Bioinformatician & Postdoctoral Researcher
Manan Shah, PhD
Exploring microbial life.
Building the tools to understand it.
I study freshwater microorganisms, build bioinformatics workflows, and develop the data infrastructure that keeps research moving—from samples and sequencing to analysis, documentation, and reuse.
University of Duisburg-Essen · Germany
Curiosity meets practical problem-solving.
How do microbial communities respond to environmental change—and how can we make the data behind those answers easier to work with? These questions connect my research and the tools I build.
I am a postdoctoral researcher at the University of Duisburg-Essen, working with Environmental Metagenomics (Prof. Alexander J. Probst) and Aquatic Ecosystems Research (Prof. Florian Leese). My background spans environmental sequencing, microbial ecology, scientific computing, and research data management.
I bring experience from both sides of a sequencing project: collecting samples and generating data, then writing the code and building the infrastructure to analyse and manage them. Alongside my research, I support CRC-RESIST and Archean Park, contribute to laboratory automation, and teach researchers how to work confidently with computational tools.
What motivates me: a compelling biological question, a workflow worth improving, and helping someone take their next step towards independent research.
Research & Projects
My work connects ecological questions with the computational methods and research infrastructure needed to investigate them.
MICROBIAL ECOLOGY
Understanding life in freshwater
I use metabarcoding, metagenomics, and metatranscriptomics to investigate microbial diversity, community function, and responses to environmental stressors.
Research highlight: First-author work on bacterial genomic properties across 44 European freshwater lakes.
CURRENT RESEARCH
Generalists, specialists & microbial genomes
I investigate how microbial ecological strategies relate to environmental conditions, using genome-resolved metagenomics to explore generalist and specialist patterns in lake communities.
Focus: Connecting genomic information with ecological interpretation.
RESEARCH DATA MANAGEMENT
Making FAIR work in practice
For CRC-RESIST and Archean Park, I develop metadata structures, support repository workflows, and help researchers organise, document, and share their data.
Focus: Translating FAIR principles into practical routines using Dataverse, eLabFTW, and Nextcloud.
PIPELINES & AUTOMATION
Less repetition. More time for science.
I develop amplicon and metagenomics workflows and integrations connecting data collection, computational processing, repository uploads, and laboratory documentation.
In development: Nextcloud → computational analysis → Dataverse → eLabFTW workflows, with logs and metadata to keep analysis steps traceable.
METHODS & EVALUATION
Looking closely at long-read workflows
I evaluate long-read metagenomics approaches through practical analyses and student projects, examining assembly and annotation quality and frameshift-related issues in recovered genes.
Focus: Understanding how processing choices affect biological interpretation.
LABORATORY AUTOMATION
Connecting the bench to the data
Within the Genomics Core Facility, I contribute to automation tools for liquid-handling systems and workflows for sequencing data delivery.
Focus: Connecting laboratory protocols, sample metadata, sequencing outputs, and downstream analysis.
Technical Toolkit
- Bioinformatics & ecology: Metagenomics, genome-resolved metagenomics, metatranscriptomics, metabarcoding, microbial genomics, and taxonomic and functional community analysis.
- Programming & reproducibility: Python, R, Bash, Perl, Snakemake, Git, Conda environments, and container-based workflows with Singularity.
- Research data management: Metadata organisation, FAIR data practices, Dataverse, eLabFTW, Nextcloud, API integrations, and automated data transfer.
- Computing & infrastructure: Linux, high-performance computing, virtual machines, databases, web servers, and workflow troubleshooting.
- Sequencing & laboratory work: Illumina, Oxford Nanopore, Sanger sequencing, environmental sampling, mesocosm experiments, DNA extraction, and library preparation.
- Training & collaboration: Practical workshops, researcher onboarding, bioinformatics support, documentation, and student supervision.
Experience
Postdoctoral Researcher — Bioinformatics, Research Data Management & Automation
University of Duisburg-Essen | 2025–present
Environmental Metagenomics, Research Center One Health Ruhr, and Aquatic Ecosystems Research
- Manage research data and carry out initial amplicon sequencing analyses within the CRC-RESIST INF sub-project.
- Develop workflows connecting research data storage, computational analysis, metadata documentation, and repository-based data delivery.
- Help researchers adopt Dataverse, eLabFTW, and Nextcloud through practical workshops, onboarding, and clear documentation.
- Contribute to liquid-handling automation and sequencing data delivery within the Genomics Core Facility.
- Teach computational methods and guide student projects in bioinformatics, microbial ecology, and reproducible data analysis.
