The role of pH in determining the species composition of the human colonic microbiota

Early life gut microbiome and its impact on childhood health and chronic conditions

The development of the gut microbiome is crucial to human health, particularly during the first three years of life. Given its role in immune development, disturbances in the establishment process of the gut microbiome may have long term consequences. This review summarizes evidence for these claims, highlighting compositional changes of the gut microbiome during this critical period of life as well as factors that affect gut microbiome development. Based on human and animal data, we conclude that the early-life microbiome is a determinant of long-term health, impacting physiological, metabolic, and immune processes. The early-life gut microbiome field faces challenges. Some of these challenges are technical, such as lack of standardized stool collection protocols, inconsistent DNA extraction methods, and outdated sequencing technologies. Other challenges are methodological: small sample sizes, lack of longitudinal studies, and poor control of confounding variables. To address these limitations, we advocate for more robust research methodologies to better understand the microbiome's role in health and disease. Improved methods will lead to more reliable microbiome studies and a deeper understanding of its impact on health outcomes.

Therapeutic Strategies to Modulate Gut Microbial Health: Approaches for Chronic Metabolic Disorder Management

Numerous recent studies have suggested that the composition of the intestinal microbiota can trigger metabolic disorders, such as diabetes, prediabetes, obesity, metabolic syndrome, sarcopenia, dyslipidemia, hyperhomocysteinemia, and non-alcoholic fatty liver disease. Since then, considerable effort has been made to understand the link between the composition of intestinal microbiota and metabolic disorders, as well as the role of probiotics in the modulation of the intestinal microbiota. The aim of this review was to summarize the reviews and individual articles on the state of the art regarding ideal therapy with probiotics and prebiotics in order to obtain the reversion of dysbiosis (alteration in microbiota) to eubiosis during metabolic diseases, such as diabetes, prediabetes, obesity, hyperhomocysteinemia, dyslipidemia, sarcopenia, and non-alcoholic fatty liver diseases. This review includes 245 eligible studies. In conclusion, a condition of dysbiosis, or in general, alteration of the intestinal microbiota, could be implicated in the development of metabolic disorders through different mechanisms, mainly linked to the release of pro-inflammatory factors. Several studies have already demonstrated the potential of using probiotics and prebiotics in the treatment of this condition, detecting significant improvements in the specific symptoms of metabolic diseases. These findings reinforce the hypothesis that a condition of dysbiosis can lead to a generalized inflammatory picture with negative consequences on different organs and systems. Moreover, this review confirms that the beneficial effects of probiotics on metabolic diseases are promising, but more research is needed to determine the optimal probiotic strains, doses, and administration forms for specific metabolic conditions.

Modulation of microbiota composition and markers of gut health after in vitro dynamic colonic fermentation of plant sterol-enriched wholemeal rye bread

A human oral phase followed by a dynamic gastrointestinal digestion and colonic fermentation (simgi®) has been applied to wholemeal rye bread (WRB) and PS-enriched WRB (PS-WRB). The aim of this study was to evaluate the impact of these solid and high-fiber food matrices on the metabolism of PS, modulation of the microbiota and production of short-chain fatty acids (SCFA) and ammonium ion after a simulated chronic intake (5 days). In both breads, campesterol, campestanol, stigmasterol, β-sitosterol, sitostanol, Δ5-avenasterol, Δ5,24-stigmastadienol, Δ7-stigmastenol, and Δ7-avenasterol were identified, of which only β-sitosterol was metabolized to sitostenone after PS-WRB treatment. The presence of fiber in both breads exerted a prebiotic effect after fermentation by the increase in Firmicutes (Lactobacillus genus, maximum abundance of 89-99 %) and Actinobacteria (Bifidobacterium genus, maximum abundance of 30-31 %), reflected in an increase of SCFA content. The reduction of proteolytic activity confirmed by the decrease in ammonium ion contents is related to a reduction in the Proteobacteria phylum. Thus, PS-WRB could be considered as a healthy staple food choice since, besides the known hypocholesterolemic effect of PS, rye bread fiber preserves the beneficial microbiota and exerts a positive impact on markers of gut health.

Dynamics of Intestinal Mucosa Microbiota in Juvenile Sika Deer During Early Growth

The establishment of gut microbiota in young ruminants has a profound impact on their productive performance in adulthood. The microbial communities of ruminants differ significantly across the different regions of the digestive tract, as well as between the mucosa and lumen. In this study, we analyzed the characteristics of the microbiota of the small intestine (jejunum and ileum) and large intestine (cecum and colon) of sika deer on day 1 (birth), day 42 (transition period) and day 70 (rumination period) using 16S rRNA gene sequencing. The results showed that the microbial diversity of the mucosa in the jejunum, ileum, cecum and colon of sika deer was higher on day 70 than on day 1, and the diversity of the cecal mucosa was significantly higher than that in the small intestine. Principal coordinates analysis (PCoA) showed that the microbial community structures of the small and large intestinal mucosa were significantly different, and the microbial community structure of sika deer on day 1 was significantly different from that on days 42 and 70. The relative abundances of Methylobacterium-Methylorubrum, Pelagibacterium, Acinetobacter and Staphylococcus were higher in the small intestinal mucosa, while Alistipes, Prevotellaceae UCG-004, Eubacterium coprostanoligenes group and Lachnospiraceae unclassified were higher in the large intestinal mucosa. We also observed increased levels of specific microbiota in the small intestinal (Turicibacter and Cellulosilyticum) and large intestinal mucosa (Treponema, Romboutsia, Oscillospirales UCG-005 and Peptostreptococcaceae unclassified) with animal growth. A comparison of the predicted function showed that the microbiota of the small intestinal mucosa was enriched for replication and repair, while carbohydrate metabolism was enriched in the microbiota of the large intestinal mucosa. In addition, the relative abundances of amino acid and energy metabolism were significantly higher on days 42 and 70 than on day 1. Our results revealed that the microbial community composition and the dynamics of the intestinal mucosa from birth to rumination in juvenile sika deer, which may provide insights into similar processes in other juvenile ruminants.

Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiome modulation

Industrialization adversely affects the gut microbiome and predisposes individuals to chronic non-communicable diseases. We tested a microbiome restoration strategy comprising a diet that recapitulated key characteristics of non-industrialized dietary patterns (restore diet) and a bacterium rarely found in industrialized microbiomes (Limosilactobacillus reuteri) in a randomized controlled feeding trial in healthy Canadian adults. The restore diet, despite reducing gut microbiome diversity, enhanced the persistence of L. reuteri strain from rural Papua New Guinea (PB-W1) and redressed several microbiome features altered by industrialization. The diet also beneficially altered microbiota-derived plasma metabolites implicated in the etiology of chronic non-communicable diseases. Considerable cardiometabolic benefits were observed independently of L. reuteri administration, several of which could be accurately predicted by baseline and diet-responsive microbiome features. The findings suggest that a dietary intervention targeted toward restoring the gut microbiome can improve host-microbiome interactions that likely underpin chronic pathologies, which can guide dietary recommendations and the development of therapeutic and nutritional strategies.

Study on the Effect of Radish Sprouts on Short-Chain Fatty Acids and Gut Microbial Diversity in Healthy Individuals

This study aimed to assess the impact of radish sprouts on the gut microbiota of healthy individuals. Radish sprout additives, subjected to short-term storage and steam treatment, were used to intervene in an in vitro culture of human gut microbiota. The influence of radish sprouts on the gut microbiota was evaluated by monitoring short-chain fatty acid (SCFA) content and proportion in the fermentation broth, and microbial diversity was assessed using 16S rDNA amplicon sequencing. The results indicated that the gut microbiota produced a substantial amount of SCFA within 48 h of fermentation, with a right-skewed distribution across all groups. The addition of both digestates enhanced Firmicutes diversity, while Bacteroidetes and Proteobacteria diversity remained stable between the control and fresh sprout groups. The 30 s steam treatment group showed an increase in Bacteroidetes and a decrease in Proteobacteria diversity. The abundance of Bacilli, Bacillaceae, and Bacillus was significantly higher in both the fresh and steam-treated groups compared to the control. Both fresh and steam-treated radish sprout digestates enriched gut microbiota diversity, with steam treatment showing superior effects. These findings suggest that radish sprout consumption may positively influence gut microbiota, with steam treatment potentially enhancing these benefits.

