A. Walker

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Dominant and diet-responsive groups of bacteria within the human colonic microbiota

J. Parkhill, H. Flint, A. Walker, 2011, The ISME Journal.

Patent Human Infections with the Whipworm, Trichuris trichiura, Are Not Associated with Alterations in the Faecal Microbiota

Julian Parkhill, J. Parkhill, A. Walker, 2013, PloS one.

Explorer The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16 S rRNA Gene Sequencing

C. Lees, J. Satsangi, J. Parkhill, 2017 .

Shotgun metagenomics, from sampling to analysis

N. Segata, N. Loman, C. Quince, 2017, Nature Biotechnology.

Shotgun metagenomics , from sampling to sequencing and analysis

N. Segata, N. Loman, C. Quince, 2017 .

The impact of the Fungus-Host-Microbiota interplay upon Candida albicans infections: current knowledge and new perspectives

Alistair J. P. Brown, C. Manichanh, M. Netea, 2020, FEMS microbiology reviews.

TLR Signaling Modulates Side Effects of Anticancer Therapy in the Small Intestine

J. Parkhill, G. Gerken, A. Walker, 2015, The Journal of Immunology.

Corrigendum: Shotgun metagenomics, from sampling to analysis

N. Segata, N. Loman, C. Quince, 2017, Nature Biotechnology.

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

R. Dewhurst, A. Walker, M. Watson, 2018, Nature Communications.

Antibiotic Treatment of Clostridium difficile Carrier Mice Triggers a Supershedder State, Spore-Mediated Transmission, and Severe Disease in Immunocompromised Hosts

N. Fairweather, S. Clare, G. Dougan, 2009, Infection and Immunity.

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

Paul Turner, Julian Parkhill, Nicholas J Loman, 2014, BMC Biology.

Time between Collection and Storage Significantly Influences Bacterial Sequence Composition in Sputum Samples from Cystic Fibrosis Respiratory Infections

L. Hoffman, J. Parkhill, A. Walker, 2014, Journal of Clinical Microbiology.

Identification of Rumen Microbial Genes Involved in Pathways Linked to Appetite, Growth, and Feed Conversion Efficiency in Cattle

R. Dewhurst, T. Freeman, A. Walker, 2019, Front. Genet..

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

Karen P. Scott, Julian Parkhill, Paul Scott, 2015, Microbiome.

Phylogeny, culturing, and metagenomics of the human gut microbiota.

Alan W Walker, Harry J Flint, H. Flint, 2014, Trends in microbiology.

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition

Jukka Corander, Mikko Vehkaperä, Saikat Chatterjee, 2015, PloS one.

Wheat bran promotes enrichment within the human colonic microbiota of butyrate‐producing bacteria that release ferulic acid

J. Parkhill, H. Flint, A. Walker, 2016, Environmental microbiology.

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations

Edoardo Pasolli, P. Manghi, C. Huttenhower, 2020, Genome Biology.

The environmental stress sensitivities of pathogenic Candida species, including Candida auris, and implications for their spread in the hospital setting

Alistair J. P. Brown, J. Laing, A. Walker, 2020, Medical mycology.

Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome

A. Walker, M. Watson, L. Glendinning, 2022, bioRxiv.

Sporulation capability and amylosome conservation among diverse human colonic and rumen isolates of the keystone starch‐degrader Ruminococcus bromii

E. Bayer, H. Flint, A. Walker, 2017, Environmental microbiology.

A non-endoscopic sampling device to sample the oesophageal microbiota : a case-control study

A. Walker, M. O’Donovan, R. Fitzgerald, 2016 .

The genomic and proteomic landscape of the rumen microbiome revealed by comprehensive genome-resolved metagenomics

A. Walker, M. Watson, Robert D. Stewart, 2018, bioRxiv.

Fibrinogen‐binding and platelet‐aggregation activities of a Lactobacillus salivarius septicaemia isolate are mediated by a novel fibrinogen‐binding protein

J. Parkhill, A. Walker, Yin Li, 2012, Molecular microbiology.

Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism

R. Dewhurst, A. Walker, M. Watson, 2017, bioRxiv.

Anticancer Therapy in the Small Intestine TLR Signaling Modulates Side Effects of

J. Parkhill, G. Gerken, A. Walker, 2015 .

Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

Mihai Pop, Julian Parkhill, Hector Corrada Bravo, 2014, Genome Biology.

