βΌοΈDiamond Lab is considering potential a new postdoctoral researcher. If you have strong interests in microbiomes, metagenomics, machine learning, or rumen biology drop us a line and shoot us a CV!
01.08.2025 22:57 β π 4 π 4 π¬ 0 π 1
Phage-based delivery of CRISPR-associated transposases for targeted bacterial editing
"Here, we engineer phage Ξ» with CRISPR-associated transposases to enable flexible bacterial genome manipulation, including in a mixed microbial community context."
www.pnas.org/doi/10.1073/...
29.07.2025 17:26 β π 10 π 4 π¬ 1 π 0
We (with Clement Coclet, not on Bsky) had the chance to work on a broad "state of viromics" review. We tried to use this to give an overview of how the field changed over the last ~ 15 years, and also what we think are some of the major remaining challenges. Full-text access at -> rdcu.be/excHt
22.07.2025 15:06 β π 79 π 39 π¬ 2 π 2
New review article with @mmdesai.bsky.social is out today! Grateful for the opportunity to contribute something we hope will serve the community well
21.07.2025 17:30 β π 43 π 15 π¬ 3 π 0
Junior, Assistant, or Associate Specialist β Xue Lab
University of California, Irvine is hiring. Apply now!
The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more.
recruit.ap.uci.edu/JPF09601
17.07.2025 20:32 β π 113 π 111 π¬ 0 π 3
π¨ Fresh from the press! We created and analyzed over 100 in vitro cyanobacterial consortia using well-characterized model cyanobacterial hosts to better understand how cyanobacteria recruit and interact with their microbiomes.
Check it out: doi.org/10.1093/isme...
11.07.2025 13:07 β π 43 π 22 π¬ 3 π 4
Bridging the scales: what can microbial ecologists learn from classic ecology?
Beautiful new review paper in preprint bridging microbial ecology and classic ecology led by Maggie Vogel, @olimeacock.bsky.social and @annasophieweiss.bsky.social, also by @juliensluneau.bsky.social and @lambdapp.bsky.social from our lab (not me :)) ecoevorxiv.org/repository/v...
01.07.2025 08:25 β π 39 π 26 π¬ 1 π 0
Weβre happy to share our preprint where applied phages to Microbiomes to test microbial interaction hypotheses - without losing the relevance of the community.
Bonus: using SNPs we studied how our targeted organism recovers from infection, and find how the community likely influences this process.
22.06.2025 20:49 β π 14 π 4 π¬ 0 π 0
over a year later, this one out today!
link.springer.com/article/10.1...
16.06.2025 16:35 β π 33 π 14 π¬ 3 π 0
Our structural core gene pipeline Unicode is now published at GBE
π doi.org/10.1093/gbe/...
Please also check out @dongwookkim.bsky.socialβs
𧡠bsky.app/profile/dong...
03.06.2025 17:19 β π 43 π 19 π¬ 2 π 0
Microbial model communities reveal widespread auxotrophies in abundant bacteria
Our results highlight the value of cultivating microorganisms in groups to cultivate:
1) abundant microorganisms
tinyurl.com/miintmodcom
29.04.2025 05:00 β π 23 π 11 π¬ 2 π 0
A graph showing reported measles cases in the United States. The line shows that there were regularly 400-600,000 cases each year until 1963, when the measles vaccine was licensed, at which point cases plummet. In 2000, the elimination of measles was declared.
Vaccines have granted families in wealthy countries the luxury of forgetting what measles, polio, rubella, and other preventable diseases are like.
We're looking at how many millions of lives vaccines have saved.
Read the full story: https://go.nature.com/42Aj3Y8
08.04.2025 09:55 β π 232 π 88 π¬ 3 π 9
Beautiful new study reveals how ππ΅π³π¦π±π΅π°π€π°π€π€πΆπ΄ π±πΊπ°π¨π¦π―π¦π΄ bacteria prefer to acquire CRISPR immunity from dormant (lysogenic) phagesβnot active lytic ones. A clever way to survive and remember without getting destroyed.
Keith et al., Cell Host Microbe
#CRISPR #phage
www.cell.com/cell-host-mi...
23.03.2025 00:07 β π 36 π 13 π¬ 1 π 1
Ben Adler & Muntathar Jamal Al-Shimary
Phage genomes are full of mysterious proteins that could be harnessed to create new genomic tools. IGI's @doudna-lab.bsky.social & @cresslab.bsky.social with co-first authors @benadler.bsky.social & Muntathar Jamal Al-Shimary detail a new way to exploring phage genomes: ow.ly/uucL50V77n0 π§ͺπ¦ π§¬
13.03.2025 17:58 β π 22 π 7 π¬ 0 π 0
Our Phage infection/T6S story is finally out @embojournal.org! "Surface-mediated bacteriophage defense incurs fitness tradeoffs for interbacterial antagonism" Led by my wonderful team at Academia Sinica!
www.embopress.org/doi/full/10....
10.03.2025 13:43 β π 10 π 7 π¬ 2 π 0
PLOS statement on recent US Executive Orders and scientific integrity - The Official PLOS Blog
Since its founding over twenty five years ago PLOS has been dedicated to advancing open science, ensuring that knowledge is accessible toβ¦
PLOS has issued a statement on recent US Executive Orders and scientific integrity.
