Intake of high quantities of dietary proteins sourced from dairy, meat or plants can affect body weight and metabolic health in humans. To improve our understanding of how this may be achieved, we reviewed the data related to the availability of nutrients and metabolites in the faeces, circulation and urine. All protein sources (≥20% by energy) increased faecal levels of branched chain fatty acids and ammonia, and decreased the levels of butyrate. There were metabolites responding to dairy and meat proteins (branch chain amino acids) as well as dairy and plant proteins (p-cresol), which were increased in faecal matter. Specific to dairy protein intake, the faecal levels of acetate, indole and phenol were increased, whereas plant protein intake specifically increased the levels of kynurenine and tyramine. Meat protein intake increased the faecal levels of methionine, cysteine and alanine, and decreased the levels of propionate and acetate. The metabolite profile in the faecal matter following dairy protein intake mirrored availability in circulation or urine. These findings provide an understanding of the contrasting gut versus systemic effects of different dietary proteins, which we know to show different physiological effects. In this regard, we provide directions to determining the mechanisms for the effects of different dietary proteins.

Metabolic dietary patterns, including the Empirical Dietary Index for Hyperinsulinaemia (EDIH) and Empirical Dietary Inflammatory Pattern (EDIP), are known to impact multiple chronic diseases, but the role of the colonic microbiome in mediating such relationships is poorly understood. Among 1,610 adults with faecal 16S rRNA data in the TwinsUK cohort, we identified the microbiome profiles for EDIH and EDIP (from food frequency questionnaires) cross-sectionally using elastic net regression. We assessed the association of the dietary pattern-related microbiome profile scores with circulating biomarkers in multivariable-adjusted linear regression. In addition, we used PICRUSt2 to predict biological pathways associated with the enriched microbiome profiles, and further screened pathways for associations with the dietary scores in linear regression analyses. Microbiome profile scores developed with 32 (EDIH) and 15 (EDIP) genera were associated with higher insulin and homeostatic model assessment of insulin resistance. Six genera were associated with both dietary scores: Ruminococcaceae_UCG-008, Lachnospiraceae_UCG-008, Defluviitaleaceae_UCG-011 Anaeroplasma, inversely and Negativibacillus, Streptococcus, positively. Further, pathways in fatty acid biosynthesis, sugar acid degradation, and mevalonate metabolism were associated with insulinaemic and inflammatory diets. Dietary patterns that exert metabolic effects on insulin and inflammation may influence chronic disease risk by modulating gut microbial composition and function.

This research communication aimed at assessing the microbial quality and preparation practices of dahi/thayir, a popular traditional fermented milk product, in households from two distinct agroecological zones in Kerala, India, namely the high-range and central midland, We highlighted the significant variations and potential food safety concerns associated with regional differences in production methods. The local climate significantly influenced the incubation temperature of dahi/thayir, thereby influencing the types of microflora involved in the fermentation process. Data on preparation practices and sensory preferences were collected from producers during the sampling process, covering 200 households. There were significant variations in preparation practices between the two regions, particularly concerning the type of container used, inoculation rate and incubation period. Samples from the high-range region exhibited significantly higher acidity and coliform count as well as yeast and mold count than the central midland region. The household fermentation of milk is often uncontrolled, causing increased acidity levels. This uncontrolled fermentation favored the growth of contaminants such as coliforms and yeast, posing a potential threat to food safety. This study underscores the importance of understanding microbial quality variations and preparation practices in dahi/thayir production, emphasizing the need for proper fermentation techniques and hygienic practices to ensure the safety and quality of this traditional fermented milk product.

