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PhD Studentship: Single Cell Transcriptomics for Microbiomics Approaches

University of Essex - Biological Sciences

Qualification Type: PhD
Location: Colchester
Funding for: UK Students, EU Students, International Students
Funding amount: £15,009 per annum
Hours: Full Time
Placed On: 31st May 2019
Closes: 22nd July 2019
Reference: 11287


The microbiome has emerged as an important factor in health and disease, affecting aspects such as obesity, metabolic disease, cancer and, potentially, brain health.

The microbiome composition is highly dynamic and affected by nutrition, co-housing, age and life style. The microbiome is an important factor in inflammatory bowel diseases (IBD), conditions that are quite prevalent (one in 250 of the population) can be severe and cannot be cured.

IBD is promoted by colitogenic bacteria, some of these, such as members of the TM7 phylum, are not well understood. Therefore, technologies that can provide new insights into microbiome diversity are much needed. Microbiomics is most commonly performed by 16S sequencing. However, this will not discover functional aspects of diversity that are likely important.

We propose to develop single cell transcriptomics for microbiomics approaches, building on recent progress on drop based sequencing technology.

Single cell transcriptomic approaches on bacteria provide many challenges, such as low abundance of transcripts and efficient amplification of material, but some of these have recently been addressed (“Single prokaryotic cell isolation and total transcript amplification protocol for transcriptomic analysis”, Kang et al., Nature Protocols volume 10, pages 974–984, 2015).

Combining such breakthroughs with drop technologies and next generation sequencing will provide further breakthroughs. We are at the right moment in time to further invest in the development of such technologies. 

You are encouraged to contact the supervisors before application: or  If you have any queries with the online application process, please contact

For general information about the School of Biological Sciences at the University please visit our webpages


Home/EU fee waiver or equivalent fee discount for overseas students (a doctoral stipend equivalent to RCUK (£15,009 in 2019-20), plus £2,500 training bursary via Proficio funding.  This is a competition funded studentship.


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