Role of Dietary Nutrients in the Modulation of Gut Microbiota: A Narrative Review

Intestinal Permeability in Children with Functional Gastrointestinal Disorders: The Effects of Diet

Functional gastrointestinal disorders (FGIDs) are very common and life-impacting in children and young adults, covering 50% of pediatric gastroenterologist consultations. As it is known, FGIDs may be due to alterations in the gut–brain axis, dysbiosis and dysregulation of intestinal barrier, causing leaky gut. This may enhance increased antigen and bacterial passage through a damaged mucosa, worsening the impact of different medical conditions such as FGIDs. Little is known about the role of nutrients in modifying this “barrier disruption”. This narrative review aims to analyze the clinical evidence concerning diet and Intestinal Permeability (IP) in FGIDs in children. We searched the PubMed/Medline library for articles published between January 2000 and November 2021 including children aged 0–18 years old, using keywords related to the topic. Since diet induces changes in the intestinal barrier and microbiota, we aimed at clarifying how it is possible to modify IP in FGIDs by diet modulation, and how this can impact on gastrointestinal symptoms. We found that) is that small changes in eating habits, such as a low-FODMAP diet, an adequate intake of fiber and intestinal microbiota modulation by prebiotics and probiotics, seem to lead to big improvements in quality of life.

Effects of Non-Polar Dietary and Endogenous Lipids on Gut Microbiota Alterations: The Role of Lipidomics

Advances in sequencing technologies over the past 15 years have led to a substantially greater appreciation of the importance of the gut microbiome to the health of the host. Recent outcomes indicate that aspects of nutrition, especially lipids (exogenous or endogenous), can influence the gut microbiota composition and consequently, play an important role in the metabolic health of the host. Thus, there is an increasing interest in applying holistic analytical approaches, such as lipidomics, metabolomics, (meta)transcriptomics, (meta)genomics, and (meta)proteomics, to thoroughly study the gut microbiota and any possible interplay with nutritional or endogenous components. This review firstly summarizes the general background regarding the interactions between important non-polar dietary (i.e., sterols, fat-soluble vitamins, and carotenoids) or amphoteric endogenous (i.e., eicosanoids, endocannabinoids-eCBs, and specialized pro-resolving mediators-SPMs) lipids and gut microbiota. In the second stage, through the evaluation of a vast number of dietary clinical interventions, a comprehensive effort is made to highlight the role of the above lipid categories on gut microbiota and vice versa. In addition, the present status of lipidomics in current clinical interventions as well as their strengths and limitations are also presented. Indisputably, dietary lipids and most phytochemicals, such as sterols and carotenoids, can play an important role on the development of medical foods or nutraceuticals, as they exert prebiotic-like effects. On the other hand, endogenous lipids can be considered either prognostic indicators of symbiosis or dysbiosis or even play a role as specialized mediators through dietary interventions, which seem to be regulated by gut microbiota.

Involvement of the Liver in COVID-19: A Systematic Review

COVID-19, a respiratory viral infection, has affected 388 million individuals worldwide as of the February 4, 2022. In this review, we have outlined the important liver manifestations of COVID-19 and discussed the possible underlying pathophysiological mechanisms and their diagnosis and management. Factors that may contribute to hepatic involvement in COVID-19 include direct viral cytopathic effects, exaggerated immune responses/systemic inflammatory response syndrome, hypoxia-induced changes, vascular changes due to coagulopathy, endothelitis, cardiac congestion from right heart failure, and drug-induced liver injury. The majority of COVID-19-associated liver symptoms are mild and self-limiting. Thus management is generally supportive. Liver function tests and abdominal imaging are the primary investigations done in relation to liver involvement in COVID-19 patients. However, imaging findings are nonspecific. Severe acute respiratory syndrome coronavirus 2 RNA has been found in liver biopsies. However, there is limited place for liver biopsy in the clinical context, as it does not influence management. Although, the management is supportive in the majority of patients without previous liver disease, special emphasis is needed in those with nonalcoholic fatty liver disease, cirrhosis, hepatocellular carcinoma, hepatitis B and C infections, and alcoholic liver disease, and in liver transplant recipients.

Functional properties of miscanthus fiber and prebiotic blends in extruded canine diets

Dietary fiber has become increasingly recognized as a key factor in maintaining gastrointestinal health. Dietary fiber sources are often comprised of several different fiber fractions, each with unique physicochemical properties. These properties can have varying physiological effects on the gastrointestinal tract that include modulation of microbiota, production of fermentation-derived metabolites, and laxation. The objectives of this study were 1) to determine the effects of a novel dietary fiber source, miscanthus grass fiber (MF), and prebiotic and fiber blends on gastrointestinal tolerance, apparent total tract digestibility, fecal metabolites, and fecal microbiota and 2) to evaluate the palatability of extruded diets containing MF in comparison to traditional dietary fiber sources. All animal procedures were approved by the University of Illinois Institutional Animal Care and Use Committee. Six dietary treatments were formulated to meet or exceed the AAFCO nutrient profile of 2018 and included either cellulose (CO), beet pulp (BP), MF, or a blend of MF and tomato pomace, MF and resistant starch, or MF and fructooligosaccharide. A total of 12 adult neutered female beagles (mean age 5.8 ± 1.1 yr; mean body weight 10.9 ± 1.0 kg; mean body condition score 5.7 ± 0.7) were randomly assigned to one of the six treatment diets in a replicated 6 × 6 Latin square design. Each dog was fed their assigned diet for a treatment period of 21 d with 17 d of diet adaptation followed by 4 d of total and fresh fecal collection. All diets were well accepted and digested by the dogs. Dogs fed BP had greater fecal total short-chain fatty acid concentration than the CO treatment (P < 0.05), while the dogs fed diets containing MF were intermediate. In a two-bowl palatability trial, no significant preference was observed between the extruded diets containing MF and CO (P > 0.05). However, a significant preference for the extruded diet containing BP over the diet containing only MF was observed (P < 0.05). The α-diversity of fecal microbial communities was not impacted by treatment (P > 0.05), but β-diversity indicated that dogs fed the BP diet differed from the other treatment groups (P < 0.05). The data from this study suggest that miscanthus grass can be successfully utilized in fiber blends in extruded diets for adult dogs, with modulatory effects similar to the traditional dietary fiber source, cellulose.

An anxious relationship between Autism Spectrum Disorder and Gut Microbiota: A tangled chemistry?

Autism spectrum disorder (ASD) is a serious multifactorial neurodevelopmental disorder often accompanied by strained social communication, repetitive behaviour, immune dysregulation, and gastrointestinal (GI) issues. Recent studies have recorded a link between dysbiosis in the gut microbiota (gm) and the primary stages of ASD. A bidirectional connection (also called microbiota-gut-brain-axis) exchanges information between the gut bacteria and central nervous system. When the homeostasis of the microenvironment of the gut is dysregulated, it causes oxidative stress, affecting neuronal cells and neurotransmitters, thereby causing neurodevelopmental disorders. Studies have confirmed a difference in the constitution of gut bacteria among ASD cases and their controls. Numerous studies on animal models of ASD have shown altered gm and its association with abnormal metabolite profile and altered behaviour phenotype. This process happens due to an abnormal metabolite production in gm, leading to changes in the immune system, especially in ASD. Hence, this review aims to question the current knowledge on gm dysbiosis and its related GI discomforts and ASD behavioural symptoms and shed light on the possible therapeutic approaches available to deal with this situation. Thereby, though it is understood that more research might be needed to prove an association or causal relationship between gm and ASD, therapy with the microbiome may also be considered as an effective strategy to combat this issue.

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.

