Plant Glycan Metabolism by Bifidobacteria

Effects of defatted rice bran-fortified bread on gut microbiome, cardiovascular risk, gut discomfort, wellbeing and gut physiology in healthy adults with low dietary fibre intake

BACKGROUND & AIMS

Inadequate dietary fibre (DF) intake is associated with suboptimal gut function and increased risk of several human diseases. Bread is commonly consumed and is ideal to incorporate cereal bran to increase DF content. No human studies have investigated the effects of defatted rice bran (DRB) in bread, which has triple the DF of white bread, purported hypo-allergenicity and a unique nutrient profile, as a dietary intervention in healthy adults. This study aims to assess the relative abundances of a composite of key faecal microbial genera and species involved in DF fermentation and metabolism following the habitual intake of DRB-fortified bread and its influence on other biological markers of host and microbial interactions, cardiovascular risk profile, patient-reported outcomes, total DF intake, and gut physiology in healthy adults with low baseline DF intake.

METHODS

Fifty-six healthy adults with low baseline DF intake (<18 g/day (females), <22 g/day (males)) completed a two-arm, placebo-controlled, double-blind, randomised, crossover study. Participants consumed three (females) or four (males) slices of DRB-fortified bread or control bread daily as part of their usual diet for four weeks, with the intervention periods separated by a two-week washout. Outcomes included faecal microbiota composite (primary outcome); relative abundances (taxa and gene); faecal moisture content and bile acid concentrations; plasma and faecal organic acid concentrations; cardiovascular risk profile; gut comfort, psychological wellbeing parameters; total DF intake; whole gut transit time, and were measured at baseline and following each intervention phase. Additionally, in a sub-study, 15 participants ingested gas-sensing capsules to assess whole and regional gut transit times, and total and regional colonic hydrogen and carbon dioxide concentrations at the same timepoints.

RESULTS

DRB-fortified bread consumption significantly increased total DF intake from 20.7 g/day to 43.4 g/day (p < 0.001). No significant differences were observed in the primary outcome, microbial taxa composite within and between groups (False Discovery Rate (FDR) correction, p > 0.10). As compared to control, the DRB group had increased relative abundances of Faecalibacterium prausnitzii (unadjusted p = 0.04), Bifidobacterium longum (unadjusted p = 0.12), and Bacteroides ovatus (unadjusted p = 0.10); lower relative abundances in Coprococcus genus (unadjusted p = 0.09), Roseburia faecis (unadjusted p = 0.02) and Prevotella copri species (unadjusted p = 0.05). However, no significant differences were observed in the relative abundances of these taxa within and between groups (FDR correction p > 0.10) and for most of the other outcomes between groups (p > 0.05). Only mean serum high-density lipoprotein (HDL) concentrations significantly increased (p = 0.006), and mean total cholesterol (TC) to HDL concentration ratio significantly lowered (p = 0.02) in the DRB group compared to the control group.

CONCLUSION

This is the first human study to show that a high-DF DRB-fortified bread improved DF intake, HDL cholesterol profiles, and may affect the gut microbiota composition in healthy adults with low DF intake. These findings support the substitution of white bread with DRB-fortified bread as an effective method to improve DF intake, which may have subsequent benefits on gut physiology and metabolic health.

A diverse set of solubilized natural fibers drives structure-dependent metabolism and modulation of the human gut microbiota

Growing evidence suggests that inadequate dietary fiber intake, termed the "fiber gap," is linked to disease states through disruption of the gut microbiota. Despite this, our understanding of how various fiber structures influence the microbiota and health is limited by the lack of diverse commercially available fibers. Studies have primarily focused on a limited range of fibers, rather than the diverse array of fibers representative of those commonly found in our diets. In this study, we aimed to investigate how naturally derived fibers impact the human microbiota and their metabolic products. We performed a comprehensive structural characterization and functional evaluation of a unique and highly diverse set of new, highly soluble fibers with varied monosaccharide compositions, glycosidic linkages, and polymer lengths. Using an ex vivo high-throughput human microbiota platform coupled with metabolomic profiling, we demonstrate that these diverse fibers drive distinct and consistent microbial and metabolic profiles across cohorts of donors in a structure-dependent manner. These metabolic effects were accompanied by both general and donor-specific changes in microbial taxa. Finally, we demonstrate that integrating detailed glycomic characterization with microbial and metabolomic data allowed for prediction of functional outcomes driven by a novel material, pineapple pulp fiber. This work highlights the potential for targeted dietary fiber interventions to modulate the microbiota and improve health outcomes, paving the way for the development of new fiber-rich products with specific health benefits.IMPORTANCEFiber deficiency is associated with numerous disease states, many of which are linked to disruption of the gut microbiota. This study encompasses the first systematic and comprehensive characterization of a diverse collection of naturally derived solubilized fibers and their impacts on the microbiota. The results expand our understanding of the beneficial effects of specific carbohydrate structures naturally found in the human diet, highlighting the potential for designing fiber-based health interventions. The high solubility of these fibers increases both the range of products they can be incorporated in as well as their assayability in experiments, enabling a widespread increase in fiber consumption and positive health impacts.

Yeast mannans promote laxation and specifically modulate microbiota composition in older adults: An open-label pilot study

Yeast mannans (YM) are potential prebiotics that may improve laxation. The aim was to evaluate the effects of YM on gastrointestinal symptoms, with a hypothesis of high tolerance. A secondary aim assessed stool frequency. Fecal microbiota composition (16S rRNA gene amplicon sequencing) and targeted urine metabolites (LC-MS/MS) were explored. An ex vivo simulation of digestion and fermentation (6 donors) compared YM to the reference prebiotic inulin followed by an open-label pilot study, with a 1-week baseline and 2-week intervention of 15 g/d of YM. Ex vivo findings showed increased Bacteroides faecis, B. ovatus, Parabacteroides merdae, P. distasonis, Blautia faecis, and Bifidobacterium spp. in response to YM. Participants (n = 20, 71.4 ± 11.0 y) reported no change with YM for burping, constipation, diarrhea, flatulence/gas, nausea, reflux/heartburn, or rumblings/noise, rated from 0 for none to 3 for severe symptoms. Cramping/pain marginally increased from baseline (0.02 ± 0.01) to intervention (0.05 ± 0.02; P = .046), as did distention/bloating (baseline, 0.07 ± 0.03; intervention week 2, 0.15 ± 0.05; P = .037). This high tolerability was explained by the ex vivo finding that YM induced less gas production than inulin (-45%). Stool frequency trended higher with YM (1.53 ± 0.15 stools/d) compared to baseline (1.35 ± 0.11) (P = .079); participants with ≤1 stools/d (n = 8) showed an increase (0.84 ± 0.14 to 1.19 ± 0.32; P = .016). In vivo compositional changes in fecal microbiota suggest increased B. faecis, B. ovatus, P. merdae, and P. distasonis levels in response to YM. Overall, YM elicited specific microbiota modulation with minimal gastrointestinal symptoms and the potential to increase stool frequency, supporting its prebiotic potential. This trial was registered at clinicaltrials.gov (NCT05939336).

The Lost Kingdom: commensal protists in the gut microbiota

The gut microbiota critically influences many aspects of host biology, from nutrient acquisition to immunological function, and is integral to metazoan life. While most microbiome research has focused on bacteria, the intestinal microbiota encompasses a diverse constellation of microorganisms, including viruses, fungi, archaea, and protists. Among these microbes, commensal protists have been particularly neglected, to the point that their status as true members of the microbiota remained contentious. However, findings over the past decade revealed that commensal protists, particularly those in the Parabasalia phylum (parabasalids), perform keystone roles within the intestinal ecosystem. Emerging evidence highlights how parabasalids dramatically impact host immunity, gut microbiome ecology, and host susceptibility to both infectious and inflammatory diseases. In this review, we discuss the recent discoveries of the varied and powerful roles of commensal parabasalids in the intestinal microbiota and outline the challenges and opportunities in this burgeoning new area of the microbiome field.

Gut Barrier Dysfunction and Microbiota Variations in Cryptosporidiosis: A Comprehensive Review

Cryptosporidiosis is a zoonotic protozoan parasite-born disease, equally significant in both animals and humans, especially affecting immunocompromised individuals (e.g., AIDS patients) and neonates. The prime concerns of this review article are to demonstrate the disruption of the intestinal barrier and variations in the gut microbiome during cryptosporidiosis, and to explore host gut-parasite interactions that can lead to the development of novel therapeutics. The review concluded that the enteric barrier is particularly maintained by tight junction proteins (e.g., occludin, claudin, and ZO-1, etc.) and mucosal immunity, both of which are severely compromised during Cryptosporidium spp. infections, resulting in increased intestinal barrier permeability, inflammatory responses, diarrhea, and ultimately death in severe cases. Cryptosporidium-induced dysbiosis is characterized by reduced microbial diversity and richness, a shift from commensal to pathogenic bacteria, as evidenced by increased pro-inflammatory taxa like Proteobacteria, and reduced proportions of beneficial SCFAs producing bacteria, e.g., Firmicutes. Recent investigations have highlighted the interrelations between gut microbiota and epithelial barrier integrity, especially during cryptosporidiosis, demonstrating the modulations regarding tight junctions (TJs), immune reactions, and SCFA production, all of which are main players in alleviating this protozoal parasitic infection. This review comprehensively describes the fine details underlying these impairments, including autophagy-mediated TJs' degradation, inflammasome activation, and gut microbiome-driven alterations in metabolic pathways, providing the latest relevant, and well-organized piece of knowledge regarding intestinal barrier alterations and microbial shifts during cryptosporidiosis. This work emphasizes the future need for longitudinal studies and advanced sequencing techniques to understand host gut microbiota-parasite interactions, aiming to formulate innovative strategies to mitigate cryptosporidiosis.

