JS Gounot
@jsgounot.bsky.social
Microbiology x population genetic Post-doctoral fellow in the Genome Institute of Singapore.
It's my pleasure to introduce for the first time r-news.net, a project I had in my head for quite a long time (since my PhD!). With AI improving literature review quite substantially, we still miss a critical step: What does the community as a whole like the most?
Top Stories — RNews
r-news.net
Biologists Confirm Not Much Evolution Happened Today — theonion.com/biologists-c...
Biologists Confirm Not Much Evolution Happened Today
STANFORD, CA—Calling it a “pretty slow one” as far as natural selection and genetic drift were concerned, biologists from Stanford University confirmed Tuesday that not much evolution happened today. ...
theonion.com
Whenever I presented Phold, I was frequently asked "can you do the same beyond phages?" We ( @oschwengers.bsky.social @linsalrob.bsky.social @binomicalabs.org et al) finally did it with Baktfold github.com/gbouras13/ba... www.biorxiv.org/content/10.6...
GitHub - gbouras13/baktfold: Rapid & standardized genome annotation using protein structural information
Rapid & standardized genome annotation using protein structural information - gbouras13/baktfold
github.com
High-resolution temporal profiling reveals synchronized dynamics of the mouse gut microbiome https://www.biorxiv.org/content/10.64898/2026.03.26.714232v1
Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback. rdcu.be/famFj
High-resolution metagenome assembly for modern long reads with myloasm
Nature Biotechnology - A long-read metagenome assembly method recovers circular and complete genomes better than existing tools.
rdcu.be
Nature Biotechnology@natbiotech.nature.com · 4mo agoHigh-resolution metagenome assembly for modern long reads with myloasm - @lh3lh3.bsky.social @jimshaw.bsky.social @danafarber.bsky.social @harvardmed.bsky.social go.nature.com/3PBEwvR
How did @Nature become "prestigious" to scientists? In our opening article of Issue 09, writer Robert Reason traces the journal's history. By understanding how Nature’s prestige was constructed, we can also clarify which elements are deserved and which are entrenched.
Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm
Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology
Long-read sequence assemblies from metagenomes contain frequent errors.
go.nature.com
Our new paper on high-throughput isolation of Bifidobacterium just got published! A very nice adventure starting with the supervision of @lamhaiha.bsky.social, a talented intern, and a nice collab with our BSight expert @isaacyueyuan.bsky.social! Stay tuned for more isolation and Bifido work! :)
@isaacyueyuan.bsky.social · 7mo agoThrilled to share our high-throughput Bifidobacterium isolation work in Microbiology Spectrum! journals.asm.org/doi/10.1128/... By integrating a single-cell dispenser into a culturomics workflow, we accelerated the isolation of individual bacterial cells, allowing robust strain-level resolution.
✨ Latest exciting story of the group in @nature.com. Here, we go beyond SNPs and built a species-wide atlas of genetic variants in yeast. With >1,000 near T2T genomes, we show how large genomic variations affect trait diversity. www.nature.com/articles/s41...
From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes - Nature
A newly compiled atlas of species-wide structural variants and gene-based and graph pangenomes derived from highly complete assemblies of genomes from 1,086 natural isolates enable integrative genome-...
nature.com
www.cell.com/cell-host-mi... #microsky #microbiome
Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts
Bifidobacterium are beneficial members of the microbiota across animal hosts. Kujawska et al. demonstrate that bifidobacteria have likely co-evolved more closely with mammals, particularly primates, a...
cell.com
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 11mo agoHigh-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
The latest story from the @haploteam highlights the phenotypic impact of acquired subgenomes in allopolyploids, through the lens of 1,060 Brettanomyces bruxellensis genomes. Nice collaboration with @univbordeaux.bsky.social @unistra.fr @cnrsbiologie.bsky.social www.nature.com/articles/s41...
