Enterotype Variations of the Healthy Human Gut Microbiome in Different Geographical Regions

Microbial Ecology and Metabolism of Emerging Adulthood: Gut Microbiome Insights from a College Freshman Cohort

The human gut microbiome (GM) undergoes dynamic changes throughout life, transitioning from infancy to adulthood. Despite improved understanding over the past years about how genetics, lifestyle, and the external environment impact the GM, limited research has explored the GM's evolution during late-stage adolescence, especially among college students. This study addresses this gap by investigating the longitudinal dynamics of fecal microbial, functional, and metabolomic signatures in a diverse group of first-year, dormitory-housed college students. A total of 485 stool samples from 246 participants were analyzed, identifying four primary GM community types, predominantly led by Bacteroides (66.8% of samples), as well as Blautia and Prevotella. The Prevotella/Bacteroides (P/B) ratio emerged as a robust GM composition indicator, predictively associated with 15 metabolites. Notably, higher P/B ratios correlated negatively with p-cresol sulfate and cholesterol sulfate, implying potential health implications, while positively correlating with kynurenic acid. Distinct GM transition and stability patterns were found from a detailed longitudinal subset of 93 participants over an academic year. Parasutterella and the Ruminococcus gnavus group exhibited positive associations with compositional variability, whereas Faecalibacterium and Eubacterium ventriosum group displayed negative associations, the latter suggesting stabilizing roles in the GM. Most notably, nearly half of the longitudinal cohort experienced GM community shifts, emphasizing long-term GM adaptability. Comparing individuals with stable community types to those undergoing transitions, we observed significant differences in microbial composition and diversity, signifying substantial shifts in the microbiota during transitions. Although diet-related variables contributed to some observed variance, diet did not independently predict the probability of switching between community types within the study's timeframe via multi-state Markov modeling. Furthermore, exploration of stability within dynamic microbiomes among the longitudinal cohort experiencing shifts in community types revealed that microbiome taxa at the genus level exhibited significantly higher total variance than estimated functional and fecal metabolomic features. This suggests tight control of function and metabolism, despite community shifting. Overall, this study highlights the dynamic nature of the late-stage adolescent GM, the role of core taxa, metabolic pathways, the fecal metabolome, and lifestyle and dietary factors, contributing to our understanding of GM assembly and potential health implications during this life phase.

Survey of the fecal microbiota of indigenous small ruminants living in different areas of Guizhou

Introduction

Gut microbiota are associated with the health and performance of ruminant species, and they are affected by altitude, host genetics, and sex. However, there has been little research on comparing the fecal microbiota of indigenous small ruminants such as sheep and goats in Guizhou province, China. In the present study, we revealed the effect of altitude, genetics, and sex on fecal microbiota profiles and enterotypes in indigenous small ruminants of Guizhou province, China.

Methods

Fecal samples were collected from Hei and Qianbei Ma goats and Weining sheep in the Chinese province of Guizhou. 16S rRNA gene sequencing targeting the V3-V4 region was performed using the Illumina MiSeq platform. Sequences were processed using QIIME2, and the qualified sequences were processed using the plugin DADA2 to generate amplicon sequence variants (ASVs). The statistical analysis was performed using R studio.

Results

The fecal microbial profile was found to vary by herd (influenced by genetics/altitude) and sex. All samples were categorized into two enterotypes. The first enterotype is dominated by UCG-005, and the second enterotype is dominated by the Christensenellaceae_R-7_group, which may be highly driven by the host's genetics (breed). The predicted functional profiles of the fecal microbiota were also assigned to two clusters that corresponded exactly to the enterotypes. Cluster 1 of the functional profiling was characterized by biosynthesis pathways, and cluster 2 was characterized by energy metabolism pathways.

Discussion

Our findings may provide new insights into the fecal microbial community and enterotypes in small ruminants by herds, offering clues for understanding the mechanisms by which the fecal microbiota contribute to divergent host phenotypes in indigenous small ruminants in Guizhou.