Simulator of the Human Intestinal Microbial Ecosystem (SHIME®): Current Developments, Applications, and Future Prospects

The human gastrointestinal microbiota plays a vital role in maintaining host health and preventing diseases, prompting the creation of simulators to replicate this intricate system. The Simulator of the Human Intestinal Microbial Ecosystem (SHIME®), a multicompartment dynamic simulator, has emerged as a pivotal in vitro model for studying the interactions and interferences within the human gut microbiota. The continuous and real-time monitoring hallmarks, along with the programmatically flexible setup, bestow SHIME® with the ability to mimic the entire human intestinal ecosystem with high dynamics and stability, allowing the evaluation of various treatments on the bowel microbiota in a controlled environment. This review outlines recent developments in SHIME® systems, including the M-SHIME®, Twin-SHIME®, Triple-SHIME®, and Toddle SHIME® models, highlighting their applications in the fields of food and nutritional science, drug development, gut health research, and traditional Chinese medicine. Additionally, the prospect of SHIME® integrating with other advanced technologies is also discussed. The findings underscore the versatility of SHIME® technology, demonstrating its significant contributions to current gut ecosystem research and its potential for future innovation in microbiome-related fields.

Impact of Probiotics and Prebiotics on Gut Microbiome and Hormonal Regulation

The gut microbiome plays a crucial role in human health by influencing various physiological functions through complex interactions with the endocrine system. These interactions involve the production of metabolites, signaling molecules, and direct communication with endocrine cells, which modulate hormone secretion and activity. As a result, the microbiome can exert neuroendocrine effects and contribute to metabolic regulation, adiposity, and appetite control. Additionally, the gut microbiome influences reproductive health by altering levels of sex hormones such as estrogen and testosterone, potentially contributing to conditions like polycystic ovary syndrome (PCOS) and hypogonadism. Given these roles, targeting the gut microbiome offers researchers and clinicians novel opportunities to improve overall health and well-being. Probiotics, such as Lactobacillus and Bifidobacterium, are live beneficial microbes that help maintain gut health by balancing the microbiota. Prebiotics, non-digestible fibers, nourish these beneficial bacteria, promoting their growth and activity. When combined, probiotics and prebiotics form synbiotics, which work synergistically to enhance the gut microbiota balance and improve metabolic, immune, and hormonal health. This integrated approach shows promising potential for managing conditions related to hormonal imbalances, though further research is needed to fully understand their specific mechanisms and therapeutic potential.

Effect of Oat Hay as a Substitute for Alfalfa Hay on the Gut Microbiome and Metabolites of Yak Calves

To evaluate the impact of different roughages on the intestinal microbiota of yak calves, we fed them oat hay in substitution of alfalfa hay, in addition to milk replacer and starter powder. Twenty-one 45-day-old male yak calves were selected and randomly assigned to three groups: the milk replacer + starter + alfalfa hay group (AH), the milk replacer + starter + oat hay group (OH), and the milk replacer + starter + mixed hay group (AO), in which the alfalfa hay and oat hay were administered in a 1:1 ratio. All calves in the three groups were fed the same milk replacer and an equivalent amount of dry matter. The formal experiment commenced after a 21-day pre-test period and lasted for 120 days. Following the experiment, the contents of the jejunum and colon were collected to investigate the intestinal microbiota and metabolites using 16S rRNA sequencing and LC-MS metabolomics. The result showed that the AO group had greater final body weights overall than the AH group and OH group (p < 0.05). The AH group and OH group had considerably greater feed-to-gain ratios than the AO group (p < 0.05). At the phylum level, the OH group exhibited an increased relative abundance of Bacteroidota and Spirochaetota in the jejunum (p < 0.05). The relative abundance of Actinobacteriota in the colon was increased in the AO group (p < 0.05). At the genus level, the AO group exhibited a decreased abundance of Clostridium sensu_stricto_1 (p < 0.05), and the OH group showed an increased abundance UCG-005 and Alistipes in the jejunum. There were many differential metabolites in the OH group and AO group compared to the AH group, and the different metabolites of the OH group were associated with the metabolic pathways of the nervous system, sensory system, amino acid metabolism, and lipid metabolism in the jejunum and with lipid metabolism, amino acid metabolism, and the nervous system in the colon. In the AO group, these metabolites were associated with the digestive system and the translation and metabolism of cofactors in the jejunum and with the metabolism of cofactors and vitamins in the colon. In summary, it is feasible to replace alfalfa hay with oat hay based on milk replacer and starter. The combination of the two forages enhanced nutrient absorption, improved immune function, maintained the internal homeostasis of yak calves, and was more beneficial to their growth and development.

The ruminant gut microbiome vs enteric methane emission: The essential microbes may help to mitigate the global methane crisis

Ruminants release enteric methane into the atmosphere, significantly increasing greenhouse gas emissions and degrading the environment. A common focus of traditional mitigation efforts is on dietary management and manipulation, which may have limits in sustainability and efficacy, exploring the potential of essential microorganisms as a novel way to reduce intestinal methane emissions in ruminants; a topic that has garnered increased attention in recent years. Fermentation and feed digestion are significantly aided by essential microbes found in the rumen, such as bacteria, fungi, and archaea. The practical implications of the findings reported in various studies conducted on rumen gut concerning methane emissions may pave the way to understanding the mechanisms of CH4 production in the rumen to enhance cattle feed efficiency and mitigate CH4 emissions from livestock. This review discussed using essential bacteria to reduce intestinal methane emissions in ruminants. It investigates how particular microbial strains or consortia can alter rumen fermentation pathways to lower methane output while preserving the health and productivity of animals. We also describe the role of probiotics and prebiotics in managing methane emissions using microbial feed additives. Further, recent studies involving microbial interventions have been discussed. The use of new methods involving functional metagenomics and meta-transcriptomics for exploring the rumen microbiome structure has been highlighted. This review also emphasizes the challenges faced in altering the gut microbiome and future directions in this area.

A core microbiome signature as an indicator of health

The gut microbiota is crucial for human health, functioning as a complex adaptive system akin to a vital organ. To identify core health-relevant gut microbes, we followed the systems biology tenet that stable relationships signify core components. By analyzing metagenomic datasets from a high-fiber dietary intervention in type 2 diabetes and 26 case-control studies across 15 diseases, we identified a set of stably correlated genome pairs within co-abundance networks perturbed by dietary interventions and diseases. These genomes formed a "two competing guilds" (TCGs) model, with one guild specialized in fiber fermentation and butyrate production and the other characterized by virulence and antibiotic resistance. Our random forest models successfully distinguished cases from controls across multiple diseases and predicted immunotherapy outcomes through the use of these genomes. Our guild-based approach, which is genome specific, database independent, and interaction focused, identifies a core microbiome signature that serves as a holistic health indicator and a potential common target for health enhancement.

N-acyl glycines produced by commensal bacteria potentiate GLP-1 secretion as GPCR ligands

Commensal microbiota is crucial for nutrient digestion and production of biologically active molecules, many of which mimic endogenous ligands of human GPCRs. Bacteroides spp. are among the most abundant bacteria residing in the human gut and their absence has been positively correlated with metabolic disorders. In the present study, we focused on N-acylated glycines (NAGlys) as products of Bacteroides spp. and potential GPCR ligands modulating GLP-1 secretion. Representative strains of the most abundant commensal Bacteroides were cultured in either yeast- or animal-based nutrient broths. The broths post-culture were investigated in terms of the contents of NAGlys and stimulatory effects towards GLP-1 production in GLUTag and NCI-H716 cell lines. Pure preparations of the detected NAGlys were further studied to evaluate stimulation of GLP-1 production and related cellular signalling evoked. The most potent NAGlys were also tested as ligands of key lipid GPCRs involved in the regulation of carbohydrate metabolism: GPR40/FFAR1, GPR55, GPR119, and GPR120/FFAR4. We found that Bacteroides potentiate GLP-1 production, depending on the strain and provided nutrient mix. Long-chain unsaturated oleoyl and arachidonoyl glycines, produced by B. thetaiotaomicron and B. intestinalis in the animal-based broth, were particularly effective in stimulation of GLP-1 secretion. They served as agonists of all the receptors under study expressed in GLP-1-producing cells. The obtained results broaden the knowledge of microbial signalling molecules and their role in regulation of carbohydrate homeostasis. They also emphasise the importance of balanced diet as a source of building blocks for commensal bacteria to produce efficient agonists of lipid GPCRs.

