Single Cell Sequencing of cow gut microbiome
The cattle gastrointestinal tract harbors a diverse community of microorganisms, including pathogenic and commensal strains of Escherichia coli. The use of antimicrobials to treat infections in cattle can disrupt the gut microbiome leading to shifts in bacterial diversity and abundance. Here, we assessed how ceftiofur antibiotic treatment impacted microbiome structure (microbial diversity and antimicrobial gene distribution) and E. coli colonization dynamics using shotgun metagenomics and single cell sequencing. Ceftiofur was administered intramuscularly at the start of the experiment around the time of inoculation of a cocktail consisting of 17 different Extended Beta-Lactamase-expressing E. coli strains, and fecal samples were collected from both the antibiotic-treated (ceftiofur and inoculation) and control (inoculation only) calves over the course of 35 days (n=50). Our results showed substantial differences in microbial richness and beta diversity between treatment groups. Notably, we identified several metagenome assembled genomes (MAGs) being more abundant within the samples that did not receive ceftiofur, including Bacteroidaceae and Fibrobacter MAGs. Conversely, we identified several beta-lactamase genes enriched in ceftiofur-treated calves, including cfxA5 and cfxA6 encoded by CAG-485 (Muribaculaceae) MAGs. We further profiled individual cells using single cell sequencing, which revealed a high number of Clostridium carrying macrolide resistance genes lnu(P) and mph(N) in both ceftiofur and control samples. Strain level E. coli identification was performed by metagenomic read mapping against a strain-specific sequence database, which indicated that E. coli abundance and prevalence was greater in control samples for most strains. Although several cocktail strains were identified post inoculation, native E. coli strain sequences showed a greater prevalence and overall abundance. Collectively, this study provides insights into strain level bacterial shifts during antimicrobial treatment.