Endurance exercise associated with a fructooligosaccharide diet modulates gut microbiota and increases colon absorptive area

BACKGROUND AND AIM

Fructooligosaccharide (FOS) supplementation can stimulate beneficial intestinal bacteria growth, but little is known about its influence on training performance. Therefore, this study analyzed FOS and exercise effects on gut microbiota and intestinal morphology of C57Bl/6 mice.

METHODS

Forty male mice were divided into four groups: standard diet-sedentary (SDS), standard diet-exercised (SDE), FOS supplemented (7.5% FOS)-sedentary (FDS), and FOS supplemented-exercised (FDE), n = 10 each group. Exercise training consisted of 60 min/day, 3 days/week, for 12 weeks.

RESULTS

SDE and FDE groups had an increase in aerobic performance compared to the pretraining period and SDS and FDS groups (P < 0.01), respectively. Groups with FOS increased colonic crypts size (P < 0.05). The FDE group presented rich microbiota (α-diversity) compared to other groups. The FDE group also acquired a greater microbial abundance (β-diversity) than other groups. The FDE group had a decrease in the Ruminococcaceae (P < 0.002) and an increase in Roseburia (P < 0.003), Enterorhabdus (P < 0.004) and Anaerotruncus (P < 0.006).

CONCLUSIONS

These findings suggest that aerobic exercise associated with FOS supplementation modulates gut microbiota and can increase colonic crypt size without improving endurance exercise performance.

The microbiota-gut-brain-immune interface in the pathogenesis of neuroinflammatory diseases: a narrative review of the emerging literature

Importance

Research is beginning to elucidate the sophisticated mechanisms underlying the microbiota-gut-brain-immune interface, moving from primarily animal models to human studies. Findings support the dynamic relationships between the gut microbiota as an ecosystem (microbiome) within an ecosystem (host) and its intersection with the host immune and nervous systems. Adding this to the effects on epigenetic regulation of gene expression further complicates and strengthens the response. At the heart is inflammation, which manifests in a variety of pathologies including neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and Multiple Sclerosis (MS).

Observations

Generally, the research to date is limited and has focused on bacteria, likely due to the simplicity and cost-effectiveness of 16s rRNA sequencing, despite its lower resolution and inability to determine functional ability/alterations. However, this omits all other microbiota including fungi, viruses, and phages, which are emerging as key members of the human microbiome. Much of the research has been done in pre-clinical models and/or in small human studies in more developed parts of the world. The relationships observed are promising but cannot be considered reliable or generalizable at this time. Specifically, causal relationships cannot be determined currently. More research has been done in Alzheimer's disease, followed by Parkinson's disease, and then little in MS. The data for MS is encouraging despite this.

Conclusions and relevance

While the research is still nascent, the microbiota-gut-brain-immune interface may be a missing link, which has hampered our progress on understanding, let alone preventing, managing, or putting into remission neurodegenerative diseases. Relationships must first be established in humans, as animal models have been shown to poorly translate to complex human physiology and environments, especially when investigating the human gut microbiome and its relationships where animal models are often overly simplistic. Only then can robust research be conducted in humans and using mechanistic model systems.

Dietary methionine restriction in cancer development and antitumor immunity

Methionine restriction (MR) has been shown to suppress tumor growth and improve the responses to various anticancer therapies. However, methionine itself is required for the proliferation, activation, and differentiation of T cells that are crucial for antitumor immunity. The dual impact of methionine, that influences both tumor and immune cells, has generated concerns regarding the potential consequences of MR on T cell immunity and its possible role in promoting cancer. In this review we systemically examine current literature on the interactions between dietary methionine, cancer cells, and immune cells. Based on recent findings on MR in immunocompetent animals, we further discuss how tumor stage-specific methionine dependence of immune cells and cancer cells in the tumor microenvironment could ultimately dictate the response of tumors to MR.

Perspective: Nutrition Health Disparities Framework: A Model to Advance Health Equity

Disparities in nutrition, such as poor diet quality and inadequate nutrient intake, arise from multiple factors and are related to adverse health outcomes such as obesity, diabetes, cardiovascular disease, and some cancers. The aim of the current perspective is to present a nutrition-centric socioecological framework that delineates determinants and factors that contribute to diet and nutrition-related disparities among disadvantaged populations. The Nutrition Health Disparities Framework (NHDF) describes the domains (biological, behavioral, physical/built environment, sociocultural environment, and healthcare system) that influence nutrition-related health disparities through the lens of each level of influence (that is, individual, interpersonal, community, and societal). On the basis of the scientific literature, the authors engaged in consensus decision making in selecting nutrition-related determinants of health within each domain and socioecological level when creating the NHDF. The framework identifies how neighborhood food availability and access (individual/built environment) intersect with cultural norms and practices (interpersonal/sociocultural environment) to influence dietary behaviors, exposures, and risk of diet-related diseases. In addition, the NHDF shows how factors such as genetic predisposition (individual/biology), family dietary practices (interpersonal/behavioral), and food marketing policies (societal) may impact the consumption of unhealthy foods and beverages and increase chronic disease risk. Family and peer norms (interpersonal/behavior) related to breastfeeding and early childhood nutrition interact with resource-poor environments such as lack of access to preventive healthcare settings (societal/healthcare system) and low usage of federal nutrition programs (societal/behavioral), which may increase risk of poor nutrition during childhood and food insecurity. The NHDF describes the synergistic interrelationships among factors at different levels of the socioecological model that influence nutrition-related outcomes and exacerbate health disparities. The framework is a useful resource for nutrition researchers, practitioners, food industry leaders, and policymakers interested in improving diet-related health outcomes and promoting health equity in diverse populations.

NURECON: A Novel Online System for Determining Nutrition Requirements Based on Microbial Composition

Dietary habits have been proven to have an impact on the microbial composition and health of the human gut. Over the past decade, researchers have discovered that gut microbiota can use nutrients to produce metabolites that have major implications for human physiology. However, there is no comprehensive system that specifically focuses on identifying nutrient deficiencies based on gut microbiota, making it difficult to interpret and compare gut microbiome data in the literature. This study proposes an analytical platform, NURECON, that can predict nutrient deficiency information in individuals by comparing their metagenomic information to a reference baseline. NURECON integrates a next-generation bacterial 16S rRNA analytical pipeline (QIIME2), metabolic pathway prediction tools (PICRUSt2 and KEGG), and a food compound database (FooDB) to enable the identification of missing nutrients and provide personalized dietary suggestions. Metagenomic information from total number of 287 healthy subjects was used to establish baseline microbial composition and metabolic profiles. The uploaded data is analyzed and compared to the baseline for nutrient deficiency assessment. Visualization results include gut microbial composition, related enzymes, pathways, and nutrient abundance. NURECON is a user-friendly online platform that provides nutritional advice to support dietitians' research or menu design.

B-Group Vitamins as Potential Prebiotic Candidates: Their Effects on the Human Gut Microbiome

In recent years, thousands of studies have demonstrated the importance of the gut microbiome for human health and its relationship with certain diseases. The search for new gut microbiome modulators has thus become an objective to beneficially alter the gut microbiome composition and/or metabolic activity, which may modify intestinal physiology. Growing evidence has shown that B-group vitamins might be considered as potential candidates as gut microbiome modulators. However, the relationship between the B-group vitamins and the gut microbiome remains largely unexplored. Studies have suggested that non-absorbed B-group vitamins administered orally can reach the distal intestine or even the colon where these vitamins may have potential health benefits for the host. Clinical trials supporting this effect are still limited. In this review, we discuss evidence regarding the modulatory effects of B-group vitamins on the gut microbiome with a focus on their potential role as prebiotic candidates.