Priority effects, nutrition and milk glycan-metabolic potential drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome

Background

The initial colonization of the infant gut is a complex process that defines the foundation for a healthy microbiome development. Bifidobacterium longum is one of the first colonizers of newborns' gut, playing a crucial role in the healthy development of both the host and its microbiome. However, B. longum exhibits significant genomic diversity, with subspecies (e.g., Bifidobacterium longum subsp. infantis and subsp. longum) displaying distinct ecological and metabolic strategies including differential capabilities to break down human milk glycans (HMGs). To promote healthy infant microbiome development, a good understanding of the factors governing infant microbiome dynamics is required.

Methodology

We analyzed newly sequenced gut microbiome samples of mother-infant pairs from the Amsterdam Infant Microbiome Study (AIMS) and four publicly available datasets to identify important environmental and bifidobacterial features associated with the colonization success and succession outcomes of B. longum subspecies. Metagenome-assembled genomes (MAGs) were generated and assessed to identify characteristics of B. longum subspecies in relation to early-life gut colonization. We further implemented machine learning tools to identify significant features associated with B. longum subspecies abundance.

Results

B. longum subsp. longum was the most abundant and prevalent gut Bifidobacterium at one month, being replaced by B. longum subsp. infantis at six months of age. By utilizing metagenome-assembled genomes (MAGs), we reveal significant differences between and within B. longum subspecies in their potential to break down HMGs. We further combined strain-tracking, meta-pangenomics and machine learning to understand these abundance dynamics and found an interplay of priority effects, milk-feeding type and HMG-utilization potential to govern them across the first six months of life. We find higher abundances of B. longum subsp. longum in the maternal gut microbiome, vertical transmission, breast milk and a broader range of HMG-utilizing genes to promote its abundance at one month of age. Eventually, we find B. longum subsp. longum to be replaced by B. longum subsp. infantis at six months of age due to a combination of nutritional intake, HMG-utilization potential and a diminishment of priority effects.

Discussion

Our results establish a strain-level ecological framework explaining early-life abundance dynamics of B. longum subspecies. We highlight the role of priority effects, nutrition and significant variability in HMG-utilization potential in determining the predictable colonization and succession trajectories of B. longum subspecies, with potential implications for promoting infant health and well-being.

The gut core microbial species Bifidobacterium longum: Colonization, mechanisms, and health benefits

Bifidobacterium longum (B. longum) is a species of the core microbiome in the human gut, whose abundance is closely associated with host age and health status. B. longum has been shown to modulate host gut microecology and have the potential to alleviate various diseases. Comprehensive understanding on the colonization mechanism of B. longum and mechanism of the host-B. longum interactions, can provide us possibility to prevent and treat human diseases through B. longum-directed strategies. In this review, we summarized the gut colonization characteristics of B. longum, discussed the diet factors that have ability/potential to enrich indigenous and/or ingested B. longum strains, and reviewed the intervention mechanisms of B. longum in multiple diseases. The key findings are as follows: First, B. longum has specialized colonization mechanisms, like a wide carbohydrate utilization spectrum that allows it to adapt to the host's diet, species-level conserved genes encoding bile salt hydrolase (BSHs), and appropriate bacterial surface structures. Second, dietary intervention (e.g., anthocyanins) could effectively improve the gut colonization of B. longum, demonstrating the feasibility of diet-tuned strain colonization. Finally, we analyzed the skewed abundance of B. longum in different types of diseases and summarized the main mechanisms by which B. longum alleviates digestive (repairing the intestinal mucosal barrier by stimulating Paneth cell activity), immune (up-regulating the regulatory T cell (Treg) populations and maintaining the balance of Th1/Th2), and neurological diseases (regulating the kynurenine pathway and quinolinic acid levels in the brain through the gut-brain axis).

A Novel Lineage of Endosymbiotic Actinomycetales: Genome Reduction and Acquisition of New Functions in Bifidobacteriaceae Associated With Termite Gut Flagellates

Cellulolytic flagellates are essential for the symbiotic digestion of lignocellulose in the gut of lower termites. Most species are associated with host-specific consortia of bacterial symbionts from various phyla. 16S rRNA-based diversity studies and taxon-specific fluorescence in situ hybridization revealed a termite-specific clade of Actinomycetales that colonise the cytoplasm of Trichonympha spp. and other gut flagellates, representing the only known case of intracellular Actinomycetota in protists. Comparative analysis of eleven metagenome-assembled genomes from lower termites allowed us to describe them as new genera of Bifidobacteriaceae. Like the previously investigated Candidatus Ancillula trichonymphae, they ferment sugars via the bifidobacterium shunt but, unlike their free-living relatives, experienced significant genome erosion. Additionally, they acquired new functions by horizontal gene transfer from other gut bacteria, including the capacity to produce hydrogen. Members of the genus Ancillula (average genome size 1.56 ± 0.2 Mbp) retained most pathways for the synthesis of amino acids, including a threonine/serine exporter, providing concrete evidence for the basis of the mutualistic relationship with their host. By contrast, Opitulatrix species (1.23 ± 0.1 Mbp) lost most of their biosynthetic capacities, indicating that an originally mutualistic symbiosis is on the decline.

Role of gut microbiota in rheumatoid arthritis: Potential cellular mechanisms regulated by prebiotic, probiotic, and pharmacological interventions

Rheumatoid arthritis (RA) is a chronic autoimmune disease that primarily affects joints and multiple organs and systems, which is long-lasting and challenging to cure and significantly impacting patients' quality of life. Alterations in the composition of intestinal flora in both preclinical and confirmed RA patients indicate that intestinal bacteria play a vital role in RA immune function. However, the mechanism by which the intestinal flora is regulated to improve the condition of RA is not fully understood. This paper reviews the methods of regulating gut microbiota and its metabolites through prebiotics, probiotics, and pharmacological interventions, and discusses their effects on RA. Additionally, it explores the potential predictive role of cellular therapy mechanisms of intestinal flora in treating RA. These findings suggest that restoring the ecological balance of intestinal flora and regulating intestinal barrier function may enhance immune system function, thereby improving rheumatoid arthritis. This offers new insights into its treatment.

The Effect of Mono- and Di-Saccharides on the Microbiome of Dairy Cow Manure and Its Odor

In a previous experiment, we showed that the odor of Bos taurus manure slurries could be improved by anaerobic incubation with the sugars glucose, lactose, and sucrose. This improvement was due to reductions in the concentrations of malodorants, including dimethyl disulfide, p-cresol, p-ethylphenol, indole, and skatole, and a shift to the production of fruity esters, including ethyl butyrate and propyl propanoate. Due to large concentrations of lactic acid produced by the sugar-amended manure slurries, we inferred that lactic acid bacteria were involved in improving the manure slurry odor. Here, through 16S rRNA amplicon sequencing for microbiome analysis, we show that lactic acid bacterial growth was promoted by the addition of all three sugars. Lactobacillus buchneri and an unknown Lactobacillus sp. were the most prominent lactic acid bacteria stimulated by sugar addition. Lactobacillales were found only in trace abundances in unamended manure slurries. The relative abundance of orders such as Clostridiales, Bifidobacteriales, and Erysipelotrichales were not noticeably affected by sugar amendment. However, the disaccharides lactose and sucrose seemed to increase the relative abundance of Bifidobacterium, whereas the monosaccharide glucose did not. We conclude that lactic acid bacteria are the primary bacteria involved in improving odor in dairy cow manure slurries and present strategies to enhance their abundance in animal wastes.

