Bacterial diversity and strain dynamics in the infant respiratory microbiome during the first year of life.
Volpiano CG, Judd LM, Harshegyi-Hand T, Wick RR, Sly PD, Holt PG, Kusel M, Strickland DH, Inouye M, Holt KE, Méric G.
bioRxiv, 20 May 2026. DOI: 10.64898/2026.05.20.726687

Interplay between colorectal cancer-related lifestyles and the gut microbiome: an exploratory analysis of metagenomic data.
Tammi R, Maukonen M, Kaartinen NE, Koponen K, Niiranen T, Méric G, Albanes D, Eriksson JG, Jousilahti P, Koskinen S, Pajari AM, Knight R, Havulinna AS, Salomaa V, Männistö S.
Cancer Causes & Control, 11 March 2026.
DOI: 10.1007/s10552-026-02144-1

Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals.
Baldanzi G, Larsson A, Sayols-Baixeras S, Dekkers KF, Hammar U, Nguyen D, Graells T, Ahmad S, Volpiano CG, Méric G, Järhult JD, Tängdén T, Ludvigsson JF, Lind L, Sundström J, Michaëlsson K, Ärnlöv J, Kennedy B, Orho-Melander M, Fall T.
Nature Medicine, 11 March 2026.
DOI: 10.1038/s41591-026-04284-y
Additional content: press release UU, press coverage 1, 2, 3, 4, 5 (French), 6 (Portuguese), 7 (Spanish), 8 (Greek), 9 (French), 10 (German), 11 (Dutch), 12, 13, 14, 15 (German), 16, 17 (French), 18 (Spanish), 19 (Spanish)

Gut microbiome and risk of dementia – a prospective, population-based study.
Tynkkynen J*, Kambur O*, Niiranen T, Lahti L, Ruuskanen MO, McDonald D, Jousilahti P, Volpiano CG, Méric G, Inouye M, Liu Y, Khatib L, Patel L, Salomaa V, Knight R, Havulinna A.
medRxiv, 22 February 2026.
DOI: 10.64898/2026.02.15.26345196

Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation.
Dekkers KF*, Pertiwi K*, Baldanzi G*, Lundmark P, Hammar U, Moksnes MR, Coward E, Nethander M, Salih GA, Miari A, Nguyen D, Sayols-Baixeras S, Eklund AC, Holm JB, Nielsen HB, Volpiano CG, Méric G, Thangam M, Hakaste L, Tuomi T, Ahlqvist E, Smith CA, Allen M, Reimann F, Gribble FM, Ohlsson C, Hveem K, Melander O, Nilsson PM, Engström G, Smith JG, Michaëlsson K, Ärnlöv J, Orho-Melander M, Fall T.
Nature Genetics, 13 February 2026.
DOI: 10.1038/s41588-026-02512-2

Value of multiomics over clinical risk factors in hypertension prediction.
Vuoria M*, Ruuskanen M*, Jousilahti P, Salomaa V, Yaoa L, Vaurac F, Havulinna A, Liu Y, Méric G, Inouye M, Knight R, Lahti L, Niiranen T.
Hypertension, 11 December 2025.
DOI: 10.1161/hypertensionaha.125.25358

Variation and prognostic potential of the gut antibiotic resistome in the FINRISK 2002 cohort.
Pärnänen K, Ruuskanen M, Sommeria-Klein G, Laitinen V, Kantanen P, Méric G, Volpiano CG, Inouye M, Knight R, Salomaa V, Havulinna AS, Niiranen T, Lahti L.
Nature Communications, 01 July 2025.
DOI: 10.1038/s41467-025-61137-x

Associations of alcohol with the human gut microbiome and prospective health outcomes in the FINRISK 2002 cohort.
Koponen K, McDonald D, Jousilahti P, Meric G, Inouye M, Lahti L, Niiranen T, Männistö S, Havulinna A, Knight R, Salomaa V.
European Journal of Nutrition, 11 April 2025.
DOI: 10.1007/s00394-025-03668-z

Deep learning for polygenic prediction: The role of heritability, interaction type and sample size.
Grealey J, Abraham G, Méric G, Cánovas R, Kelemen M, Teo SM, Salim A, Inouye M*, Xu Y*.
medRxiv, 27 October 2024.
DOI: 10.1101/2024.10.25.24316156

