Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth

Faecalibacterium prausnitzii regulates carbohydrate metabolic functions of the gut microbiome in C57BL/6 mice

The probiotic impact of microbes on host metabolism and health depends on both host genetics and bacterial genomic variation. Faecalibacterium prausnitzii is the predominant human gut commensal emerging as a next-generation probiotic. Although this bacterium exhibits substantial intraspecies diversity, it is unclear whether genetically distinct F. prausnitzii strains might lead to functional differences in the gut microbiome. Here, we isolated and characterized a novel F. prausnitzii strain (UT1) that belongs to the most prevalent but underappreciated phylogenetic clade in the global human population. Genome analysis showed that this butyrate-producing isolate carries multiple putative mobile genetic elements, a clade-specific defense system, and a range of carbohydrate catabolic enzymes. Multiomic approaches were used to profile the impact of UT1 on the gut microbiome and associated metabolic activity of C57BL/6 mice at homeostasis. Both 16S rRNA and metagenomic sequencing demonstrated that oral administration of UT1 resulted in profound microbial compositional changes including a significant enrichment of Lactobacillus, Bifidobacterium, and Turicibacter. Functional profiling of the fecal metagenomes revealed a markedly higher abundance of carbohydrate-active enzymes (CAZymes) in UT1-gavaged mice. Accordingly, UT1-conditioned microbiota possessed the elevated capability of utilizing starch in vitro and exhibited a lower availability of microbiota-accessible carbohydrates in the gut. Further analysis uncovered a functional network wherein UT1 reduced the abundance of mucin-degrading CAZymes and microbes, which correlated with a concomitant reduction of fecal mucin glycans. Collectively, our results reveal a crucial role of UT1 in facilitating the carbohydrate metabolism of the gut microbiome and expand our understanding of the genetic and phenotypic diversity of F. prausnitzii.

Bacteria-derived 3-hydroxydodecanoic acid induces a potent anti-tumor immune response via the GPR84 receptor

Despite advances in cancer treatment, the development of effective therapies remains an urgent unmet need. Here, we investigate the potential of bacteria-derived metabolites as a therapeutic alternative for the treatment of cancer. We detect 3-hydroxydodecanedioic acid in the serum of tumor-bearing mice treated with serum from mice previously supplemented with a mix of Clostridiales bacteria. Further, 3-hydroxydodecanoic acid, an intermediate derivative between dodecanoic and 3-hydroxydodecanedioic acids, exhibits a strong anti-tumor response via GPR84 receptor signaling and enhances CD8+ T cell infiltration and cytotoxicity within tumor tissue in multiple cancer models. Metabolomics analysis of colorectal cancer patient serum reveals an inverse correlation between the abundance of these metabolites and advanced disease stages. Our findings provide a strong rationale for 3-hydroxydodecanoic acid and the GPR84 receptor to be considered as promising therapeutic targets for cancer treatment.

Faecalibacterium prausnitzii Is Associated with Disease Severity in MASLD but Its Supplementation Does Not Improve Diet-Induced Steatohepatitis in Mice

The gut microbiota plays an important role in the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD). In this study, we aimed to evaluate the role of the butyrate-producing bacterium Faecalibacterium prausnitzii in MASLD and whether supplementation with butyrate-producing bacteria, in particular Faecalibacterium prausnitzii, can ameliorate diet-induced steatohepatitis in mice. The relative abundance of the genus Faecalibacterium and its most abundant strain Faecalibacterium prausnitzii was determined by 16S rRNA sequencing and quantitative polymerase chain reaction (qPCR), respectively, in 95 participants with MASLD and 19 healthy control subjects. Butyrate and butyrate-producing bacteria (Faecalibacterium prausnitzii and Coprococcus comes) were gavaged to C57BL/6 mice fed a steatohepatitis-inducing diet. The fecal relative abundance of Faecalibacterium and Faecalibacterium prausnitzii was decreased in subjects with MASLD versus healthy controls and lower in individuals with MASLD and stage 3-4 fibrosis versus those with stage 0-2 fibrosis. Sodium-butyrate supplementation improved hepatic steatosis in mice on high-fat diet (HFD). Gavage of various butyrate-producing bacteria including Faecalibacterium prausnitzii and Coprococcus comes isolated from humans did not improve HFD-induced liver disease in mice. Although the abundance of Faecalibacterium prausnitzii is associated with MASLD severity in humans, its gavage to mice does not improve experimental diet-induced liver disease.

Akkermansia muciniphila: promises and pitfallsfor next-generation beneficial microorganisms

Akkermansia muciniphila, a microorganism ubiquitously colonizing the mucosal layer of the human gut, has garnered significant scientific interest as a promising candidate for probiotic therapeutics. Its persistent identification in both laboratory and living organism studies underscores its potential physiological benefits, positioning it as a bacterium of paramount importance in promoting host health. This review examines the diversity and abundance of gut microbiota members, emphasizing the identification of microbial species engaged in cross-feeding networks with A. muciniphila. Insightful exploration into the mechanisms of cross-feeding, including mucin-derived nutrient exchange and metabolite production, unveils the intricate dynamics shaping microbial community stability. Such interactions contribute not only to the availability of essential nutrients within the gut environment but also to the production of metabolites influencing microbial community dynamics and host health. In conclusion, the cumulative evidence from in vitro and in vivo perspectives substantiates the notion that A. muciniphila holds tremendous promise as a next-generation probiotic. By leveraging its unique physiological benefits, particularly in mucosal health and metabolic regulation, A. muciniphila stands poised to revolutionize the landscape of probiotic interventions for enhanced host well-being.

Gut Microbiota Predicts Treatment Response to Empagliflozin Among MASLD Patients Without Diabetes Mellitus

BACKGROUND AND AIM

We aimed to investigate whether gut microbiota could predict the treatment response to pharmacological agents among metabolic dysfunction-associated steatotic liver disease (MASLD) patients without diabetes mellitus (DM), as data are lacking.

METHODS

We prospectively followed up non-diabetic MASLD patients who used empagliflozin. Clinical, anthropometric, laboratory assessments and magnetic resonance imaging-proton density fat fraction (MRI-PDFF) were performed from baseline to week 52 (EOT). Baseline stool samples were collected, and shotgun DNA metagenomic sequencing was performed to profile microbiome. The primary outcome was treatment response to empagliflozin at EOT, defined as MRI-PDFF decline ≥ 30% at EOT from baseline. Linear discriminant analysis [LDA] effect size was used to identify putative bacterial species. Multivariable logistic regression was used to derive adjusted odds ratio (aOR) of outcome with bacterial species by adjusting for clinical factors.

RESULTS

Twenty-two (48.9%) of 45 patients (median age: 56.9 years [IQR: 51.0-63.2]; male: 23 [51.1%]) achieved treatment response at EOT. There was difference in alpha diversity (Shannon index: p < 0.001; Simpson index: p = 0.001) and beta diversity (p = 0.048) in baseline microbiome between treatment response and non-response groups. Faecalibacterium prausnitzii (log10LDAscore = 4.27), Lachnospira pectinoschiza (log10LDAscore = 3.99), Anaerostipes hadrus (log10LDAscore = 3.98), Roseburia faecis (log10LDAscore = 3.97), Roseburia inulinivorans (log10LDAscore = 3.58) and Agathobaculum butyriciproducens (log10LDAscore = 2.77) were enriched in the treatment response group. L. pectinoschiza (aOR: 34.1; p = 0.015), A. hadrus (aOR:35.0; p = 0.032) and A. butyriciproducens (aOR:22.3; p = 0.023) independently predicted treatment response but not clinical factors. These three species collectively predicted treatment response with AUROC of 0.89 (95% CI: 0.80-0.99).

CONCLUSIONS

Certain gut bacterial species, particularly the combination of A. hadrus, L. pectinoschiza and A. butyriciproducens, may predict treatment response to empagliflozin in MAFLD patients without DM.

Enterocloster clostridioformis protects against Salmonella pathogenesis and modulates epithelial and mucosal immune function

BACKGROUND

Promoting resistance to enteric pathogen infection is a core function of the gut microbiota; however, many of the specific host-commensal interactions that mediate this protection remain uncharacterised. To address this knowledge gap, we monocolonised germ-free mice with mouse-derived commensal microbes to screen for microbiota-induced resistance to Salmonella Typhimurium infection.

RESULTS

We identified Enterocloster clostridioformis as a protective species against S. Typhimurium infection. E. clostridioformis selectively upregulates resistin-like molecule β and cell cycle pathway expression at the level of caecal epithelial cells and increases T-regulatory cells in the underlying mucosal immune system, potentially contributing to reduced infection-induced pathology.

CONCLUSIONS

We highlight novel mechanisms of host-microbe interactions that can mediate microbiota-induced resistance to acute salmonellosis. In the backdrop of increasing antibiotic resistance, this study identifies novel potential avenues for further research into protective host responses against enteric infections and could lead to new therapeutic approaches. Video Abstract.

