ORCID Profile
0000-0001-6097-2539
Current Organisations
Norwegian University of Life Science
,
Cancer Council Victoria
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Publisher: Springer Science and Business Media LLC
Date: 12-10-2018
Publisher: Elsevier BV
Date: 06-2021
DOI: 10.1016/J.CELL.2021.04.024
Abstract: Plant species have evolved myriads of solutions, including complex cell type development and regulation, to adapt to dynamic environments. To understand this cellular ersity, we profiled tomato root cell type translatomes. Using xylem differentiation in tomato, ex les of functional innovation, repurposing, and conservation of transcription factors are described, relative to the model plant Arabidopsis. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Comparative translatome analyses of rice, tomato, and Arabidopsis cell populations suggest increased expression conservation of root meristems compared with other homologous populations. In addition, the functions of constitutively expressed genes are more conserved than those of cell type/tissue-enriched genes. These observations suggest that higher order properties of cell type and pan-cell type regulation are evolutionarily conserved between plants and animals.
Publisher: Cold Spring Harbor Laboratory
Date: 10-04-2020
DOI: 10.1101/2020.04.09.017285
Abstract: Plant species have evolved myriads of solutions to adapt to dynamic environments, including complex cell type development and regulation. To understand this ersity, we profiled tomato root cell type translatomes and chromatin accessibility. Using xylem differentiation in tomato, relative to Arabidopsis, ex les of functional innovation, repurposing and conservation of transcription factors are described. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Translatome analyses of rice, tomato and Arabidopsis tissues suggest that root meristems are more conserved, and that the functions of constitutively expressed genes are more conserved than those of cell type/tissue-enriched genes. These observations suggest that higher-order properties of cell type and pan-cell type regulation are conserved between plants and animals. Pan-species cell type translatome and chromatin accessibility data reveal novelty, conservation and repurposing of gene function.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 13-04-2018
Abstract: Trees become dormant in winter, with encapsulated buds protected against harsh conditions. Tylewicz et al. found that, as the days get shorter, communication channels between cells in aspen trees shut down. The blocked plasmodesmata sequester the dormant meristems from growth signals. Growth-promoting signals can be turned on and off relatively rapidly, but the closed plasmodesmata are not so nimble. Thus, despite the occasional sunny day, the trees stay dormant until spring. Science , this issue p. 212
Publisher: Cold Spring Harbor Laboratory
Date: 29-11-2019
DOI: 10.1101/857599
Abstract: Microbiology is founded on well-known model organisms. For ex le, the majority of our fundamental knowledge regarding the quantitative levels of DNA, RNA, and protein backdates to keystone pure culture-based studies. Nowadays, meta-omic approaches allow us to directly access the molecules that constitute microbes and microbial communities, however due to a lack of absolute measurements, many original culture-derived “microbiology statutes” have not been updated or adapted to more complex microbiome settings. Within a cellulose-degrading and methanogenic consortium, we temporally measured genome-centric absolute RNA and protein levels per gene, and obtained a protein-to-RNA ratio of 10 2 -10 4 for bacterial populations, whereas Archaeal RNA rotein dynamics (10 3 -10 5 : Methanothermobacter thermoautotrophicus ) were more comparable to Eukaryotic representatives humans and yeast. The linearity between transcriptome and proteome had a population-specific change over time, highlighting a minimal subset of four functional carriers (cellulose degrader, fermenter, syntrophic acetate-oxidizer and methanogen) that coordinated their respective metabolisms, cumulating in the overarching community phenotype of converting polysaccharides to methane. Our findings show that upgrading multi-omic toolkits with traditional absolute measurements unlocks the scaling of core biological questions to dynamic and complex microbiomes, creating a deeper insight into inter-organismal relationships that drive the greater community function.
Publisher: Springer Science and Business Media LLC
Date: 18-09-2020
DOI: 10.1038/S41467-020-18543-0
Abstract: While the field of microbiology has adapted to the study of complex microbiomes via modern meta-omics techniques, we have not updated our basic knowledge regarding the quantitative levels of DNA, RNA and protein molecules within a microbial cell, which ultimately control cellular function. Here we report the temporal measurements of absolute RNA and protein levels per gene within a mixed bacterial-archaeal consortium. Our analysis of this data reveals an absolute protein-to-RNA ratio of 10 2 –10 4 for bacterial populations and 10 3 –10 5 for an archaeon, which is more comparable to Eukaryotic representatives’ humans and yeast. Furthermore, we use the linearity between the metaproteome and metatranscriptome over time to identify core functional guilds, hence using a fundamental biological feature (i.e., RNA rotein levels) to highlight phenotypical complementarity. Our findings show that upgrading multi-omic toolkits with traditional absolute measurements unlocks the scaling of core biological questions to dynamic and complex microbiomes, creating a deeper insight into inter-organismal relationships that drive the greater community function.
