Roseburia spp.: a marker of health?

Key Bacteria in the Gut Microbiota Network for the Transition between Sedentary and Active Lifestyle

Physical activity modifies the gut microbiota, exerting health benefits on the host; however, the specific bacteria associated with exercise are not yet known. In this work, we propose a novel method, based on hierarchical topology, to study the differences between the microbiota of active and sedentary lifestyles, and to identify relevant bacterial taxa. Our results show that the microbiota network found in active people has a significantly higher overall efficiency and higher transmissibility rate. We also identified key bacteria in active and sedentary networks that could be involved in the conversion of an active microbial network to a sedentary microbial network and vice versa.

Oral Supplements of Combined Bacillus licheniformis Zhengchangsheng® and Xylooligosaccharides Improve High-Fat Diet-Induced Obesity and Modulate the Gut Microbiota in Rats

Gut dysbiosis induced by high-fat diet (HFD) may result in low-grade inflammation leading to diverse inflammatory diseases. The beneficial effects of probiotics and prebiotics on obesity have been reported previously. However, their benefits in promoting human health and the underlying mechanisms still need to be further characterized. This study is aimed at understanding how probiotic Bacillus licheniformis Zhengchangsheng® (BL) and prebiotic xylooligosaccharides (XOS) influence the health of a rat model with HF (60 kcal %) diet-induced obesity. Five groups of male Sprague Dawley (SD) rats were fed a normal fat diet (CON) or an HFD with or without BL and XOS supplementation for 3 weeks. Lipid profiles, inflammatory biomarkers, and microbiota composition were analyzed at the end of the experiment. Rats fed an HFD exhibited increased body weight and disordered lipid metabolism. In contrast, combined BL and XOS supplementation inhibited body weight gain and returned lipid metabolism to normal. Furthermore, BL and XOS administration changed the gut microbiota composition and modulated specific bacteria such as Prevotellaceae, Desulfovibrionaceae, and Ruminococcaceae. In addition, supplements of combined BL and XOS obviously reduced the serum LPS level, which was significantly related to microbial variations. Our findings suggest that modulation of the gut microbiota as a result of probiotic BL and prebiotic XOS supplementation has a positive effect on HFD-induced obesity in rats.

Dietary Emulsifier Sodium Stearoyl Lactylate Alters Gut Microbiota in vitro and Inhibits Bacterial Butyrate Producers

Dietary emulsifiers are widely used in industrially processed foods, although the effects of these food additives on human gut microbiota are not well studied. Here, we investigated the effects of five different emulsifiers [glycerol monoacetate, glycerol monostearate, glycerol monooleate, propylene glycol monostearate, and sodium stearoyl lactylate (SSL)] on fecal microbiota in vitro. We found that 0.025% (w/v) of SSL reduced the relative abundance of the bacterial class Clostridia and others. The relative abundance of the families Clostridiaceae, Lachnospiraceae, and Ruminococcaceae was substantially reduced whereas that of Bacteroidaceae and Enterobacteriaceae was increased. Given the marked impact of SSL on Clostridia, we used genome reconstruction to predict community-wide production of short-chain fatty acids, which were experimentally assessed by GC-MS analysis. SSL significantly reduced concentrations of butyrate, and increased concentrations of propionate compared to control cultures. The presence of SSL increased lipopolysaccharide, LPS and flagellin in cultured communities, thereby enhancing the proinflammatory potential of SSL-selected bacterial communities.

Correlation of gut microbial compositions to the development of Kawasaki disease vasculitis in children

Aim: Here, we hypothesize that dysbiotic gut microbiota might contribute to the development of Kawasaki disease (KD), a pediatric disease with unknown etiology. This is the second report on gut microbiota composition in KD patients. Materials & results: 16S amplicon sequencing was performed on fecal DNA samples and revealed predominance of bacterial pathogens, such as Fusobacterium, Neisseria, Shigella and Streptococcus, in the gut of KD patients, but absent or suppressed after immunoglobulin/antibiotics therapy. In addition, beneficial bacteria propagated after the therapy. Conclusion: We conclude that prevalence of Fusobacteria, Shigella and Streptococcus might contribute to KD pathogenesis.

Microbiota Composition and Metabolism Are Associated With Gut Function in Parkinson's Disease

BACKGROUND

Parkinson's disease is characterized by a high burden of gastrointestinal comorbidities, especially constipation and reduced colonic transit time, and by gut microbiota alterations. The diverse metabolites produced by the microbiota are broadly relevant to host health. How microbiota composition and metabolism relate to gastrointestinal function in Parkinson's disease is largely unknown. The objectives of the current study were to assesses associations between microbiota composition, stool consistency, constipation, and systemic microbial metabolites in Parkinson's disease to better understand how intestinal microbes contribute to gastrointestinal disturbances commonly observed in patients.

METHODS

Three hundred participants (197 Parkinson's patients and 103 controls) were recruited for this cross-sectional cohort study. Participants supplied fecal samples for microbiota sequencing (n = 300) and serum for untargeted metabolomics (n = 125). Data were collected on motor and nonmotor Parkinson's symptoms, medications, diet, and demographics.

RESULTS

Significant microbiota taxonomic differences were observed in Parkinson's patients, even when controlling for gastrointestinal function. Parkinson's microbiota was characterized by reduced carbohydrate fermentation and butyrate synthesis capacity and increased proteolytic fermentation and production of deleterious amino acid metabolites, including p-cresol and phenylacetylglutamine. Taxonomic shifts and elevated proteolytic metabolites were strongly associated with stool consistency (a proxy for colonic transit time) and constipation among patients.

CONCLUSIONS

Compositional and metabolic alterations in the Parkinson's microbiota are highly associated with gut function, suggesting plausible mechanistic links between altered bacterial metabolism and reduced gut health in this disease. The systemic detection of elevated deleterious proteolytic microbial metabolites in Parkinson's serum suggests a mechanism whereby microbiota dysbiosis contributes to disease etiology and pathophysiology. © 2020 International Parkinson and Movement Disorder Society.

Diet, nutrients and the microbiome

Although there is associative evidence linking fecal microbiome profile to health and disease, many studies have not considered the confounding effects of dietary intake. Consuming food provides fermentable substrate which sustains the microbial ecosystem that resides with most abundance in the colon. Western, Mediterranean and vegetarian dietary patterns have a role in modulating the gut microbiota, as do trending restrictive diets such the paleolithic and ketogenic. Altering the amount or ratio of carbohydrate, protein and fat, particularly at the extremes of intake, impacts the microbiome. Diets high in fermentable carbohydrates support the relative abundance of Bifidobacterium, Prevotella, Ruminococcus, Dorea and Roseburia, among others, capable of degrading polysaccharides, oligosaccharides and sugars. Conversely, very high fat diets increase bile-resistant organisms such as Bilophila and Bacteroides. Food form, whole foods vs. ultra-processed, alters the provision of macronutrient substrate to the colon due to differing digestibility, and thereby may impact the microbiota and its metabolic activity. In addition, phytochemicals in plant-based foods have specific and possibly prebiotic effects on the microbiome. Further, food ingredients such as certain low-calorie sweeteners enhance Bifidobacterium spp. The weight of evidence to date suggests a high level of interindividual variability in the human microbiome vs. clearly defined, dietary-induced profiles. Healthful dietary patterns, emphasizing plant foods high in microbial-available carbohydrate, support favorable microbiome profiles active in saccharolytic fermentation. Future research into diet and microbiome should consider the balance of gut microbial-generated metabolites, an important link between microbiome profile and human health.

Bound Phenolics Ensure the Antihyperglycemic Effect of Rice Bran Dietary Fiber in db/db Mice via Activating the Insulin Signaling Pathway in Skeletal Muscle and Altering Gut Microbiota

Whole-grain dietary fiber intake is beneficial in the prevention of metabolic syndrome. Considering rich in bound phenolics being a special characteristic of whole-grain dietary fiber, the aim of this study was to evaluate the effects of the presence or absence of bound phenolics in rice bran dietary fiber (RBDF) on regulating glucose metabolism in diabetic db/db mice. In comparison to phenolics-removed RBDF (PR-RBDF) intervention without an antihyperglycemic effect, RBDF and formulated RBDF (F-RBDF, obtained by mixing PR-RBDF and hydrolyzed-bound phenolics) significantly reduced fasting blood glucose levels after 1 and 5 weeks of interventions, respectively. The presence of bound phenolics interventions could activate the IRS1/AKT/GLUT4 insulin signaling pathway in skeletal muscle and alter gut microbiota by modulating gut microbiota dysbiosis and enriching the butyric-acid-producing bacteria genera of the families Lachnospiraceae and Ruminococcaceae, thus leading to the reduction of blood glucose levels. These findings indicate that bound phenolics ensure the antihyperglycemic effect of RBDF.

The Controversial Role of Human Gut Lachnospiraceae

The complex polymicrobial composition of human gut microbiota plays a key role in health and disease. Lachnospiraceae belong to the core of gut microbiota, colonizing the intestinal lumen from birth and increasing, in terms of species richness and their relative abundances during the host's life. Although, members of Lachnospiraceae are among the main producers of short-chain fatty acids, different taxa of Lachnospiraceae are also associated with different intra- and extraintestinal diseases. Their impact on the host physiology is often inconsistent across different studies. Here, we discuss changes in Lachnospiraceae abundances according to health and disease. With the aim of harnessing Lachnospiraceae to promote human health, we also analyze how nutrients from the host diet can influence their growth and how their metabolites can, in turn, influence host physiology.

