The human large intestinal microbiota thrives on dietary carbohydrates that are converted to a range of fermentation products. Short-chain fatty acids (acetate, propionate and butyrate) are the dominant fermentation acids that accumulate to high concentrations in the colon and they have health-promoting effects on the host. Although many gut microbes can also produce lactate, it usually does not accumulate in the healthy gut lumen. This appears largely to be due to the presence of a relatively small number of gut microbes that can utilise lactate and convert it to propionate, butyrate or acetate. There is increasing evidence that these microbes play important roles in maintaining a healthy gut environment. In this review, we will provide an overview of the different microbes involved in lactate metabolism within the gut microbiota, including biochemical pathways utilised and their underlying energetics, as well as regulation of the corresponding genes. We will further discuss the potential consequences of perturbation of the microbiota leading to lactate accumulation in the gut and associated disease states and how lactate-utilising bacteria may be employed to treat such diseases.

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.

Dietary fibre is an umbrella term comprising various types of carbohydrate polymers that cannot be digested nor absorbed by the human small intestine. Consumption of dietary fibre is linked to beneficial effects on cognitive and affective processes, although not all fibres produce the same effects. Fibres that increase short-chain fatty acid (SCFA) production following modulation of the gut microbiota are thought to be the most potent fibres to induce effects on cognitive and affective processes. SCFAs can exert their effects by improving central, peripheral and systemic immunity, lowering hypertension and enhancing intestinal barrier integrity. Here, we propose additional mechanisms by which dietary fibres may contribute to improvements in affective and cognitive processes. Fibre-induced modulation of the gut microbiota may influence affective processes and cognition by increasing brain-derived neurotrophic factor levels. Depending on the physicochemical properties of dietary fibre, additional effects on affect and cognition may occur via non-microbiota-related routes, such as enhancement of the immune system and lowering cholesterol levels and subsequently lowering blood pressure. Mechanistic randomised placebo-controlled trials are needed to establish the effects of dietary fibre consumption and the magnitude of explained variance in affect and cognition when incorporating measurements of microbiota-dependent and microbiota-independent mechanisms in humans.

Metabolites produced by microbial fermentation in the human intestine, especially short-chain fatty acids (SCFAs), are known to play important roles in colonic and systemic health. Our aim here was to advance our understanding of how and why their concentrations and proportions vary between individuals. We have analysed faecal concentrations of microbial fermentation acids from 10 human volunteer studies, involving 163 subjects, conducted at the Rowett Institute, Aberdeen, UK over a 7-year period. In baseline samples, the % butyrate was significantly higher, whilst % iso-butyrate and % iso-valerate were significantly lower, with increasing total SCFA concentration. The decreasing proportions of iso-butyrate and iso-valerate, derived from amino acid fermentation, suggest that fibre intake was mainly responsible for increased SCFA concentrations. We propose that the increase in % butyrate among faecal SCFA is largely driven by a decrease in colonic pH resulting from higher SCFA concentrations. Consistent with this, both total SCFA and % butyrate increased significantly with decreasing pH across five studies for which faecal pH measurements were available. Colonic pH influences butyrate production through altering the stoichiometry of butyrate formation by butyrate-producing species, resulting in increased acetate uptake and butyrate formation, and facilitating increased relative abundance of butyrate-producing species (notably Roseburia and Eubacterium rectale).

This study aimed to investigate the relationships between diet quality, the relative abundance of butyrate-producing bacteria of the gut microbiome and muscle mass, strength and function. In this cross-sectional study, n = 490 men (64.4 ± 13.5 years) from the Geelong Osteoporosis Study provided food frequency questionnaire data, from which the Australian Recommended Food Score (ARFS) and Dietary Inflammatory Index (DII) score were calculated. Muscle mass (skeletal muscle index from DXA-derived lean mass), muscle strength (handgrip strength) and muscle function (Timed Up-and-Go test) were measured. Participants provided stool samples for 16S rRNA gene sequencing. There was no evidence of associations between alpha or beta diversity and muscle health measures. A healthier ARFS score was positively associated with the relative abundance of butyrate-producing bacteria (β 0.09, 95%CI 0.03, 0.15) and a higher (pro-inflammatory) DII score was associated with lower relative abundance of butyrate-producing bacteria (β −0.60, 95%CI −1.06, −0.15). The relative abundance of butyrate-producing bacteria was positively associated with healthier muscle mass, strength and function; however, these relationships were attenuated in multivariable models. These findings support the role of diet quality in achieving a healthier gut microbiome, however, further evidence is required for a gut-muscle axis in humans.