Associations of plant-based foods, red and processed meat, and dairy with gut microbiome in Finnish adults.
Maukonen M, Koponen KK, Havulinna AS, Kaartinen NE, Niiranen T, Meric G, Pajari A-M, Knight R, Salomaa V, Männistö S.
European Journal of Nutrition, 16 May 2024.
DOI: 10.1007/s00394-024-03406-x

Integration of polygenic and gut metagenomic risk prediction for common diseases.
Liu Y, Ritchie SC, Teo SM, Ruuskanen MO, Kambur O, Zhu Q, Sanders J, Vazquez-Baeza Y, Verspoor KM, Jousilahti P, Lahti L, Niiranen T, Salomaa V, Havulinna A, Knight R, Méric G, Inouye M.
Nature Aging, 25 March 2024.
DOI: 10.1038/s43587-024-00590-7
Additional content: Baker press release, ASU press release

Exploring the effects of antimicrobial treatment on the gut and oral microbiomes and resistomes from elderly long-term care facility residents via shotgun DNA sequencing.
Kitamura N, Kajihara T, Volpiano CG, Naung M, Méric G, Hirabayashi A, Yano H, Yamamoto M, Yoshida F, Kobayashi T, Yamanashi S, Kawamura T, Matsunaga N, Okochi J, Sugai M, Yahara K.
Microbial Genomics, 01 February 2024.
DOI: 10.1099/mgen.0.001180

Harnessing human microbiomes for disease prediction.
Liu Y, Fachrul M, Inouye M, Méric G.
Trends in Microbiology, 20 January 2024.
DOI: 10.1016/j.tim.2023.12.004

Role of gut microbiota in statin-associated new-onset diabetes – a cross-sectional and prospective analysis of the FINRISK 2002 cohort.
Koponen K, Kambur O, Joseph B, Ruuskanen MO, Jousilahti P, Salido R, Sanders K, Brennan C, Humphrey G, Sanders J, Jain M, Méric G, Inouye M, Lahti L, Niiranen T, Havulinna AS, Knight R, Salomaa V.
Arteriosclerosis, Thrombosis, and Vascular Biology, 16 November 2023.
DOI: 10.1161/atvbaha.123.319458
Additional content: Editorial commentary.

Guidelines for microbiome studies in renal physiology.
Muralitharan R*, Snelson M*, Méric G, Coughlan MT, Marques FZ
American Journal of Physiology-Renal Physiology, 13 July 2023.
DOI: 10.1152/ajprenal.00072.2023

The gut microbiome and hypertension.
O’Donnell JA, Zheng T, Méric G, Marques FZ
Nature Reviews Nephrology, 11 January 2023.
DOI: 10.1038/s41581-022-00654-0

The gut microbiome is a significant risk factor for future chronic lung disease.
Liu Y, Teo SM, Méric G, Tang HHF, Zhu Q, Sanders JG, Vazquez-Baeza Y, Verspoor K, Vartiainen VA, Jousilahti P, Lahti L, Niiranen T, Havulinna AS, Knight R, Salomaa V, Inouye M.
Journal of Allergy and Clinical Immunology, 29 December 2022.
DOI: 10.1016/j.jaci.2022.12.810

Assessing and removing the effect of unwanted technical variations in microbiome data.
Fachrul M, Méric G, Inouye M, Pamp SJ, Salim A.
Scientific Reports, 23 December 2022.
DOI: 10.1101/2021.05.21.445058
Additional content: Twitter/X thread, 2021 bioRxiv preprint.

Genetic diversity and variation in antimicrobial-resistance determinants of non-serotype 2 Streptococcus suis isolates from healthy pigs.
Kittiwan N, Calland JK, Mourkas E, Hitchings MD, Murray S, Tadee P, Tadee P, Duangsonk K, Méric G, Sheppard SK, Patchanee P, Pascoe B
Microbial Genomics, 01 November 2022.
DOI: 10.1099/mgen.0.000882

A two-hit epistasis model prevents core genome disharmony in recombining bacteria.
Taylor AJ*, Meric G*, Yahara K, Pascoe B, Mageiros L, Mourkas E, Calland JK, Puranen S, Hitchings MD, Jolley KA, Kabros CM, Williams NJ, van Vliet AHM, Parkhill J, Maiden MCJ, Corander J, Hurst LD, Falush D, Didelot X, Kelly DJ, Sheppard SK.
bioRxiv, 10 May 2022.
DOI: 10.1101/2021.03.15.435406

