Journal Articles
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Item Dietary patterns influencing the human colonic microbiota from infancy to centenarian age: a narrative review(Frontiers Media S A, 2025-06-04) Geniselli da Silva V; Roy NC; Smith NW; Wall C; Mullaney JA; McNabb WC; Benítez-Páez AOur dietary choices not only affect our body but also shape the microbial community inhabiting our large intestine. The colonic microbiota strongly influences our physiology, playing a crucial role in both disease prevention and development. Hence, dietary strategies to modulate colonic microbes have gained notable attention. However, most diet-colonic microbiota research has focused on adults, often neglecting other key life stages, such as infancy and older adulthood. In this narrative review, we explore the impact of various dietary patterns on the colonic microbiota from early infancy to centenarian age, aiming to identify age-specific diets promoting health and well-being by nourishing the microbiota. Diversified diets rich in fruits, vegetables, and whole grains, along with daily consumption of fermented foods, and moderate amounts of fish and lean meats (two to four times a week), increase colonic microbial diversity, the abundance of saccharolytic taxa, and the production of beneficial microbial metabolites. Most of the current knowledge of diet-microbiota interactions is limited to studies using fecal samples as a proxy. Future directions in colonic microbiota research include personalized in silico simulations to predict the impact of diets on colonic microbes. Complementary to traditional methodologies, modeling has the potential to reduce the costs of colonic microbiota investigations, accelerate our understanding of diet-microbiota interactions, and contribute to the advancement of personalized nutrition across various life stages.Item Complementary foods in infants: an in vitro study of the faecal microbial composition and organic acid production(Royal Society of Chemistry, 2025-05-07) Geniselli da Silva V; Mullaney JA; Roy NC; Smith NW; Wall C; Tatton CJ; McNabb WCThe transition from breastmilk to complementary foods is critical for maturing the colonic microbiota of infants. Dietary choices at weaning can lead to long-lasting microbial changes, potentially influencing health later in life. However, the weaning phase remains underexplored in colonic microbiome research, and the current understanding of how complementary foods impact the infant's colonic microbiota is limited. To address this knowledge gap, this study assessed the influence of 13 food ingredients on the in vitro microbial composition and production of organic acids by the faecal microbiota in New Zealand infants aged 5 to 11 months. To better represent real feeding practices, ingredients were combined with infant formula, other complementary foods, or both infant formula and other foods. Among the individual food ingredients, fermentation with peeled kūmara (sweet potato) increased the production of lactate and the relative abundance of the genus Enterococcus. Fermentation with blackcurrants, strawberries, or raspberries enhanced acetate and propionate production. Additionally, fermentation with blackcurrants increased the relative abundance of the genus Parabacteroides, while raspberry fermentation increased the relative abundance of the genera Parabacteroides and Eubacterium. When combined with infant formula or with blackcurrants, fermenting black beans increased butyrate production and stimulated the relative abundance of Clostridium sensu stricto 1. These foods are promising candidates for future clinical trials.Item Effects of defatted rice bran-fortified bread on gut microbiome, cardiovascular risk, gut discomfort, wellbeing and gut physiology in healthy adults with low dietary fibre intake(Elsevier Ltd on behalf of the European Society for Clinical Nutrition and Metabolism, 2025-06) Ng HM; Maggo J; Wall CL; Bayer SB; Mullaney JA; Cabrera D; Fraser K; Cooney JM; Günther CS; McNabb WC; Foster M; Frampton C; Gearry RB; Roy NCBackground & aims: Inadequate dietary fibre (DF) intake is associated with suboptimal gut function and increased risk of several human diseases. Bread is commonly consumed and is ideal to incorporate cereal bran to increase DF content. No human studies have investigated the effects of defatted rice bran (DRB) in bread, which has triple the DF of white bread, purported hypo-allergenicity and a unique nutrient profile, as a dietary intervention in healthy adults. This study aims to assess the relative abundances of a composite of key faecal microbial genera and species involved in DF fermentation and metabolism following the habitual intake of DRB-fortified bread and its influence on other biological markers of host and microbial interactions, cardiovascular risk