Our Publications

Gut microbes may influence how genes work in the brain.

A new review in 𝐇𝐚𝐧𝐝𝐛𝐨𝐨𝐤 𝐨𝐟 𝐂𝐥𝐢𝐧𝐢𝐜𝐚𝐥 𝐍𝐞𝐮𝐫𝐨𝐥𝐨𝐠𝐲 examines the links between the gut microbiota and epigenetics, which controls gene activity without changing the DNA sequence.

The authors explore DNA methylation, histone modification and non-coding RNA, and how these processes may connect microbial activity with brain signalling, inflammation and the blood-brain barrier.

The review brings evidence together across brain physiology and neurological and psychiatric conditions, helping researchers examine possible mechanisms without assuming that associations establish cause and effect.

The chapter is authored by APC Microbiome Ireland and University College Cork researchers Gerard Moloney, Gerard Clarke and John Cryan.

📰 Read the paper: https://buff.ly/6qah2r2

Bacteria used in dairy fermentation have different ways of defending themselves against viruses.

A new study published in 𝐌𝐢𝐜𝐫𝐨𝐛𝐢𝐚𝐥 𝐆𝐞𝐧𝐨𝐦𝐢𝐜𝐬 explores how bacteria from the Lactococcus and Pseudolactococcus groups interact with bacteriophages, viruses that infect bacteria.

Researchers analysed 495 bacterial genomes, examining cell surface structures, viral DNA and defence systems. They found that dairy-associated strains carried more phage-related genetic material and defence systems than plant-associated strains.

These differences help explain how bacteria and their viruses adapt to different environments.

The research involved APC Microbiome Ireland scientists José Augusto Gonzales Castillo, Douwe van Sinderen and Jennifer Mahony, working with Axel Soto Serrano, Lukasz Krych and Paulina Deptula at the University of Copenhagen.

📰 Read the paper: https://buff.ly/tj4BNUj

Gut microbes can turn peanut components into metabolites linked with immune signalling.

A new study published in 𝐆𝐮𝐭 𝐌𝐢𝐜𝐫𝐨𝐛𝐞𝐬 examined how peanut consumption shapes the early-life gut microbiome and microbial metabolism.

Researchers analysed faecal samples from 343 children aged 12 months. They also found that peanut fermentation altered 188 metabolites and increased the production of short-chain fatty acids.

The findings improve our understanding of how gut microbes may connect early diet with immune signalling.

This APC Microbiome Ireland-led research includes Emer Shannon, Hannah Devotta, Cebile Ndwandwe, Songhui Kim, Lu Yao, Lamiah Kareem, Avril Walters, Nonhlanhla Lunjani, Lisa Friess, Douwe van Sinderen, Catherine Stanton, Jens Walter and Liam O'Mahony, alongside collaborators Sadhbh Hurley, Katri Korpela, Fatma Koç, Harsh Mathur, Anoop Ambikan, Ujjwal N., Carina Venter and Jonathan Hourihane.

📰 Read the paper: https://buff.ly/M1tNd0r

📱 Read the webstory: https://buff.ly/OqUaSM0

Personalised models suggest gut microbes may influence metabolic changes linked to Alzheimer’s disease.

A new study published in 𝐆𝐮𝐭 𝐌𝐢𝐜𝐫𝐨𝐛𝐞𝐬 created personalised whole-body metabolic models for 34 people with Alzheimer’s dementia, 51 with mild cognitive impairment and 298 healthy controls.

The models predicted greater capacity for host-microbiome metabolism to produce five blood metabolites, including arginine, creatine and taurine. They also identified Bacteroides uniformis and Bacteroides thetaiotaomicron as key microbial contributors to these predicted shifts.

The work provides a framework for studying how microbiome differences may connect to host metabolism in Alzheimer’s disease.

Authors: Tim Hensen, Lora Khatib, Lucas Patel, Daniel McDonald, Antonio González, Siamak Mahmoudian Dehkordi, Colette Blach, Rob Knight, RIMA Kaddurah- Daouk and APC Group Leader Prof. Ines Thiele.

