Rauf Salamzade
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raufs.bsky.social
Rauf Salamzade
@raufs.bsky.social
Interested in microbial ecology & evolution. Views are only my own. (he/him)

🎓: https://scholar.google.com/citations?hl=en&user=OBPpZq4AAAAJ&view_op=list_works&sortby=pubdate
👨‍💻: https://github.com/raufs
Reposted by Rauf Salamzade
Happy Darwin Day to all! To celebrate can you comment with your favorite paper on evolutionary biology from the last few years? Whatever comes to mind and whichever paper that really changed your view of evolution.
February 12, 2026 at 7:18 PM
Reposted by Rauf Salamzade
Reading this for my ecological genomics class. Pretty mind-blowing stuff, even identifying insect-bacterial symbionts from high covariance in airborne eDNA!
Airborne eDNA captures three decades of ecosystem biodiversity - Nature Communications
Quantifying ecosystem dynamics is critical in the face of rapid environmental change. This study uses airborne eDNA to quantify changes in organism abundances across the tree of life and reveal a regi...
doi.org
February 12, 2026 at 4:48 PM
Reposted by Rauf Salamzade
The science writing over at @asimovpress.bsky.social is fantastic!

From the origin of the lab vortex, to the history of Xenopus, their content is creative, beautiful, and thoughtfully researched.

Consider assigning some of their pieces in science courses.

www.asimov.press/p/vortex?utm...
Making the Vortex Mixer
The forgotten story of an invention found in every biology lab.
www.asimov.press
February 12, 2026 at 3:45 PM
Reposted by Rauf Salamzade
Evolution and diversity of oxidoreductases involved in redox balance and energy conservation www.nature.com/articles/s41... #jcampubs
Evolution and diversity of oxidoreductases involved in redox balance and energy conservation - Nature Ecology & Evolution
HORBEC are protein complexes involved in the regulation of redox balance and energy conservation. The authors develop a bioinformatic tool for HORBEC annotation in bacterial and archaeal genomes and r...
www.nature.com
February 11, 2026 at 11:32 PM
Reposted by Rauf Salamzade
Check out our latest preprint from @jnvmartinson.bsky.social and @leosong.bsky.social! 🌟🦠

We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵
February 12, 2026 at 12:42 AM
Reposted by Rauf Salamzade
Check out this cool new preprint from @therubinlab.bsky.social led by @jnvmartinson.bsky.social

They shielded recipient strains from lethal zygosis (conjugative killing of the recipient) by encoding protective DNA cargo via CASTs 🧪🦠🧬🧫
Plasmids weaponize conjugation to eliminate non-permissive recipients https://www.biorxiv.org/content/10.64898/2026.02.10.705089v1
February 11, 2026 at 4:55 AM
Reposted by Rauf Salamzade
Latest work! 🧬

We uncover how evolution of translation initiation factor 2 (IF2) extensions links translation to bacterial stress response. We map 7 structural architectures & show how terminal extensions are enriched in intrinsic disorder & phase-separation features.

Link: doi.org/10.64898/202...
February 11, 2026 at 6:18 PM
Reposted by Rauf Salamzade
On International Day of Women and Girls in Science 🔬👩‍🔬
We’re launching the Women Microbiologists Network: a member-led networking and discussions event for women in microbiology by Dr. Enas Newire.
Read the news story and join:
🔗 https://microb.io/4ax5M5I
February 11, 2026 at 9:00 AM
Reposted by Rauf Salamzade
Recent microbial evolutionary insights from metagenomics academic.oup.com/gbe/advance-... #jcampubs
February 11, 2026 at 4:02 PM
Reposted by Rauf Salamzade
~50 kb genomes, 4× smaller than the genomes of 𝘕𝘢𝘳𝘥𝘰𝘯𝘦𝘭𝘭𝘢 sp. 👀 and ~3× smaller than the 𝘊𝘢𝘳𝘴𝘰𝘯𝘦𝘭𝘭𝘢 genome 👀. Elio called 𝘊𝘢𝘳𝘴𝘰𝘯𝘦𝘭𝘭𝘢 ...👇
#SymbioSky
February 11, 2026 at 1:38 PM
Reposted by Rauf Salamzade
To celebrate #IDWGS2026, we're highlighting women who shaped microbiology but never got their flowers, starting with Fanny Hesse.

