Culturing of the so-called unculturable rumen bacteria

The rumen represents the largest fermentative compartment in the ruminant stomach. It is a complex and dynamic ecosystem, comprising mainly anaerobic bacteria, protozoa, fungi, methanogenic archaea, and bacteriophages. Our current understanding of the rumen microbiome is impeded by poor culture collections and a lack of effort placed on culturing following an explosion in ‘omic’ technologies in recent years. This has led to an assumption that many microbes are unculturable, when it is recognised that with modest concentrated effort they could be cultured. In this study, we bring many of the missing bacteria from ruminal bacterial families into pure culture to enhance their current culture collection. Using the dilution to extinction method, ruminal fluid samples from sheep and cattle were plated onto three growth media namely Hobson’s M2 medium, Bovine Heart Infusion (BHI) medium, and PC basal medium to isolate anaerobic bacteria. This resulted in isolation of over 120 ruminal bacteria, with observed differences in their profile with respect to the medium used highlighting the importance of media diversification during isolation. Additionally, 16S rRNA gene sequencing analysis reveals a potential new species of ruminal bacteria with only a 94.38% identity with the most closely related bacteria, Parabacteroides goldsteinii in the NCBI database. Further characterisation of this new species may provide insight into their role in the rumen microbiome and importance to the host. Overall, our results provide an enhanced understanding of the rumen microbiome, allowing for novel research on microbiome function/role in the health, productivity, and sustainability of ruminants.