A Comprehensive Review on Dietary Polysaccharides as Prebiotics, Synbiotics, and Postbiotics in Infant Formula and Their Influences on Gut Microbiota

Human milk contains an abundance of nutrients which benefit the development and growth of infants. However, infant formula has to be used when breastfeeding is not possible. The large differences between human milk and infant formula in prebiotics lead to the suboptimal intestinal health of infant formula-fed infants. This functional deficit of infant formula may be overcome through other dietary polysaccharides that have been characterized. The aim of this review was to summarize the potential applications of dietary polysaccharides as prebiotics, synbiotics, and postbiotics in infant formula to better mimic the functionality of human milk prebiotics for infant gut health. Previous studies have demonstrated the influences of dietary polysaccharides on gut microbiota, SCFA production, and immune system development. Compared to prebiotics, synbiotics and postbiotics showed better application potential in shaping the gut microbiota, the prevention of pathogen infections, and the development of the immune system. Moreover, the safety issues for biotics still require more clinical trials with a large-scale population and long time duration, and the generally accepted regulations are important to regulate related products. Pectin polysaccharides has similar impacts to human milk oligosaccharides on gut microbiota and the repairing of a damaged gut barrier, with similar functions also being observed for inulin and β-glucan. Prebiotics as an encapsulation material combined with probiotics and postbiotics showed better potential applications compared to traditional material in infant formula.

Benefits and Challenges of Encapsulating Bifidobacterium Probiotic Strains with Bifidogenic Prebiotics

Bifidobacteria offer remarkable health benefits when added to probiotic formulations, contributing to the burgeoning market driven by increased awareness among consumers and healthcare providers. However, several pivotal challenges must be crossed: strain selection, encapsulation wall materials, compatible food matrices, and the intricate interplay among these factors. An approach to address these challenges involves exploring bifidogenic substrates as potential encapsulation materials. This strategy has the potential to enhance bifidobacteria viability within the demanding gastrointestinal environment, extend shelf life, and promote synergistic interactions that promote bifidobacteria survival. Nonetheless, it is crucial to acknowledge that the relationship between bifidogenic substrates and bifidobacterial metabolism is complex and multifaceted. Consequently, despite the promising outlook, it is important to emphasize that this approach requires in-depth investigation, as the intricate interplay between these elements constitutes a rich area of ongoing research. This pursuit aims to ultimately deliver consumers a product that can genuinely improve their health and well-being.

A Novel Bifidobacterium longum Subsp. longum T1 Strain from Cow's Milk: Homeostatic and Antibacterial Activity against ESBL-Producing Escherichia coli

Background/Objectives: The global emergence of antibiotic-resistant zooanthroponotic Escherichia coli strains, producing extended-spectrum beta-lactamases (ESBL-E) and persisting in the intestines of farm animals, has now led to the development of a pandemic of extra-intestinal infectious diseases in humans. The search for innovative probiotic microorganisms that eliminate ESBL-E from the intestines of humans and animals is relevant. Previously, we received three isolates of bifidobacteria: from milk of a calved cow (BLLT1), feces of a newborn calf (BLLT2) and feces of a three-year-old child who received fresh milk from this calved cow (BLLT3). Our goal was to evaluate the genetic identity of BLLT1, BLLT2, BLLT3 isolates using genomic DNA fingerprinting (GDF), to study the tolerance, adhesion, homeostatic and antibacterial activity of BLLT1 against ESBL-E. Methods: We used a complex of microbiological, molecular biological, and immunological methods, including next generation sequencing (NGS). Results: GDF showed that DNA fragments of BLLT2 and BLLT3 isolates were identical in number and size to DNA fragments of BLLT1. These data show for the first time the possibility of natural horizontal transmission of BLLT1 through with the milk of a calved cow into the intestines of a calf and the intestines of a child. BLLT1 was resistant to gastric and intestinal stresses and exhibited high adhesive activity to calf, pig, chicken, and human enterocytes. This indicates the unique ability of BLLT1 to inhabit the intestines of animals and humans. We are the first to show that BLLT1 has antibacterial activity against ESBL-E strains that persist in humans and animals. BLLT1 produced 145 ± 8 mM of acetic acid, which reduced the pH of the nutrient medium from 6.8 to 5.2. This had an antibacterial effect on ESBL-E. The genome of BLLT1 contains ABC-type carbohydrate transporter gene clusters responsible for the synthesis of acetic acid with its antibacterial activity against ESBL-E. BLLT1 inhibited TLR4 mRNA expression induced by ESBL-E in HT-29 enterocytes, and protected the enterocyte monolayers used in this study as a bio-model of the intestinal barrier. BLLT1 increased intestinal alkaline phosphatase (IAP) as one of the main molecular factors providing intestinal homeostasis. Conclusions: BLLT1 shows promise for the creation of innovative functional nutritional products for humans and feed additives for farm animals that will reduce the spread of ESBL-E strains in the food chain.

The pectin metabolizing capacity of the human gut microbiota

The human gastrointestinal microbiota, densely populated with a diverse array of microorganisms primarily from the bacterial phyla Bacteroidota, Bacillota, and Actinomycetota, is crucial for maintaining health and physiological functions. Dietary fibers, particularly pectin, significantly influence the composition and metabolic activity of the gut microbiome. Pectin is fermented by gut bacteria using carbohydrate-active enzymes (CAZymes), resulting in the production of short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate, which provide various health benefits. The gastrointestinal microbiota has evolved to produce CAZymes that target different pectin components, facilitating cross-feeding within the microbial community. This review explores the fermentation of pectin by various gut bacteria, focusing on the involved transport systems, CAZyme families, SCFA synthesis capacity, and effects on microbial ecology in the gut. It addresses the complexities of the gut microbiome's response to pectin and highlights the importance of microbial cross-feeding in maintaining a balanced and diverse gut ecosystem. Through a systematic analysis of pectinolytic CAZyme production, this review provides insights into the enzymatic mechanisms underlying pectin degradation and their broader implications for human health, paving the way for more targeted and personalized dietary strategies.

Synbiotic therapy with Clostridium sporogenes and xylan promotes gut-derived indole-3-propionic acid and improves cognitive impairments in an Alzheimer's disease mouse model

Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized primarily by cognitive impairment. Recent investigations have highlighted the potential of nutritional interventions that target the gut-brain axis, such as probiotics and prebiotics, in forestalling the onset of AD. In this study, whole-genome sequencing was employed to identify xylan as the optimal carbon source for the tryptophan metabolism regulating probiotic Clostridium sporogenes (C. sporogenes). Subsequent in vivo studies demonstrated that administration of a synbiotic formulation comprising C. sporogenes (1 × 1010 CFU per day) and xylan (1%, w/w) over a duration of 30 days markedly enhanced cognitive performance and spatial memory faculties in the 5xFAD transgenic AD mouse model. The synbiotic treatment significantly reduced amyloid-β (Aβ) accumulation in the cortex and hippocampus of the brain. Importantly, synbiotic therapy substantially restored the synaptic ultrastructure in AD mice and suppressed neuroinflammatory responses. Moreover, the intervention escalated levels of the microbial metabolite indole-3-propionic acid (IPA) and augmented the relative prevalence of IPA-synthesizing bacteria, Lachnospira and Clostridium, while reducing the dominant bacteria in AD, such as Aquabacterium, Corynebacterium, and Romboutsia. Notably, synbiotic treatment also prevented the disruption of gut barrier integrity. Correlation analysis indicated a strong positive association between gut microbiota-generated IPA levels and behavioral changes. In conclusion, this study demonstrates that synbiotic supplementation significantly improves cognitive and intellectual deficits in 5xFAD mice, which could be partly attributed to enhanced IPA production by gut microbiota. These findings provide a theoretical basis for considering synbiotic therapy as a novel microbiota-targeted approach for the treatment of metabolic and neurodegenerative diseases.

Unveiling metabolic pathways of selected plant-derived glycans by Bifidobacterium pseudocatenulatum

Bifidobacteria are commonly encountered members of the human gut microbiota that possess the enzymatic machinery necessary for the metabolism of certain plant-derived, complex carbohydrates. In the current study we describe differential growth profiles elicited by a panel of 21 newly isolated Bifidobacterium pseudocatenulatum strains on various plant-derived glycans. Using a combination of gene-trait matching and comparative genome analysis, we identified two distinct xylanases responsible for the degradation of xylan. Furthermore, three distinct extracellular α-amylases were shown to be involved in starch degradation by certain strains of B. pseudocatenulatum. Biochemical characterization showed that all three α-amylases can cleave the related substrates amylose, amylopectin, maltodextrin, glycogen and starch. The genes encoding these enzymes are variably found in the species B. pseudocatenulatum, therefore constituting a strain-specific adaptation to the gut environment as these glycans constitute common plant-derived carbohydrates present in the human diet. Overall, our study provides insights into the metabolism of these common dietary carbohydrates by a human-derived bifidobacterial species.

Cross-feeding of bifidobacteria promotes intestinal homeostasis: a lifelong perspective on the host health

Throughout the life span of a host, bifidobacteria have shown superior colonization and glycan abilities. Complex glycans, such as human milk oligosaccharides and plant glycans, that reach the colon are directly internalized by the transport system of bifidobacteria, cleaved into simple structures by extracellular glycosyl hydrolase, and transported to cells for fermentation. The glycan utilization of bifidobacteria introduces cross-feeding activities between bifidobacterial strains and other microbiota, which are influenced by host nutrition and regulate gut homeostasis. This review discusses bifidobacterial glycan utilization strategies, focusing on the cross-feeding involved in bifidobacteria and its potential health benefits. Furthermore, the impact of cross-feeding on the gut trophic niche of bifidobacteria and host health is also highlighted. This review provides novel insights into the interactions between microbe-microbe and host-microbe.