Influence of dietary vitamin E and selenium supplementation on broilers subjected to heat stress, Part II: Oxidative stress, immune response, gut integrity, and intestinal microbiota

This study evaluated the effects of vitamin E (Vit E) and selenium (Se) supplementation on mRNA abundance of antioxidant, immune response, and tight junction genes, as well as taxonomic and functional profiles of ileal microbiota of broilers exposed to daily 4-h elevated temperature during d 28 to 35. A total of 640-day-old Cobb male broiler chicks were randomly allocated to 32 floor pens in a 2 × 2 factorial arrangement that included ambient temperature (thermoneutral [TN] or heat stress [HS]) and dietary treatments (basal diet or Vit E + Se). Vit E and organic Se were added to the basal diet at the rate of 250 mg/kg and 1 mg/kg, respectively. Liver and jejunum tissue samples were taken on d 27 (1 bird/pen), d 28 and d 35 (2 birds/pen) from birds for qPCR analysis. Data were subjected to a 2-way ANOVA using the GLM procedure of JMP. Ileal contents were taken on d 27 and d 35 for microbial profiling. Microbiota data were analyzed in QIIME 2 and significance between treatments identified linear discriminant analysis effect size (LEfSe, P < 0.05). Dietary Vit E/Se significantly downregulated the mRNA levels of HSPs in liver and jejunal tissues of the HS-challenged birds both on d 28 and d 35. Moreover, mRNA abundance of TLR2, TNFα, IFNγ, IL-1β, IL-10, and iNOS in the liver were significantly downregulated in birds fed the Vit E/Se diet on d 35. However, dietary treatment had no significant impact on oxidative stress, immunity, and gut integrity related genes analyzed in jejunal tissues on d 28 and d 35, except downregulation of IFNγ on d 35 (P = 0.052). LEfSe analysis revealed that Lachnospiraceae FE2018 and Ruminococcaceae NK4A214 groups was enriched in the Vit E/Se birds on d 35. Moreover, PICRUSt analysis predicted significant functional differences among the treatment groups. In conclusion, dietary supplementation of Vit E/Se mitigated the negative effects of HS potentially via improving antioxidant status, regulating cytokine responses and modifying ileal microbiota and its function.

Health Benefits of Probiotics in Sport and Exercise - Non-existent or a Matter of Heterogeneity? A Systematic Review

Background

The use of probiotics in sports has been growing in recent years, as up to 50% of athletes suffer from training- and performance-limiting gastrointestinal (GI) problems. Moreover, repeated exhaustive exercise and high training loads may lead to a transiently depressed immune function, associated with an increased risk of upper respiratory tract infection (URTI).

Aim

To provide a qualitative analysis of probiotic effects on URTI, GI symptoms and the immune system in healthy individuals under consideration of performance level as main classifier.

Methods

A systematic review of the literature was conducted (PubMed, SPORTDiscus with Full Text, Web of Science) to analyze the effects of probiotics in athletes and healthy active individuals on GI problems, URTI, and the immune system. A qualitative synthesis with performance level and treatment duration as main classifiers was performed.

Results

Of 41 eligible studies, 24 evaluated the effects of probiotic supplements in athletes, 10 in recreationally active individuals and 7 in healthy untrained adults. Large heterogeneity was observed in terms of probiotic strains, mode of delivery, performance level, treatment duration and outcome assessment. Overall, studies provided inconsistent observations.

Conclusion

The effects of probiotics on immune system, URTI, and GI symptoms in athletes, healthy adults and recreationally active individuals remain inconclusive. Based on the analyzed studies and identified parameters, this article provides suggestions to align future research on the effects of probiotics in exercise.

Systematic Review Registration

PROSPERO, identifier: CRD42021245840.

The Nutrition-Microbiota-Physical Activity Triad: An Inspiring New Concept for Health and Sports Performance

The human gut microbiota is currently the focus of converging interest in many diseases and sports performance. This review presents gut microbiota as a real “orchestra conductor” in the host’s physio(patho)logy due to its implications in many aspects of health and disease. Reciprocally, gut microbiota composition and activity are influenced by many different factors, such as diet and physical activity. Literature data have shown that macro- and micro-nutrients influence gut microbiota composition. Cumulative data indicate that gut bacteria are sensitive to modulation by physical activity, as shown by studies using training and hypoactivity models. Sports performance studies have also presented interesting and promising results. Therefore, gut microbiota could be considered a “pivotal” organ for health and sports performance, leading to a new concept: the nutrition-microbiota-physical activity triad. The next challenge for the scientific and medical communities is to test this concept in clinical studies. The long-term aim is to find the best combination of the three elements of this triad to optimize treatments, delay disease onset, or enhance sports performance. The many possibilities offered by biotic supplementation and training modalities open different avenues for future research.

Vaccines, Microbiota and Immunonutrition: Food for Thought

Vaccines are among the most effective health measures and have contributed to eradicating some diseases. Despite being very effective, response rates are low in some individuals. Different factors have been proposed to explain why some people are not as responsive as others, but what appears to be of critical importance is the presence of a healthy functioning immune system. In this respect, a key factor in modulating the immune system, both in its adaptive and innate components, is the microbiota. While microbiota can be modulated in different ways (i.e., antibiotics, probiotics, prebiotics), an effective and somewhat obvious mechanism is via nutrition. The science of nutrients and their therapeutic application is called immunonutrition, and it is increasingly being considered in several conditions. Our review will focus on the importance of nutrition and microbiota modulation in promoting a healthy immune system while also discussing the overall impact on vaccination response.

Gut microbiota and vitamin status in persons with obesity: A key interplay

There are numerous factors involved in obesity progression and maintenance including systemic low-grade inflammation, adipose tissue dysfunction, or gut microbiota dysbiosis. Recently, a growing interest has arisen for vitamins' role in obesity and related disorders, both at the host and gut bacterial level. Indeed, vitamins are provided mostly by food, but some, from the B and K groups in particular, can be synthesized by the gut bacterial ecosystem and absorbed in the colon. Knowing that vitamin deficiency can alter many important cellular functions and lead to serious health issues, it is important to carefully monitor the vitamin status of patients with obesity and potentially already existing comorbidities as well as to examine the dysbiotic gut microbiota and thus potentially altered bacterial metabolism of vitamins. In this review, we examined both murine and human studies, to assess the prevalence of sub-optimal levels of several vitamins in obesity and metabolic alterations. This review also examines the relationship between vitamins and the gut microbiota in terms of vitamin production and the modulation of the gut bacterial ecosystem in conditions of vitamin shortage or supplementation. Furthermore, some strategies to improve vitamin status of patients with severe obesity are proposed within this review.

The impact of a competitive event and the efficacy of a lactic acid bacteria-fermented soymilk extract on the gut microbiota and urinary metabolites of endurance athletes: An open-label pilot study

Diet and exercise can alter the gut microbiota, but recent studies have assessed the impact of athletic competition on gut microbiota and host metabolites. We designed an open-label pilot study to investigate the effects of both official competition and a multi-strain lactic acid bacteria-fermented soymilk extract (LEX) on the gut microbiota in Japanese college endurance athletes. The analysis of fecal 16S rRNA metagenome and urinary metabolites was used to identify changes in gut microbiota composition and host metabolism. When the fecal microbiota were investigated before and after a race without using of a supplement (pre-observation period), there was an increase in the phylum Firmicutes and decrease in Bacteroidetes. However, no changes in these phyla were seen before and after a race in those who consumed LEX. Before and after LEX ingestion, changes in urinary metabolites included a significant reduction in yeast and fungal markers, neurotransmitters, and mitochondrial metabolites including the TCA cycle. There were several correlations between urinary metabolites and the composition of fecal microbiota. For example, the level of tricarballylic acid was positively correlated with the composition ratio of phylum Firmicutes (Pearson's r = 0.66; p < 0.01). The bacterial species Parabacteroides distasonis was also found to correlate moderately with several urinary metabolites. These findings suggest two possibilities. First, endurance athletes experience significant fluctuations in gut microbiota after a single competition. Second, LEX ingestion may improve yeast and fungal overgrowth in the gastrointestinal tract and enhancing mitochondrial metabolic function.

Gut Microbiota and Short Chain Fatty Acids: Implications in Glucose Homeostasis

Gut microbiota encompasses a wide variety of commensal microorganisms consisting of trillions of bacteria, fungi, and viruses. This microbial population coexists in symbiosis with the host, and related metabolites have profound effects on human health. In this respect, gut microbiota plays a pivotal role in the regulation of metabolic, endocrine, and immune functions. Bacterial metabolites include the short chain fatty acids (SCFAs) acetate (C2), propionate (C3), and butyrate (C4), which are the most abundant SCFAs in the human body and the most abundant anions in the colon. SCFAs are made from fermentation of dietary fiber and resistant starch in the gut. They modulate several metabolic pathways and are involved in obesity, insulin resistance, and type 2 diabetes. Thus, diet might influence gut microbiota composition and activity, SCFAs production, and metabolic effects. In this narrative review, we discuss the relevant research focusing on the relationship between gut microbiota, SCFAs, and glucose metabolism.