Host-pathobiont interactions in Crohn's disease

The mammalian intestine is colonized by trillions of microorganisms that are collectively referred to as the gut microbiota. The majority of symbionts have co-evolved with their host in a mutualistic relationship that benefits both. Under certain conditions, such as in Crohn's disease, a subtype of inflammatory bowel disease, some symbionts bloom to cause disease in genetically susceptible hosts. Although the identity and function of disease-causing microorganisms or pathobionts in Crohn's disease remain largely unknown, mounting evidence from animal models suggests that pathobionts triggering Crohn's disease-like colitis inhabit certain niches and penetrate the intestinal tissue to trigger inflammation. In this Review, we discuss the distinct niches occupied by intestinal symbionts and the evidence that pathobionts triggering Crohn's disease live in the mucus layer or near the intestinal epithelium. We also discuss how Crohn's disease-associated mutations in the host disrupt intestinal homeostasis by promoting the penetration and accumulation of pathobionts in the intestinal tissue. Finally, we discuss the potential role of microbiome-based interventions in precision therapeutic strategies for the treatment of Crohn's disease.

Reinventing gut health: leveraging dietary bioactive compounds for the prevention and treatment of diseases

The human gut harbors a complex and diverse microbiota essential for maintaining health. Diet is the most significant modifiable factor influencing gut microbiota composition and function, particularly through bioactive compounds like polyphenols, dietary fibers, and carotenoids found in vegetables, fruits, seafood, coffee, and green tea. These compounds regulate the gut microbiota by promoting beneficial bacteria and suppressing harmful ones, leading to the production of key microbiota-derived metabolites such as short-chain fatty acids, bile acid derivatives, and tryptophan metabolites. These metabolites are crucial for gut homeostasis, influencing gut barrier function, immune responses, energy metabolism, anti-inflammatory processes, lipid digestion, and modulation of gut inflammation. This review outlines the regulatory impact of typical bioactive compounds on the gut microbiota and explores the connection between specific microbiota-derived metabolites and overall health. We discuss how dietary interventions can affect disease development and progression through mechanisms involving these metabolites. We examine the roles of bioactive compounds and their metabolites in the prevention and treatment of diseases including inflammatory bowel disease, colorectal cancer, cardiovascular diseases, obesity, and type 2 diabetes mellitus. This study provides new insights into disease prevention and underscores the potential of dietary modulation of the gut microbiota as a strategy for improving health.

Lactiplantibacillus argentoratensis AGMB00912 alleviates diarrhea and promotes the growth performance of piglets during the weaning transition

BACKGROUND

Preventing post-weaning diarrhea (PWD) in weaned piglets is a crucial challenge in the swine production industry. The stress of weaning, dietary shifts from maternal milk to solid feed, and environmental changes lead to decreased microbial diversity, increased pathogen abundance, and compromised intestinal integrity. We have previously identified Lactiplantibacillus argentoratensis AGMB00912 (LA) in healthy porcine feces, which demonstrated antimicrobial activity against pathogens and enhanced short-chain fatty acid production. This research aimed to evaluate the efficacy of LA strain supplementation as a strategy to inhibit PWD and enhance overall growth performance in weaned piglets.

RESULTS

LA supplementation in weaned piglets significantly increased body weight gain, average daily gain, and average daily feed intake. It also alleviated diarrhea symptoms (diarrhea score and incidence). Notably, LA was found to enrich beneficial microbial populations (Lactobacillus, Anaerobutyricum, Roseburia, Lachnospiraceae, and Blautia) while reducing the abundance of harmful bacteria (Helicobacter and Campylobacter). This not only reduces the direct impact of pathogens but also improves the overall gut microbiota structure, thus enhancing the resilience of weaned piglets. LA treatment also promotes the growth of the small intestinal epithelial structure, strengthens gut barrier integrity, and increases short-chain fatty acid levels in the gut.

CONCLUSIONS

The study findings demonstrate the promising potential of LA in preventing PWD. Supplementation with the LA strain offers a promising feed additive for improving intestinal health and growth in piglets during the weaning transition, with the potential to significantly reduce the incidence and severity of PWD.

Improvement of intestinal microbial structure in patients with cerebral infarction through in vitro fermentation of anthocyanins from Lycium ruthenicum Murray

Anthocyanins in Lycium ruthenicum Murray can be degraded into metabolites by intestinal microorganisms and have a wide range of biological functions. However, there are limited studies on the effect of anthocyanins on the intestinal flora structure in patients with cerebral infarction. To explore the new probiotic effects of ACN, the gut microbiota present in fecal samples obtained from healthy volunteers and patients with acute cerebral infarction underwent in vitro fermentation analysis. The in vitro fermentation product of ACN with L. ruthenicum Murray can significantly increase the diversity of the gut flora in patients with cerebral infarction. It can also promote beneficial bacteria (e.g., Bifidobacterium) in the guts of patients with acute cerebral infarction (e.g. Bifidobacterium, Allisonella, and Prevotell), reduce the growth of potentially harmful bacteria (Dialister, Megamonas, and Clostridium), and increase the levels of SCFAs. This investigation demonstrated the capability of ACN in vitro fermentation to improve the gut microbiota structure in patients with cerebral infarction. This, in turn, furnishes new theoretical underpinnings for its potential development as a functional food component.

Polysaccharides to postbiotics: Nurturing bone health via modulating "gut-immune axis"

The increasing prevalence of individuals affected by bone pathologies globally has sparked catastrophic concerns. Ankylosing spondylitis, osteoporosis, rheumatoid arthritis, osteoarthritis, and fractures alone impact an estimated 1.71 billion people worldwide. The gut microbiota plays a crucial role in interacting with the host through the synthesis of a diverse range of metabolites called gut-associated metabolites (GAMs), which originate from external dietary substrates or endogenous host compounds. Many metabolic disorders have been linked to alterations in the gut microbiota's activity and composition. The development of metabolic illnesses has been linked to certain microbiota-derived metabolites, such as branched-chain amino acids, bile acids, short-chain fatty acids, tryptophan, trimethylamine N-oxide, and indole derivatives. Moreover, the modulation of gut microbiota through biotics (prebiotics, probiotics and postbiotics) presents a promising avenue for therapeutic intervention. Biotics selectively promote the growth of beneficial gut bacteria, thereby enhancing the production of GAMs with potential beneficial effects on bone metabolism. Understanding the intricate interplay between GAMs, and bone-associated genes through molecular informatics holds significant promise for early diagnosis, prognosis, and novel treatment strategies for various bone disorders.

The gut microbiota of healthy individuals remains resilient in response to the consumption of various dietary fibers

This study focuses on the resilience of gut microbiota during a five-month multi-interventional nutrition trial. The modulatory effects of beta-glucan, rye bran and two dietary fiber mixtures on the fecal pH and compositional changes of the microbiome of healthy subjects were studied. To analyze the stability of intestinal microbiota, we collected an extensive dataset of sequential fecal samples (23-29 from each participant) during a week of the base, beta-glucan consumption and wash-out periods accompanied by the collection of daily food diary data. Microbiota analyses were also conducted after the end of each fiber intake and wash-out period, along with measurements of fecal organic acids and pH. Based on the dominant bacterial taxa, two prevalent microbiota types were identified. The Prevotella-type microbiota responded more to the tested dietary fibers, while the Bacteroides-type microbiota was the least affected. Three microbiota types could not be clustered and behaved differently. Although we noted individual effects of definite fibers on participants' gut microbiota and metabolic profile, relative abundances of bacteria remained stable in the base period (z-scores - 2.2 to 2.3). In most cases, the bacterial abundances of the final samples remained within the normal fluctuation range stressing out the resilience of healthy microbiota. The pH of all fecal samples varied between 6.1 and 8.3 and was associated with the concentration of organic acids and microbial composition. The effect of dietary fibers on the metabolism of fecal microbiota clearly depended on the individual microbiota type. Combining the analysis of gut microbiota with knowledge of the properties of dietary fibers would provide a powerful strategy for nutrition guidance and disease prevention.

