Diet influence on the gut microbiota and dysbiosis related to nutritional disorders

Diet, microbiome, and probiotics establish a crucial link in vaccine efficacy

Vaccination plays a critical role in public health by reducing the incidence and prevalence of infectious diseases. The efficacy of a vaccine has numerous determinants, which include age, sex, genetics, environment, geographic location, nutritional status, maternal antibodies, and prior exposure to pathogens. However, little is known about the role of gut microbiome in vaccine efficacy and how it can be targeted through dietary interventions to improve immunological responses. Unveiling this link is imperative, particularly in the post-pandemic world, considering impaired COVID-19 vaccine response observed in dysbiotic individuals. Therefore, this article aims to comprehensively review how diet and probiotics can modulate gut microbiome composition, which is linked to vaccine efficacy. Dietary fiber and polyphenolic compounds derived from plant-based foods improve gut microbial diversity and vaccine efficacy by promoting the growth of short-chain fatty acids-producing microbes. On the other hand, animal-based foods have mixed effects - whey protein and fish oil promote gut eubiosis and vaccine efficacy. In contrast, lard and red meat have adverse effects. Studies further indicate that probiotic supplements exert varied effects, mostly strain and dosage-specific. Interlinking diet, microbiome, probiotics, and vaccines will reveal opportunities for newer research on diet-induced microbiome-manipulated precision vaccination strategies against infectious diseases.

Gut microbial metabolites: The bridge connecting diet and atherosclerosis, and next-generation targets for dietary interventions

Mounting evidence indicates that gut microbial metabolites are central hubs linking the gut microbiota to atherosclerosis (AS). Gut microbiota enriched with pathobiont bacteria responsible for producing metabolites like trimethylamine N-oxide and phenylacetylglutamine are related to an increased risk of cardiovascular events. Furthermore, gut microbiota enriched with bacteria responsible for producing short-chain fatty acids, indole, and its derivatives, such as indole-3-propionic acid, have demonstrated AS-protective effects. This study described AS-related gut microbial composition and how microbial metabolites affect AS. Summary findings revealed gut microbiota and their metabolites-targeted diets could benefit AS treatment. In conclusion, dietary interventions centered on the gut microbiota represent a promising strategy for AS treatment, and understanding diet-microbiota interactions could potentially be devoted to developing novel anti-AS therapies.

Flavonoids and the gut microbiome: a powerful duo for brain health

Flavonoids, a class of polyphenolic compounds, are widely distributed in plant-based foods and have been recognized for their potential to promote overall health and well-being. Flavonoids in fruits and vegetables offer various beneficial effects such as anti-aging, anticancer, and anti-inflammatory properties. Flavonoids have been extensively studied for their neuroprotective properties, which are attributed to their ability to cross the blood-brain barrier and interact with neural cells. Factors like gut microbiota composition, age, genetics, and diet can impact how well flavonoids are absorbed in the gut. The gut microbiota can enhance the absorption of flavonoids through enzymatic processes, making microbiota composition a key factor influenced by age, genetics, and diet. Flavonoids can modulate the gut microbiota through prebiotic and antimicrobial effects, affecting the production of beneficial microbial metabolites like short-chain fatty acids (SCFAs) such as butyrate, which play a role in brain function and health. The gut microbiome also modulates the immune system, which is critical for preventing neuroinflammation. Additionally, flavonoids can benefit mental and psychological health by influencing anti-inflammatory signaling pathways in brain cells and increasing the absorption of tyrosine and tryptophan, precursors to neurotransmitters like serotonin, dopamine, norepinephrine, adrenaline, and gamma-aminobutyric acid (GABA). The flavonoid-gut microbiome axis is a complex and multifaceted relationship that has significant implications for neurological health. This review will explore how genetic and environmental factors can impact flavonoid absorption and the positive effects of flavonoids on brain health and the gut microbiota network.

Dietary Inflammatory Index is associated with periodontitis risk in pregnant women with gestational diabetes mellitus

Recent studies suggest a link between periodontitis and the Dietary Inflammatory Index (DII). We hypothesize that a more proinflammatory diet is associated with periodontitis risk in pregnant women with gestational diabetes mellitus (GDM). This study aimed to explore the association between DII scores and periodontitis risk in GDM women. In this cross-sectional study, 302 eligible GDM women from a Maternal and Child Health Hospital were enrolled between February and July 2023. DII scores were calculated based on dietary intake data collected using a validated semiquantitative food frequency questionnaire. Periodontal health was assessed through periodontal parameters including bleeding on probing, probing depth, and clinical attachment loss. Logistic regression models were employed to evaluate the odds ratios (ORs) for periodontitis risk across DII tertiles. Our study found that the prevalence of periodontitis across the DII tertiles 1, 2, and 3 was 34.7%, 56.4%, and 54.0%, respectively. Comparing the highest DII tertile (tertile 3) with the lowest (tertile 1), a significant association was found between higher DII scores and periodontitis risk (univariate OR: 2.21; 95% CI: 1.25, 3.90; P = .006), which remained significant in the fully adjusted model (adjusted OR: 2.30; 95% CI: 1.21, 4.37; P = .011). In conclusion, elevated DII scores are associated with an increased risk of periodontitis, underscoring the crucial role of a proinflammatory diet in periodontitis progression. Future well-designed experimental studies are needed to verify if tailored dietary strategies can effectively reduce periodontitis risk among pregnant women with GDM.

Nutritional Management in Stricturing Crohn's Disease: A Pilot Study

BACKGROUND

More than half of patients with Crohn's disease develop intestinal fibrosis induced intestinal obstruction with debilitating symptoms throughout their disease course. The incidence of stricture formation in CD has remained unchanged over the last several decades. Factors promoting intestinal fibrosis are currently unclear, but diet may represent an underestimated risk factor for intestinal fibrosis by modification of both the host immune response and intestinal microbial composition. Evaluating the impact of diet on the course of IBD is very complex. Sarcopenia is a common problem in IBD patients and correlates with an increased rate of disease. Skeletal muscle index (SMI) is an important parameter to measure sarcopenia and is an easily accessible tool for evaluating the likelihood of complications in individuals with CD.

METHODS

Using a randomized and controlled pilot design, we aimed to investigate the efficacy of 12 months of short-term dietary intervention based on essential amino acid (EAA) and sodium butyrate (NaB) supplementation in the management of stricturing Crohn's disease patients.

RESULTS

After the treatment in the diet EAA/NaB group, we revealed a statistically significant improvement of muscle mass (61.49 ± 5.47 vs. control 86 ± 10.70, p = 0.01) and SMI index (9.97 ± 1.79 vs. control 7.60 ± 2.29, p = 0.02). In addition, the measurement of skeletal muscle mass in CD patients has been suggested to be crucial for predicting the disease course. Indeed, after one year, surgery was required in 4/10 control group patients (40%) and 1/10 study group (10%) patients, underlining the importance of body composition alterations and adequate dietary intake in the management of these patients.

CONCLUSIONS

Further prospective studies are needed to confirm these results; nonetheless this nutritional approach could become an integral part in the treatment of stricturing CD patients to improve disease outcomes and increase the quality of life in these patients.

The Role of the Gut Microbiome in the Development and Progression of Type 2 Diabetes and Liver Disease

Type 2 diabetes mellitus (T2DM) and progressive liver disease are 2 of the most significant global health concerns, and they have alarming and ever-increasing prevalence. A growing body of literature has demonstrated a potential multilateral link between gut microbiome dysbiosis and the development and progression of the above-mentioned conditions. Modulation of gut microbial composition from the norm is due to changes in diet allied with external factors such as age, genetics, and environmental changes. In this comprehensive review, we recapitulate the research to date investigating the links between gut microbiome dysbiosis and T2DM or liver disease, with special attention to the importance of diet. Additionally, we review the most commonly used tools and methodologies of investigating changes in the gut microbiome, highlighting the advantages and limitations of each strategy, before introducing a novel in vitro approach to the problem. Finally, the review offers recommendations for future research in this field that will allow better understanding of how the gut microbiota affects disease progression and of the prospects for intestinal microbiota-based therapeutic options.

