The gut microbiome is widely recognized for its significant contribution to maintaining human health across all life stages, from infancy to adulthood and beyond. This perspective article focuses on the impacts of well-supported microbiome research on global caesarean delivery rates, breastfeeding practices, and antimicrobial use. The article also explores the impact of dietary choices, particularly those involving ultra-processed foods, on the gut microbiota and their potential contribution to conditions like obesity, metabolic syndrome, and inflammatory diseases. This perspective aims to emphasize the need for updated guidelines and policy interventions to address the increasing global trends of caesarean deliveries, reduced breastfeeding, overuse of antibiotics, and consumption of highly processed foods to counter their adverse effects on gut health.

The latest Yakult Science Study Day was held virtually on 2 November 2023. Aimed at healthcare professionals, researchers, and students, a variety of experts explored the latest gut microbiome research and what it means in practice. The morning sessions discussed the role of the microbiome in health and disease, the rapid advancements in DNA sequencing and implications for personalised nutrition, the current state of evidence on health benefits associated with fermented foods, prebiotics and probiotics and the challenges involved in interpreting research in this area. The afternoon session considered the emerging research on the microbiota–gut–brain axis in mediating effects of food on mood, the bidirectional impact of menopause on the gut microbiota, and the interplay between the gut and skin with implications for the treatment of rare and common skin disorders. The session ended with an update on the use of faecal microbiota transplant in both research and clinical practice. Undoubtedly, the gut microbiome is emerging as a key conductor of human health, both in relation to gastrointestinal and non-gastrointestinal outcomes. As research continues to elucidate mechanisms of action and confirm their effects in human trials, the gut microbiome should be a key consideration within a holistic approach to health moving forward.

The role of oncobiosis, characterized by dysregulated microbial ecosystems associated with cancer, has been increasingly acknowledged in promoting the metastasis and dissemination of tumour cells. A comprehensive understanding of the complex interactions between the gut microbiome and metastatic colorectal cancer (mCRC) presents promising avenues for the development of innovative therapeutic approaches centred around modulating the gut microbiome to prevent or hinder metastatic spread. In this comprehensive review, we aim to provide a molecularly focused summary of the implications of the human gut microbiome and microbial metabolites in the initiation and advancement of mCRC. By elucidating these intricate mechanisms, we strive to establish a foundation for future research and the design of novel interventions targeting the gut microbiome to combat this devastating disease.

Eggs are highly digestible, nutrient-rich and are a valuable source of protein and choline, thereby promoting a range of health benefits. Several studies have found an association between protein intake and gastrointestinal microbial diversity(1), while bacterial fermentation of undigested protein in the large bowel can produce short-chain fatty acids, such as butyrate, positively influencing host metabolic health, gut integrity and immune function(2). On the other hand, dietary choline stimulates gastrointestinal bacterial production of trimethylamine and the prothrombotic compound trimethylamine-N-oxide (TMAO)(3). Despite these established links, limited studies have explored the effects of whole egg intake on indices of gastrointestinal health. This systematic literature review aimed to synthesise research that has investigated the impact of egg-supplemented diets or egg consumption on markers of gastrointestinal health including microbiome, function and symptoms. This review was conducted in accordance with PRISMA guidelines. Five databases (Ovid Medline, Embase, CINAHL Plus, SCOPUS, and PsychInfo), and reference lists of relevant papers, were searched from inception until April 2023. Studies were included if they examined the link between whole chicken egg consumption and gastrointestinal health in healthy adults (aged>16). Indices of gastrointestinal health were defined as any outcomes related to gastrointestinal factors, including symptoms, microbiome, inflammation, colonic fermentation and TMAO. Reviews and case studies were excluded. All studies underwent risk of bias assessment. Overall, 548 studies were identified and 19 studies were included after screening. Eight of these were randomised controlled trials (RCTs), 8 cross-sectional and 3 prospective cohort studies. Participants ranged in number between 20-32,166 and in age between 18–84 years. Study periods varied between 3–14 weeks for RCTs and 6 months–12.5 years for prospective cohort studies. RCTs examined intakes between 1–4 eggs/day, with the majority examining 3 eggs/day (n = 6). The primary outcome across 15 articles was TMAO levels, with most reporting no significant associations (n = 13). Five studies examined inflammation with inconsistent findings ranging from no alterations (in TNF-α, IL-8, CRP), increases (in anti-inflammatory marker LTB5, TNF-α), and decreases (in IL-6, CRP). Lastly, 7 studies explored alterations in microbiome. Two RCTs and 2 cross-sectional trials reported no alterations in microbial diversity in response to eggs. Meanwhile, 2 cross-sectional and 1 prospective study linked specific bacteria to consistent egg intake. Eggs were associated with species that produce butyrate (E.rectale, F.prausnitzii, M.smithii, and R.bromii), and protect against metabolic syndrome (A.muciniphila). This systematic review found that egg consumption did not increase levels of the undesirable biomarker TMAO and were associated with butyrate-producing bacteria. Evidence regarding the effect of egg intake on inflammation was inconsistent. This review revealed the general lack of available research investigating whole eggs and gastrointestinal health. Future carefully designed RCTs are required to improve understanding of how eggs may influence the gastrointestinal microbiome and colonic fermentation.