Simulated Gastrointestinal Digestion and Fecal Fermentation Characteristics of Exopolysaccharides Synthesized by Schleiferilactobacillus harbinensis Z171

Exopolysaccharides (EPSs) produced by Lactobacillus have important physiological activities and are commonly used as novel prebiotics. A strain of Lactobacillus with high EPS yield was identified as Schleiferilactobacillus harbinensis (S. harbinensis Z171), which was isolated from Chinese sauerkraut. The objective of this study was to investigate the in vitro simulated digestion and fecal fermentation behavior of the purified exopolysaccharide fraction F-EPS1A from S. harbinensis Z171 and its influence on the human intestinal flora composition. The in vitro digestion results showed that the primary structural characteristics of F-EPS1A, such as morphology, molecular weight, and monosaccharide composition remained stable after saliva and gastrointestinal digestion. Compared with the blank group, the fermentation of F-SPS1A by fecal microbiota decreased the diversity of the bacterial communities, significantly promoted the relative abundance of Bifidobacterium and Faecalibacterium, and decreased the relative abundance of Lachnospiraceae_Clostridium, Fusobacterium, and Oscillospira. Reverse transcription polymerase chain reaction (RT-PCR) analysis also showed that the population of Bifidobacterium markedly increased. Furthermore, the total short-chain fatty acid levels increased significantly, especially for butyric acid. Gas chromatography-mass spectrometry (GC-MS) results showed that F-EPS1A could be fermented by the human gut microbiota to synthesize organic acids and derivative metabolites that are beneficial to gut health. Therefore, these findings suggest that F-EPS1A could be exploited as a potential prebiotic.

High casein concentration induces diarrhea through mTOR signal pathway inhibition in post-weaning piglets

Weaning is one of the most challenging periods in a pig's life, during which piglets suffer from nutrition and other issues. Post-weaning diarrhea is one of the major health problems in the pig industry, leading to high morbidity and mortality rates. Previous studies have demonstrated that both the source and concentration of proteins are closely associated with post-weaning diarrhea in piglets. This study was conducted to prevent and control post-weaning diarrhea by selecting different dietary protein concentrations. To eliminate interference from other protein sources, casein was used as the only protein source in this study. Fourteen piglets (weighing 8.43 ± 0.3 kg, weaned on the 28th day) were randomly assigned to two dietary protein groups: a low-protein group (LP, containing 17% casein) and a high-protein group (HP, containing 30% casein). The experiment lasted 2 weeks, during which all piglets had ad libitum access to food and water. Diarrhea was scored on a scale from 1 to 3 (where 1 indicates normal stools and 3 indicates watery diarrhea), and growth performance measurements were recorded daily. The results showed that the piglets in the HP group had persistent diarrhea during the whole study, whereas no diarrhea was observed among piglets in the control group. The body weights and feed intake were significantly lower in piglets in the HP group compared to those in the LP group (p < 0.05). The gastrointestinal pH was significantly higher in piglets in the HP group than those in the LP group (p < 0.05). The intestinal tract microorganisms of the piglets in both groups were significantly affected by the protein concentration of the diet. A diet with high casein concentration significantly reduced the microbiota diversity. Compared to the LP group, the 30% casein diet decreased the abundance of Firmicutes, Bacteroidetes, and Actinobacteria at the phylum level and the relative abundance of Ruminococcus at the genus level. Diarrhea-related mRNA abundances were analyzed by the real-time polymerase chain reaction (PCR) in the intestine of piglets, and the results showed that the HP concentration markedly decreased the expression of solute carriers (SLC, p < 0.05). The mammalian target of rapamycin-mTOR signaling pathway (p < 0.01) was activated in the HP group. In conclusion, a high-protein diet induced post-weaning diarrhea, decreased growth performance, increased gastrointestinal pH, and reduced expression of solute carrier proteins. However, the relationship between high dietary casein feed and post-weaning diarrhea remains unclear and needs to be explored further.

Identification of dietary factors that impact the gut microbiota associated with vitiligo: A Mendelian randomization study and meta-analysis

Previous observational studies have suggested that gut microbiota might be associated with vitiligo. However, owing to the limitations in observational studies of reverse causality and confounders, it remains unclear that whether and how the causal relationships exist. The results suggested that pylum.Bacteroidetes, family.BacteroidalesS24.7, genus.LachnospiraceaeND3007, genus.Marvinbryantia are protective factors for vitiligo. Conversely, family.Lachnospiraceae, order.Burkholderiales, genus.Adlercreutzia, genus.Catenibacterium and genus.Lachnospira are risk factors for vitiligo. In addition, the causative connection between dietary factors and the gut microbiota associated with vitiligo was also investigated. The results revealed that 'alcohol intake versus 10 years pervious' results in a reduction in the abundance of genus.Lachnospiraceae ND3007 and family.BacteroidalesS24.7, bread intake leads to a reduction of genus.Marvinbryantia, 'average weekly red wine intake' is linked to a decrease in the abundance of order.Burkholderiales, tea intake is associated with an augmentation in the abundance of genus.Catenibacterium, salad/raw vegetable intake elevates the abundance of order.Burkholderiales. In summary, this Mendelian randomization study substantiates potential causal effects of gut microbiota on vitiligo. Modulating the gut microbiota through regulating dietary composition may be a novel strategy for preventing vitiligo.

Microbiota alterations associated with vascular diseases: postbiotics as a next-generation magic bullet for gut-vascular axis

The intestinal microbiota represents a key element in maintaining the homeostasis and health conditions of the host. Vascular pathologies and other risk factors such as aging have been recently associated with dysbiosis. The qualitative and quantitative alteration of the intestinal microbiota hinders correct metabolic homeostasis, causing structural and functional changes of the intestinal wall itself. Impairment of the intestinal microbiota, combined with the reduction of the barrier function, worsen the pathological scenarios of peripheral tissues over time, including the vascular one. Several experimental evidence, collected in this review, describes in detail the changes of the intestinal microbiota in dysbiosis associated with vascular alterations, such as atherosclerosis, hypertension, and endothelial dysfunction, the resulting metabolic disorders and how these can impact on vascular health. In this context, the gut-vascular axis is considered, for the first time, as a merged unit involved in the development and progression of vascular pathologies and as a promising target. Current approaches for the management of dysbiosis such as probiotics, prebiotics and dietary modifications act mainly on the intestinal district. Postbiotics, described as preparation of inanimate microorganisms and/or their components that confers health benefits on the host, represent an innovative strategy for a dual management of intestinal dysbiosis and vascular pathologies. In this context, this review has the further purpose of defining the positive effects of the supplementation of bacterial strains metabolites (short‑chain fatty acids, exopolysaccharides, lipoteichoic acids, gallic acid, and protocatechuic acid) restoring intestinal homeostasis and acting directly on the vascular district through the gut-vascular axis.

Specific Gut Microbiome Signatures in Children with Cow's Milk Allergy

Although gut dysbiosis is associated with cow's milk allergy (CMA), causality remains uncertain. This study aimed to identify specific bacterial signatures that influence the development and outcome of the disease. We also investigated the effect of hypoallergenic formula (HF) consumption on the gut microbiome of milk-allergic children. 16S rRNA amplicon sequencing was applied to characterize the gut microbiome of 32 milk-allergic children aged 5-12 years and 36 age-matched healthy controls. We showed that the gut microbiome of children with CMA differed significantly from that of healthy children, regardless of whether they consumed cow's milk. Compared to that of healthy cow's milk consumers, it was depleted in Bifidobacterium, Coprococcus catus, Monoglobus, and Lachnospiraceae GCA-900066575, while being enriched in Oscillibacter valericigenes, Negativibacillus massiliensis, and three genera of the Ruminococcaceae family. Of these, only the Ruminococcaceae taxa were also enriched in healthy children not consuming cow's milk. Furthermore, the gut microbiome of children who developed tolerance and had received an HF was similar to that of healthy children, whereas that of children who had not received an HF was significantly different. Our results demonstrate that specific gut microbiome signatures are associated with CMA, which differ from those of dietary milk elimination. Moreover, HF consumption affects the gut microbiome of children who develop tolerance.

Rapid GIT transit time in volant vertebrates, with implications for convergence in microbiome composition

Flying birds and bats have simplified gastrointestinal tracts (GITs) and low intestinal mass to facilitate flight. Previous work showed reduced GIT transit times in birds relative to other vertebrates-but GIT transit has never been collectively quantified for bats. Unique among mammals, bat GIT microbiomes are dominated by Pseudomonadota bacteria (previously Proteobacteria), which also dominate the microbiomes of flying birds - we hypothesized this convergence to result from rapid GIT transit times for both volant taxa. We conducted a meta-analysis of vertebrate GIT transit times which showed that bats and flying birds have significantly faster transit times relative to nonvolant vertebrates. Additionally, within the bat order (Chiroptera), we demonstrated decreasing transit times associated with increasing body mass, a pattern contrasting other vertebrates (including volant birds) and possibly influencing GIT microbiome composition. This inverted mass-transit association is likely driven by diet as fruit- and nectar-consuming Pteropodids are the largest of all bats.