Seasonal Changes and Age-Related Effects on the Intestinal Microbiota of Captive Chinese Monals (Lophophorus lhuysii)

The Chinese monal (Lophophorus lhuysii) is a large-sized and vulnerable (VU in IUCN) bird from southwestern China. This study applied 16S rRNA high-throughput sequencing to comprehensively examine the gut microbiota of captive Chinese monals (located in Baoxing, Sichuan, China) across varying seasons and life stages. Dominant bacterial phyla identified included Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Significant seasonal and age-associated shifts were observed within specific bacterial groups, particularly marked by seasonal fluctuations in beta diversity. Moreover, linear discriminant analysis effect size (LEfSe) and functional predictions highlighted distinct winter signatures, indicating possible functional shifts in energy metabolism and disease resistance. In mid-aged adults, an expansion of Gamma-Proteobacteria suggested an elevated susceptibility of the gut microbiota of Chinese monals to chronic disorders and microbial imbalance. Putative pathogenic bacteria exhibited increased abundance in spring and summer, likely driven by temperature, host physiological cycles, interspecies interactions, and competition. These findings imply that the diversity, and structure of the gut microbiota in captive Chinese monals are strongly influenced by seasonal and age-related factors. The insights provided here are essential for improving breeding strategies and preventing gastrointestinal diseases in captivity.

Implications of the microbiome and metabolic intermediaries produced by bacteria in breast cancer

The breast microbiome presents a diverse microbial community that could affects health and disease states, in the context of breast cancer. Sequencing technologies have allowed describing the diversity and abundance of microbial communities among individuals. The complex tumoral microenvironment that includes the microbial composition could influence tumor growth. The imbalance of diversity and abundance inside the microbial community, known as dysbiosis plays a crucial role in this context. One the most prevalent bacterial genera described in breast invasive carcinoma are Bacillus, Pseudomonas, Brevibacillus, Mycobacterium, Thermoviga, Acinetobacter, Corynebacterium, Paenibacillus, Ensifer, and Bacteroides. Paenibacills genus shows a relation with patient survival. When the Paenibacills genus increases its abundance in patients with breast cancer, the survival probability decreases. Within this dysbiotic environment, various bacterial metabolites could play a pivotal role in the progression and modulation of breast cancer. Key bacterial metabolites, such as cadaverine, lipopolysaccharides (LPS), and trimethylamine N-oxide (TMAO), have been found to exhibit potential interactions within breast tissue microenvironments. Understanding the intricate relationships between dysbiosis and these metabolites in breast cancer may open new avenues for diagnostic biomarkers and therapeutic targets. Further research is essential to unravel the specific roles and mechanisms of these microbial metabolites in breast cancer progression.

Summatory Effects of Anaerobic Exercise and a 'Westernized Athletic Diet' on Gut Dysbiosis and Chronic Low-Grade Metabolic Acidosis

Anaerobic exercise decreases systemic pH and increases metabolic acidosis in athletes, altering the acid-base homeostasis. In addition, nutritional recommendations advising athletes to intake higher amounts of proteins and simple carbohydrates (including from sport functional supplements) could be detrimental to restoring acid-base balance. Here, this specific nutrition could be classified as an acidic diet and defined as 'Westernized athletic nutrition'. The maintenance of a chronic physiological state of low-grade metabolic acidosis produces detrimental effects on systemic health, physical performance, and inflammation. Therefore, nutrition must be capable of compensating for systemic acidosis from anaerobic exercise. The healthy gut microbiota can contribute to improving health and physical performance in athletes and, specifically, decrease the systemic acidic load through the conversion of lactate from systemic circulation to short-chain fatty acids in the proximal colon. On the contrary, microbial dysbiosis results in negative consequences for host health and physical performance because it results in a greater accumulation of systemic lactate, hydrogen ions, carbon dioxide, bacterial endotoxins, bioamines, and immunogenic compounds that are transported through the epithelia into the blood circulation. In conclusion, the systemic metabolic acidosis resulting from anaerobic exercise can be aggravated through an acidic diet, promoting chronic, low-grade metabolic acidosis in athletes. The individuality of athletic training and nutrition must take into consideration the acid-base homeostasis to modulate microbiota and adaptive physiological responses.

Celiac Disease: The Importance of Studying the Duodenal Mucosa-Associated Microbiota

There is increasing evidence indicating that changes in both the composition and functionality of the intestinal microbiome are closely associated with the development of several chronic inflammatory diseases, with celiac disease (CeD) being particularly noteworthy. Thanks to the advent of culture-independent methodologies, the ability to identify and quantify the diverse microbial communities residing within the human body has been significantly improved. However, in the context of CeD, a notable challenge lies in characterizing the specific microbiota present on the mucosal surfaces of the intestine, rather than relying solely on fecal samples, which may not fully represent the relevant microbial populations. Currently, our comprehension of the composition and functional importance of mucosa-associated microbiota (MAM) in CeD remains an ongoing field of research because the limited number of available studies have reported few and sometimes contradictory results. MAM plays a crucial role in the development and progression of CeD, potentially acting as both a trigger and modulator of the immune response within the intestinal mucosa, given its proximity to the epithelial cells and direct interaction. According to this background, this review aims to consolidate the existing literature specifically focused on MAM in CeD. By elucidating the complex interplay between the host immune system and the gut microbiota, we aim to pave the way for new interventions based on novel therapeutic targets and diagnostic biomarkers for MAM in CeD.

Unraveling the Microbiome-Human Body Axis: A Comprehensive Examination of Therapeutic Strategies, Interactions and Implications

This review scrutinizes the intricate interplay between the microbiome and the human body, exploring its multifaceted dimensions and far-reaching implications. The human microbiome, comprising diverse microbial communities inhabiting various anatomical niches, is increasingly recognized as a critical determinant of human health and disease. Through an extensive examination of current research, this review elucidates the dynamic interactions between the microbiome and host physiology across multiple organ systems. Key topics include the establishment and maintenance of microbiota diversity, the influence of host factors on microbial composition, and the bidirectional communication pathways between microbiota and host cells. Furthermore, we delve into the functional implications of microbiome dysbiosis in disease states, emphasizing its role in shaping immune responses, metabolic processes, and neurological functions. Additionally, this review discusses emerging therapeutic strategies aimed at modulating the microbiome to restore host-microbe homeostasis and promote health. Microbiota fecal transplantation represents a groundbreaking therapeutic approach in the management of dysbiosis-related diseases, offering a promising avenue for restoring microbial balance within the gut ecosystem. This innovative therapy involves the transfer of fecal microbiota from a healthy donor to an individual suffering from dysbiosis, aiming to replenish beneficial microbial populations and mitigate pathological imbalances. By synthesizing findings from diverse fields, this review offers valuable insights into the complex relationship between the microbiome and the human body, highlighting avenues for future research and clinical interventions.

Dietary supplementation of ark clams protects gut health and modifies gut microbiota in d-galactose-induced aging rats

BACKGROUND

Ark clams, a seafood abundant in various nutrients, are widely consumed worldwide. This study aimed to investigate the protective benefits of two common ark clams in Korea, Scapharca subcrenata (SS) and Tegillarca granosa (TG), on gut health in d-galactose (d-gal)-induced aging rats.

RESULTS

Thirty-two Wistar rats (11 weeks old) were randomly allocated into four groups: a CON group (normal diet + saline intraperitoneal (i.p.) injection), a CD group (normal diet + d-gal i.p. injection), an SS group (normal diet with 5% SS supplementation + d-gal i.p. injection), and a TG group (normal diet with 5% TG supplementation + d-gal i.p. injection). After 12 weeks of treatment, histopathological results showed that gut barrier damage was alleviated in rats of the SS and TG groups, as evidenced by increases in mucus layer thickness and goblet cell numbers. Meanwhile, the two groups supplemented with ark clams showed an evident reduction in oxidative stress biomarkers (malondialdehyde and protein carbonyl content levels in the colon) and an increase in the immune-related factor (immunoglobulin A level in the plasma) in rats. The 16S ribosomal RNA analysis revealed that SS and TG ark clams significantly increased the proliferations of Bacteroidetes at the phylum level and Parabacteroides at the genus level. Additionally, the levels of the three main short-chain fatty acids in the cecal contents were also significantly increased in the SS and TG groups.

CONCLUSION

Our results indicated a potent preventive effect of SS and TG ark clams on d-gal-induced gut injury, suggesting that ark clams may be a promising dietary component for intervening in aging. © 2023 Society of Chemical Industry.