Gut microbiota in children with juvenile idiopathic arthritis: characteristics, biomarker identification, and usefulness in clinical prediction

Background

Recent studies have suggested that the gut microbiota is altered in children with juvenile idiopathic arthritis (JIA). However, age, sex, and body mass index (BMI) were not matched in the previous studies, and the results are inconsistent. We conducted an age-, sex-, and BMI-matched cross-sectional study to characterize the gut microbiota in children with JIA, and evaluate its potential in clinical prediction.

Methods

A total of 40 patients with JIA and 42 healthy controls, ranging from 1 to 16 years, were enrolled in this study. Fecal samples were collected for 16S rDNA sequencing. The data were analyzed using QIIME software and R packages. Specifically, the random forest model was used to identify biomarkers, and the receiver operating characteristic curve and the decision curve analysis were used to evaluate model performance.

Results

A total of 39 fecal samples from patients with JIA, and 42 fecal samples from healthy controls were sequenced successfully. The Chao 1 and Shannon–Wiener index in the JIA group were significantly lower than those in the control group, and the Bray-Curtis dissimilarity also differed significantly between the two groups. The relative abundance of 4 genera, Anaerostipes, Dialister, Lachnospira, and Roseburia, decreased significantly in the JIA group compared to those in the control group. The 4 genera included microbes that produce short-chain fatty acids (SCFAs) and were negatively correlated with some rheumatic indices. Moreover, 12 genera were identified as potential biomarkers by using the nested cross-validation function of the random forest. A random forest model constructed using these genera was able to differentiate the patients with JIA from the healthy controls, and the area under the receiver operating characteristic curve was 0.7975. The decision curve analysis indicated that the model had usefulness in clinical practice.

Conclusions

The gut microbiota in patients with JIA is altered and characterized by a decreased abundance of 4 SCFA-producing genera. The decreases in the 4 genera correlated with more serious clinical indices. Twelve genera could be used as biomarkers and predictors in clinical practice.

Trial registration

The study is registered online at the Chinese Clinical Trial Registry on 11 May 2018 (registration number: ChiCTR1800016110).

A Health-Conscious Food Pattern Is Associated with Prediabetes and Gut Microbiota in the Malmö Offspring Study

BACKGROUND

Diet is a determinant of gut microbiota. Both diet and gut microbiota have been linked to metabolic diseases.

OBJECTIVE

We aimed to examine data-driven food patterns in relation to the prevalence of prediabetes and gut microbiota composition and food pattern-associated bacteria in relation to prediabetes.

METHODS

Food patterns were extracted using principal component analysis in 1726 individuals (aged 18-71 y, 55% women, mean BMI = 25.5 kg/m2) without diabetes from the population-based Malmö Offspring Study. The gut (fecal) microbiota was analyzed by sequencing the 16S ribosomal RNA gene (V1-V3 region). Prediabetes classification was based on fasting glucose ≥6.0 mmol/L and/or glycated hemoglobin ≥42 mmol/L at baseline and/or type 2 diabetes diagnosis during follow-up (0-3.8 y). Logistic regression was used to investigate cross-sectional associations with prediabetes, and the general linear model to examine associations between food patterns and bacterial genera.

RESULTS

Two food patterns, the Health-conscious and the Sugar and High-Fat Dairy patterns, were identified. Adherence to the Health-conscious pattern was associated with a lower prevalence of prediabetes (OR comparing highest quintile with lowest: 0.54; 95% CI: 0.32, 0.92; P-trend = 0.03) and with the abundance of several gut bacterial genera, of which the most robust findings were with a higher abundance of Roseburia and Lachnospira and with a lower abundance of Eubacterium. Roseburia was also associated with a lower prevalence of prediabetes (OR comparing highest quintile with lowest: 0.56; 95% CI: 0.35, 0.92; P-trend = 0.01) and the association between the Health-conscious pattern and prediabetes was attenuated after adjustment for abundance of Roseburia and BMI. Adherence to the Sugar and High-Fat Dairy pattern was associated with a higher prevalence of prediabetes in women (P-trend across food pattern quintiles = 0.03).

CONCLUSIONS

In this Swedish population-based study, a Health-conscious food pattern showed an inverse association with the prevalence of prediabetes. Potential underlying explanations may involve links between healthy diet and BMI, as well as gut microbiota, especially a higher abundance of Roseburia.

Randomised Double-Blind Placebo-Controlled Trial of Inulin with Metronidazole in Non-Alcoholic Fatty Liver Disease (NAFLD)

Background: Non-alcoholic fatty liver disease (NAFLD) can be ameliorated by weight loss although difficult to maintain. Emerging evidence indicates that prebiotics and antibiotics improve NAFLD. Aim: To determine whether inulin supplementation after brief metronidazole therapy is effective in reducing alanine aminotransferase (ALT) and maintaining weight loss achieved through a very-low-calorie diet (VLCD) among people with NAFLD. Methods: Sixty-two people with NAFLD commenced 4-week VLCD using Optifast meal replacements (600 kcal/day). Sixty were then randomised into a 12-week double-blind, placebo-controlled, parallel three-arm trial: (1) 400 mg metronidazole twice daily in Week 1 then inulin 4 g twice daily OR (2) placebo twice daily in week one then inulin OR (3) placebo-placebo. Main outcomes were ALT and body weight at 12 weeks. Fecal microbiota changes were also evaluated. Results: Mean body mass index (BMI) and ALT reduced after VLCD by 2.4 kg/m² and 11 U/L, respectively. ALT further decreased after metronidazole-inulin compared to after placebo-placebo (mean ALT change -19.6 vs. -0.2 U/L, respectively; p = 0.026); however, weight loss maintenance did not differ. VLCD treatment decreased the ratio of Firmicutes/Bacteroidetes (p = 0.002). Conclusion: Brief metronidazole followed by inulin supplementation can reduce ALT beyond that achieved after VLCD in patients with NAFLD.

Preventive Role of Salsalate in Diabetes Is Associated With Reducing Intestinal Inflammation Through Improvement of Gut Dysbiosis in ZDF Rats

A safe and effective approach is needed to prevent and reduce the incidence of diabetes worldwide. The hypoglycemic efficacy of salicylic acid (salsalate, SAL), which has anti-inflammatory properties, has been empirically demonstrated in studies conducted at the Joslin Diabetes Center and elsewhere. Here, we investigated the potential role of SAL in preventing the onset of diabetes in Zucker diabetic fatty (ZDF) rats and attempted to elucidate its underlying mechanisms. ZDF and Zucker lean (ZL) rats were administered a high-fat diet with or without SAL intervention, and their relative rates of diabetes were compared. Our results showed that all rats in the placebo group developed diabetes, whereas only 10% of the SAL-treated rats presented with impaired glucose tolerance (IGT). None of the latter progressed to diabetes. Relative to the untreated rats, SAL lowered plasma glucagon and insulin while improving insulin sensitivity and β-cell function. SAL may protect against hyperglycemia by increasing the microbial diversity, ameliorating gut dysbiosis, restoring intestinal epithelial cell connections, inhibiting endotoxin influx into the blood, and attenuating inflammation. Together, these findings suggest that SAL may be a candidate prophylactic therapy against diabetes. The protective role of SAL may be attributed to its ability to reduce intestinal inflammation and improve gut dysbiosis.

Gut microbiota and lipid metabolism alterations in mice induced by oral cadmium telluride quantum dots

The potential toxicity of cadmium-containing quantum dots (QDs) has received much attention because of increasing biomedical applications. However, little has been known about how cadmium telluride (CdTe) QDs influence the gut microbiota and lipid metabolism. In this study, mice were exposed orally to CdTe QDs (200 μL of 0.2, 2, 20 or 200 μm; twice per week) for 4 weeks. The oral experiments showed CdTe QD exposure led to a decrease of the Firmicutes/Bacteroidetes (F/B) ratio of gut microbiota, which highly negatively correlated with the low-density lipoprotein (LDL), triglyceride (TG) and total cholesterol (TC) levels in serum. In addition, the low-dose (0.2 and 2 μm) CdTe QDs significantly increased the diversity of gut microbiota, and did not elevate the LDL, TG and TC levels in serum. The medium dose (20 μm) of CdTe QDs caused the biggest decrease of the F/B ratio, so it significantly increased the LDL, TG and TC levels compared with the control. Furthermore, high-dose (200 μm) CdTe QDs caused various toxicities in the histopathology of liver and intestine, liver function and intestinal immunity, but did not significantly lead to changes of the LDL, TG and TC levels in serum. This study demonstrates that high-dose oral CdTe QDs mainly lead to tissue damage of the liver and intestine, while the medium and low doses of oral CdTe QDs induce shifts of gut microbiota structure, which are associated with blood lipid levels.

Timing of complementary feeding is associated with gut microbiota diversity and composition and short chain fatty acid concentrations over the first year of life

BACKGROUND

Early introduction of complementary foods has been associated with various immune disorders, oxidative stress, and obesity in childhood. The gut microbiota and the short chain fatty acids (SCFAs) they produce are postulated to be on the causal pathway. The objective of this study was to determine if early complementary feeding (i.e. consumption of solids or non-water/formula liquids at or before 3 months) is prospectively associated with infant gut microbiota composition, diversity and SCFAs at 3 and 12 months of age in the Nurture birth cohort.

