Diet-induced dysbiosis of the intestinal microbiota and the effects on immunity and disease

From Probiotics to Psychobiotics: Live Beneficial Bacteria Which Act on the Brain-Gut Axis

There is an important relationship between probiotics, psychobiotics and cognitive and behavioral processes, which include neurological, metabolic, hormonal and immunological signaling pathways; the alteration in these systems may cause alterations in behavior (mood) and cognitive level (learning and memory). Psychobiotics have been considered key elements in affective disorders and the immune system, in addition to their effect encompassing the regulation of neuroimmune regulation and control axes (the hypothalamic-pituitary-adrenal axis or HPA, the sympathetic-adrenal-medullary axis or SAM and the inflammatory reflex) in diseases of the nervous system. The aim of this review is to summarize the recent findings about psychobiotics, the brain-gut axis and the immune system. The review focuses on a very new and interesting field that relates the microbiota of the intestine with diseases of the nervous system and its possible treatment, in neuroimmunomodulation area. Indeed, although probiotic bacteria will be concentrated after ingestion, mainly in the intestinal epithelium (where they provide the host with essential nutrients and modulation of the immune system), they may also produce neuroactive substances which act on the brain-gut axis.

High intake of dietary fructose in overweight/obese teenagers associated with depletion of Eubacterium and Streptococcus in gut microbiome

Background: A western high fat, high carbohydrate diet has been shown to be associated with decreased gut bacterial diversity and reductions in beneficial bacteria. This gut bacteria dysbiosis could develop in early life and contribute to chronic disease risk such as obesity, type 2 diabetes and non-alcoholic fatty liver disease.Objective: To determine how dietary macronutrients are associated with the relative abundance of gut bacteria in healthy adolescents.Methods: Fifty-two obese participants (12-19 years) from two studies, many who were primarily of Hispanic background, provided fecal samples for 16S rRNA gene sequencing. Dietary macronutrients were assessed using 24-hour diet recalls and body composition was assessed using DEXA. General regression models assuming a negative binomial distribution were used to examine the associations between gut bacteria and dietary fiber, saturated fat, unsaturated fats, protein, added sugar, total sugar and free fructose after adjusting for age, gender, race/ethnicity, body fat percentage, study and caloric intake.Results: The genera Eubacterium (Benjamini-Hochberg (BH) corrected p-value = 0.10) and Streptococcus (BH corrected p-value = 0.04) were inversely associated with dietary fructose intake. There were no other significant associations between abundances of gut microbes and other dietary macronutrients, including fiber, fat, protein, total sugar or added sugar.Conclusions: High dietary fructose was associated with lower abundance of the beneficial microbes Eubacterium and Streptococcus, which are involved with carbohydrate metabolism.

Contribution of Non-immune Cells to Activation and Modulation of the Intestinal Inflammation

The mucosal immune system constitutes a physical and dynamic barrier against foreign antigens and pathogens and exerts control mechanisms to maintain intestinal tolerance to the microbiota and food antigens. Chronic alterations of the intestinal homeostasis predispose to inflammatory diseases of the gastrointestinal tract, such as Inflammatory Bowel Diseases (IBD). There is growing evidence that the frequency and severity of these diseases are increasing worldwide, which may be probably due to changes in environmental factors. Several stromal and immune cells are involved in this delicate equilibrium that dictates homeostasis. In this review we aimed to summarize the role of epithelial cells and fibroblasts in the induction of mucosal inflammation in the context of IBD. It has been extensively described that environmental factors are key players in this process, and the microbiome of the gastrointestinal tract is currently being intensively investigated due to its profound impact the immune response. Recent findings have demonstrated the interplay between dietary and environmental components, the gut microbiome, and immune cells. "Western" dietary patterns, such as high caloric diets, and pollution can induce alterations in the gut microbiome that in turn affect the intestinal and systemic homeostasis. Here we summarize current knowledge on the influence of dietary components and air particulate matters on gut microbiome composition, and the impact on stromal and immune cells, with a particular focus on promoting local inflammation.

Peptidomic and glycomic profiling of commercial dairy products: identification, quantification and potential bioactivities

Peptidomics and glycomics are recently established disciplines enabling researchers to characterize functional characteristics of foods at a molecular level. Milk-derived bioactive peptides and oligosaccharides have garnered both scientific and commercial interest because they possess unique functional properties, such as anti-hypertensive, immunomodulatory and prebiotic activities; therefore, the objective of this work was to employ peptidomic and glycomic tools to identify and measure relative and absolute quantities of peptides and oligosaccharides in widely consumed dairy products. Specifically, we identified up to 2117 unique peptides in 10 commercial dairy products, which together represent the most comprehensive peptidomic profiling of dairy milk in the literature to date. The quantity of peptides, measured by ion-exchange chromatography, varied between 60 and 130 mg/L among the same set of dairy products, which the majority originated from caseins, and the remaining from whey proteins. A recently published bioactive peptide database was used to identify 66 unique bioactive peptides in the dataset. In addition, 24 unique oligosaccharide compositions were identified in all the samples by nano LC Chip QTOF. Neutral oligosaccharides were the most abundant class in all samples (66-91.3%), followed by acidic (8.6-33.7%), and fucosylated oligosaccharides (0-4.6%). Variation of total oligosaccharide concentration ranged from a high of 65.78 to a low of 24.82 mg/L. Importantly, characterizing bioactive peptides and oligosaccharides in a wider number of dairy products may lead to innovations that go beyond the traditional vision of dairy components used for nutritional purposes but that will rather focus on improving human health.

Bifidobacterium longum and VSL#3® amelioration of TNBS-induced colitis associated with reduced HMGB1 and epithelial barrier impairment

Probiotics are a beneficial treatment for inflammatory bowel disease (IBD). However, studies comparing the effects of similar doses of single and mixed probiotics on IBD are scarce. High mobility group box 1 (HMGB1) is an important proinflammatory mediator involved IBD development. The present study assessed fecal HMGB1 levels in IBD patients and compared the effects of similar doses of Bifidobacterium longum (Bif) versus VSL#3® on HMGB1 levels in 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced murine colitis. Twenty-four mice were divided into four treatment groups (n = 6 per group): ethanol (control), TNBS, TNBS + Bif, and TNBS + VSL#3®. Bif and VSL#3® (4 × 109 CFU/dose) were administered daily by intragastric gavage, beginning 3 d before TNBS treatment, for a total of 7 d. Fecal HMGB1 levels were higher in both active IBD patients and TNBS-induced colitis mice versus their respective controls. Both Bif and VSL#3® improved intestinal inflammation and fecal microbiota imbalance in TNBS-induced colitis mice. Both treatments also reduced serum and fecal HMGB1 levels as well as increased expression of zonula occludins-1, occludin, and claudin-1 in colon tissues. In Caco-2 cells, HMGB1 reduced transepithelial electrical resistance, zonula occludins-1 protein expression, and increased paracellular permeability of FITC-dextran; the opposite was found with both probiotic treatments. These findings suggest Bif and VSL#3® have similar beneficial effects on TNBS-induced colitis, possibly through inhibition of HMGB1 release and subsequent HMGB1-mediated gut barrier dysfunction. The present study provides novel insights into probiotic treatment of IBD.