Short-term dietary fiber interventions produce consistent gut microbiome responses across studies

The composition of the human gut microbiome varies tremendously among individuals, making the effects of dietary or treatment interventions difficult to detect and characterize. The consumption of fiber is important for gut health, yet the specific effects of increased fiber intake on the gut microbiome vary across studies. The variation in study outcomes might be due to inter-individual (or inter-population) variation or to the details of the interventions including the types of fiber, length of study, size of cohort, and molecular approaches. Thus, to identify generally (on average) consistent fiber-induced responses in the gut microbiome of healthy individuals, we re-analyzed 16S rRNA sequencing data from 21 dietary fiber interventions from 12 human studies, which included 2,564 fecal samples from 538 subjects across all interventions. Short-term increases in dietary fiber consumption resulted in highly consistent gut bacterial community responses across studies. Increased fiber consumption explained an average of 1.5% of compositional variation (vs 82% of variation attributed to the individual), reduced alpha-diversity, and resulted in phylogenetically conserved responses in relative abundances among bacterial taxa. Additionally, we identified bacterial clades, at approximately the genus level, that were highly consistent in their response (on average, increasing or decreasing in their relative abundance) to dietary fiber interventions across the studies.

IMPORTANCE

Our study is an example of the power of synthesizing and reanalyzing 16S rRNA microbiome data from many intervention studies. Despite high inter-individual variation of the composition of the human gut microbiome, dietary fiber interventions cause a consistent response both in the degree of change and the particular taxa that respond to increased fiber.

Identification of carbohydrate gene clusters obtained from in vitro fermentations as predictive biomarkers of prebiotic responses

BACKGROUND

Prebiotic fibers are non-digestible substrates that modulate the gut microbiome by promoting expansion of microbes having the genetic and physiological potential to utilize those molecules. Although several prebiotic substrates have been consistently shown to provide health benefits in human clinical trials, responder and non-responder phenotypes are often reported. These observations had led to interest in identifying, a priori, prebiotic responders and non-responders as a basis for personalized nutrition. In this study, we conducted in vitro fecal enrichments and applied shotgun metagenomics and machine learning tools to identify microbial gene signatures from adult subjects that could be used to predict prebiotic responders and non-responders.

RESULTS

Using short chain fatty acids as a targeted response, we identified genetic features, consisting of carbohydrate active enzymes, transcription factors and sugar transporters, from metagenomic sequencing of in vitro fermentations for three prebiotic substrates: xylooligosacharides, fructooligosacharides, and inulin. A machine learning approach was then used to select substrate-specific gene signatures as predictive features. These features were found to be predictive for XOS responders with respect to SCFA production in an in vivo trial.

CONCLUSIONS

Our results confirm the bifidogenic effect of commonly used prebiotic substrates along with inter-individual microbial responses towards these substrates. We successfully trained classifiers for the prediction of prebiotic responders towards XOS and inulin with robust accuracy (≥ AUC 0.9) and demonstrated its utility in a human feeding trial. Overall, the findings from this study highlight the practical implementation of pre-intervention targeted profiling of individual microbiomes to stratify responders and non-responders.

A methyl esterase from Bifidobacterium longum subsp. longum reshapes the prebiotic properties of apple pectin by triggering differential modulatory capacity in faecal cultures

Pectin structures have received increasing attention as emergent prebiotics due to their capacity to promote beneficial intestinal bacteria. Yet the collective activity of gut bacterial communities to cooperatively metabolize structural variants of this substrate remains largely unknown. Herein, the characterization of a pectin methylesterase, BpeM, from Bifidobacterium longum subsp. longum, is reported. The purified enzyme was able to remove methyl groups from highly methoxylated apple pectin, and the mathematical modelling of its activity enabled to tightly control the reaction conditions to achieve predefined final degrees of methyl-esterification in the resultant pectin. Demethylated pectin, generated by BpeM, exhibited differential fermentation patterns by gut microbial communities in in vitro mixed faecal cultures, promoting a stronger increase of bacterial genera associated with beneficial effects including Lactobacillus, Bifidobacterium and Collinsella. Our findings demonstrate that controlled pectin demethylation by the action of a B. longum esterase selectively modifies its prebiotic fermentation pattern, producing substrates that promote targeted bacterial groups more efficiently. This opens new possibilities to exploit biotechnological applications of enzymes from gut commensals to programme prebiotic properties.

Applications of Strain-Specific Probiotics in the Management of Cardiovascular Diseases: A Systemic Review

Cardiovascular diseases (CVDs) are a leading cause of global mortality and novel approaches for prevention and management are needed. The human gastrointestinal tract hosts a diverse microbiota that is crucial in maintaining metabolic homeostasis. The formulation of effective probiotics, alone or in combination, has been under discussion due to their impact on cardiovascular and metabolic diseases. Probiotics have been shown to impact cardiovascular health positively. An imbalance in the presence of Firmicutes and Bacteroidetes has been linked to the progression of CVDs due to their impact on bile acid and cholesterol metabolism. The probiotics primarily help in the reduction of plasma low-density lipoprotein levels and attenuation of the proinflammatory markers. These beneficial microorganisms contribute to lowering cholesterol levels and produce essential short-chain fatty acids. The impact of lipid-regulating probiotic strains on human health is quite significant. However, only a few have been tested for potential beneficial efficacy, and ambiguity exists regarding strain dosages, interactions with confounding factors, and potential adverse effects. Hence, more comprehensive studies and randomized trials are needed to understand the mechanisms of probiotics on CVDs and to ensure human health. This review assesses the evidence and highlights the roles of strain-specific probiotics in the management of CVDs.

Linking human milk oligosaccharide metabolism and early life gut microbiota: bifidobacteria and beyond

SUMMARYHuman milk oligosaccharides (HMOs) are complex, multi-functional glycans present in human breast milk. They represent an intricate mix of heterogeneous structures which reach the infant intestine in an intact form as they resist gastrointestinal digestion. Therefore, they confer a multitude of benefits, directly and/or indirectly, to the developing neonate. Certain bifidobacterial species, being among the earliest gut colonizers of breast-fed infants, have an adapted functional capacity to metabolize various HMO structures. This ability is typically observed in infant-associated bifidobacteria, as opposed to bifidobacteria associated with a mature microbiota. In recent years, information has been gleaned regarding how these infant-associated bifidobacteria as well as certain other taxa are able to assimilate HMOs, including the mechanistic strategies enabling their acquisition and consumption. Additionally, complex metabolic interactions occur between microbes facilitated by HMOs, including the utilization of breakdown products released from HMO degradation. Interest in HMO-mediated changes in microbial composition and function has been the focal point of numerous studies, in recent times fueled by the availability of individual biosynthetic HMOs, some of which are now commonly included in infant formula. In this review, we outline the main HMO assimilatory and catabolic strategies employed by infant-associated bifidobacteria, discuss other taxa that exhibit breast milk glycan degradation capacity, and cover HMO-supported cross-feeding interactions and related metabolites that have been described thus far.

Genomic and functional diversity of cultivated Bifidobacterium from human gut microbiota

The genus Bifidobacterium widely exists in human gut and has been increasingly used as the adjuvant probiotics for the prevention and treatment of diseases. However, the functional differences of Bifidobacterium genomes from different regions of the world remain unclear. We here describe an extensive study on the genomic characteristics and function annotations of 1512 genomes (clustered to 849 non-redundant genomes) of Bifidobacterium cultured from human gut. The distribution of some carbohydrate-active enzymes varied among different Bifidobacterium species and continents. More than 36% of the genomes of B. pseudocatenulatum harbored biosynthetic gene clusters of lanthipeptide-class-iv. 99.76% of the cultivated genomes of Bifidobacterium harbored genes of bile salt hydrolase. Most genomes of B. adolescentis, and all genomes of B. dentium harbored genes involved in gamma-aminobutyric acid synthesis. B. longum subsp. infantis were characterized harboring most genes related to human milk oligosaccharide utilization. Significant differences between the distribution of antibiotic resistance genes among different species and continents revealed the importance to use antibiotics precisely in the clinical treatment. Phages infecting Bifidobacterium and horizontal gene transfers occurring in genomes of Bifidobacterium were dependent on species and region sources, and might help Bifidobacterium adapt to the environment. In addition, the distribution of Bifidobacterium in human gut was found varied from different regions of the world. This study represents a comprehensive view of characteristics and functions of genomes of cultivated Bifidobacterium from human gut, and enables clinical advances in the future.

