Rauf Salamzade

A cartoon/ digital drawing summarising the findings of the paper "Defensive fungal symbiosis on insect hindlegs" by T. Nishino et al published in 2025. On the top left, a female Megymenum gracilicorne bug shows off symbiotic organs on the hind legs where she carries Ascomycota fungi. These were previously assumed to be Tympanal organs in these bugs but only females had them?; that didnt make a whole lot of sense to the authors...To the right of the bug is a row of eggs lying side by side. The paper shows that the bugs deposit the symbiotic fungi on the egg surface after egg-laying. Next on the image, fungal conidia grow on the egg surface. The eggs are pinkish in colour. A few fungi wear sunglasses like they are body guards. The paper shows that they protect the eggs from Trissolcus brevinotaulus, a parasitoid wasp, that likes to lay its eggs inside the developing bug's eggs. There are two wasps in this cartoon "eyeing" the fungi and looking frustrated. Eggs turn from whitish to pinkish within 10-days because they are reflecting the body colour of the nymph within the eggs.

Had to draw a cartoon for this fascinating finding!
Defensive fungal symbiosis on insect hindlegs: www.science.org/doi/10.1126/...
#SymbioSky

From @plos.org #Computational #Biology | Ten rules for a structural bioinformatic analysis | i like Recommendation #10: Visualize everything! | #Bioinformatics #Education #Recommendations #NotSimpleRules 🧬 🖥️ 🧪 🔓 CC/ @ppalagi.bsky.social
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journals.plos.org/ploscompbiol...

Nested Connections: Local Phage and Broad Plasmid Sharing in the Honey Bee Mobilome https://www.biorxiv.org/content/10.1101/2025.10.31.685865v1

Pleiotropic functions of glutathione in the adaptive response to long-term nitrogen starvation in Escherichia coli https://www.biorxiv.org/content/10.1101/2025.10.31.685819v1

Vibrio cholerae interaction with predatory bacteria on chitin suggests an alternative mode of biofilm formation in marine snow conditions https://www.biorxiv.org/content/10.1101/2025.10.31.685833v1

A host-directed adjuvant sensitizes intracellular bacterial persisters to antibiotics - Nature Microbiology The authors developed a screen to find compounds that modulate intracellular Staphylococcus aureus metabolism and discovered KL1, which sensitizes persisters to antibiotics by reversing host-induced tolerance.

Delighted to share our latest paper - A host-directed adjuvant sensitizes intracellular bacterial persisters to antibiotics. Excellently led by Dr. Kuan-Yi Lu. We think it's a great proof-of-concept that altering immune cell behavior can make antibiotics work better www.nature.com/articles/s41...

Methanobrevibacter smithii Methanobrevibacter smithii is one of the most prevalent and worldwide distributed archaea in the human gut. M. smithii is a strict anaerobe that obtains its energy through methanogenesis. In culture, it reduces CO2 to methane (CH4) using H2 as electron donor (i.e., CO2-reducing hydrogenotrophic methanogenesis) and to a lower extent, formate. Other potential methanogenic substrates, methanol and ethanol, are not used in culture, but genes involved in their utilization are upregulated when colonizing the mouse intestine.

Methanobrevibacter smithii

We’re thrilled to welcome Dr. Paul Bollyky, MD, DPhil, as the new Division Chief of Infectious Diseases and Geographic Medicine at Stanford Medicine.

Dr. Bollyky has been a dedicated member of our division, bringing deep expertise and a vision for advancing infectious disease research and care.

A brand-new Gordon Conference on Microbiomes!🦠 The opening session (Jan 2026) dives into microbiome editing - how fundamental research and new technologies can advance human health and environmental sustainability. Super looking forward!🧪 #microsky #microbiomesky #grc
www.grc.org/microbiome-e...

Charting the landscape of cytoskeletal diversity in microbial eukaryotes An imaging resource of over 200 microbial eukaryotic species provides a glimpse into the remarkable universe of cytoskeletal diversity.

Now online! Charting the landscape of cytoskeletal diversity in microbial eukaryotes

High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons - Microbiome Background High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. Results...

Still using 16S/ITS profiling? You might want to reconsider👀

Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable!
microbiomejournal.biomedcentral.com/articles/10....

A very proper 'All Hallow's Eve'-Eve Fish. 🐟👻🎃

The average nucleotide identity (ANI) underpins how we map microbial diversity, compare species, and connect genomes to ecology.
I wrote a short piece reflecting on the discovery and significance of this metric (and really enjoyed digging into the context and story behind it!) #microsky 🧬

A Genomic Perspective on Species Delimitation Genomic species delimitation is transforming how we understand and define species by enabling a process-oriented and efficient approach to identifying species boundaries. This review outlines the two ...

www.annualreviews.org/content/jour...

We are really proud of this report from our 3 colloquia convened by the AAM and supported by the Moore Foundation. A few experts even said they would use it as their introductory textbook for this area. Please check it out!

Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes Abstract. The classification of living systems presents significant challenges due to the prevalence of gene transfer between genomes. Traditional taxonomi

I've often wondered about what we should call organisms whose similarity might be due to acquired genetic material. It got a little complicated, but I made a stab at it here

Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes academic.oup.com/mbe/article/...

Cellulose biosynthesis and function in Streptomyces Cellulose, a ubiquitous polysaccharide with critical roles in life, provides structural integrity to cells in plants and aids biofilm formation in many bacteria. Although bacterial cellulose biosynthe...

Cellulose biosynthesis and function in Streptomyces

@cp-trendsmicrobiol.bsky.social by Chennan Yang, @xiaobozhong.bsky.social and Dennis Claessen

www.cell.com/trends/micro...

Congratulations @annazaidmanremy.bsky.social and all!

A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights Oral microbiome shows rising importance in human health. Cha et al. present the human reference oral microbiome (HROM), comprising 72,641 high-quality genomes from 3,426 species, including 2,019 previ...

Catalog of human oral microbiome:

Human reference oral microbiome (HROM) comprises 72,641 genomes from 3,426 species, including 2,019 novel species. HROM reveals disease-assoc. species & ectopic oral species in the gut predictive of systemic diseases
www.cell.com/cell-host-mi...

Meta-analysis of COVID, RSV, flu vaccines for fall provides 'sea of data' showing efficacy, safety

Thank you, @cidrap.bsky.social, for covering our new @nejm.org review of Covid-19, RSV, and influenza immunizations.

Check it out: cidrap.umn.edu/covid-19/meta-analysis-covid-rsv-flu-vaccines-fall-provides-sea-data-showing-efficacy-safety

Even as the anti-vax lobby erodes public trust, new evidence confirms that "immunizations against Covid-19, RSV, and influenza have shown consistent effectiveness & safety and are associated with a substantially reduced risk of hospitalization & severe disease"

www.nejm.org/doi/full/10....

These Bay Area Restaurants Are Offering Free Food to SNAP Recipients Amid a government shutdown that will cut off aid for 42 million Americans, local food scene folks plan to pick up the slack.

While the feds continue to play stupid games, SNAP recipients are set to lose food aid for the next month. In the Bay Area, a growing number of restaurants are stepping up to help, and we're maintaining the list. Share with anyone who needs it. www.coyotemedia.org/these-bay-ar...

Scientists had to change more than 700 grant titles to receive NIH funding. Health disparities researchers fear what’s next www.statnews.com/2025/10/29/n...

Systematic metaproteomics mapping reveals functional and ecological landscapes of Ex vivo human gut microbiota responses to therapeutic drugs Nature Communications - Here, the authors systematically map metaproteomic responses of ex vivo human gut microbiota to common therapeutics, identifying several drug classes inducing strong...

Interested in #drugs, #microbiome and #antibiotic resistance, then check out our paper on the effects of over 300 drugs on the gut microbiome. Exciting results as well on the role of antibiotic resistance defining how microbiomes respond to drugs.
@quadraminstitute.bsky.social

rdcu.be/eMmcT

Great workshop, fantastic location, amazing instructors! If you are interested in obtaining advanced training in phylogenomics / comparative genomics research, apply now!

Check out our @natbiotech.nature.com @natureportfolio.nature.com piece with Yumeng Zhang + Jiangning Song on @genentech.bsky.social's deep learning approach to accelerate antibiotic discovery. Congrats to Gabriele Scalia, Tommaso Biancalani, Man-Wah Tan, Aviv Regev, @yoshuabengio.bsky.social et al!

1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start?

We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!

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

Pseudomonas aeruginosa senses exopolysaccharide trails using type IV pili and adhesins during biofilm formation - Nature Microbiology Opposing forces generated by exopolysaccharide trail binding versus type IV pilus retraction generate a high cyclic diGMP–high cyclic AMP state in Pseudomonas aeruginosa that promotes social motility.

Cool 🦠

William Schmidt
Gerard Wong Lab @UCLA
Nature Microbiology

Pseudomonas aeruginosa lays down Psl exopolysaccharide as it crawls

Other cells detect and follow these trails using type IV pili pulling against adhesins like CdrA triggering c-di-GMP & cAMP surges to shift into early biofilm mode

Jumbo phage–mediated transduction of genomic islands | PNAS Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages, and c...

@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎

www.pnas.org/doi/10.1073/...

Host-mediated niche construction of bacterial communities in an aquatic microecosystem Abstract. Microbes coordinate homeostasis in host-associated and environmental ecosystems alike, but the connectivity of these biomes is seldom considered.

Excited to share our new paper out in @isme-microbes.bsky.social. We asked if environmental microbial communities can be adaptively modulated by host species that transiently acquire their symbionts from the environment #SymbioSky #MicrobiomeSky
doi.org/10.1093/isme...