RESULTS

Mother-infant dyads in the early complementary feeding group (n = 18) had similar baseline characteristics to those in the later feeding group (n = 49). We assessed differential abundance of microbial taxa (measured by 16S rRNA gene sequencing of the V4 region) by timing of complementary feeding using beta-binomial regression models (considering a two-sided FDR corrected p-value of < 0.05 as significant), and we fittted linear regression models to assess the association between early complementary feeding and SCFA concentrations (quantified using gas chromatography). After multivariable adjustment for breastfeeding, delivery method, birth weight, and gestational age, there were 13 differentially abundant microbial amplicon sequence variants (ASVs) by timing of introduction to complementary foods at 3 months and 20 ASVs at 12 months. Infants introduced to complementary foods early (vs. later) had higher concentrations of the SCFA butyric acid (mean difference = 0.65, 95% CI: 0.27, 1.04, p < 0.01) and total SCFAs (mean difference = 38.8, 95% CI: 7.83, 69.7) at 12 months. Bilophila wadsworthia and Lachnospiraceae Roseburia were associated with early (vs. later) complementary feeding and with higher butyric acid concentrations at 3 and 12 months, respectively.

CONCLUSIONS

Our findings are consistent with the hypothesis that early (vs. later) introduction to complementary foods is associated with altered gut microbiota composition and butyric acid concentrations measured in stool until at least 1 year of age. Further research is needed to determine if these changes mediate future development of metabolic and immune conditions.

Long-term metal exposure changes gut microbiota of residents surrounding a mining and smelting area

In this epidemiologic study, 16 S rRNA sequencing was used to investigate the changes of diversity and composition profile of gut microbiota resulting from long-term exposure to multiple metals, including arsenic (As), cadmium (Cd), cuprum (Cu), lead (Pb), and zinc (Zn). Due to long-term exposure to various metals, the relative abundances of Lachnospiraceae, Eubacterium eligens, Ruminococcaceae UGG-014, Erysipelotrichaceae UCG-003, Tyzzerella 3, Bacteroides, Slackia, italics, and Roseburia were found to become much higher, whereas the abundance of Prevotella 9 presented an opposite trend. Additionally, differences between males and female groups were found, such as the greater richness and evenness of bacteria for men subjected to long-term metal exposure in polluted areas. The changes of men’s microbiomes were more significant as a result of higher daily intake, mining and smelting activity, and living habits. This research presents a new theoretical basis for the correlation between long-term metal exposure and gut health for people living in contaminated areas.

Protective Effects of Ghrelin on Fasting-Induced Muscle Atrophy in Aging Mice

Sarcopenia is the aging-associated progressive loss of skeletal muscle; however, the pathogenic mechanism of sarcopenia is not clear. The orexigenic hormone ghrelin stimulates growth hormone secretion, increases food intake, and promotes adiposity. Here we showed that fasting-induced muscle loss was exacerbated in old ghrelin-null (Ghrl-/-) mice, exhibiting decreased expression of myogenic regulator MyoD and increased expression of protein degradation marker MuRF1, as well as altered mitochondrial function. Moreover, acylated ghrelin and unacylated ghrelin treatments significantly increased mitochondrial respiration capacity in muscle C2C12 cells. Consistently, acylated ghrelin and unacylated ghrelin treatments effectively increased myogenic genes and decreased degradation genes in the muscle in fasted old Ghrl-/- mice, possibly by stimulating insulin and adenosine monophosphate-activated protein kinase pathways. Furthermore, Ghrl-/- mice showed a profile of pro-inflammatory gut microbiota, exhibiting reduced butyrate-producing bacteria Roseburia and ClostridiumXIVb. Collectively, our results showed that ghrelin has a major role in the maintenance of aging muscle via both muscle-intrinsic and -extrinsic mechanisms. Acylated ghrelin and unacylated ghrelin enhanced muscle anabolism and exerted protective effects for muscle atrophy. Because unacylated ghrelin is devoid of the obesogenic side effect seen with acylated ghrelin, it represents an attractive therapeutic option for sarcopenia.

The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition

Despite an overall temporal stability in time of the human gut microbiota at the phylum level, strong variations in species abundance have been observed. We are far from a clear understanding of what promotes or disrupts the stability of microbiome communities. Environmental factors, like food or antibiotic use, modify the gut microbiota composition, but their overall impacts remain relatively low. Phages, the viruses that infect bacteria, might constitute important factors explaining temporal variations in species abundance. Gut bacteria harbour numerous prophages, or dormant viruses, which can evolve to become ultravirulent phage mutants, potentially leading to important bacterial death. Whether such phenomenon occurs in the mammal's microbiota has been largely unexplored. Here we studied temperate phage-bacteria coevolution in gnotoxenic mice colonised with Roseburia intestinalis, a dominant symbiont of the human gut microbiota, and Escherichia coli, a sub-dominant member of the same microbiota. We show that R. intestinalis L1-82 harbours two active prophages, Jekyll and Shimadzu. We observed the systematic evolution in mice of ultravirulent Shimadzu phage mutants, which led to a collapse of R. intestinalis population. In a second step, phage infection drove the fast counter-evolution of host phage resistance mainly through phage-derived spacer acquisition in a clustered regularly interspaced short palindromic repeats array. Alternatively, phage resistance was conferred by a prophage originating from an ultravirulent phage with a restored ability to lysogenize. Our results demonstrate that prophages are a potential source of ultravirulent phages that can successfully infect most of the susceptible bacteria. This suggests that prophages can play important roles in the short-term temporal variations observed in the composition of the gut microbiota.

Main gut bacterial composition differs between patients with type 1 and type 2 diabetes and non-diabetic adults

Background

Regarding the role of gut microbial dysbiosis in hyperglycemia, we aimed to compare the main gut bacterial composition among type 1 and type 2 diabetic patients and healthy non-diabetic adults.

Methods

A total of 110 adult subjects (49 patients diagnosed with type 2 diabetes, 21 patients diagnosed with type 1 diabetes and 40 healthy persons) were included in this case-control study. The intestinal microbiota composition was investigated by quantitative real-time polymerase chain reaction (qPCR) method targeting bacterial 16S rRNA gene. Comparison between three groups was done using one-way analysis of variance.

Results

The participants' mean age in the type 1 diabetes, type 2 diabetes and control groups was 35.4, 57.2 and 38.0 years, respectively. Higher level of Escherichia, Prevotella and Lactobacillus was observed in both type 1 and type 2 diabetic patients compared with the healthy group (P ˂0.001). In contrast, bacterial load of Bifidobacterium, Roseburia and Bacteroides was higher in healthy control group (P < 0.05). Faecalibacterium was significantly lower in type 1 diabetic patients compared with the other two groups (P ˂0.001). No significant difference was found in Akkermansia level among three groups.

Conclusions

Gut microbial alterations have been observed among patients suffering from type 1 and type 2 diabetes mellitus and healthy control adults. Butyrate producing genera including Roseburia and Faecalibacterium decreased while Escherichia, Prevotella and Lactobacillus increased in diabetic patients compared to healthy subjects. Modulating approaches of gut microbiota composition could be helpful in diabetes management.

Impact of global PTP1B deficiency on the gut barrier permeability during NASH in mice

OBJECTIVE

Non-alcoholic steatohepatitis (NASH) is characterized by a robust pro-inflammatory component at both hepatic and systemic levels together with a disease-specific gut microbiome signature. Protein tyrosine phosphatase 1 B (PTP1B) plays distinct roles in non-immune and immune cells, in the latter inhibiting pro-inflammatory signaling cascades. In this study, we have explored the role of PTP1B in the composition of gut microbiota and gut barrier dynamics in methionine and choline-deficient (MCD) diet-induced NASH in mice.

METHODS

Gut features and barrier permeability were characterized in wild-type (PTP1B WT) and PTP1B-deficient knockout (PTP1B KO) mice fed a chow or methionine/choline-deficient (MCD) diet for 4 weeks. The impact of inflammation was studied in intestinal epithelial and enteroendocrine cells. The secretion of GLP-1 was evaluated in primary colonic cultures and plasma of mice.

RESULTS

We found that a shift in the gut microbiota shape, disruption of gut barrier function, higher levels of serum bile acids, and decreased circulating glucagon-like peptide (GLP)-1 are features during NASH. Surprisingly, despite the pro-inflammatory phenotype of global PTP1B-deficient mice, they were partly protected against the alterations in gut microbiota composition during NASH and presented better gut barrier integrity and less permeability under this pathological condition. These effects concurred with higher colonic mucosal inflammation, decreased serum bile acids, and protection against the decrease in circulating GLP-1 levels during NASH compared with their WT counterparts together with increased expression of GLP-2-sensitive genes in the gut. At the molecular level, stimulation of enteroendocrine STC-1 cells with a pro-inflammatory conditioned medium (CM) from lipopolysaccharide (LPS)-stimulated macrophages triggered pro-inflammatory signaling cascades that were further exacerbated by a PTP1B inhibitor. Likewise, the pro-inflammatory CM induced GLP-1 secretion in primary colonic cultures, an effect augmented by PTP1B inhibition.

CONCLUSION

Altogether our results have unraveled a potential role of PTP1B in the gut-liver axis during NASH, likely mediated by increased sensitivity to GLPs, with potential therapeutic value.

