Milk microbiome assessed through 165 rRNA sequencing during antimicrobial treatment of mastitis

a randomized clinical trial and longitudinal follow up

Abstract

There is increasing concern regarding the use of antimicrobials in food animals and the possible implications in human health, such as antibiotic resistance in pathogens, highlighting the importance of judicious use of antimicrobials in production animals. Specific aims were to: 1) evaluate the effect of antibiotics on cure of clinical mastitis; 2) use high throughput sequencing to assess the microbiome of milk samples from a mastitic quarter and compare it to the microbiome of ipsilateral healthy quarter of cows diagnosed with clinical mastitis caused by either a Gram-negative pathogen or with no bacterial growth on conventional aerobic culture; and 3) evaluate the over-time effect of prolonged antibiotic therapy on the microbiome profile of mastitic milk.