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
Fecal microbiome transplant up-regulates immune tolerance pathways in food allergy www.science.org/doi/10.1126/... @bostonchildrens.bsky.social
Fecal microbiome transplant in food allergy in humans and mice identifies a role for bile acid metabolites in oral tolerance
Fecal microbiome transplant up-regulates immune tolerance pathways in food allergy.
science.org
Delighted to share our latest publication on the extremophilic fungus 'Whiskey Black' or 'Angel's Share' (i.e. Baudoinia spp.) that grows on ethanol vapours around distilleries and whiskey maturation warehouses. www.sciencedirect.com/science/arti...
Comparative genomics sheds new light on the microbiology of the whiskey fungus Baudoinia
Baudoinia compniacensis is a melanized saprobic fungus that causes blackening of surfaces in the vicinity of spirit maturation warehouses, commercial …
sciencedirect.com
Love this. Your skin is one of, if not the largest, organs of the human body.
Rauf Salamzade@raufs.bsky.social · 3d agoWe investigated and identified several skin-derived bacteria that antagonize common pathogenic species: www.nature.com/articles/s41... A cool highlight was that bacteria from feet, where fungi are particularly diverse, tended to be more broadly antifungal than those from other body sites! #microevo
Continuing my writing on evolutionary biology and life. Another 6-ish minute read. Always free. "Never Bet It All" open.substack.com/pub/profmcin...
Never Bet It All
What potatoes, a gambler and your own genome knows about surviving a future you can't predict
open.substack.com
Independent replication from my own hand (right) and foot (left) in a little family science project
Rauf Salamzade@raufs.bsky.social · 3d agoWe investigated and identified several skin-derived bacteria that antagonize common pathogenic species: www.nature.com/articles/s41... A cool highlight was that bacteria from feet, where fungi are particularly diverse, tended to be more broadly antifungal than those from other body sites! #microevo
New Preprint 🚨: Led by Ph.D student, Ashlynn Bruder, we explore how feast/famine cycles in our LTRS system influence temporal selection on new mutations. Reconstruction of mutations reveals environment-dependent epistasis + increased fitness during both feast and famine conditions. Summary Fig ⬇️
bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · yesterdayEnvironment-dependent epistasis shapes adaptation to fluctuating resources. https://www.biorxiv.org/content/10.64898/2026.07.31.742109v1
The latest in my “what has four billion years of evolution taught us” series. Always free. Always about evolution. Take a look. open.substack.com/pub/profmcin...
Drift and Luck
In 1968, a Japanese geneticist named Motoo Kimura published a paper that changed how every evolutionary biologist thought about evolution.
open.substack.com
Maybe late to the game, but if you have not read the 75th Anniversary special series of @systbiol.bsky.social you should. So many good ideas and history there academic.oup.com/sysbio/pages... #systematicbiology
Systematic Biology's 75th Anniversary
In celebration of Systematic Biology's 75th anniversary, the 2026 volume features a special series of discussions and essays commissioned by the Society’s Legac
academic.oup.com
In #Microbiome The Metaproteomics Initiative: five years of community-driven progress Read more 👉 doi.org/rhdg
Fantastic 🧵 👇! For more information on the role of Dutch scientists in clandestine penicillin production during WW2 see citation below. 1/
Dan Kaszeta FRHistS@dankaszeta.bsky.social · 2d agoPenicillin was not, in fact, the first antibiotic.
Proof of the 40-year old Bandelt-Dress conjecture on the maximum quartet distance between phylogenetic trees (and an interesting connection to independence testing). arxiv.org/abs/2608.03542
The maximum quartet distance between phylogenetic trees
The quartet distance counts the four-leaf subsets on which two binary phylogenetic trees display different topologies. We prove that its maximum over trees on $n$ leaves is $(2/3+o(1))\binom{n}{4}$, r...
arxiv.org
deep learning–based score to evaluate multiple sequence alignments | Molecular Biology and Evolution | Oxford Academic
A deep learning–based score to evaluate multiple sequence alignments
Abstract. Multiple sequence alignment (MSA) inference is a central task in molecular evolution and comparative genomics, and the reliability of downstream
dx.doi.org
Phylogenetic conservation of bacterial environmental responses predicts soil bacterial biogeographic patterns www.biorxiv.org/content/10.6... #jcampubs
Contrastive learning unites sequence and structure in a global representation of protein space #proteins #bioinformatics #MachineLearning #AI @pnas.org doi.org/10.1073/pnas...
Contrastive learning unites sequence and structure in a global representation of protein space | PNAS
Establishing a coherent mapping of the relationships among all known proteins is crucial for elucidating processes of protein emergence and evoluti...
doi.org
As chicken numbers have risen globally, so have the fortunes of the bacterial pathogen Campylobacter jejuni, which infects chickens and other birds. The bacteria are more prevalent, more mobile, and more genetically diverse than in 1960. In PNAS: https://ow.ly/Gaqo50Zwbn4
🚨NEW PAPER 🚨 "Deconstructing empirical fitness seascapes across scales of granularity" published in #G3 (@genetics-gsa.bsky.social) 1/2 The fitness landscape has been among the most influential instruments in evolutionary theory for nearly a century. But we often treat them as fixed and static.
Check out our new review: Impacts of pollution on the soil microbiome just out in @natrevmicro.nature.com www.nature.com/articles/s41...
