Pam Engelberts

📣 New paper alert! Just out in Cell Reports! pubmed.ncbi.nlm.nih.gov/40644298/
Thrilled to share that we have discovered a brand-new anti-phage defense system! Bacteria have evolved various defense strategies (CRISPR etc) to counter phage attacks. We found a new one - fascinating and dramatic
⚔️🦠❄️🔬

We (with Clement Coclet, not on Bsky) had the chance to work on a broad "state of viromics" review. We tried to use this to give an overview of how the field changed over the last ~ 15 years, and also what we think are some of the major remaining challenges. Full-text access at -> rdcu.be/excHt

Thank you Courtney! GenomeFISH should work on roots as well, as long as you can get the genomes of the microbes of interest for probe generation :)

Are you interested in microbes that are rare but active? We combined BONCAT with SIP and metaproteomics to improve the recovery of labeled proteins from such microbes. In this case, it illuminated a new anaerobic syntrophic acetate-oxidizing bacterium.

tinyurl.com/a8j29dsr
#microbiomesky #microsky

Logo for the Sandpiper website

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

In the target population, the GenomeFISH and DAPI signal are positively correlated, resulting in a normalised signal intensity of ~1 when dividing the GenomeFISH signal by the DAPI signal. For closely related strains, this value drops below 1, as the GenomeFISH signal reduces in strength.

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Thanks Nicholas! We normalise the GenomeFISH signal to the DAPI signal. As genome copy number and image plane orientation can all influence the signal strength in the target population and probes will also bind to closely related strains, normalisation is key.

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Thanks Steve!

No need for design :) GenomeFISH probes are generated from single amplified genomes or isolate genomes by simply fragmenting the entire genome and fluorescently labelling the fragments.

Given the high-throughput nature of GenomeFISH, its superior sensitivity, and its phylogenetic resolution, we hope it will become widely used for the visualisation of complex microbial communities.

It also enables GenomeFISH to reach superior signal intensities compared to traditional FISH, allowing it to visualise microbial lineages that are challenging to visualise with traditional FISH, such as members of the Patescibacteria.

As a result, GenomeFISH can distinguish between strains with up to 99% ANI in mock communities and environmental samples.

By targeting the entire genome, GenomeFISH overcomes the inherent limitations of traditional FISH, circumventing the need for probe design and optimisation, while increasing sensitivity and specificity.

GenomeFISH probes can be rapidly generated from single cell genomes obtained from environmental and clinical samples, which are amplified, fragmented, fluorescently labelled, and hybridised to visualise the target microorganism in situ.

GenomeFISH is an innovative, genome-based FISH approach that couples high-throughput single-cell genomics with whole-genome hybridisation to visualise microbial communities.

GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities Abstract. Fluorescence in situ hybridisation (FISH) is a powerful tool for visualising the spatial organisation of microbial communities. However, traditio

Very excited to share the first paper out of my Postdoc @CMR:

GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities.
@sjmcilroy.bsky.social @jamesvolmer.bsky.social @benjwoodcroft.bsky.social

doi.org/10.1093/isme...

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Hello BrisJAMS Community :)

BrisJAMS returns this July with an Antimicrobial Resistance Special featuring three fantastic speakers.

📅 Wednesday, 23 July 2025
🕕 6:00–7:30 PM
📍 The Burrow, West End
🍽 Free food provided!
This free event is open to all in the microbiology community.

ISME travel award application The International Society of Microbial Ecology (ISME) would like to support early career scientists to attend the MBK/CEESME joint conference, Thessaloniki, Greece, 22-24/09/2025. By investing in th...

We are happy to announce that @isme-microbes.bsky.social offers 12 travel awards for early-career scientists who will join the #mbkceesme2025 conference.
forms.gle/ExVETmU6XZYz...

First code release of "SingleM for dsDNA phage"! Lyrebird scans metagenomic reads for marker genes to give a “phage community profile”. It detects many novel phages, many more than standard contig-centric methods. @benjwoodcroft.bsky.social @emerge-bii.bsky.social wwood.github.io/singlem/Lyrebird

Short-read metagenomic sequencing cannot recover genomes from many abundant marine prokaryotes due to high strain heterogeneity and platform-inherent GC bias (likely viruses, too), but Nanopore long reads can address this. A results thread on our recent preprint 🧵.

Please check out our recent preprint from @ace-uq.bsky.social researcher’s @stevenjrobbins.bsky.social, @xrefugee13.bsky.social, and former ACEr @pam-engelberts.bsky.social on their work generating the Great Barrier Reef Microbial Genomes Database (GBR-MGD).

The planktonic microbiome of the Great Barrier Reef Large genome databases have markedly improved our understanding of marine microorganisms. Although these resources have focused on prokaryotes, genomes from many dominant marine lineages, such as Pela...

Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂

www.biorxiv.org/content/10.1...

BONCAT-Live for isolation and cultivation of active environmental bacteria In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including in association with plants and animals. Their physiological...

BONCAT-Live for isolation and cultivation of active environmental bacteria www.biorxiv.org/content/10.1... #jcampubs

📅 Join us at The Burrow | Wednesday, April 30th at 6 PM
An evening of insightful talks 🎤, great company 🧑‍🔬, and delicious food 🍽️
Come connect, learn, and enjoy the night with our fantastic line-up of speakers. We’d love to see you there!
#brisbanescience #microbiology #jams #academia

GTDB Release 10-RS226 (16th April 2025) has been published
gtdb.ecogenomic.org

Postdoc available in Grenoble (France), funded by the ERC SymbiOCEAN, to work on the metabolic connectivity in planktonic photosymbiosis. 👉Passionate by symbiosis & marine protists? skills in bioinfo and molecular biology? Join us! Info: emploi.cnrs.fr/Offres/CDD/U...

#protistsonsky #SymbioSky

Please repost: Postdoc position in antibiotic discovery in a large multidisciplinary project combining high-throughput approaches, microscopy, AI, and hit-to-lead optimization at @umontreal.ca and @mila-quebec.bsky.social. Apply to ML.Antibiotics@gmail.com. See
lnkd.in/dVVk4N3s. #microsky

Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing Abstract. Most microorganisms cannot be cultured in isolation, necessitating sophisticated methods for studying their (eco)physiology. While numerous appro

Want to know who’s replicating and who’s just hanging out in your enrichment cultures? Our new study led by @soansi.bsky.social shows how @nanoporetech.com long-read sequencing can reveal replication states, shedding light on microbial growth. 🦠🧬

See our latest publication: doi.org/10.1093/isme...

Microbiota in inflammatory bowel disease: mechanisms of disease and therapeutic opportunities Nature Reviews Microbiology, Published online: 10 March 2025; doi:10.1038/s41579-025-01163-0In this Review, Iliev, Ananthakrishnan and Guo explore the gut microbiota in inflammatory bowel disease, highlighting bacterial and fungal components, immune…

New online! Microbiota in inflammatory bowel disease: mechanisms of disease and therapeutic opportunities