Insights on Medical Nutrition Therapy for Type 2 Diabetes Mellitus: An Indian Perspective

It is critical to integrate medical nutrition therapy (MNT) provided by a registered dietician (RD) into primary care of type 2 diabetes mellitus (T2DM). This is necessary to achieve the goals of improving overall metabolic measures beyond calorie restriction and weight loss. Misconceptions about nutrition in T2DM add to the challenges of executing MNT in a culturally sensitive population. The current review provides insights into MNT for the prevention and management of T2DM in India, based on both evidence and experience. It revisits historical Indian studies and provides information on appropriate dietary intake of carbohydrates (60-70%), proteins (~ 20%) and fats (10%) that will be acceptable and beneficial in an Indian T2DM population. It discusses nuances of types of carbohydrates and fats and explains associations of increased dietary fiber intake, balanced intake of low and high glycemic index foods and substitution of saturated fats with plant-based polyunsaturated fats in improving outcomes of T2DM and attenuating risk factors. The article also deliberates upon special patient populations with comorbid conditions and diseases and the necessary adjustments needed in their nutritional care. It outlines a step-wise approach to MNT involving a careful interplay of nutrition assessment, diagnosis, individualization and patient counseling. Overall, the success of MNT relies on providing accurate, acceptable and appropriate dietary choices for continued patient adherence. Collaborative efforts from diabetologists, endocrinologists, internists and RDs are required to prioritize and implement MNT in diabetes practice in India.Funding: Signutra Inc.

Gut Mucosal Proteins and Bacteriome Are Shaped by the Saturation Index of Dietary Lipids

The dynamics of the tripartite relationship between the host, gut bacteria and diet in the gut is relatively unknown. An imbalance between harmful and protective gut bacteria, termed dysbiosis, has been linked to many diseases and has most often been attributed to high-fat dietary intake. However, we recently clarified that the type of fat, not calories, were important in the development of murine colitis. To further understand the host-microbe dynamic in response to dietary lipids, we fed mice isocaloric high-fat diets containing either milk fat, corn oil or olive oil and performed 16S rRNA gene sequencing of the colon microbiome and mass spectrometry-based relative quantification of the colonic metaproteome. The corn oil diet, rich in omega-6 polyunsaturated fatty acids, increased the potential for pathobiont survival and invasion in an inflamed, oxidized and damaged gut while saturated fatty acids promoted compensatory inflammatory responses involved in tissue healing. We conclude that various lipids uniquely alter the host-microbe interaction in the gut. While high-fat consumption has a distinct impact on the gut microbiota, the type of fatty acids alters the relative microbial abundances and predicted functions. These results support that the type of fat are key to understanding the biological effects of high-fat diets on gut health.

Metabolic Modeling of Clostridium difficile Associated Dysbiosis of the Gut Microbiota

Recent in vitro experiments have demonstrated the ability of the pathogen Clostridium difficile and commensal gut bacteria to form biofilms on surfaces, and biofilm development in vivo is likely. Various studies have reported that 3%–15% of healthy adults are asymptomatically colonized with C. difficile, with commensal species providing resistance against C. difficile pathogenic colonization. C. difficile infection (CDI) is observed at a higher rate in immunocompromised patients previously treated with broad spectrum antibiotics that disrupt the commensal microbiota and reduce competition for available nutrients, resulting in imbalance among commensal species and dysbiosis conducive to C. difficile propagation. To investigate the metabolic interactions of C. difficile with commensal species from the three dominant phyla in the human gut, we developed a multispecies biofilm model by combining genome-scale metabolic reconstructions of C. difficile, Bacteroides thetaiotaomicron from the phylum Bacteroidetes, Faecalibacterium prausnitzii from the phylum Firmicutes, and Escherichia coli from the phylum Proteobacteria. The biofilm model was used to identify gut nutrient conditions that resulted in C. difficile-associated dysbiosis characterized by large increases in C. difficile and E. coli abundances and large decreases in F. prausnitzii abundance. We tuned the model to produce species abundances and short-chain fatty acid levels consistent with available data for healthy individuals. The model predicted that experimentally-observed host-microbiota perturbations resulting in decreased carbohydrate/increased amino acid levels and/or increased primary bile acid levels would induce large increases in C. difficile abundance and decreases in F. prausnitzii abundance. By adding the experimentally-observed perturbation of increased host nitrate secretion, the model also was able to predict increased E. coli abundance associated with C. difficile dysbiosis. In addition to rationalizing known connections between nutrient levels and disease progression, the model generated hypotheses for future testing and has the capability to support the development of new treatment strategies for C. difficile gut infections.

Dynamic Development of Fecal Microbiome During the Progression of Diabetes Mellitus in Zucker Diabetic Fatty Rats

Background: Although substantial efforts have been made to link the gut microbiota to type 2 diabetes, dynamic changes in the fecal microbiome under the pathological conditions of diabetes have not been investigated.

Methods: Four male Zucker diabetic fatty (ZDF) rats received Purina 5008 chow [protein = 23.6%, Nitrogen-Free Extract (by difference) = 50.3%, fiber (crude) = 3.3%, ash = 6.1%, fat (ether extract) = 6.7%, and fat (acid hydrolysis) = 8.1%] for 8 weeks. A total of 32 stool samples were collected from weeks 8 to 15 in four rats. To decipher the microbial populations in these samples, we used a 16S rRNA gene sequencing approach.

Results: Microbiome analysis showed that the changes in the fecal microbiome were associated with age and disease progression. In all the stages from 8 to 15 weeks, phyla Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria primarily dominated the fecal microbiome of the rats. Although Lactobacillus and Turicibacter were the predominant genera in 8- to 10-week-old rats, Bifidobacterium, Lactobacillus, Ruminococcus, and Allobaculum were the most abundant genera in 15-week-old rats. Of interest, compared to the earlier weeks, relatively greater diversity (at the genus level) was observed at 10 weeks of age. Although the microbiome of 12-week-old rats had the highest diversity, the diversity in 13–15-week-old rats was reduced. Spearman’s correlation analysis showed that F/B was negatively correlated with age. Random blood glucose was negatively correlated with Lactobacillus and Turicibacter but positively correlated with Ruminococcus and Allobaculum and Simpson’s diversity index.

Conclusion: We demonstrated the time-dependent alterations of the abundance and diversity of the fecal microbiome during the progression of diabetes in ZDF rats. At the genus level, dynamic changes were observed. We believe that this work will enhance our understanding of fecal microbiome development in ZDF rats and help to further analyze the role of the microbiome in metabolic diseases. Furthermore, our work may also provide an effective strategy for the clinical treatment of diabetes through microbial intervention.

Comparison and Evaluation of Four Species of Macro-Algaes as Dietary Ingredients in Litopenaeus vannamei Under Normal Rearing and WSSV Challenge Conditions: Effect on Growth, Immune Response, and Intestinal Microbiota

The study was conducted to compare and evaluate effects of four different macro-algaes on growth, immune response, and intestinal microbiota of Litopenaeus vannamei. In the rearing trial 1, shrimp were fed five diets containing four sources of macro-algaes for 8 weeks, named D1 (without macro-algae), D2 (Porphyra haitanensis), D3 (Undaria pinnatifida), D4 (Saccharina japonica), and D5 (Gracilaria lemaneiformis), respectively. Growth performance of shrimp in D5 diet was significantly higher than that of shrimp fed the control and D4 diet (P < 0.05); however, there is no significant difference among D2, D3, and D5 diets (P > 0.05). Apparent digestibility coefficients of dry matter from the D2, D3, and D5 diets were significantly higher than that from the control and D4 diets (P < 0.05). Supplementary macro-algaes enhanced hepatopancreas immunity through positively increasing total antioxidant status (TAS) and prophenoloxidase activity (ProPO), as well as up-regulating the hepatopancreas RNA expression of ProPO and IκBα and down-regulating the expression of transforming growth factor β. Furthermore, dietary macro-algaes modified intestinal microbiota of L. vannamei, boosting the relative abundance of beneficial bacterial such as Bacteroidetes, Firmicutes, and Bacillaceae, and decreasing those detrimental bacterial such as Gammaproteobacteria and Vibrionaceae. In the white spot syndrome virus (WSSV) challenge trial, shrimps were injected for 6-day after the rearing trial. On the fourth day, shrimp death started to occur, and the mortality in D2, D3, and D5 diets was significantly lower than that in control and SJ diets during 4-6 challenged days (P < 0.05). Dietary macro-algaes ameliorated hepatopancreas damage in L. vannamei by increasing TAS and ProPO activities and decreasing SOD activity, inhibiting the lipid peroxidation (malondialdehyde), as well as regulating the immune-related genes expression. Taken together, dietary macro-algaes availably relieved enterohepatic oxidative damage by improving antioxidant ability and immunity and regulated intestinal microbiota in L. vannamei. These results indicated that G. lemaneiformis is the most suitable macro-algae and then followed by U. pinnatifida and P. haitanensis as the feed ingredient for L. vannamei.

