Alex Crits-Christoph

@acritschristoph.bsky.social

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Computational microbiologist

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Alex Crits-Christoph

'In this Essay, we propose the concept of ancestral immunity, which designates the pool of eukaryotic immune modules originating from prokaryotic immune defences. These modules are not necessarily present in all organisms but are detected across domains of life.' journals.plos.org/plosbiology/...

The immune modules conserved across the tree of life: Towards a definition of ancestral immunityjournals.plos.org A subset of prokaryotic antiviral systems are conserved in eukaryotes and have crucial roles in immune pathways. This Essay introduces the concept of ancestral immunity, which refers to the set of imm...

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Alex Crits-Christoph

Does choosing one antibiotic impact how resistance to another evolves? Short answer is yes! Was great contributing to this work led by @dralhubb.bsky.social , @blackpassiflora.bsky.social and @bethjames.bsky.social (along with others not on bluesky). www.nature.com/articles/s44...

The effect of antibiotic selection on collateral effects and evolvability of uropathogenic Escherichia coli - npj Antimicrobials and Resistancewww.nature.com npj Antimicrobials and Resistance - The effect of antibiotic selection on collateral effects and evolvability of uropathogenic Escherichia coli

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Alex Crits-Christoph

If you are interested in prophages, we have a new database: Prophage-DB. Check it out and all feedback is welcome biorxiv.org/cgi/content/...

Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophagesbiorxiv.org bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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Alex Crits-Christoph

Day 2 of Genome Science 2024! First up in the Microbes and Microbiomes session is Lauren Cowley: talking about building machine learning models for geographical source attribution from genome sequence data (published here: elifesciences.org/articles/84167)

Rapid geographical source attribution of Salmonella enterica serovar Enteritidis genomes using hierarchical machine learningelifesciences.org Application of hierarchical machine learning to the geographical source attribution of Salmonella enteritidis indicates high utility for the rapid translation of raw pathogen genome sequencing data in...

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Alex Crits-Christoph

This is astounding. Over about 10 years the use of the livestock drug diclofenac wiped out nearly 50 million vultures. The result was spread of disease among humans causing an estimated half a million deaths. Just tragic all around. www.science.org/content/arti...

Loss of India’s vultures may have led to deaths of half a million peoplewww.science.org Find could offer lessons for conserving key species in other places

A synbiotic of Anaerostipes caccae and lactulose prevents and treats food allergy in mice www.cell.com/cell-host-mi...

A synbiotic of Anaerostipes caccae and lactulose prevents and treats food allergy in micewww.cell.com Hesser et al. utilize a synbiotic composed of butyrate-producing bacteria and lactulose to treat food allergy. Cow’s milk-allergic infants lack butyrate-producing taxa. Treatment with this synbiotic i...

Genomic representativeness and chimerism in large collections of SAGs and MAGs of marine prokaryoplankton link.springer.com/article/10.1... A reasonable comparison and discussion. I'm still skeptical of SAGs because I hypothesize they often exclude filamentous and biofilm-inhabiting microbes?

Genomic representativeness and chimerism in large collections of SAGs and MAGs of marine prokaryoplankton - Microbiomelink.springer.com Background Single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are the predominant sources of information about the coding potential of uncultured microbial lineages, but their str...

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Alex Crits-Christoph

Properly pumped to get started at this year's Genome Science meeting in Bristol this afternoon: a stellar programme starting with some fantastic keynote speakers: Lucy Birkett-Gray (UK BioBank) and Richard Durbin (Cambridge) bristol.genomescience.org.uk/assets/img/P...

bristol.genomescience.org.uk

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Alex Crits-Christoph

We’re trying to make the G3 journal a home for all your fun bacterial genetics stories! Please hit us up if you have a relevant manuscript to submit!

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Alex Crits-Christoph

Over weekend, Colorado said now four H5 bird flu cases confirmed in poultry worker outbreak and fifth presumptive CDC now says: - symptoms included "coughing and sore throat" - first U.S. poultry worker cases since 2022 - sequencing attempts underway tinalexander.github.io/notes/2024/0...

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Alex Crits-Christoph

'They face a concerted effort—including by members of Congress—to undermine or silence their work documenting false and misleading internet content. The claim is that online misinformation researchers are trying to silence conservative voices. The evidence suggests just the opposite.'

American academic freedom is in perilwww.science.org Academics researching online misinformation in the US are learning a hard lesson: Academic freedom cannot be taken for granted. They face a concerted effort—including by members of Congress—to undermi...

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Reply to

Rhys White

We updated Dorado, re-basecalled & applied HERRO correction (Dorado correct) to ONT data from a recent #MRSA outbreak in the NICU. Median pairwise SNV distance dropped, improving the resolution of #outbreak genomes See our initial paper: doi.org/10.1099/mgen... 🖥️🧬💻 #AcademicSky #Microsky 🧪🧫🦠

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Alex Crits-Christoph

okay this is a wild way to synthesize 3-nitrotyrosine: translate a MRYLH pentapeptide, use one enzyme to generate NO off the Arg which reacts w/the Tyr, then cleave out the 3-NO-Tyr: (from: www.biorxiv.org/content/10.1...).

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Alex Crits-Christoph

New research from our group: We show that endemism is a major driver of viral diversity, ecology, and evolution in hydrothermal vents and the deep-sea. www.biorxiv.org/content/10.1....

Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystemswww.biorxiv.org bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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Alex Crits-Christoph

Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution #ISMEJournal from Gergely Szöllősi and collagues (Phil Hugenholtz, Anja Spang, Cecile Gubry-Rangin, Paul O Sheridan, Laura Eme, Rochelle M Soo and more academic.oup.com/ismej/advanc...

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Alex Crits-Christoph

🍄🌲🌎🧪🔬 "It's the fungal diversity; stupid": Forest tolerate droughts better when they have higher diversity of symbiotic FUNGAL mycorrhizae, not tree diversity! besjournals.onlinelibrary.wiley.com/doi/10.1111/...

Forest growth resistance and resilience to the 2018–2020 drought depend on tree diversity and mycorrhizal typebesjournals.onlinelibrary.wiley.com <em>Journal of Ecology</em> publishes original research on all aspects of the plant ecology (including algae), in both aquatic and terrestrial ecosystems.

Evolutionary dynamics of genome structure and content among closely related bacteria www.biorxiv.org/content/10.1... Interesting paper looking at bacterial evolution over ~100 years - in E. coli ST131. 1 structural change per 3 core genome SNPs.

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Alex Crits-Christoph

Our (great x gazillion) grandmother "LUCA was a prokaryote-grade anaerobic acetogen that possessed an early immune system" dating to ~4.2 billion years ago: www.nature.com/articles/s41... 🧪⚒️

The nature of the last universal common ancestor and its impact on the early Earth system - Nature Ecology & Evolutionwww.nature.com Integration of phylogenetics, comparative genomics and palaeobiological approaches suggests that the last universal common ancestor lived about 4.2 billion years ago and was a complex prokaryote-grade...

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Alex Crits-Christoph

The so-called "VGIX01" bacterial phylum from GTDB now has a name :-) First paper from my collaboration with Lei Su, Jiangtao Li, Andreas Teske, and others. Lei spent a year in Aarhus getting started on this work as part of her PhD - more papers to come! journals.asm.org/doi/10.1128/...

Genomic characterization of the bacterial phylum Candidatus Effluviviacota, a cosmopolitan member of the global seep microbiome | mBiojournals.asm.org The newly discovered bacterial phylum Candidatus Effluviviacota is widespread across diverse seepage ecosystems, marine environments, and freshwater environments, with a notable preference for cold se...

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Alex Crits-Christoph

Find out which bacteria can reflect light using structural colour and where to find them. Our latest PNAS paper provides new insights. www.uu.nl/en/news/gene...

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Alex Crits-Christoph

We are on the look out for postdocs to join the Lieberman Lab at MIT. Areas include: -Connecting bacterial warfare to strain dynamics in vivo -Evolution and transmission of microbes in humans -Revisiting role of microbes in acne vulgaris Take a look at our recent preprints and reach out!

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Going from PhD to independent postdoc has been hard, and switching bacteria didn't make it easier. Especially when I found out that my A. baumannii (5075) has/had no available phage. But, that meant I had a gap to fill! And that's resulted in this work here: www.biorxiv.org/content/10.1...

Environmental differences impact Acinetobacter baumannii phage isolation and infectivitywww.biorxiv.org bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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Alex Crits-Christoph

Do you want to run a microbial GWAS but are put off by installing a dozen different bioinformatic tools, are unsure about best practices, and how to transform the list of threshold passing variants into a neat annotated table? Then we have just the thing for you! www.biorxiv.org/content/10.1...

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Alex Crits-Christoph

It's that time of year again. The Applied Microbiology International's Horizon Award applications are due. You can nominate yourself or someone else here appliedmicrobiology.org/membership-c...

Horizon Awardsappliedmicrobiology.org The Horizon Awards recognise individuals and teams at the forefront of microbiological research.

Repeated plague infections across six generations of Neolithic Farmers www.nature.com/articles/s41... Yersinia genomes from a plague 5000 years ago:

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Alex Crits-Christoph

Our paper, Floria, is now out in the ISMB 2024 Bioinformatics proceedings! Floria can obtain strain-level haplotypes of metagenomes for *noisy long reads* or *short reads* in minutes With Jean-Sebastien Gounot, Hanrong Chen, Niranjan Nagarajan, Yun William Yu academic.oup.com/bioinformati...

Floria: fast and accurate strain haplotyping in metagenomesacademic.oup.com AbstractSummary. Shotgun metagenomics allows for direct analysis of microbial community genetics, but scalable computational methods for the recovery of ba

2025 EMBL events: www.embl.org/about/info/c...

Simultaneous multi-site editing of individual genomes using retron arrays for making multiple genomic edits concurrently www.biorxiv.org/content/10.1...

A story behind the new Loki culture: "one culture collection declined our request to deposit the strain- For the other three, two unfortunately could not preserve the strain and only one culture collection succeeded – Japan Collection of Microorganisms" microbiologysociety.org/blog/appreci...

Appreciation towards culture collectionsmicrobiologysociety.org Dr Hiroyuki Imachi and Dr Masaru K. Nobu take us behind the scenes of their latest publication '<a href="https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.006435">Promethe...

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Alex Crits-Christoph

Genome-resolved year-round dynamics reveal a broad range of giant virus microdiversity https://www.biorxiv.org/content/10.1101/2024.07.08.602415v1

Genome-resolved year-round dynamics reveal a broad range of giant virus microdiversity https://www.biorxiv.org/content/10.1101/2024.07.08.602415v1 www.biorxiv.org Giant viruses are crucial for marine ecosystem dynamics because they regulate microeukaryotic commun