Identification and characterization of Faecalibacterium prophages rich in diversity-generating retroelements

Metagenomics has revealed the incredible diversity of phages within the human gut. However, very few of these phages have been subjected to in-depth experimental characterization. One promising method of obtaining novel phages for experimental characterization is through induction of the prophages integrated into the genomes of cultured gut bacteria. Here, we developed a bioinformatic approach to prophage identification that builds on prophage genomic properties, existing prophage-detecting software, and publicly available virome sequencing data. We applied our approach to 22 strains of bacteria belonging to the genus Faecalibacterium, resulting in identification of 15 candidate prophages, and validated the approach by demonstrating the activity of five prophages from four of the strains. The genomes of three active phages were identical or similar to those of known phages, while the other two active phages were not represented in the Viral RefSeq database. Four of the active phages possessed a diversity-generating retroelement (DGR), and one retroelement had two variable regions. DGRs of two phages were active at the time of the induction experiments, as evidenced by nucleotide variation in sequencing reads. We also predicted that the host range of two active phages may include multiple bacterial species. Finally, we noted that four phages were less prevalent in the metagenomes of inflammatory bowel disease patients compared to a general population cohort, a difference mainly explained by differences in the abundance of the host bacteria. Our study highlights the utility of prophage identification and induction for unraveling phage molecular mechanisms and ecological interactions.IMPORTANCEWhile hundreds of thousands of phage genomes have been discovered in metagenomics studies, only a few of these phages have been characterized experimentally. Here, we explore phage characterization through bioinformatic identification of prophages in genomes of cultured bacteria, followed by prophage induction. Using this approach, we detect the activity of five prophages in four strains of commensal gut bacteria Faecalibacterium. We further note that four of the prophages possess diversity-generating retroelements implicated in rapid mutation of phage genome loci associated with phage-host and phage-environment interactions and analyze the intricate patterns of retroelement activity. Our study highlights the potential of prophage characterization for elucidating complex molecular mechanisms employed by the phages.

Functional foods acting on gut microbiota-related wellness: The multi-unit in vitro colon model to assess gut ecological and functional modulation

The aim of this study was to investigate the effect of a functional probiotic cheese (FPC) on gut microbiota (GM), after simulated digestion performed by a multi-unit in vitro colon model (MICODE). Squacquerone-like cheese was produced using the starter Streptococcus thermophilus (control, CTRL), and supplemented with the probiotic Lacticaseibacillus rhamnosus, which was either subjected to high pressure homogenization (LrH) or not (Lr). Samples were stratified by cheese type, storage time, and colonic fermentation phase. Samples were then digested with MICODE and digests were characterized for ecological and functional profiles. The lactobacilli detected in Lr and LrH cheeses (9.0 log CFU/g) were represented by the probiotic strain L. rhamnosus and remained unchanged after storage at 4 °C. Lactobacilli levels in CTRLs increased from 1.5 log CFU/g to 2.0 log CFU/g after six days at 4 °C, while total coliforms remained below 1.5 log CFU/g in all samples. Real-time qPCR indicated a positive GM response after FPC simulated digestion, highlighting an abundance of bifidobacteria, lactobacilli and Clostridium group IV in LrH samples. Metataxonomy revealed higher levels of Firmicutes and Proteobacteria (p ≤ 0.05) after simulated digestion, as well as Megasphaera, Escherichia, Prevotella and Dorea. Moreover, an increase of short and medium chain fatty acids were detected by metabolomics. Overexpression of inferred KEGG metabolic pathways showed mainly fatty acids, novobiocin and amino acid metabolism. Understanding how functional foods can modify the GM may lead to the development of targeted microbiome-based therapies and the exploitation of these foods for the benefit of human health.

Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status

Ruminococcus gnavus is a gut bacterium found in > 90% of healthy individuals, but its increased abundance is also associated with chronic inflammatory diseases, particularly Crohn's disease. Nevertheless, its global distribution and intraspecies genomic variation remain understudied. By surveying 12,791 gut metagenomes, we recapitulated known associations with metabolic diseases and inflammatory bowel disease. We uncovered a higher prevalence and abundance of R. gnavus in Westernized populations and observed bacterial relative abundances up to 83% in newborns. Next, we built a resource of R. gnavus isolates (N = 45) from healthy individuals and Crohn's disease patients and generated complete R. gnavus genomes using PacBio circular consensus sequencing. Analysis of these genomes and publicly available high-quality draft genomes (N = 333 genomes) revealed multiple clades which separated Crohn's-derived isolates from healthy-derived isolates. Presumed R. gnavus virulence factors could not explain this separation. Bacterial genome-wide association study revealed that Crohn's-derived isolates were enriched in genes related to mobile elements and mucin foraging. Together, we present a large R. gnavus resource that will be available to the scientific community and provide novel biological insights into the global distribution and genomic variation of R. gnavus.

Targeted prebiotic application of gluconic acid-containing oligosaccharides promotes Faecalibacterium growth through microbial cross-feeding networks

The gut microbiome plays a crucial role in human health, and certain bacterial species, such as Faecalibacterium prausnitzii, are particularly beneficial. This study conducted a comprehensive investigation of prebiotic compounds that showed potential for specifically promoting beneficial gut bacteria. Using in vitro fecal cultures and a human intervention study, we identified maltobionic acid and lactobionic acid as compounds that specifically promoted Faecalibacterium growth both in vitro and in vivo without significantly affecting Bifidobacterium, which is typically increased by traditional prebiotics. In a human intervention study (n = 27), a significant increase was observed in Faecalibacterium abundance following maltobionic acid supplementation, with effectiveness correlating with the initial Parabacteroides abundance. Mechanistic investigations revealed a cross-feeding pathway between gut bacteria. In this pathway, Parabacteroides species converted the gluconic acid moiety of maltobionic and lactobionic acids to glucuronic acid, which was then preferentially utilized by Faecalibacterium. These findings suggest that gluconic acid-containing oligosaccharides are promising prebiotics for the targeted enhancement of beneficial Faecalibacterium and underscore the importance of microbial interactions in prebiotic research, offering new avenues for personalized microbiome modulation strategies.

Effect of Postbiotic Bifidobacterium longum CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study

OBJECTIVES

A randomised, double-blind, placebo-controlled pilot trial was conducted to assess the effect of heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) in healthy adults with mild to moderate digestive symptoms. A total of 60 participants were recruited and received either HT-ES1 or an identical placebo for 8 weeks with a further follow-up at week 10.

METHODS

This study monitored changes in the total Gastrointestinal Symptom Rating Scale for IBS score (GSRS-IBS), Irritable Bowel Syndrome Symptom Severity Scale (IBS-SSS), IBS Quality of Life index (IBS-QoL), gut microbiome using 16S rRNA sequencing, and the Visceral Sensitivity Index, as well as a range of biochemical markers, anthropometric parameters, and adverse events.

RESULTS

While minimal changes were observed in gastrointestinal (GI) symptoms, the HT-ES1 group showed a significant decrease in total and non-HDL cholesterol compared to the placebo. The intervention group also exhibited a significant increase in the abundance of the genera Faecalibacterium and Anaerobutyricum, both of which were positively correlated with butyrate concentrations. Faecal calprotectin significantly increased over time in the placebo group but remained stable in the HT-ES1 group.

CONCLUSIONS

Overall, these findings suggest that HT-ES1 may promote gut health by increasing butyrate-producing bacteria in the gut, maintaining normal levels of faecal calprotectin and reducing serum cholesterol.

In vitro fecal microbiota modulation properties of pectin and xyloglucan from hazelnut (Corylus avellana L.) skin, an industrial byproduct, and their incorporation into biscuit formula

The aim of this study was to extract water-soluble dietary fibers (WSDFskin), pectin (PECskin), and xyloglucan (XGskin) from hazelnut skin and to determine their impacts on colonic microbiota and metabolic function. WSDFskin, PECskin, and XGskin were extracted by water, acid, and alkali treatments, respectively. Monosaccharide analysis revealed WSDFskin and PECskin were dominated by uronic acids, while the XGskin was found to contain xyloglucan- and pectin-associated sugars. In vitro fecal fermentation analysis showed that WSDFskin, PECskin, and XGskin are fermented to different microbial short-chain fatty acid profiles by identical microbiota. 16S rRNA sequencing demonstrated that PECskin promoted Faecalibacterium prausnitzii and Lachnospiraceae related operational taxonomic units (OTUs), which are recognized as beneficial members of the human gut, whereas WSDFskin and XGskin stimulated Bacteroides OTUs. Interestingly, increased abundances of F. prausnitzii and Lachnospiraceae OTUs in PECskin were higher than those in commercially available pectin. Finally, PECskin and XGskin were tested in a biscuit model and the results showed that either PECskin or XGskin can be incorporated into biscuit formulations without impacting physical, textural, and sensory properties of the final product. Overall, our results demonstrated that hazelnut skin, an industrial byproduct, can be utilized for the production of functional dietary fibers, especially pectin, to improve colonic health.