Pre- to Postbiotics: The Beneficial Roles of Pediatric Dysbiosis Associated with Inflammatory Bowel Diseases

Probiotics are "live microorganisms which, when administered in adequate amount, confer health benefits on the host". They can be found in certain foods like yogurt and kefir and in dietary supplements. The introduction of bacterial derivatives has not only contributed to disease control but has also exhibited promising outcomes, such as improved survival rates, immune enhancement, and growth promotion effects. It is interesting to note that the efficacy of probiotics goes beyond the viability of the bacteria, giving rise to concepts like paraprobiotics, non-viable forms of probiotics, and postbiotics. Paraprobiotics offer various health benefits in children with intestinal dysbiosis, contributing to improved digestive health, immune function, and overall well-being. In this review, the potential of these therapeutic applications as alternatives to pharmacological agents for treating pediatric intestinal dysbiosis will be thoroughly evaluated. This includes an analysis of their efficacy, safety, long-term benefits, and their ability to restore gut microbiota balance, improve digestive health, enhance immune function, and reduce inflammation. The aim is to determine if these non-pharmacological interventions can effectively and safely manage intestinal dysbiosis in children, reducing the need for conventional medications and their side effects.

Both pathogen and host dynamically adapt pH responses along the intestinal tract during enteric bacterial infection

Enteric pathogens navigate distinct regional microenvironments within the intestine that cue important adaptive behaviors. We investigated the response of Citrobacter rodentium, a model of human pathogenic Escherichia coli infection in mice, to regional gastrointestinal pH. We found that small intestinal pH (4.4-4.8) triggered virulence gene expression and altered cell morphology, supporting initial intestinal attachment, while higher pH, representative of C. rodentium's replicative niches further along the murine intestine, supported pathogen growth. Gastric pH, a key barrier to intestinal colonization, caused significant accumulation of intra-bacterial reactive oxygen species (ROS), inhibiting growth of C. rodentium and related human pathogens. Within-host adaptation increased gastric acid survival, which may be due to a robust acid tolerance response (ATR) induced at colonic pH. However, the intestinal environment changes throughout the course of infection. We found that murine gastric pH decreases postinfection, corresponding to increased serum gastrin levels and altered host expression of acid secretion-related genes. Similar responses following Salmonella infection may indicate a protective host response to limit further pathogen ingestion. Together, we highlight interlinked bacterial and host adaptive pH responses as an important component of host-pathogen coevolution.

Endogenous ethanol production in health and disease

The gut microbiome exerts metabolic actions on distal tissues and organs outside the intestine, partly through microbial metabolites that diffuse into the circulation. The disruption of gut homeostasis results in changes to microbial metabolites, and more than half of the variance in the plasma metabolome can be explained by the gut microbiome. Ethanol is a major microbial metabolite that is produced in the intestine of nearly all individuals; however, elevated ethanol production is associated with pathological conditions such as metabolic dysfunction-associated steatotic liver disease and auto-brewery syndrome, in which the liver's capacity to metabolize ethanol is surpassed. In this Review, we describe the mechanisms underlying excessive ethanol production in the gut and the role of ethanol catabolism in mediating pathogenic effects of ethanol on the liver and host metabolism. We conclude by discussing approaches to target excessive ethanol production by gut bacteria.

The Therapeutic Potential of the Specific Intestinal Microbiome (SIM) Diet on Metabolic Diseases

Exploring the intricate crosstalk between dietary prebiotics and the specific intestinal microbiome (SIM) is intriguing in explaining the mechanisms of current successful dietary interventions, including the Mediterranean diet and high-fiber diet. This knowledge forms a robust basis for developing a new natural food therapy. The SIM diet can be measured and evaluated to establish a reliable basis for the management of metabolic diseases, such as diabetes, metabolic (dysfunction)-associated fatty liver disease (MAFLD), obesity, and metabolic cardiovascular disease. This review aims to delve into the existing body of research to shed light on the promising developments of possible dietary prebiotics in this field and explore the implications for clinical practice. The exciting part is the crosstalk of diet, microbiota, and gut-organ interactions facilitated by producing short-chain fatty acids, bile acids, and subsequent metabolite production. These metabolic-related microorganisms include Butyricicoccus, Akkermansia, and Phascolarctobacterium. The SIM diet, rather than supplementation, holds the promise of significant health consequences via the prolonged reaction with the gut microbiome. Most importantly, the literature consistently reports no adverse effects, providing a strong foundation for the safety of this dietary therapy.

Anthocyanins-gut microbiota-health axis: A review

Anthocyanins are a subclass of flavonoids responsible for color in some fruits and vegetables with potent antioxidative capacity. During digestion, a larger proportion of dietary anthocyanins remains unabsorbed and reach the large intestine where they interact with the gut microbiota. Anthocyanins can modulate gut microbial populations to improve diversity and the proportion of beneficial populations, leading to alterations in short chain fatty acid and bile acid production. Some anthocyanins can be degraded into colonic metabolites, such as phenolic acids, which accumulate in the body and regulate a range of biological activities. Here we provide an overview of the effects of dietary anthocyanin consumption on gut microbial interactions, metabolism, and composition. Progression of chronic diseases has been strongly associated with imbalances in gut microbial populations. We therefore focus on the role of the gut microbiota as the 'mediator' that facilitates the therapeutic potential of anthocyanins against various chronic diseases, including obesity, type II diabetes, cardiovascular disease, neurodegenerative disease, inflammatory bowel disease, cancer, fatty liver disease, chronic kidney disease and osteoarthritis.

Metaproteomics reveals parallel utilization of colonic mucin glycans and dietary fibers by the human gut microbiota

A diet lacking dietary fibers promotes the expansion of gut microbiota members that can degrade host glycans, such as those on mucins. The microbial foraging on mucin has been associated with disruptions of the gut-protective mucus layer and colonic inflammation. Yet, it remains unclear how the co-utilization of mucin and dietary fibers affects the microbiota composition and metabolic activity. Here, we used 14 dietary fibers and porcine colonic and gastric mucins to study the dynamics of mucin and dietary fiber utilization by the human fecal microbiota in vitro. Combining metaproteome and metabolites analyses revealed the central role of the Bacteroides genus in the utilization of complex fibers together with mucin while Akkermansia muciniphila was the main utilizer of sole porcine colonic mucin but not gastric mucin. This study gives a broad overview of the colonic environment in response to dietary and host glycan availability.

The Non-Denatured Processing of Brasenia schreberi Mucilage-Characteristics of Hydrodynamic Properties and the Effect on In Vivo Functions

Food non-denatured processes, such as freeze-drying and grinding, are commonly applied to raw materials with good bioactive functions. Although the functional components are maintained, whether structural and physical changes impact the in vivo function is often ignored in practical situations. Brasenia schreberi mucilage (BSM) has a significant alleviation effect on DSS-induced colitis. This work focused on the influence of non-denatured manufacture on the colonic benefits of BSM-based products. First, three forms of products including fresh mucilage (FM), freeze-dried products (FS), and freeze-dried powder (FP) were prepared. Then, their in vitro physiochemical properties were compared, analyzing their influence on the gut inflammation degree, microbial composition, and SCFA production in mice. The results suggested that the water retention rate of FS and FP was decreased to 34.59 ± 3.85%, and 9.93 ± 1.76%. The viscosity of FM, FS, and FP was 20.14 Pa∙s, 4.92 Pa∙s, and 0.41 Pa∙s, respectively. The freeze-drying and grinding process also damaged the lamellar microstructure of BSM. Then, animal tests showed that colitis mice intervened with FM, FS, and FP had disease activity scores of 2.03, 3.95, and 4.62. Meanwhile, FM notably changed the gut microbial composition and significantly increased propionate and butyrate levels. It seemed that the distinct colitis alleviation efficacy of BSM-based products is attributed to different hydrodynamic properties in the gut. FM had relatively higher viscosity and correspondingly high nutritional density in the gut lumen, which stimulates Firmicutes growth and promotes butyrate production, and thereby exhibited the best efficiency on protecting from colitis.

