Shane Maher

Dr. Shane Maher

School of Agriculture and Food Science, University College Dublin (UCD), Dublin, Ireland
orcid

Research Focus & Metrics

Academic Career Length

5Years (2022-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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4 April 2022 in Journal of Animal Science and Biotechnology
Verified
Journal Article
Open access
PDF file
BVBrigkita Venardou
Brigkita Venardou
John O'DohertyJohn O'Doherty
John O'Doherty
Shane MaherShane Maher
Shane Maher
MRMarion Ryan
Marion Ryan
VGVivian Gath
Vivian Gath
TSTorres Sweeney
Torres Sweeney
Background: Dietary supplementation with a fucoidan-rich Ascophyllum nodosum extract (ANE), possessing an in vitro anti-Salmonella Typhimurium activity could be a promising on-farm strategy to control Salmonella infection in pigs. The objectives of this study were to: 1) evaluate the anti-S. Typhimurium activity of ANE (containing 46.6% fucoidan, 18.6% laminarin, 10.7% mannitol, 4.6% alginate) in vitro, and; 2) compare the effects of dietary supplementation with ANE and Zinc oxide (ZnO) on growth performance, Salmonella shedding and selected gut parameters in naturally infected pigs. This was established post-weaning (newly weaned pig experiment) and following regrouping of post-weaned pigs and experimental re-infection with S. Typhimurium (challenge experiment). Results: In the in vitro assay, increasing ANE concentrations led to a linear reduction in S. Typhimurium counts (P < 0.05). In the newly weaned pig experiment (12 replicates/treatment), high ANE supplementation increased gain to feed ratio, similar to ZnO supplementation, and reduced faecal Salmonella counts on d 21 compared to the low ANE and control groups (P < 0.05). The challenge experiment included thirty-six pigs from the previous experiment that remained on their original dietary treatments (control and high ANE groups with the latter being renamed to ANE group) apart from the ZnO group which transitioned onto a control diet on d 21 (ZnO-residual group). These dietary treatments had no effect on performance, faecal scores, Salmonella shedding or colonic and caecal Salmonella counts (P > 0.05). ANE supplementation decreased the Enterobacteriaceae counts compared to the control. Enterobacteriaceae counts were also reduced in the ZnO-residual group compared to the control (P < 0.05). ANE supplementation decreased the expression of interleukin 22 and transforming growth factor beta 1 in the ileum compared to the control (P < 0.05). Conclusions: ANE supplementation was associated with some beneficial changes in the composition of the colonic microbiota, Salmonella shedding, and the expression of inflammatory genes associated with persistent Salmonella infection.

13 May 2025 in Animals
Verified
Journal Article
Open access
PDF file
Shane MaherShane Maher
Shane Maher
TSTorres Sweeney
Torres Sweeney
John O'DohertyJohn O'Doherty
John O'Doherty
The intensifying global demand for food presents significant challenges for sustainable pig production, particularly in the context of escalating input costs, environmental degradation, and resource scarcity. Life cycle assessment provides a comprehensive framework for quantifying environmental impacts and identifying production hotspots within pig production systems. Feed production and manure management are consistently identified as major contributors, emphasising the need for targeted interventions. Although soybean meal remains a key protein source, its association with deforestation and biodiversity loss is driving an interest in more sustainable alternatives. In temperate climates, faba beans offer a promising, locally sourced option, though their wider adoption is limited by amino acid imbalances and anti-nutritional factors. Grain preservation is another critical consideration, as post-harvest losses and fungal contamination compromise feed quality and animal health. Organic acid preservation has emerged as an energy-efficient, cost-effective alternative to industrial drying, improving storage stability and reducing fossil fuel dependence. Additional nutritional strategies, including dietary crude protein reduction, carbohydrate source modification, feed additive inclusion, and maternal nutritional interventions, can enhance nutrient utilisation, intestinal health, and herd resilience while mitigating environmental impact. This review explores practical feed-based strategies to support sustainable, resilient, and resource-efficient pig production and contribute to global food security.

12 March 2025 in Journal of Animal Science and Biotechnology
Verified
Journal Article
Open access
Shane MaherShane Maher
Shane Maher
TSTorres Sweeney
Torres Sweeney
SVStafford Vigors
Stafford Vigors
MMMichael McDonald
Michael McDonald
John O'DohertyJohn O'Doherty
John O'Doherty
Background: Organic acids (OA) and maternal nutritional strategies have been demonstrated to promote piglet health and development. The objective of this study was to investigate the effects of incorporating OA-preserved cereal grains into sow diets during late gestation and lactation, aiming to reduce the metabolic demands of lactation while optimising offspring development and growth until slaughter. The experiment compared OA-preserved wheat and barley to conventionally dried grains, focusing on sow and offspring performance, as well as their faecal microbiota during lactation. Forty sows were blocked based on parity, body weight and back fat thickness on d 100 of gestation and assigned to one of two diets: a dried grain lactation diet and a preserved grain lactation diet. Sow faecal samples were collected at farrowing for the coefficient of apparent total tract digestibility (CATTD) of nutrients and microbial analysis. Offspring faecal samples were collected on d 10 postpartum and at weaning (d 26 postpartum) for microbial analysis. Results: Sow body weight, back fat changes, gestation and lactation length, total piglets born, wean-to-oestrus interval, and lactation efficiency were unaffected by sow diet (P > 0.05). However, sows offered the preserved grain diet exhibited improved CATTD of dry matter, nitrogen, gross energy, and neutral detergent fibre (P < 0.05). While no maternal effect was observed on offspring growth during lactation (P > 0.05), pigs from sows offered the preserved grain diet showed improved growth and feed efficiency from weaning until slaughter (d 168) compared to those from sows offered the dried grain diet (P < 0.05). The preserved grain diet also reduced the abundance of Proteobacteria in sow faeces at farrowing and in their offspring on d 10 postpartum, and improved piglet faecal scores throughout lactation (P = 0.05). At weaning, piglets from sows offered the preserved grain diet exhibited an increased abundance of Lactobacillus and reduced abundance of Alistipes in their faeces (P < 0.05). Conclusion: OA-preserved grains enhanced the CATTD of nutrients in sows, promoted healthier piglet faecal scores during lactation, and improved offspring growth performance post-weaning, potentially linked to beneficial changes observed in the faecal microbiota of sows and their offspring during lactation.