Publisher: Cold Spring Harbor Laboratory
Date: 10-10-2019
DOI: 10.1101/799023
Abstract: Beneficial modulation of the gut microbiome has high-impact implications not only in humans, but also in livestock that sustain our current societal needs. In this context, we have tailored an acetylated galactoglucomannan (AcGGM) fibre to match unique enzymatic capabilities of Roseburia and Faecalibacterium species, both renowned butyrate-producing gut commensals. The accuracy of AcGGM was tested within the complex endogenous gut microbiome of pigs, wherein we resolved 355 metagenome-assembled genomes together with quantitative metaproteomes. In AcGGM-fed pigs, both target populations differentially expressed AcGGM-specific polysaccharide utilization loci, including novel, mannan-specific esterases that are critical to its deconstruction. However, AcGGM-inclusion also manifested a “butterfly effect”, whereby numerous metabolic changes and interdependent cross-feeding pathways were detected in neighboring non-mannolytic populations that produce short-chain fatty acids. Our findings show that intricate structural features and acetylation patterns of dietary fibre can be customized to specific bacterial populations, with potential to create greater modulatory effects at large.
Publisher: Springer Science and Business Media LLC
Date: 11-05-2023
DOI: 10.1038/S41396-023-01407-Y
Abstract: Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the entodiniomorphs (order: Entodiniomorphida ) and holotrichs (order: Vestibuliferida ) are consistently observed to be dominant across a erse genetic and geographical range of ruminant hosts. Despite the apparent core role that protozoal species exert, their major biological and metabolic contributions to rumen function remain largely undescribed in vivo. Here, we have leveraged (meta)genome-centric metaproteomes from rumen fluid s les originating from both cattle and goats fed diets with varying inclusion levels of lipids and starch, to detail the specific metabolic niches that protozoa occupy in the context of their microbial co-habitants. Initial proteome estimations via total protein counts and label-free quantification highlight that entodiniomorph species Entodinium and Epidinium as well as the holotrichs Dasytricha and Isotricha comprise an extensive fraction of the total rumen metaproteome. Proteomic detection of protozoal metabolism such as hydrogenases ( Dasytricha , Isotricha, Epidinium, Enoploplastron ), carbohydrate-active enzymes ( Epidinium, Diplodinium, Enoploplastron , Polyplastron ), microbial predation ( Entodinium ) and volatile fatty acid production ( Entodinium and Epidinium ) was observed at increased levels in high methane-emitting animals. Despite certain protozoal species having well-established reputations for digesting starch, they were unexpectedly less detectable in low methane emitting-animals fed high starch diets, which were instead dominated by propionate/succinate-producing bacterial populations suspected of being resistant to predation irrespective of host. Finally, we reaffirmed our abovementioned observations in geographically independent datasets, thus illuminating the substantial metabolic influence that under-explored eukaryotic populations have in the rumen, with greater implications for both digestion and methane metabolism.
Publisher: Cold Spring Harbor Laboratory
Date: 12-03-2018
DOI: 10.1101/280602
Abstract: Microbial communities that degrade lignocellulosic biomass are typified by high levels of species- and strain-level complexity as well as synergistic interactions between both cellulolytic and non-cellulolytic microorganisms. Coprothermobacter proteolyticus frequently dominates thermophilic, lignocellulose-degrading communities with wide geographical distribution, which is in contrast to reports that it ferments proteinaceous substrates and is incapable of polysaccharide hydrolysis. Here we deconvolute a highly efficient cellulose-degrading consortium (SEM1b) that is co-dominated by Clostridium (Ruminiclostridium) thermocellum - and multiple heterogenic strains affiliated to C. proteolyticus . Metagenomic analysis of SEM1b recovered metagenome-assembled genomes (MAGs) for each constituent population, whilst in parallel two novel strains of C. proteolyticus were successfully isolated and sequenced. Annotation of all C. proteolyticus genotypes (two strains and one MAG) revealed their genetic acquisition of carbohydrate-active enzymes (CAZymes), presumably derived from horizontal gene transfer (HGT) events involving polysaccharide-degrading Firmicutes or Thermotogae-affiliated populations that are historically co-located. HGT material included a saccharolytic operon, from which a CAZyme was biochemically characterized and demonstrated hydrolysis of multiple hemicellulose polysaccharides. Finally, temporal genome-resolved metatranscriptomic analysis of SEM1b revealed expression of C. proteolyticus CAZymes at different SEM1b life-stages as well as co-expression of CAZymes from multiple SEM1b populations, inferring deeper microbial interactions that are dedicated towards community degradation of cellulose and hemicellulose. We show that C. proteolyticus , a ubiquitous keystone population, consists of closely related strains that have adapted via HGT to presumably degrade both oligo- and longer polysaccharides present in decaying plants and microbial cell walls, thus explaining its dominance in thermophilic anaerobic digesters on a global scale.
