List of works - Phillip B Pope

"Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system

scientific article published in March 2018

A polysaccharide utilization locus from an uncultured bacteroidetes phylotype suggests ecological adaptation and substrate versatility

scientific article

A stable core gut microbiota across fresh- to saltwater transition for farmed Atlantic salmon.

scientific article

An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants

scientific article published on 12 June 2021

Analysis of the bovine rumen microbiome reveals a diversity of Sus-like polysaccharide utilization loci from the bacterial phylum Bacteroidetes

scientific article published on 22 January 2014

Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure

scientific article

De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes

scientific article published on 15 February 2013

Discovery and characterization of a thermostable two-domain GH6 endoglucanase from a compost metagenome.

scientific article

Do rumen Bacteroidetes utilize an alternative mechanism for cellulose degradation?

scientific article

Draft genome sequence of the methane-oxidizing bacterium Methylococcus capsulatus (Texas)

scientific article published on December 2012

First insight into the faecal microbiota of the high Arctic muskoxen (Ovibos moschatus).

scientific article

Forecasting the dynamics of a complex microbial community using integrated meta-omics

scientific article published in January 2024

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer

scientific article

From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus

scientific article published on 12 October 2018

From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus

Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite

article

High-yield and phylogenetically robust methods of DNA recovery for analysis of microbial biofilms adherent to plant biomass in the herbivore gut.

scientific article

Host-linked soil viral ecology along a permafrost thaw gradient

article

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

scientific article published on 30 October 2016

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data

scientific article

Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders

scientific article

Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes

scientific article published on 18 September 2020

Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem

article

Major faecal microbiota shifts in composition and diversity with age in a geographically restricted cohort of mothers and their children.

scientific article

Metagenomic analysis of a freshwater toxic cyanobacteria bloom

scientific article

Metagenomics and CAZyme Discovery

scientific article published on January 2017

Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci

scientific article (publication date: 2012)

Microbial community structure and dynamics during co-digestion of whey permeate and cow manure in continuous stirred tank reactor systems

scientific article

Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut

scientific article published on 13 November 2020

Muramidases found in the foregut microbiome of the Tammar wallaby can direct cell aggregation and biofilm formation.

scientific article

Nitrous oxide respiring bacteria in biogas digestates for reduced agricultural emissions

scientific article published in 2021

Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome.

scientific article published on 13 September 2016

Omics-based interpretation of synergism in a soil-derived cellulose-degrading microbial community

scientific article

Outer membrane vesicles from Fibrobacter succinogenes S85 contain an array of carbohydrate-active enzymes with versatile polysaccharide-degrading capacity

scientific article published on 26 April 2017

Plant biomass degradation by gut microbiomes: more of the same or something new?

scientific article published on 08 June 2009

Potential applications of gut microbiota to control human physiology

scientific article

Probiotic dosing of Ruminococcus flavefaciens affects rumen microbiome structure and function in reindeer

scientific article

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

scientific article published on 14 September 2020

Proteomic Dissection of the Cellulolytic Machineries Used by Soil-Dwelling

Proteomic data on enzyme secretion and activity in the bacterium Chitinophaga pinensis

scientific article published on 17 February 2017

Proteomic insights into mannan degradation and protein secretion by the forest floor bacterium Chitinophaga pinensis

scientific article published on 6 January 2017

Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester

scientific article published on 4 November 2016

Resin acids play key roles in shaping microbial communities during degradation of spruce bark

scientific article published in 2023

Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations

scientific article published on 16 April 2015

Rumen and Cecum Microbiomes in Reindeer (Rangifer tarandus tarandus) Are Changed in Response to a Lichen Diet and May Affect Enteric Methane Emissions

scientific article

Structural Features of a Bacteroidetes-Affiliated Cellulase Linked with a Polysaccharide Utilization Locus

scientific article published on 2 July 2015

Succession of Bifidobacterium longum Strains in Response to a Changing Early Life Nutritional Environment Reveals Dietary Substrate Adaptations

scientific article published on 15 July 2020

Taxonomic metagenome sequence assignment with structured output models

scientific article published on March 2011

The Farmed Atlantic Salmon (Salmo salar) Skin-Mucus Proteome and Its Nutrient Potential for the Resident Bacterial Community

scientific article published on 07 July 2019

The Potential of Class II Bacteriocins to Modify Gut Microbiota to Improve Host Health

scientific article

The Reindeer Rumen Microbiome

The effect of storage conditions on microbial community composition and biomethane potential in a biogas starter culture

scientific article published on 7 May 2015

The human gut Firmicute Roseburia intestinalis is a primary degrader of dietary β-mannans

scientific article published on 22 February 2019

Two SusD-like proteins encoded within a polysaccharide utilization locus of an uncultured ruminant Bacteroidetes phylotype bind strongly to cellulose.