profile, patient-reported outcomes, total DF intake, and gut physiology in healthy adults with low baseline DF intake. Methods: Fifty-six healthy adults with low baseline DF intake (<18 g/day (females), <22 g/day (males)) completed a two-arm, placebo-controlled, double-blind, randomised, crossover study. Participants consumed three (females) or four (males) slices of DRB-fortified bread or control bread daily as part of their usual diet for four weeks, with the intervention periods separated by a two-week washout. Outcomes included faecal microbiota composite (primary outcome); relative abundances (taxa and gene); faecal moisture content and bile acid concentrations; plasma and faecal organic acid concentrations; cardiovascular risk profile; gut comfort, psychological wellbeing parameters; total DF intake; whole gut transit time, and were measured at baseline and following each intervention phase. Additionally, in a sub-study, 15 participants ingested gas-sensing capsules to assess whole and regional gut transit times, and total and regional colonic hydrogen and carbon dioxide concentrations at the same timepoints. Results: DRB-fortified bread consumption significantly increased total DF intake from 20.7 g/day to 43.4 g/day (p < 0.001). No significant differences were observed in the primary outcome, microbial taxa composite within and between groups (False Discovery Rate (FDR) correction, p > 0.10). As compared to control, the DRB group had increased relative abundances of Faecalibacterium prausnitzii (unadjusted p = 0.04), Bifidobacterium longum (unadjusted p = 0.12), and Bacteroides ovatus (unadjusted p = 0.10); lower relative abundances in Coprococcus genus (unadjusted p = 0.09), Roseburia faecis (unadjusted p = 0.02) and Prevotella copri species (unadjusted p = 0.05). However, no significant differences were observed in the relative abundances of these taxa within and between groups (FDR correction p > 0.10) and for most of the other outcomes between groups (p > 0.05). Only mean serum high-density lipoprotein (HDL) concentrations significantly increased (p = 0.006), and mean total cholesterol (TC) to HDL concentration ratio significantly lowered (p = 0.02) in the DRB group compared to the control group. Conclusion: This is the first human study to show that a high-DF DRB-fortified bread improved DF intake, HDL cholesterol profiles, and may affect the gut microbiota composition in healthy adults with low DF intake. These findings support the substitution of white bread with DRB-fortified bread as an effective method to improve DF intake, which may have subsequent benefits on gut physiology and metabolic health.Item Study Protocol for a Randomized Controlled Trial Investigating the Effects of the Daily Consumption of Ruminant Milk on Digestive Comfort and Nutrition in Older Women: The YUMMI Study.(MDPI (Basel, Switzerland), 2024-12-06) Ong SP; Miller JC; McNabb WC; Gearry RB; Ware LM; Mullaney JA; Fraser K; Hort J; Bayer SB; Frampton CMA; Roy NC; Miranda JMBACKGROUND: Age-related changes can lead to dietary insufficiency in older adults. The inclusion of high-quality, nutrient-dense foods such as ruminant milks can significantly improve health outcomes. However, many older adults worldwide do not meet daily milk intake recommendations because of digestive discomfort and health concerns. Ovine and caprine milks are increasingly popular for their perceived digestive and nutritional benefits. While preclinical studies suggest differences in milk digestion, human studies investigating acute postprandial responses remain inconclusive, and the impacts of sustained milk consumption remain uncertain. OBJECTIVES: Hence, we present a randomized controlled trial investigating how the sustained consumption of bovine, caprine, or ovine milk influences digestion, nutrition, and metabolism in older women. METHODS: A total of 165 healthy older women were randomized to receive bovine, caprine, or ovine milk, or no milk, twice daily for 12 weeks. The primary outcome is the impact of milk consumption on digestive comfort assessed via the Gastrointestinal Syndrome Rating Scale (GSRS). Secondary outcomes include changes in nutrient intake, plasma amino acid and lipid appearance, bowel habits, the gut microbiota, cardiometabolic health, physical function, physical activity, sleep, mood, sensory perception, and emotional response. CONCLUSIONS: The findings could inform dietary recommendations for older women and facilitate the development of targeted functional food products.Item The effect of complementary foods on the colonic microbiota of weaning infants: a systematic review.