While links have been found between the gut’s microbiome and COVID-19, as well as other diseases, this is the first published research to show a link specifically to COVID’s long-term effects, the investigators, based at the Chinese University of Hong Kong, wrote in Gut.
“To our knowledge, this is the first study to show that altered 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,” said Siew Ng, MBBS, PhD, associate director at the university’s Center for Gut Microbiota Research.
At three hospitals, the researchers enrolled 106 patients with COVID-19 from February to August 2020 with stool samples at admission and at 1 month and 6 months after discharge, and compared them with people who did not have COVID, recruited in 2019. The severity of COVID in the enrolled patients was mostly mild to moderate.
At 3 months, 86 of the patients with COVID had post–acute COVID-19 syndrome (PACS) – defined as at least one persistent, otherwise unexplained symptom 4 weeks after clearance of the virus. And 81 patients had PACS at 6 months, most commonly fatigue, poor memory, hair loss, anxiety, and trouble sleeping.
Using stool samples for their analysis, the researchers found that, broadly, the diversity of the types of bacteria, and the abundance of these bacteria, were significantly lower at 6 months for those with PACS, compared with those without PACS and with controls (P < .05 and P < .0001, respectively). Among those with PACS, 28 bacteria species were diminished and 14 were enriched, both at baseline and follow-up. Those patients who had COVID but not PACS showed just 25 alterations of bacteria species at the time of hospital admission, and they all normalized by 6 months.
Having respiratory symptoms at 6 months was linked with higher levels of opportunistic pathogens such as Streptococcus anginosus and S. vestibularis. Neuropsychiatric symptoms and fatigue were associated with nosocomial pathogens that are linked to opportunistic infections, such as Clostridium innocuum and Actinomyces naeslundii (P < .05).
Bacteria known for producing butyrate, a beneficial fatty acid, were significantly depleted in those patients with hair loss. And certain of these bacteria, including Bifidobacterium pseudocatenulatum and Faecalibacterium prausnitzii, had the largest inverse correlations with PACS at 6 months (P < .05), the researchers found.
“Particular gut microbial profiles may indicate heightened susceptibility,” Dr. Ng said.
Although the findings were drawn from patients with earlier strains of the COVID-19 virus, the findings still apply to new variants, including Omicron, since these pose the same problem of persistent disruption of the immune system, Dr. Ng said.
Her group is conducting trials to look at how modulating the microbiome might prevent long COVID and boost antibodies after vaccination in high-risk people, she said.
“Gut microbiota influences the health of the host,” Dr. Ng said. “It provides crucial benefits in the form of immune system development, prevention of infections, nutrient acquisition, and brain and nervous system functionality. 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.”
John Haran, MD, PhD, associate professor of microbiology and physiological systems and emergency medicine at the University of Massachusetts, Worcester, said the research adds to the evidence base on the gut microbiome’s links to COVID, but there was likely be no clinical impact yet. Still, he said the findings linking specific species to specific symptoms was particularly interesting.
“Very early on during hospitalization, [the researchers] saw these differences and correlated out with people who have longer symptoms, and especially different groups of people that have longer symptoms, too,” said Dr. Haran, who has done research on the topic. “It’s very different if you have different symptoms, for example, you keep coughing for months versus you have brain fog and fatigue, or other debilitating symptoms.”
Dr. Haran noted that the findings didn’t identify bacteria types especially linked to COVID, but rather species that have already been found to be associated with a “bad” microbiome. He also pointed out that the patients enrolled in the study were not vaccinated, because vaccines weren’t available at the time. Still, further study to see whether modulation of gut bacteria can be a therapy seems worthwhile.
“Microbiome modulation is pretty safe, and that’s really the next big step that needs to be taken in this,” he said.
For now, the findings don’t give the clinician much new ammunition for treatment.
“We’re not there yet,” he added. “It’s not as if clinicians are going to tell their COVID patients: ‘Go out and buy some kale.’ ”
Eugene Chang, MD, professor of medicine at the University of Chicago, who has studied the gut microbiome and gastrointestinal disease, said it’s “too preliminary” to say whether the findings could lead to a clinical impact. The measures used merely identify the microbes present, but not what they are doing.
“These measures are unlikely to perform well enough to be useful for risk assessment or predicting clinical outcomes,” he said. “That being said, advances in technology are being made where next generations of metrics could be developed and useful as stratifiers and predictors of risk.”
Seeing shifting patterns associated with certain symptoms, he said, is “notable because it suggests that the disturbances of the gut microbiota in PACS are significant.”
But he said it’s important to know whether these changes are a cause of PACS in some way or just an effect of it.
“If causative or contributory – this has to be proven – then ‘microbiota modulation’ would make sense and could be a priority for development,” he said. “If merely an effect, these metrics and better ones to come could be useful as predictors or measures of the patient’s general state of health.”
As seen in his group’s work and other work, he said, “the gut microbiota is highly sensitive to changes in their ecosystem, which is influenced by the health state of the patient.”
Dr. Ng, Dr. Haran, and Dr. Chang reported no relevant disclosures.
This article was updated Jan. 27, 2022.