Microbiota–Host Transgenomic Metabolism, Bioactive Molecules from the Inside

A 15-day pilot biodiversity intervention with horses in a farm system leads to gut microbiome rewilding in 10 urban Italian children

To provide some glimpses on the possibility of shaping the human gut microbiome (GM) through probiotic exchange with natural ecosystems, here we explored the impact of 15 days of daily interaction with horses on the GM of 10 urban-living Italian children. Specifically, the children were in close contact with the horses in an "educational farm", where they spent almost 10 h/day interacting with the animals. The children's GM was assessed before and after the horse interaction using metabarcoding sequencing and shotgun metagenomics, along with the horses' skin, oral and fecal microbiomes. Targeted metabolomic analysis for GM-produced beneficial metabolites (i.e., short-chain fatty acids) in the children's feces was also performed. Interaction with horses facilitated the acquisition of health-related traits in the children's GM, such as increased diversity, enhanced butyrate production and an increase in several health-promoting species considered to be next-generation probiotics. Among these, the butyrate producers Facecalibacterium prausnitzii and F. duncaniae and a species belonging to the order Christensenellales. Interaction with horses was also associated with increased proportions of Eggerthella lenta, Gordonibacter pamelae and G. urolithinfaciens, GM components known to play a role in the bioconversion of dietary plant polyphenols into beneficial metabolites. Notably, no increase in potentially harmful traits, including toxin genes, was observed. Overall, our pilot study provides some insights on the existence of possible health-promoting exchanges between children and horses microbiomes. It lays the groundwork for an implemented and more systematic enrollment effort to explore the full complexity of human GM rewilding through exchange with natural ecosystems, aligning with the One Health approach.

Role of gut microbiome in the outcome of lymphoma patients treated with checkpoint inhibitors-The MicroLinf Study

Biomarkers for immune checkpoint inhibitors (ICIs) response and resistance include PD-L1 expression and other environmental factors, among which the gut microbiome (GM) is gaining increasing interest especially in lymphomas. To explore the potential role of GM in this clinical issue, feces of 30 relapsed/refractory lymphoma (Hodgkin and primary mediastinal B-cell lymphoma) patients undergoing ICIs were collected from start to end of treatment (EoT). GM was profiled through Illumina, that is, 16S rRNA sequencing, and subsequently processed through a bioinformatics pipeline. The overall response rate to ICIs was 30.5%, with no association between patients clinical characteristics and response/survival outcomes. Regarding GM, responder patients showed a peculiar significant enrichment of Lachnospira, while non-responder ones showed higher presence of Enterobacteriaceae (at baseline and maintained till EoT). Recognizing patient-related factors that may influence response to ICIs is becoming critical to optimize the treatment pathway of heavily pretreated, young patients with a potentially long-life expectancy. These preliminary results indicate potential early GM signatures of ICIs response in lymphoma, which could pave the way for future research to improve patients prognosis with new adjuvant strategies.

Dietary Supplementation of Brevibacillus laterosporus S62-9 Improves Broiler Growth and Immunity by Regulating Cecal Microbiota and Metabolites

Brevibacillus laterosporus has been added as a direct-fed microbiota to chicken. Yet, few studies have reported the effects of B. laterosporus on broiler growth and gut microbiota. The aim of this study was to evaluate the effects of B. laterosporus S62-9 on growth performance, immunity, cecal microbiota, and metabolites in broilers. A total of 160 1-day-old broilers were randomly divided into S62-9 and control groups, with or without 106 CFU/g B. laterosporus S62-9 supplementation, respectively. During the 42 days feeding, body weight and feed intake were recorded weekly. Serum was collected for immunoglobulin determination, and cecal contents were taken for 16S rDNA analysis and metabolome at Day 42. Results indicated that the broilers in S62-9 group showed an increase in body weight of 7.2% and 5.19% improvement in feed conversion ratio compared to the control group. The B. laterosporus S62-9 supplementation promoted the maturation of immune organs and increased the concentration of serum immunoglobulins. Furthermore, the α-diversity of cecal microbiota was improved in the S62-9 group. B. laterosporus S62-9 supplementation increased the relative abundance of beneficial bacteria including Akkermansia, Bifidobacterium, and Lactobacillus, while decreased the relative abundance of pathogens including Klebsiella and Pseudomonas. Untargeted metabolomics revealed that 53 differential metabolites between the two groups. The differential metabolites were enriched in 4 amino acid metabolic pathways, including arginine biosynthesis and glutathione metabolism. In summary, B. laterosporus S62-9 supplementation could improve the growth performance and immunity through the regulation of gut microbiota and metabolome in broilers.

Cancer-Stem-Cell Phenotype-Guided Discovery of a Microbiota-Inspired Synthetic Compound Targeting NPM1 for Leukemia

The human microbiota plays an important role in human health and disease, through the secretion of metabolites that regulate key biological functions. We propose that microbiota metabolites represent an unexplored chemical space of small drug-like molecules in the search of new hits for drug discovery. Here, we describe the generation of a set of complex chemotypes inspired on selected microbiota metabolites, which have been synthesized using asymmetric organocatalytic reactions. Following a primary screening in CSC models, we identified the novel compound UCM-13369 (4b) whose cytotoxicity was mediated by NPM1. This protein is one of the most frequent mutations of AML, and NPM1-mutated AML is recognized by the WHO as a distinct hematopoietic malignancy. UCM-13369 inhibits NPM1 expression, downregulates the pathway associated with mutant NPM1 C+, and specifically recognizes the C-end DNA-binding domain of NPM1 C+, avoiding the nucleus-cytoplasm translocation involved in the AML tumorological process. The new NPM1 inhibitor triggers apoptosis in AML cell lines and primary cells from AML patients and reduces tumor infiltration in a mouse model of AML with NPM1 C+ mutation. The disclosed phenotype-guided discovery of UCM-13369, a novel small molecule inspired on microbiota metabolites, confirms that CSC death induced by NPM1 inhibition represents a promising therapeutic opportunity for NPM1-mutated AML, a high-mortality disease.

Effect of Stool Sampling on a Routine Clinical Method for the Quantification of Six Short Chain Fatty Acids in Stool Using Gas Chromatography-Mass Spectrometry

Short chain fatty acids (SCFAs) are primarily produced in the caecum and proximal colon via the bacterial fermentation of undigested carbohydrates that have avoided digestion in the small intestine. Increasing evidence supports the critical role that SCFAs play in health and homeostasis. Microbial SCFAs, namely butyric acid, serve as a principal energy source for colonocytes, and their production is essential for gut integrity. A direct link between SCFAs and some human pathological conditions, such as inflammatory bowel disease, irritable bowel syndrome, diarrhea, and cancer, has been proposed. The direct measurement of SCFAs in feces provides a non-invasive approach to demonstrating connections between SCFAs, microbiota, and metabolic diseases to estimate their potential applicability as meaningful biomarkers of intestinal health. This study aimed to adapt a robust analytical method (liquid-liquid extraction, followed by isobutyl chloroformate derivatization and GC-MS analysis), with comparable performances to methods from the literature, and to use this tool to tackle the question of pre-analytical conditions, namely stool processing. We focused on the methodology of managing stool samples before the analysis (fresh stool or dilution in either ethanol/methanol, lyophilized stool, or RNAlater®), as this is a significant issue to consider for standardizing results between clinical laboratories. The objective was to standardize methods for future applications as diagnostic tools. In this paper, we propose a validated GC-MS method for SCFA quantification in stool samples, including pre- and post-analytical comparison studies that could be easily used for clinical laboratory purposes. Our results show that using lyophilization as a stool-processing method would be the best method to achieve this goal.

Microbial imidazole propionate affects glomerular filtration rate in patients with diabetic nephropathy through association with HSP90α

Imidazole propionate (ImP) is a detrimental metabolite produced by the fermentation of histidine intermediates via the intestinal flora. Here, the untargeted metabolite analysis of plasma metabolites from patients with diabetic nephropathy (DN), in combination with the Human Metabolome Database, revealed significantly increased levels of ImP in patients with DN, with a positive correlation with patients' blood creatinine concentration and urinary albumin-to-creatinine ratio, and a negative correlation with the glomerular filtration rate. RNA-seq was applied to detect the effects of ImP on renal tissue transcriptome in mice with DN. It demonstrated that ImP exacerbated renal injury in mice with DN and promoted renal tubular epithelial-mesenchymal transition (EMT), leading to renal mesenchymal fibrosis and renal impairment. Furthermore, ImP was found to directly target HAP90α and activate the PI3K-Akt signalling pathway, which is involved in EMT, by the drug affinity response target stability method. The findings showed that ImP may provide a novel target for DN quality, as it can directly bind to and activate HSP90, thereby facilitating the development of DN while acting as a potential indicator for the clinical diagnosis of DN.