Abnormal metabolism of gut microbiota reveals the possible molecular mechanism of nephropathy induced by hyperuricemia

The progression of hyperuricemia disease is often accompanied by damage to renal function. However, there are few studies on hyperuricemia nephropathy, especially its association with intestinal flora. This study combines metabolomics and gut microbiota diversity analysis to explore metabolic changes using a rat model as well as the changes in intestinal flora composition. The results showed that amino acid metabolism was disturbed with serine, glutamate and glutamine being downregulated whilst glycine, hydroxyproline and alanine being upregulated. The combined glycine, serine and glutamate could predict hyperuricemia nephropathy with an area under the curve of 1.00. Imbalanced intestinal flora was also observed. Flavobacterium, Myroides, Corynebacterium, Alcaligenaceae, Oligella and other conditional pathogens increased significantly in the model group, while Blautia and Roseburia, the short-chain fatty acid producing bacteria, declined greatly. At phylum, family and genus levels, disordered nitrogen circulation in gut microbiota was detected. In the model group, the uric acid decomposition pathway was enhanced with reinforced urea liver-intestine circulation. The results implied that the intestinal flora play a vital role in the pathogenesis of hyperuricemia nephropathy. Hence, modulation of gut microbiota or targeting at metabolic enzymes, i.e., urease, could assist the treatment and prevention of this disease.

Sex-specific association between the gut microbiome and high-fat diet-induced metabolic disorders in mice

Background

Accumulating evidence indicates that high-fat diet (HFD)-induced metabolic disorders are associated with dysbiosis of the gut microbiota. However, the sex-specific characteristics of the gut microbiota and its association with a sexually dimorphic response to a HFD remain unclear.

Methods

Male and female mice were randomly assigned to receive a chow diet (CD) or HFD for 12 weeks. A group of HFD mice were pretreated with antibiotic cocktails for 4 weeks. Body weight, insulin sensitivity and the levels of serum metabolic parameters (blood glucose and insulin) were evaluated. 16S rRNA gene sequencing was performed to analyze the composition of the gut microbiota.

Results

HFD-induced body weight gain (BWG) was higher in male mice than in female mice. While insulin resistance was increased in the HFD group compared to CD group in male mice, there was no difference in insulin resistance among female mice. Antibiotic-pretreatment alleviated HFD-induced insulin resistance in male mice and elevated fasting blood glucose in female mice. The composition of the gut microbiota in male mice was remarkably different from that in female mice independent of diet. A higher abundance of the genera Parabacteroides, Lactobacillus, Bacteroides, and Bifidobacterium was observed in females than inmales. HFD feeding also influenced the structure of the gut microbiota, as it decreased the abundance of short-chain fatty acids-producing bacteria including Roseburia and Lachnospiraceae_NK4A136_group. Alterations in the gut microbiota in response to antibiotics followed by HFD were different between males and females, indicating sex-dependent sensitivity to antibiotics.

Conclusions

We identified that sex had a greater impact on the composition of gut microbiota than environmental factors (HFD and antibiotics). The enrichment of beneficial microbes in female mice may be associated with the resistance of female mice to HFD-induced metabolic disorders, which was weakened by antibiotic pretreatment.

Microbiota Induced Changes in the Immune Response in Pregnant Mice

Pregnancy is associated with adaptations of the immune response and with changes in the gutmicrobiota. We hypothesized the gut microbiota are involved in inducing (part of) the immunological adaptations during pregnancy. To test this hypothesis, we collected feces from pregnant conventional mice before and during pregnancy (days 7, 14, and 18) and microbiota were measured using 16S RNA sequencing. At day 18, mice were sacrificed and splenic (various Th cell populations) and blood immune cells (monocyte subsets) were measured by flow cytometry. The data were compared with splenic and blood immune cell populations from pregnant (day 18) germfree mice and non-pregnant conventional and germfree mice. Finally, the abundances of the individual gut bacteria in the microbiota of each conventional pregnant mouse were correlated to the parameters of the immune response of the same mouse. The microbiota of conventional mice were significantly different at the end of pregnancy (day 18) as compared with pre-pregnancy (Permanova, p < 0.05). The Shannon index was decreased and the Firmicutes/Bacteroidetes ratio was increased (Friedman followed by Dunn's test, p < 0.05), while abundances of various species (such as Allobaculum stercoricanis, Barnesiella intestihominis, and Roseburia faecis) were significantly different at day 18 compared with pre-pregnancy. In pregnant conventional mice, the percentage of Th1 cells was decreased, while the percentages of Treg cells and Th2 cells were or tended to be increased vs. non-pregnant mice. In germfree mice, only the percentage of Th1 cells was decreased in pregnant vs. non-pregnant mice, with no effect of pregnancy on Treg and Th2 cells. The percentages of monocyte subsets were affected by pregnancy similarly in conventional and germfree mice. However, the activation status of monocytes (expression of CD80 and MHCII) was affected by pregnancy mainly in conventional mice, and not in germfree mice. Correlation (Spearman's coefficient) of pregnancy affected microbiota with pregnancy affected immune cells, i.e., immune cells that were only affected differently in conventional mice and germfree mice, showed 4 clusters of bacteria and 4 clusters of immune cells, some of these clusters were correlated with each other. For instance, the microbiota in cluster 1 and 2 (in which there were various short chain fatty acid producing microbiota) are positively correlated with immune cells in cluster B, containing Treg cells and Th2 cells. Microbiota and immune cells are affected by pregnancy in mice. The different immunological adaptations to pregnancy between conventional and germfree mice, such as the increase in Treg and tendency to an increase in Th2 cells in conventional pregnant mice only, may suggest that the microbiota may play a role in adapting the maternal immune response to pregnancy.

Gut microbiota in reintroduction of giant panda

Reintroduction is a key approach in the conservation of endangered species. In recent decades, many reintroduction projects have been conducted for conservation purposes, but the rate of success has been low. Given the important role of gut microbiota in health and diseases, we questioned whether gut microbiota would play a crucial role in giant panda's wild-training process. The wild procedure is when captive-born babies live with their mothers in a wilderness enclosure and learn wilderness survival skills from their mothers. During the wild-training process, the baby pandas undergo wilderness survival tests and regular physical examinations. Based on their performance through these tests, the top subjects (age 2-3 years old) are released into the wild while the others are translocated to captivity. After release, we tracked one released panda (Zhangxiang) and collected its fecal samples for 5 months (January 16, 2013 to March 29 2014). Here, we analyzed the Illumina HiSeq sequencing data (V4 region of 16S rRNA gene) from captive pandas (n = 24), wild-training baby pandas (n = 8) of which 6 were released and 2 were unreleased, wild-training mother pandas (n = 8), one released panda (Zhangxiang), and wild giant pandas (n = 18). Our results showed that the gut microbiota of wild-training pandas is significantly different from that of wild pandas but similar to that of captive ones. The gut microbiota of the released panda Zhangxiang gradually changed to become similar to those of wild pandas after release. In addition, we identified several bacteria that were enriched in the released baby pandas before release, compared with the unreleased baby pandas. These bacteria include several known gut-health related beneficial taxa such as Roseburia, Coprococcus, Sutterella, Dorea, and Ruminococcus. Therefore, our results suggest that certain members of the gut microbiota may be important in panda reintroduction.

Baicalin Protects Against Hypertension-Associated Intestinal Barrier Impairment in Part Through Enhanced Microbial Production of Short-Chain Fatty Acids

Impaired intestinal barrier plays an important role in the pathogenesis of hypertension primarily through promoting the development of chronic low-grade inflammation. Baicalin is the major flavonoid component of Scutellaria baicalensis Georgi, a medicinal plant commonly used for the treatment of inflammatory intestinal disorders and hypertension in traditional Chinese medicine. However, it remains to be elucidated whether baicalin alleviates hypertension-associated intestinal barrier impairment. The current study thus investigated the effects of baicalin on the intestinal barrier integrity, the intestinal expression of genes encoding proinflammatory factors and tight junction proteins, the serum levels of the inflammatory markers, the amount of fecal short-chain fatty acids (SCFAs) and the abundance of SCFAs-producing bacteria in the spontaneously hypertensive rats (SHRs). The results showed that baicalin alleviated the pathological lesions in the ilium and the proximal colon in the SHRs. Baicalin treatment resulted in decreased ileal and colonic expression of proinflammatory genes in the SHRs. In addition, baicalin treatment attenuated hypertension-associated intestinal hyperpermeability and decreased the serum levels of inflammatory indicators such as high-sensitivity C-reactive protein (hs-CRP), interleukin 1 beta, and IL-6 in the SHRs. The protective effect of baicalin on the intestinal integrity was also supported by well-preserved intestinal ultrastructure and increased intestinal expression of genes encoding tight junction proteins such as zonula occludens-1 (ZO-1), cingulin, and occludin in the SHRs. Lastly, baicalin treatment increased the amount of fecal SCFAs and the abundance of SCFAs-producing bacteria in the SHRs. In conclusion, the work here provides for the first time the morphological, biochemical, and molecular evidence supporting the protective effects of baicalin on the intestinal integrity in the SHRs, which may help better understand the therapeutic effects of S. baicalensis Georgi in the treatment of hypertension.

