Modulation of Gut Microbiota by Lactobacillus casei Fermented Raspberry Juice In Vitro and In Vivo

Synbiotic Sapota-do-Solimões (Quararibea cordata Vischer) Juice Improves Gut Microbiota and Short-Chain Fatty Acid Production in an In Vitro Model

Sapota-do-Solimões (Quararibea cordata Vischer) is Amazon South América fruit found in Brazil, Colombia, Ecuador, and Peru. The orange-yellow fruit is usually eaten out of hand or as juice. Despite being a source of carotenoids and dietary fibers (pectin) that can reach the colon and act as an energy source for intestinal microbiota, the fruit is rarely known outside of South America. The symbiotic juice was prepared by fermenting the fruit juice with Lacticaseibacillus casei B-442 and adding prebiotic fructooligosaccharides (FOS, 7% w/v). This study evaluated the functional juice immediately after L. casei fermentation (SSJ0) and after 30 days of cold storage (SSJ30) regarding its effect on human colonic microbiota composition after in vitro fermentation. Fecal samples were collected from two healthy female volunteers, and the 16s rRNA gene sequencing analyzed the fecal microbiota composition. In vitro, colonic fermentation was performed using a batch bioreactor to simulate gastrointestinal conditions. The L. casei viability did not change significantly after 30 days of the synbiotic juice cold storage (4 °C). After the colonic fermentation, the relative abundance of Firmicutes decreased while Proteobacteria and Actinobacteria increased. Regarding short-chain fatty acid (SCFA) production by fecal colonic microbiota, the butyric acid was higher after sample SSJ0 fecal fermentation. In contrast, propionic, isobutyric, and acetic acids were higher after SSJ30 sample fecal fermentation. This study contributes to understanding the interactions between specific foods and the gut microbiota, which can affect human health and well-being.

Correlation analysis of the impact of Clonorchis sinensis juvenile on gut microbiota and transcriptome in mice

Clonorchiasis remains a non-negligible global zoonosis, imposing serious socio-economic burdens in endemic regions. The interplay between gut microbiota and the host transcriptome is crucial for maintaining health; however, the impact of Clonorchiasis sinensis juvenile infection on these factors is still poorly understood. This study aimed to investigate their relationship and potential pathogenic mechanisms. The BALB/c mouse model of early infection with C. sinensis juvenile was constructed. Pathological analyses revealed that C. sinensis juvenile triggered liver inflammation, promoted intestinal villi growth, and augmented goblet cell numbers in the ileum. Additionally, the infection altered the diversity and structure of gut microbiota, particularly affecting beneficial bacteria that produce short-chain fatty acids, such as Lactobacillus and Muribaculaceae, and disrupted the Firmicutes/Bacteroidetes ratio. Gut transcriptome analysis demonstrated an increase in the number of differentially expressed genes (DEGs) as infection progressed. Enriched Gene Ontology items highlighted immune and detoxification-related processes, including immunoglobulin production and xenobiotic metabolic processes. Kyoto Encyclopedia of Genes and Genomes pathway analysis further indicated involvement in circadian rhythm, as well as various detoxification and metabolic-related pathways (e.g., glutathione metabolism and glycolysis/gluconeogenesis). Prominent DEGs associated with these pathways included Igkv12-41, Mcpt2, Arntl, Npas2, Cry1, and Gsta1. Correlation analysis additionally identified Bacteroides_sartorii as a potential key regulator in the interaction between gut microbiota and transcriptome. This study sheds light on the alterations in gut microbiota and transcriptome in mice following C. sinensis juvenile infection, as well as their correlation, laying a foundation for a better understanding of their interaction during infection.

IMPORTANCE

This study highlighted the impact of C. sinensis juvenile infection on the gut microbiota and transcriptome of BALB/c mice. It induced liver inflammation, promoted intestinal villi growth, and altered goblet cell numbers. The infection also disrupted the diversity and structure of gut microbiota, particularly affecting beneficial bacteria. Transcriptome analysis revealed increased expression of genes related to immune response and detoxification processes. Important pathways affected included circadian rhythm, glutathione metabolism, and glycolysis/gluconeogenesis. Notable genes implicated included Igkv12-41, Mcpt2, Arntl, Npas2, Cry1, and Gsta1. Bacteroides_sartorii emerged as a potential key regulator in this interaction.

