Items where Author is "Hall, Lindsay"

Published

Lopez-Tello, Jorge, Kiu, Raymond, Schofield, Zoe, Zhang, Cindy X. W., van Sinderen, Douwe, Le Gall, Gwénaëlle ORCID: https://orcid.org/0000-0002-1379-2196, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Sferruzzi-Perri, Amanda N. (2024) Maternal gut Bifidobacterium breve modifies fetal brain metabolism in germ-free mice. Molecular Metabolism, 88. ISSN 2212-8778

Kujawska, Magdalena, Neuhaus, Klaus, Huptas, Christopher, Jiménez, Esther, Arboleya, Silvia, Schaubeck, Monika and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2024) Exploring the potential probiotic properties of Bifidobacterium breve DSM 32583—A novel strain isolated from human milk. Probiotics and Antimicrobial Proteins. ISSN 1867-1306

Dalby, Matthew J., Kiu, Raymond, Serghiou, Iliana R., Miyazaki, Asuka, Acford-Palmer, Holly, Tung, Rathavy, Caim, Shabhonam, Phillips, Sarah, Kujawska, Magdalena, Matsui, Mitsuaki, Iwamoto, Azusa, Taking, Bunsreng, Cox, Sharon E. and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2024) Faecal microbiota and cytokine profiles of rural Cambodian infants linked to diet and diarrhoeal episodes. npj Biofilms and Microbiomes, 10. ISSN 2055-5008

Mudhluli, Taona Emmah, Kujawska, Magdalena, Mueller, Julia, Felsl, Angela, Truppel, Bastian-Alexander, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Chitsike, Inam, Gomo, Exnevia and Zhou, Danai Tavonga (2024) Exploring the genomic traits of infant-associated microbiota members from a Zimbabwean cohort. BMC Genomics, 25. ISSN 1471-2164

Gooch, Harriet C. C., Labedan, Marjorie, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Maxwell, Anthony (2024) Transplanting human infant gut microbiome species into Galleria mellonella. BMC Research Notes, 17. ISSN 1756-0500

Camargo, Anny, Ramírez, Juan David, Kiu, Raymond, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Muñoz, Marina (2024) Unveiling the pathogenic mechanisms of Clostridium perfringens toxins and virulence factors. Emerging Microbes and Infections, 13 (1). ISSN 2222-1751

Kadia, Benjamin Momo, Otiti, Mary Iwaret, Ramsteijn, Anouschka, Sow, Doudou, Faye, Babacar, Heffernan, Claire, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Webster, Joanne P., Walker, Alan W. and Allen, Stephen (2024) Modulating the early-life gut microbiota using pro-, pre-, and synbiotics to improve gut health, child development, and growth. Nutrition Reviews, 82 (2). pp. 244-247. ISSN 0029-6643

Kujawska, Magdalena, Schaubeck, Monika, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Neuhaus, Klaus (2023) Draft genome sequence of Bifidobacterium breve DSM 32583, isolated from human milk. Microbiology Resource Announcements, 12 (11). ISSN 2576-098X

Serghiou, Iliana R., Webber, Mark A. and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2023) An update on the current understanding of the infant skin microbiome and research challenges. Current Opinion in Microbiology, 75. ISSN 1369-5274

Elek, Claire K. A., Brown, Teagan L., Viet, Thanh Le, Evans, Rhiannon, Baker, David J., Telatin, Andrea, Tiwari, Sumeet K., Al-Khanaq, Haider, Thilliez, Gaëtan, Kingsley, Robert A. ORCID: https://orcid.org/0000-0002-0194-6485, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Webber, Mark A. and Adriaenssens, Evelien M. (2023) A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses. Microbial Genomics, 9 (7). ISSN 2057-5858

Serghiou, Iliana R., Baker, Dave, Evans, Rhiannon, Dalby, Matthew J., Kiu, Raymond, Trampari, Eleftheria, Phillips, Sarah, Watt, Rachel, Atkinson, Thomas, Murphy, Barry, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Webber, Mark A. (2023) An efficient method for high molecular weight bacterial DNA extraction suitable for shotgun metagenomics from skin swabs. Microbial Genomics, 9 (7). ISSN 2057-5858

Teng, Nancy M. Y., Kiu, Raymond, Evans, Rhiannon, Baker, David J., Zenner, Christian, Robinson, Stephen D. ORCID: https://orcid.org/0000-0002-6606-7588 and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2023) Allocoprobacillus halotolerans gen. nov., sp. nov and Coprobacter tertius sp. nov., isolated from human gut microbiota. International Journal of Systematic and Evolutionary Microbiology, 73 (7). ISSN 1466-5026

