Professor Lindsay Hall

Professor Lindsay Hall

Institute of Microbiology and Infection
Chair of Microbiome Research

Contact details

University of Birmingham
B15 2TT

Professor Lindsay Hall is Chair of Microbiome Research and a Wellcome Investigator. Leading a dynamic, multidisciplinary team, she is on a mission to unravel the mysteries of how host-associated microbial communities foster well-being. Her research is focused on the critical early stages of life, including pregnancy and infancy, where the colonisation of microbes like Bifidobacterium coincides with pivotal physiological programming, laying the foundation for future health and vitality.

Beyond these foundational aspects, Professor Hall and her team delve into the potential of early life microbes to positively influence the risk and progression of chronic diseases, including cancer. Her work has garnered support from various grant and charitable organisations, underscoring the significance of her research in the scientific community.

Professor Hall's collaborative network stretches across the globe to like-minded researchers who share her passion for microbiome investigation and the development of innovative dietary and microbial therapies.

Lindsay also has a strong commitment to making the captivating world of the microbiome accessible to diverse audiences. She passionately engages with the public and schoolchildren, bringing the magic of microbiome science to life in an educational and inspiring manner. 


2011-2014: Postgraduate Certificate in Higher Education Practice, University of East Anglia

2003-2007: PhD, Microbiology and Immunology, University of Cambridge

1999-2003: BSc (Hons), Microbiology, University of Glasgow


Professor Lindsay Hall assumed the role of Chair of Microbiome Research at the University of Birmingham in 2023, marking another major milestone in her academic journey. Her exploration of the microbial world began at the University of Glasgow, where she earned her BSc in Microbiology, followed by a PhD in Microbiology and Immunology from the University of Cambridge at the Wellcome Trust Sanger Institute.

Lindsay's intellectual journey took her to the dramatic landscapes of South Ireland, where she embarked on a postdoctoral fellowship at University College Cork within the APC Microbiome Institute. It was during this period that her fascination with gut-associated microbial communities was ignited. Her return to the UK saw her take up her first independent role, a lectureship at the University of East Anglia in Norwich. Here, she dedicated herself to expanding her research portfolio, with a particular focus on the intricate world of the gut microbiota, especially during the critical early stages of life.

In 2015, Lindsay's curiosity and dedication to microbiome research led her to the Quadram Institute in Norwich. During her tenure, she made significant strides in her research agenda, establishing several clinical cohort studies that would further our understanding of the gut microbiota's role in human health. Beyond her research, Lindsay embraced the opportunity to engage with the public and share the wonders of science through various outreach and educational initiatives, all under the captivating theme of 'Guardians of the Gut.'

Before her arrival at the University of Birmingham, Lindsay held the prestigious position of Chair of Intestinal Microbiome at the Technical University of Munich in Germany. In this role, she continued her pioneering research into the world of beneficial microbes and developed innovative therapies to enhance infant health.

Her academic journey is a testament to her unwavering commitment to advancing our understanding of microbiomes, their impact on human health, and their potential to shape the future of medicine. As a distinguished microbiologist and educator, Professor Lindsay Hall brings a wealth of knowledge and experience to her role, enriching the University of Birmingham's academic community and contributing to ground-breaking research in microbiome science.

Postgraduate supervision

Prof Hall has a distinguished record of guiding and nurturing postgraduate scholars through their academic journeys. She welcomes aspiring students who share her deep enthusiasm for the captivating realm of microbiome research. Specifically, Lindsay is keen to collaborate with those driven by curiosity for unravelling the intricate mechanisms by which beneficial microbes communicate with their host. Additionally, she seeks students who share her interest about the dynamic interactions among microorganisms, as they work together to foster the development of robust and harmonious microbial ecosystems. Ultimately, these ecosystems play a pivotal role in enhancing the well-being of infants, making this an exciting and impactful area of study. If you share Lindsay's passion for microbiome research and aspire to make meaningful contributions in these topics, she looks forward to hearing from you directly, or for any general doctoral research enquiries, please email