Dietary quality of predominantly traditional diets is associated with blood glucose profiles, but not with total fecal Bifidobacterium in Indonesian women

Background

A high quality modern diet is associated with reduced risk of metabolic disease and diabetes. However, it remains unclear whether the quality of predominantly traditional ethnic diets is associated with such conditions. Moreover, the relationship between dietary quality and microbiota, a potential mediator of metabolic disease, has not been studied.

Objective

We investigated the relationship of dietary quality of traditional ethnic diets in Indonesia with fasting blood glucose (FBG), HbA1c, and the number of fecal Bifidobacterium.

Design

A cross-sectional study was conducted in selected districts with predominantly animal- or plant-based traditional diets of West Sumatera and West Java provinces, respectively. A total of 240 apparently healthy women aged 19–50 years were randomly selected from 360 women screened by a cluster sampling design. Dietary quality was assessed by 2-day repeated 24-hour food recall, and scored using the Healthy Eating Index (HEI) 2010. FBG was quantified with the enzymatic colorimetric method, and HbA1c by using hexokinase and high-performance liquid chromatography, and total fecal Bifidobacterium by real-time quantitative polymerase chain reaction.

Results

The HEI scores of 99% of women were <51, indicating a low-quality diet. In adjusted multivariate regression, HEI was inversely associated with FBG (ß = -0.403; 95% CI = -0.789 to -0.016; p = 0.041) and HbA1c (ß = -0.018; 95% CI = -0.036 to 0.000; p = 0.048) but was not significantly associated with total levels of Bifidobacterium (ß = -0.007, p = 0.275). Bifidobacterium count was not significantly associated with either FBG or HbA1c levels.

Conclusion

Low dietary quality is clearly associated with risk of increased markers of blood glucose. However, any mediating role of Bifidobacterium between dietary quality and glucose outcomes was not apparent. Innovative interventions for healthy eating should be implemented to increase dietary quality of populations transitioning from predominantly traditional to modern diets, to reduce the risk of diabetes, especially in women.

A systematic review of enteric dysbiosis in chronic fatigue syndrome/myalgic encephalomyelitis

BACKGROUND

Chronic fatigue syndrome or myalgic encephalomyelitis (CFS/ME) is an illness characterised by profound and pervasive fatigue in addition to a heterogeneous constellation of symptoms. The aetiology of this condition remains unknown; however, it has been previously suggested that enteric dysbiosis is implicated in the pathogenesis of CFS/ME. This review examines the evidence currently available for the presence of abnormal microbial ecology in CFS/ME in comparison to healthy controls, with one exception being probiotic-supplemented CFS/ME patients, and whether the composition of the microbiome plays a role in symptom causation.

METHODS

EMBASE, Medline (via EBSCOhost), Pubmed and Scopus were systematically searched from 1994 to March 2018. All studies that investigated the gut microbiome composition of CFS/ME patients were initially included prior to the application of specific exclusion criteria. The association between these findings and patient-centred outcomes (fatigue, quality of life, gastrointestinal symptoms, psychological wellbeing) are also reported.

RESULTS

Seven studies that met the inclusion criteria were included in the review. The microbiome composition of CFS/ME patients was compared with healthy controls, with the exception of one study that compared to probiotic-supplemented CFS/ME patients. Differences were reported in each study; however, only three were considered statistically significant, and the findings across all studies were inconsistent. The quality of the studies included in this review scored between poor (< 54%), fair (54-72%) and good (94-100%) using the Downs and Black checklist.

CONCLUSIONS

There is currently insufficient evidence for enteric dysbiosis playing a significant role in the pathomechanism of CFS/ME. Recommendations for future research in this field include the use of consistent criteria for the diagnosis of CFS/ME, reduction of confounding variables by controlling factors that influence microbiome composition prior to sample collection and including more severe cases of CFS/ME.

The role of diet in the prevention and treatment of Inflammatory Bowel Diseases

Inflammatory bowel diseases (IBD) - Crohn's disease (CD) and ulcerative colitis (UC) - are chronic conditions characterised by relapsing inflammation of the gastrointestinal tract. They represent an increasing public health concern and an aetiological enigma due to unknown causal factors. The current knowledge on the pathogenesis of IBD is that genetically susceptible individuals develop intolerance to a dysregulated gut microflora (dysbiosis) and chronic inflammation develops as a result of environmental triggers. Among the environmental factors associated with IBD, diet plays an important role in modulating the gut microbiome, and, consequently, it could have a therapeutic impact on the disease course. An overabundance of calories and some macronutrients typical of the Western dietetic pattern increase gut inflammation, whereas several micronutrients characteristic of the Mediterranean Diet have the potential to modulate gut inflammation, according to recent evidence. Immunonutrition has emerged as a new concept putting forward the role of vitamins such as vitamins A, C, E, and D, folic acid, beta carotene and trace elements such as zinc, selenium, manganese and iron. However, when assessed in clinical trials, specific micronutrients showed a limited benefit. Further research is required to evaluate the role of individual food compounds and complex nutritional interventions with the potential to decrease inflammation as a means of prevention and management of IBD. The current dietary recommendations for disease prevention and management are scarce and non evidence-based. This review summarizes the current knowledge on the complex interaction between diet, microbiome and immune-modulation in IBD, with particular focus to the role of the Mediterranean Diet as a tool for prevention and treatment of the disease.

PGlyRP3 concerts with PPARγ to attenuate DSS-induced colitis in mice

Nutrients may modulate immunity through their transcription factors that act on both metabolic and immunity genes. It has been shown that the transcription factor of lipid ligands PPARγ physically binds the gene promoter of the peptidoglycan recognition protein (PGlyRP3), which showed anti-inflammatory action in vitro. It is hypothesized in the present work that olive oil feeding protects against toxicity of DSS-induced colitis via activation of the lipid transcription factor PPARγ that stimulates the anti-inflammatory PGlyRP3. Results: PGlyRP3 is expressed in mouse colon and up-regulated by olive oil feeding. Olive oil reduced mortality and severity scores of DSS-induced colitis and down-regulated the proinflammatory IL-1b, IL-6 and TNFα genes. This protective effect was accompanied by up-regulation of both PPARγ and PGlyRP3. Inhibition of PPARγ by its antagonist BADGE down-regulated PGlyRP3 and abolished the anti-inflammatory effect of olive oil feeding in this DSS-induced colitis model, reflecting the pivotal role of PPARγ binding nutrition and inflammation. Activation of PGlyRP3 by its ligand peptidoglycan was not responsible for the inflammation caused by peptidoglycan, since neutralization of TLR2 attenuated this inflammatory response without affecting the peptidoglycan-induced PGlyRP3 level. Olive oil activated the IκBα and inhibited NF-κB and cox-2 gene expressions, and p65 nuclear translocation in DSS-colitis mice, reflecting the involvement of the inhibition of NF-κB signaling pathway in the anti-inflammatory olive oil - PPARγ - PGlyRP3 access. This pathway was reactivated by the PPARγ antagonist BADGE. Conclusions: Olive oil regulates by the same transcription factor (PPARγ) both lipid metabolic and immune gene (PGlyRP3) expressions, exerting the anti-inflammatory effect, and protecting against DSS-induced colitis in mice.

