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.

Associations between Accelerometer-Measured Physical Activity and Fecal Microbiota in Adults with Overweight and Obesity

PURPOSE

We aimed to assess whether total daily physical activity (PA), PA intensities, sedentary time (ST), and prolonged ST are associated with differences in the gut microbiota composition or short-chain fatty acid (SCFA) profile of adults with overweight or obesity.

METHODS

Cross-sectional associations between total daily PA (counts per minute), PA intensities (light and moderate-to-vigorous (MVPA)), ST, prolonged ST, and fecal microbiota composition were assessed in adults ( n = 124) between 25 and 45 yr of age with body mass index ≥25 kg·m -2 . Fecal microbiota composition was assessed with 16S rRNA gene sequencing. Daily PA and ST were measured with a hip-worn ActiGraph wGT3X-BT accelerometer.

RESULTS

Daily PA volume and intensity were positively associated with relative abundance of Faecalibacterium ( P = 0.04) and negatively associated with the abundances of Alistipes , Parabacteroides , and Gemmiger ( P = 0.003-0.04) as well as the concentrations of acetate, butyrate, and total SCFA (all P = 0.04). Conversely, ST was negatively associated with abundance of Faecalibacterium but positively associated with the abundances of taxa, including Ruminococcaceae, Parabacteroides , Alistipes , and Gemmiger . Clustering of participants based on whether they met PA recommendations suggested that SCFA profiles differed between individuals who did and did not meet PA recommendations. K-means clustering based on percent of time spent in MVPA and ST also identified differences in fecal microbiota composition between cluster 1 (lower MVPA, higher ST) and cluster 2 (higher MVPA, lower ST), including a higher abundance of Alistipes in cluster 1.

CONCLUSIONS

The current analysis suggests a beneficial association of daily PA on the fecal microbiota and a negative association of ST, particularly with respect to the associations of these variables with the genera Faecalibacterium , a butyrate-producing taxon.

Faecalibacterium prausnitzii prevents hepatic damage in a mouse model of NASH induced by a high-fructose high-fat diet

Introduction

Nonalcoholic steatohepatitis (NASH) is an advanced nonalcoholic fatty liver disease characterized by chronic inflammation and fibrosis. A dysbiosis of the gut microbiota has been associated with the pathophysiology of NASH, and probiotics have proven helpful in its treatment and prevention. Although both traditional and next-generation probiotics have the potential to alleviate various diseases, studies that observe the therapeutic effect of next-generation probiotics on NASH are lacking. Therefore, we investigated whether a next-generation probiotic candidate, Faecalibacterium prausnitzii, contributed to the mitigation of NASH.

Methods

In this study, we conducted 16S rRNA sequencing analyses in patients with NASH and healthy controls. To test F. prausnitzii could alleviate NASH symptoms, we isolated four F. prausnitzii strains (EB-FPDK3, EB-FPDK9, EB-FPDK11, and EB-FPYYK1) from fecal samples collected from four healthy individuals. Mice were maintained on a high-fructose high-fat diet for 16 weeks to induce a NASH model and received oral administration of the bacterial strains. Changes in characteristic NASH phenotypes were assessed via oral glucose tolerance tests, biochemical assays, and histological analyses.

Results

16S rRNA sequencing analyses confirmed that the relative abundance of F. prausnitzii reduced significantly in patients with NASH compared to healthy controls (p < 0.05). In the NASH mice, F. prausnitzii supplementation improved glucose homeostasis, prevented hepatic lipid accumulation, curbed liver damage and fibrosis, restored damaged gut barrier functions, and alleviated hepatic steatosis and liver inflammation. Furthermore, real-time PCR assays documented that the four F. prausnitzii strains regulated the expression of genes related to hepatic steatosis in these mice.

Discussion

Our study, therefore, confirms that the administration of F. prausnitzii bacteria can alleviate NASH symptoms. We propose that F. prausnitzii has the potential to contribute to the next-generation probiotic treatment of NASH.

Metagenomic association analysis of cognitive impairment in community-dwelling older adults

The gut microbiota is reportedly involved in neurodegenerative disorders, and exploration of differences in the gut microbiota in different cognitive status could provide clues for early detection and intervention in cognitive impairment. Here, we used data from the Taizhou Imaging Study (N = 516), a community-based cohort, to compare the overall structure of the gut microbiota at the species level through metagenomic sequencing, and to explore associations with cognition. Interestingly, bacteria capable of producing short-chain fatty acids (SCFAs), such as Bacteroides massiliensis, Bifidobacterium pseudocatenulatum, Fusicatenibacter saccharivorans and Eggerthella lenta, that can biotransform polyphenols, were positively associated with better cognitive performance (p < 0.05). Although Diallister invisus and Streptococcus gordonii were not obviously related to cognition, the former was dominant in individuals with mild cognitive impairment (MCI), while the later was more abundant in cognitively normal (CN) than MCI groups, and positively associated with cognitive performance (p < 0.05). Functional analysis further supported a potential role of SCFAs and lactic acid in the association between the gut microbiota and cognition. The significant associations persisted after accounting for dietary patterns. Collectively, our results demonstrate an association between the gut microbiota and cognition in the general population, indicating a potential role in cognitive impairment. The findings provide clues for microbiome biomarkers of dementia, and insight for the prevention and treatment of dementia.

Berberine regulates glucose metabolism in largemouth bass by modulating intestinal microbiota

This study examined the role of intestinal microbiota in berberine (BBR)-mediated glucose (GLU) metabolism regulation in largemouth bass. Four groups of largemouth bass (133.7 ± 1.43 g) were fed with control diet, BBR (1 g/kg feed) supplemented diet, antibiotic (ATB, 0.9 g/kg feed) supplemented diet and BBR + ATB (1g/kg feed +0.9 g/kg feed) supplemented diet for 50 days. BBR improved growth, decreased the hepatosomatic and visceral weight indices, significantly downregulated the serum total cholesterol and GLU levels, and significantly upregulated the serum total bile acid (TBA) levels. The hepatic hexokinase, pyruvate kinase, GLU-6-phosphatase and glutamic oxalacetic transaminase activities in the largemouth bass were significantly upregulated when compared with those in the control group. The ATB group exhibited significantly decreased final bodyweight, weight gain, specific growth rates and serum TBA levels, and significantly increased hepatosomatic and viscera weight indices, hepatic phosphoenolpyruvate carboxykinase, phosphofructokinase, and pyruvate carboxylase activities, and serum GLU levels. Meanwhile, the BBR + ATB group exhibited significantly decreased final weight, weight gain and specific growth rates, and TBA levels and significantly increased hepatosomatic and viscera weight indices and GLU levels. High-throughput sequencing revealed that compared with those in the control group, the Chao one index and Bacteroidota contents were significantly upregulated and the Firmicutes contents were downregulated in the BBR group. Additionally, the Shannon and Simpson indices and Bacteroidota levels were significantly downregulated, whereas the Firmicutes levels were significantly upregulated in ATB and BBR + ATB groups. The results of in-vitro culture of intestinal microbiota revealed that BBR significantly increased the number of culturable bacteria. The characteristic bacterium in the BBR group was Enterobacter cloacae. Biochemical identification analysis revealed that E. cloacae metabolizes carbohydrates. The size and degree of vacuolation of the hepatocytes in the control, ATB, and ATB + BBR groups were higher than those in the BBR group. Additionally, BBR decreased the number of nuclei at the edges and the distribution of lipids in the liver tissue. Collectively, BBR reduced the blood GLU level and improved GLU metabolism in largemouth bass. Comparative analysis of experiments with ATB and BBR supplementation revealed that BBR regulated GLU metabolism in largemouth bass by modulating intestinal microbiota.

Development of the Anaerobic Microbiome in the Infant Gut

Ninety-five percent of gut microbiota are anaerobes and vary according to age and diet. Complex carbohydrates in human milk enhance the growth of Bifidobacterium and Bacteroides in the first year. Complex carbohydrates in solid foods enhance the growth of Bacteroides and Clostridium in the second year. Short-chain fatty acids produced by Akkermansia and Faecalibacterium may reduce obesity, diabetes and IBD.