Microbial lactate utilisation and the stability of the gut microbiome

H. Flint, A. Walker, S. Duncan, 2022, Gut Microbiome.

Enhanced Susceptibility to Citrobacter rodentium Infection in MicroRNA-155-Deficient Mice

A. Enright, C. Abreu-Goodger, E. Vigorito, 2012, Infection and Immunity.

Analysis of pit latrine microbiota reveals depth-related variation in composition, and key parameters and taxa associated with latrine fill-up rate

C. Quince, J. Parkhill, A. Walker, 2022, Frontiers in Microbiology.

TPL-2 restricts Ccl24-dependent immunity to Heligmosomoides polygyrus

A. Walker, S. Ley, Mark S. Wilson, 2017, PLoS pathogens.

Impact of changes at the Candida albicans cell surface upon immunogenicity and colonisation in the gastrointestinal tract

A. Walker, S. Duncan, N. Gow, 2022, Cell surface.

Objections to the proposed reclassification of Eubacterium rectale as Agathobacter rectalis.

H. Flint, A. Walker, S. Duncan, 2016, International journal of systematic and evolutionary microbiology.

CCR2 mediates dendritic cell recruitment to the human colon but is not responsible for differences observed in dendritic cell subsets, phenotype and function between the proximal and distal colon

J. Parkhill, A. Walker, P. Scott, 2015 .

Higher total faecal short-chain fatty acid concentrations correlate with increasing proportions of butyrate and decreasing proportions of branched-chain fatty acids across multiple human studies

H. Flint, A. Walker, S. Duncan, 2022, Gut Microbiome.

Whole Genome Amplification of Single Bacterial Cells

A. Walker, P. Scott, 2015 .

Food additives: Assessing the impact of exposure to permitted emulsifiers on bowel and metabolic health – introducing the FADiets study

A. Walker, A. Johnstone, J. Rhodes, 2019, Nutrition bulletin.

High-fat diet induced changes in gut microbiota and pathogen associate molecular patterns (PAMPS)

H. Flint, A. Walker, C. Erridge, 2014, Proceedings of the Nutrition Society.

Survival Strategies and Metabolic Interactions between Ruminococcus gauvreauii and Ruminococcoides bili, Isolated from Human Bile

A. Walker, S. Duncan, E. Conti, 2022, Microbiology spectrum.

Implications of multiple freeze-thawing on respiratory samples for culture-independent analyses✩

L. Hoffman, J. Parkhill, A. Walker, 2014, Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society.

Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

Mick Watson, Rainer Roehe, Alan W Walker, 2019, Nature Biotechnology.

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

Keith Dobney, Julian Parkhill, Grant Townsend, 2013, Nature Genetics.

Lung infections in cystic fibrosis: deriving clinical insight from microbial complexity

A. Walker, G. Rogers, K. Bruce, 2010, Expert review of molecular diagnostics.

Dietary fibre complexity and its influence on functional groups of the human gut microbiota

A. Walker, S. Duncan, P. Louis, 2021, Proceedings of the Nutrition Society.

Fighting Obesity with Bacteria

J. Parkhill, A. Walker, 2013, Science.

pH and Peptide Supply Can Radically Alter Bacterial Populations and Short-Chain Fatty Acid Ratios within Microbial Communities from the Human Colon

H. Flint, A. Walker, S. Duncan, 2005, Applied and Environmental Microbiology.

The Transcription Factor T-bet Regulates Intestinal Inflammation Mediated by Interleukin-7 Receptor+ Innate Lymphoid Cells

Graham M Lord, Richard G. Jenner, J. Parkhill, 2012, Immunity.

Colitis susceptibility in mice with reactive oxygen species deficiency is mediated by mucus barrier and immune defense defects

A. Walker, U. Knaus, G. D'Agostino, 2019, Mucosal Immunology.

A Common Genomic Framework for a Diverse Assembly of Plasmids in the Symbiotic Nitrogen Fixing Bacteria

Georgios S. Vernikos, Lisa C. Crossman, J. Parkhill, 2008, PloS one.

Interleukin 6 Increases Production of Cytokines by Colonic Innate Lymphoid Cells in Mice and Patients With Chronic Intestinal Inflammation

Graham M Lord, J. Sanderson, J. Parkhill, 2015, Gastroenterology.

Therapeutic modulation of intestinal dysbiosis.

A. Walker, T. Lawley, A. Walker, 2013, Pharmacological research.

Pivotal Roles for pH, Lactate, and Lactate-Utilizing Bacteria in the Stability of a Human Colonic Microbial Ecosystem

J. Parkhill, H. Flint, A. Walker, 2020, mSystems.

Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements

R. Dewhurst, A. Walker, M. Watson, 2019, Animal microbiome.

Chemokine (C-C Motif) Receptor 2 Mediates Dendritic Cell Recruitment to the Human Colon but Is Not Responsible for Differences Observed in Dendritic Cell Subsets, Phenotype, and Function Between the Proximal and Distal Colon