Are We What We Eat? Impact of Diet on the Gut-Brain Axis in Parkinson's Disease

Parkinson’s disease is characterized by motor and non-motor symptoms, such as defects in the gut function, which may occur before the motor symptoms. To date, there are therapies that can improve these symptoms, but there is no cure to avoid the development or exacerbation of this disorder. Dysbiosis of gut microbiota could have a crucial role in the gut–brain axis, which is a bidirectional communication between the central nervous system and the enteric nervous system. Diet can affect the microbiota composition, impacting gut–brain axis functionality. Gut microbiome restoration through probiotics, prebiotics, synbiotics or other dietary means could have the potential to slow PD progression. In this review, we will discuss the influence of diet on the bidirectional communication between gut and brain, thus supporting the hypothesis that this disorder could begin in the gut. We also focus on how food-based therapies might then have an influence on PD and could ameliorate non-motor as well as motor symptoms.

Gut Microbiome in Retina Health: The Crucial Role of the Gut-Retina Axis

The term microbiome means not only a complex ecosystem of microbial species that colonize our body but also their genome and the surrounding environment in which they live. Recent studies support the existence of a gut-retina axis involved in the pathogenesis of several chronic progressive ocular diseases, including age-related macular disorders. This review aims to underline the importance of the gut microbiome in relation to ocular health. After briefly introducing the characteristics of the gut microbiome in terms of composition and functions, the role of gut microbiome dysbiosis, in the development or progression of retinal diseases, is highlighted, focusing on the relationship between gut microbiome composition and retinal health based on the recently investigated gut-retina axis.

Association between Fecal Short-Chain Fatty Acid Levels, Diet, and Body Mass Index in Patients with Inflammatory Bowel Disease

Simple Summary

Inflammatory bowel disease (IBD) is a chronic disorder of the gastrointestinal tract associated with gut inflammation and a disturbance in the amount of bacteria living in the human intestines. As a result, there is a reduction in the production of bacterial metabolites, especially short-chain fatty acids (SCFAs), which are formed from dietary fiber. The aim of our study was to assess the relationship between body mass index (BMI), the type of diet used, and changes in fecal SCFA levels in patients with IBD. We enrolled 61 patients with IBD and 16 patients as a control group. We asked all participants about their daily diet, using the simplified FF questionnaire, and measured the levels of SCFA in their stool samples. Our results revealed that underweight subjects had higher levels of isobutyric acid, whereas those with excessive weight had lower level of butyric, isovaleric, and propionic acids. Furthermore, we observed higher levels of valeric acid in controls than in IBD patients. However, we did not observe a relationship between diet habits and fecal SCFA levels. In conclusion, we demonstrated that BMI is associated with SCFA levels in patients with IBD.

Abstract

Disturbances in the production of bacterial metabolites in the intestine have been reported in diseases associated with dysbiosis, such as inflammatory bowel diseases (IBDs) that include two conditions: Crohn disease (CD) and ulcerative colitis (UC). Short-chain fatty acids (SCFAs) are the main dietary-fiber-derived bacterial metabolites associated with the course of intestinal inflammation. In this study, we assessed the relationship between body mass index (BMI), the type of diet used, and changes in fecal SCFA levels in patients with IBD. We performed nutritional assessments using a nutritional questionnaire and determined fecal SCFA levels in 43 patients with UC, 18 patients with CD, and 16 controls. Our results revealed that subjects with a BMI > 24.99 kg/m² had higher levels of isobutyric acid, whereas those with a BMI < 18.5 kg/m² had lower level of butyric, isovaleric, and propionic acids. Furthermore, we observed higher levels of valeric acid in controls than in IBD patients. We did not reveal a relationship between a specific SCFA and the type of diet, but eating habits appear to be related to the observed changes in the SCFA profile depending on BMI. In conclusion, we demonstrated that BMI is associated with SCFA levels in patients with IBD.

Musings in the twilight of my career

I present a summary of my research during the last few decades of research which focused on understanding the biochemical basis for maintaining an optimum metabolism to support long-term health. I realized that adequate levels of ∼40 vitamins and minerals needed as cofactors in thousands of metabolic reactions were critical for maintaining a healthy metabolism, and thus for longevity and prevention of chronic disease. Inadequate dietary intake of vitamins and minerals accelerates the risk of aging-associated diseases, leading to insidious damage. The Triage Theory provides a mechanistic rationale for such damage: shortage of a nutrient triggers a built-in rationing mechanism that allocates the scarce nutrient to proteins needed for immediate survival (survival proteins), at the expense of those needed for long-term survival (longevity proteins). Many as-yet-unknown longevity vitamins and proteins likely remain to be discovered. The fiber and nutrient-rich CHORI-bar was developed to fill gaps in inadequate diets; it yielded broadscale metabolic improvements. The health-related damages resulting from vitamin D deficiency and the positive effects of vitamin D supplementation were connected to numerous health-related problems, including the higher level of deficiency in people of color residing at northern latitudes. In general, prevention of degenerative diseases of aging requires expertise in metabolism, nutrition, biochemistry and regulatory functions.

The benefits of the Mediterranean diet in first episode psychosis patients taking antipsychotics

Background

The side effects of antipsychotics (APs), related to weight gain and metabolic disturbances, can contribute to the health burden of psychotic people.

Objective

To explore a) the level of adherence to the Mediterranean Diet (MedDiet) and consumption of fermented foods by first episode of psychosis (FEPs) patients taking APs, in comparison to matched -for age and BMI- healthy controls (HCs), and b) the effect of this dietary pattern on the biochemical and metabolic profile of FEPs.

Method

The study population consisted of 33 FEPs treated with APs for less than 5 years, with no history of other chronic diseases, and an equal number of HCs. The FEPs were classified into two subgroups, according to their AP medication, depending on the documented risk of weight gain. A validated questionnaire for the adherence to Mediterranean diet and a food frequency questionnaire for selected fermented foods were completed by FEPs and HC. Anthropometric data and blood measurements were recorded for all participants.

Results and conclusions

The FEPs showed a relevant lower overall adherence to the MedDiet, but no differences in consumption of fermented foods. Type of antipsychotic therapy uncovered differences in platelet count, vitamin B12, HDL and glucose (p < 0.05) between the subgroups of FEPs and HCs, although no values were abnormal. The MedDiet score was found to act as a prognostic factor for abnormal glucose levels in FEPs treated with APs associated with weight gain (p = 0.04). These results need to be confirmed by observations after long term adherence to MedDiet.

Diet and gut microbiome in fatty liver and its associated liver cancer

Non-alcoholic fatty liver disease (NAFLD) is the major cause of chronic liver disease worldwide as a consequence of a sedentary lifestyle and overnutrition. NAFLD could progress to non-alcoholic steatohepatitis (NASH), which may further develop to cirrhosis and hepatocellular carcinoma (HCC). The gut microbiome is one of the central regulators in host metabolism. Diet could change human gut microbiome rapidly and reproducibly and modulate several metabolic pathways. Both diet and gut microbiome dysbiosis are associated with NAFLD and its related HCC (NAFLD-HCC). Dietary cholesterol, fiber, fat, or carbohydrate could change the microbiome composition to contribute to the development of NASH and NAFLD-HCC. Hence, identification of elements of the gut-liver axis that are primarily damaged in NASH and NAFLD-HCC offers new possibility for therapeutic intervention. In this review, the roles of gut microbiome and microbial metabolites in the development and progression of NAFLD and NAFLD-HCC are first discussed. The impacts of different diet compositions including cholesterol, fiber, fat, and sugar on the gut microbiome that leads to predisposition to NASH and NAFLD-HCC are also explored. We summarized the article by discussing potential therapeutic implication of diet and microbiome modulation in fatty liver and liver cancer.

Large-scale correlation analysis of deep venous thrombosis and gut microbiota

Objective

Although previous studies have shown that gut microbiota may be involved in the occurrence of deep venous thrombosis (DVT), the specific link between the two remains unclear. The present study aimed to explore this question from a genetic perspective.

