Introductory description

The aim of this module is to provide students with an understanding of the role of environmental and host-associated microbial communities in driving processes in the environment and affecting the physiology and health of plants, animal and human hosts. The module also showcases how the analysis of microbial diversity and function is critically dependent on the application of cultivation-independent approaches for linking identity and function of uncultivated microorganisms, including high throughput DNA sequencing methodologies for community profiling and metagenomics and a range of other approaches.

Module web page

Module aims

Outline syllabus

This is an indicative module outline only to give an indication of the sort of topics that may be covered. Actual sessions held may differ.

Microbial diversity, and systematics; ribosomal RNA as a conserved phylogenetic marker

Culturability (and non-culturability) of microorganisms; the case for microbial community analysis using molecular biological, cultivation-independent approaches

Distribution of microorganisms in the environment and role in biogeochemical cycling (case studies)

Diversity of plant, animal, human-associated microbiomes (case studies)

Establishing gene function in model organisms and translation of findings to microbial communities (incl tutorial case study)

Stable isotope and radioisotope approaches to linking microbial identity and function

Metagenomics approaches for studying composition and metabolic potential (metagenomics)

IT workshop: practical examples of databases, online resources used for diversity and metagenomics studies; gene finding and annotation of DNA sequence data.

Learning outcomes

By the end of the module, students should be able to:

• After taking this module, students should be able to critically evaluate how different methodological approaches can help to dissect structure/function relationships in microbial communities and identify the biases associated with different methods.
• After taking this module, students should be able to autonomously interpret original research outputs of advanced microbiomics studies and critically evaluate the findings.
• After taking this module, students should be able assess the identity and functional potential of uncultivated microorganisms based on analysis of DNA sequence data.

Indicative reading list

Madigan, M. T. et al. (2018) Brock biology of microorganisms. Fifteenth edition. NY, NY:
Pearson. Available at: http://encore.lib.warwick.ac.uk/iii/encore/record/C__Rb3229767.

Vorholt, J. A. (2012) ‘Microbial life in the phyllosphere’, Nature Reviews Microbiology, 10(12), pp. 828–840. doi: 10.1038/nrmicro2910.

Brown, C. T. et al. (2015) ‘Unusual biology across a group comprising more than 15% of domain Bacteria’, Nature, 523(7559), pp. 208–211. doi: 10.1038/nature14486.

Bulgarelli, D. et al. (2012) ‘Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota’, Nature, 488(7409), pp. 91–95. doi: 10.1038/nature11336.

Caporaso, J. G. et al. (2012) ‘Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms’, The ISME Journal, 6(8), pp. 1621–1624. doi:10.1038/ismej.2012.8.

Chen, Y. and Murrell, J. C. (2010) ‘When metagenomics meets stable-isotope probing: progress and perspectives’, Trends in Microbiology, 18(4), pp. 157–163. doi:10.1016/j.tim.2010.02.002.

Davide Bulgarelli (2015) ‘Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley’, Cell Host & Microbe. Elsevier, 17(3). doi: 10.1016/j.chom.2015.01.011.

Escobar-Zepeda, A., Vera-Ponce de León, A. and Sanchez-Flores, A. (2015) ‘The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics’, Frontiers in Genetics, 6. doi: 10.3389/fgene.2015.00348.

Eyice, Ö. et al. (2018) ‘Bacterial SBP56 identified as a Cu-dependent methanethiol oxidase widely distributed in the biosphere’, The ISME Journal, 12(1), pp. 145–160. doi: 10.1038/ismej.2017.148.

Hug, L. A. et al. (2016) ‘A new view of the tree of life’, Nature Microbiology, 1(5). doi: 10.1038/nmicrobiol.2016.48.

Lundberg, D. S. et al. (2012) ‘Defining the core Arabidopsis thaliana root microbiome’, Nature, 488(7409), pp. 86–90. doi: 10.1038/nature11237.

Meyer, F. et al. (2008) ‘The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes’, BMC Bioinformatics, 9(1). doi: 10.1186/1471-2105-9-386.

Parks, D. H. et al. (2017) ‘Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life’, Nature Microbiology, 2(11), pp. 1533–1542. doi: 10.1038/s41564-017-0012-7.

Valles-Colomer, M. et al. (2019) ‘The neuroactive potential of the human gut microbiota in quality of life and depression’, Nature Microbiology, 4(4), pp. 623–632. doi: 10.1038/s41564-018-0337-x.

Yarza, P. et al. (2014) ‘Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences’, Nature Reviews Microbiology, 12(9), pp. 635–645. doi: 10.1038/nrmicro3330.

View reading list on Talis Aspire

Subject specific skills

Identify the role that microbiota associated with animals, plants and humans have for host physiology and understand how knowledge of the microbiome may be exploitable in order to bring about beneficial changes to host physiology, health and — in case of crop plants, to crop yield and disease resistance.

Transferable skills

Autonomously interpret original research
Critically evaluate different methodological approaches