(Taylor & Francis Group, LLC, 2024-12-16) Geniselli da Silva V; Tonkie JN; Roy NC; Smith NW; Wall C; Kruger MC; Mullaney JA; McNabb WCThe transition from breastmilk to solid foods (weaning) is a decisive stage for the development of the colonic microbiota. However, little is known about how complementary foods influence the composition and function of the colonic microbiota in infants. This systematic review collected evidence of the effect of individual foods on the fecal microbiota of weaning infants (4-12 months old) using five databases: PubMed, CENTRAL, Scopus, Web of Science, and ScienceDirect. A total of 3625 records were examined, and seven randomized clinical trials met the review's eligibility criteria. Altogether, 983 participants were enrolled, and plant-based foods, meats, and dairy products were used as interventions. Wholegrain cereal increased the fecal abundance of the order Bacteroidales in the two included studies. Pureed beef increased the fecal abundances of the genus Bacteroides and the Clostridium XIVa group, as well as microbial richness in two of the three included studies. However, the conclusions of this review are limited by the small number of studies included. No conclusions could be drawn about the impact of complementary foods on fecal metabolites. Further clinical trials assessing the effect of dietary interventions on both fecal microbial composition and function are needed to fill this knowledge gap in infant nutrition.Item Heat-Treatments Affect Protease Activities and Peptide Profiles of Ruminants' Milk(Frontiers Media S.A., 2021-03-10) Leite JAS; Montoya CA; Loveday SM; Maes E; Mullaney JA; McNabb WC; Roy NC; Abd El-Aty, AMProteases present in milk are heat-sensitive, and their activities increase or decrease depending on the intensity of the thermal treatment applied. The thermal effects on the protease activity are well-known for bovine milk but poorly understood for ovine and caprine milk. This study aimed to determine the non-specific and specific protease activities in casein and whey fractions isolated from raw bovine, ovine, and caprine milk collected in early lactation, and to determine the effects of low-temperature, long-time (63°C for 30 min) and high-temperature, short-time (85°C for 5 min) treatments on protease activities within each milk fraction. The non-specific protease activities in raw and heat-treated milk samples were determined using the substrate azocasein. Plasmin (the main protease in milk) and plasminogen-derived activities were determined using the chromogenic substrate S-2251 (D-Val-Leu-Lys-pNA dihydrochloride). Peptides were characterized using high-resolution liquid chromatography coupled with tandem mass spectrometry. The activity of all native proteases, shown as non-specific proteases, was similar between raw bovine and caprine milk samples, but lower (P < 0.05) than raw ovine milk in the whey fraction. There was no difference (P > 0.05) between the non-specific protease activity of the casein fraction of raw bovine and caprine milk samples; both had higher activity than ovine milk. After 63°C/30 min, the non-specific protease activity decreased (44%; P > 0.05) for the bovine casein fraction only. In contrast, the protease activity of the milk heated at 85°C/5 min changed depending on the species and fraction. For instance, the activity decreased by 49% for ovine whey fraction, but it increased by 68% for ovine casein fraction. Plasmin and plasminogen were in general inactivated (P > 0.05) when all milk fractions were heated at 85°C/5 min. Most of the peptides present in heat-treated milk were derived from β-casein and αS1-casein, and they matched the hydrolysis profile of cathepsin D and plasmin. Identified peptides in ruminant milk samples had purported immunomodulatory and inhibitory functions. These findings indicate that the non-specific protease activity in whey and casein fractions differed between ruminant milk species, and specific thermal treatments could be used to retain better protease activity for all ruminant milk species.Item The impact of heating and drying on protease activities of ruminant milk before and after in vitro infant digestion(Elsevier Ltd, 2023-12-15) Leite JAS; Montoya CA; Loveday SM; Mullaney JA; Loo TS; McNabb WC; Roy NCThis study investigated the effect of heating (63°C/30 min or 75°C/15 s) and drying (spray-drying or freeze-drying) on plasmin, cathepsin D, and elastase activities in bovine, ovine, and caprine milk, compared to non-dried raw milk counterparts. Protease activities and protein hydrolysis were assessed before and after in vitro infant digestion with or without gastric and pancreatic enzymes. At 75°C/15 s, plasmin activity in caprine and ovine milk decreased (69-75%, p<0.05), while cathepsin D activity in spray-dried bovine milk heated increased (2.8-fold, p<0.05). Plasmin and cathepsin D activities increased (<1.2-fold, p<0.05) after in vitro digestion with pancreatin, regardless of milk species. Endogenous milk enzymes hydrolyzed more proteins than gastric enzymes during gastric