow-up samples, which varied in number based on when the patient was ultimately discharged.

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