Noxious ramifications of cosmetic pollutants on gastrointestinal microbiome: A pathway to neurological disorders

On exposure to cosmetic pollutants, gastrointestinal dysbiosis, which is characterised by a disturbance in the gut microbiota, has come into focus as a possible contributor to the occurrence of neurotoxic consequences. It is normal practice to use personal care products that include parabens, phthalates, sulphates, triclosans/triclocarbans and micro/nano plastics. These substances have been found in a variety of bodily fluids and tissues, demonstrating their systemic dispersion. Being exposed to these cosmetic pollutants has been linked in recent research to neurotoxicity, including cognitive decline and neurodevelopmental problems. A vital part of sustaining gut health and general well-being is the gut flora. Increased intestinal permeability, persistent inflammation, and impaired metabolism may result from disruption of the gut microbial environment, which may in turn contribute to neurotoxicity. The link between gastrointestinal dysbiosis and the neurotoxic effects brought on by cosmetic pollutants may be explained by a number of processes, primarily the gut-brain axis. For the purpose of creating preventative and therapeutic measures, it is crucial to comprehend the intricate interactions involving cosmetic pollutants, gastrointestinal dysbiosis, and neurotoxicity. This review provides an in-depth understanding of the various hazardous cosmetic pollutants and its potential role in the occurrence of neurological disorders via gastrointestinal dysbiosis, providing insights into various described and hypothetical mechanisms regarding the complex toxic effects of these industrial pollutants.

Diet-microbiota associations in gastrointestinal research: a systematic review

Interactions between diet and gastrointestinal microbiota influence health status and outcomes. Evaluating these relationships requires accurate quantification of dietary variables relevant to microbial metabolism, however current dietary assessment methods focus on dietary components relevant to human digestion only. The aim of this study was to synthesize research on foods and nutrients that influence human gut microbiota and thereby identify knowledge gaps to inform dietary assessment advancements toward better understanding of diet-microbiota interactions. Thirty-eight systematic reviews and 106 primary studies reported on human diet-microbiota associations. Dietary factors altering colonic microbiota included dietary patterns, macronutrients, micronutrients, bioactive compounds, and food additives. Reported diet-microbiota associations were dominated by routinely analyzed nutrients, which are absorbed from the small intestine but analyzed for correlation to stool microbiota. Dietary derived microbiota-relevant nutrients are more challenging to quantify and underrepresented in included studies. This evidence synthesis highlights advancements needed, including opportunities for expansion of food composition databases to include microbiota-relevant data, particularly for human intervention studies. These advances in dietary assessment methodology will facilitate translation of microbiota-specific nutrition therapy to practice.

Factors influencing oral microbiome analysis: from saliva sampling methods to next-generation sequencing platforms

The exploration of oral microbiome has been increasing due to its relatedness with various systemic diseases, but standardization of saliva sampling for microbiome analysis has not been established, contributing to the lack of data comparability. Here, we evaluated the factors that influence the microbiome data. Saliva samples were collected by the two collection methods (passive drooling and mouthwash) using three saliva-preservation methods (OMNIgene, DNA/RNA shield, and simple collection). A total of 18 samples were sequenced by both Illumina short-read and Nanopore long-read next-generation sequencing (NGS). The component of the oral microbiome in each sample was compared with alpha and beta diversity and the taxonomic abundances, to find out the effects of factors on oral microbiome data. The alpha diversity indices of the mouthwash sample were significantly higher than that of the drooling group with both short-read and long-read NGS, while no significant differences in microbial diversities were found between the three saliva-preservation methods. Our study shows mouthwash and simple collection are not inferior to other sample collection and saliva-preservation methods, respectively. This result is promising since the convenience and cost-effectiveness of mouthwash and simple collection can simplify the saliva sample preparation, which would greatly help clinical operators and lab workers.

Metabolic landscape of the male mouse gut identifies different niches determined by microbial activities

Distinct niches of the mammalian gut are populated by diverse microbiota, but the contribution of spatial variation to intestinal metabolism remains unclear. Here we present a map of the longitudinal metabolome along the gut of healthy colonized and germ-free male mice. With this map, we reveal a general shift from amino acids in the small intestine to organic acids, vitamins and nucleotides in the large intestine. We compare the metabolic landscapes in colonized versus germ-free mice to disentangle the origin of many metabolites in different niches, which in some cases allows us to infer the underlying processes or identify the producing species. Beyond the known impact of diet on the small intestinal metabolic niche, distinct spatial patterns suggest specific microbial influence on the metabolome in the small intestine. Thus, we present a map of intestinal metabolism and identify metabolite-microbe associations, which provide a basis to connect the spatial occurrence of bioactive compounds to host or microorganism metabolism.

Capsules with Ileocolonic-Targeted Release of Vitamin B2, B3, and C (ColoVit) Intended for Optimization of Gut Health: Development and Validation of the Production Process

The ileocolonic-targeted delivery of vitamins can establish beneficial alterations in gut microbial composition. Here, we describe the development of capsules containing riboflavin, nicotinic acid, and ascorbic acid covered with a pH-sensitive coating (ColoVit) to establish site-specific release in the ileocolon. Ingredient properties (particle size distribution, morphology) relevant for formulation and product quality were determined. Capsule content and the in vitro release behaviour were determined using a HPLC-method. Uncoated and coated validation batches were produced. Release characteristics were evaluated using a gastro-intestinal simulation system. All capsules met the required specifications. The contents of the ingredients were in the 90.0-120.0% range, and uniformity requirements were met. In the dissolution test a lag-time in drug release of 277-283 min was found, which meets requirements for ileocolonic release. The release itself is immediate as shown by dissolution of the vitamins of more than 75% in 1 h. The production process of the ColoVit formulation was validated and reproducible, it was shown that the vitamin blend was stable during the production process and in the finished coated product. The ColoVit is intended as an innovative treatment approach for beneficial microbiome modulation and optimization of gut health.

Meat Consumption and Gut Microbiota: a Scoping Review of Literature and Systematic Review of Randomized Controlled Trials in Adults

Emerging research indicates the importance of gut microbiota in mediating the relationship between meat intake and human health outcomes. We aimed to assess the state of available scientific literature on meat intake and gut microbiota in humans (PROSPERO, International Prospective Register of Systematic Reviews, CRD42020135649). We first conducted a scoping review to identify observational and interventional studies on this topic. Searches were performed for English language articles using PubMed, Cochrane Library, Scopus, and CINAHL (Cumulated Index to Nursing and Allied Health Literature) databases from inception to August 2021 and using keywords related to meat (inclusive of mammalian, avian, and aquatic subtypes) and gut microbiota. Of 14,680 records, 85 eligible articles were included in the scoping review, comprising 57 observational and 28 interventional studies. One prospective observational study and 13 randomized controlled trials (RCTs) were identified in adults without diagnosed disease. We included the 13 RCTs, comprising 18 comparisons, in the systematic review to assess the effects of higher and lower intakes of total meat and meat subtypes on the gut microbiota composition. The bacterial composition was differentially affected by consuming diets with and without meat or with varied meat subtypes. For example, higher meat intake tended to decrease population sizes of genera Anerostipes and Faecalibacterium, but it increased the population size of Roseburia across studies. However, the magnitude and directionality of most microbial responses varied, with inconsistent patterns of responses across studies. The data were insufficient for comparison within or between meat subtypes. The paucity of research, especially among meat subtypes, and heterogeneity of findings underscore the need for more well-designed prospective studies and full-feeding RCTs to address the relationships between and effects of consuming total meat and meat subtypes on gut microbiota, respectively.

