Microbiota and Systems Biology

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 remain to be grown in the laboratory, let alone genome sequenced or their interactions with the human immune system characterised. Research within the Microbiota and Systems Biology laboratory applies genomics, computational and systems biology, microbiology and immunology to develop our 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, our research builds on a strong, fundamental understanding of basic microbiology, immunology and systems biology to develop 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 and the development of conventional and bacteriotherapy based clinical interventions to improve human health.

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Research Group

• Dr Marina Iacovou, Senior Research Scientist
• Dr Michelle Chonwerawong, Postdoctoral Scientist
• Dr Emily Gulliver, Postdoctoral Scientist
• Dr Nicole Kellow, Honorary Clinical Associate
• Dr Maurizio Pacilli, Honorary Clinical Associate
• Emily Rutten, Junior Research Assistant, Research Support Staff
• Tamblyn Thomason, Research Assistant, Research Support Staff
• Jodee Gould, Senior Research Specialist, Research Support Staff
• Gemma D'Adamo, PhD Student
• Sofia Dahlman, PhD Student
• Laura Franco, PhD Student
• Jamia Hemphill, PhD Student
• Patricia Khoo, PhD Student
• Emma Saltzman, PhD Student
• Sean Solari, PhD Student
• Remy Young, PhD Student
• Sara Di Simone, PhD Student
• Molly Horne, Honours Student
• Jack Cameron, Undergraduate Research Opportunities Program (UROP) Student

Selected publications

• 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

• 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.

• Pike LJ & Forster SC (2018) A new piece in the microbiome puzzle. Nat Rev Microbiol 16(4): 186.

• 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

• Forster SC (2017) Illuminating microbial diversity. Nat Rev Microbiol 15(10):578.

• Iraola G*, Forster SC*, Kumar N, Lehours P, Bekal S, García-Peña FJ, Paolicchi F, Morsella C, Hotzel H, Hsueh PR, Vidal A, Lévesque S, Yamazaki W, Balzan C, Vargas A, Piccirillo A, Chaban B, Hill JE, Betancor L, Collado L, Truyers I, Midwinter AC, Dagi HT, Mégraud F, Calleros L, Pérez R, Naya H & Lawley TD (* co-first authors) (2017) Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota. Nature Commun 8 (1): 1367

• 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.

• Forster SC*, Browne HP, Kumar N, Hunt M, Denise H, Mitchell A, Finn RD, Lawley TD* (*co-corresponding authors) (2016) HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes. Nucleic Acids Res D1:604-609.

• Giles EM, D’Adamo GL, Forster SC (2019) The future of faecal transplants. Nat Rev Microbiol 17(12):719.

• 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.

• Kumar N, Browne HP, Viciani E, Forster SC, Clare S, Harcourt K, Stares MD, Dougan G, Fairley DJ, Roberts P, Pirmohamed M, Clokie MRJ, Jensen MBF, Hargreaves KR, Ip M, Wieler LH, Seyboldt C, Norén T, Riley TV, Kuijper EJ, Wren BW, Lawley TD (2019) Adaptation of host transmission cycle during Clostridium difficile speciation. Nat Genet 51(9):1315-1320.

• 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.