Gut microbiome and antimicrobial impacts
The microbiome is the diverse community of microbes—bacteria, fungi, viruses, and more—that live on and inside humans and animals, especially in the gut. These microbes work with our bodies as a "supraorganism," helping digest food, produce vitamins, train the immune system, and even influence brain function and behavior. A healthy microbiome supports overall resilience and has been linked to lower risks of infections, allergies, obesity, diabetes, and mental health conditions. In both people and animals, antibiotics can disrupt the microbiome by wiping out beneficial microbes along with harmful ones, sometimes leading to imbalances or antibiotic-resistant infections. We study the microbiome from multiple angles, examining the impact of specific bacteria, dietary supplements, and antibiotics on its composition.
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C. difficile and the Microbiome
​​Clostridioides difficile is a pathogen that is very strongly associated with the state of the microbiome. In a healthy microbiome, C. diff is generally "kept in check" by the other bacteria, while in a disrupted microbiome, C. diff can "take over" and cause gastrointestinal disease.
We've shown that even asymptomatic colonization with C. diff is associated with subtle differences in microbiome composition in different species, including in species where it is not generally known to cause disease.
Gut microbiota features associated with Clostridioides difficile colonization in dairy calves
Gut microbiota features associated with Clostridioides difficile colonization in puppies
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Modifiers of the Microbiome in Food Animal Species
In the food animal industry, alternatives to antibiotics are constantly being evaluated in an attempt to decrease antibiotic use and improve animal health. Dietary zinc is one such option. This trace element is often used in young animals around weaning to prevent diarrhea. We showed that in gestating cows and sows, high levels of this trace element do not adversely affect the microbiome and can even have modestly beneficial effects in dams and offspring. ​
​A review of the impact of dietary zinc on livestock health
​ Effects of dietary zinc on the gut microbiome and resistome of the gestating cow and
The effect of dietary zinc on the microbiome and resistome of the gestating sow and neonatal piglets
Zinc fingers
Response of the microbiome to antibiotics
Antibiotics are a well-known disruptor of the gut microbiome. Most people recover uneventfully from antibiotics, but some experience profound disruption (also called "dysbiosis") that can lead to clinical disease. In the REMBRANDT study (REcovery of the MicroBiome fRom ANtibiotics for Dental implanTs), we are enrolling patients receiving antibiotics and examining the disruption and recovery of their gut and oral microbiomes. In particular, we hope to examine factors that result in milder disruption and faster recovery of the microbiome. One such potential factor could be pet ownership. We previously found that pet ownership was protective against the recurrence of C. diff infection. Hypothesizing that this was because pets shared their healthy microbiota with their owner, we will be comparing pet owners and non-pet owners in the REMBRANDT study to see whether having a pet protects against some of the adverse effects of antibiotics.
Pet Ownership Protects Against Recurrence of Clostridioides difficile Infection