We investigated cross-sectional and longitudinal associations between neonate microbial exposure and emerging behavioral temperament measures at the ages of 1, 2, and 3 years. Infants and mothers (n = 335) were extracted from the Kuopio Birth Cohort Study. Temperament was assessed using the Infant Behavioral and Early Childhood Behavioral Questionnaires. Microbial samples were collected from oral cavity at birth and the bacterial profiles were assessed using 16S rRNA gene sequencing. Microbial diversity was characterized using alpha and beta diversity metrics. Analyses were performed for the most abundant genera. The sample was analyzed as a whole, as well as divided into subgroups representing no antibiotic use during birth (n = 198) and those with antibiotic use during birth (n = 137). No significant associations were observed between microbial profiles and behavioral measures after Bonferroni corrections. Nevertheless, our pre-correction results indicated an association between increased behavioral temperament surgency in the first year and beta diversity (high abundance of Bacteroides, Faecalibacterium and Blautia, low abundance of Lactobacillus) in the antibiotic use group. Additionally, pre-corrections, a high relative abundance of Staphylococcus was associated with increased surgency through years 1, 2, and 3 in the no antibiotics group, prompting consideration into a possible link between antibiotic use and emerging behavioral temperament.

Uncontrolled hypertension is a primary cause of non-communicable diseases and death globally(1). The gut microbiota plays a role in hypertension and dietary interventions high in fibre have been shown to lower blood pressure (BP)(2). Not all participants respond to dietary fibre interventions, for reasons which are unclear. Here we aimed to identify responders of a high fibre intervention based on their baseline gut microbiome. Twenty treatment-naive participants with hypertension received either placebo or 40g per day of prebiotic acetylated and butyrylated high amylose maize starch (HAMSAB) supplementation for 3 weeks in a phase II randomised cross-over double-blind placebo-controlled trial. Blood pressure was monitored at baseline and each endpoint by 24-hour ambulatory BP monitoring, with those experiencing a reduction between timepoints of ≥ 2 mmHg classified as responders. Baseline stool samples were collected and the V4-V5 region of the 16S gene sequenced. Taxonomy was assigned by reference to the SILVA database. The MaAsLin2 package was used for assessing the relationship between baseline gut microbiota and response to dietary intervention. Overall participants had significant reduction in 24-hour systolic BP (–6.1 mmHg, p = 0.03), with 14 individuals classified as responders and six individuals as non-responders. 13 genera were found to be differentially abundant between responders and non-responders. Genera significantly enriched in responders included Dialister (β = 1.29, q = 1.921x10-134), Coprococcus (β = 1.26, q = 3.282x10-121), Bifidobacterium (β = 1.67, q = 1.11x10-81), Ruminococcus (β = 0.161, q = 1.11x10-8) and Roseburia (β = 0.82, q = 4.275x10-2). Participants who experienced a decrease in systolic BP following a dietary fibre intervention had increased level of bacterial genera known to contain species that produce short-chain fatty acids (e.g. Bifidobacterium, Roseburia and Ruminococcus) at baseline. These data suggest that baseline microbiota composition contributes to the response to dietary fibre intervention trials in people with hypertension.

The sophisticated relationship between the intake of dietary carbohydrates and host immunity is mediated in large part by the gut microbiota. This comprehensive review explores the multifaceted connections linking human gut microbiota with nondigestible carbohydrate metabolism and immune responses, highlighting the critical importance of this symbiotic relationship in maintaining overall host health. Understanding the mechanisms by which gut microbiota act as a bridge between carbohydrate intake and host immunity has significant implications for precision nutrition strategies and the development of therapeutic interventions.

Camelina cake (CAM) is a co-product proposed as an alternative protein source; however, piglet data are still limited. This study aimed to evaluate the effect of different doses of CAM in substitution of soyabean meal on the growth, health and gut health of weaned pigs. At 14 d post-weaning (d0), sixty-four piglets were assigned either to a standard diet or to a diet with 4 %, 8 % or 12 % of CAM. Piglets were weighed weekly. At d7 and d28, faeces were collected for microbiota and polyamine and blood for reactive oxygen metabolites (ROM) and thyroxine analysis. At d28, pigs were slaughtered, organs were weighed, pH was recorded on gut, colon was analysed for volatile fatty acids (VFA) and jejunum was used for morphological and gene expression analysis. Data analysis was carried out using a mixed model including diet, pen and litter as factors; linear and quadratic contrasts were tested. CAM linearly reduced the average daily gain from d0–d7, d0–d14, d0–d21 and d0–d28 (P ≤ 0·01). From d0–d7 increasing CAM linearly decreased feed intake (P = 0·04) and increased linearly the feed to gain (P = 0·004). CAM increased linearly the liver weight (P < 0·0001) and affected the cadaverine (P < 0·001). The diet did not affect the ROM, thyroxine, intestinal pH, VFA and morphology. All doses of CAM increased the α diversity indices at d28 (P < 0·05). CAM at 4 % promoted the abundance of Butyricicoccaceae_UCG-008. Feeding with CAM enhanced resilience in the gut microbiome and can be evaluated as a potential alternative protein source with dose-dependent limitations on piglet growth performance.

