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Updated: Sep 28, 2025
Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing
Published on: March 19, 2018
Pre-Existing Microbiome Signature in a SARS-CoV-2 Discordant Family
1Progenabiome, Ventura Clinical Trials, Ventura, California, USA.
Insights
Individuals with Crohn's disease and COVID-19 showed distinct gut microbiome differences compared to healthy family members. This suggests a potential link between gut bacteria and SARS-CoV-2 infection susceptibility.
Area of Science:
- Microbiology
- Virology
- Gastroenterology
Background:
- Investigating the relationship between host microbiome and susceptibility to viral infections.
- Understanding factors influencing SARS-CoV-2 transmission within households.
Observation:
- A 19-year-old male with Crohn's disease (CD) tested positive for SARS-CoV-2 along with his father and sister.
- His mother (asthma history) and healthy siblings remained negative despite shared living conditions.
- Fecal microbiome analysis revealed significant differences between the SARS-CoV-2-positive patient and his negative family members.
Findings:
- SARS-CoV-2-positive individuals exhibited altered fecal microbiota composition compared to negative family members.
- Key differences were observed at multiple taxonomic levels, including phylum, class, order, family, and genus.
- Specifically, an increased relative abundance of Bacteroidetes and reduced bacterial diversity, notably in the Bifidobacterium family, were noted in the positive case.
Implications:
- The gut microbiome may play a role in modulating susceptibility to SARS-CoV-2 infection.
- Alterations in gut bacterial composition, such as reduced diversity and changes in specific phyla, could be associated with COVID-19 outcomes.
- Further research into the gut microbiome could reveal novel strategies for the prevention or treatment of SARS-CoV-2 infections.
Abstract:
Our index patient is a 19-year-old man with Crohn's disease. After developing symptoms consistent with COVID-19, he, his 62-year-old father, and 14-year-old sister tested positive for SARS-CoV-2 in May 2020. Despite a shared household, his 50-year-old mother with a history of asthma and his healthy brother and sister-in-law (a married couple) remained negative. The index patient and his mother had undergone microbiome analysis in May 2019, following his brother and his sister-in-law in November 2020. We observed significant differences between the fecal microbiota of the SARS-CoV-2-positive son and those of his healthy family. There were differences in the bacterial phylum, class, order, family, and genus level with the increased relative abundance of Bacteroidetes and reductions or deletions in bacterial diversity, particularly of the Bifidobacterium family. This unique study may signal a new exploratory avenue for the prevention or treatment of SARS-CoV-2 infections.
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