Persistent Gut Dysbiosis Observed 6 Months After Recovery From COVID-19

gut microbiome
gut microbiome
Investigators assessed whether alterations in gut microbiome composition were linked to postacute COVID-19 syndrome.

Patients with long-term complications of COVID-19 have compositional alterations of the gut microbiome, researchers reported in Gut.

The prospective cohort study investigated whether gut microbiome composition was linked to postacute COVID-19 syndrome (PACS). Patients with a confirmed diagnosis of COVID-19 were enrolled from February 1, 2020, to August 31, 2020, from 3 hospitals in Hong Kong, China. Control individuals matched for age and sex with normal colonoscopy results were recruited before the COVID-19 pandemic (September 2019 to November 2019).

The investigators assessed the presence of the 30 most frequently reported symptoms 3 and 6 months after COVID-19 onset. PACS was defined as having at least 1 persistent symptom that could not be explained by an alternative diagnosis 4 weeks after clearance of SARS-CoV-2.

A total of 258 stool samples were collected and sequenced. The cohort included 106 patients who were followed up for 6 months. Their median age was 48.3 years (IQR, 33-62 years) and 56 (52.9%) were women.

Of the 68 patients with COVID-19 who had stool samples analyzed at 6 months, 50 (73.5%) had PACS. The patients without PACS had recovered gut microbiomes similar to those of non-COVID-19 control group individuals (P =.470). The gut microbiome composition of patients with PACS was unique from that of non-COVID-19 control group individuals at 6 months (P <.001). Bacteria diversity and richness in patients with PACS were significantly lower than in those who did not have PACS as well as members of the control group at 6 months follow-up.

Patients with PACS had significantly reduced levels of Collinsella aerofaciens, Faecalibacterium prausnitzii, and Blautia obeum and increased levels of Ruminococcus gnavus and Bacteroides vulgatus compared with non-COVID-19 control group individuals at 6 months (P <.05).

A total of 81 bacterial species were associated with different PACS categories. The gut microbiome composition of patients who had persistent respiratory symptoms was positively correlated with a number of opportunistic pathogens at 6 months, including Streptococcus anginosus, Streptococcus vestibularis, Streptococcus gordonii, and Clostridium disporicum. Nosocomial pathogens associated with opportunistic infections including Clostridium innocuum and Actinomyces naeslundii were correlated with neuropsychiatric symptoms and fatigue.

Multiple bacterial species beneficial to host immunity such as Bifidobacterium pseudocatenulatum, Faecalibacterium prausnitzii, Roseburia inulinivorans, and Roseburia hominis had the largest inverse correlations with PACS at 6 months.

The researchers noted that their small sample size is a limitation. Additionally, the power of their study might be limited by unrecognized factors unrelated to COVID-19 that affect the bacterial microbiome, such as host milieu, diet, lifestyle, and medication use.

“[A]ltered gut microbiome composition is strongly associated with persistent symptoms in patients with COVID-19 up to 6 months after clearance of SARS-CoV-2 virus,” stated the study authors. “Considering the millions of people infected during the ongoing pandemic, our findings are a strong impetus for consideration of microbiota modulation to facilitate timely recovery and reduce the burden of post-acute COVID-19 syndrome.”


Liu Q, Mak JWY, Su Q, et al. Gut microbiota dynamics in a prospective cohort of patients with post-acute COVID-19 syndrome. Gut. 2022;71(3):544-552. doi: 10.1136/gutjnl-2021-325989

This article originally appeared on Gastroenterology Advisor