Publisher: Springer Science and Business Media LLC
Date: 13-11-2020
DOI: 10.1038/S41467-020-19585-0
Abstract: Beneficial modulation of the gut microbiome has high-impact implications not only in humans, but also in livestock that sustain our current societal needs. In this context, we have tailored an acetylated galactoglucomannan (AcGGM) fibre to match unique enzymatic capabilities of Roseburia and Faecalibacterium species, both renowned butyrate-producing gut commensals. Here, we test the accuracy of AcGGM within the complex endogenous gut microbiome of pigs, wherein we resolve 355 metagenome-assembled genomes together with quantitative metaproteomes. In AcGGM-fed pigs, both target populations differentially express AcGGM-specific polysaccharide utilization loci, including novel, mannan-specific esterases that are critical to its deconstruction. However, AcGGM-inclusion also manifests a “butterfly effect”, whereby numerous metabolic changes and interdependent cross-feeding pathways occur in neighboring non-mannanolytic populations that produce short-chain fatty acids. Our findings show how intricate structural features and acetylation patterns of dietary fibre can be customized to specific bacterial populations, with potential to create greater modulatory effects at large.
Publisher: Cold Spring Harbor Laboratory
Date: 22-06-2022
DOI: 10.1101/2022.06.22.497163
Abstract: Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the entodiniomorphs (order: Entodiniomorphida ) and holotrichs (order: Vestibuliferida ) are consistently observed to be dominant across a erse genetic and geographical range of ruminant hosts. Despite the apparent core role that protozoal species exert, their major biological and metabolic contributions to rumen function remain largely undescribed in vivo . Here, we have leveraged (meta)genome-centric metaproteomes from rumen fluid s les originating from both cattle and goats fed diets with varying inclusion levels of lipids and starch, to detail the specific metabolic niches that protozoa occupy in the context of their microbial co-habitants. Initial proteome estimations via total protein counts and label-free quantification highlight that entodiniomorph species Entodinium and Epidinium as well as the holotrichs Dasytricha and Isotricha comprise an extensive fraction of the total rumen metaproteome. Proteomic detection of protozoal metabolism such as hydrogenases ( Dasytricha, Isotricha, Epidinium, Enoploplastron ), carbohydrate-active enzymes ( Epidinium, Diplodinium, Enoploplastron, Polyplastron ), microbial predation ( Entodinium ) and volatile fatty acid production ( Entodinium and Epidinium ) was observed at increased levels in high methane-emitting animals. Despite certain protozoal species having well-established reputations for digesting starch, they were unexpectedly less detectable in low methane emitting-animals fed high starch diets, which were instead dominated by propionate/succinate-producing bacterial populations suspected of being resistant to predation irrespective of host. Finally, we reaffirmed our abovementioned observations in geographically independent datasets, thus illuminating the substantial metabolic influence that under-explored eukaryotic populations have in the rumen, with greater implications for both digestion and methane metabolism.
Publisher: Cold Spring Harbor Laboratory
Date: 11-05-2021
DOI: 10.1101/2021.05.11.443593
Abstract: Manipulating soil metabolism by heavy inoculation with microbes is deemed realistic if waste from anaerobic digestion (digestate) is utilized as substrate and vector, but requires organisms that can grow both in digestate and soil (=generalist). We designed a strategy to enrich and isolate such generalist N 2 O-respiring bacteria (NRB) in soil and digestate, to provide inoculum for reducing N 2 O-emissions from agricultural soil. Sequential anaerobic enrichment cultures were provided with a small dose of O 2 and unlimited N 2 O, alternating between sterilized digestate and soil as substrates. The cultures were monitored for gas kinetics and community composition (16SrDNA), and cluster-analysis identified generalist-OTUs which became dominant, digestate/soil-specialists which did not, and a majority that were diluted out. Several NRBs circumscribed by generalist-OTU’s were isolated, genome sequenced to screen for catabolic capacity, and phenotyped, to assess their capacity as N 2 O-sinks in soil. The two isolates Cloacibacterium sp., carrying only N 2 O-reductase (Clade-II) and Pseudomonas sp ., with full-fledged denitrification-pathway, were both very effective N 2 O-sinks in soil, with Pseudomonas sp., showing a long-lasting sink effect, suggesting better survival in soil. This avenue for utilizing waste to bioengineer the soil microbiota holds promise to effectively combat N 2 O-emissions but could also be utilized for enhancing other metabolic functions in soil.
No related grants have been discovered for Torgeir R Hvidsten.