The oral delivery of compounds associated with diet or medication have an impact on the gut microbiota balance, which in turn, influences the physiologic process. Several reports have shown significant advances in clarifying the impact, interactions and outcomes of oral intake of nanoparticles and the human gut. These interactions may affect the bioavailability of the delivered compounds. In addition, there is a considerable breakthrough in the development of antimicrobial nanoparticles for intestinal pathogenic bacteria. Several in vitro fermentation and in vivo models have been developed throughout the years and were used to test these systems. The methodologies and studies carried out so far on the modulation of human and animal gut microbiome by oral delivery nanosized materials were reviewed. Overall, the available in vitro studies mimic the real physiological events enabling to select the best production conditions of nanoparticulate systems in a preliminary stage of research. On the other hand, animal studies can be used to access the dosage effect, safety and correlation between haematological, biochemical and symptoms, with gut microbiota groups and metabolites.

We investigated the impact of dried chicory root in a randomised, placebo-controlled trial with 55 subjects at risk for type 2 diabetes on bowel function, gut microbiota and its products, and glucose homeostasis. The treatment increased stool softness (+1.1 ± 0.3 units; p = 0.034) and frequency (+0.6 ± 0.2 defecations/day; p < 0.001), strongly modulated gut microbiota composition (7 % variation; p = 0.001), and dramatically increased relative levels (3-4-fold) of Anaerostipes and Bifidobacterium spp., in a dose-dependent, reversible manner. A synthetic community, including selected members of these genera and a Bacteroides strain, generated a butyrogenic trophic chain from the product. Faecal acetate, propionate and butyrate increased by 25.8 % (+13.0 ± 6.3 mmol/kg; p = 0.023) as did their fasting circulating levels by 15.7 % (+7.7 ± 3.9 μM; p = 0.057). In the treatment group the glycaemic coefficient of variation decreased from 21.3 ± 0.94 to 18.3 ± 0.84 % (p = 0.004), whereas fasting glucose and HOMA-ir decreased in subjects with low baseline Blautia levels (−0.3 ± 0.1 mmol/L fasting glucose; p = 0.0187; −0.14 ± 0.1 HOMA-ir; p = 0.045). Dried chicory root intake rapidly and reversibly affects bowel function, benefits butyrogenic trophic chains, and promotes glycaemic control.

Dietary patterns influence gut microbiota composition. To date, there has not been an assessment of diet and gut microbiota in Veterans, who have a history of unique environmental exposures, including military deployment, that may influence associations between diet and gut microbiota. Our aim was to characterise Veteran habitual dietary intake and quality, and to evaluate correlations between diet and gut microbiota. We administered Food Frequency Questionnaires (FFQs) and collected stool samples from 330 Veterans. FFQ data were used to generate Healthy Eating Indices (HEI) of dietary quality. Exploratory factor analysis was used to identify two dietary patterns we defined as “Western” and “Prudent.” Stool samples underwent 16S rRNA gene sequencing, and the resulting data were used to evaluate associations with dietary variables/indices. Analyses included linear regression of α-diversity, constrained analysis of principal coordinates of β-diversity, and multivariate association with linear models and Analysis of Composition of Microbiomes analyses of dietary factors and phylum- and genus-level taxa. There were no significant associations between dietary patterns or factors and α- or β-diversity. At the phylum level, increasing HEI scores were inversely associated with relative abundance of Actinobacteria, and added sugar was inversely associated with abundance of Verrucomicrobia. Veterans largely consumed a Western-style diet, characterised by poor adherence to nutritional guidelines.

Despite extensive research into the toxicology of the herbicide glyphosate, there are still major unknowns regarding its effects on the human gut microbiome. We describe the effects of glyphosate and a Roundup glyphosate-based herbicide on infant gut microbiota using SHIME technology. SHIME microbiota culture was undertaken in the presence of a concentration of 100-mg/L glyphosate and the same glyphosate equivalent concentration of Roundup. Roundup and to a lesser extent glyphosate caused an increase in fermentation activity, resulting in acidification of the microbial environment. This was also reflected by an increase in lactate and acetate production concomitant to a decrease in the levels of propionate, valerate, caproate and butyrate. Ammonium production reflecting proteolytic activities was increased by Roundup exposure. Global metabolomics revealed large-scale disturbances, including an increased abundance of long-chain polyunsaturated fatty acids. Changes in bacterial composition measured by qPCR and 16S rRNA suggested that lactobacilli had their growth stimulated as a result of microenvironment acidification. Co-treatment with the spore-based probiotic formulation MegaSporeBiotic reverted some of the changes in short-chain fatty acid levels. Altogether, our results suggest that glyphosate can exert effects on human gut microbiota.