Kiu, Raymond, Shaw, Alexander G., Sim, Kathleen, Acuna-Gonzalez, Antia, Price, Christopher A., Bedwell, Harley, Dreger, Sally A., Fowler, Wesley J., Cornwell, Emma, Pickard, Derek, Belteki, Gusztav, Malsom, Jennifer, Phillips, Sarah, Young, Gregory R., Schofield, Zoe, Alcon-Giner, Cristina, Berrington, Janet E., Stewart, Christopher J., Dougan, Gordon, Clarke, Paul ORCID: https://orcid.org/0000-0001-6203-7632, Douce, Gillian, Robinson, Stephen D. ORCID: https://orcid.org/0000-0002-6606-7588, Kroll, J. Simon and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2023) Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains. Nature Microbiology, 8 (6). pp. 1160-1175. ISSN 2058-5276

Acuna-Gonzalez, Antia, Kujawska, Magdalena, Youssif, Mayada, Atkinson, Thomas, Grundy, Sara, Hutchison, Alexandra, Tremlett, Catherine, Clarke, Paul ORCID: https://orcid.org/0000-0001-6203-7632 and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2023) Bifidobacterium bacteraemia is rare with routine probiotics use in preterm infants: A further case report with literature review. Anaerobe, 80. ISSN 1075-9964

Seki, David, Errerd, Theresa and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2023) The role of human milk fats in shaping neonatal development and the early life gut microbiota. Microbiome Research Reports, 2 (2). ISSN 2771-5965

Neumann, Charlotte J., Mahnert, Alexander, Kumpitsch, Christina, Kiu, Raymond, Dalby, Matthew J., Kujawska, Magdalena, Madl, Tobias, Kurath-Koller, Stefan, Urlesberger, Berndt, Resch, Bernhard, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Moissl-Eichinger, Christine (2023) Clinical NEC prevention practices drive different microbiome profiles and functional responses in the preterm intestine. Nature Communications, 14. ISSN 2041-1723

James, Steve A., Telatin, Andrea, Baker, David, Evans, Rhiannon, Clarke, Paul ORCID: https://orcid.org/0000-0001-6203-7632, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Carding, Simon R. (2023) Draft genome sequence of a preterm infant-derived isolate of Candida parapsilosis. Microbiology Resource Announcements, 12 (3). ISSN 2576-098X

Kennedy, Katherine M., de Goffau, Marcus C., Perez-Muñoz, Maria Elisa, Arrieta, Marie-Claire, Bäckhed, Fredrik, Bork, Peer, Braun, Thorsten, Bushman, Frederic D., Dore, Joel, de Vos, Willem M., Earl, Ashlee M., Eisen, Jonathan A., Elovitz, Michal A., Ganal-Vonarburg, Stephanie C., Gänzle, Michael G., Garrett, Wendy S., Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Hornef, Mathias W., Huttenhower, Curtis, Konnikova, Liza, Lebeer, Sarah, Macpherson, Andrew J., Massey, Ruth C., McHardy, Alice Carolyn, Koren, Omry, Lawley, Trevor D., Ley, Ruth E., O'Mahony, Liam, O'Toole, Paul W., Pamer, Eric G., Parkhill, Julian, Raes, Jeroen, Rattei, Thomas, Salonen, Anne, Segal, Eran, Segata, Nicola, Shanahan, Fergus, Sloboda, Deborah M., Smith, Gordon C. S., Sokol, Harry, Spector, Tim D., Surette, Michael G., Tannock, Gerald W., Walker, Alan W., Yassour, Moran and Walter, Jens (2023) Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature, 613 (7945). 639–649. ISSN 0028-0836

Roager, Henrik M., Stanton, Catherine and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2023) Microbial metabolites as modulators of the infant gut microbiome and host-microbial interactions in early life. Gut Microbes, 15 (1). ISSN 1949-0976

Saeed, Muhammad Hassan and Hall, Lindsay J ORCID: https://orcid.org/0000-0001-8938-5709 (2023) Early-life antibiotic usage and impact on the gut microbiota, including emergence of antimicrobial resistant Enterococcus. Microbiota and Host, 1 (1). ISSN 2753-6955

Zenner, Christian, Chalklen, Lisa, Adjei, Helena, Dalby, Matthew J., Mitra, Suparna, Cornwell, Emma, Shaw, Alexander G., Sim, Kathleen, Kroll, J. Simon and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2023) Non-invasive faecal cytokine and microbiome profiles predict commencement of necrotizing enterocolitis in a proof-of-concept study. Gastro Hep Advances, 2 (5). pp. 666-675. ISSN 2772-5723

Clarke, Paul ORCID: https://orcid.org/0000-0001-6203-7632, Shearer, Martin J., Card, David J., Nichols, Amy, Ponnusamy, Vennila, Mahaveer, Ajit, Voong, Kieran, Dockery, Karen, Holland, Nicky, Mulla, Shaveta, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Maassen, Cecile, Lux, Petra, Schurgers, Leon J. and Harrington, Dominic J. (2022) Exclusively breastmilk-fed preterm infants are at high risk of developing subclinical vitamin K deficiency despite intramuscular prophylaxis at birth. Journal of Thrombosis and Haemostasis, 20 (12). pp. 2773-2785. ISSN 1538-7933

Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Schirmer, Melanie (2022) Current state and future of the microbiome field: Why context matters. Current Opinion in Microbiology, 70. ISSN 1369-5274

Kujawska, Magdalena, Raulo, Aura, Millar, Molly, Warren, Fred, Baltrūnaitė, Laima, Knowles, Sarah C. L. and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2022) Bifidobacterium castoris strains isolated from wild mice show evidence of frequent host switching and diverse carbohydrate metabolism potential. ISME Communications, 2. ISSN 2730-6151

Hitch, Thomas C. A., Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Walsh, Sarah Kate, Leventhal, Gabriel E., Slack, Emma, de Wouters, Tomas, Walter, Jens and Clavel, Thomas (2022) Microbiome-based interventions to modulate gut ecology and the immune system. Mucosal Immunology, 15 (6). 1095–1113. ISSN 1933-0219

Tran, Hoang N. H., Thu, Trang Nguyen Hoang, Nguyen, Phu Huu, Vo, Chi Nguyen, Doan, Khanh Van, Nguyen Ngoc Minh, Chau, Nguyen, Ngoc Tuan, Ta, Van Ngoc Duc, Vu, Khuong An, Hua, Thanh Danh, Nguyen, To Nguyen Thi, Van, Tan Trinh, Pham Duc, Trung, Duong, Ba Lap, Nguyen, Phuc Minh, Hoang, Vinh Chuc, Pham, Duy Thanh, Thwaites, Guy E., Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Slade, Daniel J., Baker, Stephen, Tran, Vinh Hung and Chung The, Hao (2022) Tumour microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients. npj Biofilms and Microbiomes, 8. ISSN 2055-5008

Jordan, Anne, Carding, Simon R and Hall, Lindsay J ORCID: https://orcid.org/0000-0001-8938-5709 (2022) The early-life gut microbiome and vaccine efficacy. The Lancet Microbe, 3 (10). E787-E794. ISSN 2666-5247

Lopez-Tello, Jorge, Schofield, Zoe, Kiu, Raymond, Dalby, Matthew J., van Sinderen, Douwe, Le Gall, Gwenaelle ORCID: https://orcid.org/0000-0002-1379-2196, Sferruzzi-Perri, Amanda N. and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2022) Maternal gut microbiota Bifidobacterium promotes placental morphogenesis, nutrient transport and fetal growth in mice. Cellular and Molecular Life Sciences, 79 (7). ISSN 1420-682X

Scott, Nicholas A., Lawson, Melissa A. E., Hodgetts, Ryan James, Le Gall, Gwénaëlle ORCID: https://orcid.org/0000-0002-1379-2196, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Mann, Elizabeth R. (2022) Macrophage metabolism in the intestine is compartment specific and regulated by the microbiota. Immunology, 166 (1). pp. 138-152. ISSN 0019-2805

Brooks-Warburton, Johanne, Modos, Dezso, Sudhakar, Padhmanand, Madgwick, Matthew, Thomas, John P., Bohar, Balazs, Fazekas, David, Zoufir, Azedine, Kapuy, Orsolya, Szalay-Beko, Mate, Verstockt, Bram, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Watson, Alastair ORCID: https://orcid.org/0000-0003-3326-0426, Tremelling, Mark, Parkes, Miles, Vermeire, Severine, Bender, Andreas, Carding, Simon R. and Korcsmaros, Tamas (2022) A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis. Nature Communications, 13 (1). ISSN 2041-1723

Otiti, Mary Iwaret, Kariuki, Simon, Wang, Duolao, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Ter Kuile, Feiko O. and Allen, Stephen (2022) PRObiotics and SYNbiotics to improve gut health and growth in infants in western Kenya (PROSYNK Trial): Study protocol for a 4-arm, open-label, randomised, controlled trial. Trials, 23 (1). ISSN 1745-6215

Gooch, Harriet C. C., Kiu, Raymond, Rudder, Steven, Baker, David J., Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Maxwell, Anthony (2021) Enterococcus innesii sp. nov., isolated from the wax moth Galleria mellonella. International Journal of Systematic and Evolutionary Microbiology, 71 (12). ISSN 1466-5026

Nikolova, Viktoriya L., Smith, Megan R. B., Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Cleare, Anthony J., Stone, James M. and Young, Allan H. (2021) Perturbations in gut microbiota composition in psychiatric disorders: A review and meta-analysis. JAMA Psychiatry, 78 (12). pp. 1343-1354. ISSN 2168-622X

The, Hao Chung, Minh, Chau Nguyen Ngoc, Hong, Chau Tran Thi, Nguyen, To Nguyen Thi, Pike, Lindsay J., Zellmer, Caroline, Duc, Trung Pham, Tran, Tuan Anh, Thanh, Tuyen Ha, Van, Minh Pham, Thwaites, Guy E., Rabaa, Maia A., Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Baker, Stephen (2021) Exploring the genomic diversity and antimicrobial susceptibility of bifidobacterium pseudocatenulatum in a Vietnamese population. Microbiology Spectrum, 9 (2). ISSN 2165-0497