Materials and methods

Genome-wide association study (GWAS) summary data of DVT were obtained from the UK Biobank (N = 9,059). GWAS summary data of the gut microbiota were obtained from the Flemish Gut Flora Project (N = 2,223) and two German cohorts (FoCus, N = 950; PopGen, N = 717). All the participants were of European ancestry. Linkage disequilibrium score (LDSC) regression has great potential for analyzing the heritability of disease or character traits. LDSC regression was used to analyze the genetic correlation between DVT and the gut microbiota based on the GWAS summary data obtained from previous studies. Mendelian randomization (MR) was used to analyze the genetic causal relationship between DVT and the gut microbiota. We used the random effects inverse variance weighted, MR Egger, weighted median, simple mode, and weighted mode to perform MR analysis. We performed a sensitivity analysis of the MR analysis results by examining heterogeneity and horizontal pleiotropy.

Results

Linkage disequilibrium score analysis showed that Streptococcaceae (correlation coefficient = -0.542, SE = 0.237, P = 0.022), Dialister (correlation coefficient = -0.623, SE = 0.316, P = 0.049), Streptococcus (correlation coefficient = -0.576, SE = 0.264, P = 0.029), and Lactobacillales (correlation coefficient = -0.484, SE = 0.237, P = 0.042) had suggestive genetic correlation with DVT. In addition, the MR analysis showed that Streptococcaceae had a positive genetic causal relationship with DVT (P = 0.027, OR = 1.005). There was no heterogeneity or horizontal pleiotropy in the MR analysis (P > 0.05).

Conclusion

In this study, four gut microbes (Streptococcaceae, Dialister Streptococcus, Lactobacillales) had suggestive genetic correlations with DVT, and Streptococcaceae had a positive causal relationship with DVT. Our findings provide a new research direction for the further study of and prevention of DVT.

Taxonomy and Functional Diversity in the Fecal Microbiome of Beef Cattle Reared in Brazilian Traditional and Semi-Intensive Production Systems

The importance of beef production for economy of Brazil and the growing demand for animal protein across the globe warrant an improvement in the beef production system. Although most attention has been on modulation of the rumen microbiome to improve ruminant production, the role of the lower gut microbiome in host health and nutrition remains relatively unexplored. This work aimed to investigate the taxonomy and functional variations in the fecal microbiome of Brazilian beef cattle reared in two different production systems using a metagenomic approach. Sixty male beef cattle from six farms representing semi-intensive (I, n = 2) and traditional (T, n = 4) Brazilian beef production systems were enrolled in the study. Shotgun sequencing was used to characterize taxonomic and functional composition and diversity of the microbiome in fecal samples collected from each animal. Fecal samples were analyzed for copper (Cu), lead (Pb), nitrogen (N), phosphorous (P), selenium (Se), and zinc (Zn) and stable isotopes of carbon (¹³C) and nitrogen (¹⁵N). The fecal microbiome was influenced by the beef production systems with greater functional and lower taxonomic diversity in beef cattle feces from I systems compared with that from T systems. The concentration of N, P, and Zn was higher in beef cattle feces from I systems compared with that from T systems and was associated with taxonomic and functional profile of fecal microbiome in I system, suggesting the role of fecal nutrients in shaping system-specific microbiome. Semi-intensive management practices led to a more complex but less connected fecal microbiome in beef cattle. The microbial community in beef cattle feces from I systems was characterized by greater abundance of beneficial bacteria (phylum Firmicutes and butyrate-producing bacteria family Lachnospiraceae and genera Anaerostipes, Blautia, Butyrivibrio, Eubacterium, Roseburia, and Ruminococcus). In addition, the fecal abundance of microbial genes related to immune system, nutrient metabolism, and energy production was greater in beef cattle raised under I systems compared with that under T systems. Findings of the current study suggest that semi-intensive management practices could facilitate the development of a healthier and more efficient fecal microbiome in beef cattle by driving an increase in the abundance of beneficial bacteria and functional genes.

Djulis Hull Improves Insulin Resistance and Modulates the Gut Microbiota in High-Fat Diet (HFD)-Induced Hyperglycaemia

In this study, we annotated the major flavonoid glycoside, rutin, of djulis hull crude extract using a Global Natural Products Social Molecular Networking (GNPS) library and its MS/MS spectra. To evaluate the protective effect of djulis hull crude extract and rutin on glucose tolerance, we fed mice a high-fat diet (HFD) for 16 weeks to induce hyperglycaemia. These results showed that crude extract significantly decreased HFD-induced elevation in the area under the curve (AUC) of weekly random blood glucose and oral glucose tolerance tests (OGTT), homeostasis model assessment (HOMA-IR), and advanced glycation end product (AGE) levels, and significantly increased pIRS1 and Glut4 protein expression in epididymal white adipose tissue (eWAT) and liver. Furthermore, the HFD-induced reduction in the activity of glutathione peroxidase (GPx) and catalase (CAT) was reversed by crude extract. In addition, ZO-1 and occludin protein expression in the colon was markedly downregulated in HFD-fed mice, resulting in decreased intestinal permeability and lipopolysaccharide (LPS) translocation, but were restored following crude extract. Moreover, the crude extract intervention had a profound effect on the alpha diversity and microbial community in the gut microbiota. Therefore, djulis hull crude extract could improve blood glucose and increase insulin receptor sensitivity in HFD-induced hyperglycaemia, which is likely due to its modulation of the gut microbiota, preservation of the integrity of the intestinal barrier to reduce body inflammation, increased antioxidant activity, and modulation of insulin signalling.

Sleep, circadian rhythm and gut microbiota: alterations in Alzheimer's disease and their potential links in the pathogenesis

ABSTRATCIn recent years, emerging studies have observed gut microbiota (GM) alterations in Alzheimer's disease (AD), even in individuals with mild cognitive impairment (MCI). Further, impaired sleep and circadian patterns are common symptoms of AD, while sleep and circadian rhythm disruption (SCRD) is associated with greater β-amyloid (Aβ) burden and AD risk, sometimes years before the clinical onset of AD. Moreover, reports have demonstrated that GM and its metabolites exhibit diurnal rhythmicity and the role of SCRD in dampening the GM rhythmicity and eubiosis. This review will provide an evaluation of clinical and animal studies describing GM alterations in distinct conditions, including AD, sleep and circadian disruption. It aims to identify the overlapping and distinctive GM alterations in these conditions and their contributions to pathophysiology. Although most studies are observational and use different methodologies, data indicate partial commonalities in GM alterations and unanimity at functional level. Finally, we discuss the possible interactions between SCRD and GM in AD pathogenesis, as well as several methodological improvements that are necessary for future research.

Insights into Health-Promoting Effects of Plant MicroRNAs: A Review

Plant-derived microRNAs (miRNAs) play a significant role in human health and are "dark nutrients", as opposed to traditional plant nutrients, as well as important components of food diversification. Studies have revealed that multiple plant-derived miRNA pathways affect human health. First, plant miRNAs regulate plant growth and development and accumulation of metabolites, which alters the food quality and thus indirectly interferes with the health of the host. Moreover, when absorbed in vivo, some miRNAs may target the host cell mRNAs to affect protein expression. In addition, plant miRNAs target and reshape the human gut microbiota (GM), which interferes with the physiology and metabolism of the host. Therefore, miRNAs play a significant role in the cross-kingdom communication of plants, GM, and the host and in maintaining a balance of the three. Future contributions of plant miRNAs can bring new perspectives and opportunities to better understand food nutrition and health care research, which will facilitate the right exploitation of plant resources.

Next-generation microbial drugs developed from microbiome's natural products

Scientists working in natural products chemistry have been enticed by the current advancements being made in the discovery of novel "magic bullets" from microbes homed to all conceivable environments. Even though researchers continue to face challenges funneling the novel bioactive compounds in the global therapeutic industries, it seems most likely that the discovery of some "hit molecules" with significant biomedical applications is not that far. We applaud novel natural products for their ability to combat the spread of superbugs and aid in the prevention of currently observed antibiotic resistance. This in-depth investigation covers a wide range of microbiomes with a proclivity for synthesizing novel compounds to combat the spread of superbugs. Furthermore, we use this opportunity to explore various groups of secondary metabolites and their biosynthetic pathways in various microbiota found in mammals, insects, and humans. This systematic study, when taken as a whole, offers detail understanding on the biomedical fate of various groups of compounds originated from diverse microbiomes. For gathering all information that has been uncovered and released so far, we have also presented the huge diversity of microbes that are associated with humans and their metabolic products. To conclude, this concrete review suggests novel ideas that will prove immensely helpful in reducing the danger posed by superbugs while also improving the efficacy of antibiotics.