Midwest Microbial Pathogenesis Conference (MMPC) September 25-27, 2026 University of Minnesota Minneapolis, MN Register now! #MicroSky
Julia Willett@jlewillett.bsky.social · 2d agoI'm excited to be co-organizing the 2026 Midwest Microbial Pathogenesis Conference, which will take place Sept 25-27 on the UMN campus in Minneapolis! Poster abstracts due Aug 7! Submit yours & register here ➡️ mmpc2026.umn.edu
Preprint 🦠🚨: We are diving deeper into #T6SS effectors, and now in #Pantoea. We describe the largest, most diverse effector arsenal associated with a single T6SS, and it's in a plant pathogen that forms galls on beet roots. Sweet! 1/8 www.biorxiv.org/content/10.6...
Pantoea agglomerans T6SS effectors reside in hotspots with combinatorial offensive and defensive arsenals
Gram-negative bacteria deploy type VI secretion systems (T6SSs) to mediate interbacterial competition. Although numerous T6SS effectors have been identified, their pan-genomic repertoires and evolutio...
biorxiv.org
😳 Specific nonantibiotics can potentially pose a risk for the emergence of multidrug resistance! journals.asm.org/doi/10.1128/... @mbio.bsky.social
Nonantibiotic-driven evolution reveals rare but predictable routes to broad antibiotic resistance | mBio
Many medications not typically prescribed to treat infectious diseases have potent antimicrobial activity at physiological concentrations. This anti-bacterial activity raises concern that long-term administration of such nonantibiotics might unintentionally select for multidrug resistance, including resistance to antibiotics. Using Escherichia coli, we show that in most cases, these nonantibiotics do not broadly select for resistance to antibiotics in vitro. However, we identified five nonantibiotics that repeatedly selected for resistance to multiple antibiotics through a shared mechanism of action—upregulation of the multidrug efflux pump AcrAB-TolC. These findings highlight that while the overall risk is low, certain nonantibiotics may still contribute to the emergence of multidrug resistance. Identifying these high-risk drugs can help guide safer prescribing practices and inform strategies to limit the spread of antibiotic resistance.
journals.asm.org
Beautiful work (Petrungaro, Bollenbach lab) on evo trajectories toward abx resistance (E. coli). Goes beyond many other studies in its attention to the experimental setup (identical selective pressure across all lines). I strongly recommend reading the entire paper! www.nature.com/articles/s41...
Function-specific epistasis shapes evolutionary trajectories towards antibiotic resistance - Nature Communications
Antibiotic resistance can evolve through the combination of factors but the predictability of this is unclear. Here, the authors used high-throughput evolution experiments to reveal that antibiotic re...
nature.com
DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation Out now: how DNA sequencing can transform microbial surveillance in lung disease and what must change for clinical use. journals.asm.org/doi/10.1128/...
DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation | Clinical Microbiology Reviews
SUMMARYDNA sequencing has revolutionized microbial surveillance in cystic fibrosis (CF), transforming pathogen identification from culture-dependent to total microbial community identification using m...
journals.asm.org
Phage terminase recognition by the bacterial immune sensors Avs2 and Upx | Nature Communications
Phage terminase recognition by the bacterial immune sensors Avs2 and Upx - Nature Communications
Direct recognition of viral proteins is key to bacterial immunity. Here, Evans et al. uncover the mechanisms used by two distinct defense proteins to detect the phage DNA packaging motor mechanisms: bridging ATP ligand or binding an unfolded state.
nature.com
We derive a working hypothesis for how the genetic code evolved, by assuming LUCA-depleted amino acids came early, using codons we infer via the 2-1-3 rule. We validate with independent data and a control ordering ecoevorxiv.org/repository/v... @seekingluca.bsky.social @hanonmcshea.bsky.social 1/13
The series of genetic codes that preceded our own
ecoevorxiv.org
Why do intrinsically disordered proteins behave so weirdly during SDS-PAGE? This is the question we aim to answer in our recent paper: onlinelibrary.wiley.com/doi/10.1002/...
Sequence determinants of the hypomobility of intrinsically disordered proteins in <fc>SDS</fc>‐<fc>PAGE</fc>
Proteins with intrinsically disordered regions (IDRs) migrate at a higher apparent molecular weight in sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis, complicating their analysis and...
onlinelibrary.wiley.com
𝘔𝘺𝘹𝘰𝘤𝘰𝘤𝘤𝘶𝘴 𝘹𝘢𝘯𝘵𝘩𝘶𝘴 as self-propelling archimedes' screw 👇 – much like its flagellated (distant) cousin 𝘊𝘢𝘣𝘢𝘭𝘭𝘦𝘳𝘰𝘯𝘪𝘢 𝘪𝘯𝘴𝘦𝘤𝘵𝘪𝘤𝘰𝘭𝘢 that we featured recently...
Backstroke Swimming
by Christoph — It is not widely known that sporty bacteria have also mastered the art of backstroke swimming. Among them is Caballeronia insecticola...
smallthingsconsidered.blog
Ricard Alert Zenón@ricardalert.bsky.social · 2d agoNew paper! Inspired by gliding bacteria, we introduce active screws: Particles that self-propel by spinning around their propulsion axis. We show that active screws form active chiral nematics. With Debu Banerjee and @lauritzh.bsky.social @mpipks.bsky.social journals.aps.org/prresearch/a...
Habitat-specific patterns of horizontal gene transfer revealed by metagenomics across aquatic and terrestrial ecosystems www.sciencedirect.com/science/arti... #jcampubs
Habitat-specific patterns of horizontal gene transfer revealed by metagenomics across aquatic and terrestrial ecosystems
Horizontal gene transfer (HGT) is a major driver of microbial adaptation and evolution, yet how habitat type and anthropogenic pressures shape communi…
sciencedirect.com
"When a conversation slows, I no longer see it as a sign of failure. I see it as evidence that we are finally doing the harder work of understanding one another." #ScienceWorkingLife https://scim.ag/4x9jwgp
