Microbiota and Systems Biology

Understanding the microbiome has the potential to revolutionise medicine. However, this opportunity is limited by a lack of fundamental knowledge. The Microbiota and Systems Biology group is building this knowledge and translating breakthroughs into new patient treatments.

Overview

The gastrointestinal microbiota plays an essential, though poorly understood, role in many aspects of human biology. Emerging evidence suggests the bacterial community structure can impact diseases as diverse as autoimmune diseases, cancers, and infections. Despite this importance, many of the species of bacteria that inhabit this environment are yet to be grown in the laboratory, let alone genome sequenced or their interactions with the human body characterised.

Research within the Microbiota and Systems Biology laboratory applies genomics, computational and systems biology, microbiology, and immunology to develop an understanding of these bacteria, their genomes and reciprocal interactions with the human immune system that lead to disease or maintain health.

Using cutting edge bacterial culturing, genomics and host-transcriptomics, the Microbiota and Systems Biology lab’s research builds on a strong, fundamental understanding to develop new therapeutic options for many conditions and diseases.

Potential treatment options developed through this work range from methods of biomarker detection to guide therapy or control the spread of antimicrobial resistance within the healthcare system, through to identification of optimal bacterial communities, diets that support them and the development of conventional and live biotherapeutic based clinical interventions to improve human, animal and environmental health.

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Diseases we research

Areas of focus

Microbiome-based therapies for Inflammatory Bowel Disease
Microbiome therapies for early life disease
Antibiotic resistance in the microbiome
Dietary interventions to modify the microbiome
Understanding the structure and function of the microbiome
Phage in the microbiome

Research Group Head | Associate Professor Samuel Forster

We all have our own unique, diverse communities of microbes, our microbiomes, which are key to our health. I work to understand these species, how we can help them and how they can help us as treatments for disease.

Meet the team

News from the lab

28 February 2024

Hudson Institute’s 2023 Emerging Leaders

See more news articles about Microbiota and Systems Biology

Student opportunities

Collaborators

Publication highlights

Gulliver, E. L., Adams, V., Marcelino, V. R., Gould, J., Rutten, E. L., Powell, D. R., Young, R. B., D’Adamo, G. L., Hemphill, J., Solari, S. M., Revitt-Mills, S. A., Munn, S., Jirapanjawat, T., Greening, C., Boer, J. C., Flanagan, K. L., Kaldhusdal, M., Plebanski, M., Gibney, K. B., Moore, R. J., Rood, J. I. and Forster S. C., (2023), Extensive genome analysis identifies novel plasmid families in Clostridium perfringens, Microbial Genomics. 9, 4, 16 p., 000995.
Di Simone, S. K., Rudloff, I., Nold-Petry, C. A., Forster, S. C. & Nold, M. F., (11 Jan 2023) Understanding respiratory microbiome-immune system interactions in health and disease, Science Translational Medicine. 15, 678, 15 p., eabq5126.
Solari, S. M., Young, R. B., Marcelino, V. R. & Forster, S. C., (2022) expam-high-resolution analysis of metagenomes using distance trees, Bioinformatics. 38, 20, p. 4814-4816 3 p.
Forster, S.C., Clare, S., Beresford-Jones, B.S. et al. Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis. Nat Microbiol 7, 590 – 599 (2022). https://doi.org/10.1038/s41564-022-01094-z
Forster, S.C., Liu, J., Kumar, N. et al. Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome. Nat Commun 13, 1445 (2022). https://doi.org/10.1038/s41467-022-29096-9
James KR, Gomes T, Elmentaite R, Kumar N, Gulliver EL, King HW, Stares MD, Bareham BR, Ferdinand JR, Petrova VN, Polański K, Forster SC, Jarvis LB, Suchanek O, Howlett S, James LK, Jones JL, Meyer KB, Clatworthy MR, Saeb-Parsy K, Lawley TD, Teichmann SA (2020) Distinct microbial and immune niches of the human colon. Nat Immunology 21 (3): 343-353.
Forster SC*, Kumar N, Anonye BO, Almeida A, Viciani E, Stares MD, Dunn M, Mkandawire TT, Zhu A, Shao Y, Pike LJ, Louie T, Browne HP, Mitchell AL, Neville BA, Finn RD & Lawley TD* (*co-corresponding authors) (2019) A human gut bacterial genome and culture collection for improved metagenomic analyses. Nature Biotech 37 (2): 186-192
Shao Y, Forster SC, Tsaliki E, Vervier K, Strang A, Simpson N, Kumar N, Stares MD, Rodger A, Brocklehurst P, Field N, Lawley TD (2019) Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. Nature 574(7776):117-121.
Giles EM, D’Adamo GL, Forster SC (2019) The future of faecal transplants. Nat Rev Microbiol 17(12):719.
Almeida A, Mitchell AL, Boland M, Forster SC, Gloor GB, Tarkowska A, Lawley TD & Finn RD (2019) A new genomic blueprint of the human gut microbiota. Nature 566 (7753): 499-504.
Thomas-White K*, Forster SC*, Kumar N*, Van Kuiken M, Putonti C, Stares MD, Hilt EE, Price TK, Wolfe AJ & Lawley TD (* co-first authors) (2018) Culturing of female bladder bacteria reveals an interconnected urogenital microbiota. Nature Commun 9 (1): 1557
Browne HP*, Forster SC*, Anonye BO, Kumar N, Neville BA, Stares MD, Goulding D, Lawley TD (* co-first authors) (2016) Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation. Nature 533(7604):543-546.

Our research group is keen to discuss funding opportunities

Support our research

Microbiota and Systems Biology

Overview

Diseases we research

Areas of focus

Research Group Head | Associate Professor Samuel Forster

Meet the team

News from the lab

New CRC-P Grant accelerates Microbiome therapeutics

Strength in diversity – computing healthy microbiome relationships

Does broccoli boost bad gut bacteria?

New precision identifies the microbiome keys to IBD

New anti-inflammatory drug – one medicine to rule them all

What’s the link between diet and the gut microbiome?

Where the microbiome meets the immune system

Hudson Institute’s 2023 Emerging Leaders

Student opportunities

Collaborators

Publication highlights

Our research group is keen to discuss funding opportunities