BDB-Lab Updates June 2025
Microbial functional role attribution and other updates
Upcoming
July 14–17. Anna will be at FEMS Micro in Milan and present a poster on long-read metagenomics of Shanghai pet dogs. Feel free to get in touch with Anna if you will be there!
July 20–24. Luis will present an abstract on our dog gut microbiome work at ISMB/ECCB2025. Before that, Luis will be in London (15–20 July) and will visit the University of Warwick on the 25th of July before returning to Australia.
Aug 17–22. Luis will be a speaker at the Decoding Microproteins Across Evolution and Disease GRC.
Sep 16–19. Luis will be a speaker at the EMBL Human Microbiome Symposium.
If you will be at any of these events, do get in touch!
Focus of the Quarter: Microbial functional role attribution by Alexandre Castro
Can you tell us a bit about yourself: what was your path to get here? I'm an applied biologist with a master's degree in bioinformatics (both degrees from Universidade do Minho, Braga, Portugal). During my master's, I started working on metabolic modelling. For my thesis, I worked on the development of a method to enhance metabolic models with enzyme constraints in an automated way, to characterise and analyse the effects of fluctuating trace metals in human gut microbial communities.
After concluding my degree, I had a short passage through the cybersecurity industry, where I worked as an application security analyst. After this experience, I decided to return to academia, as I wanted to expand my knowledge and capabilities, as well as contribute to scientific knowledge to the best of my ability. So, in 2023, when the opportunity to join Big Data Biology in Brisbane, Australia came up, I decided to join. I have been here since October 2024 and am currently working on my PhD thesis.
Despite my wet-lab background in my bachelor's, the shift to dry lab work, along with my experience in the tech industry, has allowed me to combine the use of computational tools and methods to expand our current knowledge and provide biological relevance to many of our observations.
What is microbial functional role attribution? Why is it important?
Microbial characterisation is a vital part of our work as microbiologists. When we take into account the communal nature in which microbes generally live, it is easy to understand that there is an underlying complexity.
Traditionally, when we look at microbes inside a community, we focus on either taxonomic composition or functional potential (the function of the genes). However, this ignores that microbial activity is highly contextual. A particular microbe can behave differently depending on metabolite availability, presence or absence of other microbes, and other factors, which are not taken into account by static analyses of communities. Therefore, we will establish functional roles, which characterise microbes by activity and move beyond current methods. These can be defined as the set of properties that a specific microbe possesses within a specific community setting and its impact in the whole community; for example, how independent a microbe is by observing how well it performs under different community settings.
How can we establish these roles, and what knowledge could they bring us?
Microbial functional roles can be assigned by looking at the simulated behaviour of a microbe under specific contexts. For that, this characterisation needs to be done in a dynamic way. By employing metabolic modelling and metagenomics, we will be able to provide evaluation scores for various parameters like the uptake profile of a certain microbe, its independence, and even factors like resistance to metabolic stress.
The final aim is a novel approach to characterise microbial units beyond traditional taxonomic classification, and instead characterising them by behaviour.
For readers interested in an overview of this approach, I have written an introductory blog post on metabolic modelling titled A (not so) short introduction to Metabolic Modelling.
Where can people find you and get in touch? Feel free to contact me by e-mail, or you can also find me on Twitter!
Updates
People
Vedanth was accepted at Stanford University to pursue his undergraduate studies, congrats!
Hongjie Zhang and Yaozhong Zhang, both from Nanjing, will be joining us for a one-year research visit in Brisbane. Hongjie is a PhD student at Hohai University, focusing on microbial community structure, function, assembly mechanisms, and potential interactions in aquatic ecosystems. Yaozhong is a direct PhD student at Nanjing Agricultural University, focusing on One Health, soil pathogens, antibiotic resistance genes, and microbial ecology, especially the environmental risks and transmission of soil-borne pathogens.
Milestones
Yiqian defended her PhD thesis. Congratulations, Dr. Yiqian Duan!
Anil successfully articulated from the MPhil to the PhD.
Papers & tools
argNorm 0.8.0, v1.0.0, and v1.1.0 released (with the latest release, v1.1.0 having been done today, 24 June). And the paper is now published at Bioinformatics. Congrats to Svetlana & Vedanth!
Review paper co-authored by Yiqian & Luis is now published at ACS Accounts of Chemical Research.
We just released the first version of SPIREpy, a command-line tool and Python library to query the SPIRE database (see also Schmidt et al., 2024).
Alumni news
Célio Dias Santos Júnior is now a Full Professor in the College of Food Science and Technology at Huazhong Agricultural University (Wuhan). Congrats, Prof. Célio!
Conferences & talks
Vedanth presented an online poster on argNorm at the Applied Bioinformatics and Public Health Microbiology conference.
Anil presented at the Crop-to-Kitchen symposium organised by Coronial and Public Health Sciences Services, Queensland Health.
Juan is invited in CARe (Centre for Antimicrobial Resistance Research) meeting, at the University of Gothenburg.
Luis delivered a remote presentation at the 15th International Conference of Pakistan Society for Microbiology (FIBC-PSM 2025) in Pakistan.
Other
Luis has joined the editorial board of Microbiome as an Associate Editor.