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 Gut Microbial Metabolites and Biochemical Pathways Involved in Irritable Bowel Syndrome: Effects of Diet and Nutrition on the Microbiome(Elsevier Inc on behalf of the American Society for Nutrition, 2020-05) James SC; Fraser K; Young W; McNabb WC; Roy NCThe food we consume and its interactions with the host and their gut microbiota affect normal gut function and health. Functional gut disorders (FGDs), including irritable bowel syndrome (IBS), can result from negative effects of these interactions, leading to a reduced quality of life. Certain foods exacerbate or reduce the severity and prevalence of FGD symptoms. IBS can be used as a model of perturbation from normal gut function with which to study the impact of foods and diets on the severity and symptoms of FGDs and understand how critical processes and biochemical mechanisms contribute to this impact. Analyzing the complex interactions between food, host, and microbial metabolites gives insights into the pathways and processes occurring in the gut which contribute to FGDs. The following review is a critical discussion of the literature regarding metabolic pathways and dietary interventions relevant to FGDs. Many metabolites, for example bile acids, SCFAs, vitamins, amino acids, and neurotransmitters, can be altered by dietary intake, and could be valuable for identifying perturbations in metabolic pathways that distinguish a "normal, healthy" gut from a "dysfunctional, unhealthy" gut. Dietary interventions for reducing symptoms of FGDs are becoming more prevalent, but studies investigating the underlying mechanisms linked to host, microbiome, and metabolite interactions are less common. Therefore, we aim to evaluate the recent literature to assist with further progression of research in this field.Item Effects of Defatted Rice Bran-Fortified Bread on the Gut Microbiota Composition of Healthy Adults With Low Dietary Fiber Intake: Protocol for a Crossover Randomized Controlled Trial(JMIR Publications, 2024-08-29) Ng HM; Maggo J; Wall CL; Bayer SB; McNabb WC; Mullaney JA; Foster M; Cabrera DL; Fraser K; Cooney J; Trower T; Günther CS; Frampton C; Gearry RB; Roy NCBACKGROUND: Inadequate dietary fiber (DF) intake is associated with several human diseases. Bread is commonly consumed, and its DF content can be increased by incorporating defatted rice bran (DRB). OBJECTIVE: This first human study on DRB-fortified bread primarily aims to assess the effect of DRB-fortified bread on the relative abundance of a composite of key microbial genera and species in fecal samples. Secondary outcomes include clinical (cardiovascular risk profile), patient-reported (daily bread consumption and bowel movement, gut comfort, general well-being, and total DF intake), biological (fecal microbiota gene abundances, and fecal and plasma metabolites), and physiome (whole-gut and regional transit time and gas fermentation profiles) outcomes in healthy adults with low DF intake. METHODS: This is a 2-armed, placebo-controlled, double-blinded, crossover randomized controlled trial. The study duration is 14 weeks: 2 weeks of lead-in, 4 weeks of intervention per phase, 2 weeks of washout, and 2 weeks of follow-up. Overall, 60 healthy adults with low DF intake (<18 g [female individuals] or <22 g [male individuals] per day) were recruited in Christchurch, New Zealand, between June and December 2022. Randomly assigned participants consumed 3 (female individuals) or 4 (male individuals) slices of DRB-fortified bread per day and then placebo bread, and vice versa. The DRB-fortified bread provided 8 g (female individuals) or 10.6 g (male individuals) of total DF, whereas the placebo (a matched commercial white toast bread) provided 2.7 g (female individuals) or 3.6 g (male individuals) of total DF. Before and after each intervention phase, participants provided fecal and blood samples to assess biological responses; completed a 3-day food diary to assess usual intakes and web-based questionnaires to assess gut comfort, general and mental well-being, daily bread intake, and bowel movement via an app; underwent anthropometry and blood pressure measurements; and drank blue food dye to assess whole-gut transit time. Additionally, 25% (15/60) of the participants ingested Atmo gas-sensing capsules to assess colonic gas fermentation profile and whole-gut and regional transit time. Mean differences from baseline will be compared between the DRB and placebo groups, as well as within groups (after the intervention vs baseline). For metabolome analyses, comparisons will be made within and between groups using postintervention values. RESULTS: Preliminary analysis included 56 participants (n=33, 59% female; n=23, 41% male). Due to the large dataset, data analysis was planned to be fully completed by the last quarter of 2024, with full results expected to be published in peer-reviewed journals by the end of 2024. CONCLUSIONS: This first human study offers insights into the prospect of consuming DRB-fortified bread to effectively modulate health-promoting gut microbes, their metabolism, and DF intake in healthy adults with low DF intake. TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry ACTRN12622000884707; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=383814. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/59227.Item Nourishing the Infant Gut Microbiome to Support Immune Health: Protocol of SUN (Seeding Through Feeding) Randomized Controlled Trial.(JMIR Publications, 2024-09-02) Wall CR; Roy NC; Mullaney JA; McNabb WC; Gasser O; Fraser K; Altermann E; Young W; Cooney J; Lawrence R; Jiang Y; Galland BC; Fu X; Tonkie JN; Mahawar N; Lovell AL; Ma SBackground: The introduction of complementary foods during the first year of life influences the diversity of the gut microbiome. How this diversity affects immune development and health is unclear. Objective: This study evaluates the effect of consuming kūmara or kūmara with added banana powder (resistant starch) compared to a reference control at 4 months post randomization on the prevalence of respiratory tract infections and the development of the gut microbiome. Methods: This study is a double-blind, randomized controlled trial of mothers and their 6-month-old infants (up to n=300) who have not yet started solids. Infants are randomized into one of 3 groups: control arm (C), standard kūmara intervention (K), and a kūmara intervention with added banana powder product (K+) to be consumed daily for 4 months until the infant is approximately 10 months old. Infants are matched for sex using stratified randomization. Data are collected at baseline (prior to commencing solid food) and at 2 and 4 months after commencing solid food (at around 8 and 10 months of age). Data and samples collected at each timepoint include weight and length, intervention adherence (months 2 and 4), illness and medication history, dietary intake (months 2 and 4), sleep (diary and actigraphy), maternal dietary intake, breast milk, feces (baseline and 4 months), and blood samples (baseline and 4 months). Results: The trial was approved by the Health and Disability Ethics Committee of the Ministry of Health, New Zealand (reference 20/NTA/9). Recruitment and data collection did not commence until January 2022 due to the COVID-19 pandemic. Data collection and analyses are expected to conclude in January 2024 and early 2025, respectively. Results are to be published in 2024 and 2025. Conclusions: The results of this study will help us understand how the introduction of a specific prebiotic complementary food affects the microbiota and relative abundances of the microbial species, the modulation of immune development, and infant health. It will contribute to the expanding body of research that aims to deepen our understanding of the connections between nutrition, gut microbiota, and early-life postnatal health. Trial Registration: Australian New Zealand Clinical Trials Registry ACTRN12620000026921; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=378654 International Registered Report Identifier (IRRID): DERR1-10.2196/56772 JMIR Res Protoc 2024;13:e56772Item Impact of Gut Recolonization on Liver Regeneration: Hepatic Matrisome Gene Expression after Partial Hepatectomy in Mice.(MDPI (Basel, Switzerland), 2023-06-28) Amin AR; Hairulhisyam NM; Aqilah RNF; Nur Fariha MM; Mallard BL; Shanahan F; Wheatley AM; Marlini M; Neuman M; Malnick SThe hepatic matrisome is involved in the remodeling phase of liver regeneration. As the gut microbiota has been implicated in liver regeneration, we investigated its role in liver regeneration focusing on gene expression of the hepatic matrisome after partial hepatectomy (PHx) in germ-free (GF) mice, and in GF mice reconstituted with normal gut microbiota (XGF). Liver mass restoration, hepatocyte proliferation, and immune response were assessed following 70% PHx. Hepatic matrisome and collagen gene expression were also analyzed. Reduced liver weight/body weight ratio, mitotic count, and hepatocyte proliferative index at 72 h post PHx in GF mice were preceded by reduced expression of cytokine receptor genes Tnfrsf1a and Il6ra, and Hgf gene at 3 h post PHx. In XGF mice, these indices were significantly higher than in GF mice, and similar to that of control mice, indicating normal liver regeneration. Differentially expressed genes (DEGs) of the matrisome were lower in GF compared to XGF mice at both 3 h and 72 h post PHx. GF mice also demonstrated lower collagen expression, with significantly lower expression of Col1a1, Col1a2, Col5a1, and Col6a2 compared to WT mice at 72 h post PHx. In conclusion, enhanced liver regeneration and matrisome expression in XGF mice suggests that interaction of the gut microbiota and matrisome may play a significant role in the regulation of hepatic remodeling during the regenerative process.Item Gut microbiome signature and nasal lavage inflammatory markers in young people with asthma(Elsevier Inc on behalf of the American Academy of Allergy, Asthma & Immunology (AAAAI), 2024-05) Sampaio Dotto Fiuza B; Machado de Andrade C; Meirelles PM; Santos da Silva J; de Jesus Silva M; Vila Nova Santana C; Pimentel Pinheiro G; Mpairwe H; Cooper P; Brooks C; Pembrey L; Taylor S; Douwes J; Cruz