Doctoral Researcher
University of Duisburg-Essen | 2020–2025
Completed my PhD under the supervision of Prof. Dr. Jens Boenigk and Prof. Dr. Daniela Beisser, supported by a scholarship from the Bauer-Stemmler Stiftung. My thesis, Hidden Signals: Employing Taxonomy and Functions to Reveal Freshwater Ecosystem Resilience Using Meta-Omics Methods, explored microbial responses to environmental stressors using metabarcoding, metatranscriptomics, and metagenomics.
My research involved designing and running mesocosm experiments, generating RNA and DNA sequencing data, and developing bioinformatics workflows to investigate taxonomic and functional resilience. In parallel, I contributed to CRC-RESIST as a Research Data Manager, supporting data organisation, structured storage, and research data infrastructure.
Bioinformatician
PierianDx India Pvt. Ltd. | 2019, 2 months
Customised directed acyclic graphs for the Clinical Genomics Workbench to meet the requirements of participating institutes and hospitals.
Project Assistant II
National Collection of Industrial Microorganisms, CSIR–National Chemical Laboratory | 2016–2018
Worked with Dr. Mahesh Dharne on microbial genomics and environmental sequencing projects, analysing 16S, 18S, and ITS amplicons, shotgun metagenomes, and bacterial and viral genomes generated using Illumina and Oxford Nanopore platforms.
Contributed to sampling, DNA extraction, library preparation, and sequencing of material from rivers, hot springs, hypersaline lakes, and glaciers. Set up and maintained Linux-based HPC infrastructure, developed pipelines using Python, R, and Perl, maintained internal databases, and supported doctoral researchers with bioinformatics methods and custom scripts.
Trainee & Domain Analyst
Persistent Systems Ltd. | 2015–2016
Trainee: 3 months; Domain Analyst: 9 months
Supported bioinformatics and clinical research platforms, including caTissue for biobanking, InfoEd for research administration, OnCore for oncology clinical research management, and InForm for electronic patient data collection. Also contributed to testing and quality assurance for OncDRS.
Responsibilities included application administration, database management, troubleshooting, and end-user support.
Teaching & Supervision
I enjoy making computational methods approachable. My teaching combines practical exercises with the reasoning behind each step, helping students and researchers move from following commands to understanding and adapting their own analyses.
- Linux & scripting: The command line, remote computing with SSH, Bash scripting, text processing, and computational environments.
- Bioinformatics & metabarcoding: Sequencing data processing, analysis workflows, and interpretation of microbial community data.
- Research data management: Dataverse and eLabFTW workshops, metadata documentation, and practical data organisation.
- Student projects: Supervision and methodological support for microbial ecology and bioinformatics projects, including generalist–specialist analyses and long-read workflow evaluation.
- Course development: Contributing to a master’s-level Microbial Bioinformatics course connecting microbial ecology, genomics, and practical computational analysis.
Education & Training
- PhD in Biodiversity and Bioinformatics, 2025
University of Duisburg-Essen, Germany - Master’s in Bioinformatics
Bioinformatics Centre, Pune University, India - Bachelor’s in Biotechnology
Jai Hind College, Mumbai University, India
Additional training: Python Certification Training, TryCatch Institute, Mumbai; Diploma in Basic Web Designing, Computer Station Inc., Mumbai.
Languages: English (native), Hindi (native), Gujarati (mother tongue), German (A2).
Tools I Build & Share
- GitHub — mbshah: Scripts and tools developed during my research at NCIM and UDE.
- eLabFTW-ude-cli: CRC-RESIST tools for working with eLabFTW through its API.
- Dataverse Batch Uploads: Tools supporting batch uploads and research data delivery to Dataverse.
Some UDE GitLab resources are internal and may require institutional access.
Publications
- A roadmap for equitable reuse of public microbiome data
- Authors: Laura A Hug, Roland Hatzenpichler, Cristina Moraru, André R Soares, Folker Meyer, Anke Heyder, Data Reuse Consortium, Alexander J Probst.
- Journal: Nature Microbiology (2025)
- DOI: 10.1038/s41564-025-02116-2
- Unravelling the temporal dynamics of community functions in protists induced by treated wastewater exposure using metatranscriptomics
- Authors: Manan Shah, Guido Sieber, Aman Deep, Daniela Beisser, Jens Boenigk.
- Journal: Scientific Reports (2025)
- DOI: 10.1038/s41598-025-10083-1
- Breaking the Standard: Can Oxford Nanopore Technologies Sequencing Compete With Illumina in Protistan Amplicon Studies?
