Jackson Tsuji

Nanopore sequencing reaches amplicon sequence variant (ASV) resolution www.biorxiv.org/content/10.6... #jcampubs

So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here: artic-network.github.io/peartree (click the “Example...” button for immediate candy and then click every button you can find).

Ktedonobacteria are so freaking cool, with 10+ Mbp genomes, interesting morphologies and tons of BGCs

Chromid-like secondary replicons as key sites of biosynthetic gene clusters in Ktedonobacteria https://www.biorxiv.org/content/10.64898/2026.02.02.703402v1

The Dayhoff Exchange Score: A new metric to quantify entropic site saturation in amino acid datasets prior to phylogenetic analysis Abstract. Entropic site saturation is a persistent problem in phylogenetic analyses, where it can hinder the accuracy of topology reconstruction. It is fun

New research published! I wanted to write about this, because I think the DE-Score *might* be the thing I'm proudest of so far!
All my career I have dreamt of finding something so clean. The DE-Score is a way to tell when amino acid data stops being informative. 1/7
academic.oup.com/sysbio/advan...

Resurrected nitrogenases recapitulate canonical N-isotope biosignatures over two billion years - Nature Communications The study shows that nitrogenase enzymes have maintained stable isotope signatures over billions of years, revealing how ancient microbes shaped Earth’s nitrogen cycle and offering a new experimental ...

Our new paper, out today! We resurrected ancient nitrogenases first used by life on Earth 3 billion years ago. We combined synthetic biology and geology & validated their chemical #biosignature in rocks that helps reveal ancient life on Earth!(and beyond!)

Link: www.nature.com/articles/s41...

It might be a while before I can try another amplicon run (my previous data was with R9 flow cells), but I will let you know once I can give it a shot!

This looks like it could be an incredibly helpful tool -- thanks very much for your work on this! I will have to try it out the next time I have long-read amplicon data.

GitHub - bluenote-1577/savont: Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads - bluenote-1577/savont

Announcing a new tool for "denoising" long-read amplicon sequences: savont.

Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.

1/4

github.com/bluenote-157...

Emil Ruff Leads Team to Explore Dark Oxygen Through NASA Collaborative Award | Marine Biological Laboratory For more than a century, textbooks asserted that molecular oxygen (O2) on Earth is produced almost entirely by photosynthesis, through plants and microbes. But discoveries over the past decade have ov...

Meet "OxyMoRon" our 5-year NASA ICAR program to study dark oxygen production in Earth's hidden ecosystems. We have multiple positions and are happy about collabs.

Co-PIs:@valdeanda.bsky.social @microbiaki.bsky.social @valiergaly.bsky.social Ranjani Murali, Scott Wankel

www.mbl.edu/news/emil-ru...

Looking for a tool to estimate abundances of aerobes versus anaerobes directly from metagenomes? Here you go: www.biorxiv.org/content/10.6...

Chloracidobacterium validum sp. nov., a thermophilic chlorophotoheterotrophic bacterium of the phylum Acidobacteriota
#microbiology #bacteria #taxonomy #MicroSky
@microbiologysociety.org
doi.org/10.1099/ijse...

Highly efficient bio-catalytic oxygen reduction coupled to long-range electron transport in cable bacteria www.biorxiv.org/content/10.6... #jcampubs

Isolation of ‘Candidatus Ferrigenium straubiae’ – a microaerophilic Fe(II)-oxidizing bacterium and nitrate-reducing Fe(II)-oxidizer within the community of culture KS www.microbiologyresearch.org/content/jour... #jcampubs

#MicroSky #methane #wetland #Crenothrix

...and open many questions/possibilities for future research in CH4 metabolism. Still a pre-print, but have a look if curious, especially if you want to see microscopy images of these beautiful filamentous bacteria. Happy holidays! (Collaboration with K. Umezawa, M. Fukui, and others not on Bluesky)

Isolation of Crenothrix bacteria reveals the distinct ecophysiologies of filamentous methanotrophs and adaptations to redox stress At the dawn of modern microbiology, Cohn observed abundant filamentous bacteria in drinking water wells that he named Crenothrix polyspora. Subsequent research has revealed the methanotrophic metaboli...