Intestinal microbiota mediates Enterotoxigenic Escherichia coli-induced diarrhea in piglets

Background

Enterotoxigenic Escherichia coli (ETEC) causes diarrhea in humans, cows, and pigs. The gut microbiota underlies pathology of several infectious diseases yet the role of the gut microbiota in the pathogenesis of ETEC-induced diarrhea is unknown.

Results

By using an ETEC induced diarrheal model in piglet, we profiled the jejunal and fecal microbiota using metagenomics and 16S rRNA sequencing. A jejunal microbiota transplantation experiment was conducted to determine the role of the gut microbiota in ETEC-induced diarrhea. ETEC-induced diarrhea influenced the structure and function of gut microbiota. Diarrheal piglets had lower Bacteroidetes: Firmicutes ratio and microbiota diversity in the jejunum and feces, and lower percentage of Prevotella in the feces, but higher Lactococcus in the jejunum and higher Escherichia-Shigella in the feces. The transplantation of the jejunal microbiota from diarrheal piglets to uninfected piglets leaded to diarrhea after transplantation. Microbiota transplantation experiments also supported the notion that dysbiosis of gut microbiota is involved in the immune responses in ETEC-induced diarrhea.

Conclusion

We conclude that ETEC infection influences the gut microbiota and the dysbiosis of gut microbiota after ETEC infection mediates the immune responses in ETEC infection.

Electronic supplementary material

The online version of this article (10.1186/s12917-018-1704-9) contains supplementary material, which is available to authorized users.

Novel perspectives on fermented milks and cardiometabolic health with a focus on type 2 diabetes

This review will explore the observational and mechanistic evidence supporting the hypothesis that fermented milk consumption has beneficial effects on metabolism. Live cultures in fermented dairy are thought to contribute to gut microbial balance, which is likely an instrumental mechanism that protects the host against gut dysbiosis and systemic inflammation associated with cardiometabolic diseases. Lactic acid bacteria (LAB) release bioactive metabolites, such as exopolysaccharides and peptides, that have the potential to exert a wide range of metabolic and regulatory functions. In particular, peptides derived from fermented dairy products are likely to exert greater cardiometabolic and anti-inflammatory effects than nonfermented dairy. It is hypothesized that LAB-derived bioactive peptides have the potential to protect the host against cardiometabolic diseases through antimicrobial actions and to effect changes in gene expression of glucose regulatory and anti-inflammatory signaling pathways. The peptides released through fermentation may explain some of the health effects of fermented dairy products on cardiometabolic disease risk observed in epidemiological studies, particularly type 2 diabetes; however, mechanisms have yet to be explored in detail.

Iron Dysregulation and Dormant Microbes as Causative Agents for Impaired Blood Rheology and Pathological Clotting in Alzheimer's Type Dementia

Alzheimer’s disease and other similar dementias are debilitating neurodegenerative disorders whose etiology and pathogenesis remain largely unknown, even after decades of research. With the anticipated increase in prevalence of Alzheimer’s type dementias among the more susceptible aging population, the need for disease-modifying treatments is urgent. While various hypotheses have been put forward over the last few decades, we suggest that Alzheimer’s type dementias are triggered by external environmental factors, co-expressing in individuals with specific genetic susceptibilities. These external stressors are defined in the Iron Dysregulation and Dormant Microbes (IDDM) hypothesis, previously put forward. This hypothesis is consistent with current literature in which serum ferritin levels of individuals diagnosed with Alzheimer’s disease are significantly higher compared those of age- and gender-matched controls. While iron dysregulation contributes to oxidative stress, it also causes microbial reactivation and virulence of the so-called dormant blood (and tissue) microbiome. Dysbiosis (changes in the microbiome) or previous infections can contribute to the dormant blood microbiome (atopobiosis¹), and also directly promotes systemic inflammation via the amyloidogenic formation and shedding of potent inflammagens such as lipopolysaccharides. The simultaneous iron dysregulation and microbial aberrations affect the hematological system, promoting fibrin amylodiogenesis, and pathological clotting. Systemic inflammation and oxidative stress can contribute to blood brain barrier permeability and the ensuing neuro-inflammation, characteristic of Alzheimer’s type dementias. While large inter-individual variability exists, especially concerning disease pathogenesis, the IDDM hypothesis acknowledges primary causative factors which can be targeted for early diagnosis and/or for prevention of disease progression.

Functional eubacteria species along with trans-domain gut inhabitants favour dysgenic diversity in oxalate stone disease

Analyses across all three domains of life are necessary to advance our understanding of taxonomic dysbiosis in human diseases. In the present study, we assessed gut microbiota (eubacteria, archaea, and eukaryotes) of recurrent oxalate kidney stone suffers to explore the extent of trans-domain and functional species dysbiosis inside the gut. Trans-domain taxonomic composition, active oxalate metabolizer and butyrate-producing diversity were explored by utilizing frc-, but-, and buk- functional gene amplicon analysis. Operational taxonomic units (OTUs) level analyses confound with the observation that dysbiosis in gut microbiota is not just limited to eubacteria species, but also to other domains like archaea and eukaryotes. We found that some of healthy eubacterial population retained together with Oxalobacter formigenes and Lactobacillus plantarum colonization in disease condition (p < 0.001 & FDR = 0.05). Interestingly, trans-domain species diversity has been less shared and dysgenic taxa augmentation was found to be higher. Oxalate metabolizing bacterial species (OMBS) and butyrate-producing eubacteria species were found to be decreased in Oxalobacter non-colonizers; and Prevotella and Ruminococcus species which may contribute to oxalate metabolism and butyrate synthesis as well. Our study underscores fact that microbial dysbiosis is not limited to eubacteria only hence suggest the necessity of the trans-domain surveillance in metabolic diseases for intervention studies.

Gut microbes as future therapeutics in treating inflammatory and infectious diseases: Lessons from recent findings

The human gut microbiota has been the interest of extensive research in recent years and our knowledge on using the potential capacity of these microbes are growing rapidly. Microorganisms colonized throughout the gastrointestinal tract of human are coevolved through symbiotic relationship and can influence physiology, metabolism, nutrition and immune functions of an individual. The gut microbes are directly involved in conferring protection against pathogen colonization by inducing direct killing, competing with nutrients and enhancing the response of the gut-associated immune repertoire. Damage in the microbiome (dysbiosis) is linked with several life-threatening outcomes viz. inflammatory bowel disease, cancer, obesity, allergy, and auto-immune disorders. Therefore, the manipulation of human gut microbiota came out as a potential choice for therapeutic intervention of the several human diseases. Herein, we review significant studies emphasizing the influence of the gut microbiota on the regulation of host responses in combating infectious and inflammatory diseases alongside describing the promises of gut microbes as future therapeutics.

Longitudinal Effects of Supplemental Forage on the Honey Bee (Apis mellifera) Microbiota and Inter- and Intra-Colony Variability

Honey bees (Apis mellifera) provide vital pollination services for a variety of agricultural crops around the world and are known to host a consistent core bacterial microbiome. This symbiotic microbial community is essential to many facets of bee health, including likely nutrient acquisition, disease prevention and optimal physiological function. Being that the bee microbiome is likely involved in the digestion of nutrients, we either provided or excluded honey bee colonies from supplemental floral forage before being used for almond pollination. We then used 16S rRNA gene sequencing to examine the effects of forage treatment on the bees' microbial gut communities over four months. In agreement with previous studies, we found that the honey bee gut microbiota is quite stable over time. Similarly, we compared the gut communities of bees from separate colonies and sisters sampled from within the same hive over four months. Surprisingly, we found that the gut microbial communities of individual sisters from the same colony can exhibit as much variation as bees from different colonies. Supplemental floral forage had a subtle effect on the composition of the microbiome during the month of March only, with strains of Gilliamella apicola, Lactobacillus, and Bartonella being less proportionally abundant in bees exposed to forage in the winter. Collectively, our findings show that there is unexpected longitudinal variation within the gut microbial communities of sister honey bees and that supplemental floral forage can subtly alter the microbiome of managed honey bees.