McKee, Alastair M., Kirkup, Benjamin M., Madgwick, Matthew, Fowler, Wesley J., Price, Christopher A., Dreger, Sally A., Ansorge, Rebecca, Makin, Kate A., Caim, Shabhonam, Le Gall, Gwenaelle ORCID: https://orcid.org/0000-0002-1379-2196, Paveley, Jack, Leclaire, Charlotte, Dalby, Matthew J., Alcon-Giner, Cristina, Andrusaite, Anna, Feng, Tzu-Yu, Di Modica, Martina, Triulzi, Tiziana, Tagliabue, Elda, Milling, Simon W. F., Weilbaecher, Katherine N., Rutkowski, Melanie R., Korcsmaros, Tamas, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Robinson, Stephen D. ORCID: https://orcid.org/0000-0002-6606-7588 (2021) Antibiotic-induced disturbances of the gut microbiota result in accelerated breast tumor growth. iScience, 24 (9). ISSN 2589-0042

Phillips, Sarah, Watt, Rachel, Atkinson, Thomas, Savva, George M., Hayhoe, Antonietta and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and PEARL study team (2021) The Pregnancy and EARly Life study (PEARL) - A longitudinal study to understand how gut microbes contribute to maintaining health during pregnancy and early life. BMC Pediatrics, 21 (1). ISSN 1471-2431

Teng, Nancy, Price, Christopher, Mckee, Alastair, Hall, Lindsay ORCID: https://orcid.org/0000-0001-8938-5709 and Robinson, Stephen ORCID: https://orcid.org/0000-0002-6606-7588 (2021) Exploring the impact of gut microbiota and diet on breast cancer risk and progression. International Journal of Cancer, 149 (3). pp. 494-504. ISSN 0020-7136

Shibu, Preetha, McCuaig, Frazer, McCartney, Anne L., Kujawska, Magdalena, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Hoyles, Lesley (2021) Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster. Microbial Genomics, 7 (6). ISSN 2057-5858

Henneke, Philipp, Kierdorf, Katrin, Hall, Lindsey ORCID: https://orcid.org/0000-0001-8938-5709, Sperandio, Markus and Hornef, Mathias (2021) Perinatal development of innate immune topology. eLife, 10. ISSN 2050-084X

Dalby, Matthew J. and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2021) Populating preterm infants with probiotics. Cell Reports Medicine, 2 (3). ISSN 2666-3791

Hall, Lindsay ORCID: https://orcid.org/0000-0001-8938-5709 and Robinson, Stephen ORCID: https://orcid.org/0000-0002-6606-7588 (2021) Bacterial strains augment cancer therapeutics. Nature Microbiology, 6 (3). pp. 275-276. ISSN 2058-5276

Osborne, Peter, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Kronfeld-Schor, Noga, Thybert, David and Haerty, Wilfried ORCID: https://orcid.org/0000-0003-0111-191X (2020) A rather dry subject; investigating the study of arid-associated microbial communities. Environmental Microbiomes, 15 (1). ISSN 2524-6372

James, Stephen A., Phillips, Sarah, Telatin, Andrea, Baker, David, Ansorge, Rebecca, Clarke, Paul ORCID: https://orcid.org/0000-0001-6203-7632, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Carding, Simon R. (2020) Preterm infants harbour a rapidly changing mycobiota that includes Candida pathobionts. Journal of Fungi, 6 (4). ISSN 2309-608X

Kujawska, Magdalena, Collado, Maria Carmen and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2020) Microbes, Human Milk, and Prebiotics. In: The Human Microbiome in Early Life. Elsevier, pp. 197-237. ISBN 9780128180976

Alcon-Giner, Cristina, Dalby, Matthew J., Caim, Shabhonam, Ketskemety, Jennifer, Shaw, Alex, Sim, Kathleen, Lawson, Melissa A. E., Kiu, Raymond, Leclaire, Charlotte, Chalklen, Lisa, Kujawska, Magdalena, Mitra, Suparna, Fardus-Reid, Fahmina, Belteki, Gustav, Mccoll, Katherine, Swann, Jonathan R., Kroll, J. Simon, Clarke, Paul ORCID: https://orcid.org/0000-0001-6203-7632 and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2020) Microbiota supplementation with Bifidobacterium and Lactobacillus modifies the preterm infant gut microbiota and metabolome: An observational study. Cell Reports Medicine, 1 (5). ISSN 2666-3791

Kujawska, Magdalena, La Rosa, Sabina Leanti, Roger, Laure C., Pope, Phillip B., Hoyles, Lesley, McCartney, Anne L. and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2020) Succession of Bifidobacterium longum strains in response to a changing early life nutritional environment reveals dietary substrate adaptations. iScience, 23 (8). ISSN 2589-0042

