@linsalrob

Matthew Flinders Fellow in Bioinformatics. 'The David Attenborough of Phages' mastadon: @linsalrob@genomic.social

 Adelaide, South Australia
edwards.sdsu.edu/research
Joined June 2008
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🔬 Meet Prof. @linsalrob: A creator of RAST and MG-RAST 🌟 🌐 From coral reefs to remote islands, he's pushed the limits of sequencing and bioinformatics. 🔬 Catch his talk at #ICBRAR2023: "PhageCraft: From Sewage to Synthesis." Get ready for a journey that goes beyond the lab!
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Prophages are phages hidden in bacterial genomes, and they affect our health! We explored where they hang out in the human microbiome biorxiv.org/content/10.1101/…

Prophage rates in the human microbiome vary by body site and host health

Phages integrated into a bacterial genome–called prophages–continuously monitor the health of the host bacteria to determine when to escape the genome, protect their host from other phage infections,...

biorxiv.org
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RT @feargal@genomic.social My old lab from Cork, Ireland in Nature this week with "Structural atlas of a human gut crassvirus". Really great team, always so supportive, friendly and hard working, really well earned! Plus such nice pictures. (Damn maybe I should have stayed (1/2)
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🤣 ) nature.com/articles/s41586-0… #microbiome #research #virome #microbiology #viruses #sciart genomic.social/@feargal/1103… (2/2)
Structural atlas of a human gut crassvirus

ALT Structural atlas of a human gut crassvirus

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RT @[email protected] Artículo que guardo por interesante, para leer para cuando la vida de tiempo.. 😉 The Promise and Pitfalls of Prophages | bioRxiv biorxiv.org/content/10.1101/… "Mientras que los fagos virulentos esculpen el microbioma al matar a sus anfitriones (1/2)

The Promise and Pitfalls of Prophages

Phages dominate every ecosystem on the planet. While virulent phages sculpt the microbiome by killing their bacterial hosts, temperate phages provide unique growth advantages to their hosts through...

biorxiv.org
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bacterianos, los fagos templados brindan ventajas de crecimiento únicas a sus anfitriones a través de la conversión lisogénica." mstdn.science/@cientounero/1… (2/2)
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RT @[email protected] Scientists discover why sea urchins are dying off from US to the Caribbean Nice quotes from virome_girl on the recent study! theguardian.com/environment/… And the Sci Adv paper: doi.org/10.1126/sciadv.adg32… #marine #ecology genomic.social/@foaylward/11…

Scientists discover why sea urchins are dying off from US to the Caribbean

A research team has discovered a parasite that’s been killing off sea urchins, but there’s no method to eliminate it yet

theguardian.com
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RT @[email protected] 🔬🔬Microbiology PIs looking for a great way to show your students you care? Nominate them for the TOP prize in prokaryotic molecular biology, the Nat L. Sternberg Award! Nominations due May 1, 2023 conferences.union.wisc.edu/p… mstdn.science/@Redrockcity/1…
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RT @[email protected] Our manuscript 'Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data' has now been published in Microbiome. You can read it here microbiomejournal.biomedcent…. mstdn.science/@wvschaik/1102…

Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data

Microbiome - The prediction of bacteriophage sequences in metagenomic datasets has become a topic of considerable interest, leading to the development of many novel bioinformatic tools. A...

link.springer.com
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Phages... So many #phage and they are all #prophage integrated into a #bacteria #genome A few million prophages from > million bacterial genomes Are prophages good or bad for bacteria? The data shows they provide heaps of benefits The paper is in #biorxiv and the data (1/2)
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is on #figshare biorxiv.org/content/10.1101/… open.flinders.edu.au/project… (2/2)

The Promise and Pitfalls of Prophages

Phages dominate every ecosystem on the planet. While virulent phages sculpt the microbiome by killing their bacterial hosts, temperate phages provide unique growth advantages to their hosts through...

biorxiv.org
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RT @[email protected] #ARCschedule Apr23 v2: Updated with projected opening, closing & outcome dates for schemes through to end of next year (2024). (It's very possible there's errors here. Let me know if so!) aus.social/@ARC_Tracker/1101…
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RT @feargal@genomic.social The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice. New study at Nature Microbiology. Faecal metagenomics & serum metabolomics (77 cases, 70 controls) + FMT to GF mice to show casual relationship. (1/2)
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#science #research #microbiome #metagenomics nature.com/articles/s41564-0… genomic.social/@feargal/1102… (2/2)
Figure 1 from paper. Boxplots, heatplot and barplot.

ALT Figure 1 from paper. Boxplots, heatplot and barplot.

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What would it take to add a #mastadon toot box to the #biorxiv website where the bird site one is? can you add that to metrics? @[email protected] @[email protected]
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Not all proteins arise from consecutive codons. We developed a new tool - PRFect - to identify programmed ribosomal frameshifts. Designed, built, trained, and tested with #phage genomes, it also works on #bacteria and #eukaryotes too. biorxiv.org/content/10.1101/…

Programmed ribosomal frameshifts, and how to find them

One of the stranger phenomena that can occur during gene translation is where, as a ribosome reads along the mRNA, various cellular and molecular properties contribute to stalling the ribosome on a...

biorxiv.org
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Rob Edwards retweeted
Zamin Iqbal@ZaminIqbal12 Apr 2023
Replying to @linsalrob
(I have no expertise but) maybe one that relies on plasmid encoded genes to get in? Eg biorxiv.org/content/10.1101/… From @baym and Natalia QO , whose twitter is I can't find oddly

Diverse and abundant viruses exploit conjugative plasmids

Viruses exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of bacterial viruses, phages, use chromosomally-...

biorxiv.org
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Rob Edwards retweeted
Xin😼@EnViruSoil12 Apr 2023
Replying to @linsalrob
One idea: you may have a look at the tremendous EOP assays (S1 data) performed for the BASEL E.coli phage collection by @AHarms485 & colleagues @PLOSBiology journals.plos.org/plosbiolog…

Systematic exploration of Escherichia coli phage–host interactions with the BASEL phage collection

This study presents the BASEL collection of phages that infect the model bacterium Escherichia coli; this resource for the community is representative of natural E. coli phage diversity and has been...

journals.plos.org
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Replying to @linsalrob
That depends a bit on your definition of host range. Just recognition / lysis or also plaque formation? Phages targeting the highly conserved NGR glycan of enterobacteria are quite broad or those targeting conjugative pili of broad host-range plasmids (even cross-genus for PRD1).
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