Spatiotemporal investigation of antibiotic resistance in the urban water cycle influenced by environmental and anthropogenic activity.
Tucker K, Mageiros L, Carstens A, Bröcker L, Archer E, Smith K, Mourkas E, Pascoe B, Nel D, Méric G, Sheppard SK, Kasprzyk-Hordern B, Botes M, Feil EJ, Wolfaardt G
Microbiology Spectrum, 29 August 2022.
DOI: 10.1128/spectrum.02473-22

Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy.
Zhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Balda-Ferre P, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Kim HC, Jain M, Inouye M, Gilbert JA, Knight R.
mSystems, 04 April 2022.
DOI: 10.1128/msystems.00167-22
Additional content: 2021 bioRxiv preprint, Twitter/X thread, press coverage.

Gut microbiome composition is predictive of incident type 2 diabetes in a population cohort of 5,572 Finnish adults.
Ruuskanen MO, Erawijantari PP, Havulinna AS, Liu Y, Méric G, Tuomilehto J, Inouye M, Jousilahti P, Salomaa V, Jain M, Knight R, Lahti L, Niiranen TJ.
Diabetes Care, 01 April 2022.
DOI: 10.2337/dc21-2358
Additional content: 2021 medRxiv preprint

Early prediction of liver disease using conventional risk factors and gut microbiome-augmented gradient boosting.
Liu Y, Méric G, Havulinna AS, Teo SM, Ruuskanen M, Sanders J, Zhu Q, Tripathi A, Verspoor K, Cheng S, Jain M, Jousilahti P, Vazquez-Baeza Y, Loomba R, Lahti L, Niiranen T, Salomaa V, Knight R, Inouye M.
Cell Metabolism, 29 March 2022.
DOI: 10.1016/j.cmet.2022.03.002
Additional content: Baker press release, 2020 medRxiv preprint

The carbon footprint of bioinformatics.
Grealey JG*, Lannelongue L*, Saw W-Y, Marten J, Méric G, Ruiz-Carmona S, Inouye M.
Molecular Biology and Evolution, 01 March 2022.
DOI: 10.1093/molbev/msac034
Additional content: Twitter/X thread, Green Algorithms website.
Impact on policy: Scottish Government (2023), Canadian Institut National d’Excellence en Santé et en Services Sociaux (INESSS) (2025)

Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter.
Mourkas E, Yahara K, Bayliss SC, Calland JK, Johansson H, Mageiros L, Munoz-Ramirez Y, Futcher G, Méric G, Hitchings MD, Sandoval-Motta S, Torres J, Jolley KA, Maiden MCJ, Ellstrom P, Waldenstrom J, Pascoe B, Sheppard SK.
eLife, 22 February 2022.
DOI: 10.1101/2021.08.24.457495
Additional content: 2021 bioRxiv preprint

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort.
Qin Y, Havulinna AS, Liu Y, Jousilahti P, Ritchie SC, Tokolyi A, Sanders JG, Valsta L, Brozynska M, Zhu Q, Tripathi A, Vazquez-Baeza Y, Loomba R, Cheng S, Jain M, Niiranen T, Lahti L, Knight R, Salomaa V, Inouye M*, Méric G*.
Nature Genetics, 03 February 2022.
DOI: 10.1038/s41588-021-00991-z
Additional content: Nature Genetics issue cover, GWAS Catalog, 2020 medRxiv preprint, Baker press release, press coverage 1 (Science), 2 (French), 3 (German), 4 (French), 5 (French), 6 (Finnish)
Impact on policy: US CDC (2022)

High-resolution sweep metagenomics using fast probabilistic inference.
Mäklin T, Kallonen T, David S, Boinett CJ, Pascoe B, Méric G, Aanensen DM, Feil EJ, Baker S, Parkhill J, Sheppard SK, Corander J, Honkela A.
Wellcome Open Research, 08 October 2021.
DOI: 10.12688/wellcomeopenres.15639.2
Additional content: mSWEEP github, 2018 bioRxiv preprint

Trycycler: consensus long-read assemblies for bacterial genomes.
Wick RR, Judd LM, Cerdeira LT, Hawkey J, Méric G, Vezina B, Wyres KL, Holt KE.
Genome Biology, 14 September 2021.
DOI: 10.1101/2021.07.04.451066
Additional content: Trycycler github, Twitter/X thread.