Quorum sensing-based interactions among drugs, microbes, and diseases

Many diseases and health conditions are closely related to various microbes, which participate in complex interactions with diverse drugs; nonetheless, the detailed targets of such drugs remain to be elucidated. Many existing studies have reported causal associations among drugs, gut microbes, or diseases, calling for a workflow to reveal their intricate interactions. In this study, we developed a systematic workflow comprising three modules to construct a Quorum Sensing-based Drug-Microbe-Disease (QS-DMD) database ( http://www.qsdmd.lbci.net/ ), which includes diverse interactions for more than 8,000 drugs, 163 microbes, and 42 common diseases. Potential interactions between microbes and more than 8,000 drugs have been systematically studied by targeting microbial QS receptors combined with a docking-based virtual screening technique and in vitro experimental validations. Furthermore, we have constructed a QS-based drug-receptor interaction network, proposed a systematic framework including various drug-receptor-microbe-disease connections, and mapped a paradigmatic circular interaction network based on the QS-DMD, which can provide the underlying QS-based mechanisms for the reported causal associations. The QS-DMD will promote an understanding of personalized medicine and the development of potential therapies for diverse diseases. This work contributes to a paradigm for the construction of a molecule-receptor-microbe-disease interaction network for human health that may form one of the key knowledge maps of precision medicine in the future.

Microbiota analysis for risk assessment of xenobiotics: toxicomicrobiomics, incorporating the gut microbiome in the risk assessment of xenobiotics and identifying beneficial components for One Health

This work explores three areas of relevance to the gut microbiome in the context of One Health; the incorporation of the microbiome in food safety risk assessment of xenobiotics; the identification and application of beneficial microbial components to various areas under One Health, and specifically, in the context of antimicrobial resistance. We conclude that, although challenging, focusing on the microbiota resilience, function and active components, are critical for advancing the incorporation of the gut microbiome in the risk assessment of xenobiotics. Moreover, research technologies, such as toxicomicrobiomics, culturomics and genomics, especially in combination, have revealed that the human microbiota may be a promising source of beneficial taxa or other components, with the potential to metabolise and biodegrade xenobiotics. These may have possible applications in several health areas, including in animals or plants for detoxification or in the environment for bioremediation. This approach would be of particular interest for antimicrobials, with the potential to ameliorate antimicrobial resistance development. Finally, we propose that the concept of resistance to xenobiotics in the context of the gut microbiome may deserve further investigation in the pursuit of holistically elucidating their involvement in the balance between health and disease.

Interactions between central nervous system and peripheral metabolic organs

According to Descartes, minds and bodies are distinct kinds of "substance", and they cannot have causal interactions. However, in neuroscience, the two-way interaction between the brain and peripheral organs is an emerging field of research. Several lines of evidence highlight the importance of such interactions. For example, the peripheral metabolic systems are overwhelmingly regulated by the mind (brain), and anxiety and depression greatly affect the functioning of these systems. Also, psychological stress can cause a variety of physical symptoms, such as bone loss. Moreover, the gut microbiota appears to play a key role in neuropsychiatric and neurodegenerative diseases. Mechanistically, as the command center of the body, the brain can regulate our internal organs and glands through the autonomic nervous system and neuroendocrine system, although it is generally considered to be outside the realm of voluntary control. The autonomic nervous system itself can be further subdivided into the sympathetic and parasympathetic systems. The sympathetic division functions a bit like the accelerator pedal on a car, and the parasympathetic division functions as the brake. The high center of the autonomic nervous system and the neuroendocrine system is the hypothalamus, which contains several subnuclei that control several basic physiological functions, such as the digestion of food and regulation of body temperature. Also, numerous peripheral signals contribute to the regulation of brain functions. Gastrointestinal (GI) hormones, insulin, and leptin are transported into the brain, where they regulate innate behaviors such as feeding, and they are also involved in emotional and cognitive functions. The brain can recognize peripheral inflammatory cytokines and induce a transient syndrome called sick behavior (SB), characterized by fatigue, reduced physical and social activity, and cognitive impairment. In summary, knowledge of the biological basis of the interactions between the central nervous system and peripheral organs will promote the full understanding of how our body works and the rational treatment of disorders. Thus, we summarize current development in our understanding of five types of central-peripheral interactions, including neural control of adipose tissues, energy expenditure, bone metabolism, feeding involving the brain-gut axis and gut microbiota. These interactions are essential for maintaining vital bodily functions, which result in homeostasis, i.e., a natural balance in the body's systems.

Review of the Current State of Freely Accessible Web Tools for the Analysis of 16S rRNA Sequencing of the Gut Microbiome

Owing to the emergence and improvement of high-throughput technology and the associated reduction in costs, next-generation sequencing (NGS) technology has made large-scale sampling and sequencing possible. With the large volume of data produced, the processing and downstream analysis of data are important for ensuring meaningful results and interpretation. Problems in data analysis may be encountered if researchers have little experience in using programming languages, especially if they are clinicians and beginners in the field. A strategy for solving this problem involves ensuring easy access to commercial software and tools. Here, we observed the current status of free web-based tools for microbiome analysis that can help users analyze and handle microbiome data effortlessly. We limited our search to freely available web-based tools and identified MicrobiomeAnalyst, Mian, gcMeta, VAMPS, and Microbiome Toolbox. We also highlighted the various analyses that each web tool offers, how users can analyze their data using each web tool, and noted some of their limitations. From the abovementioned list, gcMeta, VAMPS, and Microbiome Toolbox had several issues that made the analysis more difficult. Over time, as more data are generated and accessed, more users will analyze microbiome data. Thus, the availability of free and easily accessible web tools can enable the easy use and analysis of microbiome data, especially for those users with less experience in using command-line interfaces.

Food and Gut Microbiota-Derived Metabolites in Nonalcoholic Fatty Liver Disease

Diet and lifestyle are crucial factors that influence the susceptibility of humans to nonalcoholic fatty liver disease (NAFLD). Personalized diet patterns chronically affect the composition and activity of microbiota in the human gut; consequently, nutrition-related dysbiosis exacerbates NAFLD via the gut–liver axis. Recent advances in diagnostic technology for gut microbes and microbiota-derived metabolites have led to advances in the diagnosis, treatment, and prognosis of NAFLD. Microbiota-derived metabolites, including tryptophan, short-chain fatty acid, fat, fructose, or bile acid, regulate the pathophysiology of NAFLD. The microbiota metabolize nutrients, and metabolites are closely related to the development of NAFLD. In this review, we discuss the influence of nutrients, gut microbes, their corresponding metabolites, and metabolism in the pathogenesis of NAFLD.