Description of Faecalibacterium wellingii sp. nov. and two Faecalibacterium taiwanense strains, aiding to the reclassification of Faecalibacterium species

OBJECTIVES

The genus Faecalibacterium is one of the most important butyrate producers in the human intestinal tract and has been widely linked to health. Recently, several different species have been described, but still more phylogroups have been identified, suggesting that additional species may exist. Four strains HTF-FT, HTF-128, HTF-75H and HTF-76H, representing two different phylogenetic clusters, are evaluated in this study.

METHODS

Phylogenomic analysis was performed using whole-genome sequences and 16S rRNA gene sequences. Chemotaxonomic analysis was done based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Physiological and phenotypical characteristics of these strains were also determined. All characteristics of these strains were compared with other validly published species within the genus Faecalibacterium.

RESULTS

On a genomic level, the strains HTF-FT and HTF-128 shared an average nucleotide identity (ANI) of <95.0 % and digital DNA-DNA hybridization (dDDH) of <70.0 with other Faecalibacterium species, while between HTF-FT and HTF-128 the ANI-value was 97.18 % and the dDDH was 76.8 %. HTF-75H and HTF-76H had an ANI and dDDH value of 100 % (99.96 %) and 100 % (99.99 %) respectively. Both HTF-75H and HTF-76H were closely related to Faecalibacterium taiwanense HLW78T. 16S rRNA gene and chemotaxonomic analysis were in accordance with the genomic data, confirming that HTF-FT and HTF-128 represent a novel Faecalibacterium species and HTF-75H and HTF-76H belong to F. taiwanense.

CONCLUSIONS

Faecalibacterium strains HTF-FT (=DSM 117771T = NCIMB 15531T) and HTF-128 represent a novel species. The name Faecalibacterium wellingii with HTF-FT as type strain is proposed. Two novel isolates HTF-75H (=DSM 17770 = NCIMB 15530) and HTF-76H are described in this study and belong to the recently described Faecalibacterium taiwanense.

Host-diet-microbiota interplay in intestinal nutrition and health

The intestine is populated by a complex and dynamic assortment of microbes, collectively called gut microbiota, that interact with the host and contribute to its metabolism and physiology. Diet is considered a key regulator of intestinal microbiota, as ingested nutrients interact with and shape the resident microbiota composition. Furthermore, recent studies underscore the interplay of dietary and microbiota-derived nutrients, which directly impinge on intestinal stem cells regulating their turnover to ensure a healthy gut barrier. Although advanced sequencing methodologies have allowed the characterization of the human gut microbiome, mechanistic studies assessing diet-microbiota-host interactions depend on the use of genetically tractable models, such as Drosophila melanogaster. In this review, we first discuss the similarities between the human and fly intestines and then we focus on the effects of diet and microbiota on nutrient-sensing signaling cascades controlling intestinal stem cell self-renewal and differentiation, as well as disease. Finally, we underline the use of the Drosophila model in assessing the role of microbiota in gut-related pathologies and in understanding the mechanisms that mediate different whole-body manifestations of gut dysfunction.

The complex link between the gut microbiome and obesity-associated metabolic disorders: Mechanisms and therapeutic opportunities

Microbial interactions are widespread and important processes that support the link between disease and microbial ecology. The gut microbiota is a major source of microbial stimuli that can have detrimental or beneficial effects on human health. It is also an endocrine organ that maintains energy homeostasis and host immunity. Obesity is a highly and increasingly prevalent metabolic disease and the leading cause of preventable death worldwide. An imbalance in the gut microbiome is associated with several diseases including obesity-related metabolic disorders. This review summarizes the complex association between the gut microbiome and obesity-associated metabolic diseases and validates the role and mechanisms of ecological dysregulation in the gut in obesity-associated metabolic disorders. Therapies that could potentially alleviate obesity-associated metabolic diseases by modulating the gut microbiota are discussed.

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.

Next generation probiotics for human health: An emerging perspective

Over recent years, the scientific community has acknowledged the crucial role of certain microbial strains inhabiting the intestinal ecosystem in promoting human health, and participating in various beneficial functions for the host. These microorganisms are now referred to as next-generation probiotics and are currently considered as biotherapeutic products and food or nutraceutical supplements. However, the majority of next-generation probiotic candidates pose nutritional demands and exhibit high sensitivity towards aerobic conditions, leading to numerous technological hurdles in large-scale production. This underscores the need for the development of suitable delivery systems capable of enhancing the viability and functionality of these probiotic strains. Currently, potential candidates for next generation probiotics (NGP) are being sought among gut bacteria linked to health, which include strains from the genera Bacteroids, Faecalibacterium, Akkermansia and Clostridium. In contrast to Lactobacillus spp. and Bifidobacterium spp., NGP, particularly Bacteroids spp. and Clostridium spp., appear to exhibit greater ambiguity regarding their potential to induce infectious diseases. The present review provides a comprehensive overview of NGPs in terms of their health beneficial effects, regulation framework and risk assessment targeting relevant criteria for commercialization in food and pharmaceutical markets.

Natural Foraging Selection and Gut Microecology of Two Subterranean Rodents from the Eurasian Steppe in China

As the most abundant group of mammals, rodents possess a very rich ecotype, which makes them ideal for studying the relationship between diet and host gut microecology. Zokors are specialized herbivorous rodents adapted to living underground. Unlike more generalized herbivorous rodents, they feed on the underground parts of grassland plants. There are two species of the genus Myospalax in the Eurasian steppes in China: one is Myospalax psilurus, which inhabits meadow grasslands and forest edge areas, and the other is M. aspalax, which inhabits typical grassland areas. How are the dietary choices of the two species adapted to long-term subterranean life, and what is the relationship of this diet with gut microbes? Are there unique indicator genera for their gut microbial communities? Relevant factors, such as the ability of both species to degrade cellulose, are not yet clear. In this study, we analyzed the gut bacterial communities and diet compositions of two species of zokors using 16S amplicon technology combined with macro-barcoding technology. We found that the diversity of gut microbial bacterial communities in M. psilurus was significantly higher than that in M. aspalax, and that the two species of zokors possessed different gut bacterial indicator genera. Differences in the feeding habits of the two species of zokors stem from food composition rather than diversity. Based on the results of Mantel analyses, the gut bacterial community of M. aspalax showed a significant positive correlation with the creeping-rooted type food, and there was a complementary relationship between the axis root-type-food- and the rhizome-type-food-dominated (containing bulb types and tuberous root types) food groups. Functional prediction based on KEGG found that M. psilurus possessed a stronger degradation ability in the same cellulose degradation pathway. Neutral modeling results show that the gut flora of the M. psilurus has a wider ecological niche compared to that of the M. aspalax. This provides a new perspective for understanding how rodents living underground in grassland areas respond to changes in food conditions.

Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition

The duck gastrointestinal tract (GIT) harbors an abundance of microorganisms that play an important role in duck health and production. Here, we constructed the first relatively comprehensive duck gut microbial gene catalog (24 million genes) and 4437 metagenome-assembled genomes using 375 GIT metagenomic samples from four different duck breeds across five intestinal segments under two distinct rearing conditions. We further characterized the intestinal region-specific microbial taxonomy and their assigned functions, as well as the temporal development and maturation of the duck gut microbiome. Our metagenomic analysis revealed the similarity within the microbiota of the foregut and hindgut compartments, but distinctive taxonomic and functional differences between distinct intestinal segments. In addition, we found a significant shift in the microbiota composition of newly hatched ducks (3 days), followed by increased diversity and enhanced stability across growth stages (14, 42, and 70 days), indicating that the intestinal microbiota develops into a relatively mature and stable community as the host duck matures. Comparing the impact of different rearing conditions (with and without water) on duck cecal microbiota communities and functions, we found that the bacterial capacity for lipopolysaccharide biosynthesis was significantly increased in ducks that had free access to water, leading to the accumulation of pathogenic bacteria and antibiotic-resistance genes. Taken together, our findings expand the understanding of the microbiome signatures linked to intestinal regional, temporal development, and rearing conditions in ducks, which highlight the significant impact of microbiota on poultry health and production.

A Critical Review on Akkermansia muciniphila: Functional Mechanisms, Technological Challenges, and Safety Issues

Due to its physiological benefits from in vitro and in vivo points of view, Akkermansia muciniphila, a common colonizer in the human gut mucous layer, has consistently been identified as an option for the next-generation probiotic. A. muciniphila is a significant bacterium that promotes host physiology. However, it also has a great deal of potential to become a probiotic due to its physiological advantages in a variety of therapeutic circumstances. Therefore, it can be established that the abundance of A. muciniphila in the gut environment, which is controlled by many genetic and dietary variables, is related to the biological behaviors of the intestinal microbiota and gut dysbiosis/eubiosis circumstances. Before A. muciniphila is widely utilized as a next-generation probiotic, regulatory obstacles, the necessity for significant clinical trials, and the sustainability of manufacturing must be eliminated. In this review, the outcomes of recent experimental and clinical reports are comprehensively reviewed, and common colonization patterns, main factors involved in the colonization of A. muciniphila in the gut milieu, their functional mechanisms in establishing homeostasis in the metabolic and energy pathways, the promising delivery role of microencapsulation, potential genetic engineering strategies, and eventually safety issues of A. muciniphila have been discussed.