A growing body of research has identified interactions between microorganisms and nutrients within the gut, collectively referred to as the ‘gut microbiome’(1). Alongside this, distinct structural characteristics/components of dietary fibre have been recognised to exhibit various physiological effects on the body(1). These inherent physiological properties have the potential to result in diverse health benefits through the consumption of resistant starch, a specific form of dietary fibre(2). It is important to note that the laboratory-based techniques employed to assess resistant starch content from current Australian dietary composition data are antiquated and have not been conducted using updated testing methods(3). Results from updated testing methods may contribute to and inform nutritional recommendations to support and improve health outcomes. To assess the resistant starch content of starch-containing Australian foods using the updated Association of Analytical Chemists (AOAC) 2002.02 testing methods approved by Food Standards Australia New Zealand(3). Standardised kits (K-RSTAR) and control flours were used for assaying. Forty commonly consumed and available Australian foods were tested in duplicate for their resistant starch content. Calculated resistant starch values (in grams) were recorded using calculation tools provided by Megazyme. Means, standard deviations, and coefficient of variations between duplicate samples were recorded in a Microsoft Excel spreadsheet. The resistant starch content of foods varied from 0-13.72g/100g for rice crackers, beetroot, and hi-maize pancakes, respectively. Foods with the highest resistant starch were hi-maize flour pancakes, red kidney beans, Lebanese bread, and Cornflakes cereal, which ranged from 2.30-13.72g/100g. The lowest resistant starch foods included beetroot, rice crackers, All Bran cereal, and Nutri-grain cereal, ranging from 0-0.04g/100g. Changes in the foods’ natural chemical, physical, and enzymatic qualities may have led to slight batch variations and deviations from the literature available. This study is the first known Australian study to investigate the resistant starch content of selected Australian foods using the AOAC 2002.02 assay method. This data can be used to assess resistant starch consumption in the Australian population, inform gut microbiome research, and guide clinical practice recommendations for fibre intake.