J. Parkhill, A. Walker, P. Scott, 2015, Cellular and molecular gastroenterology and hepatology.

The Intestinal Microbiota Contributes to the Ability of Helminths to Modulate Allergic Inflammation

J. Rougemont, A. Loukas, K. McCoy, 2015, Immunity.

Human gut bifidobacteria inhibit the growth of the opportunistic fungal pathogen Candida albicans

A. Walker, S. Duncan, K. Mezerová, 2021, bioRxiv.

Relative abundance of the Prevotella genus within the human gut microbiota of elderly volunteers determines the inter-individual responses to dietary supplementation with wheat bran arabinoxylan-oligosaccharides

J. Parkhill, H. Flint, A. Walker, 2020, BMC Microbiology.

The human microbiota and pathogen interactions

A. Walker, A. Walker, 2015 .

Intestinal colonization resistance

A. Walker, T. Lawley, A. Walker, 2013, Immunology.

Intestinal Microbiology and Ecology in Inflammatory Bowel Disease

A. Walker, 2012 .

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

M. Yassour, F. Bushman, P. Bork, 2023, Nature.

Gut microbiota trajectory in early life may predict development of celiac disease

J. Parkhill, A. Walker, Y. Sanz, 2018, Microbiome.

Modulation of the human gut microbiota by dietary fibres occurs at the species level

J. Parkhill, H. Flint, A. Walker, 2016, BMC Biology.

Dietary fibers inhibit obesity in mice, but host responses in the cecum and liver appear unrelated to fiber-specific changes in cecal bacterial taxonomic composition

C. Mayer, H. Flint, A. Walker, 2018, Scientific Reports.

The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water

N. Ferguson, J. Parkhill, S. Baker, 2016, PLoS neglected tropical diseases.

Studying the Human Microbiota.

Alan W Walker, A. Walker, A. Walker, 2016, Advances in experimental medicine and biology.

Comparing the microbiota of the cystic fibrosis lung and human gut

D. Fine, A. Walker, G. Rogers, 2010, Gut microbes.

Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

Wolf-Dietrich Hardt, Bärbel Stecher, Martin Ackermann, 2012, Proceedings of the National Academy of Sciences.

Reagent contamination can critically impact sequence-based microbiome analyses

Paul Turner, Julian Parkhill, Nicholas J. Loman, 2014, bioRxiv.

A non-endoscopic device to sample the oesophageal microbiota: a case-control study

J. Parkhill, A. Walker, M. O’Donovan, 2016, The lancet. Gastroenterology & hepatology.

Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment

M. Pop, H. Bravo, J. Parkhill, 2016, BMC Genomics.

Lung function and microbiota diversity in cystic fibrosis

L. Hoffman, J. Parkhill, C. Teneback, 2020, Microbiome.

Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities

J. Parkhill, A. Walker, P. Scott, 2010, The ISME Journal.

Dietary Uncoupling of Gut Microbiota and Energy Harvesting from Obesity and Glucose Tolerance in Mice

A. Walker, P. Morgan, A. Ross, 2017, Cell reports.

The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16S rRNA Gene Sequencing

H. Drummond, C. Lees, J. Satsangi, 2014, PloS one.

High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease

Julian Parkhill, Alan W Walker, Gordon Dougan, 2011, BMC Microbiology.

Exclusive enteral nutrition mediates gut microbial and metabolic changes that are associated with remission in children with Crohn’s disease

W. D. de Jonge, A. Walker, J. Seppen, 2020, Scientific Reports.

Microbiota That Affect Risk for Shigellosis in Children in Low-Income Countries

M. Pop, L. Magder, T. Farag, 2015, Emerging infectious diseases.

Distribution, organization and expression of genes concerned with anaerobic lactate utilization in human intestinal bacteria

H. Harmsen, H. Flint, A. Walker, 2022, Microbial genomics.

Distribution, organization and expression of genes concerned with anaerobic lactate-utilization in human intestinal bacteria

H. Harmsen, H. Flint, A. Walker, 2021, bioRxiv.

Salmonella enterica Serovar Typhimurium Exploits Inflammation to Compete with the Intestinal Microbiota

G. Dougan, J. Parkhill, J. Buer, 2007, PLoS biology.

The Bacteriology of Pouchitis: A Molecular Phylogenetic Analysis Using 16S rRNA Gene Cloning and Sequencing

Matthew W. Johnson, G. Dougan, C. Churcher, 2010, Annals of surgery.

Special issue: The Human Intestinal Microbiota.

H. Flint, A. Walker, P. O’Toole, 2010, Microbiology.

Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines‡

C. Quince, J. Parkhill, A. Walker, 2016, Microbial biotechnology.

Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice

Taane G. Clark, Julian Parkhill, Roland Rad, 2012, PLoS pathogens.