Gut microbiome in type 1 diabetes: A comprehensive review

Type 1 diabetes (T1D) is an autoimmune disease, which is characterized by the destruction of islet β cells in the pancreas triggered by genetic and environmental factors. In past decades, extensive familial and genome-wide association studies have revealed more than 50 risk loci in the genome. However, genetic susceptibility cannot explain the increased incidence of T1D worldwide, which is very likely attributed by the growing impact of environmental factors, especially gut microbiome. Recently, the role of gut microbiome in the pathogenesis of T1D has been uncovered by the increasing evidence from both human subjects and animal models, strongly indicating that gut microbiome might be a pivotal hub of T1D-triggering factors, especially environmental factors. In this review, we summarize the current aetiological and mechanism studies of gut microbiome in T1D. A better understanding of the role of gut microbiome in T1D may provide us with powerful prognostic and therapeutic tools in the near future.

The role of diet in the aetiopathogenesis of inflammatory bowel disease

Crohn's disease and ulcerative colitis, collectively known as IBD, are chronic inflammatory disorders of the gastrointestinal tract. Although the aetiopathogenesis of IBD is largely unknown, it is widely thought that diet has a crucial role in the development and progression of IBD. Indeed, epidemiological and genetic association studies have identified a number of promising dietary and genetic risk factors for IBD. These preliminary studies have led to major interest in investigating the complex interaction between diet, host genetics, the gut microbiota and immune function in the pathogenesis of IBD. In this Review, we discuss the recent epidemiological, gene-environment interaction, microbiome and animal studies that have explored the relationship between diet and the risk of IBD. In addition, we highlight the limitations of these prior studies, in part by explaining their contradictory findings, and review future directions.

Association analysis of dietary habits with gut microbiota of a native Chinese community

Environmental exposure, including a high-fat diet (HFD), contributes to the high prevalence of colorectal cancer by changing the composition of the intestinal microbiota. However, data examining the interaction between dietary habits and intestinal microbiota of the Chinese population is sparse. We assessed dietary habits using a food frequency questionnaire (FFQ) in native Chinese community volunteers. Based on the dietary fat content determined using the FFQ, the volunteers were divided into HFD group (≥40% of dietary calories came from fat) or low-fat diet (LFD) group (<40%). Fecal and colonic mucosal microbiota composition was determined using 16S rDNA based methods. In stool matter of HFD group, Prevotella and Abiotrophia showed significantly higher abundance, whereas unclassified genus of S24-7 (family level) of Bacteroidetes, Gemmiger, Akkermansia and Rothia were less abundant. On colonic mucosal tissue testing, unclassified genus of S24-7 showed significantly higher abundance while Bacteroides, Coprobacter, Abiotrophia, and Asteroleplasma were less abundant in HFD group. A high fat and low fiber diet in a native Chinese community may partially contribute to changes of intestinal microbiota composition that may potentially favor the onset and progression of gastrointestinal disorders including inflammatory, hyperplastic and neoplastic diseases.

Agaro-Oligosaccharides Regulate Gut Microbiota and Adipose Tissue Accumulation in Mice

Gut microbiota are deeply associated with the prevalence of obesity. Agarose is hydrolyzed easily to yield oligosaccharides, designated as agaro-oligosaccharides (AGO). This study evaluated the effects of AGO on obese phenotype and gut microbial composition in mice. Mice were administered AGO in drinking water (AGO-receiving mice). 16S rRNA gene sequencing analyses revealed their fecal microbiota profiles. Serum bile acids were ascertained using a LC-MS/MS system. Compared to the control group, AGO administration significantly reduced epididymal adipose tissue weights and serum non-esterified fatty acid concentrations, but the cecal content weights were increased. Data from the serum bile acid profile show that concentrations of primary bile acids (cholic acid and chenodeoxycholic acid), but not those of secondary bile acids (deoxycholic acid, lithocholic acid, and ursodeoxycholic acid), tended to increase in AGO-receiving mice. 16S rRNA gene sequencing analyses showed that the relative abundances of 15 taxa differed significantly in AGO-receiving mice. Of these, the relative abundances of Rikenellaceae and Lachnospiraceae were found to be positively correlated with epididymal adipose tissue weight. The relative abundances of Bacteroides and Ruminococcus were correlated negatively with epididymal adipose tissue weight. Although the definitive role of gut microbes of AGO-received mice is still unknown, our data demonstrate the possibility that AGO administration affects the gut microbial composition and inhibits obesity in mice.

Microbial Insights into Asthmatic Immunopathology. A Forward-Looking Synthesis and Commentary

Asthma is an aberrant inflammatory condition of the airways affecting approximately 1 in 10 children in affluent countries. An increasing body of evidence suggests that microbial exposures during a "critical window" of development in early life play a central role in determining future asthma susceptibility. However, like the disease itself, considerable heterogeneity exists among studies in which researchers have investigated the associations between particular microbial taxa and asthma immunology. As our understanding of asthmatic pathology evolves to enable clearer definition of asthma endotypes, it will be important to consider the impact of various environmental factors on each endotype. Given the strong evidence in support of the hypothesis that early-life microbial exposures predict later disease states such as asthma, consideration of these endotypes when establishing experimental outcomes in epidemiological studies could allow for increased precision when determining exposure-outcome associations and engaging in more focused follow-up mechanistic investigations.

Microbiome Composition in Both Wild-Type and Disease Model Mice Is Heavily Influenced by Mouse Facility

Murine models have become essential tools for understanding the complex interactions between gut microbes, their hosts, and disease. While many intra-facility factors are known to influence the structure of mouse microbiomes, the contribution of inter-facility variation to mouse microbiome composition, especially in the context of disease, remains under-investigated. We replicated microbiome experiments using identical mouse lines housed in two separate animal facilities and report drastic differences in composition of microbiomes based upon animal facility of origin. We observed facility-specific microbiome signatures in the context of a disease model [the Ednrb (endothelin receptor type B) Hirschsprung disease mouse] and in normal C57BL/6J mice. Importantly, these facility differences were independent of cage, sex, or sequencing-related influence. In addition, we investigated the reproducibility of microbiome dysbiosis previously associated with Ednrb-/- (knock-out; KO) mice. While we observed genotype-based differences in composition between wild-type (WT) and KO mice, these differences were inconsistent with the previously reported conclusions. Furthermore, the genotype-based differences were not identical across animal facilities. Despite this, through differential abundance testing, we identified several conserved candidate taxa and candidate operational taxonomic units that may play a role in disease promotion or protection. Overall, our findings raise the possibility that previously reported microbiome-disease associations from murine studies conducted in a single facility may be heavily influenced by facility-specific effects. More generally, these results provide a strong rationale for replication of mouse microbiome studies at multiple facilities, and for the meticulous collection of metadata that will allow the confounding effects of facility to be more specifically identified.

