The microorganisms which live in human and animal digestive tracts play a major role in health and nutrition. Why? Well, they have a vast capacity to digest and breakdown the foods we eat (catabolic potential), thereby helping us digest our food and influencing our nutrition. Side note: They also help regulate our immune system, protect us against other disease forming bacteria, produce vitamins,and impact our mental health.
In our new study, we aimed to expand our understanding of gut microorganisms’ catabolic potential so that we might use this knowledge in the future to positively influence microbiomes (the community of microorganisms living in a particular environment, for example, with prebiotics or synbiotics.
To give you an insight into our investigation, it may be easiest to dissect the title. Starting with: “Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviours of rumen bacteria.”
What is a bacterial strain?
A strain is a genetic variant or subtype of microorganism. Strains are nearly identical in their genetic content (genotype) but show differences in the genotypes’ physical expression, referred to as phenotype. Differences in phenotypes can be variations in morphology, physical form, and biochemical and physiological processes that the cell performs, such as using a specific glycan (complex sugar). We analyse strain level phenotypic variations because they are essential for determining a microorganism’s functional capacity (ability to do specific work).
In our study, we investigated different strains of B. theta (Bacteroides thetaiotaomicron), a gut microorganism specialising in glycan digestion. Specifically, we investigated B. theta strains isolated from the rumen (the largest stomach of a cow). These strains are highly similar in their genetic content (genotype, (>98% identity)) but showed different growth phenotypes on a specific glycan – yeast mannan. This difference in growth is a variation in foraging behaviour.
Which brings me to the second key part of our title: “Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviours of rumen bacteria.”
What is a foraging behaviour?
Simply put it is a microorganism’s ability to use a specific substrate, in our case, a particular complex sugar – yeast mannan. Interestingly our near-identical strains show two foraging behaviours, high grower and medium grower, indicating one is more efficient at growing on yeast mannan than the other.
So, we asked ourselves, why do they show these phenotypic differences?
And what does this mean for the microbiome as a whole?
To answer these questions, we used a combination of several microbiological techniques, including comparative whole-genome sequencing (looking at all the genes in the strains), RNA-seq (looking at what genes are expressed), and carbohydrate-active enzyme fingerprinting (looking specifically at the genes used for glycan degradation). We also used a novel approach to track the uptake of a specific glycan into individual bacterial cells. This method uses fluorescently labelled polysaccharide (glycan) probes or FLA-PS.
Which leads me to the final part of the title “Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviours of rumen bacteria.”
Using fluorescently-labelled polysaccharide probes (FLA-PS), we could track yeast mannan uptake by rumen microbiomes, directly watching it be eaten up and letting us assign metabolic traits to bacterial populations. We could also quantify (measure) the difference in uptake between our B. theta strains and calculate their phenotypic differences. In the end, we can predict the bacterial strains’ individual nutrient acquisition strategies.
Why is this important?
As I mentioned, our overall aim is to expand our understanding of gut microorganisms’ catabolic potential so that we can influence them in a beneficial way. One example of how we influence a microbiome is with prebiotics; for example, in cattle, we use complex dietary glycans such as yeast mannan to promote the growth of beneficial microorganisms much the same way as humans eat probiotic yoghurt. To understand the effect that yeast mannan has on a microbiome, we need to know which organisms interact with it; we accomplished this in our study using the fluorescently labelled glycan. Furthermore, by combining phenotypic and genotypic approaches, we could predict the foraging behaviours of closely related bacterial strains and understand how they process a specific prebiotic. Our research gives us a new method to study microbial-prebiotic interactions and enhances our knowledge of how prebiotics affect and influence a microbiome.
Read more in our publication:
Klassen, L., Reintjes, G., Tingley, J.P. et al. Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria. Microbiome 9, 23 (2021). https://doi.org/10.1186/s40168-020-00975-x