Effects of continuous and pulse lead exposure on the swimming behavior of tadpoles revealed by brain-gut axis analysis

Lead (Pb) is present in aquatic environments with a continuous or pulse form due to the regular or irregular discharge of wastewater. These two modes of exposure result in different toxicological effects on aquatic animals. To compare the effects of Pb exposure mode on the swimming behavior of amphibian larvae, this study proposed a combination method to examine the brain-gut axis (gut bacteria, histopathology, metabolomics, and ethology) in order to evaluate the ecotoxic differences in Pelophylax nigromaculatus tadpoles (Gs 21-28) when exposed to continuous (CE100) versus pulse exposure (PE100) of environmental concentrations of Pb (100 μg/L). The results showed that: 1) CE100 significantly decreased the movement distance and swimming activity of the tadpoles compared to PE100 and the control, while there were no significant differences between the control group and PE100. 2) At the phyla level, compared to PE100, CE100 treatment significantly decreased the abundance of Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes and increased the abundance of Fusobacteria in the gut. At the genus level, compared to PE100, CE100 significantly increased the abundance of U114 and decreased the abundance of Anaerorhabdus, Exiguobacterium and Microbacterium. 3) Compared to PE100, CE100 changed the metabolites of the brain-gut axis pathway, such as quinolinic acid, L-valine, L-dopa, L-histidine, urocanic acid, L-threonine, γ-aminobutyric acid (GABA), L-glutamate (Glu), acetylcholine (Ach), L-tyrosine (Tyr), L-tryptophan (Trp), and levodopa (DOPA). 4) CE100 and PE100 played a repressive role in the histidine metabolism and tyrosine metabolism pathways and played a promoting role in the purine metabolism and pyrimidine metabolism pathways. This study provides a method for evaluating the toxic effects of heavy metal exposure via two different exposure modes (pulse versus continuous) which tadpoles may encounter in the natural environment from a combined study examining the brain-gut axis.

Integrated rumen microbiome and serum metabolome analysis responses to feed type that contribution to meat quality in lambs

BACKGROUND

Lifestyle factors, such as diet, are known to be a driver on the meat quality, rumen microbiome and serum metabolites. Rumen microbiome metabolites may be important for host health, the correlation between rumen microbiome and production of rumen metabolites are reported, while the impact of rumen microbiome on the serum metabolome and fatty acid of meat are still unclear. This study was designed to explore the rumen microbiome, serum metabolome and fatty acid of meat in response to the grass diet and concentrate diet to lambs, and the relationship of which also investigated.

METHODS

In the present study, 12 lambs were randomly divided into two groups: a grass diet (G) and a concentrate diet (C). Here, multiple physicochemical analyses combined with 16S rRNA gene sequences and metabolome analysis was performed to reveal the changes that in response to feed types.

RESULTS

The concentrate diet could improve the growth performance of lambs compared to that fed with the grass diet. The microbiome composition was highly individual, compared to the concentrate group, the abundance of Rikenellaceae_RC9_gut_group, F082_unclassified, Muribaculaceae_unclassified, Ruminococcaceae_NK4A214_group, Bacteroidetes_unclassified, and Bacteroidales_UCG-001_unclassified were significantly (P < 0.05) lower in the grass group, while, the abundance of Succinivibrio, Succinivibrionaceae_UCG-002, Fibrobacter and Christensenellaceae_R-7_group were significantly (P < 0.05) higher in the grass group. Serum metabolomics analysis combined with enrichment analysis revealed that serum metabolites were influenced by feed type as well as the metabolic pathway, and significantly affected serum metabolites involved in amino acids, peptides, and analogues, bile acids, alcohols and derivatives, linoleic acids derivatives, fatty acids and conjugates. Most of the amino acids, peptides, and analogues metabolites were positively associated with the fatty acid contents. Among the bile acids, alcohols and derivatives metabolites, glycocholic was positively associated with all fatty acid contents, except C18:0, while 25-Hydroxycholesterol and lithocholic acid metabolites were negatively associated with most of the fatty acid contents.

CONCLUSION

Correlation analysis of the association of microbiome with metabolite features, metabolite features with fatty acid provides us with comprehensive understanding of the composition and function of microbial communities. Associations between utilization or production were widely identified among affected microbiome, metabolites and fatty acid, and these findings will contribute to the direction of future research in lamb.

Disruption of the microbiota-gut-brain axis is a defining characteristic of the α-Gal A (-/0) mouse model of Fabry disease

Fabry disease (FD) is an X-linked metabolic disease caused by a deficiency in α-galactosidase A (α-Gal A) activity. This causes accumulation of glycosphingolipids, especially globotriaosylceramide (Gb3), in different cells and organs. Neuropathic pain and gastrointestinal (GI) symptoms, such as abdominal pain, nausea, diarrhea, constipation, and early satiety, are the most frequent symptoms reported by FD patients and severely affect their quality of life. It is generally accepted that Gb3 and lyso-Gb3 are involved in the symptoms; nevertheless, the origin of these symptoms is complex and multifactorial, and the exact mechanisms of pathogenesis are still poorly understood. Here, we used a murine model of FD, the male α-Gal A (-/0) mouse, to characterize functionality, behavior, and microbiota in an attempt to elucidate the microbiota-gut-brain axis at three different ages. We provided evidence of a diarrhea-like phenotype and visceral hypersensitivity in our FD model together with reduced locomotor activity and anxiety-like behavior. We also showed for the first time that symptomology was associated with early compositional and functional dysbiosis of the gut microbiota, paralleled by alterations in fecal short-chain fatty acid levels, which partly persisted with advancing age. Interestingly, most of the dysbiotic features suggested a disruption of gut homeostasis, possibly contributing to accelerated intestinal transit, visceral hypersensitivity, and impaired communication along the gut-brain axis.

A personalized diet intervention improves depression symptoms and changes microbiota and metabolite profiles among community-dwelling older adults

Introduction

The impact of diet on mental well-being and gut microorganisms in humans is well recognized. However, research on the connections between food nutrients, gut microbiota, and mental health remains limited. To address this, the present study aimed to assess the effects of a personalized diet, based on individual needs and aligned with the Mediterranean diet principles, on depression symptoms, quality of life, nutritional intake, and gut microbiota changes among older adults living in the community.

Methods

The intervention involved regular visits from a registered dietitian, who provided tailored dietary recommendations. During the 6-month study, participants completed questionnaires to evaluate their depression levels, quality of life, and dietary habits. Additionally, they provided stool samples for analysis of gut microbiota and metabolites.

Results

The results demonstrated that the personalized dietary intervention reduced depression symptoms and improved the quality of life among older adults. Furthermore, significant changes in the intake of certain nutrients, such as folate, lutein, zeaxanthin, EPA, and DHA, were observed following the intervention. Moreover, the intervention was associated with increased diversity in the gut microbiome and reduced total short-chain fatty acids, the main metabolites produced by gut microorganisms. The study also revealed correlations between food nutrients, gut microbiota, and mental health parameters.

Discussion

In conclusion, this research highlights the potential advantages of personalized dietary interventions in managing depression and enhancing overall well-being among older populations. It also sheds light on the role of gut microbiota and its metabolites in these effects. The findings offer valuable insights into the significance of nutrition and gut health for mental well-being in older adults.

Exploring Gut Microbiota and the Influence of Physical Activity Interventions on Overweight and Obese Children and Adolescents: A Systematic Review

The recognition that the gut microbiota of obese children differs from lean children has grown, and some studies suggest that physical activity positively influences the gut microbiota. This systematic review explores the changes in the gut microbiota composition of obese and non-obese children and adolescents and provides an understanding of the effects of physical activity interventions in modulating their microbiota. The PRISMA protocol was used across PubMed, Scopus, and Web of Science. Overall, twenty-four research papers were included in accordance with the chosen inclusion and exclusion criteria, eighteen studies compared the gut microbiota of obese and normal-weight children and adolescents, and six studies explored the effect of physical activity interventions on the gut microbiota. The analysis indicated that obese gut microbiota is reduced in Bacteroidetes, Bifidobacterium and alpha diversity but enriched in Proteobacteria and Lactobacillus. Interventions with physical activity seem to improve the alpha diversity and beneficial bacteria linked to body weight loss in children and adolescents. The gut microbiota of obese children exhibited a remarkably individual variation. More interventions are needed to clearly and accurately explore the relationships between child obesity, gut microbiota, and physical activity and to develop approaches to decrease the incidence of paediatric obesity.