Efficient computation of Faith’s phylogenetic diversity with applications in characterizing microbiomes.
Armstrong GW, Cantrell K, Huang S, McDonald D, Haiminen N, Carrieri AP, Zhu Q, Gonzalez A, McGrath I, Beck K, Hakim D, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Jain M, Inouye M, Swafford AD, Kim HC, Parida L, Vàzquez-Baeza Y, Knight R.
Genome Research, 03 September 2021.
DOI: 10.1101/gr.275777.121

Associations of healthy food choices with gut microbiome profiles.
Koponen K, Salosensaari A, Ruuskanen M, Havulinna AS, Männistö S, Jousilahti P, Palmu J, Salido R, Sanders K, Brennan C, Humphrey G, Sanders J, Méric G, Cheng S, Inouye M, Jain M, Niiranen T, Valsta L, Knight R, Salomaa V.
The American Journal of Clinical Nutrition, 01 August 2021.
DOI: 10.1093/ajcn/nqab077
Additional content: AJCN editorial.
Impact on policy: Federal Food Safety and Veterinary Office from Government of Switzerland, 2020 and 2021.

Taxonomic signatures of long-term mortality risk in human gut microbiota.
Salosensaari A*, Laitinen V*, Havulinna AS, Méric G, Cheng S, Perola M, Valsta L, Alfthan G, Inouye M, Watrous JD, Long T, Salido R, Sanders K, Brennan C, Humphrey GC, Sanders JG, Jain M, Jousilahti P, Salomaa V, Knight R, Lahti L*, Niiranen T*.
Nature Communications, 11 May 2021.
DOI: 10.1038/s41467-021-22962-y
Additional content: Press coverage, EGA repository, 2020 medRxiv preprint.

Genome evolution and the emergence of pathogenicity in avian Escherichia coli.
Mageiros L, Méric G, Bayliss SC, Pensar J, Pascoe B, Mourkas E, Calland JK, Yahara K, Murray S, Hitchings MD, Elvidge J, Kemmett K, Feil E, Jolley KA, Williams NJ, Corander J, Sheppard SK.
Nature Communications, 03 February 2021.
DOI: 10.1038/s41467-021-20988-w
Additional content: NCBI Bioproject, Figshare.
Impact on policy: Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), 2024.

Links between gut microbiome composition and fatty liver disease in large population sample.
Ruuskanen MO, Åberg F, Männistö V, Havulinna AS, Méric G, Liu Y, Loomba R, Vázquez-Baeza Y, Tripathi A, Valsta LM, Inouye M, Jousilahti P, Salomaa V, Jain M, Knight R, Lahti L, Niiranen TJ.
Gut Microbes, 01 January 2021.
DOI: 10.1080/19490976.2021.1888673
Additional content: Twitter thread, 2020 medRxiv preprint.

Genomic epidemiology of Campylobacter jejuni associated with asymptomatic paediatric infection in the Peruvian Amazon.
Pascoe B, Schiaffino F, Murray S, Méric G, Bayliss SC, Hitchings MD, Mourkas E, Calland JK, Burga R, Yori PP, Jolley KA, Cooper K, Parker CT, Olortegui MP, Kosek MN, Sheppard SK.
Plos Neglected Tropical Diseases, 10 August 2020.
DOI: 10.1371/journal.pntd.0008533
Additional content: 2020 medRxiv preprint.

Genome-wide association and Mendelian randomisation analysis prioritises bioactive metabolites with putative causal effects on common diseases.
Qin Y, Méric G, Long T, Watrous JD, Burgess S, Havulinna AS, Ritchie SC, Brozynska M, Jousilahti P, Perola M, Lahti L, Niiranen T, Cheng S, Salomaa V, Jain M, Inouye M.
medRxiv, 04 August 2020.
DOI: 10.1101/2020.08.01.20166413 .

Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni.
Mourkas E, Taylor AJ, Méric G, Bayliss SC, Pascoe B, Mageiros L, Calland JK, Hitchings MD, Ridley A, Vidal A, Forbes KJ, Strachan NJC, Parker CT, Parkhill J, Jolley KA, Cody AJ, Maiden MCJ, Kelly DJ*, Sheppard SK* .
PNAS, 04 May 2020.
DOI: 10.1073/pnas.1917168117
Additional content: NCBI Bioproject, figshare, press release.
Impact on policy: EU Parliement, 2020.