Evidence for a Causal Role for Escherichia coli Strains Identified as Adherent-Invasive (AIEC) in Intestinal Inflammation

Enrichment of adherent-invasive Escherichia coli (AIEC) has been consistently detected in subsets of inflammatory bowel disease (IBD) patients. Although some AIEC strains cause colitis in animal models, these studies did not systematically compare AIEC with non-AIEC strains, and causal links between AIEC and disease are still disputed. Specifically, it remains unclear whether AIEC shows enhanced pathogenicity compared to that of commensal E. coli found in the same ecological microhabitat and if the in vitro phenotypes used to classify strains as AIEC are pathologically relevant. Here, we utilized in vitro phenotyping and a murine model of intestinal inflammation to systematically compare strains identified as AIEC with those identified as non-AIEC and relate AIEC phenotypes to pathogenicity. Strains identified as AIEC caused, on average, more severe intestinal inflammation. Intracellular survival/replication phenotypes routinely used to classify AIEC positively correlated with disease, while adherence to epithelial cells and tumor necrosis factor alpha production by macrophages did not. This knowledge was then applied to design and test a strategy to prevent inflammation by selecting E. coli strains that adhered to epithelial cells but poorly survived/replicated intracellularly. Two E. coli strains that ameliorated AIEC-mediated disease were subsequently identified. In summary, our results show a relationship between intracellular survival/replication in E. coli and pathology in murine colitis, suggesting that strains possessing these phenotypes might not only become enriched in human IBD but also contribute to disease. We provide new evidence that specific AIEC phenotypes are pathologically relevant and proof of principle that such mechanistic information can be therapeutically exploited to alleviate intestinal inflammation. IMPORTANCE Inflammatory bowel disease (IBD) is associated with an altered gut microbiota composition, including expansion of Proteobacteria. Many species in this phylum are thought to contribute to disease under certain conditions, including adherent-invasive Escherichia coli (AIEC) strains, which are enriched in some patients. However, whether this bloom contributes to disease or is just a response to IBD-associated physiological changes is unknown. Although assigning causality is challenging, appropriate animal models can test the hypothesis that AIEC strains have an enhanced ability to cause colitis in comparison to other gut commensal E. coli strains and to identify bacterial traits contributing to virulence. We observed that AIEC strains are generally more pathogenic than commensal E. coli and that bacterial intracellular survival/replication phenotypes contributed to disease. We also found that E. coli strains lacking primary virulence traits can prevent inflammation. Our findings provide critical information on E. coli pathogenicity that may inform development of IBD diagnostic tools and therapies.

The Development of Gut Microbiota and Its Changes Following C. jejuni Infection in Broilers

The gut is home to more than millions of bacterial species. The gut bacteria coexist with the host in a symbiotic relationship that can influence the host’s metabolism, nutrition, and physiology and even module various immune functions. The commensal gut microbiota plays a crucial role in shaping the immune response and provides a continuous stimulus to maintain an activated immune system. The recent advancements in high throughput omics technologies have improved our understanding of the role of commensal bacteria in developing the immune system in chickens. Chicken meat continues to be one of the most consumed sources of protein worldwide, with the demand expected to increase significantly by the year 2050. Yet, chickens are a significant reservoir for human foodborne pathogens such as Campylobacter jejuni. Understanding the interaction between the commensal bacteria and C. jejuni is essential in developing novel technologies to decrease C. jejuni load in broilers. This review aims to provide current knowledge of gut microbiota development and its interaction with the immune system in broilers. Additionally, the effect of C. jejuni infection on the gut microbiota is addressed.

Fecal Microbiota Composition as a Metagenomic Biomarker of Dietary Intake

Gut microbiota encompasses the set of microorganisms that colonize the gastrointestinal tract with mutual relationships that are key for host homeostasis. Increasing evidence supports cross intercommunication between the intestinal microbiome and the eubiosis-dysbiosis binomial, indicating a networking role of gut bacteria as potential metabolic health surrogate markers. The abundance and diversity of the fecal microbial community are already recognized to be associated with several disorders, such as obesity, cardiometabolic events, gastrointestinal alterations, and mental diseases, which suggests that intestinal microbes may be a valuable tool as causal or as consequence biomarkers. In this context, the fecal microbiota could also be used as an adequate and informative proxy of the nutritional composition of the food intake and about the adherence to dietary patterns, such as the Mediterranean or Western diets, by displaying specific fecal microbiome signatures. The aim of this review was to discuss the potential use of gut microbial composition as a putative biomarker of food intake and to screen the sensitivity value of fecal microbiota in the evaluation of dietary interventions as a reliable and precise alternative to subjective questionnaires.

Vitamin D and Microbiome: Molecular Interaction in Inflammatory Bowel Disease Pathogenesis

Studies of systemic autoimmune diseases point to characteristic microbial patterns in various diseases, including inflammatory bowel disease (IBD). Autoimmune diseases, and IBD in particular, show a predisposition to vitamin D deficiency, leading to alterations in the microbiome and disruption of intestinal epithelial barrier integrity. In this review, we examine the role of the gut microbiome in IBD and discuss how vitamin D-vitamin D receptor (VDR)-associated molecular signaling pathways contribute to the development and progression of IBD through their effects on gut barrier function, the microbial community, and immune system function. The present data demonstrate that vitamin D promotes the proper function of the innate immune system by acting as an immunomodulator, exerting anti-inflammatory effects, and critically contributing to the maintenance of gut barrier integrity and modulation of the gut microbiota, mechanisms that may influence the IBD development and progression. VDR regulates the biological effects of vitamin D and is related to environmental, genetic, immunologic, and microbial aspects of IBD. Vitamin D influences the distribution of the fecal microbiota, with high vitamin D levels associated with increased levels of beneficial bacterial species and lower levels of pathogenic bacteria. Understanding the cellular functions of vitamin D-VDR signaling in intestinal epithelial cells may pave the way for the development of new treatment strategies for the therapeutic armamentarium of IBD in the near future.

A clinical trial about effects of prebiotic and probiotic supplementation on weight loss, psychological profile and metabolic parameters in obese subjects

INTRODUCTION

The management of obesity is difficult with many failures of lifestyle measures, hence the need to broaden the range of treatments prescribed. The aim of our work was to study the influence of pre and probiotics on weight loss psychological profile and metabolic parameters in obese patients.

METHODS

It is a clinical trial involving 45 obese patients, recruited from the Obesity Unit of the National Institute of Nutrition between March and August 2022 divided into three groups: diet only (low-carbohydrate and reduced energy diet), prebiotics (30 g of carob/day) and probiotics (one tablet containing Bifidobacterium longum, Lactobacillus helveticus, Lactococcus lactis, Streptococcus thermophilus/day). The three groups were matched for age, sex and BMI. Patients were seen after 1 month from the intervention. Anthropometric measures, biological parameters, dietary survey and psychological scores were performed.

RESULTS

The average age of our population was 48.73 ± 7.7 years, with a female predominance. All three groups showed a significant decrease in weight, BMI and waist circumference with p < .05. Only the prebiotic and probiotic group showed a significant decrease in fat mass (p = .001) and a significant increase in muscle strength with p = .008 and .004, but the differences were not significant between the three groups. Our results showed also a significant decrease in insulinemia and HOMA-IR in the prebiotic group compared to the diet-alone group (p = .03; p = .012) and the probiotic group showed a significant decrease in fasting blood glucose compared to the diet alone group (p = .02). A significant improvement in sleep quality was noted in the prebiotic group (p = .02), with a significant decrease in depression, anxiety and stress in all three groups.

CONCLUSIONS

The prescription of prebiotics and probiotics with the lifestyle measures seems interesting for the management of obesity especially if it is sarcopenic, in addition to the improvement of metabolic parameters and obesity-related psychiatric disorders.

Modulation of the gut microbiota: opportunities and regulatory aspects

The human gut is an intensively colonized organ containing microorganisms that can be health-promoting or pathogenic. This feature led to the development of functional foods aiming to fortify the former category at the expense of the latter. Since long, cultured products, including probiotics fortification, have been used for humans as live microbial feed additions. This review presents some of the microbes used as probiotics and discusses how supplementation with probiotics may help initiate and/or restore eubiotic composition of gut microbiota. Additionally, it considers safety and regulatory aspects of probiotics.

Role of Interleukin-22 in ulcerative colitis

Ulcerative Colitis (UC) is a chronic disease, in the progression of which an immune overreaction may play an important role. IL-22 is a member of the IL-10 superfamily of cytokines and is pleiotropic in immune regulation and inflammatory responses. IL-22 can produce protective effects, promote wound healing and tissue regeneration, while it can also induce inflammatory reactions when it is chronically overexpressed. Extensive literatures reported that IL-22 played an essential role in the pathogenic development of UC. IL-22 participates in the whole disease process of UC involving signaling pathways, gene expression regulation, and intestinal flora imbalance, making IL-22 a possible candidate for the treatment of UC. In this paper, the latest knowledge to further elucidate the role of IL-22 in UC was summarized and analyzed.