A majority of Australians consume a limited range of different dietary fibres and insufficient total dietary fibre(1). This contributes to low intestinal microbial diversity and impaired microbial function, such as capability in producing beneficial metabolites like short-chain fatty acids (SCFA). This diet-induced dysbiosis is associated with poor gastrointestinal health and a broad range of non-communicable diseases(2). Our study aimed to determine whether one dietary change, substitution of white bread with a high fibre bread improves faecal microbial diversity and butyrate-producing capability. Twenty-six healthy adults completed a randomised, cross-over, single-blinded intervention. Over the two intervention phases separated with a 4-wk washout, participants consumed either 3 slices of a high fibre bread (Prebiotic Cape Seed Loaf with BARLEYmax®) or control white bread as part of the usual diet, each for 2 weeks. At the beginning and end of each intervention period, participants completed a 24-h diet recall, a gut symptoms rating questionnaire and provided a faecal sample for microbiome analysis. The composition of faecal microbiome was characterised using 16S rRNA amplicon sequencing (V3-V4) and a marker of butyrate synthesis capability, the faecal content of butyryl-CoA:acetate CoA-transferase (BCoAT) gene was assessed using Real-time PCR. The high fibre bread intervention increased the servings of whole grain from 1.5 to 4 per day and increased total dietary fibre intake to 40 g/d which was double the amount of fibre consumed by participants at baseline or during the white bread intervention. Compared to white bread, the high fibre bread increased richness and evenness (Shannon, p = 0.014) of the gut microbiota and increased the relative abundance of SCFA producing taxa Lachnospiracae ND3007 group (p <0.001, FDR = 0.019). In addition, the high-fibre bread tended to increase relative abundance of butyrate-producing genus Roseburia, and microbial BCoAT gene content compared to white bread. In conclusion, the substitution of white bread with high-fibre bread improved the diversity of gut microbiota, specific microbes involved in SCFA production and may enhance the butyrate production capability of gut microbiota in healthy adults.

Prebiotic fibre represents a promising and efficacious treatment to manage pre-diabetes, acting via complementary pathways involving the gut microbiome and viscosity-related properties. In this study, we evaluated the effect of using a diverse prebiotic fibre supplement on glycaemic, lipid and inflammatory biomarkers in patients with pre-diabetes. Sixty-six patients diagnosed with pre-diabetes (yet not receiving glucose-lowering medications) were randomised into treatment (thirty-three) and placebo (thirty-three) interventions. Participants in the treatment arm consumed 20 g/d of a diverse prebiotic fibre supplement, and participants in the placebo arm consumed 2 g/d of cellulose for 24 weeks. A total of fifty-one and forty-eight participants completed the week 16 and week 24 visits, respectively. The intervention was well tolerated, with a high average adherence rate across groups. Our results extend upon previous work, showing a significant change in glycated haemoglobin (HbA1c) in the treatment group but only in participants with lower baseline HbA1c levels (< 6 % HbA1c) (P = 0·05; treatment –0·17 ± 0·27 v. placebo 0·07 ± 0·29, mean ± sd). Within the whole cohort, we showed significant improvements in insulin sensitivity (P = 0·03; treatment 1·62 ± 5·79 v. placebo –0·77 ± 2·11) and C-reactive protein (PFWE = 0·03; treatment –2·02 ± 6·42 v. placebo 0·94 ± 2·28) in the treatment group compared with the placebo. Together, our results support the use of a diverse prebiotic fibre supplement for physiologically relevant biomarkers in pre-diabetes.

The gut microbiome is a key element for health preservation and disease prevention. Nevertheless, defining a healthy gut microbiome is complex since it is modulated by several factors, such as host genetics, sex, age, geographical zone, drug use, and, especially, diet. Although a healthy diet has proven to increase microbial alpha and beta diversity and to promote the proliferation of health-related bacteria, considering the current environmental and nutritional crisis, such as climate change, water shortage, loss of diversity, and the obesity pandemic, it should be highlighted that a healthy diet is not always sustainable. Sustainable diets are dietary patterns that promote all dimensions of people’s health and well-being while exerting low pressure on the environment, and being accessible, affordable, safe, equitable, and culturally acceptable. Examples of diets that tend to be sustainable are the Planetary Health Diet of the EAT-Lancet Commission or territorial diets such as the Mediterranean and the Traditional Mexican diet (milpa diet), adapted to specific contexts. These diets are principally plant-based but include small or moderate amounts of animal-based foods. Characterising the effects of sustainable diets on gut microbiota is urgent to ensure that the benefits for human health are aligned with environmental preservation and respect the sociocultural aspects of individuals.

