joshnhamm.bsky.social
Joshua Hamm
@joshnhamm.bsky.social
110 followers 67 following 10 posts
Post-Doctoral Researcher in the EvoSym Group. Investigating DPANN-host interactions. jnhamm.wordpress.com
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Reposted by Joshua Hamm
alexjprobst.bsky.social
Alex Probst @alexjprobst.bsky.social · 12d
New article on equitable reuse of public sequencing data, published in @natmicrobiol.nature.com!
Led by the Data reuse core team @lhug.bsky.social @environmicrobio.bsky.social Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and with Anke Heyer and The Data Reuse Consotrium!
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Reposted by Joshua Hamm
environmicrobio.bsky.social
Roland Hatzenpichler @environmicrobio.bsky.social · 12d
Our article on equitable reuse of public sequencing data is out! Led by @alexjprobst.bsky.social, @lhug.bsky.social, Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and myself -, co-authored by Anke Heyder, and developed in consultation with 167 scientists. tinyurl.com/n6yeanmk
A roadmap for equitable reuse of public microbiome data - Nature Microbiology
In this Consensus Statement, a consortium of microbiome scientists discuss current sequencing data sharing policies and propose the use of a Data Reuse Information (DRI) tag to promote equitable and collaborative data sharing.
tinyurl.com
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Reposted by Joshua Hamm
msmjetten.bsky.social
Mike Jetten @msmjetten.bsky.social · 21d
Great new trait of #Methanoperedens archaea: Carbon monoxide metabolism in freshwater anaerobic #methanotrophic archaea #aom #anme
Egas @cuwelte.bsky.social et al #microbiology @ribesresearch.bsky.social
www.biorxiv.org/content/10.1...
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Reposted by Joshua Hamm
archaellum.bsky.social
Sonja-Verena Albers @archaellum.bsky.social · 21d
Happy to share that our story on the bacterial archaellum was published today in @natmicrobiol.nature.com
www.nature.com/articles/s41...

Congrats to the authors: @sshamphavi.bsky.social @loumollat.bsky.social @mariejoest.bsky.social Najwa Taib and @sgribaldo.bsky.social
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Reposted by Joshua Hamm
rodrisanchez95.bsky.social
Rodrigo Sánchez Martínez @rodrisanchez95.bsky.social · 28d
🦠➡️🧬 Community context matters!
In the second part of my PhD, we show how microbial complexity drives phage–bacteria ecology & evolution.
Check out the preprint 👇🏼
biorxiv-microbiol.bsky.social
bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 28d
Biological context modulates virus-host dynamics and diversification https://www.biorxiv.org/content/10.1101/2025.09.10.675297v1
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Reposted by Joshua Hamm
molbioevol.bsky.social
Molecular Biology and Evolution @molbioevol.bsky.social · Sep 8
Huang, @tweethinking.bsky.social, Sepang et al. use phylogenetic analyses to reveal that the Njordarchaeales and Panguiarchaeales constitute the new class Njordarchaeia within Asgard archaea.

🔗 doi.org/10.1093/molbev/msaf201

#evobio #molbio #archaea
Phylogenomic Analyses Reveal that Panguiarchaeum Is a Clade of Genome-Reduced Asgard Archaea Within the Njordarchaeia
Abstract. The Asgard archaea are a diverse archaeal phylum important for our understanding of cellular evolution because they include the lineage that gave
doi.org
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Reposted by Joshua Hamm
taylorpriest.bsky.social
Taylor priest @taylorpriest.bsky.social · Aug 14
The JEDI marker - a new approach for measuring #biodiversity that captures all domains of life and is applicable across biological and ecological scales. It's time to change the way we perceive biodiversity - www.biorxiv.org/content/10.1...
The JEDI marker as a universal measure of planetary biodiversity
Despite its critical importance in the formation and maintenance of ecosystems and homeostasis on Earth, biodiversity remains a complex and non-unified concept. Consequently, standards for measuring b...
www.biorxiv.org
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Reposted by Joshua Hamm
loreoliv.bsky.social
Lorenzo Olivi @loreoliv.bsky.social · Aug 22
🧵 Our study on the elusive titration control mechanism of the replication initiator DnaA in Escherichia coli is now out on @natcomms.nature.com‬! @stephkoe.bsky.social
@hohlbeinlab.bsky.social‬ @nicoc-micsynmet.bsky.social @ettema.bsky.social‬ @mib-wur.bsky.social
doi.org/10.1038/s414...
The Escherichia coli replication initiator DnaA is titrated on the chromosome - Nature Communications
A DNA-binding protein, DnaA, regulates the initiation of chromosomal replication in bacteria. Here, Olivi et al. show that the bacterial chromosome sequesters DnaA in a growth rate-dependent manner, s...
doi.org
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Reposted by Joshua Hamm
wentsunghwang.bsky.social
Wen-Cong Huang | 黄文聪 @wentsunghwang.bsky.social · Aug 14
academic.oup.com/mbe/advance-...

