Rubin Lab
@therubinlab.bsky.social
News from the Rubin Lab 🧬🧫 We conduct DNA-level editing of microbial communities for understanding and control. Managed by lab members. @innovativegenomics.bsky.social @ucberkeleyofficial.bsky.social 🔬🌁 🔗 therubinlab.org
We are PUBLISHED!!! Our mechanistic work on how CRISPR-Cas ancestors unwind DNA and how this can be used to engineer hypercompact plant editors can now be found on Mol Cell- if you are interested in what defines a good genome editor, this read is for you 😎 🔗 www.sciencedirect.com/science/arti...
sciencedirect.com
A stool transplant delivers billions of microbes into a sick gut. Almost none move in for good. We followed donor-recipient pairs from whole communities down to single nucleotides, and found the gut runs a ruthless strain-level filter. Out now in Cell Reports 🧵 www.cell.com/cell-reports...
Strain-level ecological filtering governs microbial colonization of the human gut
Baertschi et al. demonstrate that microbiota transplantation functions as a selective ecological filter. Although donor species frequently appear, only specific lineages achieve stable strain integrat...
cell.com
Universität Bern@unibe.ch · 3d agoA strict “gatekeeper” decides whether a #fecaltransplant is effective: sohub.io/wruy. This is shown by a new study led by @bahtiyil.bsky.social from #unibern & @inselgruppe.bsky.social @dbmr-unibe.bsky.social
1st genome sequenced (Sanger 1977), 1st genome synthesised (Venter 2003), 1st genome + proteome fully mutated (Huijin Xiangua 2026!) @crg.eu @sangerinstitute.bsky.social Complete Mutagenesis of the Genome and Proteome of ΦX174 www.biorxiv.org/content/10.6...
Complete Mutagenesis of the Genome and Proteome of ΦX174
The bacteriophage ΦX174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the ΦX174 ge...
biorxiv.org
Out now! In collaboration with Hiroshi Nishimasu's lab, we uncover how a dual reverse transcriptase immune system builds double-stranded DNA from both RNA and protein templates. www.cell.com/cell/abstrac... Previous thread for the preprint: bsky.app/profile/ster...
Coordinated RNA- and protein-templated synthesis of double-stranded DNA by a dual reverse transcriptase immune system
Bacterial reverse transcriptases defend against viruses, yet how their DNA products stop infection remains unknown. Bacteriophage inhibition of a host recombination enzyme activates the DRT3 defense s...
cell.com
New study by UC Berkeley researchers pinpoints human DNA inherited from ‘ghost’ ancestors. bit.ly/450g7Vp
New technique pinpoints human DNA inherited from ‘ghost’ ancestors - Berkeley News
Neanderthals and Denisovans interbred with modern human ancestors, leaving behind telltale DNA in our genomes. Now we have evidence of modern human interbreeding with two much older but unknown ancest...
bit.ly
Did you know all living things emit a faint glow? They're called 'biophotons,' and ultra-weak ‘biophotons’ might be used to diagnose disease or could even represent a new signalling mechanism in cells, according to a feature in Nature. ⚛️ 🧪
All living things emit a faint glow. Could this light be useful?
Ultra-weak ‘biophotons’ might be used to diagnose disease, or could even represent a new signalling mechanism in cells.
go.nature.com
Antibiotic resistance gene acquisition by Pseudomonas aeruginosa and Achromobacter from transiently infecting bacteria drives rapid and extreme resistance to the antibiotic tobramycin during chronic lung infection within patients. #microsky #medsky 🧪
Within-patient gene transfer between transiently and chronically infecting bacteria causes extreme antibiotic resistance during lung infections - Nature Microbiology
Antibiotic resistance gene acquisition by Pseudomonas aeruginosa and Achromobacter from transiently infecting bacteria drives rapid and extreme resistance to tobramycin during chronic lung infection within patients.
go.nature.com
Out Now! Cell-autonomous immunity as an integrated immune network against bacterial and viral pathogens #MicroSky
Cell-autonomous immunity as an integrated immune network against bacterial and viral pathogens
Nature Microbiology, Published online: 30 July 2026; doi:10.1038/s41564-026-02428-xThis Review summarizes the current knowledge about the cell-intrinsic factors that act against pathogenic bacteria and viruses and the immune evasion strategies that pathogens have to counteract cell-autonomous immunity.