26 September 2026 in Animal Feed Science and Technology
Verified
Journal Article
Closed access
Shane MaherShane Maher
Shane Maher
Nicholas HoldenNicholas Holden
Nicholas Holden
TSTorres Sweeney
Torres Sweeney
John O'DohertyJohn O'Doherty
John O'Doherty

6 May 2026 in Preprints.org
Verified
Preprint
Open access
PDF file
KCKathryn Ruth Connolly
Kathryn Ruth Connolly
Shane MaherShane Maher
Shane Maher
TSTorres Sweeney
Torres Sweeney
John O'DohertyJohn O'Doherty
John O'Doherty
In commercial pig production systems, early weaning disrupts the coordinated maturation of the gastrointestinal tract, resulting in reduced feed intake, impaired digestive capacity, altered microbial ecology and increased susceptibility to post-weaning diarrhoea (PWD). Although enterotoxigenic Escherichia coli (ETEC) is frequently implicated, variation in disease expression is not explained by pathogen presence alone, but reflects interactions among host physiology, nutrient flow and microbial metabolism. This review examines the regulation of the gut microbiota in post-weaned pigs through the interaction between digestive capacity and dietary substrate supply. It proposes substrate flow as the organising principle linking digestive function, diet composition and microbial metabolism. Gut microbial function is regulated primarily by substrate availability, which is determined by the alignment between diet composition and host digestive capacity. When this alignment is disrupted, undigested nutrients are redistributed to the hindgut, driving a shift from saccharolytic to proteolytic fermentation. This transition generates metabolites that impair epithelial integrity, increase luminal pH and favour proliferation of opportunistic bacteria, thereby promoting intestinal dysfunction. Within this context, nutritional strategies, including optimisation of dietary protein, provision of fermentable carbohydrates and support of gastric function, act by regulating substrate flow rather than directly modifying microbial composition. Organic acids, functional ingredients and maternal influences operate through the same mechanisms, shaping nutrient digestion, microbial exposure and metabolic outcomes. The characteristic post-weaning increase in Enterobacteriaceae and reduction in microbial diversity are therefore best understood as consequences of altered substrate flow and luminal conditions, rather than primary initiating events. This interpretation provides a mechanistic basis for the design of integrated nutritional and management strategies to improve gut health and reduce antimicrobial reliance in pig production systems.

5 June 2026 in Agriculture
Verified
Journal Article
Open access
PDF file
KCKathryn Ruth Connolly
Kathryn Ruth Connolly
Shane MaherShane Maher
Shane Maher
TSTorres Sweeney
Torres Sweeney
John O'DohertyJohn O'Doherty
John O'Doherty
In commercial pig production systems, early weaning imposes abrupt nutritional, environmental and social challenges before full gastrointestinal maturation has occurred, increasing susceptibility to post-weaning diarrhoea (PWD) and impaired growth performance. Although enterotoxigenic Escherichia coli (ETEC) is frequently implicated in PWD, pathogen presence alone does not adequately explain variation in disease expression among pigs and production systems. Increasing evidence indicates that gastrointestinal stability following weaning is determined by interactions among digestive capacity, substrate flow, microbial metabolism, epithelial integrity and host immune responses. In this review, substrate flow refers to the quantity, composition and regional distribution of undigested dietary and endogenous substrates moving through the gastrointestinal tract (GIT) and becoming available for microbial fermentation. The review proposes substrate flow as the central mechanistic interface linking digestive physiology with microbial metabolic activity during the post-weaning transition. Commercial weaning frequently occurs before complete adaptation to cereal- and plant-based diets has developed. Reduced feed intake, elevated gastric pH, incomplete pancreatic adaptation and reduced brush-border enzyme activity impair nutrient digestion during this transition, increasing nutrient overflow to the distal intestine. Under these conditions, microbial metabolism shifts from predominantly saccharolytic fermentation towards proteolytic pathways associated with production of ammonia, phenols, indoles and branched-chain fatty acids. These metabolites impair epithelial integrity, alter luminal conditions and favour proliferation of opportunistic bacteria. Conversely, effective digestion supports saccharolytic fermentation, short-chain fatty acid production, epithelial integrity and microbial stability. Microbial dysbiosis is therefore more accurately interpreted as a metabolic consequence of altered substrate availability and fermentation dynamics rather than solely as a compositional imbalance of bacterial taxa. By integrating digestive physiology, microbial ecology and nutritional management, the substrate-flow concept provides a mechanistic framework for development of more biologically coherent nutritional strategies aimed at improving gastrointestinal resilience and reducing antimicrobial reliance in modern pig production systems.