Human milk oligosaccharides (HMOs) are a class of structurally diverse and complex unconjugated glycans present in breast milk, which act as selective substrates for several genera of select microbes and inhibit the colonisation of pathogenic bacteria. Yet, not all infants are breastfed, instead being fed with formula milks which may or may not contain HMOs. Currently, formula milks only possess two HMOs: 2′-fucosyllactose (2’FL) and lacto-N-neotetraose (LNnT), which have been suggested to be similarly effective as human breast milk in supporting age-related growth. However, the in vivo evidence regarding their ability to beneficially reduce respiratory infections along with altering the composition of an infant’s microbiota is limited at best. Thus, this review will explore the concept of HMOs and their metabolic fate, and summarise previous in vitro and in vivo clinical data regarding HMOs, with specific regard to 2’FL and LNnT.

The human microbiome is one of the most exciting areas of microbiology. From a starting point of tens of papers annually a couple of decades ago, there are now thousands of papers published every year on the microbiome. Huge strides have been made in terms of defining the individual members of complex human microbiomes from different body sites. The individuality and diversity of the human microbiome almost surpasses our ability to comprehend it. Advances in metagenomics and computational sciences have increased the complexity of the field, while at the same time we have moved from regarding the human microbiome as a benign passenger to a situation where it has been linked to almost every chronic disease, including obesity, cancer and infectious disease. The microbiome tantalizes us with the promise of novel therapeutic molecules and modalities for a range of intractable diseases. And yet, very few microbiome-based therapies have made it to the clinic or the pharmacy and we still cannot really define a healthy microbiome. We are entering the most exciting phase of microbiome research, as we develop effective, evidence-based interventions to preserve and restore human health. But we need rigour and numeracy if we are to realize this vision.

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 identification of functional processes taking place in microbiome communities augment traditional microbiome taxonomic studies, giving a more complete picture of interactions taking place within the community. While there are applications that perform functional annotation on metagenomes or metatranscriptomes, very few of these are able to link taxonomic identity to function or are limited by their input types or databases used. Here we present MetaFunc, a workflow which takes RNA sequences as input reads, and from these (1) identifies species present in the microbiome sample and (2) provides gene ontology annotations associated with the species identified. In addition, MetaFunc allows for host gene analysis, mapping the reads to a host genome, and separating these reads, prior to microbiome analyses. Differential abundance analysis for microbe taxonomies, and differential gene expression analysis and gene set enrichment analysis may then be carried out through the pipeline. A final correlation analysis between microbial species and host genes can also be performed. Finally, MetaFunc builds an R shiny application that allows users to view and interact with the microbiome results. In this paper, we showed how MetaFunc can be applied to metatranscriptomic datasets of colorectal cancer.

Knowledge of the intra-individual spatial and regional distribution of intestinal microbial populations is essential to understand gut host–microbial interactions. In this study, we performed a compositional analysis of luminal and mucosal samples from the small and large intestine of four organ donors by 16S rRNA amplicon sequencing and high-throughput quantitative polymerase chain reaction. Since the human microbiota is subject to selection pressure at lower taxonomic levels, we isolated over 400 bacterial strains and investigated strain-level variation of 11 Lactobacillus rhamnosus from different intestinal regions. Results substantiate reported inter-individual variability as well as intra-individual differences along the gastrointestinal tract. Although the luminal and mucosal-associated communities were similar within individuals, relative abundance reflected the donors’ demographic and potential pathologies. The total bacterial load of all donors increased from small intestine to colon, while Bifidobacterium was in greater abundance in the small intestine. Comparative genomic analysis of L. rhamnosus showed the strains segregated into two distinct clusters and identified no features specific to location. Analysis revealed genetic differences for exopolysaccharide production, carbohydrate utilization, pilus formation and vitamin K biosynthesis between clusters. This study contributes to the understanding of niche-specific microbial communities, encouraging subsequent studies to better understand microbial signatures at lower taxonomic levels.

The 10th International Yakult Symposium was held in Milan, Italy, on 13–14 October 2022. Two keynote lectures covered the crewed journey to space and its implications for the human microbiome, and how current regulatory systems can be adapted and updated to ensure the safety of microorganisms used as probiotics or food processing ingredients. The remaining lectures were split into sections entitled “Chances” and “Challenges.” The “Chances” section explored opportunities for the science of probiotics and fermented foods to contribute to diverse areas of health such as irritable bowel syndrome, major depression, Parkinson’s disease, immune dysfunction, infant colic, intensive care, respiratory infections, and promoting healthy longevity. The “Challenges” section included selecting appropriate clinical trial participants and methodologies to minimise heterogeneity in responses, how to view probiotics in the context of One Health, adapting regulatory frameworks, and understanding how substances of bacterial origin can cross the blood–brain barrier. The symposium provided evidence from cutting-edge research that gut eubiosis is vital for human health and, like space, the microbiota deserves further exploration of its vast potential.