Ecology- and genome-based identification of the Bifidobacterium adolescentis prototype of the healthy human gut microbiota

Bifidobacteria are among the first microbial colonizers of the human gut, being frequently associated with human health-promoting activities. In the current study, an in silico methodology based on an ecological and phylogenomic-driven approach allowed the selection of a Bifidobacterium adolescentis prototype strain, i.e., B. adolescentis PRL2023, which best represents the overall genetic content and functional features of the B. adolescentis taxon. Such features were confirmed by in vitro experiments aimed at evaluating the ability of this strain to survive in the gastrointestinal tract of the host and its ability to interact with human intestinal cells and other microbial gut commensals. In this context, co-cultivation of B. adolescentis PRL2023 and several gut commensals revealed various microbe-microbe interactions and indicated co-metabolism of particular plant-derived glycans, such as xylan.IMPORTANCEThe use of appropriate bacterial strains in experimental research becomes imperative in order to investigate bacterial behavior while mimicking the natural environment. In the current study, through in silico and in vitro methodologies, we were able to identify the most representative strain of the Bifidobacterium adolescentis species. The ability of this strain, B. adolescentis PRL2023, to cope with the environmental challenges imposed by the gastrointestinal tract, together with its ability to switch its carbohydrate metabolism to compete with other gut microorganisms, makes it an ideal choice as a B. adolescentis prototype and a member of the healthy microbiota of adults. This strain possesses a genetic blueprint appropriate for its exploitation as a candidate for next-generation probiotics.

Bifidobacterium species viability in dairy-based probiotic foods: challenges and innovative approaches for accurate viability determination and monitoring of probiotic functionality

Bifidobacterium species are essential members of a healthy human gut microbiota. Their presence in the gut is associated with numerous health outcomes such as protection against gastrointestinal tract infections, inflammation, and metabolic diseases. Regular intake of Bifidobacterium in foods is a sustainable way of maintaining the health benefits associated with its use as a probiotic. Owing to their global acceptance, fermented dairy products (particularly yogurt) are considered the ideal probiotic carrier foods. As envisioned in the definition of probiotics as "live organisms," the therapeutic functionalities of Bifidobacterium spp. depend on maintaining their viability in the foods up to the point of consumption. However, sustaining Bifidobacterium spp. viability during the manufacture and shelf-life of fermented dairy products remains challenging. Hence, this paper discusses the significance of viability as a prerequisite for Bifidobacterium spp. probiotic functionality. The paper focuses on the stress factors that influence Bifidobacterium spp. viability during the manufacture and shelf life of yogurt as an archetypical fermented dairy product that is widely accepted as a delivery vehicle for probiotics. It further expounds the Bifidobacterium spp. physiological and genetic stress response mechanisms as well as the methods for viability retention in yogurt, such as microencapsulation, use of oxygen scavenging lactic acid bacterial strains, and stress-protective agents. The report also explores the topic of viability determination as a critical factor in probiotic quality assurance, wherein, the limitations of culture-based enumeration methods, the challenges of species and strain resolution in the presence of lactic acid bacterial starter and probiotic species are discussed. Finally, new developments and potential applications of next-generation viability determination methods such as flow cytometry, propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR), next-generation sequencing, and single-cell Raman spectroscopy (SCRS) methods are examined.

In Vitro Assessment of Postbiotic and Probiotic Commercial Dietary Supplements Recommended for Counteracting Intestinal Dysbiosis in Dogs

Many environmental aspects influence the preservation of a beneficial microbiome in dogs, and gut dysbiosis occurs when imbalances in the intestinal ecosystem cause functional changes in the microbial populations. The authors evaluated the effects of two specific commercial dietary supplements: a combination of a postbiotic and prebiotics (Microbiotal cane®) and a probiotic product (NBF 1®) recommended for counteracting intestinal dysbiosis in dogs, on the gut canine microbiota composition and its metabolic activities (production of short-chain fatty acids). The investigation was performed using an in vitro fermentation system inoculated with dog fecal samples. Microbiotal cane® promoted a more immediate increase in Lactobacillus spp. after the first 6 h of fermentation, whereas NBF 1® promoted the increase at the end of the process only. The two supplements supported an increase in the Bifidobacterium spp. counts only after 24 h. The in vitro abilities of Microbiotal cane® and NBF 1® to increase selectively beneficial bacterial groups producing acetic, propionic, and butyric acids suggest a possible positive effect on the canine gut microbiota, even if further in vivo studies are needed to confirm the beneficial effects on the intestinal health.

Microbiome diversity is a modifiable virulence factor for cryptosporidiosis

Cryptosporidium spp. infection causes significant disease in immunosuppressed individuals and children under the age of 5 years. The severity of the pathological presentation of cryptosporidiosis is a function of the host and parasite genotypes, host immune status, and the enteric environment or microbiome of the host. Cryptosporidiosis often presents with abdominal pain and severe diarrhoea and is associated with intestinal dysbiosis and inflammation. Our systematic analysis of the available literature revealed that bacterial diversity is reduced during infection in larger animal models, lending support to recent studies which indicate that the use of probiotics or the presence of a naturally diverse gut microbiome can prevent or minimise pathology caused by gastrointestinal pathogens. In summary, we present evidence that the presence of a diverse gut microbiome, natural or induced, reduces both symptomatic pathology and oocyst output.

Role of Bifidobacterium in Modulating the Intestinal Epithelial Tight Junction Barrier: Current Knowledge and Perspectives

The intestinal tight junction (TJ) barrier is a crucial defense mechanism that prevents the passage of intestinal content into the intestinal wall, tissue, and systemic circulation. A compromised intestinal TJ barrier has been identified as a significant factor in inflammatory bowel disease (IBD), necrotizing enterocolitis, and other gut-related inflammatory conditions. Recent studies have revealed the importance of the probiotic bacterial strains of Bifidobacterium in protecting against intestinal inflammation and IBD pathogenesis via the regulation of intestinal TJ barrier function. Numerous species and strains of Bifidobacterium have been found to regulate TJ proteins and the signaling pathways responsible for maintaining intestinal barrier integrity and permeability. In this review, we provide a summary of recent studies that highlight the regulatory role of Bifidobacterium species and the strain effect on the intestinal TJ barrier. We also discuss the intracellular mechanisms involved in Bifidobacterium modulation of the intestinal barrier and the potential therapeutic efficacy of targeting the barrier function to regulate intestinal inflammation.

Probiotics in prevention and treatment of COVID-19: a systematic review of current evidence

Introduction. Clinical evidence suggests that certain probiotics may help treat and prevent viral infections. To date, the effectiveness of probiotics in the alleviation of COVID-19 has not been established. The aim of this systematic review was to assess the role of probiotics in the prevention and treatment of COVID-19. Materials and methods. An extensive search of four electronic databases was performed which included Embase, Scopus, Web of Science, and PubMed from November 2019 to June 2022. After reviewing the references list of related articles additional studies were identified. A multiple combination of keywords validated by MESH were used to search the databases. Study selection was performed according to an inclusion and exclusion criteria. Results. Twenty-three articles met the study inclusion criteria. Six articles were conducted in vitro while the remaining studies were conducted in the human population (in vivo). The type of probiotic was defined in eighteen studies. There were two studies that used supplements (vitamins, herbals, minerals, etc.) in addition to probiotics. The largest sample size was 445 850 participants which were from a study that used an application-based survey. The majority of studies found that probiotics had a positive effect on the COVID-19 disease. The benefits included early remission of COVID-19 symptoms and a shorter duration of sickness (10 studies), lower mortality rates (3 studies), and decreased hospitalization and length of stay (3 studies). Six in vitro studies found that probiotics were beneficial against SARS-CoV-2 through antiviral effects. There were only two studies that found probiotics to be ineffective or caused negative effects when consumed in COVID-19 patients. Conclusion. Available evidence supports the antiviral role of probiotics on prevention and treatment of COVID-19. The antiviral potential of Lactobacillus paracasei metabolite PlnE and PlnF against SARS-CoV-2 may explain the effectiveness of probiotics on COVID-19.

Insights into the fermentation patterns of wheat bran cell wall polysaccharides using an in-vitro batch fermentation model

We aimed to study the structural characteristics and fermentation properties of wheat bran cell wall polysaccharides (CWPs). Sequential extractions of CWPs from wheat bran produced the water-extractable (WE) and alkali-extractable (AE) fractions. The extracted fractions were structurally characterized based on their molecular weight (Mw) and monosaccharide composition. Our findings revealed that the Mw and the ratio of arabinose to xylose (A/X) of AE were higher than those of WE and that the two fractions were mainly composed of arabinoxylans (AXs). The substrates were then subjected to in vitro fermentation by human fecal microbiota. As fermentation progressed, the total carbohydrates of WE were significantly more utilized than that of AE (p < 0.05). The AXs in WE were utilized at a higher rate than those in AE. The relative abundance of Prevotella_9, which can efficiently utilize AXs, was significantly increased in AE. The presence of AXs in AE shifted the balance away from protein fermentation and caused a delay in protein fermentation. Our study demonstrated that wheat bran CWPs can modulate the gut microbiota in a structure-dependent manner. However, future studies should further characterize the fine structure of wheat CWPs to clarify their detailed relationship with gut microbiota and metabolites.