Camellia Oil ( Camellia oleifera Abel.) Modifies the Composition of Gut Microbiota and Alleviates Acetic Acid-Induced Colitis in Rats

Ulcerative colitis (UC), one type of chronic inflammatory bowel disease (IBD), is a chronic and recurrent disorder of the gastrointestinal (GI) tract. As camellia oil (CO) is traditionally used to treat GI disorders, this study investigated the role of CO on acetic acid-induced colitis in the rat. The composition of the gut microbial community is related to many diseases; thus, this study also investigated the effects of CO on the composition of the gut microbiota. The rats were fed a dose of 2 mL/kg body weight CO, olive oil (OO), or soybean oil (SO) once a day for 20 days, and the gut microbiota was analyzed using 16S rRNA gene sequencing. Results of the gut microbiota examination showed significant clustering of feces after treatment with CO and OO; however, individual differences with OO varied considerably. Compared to SO and OO, the intake of CO increased the ratio of Firmicutes/Bacteroidetes, the α-diversity, relative abundance of the Bifidobacterium, and reduced Prevotella of the gut microbiota. On day 21, colitis was induced by a single transrectal administration of 2 mL of 4% acetic acid. However, pretreatment of rats with CO or OO for 24 days slightly enhanced antioxidant and antioxidant enzyme activities and significantly reduced inflammatory damage and lipid peroxidation, thus ameliorating acetic acid-induced colitis. These results indicated that CO was better able to ameliorate impairment of the antioxidant system induced by acetic acid compared to OO and SO, which may have been due to CO modifying the composition of the gut microbiota or CO being a rich source of phytochemicals.

Counting the Countless: Bacterial Quantification by Targeting rRNA Molecules to Explore the Human Gut Microbiota in Health and Disease

Over the past decade, the advent of next-generation-sequencing tools has revolutionized our approach to understanding the human gut microbiota. However, numerical data on the gut bacterial groups-particularly low-cell-count microbiota, such as indigenous pathobionts, that are otherwise important components of the microbiota-are relatively limited and disparate. As a result, the comprehensive quantitative structure of the human gut microbiota still needs to be fully defined and standardized. With the aim of filling this knowledge gap, we have established a highly sensitive quantitative analytical system that is based on reverse transcription-quantitative PCR and targets microbial rRNA molecules. The system has already been validated in the precise, sensitive, and absolute quantification of more than 70 target bacterial groups belonging to various human gut bacterial clades, including predominant obligate and facultative anaerobes. The system demonstrates sensitivity several hundred times greater than that of other rRNA-gene-targeting methods. It is thus an efficient and valuable tool for exhaustive analysis of gut microbiota over a wide dynamic range. Using this system, we have to date quantified the gut microbiota of about 2,000 healthy Japanese subjects ranging in age from 1 day to over 80 years. By integrating and analyzing this large database, we came across several novel and interesting features of the gut microbiota, which we discuss here. For instance, we demonstrated for the first time that the fecal counts of not only the predominant bacterial groups but also those at lower cell counts conform to a logarithmically normal distribution. In addition, we revealed several interesting quantitative differences in the gut microbiota of people from different age groups and countries and with different diseases. Because of its high analytic sensitivity, the system has also been applied successfully to other body niches, such as in characterizing the vaginal microbiota, detecting septicemia, and monitoring bacterial translocation. Here, we present a quantitative perspective on the human gut microbiota and review some of the novel microbial insights revealed by employing this promising analytical approach.

Intestinal microbiota composition is altered according to nutritional biorhythms in the leopard coral grouper (Plectropomus leopardus)

Aquaculture is currently a major source of fish and has the potential to become a major source of protein in the future. These demands require efficient aquaculture. The intestinal microbiota plays an integral role that benefits the host, providing nutrition and modulating the immune system. Although our understanding of microbiota in fish gut has increased, comprehensive studies examining fish microbiota and host metabolism remain limited. Here, we investigated the microbiota and host metabolism in the coral leopard grouper, which is traded in Asian markets as a superior fish and has begun to be produced via aquaculture. We initially examined the structural changes of the gut microbiota using next-generation sequencing and found that the composition of microbiota changed between fasting and feeding conditions. The dominant phyla were Proteobacteria in fasting and Firmicutes in feeding; interchanging the dominant bacteria required 12 hours. Moreover, microbiota diversity was higher under feeding conditions than under fasting conditions. Multivariate analysis revealed that Proteobacteria are the key bacteria in fasting and Firmicutes and Fusobacteria are the key bacteria in feeding. Subsequently, we estimated microbiota functional capacity. Microbiota functional structure was relatively stable throughout the experiment; however, individual function activity changed according to feeding conditions. Taken together, these findings indicate that the gut microbiota could be a key factor to understanding fish feeding conditions and play a role in interactions with host metabolism. In addition, the composition of microbiota in ambient seawater directly affects the fish; therefore, it is important to monitor the microbiota in rearing tanks and seawater circulating systems.

Physicochemical differences between malanga (Xanthosoma sagittifolium) and potato (Solanum tuberosum) tubers are associated with differential effects on the gut microbiome

Malanga (Xanthosoma sagittifolium) is used as a medicinal food for infant development and gastritis. We compared the physicochemical properties and gut microbial effects of malanga versus potato (Solanum tuberosum) using nutritional analysis, rheometry, in vitro TNO Intestinal Model, and C57Bl/6J mouse models. Malanga was characterized by higher starch (70.7% v. 66.3%), lower amylose:amylopectin (0.33 v. 0.59), higher free sugar (5.44% v. 3.23%), lower viscosity (271.0 v. 863.0 mPa.s), and higher bioaccessible and bioavailable sugar (0.89 v. 0.11 g bioaccessible sucrose per 20 g load in vitro; blood glucose levels of 129.1 v. 95.2 and 133.8 v. 104.3 mg/dL after 20 and 60 min in vivo). Gut microbiota of mice fed a high fat diet containing 20% malanga for 14 d exhibited significantly higher α diversity than those fed 20% potato, indicating that minor physicochemical differences between similar tuber crops are associated with significantly different effects on the gut microbiome.

Dietary soy, meat, and fish proteins modulate the effects of prebiotic raffinose on composition and fermentation of gut microbiota in rats

Soy, meat (mixture of pork and beef), and fish proteins were fed to rats with and without prebiotic raffinose (RAF), and the composition and fermentation of gut microbiota were examined. Bifidobacterium spp. populations were higher, and propionic acid concentration was lower in soy protein-fed than meat protein-fed rats. Likewise, Enterobacteriaceae populations were higher in fish protein-fed rats than other rats. RAF feeding increased Bifidobacterium spp. and decreased Faecalibacterium prausnitzii populations regardless of the dietary protein source. Interactions between dietary proteins and RAF were shown for Lactobacillus spp. and Clostridium perfringens group; the increase of Lactobacillus spp. populations by RAF was seen only for soy protein-fed rats, whereas the reduction of C. perfringens group by RAF was evident in fish and meat protein-fed rats. It is concluded that dietary proteins may differentially modulate the effects of prebiotic oligosaccharides on gut fermentation and microbiota, with differences observed between plant and animal proteins.

Biases from different DNA extraction methods in intestine microbiome research based on 16S rDNA sequencing: a case in the koi carp, Cyprinus carpio var. Koi

This study examined the technical bias associated with different DNA extraction methods used in microbiome research. Three methods were used to extract genomic DNA from the same intestinal microbiota sample that was taken from the koi carp Cyprinus carpio var. koi, after which their microbial diversity and community structure were investigated on the basis of a 16S rDNA high‐throughput sequencing analysis. Biased results were observed in relation to the number of reads, alpha diversity indexes and taxonomic composition among the three DNA extraction protocols. A total of 1,381 OTUs from the intestinal bacteria were obtained, with 852, 759, and 698 OTUs acquired, using the Lysozyme and Ultrasonic Lysis method, Zirmil‐beating Cell Disruption method, and a QIAamp Fast DNA Stool Mini Kit, respectively. Additionally, 336 OTUs were commonly acquired, using the three methods. The results showed that the alpha diversity indexes (Rarefaction, Shannon, and Chao1) of the community that were determined using the Lysozyme and Ultrasonic Lysis method were higher than those obtained with the Zirmil‐beating Cell Disruption method, while the Zirmil method results were higher than those measured, using the QIAamp Fast DNA Stool Mini Kit. Moreover, all the major phyla (ratio>1%) could be identified with all three DNA extraction methods, but the phyla present at a lower abundance (ratio <1%) could not. Similar findings were observed at the genus level. Taken together, these findings indicated that the bias observed in the results about the community structure occurred primarily in OTUs with a lower abundance. The results of this study demonstrate that possible bias exists in community analyses, and researchers should therefore be conservative when drawing conclusions about community structures based on the currently available DNA extraction methods.

