Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation

Söllinger, Andrea; Tveit, Alexander Tøsdal; Poulsen, Morten; Noel, Samantha Joan; Bengtsson, Mia M.; Bernhardt, Jörg; Hellwing, Anne Louise Frydendahl; Lund, Peter; Riedel, Katharina; Schleper, Christa; Højberg, Ole; Urich, Tim

doi:10.1128/msystems.00038-18

Cited by 83 publications

(88 citation statements)

References 69 publications

(87 reference statements)

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“…The initial degradation of complex plant fiber makes the carbon pool available for downstream metabolism that encompasses the intricate microbial food web within the rumen, ultimately providing access to otherwise inaccessible nutrients to the host. Concurrent with previous rumen metaproteome and -transcriptome studies 23,63 , our analysis revealed that the prokaryotic population in the rumen plays significant roles in many of the key reactions in the rumen system (Figure 4). (Figure 4).…”

Section: Towards a Holistic Understanding Of The Functional Roles Ofsupporting

confidence: 79%

“…Overall, it appears that within our experimental constraints (switchgrass incubated for 48 hours), bacterial populations contributed CAZymes that primarily modified non-cellulosic plant carbohydrates. It should be emphasized that the metaproteome data analyzed here represents only a snapshot of the community metabolism, and that the protein profiles of different rumen populations most likely have undergone temporal transformations in the time period between the plant material being introduced into the rumen environment and our analysis 23,47 .…”

Section: Metaproteome-generated Cazyme Profile Indicates Compartmentamentioning

confidence: 99%

“…The impact of fungi in the rumen ecosystem was already demonstrated in the early 1990s by Gordon and Phillips who reported a significant decrease in fiber digestion within the rumen after anaerobic fungi had been removed by the administration of fungicides 22 . The importance of rumen fungi for biomass degradation has since the been supported by in vivo studies [23][24][25] , and recently reinforced in transcriptome studies revealing that the fungi express a range of CAZymes when grown on different carbon sources 9,26 . Although enzymes of fungal origin have been regularly explored for their remarkable capacity to degrade lignocellulosic fiber 12,27,28 , their functional role in native anaerobic habitats and within the biomass-degrading enzyme repertoire of the rumen microbiome remains unclear.…”

Section: Introductionmentioning

confidence: 97%

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Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

Hagen

Brooke

Shaw

et al. 2020

Preprint

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The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 hours in nylon bags within the rumen of cannulated dairy cows. Across a gene catalogue covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of polysaccharides such as hemicellulose, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo-and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8 and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryoteselected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggests that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.

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Section: Towards a Holistic Understanding Of The Functional Roles Ofsupporting

confidence: 79%

Section: Metaproteome-generated Cazyme Profile Indicates Compartmentamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

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Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

Hagen

Brooke

Shaw

et al. 2020

Preprint

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“…Immediately after feed ingestion, the most readily digestible feed components are rapidly digested and fermented, and H 2 concentration rises (Robinson et al, 1981;Janssen, 2010;Guyader et al, 2015). After feed ingestion, increases in H 2 emissions have been shown to occur earlier and faster than increases in CH 4 (Rooke et al, 2014;Van Lingen et al, 2017;Söllinger et al, 2018), although this pattern has not occurred in all studies (Hillman et al, 1985). The peak in H 2 emission preceding the evolution of CH 4 production has been modeled by Van Lingen et al (2019), and interpreted by Rooke et al (2014) as the consequence of rapid fermentation and H 2 production exceeding the capacity of methanogens to utilize all the H 2 produced.…”

Section: The Control Of the Rumen Fermentation Profilementioning

confidence: 99%

Metabolic Hydrogen Flows in Rumen Fermentation: Principles and Possibilities of Interventions

2020

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Rumen fermentation affects ruminants productivity and the environmental impact of ruminant production. The release to the atmosphere of methane produced in the rumen is a loss of energy and a cause of climate change, and the profile of volatile fatty acids produced in the rumen affects the post-absorptive metabolism of the host animal. Rumen fermentation is shaped by intracellular and intercellular flows of metabolic hydrogen centered on the production, interspecies transfer, and incorporation of dihydrogen into competing pathways. Factors that affect the growth of methanogens and the rate of feed fermentation impact dihydrogen concentration in the rumen, which in turn controls the balance between pathways that produce and incorporate metabolic hydrogen, determining methane production and the profile of volatile fatty acids. A basic kinetic model of competition for dihydrogen is presented, and possibilities for intervention to redirect metabolic hydrogen from methanogenesis toward alternative useful electron sinks are discussed. The flows of metabolic hydrogen toward nutritionally beneficial sinks could be enhanced by adding to the rumen fermentation electron acceptors or direct fed microbials. It is proposed to screen hydrogenotrophs for dihydrogen thresholds and affinities, as well as identifying and studying microorganisms that produce and utilize intercellular electron carriers other than dihydrogen. These approaches can allow identifying potential microbial additives to compete with methanogens for metabolic hydrogen. The combination of adequate microbial additives or electron acceptors with inhibitors of methanogenesis can be effective approaches to decrease methane production and simultaneously redirect metabolic hydrogen toward end products of fermentation with a nutritional value for the host animal. The design of strategies to redirect metabolic hydrogen from methane to other sinks should be based on knowledge of the physicochemical control of rumen fermentation pathways. The application of new -omics techniques together with classical biochemistry methods and mechanistic modeling can lead to exciting developments in the understanding and manipulation of the flows of metabolic hydrogen in rumen fermentation.