📰 Read the paper: https://buff.ly/ffFQsUH

Could fermented protein foods influence the connection between your gut microbiome and your muscles?

A new paper in 𝐂𝐨𝐦𝐦𝐮𝐧𝐢𝐜𝐚𝐭𝐢𝐨𝐧𝐬 𝐁𝐢𝐨𝐥𝐨𝐠𝐲 examines the evidence linking fermented protein foods with the gut-muscle axis.

Dominic Farsi, Paul Cotter and Orla O'Sullivan explore how microbial metabolites, gut barrier function, metabolic signalling and changes in protein digestion could connect the gut microbiome with skeletal muscle.

The review finds several plausible biological pathways, while direct evidence for effects on muscle protein synthesis, mass or function remains limited.

The work brings together current evidence and identifies key gaps for gut-muscle axis research.

📰 Read the paper: https://buff.ly/xl3mbd0

Fermented foods can affect the gut microbiome differently depending on the food itself.

A new study published in 𝐧𝐩𝐣 𝐒𝐜𝐢𝐞𝐧𝐜𝐞 𝐨𝐟 𝐅𝐨𝐨𝐝 compared kimchi, sauerkraut, water kefir and kombucha with their unfermented controls.

Kimchi altered gut microbiota structure and acetate production. The fermented beverages showed similar responses to their unfermented controls. The findings show why the food matrix and carefully matched controls matter when researchers study fermentation and the gut microbiome.

The study involved APC Microbiome Ireland researchers Ramya Balasubramanian, Paul Cotter and John Cryan, with Francesca Bietto , Luiza de Paula Dias Moreira, Linda Giblin and Kanishka Nilaweera at Teagasc.

📰 Read the paper: https://buff.ly/B2UAv3v

As solid foods enter the diet, the infant gut microbiome changes what it can do.

A new study published in 𝐒𝐜𝐢𝐞𝐧𝐭𝐢𝐟𝐢𝐜 𝐑𝐞𝐩𝐨𝐫𝐭𝐬 followed these changes during the first year of life.

Using metagenomic data from 125 Irish infants in the COMBINE cohort, researchers found a shift from simple sugar breakdown towards complex carbohydrate metabolism and short-chain fatty acid fermentation.

Feeding mode also shaped these functional changes. The findings add to our understanding of how diet and milk feeding help shape microbiome development during infancy.

The research involved APC Microbiome Ireland researchers Raphaela Joos, Anubhav Das, Eugene Dempsey, Aonghus Lavelle, Paul Ross and Catherine Stanton, alongside Grace Ahern, Deirdre Murray and Mairead Kiely.

📰 Read the paper: https://buff.ly/EomXRJr

Could molecules produced by our gut microbiota help regulate allergic responses?

In a new study published in 𝐌𝐮𝐜𝐨𝐬𝐚𝐥 𝐈𝐦𝐦𝐮𝐧𝐨𝐥𝐨𝐠𝐲, APC researchers and international collaborators show that microbial metabolites produced from tryptophan can directly influence key immune cells involved in allergy. The team found that these metabolites reduced Th2-associated responses and altered cellular metabolism, providing new insights into how the microbiome may shape immune health.

The findings strengthen the growing evidence that microbial metabolism plays an important role in immune regulation and may offer new opportunities for preventing or treating allergic diseases.

Congratulations to APC authors Lu Yao, Avril Walters, Kristoff Nieves, Hannah Devotta, Songhui Kim, Emer Shannon, Jens Walter and Liam O'Mahony, and all collaborators at Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich, Nencki Institute of Experimental Biology PAS and University of Cape Town.

📰 Read the paper: https://buff.ly/sU7xFhD

The gut microbiome may be part of the connection between heart and brain health in children with congenital heart disease.