Consumption of probiotics and/or yogurt could be a solution for restoring the balance of the gut microbiota. This study examined associations of regular intake of probiotic supplements or yogurt with the gut microbiota among a diverse population of older adults (N=1,861; 60–72 years). Faecal microbial composition was obtained from 16S rRNA gene sequencing (V1–V3 region). General linear models were used to estimate the associations of probiotic supplement or yogurt intake with microbiome measures adjusting for covariates. Compared to non-yogurt consumers (N=1,023), regular yogurt consumers (≥once/week, N=818) had greater Streptococcus (β=0.29, P=0.0003) and lower Odoribacter (β=−0.33, P<0.0001) abundance. The directions of the above associations were consistent across the five ethnic groups but stronger among Japanese Americans (Streptococcus: β=0.56, P=0.0009; Odoribacter: β=−0.62, P=0.0005). Regular intake of probiotic supplements (N=175) was not associated with microbial characteristics (i.e., alpha diversity and the abundance of 152 bacteria genera). Streptococcus is one of the predominant bacteria genera in yogurt products, which may explain the positive association between yogurt consumption and Streptococcus abundance. Our analyses suggest that changes in Odoribacter were independent of changes in Streptococcus abundance. Future studies may investigate whether these microbial genera and their sub-level species mediate potential pathways between yogurt consumption and health.

The industrialisation of Western food systems has reduced the regular consumption of lacto-fermented vegetables (LFV). Consuming LFV may exert health benefits through the alteration of the gut microbiome, but the mechanisms involved remain unclear. To start understanding the possible benefits of LFV, we compared faecal microbial diversity and composition, as well as dietary habits between individuals who regularly consume LFV (n = 23) and those who do not (n = 24). We utilised microbial DNA amplicon sequencing (16S rRNA and ITS2) and untargeted metabolomics (LC–MS) to analyse stool samples. Study participants also provided three consecutive days of dietary data. Results show minor effects on microbiome composition; with the enrichment of a few microorganisms potentially associated with vegetable ferments, such as Leuconostoc mesenteroides and Rhodotorula mucilaginosa (P < 0.05), in LFV consumers. However, LFV consumption had greater effects on the faecal metabolome, with higher abundances of butyrate, acetate, and valerate (P < 0.05) and significantly greater metabolome diversity (P < 0.001). Overall, the observations of minor changes in the faecal microbiome and greater effects on the faecal metabolome from LFV consumption warrant further investigations on the health significance of LFV as regular components of the daily diet in humans.

The gut microbiota plays crucial roles in maintaining the health and homeostasis of its host throughout lifespan, including through its ability to impact brain function and regulate behaviour during ageing. Studies have shown that there are disparate rates of biologic ageing despite equivalencies in chronologic age, including in the development of neurodegenerative diseases, which suggests that environmental factors may play an important role in determining health outcomes in ageing. Recent evidence demonstrates that the gut microbiota may be a potential novel target to ameliorate symptoms of brain ageing and promote healthy cognition. This review highlights the current knowledge around the relationships between the gut microbiota and host brain ageing, including potential contributions to age-related neurodegenerative diseases. Furthermore, we assess key areas for which gut microbiota-based strategies may present as opportunities for intervention.

Acute appendicitis is a common acute surgical emergency; however, the pathogenesis of adult appendicitis remains poorly understood. The microbiome is increasingly thought to play a key role in inflammatory disease of the bowel and similarly, may play a role in appendicitis. This study aimed to characterise the microbiome of adult acute appendicitis in a prospective cohort. We recruited 60 adults with acute appendicitis and 20 healthy controls. Rectal swabs were taken from each patient. After DNA extraction, 16S rRNA amplicon sequencing was carried out for analysis of diversity and taxonomic abundance. Phylogenetic sequencing of the samples indicated that there is a difference between the microbial composition of those with acute appendicitis and healthy controls, with a statistically significant decrease in alpha diversity in rectal swabs of appendicitis patients compared to healthy controls. At the genus level, we saw an increased abundance of potential pathogens, for example, Parvimonas and Acinetobacter, and a decrease in commensal taxa such as Faecalibacterium, Blautia and Lachnospiraceae in appendicitis patients compared to healthy controls. There was a reduction in diversity and loss of commensals in the microbiome of those with acute appendicitis, which may play a role in the cascade leading to acute appendicitis or the result of this.