Effects of vaccination, new SARS-CoV-2 variants and reinfections on post-COVID-19 complications

Post-COVID-19 complications involve a variety of long-lasting health complications emerging in various body systems. Since the prevalence of post-COVID-19 complications ranges from 8-47% in COVID-19 survivors, it represents a formidable challenge to COVID-19 survivors and the health care system. Post-COVID-19 complications have already been studied in the connection to risk factors linked to their higher probability of occurrence and higher severity, potential mechanisms underlying the pathogenesis of post-COVID-19 complications, and their functional and structural correlates. Vaccination status has been recently revealed to represent efficient prevention from long-term and severe post-COVID-19 complications. However, the exact mechanisms responsible for vaccine-induced protection against severe and long-lasting post-COVID-19 complications remain elusive. Also, to the best of our knowledge, the effects of new SARS-CoV-2 variants and SARS-CoV-2 reinfections on post-COVID-19 complications and their underlying pathogenesis remain to be investigated. This hypothesis article will be dedicated to the potential effects of vaccination status, SARS-CoV-2 reinfections, and new SARS-CoV-2 variants on post-COVID-19 complications and their underlying mechanisms Also, potential prevention strategies against post-COVID complications will be discussed.

Unlocking the Potential of the Human Microbiome for Identifying Disease Diagnostic Biomarkers

The human microbiome encodes more than three million genes, outnumbering human genes by more than 100 times, while microbial cells in the human microbiota outnumber human cells by 10 times. Thus, the human microbiota and related microbiome constitute a vast source for identifying disease biomarkers and therapeutic drug targets. Herein, we review the evidence backing the exploitation of the human microbiome for identifying diagnostic biomarkers for human disease. We describe the importance of the human microbiome in health and disease and detail the use of the human microbiome and microbiota metabolites as potential diagnostic biomarkers for multiple diseases, including cancer, as well as inflammatory, neurological, and metabolic diseases. Thus, the human microbiota has enormous potential to pave the road for a new era in biomarker research for diagnostic and therapeutic purposes. The scientific community needs to collaborate to overcome current challenges in microbiome research concerning the lack of standardization of research methods and the lack of understanding of causal relationships between microbiota and human disease.

Trimethylamine N-Oxide Reduces the Susceptibility of Escherichia coli to Multiple Antibiotics

Trimethylamine N-oxide (TMAO), an important intestinal flora-derived metabolite, plays a role in the development of cardiovascular disease and tumor immunity. Here, we determined the minimum inhibitory concentration (MIC) of antibiotics against Escherichia coli under gradient concentrations of TMAO and performed a bacterial killing analysis. Overall, TMAO (in the range of 10 ~ 100 mM) increased the MIC of quinolones, aminoglycosides, and β-lactams in a concentration-dependent manner, and increased the lethal dose of antibiotics against E. coli. It implies that TMAO is a potential risk for failure of anti-infective therapy, and presents a case for the relationship between intestinal flora-derived metabolites and antibiotic resistance. Further data demonstrated that the inhibition of antibiotic efficacy by TMAO is independent of the downstream metabolic processes of TMAO and the typical bacterial resistance mechanisms (mar motif and efflux pump). Interestingly, TMAO protects E. coli from high-protein denaturant (urea) stress and improves the viability of bacteria following treatment with two disinfectants (ethanol and hydrogen peroxide) that mediate protein denaturation by chemical action or oxidation. Since antibiotics can induce protein inactivation directly or indirectly, our work suggests that disruption of protein homeostasis may be a common pathway for different stress-mediated bacterial growth inhibition/cell death. In addition, we further discuss this possibility, which provides a different perspective to address the global public health problem of antibiotic resistance.

Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota

The gut microbiota contributes to diverse aspects of host physiology, ranging from immunomodulation to drug metabolism. Changes in the gut microbiota composition are associated with various diseases as well as with the response to medications. It is therefore important to understand how different lifestyle and environmental factors shape gut microbiota composition. Beyond the commonly considered factor of diet, small-molecule drugs have recently been identified as major effectors of the microbiota composition. Other xenobiotics, such as environmental or chemical pollutants, can also impact gut bacterial communities. Here, we review the mechanisms of interactions between gut bacteria and antibiotics, host-targeted drugs, natural food compounds, food additives and environmental pollutants. While xenobiotics can impact bacterial growth and metabolism, bacteria in turn can bioaccumulate or chemically modify these compounds. These reciprocal interactions can manifest in complex xenobiotic-microbiota-host relationships. Our Review highlights the need to study mechanisms underlying interactions with pollutants and food additives towards deciphering the dynamics and evolution of the gut microbiota.

Therapeutic Benefits and Dietary Restrictions of Fiber Intake: A State of the Art Review

Throughout history, malnutrition and deficiency diseases have been a problem for our planet’s population. A balanced diet significantly influences everyone’s health, and fiber intake appears to play a more important role than previously thought. The natural dietary fibers are a category of carbohydrates in the constitution of plants that are not completely digested in the human intestine. High-fiber foods, such as fruits, vegetables and whole grains, have consistently been highly beneficial to health and effectively reduced the risk of disease. Although the mode of action of dietary fiber in the consumer body is not fully understood, nutritionists and health professionals unanimously recognize the therapeutic benefits. This paper presents the fiber consumption in different countries, the metabolism of fiber and the range of health benefits associated with fiber intake. In addition, the influence of fiber intake on the intestinal microbiome, metabolic diseases (obesity and diabetes), neurological aspects, cardiovascular diseases, autoimmune diseases and cancer prevention are discussed. Finally, dietary restrictions and excess fiber are addressed, which can cause episodes of diarrhea and dehydration and increase the likelihood of bloating and flatulence or even bowel obstruction. However, extensive studies are needed regarding the composition and required amount of fiber in relation to the metabolism of saprotrophic microorganisms from the enteral level and the benefits of the various pathologies with which they can be correlated.

A Low-FODMAP Diet Provides Benefits for Functional Gastrointestinal Symptoms but Not for Improving Stool Consistency and Mucosal Inflammation in IBD: A Systematic Review and Meta-Analysis

Background: A low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols diet (LFD) is claimed to improve functional gastrointestinal symptoms (FGSs). However, the role of LFD in inflammatory bowel disease (IBD) patients with FGSs remains unclear. Objective: To systematically assess the efficacy of LFD in IBD patients with FGSs. Methods: Six databases were searched from inception to 1 January 2022. Data were synthesized as the relative risk of symptoms improvement and normal stool consistency, mean difference of Bristol Stool Form Scale (BSFS), Short IBD Questionnaire (SIBDQ), IBS Quality of Life (IBS-QoL), Harvey-Bradshaw index (HBi), Mayo score, and fecal calprotectin (FC). Risk of bias was assessed based on study types. A funnel plot and Egger’s test were used to analyze publication bias. Results: This review screened and included nine eligible studies, including four randomized controlled trials (RCTs) and five before–after studies, involving a total of 446 participants (351 patients with LFD vs. 95 controls). LFD alleviated overall FGSs (RR: 0.47, 95% CI: 0.33–0.66, p = 0.0000) and obtained higher SIBDQ scores (MD = 11.24, 95% CI 6.61 to 15.87, p = 0.0000) and lower HBi score of Crohn’s disease (MD = −1.09, 95% CI −1.77 to −0.42, p = 0.002). However, there were no statistically significant differences in normal stool consistency, BSFS, IBS-QoL, Mayo score of ulcerative colitis, and FC. No publication bias was found. Conclusions: LFD provides a benefit in FGSs and QoL but not for improving stool consistency and mucosal inflammation in IBD patients. Further well-designed RCTs are needed to develop the optimal LFD strategy for IBD.

