Forming links in the forage : a (meta)genome-centric metaproteomic approach to connect rumen microbial functions
Abstract
The rumen microbiome operates in close symbiosis with its ruminant
host, where the rumen functions as a fermentation chamber for the
conversion of complex recalcitrant carbohydrates into nutrients that
represent the primary source of energy for the animal. Dynamic
interactions between bacterial, protozoal, fungal, viral and archaeal
microorganisms in the rumen are associated with important host
productivity traits, such as feed efficiency, animal health and greenhouse
gas production (Dillard, 2019; FAO, 2020; Huws et al., 2018; Jami et al.,
2014; Matthews et al., 2019; McCann et al., 2016). Therefore,
understanding and unravelling the metabolic functions carried out by
the complex rumen microbiome is of both industrial and scientific
interest. Such knowledge can contribute to strategies to circumvent
substantial challenges related to greenhouse gas mitigation from
agriculture as well as advancing the livestock industry to securely meet
the dietary requirements of a growing human population, without
compromising animal health and wellbeing.
Advances in modern molecular techniques have enabled the study and
insight into genetic information and functional activity of complex
microbiomes. The application of so-called “meta-omics” approaches
enhances the recovery of the molecules that constitute a microbiome,
and their interpretation facilitates improved predictions of the metabolic
functions of intricate microbiomes in their natural ecosystems.
Furthermore, untangling the dynamic interactions between microbial
members in host associated microbiomes such as the rumen of
herbivores can contribute to forming valuable links to host metabolism.
In this thesis, the functions of the host associated rumen have been
explored microbiome utilizing a combined metagenomic and
metaproteomic approach. First, Paper I present key methods and
considerations for meaningful metaproteomic analysis and consequent
reconstruction of metabolically active populations of the rumen. Further
the (meta)genome centric metaproteomic approach was applied to
different rumen microbiome datasets to investigate the effects of dietary
modulation and how they relate to key metabolism in connection to host
metabolism in Paper II. Specifically, this enabled the exploration of the
role of understudied rumen ciliate protozoal populations in the rumen
microbiome of cattle and goats fed a starch-rich diet. Further, this led to
the reconstruction of key protozoal metabolism related to carbohydrate
and hydrogen metabolism, in addition to bacterial predation and volatile
fatty acid production. Despite the starch degrading reputation of certain
protozoal species, we observed a decrease in protozoal populations in
low methane-emitting animals that were fed starch-rich feeds. In
contrast, an increase in starch degrading bacterial populations
producing succinate and propionate indicated a putative shift in
hydrogen metabolism with broader implications for methane
production.
Lastly, Paper III investigated carbohydrate degradation of the red
seaweed Mazzaella japonica through the rumen as well as the distal
regions of the gastrointestinal tract in cattle. Contrary to initial
assumptions, we observed higher activity of seaweed degradation in the
lower gastrointestinal tract than in the rumen. We were further able to
reconstruct an expressed co-regulated polysaccharide utilization locus
with putative seaweed degrading properties from a Bacteroides-
affiliated species, emphasising the influence of the lower gastrointestinal
tract on degradation of complex carbohydrates and putative effects on
host metabolism.
Overall, the results presented in thesis show how the integration of
metagenomics to metaproteomic dataset can provide added resolution
to understand the functional contributions of understudied microbial
populations or metabolic niches of the host-associated microbiomes in
ruminants. Further, the results presented can contribute to the
identification of microbial populations and changes in microbial
structure are associated with the host, towards sustainable
improvements of animal health and productivity and development of
strategies to mitigate greenhouse gas emissions from agriculture. Mikrobiomet i vomma fungerer i symbiose med sin drøvtyggende vert, der vomma fungerer som et fermenteringskammer for omdannelsen av komplekse karbohydrater til næringsstoffer, som representerer dyrets
hovedkilde for energi. Dynamiske interaksjoner mellom mikroorganismer i vomma, som bakterier, protozoer, mikrobielle sopper, virus og arker, er assosierte med viktige produktivitetstrekk for verten, slik som fôrutnyttelse, dyrehelse og klimagassutslipp (Dillard, 2019; FAO, 2020; Huws et al., 2018; Jami et al., 2014; Matthews et al., 2019; McCann et al., 2016). Derfor er forståelsen av de metabolske funksjonene som utføres av den komplekse vommikrobiotaen både av industriell og vitenskapelig interesse. Denne kunnskapen kan bidra til å utvikle strategier for å imøtegå betydelige utfordringer knyttet til klimagassutslipp fra landbruket. Dette vil også kunne forbedre husdyrnæringen i møte med et økende behov for mat til en stadig voksende befolkning, uten å gå på bekostning av dyrehelse og dyrevelferd.
Utvikling av moderne molekylære teknikker har muliggjort studier av og innsikt i genetisk informasjon og funksjonell aktivitet i komplekse mikrobiom. Utnyttelsen av såkalte ‘meta-omics’-tilnærminger gjør at vi kan øke gjenskaping av molekyler som utgjør et mikrobiom, og tolkningen av disse fasiliterer bedre prediksjoner av de metabolske funksjonene til intrikate mikrobiom i deres naturlige økosystem. Oppklaring av de dynamiske interaksjonene mellom mikrobielle medlemmer i vertsassosierte mikrobiom, slik som i vomma av planteetere, kan bidra til å danne verdifulle koblinger til vertsmetabolismen.