Short-term dietary fiber interventions produce consistent gut microbiome responses across studies

Background

The composition of the human gut microbiome varies tremendously among individuals, making the effects of dietary or treatment interventions difficult to detect and characterize. The consumption of fiber is important for gut health, yet the specific effects of increased fiber intake on the gut microbiome vary across studies. The variation in study outcomes might be due to inter-individual (or inter-population) variation or to the details of the interventions including the types of fiber, length of study, size of cohort, and molecular approaches. Thus, to identify consistent fiber-induced responses in the gut microbiome of healthy individuals, we re-analyzed 16S rRNA sequencing data from 21 dietary fiber interventions from 12 human studies, which included 2564 fecal samples from 538 subjects across all interventions.

Results

Short-term increases in dietary fiber consumption resulted in highly consistent gut microbiome responses across studies. Increased fiber consumption explained an average of 1.5% of compositional variation (versus 82% of variation attributed to the individual), reduced alpha diversity, and resulted in phylogenetically conserved responses in relative abundances among bacterial taxa. Additionally, we identified bacterial clades, at approximately the genus level, that were highly consistent in their response (increasing or decreasing in their relative abundance) to dietary fiber interventions across the studies.

Conclusions

Our study is an example of the power of synthesizing and reanalyzing microbiome data from many intervention studies. Despite high inter-individual variation of the composition of the human gut microbiome, dietary fiber interventions cause a consistent response both in the degree of change as well as the particular taxa that respond to increased fiber.

Preferential sugar utilization by bifidobacterial species

Aim: Bifidobacteria benefit host health and homeostasis by breaking down diet- and host-derived carbohydrates to produce organic acids in the intestine. However, the sugar utilization preference of bifidobacterial species is poorly understood. Thus, this study aimed to investigate the sugar utilization preference (i.e., glucose or lactose) of various bifidobacterial species. Methods: Strains belonging to 40 bifidobacterial species/subspecies were cultured on a modified MRS medium supplemented with glucose and/or lactose, and their preferential sugar utilization was assessed using high-performance thin-layer chromatography. Comparative genomic analysis was conducted with a focus on genes involved in lactose and glucose uptake and genes encoding for carbohydrate-active enzymes. Results: Strains that preferentially utilized glucose or lactose were identified. Almost all the lactose-preferring strains harbored the lactose symporter lacS gene. However, the comparative genomic analysis could not explain all their differences in sugar utilization preference. Analysis based on isolate source revealed that all 10 strains isolated from humans preferentially utilized lactose, whereas all four strains isolated from insects preferentially utilized glucose. In addition, bifidobacterial species isolated from hosts whose milk contained higher lactose amounts preferentially utilized lactose. Lactose was also detected in the feces of human infants, suggesting that lactose serves as a carbon source not only for infants but also for gut microbes in vivo. Conclusion: The different sugar preference phenotypes of Bifidobacterium species may be ascribed to the residential environment affected by the dietary habits of their host. This study is the first to systematically evaluate the sugar uptake preference of various bifidobacterial species.

Combination of Lycium barbarum L. and Laminaria japonica polysaccharides as a highly efficient prebiotic: Optimal screening and complementary regulation of gut probiotics and their metabolites

The combination of polysaccharides is an effective way to develop prebiotics with stable performance during processing and digestion for human wellness. However, there is little information on optimal screening and complementary regulation of compound polysaccharides. This study aimed to optimally select a combination of Lycium barbarum L. polysaccharide (LBP) and Laminaria japonica polysaccharide (LJP) as a highly efficient prebiotic to regulate the gut probiotics and their metabolites. Two LBPs characterized as rhamnogalacturonan I enriched pectins and two LJPs characterized as fucoidans were obtained by enzyme-assisted acid extraction at moderate and dramatic temperatures and combined in pairs to obtain 4 groups containing 4 proportional combinations. All combinations showed better prebiotic effects than individual LJP. The combination of LBP and LJP extracted at 50 °C at a ratio of 4:1 exhibited the strongest prebiotic effect. The optimal compound polysaccharide achieved superior effect and complementary function via LBP-targeted proliferation of Bifidobacterium, Lactobacillus, and Bacteroides and production of SCFAs and non-SCFA health-associated metabolites, LJP-targeted accumulation of butyrate-producing bacteria and corresponding metabolites, as well as synergistic effect of LJP and LBP at exact proportion. Our study provided theoretical and methodological guidance for optimal screening of compound polysaccharides as new prebiotics.

Bifidobacterium longum LBUX23 Isolated from Feces of a Newborn; Potential Probiotic Properties and Genomic Characterization

Bifidobacterium longum is considered a microorganism with probiotic potential, which has been extensively studied, but these probiotic effects are strain dependent. This work aims to characterize the probiotic potential, based on the biochemical and genomic functionality, of B. longum LBUX23, isolated from neonates' feces. B. longum LBUX23 contains one circular genome of 2,287,838 bp with a G+C content of 60.05%, no plasmids, no CRISPR-Cas operon, possesses 56 tRNAs, 9 rRNAs, 1 tmRNA and 1776 coding sequences (CDSs). It has chromosomally encoded resistance genes to ampicillin and dicloxacillin, non-hemolytic activity, and moderate inhibition of Escherichia coli ATCC 25922 and to some emergent pathogen's clinical strains. B. longum LBUX23 was able to utilize lactose, sucrose, fructooligosaccharides (FOS), and lactulose. The maximum peak of bacterial growth was observed in sucrose and FOS at 6 h; in lactose and lactulose, it was shown at 8 h. B. longum LBUX23 can survive in gastrointestinal conditions (pH 4 to 7). A decrease in survival (96.5 and 93.8%) was observed at pH 3 and 3.5 during 120 min. argC, argH, and dapA genes could be involved in this tolerance. B. longum LBUX23 can also survive under primary and secondary glyco- or tauro-conjugated bile salts, and a mixture of bile salts due to the high extracellular bile salt hydrolase (BSH) activity (67.3 %), in taurocholic acid followed by taurodeoxycholic acid (48.5%), glycocholic acid (47.1%), oxgall (44.3%), and glycodeoxycholic acid (29.7%) probably due to the presence of the cbh and gnlE genes which form an operon (start: 119573 and end: 123812). Low BSH activity was determined intracellularly (<7%), particularly in glycocholic acid; no intracellular activity was shown. B. longum LBUX23 showed antioxidant effects in DPPH radical, mainly in intact cells (27.4%). In the case of hydroxyl radical scavenging capacity, cell debris showed the highest reduction (72.5%). In the cell-free extract, superoxide anion radical scavenging capacity was higher (90.5%). The genome of B. longum LBUX23 contains PNPOx, AhpC, Bcp, trxA, and trxB genes, which could be involved in this activity. Regarding adherence, it showed adherence up to 5% to Caco-2 cells. B. longum LBUX23 showed in vitro potential probiotic properties, mainly in BSH activity and antioxidant capacity, which indicates that it could be a good candidate for antioxidant or anti-cholesterol tests using in vivo models.

Carrot RG-I Reduces Interindividual Differences between 24 Adults through Consistent Effects on Gut Microbiota Composition and Function Ex Vivo

The human gut microbiota is characterized by large interpersonal differences, which are not only linked to health and disease but also determine the outcome of nutritional interventions. In line with the growing interest for developing targeted gut microbiota modulators, the selectivity of a carrot-derived rhamnogalacturonan I (cRG-I) was compared to substrates with demonstrated low (inulin, IN) and high selectivity (xanthan, XA), at a human equivalent dose (HED) of 1.5 g/d. The high throughput of the ex vivo SIFR® technology, validated to generate predictive insights for clinical findings, enabled the inclusion of 24 human adults. Such an unprecedented high number of samples in the context of in vitro gut microbiota modelling allowed a coverage of clinically relevant interpersonal differences in gut microbiota composition and function. A key finding was that cRG-I supplementation (already at an HED of 0.3 g/d) lowered interpersonal compositional differences due to the selective stimulation of taxa that were consistently present among human adults, including OTUs related to Bacteroides dorei/vulgatus and Bifidobacterium longum (suspected keystone species), Bacteroides thetaiotaomicron, Bifidobacterium adolescentis and butyrate-producing taxa such as Blautia sp., Anaerobutyricum hallii, and Faecalibacterium prausnitzii. In contrast, both IN and XA treatments increased interpersonal compositional differences. For IN, this followed from its low specificity. For XA, it was rather the extremely high selectivity of XA fermentation that caused large differences between 15 responders and 9 nonresponders, caused by the presence/absence of highly specific XA-fermenting taxa. While all test compounds significantly enhanced acetate, propionate, butyrate, and gas production, cRG-I resulted in a significantly higher acetate (+40%), propionate (+22%), yet a lower gas production (-44%) compared to IN. cRG-I could thus result in overall more robust beneficial effects, while also being better tolerated. Moreover, owing to its remarkable homogenization effect on microbial composition and metabolite production, cRG-I could lead to more predictable outcomes compared to substrates that are less specific or overly specific.