Impact of caloric restriction on the gut microbiota

Caloric restriction (CR) and related time-restricted diets have been popularized as means of preventing metabolic disease while improving general well-being. However, evidence as to their long-term efficacy, adverse effects, and mechanisms of activity remains incompletely understood. The gut microbiota is modulated by such dietary approaches, yet causal evidence to its possible downstream impacts on host metabolism remains elusive. Herein, we discuss the positive and adverse influences of restrictive dietary interventions on gut microbiota composition and function, and their collective impacts on host health and disease risk. We highlight known mechanisms of microbiota influences on the host, such as modulation of bioactive metabolites, while discussing challenges in achieving mechanistic dietary-microbiota insights, including interindividual variability in dietary responses as well as other methodological and conceptual challenges. In all, causally understanding the impact of CR approaches on the gut microbiota may enable to better decode their overall influences on human physiology and disease.

coli load

Graft versus host disease (GVHD) remains the major cause of morbidity and mortality after allogeneic stem cell transplantation, especially for intestinal GVHD, as steroid resistant GVHD results in high mortality. For this reason, new treatments of GVHD are needed. One approach is the reduction of pathogenic bacteria using anti-E. coli Immunoglobulin Yolk (IgY). In a haploidentical murine model, B6D2F1 mice conditioned with total body irradiation (TBI), received bone marrow cells (BM) and splenocytes (SC) from either syngeneic (Syn = B6D2F1) or allogeneic (Allo = C57BL/6) donors. Following this, animals received from day -2 until day +28 chow contained IgY or control chow. Thereafter the incidence and severity of aGVHD, the cytokines, chemokines, IDO1 and different pathogen-recognition receptors (PRR) were analyzed and compared to control animals (received chow without IgY). We found that animals receiving chow with IgY antibody showed reduced GVHD severity compared to control animals. On day28 after alloBMT, IDO, NOD2, TLR2, TLR4 and the inflammatory chemokine CCL3, were reduced in the colon and correlated with a significant decrease in E. coli bacteria. In summary chow containing chicken antibodies (IgY) improved GVHD via decrease in bacterial load of E coli conducting to reduction of pathogen receptors (NOD2, TLR2 and 4), IDO, chemokines and cytokines.

A multi-omic brain gut microbiome signature differs between IBS subjects with different bowel habits

Alterations of the brain-gut-microbiome system (BGM) have been implicated in the pathophysiology of irritable bowel syndrome (IBS), yet bowel habit-specific alterations have not been elucidated. In this cross-sectional study, we apply a systems biology approach to characterize BGM patterns related to predominant bowel habit. Fecal samples and resting state fMRI were obtained from 102 premenopausal women (36 constipation-predominant IBS (IBS-C), 27 diarrhea-predominant IBS (IBS-D), 39 healthy controls (HCs)). Data integration analysis using latent components (DIABLO) was used to integrate data from the phenome, microbiome, metabolome, and resting-state connectome to predict HCs vs IBS-C vs IBS-D. Bloating and visceral sensitivity, distinguishing IBS from HC, were negatively associated with beneficial microbes and connectivity involving the orbitofrontal cortex. This suggests that gut interactions may generate aberrant central autonomic and descending pain pathways in IBS. The connection between IBS symptom duration, key microbes, and caudate connectivity may provide mechanistic insight to the chronicity of pain in IBS. Compared to IBS-C and HCs, IBS-D had higher levels of many key metabolites including tryptophan and phenylalanine, and increased connectivity between the sensorimotor and default mode networks; thus, suggestingan influence on diarrhea, self-related thoughts, and pain perception in IBS-D ('bottom-up' mechanism). IBS-C's microbiome and metabolome resembled HCs, but IBS-C had increased connectivity in the default mode and salience networks compared to IBS-D, which may indicate importance of visceral signals, suggesting a more 'top-down' BGM pathophysiology. These BGM characteristics highlight possible mechanistic differences for variations in the IBS bowel habit phenome. This article is part of the Special Issue on 'Microbiome & the Brain: Mechanisms & Maladies'.

Food as Medicine: How to Influence the Microbiome and Improve Symptoms in Patients with Irritable Bowel Syndrome

PURPOSE OF REVIEW

This review highlights effects of dietary interventions on the gut microbiome and gastrointestinal symptoms in those with irritable bowel syndrome (IBS).

RECENT FINDINGS

It is hypothesized that gut dysbiosis factors into the pathophysiology of IBS. Various diets that influence the microbiome and intestinal physiology may have therapeutic properties. At present, data suggests that implementation of personalized dietary interventions have a mixed, but overall positive effect on the gut microbiome and IBS symptoms. The effect of dietary modification on the gut microbiome and GI symptoms in patients with IBS is a topic that has garnered interest due to the increasing prevalence of IBS and heightened awareness of the importance of gut health. The composition of the gut microbiome may be modulated by promoting fiber intake and implementation of exclusionary diets and dietary supplements; however, additional studies are needed to provide evidence-based guidelines in this patient population.

Dietary nucleotides influences intestinal barrier function, immune responses and microbiota in 3-day-old weaned piglets

Nucleotides (NTs) play a pivotal role in the growth and development of the intestine. This study aimed to evaluate the effects of nucleotides supplementation on the intestinal barrier function, immune responses and microbiota in 3-day-old weaned piglets. Ninety-six piglets weaned at 3-days after birth were randomly assigned to 2 treatments (6 replicates/treatment, 8 piglets/replicate) according to the average body weight. The dietary treatments consisted of the control (CON; fed a basal artificial milk) and nucleotides groups (NT; fed a basal artificial milk with 0.035 % nucleotides, the contents of CMP, UMP, AMP, GMP, and IMP were 1:1:1:1:1, respectively). Diarrhea rates were recorded, and blood and intestinal samples were collected on day 35 of the piglets. The current study showed that NTs supplementation tended to decrease the diarrhea rate of weaned piglets (P < 0.10). NTs increased villus height and the villus height-to-crypt depth (V/C) ratio in the ileum (P < 0.05). Dietary NTs up-regulated protein expression of ZO-1 in ileal mucosa (P < 0.05), and the protein expression of Occludin tended to increase. Furthermore, NTs up-regulated the mRNA expression of Mucin (MUC)2, while the mRNA expression of MUC4 was down-regulated in the ileal mucosa (P < 0.05). Besides, supplementation with NTs increased the ileal mucosa genes expression of IL-21, INF-γ, IL-10, IL-4, IL-6 and TNF-α (P < 0.05). Furthermore, dietary NTs increased the protein expression of NF-κB, IL-6 and TNF-α (P < 0.05), and the proteins expression of Occludin and p-NF-κB tended to be up-regulated in the ileal mucosa (P < 0.10). Furthermore, NTs supplementation increased short chain fatty acid in the colonic (P < 0.05). And NTs supplementation reduced the Firmicutes/Bacteroidota ratio in the colon, at the genus level, NTs enriched the relative abundance of Prevotella, Faecalibacterium and Olsenella (P < 0.05). These data indicate that NTs could increase the villus height, increase the V/C, regulate the expression of tight junction protein and mucin, improve the intestinal barrier of piglets, regulate the secretion of cytokines, improve the biological immunity, increase the abundance of beneficial bacteria, and thus reduce the diarrhea of piglets.

Novel Epitopes Mapping of African Swine Fever Virus CP312R Protein Using Monoclonal Antibodies

African Swine Fever (ASF) is a highly contagious and lethal pig disease and poses a huge threat to the pig industry worldwide. ASF virus (ASFV) encodes more than 150 different proteins, but the biological properties of most viral proteins are still unknown. ASFV CP312R protein has been proven to be one of the most immunogenic proteins during ASFV infection in pigs; however, its specific epitopes have yet to be identified. In this study, we verified the immunogenicity of CP312R protein in the sera from attenuated ASFV-inoculated pigs. We generated seven anti-ASFV CP312R mouse monoclonal antibodies (mAbs) from mice immunized with recombinant CP312R protein (rCP312R). All seven mAbs are the IgG2b-Kappa isotype and specifically interacted with the CP312R protein expressed in various cells that were infected by ASFVs or transfected with plasmid CP312R. The epitope mapping was performed by using these characterized mAbs and the peptide scanning (Pepscan) method followed by Western blot. As a result, two antigenic determinant regions were identified: two of the seven mAbs recognized the ¹²²KNEQGEEIYP¹³¹ amino acids, and the remaining five mAbs recognized the ⁷⁸DEEVIRMNAE⁸⁷ amino acids of the CP312R protein. These antigenic determinants of CP312R are conserved in different ASFV strains of seven genotypes. By using the characterized mAb, confocal microscopy observation revealed that the CP312R was mainly localized in the cytoplasm and, to some extent, in nuclei and on the nuclear membrane of infected host cells. In summary, our results benefit our understanding on the antigenic regions of ASFV CP312R and help to develop better serological diagnosis of ASF and vaccine research.

Akkermansia muciniphila as a Next-Generation Probiotic in Modulating Human Metabolic Homeostasis and Disease Progression: A Role Mediated by Gut-Liver-Brain Axes?

Appreciation of the importance of Akkermansia muciniphila is growing, and it is becoming increasingly relevant to identify preventive and/or therapeutic solutions targeting gut-liver-brain axes for multiple diseases via Akkermansia muciniphila. In recent years, Akkermansia muciniphila and its components such as outer membrane proteins and extracellular vesicles have been known to ameliorate host metabolic health and intestinal homeostasis. However, the impacts of Akkermansia muciniphila on host health and disease are complex, as both potentially beneficial and adverse effects are mediated by Akkermansia muciniphila and its derivatives, and in some cases, these effects are dependent upon the host physiology microenvironment and the forms, genotypes, and strain sources of Akkermansia muciniphila. Therefore, this review aims to summarize the current knowledge of how Akkermansia muciniphila interacts with the host and influences host metabolic homeostasis and disease progression. Details of Akkermansia muciniphila will be discussed including its biological and genetic characteristics; biological functions including anti-obesity, anti-diabetes, anti-metabolic-syndrome, anti-inflammation, anti-aging, anti-neurodegenerative disease, and anti-cancer therapy functions; and strategies to elevate its abundance. Key events will be referred to in some specific disease states, and this knowledge should facilitate the identification of Akkermansia muciniphila-based probiotic therapy targeting multiple diseases via gut-liver-brain axes.

