Integrative Microbiology, Multi-Omics & Applied Bioinformatics
MicroBiomica Lab at UCD studies microbial systems that affect food safety, public health, antimicrobial resistance and One Health.
We combine culture-based microbiology, direct-from-sample sequencing, long-read genomics, multi-omics and reproducible bioinformatics to make complex microbial communities easier to detect, interpret and act on.
Selected funders, collaborators and project partners
Explainer
Many microbial systems remain poorly characterised. This includes organisms that are difficult to culture, complex microbiomes, mobile genetic elements, antimicrobial resistance genes and microbial interactions that are not visible using standard approaches.
MicroBiomica Lab investigates these systems by connecting laboratory microbiology with computational analysis.
Our work asks:
Latest Updates
A quick snapshot of recent lab news, public engagement, and media mentions. See the full news page for the latest stories and archive.
MicroBiomica contribution to a €2.44 million programme in long-read metagenomics, microbial dark matter and predictive modelling.
Read the project story TalksPublic lecture exploring how beneficial and harmful microbes shape food systems and health.
Watch the talk BlogA blog reflection on belonging, inclusion and the culture of scientific meetings.
Read the blogResearch
Our work connects microbial discovery, food-system safety, pathogen genomics, antimicrobial resistance and reproducible analysis to generate insight for public health and safer food systems.
We study hidden and poorly characterised microbial diversity in complex communities. Fermented foods, model microbiomes and environmental systems are used to investigate microbial function, resilience and interaction.
We examine microbial communities across food systems to understand safety, spoilage, persistence and microbial risk.
We use genome sequencing, metagenomics and bioinformatics to study pathogens, antimicrobial resistance and biological risk across food, animal, human, environmental and built-environment contexts.
We develop and apply reproducible workflows for microbial genomics, microbiome analysis, long-read sequencing and multi-omics integration.
People & Culture
MicroBiomica Lab at UCD is a collaborative research environment for students, researchers and partners working across microbiology, bioinformatics, food safety and public health.
Principal Investigator
Assistant Professor, UCD School of Biology and Environmental Science
Principal
Investigator, MicroBiomica Lab at UCD
Dr Guerrino Macori leads research in applied bioinformatics, food microbiology, pathogen genomics and microbiome analysis. His work focuses on microbial systems relevant to food safety, public health and One Health.
The lab integrates experimental and computational approaches to study microbial communities, biological risk, antimicrobial resistance and the interpretation of complex sequencing data.
Guerrino teaches and supervises students in applied bioinformatics, pathogen genomics, food safety and microbiome analysis.
Outside the lab: Guerrino enjoys travelling, riding his Vespa, exploring new technologies and creative projects, and finding unexpected links between science, nature and everyday life. He enjoys cooking for friends, spending time outdoors and travelling with Geoffrey, his sweet Standard Poodle, who brings plenty of joy and adventure into daily life whenever possible. He is involved in his local community and volunteers with Parkrun, where both Guerrino and Geoffrey also enjoy taking part on Saturday mornings - although usually not for distances much beyond 5 km.
PhD Candidate
Computational Reconstruction of Synthetic Microbiomes for Predicting Pathogen Dynamics
Mingwei explores synthetic microbiomes as controlled model systems for investigating microbial community dynamics and pathogen behaviour.
PhD Candidate
AI-Enhanced Deciphering of Microbial Dark Matter
Jacques investigates microbial dark matter to understand how functional traits, particularly antimicrobial resistance, disseminate through complex microbiomes.
Outside the lab: Jacques enjoys cooking, home fermentation and collecting houseplants, with a long-term goal of making the office just slightly more botanical. He also likes exploring Ireland, especially places with good scenery, good food or both.
Visiting PhD Researcher
Tallinn University of Technology, Estonia
Psychrotrophic bacteria in food spoilage and safety
Atefeh’s research focuses on applying advanced sequencing and multi-omics approaches, including full-length 16S rRNA and ITS sequencing, whole-genome sequencing, and shotgun metagenomics, to investigate microbial succession and the functional adaptation of spoilage-associated microorganisms in ready-to-eat foods.
Outside the lab: Atefeh enjoys cooking and baking so much that, if she had another chance, she would probably become a baker instead of a microbiologist.