Comparative effects of non-fermented and Lacticaseibacillus paracasei-fermented pomelo juice on gut microbiota composition and short-chain fatty acid production: An in vitro colonic model

Pomelo juice, especially from the Tubtim Siam cultivar, may offer prebiotic benefits by promoting beneficial gut bacteria. This study evaluated the impact of non-fermented and Lacticaseibacillus paracasei (L. paracasei)-fermented pomelo juice on gut microbiota using an in vitro colonic fermentation model. The L. paracasei-fermented juice significantly increased lactobacilli levels compared to the non-fermented juice, while both treatments similarly suppressed coliforms within 24 h. Microbiota analysis revealed increased richness and significant community shifts in both treatments. Moreover, the fermented juice demonstrated a greater decrease in the Firmicutes/Bacteroidetes ratio, indicating a greater impact on gut metabolism. Fermented juice promoted beneficial bacteria like L. paracasei, Bifidobacterium longum, and Faecalibacterium prauznitzii while inhibiting pathogens. These changes coincided with higher production of short-chain fatty acids (SCFAs), including acetic, propionic, and n-butyric acids. Therefore, fermenting pomelo juice with L. paracasei improves its ability to beneficially influence the gut microbiota, suggesting its potential for gut health enhancement.

Natural pigments in the food industry: Enhancing stability, nutritional benefits, and gut microbiome health

Natural pigments are increasingly favored in the food industry for their vibrant colors, fewer side effects and potential health benefits compared to synthetic pigments. However, their application in food industry is hindered by their instability under harsh environmental conditions. This review evaluates current strategies aimed at enhancing the stability and bioactivity of natural pigments. Advanced physicochemical methods have shown promise in enhancing the stability of natural pigments, enabling their incorporation into food products to enhance sensory attributes, texture, and bioactive properties. Moreover, recent studies demonstrated that most natural pigments offer health benefits. Importantly, they have been found to positively influence gut microbiota, in particular their regulation of the beneficial and harmful flora of the gut microbiome, the reduction of ecological dysbiosis through changes in the composition of the gut microbiome, and the alleviation of systemic inflammation caused by a high-fat diet in mice, suggesting a beneficial role in dietary interventions.

The impact of botanical fermented foods on metabolic syndrome and type 2 diabetes: a systematic review of randomised controlled trials

Our systematic review assessed the impact of botanical fermented food (BFF) consumption on glucose, lipid, anthropometric, inflammatory and gut microbiota parameters, in adults with metabolic syndrome (MetS), MetS components or type 2 diabetes mellitus (T2DM). Embase, MEDLINE, Cochrane CENTRAL and Google Scholar were searched with no language limits, from inception to 31 August 2022, for eligible randomised controlled trials (RCTs). Two independent reviewers screened 6873 abstracts and extracted relevant data. Risk of bias (ROB) was assessed using the Cochrane Collaboration's ROB2 tool. The final review included twenty-six RCTs, with thirty-one reports published between 2001 and 2022. Significant (p < 0·05) within-group and between-group changes in cardiometabolic outcome means were reported in twenty-three and nineteen studies, respectively. Gut microbiota composition was assessed in four studies, with two finding significant between-group differences. No significant difference between groups of any measured outcomes was observed in five studies. There were fourteen studies at low ROB; ten were of some concern; and two were at high ROB. In 73% of included studies, BFF consumption by participants with obesity, MetS or T2DM led to significant between-group improvements in discrete cardiometabolic outcomes, including fasting blood glucose, lipid profile, blood pressure, waist circumference, body fat percentage and C-reactive protein. BFF consumption increased the abundance of beneficial gut bacteria, such as Bifidobacterium and LAB, whilst reducing potential pathogens such as Bacteroides. To determine the clinical significance of BFFs as therapeutic dietary adjuncts, their safety, tolerability and affordability must be balanced with the limited power and magnitude of these preliminary findings.

Are Aptamer-Based Biosensors the Future of the Detection of the Human Gut Microbiome?-A Systematic Review and Meta-Analysis