The Use of Mushrooms and Spirulina Algae as Supplements to Prevent Growth Inhibition in a Pre-Clinical Model for an Unbalanced Diet

Today’s eating patterns are characterized by the consumption of unbalanced diets (UBDs) resulting in a variety of health consequences on the one hand, and the consumption of dietary supplements in order to achieve overall health and wellness on the other. Balanced nutrition is especially crucial during childhood and adolescence as these time periods are characterized by rapid growth and development of the skeleton. We show the harmful effect of UBD on longitudinal bone growth, trabecular and cortical bone micro-architecture and bone mineral density; which were analyzed by micro-CT scanning. Three point bending tests demonstrate the negative effect of the diet on the mechanical properties of the bone material as well. Addition of Spirulina algae or Pleurotus eryngii or Agaricus bisporus mushrooms, to the UBD, was able to improve growth and impaired properties of the bone. 16SrRNA Sequencing identified dysbiosis in the UBD rats’ microbiota, with high levels of pro-inflammatory associated bacteria and low levels of bacteria associated with fermentation processes and bone related mechanisms. These results provide insight into the connection between diet, the skeletal system and the gut microbiota, and reveal the positive impact of three chosen dietary supplements on bone development and quality presumably through the microbiome composition.

Parsed synthesis of pyocyanin via co-culture enables context-dependent intercellular redox communication

Background

Microbial co-cultures and consortia are of interest in cell-based molecular production and even as “smart” therapeutics in that one can take advantage of division of labor and specialization to expand both the range of available functions and mechanisms for control. The development of tools that enable coordination and modulation of consortia will be crucial for future application of multi-population cultures. In particular, these systems would benefit from an expanded toolset that enables orthogonal inter-strain communication.

Results

We created a co-culture for the synthesis of a redox-active phenazine signaling molecule, pyocyanin (PYO), by dividing its synthesis into the generation of its intermediate, phenazine carboxylic acid (PCA) from the first strain, followed by consumption of PCA and generation of PYO in a second strain. Interestingly, both PCA and PYO can be used to actuate gene expression in cells engineered with the soxRS oxidative stress regulon, although importantly this signaling activity was found to depend on growth media. That is, like other signaling motifs in bacterial systems, the signaling activity is context dependent. We then used this co-culture’s phenazine signals in a tri-culture to modulate gene expression and production of three model products: quorum sensing molecule autoinducer-1 and two fluorescent marker proteins, eGFP and DsRed. We also showed how these redox-based signals could be intermingled with other quorum-sensing (QS) signals which are more commonly used in synthetic biology, to control complex behaviors. To provide control over product synthesis in the tri-cultures, we also showed how a QS-induced growth control module could guide metabolic flux in one population and at the same time guide overall tri-culture function. Specifically, we showed that phenazine signal recognition, enabled through the oxidative stress response regulon soxRS, was dependent on media composition such that signal propagation within our parsed synthetic system could guide different desired outcomes based on the prevailing environment. In doing so, we expanded the range of signaling molecules available for coordination and the modes by which they can be utilized to influence overall function of a multi-population culture.

Conclusions

Our results show that redox-based signaling can be intermingled with other quorum sensing signaling in ways that enable user-defined control of microbial consortia yielding various outcomes defined by culture medium. Further, we demonstrated the utility of our previously designed growth control module in influencing signal propagation and metabolic activity is unimpeded by orthogonal redox-based signaling. By exploring novel multi-modal strategies for guiding communication and consortia outcome, the concepts introduced here may prove to be useful for coordination of multiple populations within complex microbial systems.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01703-2.

Untargeted Gut Metabolomics to Delve the Interplay between Selenium Supplementation and Gut Microbiota

Selenium (Se) is an essential trace element with important health roles due to the antioxidant properties of selenoproteins. To analyze the interplay between Se and gut microbiota, gut metabolomic profiles were determined in conventional (C) and microbiota depleted mice (Abx) after Se-supplementation (Abx-Se) by untargeted metabolomics, using an analytical multiplatform based on GC-MS and UHPLC-QTOF-MS (MassIVE ID MSV000087829). Gut microbiota profiling was performed by 16S rRNA gene amplicon sequencing. Significant differences in the levels of about 70% of the gut metabolites determined, including fatty acyls, glycerolipids, glycerophospholipids, and steroids, were found in Abx-Se compared to Abx, and only 30% were different between Abx-Se and C, suggesting an important effect of Se-supplementation on Abx mice metabolism. At genus level, the correlation analysis showed strong associations between metabolites and gut bacterial profiles. Likewise, higher abundance of Lactobacillus spp., a potentially beneficial genus enriched after Se-supplementation, was associated with higher levels of prenol lipids, phosphatidylglycerols (C-Se), steroids and diterpenoids (Abx-Se), and also with lower levels of fatty acids (Abx-Se). Thus, we observed a crucial interaction between Se intake-microbiota-metabolites, although further studies to clarify the specific mechanisms are needed. This is the first study about untargeted gut metabolomics after microbiota depletion and Se-supplementation.

Dietary calcium phosphate strongly impacts gut microbiome changes elicited by inulin and galacto-oligosaccharides consumption

BACKGROUND

Fructo-oligosaccharides (FOS), inulin, and galacto-oligosaccharides (GOS) are widely recognized prebiotics that profoundly affect the intestinal microbiota, including stimulation of bifidobacteria and lactobacilli, and are reported to elicit several health benefits. The combination of dietary FOS and inulin with calcium phosphate was reported to stimulate commensal Lactobacillus populations and protect the host against pathogenic Enterobacteriaceae, but little is known about the effects of GOS in diets with a different level of calcium phosphate.

METHODS

We investigated the microbiome changes elicited by dietary supplementation with GOS or inulin using diets with high (100 mmol/kg) and low (30 mmol/kg) calcium phosphate levels in adult Wistar rats. Rats were acclimatized to the respective experimental diets for 14 days, after which fecal material was collected, DNA was extracted from fecal material, and the V3‑V4 region of the bacterial 16S rRNA gene was amplified with PCR, followed by microbial composition analysis. In tandem, the organic acid profiles of the fecal material were analyzed.

RESULTS

Feeding rats non-supplemented (no prebiotic-added) diets revealed that diets rich in calcium phosphate favored members of the Firmicutes and increased fecal lactic, succinic, acetic, propionic, and butyric acid levels. In contrast, relatively low dietary calcium phosphate levels promoted the abundance of mucin degrading genera like Akkermansia and Bacteroides, and resulted in increased fecal propionic acid levels and modest increases in lactic and butyric acid levels. Irrespective of the calcium phosphate levels, supplementation with GOS or inulin strongly stimulated Bifidobacterium, while only high calcium phosphate diets increased the endogenous Faecalibaculum populations.

CONCLUSIONS

Despite the prebiotic's substantial difference in chemical structure, sugar composition, oligomer size, and the microbial degradation pathway involved in their utilization, inulin and GOS modulated the gut microbiota very similarly, in a manner that strongly depended on the dietary calcium phosphate level. Therefore, our study implies that the collection of detailed diet information including micronutrient balance is necessary to correctly assess diet-driven microbiota analysis. Video Abstract.

High association of COVID-19 severity with poor gut health score in Lebanese patients

Background

Coronavirus disease 2019 (COVID-19) has affected millions of lives globally. However, the disease has presented more extreme challenges for developing countries that are experiencing economic crises. Studies on COVID-19 symptoms and gut health are scarce and have not fully analyzed possible associations between gut health and disease pathophysiology. Therefore, this study aimed to demonstrate a potential association between gut health and COVID-19 severity in the Lebanese community, which has been experiencing a severe economic crisis.

Methods

This cross-sectional study investigated SARS-CoV-2 PCR-positive Lebanese patients. Participants were interviewed and gut health, COVID-19 symptoms, and different metrics were analyzed using simple and multiple logistic regression models.