Visiting PhD Researcher
Università di Padova, Italy
Pathogens and spoilers persist in food environments, posing challenges for food safety
Sara’s research investigates how foodborne pathogens and spoilage bacteria persist in food-processing environments despite exposure to cleaning, processing and other stress conditions. Her project focuses on bacterial dormancy as a possible survival strategy, using microbiology and molecular biology approaches to explore the pathways that allow persistent bacteria to withstand stress and reappear over time.
Outside the lab: Sara enjoys travelling, good food, live music, and spending time with her dog, Hubble. Her beloved companion often accompanies her to the office, where he doubles as an unofficial therapy dog, always ready to offer a cuddle to anyone in need.
MSc Student
Validation and optimisation of Oxford Nanopore sequencing workflows for serotyping of porcine bacterial pathogens
Mahevish’s research focuses on validating and optimising Oxford Nanopore sequencing workflows for serotyping the porcine pathogens Streptococcus suis and Actinobacillus pleuropneumoniae. The project evaluates laboratory and bioinformatics workflows, comparing Nanopore predictions with conventional serotyping and public genome datasets to support reliable serotyping.
Professional Profiles:
LinkedInOutside the lab: Mahevish enjoys gardening, painting, reading and creative activities. She also loves community work, spending time with children, and outdoor adventures like mountain biking.
For funded PhD, postdoctoral and research staff opportunities, see Join the Lab and follow official UCD recruitment channels and announcements shared by the PI or School. Academic collaboration and project enquiries are welcome by email.
A few short alumni spotlights give a quick sense of the people who have trained in the lab and where their experience has taken them next.
Katia explored probiotic bacteria in water kefir using culture-based and sequencing methods, learning culturing, DNA extraction, and full-length 16S rRNA sequencing while also writing a literature review and final poster.
"My time in Dr. Macori's lab enhanced me as a scientist and gave me the skill set that helped me pursue my PhD in food science at the University of Illinois, Urbana-Champaign."
Rayna wrote her thesis on novel sequencing technologies to explore the microbiome of water kefir, building confidence and independence through close supervision and a structured experimental workflow.
"Working with Dr. Macori was very beneficial for me, as it allowed me to become more independent and confident in my research skills. I am currently working in a microbiology lab."
Marine explored microbial diversity in water kefir using advanced sequencing approaches for food safety and probiotic strain identification during an international training placement.
Project focus: Explore microbial diversity in water kefir using advanced sequencing techniques for food safety and probiotic strain identification.
Samuel completed a taught MSc thesis on bacteriophages from campus water sources and later progressed to a PhD within the SAFEGREEN project at Teagasc under Dr Kaye Burgess, with Dr Guerrino Macori as academic advisor.
His current PhD examines environmental contamination sources in fresh produce systems, with a focus on Listeria, pathogenic E. coli and Salmonella at the interface of microbiology, environmental monitoring, and metagenomics.
Hatay used water kefir as a model system to study how environmental conditions and substrates shape microbial diversity, and how communities can be deconstructed and reconstructed.
The project highlighted resilient lactic and acetic acid bacteria, substrate-dependent shifts in diversity, and the value of functional profiling for designing synthetic communities with desired metabolic properties.
Holly's thesis focused on environmental bacteriophages from a man-made lake on UCD campus, assessing their activity against antimicrobial-resistant bacteria and analysing prophage content in Aeromonas strains.
She later accepted a research assistant position in Maynooth University and will start a PhD at the University of Galway in September 2026.
Xiaopeng evaluated propidium monoazide treatment combined with full-length 16S rRNA gene sequencing to distinguish viable bacterial populations in complex microbial communities.
The project explored how viability-focused sequencing can improve interpretation of mixed microbial systems and support more accurate community profiling.
Hover or focus a card to flip and read the short story behind each alumni profile.
Teaching
Alongside research supervision, Dr Guerrino Macori contributes to undergraduate and graduate teaching across microbiology, genomics and environmental biology at UCD.
Introduction to microbiome analysis, experimental design, techniques, bioinformatics and case studies.
Introduction to pathogen genomics, sequencing approaches and bioinformatics applications for detecting and studying pathogens.
Introduction to microbiology of foods, spoilage, foodborne organisms and the role of microbes in food production.
Research training and advanced project work, literature review, practical skills and thesis development for the MSc Biological & Biomolecular Science.
Selected Outputs
This section highlights selected publications, educational resources, commentary and public-engagement outputs associated with the lab’s research and teaching. For a complete publication record, see the external researcher profiles linked on the site.