The gut microbiome is shaped early in life by dietary and lifestyle factors. Specific compounds in the gut affect the growth of different bacterial species and the production of beneficial or harmful byproducts. Dysbiosis of the gut microbiome has been linked to various diseases resulting from the presence of harmful bacteria and their byproducts. Existing methods for detecting microbial species, such as microscopic observation and molecular biological techniques, are costly, labor-intensive, and require skilled personnel. Biosensors, which integrate a recognition element, transducer, amplifier, signal processor, and display unit, can convert biological events into electronic signals. This review provides a comprehensive and systematic survey of scientific publications from 2018 to June 2024, obtained from ScienceDirect, PubMed, and Scopus databases. The aim was to evaluate the current state-of-the-art and identify knowledge gaps in the application of aptamer biosensors for the determination of gut microbiota. A total of 13 eligible publications were categorized based on the type of study: those using microbial bioreceptors (category 1) and those using aptamer bioreceptors (category 2) for the determination of gut microbiota. Point-of-care biosensors are being developed to monitor changes in metabolites that may lead to disease. They are well-suited for use in the healthcare system and offer an excellent alternative to traditional methods. Aptamers are gaining attention due to their stability, specificity, scalability, reproducibility, low production cost, and low immunogenicity. While there is limited research on using aptamers to detect human gut microbiota, they show promise for providing accurate, robust, and cost-effective diagnostic methods for monitoring the gut microbiome.

Prebiotic saccharides polymerization improves the encapsulation efficiency, stability, bioaccessibility and gut microbiota modulation of urolithin A liposomes

This work was to investigate the effect of four prebiotic saccharides gum arabic (GA), fructooligosaccharide (FOS), konjac glucomannan (KGM), and inulin (INU) incorporation on the encapsulation efficiency (EE), physicochemical stability, and in vitro digestion of urolithin A-loaded liposomes (UroA-LPs). The regulation of liposomes on gut microbiota was also investigated by in vitro colonic fermentation. Results indicated that liposomes coated with GA showed the best EE, bioaccessibility, storage and thermal stability, the bioaccessibility was 1.67 times of that of UroA-LPs. The UroA-LPs coated with FOS showed the best freeze-thaw stability and transformation. Meanwhile, saccharides addition remarkably improved the relative abundance of Bacteroidota, reduced the abundances of Proteobacteria and Actinobacteria. The UroA-LPs coated with FOS, INU, and GA exhibited the highest beneficial bacteria abundance of Parabacteroides, Monoglobus, and Phascolarctobacterium, respectively. FOS could also decrease the abundance of harmful bacteria Collinsella and Enterococcus, and increase the levels of acetic acid, butyric acid and iso-butyric acid. Consequently, prebiotic saccharides can improve the EE, physicochemical stability, gut microbiota regulation of UroA-LPs, and promote the bioaccessibility of UroA, but the efficiency varied based on saccharides types, which can lay a foundation for the application of UroA in foods industry and for the enhancement of its bio-activities.

Red raspberry (Rubus idaeus) preserves intestinal barrier integrity and reduces oxidative stress in Caco-2 cells exposed to a proinflammatory stimulus

Growing evidence showed the capacity of (poly)phenols to exert a protective role on intestinal health. Nevertheless, the existing findings are still heterogeneous and the underlying mechanisms remain unclear. This study investigated the potential benefits of a red raspberry (Rubus idaeus) powder on the integrity of the intestinal barrier, focusing on its ability to mitigate the effects of tumor necrosis factor-α (TNF-α)-induced intestinal permeability. Human colorectal adenocarcinoma cells (i.e., Caco-2 cells) were used as a model to assess the impact of red raspberry on intestinal permeability, tight junction expression, and oxidative stress. The Caco-2 cells were differentiated into polarized monolayers and treated with interferon-γ (IFN-γ) (10 ng mL-1) for 24 hours, followed by exposure to TNF-α (10 ng mL-1) in the presence or absence of red raspberry extract (1-5 mg mL-1). The integrity of the intestinal monolayer was evaluated using transepithelial electrical resistance (TEER) and fluorescein isothiocyanate-dextran (FITC-D) efflux assay. Markers of intestinal permeability (claudin-1, occludin, and zonula occludens-1 (ZO-1)) and oxidative stress (8-hydroxy-2-deoxyguanosine (8-OHdG) and protein carbonyl) were assessed using ELISA kits. Treatment with red raspberry resulted in a significant counteraction of TEER value loss (41%; p < 0.01) and a notable reduction in the efflux of FITC-D (-2.5 times; p < 0.01). Additionally, red raspberry attenuated the levels of 8-OHdG (-48.8%; p < 0.01), mitigating the detrimental effects induced by TNF-α. Moreover, red raspberry positively influenced the expression of the integral membrane protein claudin-1 (+18%; p < 0.01), an essential component of tight junctions. These findings contribute to the growing understanding of the beneficial effects of red raspberry in the context of the intestinal barrier. The effect of red raspberry against TNF-α-induced intestinal permeability observed in our in vitro model suggests, for the first time, its potential as a dietary strategy to promote gastrointestinal health.