The aim of this review is to provide an overview of how person-specific interactions between diet and the gut microbiota could play a role in affecting diet-induced weight loss responses. The highly person-specific gut microbiota, which is shaped by our diet, secretes digestive enzymes and molecules that affect digestion in the colon. Therefore, weight loss responses could in part depend on personal colonic fermentation responses, which affect energy extraction of food and production of microbial metabolites, such as short-chain fatty acids (SCFAs), which exert various effects on host metabolism. Colonic fermentation is the net result of the complex interplay between availability of dietary substrates, the functional capacity of the gut microbiome and environmental (abiotic) factors in the gut such as pH and transit time. While animal studies have demonstrated that the gut microbiota can causally affect obesity, causal and mechanistic evidence from human studies is still largely lacking. However, recent human studies have proposed that the baseline gut microbiota composition may predict diet-induced weight loss-responses. In particular, individuals characterised by high relative abundance of Prevotella have been found to lose more weight on diets rich in dietary fibre compared to individuals with low Prevotella abundance. Although harnessing of personal diet–microbiota interactions holds promise for more personalised nutrition and obesity management strategies to improve human health, there is currently insufficient evidence to unequivocally link the gut microbiota and weight loss in human subjects. To move the field forward, a greater understanding of the mechanistic underpinnings of personal diet–microbiota interactions is needed.

As past usual diet quality may affect gut microbiome (GM) composition, we examined the association of the Healthy Eating Index (HEI)-2015 assessed 21 and 9 years before stool collection with measures of fecal microbial composition in a subset of the Multiethnic Cohort. A total of 5936 participants completed a validated quantitative FFQ (QFFQ) at cohort entry (Q1, 1993–1996), 5280 at follow-up (Q3, 2003–2008) and 1685 also at a second follow-up (Adiposity Phenotype Study (APS), 2013–2016). All participants provided a stool sample in 2013–2016. Fecal microbial composition was obtained from 16S rRNA gene sequencing (V1–V3 regions). HEI-2015 scores were computed based on each QFFQ. Using linear regression adjusted for relevant covariates, we calculated associations of HEI-2015 scores with gut microbial diversity and 152 individual genera. The mean HEI-2015 scores increased from Q1 (67 (sd 10)) to Q3 (71 (sd 11)) and APS (72 (sd 10)). Alpha diversity assessed by the Shannon Index was significantly higher with increasing tertiles of HEI-2015. Of the 152 bacterial genera tested, seven (Anaerostipes, Coprococcus_2, Eubacterium eligens, Lachnospira, Lachnospiraceae_ND3007, Ruminococcaceae_UCG-013 and Ruminococcus_1) were positively and five (Collinsella, Parabacteroides, Ruminiclostridium_5, Ruminococcus gnavus and Tyzzerella) were inversely associated with HEI-2015 assessed in Q1, Q3 and APS. The estimates of change per unit of the HEI-2015 score associated with the abundance of these twelve genera were consistent across the three questionnaires. The quality of past diet, assessed as far as ∼20 years before stool collection, is equally predictive of GM composition as concurrently assessed diet, indicative of the long-term consistency of this relation.