We're not stopping there; help us continue the work. Nominate a female microbiologist you know for a feature on our blog: buff.ly/kk7Ieye

#IDWGS #WomenInSTEM
February 11, 2026 at 2:42 PM
Reposted by Rauf Salamzade
February 11, 2026 at 8:40 AM
Reposted by Rauf Salamzade
This is troubling for multiple reasons, but one big one is companies won’t want to invest in R&D and clinical trials if they don’t think they can get a fair regulatory review—which is at the end of a long and extremely expensive process.

www.nytimes.com/2026/02/10/h...
F.D.A. Refuses to Review Moderna Flu Vaccine
www.nytimes.com
February 11, 2026 at 12:37 AM
Reposted by Rauf Salamzade
Reposted by Rauf Salamzade
Ever struggled with a good SNP threshold for transmission analysis? As part of our paper, we made the bioinformatics pipeline available and we deeply investigated and developed new methods for this purpose. Check it out!
We’ve made our analytical pipeline THRESHER publicly available! Just provide your genomes and it handles strain and/or cluster composition, and generates quality visualizations for you. Easy to install,thoroughly documented,and validated on published datasets and simulations. Manuscript coming soon!
GitHub - microbialARC/THRESHER: THRESHER is a bacterial phylogenomics toolkit for strain and/or transmission clusters identification, genome profiling of substitution rates and MGEs, and bacterial evo...
THRESHER is a bacterial phylogenomics toolkit for strain and/or transmission clusters identification, genome profiling of substitution rates and MGEs, and bacterial evolution simulation. - microbia...
github.com
February 10, 2026 at 6:06 PM
Reposted by Rauf Salamzade
New in JB: Latimer, Agbavor & Cahoon discuss the HtrA protein, which serves double duty as a protease and chaperone and plays key roles in maintaining envelope integrity, stress resistance, and virulence in Gram-positive organisms.
journals.asm.org/doi/10.1128/...
@asm.org #JBacteriology
February 10, 2026 at 3:43 PM
Reposted by Rauf Salamzade
Reposted by Rauf Salamzade
The Journal of Infectious Diseases has just released a special collection of papers devoted to "Contemporary Research on #AMR", covering mechanisms of resistance and virulence, pharmacokinetics, drug development, and wastewater surveillance
@jidjournal.bsky.social
#IDEpi #MedSky #IDSky #AMS
Validate User
academic.oup.com
February 10, 2026 at 5:44 AM
Reposted by Rauf Salamzade
STEM Black History Fact 9/28

Dr. Jane Cooke Wright pioneered chemotherapy techniques and helped establish personalized cancer treatment as a scientific discipline.
Ten Black Scientists That Science Teachers Should Know About
Help your students see the possibilities of careers in STEM fields by providing them with diverse role models.
www.pbs.org
February 10, 2026 at 2:44 AM
Reposted by Rauf Salamzade
Now out & nicely formatted in @isme-microbes.bsky.social

A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.

A few highlights... 🧵 (1/n)

doi.org/10.1093/isme...
Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny
Abstract. Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring
doi.org
February 9, 2026 at 8:31 PM
Reposted by Rauf Salamzade
How do bacterial pangenomes evolve, what controls their dynamics, why do they exist?
Fitting a mechanistic model to 450 species from allthebacteria.org suggesting fast vs slow gene exchange (i.e. amount of MGEs) is a major differentiating factor, correlated with phylogeny rather than lifestyle
February 9, 2026 at 10:55 AM
Reposted by Rauf Salamzade
This study looks at microbiomes in aerial surfaces of plants and their roles in environmental processes, in order to advance microbiome utility across the bioeconomy. @ucmerced.bsky.social
🖥️🧬 🦠 🌱

https://jgi.doe.gov/user-science/science-stories/secrets-needles-what-microbes-do-conifer-leaves
Secrets of the Needles: What Microbes do on Conifer Leaves | Joint Genome Institute
Novel study looks at microbiomes in aerial surfaces of plants, and their roles in plant health and environmental processes
jgi.doe.gov
February 9, 2026 at 9:15 PM
Reposted by Rauf Salamzade
Just published: "Planetary microbiome structure and generalist-driven gene flow across disparate habitats" by @podlesny.bsky.social @chanyeong-kim.bsky.social and @jonas-bio.bsky.social www.cell.com/cell/fulltex...

See the quoted post below for a thread on the preprint!
February 9, 2026 at 5:08 PM
Reposted by Rauf Salamzade
Excited to share the newest paper from our team, where we uncovered a potential role of the uncultured gut #microbiome in health: www.cell.com/cell-host-mi.... Out now in @cp-cellhostmicrobe.bsky.social @cellpress.bsky.social. With Ana C. da Silva, Jacob Lapkin, Qi Yin and Efrat Muller.
Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a candidate signature of health
Silva et al. perform a global analysis of over 11,000 gut microbiomes and reveal that uncultured bacteria are key markers of gut health. The uncultured genus CAG-170 is strongly linked to low gut dysb...
www.cell.com
February 9, 2026 at 4:46 PM