A modified method for genomic DNA extraction from the fish intestinal microflora

A modified genomic DNA extraction method named the combination of lysozyme and ultrasonic lysis (CLU) method was used to analyze the fish intestinal microflora. In this method, the physical disruption and chemical lysis steps were combined, and some parameters in the key steps were adjusted. In addition, the results obtained by this method were compared with the results obtained by the Zirmil-beating cell disruption method and the QIAamp Fast DNA Stool Mini Kit. The OD₂₆₀/OD₂₈₀ ratio and concentration of the DNA extracted using the CLU method were 2.02 and 282.8 µg/µL, respectively; when the incubation temperatures for lysozyme and RNase were adjusted to 37 °C, those values were 2.08 and 309.8 µg/µL, respectively. On the agarose gel, a major high-intensity, discrete band of more than 10 kb was found for the CLU method. However, the smearing intensity of degraded DNA was lower when the incubation temperatures were 60 °C for lysozyme and 30 °C for RNase than when incubation temperatures of 37 °C for lysozyme and 37 °C for RNase were used. The V3 variable region of the prokaryotic 16S rDNA was amplified, and an approximately 600-bp fragment was observed when the DNA extracted using the CLU method was used as a template. The CLU method is simple and cost effective, and it yields high-quality, unsheared, high-molecular-weight DNA, which is comparable to that obtained with a commercially available kit. The extracted DNA has potential for applications in critical molecular biology techniques.

Kawasaki disease: Epidemiological differences between past and recent periods, and implications of distribution dynamism

BACKGROUND

Epidemiological findings suggest that Kawasaki disease (KD) is mediated by infection, which triggers its onset. Although the mechanism of onset seems to involve preconditioning factors and triggering factors, the details remain unclarified.

METHODS

Data for 330 662 patients reported in KD nationwide surveys in Japan implemented between 1961 and 2014 were chronologically compared in terms of patient age distribution, estimated mean onset age, and male-to-female ratio during four periods: pre-epidemic (P1), epidemic (P2), stable (P3), and recent (P4): 1961-1978, 1979-1986, 1987-1997, and 1998-2014, respectively.

RESULTS

During P2, the number of patients aged 6 months-2 years increased, and the mean onset age was younger; during P4, however, the number of patients aged ≤1 year decreased, but the number of patients ≥2 years increased, with a flat onset age distribution chart, and the mean onset age was older. During P2, increases in the number of patients were accompanied by younger mean onset age, whereas during P4, increases in the number of patients were conversely accompanied by older mean onset ages. The male: female ratio tended to decrease during P2, but this tendency was not seen in P4. No outbreak occurred during a recent 28 year period (P3, P4). Specific preconditioning factors might have been present during the 8 years (P2) of the past three outbreaks.

CONCLUSION

P2 and P4 were significantly different in epidemiological features. It is likely that they do not share the same mechanism of onset (preconditioning and/or trigger factors).

Mechanisms underlying the effects of n-3 polyunsaturated fatty acids on fear memory processing and their hypothetical effects on fear of cancer recurrence in cancer survivors

The relationship of n-3 polyunsaturated fatty acids (PUFAs) and gut microbiota with brain function has been extensively reported. Here, we review how n-3 polyunsaturated fatty acids affect fear memory processing. n-3 PUFAs may improve dysfunctional fear memory processing via immunomodulation/anti-inflammation, increased BDNF, upregulated adult neurogenesis, modulated signal transduction, and microbiota-gut-brain axis normalization. We emphasize how n-3 PUFAs affect this axis and also focus on the hypothetical effects of PUFAs in fear of cancer recurrence (FCR), the primary psychological unmet need of cancer survivors. Its pathophysiology may be similar to that of post-traumatic stress disorder (PTSD), which involves dysfunctional fear memory processing. Due to fewer adverse effects than psychotropic drugs, nutritional interventions involving n-3 PUFAs should be acceptable for physically vulnerable cancer survivors. We are currently studying the relationship of FCR with n-3 PUFAs and gut microbiota in cancer survivors to provide them with a nutritional intervention that protects against FCR.

Phenylketonuric diet negatively impacts on butyrate production

BACKGROUND AND AIMS

Phenylalanine (Phe) restricted diet, combined with Phe-free l-amino acid supplementation, is the mainstay of treatment for phenylketonuria (PKU). Being the diet a key factor modulating gut microbiota composition, the aim of the present paper was to compare dietary intakes, gut microbiota biodiversity and short chain fatty acids (SCFAs) production in children with PKU, on low-Phe diet, and in children with mild hyperphenylalaninemia (MHP), on unrestricted diet.

METHODS AND RESULTS

We enrolled 21 PKU and 21 MHP children matched for gender, age and body mass index z-score. Dietary intakes, including glycemic index (GI) and glycemic load (GL), and fecal microbiota analyses, by means of denaturing gradient gel electrophoresis (DGGE) and Real-time PCR were assessed. Fecal SCFAs were quantified by gas chromatographic analysis.

RESULTS

We observed an increased carbohydrate (% of total energy), fiber and vegetables intakes (g/day) in PKU compared with MHP children (p = 0.047), as well a higher daily GI and GL (maximum p < 0.001). Compared with MHP, PKU showed a lower degree of microbial diversity and a decrease in fecal butyrate content (p = 0.02). Accordingly, two of the most abundant butyrate-producing genera, Faecalibacterium spp. and Roseburia spp., were found significantly depleted in PKU children (p = 0.02 and p = 0.03, respectively).

CONCLUSION

The low-Phe diet, characterized by a higher carbohydrate intake, increases GI and GL, resulting in a different quality of substrates for microbial fermentation. Further analyses, thoroughly evaluating microbial species altered by PKU diet are needed to better investigate gut microbiota in PKU children and to eventually pave the way for pre/probiotic supplementations.

Removal of the cecum affects intestinal fermentation, enteric bacterial community structure, and acute colitis in mice

The murine cecum is a major site of fermentation of dietary materials, and production of short chain fatty acids (SCFAs). To examine the role that the cecum plays in acute bacterial infection in mice, the cecum was surgically removed, and changes in bacterial communities and production of SCFAs were analyzed relative to surgical sham animals. To incite bacterial colitis, mice were orally challenged with Citrobacter rodentium. The impact of butyrate administered directly into the colon was also examined. Concentrations of SCFAs in feces were substantially lower in mice with an excised cecum. Bacterial communities were also less diverse in cecectomized mice, and densities of major SCFA-producing taxa including bacteria within the Ruminococcaceae and Lachnospiraceae families were reduced. Colonization of the intestine by C. rodentium was not affected by removal of the cecum, and the bacterium equally incited acute colitis in mice with and without a cecum. However, cecectomized mice exhibited lower body weights at later stages of infection indicating an impaired ability to recover following challenge with C. rodentium. Furthermore, removal of the cecum altered immune and inflammatory responses to infection including increased inflammatory markers in the proximal colon (Tnfα, Il10, βd1), and heightened inflammatory response in the proximal and distal colon (Ifnγ, Tnfα, Relmβ). Exogenous administration of butyrate was insufficient to normalize responses to C. rodentium in cecectomized mice. The murine cecum plays a critical role in maintaining intestinal health, and the murine cecectomy model may be a useful tool in elucidating key aspects of intestine-pathogen-microbiota interactions.