In a rodent model of autism, probiotics decrease gut leakiness in relation to gene expression of GABA receptors: Emphasize how crucial the gut-brain axis

Objective

Rodent models may help investigations on the possible link between autism spectrum disorder and increased permeability of the gastrointestinal (GI) tract since autistic patients frequently manifested GI troubles as comorbidities.

Methods

Forty young male western Albino rats, weighing approximately 60-70 g and aged 3-4 weeks, were used. In each of the six experimental groups, eight animals were treated as follows. The mice in the control group (I) received phosphate-buffered saline orally. For 3 days, the animals in the propionic acid (PPA)-treated groups (II and III) were given an oral neurotoxic dose of PPA (250 mg/kg body weight each day). Group II was euthanized after 3 days; however, Group III was left alive to be euthanized alongside the other groups. The animals were kept at 22 ± 1°C and allowed to access water and normal food as needed. Identical dosages of PPA were given to the rats in the three treatment groups (IV, V, and VI), and for 3 weeks, they were given the following treatments: 0.2 g/kg body weight of pure Bifidobacterium infantis, a probiotic mixture of PROTEXIN®, Somerset, UK and pure Lactobacillus bulgaricus, respectively. The six groups underwent measurements of serum zonulin and occludin as variables associated with leaky gut, glutathione, malondialdehyde, and catalase as oxidative stress-related variables, with gamma-aminobutyric acid (GABA) receptor gene expression.

Results

This study demonstrated the potential effects of pure or mixed probiotics in lowering zonulin and occludin as markers of increased intestinal permeability, enhancing GABA receptor expression, and reducing oxidative stress as neurotoxic effects of PPA.

Conclusions

This study demonstrates that various probiotics protect gut barrier function and could be used to alleviate increased intestinal permeability caused by oxidative stress and impaired GABA signaling as a result of PPA neurotoxicity, addressing the clinical implications of probiotic supplements.

Ready-to-use therapeutic/supplementary foods from local food resources: Technology accessibility, program effectiveness, and sustainability, a review

Ready-to-Use Therapeutic Food (RUTF) or Ready-to-Use Supplementary Food (RUSF) has been widely used in home-based treatment for severely and moderately acute malnourished children. These programs showed positive results in short term nutritional recovery in children, which were reported in some research settings. Nowadays, the RUTF/RUSF formulation has been improved using a variety of RUTF/RUSF from locally available food ingredients. This paper aims to review the essential aspects of the development and provision of RUTF/RUSF made from local food resources and monitor program effectiveness that warrants the program's sustainability. The modified recipes of RUTF/RUSF were developed following the international dietary guidelines for the rehabilitation of severely and moderately acute malnourished children. The local production of RUTF/RUSF provided some benefits that include empowering the local community, consideration of the common eating pattern, promoting the diversification of food consumption, strengthening food security, as well as supporting the sustainability of RUTF/RUSF production. Results of the PRISMA-based systematic literature review revealed various ingredient developments and processing techniques which could improve the product characteristics and sensory evaluation. RUTF/RUSF in local food production provided different food carriers (e.g., biscuits, wafers) and seemed to be more readily accepted by the children. Furthermore, the program sustainability of RUTF/RUSF depends on a continuous ingredients supply and support from the local government. The findings presented the importance of development of such food supplements based on the local food resources and with improved technology for prevention and rehabilitation of malnourished children.

Consumption of yacon flour and energy-restricted diet increased the relative abundance of intestinal bacteria in obese adults

Prebiotics can alter the gastrointestinal environment, favoring the growth of health-promoting bacteria. Although yacon is a functional food, with prebiotic properties (fructooligosaccharides), its effects on the intestinal microbiota have not been investigated yet. The objective of this study was to evaluate the effects of yacon flour consumption and energy-restricted diet in the intestinal microbiota in adults with excess body weight. Twenty-one adults with excess body weight were included in this randomized, parallel, double-blind, placebo-controlled, 6-week clinical trial. Subjects daily consumed at breakfast a drink containing 25 g of yacon flour (n = 11) or not containing yacon (n = 10) and received the prescription of energy-restricted diets. Fecal samples were collected on the first and on last day of the study. 16S rRNA sequencing was assessed to evaluate the effect of yacon fermentation on intestinal microbiota bacterial composition. There was an increase in the genera Bifidobacterium, Blautia, Subdoligranulum, and Streptococcus after the consumption of yacon and energy-restricted diet. In the yacon group, we also observed a positive correlation between the concentrations of short-chain fatty acids versus the genera Coprococcus and Howardella, besides a negative correlation between the concentrations of advanced glycation end products and early glycation products versus the genera Ruminococcus and Prevotella, respectively. Consumption of yacon flour and energy-restricted diet selectively changed the intestinal microbiota composition in adults with excess body weight. TRIAL REGISTRATION: Register number: RBR-6YH6BQ. Registered 23 January, 2018.

Gut Microbiota and Its Role in Anti-aging Phenomenon: Evidence-Based Review

The gut microbiota widely varies from individual to individual, but the variation shows stability over a period of time. The presence of abundant bacterial taxa is a common structure that determines the microbiota of human being. The presence of this microbiota greatly varies from geographic location, sex, food habits and age. Microbiota existing within the gut plays a significant role in nutrient absorption, development of immunity, curing of diseases and various developmental phases. With change in age, chronology diversification and variation of gut microbiota are observed within human being. But it has been observed that with the enhancement of age the richness of the microbial diversity has shown a sharp decline. The enhancement of age also results in the drift of the characteristic of the microbes associated with the microbiota from commensals to pathogenic. Various studies have shown that age associated gut-dysbiosis may result in decrease in tlongevity along with unhealthy aging. The host signalling pathways regulate the presence of the gut microbiota and their longevity. The presence of various nutrients regulates the presence of various microbial species. Innate immunity can be triggered due to the mechanism of gut dysbiosis resulting in the development of various age-related pathological syndromes and early aging. The gut microbiota possesses the ability to communicate with the host system with the help of various types of biomolecules, epigenetic mechanisms and various types of signalling-independent pathways. Drift in this mechanism of communication may affect the life span along with the health of the host. Thus, this review would focus on the use of gut-microbiota in anti-aging and healthy conditions of the host system.

Ethanol-Producing Enterocloster bolteae Is Enriched in Chronic Hepatitis B-Associated Gut Dysbiosis: A Case-Control Culturomics Study

BACKGROUND

Hepatitis B virus (HBV) infection is a global health epidemic that causes fatal complications, leading to liver cirrhosis and hepatocellular carcinoma. The link between HBV-related dysbiosis and specific bacterial taxa is still under investigation. Enterocloster is emerging as a new genus (formerly Clostridium), including Enterocloster bolteae, a gut pathogen previously associated with dysbiosis and human diseases such as autism, multiple sclerosis, and inflammatory bowel diseases. Its role in liver diseases, especially HBV infection, is not reported.

METHODS

The fecal samples of eight patients with chronic HBV infection and ten healthy individuals were analyzed using the high-throughput culturomics approach and compared to 16S rRNA sequencing. Quantification of ethanol, known for its damaging effect on the liver, produced from bacterial strains enriched in chronic HBV was carried out by gas chromatography-mass spectrometry.

RESULTS

Using culturomics, 29,120 isolated colonies were analyzed by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-TOF); 340 species were identified (240 species in chronic HBV samples, 254 species in control samples) belonging to 169 genera and 6 phyla. In the chronic HBV group, 65 species were already known in the literature; 48 were associated with humans but had not been previously found in the gut, and 17 had never been associated with humans previously. Six species were newly isolated in our study. By comparing bacterial species frequency, three bacterial genera were serendipitously found with significantly enriched bacterial diversity in patients with chronic HBV: Enterocloster, Clostridium, and Streptococcus (p = 0.0016, p = 0.041, p = 0.053, respectively). However, metagenomics could not identify this enrichment, possibly concerning its insufficient taxonomical resolution (equivocal assignment of operational taxonomic units). At the species level, the significantly enriched species in the chronic HBV group almost all belonged to class Clostridia, such as Clostridium perfringens, Clostridium sporogenes, Enterocloster aldenensis, Enterocloster bolteae, Enterocloster clostridioformis, and Clostridium innocuum. Two E. bolteae strains, isolated from two patients with chronic HBV infection, showed high ethanol production (27 and 200 mM).