Gut health benefits and associated systemic effects provided by functional components from the fermentation of natural matrices

Recently, the role of the gut microbiota in metabolic health, immunity, behavioral balance, longevity, and intestine comfort has been the object of several studies from scientific communities. They were encouraged by a growing interest from food industries and consumers toward novel fermented ingredients and formulations with powerful biological effects, such as pre, pro, and postbiotic products. Depending on the selected strains, the operating conditions, the addition of suitable reagents or enzymes, the equipment, and the reactor configurations, functional compounds with high bioactivity, such as short-chain fatty acids, gamma-aminobutyric acid, bioactive peptides, and serotonin, can be enhanced and/or produced through fermentation of several vegetable matrices. Otherwise, their formation can also be promoted directly in the gut after the dietary intake of fermented foods: In this case, fermentation will aim to increase the content of precursor substances, such as indigestible fibers, polyphenols, some amino acids, and resistant starch, which can be potentially metabolized by endogenous gut microorganisms and converted in healthy molecules. This review provides an overview of the main functional components currently investigated in literature and the associated gut health benefits. The current state of the art about fermentation technology as a promising functionalization tool to promote the direct or indirect formation of gut-health-enhancing components was deepened, highlighting the importance of optimizing microorganism selection, system setups, and process conditions according to the target compound of interest. The collected data suggested the possibility of gaining novel functional food ingredients or products rich in functional molecules through fermentation without performing additional extraction and purification stages, which are needed when conventional culture broths are used.

Fermented foods: Harnessing their potential to modulate the microbiota-gut-brain axis for mental health

Over the past two decades, whole food supplementation strategies have been leveraged to target mental health. In addition, there has been increasing attention on the ability of gut microbes, so called psychobiotics, to positively impact behaviour though the microbiota-gut-brain axis. Fermented foods offer themselves as a combined whole food microbiota modulating intervention. Indeed, they contain potentially beneficial microbes, microbial metabolites and other bioactives, which are being harnessed to target the microbiota-gut-brain axis for positive benefits. This review highlights the diverse nature of fermented foods in terms of the raw materials used and type of fermentation employed, and summarises their potential to shape composition of the gut microbiota, the gut to brain communication pathways including the immune system and, ultimately, modulate the microbiota-gut-brain axis. Throughout, we identify knowledge gaps and challenges faced in designing human studies for investigating the mental health-promoting potential of individual fermented foods or components thereof. Importantly, we also suggest solutions that can advance understanding of the therapeutic merit of fermented foods to modulate the microbiota-gut-brain axis.

Probiotic-fermented edible herbs as functional foods: A review of current status, challenges, and strategies

Recently, consumers have become increasingly interested in natural, health-promoting, and chronic disease-preventing medicine and food homology (MFH). There has been accumulating evidence that many herbal medicines, including MFH, are biologically active due to their biotransformation through the intestinal microbiota. The emphasis of scientific investigation has moved from the functionally active role of MFH to the more subtle role of biotransformation of the active ingredients in probiotic-fermented MFH and their health benefits. This review provides an overview of the current status of research on probiotic-fermented MFH. Probiotics degrade toxins and anti-nutritional factors in MFH, improve the flavor of MFH, and increase its bioactive components through their transformative effects. Moreover, MFH can provide a material base for the growth of probiotics and promote the production of their metabolites. In addition, the health benefits of probiotic-fermented MFH in recent years, including antimicrobial, antioxidant, anti-inflammatory, anti-neurodegenerative, skin-protective, and gut microbiome-modulating effects, are summarized, and the health risks associated with them are also described. Finally, the future development of probiotic-fermented MFH is prospected in combination with modern development technologies, such as high-throughput screening technology, synthetic biology technology, and database construction technology. Overall, probiotic-fermented MFH has the potential to be used in functional food for preventing and improving people's health. In the future, personalized functional foods can be expected based on synthetic biology technology and a database on the functional role of probiotic-fermented MFH.