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“…For instance, microbial diversity analysis has revealed that basal diet and diurnal rumen pH patterns can be somewhat independent of bacterial community profile 13 , while more recently, Söllinger et al 14 paired metabolomics with quantitative metatranscriptomics to assess the diurnal fluctuations of individual rumen microorganisms and also reported a dissociation between the functional microbial transcripts and microbiome pathway products such as methane. Layered within these challenges, the central dogma of translation appears to be disjointed, with microbial RNA not reflective of protein abundances within the rumen, possibly due to post-translational modifications along with other adaptations [14][15][16] . In addition, issues such as a limitation in analytic capabilities to discern in vivo complexities and variations due to external drivers such as endogenous and management influences, have slowed progress and the application of knowledge to commercial systems.Proteomic techniques are now integrated in livestock research, with published applications in milk [17][18][19] , urine 20-22 , plasma 23,24 , and reproductive fluid 25,26 .…”

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confidence: 99%

Characterization of variations within the rumen metaproteome of Holstein dairy cattle relative to morning feed offering

Honan

Greenwood

2020

Sci Rep

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few studies have utilized proteomic techniques to progress our knowledge of protein-mediated pathways within the rumen microbial community, and no previous research has used these techniques to investigate the patterns or variations of these proteins within this community. it was hypothesized that there would be fluctuations of rumen microbial protein abundances due to feed intake-mediated nutrient availability and that these could be identified using non gel-based proteomic techniques. This study investigated the fluctuations of bovine rumen metaproteome utilizing three mid to late-lactation Holsteins. Rumen fluid was collected at three timepoints on three days relative to their first morning feed offering (0 h, 4 h, and 6 h). Samples were pooled within timepoint within cow across day, analyzed using Lc-MS/MS techniques, and analyzed for variations across hour of sampling using pRoc MiXeD of SAS with orthogonal contrasts to determine linear and quadratic effects. A total of 658 proteins were characterized across 19 microbial species, with 68 proteins identified from a variety of 15 species affected by time of collection. Translation-related proteins such as 50S and 30S ribosomal protein subunit variants and elongation factors were positively correlated with hour of sampling. Results suggest that as nutrients become more readily available, microbes shift from conversion-focused biosynthetic routes to more encompassing DnA-driven pathways.The pregastric rumen is the dominant site of microbial colonization and microbe-mediated fermentation within the ruminant digestive tract, and functionality of this chamber is a key factor that dictates the animal's efficiency of nutrient utilization and production 1-4 . Feed and production efficiency, ruminant animal health, and environmental emissions are all affected by rumen ecology, hence there is growing interest within the ruminant livestock sector to understand the in situ or vivo functionality within and among rumen microbes. Current knowledge of the rumen microbiome is cross-disciplinary and rapidly expanding, with novel research emerging that is focused on diversity analysis and community structures of the microbiota 5-8 , as well as metabolic pathway analysis and metatranscriptomics 9-12 .Despite advances in our understanding, there is still a gap in knowledge regarding the undercurrents and interplay of microbe-specific metabolic pathways because of their dynamicity, adaptability, and complexity. Utilizing a variety of approaches to characterize the rumen in terms of microbial ecology and pathway dynamics appears to be necessary. For instance, microbial diversity analysis has revealed that basal diet and diurnal rumen pH patterns can be somewhat independent of bacterial community profile 13 , while more recently, Söllinger et al. 14 paired metabolomics with quantitative metatranscriptomics to assess the diurnal fluctuations of individual rumen microorganisms and also reported a dissociation between the functional microbial transcripts and microbiome pathway products ...

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Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation

Cited by 83 publications

References 69 publications

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

Metabolic Hydrogen Flows in Rumen Fermentation: Principles and Possibilities of Interventions

Characterization of variations within the rumen metaproteome of Holstein dairy cattle relative to morning feed offering

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