A new paper in 𝐇𝐞𝐚𝐫𝐭 reviews evidence for a gut-brain-heart axis in congenital heart disease. The authors highlight early life as a key window.

Altered gut blood flow, antibiotic exposure, disrupted feeding and cardiopulmonary bypass can all affect the gut microbiome.

The review examines how these changes may relate to inflammation, cardiac physiology and neurodevelopment.

This synthesis gives researchers a clearer framework for studying congenital heart disease as a multisystem condition.

Authors: Sean Kelleher, Dhrati Patangia, Paul Ross, Adam James, Catherine Stanton and Colin McMahon.

📰 Read the paper: https://buff.ly/WoJzIHp

By 6 months, antibiotic exposure was twice as common and peanut introduction more than three times as common in the 2025 FLORAL cohort than in the 2020 CORAL cohort.

A new study published in 𝐏𝐞𝐝𝐢𝐚𝐭𝐫𝐢𝐜 𝐀𝐥𝐥𝐞𝐫𝐠𝐲 𝐚𝐧𝐝 𝐈𝐦𝐦𝐮𝐧𝐨𝐥𝐨𝐠𝐲 compared early-life exposures in the two birth cohorts.

Among FLORAL infants, hospitalisation was 13.1% compared with 5.1% in CORAL, antibiotic exposure was 13.1% vs 6.2%, and peanut had been introduced in 44% vs 13.6%.

These data give researchers a clearer picture of how early-life healthcare and feeding exposures changed after lockdown, with relevance for microbiome and allergy research.

APC Microbiome Ireland Group Leader Prof Liam O'Mahony contributed with collaborators at RCSI and Children’s Health Ireland.

📰 Read the paper: https://buff.ly/VY3wiE5

What happened to allergy outcomes as children born during Ireland’s first COVID-19 lockdown grew older?

A new study published in 𝐏𝐞𝐝𝐢𝐚𝐭𝐫𝐢𝐜 𝐀𝐥𝐥𝐞𝐫𝐠𝐲 𝐚𝐧𝐝 𝐈𝐦𝐦𝐮𝐧𝐨𝐥𝐨𝐠𝐲 provides the first longitudinal evaluation of pandemic-associated early-life exposures and atopic outcomes in children.

Researchers followed the CORAL cohort to age 5. Aeroallergen sensitisation rose from 8.9% at age 2 to 24% at age 5, while food allergy remained uncommon and most atopic dermatitis had resolved.

Following the same children over time helps researchers understand how early allergy patterns developed through childhood after an unusual period of environmental exposure.

Authors: Anitha Sokay, Sinead Burke, Maria Iatan, Sarah Byrne, Siobhan Verdon, Jordan Crupper, Susan Byrne, Liam O'Mahony and Jonathan O'B Hourihane.

The work includes APC Group Leader Prof. Liam O'Mahony, with colleagues at RCSI and Children’s Health Ireland.

📰 Read the paper: https://buff.ly/oLSHemz

A 12-week clinical trial has added new evidence on a specific probiotic strain and cholesterol.

A new study published in 𝐒𝐜𝐢𝐞𝐧𝐭𝐢𝐟𝐢𝐜 𝐑𝐞𝐩𝐨𝐫𝐭𝐬 tested Limosilactobacillus mucosae DPC 6426 in 94 adults with mildly raised cholesterol.

In this randomised, double-blind, placebo-controlled trial, researchers assessed blood lipid profiles alongside gut microbiota composition. The probiotic was not superior to placebo for these outcomes.

The study provides controlled human evidence that helps define the effects of this specific strain under the conditions tested.

Authors: Aoife O Donovan, Fiona Fouhy, Ghjuvan Grimaud, Lis London, Andrea Doolan, Andrea Anesi, Fulvio Mattivi, Paul Ross, Noel Caplice and Catherine Stanton.

📰 Read the paper: https://buff.ly/ApqzNH6

Brain-gut crosstalk associated with brain ageing in young and mid-life adults: a multicohort cross-sectional study