Author | Lightnews

Marco Gabrielli @mgabrielli.bsky.social · 4d

Have you ever wondered what is the best way to sample a biofilm?

Here we take real cm-scale biofilm sequencing data to show the impact of sampling strategies.
Better check this out before your next sampling campaign!

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 11d

Small-scale biogeography of biofilms and its implications for sequencing-based studies https://www.biorxiv.org/content/10.1101/2025.10.13.682146v1

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Marco Gabrielli @mgabrielli.bsky.social · 20d

Does the sense of cringiness when doing that in fromt of another person decrease?

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Reposted by Marco Gabrielli

Eawag Aquatic Research @eawag.bsky.social · Sep 5

Eawag scientist Serina Robinson receives the ERC Starting Grant. She is investigating how microbial enzymes bind PFAS.

👉 www.eawag.ch/en/info/port...

@erc.europa.eu @ethz.ch #Eawag #pollutants #foreverchemicals #ERCStG

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Reposted by Marco Gabrielli

Julie Johnston @queermsfrizzle.bsky.social · Jun 19

Protect Trans Scientists.

cowritten with a lot of amazing people (I tagged those I could find but there are so many more incredible folks)
www.science.org/doi/10.1126/...
@thepunkscientist.bsky.social @jlw-ecoevo.bsky.social @bfrancescol.bsky.social @drsueishaq.bsky.social

Protect transgender scientists

Transgender and gender nonconforming (TGnC) people are a primary target of the Trump administration. Multiple executive orders seek to erase TGnC protections; mandate denial of gender identity; and ba...

www.science.org

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Reposted by Marco Gabrielli

Rolf Kümmerli @rkmicrobes.bsky.social · Jun 10

We are looking for a highly motivated postdoc to work on pathogen interactions. Please send in your application via

jobs.uzh.ch/job-vacancie...

UZH: Postdoctoral researcher in microbiology

The Department of Quantitative Biomedicine is an interdisciplinary biomedical research unit that combines basic science with biotechnological and medical research, using both experimental and computat...

jobs.uzh.ch

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Reposted by Marco Gabrielli

Caitlin R Proctor @caith2o.bsky.social · Jun 5

Having fun catching up with #Eawag at #MEWE11

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Reposted by Marco Gabrielli

Segata Lab @cibiocm.bsky.social · May 19

There is still time to apply for #PhD studentships with us!

Thanks for spreading the word.

#phdchat #phdlife #academiclife

Segata Lab @cibiocm.bsky.social · Apr 18

OPEN CALL for PhD positions in our lab through the semm_it program:

1️⃣ Microbiome signatures of early on-set colorectal cancer
2️⃣ High-resolution computational metagenomics for the study of human microbiome transmission

More info: www.semm.it/education/op...

Apply by June 9!

Open Positions | SEMM European School of Molecular Medicine

www.semm.it

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Reposted by Marco Gabrielli

Julie Johnston @queermsfrizzle.bsky.social · May 11

Please support my students kickstarter to finish an educational wastewater video game we started building!

I taught an interdisciplinary capstone class video game where programmers, artists, sound designers, and education students could work together!

www.kickstarter.com/projects/que...

What the Floc: Educational Wastewater Video Game

Educational video game where players operate a wastewater treatment plant to protect the city and environment from pollution!

www.kickstarter.com

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Marco Gabrielli @mgabrielli.bsky.social · Apr 4

Never used for isolates, but yes, I also agree with your assumption

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Marco Gabrielli @mgabrielli.bsky.social · Apr 4

In case of metagenomes, phyloflash (hrgv.github.io/phyloFlash/) is an option

phyloFlash

phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore the phylogenetic composition of an Illumina (meta)genomic dataset.

hrgv.github.io

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Marco Gabrielli @mgabrielli.bsky.social · Mar 21

This might be very basic, but what about generating different scenarios with different hypothesis (e.g., different eqs to describe a given phenomenon) and focusing on comparing the impact of those hypothesis?
Could also be couple with sensitivity and uncertainty analysis for various parameters

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Reposted by Marco Gabrielli

Michael Brockhurst @brockhurstlab.bsky.social · Feb 6

☎️ Calling #MEvoSky ☎️

2x 5-year research associate / research assistant positions in experimental evolution

ERC-funded project: How do mobile genetic elements and defence systems shape bacterial genome evolution?

Join the friendly and exciting @mermanchester.bsky.social community in Manchester!

Michael Brockhurst @brockhurstlab.bsky.social · Feb 6

🚨 Job alert 🚨 — are you interested in understanding how mobile genetic elements and defence systems shape bacterial genome evolution? 🧬 🧪 🧫 🦠 2x 5-year research positions available in experimental evolution @mermanchester.bsky.social Join us! #microsky
www.jobs.manchester.ac.uk/Job/JobDetai...