Bifidobacterium longum-fermented rice bran and rice bran supplementation affects the gut microbiome and metabolome

This study investigated gut microbiota composition along with food, host, and microbial derived metabolites in the colon and systemic circulation of healthy mice following dietary rice bran and fermented rice bran intake. Adult male BALB/c mice were fed a control diet or one of two experimental diets containing 10% w/w rice bran fermented by Bifidobacterium longum or 10% w/w non-fermented rice bran for 15 weeks. Metabolomics was performed on the study diets (food), the murine colon and whole blood. These were analysed in concert with 16S rRNA amplicon sequencing of faeces, caecum, and colon microbiomes. Principal components analysis of murine microbiota composition displayed marked separation between control and experimental diets, and between faecal and tissue (caecum and colon) microbiomes. Colon and caecal microbiomes in both experimental diet groups showed enrichment of Roseburia, Lachnospiraceae, and Clostridiales related amplicon sequence variants compared to control. Bacterial composition was largely similar between experimental diets. Metabolite profiling revealed 530 small molecules comprising of 39% amino acids and 21% lipids that had differential abundances across food, colon, and blood matrices, and statistically significant between the control, rice bran, and fermented rice bran groups. The amino acid metabolite, N-delta-acetylornithine, was notably increased by B. longum rice bran fermentation when compared to non-fermented rice bran in food, colon, and blood. These findings support that dietary intake of rice bran fermented with B. longum modulates multiple metabolic pathways important to the gut and overall health.

Effect of rice bran fermented with Saccharomyces cerevisiae and Lactobacillus plantarum on gut microbiome of mice fed high-sucrose diet

To clarify the effect of rice bran (RB) and fermented RB (FRB) in a high-sucrose and low-dietary fibre diet on the gut microbiome, the in vitro bile acid-lowering capacity and caecal microbiota of ICR mice fed with 20% RB or FRB diets for two weeks were determined. The caecal microbiome was analysed by 16S rRNA gene amplicon sequencing. The in vitro bile acid-lowering capacity was high for FRB. In mouse experiments, triacylglycerol and total cholesterol were generally lower with FRB, although the faecal frequency was highest in mice fed with RB. The Shannon-Wiener and Simpson's indices for alpha-diversity in the microbiome of mice fed with RB and FRB, were higher than mice fed the control diet. At the phylum level in the caecal microbiome, Firmicutes and Bacteroidetes were high with FRB and RB, respectively. At the operational taxonomic unit level, some bacterial groups related to diabetes and gut toxicity, such as Lachnospiraceae and Enterorhabdus mucosicola, were high for RB but not for FRB diets. These results suggest that FRB, rather than RB, intake improve the intestinal environment and blood lipid condition.

New and Preliminary Evidence on Altered Oral and Gut Microbiota in Individuals with Autism Spectrum Disorder (ASD): Implications for ASD Diagnosis and Subtyping Based on Microbial Biomarkers

Autism Spectrum Disorder (ASD) is a complex neurological and developmental disorder characterized by behavioral and social impairments as well as multiple co-occurring conditions, such as gastrointestinal abnormalities, dental/periodontal diseases, and allergies. The etiology of ASD likely involves interaction between genetic and environmental factors. Recent studies suggest that oral and gut microbiome play important roles in the pathogenesis of inflammation, immune dysfunction, and disruption of the gut–brain axis, which may contribute to ASD pathophysiology. The majority of previous studies used unrelated neurotypical individuals as controls, and they focused on the gut microbiome, with little attention paid to the oral flora. In this pilot study, we used a first degree-relative matched design combined with high fidelity 16S rRNA (ribosomal RNA) gene amplicon sequencing in order to characterize the oral and gut microbiotas of patients with ASD compared to neurotypical individuals, and explored the utility of microbiome markers for ASD diagnosis and subtyping of clinical comorbid conditions. Additionally, we aimed to develop microbiome biomarkers to monitor responses to a subsequent clinical trial using probiotics supplementation. We identified distinct features of gut and salivary microbiota that differed between ASD patients and neurotypical controls. We next explored the utility of some differentially enriched markers for ASD diagnosis and examined the association between the oral and gut microbiomes using network analysis. Due to the tremendous clinical heterogeneity of the ASD population, we explored the relationship between microbiome and clinical indices as an attempt to extract microbiome signatures assocociated with clinical subtypes, including allergies, abdominal pain, and abnormal dietary habits. The diagnosis of ASD currently relies on psychological testing with potentially high subjectivity. Given the emerging role that the oral and gut microbiome plays in systemic diseases, our study will provide preliminary evidence for developing microbial markers that can be used to diagnose or guide treatment of ASD and comorbid conditions. These preliminary results also serve as a starting point to test whether altering the oral and gut microbiome could improve co-morbid conditions in patients with ASD and further modify the core symptoms of ASD.

Batch effect exerts a bigger influence on the rat urinary metabolome and gut microbiota than uraemia: a cautionary tale

BACKGROUND

Rodent models are invaluable for studying biological processes in the context of whole organisms. The reproducibility of such research is based on an assumption of metabolic similarity between experimental animals, controlled for by breeding and housing strategies that minimise genetic and environmental variation. Here, we set out to demonstrate the effect of experimental uraemia on the rat urinary metabolome and gut microbiome but found instead that the effect of vendor shipment batch was larger in both areas than that of uraemia.

RESULTS

Twenty four Wistar rats obtained from the same commercial supplier in two separate shipment batches underwent either subtotal nephrectomy or sham procedures. All animals undergoing subtotal nephrectomy developed an expected uraemic phenotype. The urinary metabolome was studied using ¹H-NMR spectroscopy and found to vary significantly between animals from different batches, with substantial differences in concentrations of a broad range of substances including lactate, acetate, glucose, amino acids, amines and benzoate derivatives. In animals from one batch, there was a complete absence of the microbiome-associated urinary metabolite hippurate, which was present in significant concentrations in animals from the other batch. These differences were so prominent that we would have drawn quite different conclusions about the effect of uraemia on urinary phenotype depending on which batch of animals we had used. Corresponding differences were seen in the gut microbiota between animals in different batches when assessed by the sequencing of 16S rRNA gene amplicons, with higher alpha diversity and different distributions of Proteobacteria subtaxa and short-chain fatty acid producing bacteria in the second batch compared to the first. Whilst we also demonstrated differences in both the urinary metabolome and gut microbiota associated with uraemia, these effects were smaller in size than those associated with shipment batch.

CONCLUSIONS

These results challenge the assumption that experimental animals obtained from the same supplier are metabolically comparable, and provide metabolomic evidence that batch-to-batch variations in the microbiome of experimental animals are significant confounders in an experimental study. We discuss strategies for reducing such variability and the need for transparency in research publications about the supply of experimental animals.

Dietary quality and the colonic mucosa-associated gut microbiome in humans

BACKGROUND

Despite tremendous interest in modulating the microbiome to improve health, the association between diet and the colonic mucosa-associated gut microbiome in healthy individuals has not been examined.

OBJECTIVE

To investigate the associations between Healthy Eating Index (HEI)-2005 and the colonic mucosa-associated microbiota.

METHODS

In this cross-sectional observational study, we analyzed bacterial community composition and structure using 16S rRNA gene (V4 region) sequencing of 97 colonic mucosal biopsies obtained endoscopically from different colon segments of 34 polyp-free participants. Dietary consumption was ascertained using an FFQ. Differences in α- and β-diversity and taxonomic relative abundances between the higher and lower score of total HEI and its components were compared, followed by multivariable analyses.

RESULTS

The structure of the microbiota significantly differed by the scores for total HEI, total and whole fruits (HEI 1 and HEI 2), whole grains (HEI 6), milk products and soy beverages (HEI 7), and solid fat, alcohol, and added sugar (HEI 12). A lower score for total HEI and HEIs 2, 7, and 12 was associated with significantly lower richness. A lower score for total HEI was associated with significantly reduced relative abundance of Parabacteroides, Roseburia, and Subdoligranulum but higher Fusobacterium. A lower score for HEI 2 was associated with lower Roseburia but higher Bacteroides. A lower score for HEI 7 was associated with lower Faecalibacterium and Fusobacterium but higher Bacteroides. A lower score for HEI 12 was associated with lower Subdoligranulum but higher Escherichia and Fusobacterium (false discovery rate-adjusted P values <0.05). The findings were confirmed by multivariate analysis. Less abundant bacteria such as Alistipes, Odoribacter, Bilophila, and Tyzzerella were also associated with dietary quality.

CONCLUSIONS

A lower score for total HEI-2005 was significantly associated with reduced relative abundance of potentially beneficial bacteria but increased potentially harmful bacteria in the colonic mucosa of endoscopically normal individuals.

Microbial Mechanistic Insights into the Role of Sweet Potato Vine on Improving Health in Chinese Meishan Gilt Model

Simple Summary

Sweet potato vine as a source of fiber had been used in China for many years. We investigated the effects of fresh sweet potato vine on intestinal and plasma metabolites as well as colon microbial composition in Chinese Meishan gilts. Results suggest that sweet potato vine promoted intestinal muscle development, decreased gut permeability, endotoxin and pro-inflammatory cytokines concentrations, and increased butyrate production as well as beneficial flora, thus improving gut health.

