A really interesting study found that in humans, taking antibiotics (which reduces the gut bacteria) may result in the flu vaccine not being as effective as in people who did not take antibiotics. An earlier similar study had found that this was true for mice, which is why the researchers did the study on humans.
The Stanford University and Emory University researchers studied healthy people who had recent (in last few years) flu vaccinations and those who hadn't had a flu vaccine for several years prior to the study. Some individuals took 5 days of broad spectrum antibiotics, and on day 4 received a flu vaccine, while others did not take antibiotics, but did receive the flu vaccine on day 4.
Not surprisingly: The antibiotics lowered the gut-bacterial population by 10,000-fold. While month by month there was increasing recovery, the resulting loss of overall diversity was detectable for up to one year after the antibiotics were taken. Keep in mind that they found that: "Notably, species richness and biodiversity were not fully recovered at 6 months, indicating long-lasting loss of unique bacterial species, consistent with previous studies." [BOTTOM LINE: Only take antibiotics when necessary.]
Interestingly, after antibiotic use, the researchers found other changes besides an alteration in gut bacteria populations. They also found changes within the immune system which resulted in an inflammatory state, which was due to "impairments in bile acid metabolism by the gut flora". In other words, taking antibiotics has a number of effects beyond treating an infection (the reason they were taken).
By the way, those who had taken flu vaccines in prior years had much better responses to the vaccines - they only had a minimal impact on vaccine response, even though they took antibiotics, than those who had not. Those who had not received flu vaccines or the flu in recent years had "low preexisting immunity", and taking the antibiotics (which resulted in loss of gut bacterial species) impaired their antibody response to the flu vaccine. The researchers said: "The results of this study are consistent with the concept of immune responses in adults being largely determined by immune history and resilient to transient changes in the microbiome."