Kiu, Raymond, Treveil, Agatha, Harnisch, Lukas C., Caim, Shabhonam, Leclaire, Charlotte, van Sinderen, Douwe, Korcsmaros, Tamas and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2020) Bifidobacterium breve UCC2003 induces a distinct global transcriptomic programme in neonatal murine intestinal epithelial cells. iScience, 23 (7). ISSN 2589-0042

Robertson, Claire, Savva, George M., Clapuci, Raducu, Jones, Jacqueline, Maimouni, Hassan, Brown, Eleanor, Minocha, Ashish, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Clarke, Paul ORCID: https://orcid.org/0000-0001-6203-7632 (2020) Incidence of necrotising enterocolitis before and after introducing routine prophylactic Lactobacillus and Bifidobacterium probiotics. Archives of Disease in Childhood: Fetal and Neonatal Edition, 105 (4). pp. 380-386. ISSN 1359-2998

Chen, Yuhao, Brook, Thomas C., Soe, Cho Zin, O'Neill, Ian, Alcon-Giner, Cristina, Leelastwattanagul, Onnicha, Phillips, Sarah, Caim, Shabhonam, Clarke, Paul ORCID: https://orcid.org/0000-0001-6203-7632, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Hoyles, Lesley (2020) Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors. Microbial Genomics, 6 (6). ISSN 2057-5858

Dalby, Matthew J. and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2020) Recent advances in understanding the neonatal microbiome. F1000Research, 7. ISSN 2046-1402

Hughes, Kevin R., Schofield, Zoe, Dalby, Matthew J., Caim, Shabhonam, Chalklen, Lisa, Bernuzzi, Federico, Alcon-Giner, Cristina, Le Gall, Gwénaëlle ORCID: https://orcid.org/0000-0002-1379-2196, Watson, Alastair J.M. ORCID: https://orcid.org/0000-0003-3326-0426 and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2020) The early life microbiota protects neonatal mice from pathological small intestinal epithelial cell shedding. FASEB Journal, 34 (5). pp. 7075-7088. ISSN 0892-6638

Wade, Kaitlin H. and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2020) Improving causality in microbiome research: Can human genetic epidemiology help? Wellcome Open Research, 4.

Püngel, Deborah, Treveil, Agatha, Dalby, Matthew J., Caim, Shabhonam, Colquhoun, Ian J., Booth, Catherine, Ketskemety, Jennifer, Korcsmaros, Tamas, van Sinderen, Douwe, Lawson, Melissa A. E. and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2020) Bifidobacterium breve UCC2003 exopolysaccharide modulates the early life microbiota by acting as a potential dietary substrate. Nutrients, 12 (4). ISSN 2072-6643

Leggett, Richard M, Alcon-Giner, Cristina, Heavens, Darren, Caim, Shabhonam, Brook, Thomas C, Kujawska, Magdalena, Martin, Samuel, Peel, Ned, Acford-Palmer, Holly, Hoyles, Lesley, Clarke, Paul ORCID: https://orcid.org/0000-0001-6203-7632, Hall, Lindsay ORCID: https://orcid.org/0000-0001-8938-5709 and Clark, Matthew D (2020) Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens. Nature Microbiology, 5 (3). 430–442. ISSN 2058-5276

Lawson, Melissa A. E., O’Neill, Ian J., Kujawska, Magdalena, Gowrinadh Javvadi, Sree, Wijeyesekera, Anisha, Flegg, Zak, Chalklen, Lisa and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2020) Breast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem. The ISME Journal, 14 (2). pp. 635-648. ISSN 1751-7362

Greenhough, Beth, Read, Cressida Jervis, Lorimer, Jamie, Lezaun, Javier, McLeod, Carmen, Benezra, Amber, Bloomfield, Sally, Brown, Tim, Clinch, Megan, D'Acquisto, Fulvio, Dumitriu, Anna, Evans, Joshua, Fawcett, Nicola, Fortane, Nicolas, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Herrera, Cesar E. Giraldo, Hodgetts, Timothy, Johnson, Katerina Vicky-Ann, Kirchhelle, Claas, Krzywoszynska, Anna, Lambert, Helen, Monaghan, Tanya, Nading, Alex, Nerlich, Brigitte, Singer, Andrew C., Szymanski, Erika and Wills, Jane (2020) Setting the agenda for social science research on the human microbiome. Palgrave Communications, 6. ISSN 2055-1045

Carruthers, Lauren, Moses, Arinaitwe, Adriko, Moses, Faust, Christina L., Tukahebwa, Edridah M., Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Ranford-Cartwright, Lisa C. and Lamberton, Poppy H. L. (2019) The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity. PeerJ, 7. ISSN 2167-8359

McKee, Alastair M., Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Robinson, Stephen D. ORCID: https://orcid.org/0000-0002-6606-7588 (2019) The microbiota, antibiotics and breast cancer. Breast Cancer Management, 8 (3). ISSN 1758-1923

