@bretthale.bsky.social
Molecular plant-microbe interactions, plant immunity, and sustainable agriculture. Molecular Bioscience PhD. Head of R&D @AgriGro, Inc.
Reposted
Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes. #Long-read #Sequencing #Metagenomics #SoilMicrobiome #Genomics #Bioinformatics @biorxivpreprint.bsky.social 🧪🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 24, 2025 at 9:15 AM
Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes. #Long-read #Sequencing #Metagenomics #SoilMicrobiome #Genomics #Bioinformatics @biorxivpreprint.bsky.social 🧪🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted
Interested in Nanopore long-read ITS fungal metabarcode analysis? Our preprint is now out as journal article www.sciencedirect.com/science/arti.... There is more to do for improving long-read ITS analysis and we hope to advertise a PhD project around this soon.
Benchmarking fungal species classification using Oxford nanopore technologies long-read ITS metabarcodes
The gold standard for fungal classification has long been specimen or culture-based, however, many Fungi display simple morphological characteristics,…
www.sciencedirect.com
October 26, 2025 at 9:38 PM
Interested in Nanopore long-read ITS fungal metabarcode analysis? Our preprint is now out as journal article www.sciencedirect.com/science/arti.... There is more to do for improving long-read ITS analysis and we hope to advertise a PhD project around this soon.
Reposted
I am happy to see this out!
Plant-microbe relationship (mutualistic, commensalistic, parasitic) is not fixed, but rather dynamic, depending on the specific context.
We summarize the current knowledge on this.
Hope you enjoy~
www.jstage.jst.go.jp/article/plan...
Plant-microbe relationship (mutualistic, commensalistic, parasitic) is not fixed, but rather dynamic, depending on the specific context.
We summarize the current knowledge on this.
Hope you enjoy~
www.jstage.jst.go.jp/article/plan...
Dynamic shifts in plant-microbe relationships
Plant-microbe interactions encompass a continuum from mutualism and commensalism to parasitism. Mutualists confer benefits such as nutrient acquisitio …
www.jstage.jst.go.jp
September 25, 2025 at 12:52 AM
I am happy to see this out!
Plant-microbe relationship (mutualistic, commensalistic, parasitic) is not fixed, but rather dynamic, depending on the specific context.
We summarize the current knowledge on this.
Hope you enjoy~
www.jstage.jst.go.jp/article/plan...
Plant-microbe relationship (mutualistic, commensalistic, parasitic) is not fixed, but rather dynamic, depending on the specific context.
We summarize the current knowledge on this.
Hope you enjoy~
www.jstage.jst.go.jp/article/plan...
Reposted
Just about to push a big update to our R package TaxSEA where we've spent a lot of time collating data from the BacDive database so it's readily usable in a metagenomics analysis. See example below from the HMP IBD data. #metagenomics #bioinformatics #microbiome #microbiota
August 7, 2025 at 2:50 AM
Just about to push a big update to our R package TaxSEA where we've spent a lot of time collating data from the BacDive database so it's readily usable in a metagenomics analysis. See example below from the HMP IBD data. #metagenomics #bioinformatics #microbiome #microbiota
Reposted
Just your regular reminder that 'sterile' doesn't mean 'DNA-free'! (this rant brought to you by yet another published DNA-based study conducted in a low biomass system where appropriate controls do not appear to have been included)
May 8, 2025 at 8:44 PM
Just your regular reminder that 'sterile' doesn't mean 'DNA-free'! (this rant brought to you by yet another published DNA-based study conducted in a low biomass system where appropriate controls do not appear to have been included)
Reposted
New paper in Microbiome (with fancy summary video): doi.org/10.1186/s401...
1. Many bacteria can realistically transition from soil to mature leaves.
2. Early stages post-germination shape colonization processes and diversity.
3. P-M-M interactions affect mostly deterministic colonzers.
Enjoy!
1. Many bacteria can realistically transition from soil to mature leaves.
2. Early stages post-germination shape colonization processes and diversity.
3. P-M-M interactions affect mostly deterministic colonzers.
Enjoy!
