Prebiotic Functional Enhancement of Rumen Microbiomes

Project Information

RUMIC

Grant agreement ID: 840804

DOI

10.3030/840804

Project closed

EC signature date 4 April 2019

Start date 1 May 2019

End date 31 March 2023

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 251 434,56

EU contribution

€ 251 434,56

Coordinated by

MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV
Germany

Periodic Reporting for period 2 - RUMIC (Prebiotic Functional Enhancement of Rumen Microbiomes)

Reporting period: 2021-05-01 to 2022-04-30

Summary of the context and overall objectives of the project

The research project entitled RUMIC: Prebiotic Functional Enhancements of Rumen Microbiomes investigates how prebiotics act upon the rumen microbiome of food-producing animals to determine how we can use prebiotics to address the world's growing demand for sustainable food production.
In recent years research has shown that the microbiome - the community of microorganisms in animal and human digestive systems - is an integral component of animal health and production. Yet, our investigation of animal microbiomes and how they are affected by diet and supplements is still in its infancy. To move towards a greener economy, we must rethink our livestock production to include microbiomes and focus on sustainable and secure food production.
One approach is the application of prebiotics, “a substrate that is selectively used by host microorganisms conferring a health benefit” (Gibson 2018). Prebiotics function by modulating an animal’s microbiome towards improved food digestion and increase milk and meat production. They can also confer added health benefits such as antipathogenic and anti-inflammatory effects. Furthermore, prebiotics can be sourced from agricultural residues or sustainable sources such as seaweeds, adding economic value to agricultural waste streams.
Prebiotics are a promising tool to sustainably increase animal health, performance, and productivity. The RUMIC project aims to investigate how prebiotics affect rumen microbiomes and their function in animals, to provide evidence-based research tools to study the direct effect of prebiotics and help address the worlds growing demand for food production.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

In the outgoing phase, the RUMIC project investigated whether glycans found in human and livestock diets could be fluorescently labelled and whether the produced fluorescently labelled polysaccharides (FLAPS) enable visualisation of selective glycan metabolism in rumen isolates and complex rumen microbiomes.
Dr Greta Reintjes, in collaboration with the Abbott Lab of the Lethbridge Research and Development Center, Agriculture and Agri-Food Canada, successfully labelled two prominent dietary glycans, yeast-mannan (YM) and rhamnogalacturonan-II (RGII), and incubated these with the model gut microbe; Bacteroidetes thetaiotaomicron VPI-5482 (B.theta). For the first time, they showed that FLAPS can be used to visualise the selective glycan metabolism of B.theta. They demonstrated the differential uptake of FLAPS by individual cells through super-resolution microscopy and flow cytometry. Furthermore, investigations with genetically modified B.theta strains showed that FLAPS uptake was highly specific and dependent on the presence of polysaccharide utilisation loci (PULs).
This investigation of the RUMIC project highlighted that FLAPS are a novel functional tool that can be applied to rapidly assign metabolic phenotypes in rumen microorganisms and can be used to decipher glycan-microbial interactions in microbiomes.
Hehemann, J.H. Reintjes, G., et al., (2019) 'Single cell fluorescence imaging of glycan uptake by intestinal bacteria', ISME J, 13(7), pp. 1883-1889. https://doi.org/10.1038/s41396-019-0406-z

In a further investigation, Dr Reintjes tested whether the novel FLAPS could be used to identify individual cell physiologies in bovine B.theta strains. The bovine B.theta isolates consume YM using the same proteins encoded on PULs as the model B.theta strain. Compellingly, however, the bovine B.theta strains showed two distinct growth phenotypes on YM for which there were no distinct genotypic explanations. Using FLAPS, Dr Reintjes could visualise the metabolism of YM by individual bovine B.theta strains and identify strain-level variability in the carbohydrate utilisation systems of the two foraging phenotypes. Furthermore, this new next-generation physiology approach combined with "omics" approaches enabled her to characterise microbial adaptations to a prebiotic in the rumen ecosystem.
Klassen, L., Reintjes, G., et al., (2021) 'Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria', Microbiome, 9(1), pp. 23. https://doi.org/10.1186/s40168-020-00975-x

In the return phase, Dr Reintjes used culture-independent approaches to identify prebiotic-microbial interactions in simplified artificial and complex rumen communities. Benefiting from the expertise of the Lethbridge Research and Development Center, Dr Reintjes worked with an in vitro artificial rumen system that simulates the microbial rumen processes in a regulated environment (rumen-simulated technique) and live animal feed trials. FLAPS were applied to the complex communities in these trials to illuminate the functional potential encoded within each microbial community. Dr Reintjes found that both artificial and native rumen microbiomes respond rapidly to the addition of prebiotics and that there is a functional adaptation to specific prebiotics from agricultural and seaweed sources. Furthermore, the metabolically active cells were functionally sorted from these complex microbial communities, as proposed in the RUMIC project. The sorted microbes could be directly identified using 16S rRNA sequencing and characterised using proteomic analysis.
Klassen, L., Reintjes, G., et al., (2023). Fluorescence-activated cell sorting and fermentation analysis to study rumen microbiome responses to administered live microbial and yeast cell wall derived prebiotics. Frontiers in Microbiology 13. DOI 10.3389/fmicb.2022.1020250

Finally, the new FLAPS methodological developments achieved in the outgoing phase in the Abbott Lab of the Lethbridge Research and Development Center, Agriculture and Agri-Food Canada and return phase at the Max Planck Institute for Marine Microbiology, Bremen, Germany, are available here: Klassen, L., et al.,(2021) 'Approaches to Investigate Selective Dietary Polysaccharide Utilization by Human Gut Microbiota at a Functional Level', Frontiers in Microbiology, 12(308). https://doi.org/10.3389/fmicb.2021.632684
Visualisation of Carbohydrate Uptake Using Fluorescent Polysaccharides” in Carbohydrate-Protein Interactions: Methods and Protocols. Springer US. (2023) Editors Abbott, D.W. and Zandberg, W.F

This work could not have been achieved without access to the outstanding facilities, excellent supervision and tremendous day-to-day support from the Abbott Lab at the Lethbridge Research and Development Center, Agriculture and Agri-Food Canada and the Max Planck Institute for Marine Microbiology, Bremen, Germany. Thank you for being so supportive.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

RUMIC is a transatlantic collaboration between research labs in Germany and Canada, which has ushered in a next-generation physiological approach to study prebiotic metabolism in complex microbial communities. The scientific discoveries of RUMIC have provided direct evidence of prebiotic effects in livestock and increased our knowledge of how prebiotics are metabolised within the rumen microbiome and what effect this can potentially have on the host. The RUMIC project provides evidence-based tools to study the effect of prebiotics on feed efficiency, aiming to enhance animal health and enable more sustainable and secure food production.

RUMIC: Prebiotic Functional Enhancements of Rumen Microbiomes