Determining the culturability of the bovine rumen bacterial and archaeal microbiota

Ruminants play an important part in global food security, but also emit methane which contributes to global warming. Microbes in the rumen play a key role in energy retention from the host's plant-based diet and the produce methane as a by-product of this digestion. While many thousands of novel microbial genomes have been assembled from metagenome sequence data, the extent to which these can be cultured is ill-defined. Here different media were used to study their effect on the bacterial and archaeal populations isolated; two non-selective media, one containing rumen fluid and the other not, and one selective medium which contained rumen fluid as well as a range of other substrates not present in the non-selective. Bacteroidota (52.53% ± 5.10) was the most common phylum found in the rumen fluid used as an inoculum, followed by Bacillota (41.00% ± 3.96), the archaeal phylum Euryarchaeota (5.12% ± 1.94), and Pseudomonadota (1.22% ± 0.78). The most common genera were bacterial, and included Prevotella (29.13% ± 4.16), Butyrivibrio (18.21% ± 2.08), Succiniclasticum (15.57% ± 5.03), unclassified Bacteroidota (13.91% ± 1.67), and unclassified Prevotellaceae (9.50% ± 2.01). All the operational taxonomic units in the rumen fluid were also found in the cultures. However, there was a significant difference between the communities of microbes grown on the different media, irrespective of the source cow. Of the 34 taxa isolated, 31 were found in a significantly different mean relative abundance in at least one medium compared to the others. These data further emphasise the importance of using defined media to selectively enrich for different microbial taxa, and only when used in combination is the true diversity of the rumen microbiota likely to be explored. This is essential in order to understand the complex workings of the rumen microbes, and how they interact, to enhance digestion efficiency and reduce the loss of energy as methane.