APC Microbiome Ireland

24/04/2026

New blog from APC Project Leader Des Field, exploring how microbiology and bioengineering can work together to tackle bacterial resistance.

Des breaks down how nisin, a natural antimicrobial peptide, can be precisely redesigned to improve its stability and activity, and to help it evade bacterial defence systems. The piece focuses on how small molecular changes can lead to meaningful shifts in function.

Clear science. Real insight. No hype.
💻️ Read it here:
https://blog.genewiz.com/engineering-nisin-how-bio-designed-antimicrobial-peptides-are-rewriting-the-rules-against-superbugs (🔗 link in bio)

24/04/2026

Raw milk microbes can reduce chlorate already present in the dairy chain.

A new study published in 𝐀𝐜𝐜𝐞𝐬𝐬 𝐌𝐢𝐜𝐫𝐨𝐛𝐢𝐨𝐥𝐨𝐠𝐲 explores how bacteria naturally found in raw milk respond to chlorate, a residue linked to chlorine‑based cleaning products.

Researchers used shotgun metagenomic sequencing on chlorate‑spiked milk from multiple farms. Chlorate levels dropped after 10 days at 4 °C and within 24 hours at 25 °C. Different bacteria dominated at each temperature, with clear links to genes involved in chlorate reduction, including napA, narG and ydeP.

The work adds detail to how food microbiomes respond to chemical stress under common storage conditions.

The study was carried out by APC researchers , , , Douwe van Sinderen and John Kenny.

📰 Read the paper: https://pubmed.ncbi.nlm.nih.gov/42016597/(🔗 Link in bio)



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23/04/2026

Today we’re celebrating the people behind the science 🧪✨

From early starts to careful steps, every breakthrough begins in the lab.
Happy World Laboratory Day to all who explore, test, discover, and keep science moving forward.

23/04/2026

Some upper GI cancers are linked with a distinct gut microbiota pattern.

A new paper in 𝐈𝐫𝐢𝐬𝐡 𝐉𝐨𝐮𝐫𝐧𝐚𝐥 𝐨𝐟 𝐌𝐞𝐝𝐢𝐜𝐚𝐥 𝐒𝐜𝐢𝐞𝐧𝐜𝐞 looked at stool samples from people with newly diagnosed hepato-pancreatico-biliary and gastric cancers. The researchers compared 37 treatment-naïve patients with 47 age-matched non-cancer controls using 16S rRNA amplicon sequencing. They found more Enterococcus, Enterobacter, Streptococcus and Lactobacillus, and less Faecalibacterium, Bacteroides and several Lachnospiraceae groups. The team also saw a trend towards lower diversity and richness with increasing cancer stage.

That matters because it adds to the evidence that gut microbiota changes are linked with these cancers and helps build a clearer picture of disease-associated microbial patterns.

APC researchers on the study include Louise Daly, Fiona Fouhy, , Daniel Linaries, Paul O’Toole, Paul Ross, Catherine Stanton and Aoife Ryan.

📰 Read the paper: https://link.springer.com/article/10.1007/s11845-025-04166-1 (🔗 Link in bio)


| | cork_university_hospital | Mercy University Hospital |

23/04/2026

Faecal microbiota transplantation may involve more than bacteria alone.

A new review in 𝐂𝐞𝐥𝐥 𝐇𝐨𝐬𝐭 & 𝐌𝐢𝐜𝐫𝐨𝐛𝐞 explores the role of bacteriophages in FMT. It focuses on phage-mediated horizontal gene transfer, where donor phages may help move genes between gut bacteria after transplant. The paper suggests this could influence microbial fitness and function, including traits linked to metabolism, virulence and antimicrobial resistance.

That matters because it gives researchers a fuller picture of what may transfer during FMT, and what should be tracked when studying how these treatments work.

The review is from Belen Gonzalez Pastor, Andrey N. Shkoporov and .

📰 Read the paper: https://pubmed.ncbi.nlm.nih.gov/41990750/ (🔗 link in bio)



| | UCC Medicine and Health

22/04/2026

Water kefir is more than a drink. It is also a useful model for studying fermented foods.

A new study published in 𝐧𝐩𝐣 𝐁𝐢𝐨𝐟𝐢𝐥𝐦𝐬 𝐚𝐧𝐝 𝐌𝐢𝐜𝐫𝐨𝐛𝐢𝐨𝐦𝐞𝐬 explores how water kefir can be used for multi-omics and genome-scale metabolic modelling.