Distinct phenotypic and genomic signatures underlie contrasting pathogenic potential of Staphylococcus epidermidis clonal lineages.
Espadinha D, Sobral R, Mendes C, Méric G, Sheppard SK, Carrico J, de Lencastre H, Miragaia M.
Frontiers in Microbiology, 27 August 2019.
DOI: 10.3389/fmicb.2019.01971
Additional content: NCBI Bioproject.

Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease.
Mourkas E*, Florez-Cuadrado D*, Pascoe B, Calland JK, Bayliss SC, Mageiros L, Méric G, Hitchings MD, Ugarte-Ruiz M, Dominguez L, Sheppard SK.
Environmental Microbiology, 27 August 2019.
DOI: 10.3389/fmicb.2019.01971
Additional content: NCBI Bioproject.

Correcting index databases improves metagenomic studies.
Méric G*, Wick RR*, Watts SC, Holt KE, Inouye M.
bioRxiv, 23 July 2019.
DOI: 10.1101/712166 .
Additional content: Twitter/X thread, github, figshare.

Domestication of Campylobacter jejuni NCTC 11168.
Pascoe B*, Williams LK*, Calland JK, Méric G, Hitchings MD, Dyer M, Ryder J, Allan E, Vidal A, Fearnley C, Everest P, Linton D, Pachebat JA, Cogan TA, Stevens MP, Wilkinson TS, Humphrey TJ, Cody AJ, Colles FM, Jolley KA, Maiden MCJ, Forbes K, Strachan N, Pearson BM, Wren BW, Parkhill J, Kelly DJ, van Vliet AH, Sheppard SK.
Environmental Microbiology, 16 July 2019.
DOI: 10.1099/mgen.0.000279
Additional content: NCBI Bioproject, ENA repository, microreact tree, figshare.

Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis.
Méric G*, Mageiros L*, Pensar J, Laabei M, Yahara K, Pascoe B, Kittiwan N, Tadee P, Post V, Lamble S, Bowden R, Bray JE, Morgenstern M, Jolley KA, Maiden MCJ, Feil EJ, Didelot X, Miragaia M, de Lencastre H, Moriarty TF, Rohde H, Massey R, Mack D, Corander J, Sheppard SK.
Nature Communications, 28 November 2018.
DOI: 10.1038/s41467-018-07368-7
Additional content: NCBI Bioproject, github, press release.

A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk.
Berthenet E, Yahara K, Thorell K, Pascoe B, Méric G, Mikhail J, Engstrand L, Enroth H, Burette A, Megraud F, Atherton J, Smith S, Wilkinson TS, Hitchings MD, Falush D, Sheppard SK.
BMC Biology, 02 August 2018.
DOI: 10.1186/s12915-018-0550-3
Additional content: NCBI Bioproject, figshare.

Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA.
Yokohama M, Laabei M, Stevens E, Bacon L, Heesom K, Bayliss S, Ooi N, O’Neill AJ, Murray E, Williams P, Lubben A, Reeksting S, Méric G, Pascoe B, Sheppard SK, Recker M, Hurst LD, Massey RC.
Genome Biology, 18 July 2018.
DOI: 10.1186/s13059-018-1469-2
Additional content: NCBI Bioproject, figshare, 2017 bioRxiv preprint.

Ruminant and chicken: important sources of campylobacteriosis in France despite a variation of source attribution in 2009 and 2015.
Thépault A, Rose V, Quesne S, Poezevara T, Béven V, Hirchaud E, Touzain F, Lucas P, Méric G, Mageiros L, Sheppard SK, Chemaly M, Rivoal K.
Scientific Reports, 18 June 2018.
DOI: 10.1038/s41598-018-27558-z
Impact on policy: European eCDC, 2024.

Lineage-specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group.
Méric G, Mageiros L, Pascoe B, Mourkas E, Lamble S, Bowden R, Jolley KA, Raymond B, Sheppard SK.
Molecular Ecology, 02 April 2018.
DOI: 10.1111/mec.14546
Additional content: NCBI Bioproject.
Impact on policy: European Food Safety Authority (2025).

The potential of isolation source to predict colonization in avian hosts: a case study in Campylobacter jejuni strains from three bird species.
Thépault A, Rose V, Quesne S, Poezevara T, Béven V, Hirchaud E, Touzain F, Lucas P, Méric G, Mageiros L, Sheppard SK, Chemaly M, Rivoal K.
Frontiers in Microbiology, 29 March 2018.
DOI: 10.3389/fmicb.2018.00591.

