Are you planning on doing some fecal microbiota transplant studies? Unsure whether to use germ-free or antibiotic treated mice for your studies? In a recent review paper (Gut Microbes, March 2016), Randi Lundberg and her coauthors present the pros and cons for using antibiotic-treated or germ-free mice in fecal microbiota transplant (FMT) studies. Neither model truly represents physiological nor immunological conditions found in SPF mice, but can be very useful in understanding how the microbiota affects or is affected in certain disease states.
The article is comprehensive and should be read in its entirety. Here are the seven essential takeaways, along with a handy chart noting when it is best to use germ-free or antibiotic treated mice.
7 Takeaways from Gut Microbes
- Though a broad-spectrum antibiotic approach reduces the majority of the bacterial species considerably, gut flora will not be completely depleted.
- As the immune system is primed by gut microbiota in early life, exposure to microbes before depletion with antibiotics can have long-lasting effects on the host physiology. This has to be controlled or taken into consideration.
- Antibiotic treatment can lead to overgrowth of a some species, such as Klebsiella spp. which may have a substantial contaminating role in the microbial profile after colonization.
- Oral administration of antibiotics disrupts the gut microbiota, but other microbial communities such as the skin and lung microbiota are not always directly affected.
- Increasing evidence points to the fact that fungi, bacteriophages and eukaryotic viruses which are not directly targeted by bacterial antibiotics cannot be ignored in gut microbiota homeostasis and immune priming.
- Direct effects of antibiotics on host physiology should be taken into consideration.
- When treating mice with antibiotics, the risk of favoring bacteria with antibiotic resistance genes cannot be ignored.
Applicability of antibiotic-treated or germ-free rodents. Different research aims within translational microbiome research and the recommended use of either antibiotic-treated or germ-free rodent hosts for the purpose.
| Status of Host | ||
|---|---|---|
| Research Aim | Antibiotic-treated | Germ-free |
| Investigate microbial phenotype transfer of manifestations known to be microbiota dependent | X | X |
| Investigate microbial phenotype transfer of manifestations not known to be microbiota dependent | X | |
| Investigate effect of disrupting the microbiome in certain life stages of the host | X | |
| Investigate effect of targeting certain groups of bacteria | X | |
| Investigate effect of monocolonization | X | |
| Investigate effect of colonization with a few, defined organisms | X |
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