Happy to share this one. We investigated the #phylogenetic placement and #genome_evolution of Pangui/Njordarchaea-unique #Asgardarchaea that might have undergone genome reduction...
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Reposted by Joshua Hamm
archaellum.bsky.social
Sonja-Verena Albers @archaellum.bsky.social · Aug 20
Who would have thought I would ever publish an article about a bacterium?
But here it is, but of course only because Litorilinea aerophilum actually has an archaellum!

Here is what we learned about its cell structure and other surface appendages:
www.biorxiv.org/content/10.1...
Filamentous growth, cell envelope architecture, and surface appendages of a member of the Chloroflexota, Litorilinea aerophila
Litorilinea aerophila, a filamentous bacterium of the phylum Chloroflexota (class Caldilineae), exhibits unique morphological and cell envelope features that challenge traditional bacterial models. In...
www.biorxiv.org
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joshnhamm.bsky.social
Joshua Hamm @joshnhamm.bsky.social · Aug 8
Many thanks to my co-authors @ndombrowski.bsky.social, @luisvalentin.bsky.social, @greening.bsky.social, @tweethinking.bsky.social, and @anja1.bsky.social!
joshnhamm.bsky.social
Joshua Hamm @joshnhamm.bsky.social · Aug 8
Our results provide insight into a currently understudied DPANN lineage (Caliditerrarchaeota) and highlight similarities and differences in how DPANN halophiles achieved their tolerance to the hypersaline systems they inhabit.
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joshnhamm.bsky.social
Joshua Hamm @joshnhamm.bsky.social · Aug 8
Additionally, using gene trees from ALE analysis, we examined sisterhood rates across all archaea in the dataset. The results confirm higher rates of sisterhood in single gene trees for many DPANN-host pairs and reveal a potential association of Haloaenigmatarchaeaceae with Halarchaeoplasmatales.
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joshnhamm.bsky.social
Joshua Hamm @joshnhamm.bsky.social · Aug 8
However, for both lineages the gene with the highest increase in copy number was the Kef type K+ transporter, implicating this system as key in the adaptation to hypersaline environments for halophilic DPANN.
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joshnhamm.bsky.social
Joshua Hamm @joshnhamm.bsky.social · Aug 8
The results indicate for the Nanohaloarchaeota and Haloaenigmatarchaeaceae different genes were associated with transition to hypersaline environments. For Nanohaloarchaeota this includes oxygen tolerance and DNA repair systems. For Haloaenigmatarchaeaceae this includes a specific Na+ transporter.
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joshnhamm.bsky.social
Joshua Hamm @joshnhamm.bsky.social · Aug 8
Our analysis of public MAGs shows these DPANN are mostly sediment associated thermophiles with no signatures of halophily. We then used gene tree/species tree reconciliations to predict ancestral genome content and compare the two known DPANN halophiles to their last non-halophilic ancestors.
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joshnhamm.bsky.social
Joshua Hamm @joshnhamm.bsky.social · Aug 8
New preprint up now!

