Recent publications
Article
Kimble, AD, Kiu, R, Aguilar, D, Barquero-Calvo, E, Hall, LJ & Rodríguez, C 2026, 'A longitudinal One Health genomic survey of Clostridium perfringens reveals extensive genomic diversity and novelty, frequent plasmid carriage, and source-structured resistome signatures', IJID One Health, vol. 11, 100123. https://doi.org/10.1016/j.ijidoh.2026.100123
Millar, ME, Abele, M, Harris, HC, Koev, TT, Telatin, A, Kiu, R, Van Sinderen, D, Khimyak, YZ, Ludwig, C, Hall, LJ & Warren, FJ 2026, 'Bifidobacterial genes upregulated by resistant starch investigated using multi-omics have orthologs in infant gut isolates', ISME Communications, vol. 6, no. 1, ycag136. https://doi.org/10.1093/ismeco/ycag136
Chapman, JA, Masi, AC, Beck, LC, Watson, H, Young, GR, Browne, HP, Shao, Y, Kiu, R, Nelson, A, Doyle, JA, Palmowski, P, Lengyel, M, Connolly, JPR, Lamb, CA, Porter, A, Lawley, TD, Hall, LJ, Embleton, ND, Perry, JD, Berrington, JE & Stewart, CJ 2026, 'Clostridia from preterm infants metabolize human milk oligosaccharides to suppress pathobionts and modulate intestinal function in organoids', Nature Microbiology, vol. 11, no. 4, pp. 940-959. https://doi.org/10.1038/s41564-026-02297-4
Trivett, H, Dalby, MJ, Peel, N, Heavens, D, Kiu, R, Acuna-Gonzalez, A, Mohamad, M, Humayun, G, Leggett, RM, Patel, VC & Hall, LJ 2026, 'Decoding the microbiome and resistome of advanced chronic liver disease through long-read metagenomics', Genome medicine. https://doi.org/10.1186/s13073-026-01724-9
Mijić, L, Shaheen, M, Chunga, A, Kiu, R & Hall, LJ 2026, 'Early-life Gut Microbiome Assembly in Low- and Middle-Income Countries: Interactions Between Undernutrition, Infection, and Environmental Enteric Dysfunction', Gut Microbiology. https://doi.org/10.1016/j.gutmic.2026.100020
Senoo, DKJ, Acton, L & Hall, LJ 2026, 'From diet to function: using synthetic microbial communities to map gut microbial interactions', npj Biofilms and Microbiomes, vol. 12, no. 1, 189. https://doi.org/10.1038/s41522-026-01012-9
Seki, D, Pollak, S, Kujawska, M, Kiu, R, Acuna-Gonzales, A, Crouch, LI, Bakshani, CR, Chivers, PT, Mommers, M, van Best, N, Penders, J & Hall, LJ 2026, 'Human milk oligosaccharide mediated mutualism between Escherichia coli and Bifidobacterium bifidum', Nature Communications, vol. 17, 3489. https://doi.org/10.1038/s41467-026-71764-7
Otiti, MI, June, M, K'Oloo, A, Chomba, M, Dodd, J, Luo, Y, Kiu, R, Hall, L, Wang, D, Otieno, K, Kariuki, S, ter Kuile, FO & Allen, S 2026, 'Pro/synbiotics reduce systemic inflammation and improve gut health in Kenyan infants: An open label, randomized, 4-arm, phase II trial', Cell Reports Medicine, vol. 7, no. 6, 102834. https://doi.org/10.1016/j.xcrm.2026.102834
Alexander, JL, Mullish, BH, Thomas, L, Weersma, RK, Sokol, H, Roberts, LA, Edwards, LA, Emmanuel, A, Gerasimidis, K, Hall, LJ, Iqbal, TH, Kinross, JM, McIlroy, J, Monaghan, TM, Sergaki, C, Shawcross, DL, Stewart, CJ, Lamb, CA, Williams, HRT, Hansen, R & Hold, G 2026, 'Recent advances in our understanding of the gut microbiome: an analysis from the Gut Microbiota for Health Expert Panel of the British Society of Gastroenterology', Gut. https://doi.org/10.1136/gutjnl-2026-338252
Price, CA, Jones, EJ, Ilker, N, Nicklin, AD, Juodeikis, R, McKee, AM, Mitchell, LJ, Stentz, R, Hall, LJ, Carding, SR, Robinson, SD & Claesen, J (ed.) 2026, 'Systemically delivered Bacteroides thetaiotaomicron-derived bacterial extracellular vesicles inhibit primary and metastatic melanoma growth', Microbiology spectrum. https://doi.org/10.1128/spectrum.02512-26
Shimpo, A, Augustine, J, Acton, LJ, Hall, LJ & Chivers, P 2026, 'The metal-uptake-deficient Escherichia coli strain GR536 contains the ϕ80 prophage', Access Microbiology, vol. 8, no. 8, 001204.v3. https://doi.org/10.1099/acmi.0.001204.v3
Comment/debate
Valderrama, B, Morais, LH, Lavelle, A, Hemmings, SMJ, Hall, LJ, Merali, Z, Clarke, G & Cryan, JF 2026, 'Global mental health benefits from expanding microbiome–gut–brain axis research to the global south', Nature Mental Health, vol. 4, no. 8, pp. 1207-1215. https://doi.org/10.1038/s44220-026-00690-w
Review article
Whelan, FJ & Hall, LJ 2026, 'An ode to the 16S rRNA gene: its history, importance, caveats and future in microbiome research', Microbial Genomics, vol. 12, no. 8, 001823. https://doi.org/10.1099/mgen.0.001823
Tarracchini, C, Milani, C, Jones, CNL, Turroni, F, Burgess, G, Mahony, J, Hall, LJ, Ventura, M & van Sinderen, D 2026, 'Bifidobacteria: biogeography, host adaptation and ecological functions', Nature Reviews Microbiology. https://doi.org/10.1038/s41579-026-01367-y
Theodosiou, A, Bogaert, D, Cleary, D, Fady, P-E, Feehily, C, Gilbert, J, Greenhough, B, Guardabassi, L, Hall, L, Harman, T, Kuijper, E, Lebeer, S, Lorimer, J, Spector, T & Jones, C 2026, 'Microbiome research in practice: priorities for clinical translation and impact', Clinical Microbiology and Infection. https://doi.org/10.1016/j.cmi.2026.01.021
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