CONCLUSIONS

Culturomics allowed us to identify Enterocloster species, specifically, E. bolteae, enriched in the gut microbiota of patients with chronic HBV. These species had never been isolated in chronic HBV infection before. Moreover, ethanol production by E. bolteae strains isolated from the chronic HBV group could contribute to liver disease progression. Additionally, culturomics might be critical for better elucidating the relationship between dysbiosis and chronic HBV infection in the future.

Gut microbes predominantly act as living beneficial partners rather than raw nutrients

Animals and their gut microbes mutually benefit their health. Nutrition plays a central role in this, directly influencing both host and microbial fitness and the nature of their interactions. This makes nutritional symbioses a complex and dynamic tri-system of diet-microbiota-host. Despite recent discoveries on this field, full control over the interplay among these partners is challenging and hinders the resolution of fundamental questions, such as how to parse the gut microbes' effect as raw nutrition or as symbiotic partners? To tackle this, we made use of the well-characterized Drosophila melanogaster/Lactiplantibacillus plantarum experimental model of nutritional symbiosis to generate a quantitative framework of gut microbes' effect on the host. By coupling experimental assays and Random Forest analysis, we show that the beneficial effect of L. plantarum strains primarily results from the active relationship as symbionts rather than raw nutrients, regardless of the bacterial strain. Metabolomic analysis of both active and inactive bacterial cells further demonstrated the crucial role of the production of beneficial bacterial metabolites, such as N-acetylated-amino-acids, as result of active bacterial growth and function. Altogether, our results provide a ranking and quantification of the main bacterial features contributing to sustain animal growth. We demonstrate that bacterial activity is the predominant and necessary variable involved in bacteria-mediated benefit, followed by strain-specific properties and the nutritional potential of the bacterial cells. This contributes to elucidate the role of beneficial bacteria and probiotics, creating a broad quantitative framework for host-gut microbiome that can be expanded to other model systems.

Effect of Red-Beetroot-Supplemented Diet on Gut Microbiota Composition and Metabolite Profile of Weaned Pigs-A Pilot Study

Red beetroot is a well-recognized and established source of bioactive compounds (e.g., betalains and polyphenols) with anti-inflammatory and antimicrobial properties. It is proposed as a potential alternative to zinc oxide with a focus on gut microbiota modulation and metabolite production. In this study, weaned pigs aged 28 days were fed either a control diet, a diet supplemented with zinc oxide (3000 mg/kg), or 2% and 4% pulverized whole red beetroot (CON, ZNO, RB2, and RB4; respectively) for 14 days. After pigs were euthanized, blood and digesta samples were collected for microbial composition and metabolite analyses. The results showed that the diet supplemented with red beetroot at 2% improved the gut microbial richness relative to other diets but marginally influenced the cecal microbial diversity compared to a zinc-oxide-supplemented diet. A further increase in red beetroot levels (4%-RB4) led to loss in cecal diversity and decreased short chain fatty acids and secondary bile acid concentrations. Also, an increased Proteobacteria abundance, presumably due to increased lactate/lactic-acid-producing bacteria was observed. In summary, red beetroot contains several components conceived to improve the gut microbiota and metabolite output of weaned pigs. Future studies investigating individual components of red beetroot will better elucidate their contributions to gut microbiota modulation and pig health.

Evidence for proton-pump inhibitor (PPI)-associated dysbiosis in metabolically unhealthy obesity

Obesity adversely impacts millions of American adults by predisposing them to significant health risks and further complications. Obesity is differentiated into two groups: metabolically healthy and metabolically unhealthy. In contrast to metabolically healthy counterparts, obese individuals who are metabolically unhealthy display hallmark symptoms of metabolic syndrome (e.g., hypertension, dyslipidemia, hyperglycemia, abdominal obesity). Gastroesophageal reflux disease (GERD) commonly occurs in all obese populations, as do poor dietary habits. Proton-pump inhibitors (PPIs), due to their wide availability, are most often used to treat GERD-related heartburn and other symptoms. Here, we review the evidence on how poor diet as well as short- and long-term use of PPIs adversely affect the gastrointestinal microbiota to cause dysbiosis. Key components of dysbiosis-induced metabolically unhealthy obesity (MUO) associated with PPI use include "leaky gut," systemic low-grade inflammation, and reduced amounts of short-chain fatty acids (SCFAs) such as butyrate that promote metabolic health. The benefit of using probiotics to mitigate PPI-induced dysbiosis and MUO is also discussed.

Microbial inoculums improve growth and health of Heteropneustes fossilis via biofloc-driven aquaculture

Biofloc technology aims to maximize fish farming productivity by effectively breaking down ammonia and nitrite, promoting healthy flocculation, and enhancing the growth and immunity of cultured animals. However, a major limitation in this field is the suitable starter microbial culture and narrow number of fish species that have been tested with the biofloc system. Here, we investigated various microbial inoculum containing beneficial microbes with probiotics, immunostimulatory and flocs development and bioremediation properties would lead to the development of ideal biofloc development. Three treatment groups with different microbial combinations, viz., group 1 [Bacillus subtilis (AN1) + Pseudomonas putida (PB3) + Saccharomyces cerevisiae (ATCC-2601)], group 2 [B. subtilis (AN2) + P. fluorescens (PC3) + S. cerevisiae (ATCC-2601)] and group 3 [B. subtilis (AN3) + P. aeruginosa (PA2) + S. cerevisiae (ATCC-2601)] were used and compared with the positive control (pond water without microbial inoculums) and negative control (clear water: without microbial inoculums and carbon sources) on biofloc development and its characteristic features to improve the water quality and growth of fish. We demonstrated that microbial inoculums, especially group 2, significantly improve the water quality and microbiota of flocs and gut of the test animal, Heteropneustes fossilis. The study further demonstrates that biofloc system supplemented with microbial inoculums positively regulates gut histomorphology and growth performance, as evidenced by improved villous morphology, amylase, protease and lipase activity, weight gain, FCR, T3, T4 and IGF1 levels. The inoculums induced an antioxidative response marked by significantly higher values of catalase (CAT) and superoxide dismutase (SOD) activity. Furthermore, the supplementation of microbial inoculums enhances both specific and non-specific immune responses and significantly elevated levels of immune genes (transferrin, interleukin-1β and C3), and IgM was recorded. This study provides a proof-of-concept approach for assessing microbial inoculums on fish species that can be further utilized to develop biofloc technology for use in sustainable aquaculture.

Toxicity and Impact of Silica Nanoparticles on the Configuration of Gut Microbiota in Immunodeficient Mice

Nanoparticles (NPs), having exceptional physicochemical and electrical characteristics with lower toxicity, have evolved as dynamic drug delivery carriers in living organisms. Potentially, the intragastric gavage of silica nanoparticles (SiNPs) affects gut microbiota profiles in immunodeficient mice. In this study, the impact of SiNPs of variable size and dosage was investigated in cyclophosphamide (Cy)-induced immunodeficient mice, specifically on their immune functions and gut microbiota, through physicochemical and metagenomic analysis. SiNPs of different sizes and doses were gavaged to Cy-induced immunodeficient mice for 12 days at an interval of 24 h to investigate their effects on immunological functions and the gut microbiome of mice. Our results showed that SiNPs had no significant toxicological effects on the cellular and hematological activities of immunodeficient mice. Furthermore, after the administration of different levels of SiNPs, no immune dysfunction was found in the immunosuppressed mice groups. However, gut-microbial studies and comparisons of characteristic bacterial diversity and compositions demonstrated that SiNPs significantly affect the abundance of different bacterial communities. LEfSe analysis revealed that SiNPs significantly increased the abundance of Lactobacillus, Sphingomonas, Sutterella, Akkermansia, and Prevotella, and potentially reduced Ruminococcus and Allobaculum. Thus, SiNPs significantly regulate and modify the configuration of the gut microbiota in immunodeficient mice. These dynamic variations in the intestinal bacterial community, abundance, and diversity provide new insight into the regulation and administration of silica-based NPs. This would be helpful for the further demonstration of the mechanism of action and prediction of the potential effects of SiNPs.