go.nature.com
Out Now! Combined phage therapy and faecal microbiota transplantation to treat recurrent urinary tract infection: a case series #MicroSky
Combined phage therapy and faecal microbiota transplantation to treat recurrent urinary tract infection: a case series
Nature Microbiology, Published online: 30 July 2026; doi:10.1038/s41564-026-02409-0In a small case series, combined phage therapy and faecal microbiota transplantation was safe and led to sustained reductions in recurrence, severity and antibiotic use in women with recurrent urinary tract infections, even without complete eradication of Escherichia coli.
go.nature.com
Nature research paper: Diverse bacterial pattern recognition receptors sense the core phage proteome go.nature.com/45fpXCZ
Diverse bacterial pattern recognition receptors sense the core phage proteome - Nature
Systematic analysis of prokaryotic STAND NTPases — relatives of animal and plant immune receptors — uncovers diverse antiviral sensors that detect most of the core structural and replicative proteins of bacteriophages.
go.nature.com
Avocados come in 2 varieties - A-types start each day female and switch to male midday. B-types do the reverse. In work just published from the last chapter of my PhD, we show this system evolved 40+million yrs ago and is regulated by alleles of 1 transcription factor www.pnas.org/doi/10.1073/...
Balanced polymorphism in a floral transcription factor underlies the ancient rhythm of daily sex alternation in avocado | PNAS
In avocado and certain wild relatives in Lauraceae, a highly synchronized daily rhythm of floral sex timing promotes cross-pollination between two ...
pnas.org
🌱🌍 Published in Nature Reviews Bioengineering, "Genome engineering of plant photosynthesis for carbon sequestration" from IGI researchers from co-first authors Evan Groover and Flora Zhiqi Wang, and the Savage Lab, Niyogi & Lemaux labs! Read here: https://www.nature.com/articles/s44222-026-00453-3
An RNA editing enzyme restrains the excessive proliferation of intestinal stem cells—a major hallmark of #aging in humans and other organisms—according to new work in #ScienceSignaling involving fruit flies and data from mice and human samples. https://scim.ag/44VKex1
A reduction in A-to-I RNA editing by ADAR disrupts Pumilio-mediated inhibition of MAPK signaling to drive intestinal stem cell aging
The RNA editing enzyme ADAR slows intestinal stem cell aging by reducing proliferative MAPK signaling.
scim.ag
🎉final print version in PLOS Genetics @sullivan-lab.bsky.social @biosci.lbl.gov journals.plos.org/plosgenetics...
Cross-family and phage-specific gene requirements for Klebsiella infection revealed by scalable RB-TnSeq genetic screens
Author summary Bacteriophages, or phages, are viruses that infect bacteria and play central roles in shaping microbial communities across ecosystems. Despite their ecological importance, the bacterial...
journals.plos.org
Vivek Mutalik@vivekmutalik.bsky.social · 5mo agoNew paper 🔔 Collaboration @sullivan-lab.bsky.social Marissa Gittrich led the work Klebsiella phage biology has focused almost entirely on capsulated strains, but capsule loss is the #1 resistance mechanism under phage predation. We used a naturally acapsular host to reveal the receptor landscape
Some bacteria use the CRISPR/Cas systems as transcriptional repressors of other anti-phage systems, such that when CRISPR interfered with, gene expression of repressed anti-phage systems goes up www.nature.com/articles/s41...
CRISPR–Cas regulates expression of embedded anti-phage defence systems - Nature
CRISPR–Cas systems transcriptionally tune diverse innate defences using CRISPR RNA-like guides to balance antiviral protection with fitness, and hyperactivate these defences when compromised, establis...
nature.com
New online! Eggerthella lenta: metabolism, pathogenesis and therapeutic implications
Eggerthella lenta: metabolism, pathogenesis and therapeutic implications
Nature Reviews Microbiology, Published online: 23 July 2026; doi:10.1038/s41579-026-01344-5Advancing microbiome research beyond well-studied bacterial species is key to understanding the full functional diversity and potential of the human gut microbiome. In this Review, Turnbaugh and colleagues explore the unique metabolism and pathogenic potential of Eggerthella lenta, supporting the feasibility and utility of studying diverse human-associated bacterial species.
