Determining the Relationship Between Gut Microbiota and Immune Response to Influenza or COVID-19 Vaccine

The overall objective of this study is to evaluate the role of gut microbiome in influenza or COVID-19 vaccine response in immunosuppressed populations. Microbial diversity (alpha diversity) is decreased in immunosuppressed patients and might be associated with lower immunogenicity to vaccines.

It is known that patients with IBD have dysbiosis of their gut microbiome and those immunosuppressed may have a lower vaccine response. In this aim, the investigators will evaluate whether differences in microbial diversity predict immune response to the influenza and COVID-19 vaccine.

In this prospective study, immunosuppressed IBD patients will be vaccinated per standard of care and blood will be collected to measure the immune response. A fecal and saliva sample will be collected to characterize the gut microbiome. The investigators hypothesize that reduced richness / alpha-diversity in gut microbiota will correlate with those with a blunted vaccine response.

Inclusion criteria

• A history of chronic (greater than 3 month) ulcerative colitis or Crohn's disease diagnosed and documented by the standard clinical, radiographic, endoscopic, and histopathologic criteria
• Currently one of the following groups:

• Group A: Anti-TNF Therapy Group

• Maintenance monotherapy: infliximab (at least every 8 weeks), golimumab (at least monthly), adalimumab (at least every 2 weeks), or certolizumab (at least monthly)
• Combination Therapy: Anti-TNF Combination Therapy Group on anti-TNF therapy as described above along with either methotrexate, azathioprine, or 6MP
• Group B: Non-TNG biologic

• Ustekinumab Therapy: on either ustekinumab monotherapy or combination therapy with methotrexate, azathioprine, or 6MP
• Vedolizumab Therapy: on either vedolizumab monotherapy or combination therapy with methotrexate, azathioprine, or 6MP
• Risankizumab Therapy: 360mg at least every 8 weeks
• Group C: Janus Kinase Therapy

• Tofacitinib Therapy: at least 5mg PO BID
• Upadactinib Therapy: at least 15mg PO daily
• Patient has been on stable treatment for IBD for at least three months
• Must be able to provide research samples between 28-65 days post influenza or Covid-19 vaccination.

Exclusion criteria

• Member of a vulnerable group (pregnant, lacking consent capacity, non-English speaking)
• Recent oral antibiotics within previous 2 months