Convergent amino acid signatures in paraphyletic Campylobacter jejuni sub-populations suggest human niche tropism.
Méric G, McNally A, Pessia A, Mourkas E, Pascoe B, Mageiros L, Vehkala M, Corander J, Sheppard SK.
Genome Biology and Evolution, 01 March 2018.
DOI: 10.1093/gbe/evy026

Comparative genomic survey of Bacillus cereus sensu stricto isolates from the dairy production chain in Brazil.
Rossi G, Silva HO, Aguilar EG, Pascoe B, Méric G, Mourkas E, Hitchings MD, Mathias LA, Ruiz VLA, Fukumasu H, Sheppard SK, Vical AMC.
FEMS Microbiology Letters, 01 February 2018.
DOI: 10.1093/femsle/fnx283

Molecular epidemiology and comparative genomics and typing of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease.
Kirk KF, Méric G, Nielsen HL, Pascoe B, Sheppard SK, Thorlacius-Ussing O, Nielsen H.
Scientific Reports, 30 January 2018.
DOI: 10.1038/s41598-018-20135-4
Additional content: NCBI Bioproject

Genome comparison of erythromycin resistant Campylobacter from turkeys identifies hosts and pathways for horizontal spread of erm(B) genes.
Florez-Cuadrado D, Ugarte-Ruiz M, Méric G, Quesada A, Porrero MC, Pascoe B, Sáez-Llorente JL, Orozco GL, Domínguez L, Sheppard SK.
Frontiers in Microbiology, 15 November 2017.
DOI: 10.3389/fmicb.2017.02240
Impact on policy: EU eCDC, 2023.

Genomic plasticity and rapid host switching can promote the evolution of generalism: a case study in the zoonotic pathogen Campylobacter.
Woodcock DJ, Krusche P, Strachan NJC, Forbes KJ, Cohan FM, Méric G, Sheppard SK.
Scientific Reports, 29 August 2017.
DOI: 10.1038/s41598-017-09483-9
Additional content: 2016 bioRxiv preprint

A comparative genomics study of Staphylococcus epidermidis from orthopedic device-related infections correlated with patient outcome.
Post V, Harris LG, Morgenstern M, Mageiros L, Hitchings MD, Méric G, Pascoe B, Sheppard SK, Richards RG, Moriarty TF.
Journal of Clinical Microbiology, 09 August 2017.
DOI: 10.1128/JCM.00881-17

Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations.
Pascoe B, Méric G, Yahara K, Wimalarathna H, Murray S, Hitchings MD, Sproston EL, Carrillo CD, Taboada EN, Cooper KK, Huynh S, Cody AJ, Jolley KA, Maiden MCJ, McCarthy ND, Didelot X, Parker C, Sheppard SK.
Molecular Ecology, 19 June 2017.
DOI: 10.1111/mec.14176
Additional content: 2016 PeerJ preprint.
Impact on policy: Sciensano (Belgium), 2018.

Recombination-mediated host-adaptation by avian Staphylococcus aureus.
Murray S*, Pascoe B*, Méric G, Mageiros L, Yahara K, Hitchings MD, Friedmann Y, Wilkinson TS, Gormley FJ, Mack D, Bray JE, Lamble S, Bowden R, Jolley KA, Maiden MCJ, Wendlandt S, Schwarz S, Corander J, Fitzgerald JR, Sheppard SK.
Genome Biology and Evolution, 01 April 2017.
DOI: 10.1093/gbe/evx037

Genome-wide identification of host-segregating epidemiological markers for source attribution in Campylobacter jejuni.
Thepault A, Méric G, Rivoal K, Pascoe B, Mageiros L, Touzain F, Rose V, Béven V, Chemaly M, Sheppard SK.
Applied and Environmental Microbiology, 17 March 2017.
DOI: 10.1128/AEM.03085-16
Impact on policy: European Food Safety Authority, 2021.