Effects of proton pump inhibitors on inflammatory bowel disease: An updated review

Inflammatory bowel disease (IBD) is believed to be caused by various factors, including abnormalities in disease susceptibility genes, environmental factors, immune factors, and intestinal bacteria. Proton pump inhibitors (PPIs) are the primary drugs used to treat acid-related diseases. They are also commonly prescribed to patients with IBD. Recent studies have suggested a potential association between the use of certain medications, such as PPIs, and the occurrence and progression of IBD. In this review, we summarize the potential impact of PPIs on IBD and analyze the underlying mechanisms. Our findings may provide insights for conducting further investigations into the effects of PPIs on IBD and serve as an important reminder for physicians to exercise caution when prescribing PPIs to patients with IBD.

Genetic association of the gut microbiota with epigenetic clocks mediated by inflammatory cytokines: a Mendelian randomization analysis

Background

A new aging biomarker epigenetic clock has been developed. There exists a close link between aging and gut microbiota, which may be mediated by inflammatory cytokines. However, the relationship between the epigenetic clock, gut microbiota, and the mediating substances is unclear.

Methods

Two large genome-wide association meta-analyses were analyzed by two-sample Mendelian randomization. The results between gut microbiota and epigenetic clock were investigated using the four methods (Inverse variance weighted, MR-Egger, weighted median, MR-PRESSO). Genetic correlation was measured by Linked disequilibrium score regression (LDSC). The correctness of the study direction was checked by the Steiger test. Cochran's Q statistic and MR-Egger intercept were used as sensitivity analyses of the study. The two-step method was used to examine the mediating role of inflammatory cytokines. We use the Benjamini-Hochberg correction method to correct the P value.

Results

After FDR correction, multiple bacterial genera were significantly or suggestively associated with four epigenetic clocks (GrimAge, HannumAge, IEAA, PhenoAge). And we detected several inflammatory factors acting as mediators of gut microbiota and epigenetic clocks.

Conclusion

This study provides genetic evidence for a positive and negative link between gut microbiota and aging risk. We hope that by elucidating the genetic relationship and potential mechanisms between aging and gut microbiota, we will provide new avenues for continuing aging-related research and treatment.

Co-Supplementation of Baobab Fiber and Arabic Gum Synergistically Modulates the In Vitro Human Gut Microbiome Revealing Complementary and Promising Prebiotic Properties

Arabic gum, a high molecular weight heteropolysaccharide, is a promising prebiotic candidate as its fermentation occurs more distally in the colon, which is the region where most chronic colonic diseases originate. Baobab fiber could be complementary due to its relatively simple structure, facilitating breakdown in the proximal colon. Therefore, the current study aimed to gain insight into how the human gut microbiota was affected in response to long-term baobab fiber and Arabic gum supplementation when tested individually or as a combination of both, allowing the identification of potential complementary and/or synergetic effects. The validated Simulator of the Human Intestinal Microbial Ecosystem (SHIME®), an in vitro gut model simulating the entire human gastrointestinal tract, was used. The microbial metabolic activity was examined, and quantitative 16S-targeted Illumina sequencing was used to monitor the gut microbial composition. Moreover, the effect on the gut microbial metabolome was quantitatively analyzed. Repeated administration of baobab fiber, Arabic gum, and their combination had a significant effect on the metabolic activity, diversity index, and community composition of the microbiome present in the simulated proximal and distal colon with specific impacts on Bifidobacteriaceae and Faecalibacterium prausnitzii. Despite the lower dosage strategy (2.5 g/day), co-supplementation of both compounds resulted in some specific synergistic prebiotic effects, including a biological activity throughout the entire colon, SCFA synthesis including a synergy on propionate, specifically increasing abundance of Akkermansiaceae and Christensenellaceae in the distal colon region, and enhancing levels of spermidine and other metabolites of interest (such as serotonin and ProBetaine).

Why does increased microbial fermentation in the human colon shift toward butyrate?

The microbial community of the human large intestine mainly ferments dietary fiber to short chain fatty acids (SCFAs), which are efficiently absorbed by the host. The three major SCFAs (acetate, propionate, and butyrate) have different fates within the body and different effects on health. A recent analysis of 10 human volunteer studies established that the proportions of these SCFA in fecal samples significantly shifted towards butyrate as the overall concentration of SCFA increased. Butyrate plays a key role in gut health and is preferentially utilized as an energy source by the colonic epithelium. Here we discuss possible mechanisms that underlie this 'butyrate shift'; these include the selection for butyrate-producing bacteria within the microbiota by certain types of fiber, and the possibility of additional butyrate formation from lactate and acetate by metabolite cross-feeding. However, a crucial factor appears to be the pH in the proximal colon, which decreases as the SCFA concentrations increase. A mildly acidic pH has been shown to have an important impact on microbial competition and on the stoichiometry of butyrate production. Understanding these complex interactions has been greatly aided by the refinement of theoretical models of the colonic microbiota that assume a small number (10) of microbial functional groups (MFGs).

In-depth characterization of a selection of gut commensal bacteria reveals their functional capacities to metabolize dietary carbohydrates with prebiotic potential

The microbial utilization of dietary carbohydrates is closely linked to the pivotal role of the gut microbiome in human health. Inherent to the modulation of complex microbial communities, a prebiotic implies the selective utilization of a specific substrate, relying on the metabolic capacities of targeted microbes. In this study, we investigated the metabolic capacities of 17 commensal bacteria of the human gut microbiome toward dietary carbohydrates with prebiotic potential. First, in vitro experiments allowed the classification of bacterial growth and fermentation profiles in response to various carbon sources, including agave inulin, corn fiber, polydextrose, and citrus pectin. The influence of phylogenetic affiliation appeared to statistically outweigh carbon sources in determining the degree of carbohydrate utilization. Second, we narrowed our focus on six commensal bacteria representative of the Bacteroidetes and Firmicutes phyla to perform an untargeted high-resolution liquid chromatography-mass spectrometry metabolomic analysis: Bacteroides xylanisolvens, Bacteroides thetaiotaomicron, Bacteroides intestinalis, Subdoligranulum variabile, Roseburia intestinalis, and Eubacterium rectale exhibited distinct metabolomic profiles in response to different carbon sources. The relative abundance of bacterial metabolites was significantly influenced by dietary carbohydrates, with these effects being strain-specific and/or carbohydrate-specific. Particularly, the findings indicated an elevation in short-chain fatty acids and other metabolites, including succinate, gamma-aminobutyric acid, and nicotinic acid. These metabolites were associated with putative health benefits. Finally, an RNA-Seq transcriptomic approach provided deeper insights into the underlying mechanisms of carbohydrate metabolization. Restricting our focus on four commensal bacteria, including B. xylanisolvens, B. thetaiotaomicron, S. variabile, and R. intestinalis, carbon sources did significantly modulate the level of bacterial genes related to the enzymatic machinery involved in the metabolization of dietary carbohydrates. This study provides a holistic view of the molecular strategies induced during the dynamic interplay between dietary carbohydrates with prebiotic potential and gut commensal bacteria.

IMPORTANCE

This study explores at a molecular level the interactions between commensal health-relevant bacteria and dietary carbohydrates holding prebiotic potential. We showed that prebiotic breakdown involves the specific activation of gene expression related to carbohydrate metabolism. We also identified metabolites produced by each bacteria that are potentially related to our digestive health. The characterization of the functional activities of health-relevant bacteria toward prebiotic substances can yield a better application of prebiotics in clinical interventions and personalized nutrition. Overall, this study highlights the importance of identifying the impact of prebiotics at a low resolution of the gut microbiota to characterize the activities of targeted bacteria that can play a crucial role in our health.

Impacts of pancreatic exocrine insufficiency on gut microbiota

Pancreatic exocrine insufficiency (PEI) can be induced by various kinds of diseases, including chronic pancreatitis, acute pancreatitis, and post-pancreatectomy. The main pathogenetic mechanism of PEI involves the decline of trypsin synthesis, disorder of pancreatic fluid flow, and imbalance of secretion feedback. Animal studies have shown that PEI could induce gut bacterial overgrowth and dysbiosis, with the abundance of Lactobacillus and Bifidobacterium increasing the most, which could be partially reversed by pancreatic enzyme replacement therapy. Clinical studies have also confirmed the association between PEI and the dysbiosis of gut microbiota. Pancreatic exocrine secretions and changes in duodenal pH as well as bile salt malabsorption brought about by PEI may affect and shape the abundance and composition of gut microbiota. In turn, the gut microbiota may impact the pancreatic exocrine acinus through potential bidirectional crosstalk. Going forward, more and higher-quality studies are needed that focus on the mechanism underlying the impact of PEI on the gut microbiota.

