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
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
Metris, A, Walker, AW, Showering, A, Doolan, A, McBain, AJ, Ampatzoglou, A, Murphy, B, O'Neill, C, Shortt, C, Darby, EM, Aldis, G, Hillebrand, GG, Brown, HL, Browne, HP, Tiesman, JP, Leng, J, Lahti, L, Jakubovics, NS, Hasselwander, O, Finn, RD, Klamert, S, Korcsmaros, T & Hall, LJ 2025, 'Assessing the safety of microbiome perturbations', Microbial Genomics, vol. 11, no. 5, 001405. https://doi.org/10.1099/mgen.0.001405
Jain, V, Nulty, J, Alexander, EC, Burford, C, Davenport, M, Chokshi, S, Riva, A, Dalby, MJ, Verma, A, Hall, LJ, Yuksel, M & Dhawan, A 2025, 'Claudin-3, Lipopolysaccharide Binding Protein, and Jaundice Clearance in Infants with Biliary Atresia', Journal of Pediatrics, vol. 286, 114703. https://doi.org/10.1016/j.jpeds.2025.114703
Saeed, MH, Kujawska, M, Ellen, K, Acuna-Gonzalez, A, Bernabeu Lorenzo, M, Carmen Collado, M, Mommers, M, van Best, N, Hall, LJ & Neuhaus, K 2025, 'Comprehensive analysis of Enterococcus spp. from two European healthy infant cohorts shows stable genomic traits including antimicrobial resistance (AMR)', Gut Microbes, vol. 17, no. 1, 2516699. https://doi.org/10.1080/19490976.2025.2516699
Docherty, JAD, Cook, R, Kiu, R, Dyball, X, Brown, TL, Kujawska, M, Smith, R, Phillips, S, Watt, R, Telatin, A, Tiwari, SK, Hall, LJ & Adriaenssens, EM 2025, 'Diverse defense systems and prophages in human-associated Bifidobacterium species reveal coevolutionary “arms race” dynamics', Cell Reports, vol. 44, no. 11, 116542. https://doi.org/10.1016/j.celrep.2025.116542
Kaktcham, PM, Kujawska, M, Kouam, EMF, Piame, LT, Tientcheu, MLT, Felsl, A, Truppel, B-A, Ngoufack, FZ & Hall, LJ 2025, 'Genomic insights into the beneficial potential of Bifidobacterium and Enterococcus strains isolated from Cameroonian infants', Microbial Genomics, vol. 11, no. 2, 001354. https://doi.org/10.1099/mgen.0.001354
Kujawska, M, Seki, D, Chalklen, L, Malsom, J, Kiu, R, Goatcher, S, Christoforou, I, Mitra, S, Crouch, L & Hall, LJ 2025, 'Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts', Cell Host and Microbe, vol. 33, no. 9, pp. 1502-1517.e13. https://doi.org/10.1016/j.chom.2025.08.008
Samarra, A, Renwick, S, Arzamasov, AA, Rodionov, DA, Spann, K, Cabrera-Rubio, R, Acuna-Gonzalez, A, Martínez-Costa, C, Hall, L, Segata, N, Osterman, AL, Bode, L & Collado, MC 2025, 'Human milk oligosaccharide metabolism and antibiotic resistance in early gut colonizers: insights from bifidobacteria and lactobacilli in the maternal-infant microbiome', Gut Microbes, vol. 17, no. 1, 2501192. https://doi.org/10.1080/19490976.2025.2501192
Letter
Jain, V, Alexander, EC, Burford, C, Davenport, M, Dalby, MJ, Hall, LJ & Dhawan, A 2025, 'Ethanol in biliary atresia', Archives of Disease in Childhood. https://doi.org/10.1136/archdischild-2024-328338
Review article
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
Mudhluli, TE, Mashingaidze-Mano, R, Chitsike, I, Manasa, J, Hall, LJ, Gomo, E & Zhou, DT 2025, 'Gut microbiota of sub-Saharan Africa infants exposed to antiretroviral therapy: Scoping review', African journal of primary health care & family medicine, vol. 17, no. 1, a4939. https://doi.org/10.4102/phcfm.v17i1.4939
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