Iron is essential for many physiological functions of the body, and it is required for normal growth and development. Iron deficiency (ID) is the most common form of micronutrient malnutrition and is particularly prevalent in infants and young children in developing countries. Iron supplementation is considered the most effective strategy to combat the risk of ID and ID anaemia (IDA) in infants, although iron supplements cause a range of deleterious gut-related problems in malnourished children. The purpose of this review is to assess the available evidence on the effect of iron supplementation on the gut microbiota during childhood ID and to further assess whether prebiotics offer any benefits for iron supplementation. Prebiotics are well known to improve gut-microbial health in children, and recent reports indicate that prebiotics can mitigate the adverse gut-related effects of iron supplementation in children with ID and IDA. Thus, provision of prebiotics alongside iron supplements has the potential for an enhanced strategy for combatting ID and IDA among children in the developing world. However, further understanding is required before the benefit of such combined treatments of ID in nutritionally deprived children across populations can be fully confirmed. Such enhanced understanding is of high relevance in resource-poor countries where ID, poor sanitation and hygiene, alongside inadequate access to good drinking water and poor health systems, are serious public health concerns.

Early supplementation with oregano essential oil (EO) in milk replacer (MR) may improve growth, immune responses, the microbiota and the metabolome in dairy calves during pre-weaning and in adulthood. Sixteen female dairy calves (3 days of age) were divided in two groups (n = 8/group): the control group (no EO) and the EO group (0.23 ml of EO in MR during 45 days). After weaning, calves were kept in a feedlot and fed ad libitum. The animals were weighed, and blood and faecal samples were collected on days 3 (T0), 45 (T1) and 370 (T2) to measure the biochemical profile and characterise peripheral blood mononuclear cells (PBMCs; CD4+, CD8+, CD14+, CD21+ and WC1+), the metabolome and microbiota composition. The EO group only had greater average daily weight gain during the suckling (EO supplementation) period (P = 0.030). The EO group showed higher average CD14+ population (monocytes) values, a lower abundance of Ruminococcaceae UCG-014, Faecalibacterium, Blautia and Alloprevotella and increased abundances of Allistipes and Akkermansia. The modification of some metabolites in plasma, such as butyric acid, 3-indole-propionic acid and succinic acid, particularly at T1, are consistent with intestinal microbiota changes. The data suggest that early EO supplementation increases feed efficiency only during the suckling period with notable changes in the microbiota and plasma metabolome; however, not all of these changes can be considered desirable from a gut health point of view. Additional research studies is required to demonstrate that EOs are a viable natural alternative to antibiotics for improving calf growth performance and health.

Gut microbiome changed dramatically during pregnancy and played important roles in metabolic status and reproductive endocrinology in mammals. However, investigating the functional microbiota and metabolites to improve the reproductive performance and understanding the host–microbiota interaction are still arduous tasks. This study aims to reveal the dominant strains and metabolites that improve the reproductive performance. We analyzed the fecal microbiota composition and metabolic status of higher yield Chinese pig breed Meishan (MS) sows and lower yield but widespread raised hybrid pig breed Landrace × Yorkshire (L × Y) sows on days 28 and 100 of gestation. Results showed that MS sows had higher litter sizes and steroid hormone level but lower short-chain fatty acid level in feces. Fecal metabolomic analysis revealed that MS sows showed a different metabolic status compared with L × Y sows both at early and late pregnancy, which enriched with phenylpropanoid biosynthesis, bile secretion, steroid hormone biosynthesis, and plant secondary metabolite biosynthesis. In addition, 16S rDNA and internal transcribed spacer sequencing indicated that MS sows showed different structures of microbiota community and exhibited an increased bacterial α-diversity but non-differential fungal α-diversity than L × Y sows. Moreover, we found that the litter sizes and bacteria including Sphaerochaeta, Solibacillus, Oscillospira, Escherichia–Shigella, Prevotellaceae_UCG-001, dgA-11_gut_group, and Bacteroides, as well as fungi including Penicillium, Fusarium, Microascus, Elutherascus, and Heydenia both have positive association to the significant metabolites at the early pregnancy. Our findings revealed significant correlation between reproductive performance and gut microbiome and provided microbial and metabolic perspective to improve litter sizes and steroid hormones of sows.