dlvr.it
#Throwback 🧪 PERSPECTIVE | Emerging tools and best practices for studying gut microbial community metabolism @cecilianoecker.bsky.social & P Turnbaugh
Emerging tools and best practices for studying gut microbial community metabolism - Nature Metabolism
In this Perspective, Noecker and Turnbaugh provide a detailed guide for studying microbial community metabolism and discuss the best practices in the field.
nature.com
Excited for the Rubin Lab to join this DOE Genesis Mission project led by Michelle O’Malley at UCSB! We’ll contribute bacterial genome modeling and genetic engineering to help design anaerobic microbial communities that convert plant waste into useful chemicals.🧬
UC Santa Barbara@ucsantabarbara.bsky.social · 2w agoTwo research teams led by #UCSB faculty have been selected for Phase I support through the U.S. Department of Energy’s (DOE) historic Genesis Mission, a new national initiative designed to accelerate scientific discovery with artificial intelligence. Full story: https://ow.ly/9NeG50ZrtLo
New Preprint 🥳 Here we wondered how phages that have been extensively studied in laboratory E. coli strains actually behave when they encounter a real pathogen such as O157:H7 strain...one with a far more complex cell surface & one of the most consequential foodborne pathogens in the United States.
Animated E. coli Bacteria Drawing
Alt: Animated E. coli Bacteria Drawing
static.klipy.com
How do human cells defend against viruses? @sgfern.bsky.social discovers that human immune proteins named ISGs target ancient features of replication shared between animal and bacterial viruses – opening analysis of human immunity to the power of bacterial genetics www.biorxiv.org/content/10.6...
From Nobel Prizes to national parks, here are 25 UC Berkeley breakthroughs to commemorate America’s 250th birthday. #UCBerkeley #America250 #Innovation
25 UC Berkeley breakthroughs to commemorate America's 250th birthday - Berkeley News
From Nobel Prizes to national parks, here are 25 ways Berkeley has lit the way forward throughout its history.
bit.ly
Bridge recombinase enables versatile rewriting of bacterial genomes https://www.biorxiv.org/content/10.64898/2026.04.29.721476v1
HUGE congratulations to our wonderful grad student (now PhD candidate!) @leosong.bsky.social on completing his qualifying exams with flying colors! 🥳🥂 We're so fortunate to have such an awesome member of the lab and we're looking forward to seeing his accomplishments in the coming years 💙
We said goodbye to our WONDERFUL lab manager Sarah Hasham last week as she starts a new chapter in San Diego at the @salkinstitute.bsky.social's Busch Lab! We'll miss her terribly but wish her the best of luck in her future plant endeavors 🌱👩🔬💚
The Cress lab is excited to welcome 2 new postdocs: Dr. Zach LaTurner from Rice University and Dr. Madeline Hayes from UW Madison, shared with @therubinlab.bsky.social
One of the biggest challenges in microbial biotechnology? Unlocking the potential of non-model microbes and synthetic communities! Glad to share our review @sonjablasche.bsky.social @simonemozzachiodi.bsky.social @kiranrpatil.bsky.social @cambridgebiosci.bsky.social🧵(1/7) doi.org/10.1016/j.co...
A sweeping new mural at UC Berkeley celebrates 150 years of women at the university, featuring 41 trailblazers—from pioneering architect Julia Morgan to Nobel laureate Jennifer Doudna. news.berkeley.edu/2026/03/06/sprawling-new-painting-commemorates-150-years-of-women-at-uc-berkeley
Sprawling new painting commemorates 150 years of women at UC Berkeley - Berkeley News
The mural in the new Undergraduate Academic Building in the heart of campus pays tribute to 41 women and the ways their contributions have echoed through time.
news.berkeley.edu
Early-bird registration discounts for CRISPR 2026 expire Feb 28. CRISPR 2026, held at Yale University, June 10 - 12, is the continuation of the original CRISPR meeting established in 2008. Register here: web.cvent.com/event/ac20b6...
Today in Nature Communications, a team of IGI researchers from The Banfield Lab and Pam Ronald's labs uncover a new way to reduce #methane emissions from rice by influencing the activity of rice paddy soil #microbes. Read more: https://ow.ly/45j150Y3WsI
