Phil Hugenholtz

Automated genome mining predicts structural diversity and taxonomic distribution of peptide metallophores across bacteria Automated detection of metallophore biosynthesis reveals that metal-chelating non-ribosomal peptides are widespread, chemically diverse, and deeply rooted in bacterial evolution.

Are you interested in how to predict functions of natural product biosynthetic gene clusters (BGCs) and their products? And/or do you love metallophores and would love to identify their producers in microbiomes? Check out @zachreitz.bsky.social 's new paper!
elifesciences.org/articles/109... 1/n

The recovery of 12,789 genomes revealed the diversity, function, and microbial interactions of the geothermal spring microbiome https://www.biorxiv.org/content/10.64898/2026.03.10.710734v1

A very good likeness!

Genomic insights into adaptation and microevolution of two novel non-AOA #Nitrososphaeria, Acidarchaeum fankouense and Thermosulfuris yongpingense, in acid mine drainage ecosystems www.sciencedirect.com/science/arti...

Oops, typo in the family name in the abstract

Apolloniradiicaulis salifontis gen. nov., sp. nov., a New Prosthecate Aerobic Anoxygenic Phototroph Isolated from Lake Winnipegosis Region Salt Springs
#microbiology #NewSpecies #taxonomy #MicroSky
doi.org/10.3390/micr...

Thermophilic bacteria employ a contractile injection system in hot spring microbial mats Abstract. Bacterial contractile injection systems (CISs) are multiprotein complexes that facilitate the bacterial response to environmental factors or inte

Thermophilic bacteria employ a contractile injection system in hot spring microbial mats
#microbiology #thermophiles #bacteria #MicroSky
@isme-microbes.bsky.social
doi.org/10.1093/isme...

Diversity, ecology, cell biology and evolution of the Asgard archaea Nature Reviews Microbiology, Published online: 05 March 2026; doi:10.1038/s41579-026-01288-wThe Asgard archaea have become a cornerstone of archaeal research, particularly for studies aiming to unravel the origin and early evolution of eukaryotes. This Review outlines the current state of the research field focusing on these intriguing microorganisms and discusses future research directions aiming to resolve their diversity, ecology, cell biology and evolution.

New online! Diversity, ecology, cell biology and evolution of the Asgard archaea

Phenogenomics reveals the ecology and evolution of Trichoderma fungi for sustainable agriculture - Nature Microbiology Analysis of 37 genomes together with more than 140 phenotypic traits links genomic features to ecological fitness and lifestyle diversity in Trichoderma fungi.

Phenogenomics reveals the ecology and evolution of Trichoderma fungi for sustainable agriculture

-in @natmicrobiol.nature.com by Andrei Steindorff (@jgi.doe.gov) et al from Irina Druzhinina (at @rbgkew.bsky.social), Feng Cai, Igor Grigoriev, and a large network

www.nature.com/articles/s41...

With Eugene Koonin, we propose a concept of “the selfish ribosome”, under which evolution of life is viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensures the propagation of the ribosome. arxiv.org/abs/2602.23268

Calibrating for absolute microbiome abundances without spike-ins www.biorxiv.org/content/10.6... #jcampubs

I have the same cat

Huge news 🌍🧬
The Protist 10,000 Genomes Project is joining the Earth BioGenome Project.
Protists may represent the majority of eukaryotic diversity — yet only a tiny fraction have reference genomes.
Time to change that. 🚀✨
Learn more 👉 ngdc.cncb.ac.cn/p10k/
#EBP #Protists #Genomics #TreeOfLife

Metax looks really nice for taxonomic profiling: www.biorxiv.org/content/10.6...

Beyond thrilled to share that our study has been published!
This project encompasses years of work, including my thesis research on Asgard archaea in the @archaeal.bsky.social lab at @utmsi.bsky.social and
@texasscience.bsky.social!!!
#MicroSky #ArchaeaSky 1/12

Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor - Nature Sequencing of marine sediments finds 136 newly identified Heimdallarchaeia and several novel lineages, and indicates that Heimdallarchaeia evolved distinct metabolic capabilities from other Asgar...

#NatMicroPicks

Aerobic archaeal-eukaryotic ancestor? 🦠🫁

The ancestor of eukaryotes may have combined hydrogen metabolism with aerobic respiration, shaping early cellular complexity.

#MicroSky

www.nature.com/articles/s41...

Robust estimation of microbial diversity in theory and in practice AbstractQuantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of micro

hey @joshuasweitz.bsky.social this paper rocks. empirical confirmation of an intuition that is currently load-bearing in a paper i've been scared to finish. i love it academic.oup.com/ismej/articl...

To add one thing: if you have the data to run both classic dN/dS tests and MK tests, choose the latter. dN/dS tests are blind to positive selection in the important, constrained proteome, while MK test will work regardless of constraint, if DFE well estimated.
#evolution #adaptation #popgen

I am delighted to share our pre-print on a LIN code system for C. jejuni and C. coli 🎊

The ISME20 abstract submission deadline has been extended to 22 February. Microbial ecologists worldwide are invited to submit abstracts for oral, short talk, or poster presentations and contribute to the ISME20 programme.
isme-microbes.org/isme20-abstr...
#ISME20 #MicrobialEcology

Today we published a Correction on our 2023 @nature.com paper reporting the heimdallarchaeial ancestry of eukaryotes: www.nature.com/articles/s41...

Corrected paper: www.nature.com/articles/s41...

Importantly, the re-analyses of the corrected dataset are consistent with the original findings.

#microsky
Prokaryotic nomenclature in 2050

Just published: "Planetary microbiome structure and generalist-driven gene flow across disparate habitats" by @podlesny.bsky.social @chanyeong-kim.bsky.social and @jonas-bio.bsky.social www.cell.com/cell/fulltex...

See the quoted post below for a thread on the preprint!

Normally a Cell paper with one's name as corr. author would be a reason to break out the champagne. But today I have rather mixed feelings, as I inherited that spot from Peer Bork upon his untimely death. Still, congrats to all the authors! May we finish all the projects that we started with Peer!

Quantum computers will finally be useful: what’s behind the revolution A string of surprising advances suggests usable quantum computers could be here in a decade.

A feature in Nature outlines the advances that suggest usable quantum computers could be here in a decade. ⚛️ 🧪

The paradox of immune systems conservation between prokaryotes and eukaryotes - Nature Reviews Microbiology The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Arg...

Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity!

www.nature.com/articles/s41...

Ziplign published in JOSS. Tool to easily interactively compare two bacteria genomes. Inspired by ACT, but easier to install and use. Drag and drop files, or download using accessions. It runs blast for you. No terminal needed. github.com/martinghunt/...

A surface-exposed cardiolipin synthase provides an unexpected paradigm for maintaining the Gram-negative outer membrane www.pnas.org/doi/abs/10.1... #jcampubs

Effector–host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation Nature Microbiology, Published online: 26 January 2026; doi:10.1038/s41564-025-02241-yLarge-scale computational and in vitro analyses identify commensal type III secretion systems and substrates in the human gut microbiome that can interact with human proteins to modulate immune pathways.

Out Now! Effector–host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation #MicroSky

Phylogenetic tree of 8,943 bacterial genomes. The shaded branches in the tree represent different types of oxygen requirements, and the outermost ring indicates taxonomic lineages.

Using machine learning to sort over 80,000 bacterial genomes into aerobes and anaerobes, researchers find that oxygen-breathing bacteria likely evolved in local oxygen-rich environments 200–400 million years before the Great Oxidation Event. In PNAS: https://ow.ly/jZWQ50Y3LhU