Potential use of seaweed polysaccharides as prebiotics for management of metabolic syndrome: a review

Seaweed polysaccharides (SPs) obtained from seaweeds are a class of functional prebiotics. SPs can regulate glucose and lipid anomalies, affect appetite, reduce inflammation and oxidative stress, and therefore have great potential for managing metabolic syndrome (MetS). SPs are poorly digested by the human gastrointestinal tract but are available to the gut microbiota to produce metabolites and exert a series of positive effects, which may be the mechanism by which SPs render their anti-MetS effects. This article reviews the potential of SPs as prebiotics in the management of MetS-related metabolic disturbances. The structure of SPs and studies related to the process of their degradation by gut bacteria and their therapeutic effects on MetS are highlighted. In summary, this review provides new perspectives on SPs as prebiotics to prevent and treat MetS.

Production of a selective antibacterial fatty acid against Staphylococcus aureus by Bifidobacterium strains

Aims: C16 monounsaturated fatty acid (C16:1) show antibacterial activity against Staphylococcus aureus, a pathogen associated with various diseases such as atopic dermatitis and bacteremia, while the compound does not exhibit antibacterial activity against Staphylococcus epidermidis, an epidermal commensal that inhibits the growth of S. aureus. In this study, we aimed to find bifidobacterial strains with the ability to produce C16:1 and to find a practical manner to utilize C16:1-producing strains in industry. Methods: Various Bifidobacterium strains were screened for their content of C16:1. The chemical identity of C16:1 produced by a selected strain was analyzed by gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). Medium components that affect the C16:1 content of the selected strain were investigated. Antibacterial activity against staphylococci was compared between the authentic C16:1 isomers and total fatty acids (TFA) extracted from the selected strain. Results: B. adolescentis 12451, B. adolescentis 12-111, B. boum JCM 1211, and Bifidobacterium sp. JCM 7042 showed high C16:1 content among the tested strains. TFA extracted from Bifidobacterium sp. JCM 7042 contained C16:1 at 2.3% as the fatty acid constituent (2.4 mg/L of broth). Through GC-MS and LC-MS analyses, the C16:1 synthesized by Bifidobacterium sp. JCM 7042 was identified as 7-cis-hexadecenoic acid (7-cis-C16:1). The authentic 7-cis-C16:1 showed strong and selective antibacterial activity against S. aureus, similar to 6-cis-C16:1, with a minimum inhibitory concentration (MIC) of < 10 µg/mL. Components that increase C16:1 productivity were not found in the MRS and TOS media; however, Tween 80 was shown to considerably reduce the C16:1 ratio in TFA. Antibacterial activity against S. aureus was observed when the TFA extracted from Bifidobacterium sp. JCM 7042 contained high level of 7-cis-C16:1 (6.1% in TFA) but not when it contained low level of 7-cis-C16:1 (0.1% in TFA). Conclusion: The fatty acid, 7-cis-C16:1, which can selectively inhibit the S. aureus growth, is accumulated in TFA of several bifidobacteria. The TFA extracted from cultured cells of Bifidobacterium sp. JCM 7042 demonstrated antibacterial activity. From a practical viewpoint, our findings are important for developing an efficient method to produce novel skin care cosmetics, functional dairy foods, and other commodities.

Advances in extraction, purification, structural characteristics and biological activities of hemicelluloses: A review

Hemicelluloses, a major component of plant cell walls, are a non-cellulosic heteropolysaccharide composed of several distinct sugars that is second in abundance to cellulose, which are one of the most abundant and cheapest renewable resources on earth. Hemicelluloses structure is complex and its chemical structure varies greatly among the different plant species. In addition to its wide use in production of feed and other chemical materials, hemicelluloses are known for its remarkable biological activities that remain largely underutilised to date. Therefore, comprehensive investigations of hemicelluloses structural and biological properties would be helpful for achieving rational utilisation and high-value conversion of this underutilised substance into agents with enhanced health benefits for incorporation in drugs and health foods. In this review, details of diverse research initiatives that have enhanced our understanding of hemicelluloses properties are summarised, including hemicelluloses sources, extraction and purification methods, structural characteristics and biological activities. Furthermore, hemicelluloses structure-activity relationships and new directions for future hemicelluloses research studies are discussed.

Isolation and purification of Tartary buckwheat polysaccharides and their effect on gut microbiota

Tartary buckwheat (Fagopyrum tataricum) is rich in polysaccharides that can be utilized by the gut microbiota (GM) and provide several health benefits. However, the mechanisms underlying the action of these polysaccharides remain unclear to date. In this study, Tartary buckwheat polysaccharides (TBP) were purified, and five fractions were obtained. The composition of these fractions was determined using ion chromatography. Different TBP components were investigated regarding their probiotic effect on three species of Bifidobacteria and Lactobacillus rhamnosus. In addition, the effect of TBP on GM and short-chain fatty acids (SCFAs) was evaluated. Results showed that the probiotic effect of TBP fraction was dependent on their composition. The polysaccharides present in different fractions had specific probiotic effects. TBP-1.0, mainly composed of fucose, glucose, and d-galactose, exhibited the strongest proliferation effect on L. rhamnosus, while TBP-W, rich in glucose, d-galactose, and fructose, had the best promoting effect on Bifidobacterium longum and Bifidobacterium adolescentis growth. Furthermore, TBP-0.2, composed of d-galacturonic acid, d-galactose, xylose, and arabinose, exhibited its highest impact on Bifidobacterium breve growth. The composition of GM was significantly altered by adding TBP during fecal fermentation, with an increased relative abundance of Lactococcus, Phascolarctobacterium, Bacteroidetes, and Shigella. Simultaneously, the level of SCFA was also significantly increased by TBP. Our findings indicate that Tartary buckwheat can provide specific dietary polysaccharide sources to modulate and maintain GM diversity. They provide a basis for Tartary buckwheat commercial utilization for GM modulation.

Efficacy of Bifidobacterium longum alone or in multi-strain probiotic formulations during early life and beyond

The significance of Bifidobacterium to human health can be appreciated from its early colonization of the neonatal gut, where Bifidobacterium longum represents the most abundant species. While its relative abundance declines with age, it is further reduced in several diseases. Research into the beneficial properties of B. longum has unveiled a range of mechanisms, including the production of bioactive molecules, such as short-chain fatty acids, polysaccharides, and serine protease inhibitors. From its intestinal niche, B. longum can have far-reaching effects in the body influencing immune responses in the lungs and even skin, as well as influencing brain activity. In this review, we present the biological and clinical impacts of this species on a range of human conditions beginning in neonatal life and beyond. The available scientific evidence reveals a strong rationale for continued research and further clinical trials that investigate the ability of B. longum to treat or prevent a range of diseases across the human lifespan.

Manipulation of the diet-microbiota-brain axis in Alzheimer's disease

Several studies investigating the pathogenesis of Alzheimer's disease have identified various interdependent constituents contributing to the exacerbation of the disease, including Aβ plaque formation, tau protein hyperphosphorylation, neurofibrillary tangle accumulation, glial inflammation, and the eventual loss of proper neural plasticity. Recently, using various models and human patients, another key factor has been established as an influential determinant in brain homeostasis: the gut-brain axis. The implications of a rapidly aging population and the absence of a definitive cure for Alzheimer's disease have prompted a search for non-pharmaceutical tools, of which gut-modulatory therapies targeting the gut-brain axis have shown promise. Yet multiple recent studies examining changes in human gut flora in response to various probiotics and environmental factors are limited and difficult to generalize; whether the state of the gut microbiota in Alzheimer's disease is a cause of the disease, a result of the disease, or both through numerous feedback loops in the gut-brain axis, remains unclear. However, preliminary findings of longitudinal studies conducted over the past decades have highlighted dietary interventions, especially Mediterranean diets, as preventative measures for Alzheimer's disease by reversing neuroinflammation, modifying the intestinal and blood-brain barrier (BBB), and addressing gut dysbiosis. Conversely, the consumption of Western diets intensifies the progression of Alzheimer's disease through genetic alterations, impaired barrier function, and chronic inflammation. This review aims to support the growing body of experimental and clinical data highlighting specific probiotic strains and particular dietary components in preventing Alzheimer's disease via the gut-brain axis.

