BDB-Lab January 2024 Updates
We have been naming our updates after the seasons, like (e.g., the Winter Update). But now, with our expansion across both Northern and Southern hemispheres, we're embracing a more global perspective. For instance, January brings winter in one hemisphere and summer in another!
Looking forward.
Luis will be in Heidelberg 22 January and Berlin 23-25. Time is very limited, but if you want to meet, get in touch. We're also open to virtual meetups for those who can't join in person.
At the end of January, we will start a new project, Extremely Open Science, where we will work on a scientific question (first question: what antimicrobial resistance genes co-occur in genomes and metagenomes and does it matter?). Join the EOS mailing-list to participate (or see the introductory video). The first stream will be on 29 January.
Focus of the Quarter: new projects
In the last few months, we have gotten two new grants to expand our work.
First, Luis got an ARC Future Fellowship to work on the small proteins of the global microbiome. This has become one of the central research aims in the group. We published macrel already in 2020, which was our first foray into this field. We wanted a tool that could be used for high-throughput mining of peptides from the microbiome and, since we couldn’t find one, we wrote our own: the main issue when using a tool for mining large scale datasets is the risk of false positives (while we can afford to miss some peptides given how much data is available). We then used it to build the AMPSphere and the GMSC. We are very proud of these steps, but, if anything, they have highlighted how little is still known about small proteins and peptides. This Future Fellowship will thus build on this and develop better methods to (i) predict small proteins in the genome, (ii) predict functions of small proteins, and (iii) validate them in the wet lab.
Then, we also got funding for SEARCHER to study antimicrobial resistance in the microbiome. Again, this builds on our past research on antimicrobial resistance (the EMBARK project). We have already seen that there are large differences between the outputs of different antibiotic resistance gene (ARG) predictors. Importantly, not all ARGs are the same, only some are truly dangerous to human health. This is mostly when they are on mobile elements, but understanding what makes an ARG dangerous will be a big question for us to tackle as part of the larger consortium, which keeps using multiple technologies (such as culturing, shotgun or functional metagenomics) towards monitoring antimicrobial resistance in the environment.
Both of these projects include PhD studentships and SEARCHER includes funding for a postdoctoral researcher. Contact us if this could be interesting for you.
People.
We are happy to welcome Alexandre Areias Castro to the Big Data Biology Lab. He is a computational biologist who will join the group as a PhD student in 2024. His main research interest is in microbial communities, and is currently working on a project regarding the effects of transition metals in gut microbiota. You can learn more about him here.
John Paul Makumbi (JP) is joining our lab as a visitor and will visit us in Australia in 2024. JP is a PhD student in the Microbiome@UP lab (University of Pretoria, South Africa). His project aims to characterise aquatic resistomes in African freshwater and wastewater microbiomes using metagenomics, metatranscriptomics, and ecotoxicology techniques.
In November, Svetlana joined the Segata lab (University of Trento, Italy) and will continue doing open source and open science in the global microbiome and metagenomics.
Congratulations to Anna, who got the Fudan super-postdoc grant to continue her work on the gut microbiome of Shanghai pet dogs.
Manuscripts.
Take a look at our new preprint: A catalogue of small proteins from the global microbiome, which is now available in Biorxiv. This manuscript describes the GMSC, which we described in an earlier newsletter.
SPIRE: a Searchable, Planetary-scale mIcrobiome REsource is now published at Nucleic Acids Research. SPIRE is a resource (see spire.embl.de) of annotated metagenomes and their downstream products (like MAGs) from the global microbiome.
Functional and evolutionary significance of unknown genes from uncultivated taxa is finally out in Nature. There are many ubiquitous, conserved, but previously unknown, proteins in microbiome data and we attempted to shed some light into them.
Conferences/talks.
Luis attended three conferences in Brisbane (Australia): International Peptide Symposium 2023, incob23, and ABACBS. He gave talks about the AMPSphere project (IPS and incob23) and presented the last work on SemiBin2 (talk at incob23 and poster at ABACBS).
Software tools.
SemiBin 2.0 was released (including bugfix releases 2.0.1-2). Several small improvements internally, including better error messages in many situations to help users debug issues they face. Also, SemiBin2 is now recommended.
Jug 2.3.1 was released, which adds support for Python 3.12
macrel 1.3.0 was released, which outputs the AMP density and is compatible with newer versions of Pyrodigal
argNorm 0.1.0 released. This enables users to compare the output of different ARG annotation tools. Vedanth also posted a video on what argNorm is and how to use it.