No abstract

Antibiotics are our primary approach to treating complex infections, yet we have a poor understanding of how these drugs affect microbial communities. To better understand antimicrobial effects on host-associated microbial communities we treated cultured sputum microbiomes from people with cystic fibrosis (pwCF, n = 24) with 11 different antibiotics, supported by theoretical and mathematical modeling-based predictions in a mucus-plugged bronchiole microcosm. Treatment outcomes we identified in vitro that were predicted in silico were: 1) community death, 2) community resistance, 3) pathogen killing, and 4) fermenter killing. However, two outcomes that were not predicted when antibiotics were applied were 5) community profile shifts with little change in total bacterial load (TBL), and 6) increases in TBL. The latter outcome was observed in 17.8% of samples with a TBL increase of greater than 20% and 6.8% of samples with an increase greater than 40%, demonstrating significant increases in community carrying capacity in the presence of an antibiotic. An iteration of the mathematical model showed that TBL increase was due to antibiotic-mediated release of pH-dependent inhibition of pathogens by anaerobe fermentation. These dynamics were verified in vitro when killing of fermenters resulted in a higher community carrying capacity compared to a no antibiotic control. Metagenomic sequencing of sputum samples during antibiotic therapy revealed similar dynamics in clinical samples. This study shows that the complex microbial ecology dictates the outcomes of antibiotic therapy against a polymicrobial infection.

Bile acids are steroid detergents in bile that contribute to fat absorption, cell signaling and microbiome interactions in mammals. The final step in their synthesis is amino acid conjugation with either glycine or taurine to a cholic acid or chenodeoxycholic acid backbone in the liver by the enzyme bile acid-CoA:amino acid N-acyltransferase (BAAT). Here, we describe the microbial, chemical, and physiological consequences of BAAT gene deletion in mice. BAAT-/- mice were underweight after weaning but quickly exhibited catch-up growth. At 3-weeks-of-age, KO animals had increased phospholipid excretion and decreased subcutaneous fat pad mass, glycogen staining in hepatocytes and vitamin A stores in the liver, but these phenotypes were less marked in adulthood. Their bile acid (BA) pool was highly altered throughout the 8-weeks of life but was not completely devoid of conjugated BAs. These animals had 27-fold lower amounts of taurine-conjugated BAs than wildtype in their liver, but similar concentrations of glycine-conjugated BAs and higher microbially-conjugated BAs. The BA pool in BAAT-/- was enriched in a variety of unusual bile acids that were putatively sourced from cysteamine conjugation with subsequent oxidation and methylation of the sulfur group to mimic taurine. KO mice also had an altered microbiome, but most strongly in the first 3-weeks, indicating bile acid conjugation is important for proper microbiome development during the postnatal period. Finally, antibiotic treatment increased taurine, glycine, and the unusually conjugated BAs in BAAT-/- animals, indicating the microbiome was not the likely source of the conjugation. Instead, BA conjugation in KO animals was likely derived from the peroxisomal acyltransferases ACNAT1 and ACNAT2, which are duplications of BAAT in the mouse genome, but inactivated in humans. This study demonstrates that BA conjugation is important for early life development in mice and is facilitated by other host or microbial enzymes besides BAAT in a manner that results in molecular mimics of taurine that may rescue pathological phenotypes.