Immunomagnetic Capture of Faecalibacterium prausnitzii Selectively Modifies the Fecal Microbiota and Its Immunomodulatory Profile

Faecalibacterium represents one of the most abundant bacterial groups in the human intestinal microbiota of healthy adults and can represent more than 10% of the total bacterial population, Faecalibacterium prausnitzii being the only recognized species up to the past year. Reduction in the abundance of F. prausnitzii in the human gut has been linked to several human disorders, such as Crohn's disease. In this study, we developed a strategy to modify the relative abundance of F. prausnitzii in fecal microbiotas as a means of evaluating its contribution to the immunomodulatory effect of intestinal microbiotas with different F. prausnitzii contents using a peripheral blood mononuclear cell (PBMC) model. We used a polyclonal antibody against the surface of F. prausnitzii M21 to capture the bacterium from synthetic and human fecal microbiotas using immunoseparation techniques. As a proof-of-principle study, the levels of immunomodulation exerted by microbiotas of healthy donors (HDs) with different relative abundances of F. prausnitzii, achieved with the above-mentioned immunoseparation technique, were evaluated in a PBMC model. For this purpose, PBMCs were cocultivated with the modified microbiotas or a pure culture of F. prausnitzii and, subsequently, the microbiota of Crohn's donors was added to the coculture. The cytokine concentration was determined, showing that our experimental model supports the anti-inflammatory effects of this bacterium. IMPORTANCE There is increasing interest in deciphering the contribution of gut microbiota species to health and disease amelioration. The approach proposed herein provides a novel and affordable strategy to probe deeply into microbiota-host interactions by strategically modifying the relative abundance of specific gut microbes, hence facilitating the study of their contribution to a given trait of the microbiota.

paratuberculosis in Cattle

Although Mycobacterium avium subsp. paratuberculosis (MAP) has threatened public health and the livestock industry, the current diagnostic tools (e.g., fecal PCR and enzyme-linked immunosorbent assay [ELISA]) for MAP infection have some limitations, such as inconsistent results due to intermittent bacterial shedding or low sensitivity during the early stage of infection. Therefore, this study aimed to develop a novel biomarker focusing on elucidating the gut microbial signature of MAP-positive ruminants, since the clinical signs of MAP infection are closely related to dysbiosis. 16S rRNA-based gut microbial community analysis revealed both a decrease in microbial diversity and the emergence of several distinct taxa following MAP infection. To determine the discriminant taxa diagnostic of MAP infection, machine learning-based feature selection and predictive model construction were applied to taxon abundance data or their transformed derivatives. The selected taxa, such as Clostridioides (formerly Clostridium) difficile, were used to build models using a support vector machine, linear support vector classification, k-nearest neighbor, and random forest with 10-fold cross-validation. The receiver operating characteristic-area under the curve (ROC-AUC) analysis of the models revealed their high accuracy, up to approximately 96%. Collectively, taxonomic signatures of cattle gut microbiotas according to MAP infection status could be identified by feature selection tools and applied to establish a predictive model for the infection state. IMPORTANCE Due to the limitations, such as intermittent bacterial shedding or poor sensitivity, of the current diagnostic tools for Johne's disease, novel biomarkers are urgently needed to aid control of the disease. Here, we explored the fecal microbiota of Johne's disease-affected cattle and tried to discover distinct microbial characteristics which have the potential to be novel noninvasive biomarkers. Through 16S rRNA sequencing and machine learning approaches, a dozen taxa were selected as taxonomic signatures to discriminate the disease state. In addition, when constructing predictive models using relative abundance data of the corresponding taxa, the models showed high accuracy for classification, even including animals with subclinical infection. Thus, our study suggested novel noninvasive microbiological biomarkers that are robustly expressed regardless of subclinical infection and the applicability of machine learning for diagnosis of Johne's disease.

Visual detection of Cronobacter sakazakii on a microfluidic chip fabricated by a 3D molding method

Cronobacter sakazakii (C. sakazakii) is a pathogenic bacterium associated with life-threatening neonatal infections that have been linked to contaminated powdered infant formula (PIF). Most C. sakazakii testing is still limited in microbiology laboratories due to the need for sophisticated equipment and professional technicians. Microfluidic chips combined with isothermal amplification analysis are shown to be one of the most attractive microbiological on-site detection platforms. In this study, PDMS microfluidic chips were fabricated by a simple 3D molding method and sealed with "PDMS glue". The chip consisted of an inlet, a microchannel, six reaction wells, and six vent holes. And based on the 16S rRNA and ITS genes of C. sakazakii, we have successfully proposed a multiplex competitive annealing mediated isothermal amplification (mCAMP) assay on the microfluidic chip for the visual detection of C. sakazakii in PIF samples. The primers were fixed in the reaction wells of the chip before detection, which can be preserved for 60 days at 4 °C. The results showed that the established mCAMP assay had high specificity, and the limit of detection was 2.2 × 10³ CFU g^-1. With enrichment culture, even if the initial inoculation level is 1 CFU g^-1, the mCAMP assay can still detect the presence of C. sakazakii in spiked PIF samples. The test results are visible to the naked eye, which is suitable for rapid analysis in resource-limited settings.

Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data

BACKGROUND

Gut dysbacteriosis has been reported as one of the etiologies for irritable bowel syndrome (IBS). However, the association between gut microbiota and IBS is still inconclusive.

METHOD

A paired-sample study was designed by retrieving original multicenter 16 s-rRNA data of IBS patients and healthy controls from the GMrepo database. The propensity score matching (PSM) algorithm was applied to reduce confounding bias. The differential analysis of microbiota composition was performed at different taxonomic levels. The co-occurrence network was established. Subgroup analysis was performed to identify specific microbial compositions in different IBS subtypes.

RESULTS

A total of 1522 amplicon samples were initially enrolled. After PSM, 708 individuals (354 IBS and 354 healthy controls) were eligible for further analysis. A total of 1,160 genera were identified. We identified significantly changed taxa in IBS groups (IBS-enriched: the families Enterobacteriaceae, Moraxellaceae and Sphingobacteriaceae; the genera Streptococcus, Bacillus, Enterocloster, Sphingobacterium, Holdemania and Acinetobacter. IBS-depleted: the phyla Firmicutes, Euryarchaeota, Cyanobacteria, Acidobacteria and Lentisphaerae; the families Bifidobacteriaceae, Ruminococcaceae, Methanobacteriaceae and the other 25 families; the genera Faecalibacterium, Bifidobacterium and other 68 genera). The co-occurrence network identified three hub genera and six hub species (including Faecalibacterium prausnitzii) that may be involved in IBS pathophysiology. Strong positive interactions were identified among the Bifidobacterium longum, Bifidobacterium breve and Bifidobacterium adolescentis in the Bifidobacterium community.

CONCLUSION

This study provides quantitative analysis and visualization of the interaction between the gut microbiota and IBS. The identification of key species should be further validated to evaluate their causal relationships with the pathogenesis of IBS.

Pectin mediates the mechanism of host blood glucose regulation through intestinal flora

Pectin is a complex polysaccharide found in plant cell walls and interlayers. As a food component, pectin is benefit for regulating intestinal flora. Metabolites of intestinal flora, including short-chain fatty acids (SCFAs), bile acids (BAs) and lipopolysaccharides (LPS), are involved in blood glucose regulation. SCFAs promote insulin synthesis through the intestine-GPCRs-derived pathway and hepatic adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK) pathway to promote hepatic glycogen synthesis. On the one hand, BAs stimulate intestinal L cells and pancreatic α cells to secrete Glucagon-like peptide-1 (GLP-1) and peptide YY (PYY) through receptors G protein-coupled receptor (TGR5) and farnesoid X receptor (FXR). On the other hand, BAs promote hepatic glycogen synthesis through AMPK pathway. LPS inhibits the release of inflammatory cytokines through Toll-like receptors (TLRs)-myeloid differentiation factor 88 (MYD88) pathway and mitogen-activated protein kinase (MAPK) pathway, thereby alleviating insulin resistance (IR). In brief, both SCFAs and BAs promote GLP-1 secretion through different pathways, employing strategies of increasing glucose consumption and decreasing glucose production to maintain normal glucose levels. Notably, pectin can also directly inhibit the release of inflammatory cytokines through the -TLRs-MYD88 pathway. These data provide valuable information for further elucidating the relationship between pectin-intestinal flora-glucose metabolism.

Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is characterized by unexplained debilitating fatigue, cognitive dysfunction, gastrointestinal disturbances, and orthostatic intolerance. Here, we report a multi-omic analysis of a geographically diverse cohort of 106 cases and 91 healthy controls that revealed differences in gut microbiome diversity, abundances, functional pathways, and interactions. Faecalibacterium prausnitzii and Eubacterium rectale, which are both recognized as abundant, health-promoting butyrate producers in the human gut, were reduced in ME/CFS. Functional metagenomics, qPCR, and metabolomics of fecal short-chain fatty acids confirmed a deficient microbial capacity for butyrate synthesis. Microbiome-based machine learning classifier models were robust to geographic variation and generalizable in a validation cohort. The abundance of Faecalibacterium prausnitzii was inversely associated with fatigue severity. These findings demonstrate the functional nature of gut dysbiosis and the underlying microbial network disturbance in ME/CFS, providing possible targets for disease classification and therapeutic trials.

coli pathobiont LF82 encodes a unique variant of σ (70) that results in specific gene expression changes and altered phenotypes

LF82, an adherent invasive Escherichia coli pathobiont, is associated with ileal Crohn's disease, an inflammatory bowel disease of unknown etiology. Although LF82 contains no virulence genes, it carries several genetic differences, including single nucleotide polymorphisms (SNPs), that distinguish it from nonpathogenic E. coli . We have identified and investigated an extremely rare SNP that is within the highly conserved rpoD gene, encoding σ ⁷⁰ , the primary sigma factor for RNA polymerase. We demonstrate that this single residue change (D445V) results in specific transcriptome and phenotypic changes that are consistent with multiple phenotypes observed in LF82, including increased antibiotic resistance and biofilm formation, modulation of motility, and increased capacity for methionine biosynthesis. Our work demonstrates that a single residue change within the bacterial primary sigma factor can lead to multiple alterations in gene expression and phenotypic changes, suggesting an underrecognized mechanism by which pathobionts and other strain variants with new phenotypes can emerge.

Type I Diabetes Pathoetiology and Pathophysiology: Roles of the Gut Microbiome, Pancreatic Cellular Interactions, and the 'Bystander' Activation of Memory CD8(+) T Cells

Type 1 diabetes mellitus (T1DM) arises from the failure of pancreatic β-cells to produce adequate insulin, usually as a consequence of extensive pancreatic β-cell destruction. T1DM is classed as an immune-mediated condition. However, the processes that drive pancreatic β-cell apoptosis remain to be determined, resulting in a failure to prevent ongoing cellular destruction. Alteration in mitochondrial function is clearly the major pathophysiological process underpinning pancreatic β-cell loss in T1DM. As with many medical conditions, there is a growing interest in T1DM as to the role of the gut microbiome, including the interactions of gut bacteria with Candida albicans fungal infection. Gut dysbiosis and gut permeability are intimately associated with raised levels of circulating lipopolysaccharide and suppressed butyrate levels, which can act to dysregulate immune responses and systemic mitochondrial function. This manuscript reviews broad bodies of data on T1DM pathophysiology, highlighting the importance of alterations in the mitochondrial melatonergic pathway of pancreatic β-cells in driving mitochondrial dysfunction. The suppression of mitochondrial melatonin makes pancreatic β-cells susceptible to oxidative stress and dysfunctional mitophagy, partly mediated by the loss of melatonin's induction of PTEN-induced kinase 1 (PINK1), thereby suppressing mitophagy and increasing autoimmune associated major histocompatibility complex (MHC)-1. The immediate precursor to melatonin, N-acetylserotonin (NAS), is a brain-derived neurotrophic factor (BDNF) mimic, via the activation of the BDNF receptor, TrkB. As both the full-length and truncated TrkB play powerful roles in pancreatic β-cell function and survival, NAS is another important aspect of the melatonergic pathway relevant to pancreatic β-cell destruction in T1DM. The incorporation of the mitochondrial melatonergic pathway in T1DM pathophysiology integrates wide bodies of previously disparate data on pancreatic intercellular processes. The suppression of Akkermansia muciniphila, Lactobacillus johnsonii, butyrate, and the shikimate pathway-including by bacteriophages-contributes to not only pancreatic β-cell apoptosis, but also to the bystander activation of CD8⁺ T cells, which increases their effector function and prevents their deselection in the thymus. The gut microbiome is therefore a significant determinant of the mitochondrial dysfunction driving pancreatic β-cell loss as well as 'autoimmune' effects derived from cytotoxic CD8⁺ T cells. This has significant future research and treatment implications.

Saccharomyces cerevisiae prevents postoperative recurrence of Crohn's disease modeled by ileocecal resection in HLA-B27 transgenic rats

BACKGROUND

Postoperative recurrence (POR) after ileocecal resection (ICR) affects most Crohn's disease patients within 3-5 years after surgery. Adherent-invasive Escherichia coli (AIEC) typified by the LF82 strain are pathobionts that are frequently detected in POR of Crohn's disease and have a potential role in the early stages of the disease pathogenesis. Saccharomyces cerevisiae CNCM I-3856 is a probiotic yeast reported to inhibit AIEC adhesion to intestinal epithelial cells and to favor their elimination from the gut.

AIM

To evaluate the efficacy of CNCM I-3856 in preventing POR induced by LF82 in an HLA-B27 transgenic (TgB27) rat model.

METHODS

Sixty-four rats [strain F344, 38 TgB27, 26 control non-Tg (nTg)] underwent an ICR at the 12^th wk (W12) of life and were sacrificed at the 18^th wk (W18) of life. TgB27 rats were challenged daily with oral administration of LF82 (10⁹ colony forming units (CFUs)/day (d), n = 8), PBS (n = 5), CNCM I-3856 (10⁹ CFUs/d, n = 7) or a combination of LF82 and CNCM I-3856 (n = 18). nTg rats receiving LF82 (n = 5), PBS (n = 5), CNCM I-3856 (n = 7) or CNCM I-3856 and LF82 (n = 9) under the same conditions were used as controls. POR was analyzed using macroscopic (from 0 to 4) and histologic (from 0 to 6) scores. Luminal LF82 quantifications were performed weekly for each animal. Adherent LF82 and inflammatory/regulatory cytokines were quantified in biopsies at W12 and W18. Data are expressed as the median with the interquartile range.

RESULTS

nTg animals did not develop POR. A total of 7/8 (87%) of the TgB27 rats receiving LF82 alone had POR (macroscopic score ≥ 2), which was significantly prevented by CNCM I-3856 administration [6/18 (33%) TgB27 rats, P = 0.01]. Macroscopic lesions were located 2 cm above the anastomosis in the TgB27 rats receiving LF82 alone and consisted of ulcerations with a score of 3.5 (2 - 4). Seven out of 18 TgB27 rats (39%) receiving CNCM I-3856 and LF82 had no macroscopic lesions. Compared to untreated TgB27 animals receiving LF82 alone, coadministration of CNCM I-3856 and LF82 significantly reduced the macroscopic [3.5 (2 - 4) vs 1 (0 - 3), P = 0.002] and histological lesions by more than 50% [4.5 (3.3 - 5.8) vs 2 (1.3 - 3), P = 0.003]. The levels of adherent LF82 were correlated with anastomotic macroscopic scores in TgB27 rats (r = 0.49, P = 0.006), with a higher risk of POR in animals having high levels of luminal LF82 (71.4% vs 25%, P = 0.02). Administration of CNCM I-3856 significantly reduced the levels of luminal and adherent LF82, increased the production of interleukin (IL)-10 and decreased the production of IL-23 and IL-17 in TgB27 rats.

CONCLUSION

In a reliable model of POR induced by LF82 in TgB27 rats, CNCM I-3856 prevents macroscopic POR by decreasing LF82 infection and gut inflammation.

Definition of a microbial signature as a predictor of endoscopic post-surgical recurrence in patients with Crohn’s disease

Background and aims: Although there are several effective drugs for the treatment of Crohn’s disease (CD), almost 70% of patients will require surgical resection during their lifetime. This procedure is not always curative, as endoscopic recurrence occurs in 65%–90% of patients in the first year after surgery. The aetiology of the recurrence is unknown; however, several studies have shown how the resident microbiota is modified after surgery. The aim of this study was to evaluate samples from patients with Crohn’s disease before and after an intestinal resection to determine whether there were differences in the abundance of different microbial markers, which may predict endoscopic recurrence at baseline.

Methods: In this observational study, a stool sample was obtained from 25 patients with Crohn’s disease before undergoing surgery, recruited at three Catalan hospitals. From each sample, DNA was purified and the relative abundance of nine microbial markers was quantified using qPCR.

Results: An algorithm composed of four microbial markers (E. coli, F. prausnitzii phylogroup I, Bacteroidetes, and Eubacteria) showed a sensitivity and specificity of 90.91% and 85.71%, respectively, and a positive and negative predictive value of 83.33% and 92.31%, respectively.

Conclusion: A microbial signature to determine patients who will have post-surgical recurrence was identified. This tool might be very useful in daily clinical practice, allowing the scheduling of personalized therapy and enabling preventive treatment only in patients who really require it.

