21 AUG — #ISME20 Day 5! 🦠 Today we're exploring antibiotic resistance, virus visualisation and a new reversible fixation method. Check out our presentations below! 🔬🌏

20 AUG — #ISME20 Day 4! 🦠 Today we're exploring human microbiomes and their plasmids, microbial biogeography, methane cycling and high throughput isolation. Check out our presentations below! 🔬🌏

18 AUG — #ISME20 Day 2! 🦠 Today we're exploring microbial functional roles, 16S and gene cluster tools, foodborne pathogens and rumen microbiomes rewiring. Check out our presentations below! 🔬🌏

17 AUG — #ISME20 Day 1! 🦠 Today we're exploring AI (machine learning and LLMs), phage phylogeny, novel species recovery and the complex rumen microbiome. Check out our presentations below! 🔬🌏

The Centre for Microbiome Research has a large contingent going to #ISME20 in Auckland next week. See below for our talks, posters and panels! 🌏🔬🦠 Discover new tools and methods to uncover microbial diversity, interactions and function, from individual cells and viruses to global microbiomes.

Out today in Nature Microbiology: a paper that started in 2021 with an email from @sullivan-lab.bsky.social. Subject line: "Crazy ideas". www.nature.com/articles/s41... 1/23

🎉 Big congratulations to Dr James Volmer and @luispedrocoelho ! James has been awarded a TRI LINC Grant, and Luis has received a TRI Translation Fellowship. Both are fantastic opportunities to translate their research into clinical applications and drive real-world impact.👏🚀

New paper in mSystems! 🧵 - how much of your metagenome is actually bacterial/archaeal DNA? For many samples, nobody knows. We built SingleM prokaryotic_fraction (SPF) to answer this, then ran it on >100,000 public metagenomes. 🧬🖥️🦠 Here's what we found 👇 doi.org/10.1128/msystems.01062-25

First cake of the year! Thanks Pam!

The ISME Early Career Scientist Committee is glad to begin the year by spotlighting @aroneys.bsky.social, a Postdoctoral Researcher at QUT, and his paper, “Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes.” doi.org/10.1038/s415... (1/2)

Celebrating Excellence at the Centre for Microbiome Research! We’re thrilled to share that Gene Tyson, @benjwoodcroft.bsky.social and @luispedrocoelho.bsky.social have once again been named Highly Cited Researchers for 2025 by Clarivate! #HighlyCited2025

“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla. doi.org/10.1038/s415... @benjwoodcroft.bsky.social @rhysnewell.bsky.social 🧵1/6

Spoiled today by two fantastic talks! Second by Prof Greg Cook about inhibiting greenhouse gas emissions in agricultural soils.

Excited to hear from Prof Lindsay Hall at our combined CMR and @ace-uq.bsky.social meeting! Bifidobacterium is really important for setting up our gut in early life.

Check out our teams paper on SingleM, a metagenomic taxonomy profiler that doesn't ignore unknown species! @benjwoodcroft.bsky.social @aroneys.bsky.social doi.org/10.1038/s41587-025-02738-1

Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper - Nature Biotechnology

Novel microbial species in metagenomes are identified using conserved regions within universal marker genes.

doi.org

Ben J Woodcroft@benjwoodcroft.bsky.social · last yr.

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 🧵

Check out our team's latest paper, published in @ISMEJournal, introducing GenomeFISH—an innovative, genome-based FISH technique enabling strain-level visualisation of microbial communities @pam-engelberts.bsky.social doi.org/10.1093/isme...

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

doi.org

We used Great Oxidation Event as a planet-sized "fossil" to add ancient dates to the Bacterial tree of life. @theconversation.com and @science.org articles show oxygen was used by non-cyanos before that cataclysm, surprisingly. theconversation.com/1-trillion-s... www.science.org/doi/10.1126/...

1 trillion species, 3 billion years: how we used AI to trace the evolution of bacteria on Earth

Until now, it’s been very hard for scientists to establish a detailed timeline of the early evolution of bacteria.

theconversation.com

A fantastic talk from CMR's Prof Phil Pope (@microbesrule.bsky.social) at today’s QUT School of Biomedical Sciences seminar series. Phil shared how his team uses meta-omic technologies to interrogate the complex microbial communities that are integral to animal health, nutrition and gut function.

New Postdoctoral Research Fellow opportunity at CMR! We are looking for a Gut Microbiome Specialist and Microbial Ecologist to join our team as we aim to unravel the complex mechanisms of methanogenesis in the cow rumen. Learn more and apply here: lnkd.in/gs83q68J

Don't miss the 2025 Science Festival Brisbane! CMR's Prof Gene Tyson will take part in a panel discussion at the session "Love Your Guts: Health and the Microbiome"—a fascinating exploration of how microbes in our gut shape our health. Find the full program below. worldsciencefestival.com.au

World Science Festival Brisbane 2025

World Science Festival Brisbane (WSFB) celebrates its spectacular 10th anniversary in 2025 with the vision, Infinite Awe. There are over 200 ways to experience this epic 10 day festival, which brings ...

worldsciencefestival.com.au

Congrats to CMR's Camila Ayala Pintos on submitting her PhD thesis! It has been a pleasure to watch your hard work and dedication over the past few years, and we are so proud of everything you've accomplished. And, as always, thank you to Pam for an incredible cake 🎂🎉

Congrats to CMR PhD student @iambrettb.bsky.social for taking home the best student speaker prize at this year's MGE Aus meeting 🥳 And another congrats to Ms Lara Carrington on securing the Australian Society for Microbiology Queensland Branch Mobile Genetic Elements Award. Excellent work both 👏👏

Ben J Woodcroft@benjwoodcroft.bsky.social · 2y ago

Wrapt for @iambrettb.bsky.social winning the student prize at @mgeaus.bsky.social - "Estimation of phage species trees using gene/species tree reconciliation". Hoping we can have an impact on viral phylogeny with these new methods, carefully applied.

The Centre for Microbiome Research (CMR) is now engaging with our community on Bluesky! We look forward to using this platform to have meaningful conversations and build stronger connections with researchers and community members around the world. CMR: Asking questions no one has asked 🦠🔬