Food, gut barrier dysfunction, and related diseases: A new target for future individualized disease prevention and management

Dysfunction of gut barrier is known as "leaky gut" or increased intestinal permeability. Numerous recent scientific evidences showed the association between gut dysfunction and multiple gastrointestinal tract (GI) and non-GI diseases. Research also demonstrated that food plays a crucial role to cause or remedy gut dysfunction related to diseases. We reviewed recent articles from electronic databases, mainly PubMed. The data were based on animal models, cell models, and human research in vivo and in vitro models. In this comprehensive review, our aim focused on the relationship between dietary factors, intestinal permeability dysfunction, and related diseases. This review synthesizes currently available literature and is discussed in three parts: (a) the mechanism of gut barrier and function, (b) food and dietary supplements that may promote gut health, and food or medication that may alter gut function, and (c) a table that organizes the synthesized information by general mechanisms for diseases related to leaky gut/intestinal permeability and associated dietary influences. With future research, dietary intervention could be a new target for individualized disease prevention and management.

About Functional Foods: The Probiotics and Prebiotics State of Art

Poor diet, obesity and a sedentary lifestyle have a significant impact on natural microbiota disorders; specifically, the intestinal one. This in turn can lead to a multitude of organ dysfunctions. The gut microbiota contains more than 500 species of bacteria and constitutes 95% of the total number of cells in the human body, thus contributing significantly to the host's resistance to infectious diseases. Nowadays, consumers have turned to purchased foods, especially those containing probiotic bacteria or prebiotics, that constitute some of the functional food market, which is constantly expanding. Indeed, there are many products available that incorporate probiotics, such as yogurt, cheese, juices, jams, cookies, salami sausages, mayonnaise, nutritional supplements, etc. The probiotics are microorganisms that, when taken in sufficient amounts, contribute positively to the health of the host and are the focus of interest for both scientific studies and commercial companies. Thus, in the last decade, the introduction of DNA sequencing technologies with subsequent bioinformatics processing contributes to the in-depth characterization of the vast biodiversity of the gut microbiota, their composition, their connection with the physiological function-known as homeostasis-of the human organism, and their involvement in several diseases. Therefore, in this study, we highlighted the extensive investigation of current scientific research for the association of those types of functional foods containing probiotics and prebiotics in the diet and the composition of the intestinal microbiota. As a result, this study can form the foundation for a new research path based on reliable data from the literature, acting a guide in the continuous effort to monitor the rapid developments in this field.

Modified cereal bran (MCB) from finger millet, kodo millet, and rice bran prevents high-fat diet-induced metabolic derangements

Cereal bran consumption improves gastrointestinal and metabolic health. Unprocessed cereal brans have a limited shelf-life and contain anti-nutrient phytochemicals. In the present study, lipids and antinutrients (flavonoids, tannin, and polyphenol) were removed from finger millet, kodo millet and rice bran using chemo-enzymatic processing. The thus-obtained modified cereal brans (MCBs) were evaluated for their potential in preventing high fat diet (HFD)-induced obesity. C57BL/6 mice were fed a HFD or a HFD supplemented with 10% w/w modified finger millet bran (mFMB), modified kodo millet bran (mKMB), modified rice bran (mRB), or a combination of the modified brans (1 : 1 : 1) for twelve weeks. The MCBs reduced HFD-induced body weight gain, improved glucose homeostasis, decreased the Firmicutes/Bacteroidetes ratio, and increased the short chain fatty acid (SCFA) levels in the cecum. Liver dyslipidemia, oxidative stress, inflammation, visceral white adipose tissue (vWAT) hypertrophy, and lipolysis were also prevented by the MCBs. Among the individual MCBs, mRB showed a greater effect in preventing HFD-induced increase in the inflammatory cytokines (IL-6, TNF-α, and LPS) than mFMB and mKMB. mFMB and mKMB supplementation more significantly restored the relative abundance of Akkermansia muciniphila and butyrate-producing genera such as Lachnospiraceae, Eubacterium, and Ruminococcus than mRB. Ex vivo gut permeability assay, immunohistochemistry of tight junction proteins, and gene expression analysis in the colon revealed that the combination of three brans was better in preventing HFD-induced leaky gut in comparison to the individual brans. Hierarchical clustering analysis showed that the combination group was clustered closest to the NPD group, suggesting an additive effect. Our study implies that a combination of mFMB, mKMB, and mRB could be used as a nutraceutical or functional food ingredient for preventing HFD-induced gut derangements and associated metabolic complications.

Fermented Foods in the Management of Obesity: Mechanisms of Action and Future Challenges

Fermented foods are part of the staple diet in many different countries and populations and contain various probiotic microorganisms and non-digestible prebiotics. Fermentation is the process of breaking down sugars by bacteria and yeast species; it not only enhances food preservation but can also increase the number of beneficial gut bacteria. Regular consumption of fermented foods has been associated with a variety of health benefits (although some health risks also exist), including improved digestion, enhanced immunity, and greater weight loss, suggesting that fermented foods have the potential to help in the design of effective nutritional therapeutic approaches for obesity. In this article, we provide a comprehensive overview of the health effects of fermented foods and the corresponding mechanisms of action in obesity and obesity-related metabolic abnormalities.

Serum Vitamin D Level and Gut Microbiota in Women

Obesity and vitamin D deficiency are two major public health concerns. Evidence suggests that alteration in gut microbiota composition is a possible risk factor for obesity. Additionally, altered vitamin D status has a potential role in shaping the gut microbial community. Further, the prevalence of obesity has been rising in the Middle East, especially among women of reproductive age, which is of specific concern due to its adverse effects on the health of their offspring. To date, limited evidence is available on the association between gut microbiota composition and vitamin D levels in Arab women. This study aims to identify the associations between serum vitamin D, gut microbiota, and obesity among Saudi females. The current study is a case-control study including 92 women aged 18 to 25 years, (n = 48) with normal weight and (n = 44) with obesity. Anthropometric, biochemical, lifestyle data, and fecal samples were collected and analyzed. We used shotgun metagenomic sequencing to characterize microbial communities of stool samples. Vitamin D levels were significantly associated with alpha and beta diversities. Serum vitamin D levels were positively associated with bacteria known to regulate immunological responses; Bacteroides thetaiotaomicron in the normal weight group (r = 0.34, p = 0.03) and Bifidobacterium adolescentis in the obesity group (r = 0.33, p = 0.04). In conclusion, the findings suggest that vitamin D status may play a role in regulating the gut microbiota composition by inhibiting the growth of pathogenic bacteria while nourishing the beneficial strains.

Hearing rehabilitation and microbial shift after middle ear surgery with Vibrant Soundbridge in patients with chronic otitis media

INTRODUCTION

Patients with otitis media (OM) encounter significant functional hearing impairment with conductive, or a combined hearing loss and long-term sequelae involving impaired speech/language development in children, reduced academic achievement and irreversible disorders of middle and inner ear requiring a long time therapy and/or multiple surgeries. In its persistent chronic form, Otitis media (COM) can often only be treated by undergoing ear surgery for hearing restoration. The persistent inflammatory reaction plays a major role, often caused by multi-resistant pathogens in the ear. Herein, we present outcomes of patients implanted with currently the only FDA approved active Middle Ear Implant Vibrant Soundbridge (VSB), suffering from persistent COM.

METHODS

The study enrolled 42 patients, treated by performing middle ear (ME) surgery to different extents and implanted with the VSB to various structures in the ME. Included were 17 children and 25 adults that had recurrent and/or persisting OM and significant hearing loss. Preoperative and postoperative patients' audiometric data were evaluated and the benefit with VSB assessed using the Glasgow Benefit Inventory for adults and pediatric cohorts. The microbial spectrum of pathogens was assessed before and after surgery, exploring the colonization of the otopathogens, as well as the intestinal microbiome from individually burdened patients.

RESULTS

The mean functional gain is 29.7 dB HL (range from 10 to 56.2 dB HL) with a significant improvement in speech intelligibility in quiet. Following VSB implantation, no significant differences in coupling were observed at low complication rates. Postoperatively patients showed significantly increased benefit with VSB compared to the untreated situation, including less otorrhea, pain, medical visits, and medication intake, with no recurrent OM and significant bacterial shift in otopathogens. The analysis of the intestinal microbiome displayed a high abundance of bacterial strains that might be linked to chronic and persistent inflammation.

