Dysbiosis of gut microbiota in COVID-19 is associated with intestinal DNA phage dynamics of lysogenic and lytic infection

• Published in: Microbiology spectrum Vol. 13; no. 1; p. e0099824
• Main Authors: Ishizaka, Aya, Tamura, Azumi, Koga, Michiko, Mizutani, Taketoshi, Yamayoshi, Seiya, Iwatsuki-Horimoto, Kiyoko, Yasuhara, Atsuhiro, Yamamoto, Shinya, Nagai, Hiroyuki, Adachi, Eisuke, Suzuki, Yutaka, Kawaoka, Yoshihiro, Yotsuyanagi, Hiroshi
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 07.01.2025
• Subjects: Adult; Aged; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Bacteria - virology; bacteriophages; Bacteriophages - genetics; Bacteriophages - isolation & purification; Bacteriophages - physiology; Clinical Microbiology; COVID-19; COVID-19 - microbiology; COVID-19 - virology; DNA, Viral - genetics; Dysbiosis - microbiology; Dysbiosis - virology; Feces - microbiology; Feces - virology; Female; Gastrointestinal Microbiome; gut microbiome; Humans; Intestines - microbiology; Intestines - virology; Lysogeny; Male; Middle Aged; Research Article; SARS-CoV-2; SARS-CoV-2 - genetics; SARS-CoV-2 - physiology; Virome; COVID-19; SARS-CoV-2; gut microbiome; bacteriophages
• ISSN: 2165-0497; 2165-0497
• DOI: 10.1128/spectrum.00998-24

Bacteriophages infect and replicate with bacteria and archaea and are closely associated with intestinal bacteria. The symbiotic relationship between gut microbiota and bacteriophages is of interest, but it is challenging to study their dynamics in the human body over time. SARS-CoV-2 infection has been reported to alter the gut microbiota, which is involved in gut immune regulation and pathophysiology, although changes in the intestinal phages of patients with SARS-CoV-2 and their dynamic relationship with the gut microbiota remain unclear. SARS-CoV-2 infection, which follows a transient pathological course from disease onset to cure, may provide a reliable model to investigate these interactions in the gut environment. Therefore, this study aimed to elucidate the correlation between gut microbiota and intestinal DNA virome dynamics in COVID-19 pathogenesis. This study found that the dysbiosis observed in SARS-CoV-2 infection involves a growth strategy that depends on the phage or bacterial dominance.