Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria

Citation

Klassen, L., Reintjes, G., Tingley, J.P., Jones, D.R., Hehemann, J.H., Smith, A.D., Schwinghamer, T.D., Arnosti, C., Jin, L., Alexander, T.W., Amundsen, C., Thomas, D., Amann, R., McAllister, T.A., Abbott, D.W. (2021). Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria, 9(1), http://dx.doi.org/10.1186/s40168-020-00975-x

Plain language summary

The rumen microbiome plays a vital role in fiber digestion and host health. By expanding our understanding of the carbohydrate metabolic pathways encoded within the rumen microbiome we will learn foundational information about how the microbiome functions to digest feed and how glycans in the diet influences cattle physiology. Currently, our knowledge of rumen microbial pathways relies heavily on inferences derived from sequencing data or culturing bacteria in the lab. Novel, more direct approaches can help illuminate the function of bacterial cells in these communities to provide accurate and rapid assessments of metabolic abilities. In this study, we used fluorescently labeled polysaccharides to visualize carbohydrate metabolism by bacterial cells in complex rumen samples. Strains of Bacteroides thetaiotaomicron that could metabolize yeast mannan, a carbohydrate with prebiotic potential, were isolated from the rumen of beef cattle and characterized using whole-genome sequencing, RNA-seq, and carbohydrate-active enzyme fingerprinting to elucidate the strain-level differences in yeast mannan metabolism. Using this combination of techniques, we were able to determine that the transport of carbohydrates into the cell is the limiting process for determining the growth potential of different rumen bacteria.

Abstract

© 2021, The Author(s).Gut microbiomes, such as the microbial community that colonizes the rumen, have vast catabolic potential and play a vital role in host health and nutrition. By expanding our understanding of metabolic pathways in these ecosystems, we will garner foundational information for manipulating microbiome structure and function to influence host physiology. Currently, our knowledge of metabolic pathways relies heavily on inferences derived from metagenomics or culturing bacteria in vitro. However, novel approaches targeting specific cell physiologies can illuminate the functional potential encoded within microbial (meta)genomes to provide accurate assessments of metabolic abilities. Using fluorescently labeled polysaccharides, we visualized carbohydrate metabolism performed by single bacterial cells in a complex rumen sample, enabling a rapid assessment of their metabolic phenotype. Specifically, we identified bovine-adapted strains of Bacteroides thetaiotaomicron that metabolized yeast mannan in the rumen microbiome ex vivo and discerned the mechanistic differences between two distinct carbohydrate foraging behaviors, referred to as “medium grower” and “high grower.” Using comparative whole-genome sequencing, RNA-seq, and carbohydrate-active enzyme fingerprinting, we could elucidate the strain-level variability in carbohydrate utilization systems of the two foraging behaviors to help predict individual strategies of nutrient acquisition. Here, we present a multi-faceted study using complimentary next-generation physiology and “omics” approaches to characterize microbial adaptation to a prebiotic in the rumen ecosystem. [MediaObject not available: see fulltext.]