The microbiome includes all microorganisms within a resident habitant. Advantages of high-throughput sequencing technologies are that we can detect the gut microbiome composition and its relationship with human health and disease. Our overall goal is to study how the gut microbiome compositions are altered by environmental factors and how the altered microbiome affects the host and to apply this knowledge to improve clinical outcomes.
Obesity is a risk factor for kidney transplantation as well as many comorbidities. Bariatric surgery has proven to be an effective method of weight management. The combination of BS with kidney transplantation may be a promising way of improving renal function and reducing obesity. In our follow-up study of obese subjects with BS, we observed increased species diversity post-surgery within 6 months with the appearance of Streptococcus species. Eubacterium rectale and Megamonas hypermegale were positively associated with BMI, whereas Streptococcus salivarius was negatively correlated with BMI. Microbial species are also associated with serum cytokine levels. Bacteroides thetataomicron is positively correlated with the anti-inflammatory cytokine IL-13.
In the study of infants with cystic fibrosis (CF), we detected associations between growth and gut microbiome in CF infants. The gut microbiome is affected by age, antibiotic prophylaxis, malnutrition, and diet at the genus level. Compared to US-CF infants, AUS-CF infants had lower gut microbiome diversity with a higher abundance of Proteobacteria and a lower abundance of Firmicutes, which may be due to treatment with prophylactic antibiotics. Specifically, enrichment of Klebsiella in Proteobacteria in the AUS-CF was associated with antibiotic prophylaxis treatment.
Using allogeneic transplants murine model, we identified the effective Abx components vancomycin and metronidazole to highly prolong graft survival when both were present. Abx treatment reduced bacterial diversity with increased Bacteroides species, including Parabacteroides distasonis and Alistipes finegoldii. Enrichment of commensal bacteria may help alleviate inflammation and thus prolong graft survival.
To conclude, we identified the gut microbiome changes upon multiple environmental factors of diseases and medications including antibiotics and how they may improve clinical outcome. Understanding their changes and metabolic functions will highlight future medical applications with disease monitoring, prevention, and intervention