scientific article published on 8 June 2012

Wood-Derived Dietary Fibers Promote Beneficial Human Gut Microbiota

scientific article published on 23 January 2019

microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data ⬇️

scientific article published in 2024

List of works by Phillip B Pope

"Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system

A polysaccharide utilization locus from an uncultured bacteroidetes phylotype suggests ecological adaptation and substrate versatility

A stable core gut microbiota across fresh- to saltwater transition for farmed Atlantic salmon.

An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants

Analysis of the bovine rumen microbiome reveals a diversity of Sus-like polysaccharide utilization loci from the bacterial phylum Bacteroidetes

Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure

De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes

Discovery and characterization of a thermostable two-domain GH6 endoglucanase from a compost metagenome.

Do rumen Bacteroidetes utilize an alternative mechanism for cellulose degradation?

Draft genome sequence of the methane-oxidizing bacterium Methylococcus capsulatus (Texas)

First insight into the faecal microbiota of the high Arctic muskoxen (Ovibos moschatus).

Forecasting the dynamics of a complex microbial community using integrated meta-omics

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer

From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus

From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus

Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite

High-yield and phylogenetically robust methods of DNA recovery for analysis of microbial biofilms adherent to plant biomass in the herbivore gut.

Host-linked soil viral ecology along a permafrost thaw gradient

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data

Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders

Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes

Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem

Major faecal microbiota shifts in composition and diversity with age in a geographically restricted cohort of mothers and their children.

Metagenomic analysis of a freshwater toxic cyanobacteria bloom

Metagenomics and CAZyme Discovery

Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci

Microbial community structure and dynamics during co-digestion of whey permeate and cow manure in continuous stirred tank reactor systems

Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut

Muramidases found in the foregut microbiome of the Tammar wallaby can direct cell aggregation and biofilm formation.

Nitrous oxide respiring bacteria in biogas digestates for reduced agricultural emissions

Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome.

Omics-based interpretation of synergism in a soil-derived cellulose-degrading microbial community

Outer membrane vesicles from Fibrobacter succinogenes S85 contain an array of carbohydrate-active enzymes with versatile polysaccharide-degrading capacity

Plant biomass degradation by gut microbiomes: more of the same or something new?

Potential applications of gut microbiota to control human physiology

Probiotic dosing of Ruminococcus flavefaciens affects rumen microbiome structure and function in reindeer

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

Proteomic Dissection of the Cellulolytic Machineries Used by Soil-Dwelling

Proteomic data on enzyme secretion and activity in the bacterium Chitinophaga pinensis

Proteomic insights into mannan degradation and protein secretion by the forest floor bacterium Chitinophaga pinensis

Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester

Resin acids play key roles in shaping microbial communities during degradation of spruce bark

Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations

Rumen and Cecum Microbiomes in Reindeer (Rangifer tarandus tarandus) Are Changed in Response to a Lichen Diet and May Affect Enteric Methane Emissions

Structural Features of a Bacteroidetes-Affiliated Cellulase Linked with a Polysaccharide Utilization Locus

Succession of Bifidobacterium longum Strains in Response to a Changing Early Life Nutritional Environment Reveals Dietary Substrate Adaptations

Taxonomic metagenome sequence assignment with structured output models

The Farmed Atlantic Salmon (Salmo salar) Skin-Mucus Proteome and Its Nutrient Potential for the Resident Bacterial Community

The Potential of Class II Bacteriocins to Modify Gut Microbiota to Improve Host Health

The Reindeer Rumen Microbiome

The effect of storage conditions on microbial community composition and biomethane potential in a biogas starter culture

The human gut Firmicute Roseburia intestinalis is a primary degrader of dietary β-mannans

Two SusD-like proteins encoded within a polysaccharide utilization locus of an uncultured ruminant Bacteroidetes phylotype bind strongly to cellulose.

Wood-Derived Dietary Fibers Promote Beneficial Human Gut Microbiota

microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data ⬇️