Incorporating the Gut Microbiome in the Risk Assessment of Xenobiotics and Identifying Beneficial Components for One Health

Three areas of relevance to the gut microbiome in the context of One Health were explored; the incorporation of the microbiome in food safety risk assessment of xenobiotics; the identification and application of beneficial microbial components to various areas under One Health, and; specifically, in the context of antimicrobial resistance. Although challenging, focusing on the microbiota resilience, function and active components is critical for advancing the incorporation of microbiome data in the risk assessment of xenobiotics. Moreover, the human microbiota may be a promising source of beneficial components, with the potential to metabolize xenobiotics. These may have possible applications in several areas, e.g., in animals or plants for detoxification or in the environment for biodegradation. This approach would be of particular interest for antimicrobials, with the potential to ameliorate antimicrobial resistance development. Finally, the concept of resistance to xenobiotics in the context of the gut microbiome may deserve further investigation.

The Effects of Probiotics on Inflammation, Endothelial Dysfunction, and Atherosclerosis Progression: A Mechanistic Overview

INTRODUCTION

The relationship between the intestinal microbiota dysbiosis, inflammation, and cardiovascular disorders (CVDs) has become evident, based on a growing body of literature from animal models and human studies. On the other hand, probiotics are believed to have promising effects on modifying dysbiosis and protecting against CVDs.

OBJECTIVE

This narrative review provides an overview of the link between gut microbiota, inflammation, endothelial dysfunction, and atherosclerosis. The influences of probiotic supplementation on biomarkers contributing to these conditions as the primary underlying risk factors for developing CVDs are also discussed.

METHODS

An up-to-date review was performed of the available evidence from experimental studies, clinical trials, and meta-analyses, considering their challenges and limitations. It also aimed to provide mechanistic insight into the likely mechanisms of probiotics that could prevent atherosclerosis initiation and progression.

RESULTS

Probiotic supplementation seems to be associated with reduced levels of inflammation and oxidative stress biomarkers (C-reactive protein, tumour necrosis factor-α, interleukin (IL)-6, IL-12, and malondialdehyde). Further, these agents might enhance antioxidant factors (IL-10, total antioxidant status, total antioxidant capacity, glutathione, and nitric oxide). Probiotics also appear to improve intestinal barrier integrity, reduce leakage of harmful metabolites (e.g., lipopolysaccharides), inhibit pro-inflammatory signalling pathways, and possibly suppress the formation of trimethylamine/trimethylamine oxide. Probiotics have also been found to enhance endothelial function and halter thrombosis.

CONCLUSION

The current clinical evidence underlines belief that probiotics might be associated with reduced levels of inflammation biomarkers. Experimental evidence reports that the beneficial effects of probiotics seem to be mainly imposed by triggering the secretion of short-chain fatty acids and bile acids, in addition to suppressing the NF-κB signalling pathway. However, the current studies are still in their infancy and it is of high priority to design further research on the topic.

Ornipural® Mitigates Malathion-Induced Hepato-Renal Damage in Rats via Amelioration of Oxidative Stress Biomarkers, Restoration of Antioxidant Activity, and Attenuation of Inflammatory Response

The current study was instigated by investigating the ameliorative potential of Ornipural^® solution against the hepato-renal toxicity of malathion. A total number of 35 male Wistar albino rats were divided equally into five groups. Group 1 served as control and received normal saline intraperitoneally. Group 2, the sham group, were administered only corn oil (vehicle of malathion) orally. Group 3 was orally intoxicated by malathion in corn oil at a dose of 135 mg/kg BW via intra-gastric gavage. Group 4 received malathion orally concomitantly with Ornipural^® intraperitoneally. Group 5 was given Ornipural^® solution in saline via intraperitoneal injection at a dose of (1 mL/kg BW). Animals received the treatment regime for 30 days. Histopathological examination revealed the harmful effect of malathion on hepatic and renal tissue. The results showed that malathion induced a significant decrease in body weight and marked elevation in the activity of liver enzymes, LDH, and ACP. In contrast, the activity of AchE and Paraoxonase was markedly decreased. Moreover, there was a significant increase in the serum content of bilirubin, cholesterol, and kidney injury markers. A significant elevation in malondialdehyde, nitric oxide (nitrite), and 8-hydroxy-2-deoxyguanosine was observed, along with a substantial reduction in antioxidant activity. Furthermore, malathion increased tumor necrosis factor-alpha, the upregulation of IL-1B, BAX, and IFN-β genes, and the downregulation of Nrf2, Bcl2, and HO-1 genes. Concurrent administration of Ornipural^® with malathion attenuated the detrimental impact of malathion through ameliorating metabolic biomarkers, restoring antioxidant activity, reducing the inflammatory response, and improving pathologic microscopic alterations. It could be concluded that Ornipural^® solution demonstrates hepatorenal defensive impacts against malathion toxicity at biochemical, antioxidants, molecular, and cellular levels.

Perspective: Is it Time to Expand Research on "Nuts" to Include "Seeds"? Justifications and Key Considerations

The health benefits of nuts reported throughout the literature are extensive and well established for reducing the risk of, and managing several chronic conditions such as cardiovascular disease, type 2 diabetes, nonalcoholic fatty liver disease, and cognition. Despite their comparable nutrient profile to nuts, seeds are often not assessed in clinical and epidemiological studies. Interestingly, dietary guidelines and recommendations often refer to "nuts and seeds" collectively, even though they are not consistently examined together in nutrition research when determining associated health benefits. The purpose of this review is to call for future nutrition research to consider combining nuts and seeds. This review provides justification for this proposal by summarizing current definitions for nuts and seeds and highlighting the similarities or dissimilarities in their nutrient compositions. Following this, we summarize current evidence on the health benefits of nuts and seeds, research gaps that should be addressed, and considerations for future research using both epidemiological and interventional study designs.

The Gut-Brain Axis and Its Relation to Parkinson's Disease: A Review

Parkinson's disease is a chronic neurodegenerative disease characterized by the accumulation of misfolded alpha-synuclein protein (Lewy bodies) in dopaminergic neurons of the substantia nigra and other related circuitry, which contribute to the development of both motor (bradykinesia, tremors, stiffness, abnormal gait) and non-motor symptoms (gastrointestinal issues, urinogenital complications, olfaction dysfunction, cognitive impairment). Despite tremendous progress in the field, the exact pathways and mechanisms responsible for the initiation and progression of this disease remain unclear. However, recent research suggests a potential relationship between the commensal gut bacteria and the brain capable of influencing neurodevelopment, brain function and health. This bidirectional communication is often referred to as the microbiome-gut-brain axis. Accumulating evidence suggests that the onset of non-motor symptoms, such as gastrointestinal manifestations, often precede the onset of motor symptoms and disease diagnosis, lending support to the potential role that the microbiome-gut-brain axis might play in the underlying pathological mechanisms of Parkinson's disease. This review will provide an overview of and critically discuss the current knowledge of the relationship between the gut microbiota and Parkinson's disease. We will discuss the role of α-synuclein in non-motor disease pathology, proposed pathways constituting the connection between the gut microbiome and the brain, existing evidence related to pre- and probiotic interventions. Finally, we will highlight the potential opportunity for the development of novel preventative measures and therapeutic options that could target the microbiome-gut-brain axis in the context of Parkinson's disease.