Kiu, Raymond, Brown, Joseph, Bedwell, Harley, Leclaire, Charlotte, Caim, Shabhonam, Pickard, Derek, Dougan, Gordon, Dixon, Ronald A. and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2019) Genomic analysis on broiler-associated Clostridium perfringens strains and exploratory caecal microbiome investigation reveals key factors linked to poultry necrotic enteritis. Animal Microbiome, 1. ISSN 2524-4671

Kiu, Raymond, Caim, Shabhonam, Painset, Anais, Pickard, Derek, Swift, Craig, Dougan, Gordon, Mather, Alison E., Amar, Corinne and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2019) Phylogenomic analysis of gastroenteritis-associated Clostridium perfringens in England and Wales over a 7-year period indicates distribution of clonal toxigenic strains in multiple outbreaks and extensive involvement of enterotoxin-encoding (CPE) plasmids. Microbial Genomics, 5 (10). ISSN 2057-5858

Kiu, Raymond, Sim, Kathleen, Shaw, Alex, Cornwell, Emma, Pickard, Derek, Kroll, J. Simon and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2019) Genomic analysis of Clostridium perfringens BEC/CPILE-positive, toxinotype D and E strains isolated from healthy children. Toxins, 11 (9). ISSN 2072-6651

Chen, Yuhao, Brook, Thomas C., Alcon-Giner, Cristina, Clarke, Paul ORCID: https://orcid.org/0000-0001-6203-7632, Hall, Lindsay ORCID: https://orcid.org/0000-0001-8938-5709 and Hoyles, Lesley (2019) Draft genome sequences of Citrobacter freundii and Citrobacter murliniae strains isolated from the feces of preterm infants. Microbiology Resource Announcements, 8 (33).

Chen, Yuhao, Brook, Thomas C., Alcon-Giner, Cristina, Clarke, Paul ORCID: https://orcid.org/0000-0001-6203-7632, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Hoyles, Lesley (2019) Draft genome sequence of Raoultella ornithinolytica P079F W, isolated from the feces of a preterm infant. Microbiology Resource Announcements, 8 (33).

Sultan, Alyshah Abdul, Mallen, Christian, Muller, Sara, Hider, Samantha, Scott, Ian, Helliwell, Toby and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2019) Antibiotic use and the risk of rheumatoid arthritis: a population-based case-control study. BMC Medicine, 17 (1). ISSN 1741-7015

Jones, Emily J, Matthews, Zoe J, Gul, Lejla, Sudhakar, Padhmanand, Treveil, Agatha, Divekar, Devina, Buck, Jasmine, Wrzesinski, Tomasz, Jefferson, Matthew, Armstrong, Stuart D, Hall, Lindsay J ORCID: https://orcid.org/0000-0001-8938-5709, Watson, Alastair J M ORCID: https://orcid.org/0000-0003-3326-0426, Carding, Simon R, Haerty, Wilfried, Di Palma, Federica, Mayer, Ulrike ORCID: https://orcid.org/0000-0003-2328-0052, Powell, Penny P ORCID: https://orcid.org/0000-0002-5347-0490, Hautefort, Isabelle, Wileman, Tom and Korcsmaros, Tamas (2019) Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy. Disease Models & Mechanisms, 12 (3). ISSN 1754-8403

Rowe, Will P. P., Carrieri, Anna Paola, Alcon-Giner, Cristina, Caim, Shabhonam, Shaw, Alex, Sim, Kathleen, Kroll, J. Simon, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Pyzer-Knapp, Edward O. and Winn, Martyn D. (2019) Streaming histogram sketching for rapid microbiome analytics. Microbiome, 7 (1). ISSN 2049-2618

Scott, Nicholas A., Andrusaite, Anna, Andersen, Peter, Lawson, Melissa, Alcon-Giner, Cristina, Leclaire, Charlotte, Caim, Shabhonam, Le Gall, Gwenaelle ORCID: https://orcid.org/0000-0002-1379-2196, Shaw, Tovah, Connolly, James P. R., Roe, Andrew J., Wessel, Hannah, Bravo-Blas, Alberto, Thomson, Carolyn A., Kästele, Verena, Wang, Ping, Peterson, Daniel A., Bancroft, Allison, Li, Xuhang, Grencis, Richard, Mowat, Allan McI., Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Travis, Mark A., Milling, Simon W. F. and Mann, Elizabeth R. (2018) Antibiotics induce sustained dysregulation of intestinal T cell immunity by perturbing macrophage homeostasis. Science Translational Medicine, 10 (464). ISSN 1946-6234

Kiu, Raymond and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2018) Response: Commentary: Probing genomic aspects of the multi-host pathogen Clostridium perfringens reveals significant pangenome diversity, and a diverse array of virulence factors. Frontiers in Microbiology, 9 (AUG). ISSN 1664-302X

Kiu, Raymond and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2018) An update on the human and animal enteric pathogen Clostridium perfringens. Emerging Microbes & Infections, 7. ISSN 2222-1751

