Antibiotic-induced gut microbiome perturbation alters the immune responses to the rabies vaccine (Apr 2025, n=18) Antibiotics

[Michael Harrop]

https://www.sciencedirect.com/science/article/abs/pii/S193131282500126X

Highlights​

• Gut microbiome disruption impairs humoral responses to primary rabies vaccination
• Gut microbiome disruption skews the Th1/Tfh balance to primary rabies vaccination
• MMRN links the microbiome, transcriptome, and metabolome to human immunity to vaccines

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Summary​

The gut microbiome plays a crucial role in modulating human immunity. Previously, we reported that antibiotic-induced microbiome perturbation affects influenza vaccine responses, depending on pre-existing immunity levels.

Here, we employed a systems biology approach to analyze the impact of antibiotic administration on both primary and secondary immune responses to the rabies vaccine in humans. Antibiotic administration reduced the gut bacterial load, with a long-lasting reduction in commensal diversity. This alteration was associated with reduced rabies-specific humoral responses.

Multi-omics profiling revealed that antibiotic administration induced (1) an enhanced pro-inflammatory signature early after vaccination, (2) a shift in the balance of vaccine-specific T-helper 1 (Th1) to T-follicular-helper response toward Th1 phenotype, and (3) profound alterations in metabolites, particularly in secondary bile acids in the blood.

By integrating multi-omics datasets, we generated a multiscale, multi-response network that revealed key regulatory nodes, including the microbiota, secondary bile acids, and humoral immunity to vaccination.

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Nine participants were randomized to receive a 5-day course of antibiotics treatment

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Wow, that is so unethical. It is alarming that this kind of thing (antibiotics to healthy people) is still being allowed.

Most of the study is paywalled but you can see many of the authors are from Stanford, and they mention Emory Hope Clinic, which is in Atlanta, GA.

I would report it to some authority, but since it's paywalled I have no clue who to report it to.

 

[NiroZ]

The lead contact is Bali Pulendran ([email protected]), and if you don't get a response there you could try contacting the editors of the journal (https://www.cell.com/cell-host-microbe/editors-and-staff) to make a complaint through them. At the very least they should be able to tell you the ethics approval number and which university ethics board so that you can contact them to make a complaint. Unfortunately I couldn't get access to the article either so I can't tell you.

 

[indigo34]

Interesting this probably helps explain the mechanism by which vaccines can lead to autoimmune disease in some individuals.

Not surprised at all that they gave antibiotics to healthy people. I was prescribed amoxicillin for a bacterial sinus infection that I was told would clear up on its own in a few weeks. Similarly prescribed cipro/flagyl for enteritis even when stool testing came back negative. Also was told I would need to take antibiotics for at least a month, preferably longer, before being considered for an allergist referral for nasal congestion. I didn't take any of the antibiotics, not sure if it matters at this point because my gut is f***** already but no point taking the chance when I didn't need them. The sinus infection went away on its own, the enteritis comes and goes (probably diet related) and it's highly doubtful the antibiotics would have helped with congestion long-term.

I know my situation is different from the article because I had health issues they were attempting to address, but the doctors did not have a sound scientific basis for believing they would help me long term in any of those cases. The medical profession absolutely loves prescribing antibiotics. I believe it actually makes nurses and doctors feel good and feel like they are helping people when doing nothing in most cases is the safest option. I do not believe they have any understanding of the immense harm they are inflicting on society every day.

 

[s1ag]

I was able to access the article through my institution but as NiroZ already said, the main contact is Bali Pulendran via the email above.

The article had the Clinical Trial ID so I was able to find it on clinicaltrials.gov which I've linked below. There should be more contacts there from what I briefly saw.
https://clinicaltrials.gov/study/NCT03557008?id=NCT03557008&rank=1

From what I saw when briefly scanning the methods section, the line below would probably give you a point of contact regarding ethics etc.

Written informed consent was obtained from each participant, and the study protocols were approved by the Institutional Review Boards (IRB) of Emory University.

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[Michael Harrop]

Thank you! I wrote to the Cell journal editors but haven't received a response yet. I just wrote to the Emory IRB. Do you see information about the funding source?

Per https://irb.emory.edu/about/contact/index.html, the main contact is [email protected], but there are numerous divisions with dozens of people. I guess I'll contact the 3 members of the Education and Quality Assurance Team too.

I also submitted a comment on Pubpeer (currently awaiting moderation).

an antibiotic regimen consisting of metronidazole, vancomycin, and neomycin sulfate.

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Oh my god. That's an extremely harsh regimen. That is something you give when trying to completely wipe out the microbiome prior to FMT.

 

[s1ag]

I took a quick look at the funding information.

On clinicaltrails.gov, the only sponsor listed is Emory University which I assume you would have seen already.

I checked the acknowledgements section of the paper and noted this line.

This work was supported by the NIH (R01 AI048638, U19 AI057266, and U19 AI167903),Open Philanthropy, Anonymous Donor, and the Violetta L. Horton and Soffer Endowments to B.P.

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Seems like there was multiple avenues of funding with some of them being independent parties.

I guess the IRB contact would be difficult with the amount of people involved. There seems to be dedicated numbers for complaints on the Participants FAQ page in the section "What if I don't like something about the study?" (https://irb.emory.edu/participants/participant-faq.html).
There's also the faculty leadership members (https://irb.emory.edu/about/contact/faculty-leadership.html). You'd be looking at contacting the biomedical committee members if you think it's worth it.