CONCLUSIONS

Functional ear surgery including rehabilitation with a VSB in patients suffering from COM present to be safe and effective. The successful acceptance accompanied by the improved audiological performance resulted in significant benefit with VSB, with a shift in the ear pathogens and altered microbiome and thus is a great opportunity to be treated.

The gut microbiota-artery axis: A bridge between dietary lipids and atherosclerosis?

Atherosclerotic cardiovascular disease is one of the major leading global causes of death. Growing evidence has demonstrated that gut microbiota (GM) and its metabolites play a pivotal role in the onset and progression of atherosclerosis (AS), now known as GM-artery axis. There are interactions between dietary lipids and GM, which ultimately affect GM and its metabolites. Given these two aspects, the GM-artery axis may play a mediating role between dietary lipids and AS. Diets rich in saturated fatty acids (SFAs), omega-6 polyunsaturated fatty acids (n-6 PUFAs), industrial trans fatty acids (TFAs), and cholesterol can increase the levels of atherogenic microbes and metabolites, whereas monounsaturated fatty acids (MUFAs), ruminant TFAs, and phytosterols (PS) can increase the levels of antiatherogenic microbes and metabolites. Actually, dietary phosphatidylcholine (PC), sphingomyelin (SM), and omega-3 polyunsaturated fatty acids (n-3 PUFAs) have been demonstrated to affect AS via the GM-artery axis. Therefore, that GM-artery axis acts as a communication bridge between dietary lipids and AS. Herein, we will describe the molecular mechanism of GM-artery axis in AS and discuss the complex interactions between dietary lipids and GM. In particular, we will highlight the evidence and potential mechanisms of dietary lipids affecting AS via GM-artery axis.

Fecal Microbiota Transplantation and Other Gut Microbiota Manipulation Strategies

The gut microbiota is composed of bacteria, archaea, phages, and protozoa. It is now well known that their mutual interactions and metabolism influence host organism pathophysiology. Over the years, there has been growing interest in the composition of the gut microbiota and intervention strategies in order to modulate it. Characterizing the gut microbial populations represents the first step to clarifying the impact on the health/illness equilibrium, and then developing potential tools suited for each clinical disorder. In this review, we discuss the current gut microbiota manipulation strategies available and their clinical applications in personalized medicine. Among them, FMT represents the most widely explored therapeutic tools as recent guidelines and standardization protocols, not only for intestinal disorders. On the other hand, the use of prebiotics and probiotics has evidence of encouraging findings on their safety, patient compliance, and inter-individual effectiveness. In recent years, avant-garde approaches have emerged, including engineered bacterial strains, phage therapy, and genome editing (CRISPR-Cas9), which require further investigation through clinical trials.

Colonic Microflora Protagonist of Liver Metabolism and Gut Permeability: Study on Mice Model

Alteration of gut microflora results in a metabolic imbalance in the liver. In the present study, we investigate the reversal potential of alteration of the colonic microflora via improving metabolism balance and regulating the altered tight junction of the intestinal tract. Animals were fed with high sugar diet to mimic the onset of the pathophysiological conditions of diabetes. Following induction, animals were divided into two reversal groups i.e., crude cefdinir and colon-specific formulated cefdinir, to alter the gut microflora. In the present study, we have tried to quantify the microbial content via metagenome analysis to provide an actual picture of the alteration and subsequent reversal. Expression of mRNA of junctional protein and parameters involved in liver metabolism was determined using qPCR. Results indicated direct effect of altered composition of gut microflora on the gut permeability and metabolic alteration. Metagenomic analysis showed least evenness and richness in the HSD group whereas antibiotic-treated groups showed reversal of microflora towards control group with increased richness, evenness and decreased distance on PCoA plot. This changes in gut microflora composition changes expression of metabolic markers and thus insulin sensitivity. Targeting colonic microflora to have a reversal effect on T2D pathogenesis, found to have a positive impact on liver metabolic state with improved permeability markers of gut with SCFA alteration.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-022-01032-x.

Role of gastrointestinal microbial populations, a terra incognita of the human body in the management of intestinal bowel disease and metabolic disorders

Intestinal bowel disease (IBD) is a chronic immune-mediated clinical condition that affects the gastrointestinal tract and is mediated by an inflammatory response. Although it has been extensively studied, the multifactorial aetiology of this disorder makes it difficult to fully understand all the involved mechanisms in its development and therefore its treatment. In recent years, the fundamental role played by the human microbiota in the pathogenesis of IBD has been emphasised. Microbial imbalances in the gut bacterial communities and a lower species diversity in patients suffering from inflammatory gastrointestinal disorders compared to healthy individuals have been reported as principal factors in the development of IBD. These served to support scientific arguments for the use of probiotic microorganisms in alternative approaches for the prevention and treatment of IBD. In a homeostatic environment, the presence of bacteria (including probiotics) on the intestinal epithelial surface activates a cascade of processes by which immune responses inhibited and thereby commensal organisms maintained. At the same time these processes may support activities against specific pathogenic bacteria. In dysbiosis, these underlying mechanisms will serve to provoke a proinflammatory response, that, in combination with the use of antibiotics and the genetic predisposition of the host, will culminate in the development of IBD. In this review, we summarised the main causes of IBD, the physiological mechanisms involved and the related bacterial groups most frequently associated with these processes. The intention was to enable a better understanding of the interaction between the intestinal microbiota and the host, and to suggest possibilities by which this knowledge can be useful for the development of new therapeutic treatments.

Uncovering the biogeography of the microbial commmunity and its association with nutrient metabolism in the intestinal tract using a pig model

The gut microbiota is a complex ecosystem that is essential for the metabolism, immunity and health of the host. The gut microbiota also plays a critical role in nutrient absorption and metabolism, and nutrients can influence the growth and composition of the gut microbiota. To gain a better understanding of the relationship between the gut microbial composition and nutrient metabolism, we used a pig model by collecting the contents of the different intestinal locations from six pigs to investigate microbial composition in different intestinal locations based on 16S rRNA gene sequencing and the concentrations of short-chain fatty acids (SCFAs), amino acids, fat, and crude ash in different intestinal locations using gas chromatography and chemical analysis. The results showed that the richness and diversity of intestinal microbial communities gradually increased from the small intestine to the large intestine. The relative abundance of Proteobacteria was higher in the jejunum and ileum, whereas the proportion of Firmicutes was higher in the cecum and colon. The concentrations of SCFAs were higher in the cecum and colon (P < 0.05). The concentrations of amino acids were higher in the small intestine than in the large intestine, while the amino acid content was significantly higher in the ascending colon than in the transverse colon and descending colon. The correlation analysis revealed that Ruminococcaceae UCG-005, Coriobacteriaceae_uncultured, [Eubacterium] hallii group, Mogibacterium and Lachnospiraceae AC2044 group had a higher positive correlation with SCFAs, crude ash and fat but had a negative correlation with amino acids in different gut locations of pigs. These findings may serve as fundamental data for using nutrient metabolism to regulate human and animal gut microbes and health and provide guidance for exploring host-microbe bidirectional interaction mechanisms and driving pathways.

A, Bhardwaj S, Yadav NK, Patel A, Patel A. Gut Microbiota Interventions for the Management of Obesity: A Literature Review

The gut microbiota (GM) has been recognized as an important factor in the development of metabolic diseases such as obesity; it has been reported that the composition of the GM differs in obese and lean subjects, suggesting that microbiota dysbiosis can contribute to changes in body weight. Dysbiosis occurs due to an imbalance in the composition of gut bacteria, changes in the metabolic process, or changes in the distribution of microbiota within the gut. Dysbiosis can change the functioning of the intestinal barrier and the gut-associated lymphoid tissues (GALT). Microbial manipulation may help with preventing or treating weight gain and associated comorbidities. Approaches to this may range from dietary manipulation, which is suitable to treat the individual’s microflora, to probiotics, prebiotics, synbiotics, and fecal microbiota transplant (FMT).