Recent Review on Selected Xenobiotics and Their Impacts on Gut Microbiome and Metabolome

As it is well known, the gut is one of the primary sites in any host for xenobiotics, and the many microbial metabolites responsible for the interactions between the gut microbiome and the host. However, there is a growing concern about the negative impacts on human health induced by toxic xenobiotics. Metabolomics, broadly including lipidomics, is an emerging approach to studying thousands of metabolites in parallel. In this review, we summarized recent advancements in mass spectrometry (MS) technologies in metabolomics. In addition, we reviewed recent applications of MS-based metabolomics for the investigation of toxic effects of xenobiotics on microbial and host metabolism. It was demonstrated that metabolomics, gut microbiome profiling, and their combination have a high potential to identify metabolic and microbial markers of xenobiotic exposure and determine its mechanism. Further, there is increasing evidence supporting that reprogramming the gut microbiome could be a promising approach to the intervention of xenobiotic toxicity.

Dietary protein levels modulate the gut microbiome composition through fecal samples derived from lactating ewes

In ruminants, the digestion and utilization of dietary proteins are closely linked to the bacterial populations that are present in the gastrointestinal tract. In the present study, 16S rDNA sequencing, together with a metagenomic strategy was used to characterize the fecal bacteria of ewes in the early lactation stage after feeding with three levels of dietary proteins 8.58%, 10.34%, and 13.93%, in three different groups (H_1), (H_m) and (H_h), respectively. A total of 376,278,516 clean data-points were obtained by metagenomic sequencing. Firmicutes and Bacteroidetes were the dominant phyla, regardless of the dietary protein levels. In the H_h group, the phyla Proteobacteria, Caldiserica, and Candidatus_Cryosericota were less abundant than those in the H_I group. In contrast, Lentisphaerae, Chlamydiae, and Planctomycetes were significantly more abundant in the H_h group. Some genera, such as Prevotella, Roseburia, and Firmicutes_unclassified, were less abundant in the H_h group than those in the H_I group. In contrast, Ruminococcus, Ruminococcaceae_noname, Anaerotruncus, Thermotalae, Lentisphaerae_noname, and Paraprevotella were enriched in the H_h group. The acquired microbial genes were mainly clustered into biological processes; molecular functions; cytosol; cellular components; cytoplasm; structural constituents of ribosomes; plasma membranes; translation; and catalytic activities. 205987 genes were significantly enriched in the H_h group. In contrast, 108129 genes were more abundant in the H_I group. Our findings reveal that dynamic changes in fecal bacteria and their genes are strongly influenced by the levels of dietary proteins. We discovered that differentially expressed genes mainly regulate metabolic activity and KEGG demonstrated the primary involvement of these genes in the metabolism of carbohydrates, amino acids, nucleotides, and vitamins. Additionally, genes responsible for metabolism were more abundant in the H_h group. Investigating fecal bacterial characteristics may help researchers develop a dietary formula for lactating ewes to optimize the growth and health of ewes and lambs.

Gut microbiota resilience and recovery after anticancer chemotherapy

Although research on the role of the gut microbiota (GM) in human health has sharply increased in recent years, what a "healthy" gut microbiota is and how it responds to major stressors is still difficult to establish. In particular, anticancer chemotherapy is known to have a drastic impact on the microbiota structure, potentially hampering its recovery with serious long-term consequences for patients' health. However, the distinguishing features of gut microbiota recovery and non-recovery processes are not yet known. In this narrative review, we first investigated how gut microbiota layouts are affected by anticancer chemotherapy and identified potential gut microbial recovery signatures. Then, we discussed microbiome-based intervention strategies aimed at promoting resilience, i.e., the rapid and complete recovery of a healthy gut microbial network associated with a better prognosis after such high-impact pharmacological treatments.

A Bibliometric Analysis on the Research Trend of Exercise and the Gut Microbiome

This article aims to provide an overview of research hotspots and trends in exercise and the gut microbiome, a field which has recently gained increasing attention. The relevant publications on exercise and the gut microbiome were identified from the Web of Science Core Collection database. The publication types were limited to articles and reviews. VOSviewer 1.6.18 (Centre for Science and Technology Studies, Leiden University, Leiden, the Netherlands) and the R package "bibliometrix" (R Foundation: Vienna, Austria) were used to conduct a bibliometric analysis. A total of 327 eligible publications were eventually identified, including 245 original articles and 82 reviews. A time trend analysis showed that the number of publications rapidly increased after 2014. The leading countries/regions in this field were the USA, China, and Europe. Most of the active institutions were from Europe and the USA. Keyword analysis showed that the relationship between disease, the gut microbiome, and exercise occurs throughout the development of this field of research. The interactions between the gut microbiota, exercise, status of the host's internal environment, and probiotics, are important facets as well. The research topic evolution presents a trend of multidisciplinary and multi-perspective comprehensive analysis. Exercise might become an effective intervention for disease treatment by regulating the gut microbiome. The innovation of exercise-centered lifestyle intervention therapy may become a significant trend in the future.

Levofloxacin prophylaxis and parenteral nutrition have a detrimental effect on intestinal microbial networks in pediatric patients undergoing HSCT

The gut microbiome (GM) has shown to influence hematopoietic stem cell transplantation (HSCT) outcome. Evidence on levofloxacin (LVX) prophylaxis usefulness before HSCT in pediatric patients is controversial and its impact on GM is poorly characterized. Post-HSCT parenteral nutrition (PN) is oftentimes the first-line nutritional support in the neutropenic phase, despite the emerging benefits of enteral nutrition (EN). In this exploratory work, we used a global-to-local networking approach to obtain a high-resolution longitudinal characterization of the GM in 30 pediatric HSCT patients receiving PN combined with LVX prophylaxis or PN alone or EN alone. By evaluating the network topology, we found that PN, especially preceded by LVX prophylaxis, resulted in a detrimental effect over the GM, with low modularity, poor cohesion, a shift in keystone species and the emergence of modules comprising several pathobionts, such as Klebsiella spp., [Ruminococcus] gnavus, Flavonifractor plautii and Enterococcus faecium. Our pilot findings on LVX prophylaxis and PN-related disruption of GM networks should be considered in patient management, to possibly facilitate prompt recovery/maintenance of a healthy and well-wired GM. However, the impact of LVX prophylaxis and nutritional support on short- to long-term post-HSCT clinical outcomes has yet to be elucidated.

Comprehensive bibliometric and visualized analysis of research on fecal microbial transplantation published from 2000 to 2021

Background

Fecal microbial transplantation has emerged in recent years as a method of treating disease by rebuilding the intestinal flora. However, few bibliometric analyses have systematically studied this area of research. We aimed to use bibliometric analysis to visualize trends and topical research in fecal microbial transplantation to help provide insight into future trends in clinical and basic research.

Materials and methods

Articles and reviews related to fecal microbial transplantation were collected from the Web of Science Core Collection. Significant information associated with this field was visually analyzed by using Biblioshiny and CtieSpace software.

Results

A total of 3144 articles and overviews were included. The number of publications related to fecal microbial transplantation significantly increased yearly. These publications mainly came from 100 countries, led by the US and China, and 521 institutions. The most prolific and influential author is KHORUTS A. The main disciplines and application fields of fecal microbial transplantation included molecular /biology/immunology and medicine/clinical medicine, and the research foundation of fecal microbial transplantation was molecular /biology/genetics and health/nursing/medicine. An alluvial flow visualization showed several landmark articles. New developments were identified in terms of reference and keyword citation bursts. Data analysis showed that different FMT preparation and delivery methods gradually appeared as research hotspots. The main research keywords in the last 3 years were chain fatty acids, Akkermansia muciniphila, and insulin sensitivity, other keywords were current and developing research fields.

Conclusion

Research on fecal microbial transplantation is flourishing and many new applications of fecal microbial transplantation are emerging. Microbial metabolites such as short-chain fatty acids and the microbiota–gut–brain axis have become the focus of current research and are future research trends.

