Isolation, identification, and phenotyping of novel rumen bacteria

The rumen microbiome enables ruminants to make energy stored in plant material metabolically available. Current understanding of the rumen microbiome is impeded by poor culture collections and a reduced effort placed on culturing following an explosion in ‘omic’ technologies in recent years; leading to the assumption that many microbes are unculturable. This thesis addresses a critical gap in rumen microbiome research: how to improve the limited availability of cultured isolates to facilitate functional research. It is structured around three synergistic pillars: (1) the isolation and identification of rumen bacteria, (2) development of a custom MALDI-TOF MS database to facilitate their identification, and (3) phenotypic characterisation of novel isolates. Using direct plating and dilution-to-extinction approaches with diverse culture media, 354 rumen bacterial strains spanning nine phyla encompassing 59 species were isolated. Identification based on nearly full-length 16S rRNA gene sequences revealed 62 isolates with