Scholar

Simon Roux

Videos
H-index: 70
Environmental science 40%
Biology 33%
more

Reposted by: Simon Roux

dumpyunc.bsky.social
Our group at the Allen Institute is recruiting a technician and postdoc to work on light microscopy-based connectomics. Please DM me or share with anyone you think may be interested in this NIH BRAIN CONNECTS funded project.
1 18 16

Reposted by: Simon Roux

napaaqtuk.bsky.social
I have a fabulous undergrad who has a lot of experience with QIIME2 & using R to analyze microbiome data. She is looking for a job starting in January. Would love to learn more bench and field skills (will be getting some in her last 2 months). Open to academic, industry, government jobs in the US.
1 28 29

Reposted by: Simon Roux

bossdorf.bsky.social
JOB ALERT! Do you also love large ecological experiments? Become coordinator of our big new geo-biosphere experiment in @terra-cluster.org. 7-year position! Follow link for details.
@gfoesoc.bsky.social
@britishecologicalsociety.org
@ecologicalsociety.bsky.social
@uslter.bsky.social

Please repost!
Stellenangebote: Universität Hohenheim
Aktuelle Stellenangebote der Universität Hohenheim.
www.uni-hohenheim.de
1 30 20

Reposted by: Simon Roux, Joshua S. Weitz

d2mory.bsky.social
Happy to share our new work on Temperature-driven biogeography of marine viruses infecting Micromonas:
academic.oup.com/ismecommun/a...
Temperature-driven biogeography of marine giant viruses infecting picoeukaryotes Micromonas
Abstract. Climate shapes the biogeography of microbial and viral communities in the ocean. Among abiotic factors, temperature is one of the main drivers of
academic.oup.com
1 4 8

Reposted by: Simon Roux, Mart Krupovìč

daumlab.bsky.social
Out in Science Advances: Our #cryoEM structure of HFTV1, a virus infecting the halophile #archaea. *First full atomic structure (containing all structural proteins) of any tailed virus!* Congrats and thanks to all co-authors and our fantastic collaborators! www.science.org/doi/10.1126/...
Cryo-EM resolves the structure of the archaeal dsDNA virus HFTV1 from head to tail
This structure of an archaeal tailed virus (arTV) provides detailed insights into arTV assembly and infection mechanisms.
www.science.org
50 120

Reposted by: Simon Roux, Jesse M. Shapiro, José R. Penadés , and 1 more

brockhurstlab.bsky.social
New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

www.biorxiv.org/content/10.1...
Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages
Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...
www.biorxiv.org
3 46 90

Reposted by: Simon Roux, Elena Litchman, Jennifer Pett‐Ridge , and 2 more

erinrgreen.bsky.social
Job alert ‼️ UChicago Micro is hiring! Open to tenured/tenure track faculty at all levels in any area of microbiology. Come join our amazing and growing department. apply.interfolio.com/174404
4 120 120

Reposted by: Simon Roux

aventurini.bsky.social
Assembling MAGs from Amazonian soils is a challenge, but it has become one of our most useful tools to understand these complex communities. Check out our new paper at MRA @asm.org doi.org/10.1128/mra.... in collaboration with @louberrios.bsky.social @jubgontijo.bsky.social @mykophile.bsky.social
A catalog of metagenome-assembled genomes from Amazonian forest and pasture soils | Microbiology Resource Announcements
Our group previously recovered 64 bacterial and 5 archaeal metagenome-assembled genomes (MAGs) from Amazonian forest and pasture soils and evaluated their genomic traits (1). Here, we formally announc...
doi.org
3 7

Reposted by: Simon Roux

johninnescentre.bsky.social
Shortlisted candidates will be invited to give a seminar at the Fellows Conference, which will be held on 10 March 2026.

Candidates who win Fellowships will be offered a Tenure Track Group Leader position from the outset, initially for 5 years.