We are determined to stand firmly behind our mission, our values and our principles, and against any attempt at censorship or undermining of the core principles of scientific inquiry.
plos.io/3D4O8cH
21.02.2025 15:41 β π 1092 π 422 π¬ 27 π 62
Email the leadership of the ASM to protest their decision to obey in advance and pulling DEI related, previously published content and papers from their website. I personally would threaten leaving ASM, avoiding ASM meetings, and refuse reviewing for them. @vscooper.micropopbio.org
03.02.2025 05:49 β π 22 π 10 π¬ 0 π 1
SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome - Nature Microbiology
Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) can be applied to complex microbial communities to reveal spatial co-localization of microbes at the micron scale.
Happy to share our new paper in @naturemicrobiol.bsky.social on mapping spatial relationships of the human gut microbiome. We identified distinct spatial hubs between gut bacteria that reflect sub-community assemblies at the micron-scale. Led by Miles Richardson & co.
www.nature.com/articles/s41...
03.02.2025 14:46 β π 89 π 36 π¬ 0 π 0
Siderophore synthetase-receptor gene coevolution reveals habitat- and pathogen-specific bacterial iron interaction networks
Coevolving siderophore genes shape bacterial iron networks, unveiling the complexity of cheating across habitats and lifestyles.
We derive iron-siderophore interaction networks among Pseudomonas strains from sequencing data. One key insight: natural strains form dense networks, whereas pathogens are loners. With @frimanscience.bsky.social @zhiyuanli.bsky.social & Nanjing colleagues
www.science.org/doi/10.1126/...
16.01.2025 09:29 β π 58 π 35 π¬ 1 π 2
Two decades of bacterial ecology and evolution in a freshwater lake
Nature Microbiology - A 471-metagenome time series from Lake Mendota in Wisconsin, USA, reveals seasonal and decadal shifts in bacterial functional and ecological dynamics, especially in response...
After 24 years of work, Iβm thrilled to announce the TYMEFLIES dataset, which comprises metagenomes from Lake Mendota (Madison, WI), collected roughly every 10 days (471 samples) for 20 years! @quendi.bsky.social @robinrohwer.bsky.social
rdcu.be/d5put
A threadβ¦
03.01.2025 11:44 β π 246 π 101 π¬ 3 π 3
Principal Researcher in BioML at Microsoft Research. He/him/δ». πΉπΌ yangkky.github.io
SMBE fosters communication among molecular evolutionists and advances the field.
π smbe.org
π¬ smbe2025.scimeeting.cn β’ @smbe-chile2025.bsky.social
π₯ @smbe-idea.bsky.social
π @molbioevol.bsky.social β’ @genomebiolevol.bsky.social
πͺπΊ π«π· π¦πΊ in π¬π§ (he/him) | www.mericlab.com
Human microbiome(s), pathogen ecology & host-microbe genomics
Associate Professor & Senior Lecturer @uniofbath.bsky.social
Clinical Affiliate @bakerresearchau.bsky.social @cambridgebaker.bsky.social
πBath, UK
Professor of Plant Evolutionary Genetics at Michigan State University.
Do my science @ace_uq studying coral reef microbiomes. Data wrangler, meta-omics and long-read wonk, clean energy enthusiast, Saganist zealot, collector of weird zoology facts, other nonsense.
Microbiology, microbiome, antimicrobial resistance. Sometimes UK politics. Head of Research of the School of Infection, Inflammation and Immunology, University of Birmingham. Also Co-Director of @target-amr.bsky.social.
Eco-evo with microbes. I happen to like fjords, I think they give a lovely baroque feel to a continent. The University of TromsΓΈ. Opinions my own. She/her
The Diamond Lab | Innovative Genomics Institute @ UC Berkeley | Metagenomics | Microbiome Systems Ecology and Modeling | AI for Microbes | Environmental MGEs | Health and Climate Change
@innovativegenomics.bsky.social⬠| @ucberkeleyofficial.bsky.social
Metagenomics, microbes, and molecules.
Assoc Prof @CSUSM | π¦ βπ¦ MGEs & coastal metagenomes | #BlueSoup π₯£π§¬ 𧫠| R1βBiotechβPUI | Protective mama bear of students | She/Her
Science. Biology. Progress.
Founding Editor of Asimov Press. Subscribe at press.asimov.com!
omics-driven and constraint-based modeling of microbial community metabolism 𧬠post-doc in the Sunagawa Lab, Institute of Microbiology, ETH Zürich
Microbial Ecologist π¦
Research Fellow | Securing Antarctica's Environmental Future | Greening Lab | Monash University
Curious about the extremes of life πποΈβπποΈ
they/them π³οΈβππ³οΈββ§οΈ
linktr.ee/sophie.i.holland
Algae enthusiast, Associate Professor @UniofExeter, joint appointment @thembauk #ERC-CoG, former #NERC IRF
Algal ecophysiology | signalling | microbiome | molecular microbiology | diatoms!
Assistant Professor at @univmalaga.bsky.social | Exploring how photosynthetic microbes adapt to stress π§ͺ | Combining experimental evolution, ecology & cutting-edge sequencing to predict adaptation π¬
Postdoc in Kiran Patil's lab at Cambridge, UK. Previously PhD student at Gianni Liti's lab in Nice, France. Interested in microbes (genomes, evolution, communities and metabolism)
Graduate student at SSPB, Rice University. Microbe-mineral interactions | Biosensing | Bioenrichment. It's all about the 'crobes! Sapere aude.