Abstract

This study explored the impact of fresh sweet potato vine on the growth as well as the metabolites and colon microbial composition in Chinese Meishan gilt. Twenty Meishan gilts (body weight 30 ± 0.18 kg, n = 10 per treatment) were randomly assigned to a control (CON) or sweet potato vine (SPV) supplementation diet treatment. Gilts were housed in individual stalls. In the SPV treatment, 2 kg fresh sweet potato vine was used instead of 0.18 kg basal diet which provided the same amount of digestive energy and crude protein with the exception of crude fiber (CON, 51.00 g/d vs. SPV, 73.94 g/d) in terms of dry matter intake. Gilts were slaughtered and samples were collected on day 19 after the third estrus cycle. The SPV treatment tended to increase slaughter weight of gilts (p = 0.07); it also increased (p < 0.05) gastrointestinal tract weight and intestinal muscle layer thickness. SPV treatment also decreased (p < 0.05) carcass yield and subcutaneous adipose tissue. The concentration of zonulin and endotoxin in plasma was decreased (p < 0.05) as the gilt consumed the SPV diet. Colonic fecal concentrations of endotoxin, lipocalin-2, and tumor necrosis factor-α (TNF-α) were decreased (p < 0.05), and interleukin-10 (IL-10) was increased (p < 0.05) in the SPV treatment. Butyric acid and acetate concentration in colonic content as well as acetate concentration in caecal content were increased (p < 0.05) in the SPV treatment. Furthermore, the expression of carnitine palmityl transferase (CPT-1) and peroxisome proliferator-activated receptor-α (PPAR-α) in gilt liver in SPV treatment was increased (p < 0.05) in comparison with CON treatment. Meanwhile, the composition of the colon microbes was also altered by SPV; representative changes included an increase in Lactobacillus, Bacteroides, Roseburia, and Lachnospira. These results indicate that gilt fed with sweet potato vine had decreased gut permeability, endotoxin and pro-inflammatory cytokines concentrations; colonic fecal microbiota was also changed, which may be further beneficial to the intestinal health of Chinese Meishan gilt.

Relationship(s) between obesity and inflammatory bowel diseases: possible intertwined pathogenic mechanisms

The inflammatory bowel diseases, Crohn's and ulcerative colitis have increased in incidence and prevalence from the mid-eighteen to the late nineteen centuries. From then to the current twenty-first century there has been a more rapid expansion of these disease to areas previously experiencing low rates. This latter expansion coincides with the current obesity pandemic which also began toward the end of the last century. Although the two diseases have radically different frequencies, there are interesting links between them. Four areas link the diseases. On an epidemiological level, IBD tends to follow a north-south gradient raising the importance of vitamin D in protection. Obesity has very weak relationship with latitude, but both diseases follow adult lactase distributions colliding in this plane. Is it possible that obesity (a low vitamin D condition with questionable response to supplements) reduces effects in IBD? On a pathogenic level, pro-inflammatory processes mark both IBD and obesity. The similarity raises the question of whether obesity could facilitate the development of IBD. Features of the metabolic syndrome occur in both, with or without obesity in IBD. The fourth interaction between the two diseases is the apparent effect of obesity on the course of IBD. There are suggestions that obesity may reduce the efficacy of biologic agents. Yet there is some suggestion also that obesity may reduce the need for hospitalization and surgery. The apparent co-expansion of both obesity and IBD suggests similar environmental changes may be involved in the promotion of both.

Cooked Red Lentils Dose-Dependently Modulate the Colonic Microenvironment in Healthy C57Bl/6 Male Mice

Dietary pulses, including lentils, are protein-rich plant foods that are enriched in intestinal health-promoting bioactives, such as non-digestible carbohydrates and phenolic compounds. The aim of this study was to investigate the effect of diets supplemented with cooked red lentils on the colonic microenvironment (microbiota composition and activity and epithelial barrier integrity and function). C57Bl/6 male mice were fed one of five diets: a control basal diet (BD), a BD-supplemented diet with 5, 10 or 20% cooked red lentils (by weight), or a BD-supplemented diet with 0.7% pectin (equivalent soluble fiber level as found in the 20% lentil diet). Red lentil supplementation resulted in increased: (1) fecal microbiota α-diversity; (2) abundance of short-chain fatty acid (SCFA)-producing bacteria (e.g., Prevotella, Roseburia and Dorea spp.); (3) concentrations of fecal SCFAs; (4) mRNA expression of SCFA receptors (G-protein-coupled receptors (GPR 41 and 43) and tight/adherens junction proteins (Zona Occulden-1 (ZO-1), Claudin-2, E-cadherin). Overall, 20% lentil had the greatest impact on colon health outcomes, which were in part explained by a change in the soluble and insoluble fiber profile of the diet. These results support recent public health recommendations to increase consumption of plant-based protein foods for improved health, in particular intestinal health.

Gut microbiota differences in elderly subjects between rural city Kyotango and urban city Kyoto: an age-gender-matched study

Several outcomes have been reported on the role of gut microbiota in health promotion and disease prevention. Kyotango, one of the longevity areas with various centenarians, is a provincial city located in the northern part of Kyoto Prefecture in Japan. To understand the relationship between gut microbiota and urbanization, we compared the diversity, abundance, and function of gut microbiota in older healthy subjects between Kyotango and Kyoto cities; Kyoto is an urban city located in the southern part of Kyoto Prefecture. In total, 51 subjects at Kyotango and 51 subjects at Kyoto matched by age and gender were recruited, and their fecal samples were obtained to analyze the gut microbiota using 16S rRNA gene sequencing. Principal coordinate analysis for β-diversity revealed significant differences in the gut microbiota between two cities. In contrast, the analysis of α-diversity revealed no significant differences between the groups. On comparison at the phylum levels, the abundance of Firmicutes was decreased with the urbanization, whereas that of Proteobacteria and Bacteroidetes increased. On comparison at the genus levels, with urbanization, a significant decrease was observed in Lachnospiraceae families including genus Roseburia and Coprococcus, and significant increases was observed in Bacteroides, Oscillospira, Parabacteroides, and Ruminococcus. The most markedly increased functional pathway with urbanization was lipopolysaccharide biosynthesis proteins and lipopolysaccharide biosynthesis, and decreased pathway was transporters and ABC transporters. In conclusion, the present findings indicate significant differences in the gut microbiota between the provincial city and urban cities at Kyoto Prefecture. These alterations in the microbiota may provide new insights to consider the relationship between longevity and gut microbiota.

Beneficial effect of butyrate-producing Lachnospiraceae on stress-induced visceral hypersensitivity in rats

BACKGROUND AND AIM

Emerging evidence indicates that psychological stress is involved in the pathogenesis of irritable bowel syndrome, which is characterized by visceral hypersensitivity and may be accompanied by gut dysbiosis. However, how such stress contributes to the development of visceral hypersensitivity is incompletely understood. Here, we aimed to investigate the influence that stress-induced microbial changes exert on visceral sensitivity, as well as the possible underlying mechanisms associated with this effect.

METHODS

Male Sprague-Dawley rats underwent chronic water avoidance stress (WAS) to induce visceral hypersensitivity. Visceral sensitivity, colonic tight junction protein expression, and short-chain fatty acids of cecal contents were measured. Fecal samples were collected to characterize microbiota profiles. In a separate study, oral gavage of Roseburia in WAS rats was conducted to verify its potential role in the effectiveness on visceral hypersensitivity.

RESULTS

Repeated WAS caused visceral hypersensitivity, altered fecal microbiota composition and function, and decreased occludin expression in the colon. Stressed rats exhibited reduced representation of pathways involved in the metabolism of butyrate and reduced abundance of several operational taxonomic units associated with butyrate-producing bacteria, such as Lachnospiraceae. Consistently, supplementation with Roseburia hominis, a species belonging to Lachnospiraceae, significantly increased cecal butyrate content. Moreover, Roseburia supplementation alleviated visceral hypersensitivity and prevented the decreased expression of occludin.

CONCLUSIONS

Reduction in the abundance of butyrate-producing Lachnospiraceae, which is beneficial for the intestinal barrier, was involved in the formation of visceral hypersensitivity. R. hominis is a potential probiotic for treating stress-induced visceral hypersensitivity.

Influence of Traditional vs Alternative Dietary Carbohydrates Sources on the Large Intestinal Microbiota in Post-Weaning Piglets

Simple Summary

Nutritional and environmental changes result in significant physiological changes in pigs at the weaning stage. The post-weaning period is mainly characterized by low feed intake and feed efficiency, together with intestinal disturbances. Maximizing the energy intake is known to be critical for promoting growth in weaned piglets, and it is essential to formulate diets with highly digestible and absorbable nutrients/ingredients, as the degree of intestinal maturation is limited. The current challenge is to find new sustainable, effective, and simple carbohydrate sources to satisfy these conditions without producing detrimental effects on the gut ecosystem. In this research, processed and ready-to-eat food products that are no longer suitable for humans were tested, which have high potential as an alternative energy source for pig nutrition. The results demonstrated that replacing conventional ingredients with highly digestible and simple carbohydrate-rich ingredients in the diets of post-weaning piglets did not affect their growth. However, both the abundance and composition of the bacterial community in the large intestine changed. Thus, the results should be interpreted with caution, as they are case-specific, and when these alternative feed ingredients are used in the post-weaning period, their inclusion rate and their effect on microbiota must be carefully considered.

Abstract

In this study, common cereal grains were partially replaced by former foodstuffs products (FFPs) in post-weaning piglets’ diets, to investigate how these alternative ingredients influence the faecal microbiota in the post-weaning period. Twelve post-weaning piglets were housed for 16 days in individual pens and were then fed two diets: a standard wheat-barley-corn meal diet and a diet containing 30% FFPs, thus partially substituting conventional cereals. The growth performance was monitored and faecal microbiota was characterized by the next generation sequencing of the 16S rRNA gene. The results showed no detrimental effects on growth performance when FFPs were used. However, the FFP diet decreased the bacterial richness and evenness in the large intestine, while minor differences were observed in the taxa composition. The core microbiota composition was only slightly affected, and no differences between the two groups in the gut microbiota composition at the phylum level over time were observed. Thus, although these results should be interpreted with caution, as they are case-specific, FFPs can be potentially used as alternative carbohydrate sources in post-weaning piglets, but further investigations are necessary to clarify their impact on gut health when used for a longer period.