Results

Analysis of the data showed that 25% of participants were asymptomatic, while an equal proportion experienced severe symptoms, including dyspnea (22.7%), oxygen need (7.5%), and hospitalization (3.1%). The mean age of the participants was 38.3 ±0.8 years, and the majority were males (63.9%), married (68.2%), and currently employed (66.7%). A negative correlation was found between gut health score and COVID-19 symptoms (Kendall’s tau-b = -0.153, P = 0.004); indicating that low gut health was associated with more severe COVID-19 cases. Additionally, participants who reported unhealthy food intake were more likely to experience severe symptoms (Kendall’s tau-b = 0.118, P = 0.049). When all items were taken into consideration, multiple ordinal logistic regression models showed a significant association between COVID-19 symptoms and each of the following variables: working status, flu-like illness episodes, and gut health score. COVID-19 severe symptoms were more common among patients having poor gut health scores (OR:1.31, 95%CI:1.07–1.61; P = 0.008), experiencing more than one episode of flu-like illness per year (OR:2.85, 95%CI:1.58–5.15; P = 0.001), and owning a job (OR:2.00, 95%CI:1.1–3.65; P = 0.023).

Conclusions

To our knowledge, this is the first study that showed the impact of gut health and exposure to respiratory viruses on COVID-19 severity in Lebanon. These findings can facilitate combating the pandemic in Lebanon.

Intestinal microbiota as a route for micronutrient bioavailability

The deficiency of micronutrients, including vitamins and minerals, is estimated to affect two billion people worldwide and can have devastating immediate and long-term consequences. Major causes range from inadequate micronutrient consumption mostly owing to a lack of dietary diversity, to poor nutrient absorption in the gastrointestinal tract as a result of clinical or pathological conditions. Recent studies in model organisms and humans demonstrated that intestinal microbiota plays an important role in the de novo biosynthesis and bioavailability of several micronutrients and might be a major determinant of human micronutrient status. Here, we address the importance of the gut microbiome for maintaining the balance of host vitamins and minerals and explore its potential therapeutic benefits and implications on human health.

Pathobiological Relationship of Excessive Dietary Intake of Choline/L-Carnitine: A TMAO Precursor-Associated Aggravation in Heart Failure in Sarcopenic Patients

The microecological environment of the gastrointestinal tract is altered if there is an imbalance between the gut microbiota phylases, resulting in a variety of diseases. Moreover, progressive age not only slows down physical activity but also reduces the fat metabolism pathway, which may lead to a reduction in the variety of bacterial strains and bacteroidetes' abundance, promoting firmicutes and proteobacteria growth. As a result, dysbiosis reduces physiological adaptability, boosts inflammatory markers, generates ROS, and induces the destruction of free radical macromolecules, leading to sarcopenia in older patients. Research conducted at various levels indicates that the microbiota of the gut is involved in pathogenesis and can be considered as the causative agent of several cardiovascular diseases. Local and systematic inflammatory reactions are caused in patients with heart failure, as ischemia and edema are caused by splanchnic hypoperfusion and enable both bacterial metabolites and bacteria translocation to enter from an intestinal barrier, which is already weakened, to the blood circulation. Multiple diseases, such as HF, include healthy microbe-derived metabolites. These key findings demonstrate that the gut microbiota modulates the host's metabolism, either specifically or indirectly, by generating multiple metabolites. Currently, the real procedures that are an analogy to the symptoms in cardiac pathologies, such as cardiac mass dysfunctions and modifications, are investigated at a minimum level in older patients. Thus, the purpose of this review is to summarize the existing knowledge about a particular diet, including trimethylamine, which usually seems to be effective for the improvement of cardiac and skeletal muscle, such as choline and L-carnitine, which may aggravate the HF process in sarcopenic patients.

The Nasopharyngeal, Ruminal, and Vaginal Microbiota and the Core Taxa Shared across These Microbiomes in Virgin Yearling Heifers Exposed to Divergent In Utero Nutrition during Their First Trimester of Gestation and in Pregnant Beef Heifers in Response to Mineral Supplementation

In the present study, we evaluated whether the nasopharyngeal, ruminal, and vaginal microbiota would diverge (1) in virgin yearling beef heifers (9 months old) due to the maternal restricted gain during the first trimester of gestation; and (2) in pregnant beef heifers in response to the vitamin and mineral (VTM) supplementation during the first 6 months of pregnancy. As a secondary objective, using the microbiota data obtained from these two cohorts of beef heifers managed at the same location and sampled at the same time, we performed a holistic assessment of the microbial ecology residing within the respiratory, gastrointestinal, and reproductive tract of cattle. Our 16S rRNA gene sequencing results revealed that both α and β-diversity of the nasopharyngeal, ruminal and vaginal microbiota did not differ between virgin heifers raised from dams exposed to either a low gain (targeted average daily gain of 0.28 kg/d, n = 22) or a moderate gain treatment (0.79 kg/d, n = 23) during the first 84 days of gestation. Only in the vaginal microbiota were there relatively abundant genera that were affected by maternal rate of gain during early gestation. Whilst there was no significant difference in community structure and diversity in any of the three microbiota between pregnant heifers received no VTM (n = 15) and VTM supplemented (n = 17) diets, the VTM supplementation resulted in subtle compositional alterations in the nasopharyngeal and ruminal microbiota. Although the nasopharyngeal, ruminal, and vaginal microbiota were clearly distinct, a total of 41 OTUs, including methanogenic archaea, were identified as core taxa shared across the respiratory, gastrointestinal, and reproductive tracts of both virgin and pregnant heifers.

Diet, Probiotics and Their Impact on the Gut Microbiota during the COVID-19 Pandemic

SARS-CoV-2 infection is associated with diverse clinical manifestations, immune dysfunction, and gut microbiota alterations. The nutritional and biochemical quality of one's diet can influence the intestinal microbiota, which may play a role in the defense mechanisms against potential pathogens, by promoting a wide variety of immune-host interactions. In the COVID-19 pandemic, besides the development of pharmacological therapies, a healthy balanced diet, rich with food-derived antioxidants, may be a useful strategy. Many studies demonstrated that vitamins and probiotic therapies have positive effects on the treatment and prevention of oxidative stress and inflammation in COVID-19. The ecology of the gut microbiota in the digestive tract has been linked to the transport function of the host receptor known as angiotensin converting enzyme 2 (ACE2), suggesting that COVID-19 may be related to the gut microbiota. The angiotensin converting enzyme (ACE), and its receptor (ACE2), play central roles in modulating the renin-angiotensin system (RAS). In addition, ACE2 has functions that act independently of the RAS. ACE2 is the receptor for the SARS coronavirus, and ACE2 is essential for the expression of neutral amino acid transporters in the gut. In this context, ACE2 modulates innate immunity and influences the composition of the gut microbiota. Malnutrition is one of the leading underlying causes of morbidity and mortality worldwide and, including comorbidities, may be a major cause of worse outcomes and higher mortality among COVID-19 patients. This paper reviews the research on dietary components, with particular emphasis on vitamins, antioxidants, and probiotic therapies, and their impacts on the intestinal microbiota's diversity during the SARS-CoV-2 pandemic.

The Challenge of ICIs Resistance in Solid Tumours: Could Microbiota and Its Diversity Be Our Secret Weapon?

The human microbiota and its functional interaction with the human body were recently returned to the spotlight of the scientific community. In light of the extensive implementation of newer and increasingly precise genome sequencing technologies, bioinformatics, and culturomic, we now have an extraordinary ability to study the microorganisms that live within the human body. Most of the recent studies only focused on the interaction between the intestinal microbiota and one other factor. Considering the complexity of gut microbiota and its role in the pathogenesis of numerous cancers, our aim was to investigate how microbiota is affected by intestinal microenvironment and how microenvironment alterations may influence the response to immune checkpoint inhibitors (ICIs). In this context, we show how diet is emerging as a fundamental determinant of microbiota’s community structure and function. Particularly, we describe the role of certain dietary factors, as well as the use of probiotics, prebiotics, postbiotics, and antibiotics in modifying the human microbiota. The modulation of gut microbiota may be a secret weapon to potentiate the efficacy of immunotherapies. In addition, this review sheds new light on the possibility of administering fecal microbiota transplantation to modulate the gut microbiota in cancer treatment. These concepts and how these findings can be translated into the therapeutic response to cancer immunotherapies will be presented.