Microbial Dynamics in Newly Diagnosed and Treatment Naïve IBD Patients in the Mediterranean

BACKGROUND

Microbial communities have long been suspected to influence inflammatory processes in the gastrointestinal tract of patients with inflammatory bowel disease. However, these effects are often influenced by treatments and can rarely be analyzed in treatment-naïve onset cases. Specifically, microbial differences between IBD pathologies in new onset cases have rarely been investigated and can provide novel insight into the dynamics of the microbiota in Crohn's disease (CD) and ulcerative colitis (UC).

METHODS

Fifty-six treatment-naïve IBD onset patients (67.3% CD, 32.7% UC) and 97 healthy controls were recruited from the Maltese population. Stool samples were collected after diagnosis but before administration of anti-inflammatory treatments. Fecal microbial communities were assessed via 16S rRNA gene sequencing and subjected to ecological analyses to determine disease-specific differences between pathologies and disease subtypes or to predict future treatment options.

RESULTS

We identified significant differences in community composition, variability, and diversity between healthy and diseased individuals-but only small to no differences between the newly diagnosed, treatment-naïve UC and CD cohorts. Network analyses revealed massive turnover of bacterial interactions between healthy and diseased communities, as well as between CD and UC communities, as signs of disease-specific changes of community dynamics. Furthermore, we identified taxa and community characteristics serving as predictors for prospective treatments.

CONCLUSION

Untreated and newly diagnosed IBD shows clear differences from healthy microbial communities and an elevated level of disturbance, but only the network perspective revealed differences between pathologies. Furthermore, future IBD treatment is to some extent predictable by microbial community characteristics.

Comparison of the caecal microbial community structure and physiological indicators of healthy and infection Eimeria tenella chickens during peak of oocyst shedding

Eimeria tenella (E. tenella), an important intestinal parasite of chicken caeca, causes coccidiosis and brings large economic losses to the poultry industry annually. Gut microorganismal alterations directly affect the health of the body. To understand how E. tenella affects its host, we analysed the changes in caecal microbial diversity and the physiological and morphological changes during the peak of oocyst shedding. Infected and healthy chickens differed significantly in caecal pathology and blood indicators. At the genus level, the abundances of Faecalibacterium, Clostridium, Lachnoclostridium, Gemmiger, Flavonifractor, Pseudoflavonifractor and Oscillibacter were significantly decreased in the infected samples, whereas Escherichia, Nocardia and Chlamydia were significantly increased. Functional gene pathways related to replication, recombination and repair, and transcription were significantly decreased, and functional genes related to metabolism were highly significantly reduced in the infected samples. Furthermore, in the infected samples, E. tenella reduced the haemoglobin levels and red blood cell counts, greatly reduced the beneficial bacteria and increased the potentially pathogenic bacteria. This study provides a research basis for further understanding the pathogenic mechanisms of E. tenella and provides insight for potential new drug development.RESEARCH HIGHLIGHTS First simultaneous description of caecal microbiota and physiological indicators during E. tenella infection.Metagenomics used to explore functional properties of chicken caecal microbiota during E. tenella infection.Caecal microbial compositions and functional genes altered significantly after infection.Blood indicators and caecal morphology were significantly altered in the infected group.

Potential of Wood Hemicelluloses and Their Derivates as Food Ingredients

A holistic utilization of all lignocellulosic wood biomass, instead of the current approach of using only the cellulose fraction, is crucial for the efficient, ecological, and economical use of the forest resources. Use of wood constituents in the food and feed sector is a potential way of promoting the global economy. However, industrially established food products utilizing such components are still scarce, with the exception of cellulose derivatives. Hemicelluloses that include xylans and mannans are major constituents of wood. The wood hemicelluloses are structurally similar to hemicelluloses from crops, which are included in our diet, for example, as a part of dietary fibers. Hence, structurally similar wood hemicelluloses have the potential for similar uses. We review the current status and future potential of wood hemicelluloses as food ingredients. We include an inventory of the extraction routes of wood hemicelluloses, their physicochemical properties, and some of their gastrointestinal characteristics, and we also consider the regulatory route that research findings need to follow to be approved for food solutions, as well as the current status of the wood hemicellulose applications on that route.

Akkermansia muciniphila plays critical roles in host health

Akkermansia muciniphila, an intestinal microorganism, belongs to Verrucomicrobia, one of the most abundant microorganisms in the mammalian gut. It is a mucin-degrading bacterium that can colonise intestines of mammals such as humans and mice by utilising mucin as the only nitrogen and carbon source. When A. muciniphila colonises the intestine, its metabolites interact with the intestinal barrier, affecting host health by consolidating the intestinal barrier, regulating metabolic functions of the intestinal and circulatory systems, and regulating immune functions. This review summarised the mechanisms of A. muciniphila-host interactions that are relevant to host health. We focussed on characteristics of A. muciniphila in relation to its metabolites to provide a comprehensive understanding of A. muciniphila and its effects on host health and disease processes.

The role of bacterial vaccines in the fight against antimicrobial resistance: an analysis of the preclinical and clinical development pipeline

Vaccines can be highly effective tools in combating antimicrobial resistance as they reduce infections caused by antibiotic-resistant bacteria and antibiotic consumption associated with disease. This Review looks at vaccine candidates that are in development against pathogens on the 2017 WHO bacterial priority pathogen list, in addition to Clostridioides difficile and Mycobacterium tuberculosis. There were 94 active preclinical vaccine candidates and 61 active development vaccine candidates. We classified the included pathogens into the following four groups: Group A consists of pathogens for which vaccines already exist-ie, Salmonella enterica serotype Typhi, Streptococcus pneumoniae, Haemophilus influenzae type b, and M tuberculosis. Group B consists of pathogens with vaccines in advanced clinical development-ie, extra-intestinal pathogenic Escherichia coli, Salmonella enterica serotype Paratyphi A, Neisseria gonorrhoeae, and C difficile. Group C consists of pathogens with vaccines in early phases of clinical development-ie, enterotoxigenic E coli, Klebsiella pneumoniae, non-typhoidal Salmonella, Shigella spp, and Campylobacter spp. Finally, group D includes pathogens with either no candidates in clinical development or low development feasibility-ie, Pseudomonas aeruginosa, Acinetobacter baumannii, Staphylococcus aureus, Helicobacter pylori, Enterococcus faecium, and Enterobacter spp. Vaccines are already important tools in reducing antimicrobial resistance and future development will provide further opportunities to optimise the use of vaccines against resistance.

Amelioration of obesity-induced white adipose tissue inflammation by Bacillus coagulans T4 in a high-fat diet-induced obese murine model

AIM

Fresh evidence suggests that B. coagulans can be regarded as a promising therapeutic alternative for metabolic disorders. However, the possible effects of this probiotic on obesity-induced adipose tissue inflammation are unknown.

METHODS

C57BL/6j male mice were assigned to a normal-chow diet (NCD) or a high-fat diet (HFD) for 10 weeks. After this period, HFD-fed mice were randomly divided into two groups; HFD control group and HFD plus B. coagulans T4 (IBRC-N10791) for another 8 weeks. B. coagulans T4 was administrated daily by oral intragastric gavage (1 × 10⁹ colony-forming units).

KEY FINDINGS

Here, we found that B. coagulans successfully mitigated obesity and related metabolic disorder, as indicated by reduced body weight gain, decreased adiposity, and improved glucose tolerance. B. coagulans T4 administration also inhibited HFD-induced macrophage accumulation in white adipose tissue and switched M1 to M2 macrophages. In parallel, B. coagulans T4 treatment attenuated HFD-induced alteration in mRNA expression of pro/anti-inflammatory cytokines and Tlr4 in white adipose tissue. Moreover, B. coagulans T4 supplementation reduced the Firmicutes/Bacteriodetes ratio and increased the number of Lactobacillus and Faecalibacterium compared to the HFD group. Additionally, a significant increase in propionate and acetate levels in the HFD group was seen following B. coagulans T4 administration.

SIGNIFICANCE

Taken together, the present study provides evidence that B. coagulans T4 supplementation exerts anti-obesity effects in part through attenuating inflammation in adipose tissue. The present study will have significant implications for obesity management.

nov., isolated from human faeces

The human gastrointestinal tract is inhabited by various microorganisms, including thousands of bacterial taxa that have yet to be cultured and characterized. In this report, we describe the isolation, cultivation, genotypic and phenotypic characterization and taxonomy of five novel anaerobic bacterial strains that were recovered during the massive cultivation and isolation of gut microbes from human faecal samples. On the basis of the polyphasic taxonomic results, we propose two novel genera and five novel species. They are Acidaminococcus hominis sp. nov. (type strain NSJ-142^T=CGMCC 1.17903^T=KCTC 25346^T), Amedibacillus hominis sp. nov. (type strain NSJ-176^T=CGMCC 1.17933^T=KCTC 25355^T), Lientehia hominis gen. nov. sp. nov. (type strain NSJ-141^T=CGMCC 1.17902^T=KCTC 25345^T), Merdimmobilis hominis gen. nov. sp. nov. (type strain NSJ-153^T=CGMCC 1.17915^T=KCTC 25350^T) and Paraeggerthella hominis sp. nov. (type strain NSJ-152^T=CGMCC 1.17914^T=KCTC 25349^T).

Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome

Peutz-Jeghers syndrome (PJS) is a rare hereditary disorder characterized by intestinal polyposis, and intestinal intussusception is one of the most urgent complications. While it is known that imbalance of the gut microbiota is highly associated with intestinal disorders, the role of the gut microbiome in the pathogenesis of PJS has not been reported. In this study, we performed 16S rRNA sequencing on stools from 168 patients and 68 healthy family members who lived together to determine the gut microbiome composition of PJS patients. Metagenomics sequencing was further performed on the representative samples (61 PJS patients and 27 healthy family members) to analyze the functional changes. We found that the fecal microbiome of patients with PJS showed a greater variation in β-diversity. An enhancement of Escherichia coli and a reduction of Faecalibacterium prausnitzii was identified in PJS patients. Further reduction of Faecalibacterium prausnitzii was the characteristic microbial change observed in patients with intussusception. Functional analysis revealed that the abundance of propanoate metabolism was enriched in PJS patients and further enriched in those with intussusception. Escherichia coli was the major contributor to the enrichment of this metabolism pathway, which was associated with the abnormal expression of methylglyoxal synthase (encoded by mgsA) and phosphate acetyltransferase (encoded by pta). Our findings showed a distinct gut microbiome signature in PJS patients and identified the connection between the gut microbiome and intussusception. Alterations in the gut microbiome might be involved in the pathogenesis of PJS and may serve as biomarkers for gastrointestinal surveillance. IMPORTANCE Recent research has established a link between the gut microbiome and polyps and neoplasia, and antibiotic use influences the microbiome and the development of colorectal polyps. Familial adenomatous polyposis (FAP), which is characterized by the early development of benign precursor lesions (polyps), is associated with enterotoxigenic Bacteroides fragilis and Escherichia coli biofilms. However, the relationship between the gut microbiome and the pathophysiology of PJS has not yet been established. In this study, we found that PJS patients had a distinct microbiome composition, with a greater variation in β-diversity, an increase in Escherichia coli, and a decrease in Faecalibacterium prausnitzii. A further reduction of Faecalibacterium prausnitzii was observed in patients with intussusception. Moreover, PJS involved increased propanoate metabolism as well as abnormal mgsA and pta expression. These findings may contribute to a better understanding of the etiology of PJS and improve disease control strategies.

Identification of B-Cell Epitopes on Capsid Protein Reveals Two Potential Neutralization Mechanisms in Red-Spotted Grouper Nervous Necrosis Virus

Nervous necrosis virus (NNV), a formidable pathogen in marine and freshwater fish, has inflicted enormous financial tolls on the aquaculture industry worldwide. Although capsid protein (CP) is the sole structural protein with pathogenicity and antigenicity, public information on immunodominant regions remains extremely scarce. Here, we employed neutralizing monoclonal antibodies (MAbs) specific for red-spotted grouper NNV (RGNNV) CNPgg2018 in combination with partially overlapping truncated proteins and peptides to identify two minimal B-cell epitope clusters on CP, ¹²²GYVAGFL¹²⁸ and ²²⁷SLYNDSL²³³. Site-directed mutational analysis confirmed residues Y123, G126, and L128 and residues L228, Y229, N230, D231, and L233 as the critical residues responsible for the direct interaction with ligand, respectively. According to homologous modeling and bioinformatic evaluation, ¹²²GYVAGFL¹²⁸ is harbored at the groove of the CP junction with strict conservation among all NNV isolates, while ²²⁷SLYNDSL²³³ is localized in proximity to the tip of a viral protrusion having relatively high evolutionary dynamics in different genotypes. Additionally, ²²⁷SLYNDSL²³³ was shown to be a receptor-binding site, since the corresponding polypeptide could moderately suppress RGNNV multiplication by impeding virion entry. In contrast, ¹²²GYVAGFL¹²⁸ seemed dedicated only to stabilizing viral native conformation and not to assisting initial virus attachment. Altogether, these findings contribute to a novel understanding of the antigenic distribution pattern of NNV and the molecular basis for neutralization, thus advancing the development of biomedical products, especially epitope-based vaccines, against NNV. IMPORTANCE NNV is a common etiological agent associated with neurological virosis in multiple aquatic organisms, causing significant hazards to the host. However, licensed drugs or vaccines to combat NNV infection are very limited to date. Toward the advancement of broad-spectrum prophylaxis and therapeutics against NNV, elucidating the diversity of immunodominant regions within it is undoubtedly essential. Here, we identified two independent B-cell epitopes on NNV CP, followed by the confirmation of critical amino acid residues participating in direct interaction. These two sites were distributed on the shell and protrusion domains of the virion, respectively, and mediated the neutralization exerted by MAbs via drastically distinct mechanisms. Our work promotes new insights into NNV antigenicity as well as neutralization and, more importantly, offers promising targets for the development of antiviral countermeasures.

The Effects of Iron Deficiency on the Gut Microbiota in Women of Childbearing Age

Iron deficiency anemia (IDA) is the most prevalent and common nutritional deficiency worldwide and is a global health problem with significant risk, particularly among women of reproductive age. Oral iron supplementation is the most widely used and cost-effective treatment for iron deficiency and IDA. However, there are limitations regarding side effects such as enteritis, treatment compliance, and bioavailability. Intestinal microbiome characteristic research has been recently conducted to overcome these issues, but more is needed. Against this background, a metagenomics study on the 16S gene in the feces of young women vulnerable to IDA was conducted. As a result of analyzing 16 normal subjects and 15 IDA patients, significant differences in bacterial community distribution were identified. In particular, a significant decrease in Faecalibacterium was characteristic in IDA patients compared with normal subjects. Furthermore, in the case of patients who recovered from IDA following iron supplementation treatment, it was confirmed that Faecalibacterium significantly recovered to normal levels. However, no significance in beta diversity was seen compared with before treatment. There were also no differences in the beta diversity results between the recovered and normal subjects. Therefore, intestinal dysbiosis during the disease state was considered to be restored as IDA improved. Although the results were derived from a limited number of subjects and additional research is needed, the results of this study are expected to be the basis for developing treatment and prevention strategies based on host-microbiome crosstalk in IDA.

Gut Microbiota in Colorectal Cancer: Biological Role and Therapeutic Opportunities

Colorectal cancer (CRC) is the second-leading cause of cancer-related deaths worldwide. While CRC is thought to be an interplay between genetic and environmental factors, several lines of evidence suggest the involvement of gut microbiota in promoting inflammation and tumor progression. Gut microbiota refer to the ~40 trillion microorganisms that inhabit the human gut. Advances in next-generation sequencing technologies and metagenomics have provided new insights into the gut microbial ecology and have helped in linking gut microbiota to CRC. Many studies carried out in humans and animal models have emphasized the role of certain gut bacteria, such as Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli, in the onset and progression of CRC. Metagenomic studies have opened up new avenues for the application of gut microbiota in the diagnosis, prevention, and treatment of CRC. This review article summarizes the role of gut microbiota in CRC development and its use as a biomarker to predict the disease and its potential therapeutic applications.

The Diversity of Escherichia coli Pathotypes and Vaccination Strategies against This Versatile Bacterial Pathogen

Escherichia coli (E. coli) is a gram-negative bacillus and resident of the normal intestinal microbiota. However, some E. coli strains can cause diseases in humans, other mammals and birds ranging from intestinal infections, for example, diarrhea and dysentery, to extraintestinal infections, such as urinary tract infections, respiratory tract infections, meningitis, and sepsis. In terms of morbidity and mortality, pathogenic E. coli has a great impact on public health, with an economic cost of several billion dollars annually worldwide. Antibiotics are not usually used as first-line treatment for diarrheal illness caused by E. coli and in the case of bloody diarrhea, antibiotics are avoided due to the increased risk of hemolytic uremic syndrome. On the other hand, extraintestinal infections are treated with various antibiotics depending on the site of infection and susceptibility testing. Several alarming papers concerning the rising antibiotic resistance rates in E. coli strains have been published. The silent pandemic of multidrug-resistant bacteria including pathogenic E. coli that have become more difficult to treat favored prophylactic approaches such as E. coli vaccines. This review provides an overview of the pathogenesis of different pathotypes of E. coli, the virulence factors involved and updates on the major aspects of vaccine development against different E. coli pathotypes.