Find out more: www.jic.ac.uk/training-car...
Independent Research Fellowships Leading to Tenured Faculty Positions | John Innes Centre
The John Innes Centre (JIC), is a world leading centre of excellence in plant and microbial sciences based on the Norwich Research Park, UK. We are inviting applications from outstanding researchers…
www.jic.ac.uk
23 20

Reposted by: Simon Roux

doradomoralesp.bsky.social
A plasmid and an ICE teaming up... 🤯😱

www.nature.com/articles/s41...
The assembly of a hybrid type IV secretion system by a Crohn’s disease-associated Escherichia coli strain - Nature Communications
Adherent-invasive strains of E. coli are commonly isolated from patients with Crohn’s disease. Here, the authors show that an AIEC harbours a hybrid Type IV secretion system (T4SS) that mediates pilin polymerization and biofilm formation in vivo.
www.nature.com
5 11

Reposted by: Simon Roux

edrybicki.bsky.social
And, I might add, an easily engineerable solution, given our (sadly now abandoned) patent detailing our discovery that you could get efficient transformation of microalgae with Agrobacterium tumefaciens if you immobilise them in a Celite matrix 😁
patents.google.com/patent/AU201...
AU2019389307A1 - Matrix-mediated cell culture system - Google Patents
The invention relates to a matrix-mediated algal cell culture system comprising a porous matrix, a microalgal cell culture comprising cells immobilised on the porous matrix, and a vector including a n...
patents.google.com
1 2

Reposted by: Simon Roux

harvardcellbio.bsky.social
Historically, viruses were thought to primarily use host cell's translational machinery. New work from @harvardcellbio.bsky.social faculty Amy Lee reveals that a giant DNA virus encodes its own IF4F initiation complex, suggesting an unexpected evolutionary innovation. www.biorxiv.org/content/10.1...
Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life
In contrast to living organisms, viruses were long thought to lack protein synthesis machinery and instead depend on host factors to translate viral transcripts. Here, we discover that giant DNA virus...
www.biorxiv.org
39 92

Reposted by: Simon Roux

vscooper.micropopbio.org
DYK most P. aeruginosa carry filamentous phage(s) that don't need to kill the cell to reproduce?

We 👉🏻@nanamikubota.bsky.social show that these Pf phages can go ROGUE.

"Filamentous cheater phages drive bacterial and phage populations to lower fitness"

🔗 authors.elsevier.com/c/1lt5I3QW8S...
6 30 67

Reposted by: Simon Roux, Alan Richardson, Jon Agar , and 1 more

eayers0.bsky.social
Job at UC-Berkeley: Asst. Prof. in Global History of Technology, apps due 10/10 (so soon). #history #histSTM #histsci #histphilsci

aprecruit.berkeley.edu/JPF05065
Assistant Professor – Global History of Technology - Department of History
University of California, Berkeley is hiring. Apply now!
aprecruit.berkeley.edu
14 12

Reposted by: Simon Roux

evbc.bsky.social
A nationwide #HTS survey of German hopyards identified HpLV, HpMV, ApMV, ArMV and viroids HLVd and CBCVd (CBCVd confined to Hallertau), highlighting HTS as a powerful tool for #PlantPathogenSurveillance and management #PlantViromics 🧬🌾🔬
📄https://doi.org/10.1371/journal.pone.0329289
👤EVBC: Ali Pasha
Virus and viroid diversity in hops, investigating the German hop virome
Germany is worldwide one of the largest hop (Humulus lupulus L.) producers, an essential crop for the brewing industry. However, infections caused by viruses and viroids can severely impact hop yield and quality. In 2019, citrus bark cracking viroid (CBCVd) – a highly aggressive pathogen in hop – was first reported in Germany, raising concerns about its spread and prompting a broader investigation of the German hop virome.To investigate the viro-diversity in German hops, we started with a pilot study in 2021 targeting three hopyards in the Hallertau region (Bavaria), where CBCVd was previously detected. This study was expanded in 2022 and 2023 to include other main hop growing regions of Tettnang (Baden-Wuerttemberg) and Elbe-Saale (Saxony, Saxony-Anhalt, Thuringia). Leaf samples were collected from hop as well as non-hop plants inside and outside the hopyard, pooled, and proceeded for double-stranded RNAs extraction. High-throughput sequencing (HTS) was used as a diagnostic tool, followed by RT-PCR confirmation. Our analysis identified four viruses infecting hops; hop latent virus (HpLV), hop mosaic virus (HpMV), apple mosaic virus (ApMV), arabis mosaic virus (ArMV) – and two viroids; hop latent viroid (HLVd) and CBCVd. HpLV, HpMV, and HLVd were consistently found across all targeted hopyards, while CBCVd was confined to the Hallertau region. ArMV was only detected in one hopyard at one sampling timepoint. ApMV was the only virus detected in both hop and non-hop plants. Additional analysis of hop pool datasets revealed the presence of other potential hop pathogens, i.e., fungi and bacteria. The results showed a low diversity of viruses and viroids infecting hops. However, this study provides a comprehensive overview on the major viruses and viroids in German hopyards. The results may serve as a useful resource for the development of disease management strategies in hop cultivation and highlight the valuable implementation of HTS in plant pathogen surveillance.
doi.org
2 5