Exploring the resilience and stability of a defined human gut microbiota consortium: An isothermal microcalorimetric study

The gut microbiota significantly contributes to human health and well-being. The aim of this study was to evaluate the stability and resilience of a consortium composed of three next-generation probiotics (NGPs) candidates originally found in the human gut. The growth patterns of Akkermansia muciniphila, Bacteroides thetaiotaomicron, and Faecalibacterium prausnitzii were studied both individually and consortium. The growth kinetics of Akkermansia muciniphila (A. muciniphila), Bacteroides thetaiotaomicron (B. thetaiotaomicron), and Faecalibacterium prausnitzii (F. prausnitzii) were characterized both individually and in consortium using isothermal microcalorimetry and 16S ribosomal RNA next-generation sequencing. The consortium reached stability after three passages and demonstrated resilience to changes in its initial composition. The concentration of butyrate produced was nearly twice as high in the consortium compared to the monoculture of F. prausnitzii. The experimental conditions and methodologies used in this article are a solid foundation for developing further complex consortia.

Investigating the response of the butyrate production potential to major fibers in dietary intervention studies

Interventions involving dietary fibers are known to benefit host health. A leading contribution of gut microbiota is commonly recognized with production of short chain fatty acids (SCFA) suspected to play a key role. However, the detailed mechanisms are largely unknown, and apart from a well-described bifidogenic effect of some fibers, results for other bacterial taxa are often incongruent between studies. We performed pooled analyses of 16S rRNA gene data derived from intervention studies (n = 14) based on three fibers, namely, inulin-type fructans (ITF), resistant starch (RS), and arabinoxylan-oligosaccharides (AXOS), harmonizing the bioinformatics workflow to reveal taxa stimulated by those substrates, specifically focusing on the SCFA-production potential. The results showed an increased butyrate production potential after ITF (p < 0.05) and RS (p < 0.1) treatment via an increase in bacteria exhibiting the enzyme butyryl-CoA:acetate CoA-transferase (but) that was governed by Faecalibacterium, Anaerostipes (ITF) and Agathobacter (RS) respectively. AXOS did not promote an increase in butyrate producers, nor were pathways linked to propionate production stimulated by any intervention. A bifidogenic effect was observed for AXOS and ITF, which was only partly associated with the behavior of but-containing bacteria and largely represented a separate response. Low and high Ruminococcus abundances pre-intervention for ITF and RS, respectively, promoted an increase in but-containing taxa (p < 0.05) upon interventions, whereas initial Prevotella abundance was negatively associated with responses of butyrate producers for both fibers. Collectively, our data demonstrate targeted stimulation of specific taxa by individual fibers increasing the potential to synthesize butyrate, where gut microbiota composition pre-intervention strongly controlled outcomes.

Non-lactic acid bacteria probiotics isolated from intestine or various circumstances

Probiotics are live microorganisms beneficial to host health, predominantly comprising lactic acid bacteria (LAB) such as Lactobacillus. Additional non-LAB probiotics, termed intestinal isolates, encompass next-generation strains like Akkermansia muciniphila, Faecalibacterium prausnitzii, Christensenella minuta, Anaerobutyricum soehngenii, Oxalobacter formigenes, etc. and alongside externally sourced Bacillus, Saccharomyces cerevisiae, Clostridium butyricum, and Propionibacterium. Intestinal-derived probiotics represent strictly anaerobic strains with challenging culturing requirements, contrasting with the aerobic nature of Bacillus probiotics and the ease of culturing S. cerevisiae. These strains exhibit diverse health-promoting properties, encompassing antimicrobial, anticancer, antioxidant, and vitamin production capabilities, albeit contingent upon strain specificity. This review delineates the characteristics, culturing conditions, and health advantages associated with non-LAB probiotics.

Enrichment and characterization of human-associated mucin-degrading microbial consortia by sequential passage

Mucin is a glycoprotein secreted throughout the mammalian gastrointestinal tract that can support endogenous microorganisms in the absence of complex polysaccharides. While several mucin-degrading bacteria have been identified, the interindividual differences in microbial communities capable of metabolizing this complex polymer are not well described. To determine whether community assembly on mucin is deterministic across individuals or whether taxonomically distinct but functionally similar mucin-degrading communities are selected across fecal inocula, we used a 10-day in vitro sequential batch culture fermentation from three human donors with mucin as the sole carbon source. For each donor, 16S rRNA gene amplicon sequencing was used to characterize microbial community succession, and the short-chain fatty acid profile was determined from the final community. All three communities reached a steady-state by day 7 in which the community composition stabilized. Taxonomic comparisons amongst communities revealed that one of the final communities had Desulfovibrio, another had Akkermansia, and all three shared other members, such as Bacteroides. Metabolic output differences were most notable for one of the donor's communities, with significantly less production of acetate and propionate than the other two communities. These findings demonstrate the feasibility of developing stable mucin-degrading communities with shared and unique taxa. Furthermore, the mechanisms and efficiencies of mucin degradation across individuals are important for understanding how this community-level process impacts human health.

Human Gut Microbiota for Diagnosis and Treatment of Depression

Nowadays, depressive disorder is spreading rapidly all over the world. Therefore, attention to the studies of the pathogenesis of the disease in order to find novel ways of early diagnosis and treatment is increasing among the scientific and medical communities. Special attention is drawn to a biomarker and therapeutic strategy through the microbiota-gut-brain axis. It is known that the symbiotic interactions between the gut microbes and the host can affect mental health. The review analyzes the mechanisms and ways of action of the gut microbiota on the pathophysiology of depression. The possibility of using knowledge about the taxonomic composition and metabolic profile of the microbiota of patients with depression to select gene compositions (metagenomic signature) as biomarkers of the disease is evaluated. The use of in silico technologies (machine learning) for the diagnosis of depression based on the biomarkers of the gut microbiota is given. Alternative approaches to the treatment of depression are being considered by balancing the microbial composition through dietary modifications and the use of additives, namely probiotics, postbiotics (including vesicles) and prebiotics as psychobiotics, and fecal transplantation. The bacterium Faecalibacterium prausnitzii is under consideration as a promising new-generation probiotic and auxiliary diagnostic biomarker of depression. The analysis conducted in this review may be useful for clinical practice and pharmacology.

13C-Stable isotope resolved metabolomics uncovers dynamic biochemical landscape of gut microbiome-host organ communications in mice

BACKGROUND

Gut microbiome metabolites are important modulators of host health and disease. However, the overall metabolic potential of the gut microbiome and interactions with the host organs have been underexplored.

RESULTS

Using stable isotope resolved metabolomics (SIRM) in mice orally gavaged with 13C-inulin (a tracer), we first observed dynamic enrichment of 13C-metabolites in cecum contents in the amino acids and short-chain fatty acid metabolism pathways. 13C labeled metabolites were subsequently profiled comparatively in plasma, liver, brain, and skeletal muscle collected at 6, 12, and 24 h after the tracer administration. Organ-specific and time-dependent 13C metabolite enrichments were observed. Carbons from the gut microbiome were preferably incorporated into choline metabolism and the glutamine-glutamate/GABA cycle in the liver and brain, respectively. A sex difference in 13C-lactate enrichment was observed in skeletal muscle, which highlights the sex effect on the interplay between gut microbiome and host organs. Choline was identified as an interorgan metabolite derived from the gut microbiome and fed the lipogenesis of phosphatidylcholine and lysophosphatidylcholine in host organs. In vitro and in silico studies revealed the de novo synthesis of choline in the human gut microbiome via the ethanolamine pathway, and Enterococcus faecalis was identified as a major choline synthesis species. These results revealed a previously underappreciated role for gut microorganisms in choline biosynthesis.

CONCLUSIONS

Multicompartmental SIRM analyses provided new insights into the current understanding of dynamic interorgan metabolite transport between the gut microbiome and host at the whole-body level in mice. Moreover, this study singled out microbiota-derived metabolites that are potentially involved in the gut-liver, gut-brain, and gut-skeletal muscle axes. Video Abstract.