Research Associate in Experimental Evolution:Manchester

www.jobs.manchester.ac.uk

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Reposted by Marco Gabrielli

Viktoria Cologna @colognaviktoria.bsky.social · Jan 20

Our global study on the state of trust in scientists is now out in Nature Human Behaviour! 🥳

With a team of 241 researchers, we surveyed 71,922 people in 68 countries, providing the largest dataset on trust in scientists post-pandemic 👇🧵https://www.nature.com/articles/s41562-024-02090-5

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Reposted by Marco Gabrielli

IWA MEWE 2025 @mewe2025.bsky.social · Jan 8

📢 Just 2 days left for #MEWE11 abstracts! Deadline: Jan 10
Submit ASAP at mewe11.ce.gatech.edu/call-for-papers

The 11th International Water Association Conference on Microbial Ecology and Water Engineering awaits your research! 🦠💧
#microbialecology #microbiomeengineering #water #sustainability

Call for papers – IWA MEWE-11 CONFERENCE

mewe11.ce.gatech.edu

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Reposted by Marco Gabrielli

IWA MEWE 2025 @mewe2025.bsky.social · Dec 16

📢 Abstract submission deadline for #mewe11 extended to Jan 10, 2025! Early submissions (before Dec 15) are now under review. Later submissions reviewed rolling basis.

Learn more & submit: mewe11.ce.gatech.edu/call-for-papers

Call for papers – IWA MEWE-11 CONFERENCE

mewe11.ce.gatech.edu

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Reposted by Marco Gabrielli

A. Murat Eren (Meren) @merenbey.bsky.social · Dec 16

We are very happy to announce a free-to-attend #anvio workshop and ECR symposium in Oldenburg to discuss integrated microbial 'omics and learn applications of anvi'o.

More information and application link (application deadline is Jan 10): anvio.org/workshops/20...

Please apply and/or circulate 😇

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Marco Gabrielli @mgabrielli.bsky.social · Dec 6

Do you loop over the samples or parallelize them? I usually run tasksblike this in parallel using a Slurm array

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Marco Gabrielli @mgabrielli.bsky.social · Nov 30

Be sure to give a read to Alessio's latest work! Cool combination of cultivation, bioinformatics and LC-MS to understand Legionella antagonism 🦠

Alessio Cavallaro @alecava.bsky.social · Nov 30

Check our last manuscript now up on biorXiv! We analyzed the inhibitory capabilities of isolated aquatic bacteria towards different Legionella spp. and discovered variable outcomes, while reinforcing the role of biosurfactants (we specifically detected viscosin) as anti-Legionella compounds.

Variable inhibition of different Legionella species by antagonistic bacteria

The genus Legionella includes opportunistic pathogens inhabiting engineered aquatic ecosystems, where managing their presence and abundance is crucial for public health. In these environments, Legione...

www.biorxiv.org

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Reposted by Marco Gabrielli

Martin Hunt @martibartfast.bsky.social · Nov 29

I just made a first release of TNA - new tool to compare 2 bacterial genomes. Is shamelessly inspired by ACT, but should be simpler to use. Drag-n-drop two genomes: it runs BLAST for you and then you can visualize. For Mac, Windows 11, Linux tna.readthedocs.io

TNA documentation — TNA 0.0.1 documentation

tna.readthedocs.io

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Reposted by Marco Gabrielli

Microbial Systems Ecology Lab @micsysecolab.bsky.social · Oct 28

Check out our new paper, led by Astrid Stubbusch and @nonresidentdesi.bsky.social on bacterial degradation-dispersal cycles, out in @elife.bsky.social!

Glen Dsouza @nonresidentdesi.bsky.social · Oct 27

New work out in @eLife! Possibly the last one in our series on bacterial aggregation behaviours on polysaccharides. We knew cells were engaging in collective behaviours. But how do they know when to leave and why? We provide potential answers in this work

elifesciences.org/articles/93855

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Reposted by Marco Gabrielli

Anna S. Weiss @annasophieweiss.bsky.social · Nov 26

My friend & colleague @micsysecolab.bsky.social Matthias has written this extremely insightful and fascinating perspective on bacterial collective metabolism, out now in @naturemicrobiol.bsky.social. So happy to see this out & super excited for proteome allocation! www.nature.com/articles/s41...

A framework for understanding collective microbiome metabolism - Nature Microbiology

This Perspective explores why microbiome members perform partial metabolism of substrates and suggests that proteome efficiency is a driver of collective microbiome metabolism.

www.nature.com

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Reposted by Marco Gabrielli

Glen Dsouza @nonresidentdesi.bsky.social · Nov 8

New preprint! A bit of new direction for my research program: How can bacteria get nutrients when autonomous growth is not possible or passive leakage is not enough to support high growth? Shoot spearguns with toxins into other cells and leak out nutrients!

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

Antagonism as a foraging strategy in microbial communities

In natural habitats, nutrient availability limits bacterial growth. We discovered that bacteria can overcome this limitation by acquiring nutrients through lysing neighboring cells via contact-depende...

www.biorxiv.org

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Marco Gabrielli @mgabrielli.bsky.social · Oct 24

Last but not least, I want to thank @drinkmic.bsky.social
and @alecava.bsky.social for all the discussions and support through this journey into the Legionellaceae family!

n/n

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Marco Gabrielli @mgabrielli.bsky.social · Oct 24

I think these results highlight that to understand microbial ecology we he need to move beyond just tracking genera, but really move to species-level resolution.
This is not just valid for Legionella, but I think for all clades in which only a few bacteria are of interest

16/n

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Marco Gabrielli @mgabrielli.bsky.social · Oct 24

The correlation among the OTUs were quite low or negative, supporting once again that each species has its own environmental niche. Still, metabolically similar species presented higher correlations, stressing the link between functional potential and environmental niche.

15/n

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