Identification and initial characterisation of a protein involved in Campylobacter jejuni cell shape.
Esson D, Gupta S, Bailey D, Wigley P, Wedley A, Mather AE, Méric G, Mastroeni P, Sheppard SK, Thomson NR, Parkhill J, Maskell DJ, Christie G, Grant AJ.
Microbial Pathogenesis, 25 January 2017.
DOI: 10.1016/j.micpath.2017.01.042

Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork.
Yahara K*, Méric G*, Taylor AJ, de Vries SP, Murray S, Pascoe B, Mageiros L, Torralbo A, Vidal A, Ridley A, Komukai S, Wimalarathna H, Cody AJ, Colles FM, McCarthy N, Harris D, Bray JE, Jolley KA, Maiden MC, Bentley SD, Parkhill J, Bayliss CD, Grant A, Maskell D, Didelot X, Kelly DJ, Sheppard SK.
Environmental Microbiology, 01 January 2017.
DOI: 10.1111/1462-2920.13628

Genomic variations leading to alterations in cell morphology of Campylobacter spp.
Esson D, Mather AE, Scanlan E, Gupta S, de Vries SP, Bailey D, Harris SR, McKinley TJ, Méric G, Berry SK, Mastroeni P, Sheppard SK, Christie G, Thomson NR, Parkhill J, Maskell D, Grant AJ.
Scientific Reports, 02 December 2016.
DOI: 10.1038/srep38303

Population-genomic insights into emergence, crop-adaptation, and dissemination of Pseudomonas syringae pathogens
Monteil CL, Yahara K, Studholme DJ, Mageiros L, Méric G, Swingle B, Morris CE, Vinatzer BA, Sheppard SK.
Microbial Genomics, 21 October 2016.
DOI: 10.1099/mgen.0.000089

Comparative genomics of Campylobacter fetus from reptiles and mammals reveals divergent evolution in host-associated lineages
Gilbert MJ, Miller WG, Yee E, Zomer A, van der Graaf-van Bloois L, Fitzgerald C, Forbes KJ, Méric G, Sheppard SK, Wagenaar JA, Duim B.
Genome Biology and Evolution, 02 July 2016.
DOI: 10.1093/gbe/evw146

From Escherich to the Escherichia coli genome.
Méric G, Hitchings MD, Pascoe B, Sheppard SK.
The Lancet Infectious Diseases, 01 June 2016.
DOI: 10.1016/S1473-3099(16)30066-4
Additional content: Supplementary online material.

Biofilm morphotypes and population structure among Staphylococcus epidermidis from commensal and clinical samples
Harris LG, Murray S, Pascoe B, Méric G, Mageiros L, Wilkinson TS, Jeeves R, Rohde H, Schwarz S, de Lencastre H, Miragaia M, Rolo J, Bowden R, Jolley KA, Maiden MC, Mack D, Sheppard SK.
Plos One, 15 March 2016.
DOI: 10.1371/journal.pone.0151240

The impact of host metapopulation structure on the population genetics of colonizing bacteria
Numminen E, Gutmann MU, Shubin M, Marttinen P, Méric G, van Schaik W, Coque TM, Baquero F, Willems RJ, Sheppard SK, Feil EJ, Hanage WP, Corander J.
Journal of Theoretical Biology, 23 February 2016.
DOI: 10.1016/j.jtbi.2016.02.019 Additional content: 2015 bioRxiv preprint.

Enhanced biofilm formation evolves from divergent genetic backgrounds in host generalist Campylobacter jejuni
Pascoe B, Méric G, Murray S, Yahara K, Mageiros L, Bowen R, Jones NH, Jeeves RE, Lappin-Scott HM, Asakura H, Sheppard SK.
Environmental Microbiology, 14 October 2015.
DOI: 10.1111/1462-2920.13051

Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections
Dearlove B, Cody A, Pascoe B, Méric G, Wilson D, Sheppard SK.
The ISME Journal, 25 August 2015.
DOI: 10.1038/ismej.2015.149
Impact on policy: French ANSES, 2017 and EFSA, 2019.

Draft genomes, phylogenetic reconstruction and comparative genomics of two novel cohabiting bacterial symbionts isolated from Frankliniella occidentalis
Facey PD, Méric G, Hitchings MD, Pachebat JA, Hegarty MJ, Chen X, Morgan LV, Hoeppner JE, Whitten MM, Kirk WD, Dyson PJ, Sheppard SK, Del Sol R.
Genome Biology and Evolution, 15 July 2015.
DOI: 10.1093/gbe/evv136

Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis
Méric G, Miragaia M, de Been M, Yahara K, Pascoe B, Mageiros L, Mikhail J, Harris LG, Wilkinson TS, Rolo J, Lamble S, Bray JE, Jolley KA, Hanage WP, Bowden R, Maiden MC, Mack D, de Lencastre H, Feil EJ, Corander J, Sheppard SK.
Genome Biology and Evolution, 16 April 2015.
DOI: 10.1093/gbe/evv066