New Approaches to Profile the Microbiome for Treatment of Neurodegenerative Disease

Progressive neurodegenerative diseases represent some of the largest growing treatment challenges for public health in modern society. These diseases mainly progress due to aging and are driven by microglial surveillance and activation in response to changes occurring in the aging brain. The lack of efficacious treatment options for Alzheimer's disease (AD), as the focus of this review, and other neurodegenerative disorders has encouraged new approaches to address neuroinflammation for potential treatments. Here we will focus on the increasing evidence that dysbiosis of the gut microbiome is characterized by inflammation that may carry over to the central nervous system and into the brain. Neuroinflammation is the common thread associated with neurodegenerative diseases, but it is yet unknown at what point and how innate immune function turns pathogenic for an individual. This review will address extensive efforts to identify constituents of the gut microbiome and their neuroactive metabolites as a peripheral path to treatment. This approach is still in its infancy in substantive clinical trials and requires thorough human studies to elucidate the metabolic microbiome profile to design appropriate treatment strategies for early stages of neurodegenerative disease. We view that in order to address neurodegenerative mechanisms of the gut, microbiome and metabolite profiles must be determined to pre-screen AD subjects prior to the design of specific, chronic titrations of gut microbiota with low-dose antibiotics. This represents an exciting treatment strategy designed to balance inflammatory microglial involvement in disease progression with an individual's manifestation of AD as influenced by a coercive inflammatory gut.

The plant secondary compound swainsonine reshapes gut microbiota in plateau pikas (Ochotona curzoniae)

Abstract

Plants produce various plant secondary compounds (PSCs) to deter the foraging of herbivorous mammals. However, little is known about whether PSCs can reshape gut microbiota and promote gut homeostasis of hosts. Using 16S rDNA sequencing to investigate the effects of PSCs on the gut microbiota of small herbivorous mammals, we studied plateau pikas (Ochotona curzoniae) fed diets containing swainsonine (SW) extracted from Oxytropis ochrocephala. Our results showed that both long- and short-term treatment of a single artificial diet in the laboratory significantly reduced alpha diversity and significantly affected beta diversity, core bacteria abundance, and bacterial functions in pikas. After SW was added to the artificial diet, the alpha diversity significantly increased in the long-term treatment, and core bacteria (e.g., Akkermansiaceae) with altered relative abundances in the two treatments showed no significant difference compared with pikas in the wild. The complexity of the co-occurrence network structure was reduced in the artificial diet, but it increased after SW was added in both treatments. Further, the abundances of bacteria related to altered alanine, aspartate, and glutamate metabolism in the artificial diet were restored in response to SW. SW further decreased the concentration of short-chain fatty acids (SCFAs) in both treatments. Our results suggest that PSCs play a key role in regulating gut microbiota community and intestinal homeostasis, thereby maintaining host health.

Key points

• Swainsonine improves the intestinal bacterial diversity of plateau pikas.

• Swainsonine promotes the recovery of core bacterial abundances in the gut of plateau pikas.

• Swainsonine promotes the restoration of intestinal bacterial functions of plateau pikas.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11478-6.

Contribution of Biotransformations Carried Out by the Microbiota, Drug-Metabolizing Enzymes, and Transport Proteins to the Biological Activities of Phytochemicals Found in the Diet

The consumption of dietary phytochemicals has been associated with several health benefits and relevant biological activities. It is postulated that biotransformations of these compounds regulated by the microbiota, Phase I/II reactions, transport proteins, and deconjugating enzymes contribute not only to their metabolic clearance but also, in some cases, to their bioactivation. A number of factors (age, genetics, sex, physiopathological conditions, and the interplay with other dietary phytochemicals) modulating metabolic activities are important sources and contributors to the interindividual variability observed in clinical studies evaluating the biological activities of phytochemicals. In this review, we discuss all the processes that can affect the bioaccessibility and beneficial effects of these bioactive compounds. Herein, we argue that the role of these factors must be further studied to correctly understand and predict the effects observed following the intake of phytochemicals. This is, in particular, with regard to in vitro investigations, which have shown great inconsistency with preclinical and clinical studies. The complexity of in vivo metabolic activity and biotransformation should therefore be considered in the interpretation of results in vitro and their translation to human physiopathology.

Long-term changes in the gut microbiota after triple therapy, sequential therapy, bismuth quadruple therapy and concomitant therapy for Helicobacter pylori eradication in Chinese children

BACKGROUND

We previously reported that the administration of 14-day standard triple therapy (TT), sequential therapy (ST), bismuth-based quadruple therapy (BT), and concomitant therapy (CT) as the first-line therapy for Helicobacter pylori infection in Chinese children achieved eradication rates of 74.1%, 69.5%, 89.8%, and 84.6%, respectively. In this follow-up study, we further evaluated the short- and long-term effects of the four regimens on the gut microbiota in these children.

METHODS

We prospectively recruited treatment-naïve children with H. pylori infection. Fecal samples were collected at week 0, 2, 6, and 52, and alterations in the gut microbiota were analyzed by 16S rRNA gene sequencing.

RESULTS

Sixty-three patients participated in this study (16 with TT, 15 with ST, 16 with BT and 16 with CT). At week 2, the alpha diversity (Shannon and Chao 1 index) was significantly reduced in the TT (p = 0.008, p < 0.001), ST (p < 0.001, p < 0.001), BT (p < 0.001, p < 0.001) and CT groups (p < 0.001, p < 0.001). Some changes persisted in the ST, BT, and CT groups at week 6, and all were restored (expect p = 0.02 with Chao 1 index in the CT group) at week 52. The beta diversity was significantly changed in the BT (p = 0.001) and CT groups (p = 0.001) 2 weeks post-eradication and restored 1 year after therapy. Immediately after therapy, the relative abundance of Proteobacteria was strikingly increased in the ST (p = 0.005), BT (p < 0.001) and CT groups (p < 0.001), and the genus-level analysis showed that the abundances of 23.1%, 43.3%, 78.6%, and 78% of the bacterial genera in the TT, ST, BT, and CT groups were significantly changed. All these changes returned to almost the pre-eradication level 1 year post-eradication.

CONCLUSION

Eradication of H. pylori infection can lead to transient dysbiosis of gut microbiota, and these changes almost recovered 1 year post-eradication, which indicates the long-term safety of H. pylori therapy.

Exploring the impact of gut microbiota and diet on breast cancer risk and progression

There is emerging evidence that resident microbiota communities, that is, the microbiota, play a key role in cancer outcomes and anticancer responses. Although this has been relatively well studied in colorectal cancer and melanoma, other cancers, such as breast cancer (BrCa), have been largely overlooked to date. Importantly, many of the environmental factors associated with BrCa incidence and progression are also known to impact the microbiota, for example, diet and antibiotics. Here, we explore BrCa risk factors from large epidemiology studies and microbiota associations, and more recent studies that have directly profiled BrCa patients' gut microbiotas. We also discuss how in vivo studies have begun to unravel the immune mechanisms whereby the microbiota may influence BrCa responses, and finally we examine how diet and specific nutrients are also linked to BrCa outcomes. We also consider future research avenues and important considerations with respect to study design and implementation, and we highlight some of the important unresolved questions, which currently limit our overall understanding of the mechanisms underpinning microbiota-BrCa responses.

Work Stress, Dysbiosis, and Immune Dysregulation: The Interconnected Triad in COVID-19 Infection in the Medical Team Staff - A Mini-Review

The COVID-19 pandemic has hit most of the communities around the globe. Earlier researches have reported the psychological effects of pandemics either on the general populations or on specific communities such as students and health professionals. A scanty number of papers have focused on the interaction among complex factors underlying the pathogenesis of the disease. In this review, we aimed to integrate the accessible data about the possible mechanistic processes predisposing to COVID-19 infection in the health professions. We summarized these factors as "stress, microbiota, and immunity triad." We utilized the PubMed database, Google, and Google Scholar search engines to search the literature related to combinations of these keywords: "pandemics, COVID-19, coronavirus, SARS-CoV2;" "gut microbiota, gut-lung axis, dysbiosis, nutrition;" "work stress, workload, health workers, health professions, and medical team;" and "immunity, cytokine storm, and viral load." We detected no discussions combining the suggested triad concerning the medical team personnel. We cast light, for the first time to our knowledge, on the potential pathogenic role of "stress, microbiota, and immunity triad" in COVID-19-infected health workers.