Structural characterization and immunomodulatory activity of a polysaccharide from Dioscotea opposita

The purified polysaccharides fraction, DOP-2, was prepared from Dioscorea opposita Thunb (D. opposita). This study combined in vitro and in vivo experiments to comprehensively investigate the index changes in RAW264.7 cells and immunocompromised mice under DOP-2 intervention, aiming to elucidate the potential mechanisms of immunomodulatory effects of DOP-2. DOP-2 (10 ∼ 500 μg/mL) significantly elevated the levels of NO, interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) factors secreted by RAW264.7 cells, and restored the body weight of immunosuppressed mice and improve the degree of injury to the immune organ index, resulting in significant immunomodulatory effects. Notably, DOP-2 promoted the production of short-chain fatty acids (SCFAs) in immunosuppressed mice and modulated the composition of their gut microflora. These findings highlight the potential benefits of DOP-2 therapy in improving immune function and gut health, and will provide a theoretical basis for the application of D. opposita polysaccharides as an immunomodulatory adjuvant.

Cold exposure, gut microbiota and health implications: A narrative review

Temperature has been recognized as an important environmental factor affecting the composition and function of gut microbiota (GM). Although research on high-temperature impacts has been well studied, knowledge about the effect of cold exposure on GM remains limited. This narrative review aims to synthesize the latest scientific findings on the impact of cold exposure on mammalian GM, and its potential health implications. Chronic cold exposure could disrupt the α-diversity and the composition of GM in both experimental animals and wild-living hosts. Meanwhile, cold exposure could impact gut microbial metabolites, such as short-chain fatty acids. We also discussed plausible biological pathways and mechanisms by which cold-induced changes may impact host health, including metabolic homeostasis, fitness and thermogenesis, through the microbiota-gut-brain axis. Intriguingly, alterations in GM may provide a tool for favorably modulating the host response to the cold temperature. Finally, current challenges and future perspectives are discussed, emphasizing the need for translational research in humans. GM could be manipulated by utilizing nutritional strategies, such as probiotics and prebiotics, to deal with cold-related health issues and enhance well-being in populations living or working in cold environments.

The effect of in vitro simulated colonic pH gradients on microbial activity and metabolite production using common prebiotics as substrates

BACKGROUND

The interplay between gut microbiota (GM) and the metabolization of dietary components leading to the production of short-chain fatty acids (SCFAs) is affected by a range of factors including colonic pH and carbohydrate source. However, there is still only limited knowledge on how the GM activity and metabolite production in the gastrointestinal tract could be influenced by pH and the pH gradient increases along the colon.

RESULTS

Here we investigate the effect of pH gradients corresponding to levels typically found in the colon on GM composition and metabolite production using substrates inulin, lactose, galactooligosaccharides (GOS), and fructooligosaccharide (FOS) in an in vitro colon setup. We investigated 3 different pH regimes (low, 5.2 increasing to 6.4; medium, 5.6 increasing to 6.8 and high, 6.0 increasing to 7.2) for each fecal inoculum and found that colonic pH gradients significantly influenced in vitro simulated GM structure, but the influence of fecal donor and substrate was more pronounced. Low pH regimes strongly influenced GM with the decreased relative abundance of Bacteroides spp. and increased Bifidobacterium spp. Higher in vitro simulated colonic pH promoted the production of SCFAs in a donor- and substrate-dependent manner. The butyrate producer Butyricimonas was enriched at higher pH conditions, where also butyrate production was increased for inulin. The relative abundance of Phascolarctobacterium, Bacteroides, and Rikenellaceae also increased at higher colonic pH, which was accompanied by increased production of propionate with GOS and FOS as substrates.

CONCLUSIONS

Together, our results show that colonic substrates such as dietary fibres influence GM composition and metabolite production, not only by being selectively utilized by specific microbes, but also because of their SCFA production, which in turn also influences colonic pH and overall GM composition and activity. Our work provides details about the effect of the gradients of rising pH from the proximal to distal colon on fermenting dietary substrates in vitro and highlights the importance of considering pH in GM research.

Dietary Fibre for the Prevention of Post-Pancreatitis Diabetes Mellitus: A Review of the Literature and Future Research Directions

Post-pancreatitis diabetes mellitus-the most common sequela of pancreatitis-leads to poorer glycaemic control compared with type 2 diabetes. Because post-pancreatitis diabetes mellitus is an exemplar of secondary diabetes (with a clear underlying cause), much post-pancreatitis diabetes mellitus is preventable or treatable early. Earlier literature established the important role of dietary fibre in reducing plasma glucose in individuals with type 2 diabetes. The present review benchmarks available evidence on the role of habitual dietary fibre intake in pancreatitis and post-pancreatitis diabetes mellitus. It also paves the way for future research on the use of dietary fibre in the post-pancreatitis setting.

Characterization of novel endo-β-N-acetylglucosaminidases from intestinal Barnesiella intestinihominis that hydrolyze multi-branched complex-type N-glycans

Endo-β-N-acetylglucosaminidases (ENGases) are enzymes that hydrolyze N-linked glycans. Many ENGases have been characterized, but few have been identified with hydrolytic activity towards multi-branched complex-type N-glycans. In this study, three candidate ENGases were identified from Barnesiella intestinihominis based on database searches and phylogenetic analysis. A domain search identified the N x E motif in all three candidates, suggesting that they were members of glycosyl hydrolase family 85 (GH85). The three candidate ENGases, named Endo-BIN1, Endo-BIN2, and Endo-BIN3, were expressed in Escherichia coli cells, and their hydrolytic activity towards N-glycans and glycoproteins was measured by high performance liquid chromatography analysis and SDS-PAGE analysis. All ENGases showed hydrolytic activity towards glycoproteins, but only Endo-BIN2 and Endo-BIN3 showed hydrolytic activity towards pyridylaminated N-glycans. The optimum pH of Endo-BIN1, Endo-BIN2, and End-BIN3 was pH 6.5, 4.0, and 7.0, respectively. We measured substrate specificities of Endo-BIN2 and Endo-BIN3 towards pyridylaminated N-glycans, and found that the two Endo-BIN enzymes showed similar substrate specificity, preferring bi-antennary complex-type N-glycans with galactose or α2,6-linked sialic acid residues at the non-reducing ends. Endo-BIN2 and Endo-BIN3 were also able to hydrolyze multi-branched complex-type N-glycans. SDS-PAGE analysis revealed that all Endo-BIN enzymes were capable of releasing complex-type N-glycans from glycoproteins such as rituximab, transferrin, and fetuin. We expect that B. intestinihominis possesses ENGases to facilitate the utilization of complex-type N-glycans from host cells. These findings will have applications in N-glycan remodeling of glycoproteins and the development of pharmaceuticals.

Presence of digestible starch impacts in vitro fermentation of resistant starch

Starch is an important energy source for humans. Starch escaping digestion in the small intestine will transit to the colon to be fermented by gut microbes. Many gut microbes express α-amylases that can degrade soluble starch, but only a few are able to degrade intrinsic resistant starch (RS), which is insoluble and highly resistant to digestion (≥80% RS). We studied the in vitro fermentability of eight retrograded starches (RS-3 preparations) differing in rapidly digestible starch content (≥70%, 35-50%, ≤15%) by a pooled adult faecal inoculum and found that fermentability depends on the digestible starch fraction. Digestible starch was readily fermented yielding acetate and lactate, whereas resistant starch was fermented much slower generating acetate and butyrate. Primarily Bifidobacterium increased in relative abundance upon digestible starch fermentation, whereas resistant starch fermentation also increased relative abundance of Ruminococcus and Lachnospiraceae. The presence of small fractions of total digestible starch (±25%) within RS-3 preparations influenced the fermentation rate and microbiota composition, after which the resistant starch fraction was hardly fermented. By short-chain fatty acid quantification, we observed that six individual faecal inocula obtained from infants and adults were able to ferment digestible starch, whereas only one adult faecal inoculum was fermenting intrinsic RS-3. This suggests that, in contrast to digestible starch, intrinsic RS-3 is only fermentable when specific microbes are present. Our data illustrates that awareness is required for the presence of digestible starch during in vitro fermentation of resistant starch, since such digestible fraction might influence and overrule the evalution of the prebiotic potential of resistant starches.