[Exploring the causality between intestinal flora and hyperplastic scars of human based on two-sample Mendelian randomization analysis]

Objective: To investigate the causality between intestinal flora and hypertrophic scars (HS) of human. Methods: This study was a study based on two-sample Mendelian randomization (TSMR) analysis. The data on intestinal flora (n=18 473) and HS (n=208 248) of human were obtained from the genome-wide association study database. Genetically variable genes at five levels (phylum, class, order, family, and genus) of known intestinal flora, i.e., single nucleotide polymorphisms (SNPs), were extracted as instrumental variables for linkage disequilibrium (LD) analysis. Human genotype-phenotype association analysis was performed using PhenoScanner V2 database to exclude SNPs unrelated to HS in intestinal flora and analyze whether the selected SNPs were weak instrumental variables. The causal relationship between intestinal flora SNPs and HS was analyzed through four methods of TSMR analysis, namely inverse variance weighted (IVW), MR-Egger regression, weighted median, and weighted mode. Scatter plots of significant results from the four aforementioned analysis methods were plotted to analyze the correlation between intestinal flora SNPs and HS. Both IVW test and MR-Egger regression test were used to assess the heterogeneity of intestinal flora SNPs, MR-Egger regression test and MR-PRESSO outlier test were used to assess the horizontal multiplicity of intestinal flora SNPs, and leave-one-out sensitivity analysis was used to determine whether HS was caused by a single SNP in the intestinal flora. Reverse TSMR analyses were performed for HS SNPs and genus Intestinimonas or genus Ruminococcus2, respectively, to detect whether there was reverse causality between them. Results: A total of 196 known intestinal flora, belonging to 9 phyla, 16 classes, 20 orders, 32 families, and 119 genera, were obtained, and multiple SNPs were obtained from each flora as instrumental variables. LD analysis showed that the SNPs of the intestinal flora were consistent with the hypothesis that genetic variation was strongly associated with exposure factors, except for rs1000888, rs12566247, and rs994794. Human genotype-phenotype association analysis showed that none of the selected SNPs after LD analysis was excluded and there were no weak instrumental variables. IVW, MR-Egger regression, weighted median, and weighted mode of TSMR analysis showed that both genus Intestinimonas and genus Ruminococcus2 were causally associated with HS. Among them, forest plots of IVW and MR-Egger regression analyses also showed that 16 SNPs (the same SNPs number of this genus below) of genus Intestinimonas and 15 SNPs (the same SNPs number of this genus below) of genus Ruminococcus2 were protective factors for HS. Further, IVW analysis showed that genus Intestinimonas SNPs (with odds ratio of 0.62, 95% confidence interval of 0.41-0.93, P<0.05) and genus Ruminococcus2 SNPs (with odds ratio of 0.62, 95% confidence interval of 0.40-0.97, P<0.05) were negatively correlated with the risk of HS. Scatter plots showed that SNPs of genus Intestinimonas and genus Ruminococcus2 were protective factors of HS. Both IVW test and MR-Egger regression test showed that SNPs of genus Intestinimonas (with Q values of 5.73 and 5.76, respectively, P>0.05) and genus Ruminococcus2 (with Q values of 13.67 and 15.61, respectively, P>0.05) were not heterogeneous. MR-Egger regression test showed that the SNPs of genus Intestinimonas and genus Ruminococcus2 had no horizontal multiplicity (with intercepts of 0.01 and 0.06, respectively, P>0.05); MR-PRESSO outlier test showed that the SNPs of genus Intestinimonas and genus Ruminococcus2 had no horizontal multiplicity (P>0.05). Leave-one-out sensitivity analysis showed that no single intestinal flora SNP drove the occurrence of HS. Reverse TSMR analysis showed no reverse causality between HS SNPs and genus Intestinimonas or genus Ruminococcus2 (with odds ratios of 1.01 and 0.99, respectively, 95% confidence intervals of 0.97-1.06 and 0.96-1.04, respectively, P>0.05). Conclusions: There is a causal relationship between intestinal flora and HS of human, in which genus Intestinimonas and genus Ruminococcus2 have a certain effect on inhibiting HS.

Next-generation probiotics: the upcoming biotherapeutics

Recent and continuing advances in gut microbiome research have pointed out the role of the gut microbiota as an unexplored source of potentially beneficial probiotic microbes. Along the lines of these advances, both public awareness and acceptance of probiotics are increasing. That's why; academic and industrial research is dedicated to identifying and investigating new microbial strains for the development of next-generation probiotics (NGPs). At this time, there is a growing interest in NGPs as biotherapeutics that alter the gut microbiome and affect various diseases development. In this work, we have focused on some emergent and promising NGPs, specifically Eubacterium hallii, Faecalibacterium prausnitzii, Roseburia spp., Akkermansia muciniphila, and Bacteroides fragilis, as their presence in the gut can have an impact on the development of various diseases. Emerging studies point out the beneficial roles of these NGPs and open up novel promising therapeutic options. Interestingly, these NGPs were found to enhance gastrointestinal immunity, enhance immunotherapy efficacy in cancer patients, retain the intestinal barrier integrity, generate valuable metabolites, especially short-chain fatty acids, and decrease complications of chemotherapy and radiotherapy. Although many of these NGPs are considered promising for the prevention and treatment of several chronic diseases, research on humans is still lacking. Therefore, approval of these microbes from regulatory agencies is rare. Besides, some issues limit their wide use in the market, such as suitable methods for the culture and storage of these oxygen-sensitive microbes. The present review goes over the main points related to NGPs and gives a viewpoint on the key issues that still hinder their wide application. Furthermore, we have focused on the advancement in NGPs and human healthiness investigations by clarifying the limitations of traditional probiotic microorganisms, discussing the characteristics of emerging NGPs and defining their role in the management of certain ailments. Future research should emphasize the isolation, mechanisms of action of these probiotics, safety, and clinical efficacy in humans.

Gut microbiota in relationship to diabetes mellitus and its late complications with a focus on diabetic foot syndrome: A review

Diabetes mellitus is a chronic disease affecting glucose metabolism. The pathophysiological reactions underpinning the disease can lead to the development of late diabetes complications. The gut microbiota plays important roles in weight regulation and the maintenance of a healthy digestive system. Obesity, diabetes mellitus, diabetic retinopathy, diabetic nephropathy and diabetic neuropathy are all associated with a microbial imbalance in the gut. Modern technical equipment and advanced diagnostic procedures, including xmolecular methods, are commonly used to detect both quantitative and qualitative changes in the gut microbiota. This review summarises collective knowledge on the role of the gut microbiota in both types of diabetes mellitus and their late complications, with a particular focus on diabetic foot syndrome.

Prebiotic potential of pectin and cello-oligosaccharides from apple bagasse and orange peel produced by high-pressure homogenization and enzymatic hydrolysis

Apple bagasse and orange peel were subjected to high-pressure homogenization (HPH), enzymatic hydrolysis (EH) and their combination (HPHE) to study their effect on oligosaccharide production and in vitro fermentability. The application of a cellulase-pectinase mixture on the by-products generated significant quantities of cellobiose (COS-2) and pectin derived oligosaccharides (POS) which were identified as mainly methylated and acetylated oligogalacturonides with DP 2-5 (POS 2-5). When pre-treating the substrates with HPH, the release in orange peel was enhanced significantly leading to a POS content of 44.51 g/100 g peel, whereas oligosaccharide solubilization in apple bagasse was not affected. In vitro fermentation of the hydrolysates containing COS-2 and POS showed faster fermentation rates, between 6 and 10 h, and enhanced gas production, compared to those samples not subjected to enzymatic hydrolysis. Short chain fatty acid (SCFA) production was not impacted by the presence of POS and COS-2 in the induced quantities.

Strain-Specific Anti-Inflammatory Effects of Faecalibacterium prausnitzii Strain KBL1027 in Koreans

Faecalibacterium prausnitzii is one of the most dominant commensal bacteria in the human gut, and certain anti-inflammatory functions have been attributed to a single microbial anti-inflammatory molecule (MAM). Simultaneously, substantial diversity among F. prausnitzii strains is acknowledged, emphasizing the need for strain-level functional studies aimed at developing innovative probiotics. Here, two distinct F. prausnitzii strains, KBL1026 and KBL1027, were isolated from Korean donors, exhibiting notable differences in the relative abundance of F. prausnitzii. Both strains were identified as the core Faecalibacterium amplicon sequence variant (ASV) within the healthy Korean cohort, and their MAM sequences showed a high similarity of 98.6%. However, when a single strain was introduced to mice with dextran sulfate sodium (DSS)-induced colitis, KBL1027 showed the most significant ameliorative effects, including alleviation of colonic inflammation and restoration of gut microbial dysbiosis. Moreover, the supernatant from KBL1027 elevated the secretion of IL-10 cytokine more than that of KBL1026 in mouse bone marrow-derived macrophage (BMDM) cells, suggesting that the strain-specific, anti-inflammatory efficacy of KBL1027 might involve effector compounds other than MAM. Through analysis of the Faecalibacterium pan-genome and comparative genomics, strain-specific functions related to extracellular polysaccharide biosynthesis were identified in KBL1027, which could contribute to the observed morphological disparities. Collectively, our findings highlight the strain-specific, anti-inflammatory functions of F. prausnitzii, even within the same core ASV, emphasizing the influence of their human origin.