Daily intake of wheat germ-enriched bread may promote a healthy gut bacterial microbiota: a randomised controlled trial

PURPOSE

Wheat bran fibre has a beneficial effect on gastrointestinal function, but evidence for wheat germ is scarce. Accordingly, we evaluated the effects of daily intake of wheat germ on gastrointestinal discomfort and gut microbiota by adding wheat germ to refined (white) wheat bread, the most consumed bread type. We hypothesised that an improvement in the composition of refined bread could beneficially affect intestinal health without compromising consumers' acceptance.

METHODS

Fifty-five healthy adults were recruited for a randomised, double-blind, crossover, controlled trial comprising two 4-week intervention periods separated by a 5-week washout stage. During the first 4-week period, one group consumed wheat bread enriched with 6 g of wheat germ and the control group consumed non-enriched wheat bread.

RESULTS

Wheat germ-enriched bread was well-appreciated and the number of participants that demonstrated minimal gastrointestinal improvements after wheat-germ intake was higher than in the control arm. Importantly, intake of wheat germ-enriched bread decreased the perceived gastrointestinal discomfort-related quality of life (subscale worries and concerns) over refined white bread. The improvements in the gastrointestinal function were accompanied by favourable changes in gut microbiota, increasing the number of Bacteroides spp. and Bifidobacterium spp.

CONCLUSIONS

Adding wheat germ to industrially made white bread without altering sensory properties may promote a healthy gut bacterial microbiota and the gastrointestinal health.

Gut Microbiota Changes in Patients with Bipolar Depression

This study aims to characterize the gut microbiota in depressed patients with bipolar disorder (BD) compared with healthy controls (HCs), to examine the effects of quetiapine treatment on the microbiota, and to explore the potential of microbiota as a biomarker for BD diagnosis and treatment outcome. Analysis of 16S-ribosomal RNA gene sequences reveals that gut microbial composition and diversity are significantly different between BD patients and HCs. Phylum Bacteroidetes and Firmicutes are the predominant bacterial communities in BD patients and HCs, respectively. Lower levels of butyrate-producing bacteria are observed in untreated patients. Microbial composition changes following quetiapine treatment in BD patients. Notably, 30 microbial markers are identified on a random forest model and achieve an area under the curve (AUC) of 0.81 between untreated patients and HCs. Ten microbial markers are identified with the AUC of 0.93 between responder and nonresponder patients. This study characterizes the gut microbiota in BD and is the first to evaluate microbial changes following quetiapine monotherapy. Gut microbiota-based biomarkers may be helpful in BD diagnosis and predicting treatment outcome, which need further validations.

Compositional and functional features of the female premenopausal and postmenopausal gut microbiota

Endogenous estrogen deficiency accelerates many diseases in postmenopausal women, and gut microbes contribute to estrogen level modulation. However, the compositional alterations and influences of the gut microbiota in postmenopausal women remain uncertain. A metagenome-wide association study was performed to compare the gut microbiota of 24 premenopausal and 24 postmenopausal women. Firmicutes and Roseburia spp. are depleted, while Bacteroidetes and the toluene-producing genus Tolumonas are overrepresented in fecal samples from postmenopausal women. The pentose phosphate pathway is enriched in premenopausal women. Homocysteine synthesis-related processes are enriched in postmenopausal women. The gut microbiomes of premenopausal and postmenopausal women differ and produce different metabolites. The gut microbiome may be a therapeutic target to reduce risks and improve the quality of life in postmenopausal women.

Glutamic acid supplementation reduces body fat weight in finishing pigs when provided solely or in combination with arginine and it is associated with colonic propionate and butyrate concentrations

Changes in the composition of gut microbiota have been proposed as possible causes of obesity. Our previous study showed that glutamic acid (Glu) alone or a combination of Glu and arginine (Arg) decreased backfat thickness in finishing pigs. Therefore, this study aimed to investigate the effects of dietary supplementation with Glu and/or Arg on body fat weight, composition of gut microbiota, and short-chain fatty acid concentrations in the colons of finishing pigs, and to elucidate whether body fat weight was associated with changes in the colonic microbial community and concentrations of colonic metabolites. Sixty Duroc × Large White × Landrace pigs with an average initial body weight of 77.1 ± 1.3 kg were randomly assigned to one of five treatment groups (12 pigs per group). The pigs in the control group were fed a basal diet (BD group), while those in the experimental groups were fed a basal diet supplemented with either 2.05% l-alanine (Isonitrogenous, IS group), 1.00% l-arginine (Arg group), 1.00% glutamate + 1.44% l-alanine (Glu group), or 1.00% l-arginine + 1.00% glutamate (Arg_Glu group). The results showed that dietary supplementation with alanine has no effect (P > 0.05) on body fat weight, while with both Glu and Arg + Glu decreased (P < 0.05) body fat weight and increased (P < 0.05) colonic concentrations of propionate, butyrate, and valerate relative to the BD group. Negative relationships (P < 0.05) were observed between body fat weight and colonic propionate and butyrate concentrations. Compared to the IS group, dietary supplementation with Arg or Arg + Glu decreased (P < 0.05) colonic tyramine concentration. Compared to the IS group, the butyrate concentration increased (P < 0.05) in the Arg_Glu group. Compared to the BD group, the relative colonic abundance of Actinobacteria was higher (P < 0.05) in the Arg_Glu group. The abundances of Lachnospiraceae_XPB1014_group, norank_f_Erysipelotrichaceae, and Roseburia sp. were negatively (P < 0.05) correlated with body fat weight, and the abundance of norank_f_Erysipelotrichaceae was also negatively (P < 0.05) correlated with colonic butyrate concentration. These findings suggest that decreased body fat weight in finishing pigs can be induced by Glu supplementation alone or in combination with Arg. Glu + Arg supplementation was also associated with increased colonic butyrate and propionate concentrations and increased colonic Actinobacteria abundance.

Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes

The last two steps of the purine biosynthetic pathway may be catalyzed by different enzymes in prokaryotes. The genes that encode these enzymes include homologs of purH, purP, purO and those encoding the AICARFT and IMPCH domains of PurH, here named purV and purJ, respectively. In Bacteria, these reactions are mainly catalyzed by the domains AICARFT and IMPCH of PurH. In Archaea, these reactions may be carried out by PurH and also by PurP and PurO, both considered signatures of this domain and analogous to the AICARFT and IMPCH domains of PurH, respectively. These genes were searched for in 1,403 completely sequenced prokaryotic genomes publicly available. Our analyses revealed taxonomic patterns for the distribution of these genes and anticorrelations in their occurrence. The analyses of bacterial genomes revealed the existence of genes coding for PurV, PurJ, and PurO, which may no longer be considered signatures of the domain Archaea. Although highly divergent, the PurOs of Archaea and Bacteria show a high level of conservation in the amino acids of the active sites of the protein, allowing us to infer that these enzymes are analogs. Based on the results, we propose that the gene purO was present in the common ancestor of all living beings, whereas the gene encoding PurP emerged after the divergence of Archaea and Bacteria and their isoforms originated in duplication events in the common ancestor of phyla Crenarchaeota and Euryarchaeota. The results reported here expand our understanding of the diversity and evolution of the last two steps of the purine biosynthetic pathway in prokaryotes.

Strain-Specific Anti-inflammatory Properties of Two Akkermansia muciniphila Strains on Chronic Colitis in Mice

Akkermansia muciniphila is potential probiotic in that its type strain ATCC BAA-835 has beneficial effects upon obesity and diabetes. However, whether A. muciniphila can improve inflammatory bowel diseases (IBD), which is a form of chronic intestinal dysbiosis, is unknown. Hence, we used an isolated murine A. muciniphila strain (designated 139) and A. muciniphila type strain ATCC, to investigate their anti-inflammatory properties in cell models and in Dextran Sulfate Sodium (DSS)-induced chronic colitis of mice. In vitro, the two A. muciniphila strains exerted similar anti-inflammatory properties as they both reduced IL-8 production by TNF-α-stimulated HT-29 cells. However, neither of the strains showed capacity to increase the differentiation of regulatory T (Treg)-cells from CD4+ T cell populations significantly. In vivo, both A. muciniphila strains exerted anti-inflammatory effects on chronic colitis as they improved clinical parameters including spleen weight, colon inflammation index, and colon histological score. They also down-regulated the expression of the pro-inflammatory cytokines including TNF-α and IFN-γ in the colon of mice. However, the anti-inflammatory effects of strain ATCC were stronger than strain 139 in that ATCC significantly reduced spleen weight, colon inflammation index, and fecal lipocalin-2 content in mice with chronic colitis, while strain 139 was not. Dysbiosis of the gut microbiota was observed in mice with chronic colitis. Both A. muciniphila strains facilitated the normalization of the gut microbiota. The specific capacity of strain ATCC to modulate the differentiation of Tregs as well as increase production of short chain fatty acids, demonstrated strain-specific characteristics for these two A. muciniphila strains. This study suggests the potential beneficial effect of A. muciniphila on IBD and the importance of the future study of the function of A. muciniphila at the strain-level.