Impact of Antibiotic-Induced Depletion of Gut Microbiota and Selenium Supplementation on Plasma Selenoproteome and Metal Homeostasis in a Mice Model

Selenium (Se) is a micronutrient involved in important health functions and it has been suggested to shape gut microbiota. Limited information on Se assimilation by gut microbes and the possible link with selenoproteins are available. For this purpose, conventional and gut microbiota-depleted BALB/c mice were fed a Se-supplemented diet. The absolute quantification of mice plasma selenoproteins was performed for the first time using heteroatom-tagged proteomics. The gut microbiota profile was analyzed by 16S rRNA gene sequencing. Se-supplementation modulated the concentration of the antioxidant glutathione peroxidase and the Se-transporter selenoalbumin as well as the metal homeostasis, being influenced by microbiota disruption, which suggests an intertwined mechanism. Se also modulated microbiota diversity and richness and increased the relative abundance of some health-relevant taxa (e.g., families Christensenellaceae, Ruminococcaceae, and Lactobacillus genus). This study demonstrated the potential beneficial effects of Se on gut microbiota, especially after antibiotic-treatment and the first associations between specific bacteria and plasma selenoproteins.

Distinct Human Gut Microbial Taxonomic Signatures Uncovered With Different Sample Processing and Microbial Cell Disruption Methods for Metaproteomic Analysis

The use of metaproteomics for studying the human gut microbiota can shed light on the taxonomic profile and the functional role of the microbial community. Nevertheless, methods for extracting proteins from stool samples continue to evolve, in the pursuit of optimal protocols for moistening and dispersing the stool sample and for disrupting microbial cells, which are two critical steps for ensuring good protein recovery. Here, we evaluated different stool sample processing (SSP) and microbial cell disruption methods (CDMs). The combination of a longer disintegration period of the stool sample in a tube rotator with sonication increased the overall number of identified peptides and proteins. Proteobacteria, Bacteroidetes, Planctomycetes, and Euryarchaeota identification was favored by mechanical cell disruption with glass beads. In contrast, the relative abundance of Firmicutes, Actinobacteria, and Fusobacteria was improved when sonication was performed before bead beating. Tenericutes and Apicomplexa identification was enhanced by moistening the stool samples during processing and by disrupting cells with medium-sized glass beads combined with or without sonication. Human protein identifications were affected by sonication. To test the reproducibility of these gut metaproteomic analyses, we examined samples from six healthy individuals using a protocol that had shown a good taxonomic diversity and identification of proteins from Proteobacteria and humans. We also detected proteins involved in microbial functions relevant to the host and related mostly to specific taxa, such as B12 biosynthesis and short chain fatty acid (SCFA) production carried out mainly by members in the Prevotella genus and the Firmicutes phylum, respectively. The taxonomic and functional profiles obtained with the different protocols described in this work provides the researcher with valuable information when choosing the most adequate protocol for the study of certain pathologies under suspicion of being related to a specific taxon from the gut microbiota.

An evolutionary algorithm for designing microbial communities via environmental modification

Despite a growing understanding of how environmental composition affects microbial communities, it remains difficult to apply this knowledge to the rational design of synthetic multispecies consortia. This is because natural microbial communities can harbour thousands of different organisms and environmental substrates, making up a vast combinatorial space that precludes exhaustive experimental testing and computational prediction. Here, we present a method based on the combination of machine learning and metabolic modelling that selects optimal environmental compositions to produce target community phenotypes. In this framework, dynamic flux balance analysis is used to model the growth of a community in candidate environments. A genetic algorithm is then used to evaluate the behaviour of the community relative to a target phenotype, and subsequently adjust the environment to allow the organisms to approach this target. We apply this iterative process to thousands of in silico communities of varying sizes, showing how it can rapidly identify environments that yield desired taxonomic compositions and patterns of metabolic exchange. Moreover, this combination of approaches produces testable predictions for the assembly of experimental microbial communities with specific properties and can facilitate rational environmental design processes for complex microbiomes.

Probiotics as Adjunctive Treatment for Patients Contracted COVID-19: Current Understanding and Future Needs

The coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which rages all over the world and seriously threatens human life and health. Currently, there is no optimal treatment for COVID-19, and emerging evidence found that COVID-19 infection results in gut microbiota dysbiosis. The intestinal microbial richness of patients of COVID-19 does not return to normal levels even six months after recovery, but probiotic adjunctive treatment has been found to restore gut homeostasis. An updated PubMed search returned four finished clinical trials that supported the use of probiotics as adjunctive treatment for COVID-19, while at least six clinical trials aiming to investigate beneficial effects of probiotic intake in managing COVID-19 are currently in progress worldwide. Here in we tentatively summarized the understanding of the actions and potential mechanisms of probiotics in the management of COVID-19. We also highlighted some future needs for probiotic researchers in the field. The success in using probiotics as adjunctive treatment for COVID-19 has expanded the scope of application of probiotics, meanwhile deepening our knowledge in the physiological function of probiotics in modulating the gut-lung axis.

Autoimmunity and COVID-19 - The microbiotal connection

Background and aims

The novel SARS-CoV-2 has been rattling the world since its outbreak in December 2019, leading to the COVID-19 pandemic. The learning curve of this new virus has been steep, with a global scientific community desperate to learn how the virus is transmitted, how it replicates, why it causes such a wide spectrum of disease manifestations, resulting in none or few symptoms in some. Others are burdened by an intense immune response that resembles the cytokine storm syndrome (CSS), which leads to severe disease manifestations, often complicated by fatal acute respiratory distress syndrome and death. Research efforts have been focusing on finding effective cures and vaccinations for this virus.

The presence of SARS-CoV-2 in the gastrointestinal (GI) tract, represented by several GI manifestations, has led to its investigation as a target for the virus and as an indicator of disease severity. The response of the microbiome (which is heavily linked to immunity) to the novel SARS-CoV-2 virus, and its role in igniting the exaggerated immune response has therefore become a focus of interest. The objective of our study was to gather the data connecting between the microbiome, the GI tract and COVID-19 and to investigate whether these reported alterations in the gut microbiome bear any resemblance to those seen in lupus, the prototypical autoimmune disease. Confirming such changes may become the steppingstone to potential therapies that may prevent transmission, progression and immune related manifestations of COVID-19, via manipulation of the gut microbiota.

Methods

We performed an extensive literature review, utilizing the Pubmed search engine and Google Scholar for studies evaluating the microbiome in COVID-19 patients and compared results with studies evaluating the microbiome in lupus. We searched for the terms: microbiome, dysbiosis, COVID-19, SARS-CoV-2, gastrointestinal as well as lupus and autoimmune. While there were hundreds of articles which referred to gastrointestinal manifestations in COVID-19, to date only 4 studies investigated the gastrointestinal microbiome in this setting. We compared the similarities between microbiome of COVID-19 patients and lupus patients.

Results

We found that there are several similar processes of immune dysregulation in patients with COVID-19 and in those with lupus, with several other alterations seen in other pathological states. Some of these similarities include loss of microbiota biodiversity, increased representation of pathobionts, which are microbes associated with inflammation and disease (i.e Proteobacteria) and a relative decrease of symbionts, which are protective microbes, associated with anti-inflammatory properties (i.e Lactobacillus). Compromise to the intestinal barrier has also been reported in both.

Conclusions

We conclude that the gastrointestinal tract contributes to the disease manifestations in COVID-19. Whether gastrointestinal dysbiosis is the cause or effect of gastrointestinal manifestations and several severe systemic manifestations, which may be the response to an increased pro-inflammatory environment, is still debatable and warrants further investigation. Given the resemblance of the microbiome in COVID-19 patients to that seen in lupus patients, it becomes clearer why several therapies used in autoimmune conditions are currently under investigation for the treatment of COVID-19 patients. Moreover, these findings should promote further investigating the utility of manipulation of the microbiome, via nutritional supplementation or even fecal transplantations, interventions that may alter the course of the disease, and potentially prevent disease transmission at low cost and low risk.