Wholegrain fermentation affects gut microbiota composition, phenolic acid metabolism and pancreatic beta cell function in a rodent model of type 2 diabetes

The intestinal microbiota plays an important role in host metabolism via production of dietary metabolites. Microbiota imbalances are linked to type 2 diabetes (T2D), but dietary modification of the microbiota may promote glycemic control. Using a rodent model of T2D and an in vitro gut model system, this study investigated whether differences in gut microbiota between control mice and mice fed a high-fat, high-fructose (HFHFr) diet influenced the production of phenolic acid metabolites following fermentation of wholegrain (WW) and control wheat (CW). In addition, the study assessed whether changes in metabolite profiles affected pancreatic beta cell function. Fecal samples from control or HFHFr-fed mice were fermented in vitro with 0.1% (w/v) WW or CW for 0, 6, and 24 h. Microbiota composition was determined by bacterial 16S rRNA sequencing and phenolic acid (PA) profiles by UPLC-MS/MS. Cell viability, apoptosis and insulin release from pancreatic MIN6 beta cells and primary mouse islets were assessed in response to fermentation supernatants and selected PAs. HFHFr mice exhibited an overall dysbiotic microbiota with an increase in abundance of proteobacterial taxa (particularly Oxalobacteraceae) and Lachnospiraceae, and a decrease in Lactobacillus. A trend toward restoration of diversity and compositional reorganization was observed following WW fermentation at 6 h, although after 24 h, the HFHFr microbiota was monodominated by Cupriavidus. In parallel, the PA profile was significantly altered in the HFHFr group compared to controls with decreased levels of 3-OH-benzoic acid, 4-OH-benzoic acid, isoferulic acid and ferulic acid at 6 h of WW fermentation. In pancreatic beta cells, exposure to pre-fermentation supernatants led to inhibition of insulin release, which was reversed over fermentation time. We conclude that HFHFr mice as a model of T2D are characterized by a dysbiotic microbiota, which is modulated by the in vitro fermentation of WW. The differences in microbiota composition have implications for PA profile dynamics and for the secretory capacity of pancreatic beta cells.

Geraniol Treatment for Irritable Bowel Syndrome: A Double-Blind Randomized Clinical Trial

Geraniol is an acyclic monoterpene alcohol with well-known anti-inflammatory and antimicrobial properties which has shown eubiotic activity towards gut microbiota (GM) in patients with irritable bowel syndrome (IBS).

METHODS

Fifty-six IBS patients diagnosed according to Rome III criteria were enrolled in an interventional, prospective, multicentric, randomized, double-blinded, placebo-controlled trial. In the treatment arm, patients received a low-absorbable geraniol food supplement (LAGS) once daily for four weeks.

RESULTS

Patients treated with LAGS showed a significant reduction in their IBS symptoms severity score (IBS-SSS) compared to the placebo (195 vs. 265, p = 0.001). The rate of responders according to IBS-SSS (reduction ≥ 50 points) was significantly higher in the geraniol vs placebo group (52.0% vs. 16.7%, p = 0.009) mainly due to the IBS mixed subtype. There were notable differences in the microbiota composition after geraniol administration, particularly a significant decrease in a genus of Ruminococcaceae, Oscillospira (p = 0.01), a decreasing trend for the Erysipelotrichaceae and Clostridiaceae families (p = 0.1), and an increasing trend for other Ruminococcaceae taxa, specifically Faecalibacterium (p = 0.09). The main circulating proinflammatory cytokines showed no differences between placebo and geraniol arms.

CONCLUSION

LAGS was effective in treating overall IBS symptoms, together with an improvement in the gut microbiota profile, especially for the IBS mixed subtype.

Effects of early sub-therapeutic antibiotic administration on body tissue deposition, gut microbiota and metabolite profiles of weaned piglets

BACKGROUND

This study aimed to evaluate the effects of sub-therapeutic antibiotic (STA) administration and its subsequent withdrawal on the body tissue deposition, gut microbiota, and metabolite profiles of piglets. The piglets in the experimental group were fed with STA (30 mg kg^-1 bacitracin methylene disalicylate, 75 mg kg^-1 chlortetracycline, 300 mg kg^-1 calcium oxytetracycline) for 14 days and the target bodyweight of the withdrawal period was 25 kg.

RESULTS

The experiment was divided into two periods: the administration period and the withdrawal period. The results showed that STA did not improve piglets' growth performance during the two periods. Piglets treated with STA had lower body water deposition during the withdrawal period and tended to increase body lipid deposition during the withdrawal period and the whole period in comparison with the piglets in the control group. It was found that STA markedly altered the colonic microbiota and their metabolites in the piglets. Sub-therapeutic antibiotics were initially effective in decreasing the abundance of pathogenic bacteria during the administration period; however, STA could not continue the effect during the withdrawal period, leading to a rebound of pathogenic bacteria such as Alloprevotella and the increased abundance of other pathogenic bacteria like Oscillibacter. Remarkably, STA treatment decreased Blautia abundance. This bacterium plays a potential protective role against obesity. Metabolomic analysis indicated that STA mainly altered amino acid metabolism, lipid metabolism, and carbohydrate metabolism during the two periods. Spearman's correlation analysis showed that the gut microbiota was highly correlated with microbial metabolite changes.

CONCLUSION

These results suggest that early STA administration may alter body tissue deposition later in life by reshaping the gut microbiota and their metabolite profiles. © 2022 Society of Chemical Industry.

The Relationship between Gut Microbiota and Respiratory Tract Infections in Childhood: A Narrative Review

Respiratory tract infections (RTIs) are common in childhood and represent one of the main causes of hospitalization in this population. In recent years, many studies have described the association between gut microbiota (GM) composition and RTIs in animal models. In particular, the “inter-talk” between GM and the immune system has recently been unveiled. However, the role of GM in human, and especially infantile, RTIs has not yet been fully established. In this narrative review we provide an up-to-date overview of the physiological pathways that explain how the GM shapes the immune system, potentially influencing the response to common childhood respiratory viral infections and compare studies analysing the relationship between GM composition and RTIs in children. Most studies provide evidence of GM dysbiosis, but it is not yet possible to identify a distinct bacterial signature associated with RTI predisposition. A better understanding of GM involvement in RTIs could lead to innovative integrated GM-based strategies for the prevention and treatment of RTIs in the paediatric population.

Age-related diseases, therapies and gut microbiome: A new frontier for healthy aging

The gut microbiome is undoubtedly a key modulator of human health, which can promote or impair homeostasis throughout life. This is even more relevant in old age, when there is a gradual loss of function in multiple organ systems, related to growth, metabolism, and immunity. Several studies have described changes in the gut microbiome across age groups up to the extreme limits of lifespan, including maladaptations that occur in the context of age-related conditions, such as frailty, neurodegenerative diseases, and cardiometabolic diseases. The gut microbiome can also interact bi-directionally with anti-age-related disease therapies, being affected and in turn influencing their efficacy. In this framework, the development of integrated microbiome-based intervention strategies, aimed at favoring a eubiotic configuration and trajectory, could therefore represent an innovative approach for the promotion of healthy aging and the achievement of longevity.

The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept

The core microbiome, which refers to a set of consistent microbial features across populations, is of major interest in microbiome research and has been addressed by numerous studies. Understanding the core microbiome can help identify elements that lead to dysbiosis, and lead to treatments for microbiome-related health states. However, defining the core microbiome is a complex task at several levels. In this review, we consider the current state of core human microbiome research. We consider the knowledge that has been gained, the factors limiting our ability to achieve a reliable description of the core human microbiome, and the fields most likely to improve that ability. DNA sequencing technologies and the methods for analyzing metagenomics and amplicon data will most likely facilitate higher accuracy and resolution in describing the microbiome. However, more effort should be invested in characterizing the microbiome’s interactions with its human host, including the immune system and nutrition. Other components of this holobiontic system should also be emphasized, such as fungi, protists, lower eukaryotes, viruses, and phages. Most importantly, a collaborative effort of experts in microbiology, nutrition, immunology, medicine, systems biology, bioinformatics, and machine learning is probably required to identify the traits of the core human microbiome.

Gut Microbiota Dysbiosis in Childhood Vasculitis: A Perspective Comparative Pilot Study

Kawasaki disease (KD) and Henoch–Schönlein purpura (HSP) are the most frequent vasculitis in childhood. For both, a multifactorial mechanism has been hypothesised, with an abnormal immune response in genetically predisposed children. Gut microbiota (GM) alterations might trigger the hyperimmune reaction. Our aim was to explore the GM in KD and compare it with the GM of HSP and febrile children. Children diagnosed with KD, HSP and non-KD febrile illness (F) were enrolled. GM was profiled by 16S rRNA gene sequencing and compared with the profiles of healthy children from previous studies. We enrolled 13 KD, 10 HSP and 12 F children. Their GM significantly differed from controls, with an overall reduction in the relative abundance of beneficial taxa belonging to the Ruminococcaceae and Lachnospiraceae families. Potential KD and HSP signatures were identified, including smaller amounts of Dialister in the former, and Clostridium and Akkermansia in the latter. Notably, the GM structures of KD, HSP and F patients stratified by abdominal involvement, with more severe dysbiosis in those suffering from intestinal symptoms. This is the first study analysing GM in a mostly Caucasian cohort of KD and HSP children. Our data could open up new opportunities for childhood vasculitis treatment.