Interaction between dietary fiber and bifidobacteria in promoting intestinal health

Bifidobacteria are considered as probiotics due to their role in promoting intestinal health, including regulating intestinal flora, controlling glycolipid metabolism, anti-colitis effects. Dietary fiber is considered as prebiotic favoring gut health. It also can be used as carbon source to support the growth and colonization of probiotics like bifidobacteria. However, because of genetic diversity, different bifidobacterial species differ in their ability to utilize dietary fiber. Meanwhile, dietary fiber with different structural properties has different effects on the bifidobacteria proliferation. The interaction between dietary fiber and bifidobacteria will consequently lead to a synergistic or antagonistic function in promoting intestinal health, therefore affecting the application of combined use of dietary fiber and bifidobacteria. In this case, we summarize the biological function of bifidobacteria, and their interaction with different dietary fiber in promoting gut health, and finally provide several strategies about their combined use.

Role of Bifidobacterium pseudocatenulatum in Degradation and Consumption of Xylan-Derived Carbohydrates

Xylans, a family of xylose-based polysaccharides, are dietary fibers resistant to digestion. They therefore reach the large intestine intact; there, they are utilized by members of the gut microbiota. They are initially broken down by primary degraders that utilize extracellular xylanases to cleave xylan into smaller oligomers. The resulting xylooligosaccharides (XOS) can either be further metabolized directly by primary degraders or cross-feed secondary consumers, including Bifidobacterium. While several Bifidobacterium species have metabolic systems for XOS, most grow poorly on longer-chain XOS and xylan substrates. In this study, we isolated strains of Bifidobacterium pseudocatenulatum and observed that some, including B. pseudocatenulatum ED02, displayed growth on XOS with a high degree of polymerization (DP) and straight-chain xylan, suggesting a primary degrader phenotype that is rare in Bifidobacterium. In silico analyses revealed that only the genomes of these xylan-fermenting (xylan+) strains contained an extracellular GH10 endo-β-1.4 xylanase, a key enzyme for primary degradation of xylan. The presence of an extracellular xylanase was confirmed by the appearance of xylan hydrolysis products in cell-free supernatants. Extracellular xylanolytic activity was only detected in xylan+ strains, as indicated by the production of XOS fragments with a DP of 2 to 6, identified by thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC). Additionally, in vitro fecal fermentations revealed that strains with a xylan+ phenotype can persist with xylan supplementation. These results indicate that xylan+ B. pseudocatenulatum strains may have a competitive advantage in the complex environment of the gastrointestinal tract, due to their ability to act as primary degraders of xylan through extracellular enzymatic degradation. IMPORTANCE The beneficial health effects of dietary fiber are now well established. Moreover, low fiber consumption is associated with increased risks of metabolic and systemic diseases. This so-called "fiber gap" also has a profound impact on the composition of the gut microbiome, leading to a disrupted or dysbiotic microbiota. Therefore, understanding the mechanisms by which keystone bacterial species in the gut utilize xylans and other dietary fibers may provide a basis for developing strategies to restore gut microbiome function. The results described here provide biochemical and genetic evidence for primary xylan utilization by human-derived Bifidobacterium pseudocatenulatum and show also that cooperative utilization of xylans occurs among other members of this species.

Milk glycan metabolism by intestinal bifidobacteria: insights from comparative genomics

Bifidobacteria are early colonizers of the human neonatal gut and provide multiple health benefits to the infant, including inhibiting the growth of enteropathogens and modulating the immune system. Certain Bifidobacterium species prevail in the gut of breastfed infants due to the ability of these microorganisms to selectively forage glycans present in human milk, specifically human milk oligosaccharides (HMOs) and N-linked glycans. Therefore, these carbohydrates serve as promising prebiotic dietary supplements to stimulate the growth of bifidobacteria in the guts of children suffering from impaired gut microbiota development. However, the rational formulation of milk glycan-based prebiotics requires a detailed understanding of how bifidobacteria metabolize these carbohydrates. Accumulating biochemical and genomic data suggest that HMO and N-glycan assimilation abilities vary remarkably within the Bifidobacterium genus, both at the species and strain levels. This review focuses on the delineation and genome-based comparative analysis of differences in respective biochemical pathways, transport systems, and associated transcriptional regulatory networks, providing a foundation for genomics-based projection of milk glycan utilization capabilities across a rapidly growing number of sequenced bifidobacterial genomes and metagenomic datasets. This analysis also highlights remaining knowledge gaps and suggests directions for future studies to optimize the formulation of milk-glycan-based prebiotics that target bifidobacteria.

Probiotic fermentation of polyphenols: potential sources of novel functional foods

Fermented functional food products are among the major segments of food processing industry. Fermentation imparts several characteristic effects on foods including the enhancement of organoleptic characteristics, increased shelf-life, and production of novel health beneficial compounds. However, in addition to macronutrients present in the food, secondary metabolites such as polyphenols are also emerging as suitable fermentable substrates. Despite the traditional antimicrobial view of polyphenols, accumulating research shows that polyphenols exert differential effects on bacterial communities by suppressing the growth of pathogenic microbes while concomitantly promoting the proliferation and survival of probiotic bacteria. Conversely, probiotic bacteria not only survive among polyphenols but also induce their fermentation which often leads to improved bioavailability of polyphenols, production of novel metabolic intermediates, increased polyphenolic content, and thus enhanced functional capacity of the fermented food. In addition, selective fermentation of combinations of polyphenol-rich foods or fortification with polyphenols can result in novel functional foods. The present narrative review specifically explores the potential of polyphenols as fermentable substrates in functional foods. We discuss the emerging bidirectional relationship between polyphenols and probiotic bacteria with an aim at promoting the development of novel functional foods based on the amalgamation of probiotic bacteria and polyphenols.

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Assessment of the bifidogenic and antibacterial activities of xylooligosaccharide

Xylooligosaccharide (XOS) is an attractive prebiotic mainly due to its bifidogenic effect. However, commercial XOS with different compositions is often applied in the food industry at different doses without specifications. In this study, we evaluated the bifidogenic activity of XOS at different doses with either mixtures or pure fractions with different degrees of polymerization (DP), using three strains of Bifidobacterium spp., including B. breve ATCC 15700, B. bifidum ATCC 29521, and B. animalis subsp. lactis HN019. Three growth indicators showed strain-specific bifidogenic activity of XOS, and the activity was both dose- and fraction-dependent as only certain fractions stimulated significant growth. Adding 0.25% XOS (w/v) also promoted increase in total bifidobacterial population of rat fecal samples fermented in vitro. Albeit the antibacterial activity of XOS fractions can be demonstrated, significant growth inhibition can only be achieved when 4.0% XOS mixture was added in Staphylococcus aureus ATCC 6538 pure culture. In contrast, in the presence of B. lactis HN019, 1.0% XOS showed significant antibacterial activity against S. aureus ATCC 6538 in milk. In addition, RNA sequencing suggested downregulation of genes involved in S. aureus ATCC 6538 infection, pathogenesis, and quorum sensing, by XOS. In conclusion, the report urges scientific specifications on XOS chemistry for its effective application as a novel food ingredient or functional food and provides novel insights into its bifidogenic and antibacterial activities.

Effect of Fructooligosaccharides Supplementation on the Gut Microbiota in Human: A Systematic Review and Meta-Analysis

Background: Numerous studies have investigated the effects of the supplementation of fructooligosaccharides (FOS) on the number of bacteria in the gut that are good for health, but the results have been inconsistent. Additionally, due to its high fermentability, supplementation of FOS may be associated with adverse gastrointestinal symptoms such as bloating and flatulence. Therefore, we assessed the effects of FOS interventions on the composition of gut microbiota and gastrointestinal symptoms in a systematic review and meta-analysis. Design: All randomized controlled trials published before 10 July 2022 that investigated the effects of FOS supplementation on the human gut microbiota composition and gastrointestinal symptoms and met the selection criteria were included in this study. Using fixed or random-effects models, the means and standard deviations of the differences between the two groups before and after the intervention were combined into weighted mean differences using 95% confidence intervals (CIs). Results: Eight studies containing 213 FOS supplements and 175 controls remained in this meta-analysis. Bifidobacterium spp. counts significantly increased during FOS ingestion (0.579, 95% CI: 0.444−0.714) in comparison with that of the control group. Subgroup analysis showed greater variation in Bifidobacterium spp. in adults (0.861, 95% CI: 0.614−1.108) than in infants (0.458, 95% CI: 0.297−0.619). The increase in Bifidobacterium spp. counts were greater in the group with an intervention duration greater than 4 weeks (0.841, 95% CI: 0.436−1.247) than an intervention time less than or equal to four weeks (0.532, 95% CI: 0.370−0.694), and in the group with intervention doses > 5 g (1.116, 95% CI: 0.685−1.546) the counts were higher than those with doses ≤ 5 g (0.521, 95% CI: 0.379−0.663). No differences in effect were found between FOS intervention and comparators in regard to the abundance of other prespecified bacteria or adverse gastrointestinal symptoms. Conclusions: This is the first meta-analysis to explore the effect of FOS on gut microbiota and to evaluate the adverse effects of FOS intake on the gastrointestinal tract. FOS supplementation could increase the number of colonic Bifidobacterium spp. while higher dose (7.5−15 g/d) and longer duration (>4 weeks) showed more distinct effects and was well tolerated.