The rise of sequencing technologies has greatly contributed to our knowledge of the microbiota and its role in animal health and production. However, many members of the microbiota have historically been considered “unculturable.” Culturomics can be utilized to bring these fastidious microbes into cultivation and can be used in conjunction with culture-independent methods to study the microbiota in a more comprehensive manner. This review paper details culturomics’ role in revolutionizing human, swine, and bovine microbiota research and how its use has greatly increased the bacterial repertoire. Additionally, it describes how culturomics can be applied to develop microbiota-derived therapeutics, such as next-generation probiotics, and to study the role of the microbiota. Finally, this review provides potential methods and considerations for designing future culturomics studies.

Diversion of the faecal stream is associated with diversion colitis (DC). Preliminary studies indicate that microbiome dysbiosis contributes to its development and potentially treatment. This review aims to characterise these changes in the context of faecal diversion and identify their clinical impact. A systematic search was conducted using MEDLINE, EMBASE and CENTRAL databases using a predefined search strategy identifying studies investigating changes in microbiome following diversion. Findings reported according to PRISMA guidelines. Of 743 results, 6 met inclusion criteria. Five reported significantly decreased microbiome diversity in the diverted colon. At phylum level, decreases in Bacillota with a concomitant increase in Pseudomonadota were observed, consistent with dysbiosis. At genus level, studies reported decreases in beneficial lactic acid bacteria which produce short-chain fatty acid (SCFA), which inversely correlated with disease severity. Significant losses in commensals were also noted. These changes were seen to be partially reversible with restoration of bowel continuity. Changes within the microbiome were reflected by histopathological findings suggestive of intestinal dysfunction. Faecal diversion is associated with dysbiosis in the diverted colon which may have clinical implications. This is reflected in loss of microbiome diversity, increases in potentially pathogenic-associated phyla and reduction in SCFA-producing and commensal bacteria.

Age-related macular degeneration (AMD) is one of the most prevalent eye diseases among the ageing population worldwide. It is a leading cause of blindness in individuals over 55, particularly in industrialised Western countries. The prevalence of AMD increases with age, and genetic factors and environmental influences are believed to contribute to its development. Among the environmental factors, diet plays a significant role in AMD. This review explores the association between dietary components, dietary patterns and AMD. Various nutrients, non-nutrient substances and dietary models that have the potential to counteract oxidative stress and inflammation, which are underlying mechanisms of AMD, are discussed. Consuming fruits, vegetables, fish and seafood, whole grains, olive oil, nuts and low-glycaemic-index foods has been highlighted as beneficial for reducing the risk of AMD. Adhering to the Mediterranean diet, which encompasses these elements, can be recommended as a dietary pattern for AMD. Furthermore, the modulation of the gut microbiota through dietary interventions and probiotics has shown promise in managing AMD.