Effect of Probiotic Lactobacillus plantarum Dad-13 on Metabolic Profiles and Gut Microbiota in Type 2 Diabetic Women: A Randomized Double-Blind Controlled Trial

Several pathways link type 2 diabetes (T2D) mellitus to the gut microbiome. By modifying the gut microbiota (GM), probiotics may be useful in the treatment of T2D. Lactobacillus plantarum Dad-13 is an indigenous Indonesian probiotic strain that has colonized the digestive tracts of healthy Indonesian adults. Furthermore, the GM of Indonesians is dominated by L. plantarum. The probiotic L. plantarum Dad-13 is likely suitable for Indonesians. This study aimed to assess the effect of the probiotic L. plantarum Dad-13 on metabolic profiles and GM of women with T2D in Yogyakarta, Indonesia. Twenty women from each group of forty T2D patients received either a probiotic or a placebo. The probiotic group consumed 1 g skim milk powder containing 10¹⁰ CFU/g L. plantarum daily for 11 weeks. The placebo group received 1 g skim milk powder only daily for 11 weeks. At the start and end of the experiment, anthropometric measures, dietary intake surveys, blood samples, and fecal samples were obtained. The GM analysis of all samples was performed using polymerase chain reaction, and Illumina Novaseq was applied to the selected samples from each group at the beginning and end of the trial. Short-chain fatty acids (SCFAs) were analyzed with gas chromatography. The level of HbA1c in the probiotic group (n:10) significantly decreased from 9.34 ± 2.79% to 8.32 ± 2.04%. However, in comparison with the placebo (n:8), L. plantarum Dad-13 supplementation did not significantly decrease the HbA1c level. No significant change was observed in the fasting blood sugar and total cholesterol levels in either group. The GM analysis showed that L. plantarum Dad-13 supplementation resulted in a considerable increase in the L. plantarum number. No significant changes were observed in the Bifidobacterium and Prevotella populations. In addition, no significant change was observed in the fecal pH and SCFA (e.g., acetic acid, propionate, butyrate, and total SCFA) after supplementation with L. plantarum Dad-13.

Microbiomics: The Next Pillar of Precision Medicine and Its Role in African Healthcare

Limited access to technologies that support early monitoring of disease risk and a poor understanding of the geographically unique biological and environmental factors underlying disease, represent significant barriers to improved health outcomes and precision medicine efforts in low to middle income countries. These challenges are further compounded by the rich genetic diversity harboured within Southern Africa thus necessitating alternative strategies for the prediction of disease risk and clinical outcomes in regions where accessibility to personalized healthcare remains limited. The human microbiome refers to the community of microorganisms (bacteria, archaea, fungi and viruses) that co-inhabit the human body. Perturbation of the natural balance of the gut microbiome has been associated with a number of human pathologies, and the microbiome has recently emerged as a critical determinant of drug pharmacokinetics and immunomodulation. The human microbiome should therefore not be omitted from any comprehensive effort towards stratified healthcare and would provide an invaluable and orthogonal approach to existing precision medicine strategies. Recent studies have highlighted the overarching effect of geography on gut microbial diversity as it relates to human health. Health insights from international microbiome datasets are however not yet verified in context of the vast geographical diversity that exists throughout the African continent. In this commentary we discuss microbiome research in Africa and its role in future precision medicine initiatives across the African continent.

Bacteria and Methanogens in the Human Microbiome: a Review of Syntrophic Interactions

Methanogens are microorganisms belonging to the Archaea domain and represent the primary source of biotic methane. Methanogens encode a series of enzymes which can convert secondary substrates into methane following three major methanogenesis pathways. Initially recognized as environmental microorganisms, methanogens have more recently been acknowledged as host-associated microorganisms after their detection and initial isolation in ruminants in the 1950s. Methanogens have also been co-detected with bacteria in various pathological situations, bringing their role as pathogens into question. Here, we review reported associations between methanogens and bacteria in physiological and pathological situations in order to understand the metabolic interactions explaining these associations. To do so, we describe the origin of the metabolites used for methanogenesis and highlight the central role of methanogens in the syntrophic process during carbon cycling. We then focus on the metabolic abilities of co-detected bacterial species described in the literature and infer from their genomes the probable mechanisms of their association with methanogens. The syntrophic interactions between bacteria and methanogens are paramount to gut homeostasis. Therefore, any dysbiosis affecting methanogens might impact human health. Thus, the monitoring of methanogens may be used as a bio-indicator of dysbiosis. Moreover, new therapeutic approaches can be developed based on their administration as probiotics. We thus insist on the importance of investigating methanogens in clinical microbiology.

A Gut Instinct on Leukaemia: A New Mechanistic Hypothesis for Microbiota-Immune Crosstalk in Disease Progression and Relapse

Despite significant advances in the treatment of Chronic Myeloid and Acute Lymphoblastic Leukaemia (CML and ALL, respectively), disease progression and relapse remain a major problem. Growing evidence indicates the loss of immune surveillance of residual leukaemic cells as one of the main contributors to disease recurrence and relapse. More recently, there was an appreciation for how the host’s gut microbiota predisposes to relapse given its potent immunomodulatory capacity. This is especially compelling in haematological malignancies where changes in the gut microbiota have been identified after treatment, persisting in some patients for years after the completion of treatment. In this hypothesis-generating review, we discuss the interaction between the gut microbiota and treatment responses, and its capacity to influence the risk of relapse in both CML and ALL We hypothesize that the gut microbiota contributes to the creation of an immunosuppressive microenvironment, which promotes tumour progression and relapse.

Effects of Growth Stage and Rearing Pattern on Pig Gut Microbiota

Understanding the developmental period or the patterns of gut microbiota is important for nutritionists when designing a feed formula or adjusting a feeding strategy. The effects of growth stage or rearing pattern on pig gut microbiota have not been fully investigated. Herein, 39 fecal samples from pigs aged 3-9 months under two rearing patterns were collected to analyze the gut microbiome. Samples were clustered into three distinct groups, namely, early (3 months), middle (5 months), and late (7 and 9 months) stages, using principal coordinate analysis and analysis of similarities test. The rearing-pattern effects were very minimal, and no differences were observed in the alpha diversity [observed operational taxonomic units (OTUs) and Shannon index] of gut microbiota. From early and middle to late stage, Shannon index gradually decreased and OTUs gradually increased. Pigs at early stage were enriched with bacteria from family Prevotellaceae, including the genera Prevotella_9 and Prevotellaceae_NK3B31, whereas pigs at late stage were enriched with family Ruminococcaceae, including genera Ruminococcaceae_UCG-005 and Oscillospira. Pigs in the semi-free-grazing farm group were significantly enriched with bacteria from order Clostridiales. Growth stage better explained the changes in porcine gut microbiota than rearing patterns.

Enzymes-Assisted Extraction of Plants for Sustainable and Functional Applications

The scientific community and industrial companies have discovered significant enzyme applications to plant material. This rise imparts to changing consumers' demands while searching for 'clean label' food products, boosting the immune system, uprising resistance to bacterial and fungal diseases, and climate change challenges. First, enzymes were used for enhancing production yield with mild and not hazardous applications. However, enzyme specificity, activity, plant origin and characteristics, ratio, and extraction conditions differ depending on the goal. As a result, researchers have gained interest in enzymes' ability to cleave specific bonds of macroelements and release bioactive compounds by enhancing value and creating novel derivatives in plant extracts. The extract is enriched with reducing sugars, phenolic content, and peptides by disrupting lignocellulose and releasing compounds from the cell wall and cytosolic. Nonetheless, depolymerizing carbohydrates and using specific enzymes form and release various saccharides lengths. The latest studies show that oligosaccharides released and formed by enzymes have a high potential to be slowly digestible starches (SDS) and possibly be labeled as prebiotics. Additionally, they excel in new technological, organoleptic, and physicochemical properties. Released novel derivatives and phenolic compounds have a significant role in human and animal health and gut-microbiota interactions, affecting many metabolic pathways. The latest studies have contributed to enzyme-modified extracts and products used for functional, fermented products development and sustainable processes: in particular, nanocellulose, nanocrystals, nanoparticles green synthesis with drug delivery, wound healing, and antimicrobial properties. Even so, enzymes' incorporation into processes has limitations and is regulated by national and international levels.

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.

