Phyloseq 16S v5v6 accompanying paper: deGeus et al (Goat milk and fecal microbiome around parturition)

Y. de Geus, R. Blok, P. Scherpenisse, F. Harders, M.P. Spaninks, J.A. Stegeman, L. Benedictus, G. Koop, L.A.M. Smit and A. Bossers

Goat milk and fecal microbiome around parturition: a longitudinal study

Total bacterial count (TBC) in bulk milk is an important quality parameter in goat milk and is elevated around kidding. High bacterial counts can shorten shelf life and negatively impact cheese production. Knowing the bacterial composition of goat milk and its relationship with the kidding period, as well as identifying potential sources of microbial contamination, may help farmers to implement preventive measures to control TBC in both bulk milk and individual goat milk.

We conducted a longitudinal, observational study on four Dutch dairy goat farms, collecting milk and fecal samples from 67 goats before and after kidding, along with 16 bulk milk samples spanning 10 weeks around kidding. Milk samples were analyzed using conventional bacterial culturing and MALDI-TOF MS species identification, together with bacterial load (16S-qPCR) and microbiome composition (16S-rRNA amplicon sequencing). To determine potential fecal contamination of milk samples, we also analyzed the fecal microbiome and compared it with matching individual goat milk microbiomes.

Publication reference: pending.