A quick microbio present before the holidays 🎁 >150 years after their first description, filamentous "Crenothrix bacteria" are now in stable laboratory culture! In our pre-print, we probe the unique physiology & ecology of the "lacustrine" group of these enigmatic methane-oxidizing microbes... 1/2

Scikit-bio: a fundamental Python library for biological omic data analysis - Nature Methods Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis

The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource

Diving through the purple sulfur bacteria layer of Fayetteville Green Lake with our ROV last month. This is the most intense density of PSB that I've seen in many years!

Metabolic diversity of the Ferrovales and potential contributions to iron oxidation www.biorxiv.org/content/10.1... #jcampubs

Metabolic controls on the carbon isotope fractionations of bacterial fermentation | PNAS Microbial fermentation facilitates the initial breakdown of organic matter into small molecules and is thought to be the rate-limiting step of anox...

Metabolic controls on the carbon isotope fractionations of bacterial fermentation www.pnas.org/doi/abs/10.1... #jcampubs

Locating the missing chlorophylls f in far-red photosystem I The discovery of chlorophyll f-containing photosystems, with their long-wavelength photochemistry, represented a distinct, low-energy paradigm for oxygenic photosynthesis. Structural studies on chloro...

Have you ever looked at the night sky and wondered if there’s a chlorophyll f in the reaction centre of Photosystem I from far-red light adapted cyanobacteria? 🦠

Well, we did (don’t judge) and the work that followed is now out as a First Release in @science.org

www.science.org/doi/10.1126/...

Diverse bacteriohemerythrin genes of Methylomonas denitrificans FJG1 provide insight into the survival and activity of methanotrophs in low oxygen ecosystems journals.asm.org/doi/full/10.... #jcampubs

Expansion of aerobic methanotrophy to the phylum of Actinomycetota and its environmental implications | Applied and Environmental Microbiology The climate crisis is one of the most imminent threats to humanity and all life on our planet. Methane is not only the second most potent greenhouse gas (GHG) and is responsible for approximately 31% of GHG-induced global warming since the start of the industrial revolution (1) but is also the most rapid increasing GHG in the atmosphere (2). The latter is likely caused by increased microbiological production of methane from, e.g., wetlands (2). This fact stresses the importance of methanotrophic microbes that can degrade methane with and without oxygen (3, 4) and thereby fulfill a crucial role in our global climate.

Wow, our AEM paper on a new methane-oxidizing bacterium just got a Commentary! 🎉
Congrats Kambara-san—so happy to see the work getting recognized!
journals.asm.org/doi/10.1128/...

Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota - Nature Microbiology In marine bacteria, carotenoids enhance rhodopsin function by acting as light-harvesting antennae and photocycle-accelerating pigments, a dual mechanism that enhances light energy capture and expands ...

Our paper reporting a new light-harvesting system in H⁺ & Cl⁻-pumping rhodopsins of marine bacteria is now out in Nature Microbiology! So excited!!!
Key discoveries (using isolated cultures from the research cruise Mirai MR10-01 — personally, this is super exciting🔥):
www.nature.com/articles/s41...

andez, et al.: Single-cell metabolic flux analysis reveals coexisting optimal sub-groups, cross-feeding, and mixotrophy in a cyanobacterial population https://arxiv.org/abs/2506.05916 https://arxiv.org/pdf/2506.05916 https://arxiv.org/html/2506.05916

I'm happy to announce the latest release of the GlobDB, available at globdb.org.

The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.

🧪Nature, about open-minded science:
“In research, planning is indispensable, but detailed plans are useless”

Archaean green-light environments drove the evolution of cyanobacteria’s light-harvesting system - Nature Ecology & Evolution Cyanobacteria use both chlorophylls and phycobilins to absorb light energy, and authors here use cultivation experiments, numerical simulations and protein phylogenetics to argue that cyanobacteria ev...

This was another good paleobiology read

Cyanobacteria developed phycobilisomes to absorb green light 2.4B yrs ago, as iron-rich Archaean oceans filtered sunlight. Phycoerythrobilin gave them a competitive edge, fueling oxygenation/biodiversity. Green light adaptation may mark life on exoplanets
🧪⚒️