Molecular Diversity, Cultivation, and Improved Detection by Fluorescent In Situ Hybridization of a Dominant Group of Human Gut Bacteria Related to Roseburia spp. or Eubacterium rectale

H. Harmsen, H. Flint, A. Walker, 2006, Applied and Environmental Microbiology.

Studies on the effect of system retention time on bacterial populations colonizing a three-stage continuous culture model of the human large gut using FISH techniques.

A. Walker, G. Macfarlane, S. Macfarlane, 2006, FEMS microbiology ecology.

Bacterial microbiota of the upper respiratory tract and childhood asthma

W. Cookson, M. Ege, M. Moffatt, 2017, The Journal of allergy and clinical immunology.

Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention

J. Parkhill, A. Walker, Anna E. Oliver, 2015, The ISME Journal.

Cystic Fibrosis Respiratory Infections Composition in Sputum Samples from Significantly Influences Bacterial Time between Collection and Storage

L. Hoffman, J. Parkhill, A. Walker, 2014 .

Modulation of the human gut microbiota by dietary fibres occurs at the species level

J. Parkhill, H. Flint, A. Walker, 2016, BMC Biology.

The Impact of NOD2 Variants on Fecal Microbiota in Crohn’s Disease and Controls Without Gastrointestinal Disease

Julian Parkhill, Alan W Walker, Miles Parkes, 2018, Inflammatory bowel diseases.

Application of the dynamic gastrointestinal simulator (simgi®) to assess the impact of probiotic supplementation in the metabolism of grape polyphenols.

A. Walker, B. Bartolomé, M. Moreno-Arribas, 2020, Food research international.

Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection

M. Pop, D. Ecker, R. Sampath, 2013, Journal of Clinical Microbiology.

Selective colonization of insoluble substrates by human faecal bacteria.

H. Flint, A. Walker, S. Duncan, 2007, Environmental microbiology.

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

J. Parkhill, H. Flint, A. Walker, 2015, Microbiome.

Gut microbiota trajectory in early life may predict development of celiac disease

J. Parkhill, A. Walker, Y. Sanz, 2018, Microbiome.

MicroRNA-155-Deficient Mice rodentium Infection in Enhanced Susceptibility to Citrobacter

A. Enright, C. Abreu-Goodger, E. Vigorito, 2014 .

A Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence Analyses

A. Walker, A. Walker, 2019, mSystems.

Impact of carbohydrate substrate complexity on the diversity of the human colonic microbiota

J. Parkhill, H. Flint, A. Walker, 2018, FEMS microbiology ecology.

Ruminococcoides bili gen. nov., sp. nov., a bile-resistant bacterium from human bile with autolytic behavior.

A. Walker, S. Duncan, E. Conti, 2021, International journal of systematic and evolutionary microbiology.

Links between Diet, Intestinal Anaerobes, Microbial Metabolites and Health

A. Walker, S. Duncan, E. Conti, 2023, Biomedicines.

The species composition of the human intestinal microbiota differs between particle-associated and liquid phase communities.

Alan W Walker, Harry J Flint, H. Harmsen, 2008, Environmental microbiology.

Diet induced obesity is independent of metabolic endotoxemia and TLR4 signalling, but markedly increases hypothalamic expression of the acute phase protein, SerpinA3N

A. Walker, P. Morgan, P. Barrett, 2018, Scientific Reports.

Bayesian estimation of bacterial community composition from 454 sequencing data

Jukka Corander, J. Corander, A. Walker, 2012, Nucleic acids research.

Diet induced obesity is independent of metabolic endotoxemia and TLR4 signalling, but markedly increases hypothalamic expression of the acute phase protein, SerpinA3N

A. Walker, P. Morgan, P. Barrett, 2018, Scientific Reports.

Variable alterations of the microbiota, without metabolic or immunological change, following faecal microbiota transplantation in patients with chronic pouchitis

J. Parkhill, A. Walker, A. Hart, 2015, Scientific Reports.

Dietary fibers inhibit obesity in mice, but host responses in the cecum and liver appear unrelated to fiber-specific changes in cecal bacterial taxonomic composition

C. Mayer, H. Flint, A. Walker, 2018, Scientific Reports.

The Transcription Factor T-bet Regulates Intestinal Inflammation Mediated by Interleukin-7 Receptor+ Innate Lymphoid Cells

Graham M Lord, Richard G. Jenner, J. Parkhill, 2012, Immunity.

Edinburgh Research Explorer Identification of Rumen Microbial Genes Involved in Pathways Linked to Appetite, Growth, and Feed Conversion Efficiency in Cattle

R. Dewhurst, T. Freeman, A. Walker, 2022 .

Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection

D. Ecker, R. Sampath, L. Magder, 2013, Journal of Clinical Microbiology.