- Authors: Dana Bludau, Guido Sieber, Manan Shah, Aman Deep, Jens Boenigk, Daniela Beisser.
- Journal: Environmental DNA (2025)
- DOI: 10.1002/edn3.70084
- Genome-resolved metagenomics reveals the effect of nutrient availability on bacterial genomic properties across 44 European freshwater lakes
- Authors: Manan Shah, Till L. V. Bornemann, Julia K. Nuy, Martin W. Hahn, Alexander J. Probst, Daniela Beisser, Jens Boenigk.
- Journal: Environmental Microbiology (2024)
- DOI: 10.1111/1462-2920.16634
- Exploring the efficacy of metabarcoding and non-target screening for detecting treated wastewater
- Authors: Guido Sieber, Felix Drees, Manan Shah, Tom L. Stach, Lotta Hohrenk-Danzouma, Christina Bock, Maryam Vosough, Mark Schumann, Bernd Sures, Alexander J. Probst, Torsten, C. Schmidt, Daniela Beisser, Jens Boenigk.
- Journal: Science of The Total Environment (2023)
- DOI: 10.1016/j.scitotenv.2023.167457
- Temporal disturbance of a model stream ecosystem by high microbial diversity from treated wastewater
- Authors: Tom L. Stach, Guido Sieber, Manan Shah, Sophie A. Simon, André Soares, Till L. V. Bornemann, Julia Plewka, Julian Künkel, Christian Becker, Folker Meyer, Jens Boenigk, Alexander J. Probst.
- Journal: MicrobiologyOpen (2023)
- DOI: 10.1002/mbo3.1347
- The Asymmetric Response Concept explains ecological consequences of multiple stressor exposure and release
- Authors: M.Voss, CRC-RESIST Consortium, B. Suers.
- Journal: Science of the Total Environment (2023)
- DOI: 10.1016/j.scitotenv.2023.162196
- Spatio-temporal variation of the microbiome and resistome repertoire along an anthropogenically dynamic segment of the Ganges River, India
- Authors: Rachel Samson, Vinay Rajput, Rakeshkumar Yadav, Manan Shah, Mahesh Dharne.
- Journal: Science of The Total Environment (2023)
- DOI: 10.1016/j.scitotenv.2023.162125
- Microbial community shifts induced by plastic and zinc as substitutes of tire abrasion
- Authors: G. Sieber, D. Beisser, J. L. Rothenberger, M. Shah, M. Schumann, B. Sures & J. Boenigk.
- Journal: Scientific Reports (2022)
- DOI: 10.1038/s41598-022-22906-6
- Deciphering taxonomic and functional diversity of fungi as potential bioindicators within confluence stretch of Ganges and Yamuna Rivers, impacted by anthropogenic activities
- Authors:Rachel Samson, Vinay Rajput, Manan Shah, Rakeshkumar Yadav, Priyanka Sarode, Syed G Dastager, Mahesh S Dharne, Krishna Khairnar.
- Journal: Chemosphere (2020)
- DOI: 10.1016/j.chemosphere.2020.126507
- Shotgun metagenome guided exploration of anthropogenically driven resistomic hotspots within Lonar soda lake of India
- Authors: Jaya Chakraborty, Vibhavari Sapkale, Vinay Rajput, Manan Shah, Sanjay Kamble, Mahesh Dharne.
- Journal: Ecotoxicology and Environmental Safety
- DOI: 10.1016/j.ecoenv.2020.110443
- Metagenome sequencing to unveil microbial community composition and prevalence of antibiotic and metal resistance genes in hypersaline and hyperalkaline Lonar Lake, India
- Authors: Jaya Chakraborty, Vibhavari Sapkale, Manan Shah, Mahesh Dharne.
- Journal: Ecological Indicators (2019)
- DOI: 10.1016/j.ecolind.2019.105827
- Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges
- Authors: Rachel Samson, Manan Shah, Rakeshkumar Yadav, Krishna Khairnar.
- Journal: Science of The Total Environment (2019)
- DOI: 10.1016/j.scitotenv.2019.04.166
- Untapped bacterial diversity and metabolic potential within Unkeshwar hot springs, India
- Authors: Gajanan Mehetre, Manan Shah, Syed Dastager, Mahesh Dharne.
- Journal: Archives of Microbiology (2018)
- DOI: 10.1007/s00203-018-1484-4
Let’s talk science—and how to make it work.
Interested in freshwater microbial ecology, bioinformatics workflows, research data management, or laboratory automation? I would be happy to connect.