The paper explains why water kefir is a good research system. Its grains contain a relatively simple mix of bacteria and yeasts, which makes it easier to study microbial interactions and metabolism. The review also sets out a roadmap for integrated omics studies and looks at the challenges of building defined starter communities.

That matters because it gives researchers a practical way to study fermented food ecosystems with more clarity and control.

From APC Microbiome Ireland ._khan, Samuel Breselge, Kate O’Mahony, , , Jennifer Mahony, John Kenny and their colleague from Teagasc Sinéad McCarthy.

Read the paper: https://www.nature.com/articles/s41522-026-00985-x



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21/04/2026

Wishing a very fond farewell to our dear colleague and contracts manager Amanda Lohan ().

Thank you for everything you have brought to the team. We will miss working with you and wish you every success and happiness in your new role.

21/04/2026

Coffee may shape mood and stress through the gut microbiome, not just caffeine.
A new paper in 𝑵𝒂𝒕𝒖𝒓𝒆 𝑪𝒐𝒎𝒎𝒖𝒏𝒊𝒄𝒂𝒕𝒊𝒐𝒏𝒔 studied how regular coffee consumption affects the gut brain axis.

The researchers compared 31 coffee drinkers with 31 non drinkers using psychological tests, food diaries, and stool and urine samples. Coffee drinkers stopped coffee for two weeks, then restarted with either caffeinated or decaffeinated coffee.

Both types were linked to lower perceived stress and depression. The study also found shifts in gut bacteria and metabolites linked to wellbeing, including higher levels of Eggertella and Cryptobacterium.

Decaffeinated coffee was associated with improved learning and memory. Caffeinated coffee was linked to lower anxiety and better attention. This suggests coffee components beyond caffeine also play a role.

The study was led by Professor at APC Microbiome Ireland, UCC.

Congratulations to all; , Thomaz Bastiaanssen, , Federica Bergamo, Laila Zeraik, .oleary.180, .ferri, Maha Irfan, Maaike van der Rhee, Thaïs Lindemann, Elizabeth Schneider, Arthi Chinna Meyyappan, , , .carbia, , José Fernando Rinaldi de Alvarenga, Nicole Tosi, Daniele Del Rio, Alice Rosi, Letizia Bresciani, PedroMena, Gerard Clarke &

📰 Read the paper: https://doi.org/10.1038/s41467-026-71264-8 (🔗 Links in bio)
🗞️ Press release: https://buff.ly/oucNkvh


portfolio | | University of Parma

20/04/2026

Bacteria used in cheese-making have a long list of ways to fight phages.

A new review in 𝐅𝐄𝐌𝐒 𝐌𝐢𝐜𝐫𝐨𝐛𝐢𝐨𝐥𝐨𝐠𝐲 𝐑𝐞𝐯𝐢𝐞𝐰𝐬 revisits abortive infection-like antiphage systems in Lactococcus. The authors bring together 34 distinct Abi-like systems, including 11 reported recently, and examine how these systems differ in structure, predicted function, genetic location and effects on the phage life cycle.

One useful takeaway is that although many Abi-like systems were first discovered on plasmids, most antiphage defence systems in sequenced Lactococcus strains seem to be chromosomally encoded.

That gives researchers a clearer map of how these important bacteria defend themselves.

APC researchers on the paper include Andriana Grafakou, Cas Mosterd, Jennifer Mahony and Douwe van Sinderen.

📰 Read the paper: https://academic.oup.com/femsre/article/doi/10.1093/femsre/fuag009/8507239(🔗 Link in bio)



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17/04/2026

17/04/2026

6 Stories. Latest story added on 17 April 2026. See insider moments and handpicked daily stories you won't find anywhere else.

17/04/2026

The gut microbiome may be linked with mental health in older age.

A new paper in PLOS ONE looked at 153 older Chilean adults with cognitive complaints. The researchers used 16S V4 sequencing and five mental health and cognitive tests to examine how gut microbiome composition and neuroactive pathways relate to psychological and cognitive measures.

They found associations involving pathways linked to compounds such as tryptophan, short-chain fatty acids, glutamate and nitric oxide, along with differences tied to depressive symptoms and s*x.

This matters because it adds new human evidence on how gut microbial functions may relate to mental and cognitive health in ageing.

APC contributors include Benjamin Valderrama, Thomaz Bastiaanssen, Gerard Clarke and .

📰 Read the paper: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0343493 (🔗 link in bio)



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