Analysis of microbiome in GISTs: looking for different players in tumorigenesis and novel therapeutic options

Preclinical forms of gastrointestinal stromal tumor (GIST), small asymptomatic lesions, called microGIST, are detected in approximately 30% of the general population. Gastrointestinal stromal tumor driver mutation can be already detected in microGISTs, even if they do not progress into malignant cancer; these mutations are necessary, but insufficient events to foster tumor progression. Here we profiled the tissue microbiota of 60 gastrointestinal specimens in three different patient cohorts—micro, low‐risk, and high‐risk or metastatic GIST—exploring the compositional structure, predicted function, and microbial networks, with the aim of providing a complete overview of microbial ecology in GIST and its preclinical form. Comparing microGISTs and GISTs, both weighted and unweighted UniFrac and Bray–Curtis dissimilarities showed significant community‐level separation between them and a pronounced difference in Proteobacteria, Firmicutes, and Bacteroidota was observed. Through the LEfSe tool, potential microbial biomarkers associated with a specific type of lesion were identified. In particular, GIST samples were significantly enriched in the phylum Proteobacteria compared to microGISTs. Several pathways involved in sugar metabolism were also highlighted in GISTs; this was expected as cancer usually displays high aerobic glycolysis in place of oxidative phosphorylation and rise of glucose flux to promote anabolic request. Our results highlight that specific differences do exist in the tissue microbiome community between GIST and benign lesions and that microbiome restructuration can drive the carcinogenesis process.

Intestinal ELF4 Deletion Exacerbates Alcoholic Liver Disease by Disrupting Gut Homeostasis

Alcohol liver disease (ALD) is characterized by intestinal barrier disruption and gut dysbiosis. Dysfunction of E74-like ETS transcription factor 4 (ELF4) leads to colitis. We aimed to test the hypothesis that intestinal ELF4 plays a critical role in maintaining the normal function of intestinal barrier and gut homeostasis in a mouse model of ALD. Intestinal ELF4 deficiency resulted in dysfunction of the intestinal barrier. Elf4^−/− mice exhibited gut microbiota (GM) dysbiosis with the characteristic of a larger proportion of Proteobacteria. The LPS increased in Elf4^−/− mice and was the most important differential metabolite between Elf4^−/− mice and WT mice. Alcohol exposure increased liver-to-body weight ratio, and hepatic inflammation response and steatosis in WT mice. These deleterious effects were exaggerated in Elf4^−/− mice. Alcohol exposure significantly increased serum levels of TG, ALT, and AST in Elf4^−/− mice but not in WT mice. In addition, alcohol exposure resulted in enriched expression of genes associated with cholesterol metabolism and lipid metabolism in livers from Elf4^−/− mice. 16S rRNA sequencing showed a decrease abundance of Akkermansia and Bilophila in Elf4^−/− mice. In conclusion, intestinal ELF4 is an important host protective factor in maintaining gut homeostasis and alleviating alcohol exposure-induced hepatic steatosis and injury.

Nutraceuticals in the Modulation of the Intestinal Microbiota: Current Status and Future Directions

Pharmaceutical interest in the human intestinal microbiota has increased considerably, because of the increasing number of studies linking the human intestinal microbial ecology to an increasing number of non-communicable diseases. Many efforts at modulating the gut microbiota have been made using probiotics, prebiotics and recently postbiotics. However, there are other, still little-explored opportunities from a pharmaceutical point of view, which appear promising to obtain modifications of the microbiota structure and functions. This review summarizes all in vitro, in vivo and clinical studies demonstrating the possibility to positively modulate the intestinal microbiota by using probiotics, prebiotics, postbiotics, essential oils, fungus and officinal plants. For the future, clinical studies investigating the ability to impact the intestinal microbiota especially by using fungus, officinal and aromatic plants or their extracts are required. This knowledge could lead to effective microbiome modulations that might support the pharmacological therapy of most non-communicable diseases in a near future.

Linking stress and inflammation - is there a missing piece in the puzzle?

Extreme stressful incidents or even prolonged mild stress, whether physiological, psychosocial, or both, has been connected with development of chronic inflammation. Seemingly dissimilar medical conditions have been linked to this inflammatory state with weakened immune response, cancer, and metabolic and psychiatric disorders. Alteration of the gut microbiome is a common feature of these conditions and influences physiological functions throughout the body via bidirectional communication with the nervous, immune, and endocrine systems. Here, we propose that stress sensitivity, whether inborn or acquired, induces alterations in intestinal permeability and the gut microbiome to establish and stabilize chronic inflammatory states. Thus, treatment of chronic inflammation as a component of any disease should also involve the restoration of intestinal tight junction fidelity and a healthy intestinal microbial ecosystem.

Gut microbiome-micronutrient interaction: The key to controlling the bioavailability of minerals and vitamins?

Micronutrients, namely, vitamins and minerals, are necessary for the proper functioning of the human body, and their deficiencies can have dramatic short- and long-term health consequences. Among the underlying causes, certainly a reduced dietary intake and/or poor absorption in the gastrointestinal tract play a key role in decreasing their bioavailability. Recent evidence from clinical and in vivo studies suggests an increasingly important contribution from the gut microbiome. Commensal microorganisms can in fact regulate the levels of micronutrients, both by intervening in the biosynthetic processes and by modulating their absorption. This short narrative review addresses the pivotal role of the gut microbiome in influencing the bioavailability of vitamins (such as A, B, C, D, E, and K) and minerals (calcium, iron, zinc, magnesium, and phosphorous), as well as the impact of these micronutrients on microbiome composition and functionality. Personalized microbiome-based intervention strategies could therefore constitute an innovative tool to counteract micronutrient deficiencies by modulating the gut microbiome toward an eubiotic configuration capable of satisfying the needs of our organism, while promoting general health.

Consensus Prediction of Human Gut Microbiota-Mediated Metabolism Susceptibility for Small Molecules by Machine Learning, Structural Alerts, and Dietary Compounds-Based Average Similarity Methods

The human gut microbiota (HGM) colonizing human gastrointestinal tract (HGT) confers a repertoire of dynamic and unique metabolic capacities that are not possessed by the host and therefore is tentatively perceived as an alternative metabolic ″organ″ besides the liver in the host. Nevertheless, the significant contribution of HGM to the overall human metabolism is often overlooked in the modern drug discovery pipeline. Hence, a systematic evaluation of HGM-mediated drug metabolism is gradually important, and its computational prediction becomes increasingly necessary. In this work, a new data set containing both the HGM-mediated metabolism susceptible (HGMMS) and insusceptible (HGMMI) compounds (329 vs 320) was manually curated. Based on this data set, the first machine learning (ML) model, a new structural alerts (SA) model, and the K-nearest neighboring dietary compounds-based average similarity (AS) model were proposed to directly predict the HGM-mediated metabolism susceptibility for small molecules, and exhibit promising performance on three independent test sets. Finally, consensus prediction (ML/SA/AS) for DrugBank molecules revealed an intriguing phenomenon that a typical Michael acceptor ″α,β-unsaturated carbonyl group″ is a very common warhead for the design of covalent inhibitors and inclined to be metabolized by HGM in anaerobic HGT to generate the reduced metabolite without the reactive warhead, which could be a new concern to medicinal chemists. To the best of our knowledge, we gleaned the first HGMMS/HGMMI data set, developed the first HGMMS/HGMMI classification model, implemented a relatively comprehensive program based on ML/SA/AS approaches, and found a new phenomenon on the HGM-mediated deactivation of an extensively used warhead for covalent inhibitors.

Association of the Gut Microbiota With Cognitive Function in Midlife

IMPORTANCE

Animal experiments and small clinical studies support a role for the gut microbiota in cognitive functioning. Few studies have investigated gut microbiota and cognition in large community samples.

OBJECTIVE

To examine associations of gut microbial composition with measures of cognition in an established population-based study of middle-aged adults.

DESIGN, SETTING, AND PARTICIPANTS

This cross-sectional study analyzed data from the prospective Coronary Artery Risk Development in Young Adults (CARDIA) cohort in 4 US metropolitan centers between 2015 and 2016. Data were analyzed in 2019 and 2020.

EXPOSURES

Stool DNA were sequenced, and the following gut microbial measures were gathered: (1) β-diversity (between-person) derived with multivariate principal coordinates analysis; (2) α-diversity (within-person), defined as richness (genera count) and the Shannon index (integrative measure of genera richness and evenness); and (3) taxonomy (107 genera, after filtering).