Deterministic colonization arises early during the transition of soil bacteria to the phyllosphere and is shaped by plant–microbe interactions - Microbiome
Background Upon seed germination, soil bacteria are activated to transition to the plant and eventually colonize mature tissues like leaves. These bacteria are poised to significantly influence plant ...
doi.org
April 25, 2025 at 2:23 PM
New paper in Microbiome (with fancy summary video): doi.org/10.1186/s401...
1. Many bacteria can realistically transition from soil to mature leaves.
2. Early stages post-germination shape colonization processes and diversity.
3. P-M-M interactions affect mostly deterministic colonzers.
Enjoy!
1. Many bacteria can realistically transition from soil to mature leaves.
2. Early stages post-germination shape colonization processes and diversity.
3. P-M-M interactions affect mostly deterministic colonzers.
Enjoy!
Reposted
We found that many bacterial species use exogenous peptidoglycan fragments - released by lysis of neighboring cells - as a general danger signal, triggering a danger response that protects bacteria against many dangers: biofilm formation.
Details here 👇
www.nature.com/articles/s41...
Details here 👇
www.nature.com/articles/s41...
Bacteria use exogenous peptidoglycan as a danger signal to trigger biofilm formation - Nature Microbiology
Peptidoglycan released by neighbouring kin or non-kin cell lysis induces physiological changes that protect from a range of stresses, including phage predation.
www.nature.com
January 6, 2025 at 10:13 AM
We found that many bacterial species use exogenous peptidoglycan fragments - released by lysis of neighboring cells - as a general danger signal, triggering a danger response that protects bacteria against many dangers: biofilm formation.
Details here 👇
www.nature.com/articles/s41...
Details here 👇
www.nature.com/articles/s41...
Reposted
Sad news. John McDowell has passed away. He was not only a brilliant scientist, he was one of the kindest people I have ever met. He worked hard, did a tremendous job in plant pathology and was a wonderful colleague. He is gone way too soon.
www.mccoyfuneralhome.com/obituaries/J...
www.mccoyfuneralhome.com/obituaries/J...
John Matthew McDowell - View Obituary & Service Information
Share Memories and Support the Family.
www.mccoyfuneralhome.com
December 29, 2024 at 1:14 PM
Sad news. John McDowell has passed away. He was not only a brilliant scientist, he was one of the kindest people I have ever met. He worked hard, did a tremendous job in plant pathology and was a wonderful colleague. He is gone way too soon.
www.mccoyfuneralhome.com/obituaries/J...
www.mccoyfuneralhome.com/obituaries/J...
Reposted
Looks quite promising, and also highlights a problem with all metagenomic classifiers to date: only 70-80% average precision in mock communities, at genus level, and after an abundance threshold. This seems to me like a database problem, but time will hopefully tell.
Kun-peng: claims; as fast/faster than Kraken2 with the accuracy comparable to sylph! Very cool.
The design here reinforces a strong feeling I've had for a few years - moving forward in bioinfo. system-friendly & ext. memory algorithms will come to prevail. (& rust!)
www.biorxiv.org/content/10.1...
The design here reinforces a strong feeling I've had for a few years - moving forward in bioinfo. system-friendly & ext. memory algorithms will come to prevail. (& rust!)
www.biorxiv.org/content/10.1...
Kun-peng: an ultra-memory-efficient, fast, and accurate pan-domain taxonomic classifier for all
Comprehensive metagenomic sequence classification of diverse environmental samples faces significant computing memory challenges due to exponentially expanding genome databases. Here, we present Kun-p...
www.biorxiv.org
December 22, 2024 at 6:02 PM
Looks quite promising, and also highlights a problem with all metagenomic classifiers to date: only 70-80% average precision in mock communities, at genus level, and after an abundance threshold. This seems to me like a database problem, but time will hopefully tell.
Reposted
📜 Cell Wall Dynamics in the parasitic plant (Striga) and rice pathosystem
🧑🔬 Damaris Barminga, Emily S. Bellis, Steven Runo, et al.
📔 @mpmijournal.bsky.social
🔗 apsjournals.apsnet.org/doi/10.1094/...
#️⃣ #PlantScience #ParasiticPlants #Striga #PlantCellWalls #PlantImmunity
🧑🔬 Damaris Barminga, Emily S. Bellis, Steven Runo, et al.
📔 @mpmijournal.bsky.social
🔗 apsjournals.apsnet.org/doi/10.1094/...
