2020 applicants
Postgraduate Research Opportunity

Single cell transcriptomics for microbiomics approaches


Title: Single cell transcriptomics for microbiomics approaches

Funding: Full time Home/EU fees and a stipend of £15,009 p.a. (terms & conditions)

Application deadline: 22 July 2019

Start date: October 2019

Duration: 3 years (full time)

Location: Colchester Campus

Based in: School of Life Sciences


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. 


The award consists of a full Home/EU fee waiver or equivalent fee discount for overseas students (further fee details), a doctoral stipend equivalent to the Research Councils UK National Minimum Doctoral Stipend (£15,009 in 2019-20), plus £2,500 training bursary via Proficio funding, which may be used to cover the cost of advanced skills training including conference attendance and travel.


How to apply

You can apply for this postgraduate research opportunity online.

Please include your CV, covering letter, personal statement, and transcripts of UG and Masters degrees in your application.

Your personal statement should explain why you are applying for this specific project and what you could bring to the team in terms of skills, experience and enthusiasm.

Instruction to applicants

When you apply online you will be prompted to fill out several boxes in the form:

  • For "Course title" please put "PhD Biological Sciences"
  • For "Proposed research topic or area of research" please put the title of this studentship (Single cell transcriptomics for microbiomics approaches)
  • For "If you have contacted a potential supervisor..." please put the name of the lead supervisor (Dr Patrick Varga Weisz)

If you have any informal queries about this opportunity please email the lead supervisor, Dr Patrick Varga Weisz (patrick.varga-weisz@essex.ac.uk).

You can find the terms and conditions of this studentship here (.doc)