Gene loss and lineage specific restriction-modification systems associated with niche differentiation in the Campylobacter jejuni Sequence Type 403 clonal complex
Morley L, McNally A, Paszkiewicz K, Corander J, Méric G, Sheppard SK, Blom J, Manning G.
Applied and Environmental Microbiology, 20 March 2015.
DOI: 10.1128/AEM.00546-15

Variation in siderophore biosynthetic gene distribution and production across environmental and faecal populations of Escherichia coli
Searle, LJ*, Méric G*, Porcelli I, Sheppard SK, Lucchini S.
Plos One, 10 March 2015.
DOI: 10.1371/journal.pone.0117906

Higher resistance of Campylobacter coli compared to Campylobacter jejuni at chicken slaughterhouse
Torralbo A, Borge C, Garcia-Bocanegra I, Méric G, Perea A, Carbonero A.
Comparative Immunology, Microbiology and Infectious Diseases, 06 March 2015.
DOI: 10.1016/j.cimid.2015.02.003
Impact on policy: EFSA, 2017 and EFSA, 2018.

Evidence of land-sea transfer of the zoonotic pathogen Campylobacter to a wildlife marine sentinel species
Baily JL, Méric G, Bayliss S, Foster G, Moss SE, Watson E, Pascoe B, Mikhail J, Pizzi R, Goldstone RJ, Smith DG, Willoughby K, Hall AJ, Sheppard SK*, Dagleish MP*.
Molecular Ecology, 31 December 2014.
DOI: 10.1111/mec.13001
Additional content: press release, media coverage 1, 2, 3, 4, 5, live radio interview.
Impact on policy: British Whale and Dolphin Conservation, 2016.

Cryptic ecology among host generalist Campylobacter jejuni in domestic animals
Sheppard SK, Cheng L, Méric G, de Haan CP, Llarena AK, Marttwinen P, Vidal A, Ridley A, Clifton-Hadley F, Connor TR, Strachan NJ, Forbes K, Colles FM, Jolley KA, Bentley SD, Maiden MC, Hänninen ML, Parkhill J, Hanage WP, Corander J.
Molecular Ecology, 25 April 2014.
DOI: 10.1111/mec.12742

A reference pan-genome approach to comparative bacterial genomics: identification of novel epidemiological markers in pathogenic Campylobacter
Méric G, Yahara K, Mageiros L, Pascoe B, Maiden MCJ, Jolley KA, Sheppard SK.
Plos One, 27 March 2014.
DOI: 10.1371/journal.pone.0092798

Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter
Sheppard SK, Didelot X, Méric G, Torralbo A, Jolley KA, Kelly DJ, Bentley SD, Maiden MCJ, Parkhill J, Falush D.
PNAS, 01 July 2013.
DOI: 10.1073/pnas.1305559110
Impact on policy: EFSA, 2017 and EFSA, 2019.

Progressive genome-wide introgression in agricultural Campylobacter coli
Sheppard SK, Didelot X, Jolley KA, Darling AE, Pascoe B, Méric G, Kelly DJ, Cody A, Colles FM, Strachan NJ, Ogden ID, Forbes K, French NP, Carter P, Miller WG, McCarthy ND, Owen R, Litrup E, Egholm M, Affourtit JP, Bentley SD, Parkhill J, Maiden MC, Falush D.
Molecular Ecology, 20 December 2012.
DOI: 10.1111/mec.12162
Impact on policy: EFSA, 2013.

Phylogenetic distribution of traits associated with plant colonization in Escherichia coli
Méric G, Kemsley EK, Falush D, Saggers EJ, Lucchini S.
Environmental Microbiology, 30 August 2012.
DOI: 10.1111/j.1462-2920.2012.02852.x
Additional content: media coverage 1, 2
Impact on policy: Health Canada/Government of Canada (2020).

Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli
Didelot X, Méric G, Falush D, Darling AE.
BMC Genomics, 19 June 2012.
DOI: 10.1186/1471-2164-13-256
Impact on policy: US National Research Council, 2014.

luxS-based quorum-sensing signaling affects biofilm formation in Streptococcus mutans
Huang Z, Méric G, Liu Z, Ma R, Tang Z, Lejeune P.
Journal of Molecular Microbiology and Biotechnology, 26 September 2008.
DOI: 10.1159/000159193