Happy to share my first pre-print with Evelien Adriaenssens (she/her) in my new role at Quadram Institute. 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 PLOS Biology 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? Ramya Balasubramanian presents her work on understanding the role of fermented foods in modulating the microbioata-gut-brain axis… #APCSymposium2023

⁦N. Rose Edwin⁩ knocking it out of the park (digging in the weeds?) of soil microbiomes ⁦Microbiology Society⁩ Irish meeting

Our third speaker is J.O.K.Emmanuel🏳️‍🌈🏳️‍⚧️, talking about Streptococcus suis as a model for phage based biocontrol agents #MicrobioIrish23 Microbiology Society Microbiology UCC UCC Ireland (@SEFSUCC) 's Twitter Profile">SEFSUCC Ireland UCC Ireland Mahony Lab

And now Meghana Srinivas 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)

#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!

🏠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 🩷

If anyone wants to help spread the word about Skype A Scientist, it's one of two things we need the most.

You can send people to: skypeascientist.com/sign-up.html

And feel free to share this flyer with anyone who you think could benefit from our program!

Great to see this out with ⁦⁦Microbiology Society⁩ Many congrats ⁦Billy McCarthy⁩ and ⁦Meghana Srinivas⁩ Isolation and identification of chlorate-reducing Hafnia sp. from milk microbiologyresearch.org/content/journa…

How hard is it to do science in a language that’s not your first language? We quantified the severity of #languagebarriers for non-native English speakers when reading/publishing papers and attending/presenting at international conferences.
doi.org/10.1371/journa…
1/9

Nice assessment of technical bias in microbiome studies (sadly only 16S) caused by DNA extraction steps (buffers, kits and lysis conditions).
Interestingly (but not very surprisingly), composition was altered between different kits and lysis conditions, but not buffers.

Indexing and searching petabyte-scale nucleotide resources biorxiv.org/cgi/content/sh… #bioRxiv

Read our latest study on phase variation in MTBC.

We focused on phase variation that results from rapidly acquired indels in simple sequence repeats. These indels can toggle a gene ‘on’ or ‘off’ through frameshifts or dial-up or down transcription. 1/2

pnas.org/doi/10.1073/pn…

Our latest: The taxonomic resolution of 16S sequencing doesn't stop at the species level when using modern long-read techniques. Serovars from 16S...

biorxiv.org/content/10.110…

#NCStateMicrobiome

🔥🔥🔥🔥🔥Here's my second paper on rarefaction. Rather, why rarefaction should have never been called into question in the first place (as well as what rarefaction actually is) 🔥🔥🔥🔥🔥biorxiv.org/content/10.110…

If you work #norovirus what do you sequence when you want to #genotype your samples? Comment below with the primer sets you use and if you use other regions for typing! Retweet 🦠🧬👩‍🔬