Whole-genome sequencing of 1,060 Brettanomyces bruxellensis isolates reveals significant phenotypic impact of acquired subgenomes in allopolyploids - Nature Communications
The authors sequence and phenotype over 1,000 isolates of the yeast Brettanomyces bruxellensis, and show how allopolyploidization reshapes genome evolution and enhances phenotypic diversity, highlight...
nature.com
The most viruslike microbe to date was discovered by accident when researchers sequenced the DNA inside this tiny ocean critter. That story and more of the best from @science.org and science in this edition of #ScienceAdviser: www.science.org/content/arti... 🧪
Short-read metagenomic sequencing cannot recover genomes from many abundant marine prokaryotes due to high strain heterogeneity and platform-inherent GC bias (likely viruses, too), but Nanopore long reads can address this. A results thread on our recent preprint 🧵.
Steven Robbins@stevenjrobbins.bsky.social · last yr.Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.biorxiv.org/content/10.1...
Super thrilled to share our labor of love from the Asian Skin Microbiome Program! We collected >3,500 skin samples, built metagenomic libraries w/ >70 billion reads and >10TB of data to study heterogeneity of the skin microbiome in the general population (200 adults, 18 sites) t.co/ZylbJMpvpw
Large-scale skin metagenomics reveals extensive prevalence, coordination, and functional adaptation of skin microbiome dermotypes across body sites
The human skin microbiome is increasingly recognized to influence skin health, immune function and disease susceptibility. However, large-scale, multi-site metagenomic studies in the general populatio...
biorxiv.org
I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers, www.biorxiv.org/content/10.1... and tell you just a little bit about it in the following 🧵
Assemblies of long-read metagenomes suffer from diverse errors
Genomes from metagenomes have revolutionised our understanding of microbial diversity, ecology, and evolution, propelling advances in basic science, biomedicine, and biotechnology. Assembly algorithms...
biorxiv.org
LLMs hallucinating nonexistent software packages with plausible names leads to a new malware vulnerability: "slopsquatting."
LLMs can't stop making up software dependencies and sabotaging everything
: Hallucinated package names fuel 'slopsquatting'
theregister.com
Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social: rdcu.be/eg4OA 1/
Efficient and robust search of microbial genomes via phylogenetic compression
Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.
rdcu.be
In 1904, a physician took soil he had “impregnated with a living emulsion” of a virulent bacterium, Serratia marcescens, and sprinkled it in front of the UK House of Commons. This was an early experiment to study how microbes spread through buildings and cause infections...
New year, new assemblies! I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes! It's the successor to Trycycler, designed to be faster and less reliant on user intervention. Check it out: github.com/rrwick/Autoc... (1/5)
Home
A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler
github.com
Interactive online show about the microbial world from the Museum of Natural history at Oxford Uni. Cool ideas. www.oum.ox.ac.uk/bacterialwor...
A new view of #SpeciesConcepts by @jeannettewhitton.bsky.social and me, clarifying time frames while unifying interbreeding, genealogy, and traits. A general-purpose species should be a reproductive community (bound by cohesive processes) viewed retrospectively (RRCC). doi.org/10.18061/bss...
Another small and interesting historical story from Asimov press. This time about the Watson's central dogma.
Francis Crick Was Misunderstood
The Central Dogma is not a
doi.org
Excited to share our latest work, where we show how to achieve high-throughput sequencing of DNA containing non-canonical bases using Nanopore (@nanoporetech.com) and de novo basecalling enabled by spliced-based data-augmentation. #nanopore #basecaller #syntheticbiology
Direct high-throughput deconvolution of unnatural bases via nanopore sequencing and bootstrapped learning
The discovery of synthetic xeno-nucleic acids (XNAs) that can basepair as unnatural bases (UBs) to expand the genetic alphabet has spawned interest in many applications, from synthetic biology to DNA ...
biorxiv.org
A fun idea, using Bacillus subtilis to sense the TNT explosive
An autonomous microbial sensor enables long-term detection of TNT explosive in natural soil - Nature Communications
Engineered microbes can detect harmful chemicals, but may not work well in complex environments. Here, the authors built microbial sensors for detection of TNT explosive and tested their response over...
nature.com