MAIN OUTCOMES AND MEASURES

Cognitive status was assessed using 6 clinic-administered cognitive tests: Montreal Cognitive Assessment (MoCA), Digit Symbol Substitution Test (DSST), Rey-Auditory Verbal Learning Test (RAVLT), Stroop, category fluency, and letter fluency. A global score measure derived using principal components analysis was also assessed; the first principal component explained 56% of variability.

RESULTS

Microbiome data were available on 597 CARDIA participants; mean (SD) age was 55.2 (3.5) years, 268 participants (44.7%) were men, and 270 (45.2%) were Black. In multivariable-adjusted principal coordinates analysis, permutational multivariate analysis of variance tests for β-diversity were statistically significant for all cognition measures (principal component analysis, P = .001; MoCA, P = .001; DSST, P = .001; RAVLT, P = .001; Stroop, P = .007; category fluency, P = .001) with the exception of letter fluency (P = .07). After adjusting for sociodemographic variables (age, race, sex, education), health behaviors (physical activity, diet, smoking, medication use), and clinical covariates (body mass index, diabetes, hypertension), Barnesiella was positively associated with the first principal component (β, 0.16; 95% CI, 0.08-0.24), DSST (β, 1.18; 95% CI, 0.35-2.00), and category fluency (β, 0.59; 95% CI, 0.31-0.87); Lachnospiraceae FCS020 group was positively associated with DSST (β, 2.67; 95% CI, 1.10-4.23), and Sutterella was negatively associated with MoCA (β, -0.27; 95% CI, -0.44 to -0.11).

CONCLUSIONS AND RELEVANCE

In this cross-sectional study, microbial community composition, based on β-diversity, was associated with all cognitive measures in multivariable-adjusted analysis. These data contribute to a growing body of literature suggesting that the gut microbiota may be associated with cognitive aging, but must be replicated in larger samples and further researched to identify relevant pathways.

Anti-obesity natural products and gut microbiota

The link between gut microbiota and obesity or other metabolic syndromes is growing increasingly clear. Natural products are appreciated for their beneficial health effects in humans. Increasing investigations demonstrated that the anti-obesity bioactivities of many natural products are gut microbiota dependent. In this review, we summarized the current knowledge on anti-obesity natural products acting through gut microbiota according to their chemical structures and signaling metabolites. Manipulation of the gut microbiota by natural products may serve as a potential therapeutic strategy to prevent obesity.

Host microbiomes in tumor precision medicine: how far are we?

The human gut microbiome has received a crescendo of attention in recent years, due to the countless influences on human pathophysiology, including cancer. Research on cancer and anticancer therapy is constantly looking for new hints to improve the response to therapy while reducing the risk of relapse. In this scenario, the gut microbiome and the plethora of microbial-derived metabolites are considered a new opening in the development of innovative anticancer treatments for a better prognosis. This narrative review summarizes the current knowledge on the role of the gut microbiome in the onset and progression of cancer, as well as in response to chemo-immunotherapy. Recent findings regarding the tumor microbiome and its implications for clinical practice are also commented on. Current microbiome-based intervention strategies (i.e., prebiotics, probiotics, live biotherapeutics and fecal microbiota transplantation) are then discussed, along with key shortcomings, including a lack of long-term safety information in patients who are already severely compromised by standard treatments. The implementation of bioinformatic tools applied to microbiomics and other omics data, such as machine learning, has an enormous potential to push research in the field, enabling the prediction of health risk and therapeutic outcomes, for a truly personalized precision medicine.

A common fungicide tebuconazole promotes colitis in mice via regulating gut microbiota

As a common fungicide, tebuconazole are ubiquitous in the natural environment and poses many potential risks. In this study, we examined the effects of exposure to tebuconazole on colitis in mice and explored its underlying mechanism. Specifically, exposure to tebuconazole could cause structural damage and inflammatory cell infiltration in colon tissue, activate the expression of inflammation-related genes, disrupt the expression of barrier function-related genes, and induce the colonic inflammation in mice. Similarly, exposure to tebuconazole could also exacerbate DSS-induced colitis in mice. In addition, we found that tebuconazole also could change the composition of the gut microbiota. In particular, tebuconazole significantly increases the relative abundance of Akkermansia of mice. Moreover, tebuconazole resulted in metabolic profiles disorders of the serum, leading to significant changes in the relative contents of metabolites involving glycolipid metabolism and amino acid metabolism. Particularly, the results of the gut microbiota transplantation experiment showed that exposure to tebuconazole could induced colonic inflammation in mice in a gut microbiota-dependent manner. Taken together, these results indicated that tebuconazole could induce colitis in mice via regulating gut microbiota. Our findings strongly support the concept that the gut microbiota is a key trigger of inflammatory bowel disease caused by pesticide intake.

Human Gut Microbiome as an Indicator of Human Health

The undeniable achievement in the study of the gut microbiome as an association of different microorganisms, including viruses, that colonize various organs and systems of the body, is the establishment of the fact that some diseases that were consmicrobiotaidered as non-infectious can also be transmitted through microorganisms. This resulted in the gut microbiome being called a forgotten organ that could serve as an additional and kind of missing link for a more objective and better diagnosis and treatment of many diseases that were not considered infectious. The rapid development of gut microbiome research in recent years not only is connected with better understanding of the functioning of the microbiome by the scientific community, but also inseparable from the strategic support of each country. Global investment in researches, related to the human microbiome, has exceeded $1.7 billion over the past decade. These researches contribute to the development of new diagnostic methods and therapeutic interventions. Our review is dedicated to the analysis of the possibilities of application of the human gut microbiome for the diagnosis of diseases, and the role of the intestines in the provocation and causing of certain diseases. Significant differences in the composition and diversity of the human microbiome are shown depending on geographical location and the change of socio-economic formations towards a gradual decrease in the diversity of the gut microbiome due to three stages of human population’s existence: food production, agriculture and industrial urban life. We analyze the influence of dietary patterns, various diseases (including malignant neoplasms) and viral infections (in particular, coronavirus) on the gut microbiome. And vice versa – the influence of the gut microbiome on the drugs effect and their metabolism, which affects the host's immune response and course of the disease.

Searching for New Microbiome-Targeted Therapeutics through a Drug Repurposing Approach

Commonly used non-antibiotic drugs have been associated with changes in gut microbiome composition, paving the way for the possibility of repurposing FDA-approved molecules as next-generation microbiome therapeutics. Herein, we developed and validated an ex vivo high-throughput screening platform─the mini gut model─to underpin human gut microbiome response to molecular modulators. Ten FDA-approved compounds, selected based on maximum structural diversity of molecular fingerprints, were screened against the gut microbiome of five healthy subjects to characterize the ability of human-targeted drugs to modulate the human gut microbiome network. Three compounds, THIP hydrochloride, methenamine, and mesna, have shown promise as novel gut microbiome therapeutics in light of their capability of promoting health-associated features of the gut microbiome. Our findings provide a resource for future research on drug-microbiome interactions and lay the foundation for a new era of more precise gut microbiome modulation through drug repurposing, aimed at targeting specific dysbiotic events.

The Link between Gut Dysbiosis Caused by a High-Fat Diet and Hearing Loss

This review aims to provide a conceptual and theoretical overview of the association between gut dysbiosis and hearing loss. Hearing loss is a global health issue; the World Health Organisation (WHO) estimates that 2.5 billion people will be living with some degree of hearing loss by 2050. The aetiology of sensorineural hearing loss (SNHL) is complex and multifactorial, arising from congenital and acquired causes. Recent evidence suggests that impaired gut health may also be a risk factor for SNHL. Inflammatory bowel disease (IBD), type 2 diabetes, diet-induced obesity (DIO), and high-fat diet (HFD) all show links to hearing loss. Previous studies have shown that a HFD can result in microangiopathy, impaired insulin signalling, and oxidative stress in the inner ear. A HFD can also induce pathological shifts in gut microbiota and affect intestinal barrier (IB) integrity, leading to a leaky gut. A leaky gut can result in chronic systemic inflammation, which may affect extraintestinal organs. Here, we postulate that changes in gut microbiota resulting from a chronic HFD and DIO may cause a systemic inflammatory response that can compromise the permeability of the blood-labyrinth barrier (BLB) in the inner ear, thus inducing cochlear inflammation and hearing deficits.