Interested in the evolution of halophily within DPANN archaea we decided to investigate the sister phylum to the Nanohaloarchaeota, GTDB phylum EX4484-52, for which we propose the name Caliditerrarchaeota
www.biorxiv.org/content/10.1...
Caliditerrarchaeota, a new sister to Nanohaloarchaeota, provides insights into the evolution of DPANN halophily
The Nanohaloarchaeota are a clade of halophilic symbionts with small cells and genomes. Originally placed within the Euryarchaeota, they are now widely thought to belong to the DPANN archaea. However,...
www.biorxiv.org
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Reposted by Joshua Hamm
environmicrobio.bsky.social
Roland Hatzenpichler @environmicrobio.bsky.social · Aug 6
If you are a postdoc working on any topic related to environmental microbiology and are looking for exposure, the Thermal Biology Institute (tbi.montana.edu) has slots open for virtual talks via zoom this fall. Email me if you are interested! Seminars are most Mondays, 3-4 pm Mountain Time.
Thermal Biology Institute - Default | Montana State University
Index to the Thermal Biology Institute's website.
tbi.montana.edu
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Reposted by Joshua Hamm
rodrisanchez95.bsky.social
Rodrigo Sánchez Martínez @rodrisanchez95.bsky.social · Aug 4
Check out the new paper of my former lab about novel haloviruses infecting Haloquadratum walsbyi, the "square queen archaeon" of hypersaline systems 👑🟪
academic.oup.com/ismej/advanc...
Novel viruses of Haloquadratum walsbyi expand the known archaeal virosphere of hypersaline environments
Abstract. Solar salterns represent unique systems with low diversity microbial communities that serve as an excellent model for studying the evolution and
academic.oup.com
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Reposted by Joshua Hamm
danieltamarit.bsky.social
Daniel Tamarit @danieltamarit.bsky.social · May 14
New vacancy in my team!

PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.

Please repost and share with talented MSc students in #evobio, bioinformatics or related :)

www.uu.nl/en/organisat...

#MEvoSky #MicroSky
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joshnhamm.bsky.social
Joshua Hamm @joshnhamm.bsky.social · May 9
On what basis? Brett pointed out elsewhere the reads mapped are not from the sample the MAG came from. Take the B*_G* genomes for example. The SRA deposition for the metagenome for these MAGs is SAMN08040260. The SRR630144* depositions the reads are mapped from are all a different sample
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Reposted by Joshua Hamm
jvhooff.bsky.social
Jolien van Hooff @jvhooff.bsky.social · Mar 5
Exciting news! I'm looking for a computational biologist to join my lab at Wageningen University & Research! It's a 3-year postdoc position on Holomycota genome architecture and evolution. Spread the word! www.wur.nl/en/vacancy/p...
Postdoc Comparative genomics and genome architecture in early-diverging fungi and their protist relatives (3-year position)
www.wur.nl
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Reposted by Joshua Hamm
santanamolina.bsky.social
Carlos Santana Molina @santanamolina.bsky.social · Mar 3
Asgardarchaea & Alphaproteobacteria: key players for the assembly eukaryotic central carbon metabolism! Our new study reveals their gene contributions to glycolysis & TCA cycle, supporting synthrophic scenarios of eukaryogenesis.
rdcu.be/eb0aK
Chimeric origins and dynamic evolution of central carbon metabolism in eukaryotes
Nature Ecology & Evolution - Analysis of the eukaryotic gene repertoires mediating central carbon metabolism identifies ancestral contributions from Alphaproteobacteria, Asgardarchaeota and...
rdcu.be
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Reposted by Joshua Hamm
tweethinking.bsky.social
Tom Williams @tweethinking.bsky.social · Feb 17
www.biorxiv.org/content/10.1... A new collaborative paper with Anja Spang, Wen-Cong Huang, @chrisrinke.bsky.social @ettema.bsky.social @ssolo.bsky.social Zheng-Shuang Hua Maraike Probst and Lenard Szantho. We investigated the phylogenetic position and metabolic evolution of Panguiarchaeum.
Phylogenomic analyses reveal that Panguiarchaeum is a clade of genome-reduced Asgard archaea
The Asgard archaea are a diverse archaeal phylum that includes the host lineage from which eukaryotes evolved. Due to the importance of the Asgard archaea for our understanding of cellular evolution a...
www.biorxiv.org
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Reposted by Joshua Hamm
anja1.bsky.social
Anja (she/her) @anja1.bsky.social · Feb 12
Are you interested in studying archaea with their diverse symbionts? We look forward hearing from you: workingat.nioz.nl/o/postdoc-po...
NIOZ - Postdoc position: “to elucidate the role of archaeal symbionts in cellular evolution and ecology”
The EvoSym Team within the Department of Marine Microbiology and Biogeochemistry (MMB) located at the Netherlands Institute for Sea Research (NIOZ), is looking for a postdoctoral researcher with a bac
workingat.nioz.nl
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