This review will provide an overview of the immune system and then describe the effects of frailty, obesity, specific micronutrients and the gut microbiota on immunity and susceptibility to infection including data from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic where relevant. A key role for the immune system is providing host defence against pathogens. Impaired immunity predisposes to infections and to more severe infections and weakens the response to vaccination. A range of nutrients, including many micronutrients, play important roles in supporting the immune system to function. The immune system can decline in later life and this is exaggerated by frailty. The immune system is also weakened with obesity, generalised undernutrition and micronutrient deficiencies, which all result in increased susceptibility to infection. Findings obtained during the SARS-CoV-2 pandemic support what was already known about the effects of ageing, frailty and obesity on immunity and susceptibility to infection. Observational studies conducted during the pandemic also support previous findings that multiple micronutrients including vitamins C, D and E, zinc and selenium and long-chain n-3 fatty acids are important for immune health, but whether these nutrients can be used to treat those already with coronavirus disease discovered in 2019 (COVID-19), particularly if already hospitalised, is uncertain from current inconsistent or scant evidence. There is gut dysbiosis in patients with COVID-19 and studies with probiotics report clinical improvements in such patients. There is an inverse association between adherence to a healthy diet and risk of SARS-CoV-2 infection and hospitalisation with COVID-19 which is consistent with the effects of individual nutrients and other dietary components. Addressing frailty, obesity and micronutrient insufficiency will be important to reduce the burden of future pandemics and nutritional considerations need to be a central part of the approach to preventing infections, optimising vaccine responses and promoting recovery from infection.

The evolution of the understanding of the intestinal microbiota and its influence on our organism leverages it as a potential protagonist in therapies aimed at diseases that affect not only the intestine but also neural pathways and the central nervous system itself. This study, developed from a thorough systematic review, sought to demonstrate the influence of the intervention on the intestinal microbiota in subjects with Alzheimer’s disease. Clinical trials using different classes of probiotics have depicted noteworthy remission of symptoms, whose measurement was performed based on screenings and scores applied before, during, and after the period of probiotics use, allowing the observation of changes in functionality and symptomatology of patients. On the other hand, faecal microbiota transplantation requires further validation through clinical trials, even though it has already been reported in case studies as promising from the symptomatology point of view. The current compilation of studies made it possible to demonstrate the potential influence of the intestinal microbiota on Alzheimer’s pathology. However, new clinical studies with a larger number of participants are needed to obtain further clarification on pathophysiological correlations.

Dietary fiber (DF) is receiving increasing attention, and its importance in pig nutrition is now acknowledged. Although DF for pigs was frowned upon for a long time because of reductions in energy intake and digestibility of other nutrients, it has become clear that feeding DF to pigs can affect their well-being and health. This review aims to summarize the state of knowledge of studies on DF in pigs, with an emphasis on the underlying mode of action, by considering research using DF in sows as well as suckling and weaned piglets, and fattening pigs. These studies indicate that DF can benefit the digestive tracts and the health of pigs, if certain conditions or restrictions are considered, such as concentration in the feed and fermentability. Besides the chemical composition and the impact on energy and nutrient digestibility, it is also necessary to evaluate the possible physical and physiologic effects on intestinal function and intestinal microbiota, to better understand the relation of DF to animal health and welfare. Future research should be designed to provide a better mechanistic understanding of the physiologic effects of DF in pigs.

Functional constipation is a significant health issue impacting the lives of an estimated 14 % of the global population. Non-pharmaceutical treatment advice for cases with no underlying medical conditions focuses on exercise, hydration and an increase in dietary fibre intake. An alteration in the composition of the gut microbiota is thought to play a role in constipation. Prebiotics are non-digestible food ingredients that selectively stimulate the growth of a limited number of bacteria in the colon with a benefit for host health. Various types of dietary fibre, though not all, can act as a prebiotic. Short-chain fatty acids produced by these microbes play a critical role as signalling molecules in a range of metabolic and physiological processes including laxation, although details are unclear. Prebiotics have a history of safe use in the food industry spanning several decades and are increasingly used as supplements to alleviate constipation. Most scientific research on the effects of prebiotics and gut microbiota has focussed on inflammatory bowel disease rather than functional constipation. Very few clinical studies evaluated the efficacy of prebiotics in the management of constipation and their effect on the microbiota, with highly variable designs and conflicting results. Despite this, broad health claims are made by manufacturers of prebiotic supplements. This narrative review provides an overview of the literature on the interaction of prebiotics with the gut microbiota and their potential clinical role in the alleviation of functional constipation.