For a full list of available Doctoral Research opportunities, please visit our Doctoral Research programme listings


Research interests

Understanding Microbiome Interactions:

Professor Lindsay Hall leads a dynamic, multi-disciplinary team dedicated to unravelling the molecular intricacies of microbiome interactions, with a primary focus on the interface of the gut mucosa. Their research is driven by a profound interest in the critical early stages of life, particularly during pregnancy and infancy. This period, marked by the colonisation of vital microbes like Bifidobacterium, plays a pivotal role in programming essential metabolic and immune foundations for future health and well-being.

Beneficial Microbes and Disease Modulation:

The team's exploration extends to understanding how select early life microbes may positively influence the risk and progression of chronic diseases, including cancer.

Professor Hall's research program is organised into three interconnected themes:

1. Microbe-Diet Interactions: Investigating how microbes interact with dietary components.

2. Colonisation Resistance: Exploring the mechanisms that prevent harmful microbe invasion.

3. Microbiota-Host Crosstalk: Unravelling the complex communication between microbiota and the host.

Lindsay and her teams work is firmly grounded in extensive longitudinal cohort studies, including a preterm infant cohort and a mother-infant dyad cohort, where Professor Hall serves as Chief Investigator. These clinical studies underpin broader research activities.

To tackle critical outstanding questions in the microbiome field, Prof Hall and her team adopts a diverse array of multidisciplinary approaches encompassing both 'wet' and 'dry' laboratory techniques. They leverage state-of-the-art in vitro models and model colon systems to gain insights into ecological and host interactions. Additionally, they harness various 'omics technologies and employ advanced bioinformatics tools to delineate distinctive microbiome signatures associated with health. Furthermore, they draw upon preclinical and clinical samples, enabling them to translate discoveries into tangible benefits for individuals at risk.

This comprehensive approach aims to decipher the fundamental mechanisms governing microbiome-host interactions in health and disease, ultimately paving the way for intervention and therapy development. For further details visit


Recent publications


Acuna-Gonzalez, A, Kujawska, M, Youssif, M, Atkinson, T, Grundy, S, Hutchison, A, Tremlett, C, Clarke, P & Hall, LJ 2023, 'Bifidobacterium bacteraemia is rare with routine probiotics use in preterm infants: A further case report with literature review', Anaerobe, vol. 80, 102713.

Zhou, DT, Mudhluli, T, Hall, L, Manasa, J & Munyati, S 2023, 'A Scoping Review of Gut Microbiome and Bifidobacterium Research in Zimbabwe: Implications for Future Studies', Pediatric health, medicine and therapeutics, vol. 14, pp. 483—496.

Elek, CKA, Brown, TL, Viet, TL, Evans, R, Baker, DJ, Telatin, A, Tiwari, SK, Al-Khanaq, H, Thilliez, G, Kingsley, RA, Hall, LJ, Webber, MA & Adriaenssens, EM 2023, 'A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses', Microbial Genomics, vol. 9, no. 7, 001065.

Teng, NMY, Kiu, R, Evans, R, Baker, DJ, Zenner, C, Robinson, SD & Hall, LJ 2023, 'Allocoprobacillus halotolerans gen. nov., sp. nov and Coprobacter tertius sp. nov., isolated from human gut microbiota', International Journal of Systematic and Evolutionary Microbiology, vol. 73, no. 7, 005950.

Serghiou, IR, Baker, D, Evans, R, Dalby, MJ, Kiu, R, Trampari, E, Phillips, S, Watt, R, Atkinson, T, Murphy, B, Hall, LJ & Webber, MA 2023, 'An efficient method for high molecular weight bacterial DNA extraction suitable for shotgun metagenomics from skin swabs', Microbial Genomics, vol. 9, no. 7, 001058.

