Lightnews — Scholar-powered news

Reposted by Haris Zafeiropoulos

ASM @asm.org · Jun 16

#MicrobiologyMonday: Pseudomonas aeruginosa releases a surfactant that displaces Klebsiella pneumoniae from solid surfaces. By pushing K. pneumoniae away, the detergent allows P. aeruginosa to better compete for limited iron. Learn more in #mBio: asm.social/2sH

Model for the interaction between P. aeruginosa and K. pneumoniae. These bacteria can co-exist in nutrient-replete conditions. Under iron-limiting conditions, siderophore synthesis is induced in both bacteria. Iron limitation can also turn on the synthesis of biosurfactants, rhamnolipids, in P. aeruginosa, allowing it to push away K. pneumoniae.

1 8 21

Haris Zafeiropoulos @hariszaf.bsky.social · 15d

microbetag comes as a Python package you can use on your own genomes or as an on-the-fly service mapping your taxa to their closest GTDB genomes

1

Haris Zafeiropoulos @hariszaf.bsky.social · 15d

our software, microbetag, for the annotation of microbial co-occurrence networks with phenotypic traits & metabolic complementarities was just published

A Cytoscape app is also available to make your life easier (and prettier)

#microbiome #metabolic-modeling #networks

microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis - Genome Biology

Microbial co-occurrence network inference is often hindered by low accuracy and tool dependency. We introduce microbetag, a comprehensive software ecosystem designed to annotate microbial networks. No...

doi.org

1 8 15

Haris Zafeiropoulos @hariszaf.bsky.social · Aug 27

annas-archive.li/blog/an-upda...

An update from the team

About recent events.

annas-archive.li

1

Reposted by Haris Zafeiropoulos

Economic Principles in Cell Biology @economic-cell.bsky.social · Jul 1

First day of July brings us the Summer 2025 edition of our open-access textbook! Join Piglette in stargazing and exploring newest additions to our book principlescellphysiology.org/book-economi...

5 7

Haris Zafeiropoulos @hariszaf.bsky.social · Apr 8

Hi #microbiome community.

If you are interested in microbial networks, feel free to have a look and register in our summer school!

Two days with talks and hands-on on how to annotate your networks and come up with testable hypotheses.
24 and 25 Sep 2025, Leuven , Belgium

@3domics.bsky.social

Summer School on Data integration with Microbial Networks and Community Models

Bootstrap 5 Tech Conference Template

msysbiology.com

4 4

Haris Zafeiropoulos @hariszaf.bsky.social · Mar 21

microbetag.readthedocs.io

annotating microbial networksContentsMenuExpandLight modeDark modeAuto light/dark, in light modeAuto light/dark, in dark mode

microbetag.readthedocs.io

1

Haris Zafeiropoulos @hariszaf.bsky.social · Mar 19

DNNGIOR gapfiller: doi.org/10.1016/j.is...

dingo Python library for flux sampling: doi.org/10.1093/bioa...

Redirecting

doi.org

1

Haris Zafeiropoulos @hariszaf.bsky.social · Mar 19

If you're new in #metabolic #modelling or just interested, we had a workshop last week and here is a set of notebooks we wrote.

Among other things, we discussed our recently published gapfiller, DNNGIOR and the dingo flux sampling Python library we built with the GeomScale group!

#microbiome #flux

Metabolic modeling for microbiomes

Daniel Garza, Meine Boer and I, we organized a 3-days workshop at INRAE/PROSE in Antony, on the basics of metabolic modelling, our new gap-filler, called DNNGIOR and applications of the methodology on...

hariszaf.github.io

1 1

Haris Zafeiropoulos @hariszaf.bsky.social · Jan 5

If you're interested in microbial co-occurrence networks and how to make sense out of them, feel free to join my seminar at @microbiomevif.bsky.social on microbetag; a recently developed software of ours!
#microbiome #networks

Cassyni | Science starts with a seminar

Seamlessly organise, run and publish academic research seminars. Get started in minutes.

cassyni.com

3 7

Haris Zafeiropoulos @hariszaf.bsky.social · Dec 10

Here's our new tool for annotating microbial co-occurrence networks with phenotypic traits & potential metabolic complementarities.

Cytoscape App
apps.cytoscape.org/apps/mgg

Documentation
hariszaf.github.io/microbetag/

bioRxiv
doi.org/10.1101/2024...

#microbiome #microbiology #metagenomics

Cytoscape App Store - MGG

apps.cytoscape.org

1 2 9

Reposted by Haris Zafeiropoulos

Christina Pavloudi @cpavloud.bsky.social · Dec 4

Did we set fire to the rain? 🔥
Well, not exactly, but we did set it to the water. Or technically, to our artificial oil spill! 🛢️

Was there smoke on the water? 💨
Yes, there was!

Is this the first publication of, quite a few, more to come? Indeed!

Check it out here:
doi.org/10.1016/j.sc...

🧬🖥️🧪🦠🌊

Graphical abstract of a publication. The original abstract is "Major oil spills can impose a significant environmental hazard on the marine ecosystem, and a promising mitigation measure is in-situ oil burning (ISB). However, our knowledge of the impact of the burned residues and soot deposition on the marine ecosystem is still limited. We investigated the effects of burned oil residue and soot deposition on the marine plankton communities of the oligotrophic Eastern Mediterranean Sea with a mesocosm experiment. Three triplicated treatments were tested: (1) Iranian crude oil was added and burned (Burned treatment); (2) soot was collected and deposited with artificial rain (Soot); and (3) a non-contaminated Control. Results revealed that Low Nucleic Acid heterotrophic bacteria, Synechococcus spp., and pigmented pico-nano Eukaryotes (pnEuk) were negatively affected in the Burned and Soot treatments. Viruses, heterotrophic pnEuk and ciliates (in Soot) were crucial for controlling the High Nucleic Acid bacteria. Ciliates and most dinoflagellates showed a negative response to the burned residues but were less affected or were even favored when exposed to soot. Our results show that ISB affected the structure and dynamics of the plankton food web through burned residues and soot depositions. However, since the effects appeared at least three days after the ignition, ISB could be combined with subsequent burned residue collection to minimize its impact on the pelagic ecosystem."

1 1 3

Reposted by Haris Zafeiropoulos

mdboer.bsky.social @mdboer.bsky.social · Nov 26

Exciting news! 🎉 My article is out in iScience presenting DNNGIOR, a deep learning tool advancing gap-filling in metabolic models. Huge thanks to co-authors @cmelkonian.bsky.social, @hariszaf.bsky.social, Daniel Garza, Andreas Haas and @bedutilh.bsky.social. Read at shorturl.at/REOm8

Improving genome-scale metabolic models of incomplete genomes with deep learning

Microbial genomics; Biocomputational method; Computational bioinformatics; Genomic analysis.

shorturl.at

4 9

Reposted by Haris Zafeiropoulos

Steven Robbins @stevenjrobbins.bsky.social · Nov 10

Love this idea for helping the community make the transition to Bluesky, so I’ve compiled a woefully incomplete list of microbial ecologists and -omics peeps I know are here.

Please make suggestions and share. Let me know if you’d like to be added.

go.bsky.app/TQpaTqF

77 58 110

Reposted by Haris Zafeiropoulos

Will Ratcliff @wcratcliff.bsky.social · Nov 4

Excited to share: The inaugural Alma Dal Co School on Collective Behavior is coming to Venice (Sep 29-Oct 4, 2025). This unique school honors Alma (1989-2022), whose brilliant work bridging physics and microbiology revealed how metabolic interactions structure microbial communities. 1/12

2 32 50