The severity of COVID-19 is closely linked to instability and shifts in the respiratory and gut microbiomes, according to a new study published in Nature. The research highlights that patients with severe COVID-19 exhibit distinct microbial alterations compared to those with mild or asymptomatic infections, as well as healthy controls.
Microbial Shifts in Severe COVID-19
The study, which involved 98 COVID-19 patients and 34 healthy controls, categorized participants into asymptomatic, non-severe, and severe groups based on illness severity. Researchers analyzed sputum, throat swab (TS), and stool samples to characterize the respiratory and gut microbiomes. The duration of viral shedding was significantly longer in the severe group (53.6 ± 23.7 days) compared to the non-severe (11.9 ± 5.7 days) and asymptomatic groups (6.6 ± 3.8 days).
"We observed a pronounced distance boundary between the respiratory tract and stool specimens in healthy individuals," the authors noted. "However, transitioning from asymptomatic to severe cases, an increasing number of samples manifested in the boundary region, particularly prominent in the severe group, indicating microbial migration."
Key Microbial Players
Specific microorganisms were identified as indicators of severe infection. In patients C102 and C107, who did not receive antibiotic treatment, persistent Burkholderia multivorans, Enterococcus faecium, and Staphylococcus epidermidis infections were observed. Analysis of dominant species (DSs) revealed that Neisseria was frequently detected in sputum samples from the control group, while Rothia mucilaginosa was prevalent in respiratory tract specimens from mild and non-severe cases.
In the gut, Bacteroides and Prevotella are typically dominant. However, in severe COVID-19 cases, Prevotella was generally absent, and Bacteroides vulgatus showed the fastest recovery and highest abundance compared to other Bacteroides species.
Associations Between Respiratory and Intestinal Microecology
Analysis of 74 individuals with both sputum and fecal samples revealed significant differences in microbial abundance between the severe group and the control group. Bacteroides vulgatus and Escherichia coli exhibited the most significant increase in average abundance within the severe group. Correlation network analysis showed that in the control group, positive and negative relationships between microorganisms were balanced, while in the severe group, Bacteroides vulgatus suppressed Escherichia coli, Enterococcus faecium, and Klebsiella pneumoniae in the intestine, and negatively regulated Streptococcus salivarius and Streptococcus parasanguinis in the sputum.
Impact of Antibiotics on Fungal Diversity
The study also examined the impact of antibiotic treatment on fungal diversity. Saccharomyces was enriched in patients receiving antibiotics, while Malassezia and Candida were more prevalent in those without antibiotic administration. LEFSE analysis confirmed that Saccharomyces was significantly enriched in antibiotic-treated patients, likely due to the diminished bacterial competition.
These findings underscore the importance of maintaining a stable and balanced microbiome in both the respiratory and digestive tracts, particularly in the context of severe viral infections like COVID-19. Further research is needed to fully elucidate the mechanisms driving these microbial shifts and to develop targeted interventions to restore microbial balance and improve patient outcomes.