Sensory Features Introduced by Brewery Spent Grain with Impact on Consumers' Motivations and Emotions for Fibre-Enriched Products

The aim of this work was both to formulate three different fibre-enriched products by the addition of Brewery Spent Grain (BSG), and to evaluate the impact of this fibre enrichment on sensory quality, acceptability, and purchase intention under blind conditions. BSG was incorporated into bread, pasta, and chocolate milk at levels of 8.3%, 2.8%, and 0.35% (w/w), respectively. The fibre-enriched products and their regular counterparts were evaluated together by consumers through a CATA questionnaire, the EsSense 25 Profile, an overall acceptability rating, and a purchase intention ranking. Although fibre-enriched bread and chocolate milk ranked lower in overall acceptability compared with their counterparts, no significant difference was found for fibre-enriched pasta (p > 0.05). Purchase intention did not differ significantly for both bread and pasta (p > 0.05), yet the reasons for purchasing them differed significantly (p < 0.05). Consumers recognised the fibre enrichment in these two products and, therefore, were willing to partially compromise on sensory attributes. The fibre-enriched chocolate milk, nonetheless, scored significantly (p < 0.05) lower in purchase intention than the control. This work demonstrates that the effect of BSG addition is product-specific, and that fibre perception makes consumers feel more confident.

Fueling Gut Microbes: A Review of the Interaction between Diet, Exercise, and the Gut Microbiota in Athletes

The athlete's goal is to optimize their performance. Towards this end, nutrition has been used to improve the health of athletes' brains, bones, muscles, and cardiovascular system. However, recent research suggests that the gut and its resident microbiota may also play a role in athlete health and performance. Therefore, athletes should consider dietary strategies in the context of their potential effects on the gut microbiota, including the impact of sports-centric dietary strategies (e.g., protein supplements, carbohydrate loading) on the gut microbiota as well as the effects of gut-centric dietary strategies (e.g., probiotics, prebiotics) on performance. This review provides an overview of the interaction between diet, exercise, and the gut microbiota, focusing on dietary strategies that may impact both the gut microbiota and athletic performance. Current evidence suggests that the gut microbiota could, in theory, contribute to the effects of dietary intake on athletic performance by influencing microbial metabolite production, gastrointestinal physiology, and immune modulation. Common dietary strategies such as high protein and simple carbohydrate intake, low fiber intake, and food avoidance may adversely impact the gut microbiota and, in turn, performance. Conversely, intake of adequate dietary fiber, a variety of protein sources, and emphasis on unsaturated fats, especially omega-3 (ɷ-3) fatty acids, in addition to consumption of prebiotics, probiotics, and synbiotics, have shown promising results in optimizing athlete health and performance. Ultimately, while this is an emerging and promising area of research, more studies are needed that incorporate, control, and manipulate all 3 of these elements (i.e., diet, exercise, and gut microbiome) to provide recommendations for athletes on how to "fuel their microbes."

Characterization of the gut microbiota in hemodialysis patients with sarcopenia

PURPOSE

Maintenance hemodialysis (MHD) patients are at high risk of sarcopenia. Gut microbiota affects host metabolic and may act in the occurrence of sarcopenia importantly. This study aimed to study the characterization of the gut microbiota in MHD patients with sarcopenia, and to further reveal the complex pathophysiology of sarcopenia in MHD patients.

METHODS

Fecal samples and clinical data were collected from 30 MHD patients with sarcopenia, and 30 age-and-sex-matched MHD patients without sarcopenia in 1 general hospital of Jiangsu Province from December 2020 to March 2021. 16S rRNA sequencing technology was used to analyze the genetic sequence of the gut microbiota for evaluation of the diversity, species composition, and differential microbiota of the two groups.

RESULTS

Compared to MHD patients without sarcopenia, the ACE index of patients with sarcopenia was lower (P = 0.014), and there was a structural difference in the β-diversity between the two groups (P = 0.001). At the genus level, the relative abundance of Tyzzerella_4 in the sarcopenia group was significantly higher than in the non-sarcopenia group (P = 0.039), and the relative abundance of Megamonas (P = 0.004), Coprococcus_2 (P = 0.038), and uncultured_bacterium_f_Muribaculaceae (P = 0.040) decreased significantly.

CONCLUSION

The diversity and structure of the gut microbiota of MHD patients with sarcopenia were altered. The occurrence of sarcopenia in MHD patients may be influenced by gut microbiota.

Vitamins, the gut microbiome and gastrointestinal health in humans

The gut microbiome plays important roles in the maintenance of host health and the pathogenesis of many diseases. Diet is a key modulator of the gut microbiome. There is increasing evidence that nutrients other than fermentable fiber affect the gut microbial composition. In this review, we discuss the effects of vitamins on the gut microbiome, and related gastrointestinal health, based on in vitro, animal and human studies. Some vitamins, when provided in large doses or when delivered to the large intestine, have been shown to beneficially modulate the gut microbiome by increasing the abundance of presumed commensals (vitamins A, B₂, D, E, and beta-carotene), increasing or maintaining microbial diversity (vitamins A, B₂, B₃, C, K) and richness (vitamin D), increasing short chain fatty acid production (vitamin C), or increasing the abundance of short chain fatty acid producers (vitamins B₂, E). Others, such as vitamins A and D, modulate the gut immune response or barrier function, thus, indirectly influencing gastrointestinal health or the microbiome. Future research is needed to explore these potential effects and to elucidate the underlying mechanisms and host health benefits.

Nutrition and Cancer Risk from the Viewpoint of the Intestinal Microbiome

There are various important factors in reducing the risk of cancer development and progression; these factors may correct an unbalanced intake of nutrients to maintain the living body’s homeostasis, detoxify toxic materials, acting as an external factor, and maintain and strengthen the body’s immune function. In a normal cell environment, nutrients, such as carbohydrates, lipids, proteins, vitamins, and minerals, are properly digested and absorbed into the body, and, as a result, an environment in which cancer can develop and progress is prevented. It is necessary to prevent toxic materials from entering the body and to detoxify poisons in the body. If these processes occur correctly, cells work normally, and genes cannot be damaged. The most important factor in the fight against cancer and prevention of the development and progression of cancer is the immune system. This requires a nutritional state in which the immune system works well, allowing the intestinal microbiome to carry out all of its roles. In order to grow intestinal microbiota, the consumption of prebiotics, such as organic vegetables, fruits, and dietary fiber, and probiotics of effective intestinal microbiota, such as fermented foods and supplements, is required. Symbiosis, in which these organisms work together, is an effective means of reducing the risk of cancer. In addition, fecal microbiota transplantation (FMT) using ultrafine bubble water, produced specially by the Association for Clinical Research of Fecal Microbiota Transplantation Japan, is also useful for improving the nutritional condition and reducing the risk of cancer.

The gut microbiome in konzo

Konzo, a distinct upper motor neuron disease associated with a cyanogenic diet and chronic malnutrition, predominately affects children and women of childbearing age in sub-Saharan Africa. While the exact biological mechanisms that cause this disease have largely remained elusive, host-genetics and environmental components such as the gut microbiome have been implicated. Using a large study population of 180 individuals from the Democratic Republic of the Congo, where konzo is most frequent, we investigate how the structure of the gut microbiome varied across geographical contexts, as well as provide the first insight into the gut flora of children affected with this debilitating disease using shotgun metagenomic sequencing. Our findings indicate that the gut microbiome structure is highly variable depending on region of sampling, but most interestingly, we identify unique enrichments of bacterial species and functional pathways that potentially modulate the susceptibility of konzo in prone regions of the Congo.