Engineering Organoids for in vitro Modeling of Phenylketonuria

Phenylketonuria is a recessive genetic disorder of amino-acid metabolism, where impaired phenylalanine hydroxylase function leads to the accumulation of neurotoxic phenylalanine levels in the brain. Severe cognitive and neuronal impairment are observed in untreated/late-diagnosed patients, and even early treated ones are not safe from life-long sequelae. Despite the wealth of knowledge acquired from available disease models, the chronic effect of Phenylketonuria in the brain is still poorly understood and the consequences to the aging brain remain an open question. Thus, there is the need for better predictive models, able to recapitulate specific mechanisms of this disease. Human induced pluripotent stem cells (hiPSCs), with their ability to differentiate and self-organize in multiple tissues, might provide a new exciting in vitro platform to model specific PKU-derived neuronal impairment. In this review, we gather what is known about the impact of phenylalanine in the brain of patients and highlight where hiPSC-derived organoids could contribute to the understanding of this disease.

Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease

BACKGROUND

The human gut harbors trillions of microbes that play dynamic roles in health. While the microbiome contributes to many cardiometabolic traits by modulating host inflammation and metabolism, there is an incomplete understanding regarding the extent that and mechanisms by which individual microbes impact risk and development of cardiovascular disease (CVD). The Framingham Heart Study (FHS) is a multi-generational observational study following participants over decades to identify risk factors for CVD by correlating genetic and phenotypic factors with clinical outcomes. As a large-scale population-based cohort with extensive clinical phenotyping, FHS provides a rich landscape to explore the relationships between the gut microbiome and cardiometabolic traits.

METHODS

We performed 16S rRNA gene sequencing on stool from 1423 participants of the FHS Generation 3, OMNI2, and New Offspring Spouse cohorts. Data processing and taxonomic assignment were performed with the 16S bioBakery workflow using the UPARSE pipeline. We conducted statistical analyses to investigate trends in overall microbiome composition and diversity in relation to disease states and systematically examined taxonomic associations with a variety of clinical traits, disease phenotypes, clinical blood markers, and medications.

RESULTS

We demonstrate that overall microbial diversity decreases with increasing 10-year CVD risk and body mass index measures. We link lifestyle factors, especially diet and exercise, to microbial diversity. Our association analyses reveal both known and unreported microbial associations with CVD and diabetes, related prescription medications, as well as many anthropometric and blood test measurements. In particular, we observe a set of microbial species that demonstrate significant associations with CVD risk, metabolic syndrome, and type 2 diabetes as well as a number of shared associations between microbial species and cardiometabolic subphenotypes.

CONCLUSIONS

The identification of significant microbial taxa associated with prevalent CVD and diabetes, as well as risk for developing CVD, adds to increasing evidence that the microbiome may contribute to CVD pathogenesis. Our findings support new hypothesis generation around shared microbe-mediated mechanisms that influence metabolic syndrome, diabetes, and CVD risk. Further investigation of the gut microbiomes of CVD patients in a targeted manner may elucidate microbial mechanisms with diagnostic and therapeutic implications.

Which Microbes Like My Diet and What Does It Mean for My Heart?

Cardiovascular diseases are the most common causes of hospitalization, death and disability in Europe. Despite our knowledge of nonmodifiable and modifiable cardiovascular classical risk factors, the morbidity and mortality in this group of diseases remains high, leading to high social and economic costs. Therefore, it is necessary to explore new factors, such as the gut microbiome, that may play a role in many crucial pathological processes related to cardiovascular diseases. Diet is a potentially modifiable cardiovascular risk factor. Fats, proteins, carbohydrates, vitamins and minerals are nutrients that are essential to the proper function of the human body. The style and composition of the human diet has changed over time, evolving from a hunter–gatherer diet to an industrialized and Westernized modern diet that includes processed products. The relationship between the gut microbiome, diet and cardiovascular diseases is complex and still not fully understood. In this review, we discuss, in the context of diet, why particular microbes occur in individuals and how they can influence the host’s cardiovascular system in health and disease. We investigate the role of particular microorganisms and changes in the Firmicutes/Bacteroidetes ratio.

Exploration of Relationships among Clinical Gastrointestinal Indicators and Social and Sensory Symptom Severity in Children with Autism Spectrum Disorder

Autism Spectrum Disorders (ASD) are associated with co-morbidities such as gastrointestinal (GI) symptomatology, which in the absence of known causes are potential indicators of gut microbiota that may influence behavior. This study's purpose was to explore relationships among clinical GI indicators-diet, abdominal pain, and stool status-and ASD symptom severity, specifically social and sensory symptoms. Participants were 33 children with ASD, 3 to 16 years. The Social Responsiveness Scale (SRS-2) and the Child Sensory Profile Scale (CSP-2) were used to appraise social and sensory symptomatology. Significant difference was found in overall SRS-2, t(31) = -3.220, p = 0.003 when compared by abdominal pain status using independent samples t-tests. Significant difference was observed for overall CSP-2, t(31) = -2.441, p = 0.021, when grouped by stool. The three clinical GI variables predicted overall SRS-2 score using multiple linear regression, F(3, 32) = 3.257, p = 0.036; coefficient for abdominal pain significantly contributed to the outcome. Findings contribute to the growing literature signaling the need to understand occurrence of GI symptomatology more deeply, and in consideration of diet status and its implications in the children's everyday lives, behaviors, and symptom severity.

Reduced Feeding Frequency Improves Feed Efficiency Associated With Altered Fecal Microbiota and Bile Acid Composition in Pigs

A biphasic feeding regimen exerts an improvement effect on feed efficiency of pigs. While gut microbiome and metabolome are known to affect the host phenotype, so far the effects of reduced feeding frequency on fecal microbiota and their metabolism in pigs remain unclear. Here, the combination of 16S rRNA sequencing technique as well as untargeted and targeted metabolome analyses was adopted to investigate the fecal microbiome and metabolome of growing–finishing pigs in response to a biphasic feeding [two meals per day (M2)] pattern. Sixty crossbred barrows were randomly assigned into two groups with 10 replicates (three pigs/pen), namely, the free-access feeding group (FA) and the M2 group. Pigs in the FA group were fed free access while those in the M2 group were fed ad libitum twice daily for 1 h at 8:00 and 18:00. Results showed that pigs fed biphasically exhibited increased feed efficiency compared to FA pigs. The Shannon and Simpson indexes were significantly increased by reducing the feeding frequency. In the biphasic-fed pigs, the relative abundances of Subdoligranulum, Roseburia, Mitsuokella, and Terrisporobacter were significantly increased while the relative abundances of unidentified_Spirochaetaceae, Methanobrevibacter, unidentified_Bacteroidales, Alloprevotella, Parabacteroides, and Bacteroides were significantly decreased compared to FA pigs. Partial least-square discriminant analysis (PLS-DA) analysis revealed an obvious variation between the FA and M2 groups; the differential features were mainly involved in arginine, proline, glycine, serine, threonine, and tryptophan metabolism as well as primary bile acid (BA) biosynthesis. In addition, the changes in the microbial genera were correlated with the differential fecal metabolites. A biphasic feeding regimen significantly increased the abundances of primary BAs and secondary BAs in feces of pigs, and the differentially enriched BAs were positively correlated with some specific genera. Taken together, these results suggest that the improvement effect of a reduced feeding frequency on feed efficiency of pigs might be associated with the altered fecal microbial composition and fecal metabolite profile in particular the enlarged stool BA pool.

The Microbiome in Childhood Acute Lymphoblastic Leukemia

For almost 30 years, the term "holobiont" has referred to an ecological unit where a host (e.g., human) and all species living in or around it are considered together. The concept highlights the complex interactions between the host and the other species, which, if disturbed may lead to disease and premature aging. Specifically, the impact of microbiome alterations on the etiology of acute lymphoblastic leukemia (ALL) in children is not fully understood, but has been the focus of much research in recent years. In ALL patients, significant reductions in microbiome diversity are already observable at disease onset. It remains unclear whether such alterations at diagnosis are etiologically linked with leukemogenesis or simply due to immunological alteration preceding ALL onset. Regardless, all chemotherapeutic treatment regimens severely affect the microbiome, accompanied by severe side effects, including mucositis, systemic inflammation, and infection. In particular, dominance of Enterococcaceae is predictive of infections during chemotherapy. Long-term dysbiosis, like depletion of Faecalibacterium, has been observed in ALL survivors. Modulation of the microbiome (e.g., by fecal microbiota transplant, probiotics, or prebiotics) is currently being researched for potential protective effects. Herein, we review the latest microbiome studies in pediatric ALL patients.