Low dietary fiber intake increases Collinsella abundance in the gut microbiota of overweight and obese pregnant women

The gut microbiota contributes to the regulation of glucose metabolism in pregnancy. Abundance of the genus Collinsella is positively correlated with circulating insulin; however, it is unclear what determines Collinsella abundance. This study aims to validate the correlation between Collinsella and insulin and to elucidate if macronutrient intake alters Collinsella abundance and gut microbiota composition. Gut microbiota profiles were assessed by 16S rRNA sequencing in 57 overweight and 73 obese pregnant women from the SPRING (Study of PRobiotics IN Gestational diabetes) trial at 16 weeks gestation and correlated with metabolic hormone levels and macronutrient intake. Gut microbiota composition in the top and bottom 10% of dietary fiber intake was evaluated through network analysis. Collinsella abundance correlated positively with circulating insulin (rho = 0.30, p = 0.0006), independent of maternal BMI, but negatively with dietary fiber intake (rho = -0.20, p = 0.025) in this cohort. Low dietary fiber intake was associated with a gut microbiota favoring lactate fermentation while high fiber intake promotes short-chain fatty acid-producing bacteria. Low dietary fiber may enable overgrowth of Collinsella and alter the overall fermentation pattern in gut microbiota. This suggests that dietary choices during pregnancy can modify the nutritional ecology of the gut microbiota, with potential deleterious effects on the metabolic and inflammatory health of the host.

TRIAL REGISTRATION

ANZCTR 12611001208998, registered 23/11/2011.

Gut Microbial Changes, Interactions, and Their Implications on Human Lifecycle: An Ageing Perspective

Gut microbiota is established during birth and evolves with age, mostly maintaining the commensal relationship with the host. A growing body of clinical evidence suggests an intricate relationship between the gut microbiota and the immune system. With ageing, the gut microbiota develops significant imbalances in the major phyla such as the anaerobic Firmicutes and Bacteroidetes as well as a diverse range of facultative organisms, resulting in impaired immune responses. Antimicrobial therapy is commonly used for the treatment of infections; however, this may also result in the loss of normal gut flora. Advanced age, antibiotic use, underlying diseases, infections, hormonal differences, circadian rhythm, and malnutrition, either alone or in combination, contribute to the problem. This nonbeneficial gastrointestinal modulation may be reversed by judicious and controlled use of antibiotics and the appropriate use of prebiotics and probiotics. In certain persistent, recurrent settings, the option of faecal microbiota transplantation can be explored. The aim of the current review is to focus on the establishment and alteration of gut microbiota, with ageing. The review also discusses the potential role of gut microbiota in regulating the immune system, together with its function in healthy and diseased state.

The Metabolic Sensor GPR43 Receptor Plays a Role in the Control of Klebsiella pneumoniae Infection in the Lung

Pneumonia is one of the leading causes of death and mortality worldwide. The inflammatory responses that follow respiratory infections are protective leading to pathogen clearance but can also be deleterious if unregulated. The microbiota is known to be an important protective barrier against infections, mediating both direct inhibitory effects against the potential pathogen and also regulating the immune responses contributing to a proper clearance of the pathogen and return to homeostasis. GPR43 is one receptor for acetate, a microbiota metabolite shown to induce and to regulate important immune functions. Here, we addressed the role of GPR43 signaling during pulmonary bacterial infections. We have shown for the first time that the absence of GPR43 leads to increased susceptibility to Klebsiella pneumoniae infection, which was associated to both uncontrolled proliferation of bacteria and to increased inflammatory response. Mechanistically, we showed that GPR43 expression especially in neutrophils and alveolar macrophages is important for bacterial phagocytosis and killing. In addition, treatment with the GPR43 ligand, acetate, is protective during bacterial lung infection. This was associated to reduction in the number of bacteria in the airways and to the control of the inflammatory responses. Altogether, GPR43 plays an important role in the “gut–lung axis” as a sensor of the host gut microbiota activity through acetate binding promoting a proper immune response in the lungs.

Modulation of the gut microbiota by metformin improves metabolic profiles in aged obese mice

The gut microbiota is a contributing factor in obesity-related metabolic disorders. The effect of metformin on the gut microbiota has been reported; however, the relationship between the gut microbiota and the mechanism of action of metformin in elderly individuals is unclear. In this study, the effect of metformin on the gut microbiota was investigated in aged obese mice. The abundance of the genera Akkermansia, Bacteroides, Butyricimonas, and Parabacteroides was significantly increased by metformin in mice fed a high-fat diet. Metformin treatment decreased the expression of IL-1β and IL-6 in epididymal fat, which was correlated with the abundance of various bacterial genera. In addition, both fecal microbiota transplantation from metformin-treated mice and extracellular vesicles of Akkermansia muciniphila improved the body weight and lipid profiles of the mice. Our findings suggest that modulation of the gut microbiota by metformin results in metabolic improvements in aged mice, and that these effects are associated with inflammatory immune responses.

Interaction of genotype and diet on small intestine microbiota of Japanese quail fed a cholesterol enriched diet

Our previous study has shown that genetic selection for susceptibility/resistance to diet-induced atherosclerosis has affected the Japanese quail's cecal environment to accommodate distinctly different cecal microbiota. In this study, we fed the Atherosclerosis-resistant (RES) and -susceptable (SUS) quail a regular and a cholesterol enriched diet to examine the interaction of host genotype and diet on the diversity, composition, and metabolic functions of the duodenal and ileal microbiota with relations to atherosclerosis development. In the duodenal content, 9 OTUs (operational taxonomic units) were identified whose abundance had significant positive correlations with plasma total cholesterol, LDL level and/or LDL/HDL ratio. In the ileal content, 7 OTUs have significant correlation with plasma HDL. Cholesterol fed RES hosted significantly less Escherichia and unclassified Enterobacteriaceae (possibly pathogenic) in their duodenum than SUS fed the same diet. Dietary cholesterol significantly decreased the duodenal microbiome of SUS's biosynthesis of Ubiquinone and other terpenoid-quinone. Cholesterol fed RES had significantly more microbiome genes for Vitamin B6, selenocompound, taurine and hypotaurine, and Linoleic acid metabolism; Bisphenol degradation; primary bile acid, and butirosin and neomycin biosynthesis than SUS on the same diet. Microbiome in the ileum and ceca of RES contributed significantly towards the resistance to diet induced atherosclerosis.

The Inner Workings of the Outer Surface: Skin and Gill Microbiota as Indicators of Changing Gut Health in Yellowtail Kingfish

The mucosal surfaces and associated microbiota of fish are an important primary barrier and provide the first line of defense against potential pathogens. An understanding of the skin and gill microbial assemblages and the factors which drive their composition may provide useful insights into the broad dynamics of fish host–microbial relationships, and may reveal underlying changes in health status. This is particularly pertinent to cultivated systems whereby various stressors may led to conditions (like enteritis) which impinge on productivity. As an economically important species, we assessed whether the outer-surface bacterial communities reflect a change in gut health status of cultivated Yellowtail Kingfish (Seriola lalandi). Active bacterial assemblages were surveyed from RNA extracts from swabs of the skin and gills by constructing Illumina 16S rRNA gene amplicon libraries. Proteobacteria and Bacteroidetes were predominant in both the skin and gills, with enrichment of key β-proteobacteria in the gills (Nitrosomonadales and Ferrovales). Fish exhibiting early stage chronic lymphocytic enteritis comprised markedly different global bacterial assemblages compared to those deemed healthy and exhibiting late stages of the disease. This corresponded to an overall loss of diversity and enrichment of Proteobacteria and Actinobacteria, particularly in the gills. In contrast, bacterial assemblages of fish with late stage enteritis were generally similar to those of healthy individuals, though with some distinct taxa. In conclusion, gut health status is an important factor which defines the skin and gill bacterial assemblages of fish and likely reflects changes in immune states and barrier systems during the early onset of conditions like enteritis. This study represents the first to investigate the microbiota of the outer mucosal surfaces of fish in response to underlying chronic gut enteritis, revealing potential biomarkers for assessing fish health in commercial aquaculture systems.