JS Gounot

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 - Nature Biotechnology Long-read sequence assemblies from metagenomes contain frequent errors.

Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm

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! :)

Hi Sean! Looks very interesting! Will the talks be recorded and shared in some ways? Sadly it will happen during night time for some of us. Should we still register to get access to the records? Thanks!

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-...

✨ 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...

New blog post – A quick look at Roche's SBX
lh3.github.io/2025/09/11/a...

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...

www.cell.com/cell-host-mi...

#microsky #microbiome

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

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...

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...

Hidden inside this dinoflagellate is a tiny microbe so reliant on its host that scientists say it’s the most viruslike cellular organism known. Takuro Nakayama/University of Tsukuba

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 🧵.

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...

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

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...

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 🧵

LLMs can't stop making up software dependencies and sabotaging everything : Hallucinated package names fuel 'slopsquatting'

LLMs hallucinating nonexistent software packages with plausible names leads to a new malware vulnerability: "slopsquatting."

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.

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/

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...

Home A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler

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)

Interactive online show about the microbial world from the Museum of Natural history at Oxford Uni. Cool ideas. www.oum.ox.ac.uk/bacterialwor...

The Dangers of Mirrored Life Creating mirrored organisms using synthetic biology could seriously harm extant life, a 300-page report claims. While the risks from mirrored life are uncertain, it is best not to find out.

Another great piece from Asimov press: www.asimov.press/p/mirror-life

Image of first page and an illustration from our paper titled "The species as a reproductive community emerging from the past".

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...

Francis Crick Was Misunderstood The Central Dogma is not a

Another small and interesting historical story from Asimov press. This time about the Watson's central dogma.

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 ...

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

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...

A fun idea, using Bacillus subtilis to sense the TNT explosive

What is the correct meaning and interpretation of p-values? I’m posting this question, and an answer, to help dispel a few misunderstandings about what p-values are. As a hiring manager interviewing mid-level and senior data scientists, I have noticed these

BS seems a nice place to save and share some interesting links, hope this can help others as well. Starting with one more (and never-ending) reminder on p-values misconceptions, with a nice practical example.

Yes this is the main issue for most of us I guess, but I'll let you know if I think of someone.

The methodology used in previous paper is relatively easy and would probably only take few weeks or a couple of months top to reproduce. The problem is that previous methods were good enough to observe global patterns, but are subject to context-specific issues. So it's a matter of luck I think.

Fast and accurate metagenotyping of the human gut microbiome with GT-Pro - Nature Biotechnology Alignment-free SNP calling from metagenomes reduces computational time by two orders of magnitude.

If you're looking for a more "mapping-based", you can probably check this: www.nature.com/articles/s41...