digestion and contributed to small intestinal digestion. In summary, milk proteases remained active after processing with effects dependent on the species of milk, and they contributed to in vitro protein hydrolysis in the stomach and small intestine.Item Culture media and format alter cellular composition and barrier integrity of porcine colonoid-derived monolayers(Taylor and Francis Group, 2024-04-02) Barnett AM; Mullaney JA; McNabb WC; Roy NCIntestinal organoid technology has revolutionized our approach to in vitro cell culture due in part to their three-dimensional structures being more like the native tissue from which they were derived with respect to cellular composition and architecture. For this reason, organoids are becoming the new gold standard for undertaking intestinal epithelial cell research. Unfortunately, their otherwise advantageous three-dimensional geometry prevents easy access to the apical epithelium, which is a major limitation when studying interactions between dietary or microbial components and host tissues. To overcome this problem, we developed porcine colonoid-derived monolayers cultured on both permeable Transwell inserts and tissue culture treated polystyrene plates. We found that seeding density and culture format altered the expression of genes encoding markers of specific cell types (stem cells, colonocytes, goblets, and enteroendocrine cells), and barrier maturation (tight junctions). Additionally, we found that changes to the formulation of the culture medium altered the cellular composition of colonoids and of monolayers derived from them, resulting in cultures with an increasingly differentiated phenotype that was similar to that of their tissue of origin.Item Gut-Brain Axis in the Early Postnatal Years of Life: A Developmental Perspective(Frontiers Media S.A., 2020-08-05) Jena A; Montoya CA; Mullaney JA; Dilger RN; Young W; McNabb WC; Roy NC; Cammarota MEmerging evidence suggests that alterations in the development of the gastrointestinal (GI) tract during the early postnatal period can influence brain development and vice-versa. It is increasingly recognized that communication between the GI tract and brain is mainly driven by neural, endocrine, immune, and metabolic mediators, collectively called the gut-brain axis (GBA). Changes in the GBA mediators occur in response to the developmental changes in the body during this period. This review provides an overview of major developmental events in the GI tract and brain in the early postnatal period and their parallel developmental trajectories under physiological conditions. Current knowledge of GBA mediators in context to brain function and behavioral outcomes and their synthesis and metabolism (site, timing, etc.) is discussed. This review also presents hypotheses on the role of the GBA mediators in response to the parallel development of the GI tract and brain in infants.Item Adaptation of the infant gut microbiome during the complementary feeding transition(PLOS, 2022-07-14) McKeen S; Roy NC; Mullaney JA; Eriksen H; Lovell A; Kussman M; Young W; Fraser K; Wall CR; McNabb WC; xia YThe infant gut microbiome progresses in composition and function during the introduction of solid foods throughout the first year of life. The purpose of this study was to characterize changes in healthy infant gut microbiome composition, metagenomic functional capacity, and associated metabolites over the course of the complementary feeding period. Fecal samples were obtained at three 'snapshot' timepoints from infants participating in the 'Nourish to Flourish' pilot study: before the introduction of solid foods at approximately 4 months of age, after introducing solid foods at 9 months of age, and after continued diet diversification at 12 months of age. KEGG and taxonomy assignments were correlated with LC-MS metabolomic profiles to identify patterns of co-abundance. The composition of the microbiome diversified during the first year of life, while the functional capacity present in the gut microbiome remained stable. The introduction of solid foods between 4 and 9 months of age corresponded to a larger magnitude of change in relative abundance of sequences assigned to KEGG pathways and taxonomic assignments, as well as to stronger correlations with metabolites, compared to the magnitude of changes and number of correlations seen during continued diet diversification between 9 and 12 months of age. Changes in aqueous fecal metabolites were more strongly correlated with KEGG pathway assignments, while changes in lipid metabolites associated with taxonomic assignments, particularly between 9 and 12 months of age. This study establishes trends in microbiome composition and functional capacity occurring during the complementary feeding period and identifies potential metabolite targets for future investigations.