Consumption of high-energy-yielding diets, rich in fructose and lipids, is a factor contributing to the current increase in non-alcoholic fatty liver disease prevalence. Gut microbiota composition and short-chain fatty acids (SCFAs) production alterations derived from unhealthy diets are considered putative underlying mechanisms. This study aimed to determine relationships between changes in gut microbiota composition and SCFA levels by comparing rats featuring diet-induced steatohepatitis with control counterparts fed a standard diet. A high-fat high-fructose (HFHF) feeding induced higher body, liver and mesenteric adipose tissue weights, increased liver triglyceride content and serum transaminase, glucose, non-HDL-c and MCP-1 levels. Greater liver malondialdehyde levels and glutathione peroxidase activity were also observed after feeding the hypercaloric diet. Regarding gut microbiota composition, a lowered diversity and increased abundances of bacteria from the Clostridium sensu stricto 1, Blautia, Eubacterium coprostanoligenes group, Flavonifractor, and UBA1819 genera were found in rats featuring diet-induced steatohepatitis, as well as higher isobutyric, valeric and isovaleric acids concentrations. These results suggest that hepatic alterations produced by a hypercaloric HFHF diet may be related to changes in overall gut microbiota composition and abundance of specific bacteria. The shift in SCFA levels produced by this unbalanced diet cannot be discarded as potential mediators of the reported hepatic and metabolic alterations.

The ninth International Yakult Symposium was held in Ghent, Belgium in April 2018. Keynote lectures were from Professor Wijmenga on using biobanks to understand the relationship between the gut microbiota and health; and Professor Hill on phage–probiotic interactions. Session one included talks from Professor Plӧsch on epigenetic programming by nutritional and environmental factors; Professor Wilmes on the use of “omics” methodologies in microbiome research and Professor Rescigno on the gut vascular barrier. Session two explored the evidence behind Lactobacillus casei Shirota with Dr Nanno explaining the plasticity in immunomodulation that enables the strain to balance immune functions; Dr Macnaughtan outlining its potential therapeutic use in cirrhosis and Professor Nishida detailing effects in subjects under stress. The third session saw Professor Marchesi describing that both the host genes and the gut microbiota can play a role in cancer; Professor Bergheim highlighting crosstalk between the gut and the liver and Professor Cani describing the relationship between the gut microbiota and the endocrine system. The final session explored probiotic mechanisms, with Professor Lebeer dissecting the challenges in conducting mechanistic studies; Professor Wehkamp describing the mucosal defence system and Professor Van de Wiele detailing methods for modelling the gut microbiota in vitro.

Irritable bowel syndrome (IBS) is a disorder of gut–brain interaction with a complex pathophysiology. Growing evidence suggests that alterations of the gut microenvironment, including microbiota composition and function, may be involved in symptom generation. Therefore, attempts to modulate the gut microenvironment have provided promising results as an indirect approach for IBS management. Antibiotics, probiotics, prebiotics, food and faecal microbiota transplantation are the main strategies for alleviating IBS symptom severity by modulating gut microbiota composition and function (eg. metabolism), gut barrier integrity and immune activity, although with varying efficacy. In this narrative review, we aim to provide an overview of the current approaches targeting the gut microenvironment in order to indirectly manage IBS symptoms.

The gut microbiota is a dynamic ecosystem involved in multiple physiological processes that affect host health. Several factors affect intestinal microbial communities including dietary exposure to xenobiotics, which is highly concerning due to their widespread distribution. Current knowledge of this topic comes from culture-dependent methods, 16S rRNA amplicon fingerprinting, and metagenomics, but a standardised procedures framework remains lacking. This minireview integrates 45 studies from a systematic search using terms related to gut microbiota and its disruption. Only publications encompassing dietary-oral exposure and experimental gut microbiota assessments were included. The results were divided and described according to the biological model used and the disruption observed in the gut microbiota. An overall dysbiotic effect was unclear due to the variety of contaminants and hosts evaluated and the experimental gaps between publications. More standardised experimental designs, including WGS and physiological tests, are needed to establish how a particular xenobiotic can alter the gut microbiota and how the results can be extrapolated.