Polyphenols Influence the Development of Endometrial Cancer by Modulating the Gut Microbiota

Dysbiosis of the microbiota in the gastrointestinal tract can induce the development of gynaecological tumours, particularly in postmenopausal women, by causing DNA damage and alterations in metabolite metabolism. Dysbiosis also complicates cancer treatment by influencing the body's immune response and disrupting the sensitivity to chemotherapy drugs. Therefore, it is crucial to maintain homeostasis in the gut microbiota through the effective use of food components that affect its structure. Recent studies have shown that polyphenols, which are likely to be the most important secondary metabolites produced by plants, exhibit prebiotic properties. They affect the structure of the gut microbiota and the synthesis of metabolites. In this review, we summarise the current state of knowledge, focusing on the impact of polyphenols on the development of gynaecological tumours, particularly endometrial cancer, and emphasising that polyphenol consumption leads to beneficial modifications in the structure of the gut microbiota.

Health benefits of anthocyanin-containing foods, beverages, and supplements have unpredictable relation to gastrointestinal microbiota: A systematic review and meta-analysis of random clinical trials

Anthocyanins are a type of natural pigment that has numerous health benefits. In recent years, the interaction of anthocyanins with gastrointestinal (GI) microbiota has been presented as a viable paradigm for explaining anthocyanin activities. The current study performed a systematic review and meta-analysis to determine the potential modulation of GI microbiota by anthocyanins in human health improvement. Clinical trials were retrieved from PubMed, Cochrane, Web of Knowledge, China Biology Medicine, China National Knowledge Infrastructure, and ClinicalTrials.gov with no language restrictions. Eight clinical trials (252 participants) were selected from the 1121 identified studies and the relative phylum abundance extracted from the trials was analyzed using a random-effects model. Based on the analysis, anthocyanins had no effect on the relative abundance of Firmicutes (standard mean difference [SMD]: -0.46 [-1.25 to 0.34], P = .26), Proteobacteria (SMD, -0.32 [-0.73 to 0.09], P = .13), nor Actinobacteria (SMD, -0.19 [-0.50 to 0.12], P = 0.24), but influenced the abundance of Bacteroidetes (SMD, 0.84 [0.17 to 1.52], P = .01) when compared with placebo/control. No significant influence on the relative abundance was detected when the data were analyzed following the "posttreatment vs. pretreatment" strategy. Our preliminary analysis revealed that the effects of anthocyanins on human GI microbiota vary between studies and individuals, and at the current stage, the clinical trials regarding the effects of anthocyanin interventions on human GI microbiota are lacking. More trials with larger sample sizes are needed to promote the clinical application of anthocyanins.

Dietary Phenolic Compounds: Their Health Benefits and Association with the Gut Microbiota

Oxidative stress causes various diseases, such as type II diabetes and dyslipidemia, while antioxidants in foods may prevent a number of diseases and delay aging by exerting their effects in vivo. Phenolic compounds are phytochemicals such as flavonoids which consist of flavonols, flavones, flavanonols, flavanones, anthocyanidins, isoflavones, lignans, stilbenoids, curcuminoids, phenolic acids, and tannins. They have phenolic hydroxyl groups in their molecular structures. These compounds are present in most plants, are abundant in nature, and contribute to the bitterness and color of various foods. Dietary phenolic compounds, such as quercetin in onions and sesamin in sesame, exhibit antioxidant activity and help prevent cell aging and diseases. In addition, other kinds of compounds, such as tannins, have larger molecular weights, and many unexplained aspects still exist. The antioxidant activities of phenolic compounds may be beneficial for human health. On the other hand, metabolism by intestinal bacteria changes the structures of these compounds with antioxidant properties, and the resulting metabolites exert their effects in vivo. In recent years, it has become possible to analyze the composition of the intestinal microbiota. The augmentation of the intestinal microbiota by the intake of phenolic compounds has been implicated in disease prevention and symptom recovery. Furthermore, the “brain–gut axis”, which is a communication system between the gut microbiome and brain, is attracting increasing attention, and research has revealed that the gut microbiota and dietary phenolic compounds affect brain homeostasis. In this review, we discuss the usefulness of dietary phenolic compounds with antioxidant activities against some diseases, their biotransformation by the gut microbiota, the augmentation of the intestinal microflora, and their effects on the brain–gut axis.

