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Katie O'Mahony @forestsomewhere

PhD student @pharmabiotic @ucc | Microbes, Biofilms and Antimicrobial Resistance | All views my own | @aforestsomewhere@mstdn.science

Joined March 2013
  • Tweets 1,591
  • Following 1,447
  • Followers 537
41 Photos and videos
Katie O'Mahony retweeted
Thomas G. Dietterich@tdietterich
May 14
Attention @arxiv authors: Our Code of Conduct states that by signing your name as an author of a paper, each author takes full responsibility for all its contents, irrespective of how the contents were generated. 1/
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Katie O'Mahony retweeted
ASM
@ASMicrobiology
29 Oct 2025
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
Average microbiome composition for each method employed by the participants (n = 5), aligned to the ground truth (Actual) of each DNA RR. (A) Relative species level composition (%) of the DNA-Gut-HiLo and DNA-Gut-Mix RRs resulting from shotgun sequencing data analysis. (B) Relative genus level composition (%) of the DNA-Gut-HiLo and DNA-Gut-Mix RRs resulting from 16S rRNA gene amplicon sequencing data analysis.

ALT Average microbiome composition for each method employed by the participants (n = 5), aligned to the ground truth (Actual) of each DNA RR. (A) Relative species level composition (%) of the DNA-Gut-HiLo and DNA-Gut-Mix RRs resulting from shotgun sequencing data analysis. (B) Relative genus level composition (%) of the DNA-Gut-HiLo and DNA-Gut-Mix RRs resulting from 16S rRNA gene amplicon sequencing data analysis.

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Katie O'Mahony retweeted
Peter Dougherty@PeterEDougherty
2 Jan 2025
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/10.1101/…

Persistent virulent phages exist in bacterial isolates

Despite the immense diversity of tailed bacteriophages, they are traditionally classified as either virulent or temperate, with only the latter thought capable of long-term persistence in bacterial...

biorxiv.org
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Katie O'Mahony retweeted
Rainer Melzer@UCDflowerpower
9 Oct 2024
GWAS for Nobel prize laureates.
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Katie O'Mahony retweeted
Cameron Thrash@jcamthrash
25 Jun 2024
Unassigning bacterial species for microbiome studies journals.asm.org/doi/full/10…

Unassigning bacterial species for microbiome studies | mSystems

While existing methods do not provide reliable species-level assignments for 16S rRNA marker gene data, the Unassigner software solves this problem by ruling out species membership, allowing resear...

journals.asm.org
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Katie O'Mahony retweeted
Paul Cotter@pauldcotter
7 Jun 2024
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
John Kenny@jgskenny
7 Jun 2024
Some weekend reading…great to see GROND, our new database for long-read amplicon sequencing of the ribosomal operon, is out. Congrats ⁦@calumari_walsh⁩ ⁦@meghana_srini⁩ ⁦@VanSinderenLab⁩ ⁦@pauldcotter⁩ ⁦@tstinear⁩ ⁦⁦ microbiologyresearch.org/con…
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Katie O'Mahony retweeted
George Bouras@GB13Faithless
5 Jun 2024
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.0.00125…

How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies

microbiologyresearch.org
George Bouras@GB13Faithless
13 Mar 2024
Replying to @rrwick
@rrwick, myself and the team (@JuddLmj @tstinear @linsalrob & Sarah) have recently looked at the effect of depth on short-read polishing almost-perfect Nanopore bacterial genomes biorxiv.org/content/10.1101/… (1/7)
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Katie O'Mahony retweeted
Ryan Cook@RyanCookAMR
27 Nov 2023
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/10.1101/…

Nanopore and Illumina Sequencing Reveal Different Viral Populations from Human Gut Samples

The advent of viral metagenomics, or viromics, has improved our knowledge and understanding of global viral diversity. High-throughput sequencing technologies enable explorations of the ecological...

biorxiv.org
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Katie O'Mahony retweeted
bioRxiv Microbiology@biorxiv_micrbio
15 Nov 2023
MicrobeMod: A computational toolkit for identifying prokaryotic methylation and restriction-modification with nanopore sequencing biorxiv.org/cgi/content/shor… #biorxiv_micrbio
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Katie O'Mahony retweeted
Jeremy J Barr@JeremyJBarr
27 Oct 2023
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/plosbiolog… This work was led by @marion_bichet and out on World Phage Week! #WorldPhageWeek

Mammalian cells internalize bacteriophages and use them as a resource to enhance cellular growth...