ÁA; Barreto ML; Pearce N; Figueiredo CAVBACKGROUND: Asthma is a complex disease and a severe global public health problem resulting from interactions between genetic background and environmental exposures. It has been suggested that gut microbiota may be related to asthma development; however, such relationships needs further investigation. OBJECTIVE: This study aimed to characterize the gut microbiota as well as the nasal lavage cytokine profile of asthmatic and nonasthmatic individuals. METHODS: Stool and nasal lavage samples were collected from 29 children and adolescents with type 2 asthma and 28 children without asthma in Brazil. Amplicon sequencing of the stool bacterial V4 region of the 16S rRNA gene was performed using Illumina MiSeq. Microbiota analysis was performed by QIIME 2 and PICRUSt2. Type 2 asthma phenotype was characterized by high sputum eosinophil counts and positive skin prick tests for house dust mite, cockroach, and/or cat or dog dander. The nasal immune marker profile was assessed using a customized multiplex panel. RESULTS: Stool microbiota differed significantly between asthmatic and nonasthmatic participants (P = .001). Bacteroides was more abundant in participants with asthma (P < .05), while Prevotella was more abundant in nonasthmatic individuals (P < .05). In people with asthma, the relative abundance of Bacteroides correlated with IL-4 concentration in nasal lavage samples. Inference of microbiota functional capacity identified differential fatty acid biosynthesis in asthmatic compared to nonasthmatic subjects. CONCLUSION: The stool microbiota differed between asthmatic and nonasthmatic young people in Brazil. Asthma was associated with higher Bacteroides levels, which correlated with nasal IL-4 concentration.Item The Microbiome-Gut-Brain Axis and Resilience to Developing Anxiety or Depression under Stress(MDPI (Basel, Switzerland), 2021-03-31) Bear T; Dalziel J; Coad J; Roy N; Butts C; Gopal P; Adeli KEpisodes of depression and anxiety commonly follow the experience of stress, however not everyone who experiences stress develops a mood disorder. Individuals who are able to experience stress without a negative emotional effect are considered stress resilient. Stress-resilience (and its counterpart stress-susceptibility) are influenced by several psychological and biological factors, including the microbiome-gut-brain axis. Emerging research shows that the gut microbiota can influence mood, and that stress is an important variable in this relationship. Stress alters the gut microbiota and plausibly this could contribute to stress-related changes in mood. Most of the reported research has been conducted using animal models and demonstrates a relationship between gut microbiome and mood. The translational evidence from human clinical studies however is rather limited. In this review we examine the microbiome-gut-brain axis research in relation to stress resilience.Item Modulation of Bone and Joint Biomarkers, Gut Microbiota, and Inflammation Status by Synbiotic Supplementation and Weight-Bearing Exercise: Human Study Protocol for a Randomized Controlled Trial(JMIR Publications, 2021-10-26) Ilesanmi-Oyelere BL; Roy NC; Kruger MC; Eysenbach GBACKGROUND: There is strong evidence suggesting that prebiotics and probiotics regulate gut microbiota, reducing inflammation and thereby potentially improving bone health status. Similarly, mechanistic evidence suggests that either low-impact or high-impact weight-bearing exercises improve body composition and consequently increase bone mineral density in individuals with osteoporosis and osteoarthritis. OBJECTIVE: This study aims to investigate the effects of a synbiotic (probiotic+prebiotic) supplementation, an exercise intervention, or a combination of both on gut microbiota, inflammation, and bone biomarkers in postmenopausal women. METHODS: A total of 160 postmenopausal women from New Zealand will be recruited and randomized to one of four interventions or treatments for 12 weeks: control, synbiotic supplementation, exercise intervention, or synbiotic supplementation and exercise. The primary outcome measure is the bone and joint biomarkers at baseline and week 12, whereas the gut microbiota profile and inflammatory cytokine measurements will serve as the secondary outcome measures at baseline and week 12. Baseline data and exercise history will be used to assess, allocate, and stratify participants into treatment measures. RESULTS: Recruitment of participants will begin in September 2021, and the anticipated completion date is June 2022. CONCLUSIONS: To the best of our knowledge, this will be the first randomized controlled trial to analyze the effects of both a synbiotic supplement and an exercise intervention in postmenopausal women. On the basis of the results obtained, a combination of synbiotic supplements and exercise might serve as a noninvasive approach to manage and/or improve body composition and bone health in postmenopausal women. TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry ACTRN12620000998943p; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=380336&isClinicalTrial=False.