Lactate cross-feeding between Bifidobacterium species and Megasphaera indica contributes to butyrate formation in the human colonic environment

Butyrate, a physiologically active molecule, can be synthesized through metabolic interactions among colonic microorganisms. Previously, in a fermenting trial of human fecal microbiota, we observed that the butyrogenic effect positively correlated with the increasing Bifidobacterium population and an unidentified Megasphaera species. Therefore, we hypothesized that a cross-feeding phenomenon exists between Bifidobacterium and Megasphaera, where Megasphaera is the butyrate producer, and its growth relies on the metabolites generated by Bifidobacterium. To validate this hypothesis, three bacterial species (B. longum, B. pseudocatenulatum, and M. indica) were isolated from fecal cultures fermenting hydrolyzed xylan; pairwise cocultures were conducted between the Bifidobacterium and M. indica isolates; the microbial interactions were determined based on bacterial genome information, cell growth, substrate consumption, metabolite quantification, and metatranscriptomics. The results indicated that two Bifidobacterium isolates contained distinct gene clusters for xylan utilization and expressed varying substrate preferences. In contrast, M. indica alone scarcely grew on the xylose-based substrates. The growth of M. indica was significantly elevated by coculturing it with bifidobacteria, while the two Bifidobacterium species responded differently in the kinetics of cell growth and substrate consumption. Coculturing led to the depletion of lactate and increased the formation of butyrate. An RNA-seq analysis further revealed the upregulation of M. indica genes involved in the lactate utilization and butyrate formation pathways. We concluded that lactate generated by Bifidobacterium through catabolizing xylose fueled the growth of M. indica and triggered the synthesis of butyrate. Our findings demonstrated a novel cross-feeding mechanism to generate butyrate in the human colon.IMPORTANCEButyrate is an important short-chain fatty acid that is produced in the human colon through microbial fermentation. Although many butyrate-producing bacteria exhibit a limited capacity to degrade nondigestible food materials, butyrate can be formed through cross-feeding microbial metabolites, such as acetate or lactate. Previously, the literature has explicated the butyrate-forming links between Bifidobacterium and Faecalibacterium prausnitzii and between Bifidobacterium and Eubacterium rectale. In this study, we provided an alternative butyrate synthetic pathway through the interaction between Bifidobacterium and Megasphaera indica. M. indica is a species named in 2014 and is indigenous to the human intestinal tract. Scientific studies explaining the function of M. indica in the human colon are still limited. Our results show that M. indica proliferated based on the lactate generated by bifidobacteria and produced butyrate as its end metabolic product. The pathways identified here may contribute to understanding butyrate formation in the gut microbiota.

Faecalibacterium duncaniae A2-165 regulates the expression of butyrate synthesis, ferrous iron uptake, and stress-response genes based on acetate consumption

The promising next-generation probiotic Faecalibacterium prausnitzii is one of the most abundant acetate-consuming, butyrate-producing bacteria in the healthy human gut. Yet, little is known about how acetate availability affects this bacterium's gene expression strategies. Here, we investigated the effect of acetate on temporal changes in the transcriptome of F. duncaniae A2-165 cultures using RNA sequencing. We compared gene expression patterns between two growth phases (early stationary vs. late exponential) and two acetate levels (low: 3 mM vs. high: 23 mM). Only in low-acetate conditions, a general stress response was activated. In high-acetate conditions, there was greater expression of genes related to butyrate synthesis and to the importation of B vitamins and iron. Specifically, expression was strongly activated in the case of the feoAABC operon, which encodes a FeoB ferrous iron transporter, but not in the case of the feoAB gene, which encodes a second putative FeoAB transporter. Moreover, excess ferrous iron repressed feoB expression but not feoAB. Lastly, FeoB but not FeoAB peptides from strain A2-165 were found in abundance in a healthy human fecal metaproteome. In conclusion, we characterized two early-stationary transcriptomes based on acetate consumption and this work highlights the regulation of feoB expression in F. duncaniae A2-165.

An overview of microbial enzymatic approaches for pectin degradation

Pectin, a complex natural macromolecule present in primary cell walls, exhibits high structural diversity. Pectin is composed of a main chain, which contains a high amount of partly methyl-esterified galacturonic acid (GalA), and numerous types of side chains that contain almost 17 different monosaccharides and over 20 different linkages. Due to this peculiar structure, pectin exhibits special physicochemical properties and a variety of bioactivities. For example, pectin exhibits strong bioactivity only in a low molecular weight range. Many different degrading enzymes, including hydrolases, lyases and esterases, are needed to depolymerize pectin due to its structural complexity. Pectin degradation involves polygalacturonases/rhamnogalacturonases and pectate/pectin lyases, which attack the linkages in the backbone via hydrolytic and β-elimination modes, respectively. Pectin methyl/acetyl esterases involved in the de-esterification of pectin also play crucial roles. Many α-L-rhamnohydrolases, unsaturated rhamnogalacturonyl hydrolases, arabinanases and galactanases also contribute to heterogeneous pectin degradation. Although numerous microbial pectin-degrading enzymes have been described, the mechanisms involved in the coordinated degradation of pectin through these enzymes remain unclear. In recent years, the degradation of pectin by Bacteroides has received increasing attention, as Bacteroides species contain a unique genetic structure, polysaccharide utilization loci (PULs). The specific PULs of pectin degradation in Bacteroides species are a new field to study pectin metabolism in gut microbiota. This paper reviews the scientific information available on pectin structural characteristics, pectin-degrading enzymes, and PULs for the specific degradation of pectin.

Effects of dietary supplementation with Radix Isatidis polysaccharide on egg quality, immune function, and intestinal health in hens

This study aimed to investigate the effects of supplementing laying hen diets with Radix Isatidis Polysaccharide (RIPS) on egg quality, immune function, and intestinal health. The research was conducted using 288 Hyland Brown hens, which were randomly assigned to four dietary treatments: control (without RIPS), low dose (200 g/t), medium dose (500 g/t), and high dose (1000 g/t) of RIPS. Each dietary treatment was administered to eight replicates of nine hens for nine weeks. The results revealed that RIPS inclusion in diets significantly improved egg quality parameters such as egg shape index, yolk color, haugh unit, and protein height (P < 0.05). Additionally, RIPS supplementation enhanced immune function as evidenced by an alteration in serum biochemical parameters, an increase in the spleen index, and a decrease in the liver index. Further, an evaluation of intestinal health showed that RIPS fortified the intestinal barrier, thus increasing the population of beneficial intestinal bacteria and reducing the abundance of harmful ones. Such mechanisms promoted intestinal health, digestion, and nutrient absorption, ultimately leading to enhanced egg quality. In conclusion, supplementing laying hen diets with RIPS has been demonstrated to improve egg quality by boosting immunity and optimizing intestinal digestion and absorption.

Host genetic regulation of human gut microbial structural variation

Although the impact of host genetics on gut microbial diversity and the abundance of specific taxa is well established1-6, little is known about how host genetics regulates the genetic diversity of gut microorganisms. Here we conducted a meta-analysis of associations between human genetic variation and gut microbial structural variation in 9,015 individuals from four Dutch cohorts. Strikingly, the presence rate of a structural variation segment in Faecalibacterium prausnitzii that harbours an N-acetylgalactosamine (GalNAc) utilization gene cluster is higher in individuals who secrete the type A oligosaccharide antigen terminating in GalNAc, a feature that is jointly determined by human ABO and FUT2 genotypes, and we could replicate this association in a Tanzanian cohort. In vitro experiments demonstrated that GalNAc can be used as the sole carbohydrate source for F. prausnitzii strains that carry the GalNAc-metabolizing pathway. Further in silico and in vitro studies demonstrated that other ABO-associated species can also utilize GalNAc, particularly Collinsella aerofaciens. The GalNAc utilization genes are also associated with the host's cardiometabolic health, particularly in individuals with mucosal A-antigen. Together, the findings of our study demonstrate that genetic associations across the human genome and bacterial metagenome can provide functional insights into the reciprocal host-microbiome relationship.

Pectin conformation influences the bioaccessibility of cherry laurel polyphenols and gut microbiota distribution following in vitro gastrointestinal digestion and fermentation

Interactions between dietary fiber and phenolic compounds in foods can influence their gastrointestinal fate. This study aimed to examine the effect of four types of pectin on the polyphenols of cherry laurel puree and human gut microbiota during a simulated in vitro gastrointestinal digestion and large intestine fermentation. Results revealed that the combined addition of different pectins and pectinase to cherry laurel puree significantly affected the content and bioaccessibility of phenolics. The addition of pectins and pectinase distinctively impacted the phenolic subclasses in both raw and post-digested/fermented cherry laurel puree, suggesting differential interactions due to structural features. Both pectins and pectinase modulated the composition of fecal microbiota after in vitro fermentation, increasing bacterial diversity following pectinase treatment. The combined addition of pectins followed by pectinase had differential impacts on polyphenol bioaccessibility and gut microbiome diversity, hence having a potential outcome in terms of human health.

Gut firmicutes: Relationship with dietary fiber and role in host homeostasis

Firmicutes and Bacteroidetes are the predominant bacterial phyla colonizing the healthy human gut. Accumulating evidence suggests that dietary fiber plays a crucial role in host health, yet most studies have focused on how the dietary fiber affects health through gut Bacteroides. More recently, gut Firmicutes have been found to possess many genes responsible for fermenting dietary fiber, and could also interact with the intestinal mucosa and thereby contribute to homeostasis. Consequently, the relationship between dietary fiber and Firmicutes is of interest, as well as the role of Firmicutes in host health. In this review, we summarize the current knowledge regarding the molecular mechanism of dietary fiber degradation by gut Firmicutes and explain the communication pathway of the dietary fiber-Firmicutes-host axis, and the beneficial effects of dietary fiber-induced Firmicutes and their metabolites on health. A better understanding of the dialogue sustained by the dietary fiber-Firmicutes axis and the host could provide new insights into probiotic therapy and novel dietary interventions aimed at increasing the abundance of Firmicutes (such as Faecalibacterium, Lactobacillus, and Roseburia) to promote health.