Kiu, Raymond, Caim, Shabhonam, Alexander, Sarah, Pachori, Purnima and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2017) Probing genomic aspects of the multi-host pathogen Clostridium perfringens reveals significant pangenome diversity, and a diverse array of virulence factors. Frontiers in Microbiology, 8. ISSN 1664-302X

Alcon-Giner, Cristina, Caim, Shabhonam, Mitra, Suparna, Ketskemety, Jennifer, Wegmann, Udo, Wain, John, Belteki, Gusztav, Clarke, Paul ORCID: https://orcid.org/0000-0001-6203-7632 and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2017) Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants. BMC Genomics, 18. ISSN 1471-2164

Koskella, Britt, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Metcalf, C. Jessica E. (2017) The microbiome beyond the horizon of ecological and evolutionary theory. Nature Ecology & Evolution, 1 (11). pp. 1606-1615. ISSN 2397-334X

O'Neill, Ian, Schofield, Zoe and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2017) Exploring the role of the microbiota member Bifidobacterium in modulating immune-linked diseases. Emerging Topics in Life Sciences, 1 (4). pp. 333-349. ISSN 2397-8554

Kiu, Raymond, Caim, Shabhonam, Alcon-Giner, Cristina, Belteki, Gustav, Clarke, Paul ORCID: https://orcid.org/0000-0001-6203-7632, Pickard, Derek, Dougan, Gordon and Hall, Lindsay J ORCID: https://orcid.org/0000-0001-8938-5709 (2017) Preterm infant-associated Clostridium tertium, Clostridium cadaveris and Clostridium paraputrificum strains: genomic and evolutionary insights. Genome Biology and Evolution, 9 (10). 2707–2714. ISSN 1759-6653

Hughes, Kevin R., Harnisch, Lukas C., Alcon-Giner, Cristina, Mitra, Suparna, Wright, Chris J., Ketskemety, Jennifer, van Sinderen, Douwe, Watson, Alastair J. M. ORCID: https://orcid.org/0000-0003-3326-0426 and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2017) Bifidobacterium breve reduces apoptotic epithelial cell shedding in an exopolysaccharide and MyD88-dependent manner. Inflammatory Bowel Diseases, 7 (1). ISSN 1078-0998

Forde, Patrick F., Hall, Lindsay ORCID: https://orcid.org/0000-0001-8938-5709, de Kruijf, Marcel, Bourke, M. G., Doddy, T., Sadadcharam, Mira and Soden, Declan M. (2015) Non-viral immune electro-gene therapy induces potent anti-tumour responses and has a curative effect in murine colon adenocarcinoma and melanoma cancer models. Gene Therapy, 22. 29–39. ISSN 0969-7128

Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Walshaw, John and Watson, Alastair J. M. ORCID: https://orcid.org/0000-0003-3326-0426 (2014) Gut microbiome in new-onset Crohn's disease. Gastroenterology, 147 (4). 932–934. ISSN 0016-5085

Forde, Patrick F, Hall, Lindsay J ORCID: https://orcid.org/0000-0001-8938-5709, Sadadcharam, Mira, de Kruijf, Marcle, O’ Sullivan, Gerald C and Soden, Declan M (2014) Development and characterization of an enhanced nonviral expression vector for electroporation cancer treatment. Molecular Therapy — Methods & Clinical Development, 1. ISSN 2329-0501

Forde, Patrick F, Sadadcharam, Mira, Hall, Lindsay J ORCID: https://orcid.org/0000-0001-8938-5709, O'Donovan, T R, de Kruijf, Marcel, Byrne, William L, O'Sullivan, Gerald C and Soden, Declan M (2014) Enhancement of electroporation facilitated immunogene therapy via T-reg depletion. Cancer Gene Therapy, 21. pp. 349-354. ISSN 0929-1903

Williams, Jonathan M, Duckworth, Carrie A, Watson, Alastair J M ORCID: https://orcid.org/0000-0003-3326-0426, Frey, Mark R, Miguel, Jennifer C, Burkitt, Michael D, Sutton, Robert, Hughes, Kevin R, Hall, Lindsay J ORCID: https://orcid.org/0000-0001-8938-5709, Caamaño, Jorge H, Campbell, Barry J and Pritchard, D Mark (2013) A mouse model of pathological small intestinal epithelial cell apoptosis and shedding induced by systemic administration of lipopolysaccharide. Disease Models & Mechanisms, 6 (6). pp. 1388-1399. ISSN 1754-8411

Hall, L. J. ORCID: https://orcid.org/0000-0001-8938-5709, Murphy, C. T., Quinlan, A., Hurley, G., Shanahan, F., Nally, K. and Melgar, S. (2013) Natural killer cells protect mice from DSS-induced colitis by regulating neutrophil function via the NKG2A receptor. Mucosal Immunology, 6 (5). pp. 1016-1026. ISSN 1933-0219

Watson, Alastair J. M. ORCID: https://orcid.org/0000-0003-3326-0426 and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2013) Regulation of host gene expression by gut microbiota. Gastroenterology, 144 (4). pp. 841-844. ISSN 0016-5085

Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Murphy, Carola T., Hurley, Grainne, Quinlan, Aoife, Shanahan, Fergus, Nally, Kenneth and Melgar, Silvia (2013) Natural Killer cells protect against mucosal and systemic infection with the enteric pathogen Citrobacter rodentium. Infection and Immunity, 81 (2). pp. 460-469. ISSN 0019-9567

Watson, Alastair J. M. ORCID: https://orcid.org/0000-0003-3326-0426, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Hughes, Kevin R. (2012) Cell shedding: old questions answered. Gastroenterology, 143 (5). pp. 1389-1391. ISSN 1528-0012

Fanning, Saranna, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and van Sinderen, Douwe (2012) Bifidobacterium breve UCC2003 surface exopolysaccharide production is a beneficial trait mediating commensal-host interaction through immune modulation and pathogen protection. Gut Microbes, 3 (5). pp. 420-425. ISSN 1949-0976

Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 and Watson, Alastair J. M. ORCID: https://orcid.org/0000-0003-3326-0426 (2012) Role of autophagy in NOD2-induced inflammation in Crohn's disease. Gastroenterology, 142 (4). pp. 1032-1034. ISSN 1528-0012

Fanning, Saranna, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Cronin, Michelle, Zomer, Aldert, MacSharry, John, Goulding, David, O'Connell Motherway, Mary, Shanahan, Fergus, Nally, Kenneth, Dougan, Gordon and van Sinderen, Douwe (2012) Bifidobacterial surface-exopolysaccharide facilitates commensal-host interaction through immune modulation and pathogen protection. Proceedings of the National Academy of Sciences, 109 (6). pp. 2108-2113. ISSN 0027-8424

Murphy, Carola T., Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Hurley, Grainne, Quinlan, Aoife, MacSharry, John, Shanahan, Fergus, Nally, Kenneth and Melgar, Silvia (2012) The sphingosine-1-phosphate analogue FTY720 impairs mucosal immunity and clearance of the enteric pathogen Citrobacter rodentium. Infection and Immunity, 80 (8). pp. 2712-2723. ISSN 0019-9567

Jansen, Angela M., Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Clare, Simon, Goulding, David, Holt, Kathryn E., Grant, Andrew J., Mastroeni, Piero, Dougan, Gordon and Kingsley, Robert A. (2011) A Salmonella Typhimurium-Typhi genomic chimera: A model to study Vi polysaccharide capsule function in vivo. PLoS Pathogens, 7 (7).

Dougan, Gordon, Goulding, David and Hall, Lindsay ORCID: https://orcid.org/0000-0001-8938-5709 (2011) Live Vaccines and Their Role in Modern Vaccinology. In: Replicating Vaccines: A New Generation. Springer, pp. 3-14. ISBN 978-3-0346-0276-1

Hall, Lindsay J ORCID: https://orcid.org/0000-0001-8938-5709, Faivre, Emilie, Quinlan, Aoife, Shanahan, Fergus, Nally, Kenneth and Melgar, Silvia (2010) Induction and activation of adaptive immune populations during acute and chronic phases of a murine model of experimental colitis. Digestive Diseases and Sciences, 56 (1). pp. 79-89. ISSN 1573-2568

Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Clare, Simon and Dougan, Gordon (2010) Probing local innate immune responses after mucosal immunisation. Journal of Immune Based Therapies and Vaccines, 8 (5). ISSN 1476-8518

Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Clare, Simon and Dougan, Gordon (2010) NK cells influence both innate and adaptive immune responses after mucosal immunization with antigen and mucosal adjuvant. Journal of Immunology, 184 (8). pp. 4327-4337. ISSN 0022-1767

Murphy, C. T., Moloney, G., Hall, L. J. ORCID: https://orcid.org/0000-0001-8938-5709, Quinlan, A., Faivre, E., Casey, P., Shanahan, F., Melgar, S. and Nally, K. (2010) Use of bioluminescence imaging to track neutrophil migration and its inhibition in experimental colitis. Clinical and Experimental Immunology, 162 (1). pp. 188-196. ISSN 1365-2249

Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Clare, Simon, Pickard, Derek, Clark, Simon O., Kelly, Dominic L., El Ghany, Moataz Abd, Hale, Christine, Dietrich, Jes, Andersen, Peter, Marsh, Philip D. and Dougan, Gordon (2009) Characterisation of a live Salmonella vaccine stably expressing the Mycobacterium tuberculosis Ag85B-ESAT6 fusion protein. Vaccine, 27 (49). pp. 6894-6904. ISSN 1873-2518

Abd El Ghany, Moataz, Jansen, Angela, Clare, Simon, Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709, Pickard, Derek, Kingsley, Robert A. and Dougan, Gordon (2007) Candidate live, attenuated Salmonella enterica serotype Typhimurium vaccines with reduced fecal shedding are immunogenic and effective oral vaccines. Infection and Immunity, 75 (4). pp. 1835-1842. ISSN 0019-9567