Over-feeding the gut microbiome: A scoping review on health implications and therapeutic perspectives

The human gut microbiome has gained increasing attention over the past two decades. Several findings have shown that this complex and dynamic microbial ecosystem can contribute to the maintenance of host health or, when subject to imbalances, to the pathogenesis of various enteric and non-enteric diseases. This scoping review summarizes the current knowledge on how the gut microbiota and microbially-derived compounds affect host metabolism, especially in the context of obesity and related disorders. Examples of microbiome-based targeted intervention strategies that aim to restore and maintain an eubiotic layout are then discussed. Adjuvant therapeutic interventions to alleviate obesity and associated comorbidities are traditionally based on diet modulation and the supplementation of prebiotics, probiotics and synbiotics. However, these approaches have shown only moderate ability to induce sustained changes in the gut microbial ecosystem, making the development of innovative and tailored microbiome-based intervention strategies of utmost importance in clinical practice. In this regard, the administration of next-generation probiotics and engineered microbiomes has shown promising results, together with more radical intervention strategies based on the replacement of the dysbiotic ecosystem by means of fecal microbiota transplantation from healthy donors or with the introduction of synthetic communities specifically designed to achieve the desired therapeutic outcome. Finally, we provide a perspective for future translational investigations through the implementation of bioinformatics approaches, including machine and deep learning, to predict health risks and therapeutic outcomes.

The Human Microbiomes in Pancreatic Cancer: Towards Evidence-Based Manipulation Strategies?

Recent pieces of evidence have emerged on the relevance of microorganisms in modulating responses to anticancer treatments and reshaping the tumor-immune microenvironment. On the one hand, many studies have addressed the role of the gut microbiota, providing interesting correlative findings with respect to etiopathogenesis and treatment responses. On the other hand, intra-tumoral bacteria are being recognized as intrinsic and essential components of the cancer microenvironment, able to promote a plethora of tumor-related aspects from cancer growth to resistance to chemotherapy. These elements will be probably more and more valuable in the coming years in early diagnosis and risk stratification. Furthermore, microbial-targeted intervention strategies may be used as adjuvants to current therapies to improve therapeutic responses and overall survival. This review focuses on new insights and therapeutic approaches that are dawning against pancreatic cancer: a neoplasm that arises in a central metabolic "hub" interfaced between the gut and the host.

Gut Microbiota Dynamics during Chemotherapy in Epithelial Ovarian Cancer Patients Are Related to Therapeutic Outcome

Simple Summary

This pilot study on the trajectory of the gut microbiota (GM) in patients with epithelial ovarian cancer undergoing neoadjuvant and adjuvant chemotherapy highlighted peculiar dynamics associated with the therapeutic outcome. In particular, platinum-resistant patients showed a marked temporal reduction in GM diversity and increased instability with loss of health-associated taxa and increased proportions of lactate-producing microorganisms compared to those sensitive to platinum. These potential GM signatures of therapeutic failure are detectable within the first half of chemotherapy cycles, suggesting that early integrated treatments also aimed at modulating GM could influence therapeutic outcome. Further studies in larger cohorts combining multiple omics and possibly animal models are urgently needed for in-depth mechanistic understanding.

Abstract

Epithelial ovarian cancer (EOC) is one of the most lethal and silent gynecological tumors. Despite appropriate surgery and chemotherapy, relapse occurs in over half of patients with a poor prognosis. Recently, the gut microbiota (GM) was hypothesized to influence the efficacy of anticancer therapies, but no data are available in EOC. Here, by 16S rRNA gene sequencing and inferred metagenomics, we profiled the GM of EOC patients at diagnosis and reconstructed its trajectory along the course of neoadjuvant or adjuvant chemotherapy up to follow-up. Compared to healthy subjects, the GM of EOC patients appeared unbalanced and severely affected by chemotherapy. Strikingly, discriminating patterns were identified in relation to the therapeutic response. Platinum-resistant patients showed a marked temporal reduction in GM diversity and increased instability with loss of health-associated taxa and increased proportions of Coriobacteriaceae and Bifidobacterium. Notably, most of these microorganisms are lactate producers, suggesting increased lactate production as supported by inferred metagenomics. In contrast, the GM of platinum-sensitive patients appeared overall more diverse and stable and enriched in lactate utilizers from the Veillonellaceae family. In conclusion, we identified potential GM signatures of therapeutic outcome in EOC patients, which could open up new opportunities for cancer prognosis and treatment.

The gut microbiome buffers dietary adaptation in Bronze Age domesticated dogs

In an attempt to explore the role of the gut microbiome during recent canine evolutionary history, we sequenced the metagenome of 13 canine coprolites dated ca. 3,600–3,450 years ago from the Bronze Age archaeological site of Solarolo (Italy), which housed a complex farming community. The microbiome structure of Solarolo dogs revealed continuity with that of modern dogs, but it also shared some features with the wild wolf microbiome, as a kind of transitional state between them. The dietary niche, as also inferred from the microbiome composition, was omnivorous, with evidence of consumption of starchy agricultural foods. Of interest, the Solarolo dog microbiome was particularly enriched in sequences encoding alpha-amylases and complemented a low copy number of the host amylase gene. These findings suggest that Neolithic dogs could have responded to the transition to a starch-rich diet by expanding microbial functionalities devoted to starch catabolism, thus compensating for delayed host response.

•

Ancient DNA of Bronze Age canine coprolites from Solarolo was sequenced

•

Solarolo dogs share gut microbiome features with modern wolves and dogs

•

The gut microbiome of Solarolo dogs shows high number of reads for alpha-amylase

•

Neolithic canine gut microbiome complemented delay in host genome adaptation

N-Acyl-Homoserine Lactones May Affect the Gut Health of Low-Birth-Weight Piglets by Altering Intestinal Epithelial Cell Barrier Function and Amino Acid Metabolism

BACKGROUND

In piglets, low birth weight (LBW) is associated with intestinal dysfunction, which affects their growth performance and causes economic losses.

OBJECTIVES

This study was designed to test whether microbial quorum sensing (QS) affects LBW-induced intestinal developmental defects in piglets.

METHODS

Seven normal-birth-weight (NBW; 1.36 ± 0.01 kg) and 7 LBW (0.89 ± 0.01 kg) piglets were selected. Feces were collected from piglets on 2, 21, and 50 days of age for detection of the QS signaling molecules, N-acyl-homoserine lactones (AHLs), and microbiota analysis. The associations between 2 long-chain AHLs [N-3-oxo-dodecanoyl-l-homoserine lactone (3OC12-HSL) and N-3-oxo-tetradecanoyl-l-homoserine lactone (3OC14-HSL)] and the microbes were tested using Spearman correlation coefficients. The effect of 3OC12-HSL and 3OC14-HSL on intestinal porcine epithelial cell-jejunum 2 (IPEC-J2) cell viability was investigated by cholecystokinin octapeptide assay. Transcriptomic analysis was performed by RNA sequencing on cells treated with 3OC12-HSL.

RESULTS

The concentrations of 3OC12-HSL and 3OC14-HSL in the feces of LBW piglets were higher than those in NBW piglets at age 50 d by 2.5- and 2.24-fold, respectively (P < 0.05). The microbial α diversity (observed species, abundance-based coverage estimator, and Shannon index) of LBW piglets was 81-91% lower than that of NBW piglets (P < 0.05). The relative abundance of Ruminococcaceae UCG-002/UCG-013 was 43.0% and 30.0% lower, respectively, in feces from LBW compared with NBW piglets (P < 0.05). 3OC12-HSL and Ruminococcaceae UCG-002/UCG-005/UCG-010 abundance were negatively correlated (ρ  ≤  -0.58). Treatment with 400 μM 3OC12-HSL markedly reduced IPEC-J2 cell viability by 47.5%. Transcriptomic data showed that 3OC12-HSL mainly changed the "import across plasma membrane" and "arginine and proline metabolism" of IPEC-J2 cells.

CONCLUSIONS

3OC12-HSL is a QS signaling molecule with an ability to impair gut health of LBW piglets. This finding adds to our understanding of the mechanisms responsible for gut injury in LBW piglets.

Extracellular vesicles-mediated interaction within intestinal microenvironment in inflammatory bowel disease

•

EVs derived from different sources play modulatory functions in the intestine, especially interaction associated with microbiota.

•

An EV-mediated interaction system was established to describe the possible mechanism of IBD pathogenesis and its cure.

•

EVs-based treatments show great potential of clinical applications in IBD diagnosis and therapy.

Background

The intestinal tract is a complicated ecosystem with dynamic homeostasis via interaction of intestine and microbiota. Inflammatory bowel disease (IBD) is chronic intestinal inflammation involving dysbiosis of intestinal microenvironment. Extracellular vesicles (EVs), as vital characteristics of cell–cell and cell-organism communication, contribute to homeostasis in intestine. Recently, EVs showed excellent potential for clinical applications in disease diagnoses and therapies.

