Katie O'Mahony

In a study involving 23 labs, researchers tested various sequencing/bioinformatic approaches for taxonomic profiling of DNA reference reagents consisting of 20 common gut bacteria, revealing the reality of technical bias in the microbiome field. #mSystems: asm.social/2Fk

@BissonGiulia @pauldcotter @teagasc Bravissima!!!! Congratulatioms Giulia

Are there virulent phages hiding in your bacterial culture? Here we find hundreds of virulent phage genomes in bacterial genome assemblies. Bioinformatic and experimental evidence indicate these are not contaminations, but represent persistent infections. biorxiv.org/content/10.110…

GWAS for Nobel prize laureates.

Unassigning bacterial species for microbiome studies journals.asm.org/doi/full/10.11…

Great to see this finally published! GROND is a new 16S-ITS-23S rRNA database that will allow the full potential of long read sequencing be applied to amplicon-based metataxonomics

The final version of our short-read polishing manuscript (headed by @rrwick of course) is out in @MicrobioSoc MGen! Tldr: with R10.4.1+Dorado ONT assemblies, few errors remain, so short-read polishing can make assemblies worse at low depth; target >=25x doi.org/10.1099/mgen.0…

@OrlaOS @TeagascFood @pauldcotter @jgskenny @Ant__Lourenco You know when you're in a scientific meeting about fermented foods when a massive vat of fermented veg has pride of place during each lunch buffet! Thanks to Rain Kuldjärv and all at TFTAK for hosting and to new colleagues for a friendly introduction to #DOMINOEU

Happy to share my first pre-print with @EvelienAdri in my new role at @TheQuadram. We sequenced three human faecal viromes with Illumina and Nanopore, and tested a number of long, short and hybrid assembly approaches (1/10) biorxiv.org/content/10.110…

MicrobeMod: A computational toolkit for identifying prokaryotic methylation and restriction-modification with nanopore sequencing biorxiv.org/cgi/content/sh… #biorxiv_micrbio

Our latest work, out today in @PLOSBiology suggests that not only do mammalian cells absorb bacteriophages, but they appear to use them as a resource to enhance growth! journals.plos.org/plosbiology/ar… This work was led by @marion_bichet and out on World Phage Week! #WorldPhageWeek

What are fermented foods and why should we care? @RamyaBalasubr13 presents her work on understanding the role of fermented foods in modulating the microbioata-gut-brain axis… #APCSymposium2023

⁦@N_RoseEdwin⁩ knocking it out of the park (digging in the weeds?) of soil microbiomes ⁦@MicrobioSoc⁩ Irish meeting

Our third speaker is @EmmanuelKuffo15, talking about Streptococcus suis as a model for phage based biocontrol agents #MicrobioIrish23 @MicrobioSoc @UccMicrobiology @SEFSUCC @UCC @JenniferMahony7

And now @meghana_srini speaking about her work to apply long read sequencing to metagenomics #MicrobioIrish23

PSA to folks who have bioinformatics tools with required databases hosted on Zenodo: all the URLs for Zenodo data files have changed slightly. It may affect your DB set up scripts.

ggCaller paper now out in its final form genome.cshlp.org/content/33/9/1… Call your genes, get your pangenome (and a great cover thanks to laurenbellcreative.com)

@EmmanuelKuffo15 @haleybiont @RamyaBalasubr13

@haleybiont @RamyaBalasubr13 @forestsomewhere thanks for tolerating me🤭

@EmmanuelKuffo15 @PWO_Ireland 👏 well said, especially when universities and postgrad students are essentially fighting on the same team against chronic and ongoing undervalorisation and underfunding of tertiary education... And it is of such direct and concrete relevance to #EDI

One frustrating thing is the silence of some line managers&senior researchers. They know firsthand the remuneration PhDs get (or dont get), and the cost of living yet their silence is deafening. We’ve seen how valuable faculty voices were elsewhere #PGRsDeserveBetter @PWO_Ireland

#Microbiome twitter, we are looking for negative control samples from as many sources and kits as possible. If you've included blanks in your 16S or ITS amplicon seq project and the data is publicly available, drop a link in the thread! RTs appreciated!