Host Bias in Diet-Source Microbiome Transmission in Wild Cohabitating Herbivores: New Knowledge for the Evolution of Herbivory and Plant Defense

It is commonly understood that dietary nutrition will influence the composition and function of the animal gut microbiome. However, the transmission of organisms from the diet-source microbiome to the animal gut microbiome in the natural environment remains poorly understood, and elucidating this process may help in understanding the evolution of herbivores and plant defenses. Here, we investigated diet-source microbiome transmission across a range of herbivores (insects and mammals) living in both captive and wild environments. We discovered a host bias among cohabitating herbivores (leaf-eating insects and deer), where a significant portion of the herbivorous insect gut microbiome may originate from the diet, while in deer, only a tiny fraction of the gut microbiome is of dietary origin. We speculated that the putative difference in the oxygenation level in the host digestion systems would lead to these host biases in plant-source (diet) microbiome transmission due to the oxygenation living condition of the dietary plant's symbiotic microbiome. IMPORTANCE We discovered a host bias among cohabitating herbivores (leaf-eating insects and deer), where a significant portion of the herbivorous insect gut microbiome may originate from the diet, while in deer, only a tiny fraction of the gut microbiome is of dietary origin. We speculated that the putative difference in the oxygenation level in the host digestion systems would lead to these host biases in plant-source (diet) microbiome transmission due to the oxygenation living condition of the dietary plant's symbiotic microbiome. This study shed new light on the coevolution of herbivory and plant defense.

Gut Microbiota-Informed Precision Nutrition in the Generally Healthy Individual: Are We There Yet?

Since next generation sequencing facilitated high-throughput and cost-efficient genomics analyses, the human gut metagenome has become an emerging frontier to explore toward precision nutrition. Significant progress has been made in identifying gut microbial features associated with a wide spectrum of human disease. However, other than a few microbiome-disease relations, there is a dearth of confirmed causal inferences, particularly in generally healthy populations. The relatively high unexplained variability in microbiome compositions in this group warrants caution in applying this complex biomarker toward precision nutrition, because our understanding of what constitutes a healthy microbiome is still rudimentary. Although gut microbiota harbor integrated environmental and host-specific information with the potential to facilitate personalized nutritional and lifestyle advice, these data cannot yet be confidently interpreted toward precise recommendations. Thus, nutritional advice for generally healthy individuals based on personal microbiome composition analysis might not yet be appropriate unless accompanied by established blood and physiological biomarkers.

Simple Energy Balance or Microbiome for Childhood Obesity Prevention?

Obesity prevention interventions generally have either not worked or had effects inadequate to mitigate the problem. They have been predicated on the simple energy balance model, which has been severely questioned by biological scientists. Numerous other etiological mechanisms have been proposed, including the intestinal microbiome, which has been related to childhood obesity in numerous ways. Public health research is needed in regard to diet and the microbiome, which hopefully will lead to effective child obesity prevention.

SiGMoiD: A super-statistical generative model for binary data

In modern computational biology, there is great interest in building probabilistic models to describe collections of a large number of co-varying binary variables. However, current approaches to build generative models rely on modelers’ identification of constraints and are computationally expensive to infer when the number of variables is large (N~100). Here, we address both these issues with Super-statistical Generative Model for binary Data (SiGMoiD). SiGMoiD is a maximum entropy-based framework where we imagine the data as arising from super-statistical system; individual binary variables in a given sample are coupled to the same ‘bath’ whose intensive variables vary from sample to sample. Importantly, unlike standard maximum entropy approaches where modeler specifies the constraints, the SiGMoiD algorithm infers them directly from the data. Due to this optimal choice of constraints, SiGMoiD allows us to model collections of a very large number (N>1000) of binary variables. Finally, SiGMoiD offers a reduced dimensional description of the data, allowing us to identify clusters of similar data points as well as binary variables. We illustrate the versatility of SiGMoiD using multiple datasets spanning several time- and length-scales.

Collectively varying binary variables are ubiquitous in modern biology. Given that the number of possible configurations of these systems typically far exceeds the number of available samples, generative models have become an essential tool in quantitative descriptions of binary data. The state-of-the-art approaches to build generative models have several conceptual limitations. Specifically, they rely on the modeler choosing system-appropriate constraints, which can be challenging in systems with many complex interactions. Moreover, they are computationally expensive to infer when the number of variables is large (N~100). To address this issue, we propose a theoretical generalization of the maximum entropy approach that allows us to model very high dimensional data; at least an order of magnitude higher than what is currently possible. This framework will be a significant advancement in the computational analysis of covarying binary variables.

Nutritional Interventions and the Gut Microbiome in Children

The gut microbiome plays an integral role in health and disease, and diet is a major driver of its composition, diversity, and functional capacity. Given the dynamic development of the gut microbiome in infants and children, it is critical to address two major questions: (a) Can diet modify the composition, diversity, or function of the gut microbiome, and (b) will such modification affect functional/clinical outcomes including immune function, cognitive development, and overall health? We synthesize the evidence on the effect of nutritional interventions on the gut microbiome in infants and children across 26 studies. Findings indicate the need to study older children, assess the whole intestinal tract, and harmonize methods and interpretation of findings, which are critical for informing meaningful clinical and public health practice. These findings are relevant for precision health, may help identify windows of opportunity for intervention, and may inform the design and delivery of such interventions. Expected final online publication date for the Annual Review of Nutrition, Volume 41 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The Role of the Microbiota-Gut-Brain Axis in the Health and Illness Condition: A Focus on Alzheimer's Disease

Trillions of commensal microbes live in our body, the majority in the gut. This gut microbiota is in constant interaction with the homeostatic systems, the nervous, immune and endocrine systems, being fundamental for their appropriate development and function as well as for the neuroimmunoendocrine communication. The health state of an individual is understood in the frame of this communication, in which the microbiota-gut-brain axis is a relevant example. This bidirectional axis is constituted in early age and is affected by many environmental and lifestyle factors such as diet and stress, among others, being involved in the adequate maintenance of homeostasis and consequently in the health of each subject and in his/her rate of aging. For this, an alteration of gut microbiota, as occurs in a dysbiosis, and the associated gut barrier deterioration and the inflammatory state, affecting the function of immune, endocrine and nervous systems, in gut and in all the locations, is in the base of a great number of pathologies as those that involve alterations in the brain functions. There is an age-related deterioration of microbiota and the homeostatic systems due to oxi-inflamm-aging, and thus the risk of aging associated pathologies such as the neurodegenerative illness. Currently, this microbiota-gut-brain axis has been considered to have a relevant role in the pathogenesis of Alzheimer's disease and represents an important target in the prevention and slowdown of the development of this pathology. In this context, the use of probiotics seems to be a promising help.

Effect of sequentially fed high protein, hydrolyzed protein, and high fiber diets on the fecal microbiota of healthy dogs: a cross-over study

Background

Dietary content and environmental factors can shape the gut microbiota, and consequently, the way the gut microbiota metabolizes fats, carbohydrates, and proteins, affecting overall health of the host. We evaluated the impact of 3 diets (all meat [raw], high-insoluble fiber dry extruded diet and hydrolyzed protein dry extruded diet) on the gut microbiota of healthy dogs in a cross-over sequential study.

Results

We showed that diet can have an effect on the gut microbiome in dogs, which was influenced by the order of feeding. High-protein (all meat) diets were characterized by an increase in bacteria belonging to the Fusobacteria and Bacteroidetes phyla, whereas a high-insoluble fiber commercial diet correlated with increases in Firmicutes and Actinobacteria phyla. However, the individual dog’s baseline microbiota had the most impact on the magnitude and nature of the changes in response to dietary intervention.