Identification of Closed Linear Epitopes in S1-RBD and S2-HR1/2 of SARS-CoV-2 Spike Protein Able to Induce Neutralizing Abs

SARS-CoV-2 has evolved as several variants. Immunization to boost the Ab response to Spike antigens is effective, but similar vaccines could not enhance Ab efficacy enough. Effective Ab responses against the human ACE2 (hACE2)-mediated infection of the emerging SARS-CoV-2 variants are needed. We identified closed linear epitopes of the SARS-CoV-2 Spike molecule that induced neutralizing Abs (nAbs) against both S1-RBD, responsible for attachment to hACE2, and S2-HR1/2, in convalescents and vaccine recipients. They inhibited a pseudo-virus infection mediated by the hACE2 pathway. The epitope sequences included epitopes #7 (aa411-432), #11 (aa459-480) and #111 (aa1144-1161), in S1-RBD and S2-HR2. Epitope #111 was conserved in Wuhan and variant strains, whereas #7 and #11 were conserved in Wuhan carried mutations K417N and S477N/T478K in Omicron BA.4/5. These mutations were recognized by the original epitope-specific Abs. These epitopes in RBD and HR2 neither contained, nor overlapped with, those responsible for the antibody-dependent enhancement of the SARS-CoV-2 infection. The sublingual administration of multiple epitope-conjugated antigens increased the IgG and IgA Abs specific to the neutralizing epitopes in mice pre-immunized subcutaneously. The findings indicated that S1-RBD and S2-HR2 epitopes were responsible for pseudo-virus SARS-CoV-2 infections and that sublingual boosts with multiple epitope-conjugated antigens could enhance the protection by nAbs of IgG and IgA against infection by a wide range of variants.

Strains Isolated from Healthy Human Stool

Eight Faecalibacterium sp. strains were isolated from feces of healthy human volunteers. Here, we describe their genome sequences. The genome sizes ranged from 2.78 Mbp to 3.23 Mbp, with an average GC content of 56.6% and encoding 2,795 protein-coding genes on average.

Characterization of gut dominant microbiota in obese patients with nonalcoholic fatty liver disease

In obese patients, non-alcoholic fatty liver (NAFLD) is common. However, whether there is a connection between the gut microbiota and the onset of NAFLD in obese people is yet unknown. Using quantitative real-time PCR, the microbiota of feces of the eligible 181 obese individuals was identified to compare the differences in gut microbiota between obesity with NAFLD and simple obesity. According to the findings, the gut dominant microbiota was similar between obesity with NAFLD and simple obesity. Nonetheless, compared to the simple obesity group, the quantity of Faecalibacterium prausnitzii colonies was much lower in the obesity with the NAFLD group. Bacteroides were present in greater than 65% of both groups. Bacteroides, Clostridium leptum, and Clostridium butyricum accounted for more than 80% of the cases in the obesity with NAFLD group, whereas Bacteroides, Clostridium butyricum, and F. prausnitzii accounted for more than 80% of the cases in the simple obesity group. We look for potential contributing variables to obesity-related NAFLD and potential prevention measures for obese people. Based on a multi-factor logistic regression analysis, lymphocytes may be a risk factor for obesity with NAFLD while F. prausnitzii may be a protective factor. Additionally, F. prausnitzii is positively impacted by Bacteroides, Clostridium leptum, Clostridium butyricum, and Eubacterium rectale, yet adversely impacted by Enterobacteriaceae. Notably, lymphocytes and F. prausnitzii may help determine whether obese patients would develop NAFLD.

No changes in the abundance of selected fecal bacteria during increased carbohydrates consumption period associated with the racing season in amateur road cyclists

Background

Cyclists often use high-carbohydrate, low-fiber diets to optimize the glycogen stores and to avoid the gastrointestinal distress during both, the trainings and the competitions. The impact of such dietary changes on gut microbiota is not fully known.

Methods

We assessed the abundances of Faecalibacterium prausnitzii, Akkermansia muciniphila, Bifidobacterium spp., and Bacteroides spp. and the fecal pH in 14 amateur cyclists during the racing season. Eleven healthy men formed the control group.

Results

Despite significant differences in the diet composition and physical endurance levels of amateur cyclists before the competition season (1st term) and control group (carbohydrates: 52.2% ± 4.9% vs 41.9% ± 6.6%; VO₂max: 56.1 ± 6.0 vs 39.7 ± 7.7; p < 0.01; respectively), we did not observe any significant differences in studied gut bacteria abundances or fecal pH between the groups. Although the cyclists' carbohydrates consumption (2nd term) have increased throughout the season (4.48 g/kg b.w. ± 1.56 vs 5.18 g/kg b.w. ± 1.99; p < 0.05), the studied gut bacteria counts and fecal pH remained unchanged. It seems that the amateur cyclists' diet with increased carbohydrates intake does not alter the gut microbiota, but further research is needed to assess the potential impact of even higher carbohydrates consumption (over 6 g/kg b.w.).

Faecalibacterium duncaniae A2-165 regulates the expression of butyrate synthesis, ferrous iron uptake, and stress-response genes based on acetate level in early-stationary cultures.. [DOI: 10.21203/rs.3.rs-2481125/v1] [Cited by in Crossref: 0] [Impact Index Per Article: 0] Background Faecalibacterium prausnitzii, a promising next-generation probiotic, is one of the most abundant acetate-consuming, butyrate-producing bacteria in the healthy human gut. However, little is known about the gene expression strategies used by this bacterium to adapt to the availability of acetate in the human gut. Result We first established a growth model of F. duncaniae A2-165 (previously known as F. prausnitzii A2-165) using batch cultures, under high- and low-acetate conditions. Over late exponential and early stationary phases, the bacteria displayed a growth deficiency and a low butyrate production in low- compared with high-acetate conditions. Using RNA-seq, we compared expression patterns between early stationary and late exponential phases in high- and low-acetate conditions and between high- and low-acetate conditions in the early stationary phase. Functional classification of the low-acetate transcriptome revealed the specific activation of a general stress response, including upregulation of chaperones, toxin-antitoxin type II systems and downregulation of numerous protein synthesis genes. We observed two distinct import system transcriptomes, under low and high-acetate conditions, suggesting major adaptation responses to nutrient-deprived conditions of the early-stationary growth phase. Specifically, in high-acetate conditions, the feoAABC operon encoding one FeoB ferrous iron transporter was strongly activated but not the feoAB gene encoding the second FeoB transporter of F. duncaniae A2-165. This strong activation in early-stationary phase under high-acetate conditions suggested that (i) the level of extracellular ferrous iron is low (ii) FeoAABC system is required for ferrous iron uptake, in this iron-poor environment. Using RT-PCR, we demonstrated that excess ferrous iron represses feoB expression (i.e feoAABC operon) but not feoAB expression in high-acetate conditions. Finally, we conducted an integrated analysis of a healthy human fecal metaproteome, in which we were able to detect FeoB peptides from both genus Faecalibacterium and strain A2-165. Conclusion We characterized two early-stationary lifestyles of F. duncaniae A2-165 at the transcriptional level, related to acetate consumption and butyrate production. We characterized the regulation of feoAABC operon encoding an high-affinity ferrous iron transporter that may play a major role in iron homeostasis and butyrate synthesis in iron-poor and acetate-rich conditions in F. duncaniae A2-165

Background Faecalibacterium prausnitzii, a promising next-generation probiotic, is one of the most abundant acetate-consuming, butyrate-producing bacteria in the healthy human gut. However, little is known about the gene expression strategies used by this bacterium to adapt to the availability of acetate in the human gut. Result We first established a growth model of F. duncaniae A2-165 (previously known as F. prausnitzii A2-165) using batch cultures, under high- and low-acetate conditions. Over late exponential and early stationary phases, the bacteria displayed a growth deficiency and a low butyrate production in low- compared with high-acetate conditions. Using RNA-seq, we compared expression patterns between early stationary and late exponential phases in high- and low-acetate conditions and between high- and low-acetate conditions in the early stationary phase. Functional classification of the low-acetate transcriptome revealed the specific activation of a general stress response, including upregulation of chaperones, toxin-antitoxin type II systems and downregulation of numerous protein synthesis genes. We observed two distinct import system transcriptomes, under low and high-acetate conditions, suggesting major adaptation responses to nutrient-deprived conditions of the early-stationary growth phase. Specifically, in high-acetate conditions, the feoAABC operon encoding one FeoB ferrous iron transporter was strongly activated but not the feoAB gene encoding the second FeoB transporter of F. duncaniae A2-165. This strong activation in early-stationary phase under high-acetate conditions suggested that (i) the level of extracellular ferrous iron is low (ii) FeoAABC system is required for ferrous iron uptake, in this iron-poor environment. Using RT-PCR, we demonstrated that excess ferrous iron represses feoB expression (i.e feoAABC operon) but not feoAB expression in high-acetate conditions. Finally, we conducted an integrated analysis of a healthy human fecal metaproteome, in which we were able to detect FeoB peptides from both genus Faecalibacterium and strain A2-165. Conclusion We characterized two early-stationary lifestyles of F. duncaniae A2-165 at the transcriptional level, related to acetate consumption and butyrate production. We characterized the regulation of feoAABC operon encoding an high-affinity ferrous iron transporter that may play a major role in iron homeostasis and butyrate synthesis in iron-poor and acetate-rich conditions in F. duncaniae A2-165.