#️⃣ #PlantScience #ParasiticPlants #Striga #PlantCellWalls #PlantImmunity
Cell Wall Dynamics in the parasitic plant (Striga) and rice pathosystem | Molecular Plant-Microbe Interactions®
In the plant-plant pathosystem of rice (Oryza sativa) and the parasitic plant Striga hermonthica, cell walls from either plant are important defensive and offensive structures. Here we reveal cell wal...
apsjournals.apsnet.org
December 11, 2024 at 7:14 AM
📜 Cell Wall Dynamics in the parasitic plant (Striga) and rice pathosystem
🧑🔬 Damaris Barminga, Emily S. Bellis, Steven Runo, et al.
📔 @mpmijournal.bsky.social
🔗 apsjournals.apsnet.org/doi/10.1094/...
#️⃣ #PlantScience #ParasiticPlants #Striga #PlantCellWalls #PlantImmunity
🧑🔬 Damaris Barminga, Emily S. Bellis, Steven Runo, et al.
📔 @mpmijournal.bsky.social
🔗 apsjournals.apsnet.org/doi/10.1094/...
#️⃣ #PlantScience #ParasiticPlants #Striga #PlantCellWalls #PlantImmunity
Happy to share our latest manuscript in collaboration with Steven Runo’s group at Kenyatta University.
apsjournals.apsnet.org/doi/10.1094/...
apsjournals.apsnet.org/doi/10.1094/...
Cell Wall Dynamics in the parasitic plant (Striga) and rice pathosystem | Molecular Plant-Microbe Interactions®
In the plant-plant pathosystem of rice (Oryza sativa) and the parasitic plant Striga hermonthica, cell walls from either plant are important defensive and offensive structures. Here we reveal cell wal...
apsjournals.apsnet.org
December 12, 2024 at 3:34 AM
Happy to share our latest manuscript in collaboration with Steven Runo’s group at Kenyatta University.
apsjournals.apsnet.org/doi/10.1094/...
apsjournals.apsnet.org/doi/10.1094/...
Reposted
The rhizosphere has been called “one of the most complex ecosystems on earth”
But how do host plants control benefits derived from their microbial partners?
Read our paper in Nature Microbiology on how legumes mediate conflict & cooperation with N2-fixing symbionts.
Here: tinyurl.com/4y4tjx6k
But how do host plants control benefits derived from their microbial partners?
Read our paper in Nature Microbiology on how legumes mediate conflict & cooperation with N2-fixing symbionts.
Here: tinyurl.com/4y4tjx6k
December 11, 2024 at 10:39 AM
The rhizosphere has been called “one of the most complex ecosystems on earth”
But how do host plants control benefits derived from their microbial partners?
Read our paper in Nature Microbiology on how legumes mediate conflict & cooperation with N2-fixing symbionts.
Here: tinyurl.com/4y4tjx6k
But how do host plants control benefits derived from their microbial partners?
Read our paper in Nature Microbiology on how legumes mediate conflict & cooperation with N2-fixing symbionts.
Here: tinyurl.com/4y4tjx6k
Reposted
Plant microbiota feedbacks through dose-responsive expression of general non-self response genes
rdcu.be/d2gCJ
rdcu.be/d2gCJ
Plant microbiota feedbacks through dose-responsive expression of general non-self response genes
Nature Plants - The plant general non-self response system is triggered by leaf microbiota members and, in turn, impacts their colonization.
rdcu.be
December 3, 2024 at 12:40 PM
Plant microbiota feedbacks through dose-responsive expression of general non-self response genes
rdcu.be/d2gCJ
rdcu.be/d2gCJ
Reposted
Keeping your symbiosis genes on a plasmid is a smart move if you have multiple potential hosts. Here a gut bacterial symbiont, but same is true for N-fixing Rhizobia.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
A conserved bacterial genetic basis for commensal-host specificity
Animals selectively acquire specific symbiotic gut bacteria from their environments that aid host fitness. To colonize, a symbiont must locate its niche and sustain growth within the gut. Adhesins are...
www.science.org
December 7, 2024 at 1:17 PM
Keeping your symbiosis genes on a plasmid is a smart move if you have multiple potential hosts. Here a gut bacterial symbiont, but same is true for N-fixing Rhizobia.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...