Aim of Review

Our current review discusses the modulatory functions of EVs derived from different sources in intestine, especially their effects and applications in IBD clinical therapy. EV-mediated interaction systems between host intestine and microbiota were established to describe possible mechanisms of IBD pathogenesis and its cure.

Key Scientific Concepts of Review

EVs are excellent vehicles for delivering molecules containing genetic information to recipient cells. Multiple pieces of evidence have illustrated that EVs participate the interaction between host and microbiota in intestinal microenvironment. In inflammatory intestine with dysbiosis of microbiota, EVs as regulators target promoting immune response and microbial reconstruction. EVs-based immunotherapy could be a promising therapeutic approach for the treatment of IBD in the near future.

The Gut Microbiota of Critically Ill Patients With COVID-19

The SARS-CoV-2-associated COVID-19 pandemic has shaken the global healthcare system. Although the best-known symptoms are dry cough and pneumonia, viral RNA has been detected in the stool and about half of COVID-19 patients exhibit gastrointestinal upset. In this scenario, special attention is being paid to the possible role of the gut microbiota (GM). Fecal samples from 69 COVID-19 patients from three different hospitals of Bologna (Italy) were analyzed by 16S rRNA gene-based sequencing. The GM profile was compared with the publicly available one of healthy age- and gender-matched Italians, as well as with that of other critically ill non-COVID-19 patients. The GM of COVID-19 patients appeared severely dysbiotic, with reduced diversity, loss of health-associated microorganisms and enrichment of potential pathogens, particularly Enterococcus. This genus was far overrepresented in patients developing bloodstream infections (BSI) and admitted to the intensive care unit, while almost absent in other critically ill non-COVID-19 patients. Interestingly, the percentage of patients with BSI due to Enterococcus spp. was significantly higher during the COVID-19 pandemic than in the previous 3 years. Monitoring the GM of critically ill COVID-19 patients could help clinical management, by predicting the onset of medical complications such as difficult-to-treat secondary infections.

Changes in gut microbiota in the acute phase after spinal cord injury correlate with severity of the lesion

After spinal cord injury (SCI), patients face many physical and psychological issues including intestinal dysfunction and comorbidities, strongly affecting quality of life. The gut microbiota has recently been suggested to influence the course of the disease in these patients. However, to date only two studies have profiled the gut microbiota in SCI patients, months after a traumatic injury. Here we characterized the gut microbiota in a large Italian SCI population, within a short time from a not only traumatic injury. Feces were collected within the first week at the rehabilitation center (no later than 60 days after SCI), and profiled by 16S rRNA gene-based next-generation sequencing. Microbial profiles were compared to those publicly available of healthy age- and gender-matched Italians, and correlated to patient metadata, including type of SCI, spinal unit location, nutrition and concomitant antibiotic therapies. The gut microbiota of SCI patients shows distinct dysbiotic signatures, i.e. increase in potentially pathogenic, pro-inflammatory and mucus-degrading bacteria, and depletion of short-chain fatty acid producers. While robust to most host variables, such dysbiosis varies by lesion level and completeness, with the most neurologically impaired patients showing an even more unbalanced microbial profile. The SCI-related gut microbiome dysbiosis is very likely secondary to injury and closely related to the degree of completeness and severity of the lesion, regardless of etiology and time interval. This microbial layout could variously contribute to increased gut permeability and inflammation, potentially predisposing patients to the onset of severe comorbidities.

Short-chain fatty acids-producing probiotics: A novel source of psychobiotics

Psychobiotics-live microorganisms with potential mental health benefits, which can modulate the microbiota-gut-brain-axis via immune, humoral, neural, and metabolic pathways-are emerging as novel therapeutic options for the effective treatment of psychiatric disorders Recently, microbiome studies have identified numerous putative psychobiotic strains, of which short-chain fatty acids (SCFAs) producing bacteria have attracted special attention from neurobiologists. Recent studies have highlighted that SCFAs-producing bacteria such as Lactobacillus, Bifidobacterium and Clostridium have a very specific function in various psychiatric disorders, suggesting that these bacteria can be potential novel psychobiotics. SCFAs, potential mediators of microbiota-gut-brain axis, might modulate function of neurological processes. While the specific roles and mechanisms of SCFAs-producing bacteria of microbiota-targeted interventions on neuropsychiatric disease are largely unknown. This Review summarizes existing knowledge on the neuroprotective effects of the SCFAs-producing bacteria in neurological disorders via modulating microbiota-gut-brain axis and illustrate their possible mechanisms by which SCFAs-producing bacteria may act on these disorders, which will shed light on the SCFAs-producing bacteria as a promising novel source of psychobiotics.

Bi-direction effects between microbiome and MiRNAs in carcinogenesis

There is evidence from numerous studies that dysbiosis of the microbiome provokes various immune-mediated diseases, obesity, diabetes, and cancers by regulating metabolites, host genetics, environmental elements, and stress. Such reports are yet to define an accurate regulatory network for host-gut microbiome communication. miRNAs have recently emerged as crucial mediators of this communication, as portrayed by their interaction with the host microbiome. This mini-review summarizes the bi-direction effects between miRNA and microbiome and elucidates their role in carcinogenesis. An in-depth understanding of the association of miRNA with host-microbiome could be valuable to improve cancer remission, diagnosis, and treatment, and may help to potential tumor markers.

Effects of Protein Restriction and Subsequent Realimentation on Body Composition, Gut Microbiota and Metabolite Profiles in Weaned Piglets

Simple Summary

Protein restriction strategies are often used in weaned piglets to reduce the incidence of intestinal disorders that are sensitive to dietary protein supply, but may lead to a decline in production performance. Subsequent protein realimentation can alleviate the detrimental effects of reduced dietary protein on growth. However, the effects of protein realimentation on the body composition, gut microbiota and metabolite profiles of piglets are poorly understood. The present study, combining comparative slaughter methods, microbiome and metabolome analyses, demonstrated that protein restriction and subsequent realimentation lead to compensatory growth and compensatory protein deposition in piglets, and contribute to animal intestinal health by altering the gut microbiota and metabolite profiles.

Abstract

The objective of this study was to evaluate the effects of protein restriction and subsequent protein realimentation on the body composition, gut microbiota and metabolite profiles of piglets. Fifty weaned piglets were randomly assigned to two treatments: a normal protein (NP) group (20% crude protein (CP)) or a low protein (LP) group (16% CP) with five animals per pen and five pens per group. Treatment diets were fed for 14 d during the protein restriction phase, and then all pigs were fed the same nursery diets with a normal CP level (19% CP) during the protein realimentation phase until they reached an average target body weight (BW) of 25 ± 0.15 kg. At day 14 and the end of the experiment, one piglet close to the average BW of each pen was slaughtered to determine body composition, microbial composition and microbial metabolites. Results showed that there was no difference (p > 0.05) in the experimental days to reach target BW between the LP and NP groups. The average daily gain (ADG) and gain:feed ratio (G:F) during the protein restriction phase as well as BW at day 14, were significantly decreased (p < 0.05) in the LP group compared with the NP group. However, there were no significant differences (p > 0.05) during the protein realimentation phase and the overall experiment. Similarly, piglets in the LP group showed a significantly decreased body protein content (p < 0.05) at day 14, but not (p > 0.05) at the end of the experiment. The relative abundance of Parabacteroides, Butyricicoccus, Olsenella, Succinivibrio and Pseudoramibacter were significantly increased (p < 0.05), while the relative abundance of Alloprevotella and Faecalicoccus were significantly decreased (p < 0.05) in the LP group at day 14. At the end of the experiment, the piglets in the LP group showed a higher (p < 0.05) colonic relative abundances of Parabacteroides, unidentified Christensenellaceae and Caproiciproducens, and a lower (p < 0.05) relative abundance of unidentified Prevotellaceae, Haemophilus, Marvinbryantia, Faecalibaculum, Neisseria and Dubosiella than those in the NP group. Metabolomics analyses indicated that tryptophan metabolism and vitamin metabolism were enriched in the LP group at day 14, and glycerophospholipid metabolism and fatty acid esters of hydroxy fatty acid metabolism were enriched at the end of the experiment. Moreover, Spearman’s correlation analysis demonstrated that the microbial composition was highly correlated with changes in colonic metabolites. Collectively, these results indicated that protein restriction and subsequent realimentation lead to compensatory growth and compensatory protein deposition in piglets and contribute to animal intestinal health by altering the gut microbiota and its metabolites.