The relationship between the gut microbiome and resistance training: a rapid review

The human gut microbiome is attracting increasing attention because of its overall effect on health. Several reviews have investigated the impact of physical activity on the gut microbiome; however, these predominantly concentrate on either endurance or a combination of physical activities. This study aims to describe the effect of resistance or strength training on the gut microbiome of a human population. This rapid review follows the guidelines of the Cochrane Rapid Reviews Guidance along with PRISMA. A review of the literature was carried out using articles indexed by PubMed, Scopus, and Web of Science published in the last 12 years. None of the seven studies included find significant change in the gut microbiome in terms of bacterial taxa composition or overall diversity, though the results show that resistance training might decrease the zonulin level and increase mucin production and thereby reduce inflammation in the gut. Interestingly, two studies point to a gut-muscle axis connection and this is discussed in our paper. However, due to the small number of existing studies and certain methodological disagreements, it was hard to find a consensus on the relationship between the gut microbiome and resistance training.

Gut microbiota-derived butyrate selectively interferes with growth of carbapenem-resistant Escherichia coli based on their resistance mechanism

We investigated consequences of resistance acquisition in Escherichia coli clinical isolates during anaerobic (continuous culture) growth and examined their sensitivity to butyrate, a hallmark metabolite of healthy gut microbiota. Strains were stratified based on carrying either a carbapenemase (CARB) or displaying porin malfunctioning (POR). POR displayed markedly altered growth efficiencies, lower membrane stability and increased sensitivity to butyrate compared with CARB. Major differences in global gene expression between the two groups during anaerobic growth were revealed involving increased expression of alternative substrate influx routes, the stringent response and iron acquisition together with lower expression of various stress response systems in POR. Longitudinal analyses during butyrate wash-in showed common responses for all strains as well as specific features of POR that displayed strong initial "overshoot" reactions affecting various stress responses that balanced out over time. Results were partly reproduced in a mutant strain verifying porin deficiencies as the major underlying mechanism for results observed in clinical isolates. Furthermore, direct competition experiments confirmed butyrate as key for amplifying fitness disadvantages based on porin malfunctioning. Results provide new (molecular) insights into ecological consequences of resistance acquisition and can assist in developing measures to prevent colonization and infection based on the underlying resistance mechanism.

A flexible high-throughput cultivation protocol to assess the response of individuals' gut microbiota to diet-, drug-, and host-related factors

The anaerobic cultivation of fecal microbiota is a promising approach to investigating how gut microbial communities respond to specific intestinal conditions and perturbations. Here, we describe a flexible protocol using 96-deepwell plates to cultivate stool-derived gut microbiota. Our protocol aims to address gaps in high-throughput culturing in an anaerobic chamber. We characterized the influence of the gas phase on the medium chemistry and microbial physiology and introduced a modular medium preparation process to enable the testing of several conditions simultaneously. Furthermore, we identified a medium formulation that maximized the compositional similarity of ex vivo cultures and donor microbiota while limiting the bloom of Enterobacteriaceae. Lastly, we validated the protocol by demonstrating that cultivated fecal microbiota responded similarly to dietary fibers (resistant dextrin, soluble starch) and drugs (ciprofloxacin, 5-fluorouracil) as reported in vivo. This high-throughput cultivation protocol has the potential to facilitate culture-dependent studies, accelerate the discovery of gut microbiota-diet-drug-host interactions, and pave the way to personalized microbiota-centered interventions.

Gut-bacteria derived membrane vesicles and host metabolic health: a narrative review

The intestinal microbiota, consisting of an estimated 10^10-10^11 organisms, regulate physiological processes involved in digestion, metabolism, and immunity. Surprisingly, these intestinal microorganisms have been found to influence tissues that are not directly in contact with the gut, such as adipose tissue, the liver, skeletal muscle, and the brain. This interaction takes place even when intestinal barrier function is uncompromised. An increasing body of evidence suggests that bacterial membrane vesicles (bMVs), in addition to bacterial metabolites such as short-chain fatty acids, are able to mediate effects of the microbiota on these host tissues. The ability of bMVs to dissipate from the intestinal lumen into systemic circulation hereby facilitates the transport and presentation of bacterial components and metabolites to host organs. Importantly, there are indications that the interaction between bMVs and tissues or immune cells may play a role in the etiology of (chronic metabolic) disease. For example, the gut-derived bMV-mediated induction of insulin resistance in skeletal muscle cells and pro-inflammatory signaling by adipocytes possibly underlies diseases such as type 2 diabetes and obesity. Here, we review the current knowledge on bMVs in the microbiota's effects on host energy/substrate metabolism with a focus on etiological roles in the onset and progression of metabolic disease. We furthermore illustrate that vesicle production by bacterial microbiota could potentially be modulated through lifestyle intervention to improve host metabolism.

Toxic vascular effects of polystyrene microplastic exposure

Polystyrene microplastics (PSMPs) are some of the most common microplastic components, and the resulting pollution has become a global problem. Extensive studies have been conducted on the toxic effects of PSMPs on the heart, lungs, liver, kidneys, nerves, intestines and other tissues. However, the impact of PSMPs on vascular toxicity is poorly understood at present. The aim of this study was to reveal the vascular toxicity of microplastics (MPs). Patients were assigned to a calcification group (25 patients) or a non-calcification group (22 patients) based on the presence or absence of calcification in the thoracic aorta wall. We detected 7 polymer types in human feces. Patients with vascular calcification (VC) had higher levels of total MPs, polypropylene (PP) and polystyrene (PS) in feces than patients without VC. The thoracic aortic calcification score was significantly positively correlated with the total MP abundance (Spearman r = 0.8109, p < 0.0001), PP (Spearman r = 0.7211, p = 0.0160) and PS (Spearman r = 0.6523, p = 0.0471) in feces. We then explored the effects of PSMP exposure on normal and vitamin D3 + nicotine (VDN)-treated rats. PSMP exposure induced mild VC in normal rats and aggravated VC in VDN-treated rats. PSMP exposure disturbed the gut microbiota, causing Proteobacteria and Escherichia_Shigella to be the dominant phylum and genus, respectively. It also induced intestinal inflammatory responses in normal rats, aggravated intestinal inflammation in VDN-treated rats, impaired the intestinal mucosal barrier, and increased intestinal permeability. This study provides a theoretical basis for the risk assessment of MP-induced cardiovascular disease.

β-l-Arabinofurano-cyclitol Aziridines Are Covalent Broad-Spectrum Inhibitors and Activity-Based Probes for Retaining β-l-Arabinofuranosidases

GH127 and GH146 microorganismal retaining β-l-arabinofuranosidases, expressed by human gut microbiomes, feature an atypical catalytic domain and an unusual mechanism of action. We recently reported that both Bacteroides thetaiotaomicron BtGH146 and Bifidobacterium longum HypBA1 are inhibited by β-l-arabinofuranosyl cyclophellitol epoxide, supporting the action of a zinc-coordinated cysteine as a catalytic nucleophile, where in most retaining GH families, an aspartate or glutamate is employed. This work presents a panel of β-l-arabinofuranosyl cyclophellitol epoxides and aziridines as mechanism-based BtGH146/HypBA1 inhibitors and activity-based probes. The β-l-arabinofuranosyl cyclophellitol aziridines both inhibit and label β-l-arabinofuranosidase efficiently (however with different activities), whereas the epoxide-derived probes favor BtGH146 over HypBA1. These findings are accompanied by X-ray structural analysis of the unmodified β-l-arabinofuranosyl cyclophellitol aziridine in complex with both isozymes, which were shown to react by nucleophilic opening of the aziridine, at the pseudoanomeric carbon, by the active site cysteine nucleophile to form a stable thioether bond. Altogether, our activity-based probes may serve as chemical tools for the detection and identification of low-abundance β-l-arabinofuranosidases in complex biological samples.

Metabolic Syndrome: A Narrative Review from the Oxidative Stress to the Management of Related Diseases

Metabolic syndrome (MS) is a growing disorder affecting thousands of people worldwide, especially in industrialised countries, increasing mortality. Oxidative stress, hyperglycaemia, insulin resistance, inflammation, dysbiosis, abdominal obesity, atherogenic dyslipidaemia and hypertension are important factors linked to MS clusters of different pathologies, such as diabesity, cardiovascular diseases and neurological disorders. All biochemical changes observed in MS, such as dysregulation in the glucose and lipid metabolism, immune response, endothelial cell function and intestinal microbiota, promote pathological bridges between metabolic syndrome, diabesity and cardiovascular and neurodegenerative disorders. This review aims to summarise metabolic syndrome's involvement in diabesity and highlight the link between MS and cardiovascular and neurological diseases. A better understanding of MS could promote a novel strategic approach to reduce MS comorbidities.