There is a growing appreciation that the direct interaction between bacteriophages and the mammalian host can facilitate diverse and unexplored symbioses; this study shows that mammalian cells...

journals.plos.org
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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
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Katie O'Mahony retweeted
John Kenny@jgskenny
24 Oct 2023
⁦@N_RoseEdwin⁩ knocking it out of the park (digging in the weeds?) of soil microbiomes ⁦@MicrobioSoc⁩ Irish meeting
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Katie O'Mahony retweeted
microSCRUM@micro_SCRUM
25 Oct 2023
Our third speaker is @EmmanuelKuffo15, talking about Streptococcus suis as a model for phage based biocontrol agents #MicrobioIrish23 @MicrobioSoc @UccMicrobiology @SEFSUCC @UCC @JenniferMahony7
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Katie O'Mahony retweeted
John Kenny@jgskenny
25 Oct 2023
And now @meghana_srini speaking about her work to apply long read sequencing to metagenomics #MicrobioIrish23
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Katie O'Mahony retweeted
Mike Tisza@MikeTisza
18 Oct 2023
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.
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Katie O'Mahony retweeted
John Lees@johnlees6
16 Oct 2023
ggCaller paper now out in its final form genome.cshlp.org/content/33/… Call your genes, get your pangenome (and a great cover thanks to laurenbellcreative.com/)
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Katie O'Mahony retweeted
Amelia Barber@AmeliaBarberPhD
5 Oct 2023
#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!
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Katie O'Mahony retweeted
Amy Fitzpatrick@AmyHFitzpatrick
14 Aug 2023
🏠Seeking Rental Help in South Dublin. Due to a house fire, we're urgently searching for a rental from Sep to Dec/Jan. No injuries, but handling this #shitshow from Germany. If you know of any options within budget for two #academics, DM me😢 #HousingEmergency Please retweet 🩷
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Katie O'Mahony retweeted
Sarah McAnulty, Ph.D@SarahMackAttack
2 Aug 2023
If anyone wants to help spread the word about @SkypeScientist, it's one of two things we need the most. You can send people to: skypeascientist.com/sign-up.… And feel free to share this flyer with anyone who you think could benefit from our program!
An explainer for skype a scientist that says "Skype a Scientist chat with scientists FOR FREE" followed by "Skype a Scientist matches classrooms, scout troops, libraries and other groups with scientists for Q&As about science! " and then "How it works: Step 1: Sign up on SkypeAScientist.com Step 2: Pick a category of science your group would like to talk about (e.g. marine biology, chemistry, astronomy) Step 3: Get a match via email Step 4: Connect with your scientist, discuss your class's needs, and pick a time to chat Step 5: Talk to your scientist!"

ALT An explainer for skype a scientist that says "Skype a Scientist chat with scientists FOR FREE" followed by "Skype a Scientist matches classrooms, scout troops, libraries and other groups with scientists for Q&As about science! " and then "How it works: Step 1: Sign up on SkypeAScientist.com Step 2: Pick a category of science your group would like to talk about (e.g. marine biology, chemistry, astronomy) Step 3: Get a match via email Step 4: Connect with your scientist, discuss your class's needs, and pick a time to chat Step 5: Talk to your scientist!"

Sarah McAnulty, Ph.D@SarahMackAttack
2 Aug 2023
The collapse of twitter has made it much harder to publicize Skype a Scientist (she says on twitter). Very open to any ideas on how to get the word out to teachers about our program. It has to be either free or low-cost (twitter collapsing has also made fundraising harder UGH).
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Katie O'Mahony retweeted
John Kenny@jgskenny
20 Jul 2023
Great to see this out with ⁦⁦@MicrobioSoc⁩ Many congrats ⁦@BMC2203⁩ and ⁦@meghana_srini⁩ Isolation and identification of chlorate-reducing Hafnia sp. from milk microbiologyresearch.org/con…

Isolation and identification of chlorate-reducing Hafnia sp. from milk

microbiologyresearch.org
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