Isolation of Enterococcus faecium and determination of its mechanism for promoting the growth and development of Drosophila

Intestinal symbiotic microorganisms have a strong capacity to regulate the physiological functions of their host, and Drosophila serves as a useful model. Enterococcus faecium (E. faecium) is a member of the normal intestinal flora of animals. Lactic acid bacteria (LAB) such as E. faecium can promote the growth and development of Drosophila, but the mechanism of regulation of Drosophila is poorly understood. In this study, we found that E. faecium used a carbon source to produce probiotic acids. E. faecium is a symbiotic bacterium for Drosophila, and adult flies passed on parental flora to offspring. E. faecium promoted the growth and development of Drosophila, especially under poor nutritional conditions. E. faecium shortened the developmental process for Drosophila and accelerated the transformation from larva to pupa. Finally, E. faecium promoted the growth and development of Drosophila through TOR and insulin signalling pathways.

Genetic causal relationship between gut microbiome and psoriatic arthritis: a bidirectional two-sample Mendelian randomization study

Background

Several observational studies have suggested a potential relationship between gut microbiome and psoriatic arthritis (PsA). However, the causality of this relationship still remains unclear. We aim to explore if the specific gut microbiome is causally associated with PsA at the genetic level and offer valuable insights into the etiology of PsA.

Methods

In this study, we employed a bidirectional two-sample Mendelian randomization (MR) analysis to investigate the causal effects of the gut microbiome on PsA. Publicly accessible genome-wide association study summary data of gut microbiome were obtained from the MiBioGen consortium (n = 14,306), while the summary statistics of psoriatic arthropathies were sourced from the FinnGen consortium R8 release data (2,776 cases and 221,323 controls). The primary analytical method employed was inverse variance weighted (IVW), complemented by supplementary methods including MR-Egger, weighted median, weighted mode, maximum likelihood, MR-PRESSO, and cML-MA. Reverse MR analysis was performed on the bacteria that were found to be causally associated with PsA in forward MR analysis. Cochran's IVW Q statistic was utilized to assess the heterogeneity of instrumental variables among the selected single nucleotide polymorphisms.

Results

IVW estimates revealed that Ruminococcaceae_UCG-002 (odds ratio (OR) = 0.792, 95% confidence interval (CI), 0.643-0.977, p = 0.029) exhibited a protective effect on PsA. Conversely, Blautia (OR = 1.362, 95% CI, 1.008-1.842, p = 0.044), Eubacterium_fissicatena_group (OR = 1.28, 95% CI, 1.075-1.524, p = 0.006), and Methanobrevibacter (OR = 1.31, 95% CI, 1.059-1.621, p = 0.013) showed a positive correlation with the risk of PsA. No significant heterogeneity, horizontal pleiotropy, or outliers were observed, and the results of the MR analysis remained unaffected by any single nucleotide polymorphisms. According to the results of reverse MR analysis, no significant causal effect of PsA was found on gut microbiome.

Conclusion

This study establishes for the first time a causal relationship between the gut microbiome and PsA, providing potential valuable strategies for the prevention and treatment of PsA. Further randomized controlled trials are urgently warranted to support the targeted protective mechanisms of probiotics on PsA.

Anaerobic Feces Processing for Fecal Microbiota Transplantation Improves Viability of Obligate Anaerobes

Fecal microbiota transplantation (FMT) is under investigation for several indications, including ulcerative colitis (UC). The clinical success of FMT depends partly on the engraftment of viable bacteria. Because the vast majority of human gut microbiota consists of anaerobes, the currently used aerobic processing protocols of donor stool may diminish the bacterial viability of transplanted material. This study assessed the effect of four processing techniques for donor stool (i.e., anaerobic and aerobic, both direct processing and after temporary cool storage) on bacterial viability. By combining anaerobic culturing on customized media for anaerobes with 16S rRNA sequencing, we could successfully culture and identify the majority of the bacteria present in raw fecal suspensions. We show that direct anaerobic processing of donor stool is superior to aerobic processing conditions for preserving the bacterial viability of obligate anaerobes and butyrate-producing bacteria related to the clinical response to FMT in ulcerative colitis patients, including Faecalibacterium, Eubacterium hallii, and Blautia. The effect of oxygen exposure during stool processing decreased when the samples were stored long-term. Our results confirm the importance of sample conditioning to preserve the bacterial viability of oxygen-sensitive gut bacteria. Anaerobic processing of donor stool may lead to increased clinical success of FMT, which should further be investigated in clinical trials.

The digestive behavior of pectin in human gastrointestinal tract: a review on fermentation characteristics and degradation mechanism

Pectin is widely spread in nature and it develops an extremely complex structure in terms of monosaccharide composition, glycosidic linkage types, and non-glycosidic substituents. As a non-digestible polysaccharide, pectin exhibits resistance to human digestive enzymes, however, it is easily utilized by gut microbiota in the large intestine. Currently, pectin has been exploited as a novel functional component with numerous physiological benefits, and it shows a promising prospect in promoting human health. In this review, we introduce the regulatory effects of pectin on intestinal inflammation and metabolic syndromes. Subsequently, the digestive behavior of pectin in the upper gastrointestinal tract is summarized, and then it will be focused on pectin's fermentation characteristics in the large intestine. The fermentation selectivity of pectin by gut bacteria and the effects of pectin structure on intestinal microecology were discussed to highlight the interaction between pectin and bacterial community. Meanwhile, we also offer information on how gut bacteria orchestrate enzymes to degrade pectin. All of these findings provide insights into pectin digestion and advance the application of pectin in human health.

Does PM1 exposure during pregnancy impact the gut microbiota of mothers and neonates?

BACKGROUND

Ambient air pollutant exposure can change the composition of gut microbiota at 6-months of age, but there is no epidemiological evidence on the impacts of exposure to particulate matter with an aerodynamic diameter ≤1 μm (PM1) during pregnancy on gut microbiota in mothers and neonates. We aimed to determine if gestational PM1 exposure is associated with the gut microbiota of mothers and neonates.

METHODS

Leveraging a mother-infant cohort from the central region of China, we estimated the exposure concentrations of PM1 during pregnancy based on residential address records. The gut microbiota of mothers and neonates was analyzed using 16 S rRNA V3-V4 gene sequences. Functional pathway analyses of 16 S rRNA V3-V4 bacterial communities were conducted using Tax4fun. The impact of PM1 exposure on α-diversity, composition, and function of gut microbiota in mothers and neonates was evaluated using multiple linear regression, controlling for nitrogen dioxide (NO2) and ozone (O3). Permutation multivariate analysis of variance (PERMANOVA) was used to analyze the interpretation degree of PM1 on the sample differences at the OTU level using the Bray-Curtis distance algorithm.

RESULTS

Gestational PM1 exposure was positively associated with the α-diversity of gut microbiota in neonates and explained 14.8% (adj. P = 0.026) of the differences in community composition among neonatal samples. In contrast, gestational PM1 exposure had no impact on the α- and β-diversity of gut microbiota in mothers. Gestational PM1 exposure was positively associated with phylum Actinobacteria of gut microbiota in mothers, and genera Clostridium_sensu_stricto_1, Streptococcus, Faecalibacterium of gut microbiota in neonates. At Kyoto Encyclopedia of Genes and Genomes pathway level 3, the functional analysis results showed that gestational PM1 exposure significantly down-regulated Nitrogen metabolism in mothers, as well as Two-component system and Pyruvate metabolism in neonates. While Purine metabolism, Aminoacyl-tRNA biosynthesis, Pyrimidine metabolism, and Ribosome in neonates were significantly up-regulated.

CONCLUSIONS

Our study provides the first evidence that exposure to PM1 has a significant impact on the gut microbiota of mothers and neonates, especially on the diversity, composition, and function of neonatal meconium microbiota, which may have important significance for maternal health management in the future.

Role of Hydrogen Sulfide in Inflammatory Bowel Disease

Hydrogen sulfide (H2S), originally known as toxic gas, has now attracted attention as one of the gasotransmitters involved in many reactions in the human body. H2S has been assumed to play a role in the pathogenesis of many chronic diseases, of which the exact pathogenesis remains unknown. One of them is inflammatory bowel disease (IBD), a chronic intestinal disease subclassified as Crohn's disease (CD) and ulcerative colitis (UC). Any change in the amount of H2S seems to be linked to inflammation in this illness. These changes can be brought about by alterations in the microbiota, in the endogenous metabolism of H2S and in the diet. As both too little and too much H2S drive inflammation, a balanced level is needed for intestinal health. The aim of this review is to summarize the available literature published until June 2023 in order to provide an overview of the current knowledge of the connection between H2S and IBD.