Red raspberry supplementation mitigates alcohol-induced liver injury associated with gut microbiota alteration and intestinal barrier dysfunction in mice

Alcoholic liver disease (ALD) is still a global health concern. Long-term alcohol intake alters the gut microbiota diversity and metabolic activity, and causes intestinal barrier dysfunction, leading to the development of ALD. This research explored the protective effects and underlying mechanisms of red raspberry (RR) on alcohol-related disorders in mice. Male C57BL/6J mice were fed a standard diet or a standard diet supplemented with 2%, 4%, and 8% weight/weight RR. Meanwhile, mice were administered 35% (v/v) ethanol (EtOH, 10 mL per kg body weight) intragastrically once daily for six weeks, except the control group mice. The results showed that RR supplementation decreased liver injury markers (alanine and aspartate transaminases) in the serum, reduced triglyceride level in the liver and downregulated hepatic cytochrome P450 2E1 mRNA expression in mice administered EtOH. In addition, EtOH-mediated oxidative stress in the liver was attenuated by RR supplementation through decreased hepatic malondialdehyde content and increased antioxidant (glutathione, glutathione peroxidase, and catalase) levels and activities in mice exposed to EtOH. Moreover, RR supplementation reversed EtOH-induced alteration in the cecal microbial composition at the phylum, order, genus, and species levels and improved the intestinal barrier function associated with the inhibition of the NF-κB/MLCK pathway, which was accompanied by upregulation of tight junctions (zonula occludens 1, occludin, claudin-1, and claudin-4) and E-cadherin mRNA and protein expressions. Accordingly, RR supplementation resulted in a decreased level of endotoxins in the serum and attenuation of the inflammatory response in the liver, illustrated by a significant decrease in tumor necrosis factor-alpha, interleukin (IL)-1β, and IL-6 levels. Overall, RR supplementation alleviated the adverse effects of chronic alcohol intake in C57BL/6J mice and could be a potential supplement for improving ALD.

Fermented natural product targeting gut microbiota regulate immunity and anti-inflammatory activity: A possible way to prevent COVID-19 in daily diet

Low immune function makes the body vulnerable to being invaded by external bacteria or viruses, causing influenza and inflammation of various organs, and this trend is shifting to the young and middle-aged group. It has been pointed out that natural products fermented by probiotic have benign changes about their active ingredients in some studies, and it have shown strong nutritional value in anti-oxidation, anti-aging, regulating lipid metabolism, anti-inflammatory and improving immunity. In recent years, the gut microbiota plays a key role and has been extensively studied in improving immunity and anti-inflammation activity. By linking the relationship between natural products fermented by probiotic, gut microbiota, immunity, and inflammation, this review presents the modulating effects of probiotics and their fermented natural products on the body, including immunity-enhancing and anti-inflammatory activities by modulating gut microbiota, and it is discussed that the current understanding of its molecular mechanisms. It may become a possible way to prevent COVID-19 through consuming natural products fermented by probiotic in our daily diet.

Dietary Polyphenol, Gut Microbiota, and Health Benefits

Polyphenols, which are probably the most important secondary metabolites produced by plants, have attracted tremendous attention due to their health-promoting effects, including their antioxidant, anti-inflammatory, antibacterial, anti-adipogenic, and neuro-protective activities, as well as health properties. However, due to their complicated structures and high molecular weights, a large proportion of dietary polyphenols remain unabsorbed along the gastrointestinal tract, while in the large intestine they are biotransformed into bioactive, low-molecular-weight phenolic metabolites through the residing gut microbiota. Dietary polyphenols can modulate the composition of intestinal microbes, and in turn, gut microbes catabolize polyphenols to release bioactive metabolites. To better investigate the health benefits of dietary polyphenols, this review provides a summary of their modulation through in vitro and in vivo evidence (animal models and humans), as well as their possible actions through intestinal barrier function and gut microbes. This review aims to provide a basis for better understanding the relationship between dietary polyphenols, gut microbiota, and host health.

Fermented Foods, Health and the Gut Microbiome

Fermented foods have been a part of human diet for almost 10,000 years, and their level of diversity in the 21st century is substantial. The health benefits of fermented foods have been intensively investigated; identification of bioactive peptides and microbial metabolites in fermented foods that can positively affect human health has consolidated this interest. Each fermented food typically hosts a distinct population of microorganisms. Once ingested, nutrients and microorganisms from fermented foods may survive to interact with the gut microbiome, which can now be resolved at the species and strain level by metagenomics. Transient or long-term colonization of the gut by fermented food strains or impacts of fermented foods on indigenous gut microbes can therefore be determined. This review considers the primary food fermentation pathways and microorganisms involved, the potential health benefits, and the ability of these foodstuffs to impact the gut microbiome once ingested either through compounds produced during the fermentation process or through interactions with microorganisms from the fermented food that are capable of surviving in the gastro-intestinal transit. This review clearly shows that fermented foods can affect the gut microbiome in both the short and long term, and should be considered an important element of the human diet.