The recent COVID-19 pandemic has altered the face of biology, social interaction and public health worldwide. It has had a destructive effect upon millions of people and is approaching a devastating one million fatalities. Emerging evidence has suggested a link between the infection and gut microbiome status. This is one of the several factors that may contribute towards severity of infection. Given the fact that the gut is heavily linked to immunity, inflammatory status and the ability to challenge pathogens, it is worthwhile to consider dietary intervention of the gut microbiota as means of potentially challenging the viral outcome. In this context, probiotics and prebiotics have been used to mitigate similar respiratory infections. Here, we summarise links between the gut microbiome and COVID-19 infection, as well as propose mechanisms whereby probiotic and prebiotic interventions may act.

The pandemic of Coronavirus disease 2019 (COVID-19) is rapidly progressing, causing significant morbidity and mortality. Various antiviral drugs, anti-inflammatory drugs and immunomodulators have been tried without substantial clinical benefits. The severe and critical cases of COVID-19 disease are characterised by gut microbiome dysbiosis, immune dysregulation, hyper-inflammation and hypercytokinaemia (cytokine storm). Therefore, the strategies which target these pathophysiological processes may be beneficial. Probiotics are one such strategy that exerts beneficial effects by manipulation of the gut microbiota, suppression of opportunistic pathogens in the gut, decreasing translocation of opportunistic organisms, activation of mucosal immunity and modulation of the innate and adaptive immune response. Probiotics are the potential candidates to be tested in moderate and severe cases of COVID-19 due to several beneficial effects, including easy availability, easy to administer, safe and economical to use.

There is increasing evidence linking the gut microbiota to various aspects of human health. Nuts are a food rich in prebiotic fibre and polyphenols, food components which have been shown to have beneficial effects on the gut microbiota. This systematic review aimed to synthesise the evidence regarding the effect of nut consumption on the human gut microbiota. A systematic search of the databases MEDLINE, PubMed, Cochrane CENTRAL and CINAHL was performed until 28 November 2019. Eligible studies were those that investigated the effects of nut consumption in humans (aged over 3 years old), utilising next-generation sequencing technology. Primary outcome measures were between-group differences in α- and β-diversity metrics and gut microbial composition. A total of eight studies were included in the review. Included studies assessed the effects of either almonds, walnuts, hazelnuts or pistachios on the gut microbiota. Overall, nut consumption had a modest impact on gut microbiota diversity, with two studies reporting a significant shift in α-diversity and four reporting a significant shift in β-diversity. Walnuts, in particular, appeared to more frequently explain shifts in β-diversity, which may be a result of their unique nutritional composition. Some shifts in bacterial composition (including an increase in genera capable of producing SCFA: Clostridium, Roseburia, Lachnospira and Dialister) were reported following the consumption of nuts. Nut intake may yield a modulatory effect on the gut microbiota; however, results were inconsistent across studies, which may be explained by variations in trial design, methodological limitations and inter-individual microbiota.

Gastrointestinal helminth infection likely affects the gut microbiome, in turn affecting host health. To investigate the effect of intestinal parasite status on the gut microbiome, parasitic infection surveys were conducted in communities in Nan Province, Thailand. In total, 1047 participants submitted stool samples for intestinal parasite examination, and 391 parasite-positive cases were identified, equating to an infection prevalence of 37.3%. Intestinal protozoan species were less prevalent (4.6%) than helminth species. The most prevalent parasite was the minute intestinal fluke Haplorchis taichui (35.9%). Amplicon sequencing of 16S rRNA was conducted to investigate the gut microbiome profiles of H. taichui-infected participants compared with those of parasite-free participants. Prevotella copri was the dominant bacterial operational taxonomic unit (OTU) in the study population. The relative abundance of three bacterial taxa, Ruminococcus, Roseburia faecis and Veillonella parvula, was significantly increased in the H. taichui-infected group. Parasite-negative group had higher bacterial diversity (α diversity) than the H. taichui-positive group. In addition, a significant difference in bacterial community composition (β diversity) was found between the two groups. The results suggest that H. taichui infection impacts the gut microbiome profile by reducing bacterial diversity and altering bacterial community structure in the gastrointestinal tract.