A comprehensive overview of food-spoilage microorganisms and the genomic, metagenomic and multi-omics approaches used to investigate them.
A large-scale analysis showing how cheese-associated microbial communities influence product quality, sensory characteristics and safety.
A metagenomic investigation of fermented foods linking microbial community composition with substrate type, functional traits and antimicrobial-resistance genes.
A comprehensive review detailing how high-throughput sequencing technologies and multi-omics are providing novel insights into the complex microbial ecosystems of fermented dairy products, their dynamics, and their contributions to flavour and quality.
A genomic study examining colistin resistance, plasmid diversity and the distribution of the mcr-1 gene across pathogenic E. coli lineages.
The genomic and phenotypic description of a previously uncharacterised bacterial species recovered from a hospital environment.
A genomic investigation of historical foodborne Salmonella isolates identifying plasmids carrying metal-resistance and multidrug-resistance clusters.
Demonstrated the application of whole-genome sequencing to investigate and reconstruct SARS-CoV-2 transmission within healthcare settings.
A longitudinal genomic analysis of viral evolution during persistent infection in an immunocompromised patient.
Practical recommendations for improving the standardisation, portability and reproducibility of wastewater genomic-surveillance workflows.
An interactive educational resource that introduces sequencing concepts and read assembly through a practical classroom activity.
An educational technology output exploring the use of generative AI and interactive narratives to support learning and assessment.
A publication mapping the design of scientific meetings to build an inclusive culture and create welcoming environments for historically marginalised groups.
Developed by lab PhD candidate Jacques Olivier and used in Dr Guerrino Macori’s Food Microbiology module (ENVB30110) at UCD, Microdle is an interactive browser-based word puzzle where players identify a hidden food-associated microbe in eight guesses. Focusing on bacterial pathogens, spoilage organisms, yeasts, moulds, viruses and parasites across food safety, spoilage and fermentation, the game combines letter-by-letter feedback with progressive biological hints and end-of-game fact cards that explain what each microbe is and why it matters in food systems.
Public lecture with Prof Shea Fanning on the role of beneficial and harmful microbes in food systems, food safety and health.
A blog reflection on the EDI session at Annual Conference 2026, co-authored with colleagues and published by the Microbiology Society.
A Pride Month profile from the Microbiology Society highlighting Guerrino Macori's experiences and reflections as an openly LGBTQIA+ academic.
Our research outputs are widely integrated into policy frameworks to guide public health and food safety actions. A trackable count shows a robust network of scientific influence across international and local guidelines.
Note: 36 of the citing documents were subsequently cited 513 times across a further 367 policy documents, indicating sustained adoption in food safety, antimicrobial resistance, genomic surveillance, and pandemic preparedness guidelines.
Selected Media
Selected media coverage that highlights the lab's teaching, research and public-facing work.
UCD coverage of the HEA recognition of two UCD teaching and learning projects, including FAIR Game led by Guerrino Macori.
UCD coverage relating to genomic surveillance and public-health research, including SARS-CoV-2 sequencing and hospital transmission analysis.
Join the Lab
MicroBiomica Lab welcomes students and early-career researchers working across microbiology, genomics, bioinformatics and One Health. We are happy to support competitive applications for funded PhDs, postdoctoral fellowships and visiting scientist placements.
Funding & Mentorship
We are happy to supervise and mentor early-career researchers, and to support applications for scholarships and mobility funding such as Erasmus+ visitor scientist placements, Marie Skłodowska-Curie Actions postdoctoral fellowships and Research Ireland fellowships.
Get in touch
Discuss an applicationStudent Projects
We also welcome project enquiries for 4th year student projects and MSc theses across Zoology, Cell and Molecular Biology, Environmental Biology, and BBNL.
Discuss supervision
Join the lab formLab Life
A snapshot of MicroBiomica Lab at UCD across research meetings, conferences, teaching, outreach, collaboration and everyday scientific work.
We collaborate with academic, clinical, public-health, food-sector and computational partners on projects involving microbiology, sequencing, microbial ecology, genomic epidemiology, antimicrobial resistance and food-system safety.
Dr Guerrino Macori
Assistant Professor
UCD School of Biology and Environmental
Science
Affiliations: UCD Conway Institute, UCD Centre for Food Safety, and UCD Institute of Food and Health.
University College Dublin
Belfield, Dublin 4, Ireland