Spore-forming properties and enhanced oxygen tolerance of butyrate-producing Anaerostipes spp

OBJECTIVES

Butyrate producing bacteria are promising candidates for next-generation probiotics. However, they are extremely sensitive to oxygen, which is a significant obstacle to their inclusion in food matrices in a viable form. The present study characterized the spore-forming properties and stress tolerance of human gut butyrate-producing Anaerostipes spp.

METHODS

Spore formation properties in six species of Anaerostipes spp. were studied by in vitro and in silico tests.

RESULTS

Spores were observed from the cells of three species using microscopic analyses, while the remaining three did not form spores under the tested conditions. Spore-forming properties were confirmed by an ethanol treatment. The spores of Anaerostipes caccae were tolerant to oxygen and survived for 15 weeks under atmospheric conditions. Spores tolerated heat stress at 70 °C, but not at 80 °C. An in silico analysis of the conservation of potential sporulation signature genes revealed that the majority of human gut butyrate-producing bacteria were classified as potential spore formers. Comparative genomics revealed that three spore-forming Anaerostipes spp. specifically possessed the spore formation-related genes of bkdR, sodA, and splB, which may be key genes for different sporulation properties in Anaerostipes spp.

CONCLUSIONS

The present study demonstrated the enhanced stress tolerance of butyrate producing Anaerostipes spp. for future probiotic application. Presence of specific gene(s) are possibly keys for sporulation in Anaerostipes spp.

Faecalibacterium: a bacterial genus with promising human health applications

In humans, many diseases are associated with alterations in gut microbiota, namely increases or decreases in the abundance of specific bacterial groups. One example is the genus Faecalibacterium. Numerous studies have underscored that low levels of Faecalibacterium are correlated with inflammatory conditions, with inflammatory bowel disease (IBD) in the forefront. Its representation is also diminished in the case of several diseases, including colorectal cancer (CRC), dermatitis, and depression. Additionally, the relative presence of this genus is considered to reflect, at least in part, intestinal health status because Faecalibacterium is frequently present at reduced levels in individuals with gastrointestinal diseases or disorders. In this review, we first thoroughly describe updates to the taxonomy of Faecalibacterium, which has transformed a single-species taxon to a multispecies taxon over the last decade. We then explore the links discovered between Faecalibacterium abundance and various diseases since the first IBD-focused studies were published. Next, we examine current available strategies for modulating Faecalibacterium levels in the gut. Finally, we summarize the mechanisms underlying the beneficial effects that have been attributed to this genus. Together, epidemiological and experimental data strongly support the use of Faecalibacterium as a next-generation probiotic (NGP) or live biotherapeutic product (LBP).

Age-related effects on the modulation of gut microbiota by pectins and their derivatives: an in vitro study

Introduction

The present study investigates whether supplementation with pectin-type polysaccharides has potential to improve aging-associated dysbiosis of the gut microbiota. The influence of different types of pectins on the gut microbiota composition and short-chain fatty acids (SCFAs) profiles of elderly was compared to younger adults.

Methods

Pectins studied included a pectin polysaccharide (PEC), a partially hydrolyzed pectin (PPH), and a pectin oligosaccharide (POS). Additionally, inulin was used as a reference prebiotic substrate. Individual fecal samples were collected from healthy elderly volunteers (70-75 years) and younger adults (30-35 years). In vitro fermentations were performed using the CoMiniGut model with controlled temperature and pH. Samples were withdrawn at baseline and after 24 h fermentation for measurement of SCFAs production and microbiota composition by 16S rRNA gene sequencing.

Results and Discussion

The results showed that fermentations with PEC and PPH resulted in a specific stimulation of Faecalibacterium prausnitzii regardless of the age groups. Collinsella aerofaciens became a dominating species in the young adult group with fermentations of all three pectins, which was not observed in the elderly group. No significant differences in SCFAs production were found among the pectins, indicating a high level of functional redundancy. Pectins boosted various bacterial groups differently from the reference prebiotic substrate (inulin). We also found inulin had reduced butyrogenic and bifidogenic effects in the elderly group compared to the younger adult group. In conclusion, the in vitro modulating effects of pectins on elderly gut microbiota showed potential of using pectins to improve age-related dysbiosis.

Fecal carriage of extended-spectrum beta-lactamase-producing Enterobacterales in healthy Spanish schoolchildren

Background

Extended-spectrum ß-lactamase-producing Enterobacterales (ESBL-E) are a serious threat among emerging antibiotic resistant bacteria. Particularly, the number of cases of ESBL-E infections reported in children has been increasing in recent years, and approved antibiotic treatments for this age group are limited. However, information regarding the prevalence of colonization in European children, risk factors associated with colonization, and the characteristics of the colonizing strains is scarce. The aims of this study were to determine the prevalence of ESBL-E colonization in fecal samples of apparently healthy schoolchildren, to identify lifestyle routines associated with colonization, and to characterize clonal relationships and mechanisms of resistance in ESBL-E isolates.

Methods

A cohort of 887 healthy children (3-13  years old) from seven primary and secondary schools in the Madrid metropolitan area was recruited between April-June 2018, and sociodemographic information and daily habits were collected. Fecal samples were screened for ESBL-E carriage in selective medium. ESBL-E isolates were further characterized by assessing molecular epidemiology (PFGE and MLST), ESBL gene carriage, and antibiotic resistance profile. This information was analyzed in conjunction with the metadata of the participants in order to identify external factors associated with ESBL-E carriage.

Results

Twenty four ESBL-E, all but one Escherichia coli, were detected in 23 children (prevalence: 2.6%; 95% CI: 1.6-3.6%). Of these, seven contained the bla_CTX-M-14 allele, five the bla_CTX-M-15, five the bla_SHV-12, three the bla_CTX-M-27, three the bla_CTX-M-32, and one the bla_CTX-M-9. Significant clonal diversity was observed among the isolates that grouped into 22 distinct clusters (at <85% similarity of PFGE profile). ESBL-producing E. coli isolates belonged to 12 different STs, with ST10 (25%) and ST131 (17%) being the most frequent. Apart from ß-lactams, resistance to trimethoprim/sulfamethoxazole (46%), ciprofloxacin (33%), levofloxacin (33%), tobramycin (21%), and gentamicin (8%) were the most frequently detected.

Conclusion

The prevalence of ESBL-E in the studied cohort of children was lower than the average colonization rate previously detected in Europe for both children and adults. E. coli was the main ESBL-producing species detected and CTX-M were the most frequently identified ESBLs. High ST diversity suggests polyclonal dissemination. Compared to other STs, ST131 isolates were associated with resistance to various antimicrobials.

Time-dependent fermentation of different structural units of commercial pectins with intestinal bacteria

Many of the proposed health-related properties of pectins are based on their fermentability in the large intestine, but detailed structure-related studies on pectin fermentation have not been reported so far. Here, pectin fermentation kinetics were studied with a focus on structurally different pectic polymers. Therefore, six commercial pectins from citrus, apple, and sugar beet were chemically characterized and fermented in in vitro fermentation assays with human fecal samples over different periods of time (0 h, 4 h, 24 h, 48 h). Structure elucidation of intermediate cleavage products showed differences in fermentation speed and/or fermentation rate among the pectins, but the order in which specific structural pectic elements were fermented was comparable across all pectins. Neutral side chains of rhamnogalacturonan type I were fermented first (between 0 and 4 h), followed by homogalacturonan units (between 0 and 24 h) and, at last, the rhamnogalacturonan type I backbone (between 4 and 48 h). This indicates that fermentation of different pectic structural units might take place in different sections of the colon, potentially affecting their nutritional properties. For the formation of different short-chain fatty acids, mainly acetate, propionate, and butyrate, and the influence on microbiota, there was no time-dependent correlation regarding the pectic subunits. However, an increase of members of the bacterial genera Faecalibacterium, Lachnoclostridium, and Lachnospira was observed for all pectins.

Links between Diet, Intestinal Anaerobes, Microbial Metabolites and Health

A dense microbial community resides in the human colon, with considerable inter-individual variability in composition, although some species are relatively dominant and widespread in healthy individuals. In disease conditions, there is often a reduction in microbial diversity and perturbations in the composition of the microbiota. Dietary complex carbohydrates that reach the large intestine are important modulators of the composition of the microbiota and their primary metabolic outputs. Specialist gut bacteria may also transform plant phenolics to form a spectrum of products possessing antioxidant and anti-inflammatory activities. Consumption of diets high in animal protein and fat may lead to the formation of potentially deleterious microbial products, including nitroso compounds, hydrogen sulphide, and trimethylamine. Gut anaerobes also form a range of secondary metabolites, including polyketides that may possess antimicrobial activity and thus contribute to microbe-microbe interactions within the colon. The overall metabolic outputs of colonic microbes are derived from an intricate network of microbial metabolic pathways and interactions; however, much still needs to be learnt about the subtleties of these complex networks. In this review we consider the multi-faceted relationships between inter-individual microbiota variation, diet, and health.