Gut Microbiome, Short-Chain Fatty Acids, and Mucosa Injury in Young Adults with Human Immunodeficiency Virus Infection

BACKGROUND

HIV progression is characterized by immune activation and microbial translocation from the gut. Short-chain fatty acids (SCFAs) are essential for gut homeostasis. Decreased intestinal SCFAs play a role in rapid HIV progression.

AIMS

To compare the SCFA profile, intestinal microbiome, and intestinal mucosal injury between patients with HIV (but not AIDS) and healthy controls.

METHODS

This was a prospective study of 15 patients without AIDS and 10 controls conducted between July 2016 and January 2017 at the Institute of Dermatology and Venereology (Sichuan Academy of Medical Sciences). Stool specimens were collected to analyze the microbiome and SCFAs. Blood I-FABP and D-lactate (gut injury markers) were measured as well as T cells in HIV-positive patients. Intestinal mucosa was observed by colonoscopy.

RESULTS

Rikenellaceae, Microbacteriaceae, Roseburia, Lachnospiraceae, Alistipes, and Ruminococcaceae were decreased, while Moraxellaceae and Psychrobacter were increased in HIV-positive patients. Butyric acid (p = 0.04) and valeric acid (p = 0.03) were reduced in HIV-positive patients. Colonoscopy revealed no visible damage in all subjects. There were no differences in I-FABP and D-lactate between groups. Butyric and valeric acids mainly positively correlated with Rikenellaceae, Ruminococcaceae, Alistipes, Roseburia, and Lachnospiraceae. CD8+ cells were positively correlated with Proteobacteria. CD4+ cells, and CD4/CD8 were negatively correlated with acetic acid. CD8+ cells were positively correlated with valeric acid.

CONCLUSION

The differences in the distribution of intestinal flora between HIV-infected and healthy individuals, especially some SCFAs, suggest that there is already a predisposition to intestinal mucosa damage in HIV-infected individuals.

The Gut Microbiome in Inflammatory Bowel Disease: Lessons Learned From Other Immune-Mediated Inflammatory Diseases

There is a growing appreciation for the role of the gut microbiome in human health and disease. Aided by advances in sequencing technologies and analytical methods, recent research has shown the healthy gut microbiome to possess considerable diversity and functional capacity. Dysbiosis of the gut microbiota is believed to be involved in the pathogenesis of not only diseases that primarily affect the gastrointestinal tract but also other less obvious diseases, including neurologic, rheumatologic, metabolic, hepatic, and other illnesses. Chronic immune-mediated inflammatory diseases (IMIDs) represent a group of diseases that share many underlying etiological factors including genetics, aberrant immunological responses, and environmental factors. Gut dysbiosis has been reported to be common to IMIDs as a whole, and much effort is currently being directed toward elucidating microbiome-mediated disease mechanisms and their implications for causality. In this review, we discuss gut microbiome studies in several IMIDs and show how these studies can inform our understanding of the role of the gut microbiome in inflammatory bowel disease.

Effects of Intranasal Pseudorabies Virus AH02LA Infection on Microbial Community and Immune Status in the Ileum and Colon of Piglets

Pseudorabies virus (PRV) variants broke out in china since 2011, causing high fever, respiratory distress, systemic neurological symptoms, and diarrhea in piglets. This study investigated the effect of intranasal PRV variant (AH02LA) infection on ileal and colonic bacterial communities and immune status in piglets. Ten piglets (free of PRV) were assigned to PRV variant and control groups (uninfected). At day 5 after inoculation, all piglets were euthanized. No PRV was detected in the ileal and colonic mucosa. In the PRV group, we observed up-regulation of specific cytokines gene expression, down-regulation of intestinal barrier-related gene expression, and reduction of secretory immunoglobulin A (sIgA) concentration in the ileum and colon. PRV infection increased the diversity of ileal bacterial community composition. PRV infection reduced the abundance of some beneficial bacteria (Lactobacillus species in the ileum and colon; butyrate-producing bacteria species in the colon) and increased the abundance of potentially pathogenic Fusobacterium nucleatum in the ileum and Sphingomonas paucimobilis in the colon. Moreover, PRV infection decreased concentrations of the beneficial lactate in the ileum and butyrate in the colon. However, this study does not allow to evaluate whether the observed changes are directly due to the PRV infection or rather to indirect effects (fever, clinical signs and changes in diet), and will be our next research content. In summary, our findings provide evidence that intranasal PRV infection directly or indirectly brings gut health risks and implications, although no PRV was detected in the ileum and colon.

Cryopreservation of the human gut microbiota: Current state and perspectives

The human intestinal microbiota is a complex ecosystem that consists of thousands of bacterial species that are responsible for human health and disease. The intestinal microbiota is a natural resource for production of therapeutic and preventive medicals, such as probiotics and fecal transplants. Modern lifestyles have resulted in the extinction of evolutionally selected microbial populations upon exposure to environmental factors. Therefore, it is very important to preserve the human gut microbiota to have the opportunity for timely restoration with minimal safety risks. Cryopreservation techniques that are suitable for the preservation of viable, mixed microbial communities and a biobanking approach are currently under development in different countries. However, the number of studies in this area is very limited. The variety of morphological and physiological characteristics of microbes in the microbiota, the different cryopreservation goals, and the criteria for the evaluation of cryopreservation effectiveness are the main challenges in the creation of a universal and standardized cryopreservation protocol. In this review, we summarized the current progress of the main cryopreservation techniques for gut microbiota communities and the methods for the assessment of the effectiveness of these techniques in the context of practical application.

ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples

Analysis of 16S ribosomal RNA (rRNA) gene amplification data for microbial barcoding can be inaccurate across complex environmental samples. A method, ANCHOR, is presented and designed for improved species‐level microbial identification using paired‐end sequences directly, multiple high‐complexity samples and multiple reference databases. A standard operating procedure (SOP) is reported alongside benchmarking against artificial, single sample and replicated mock data sets. The method is then directly tested using a real‐world data set from surface swabs of the International Space Station (ISS). Simple mock community analysis identified 100% of the expected species and 99% of expected gene copy variants (100% identical). A replicated mock community revealed similar or better numbers of expected species than MetaAmp, DADA2, Mothur and QIIME1. Analysis of the ISS microbiome identified 714 putative unique species/strains and differential abundance analysis distinguished significant differences between the Destiny module (U.S. laboratory) and Harmony module (sleeping quarters). Harmony was remarkably dominated by human gastrointestinal tract bacteria, similar to enclosed environments on earth; however, Destiny module bacteria also derived from nonhuman microbiome carriers present on the ISS, the laboratory's research animals. ANCHOR can help substantially improve sequence resolution of 16S rRNA gene amplification data within biologically replicated environmental experiments and integrated multidatabase annotation enhances interpretation of complex, nonreference microbiomes.

Influence of Vitamin D Deficiency on Inflammatory Markers and Clinical Disease Activity in IBD Patients

Vitamin D has recently been discovered to be a potential immune modulator. Low serum vitamin D levels have been associated with risk of relapse and exacerbation of clinical outcomes in Crohn’s disease (CD) and ulcerative colitis (UC). A retrospective, longitudinal study was conducted to determine the association between vitamin D levels and inflammatory markers and clinical disease activity in inflammatory bowel disease (IBD). In addition, circulating 25(OH)D₃ progression was evaluated according to vitamin D supplementation. Participants were separated into three groups according to their vitamin D level: severe deficiency (SD), moderate deficiency (MD) and sufficiency (S). Serum 25(OH)D₃ was inversely correlated with faecal calprotectin (FC) for CD and UC but was only correlated with C-reactive protein (CRP) for UC patients. In the multivariate analysis of FC, CRP and fibrinogen (FBG), we predicted the presence of a patient in the SD group with 80% accuracy. A deficiency of 25(OH)D₃ was associated with increased hospitalisations, flare-ups, the use of steroids and escalating treatment. Supplemental doses of vitamin D were likely to be insufficient to reach adequate serum levels of 25(OH)D₃. Vitamin D intervention studies are warranted to determine whether giving higher doses of vitamin D in IBD might reduce intestinal inflammation or disease activity.

Precision Nutrition and the Microbiome, Part I: Current State of the Science

The gut microbiota is a highly complex community which evolves and adapts to its host over a lifetime. It has been described as a virtual organ owing to the myriad of functions it performs, including the production of bioactive metabolites, regulation of immunity, energy homeostasis and protection against pathogens. These activities are dependent on the quantity and quality of the microbiota alongside its metabolic potential, which are dictated by a number of factors, including diet and host genetics. In this regard, the gut microbiome is malleable and varies significantly from host to host. These two features render the gut microbiome a candidate ‘organ’ for the possibility of precision microbiomics—the use of the gut microbiome as a biomarker to predict responsiveness to specific dietary constituents to generate precision diets and interventions for optimal health. With this in mind, this two-part review investigates the current state of the science in terms of the influence of diet and specific dietary components on the gut microbiota and subsequent consequences for health status, along with opportunities to modulate the microbiota for improved health and the potential of the microbiome as a biomarker to predict responsiveness to dietary components. In particular, in Part I, we examine the development of the microbiota from birth and its role in health. We investigate the consequences of poor-quality diet in relation to infection and inflammation and discuss diet-derived microbial metabolites which negatively impact health. We look at the role of diet in shaping the microbiome and the influence of specific dietary components, namely protein, fat and carbohydrates, on gut microbiota composition.