Reposted by: Simon Roux

raw937.bsky.social
Multiomic analysis of the only megaphage in culture. In press today.

Unlocking the genomic repertoire of a cultivated megaphage | npj Viruses share.google/HgU1cjRnaHWv...

#phage #bacteriophage
Unlocking the genomic repertoire of a cultivated megaphage - npj Viruses
npj Viruses - Unlocking the genomic repertoire of a cultivated megaphage
share.google
4 10

Reposted by: Simon Roux

feldmanlab.bsky.social
I said I will never work on phages, but having @micheleleroux.bsky.social next door made me change my mind. Here is Alexis's new paper showing how different phages deal with the capsular barrier to infect Acinetobacter! A great collaboration between our labs!
journals.plos.org/plospathogen...
Acinetobacter phages use distinct strategies to breach the capsule barrier
Author summary Acinetobacter baumannii causes life-threatening and often antibiotic-resistant infections thereby posing a global threat. Accordingly, there is an urgent need for alternative treatments...
journals.plos.org
2 18 65

Reposted by: Simon Roux

evolvedbiofilm.bsky.social
The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem

#CurrOpinMicrobiol from @lgbacteria.bsky.social

www.sciencedirect.com/science/arti...
12 27

Reposted by: Simon Roux

stairwaytokevin.bsky.social
Whole-genome alignments revealed pennycress has nearly dichotomous genome compartmentalization: huge gene-poor pericentromeric regions (~300Mb; <1% genic) with frequent rearrangements and highly syntenic gene-rich chromosome arms (~150Mb; ~20% genic). What we call a "two-speed" genome structure. 3/
Figure 3 | Macrosynteny and genome structure across the Brassicaceae. Horizontal blue/black/orange bands represent the chromosomes of Arabidopsis thaliana, A. lyrata, MN106, and Brassica rapa (top to bottom). Chromosomes are ordered by their number from left to right. Colors represent genomic content binned hierarchically in sliding windows (400kb-overlapping 500kb) as follow: (1) within a gene annotation (including intron and UTR, orange), (2) within EDTA-annotated repeats categorized as Ty3, (3) Ty1 (copia), (4) within another repeat category, or (5) un-annotated. Grey bands are sequence-based syntenic blocks between each pair of genomes. Pennycress and B. rapa are phylogenetically proximate (both in Brassicodae supertribe), but have reduced synteny in part because of genome reshuffling in B. rapa following a whole-genome triplication event. The seven pennycress genome assemblies (horizontal bars) are binned into TRASH-defined centromeres (orange), pericentromeres (dark blue), chromosome arms (light blue) and telomeres (dark red). The colors along the chromosome segments scale physically with the size of the bin, except that centromeres and telomeres have a 1pt buffer to make it easier to see these typically small regions. Each genome is connected to its neighbor by grey polygons that represent sequence-based syntenic blocks. Plots, genomic bins, and syntenic blocks were built with DEEPSPACE (github.com/jtlovell/DEEPSPACE).
1 6 11

Reposted by: Simon Roux, Jesse M. Shapiro, José R. Penadés

zaminiqbal.bsky.social
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
14 150 300

Reposted by: Simon Roux

stevenjrobbins.bsky.social
Hey all! Now that i've left my position at UQ, I thought I would leverage my network here to see if anyone has leads on environmental genomics, biotech, marine policy positions in the US/Canada/Australia/Europe. I'd love to speak with anyone in those fields re openings, worthwhile recruiters, etc.
1 13 15

Reposted by: Simon Roux

c0nc0rdance.bsky.social
So, there you go:
Boring beetles bring blue wood fungus, but butterscotch brings birds that bite the beetles & burning brings more beneficial terpenes.