Conclusion

Our results suggest that the dog fecal microbiota is driven by protein and fiber composition to different degrees in individual animals, and targeted modification of these patterns could be useful in the modulation of the gut microbiota in different diseases.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00101-8.

Association of Trimethylamine N-Oxide (TMAO) with the Clinical Severity of Hidradenitis Suppurativa (Acne Inversa)

In this case-control, cross-sectional, observational study, we evaluated circulating trimethylamine n-oxide (TMAO) levels, a gut-derived metabolite associated with inflammation and cardiometabolic risk, in patients with hidradenitis suppurativa (HS), a highly disabling inflammatory skin disease associated with an elevated prevalence of comorbidities, especially cardiovascular and metabolic diseases. In this study, we enrolled 35 naive-treatment patients with HS and 35 controls, matched for sex, age, and body mass index (BMI). HS Sartorius score was 49.0 (33.0–75.0), while according to the Harley system 12 and 23 patients presented grade 1 and grade 2 severity, respectively. HS patients had a lower adherence to the Mediterranean diet (MD) (p = 0.002), lower phase angle (PhA) (p < 0.001), and higher circulating TMAO levels (p < 0.001) than the control group. HS patients with grade 2 rather than grade 1 of Harley grade severity showed a higher BMI (p = 0.007), waist circumference (p = 0.016), total energy intake (p = 0.005), and lower PhA (p < 0.001) and adherence to the MD (p = 0.003). Of interest, patients with Hurley grade 2 of severity exhibited higher circulating TMAO levels (p < 0.001) compared to grade 1. Circulating TMAO levels showed a positive correlation with HS Sartorius score even after adjustment for confounding covariates, including BMI, waist circumference, adherence to the MD, total energy intake, and PhA (r = 0.570, p = 0.001). Using a linear regression model, circulating TMAO levels and PhA were the main predictors of the clinical severity of HS.

Causal Inference in Microbiome Medicine: Principles and Applications

Microorganisms that colonize the mammalian skin and cavity play critical roles in various physiological functions of the host. Numerous studies have revealed strong associations between the microbiota and multiple diseases. However, association does not mean causation. To clarify the mechanisms underlying microbiota-mediated diseases, research is moving from associative analyses to causation studies. In this article, we first introduce the principles of the computational methods for causal inference, and then discuss the applications of these methods in microbiome medicine. Furthermore, we examine the reliability of theoretically inferred causality by the interventionist framework. Finally, we show the potential of confirmed causality in microbiota-targeted therapy, especially in personalized dietary intervention. We conclude that a comprehensive understanding of the causal relationships between diets, microbiota, host targets, and diseases is critical to future microbiome medicine.

Measuring Dietary Botanical Diversity as a Proxy for Phytochemical Exposure

The study of natural plant molecules and their medicinal properties, pharmacognosy, provides a taxonomy for botanical families that represent diverse chemical groupings with potentially distinct functions in relation to human health. Yet, this reservoir of knowledge has not been systematically applied to elucidating the role of patterns of plant food consumption on gut microbial ecology and function. All chemical classes of dietary phytochemicals can affect the composition of the microbes that colonize the gut and their function. In turn, the gut microbiome affects the host via multiple mechanisms including gut barrier function, immune function, satiety and taste regulation and the activity of biological signaling pathways that influence health and disease. Herein, we report the development of a botanical diversity index (BDI) to evaluate plant food consumption as a novel metric for identifying and quantifying phytochemicals to which an individual is exposed. A rationale is advanced for using the BDI to investigate how plant food diversity impacts gut microbial ecology and functionality.

Reframing Nutritional Microbiota Studies To Reflect an Inherent Metabolic Flexibility of the Human Gut: a Narrative Review Focusing on High-Fat Diets

There is a broad consensus in nutritional-microbiota research that high-fat (HF) diets are harmful to human health, at least in part through their modulation of the gut microbiota. However, various studies also support the inherent flexibility of the human gut and our microbiota’s ability to adapt to a variety of food sources, suggesting a more nuanced picture.

There is a broad consensus in nutritional-microbiota research that high-fat (HF) diets are harmful to human health, at least in part through their modulation of the gut microbiota. However, various studies also support the inherent flexibility of the human gut and our microbiota’s ability to adapt to a variety of food sources, suggesting a more nuanced picture. In this article, we first discuss some problems facing basic translational research and provide a different framework for thinking about diet and gut health in terms of metabolic flexibility. We then offer evidence that well-formulated HF diets, such as ketogenic diets, may provide healthful alternative fuel sources for the human gut. We place this in the context of cancer research, where this concern over HF diets is also expressed, and consider various potential objections concerning the effects of lipopolysaccharides, trimethylamine-N-oxide, and secondary bile acids on human gut health. We end by providing some general suggestions for how to improve research and clinical practice with respect to the gut microbiota when considering the framework of metabolic flexibility.

The role of gut microbiota in tumorigenesis and treatment

A large number of microbial communities exist in normal human intestinal tracts, which maintain a relatively stable dynamic balance under certain conditions. Gut microbiota are closely connected with human health and the occurrence of tumors. The colonization of certain intestinal bacteria on specific sites, gut microbiota disturbance and intestinal immune disorders can induce the occurrence of tumors. Meanwhile, gut microbiota can also play a role in tumor therapy by participating in immune regulation, influencing the efficacy of anti-tumor drugs, targeted therapy of engineered probiotics and fecal microbiota transplantation. This article reviews the role of gut microbiota in the occurrence, development, diagnosis and treatment of tumors. A better understanding of how gut microbiota affect tumors will help us find more therapies to treat the disease.

Dietary purslane (Portulaca oleracea L.) promotes the growth performance of broilers by modulation of gut microbiota

Purslane is a widespread wild vegetable with both medicinal and edible properties. It is highly appreciated for its high nutritional value and is also considered as a high-quality feed resource for livestock and poultry. In this study, Sanhuang broilers were used to investigate the effect of feeding purslane diets on the growth performance in broilers and their gut microbiota. A total of 48 birds with good growth and uniform weight were selected and randomly allocated to four treatment groups A (control), B, C and D. Dietary treatments were fed with basal diet without purslane and diets containing 1%, 2% and 3% purslane. The 16S rDNA was amplified by PCR and sequenced using the Illumina HiSeq platform to analyze the composition and diversity of gut microbiota in the four sets of samples. The results showed that dietary inclusion of 2% and 3% purslane could significantly improve the growth performance and reduce the feed conversion ratio. Microbial diversity analysis indicated that the composition of gut microbiota of Sanhuang broilers mainly included Gallibacterium, Bacteroides and Escherichia-Shigella, etc. As the content of purslane was increased, the abundance of Lactobacillus increased significantly, and Escherichia-Shigella decreased. LEfSe analysis revealed that Bacteroides_caecigallinarum, Lachnospiraceae, Lactobacillales and Firmicutes had significant differences compared with the control group. PICRUSt analysis revealed bacteria mainly enriched in carbohydrate metabolism pathway due to the additon of purslane in the diet. These results suggest that the addition of purslane to feed could increase the abundance of Lactobacillus in intestine, modulate the environment of gut microbiota and promote the metabolism of carbohydrates to improve its growth performance. This study indicates that the effect of purslane on the growth-promoting performance of broilers might depend on its modulation on gut microbiota, so as to provide a certain scientific basis for the application of purslane in the feed industry.