EBNet Webinar: Using Big Data Approaches to Understand Microbial Communities 

EBNet Webinar: Using Big Data Approaches to Understand Microbial Communities 

Thursday, 10th February 2022 at 13.00 – 14.15 – Registration now closed.

The SESSION RECORDING is available here. See Dr Sophie Nixon’s presentation here and Dr Imer Ujaz’s presentation here. Can you help inform our Bioinformatics Working Group activities? Fill in our survey here.

EBNet are hosting a series of specialist webinars to support knowledge exchange amongst members. â€œUsing Big Data Approaches to Understand Microbial Communities“. Hear the latest developments from top speakers and participate in the online chat to engage with questions.

This fascinating session is brought to you by the Chairs: Dr Sarah Forrester, the Chong Group, Dept. of Biology, University of York & Dr Bing Guo.

Dr Sarah Forrester is a PDRA within James Chong’s group within the Biology department at the University of York. She gained her PhD at the University of Liverpool in 2016 using multi ‘omic approaches to analyse parasite genomic data, and has worked since then on a range of microbial systems and used a variety of bioinformatic methods. She performs HPC driven microbial genomics research and delivers bioinformatics training. As a 2022 Software Sustainability fellow and a certified Software Carpentry instructor, she is passionate about instilling good bioinformatic practises into her training. She is also involved in the preparation and delivery of the material for Cloud-SPAN: Specialised analyses for environmental ‘omics with Cloud-based High Performance Computing , see https://cloud-span.york.ac.uk/.

Dr Bing Guo is a Lecturer in Civil and Environmental Engineering at the University of Surrey. She received her PhD in Civil Engineering from McGill University, Canada. Prior to joining Surrey in 2020, she was awarded Quebec Postdoctoral Research fellowship at Delft University of Technology, joint with the University of Alberta, Canada. Her research interests include microbial ecology modelling (immigration theory, microbial interactions and networks), syntrophic relationships and interspecies electron transfer mechanisms in anaerobic bioreactors, antimicrobial resistance (AMR) in wastewater treatment processes and receiving environments, using omics and bioinformatics tools.


Talk title: Introduction to the EBNet bioinformatics working group

Prof James Chong is a Royal Society Industry Fellow and Professor in the Department of Biology at the University of York, where he runs a research group exploiting a range of ‘omics techniques to understand microbial community dynamics, as well as leading the EBNet Working Group “Bioinformatics Training for Microbial Environmental Biotechnologies“. His group is involved in generating microbial community metagenomics, meta-transcriptomics and metabolomics datasets. His group use established analytical pipelines, but also develop their own bespoke scripts for data analysis. Insight into the application of ‘omics techniques, and the ways in which they can be applied to environmental biotechnology use cases to greater understand microbial community dynamics, has driven his desire to develop bioinformatic training resources. This is currently being supported by the UKRI Grant Cloud-SPAN: Specialised analyses for environmental ‘omics with Cloud-based High Performance Computing, and is co-led by James, see https://cloud-span.york.ac.uk/.

Talk Title: Uncovering the diversity and function of life in the deep subsurface using multi-omics approaches

Dr Sophie Nixon is a BBSRC David Philips and Dame Kathleen Ollerenshaw Research Fellow at the University of Manchester. Her research interests centre on the diversity, function and adaptation of microbial life in the deep terrestrial habitats, spanning pristine and engineered subsurface environments on Earth, and the potential for life on other planetary bodies. She combines high-pressure subsurface simulation with genomic tools and geochemistry to understand the role of microbiology in these extreme environments. Her particular areas of interest are the roles of microbial communities in hydraulically fractured shale environments and geological CO2 storage repositories. She is especially interested in how negative ‘biofouling’ processes (bio-clogging, souring, unwanted biogenic gas production, etc) can be attenuated, and ways in which positive processes (such as enhanced CO2 sequestration and conversion of CO2 into useful products) can be promoted using biotechnology. Fundamental to these research interests is the quest to understand how microorganisms cooperate with one another and function as consortia, and in particular how metabolic interdependencies drive these positive and negative processes.

Talk title: Understanding microbial communities through in-situ ‘omics data synthesis

Dr Umer Zeeshan Ijaz, Reader in Information Engineering at University of Glasgow, leads on in-situ ‘omics data analytics for microbiome research in diverse environments underpinned by expertise in numerical ecology and machine learning. Bioinformatics is becoming a vital component of a wide variety of disciplines, from engineering to medicine and ecology, and from drug delivery (pharmacogenomics) to medicinal chemistry. With theoretical foundations in information engineering (discrete mathematics, control theory, system theory, information theory and statistics), his research has delivered a suite of systems and products that has allowed him to carve out a niche within an extensive collaborative network. His research is both interdisciplinary and transdisciplinary with recent applications in water & waste water treatment, aquaculture, agriculture, dietary interventions, climate and environmental sciences, all mediated by microbial processes. The strength of his research lab is a bespoke high performance computing facility specifically for microbiome research, Orion cluster, which runs the workflows and software tailored for a ‘big data’ research projects.

Further reading

Want some in-depth background reading to get up-to-speed on the acronyms? Try these latest papers.

Challenges in microbial ecology: building predictive understanding of community function and dynamics
Stefanie Widder, et al.
The ISME Journal volume 10, pages2557–2568 (2016)

Metagenomic analysis reveals rapid development of soil biota on fresh volcanic ash
Hokyung Song et al.
Scientific Reports volume 10, Article number: 21419 (2020)

Machine Learning Approach to Predict Quality Parameters for Bacterial Consortium-Treated Hospital Wastewater and Phytotoxicity Assessment on Radish, Cauliflower, Hot Pepper, Rice and Wheat Crops
Aneeba Rashid et al.
Water 2022, 14(1), 116

Microbiomes in drinking water treatment and distribution: a meta-analysis from source to tap
Claire Thom et al.
doi: https://doi.org/10.1101/2021.08.30.457654