Now go stick your nose in some sap.

More reading here:
The Mysteries of the Ponderosa Pine
Take a look at the ponderosa pine and the many creatures that rely on it.
blog.nature.org
6 5 75

Reposted by: Simon Roux, Jonathan A. Eisen, Jesse M. Shapiro , and 2 more

vscooper.micropopbio.org
🚨 Microbiologists! We are recruiting Assistant / Associate Professors in 3 collaborative areas of our U. Pittsburgh School of Medicine.
1) MMG (my dept): fundamental research in med micro
2) Peds ID / I4Kids institute
3) Center for Vaccine Research
🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...
Faculty Professor Associate - Full-Time | Vaughn Cooper
We are recruiting Faculty microbiologists in three (3) different, complementary, and collaborative areas at the University of Pittsburgh associated with the School of Medicine. 1) Fundamental researc...
www.linkedin.com
1 130 93

Reposted by: Simon Roux

uncultured.carinilab.com
What are folks using for calling genes these days in isolate genomes: PGAP, Bakta, or Prokka? This is for a 70% GC genome of a very novel lineage.
7 7 10

Reposted by: Simon Roux

hariszaf.bsky.social
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

by Simon Roux

simrouxvirus.bsky.social
Which is actually mentioned in the paper too 😊 (despite the title maybe giving the other impression).

Also, no matter how much I wish it wasn't true, the same applies to CRISPR spacer hits 🥲
5

Reposted by: Simon Roux

contaminatedsci.bsky.social
These findings suggest phage pressure, while present, does not drive C acnes strain fitness on skin.

We propose that physical constraints — such as pore anatomy limiting phage access or skin physiology induced phage-resistant states — may explain the lack of coevolutionary arms race.
1 1 3

Reposted by: Simon Roux

contaminatedsci.bsky.social
This phage is almost never a lysogen, simplifying interpretation of viral reads as well.

Surprisingly, phage-sensitive C. acnes subphylogroups dominate across the globe.

This is true even in samples with high virus-to-microbe ratios.
1 1

Reposted by: Simon Roux

contaminatedsci.bsky.social
How much of selection in human microbiomes is driven by phage?

Excited to share our latest, led by A. Delphine Tripp, showing a case where phage is just not that important:

Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin

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

🧵
Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin
Despite Cutibacterium acnes being the most abundant and prevalent bacteria on human skin, only a single type of phage has been identified that infects this host. Here, we leverage this one-to-one syst...
www.biorxiv.org
2 17 47

Reposted by: Simon Roux, Jonathan A. Eisen

bielleogy.bsky.social
Giving a webinar on #BlueSoup this Friday, in case anyone wants to pop in during their lunch!
A promotional flyer for a webinar in the CSU Bioinformatics Webinar Series. On the left side, it shows the date and time: “26 Sep | 12 PM PST.” It includes instructions to join via Zoom with Meeting ID: 886 2442 3158 and a QR code above. On the right, there is a photo of Dr. Elinne Becket, Associate Professor in the Department of Biological Sciences at California State University San Marcos, sitting outdoors with plants and trees in the background. Below, the title of the talk is displayed: “The Soup that Blue up Twitter.” The description explains that Dr. Becket will discuss the shared curiosity of science, open science, and a story from February 2023 when leftover beef soup prepared by her mom turned bright blue. Scientists and people on Twitter collaborated to investigate, leading to a global effort among microbiologists and chemists. At the bottom, there are links to learn more about upcoming webinars at www.informatics.sdsu.edu and Dr. Becket’s website: https://elinneb.wixsite.com/becketlab
10 28 95

References

Fields & subjects

Updated 1m