Serghiou, IR, Webber, MA & Hall, LJ 2023, 'An update on the current understanding of the infant skin microbiome and research challenges', Current Opinion in Microbiology, vol. 75, 102364.

Neumann, CJ, Mahnert, A, Kumpitsch, C, Kiu, R, Dalby, MJ, Kujawska, M, Madl, T, Kurath-Koller, S, Urlesberger, B, Resch, B, Hall, LJ & Moissl-Eichinger, C 2023, 'Clinical NEC prevention practices drive different microbiome profiles and functional responses in the preterm intestine', Nature Communications, vol. 14, no. 1, 1349.

James, SA, Telatin, A, Baker, D, Evans, R, Clarke, P, Hall, LJ & Carding, SR 2023, 'Draft Genome Sequence of a Preterm Infant-Derived Isolate of Candida parapsilosis', Microbiology resource announcements, vol. 12, no. 3.

Saeed, MH & Hall, LJ 2023, 'Early-life antibiotic usage and impact on the gut microbiota, including emergence of antimicrobial resistant Enterococcus', Microbiota and Host, vol. 1, no. 1, e230002.

Kadia, BM, Otiti, MI, Ramsteijn, A, Sow, D, Faye, B, Heffernan, C, Hall, LJ, Webster, JP, Walker, AW & Allen, S 2023, 'Modulating the early-life gut microbiota using pro-, pre-, and synbiotics to improve gut health, child development, and growth', Nutrition Reviews.

Zenner, C, Chalklen, L, Adjei, H, Dalby, MJ, Mitra, S, Cornwell, E, Shaw, AG, Sim, K, Kroll, JS & Hall, LJ 2023, 'Noninvasive Fecal Cytokine and Microbiota Profiles Predict Commencement of Necrotizing Enterocolitis in a Proof-of-Concept Study', Gastro Hep Advances, vol. 2, no. 5, pp. 666-675.

Kiu, R, Shaw, AG, Sim, K, Acuna-Gonzalez, A, Price, CA, Bedwell, H, Dreger, SA, Fowler, WJ, Cornwell, E, Pickard, D, Belteki, G, Malsom, J, Phillips, S, Young, GR, Schofield, Z, Alcon-Giner, C, Berrington, JE, Stewart, CJ, Dougan, G, Clarke, P, Douce, G, Robinson, SD, Kroll, JS & Hall, LJ 2023, 'Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains', Nature Microbiology, vol. 8, no. 6, pp. 1160-1175.


Kujawska, M, Schaubeck, M, Hall, L & Neuhaus, K 2023, 'Draft genome sequence of Bifidobacterium breve DSM 32583, isolated from human milk', Microbiology resource announcements, vol. 12, no. 11, e0041223.

Review article

Roager, HM, Stanton, C & Hall, LJ 2023, 'Microbial metabolites as modulators of the infant gut microbiome and host-microbial interactions in early life', Gut Microbes, vol. 15, no. 1, 2192151.

Kennedy, KM, de Goffau, MC, Perez-Muñoz, ME, Arrieta, MC, Bäckhed, F, Bork, P, Braun, T, Bushman, FD, Dore, J, de Vos, WM, Earl, AM, Eisen, JA, Elovitz, MA, Ganal-Vonarburg, SC, Gänzle, MG, Garrett, WS, Hall, LJ, Hornef, MW, Huttenhower, C, Konnikova, L, Lebeer, S, Macpherson, AJ, Massey, RC, McHardy, AC, Koren, O, Lawley, TD, Ley, RE, O’Mahony, L, O’Toole, PW, Pamer, EG, Parkhill, J, Raes, J, Rattei, T, Salonen, A, Segal, E, Segata, N, Shanahan, F, Sloboda, DM, Smith, GCS, Sokol, H, Spector, TD, Surette, MG, Tannock, GW, Walker, AW, Yassour, M & Walter, J 2023, 'Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies', Nature, vol. 613, no. 7945, pp. 639-649.

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