Sex Differences in Cardiovascular Diseases: Exploring the Role of Microbiota and Immunity

Cardiovascular diseases (CVDs) are the most common cause of mortality and morbidity in Western countries, thus representing a global health concern. CVDs show different patterns in terms of the prevalence and presentation in men and women. The role of sex hormones has been extensively implicated in these sex-specific differences, due to the presence of the menstrual cycle and menopause in women. Moreover, the gut microbiota (GM) has been implicated in cardiovascular health, considering the growing evidence that it is involved in determining the development of specific diseases. In particular, gut-derived metabolites have been linked to CVDs and kidney disorders, which can in turn promote the progression of CVDs. Considering the differences in the composition of GM between men and women, it is possible that gut microbiota act as a mediator in regard to the sex disparities in CVDs. This narrative review aims to comprehensively review the interplay between sex, GM, and CVDs, discussing potential mechanisms and therapeutic options.

Blood Microbiota and Its Products: Mechanisms of Interference with Host Cells and Clinical Outcomes

In healthy conditions, blood was considered a sterile environment until the development of new analytical approaches that allowed for the detection of circulating bacterial ribosomal DNA. Currently, debate exists on the origin of the blood microbiota. According to advanced research using dark field microscopy, fluorescent in situ hybridization, flow cytometry, and electron microscopy, so-called microbiota have been detected in the blood. Conversely, others have reported no evidence of a common blood microbiota. Then, it was hypothesized that blood microbiota may derive from distant sites, e.g., the gut or external contamination of blood samples. Alteration of the blood microbiota's equilibrium may lead to dysbiosis and, in certain cases, disease. Cardiovascular, respiratory, hepatic, kidney, neoplastic, and immune diseases have been associated with the presence of Gram-positive and Gram-negative bacteria and/or their products in the blood. For instance, lipopolysaccharides (LPSs) and endotoxins may contribute to tissue damage, fueling chronic inflammation. Blood bacteria can interact with immune cells, especially with monocytes that engulf microorganisms and T lymphocytes via spontaneous binding to their membranes. Moreover, LPSs, extracellular vesicles, and outer membrane vesicles interact with red blood cells and immune cells, reaching distant organs. This review aims to describe the composition of blood microbiota in healthy individuals and those with disease conditions. Furthermore, special emphasis is placed on the interaction of blood microbiota with host cells to better understand disease mechanisms.

Probiotics as a Promising Therapy in Improvement of Symptoms in Children With ADHD: A Systematic Review

BACKGROUND

ADHD is widely recognized as the most prevalent neurodevelopmental disorder in children. Recently, the potential role of gut microbiota as an etiological factor in ADHD has gained attention. This systematic review aims to investigate the potential impact of probiotic supplements on alleviating ADHD symptoms and influencing behavior.

METHODS

PubMed, Web of Science, Cochrane Library, and SCOPUS were searched from inception to May 2023. Only randomized controlled trials that have suitable data of the effects of probiotics/synbiotics on children with ADHD were enrolled. The risk of bias of the included studies was assessed by Cochrane Collaboration risk of bias tool.

RESULTS

Five related randomized controlled trial were evaluated in the current review. Types of interventions ranged from single/multi strain probiotics to synbiotic. The duration of intervention in all of the studies were 2 to 3 months. The assessed outcomes were very diverse and different tools were used to report the symptoms in children. Among those which used Conners' Parent Rating Scale, a decrease in the total score occurred in the probiotic group, compared to the placebo group. An improvement in both intervention and control groups was seen in one study which used ADHD-Rating Scale.

CONCLUSION

In summary, the combined findings from the reviewed studies suggest that probiotic supplements might potentially serve as a complementary intervention for ADHD. However, given the small number of studies, limited sample sizes, and the diversity of probiotic strains, further research is needed to clarify the effects of probiotics in children with ADHD. The observed tolerability of probiotics is noteworthy as none of the studies report adverse effects.

Enterotype-Dependent Probiotic-Mediated Changes in the Male Rat Intestinal Microbiome In Vivo and In Vitro

Beneficial properties of lactic acid bacteria have been known long ago, but particular interest in probiotics has arisen in the last two decades due to the understanding of the important role of intestinal microflora in human life. Thus, the ability of probiotics to support healthy homeostasis of gut microbiomes has received particular attention. Here, we evaluated the effect of a probiotic consisting of Bifidobacterium longum and Lacticaseibacillus paracasei on the gut microbiome of male rats, assessed their persistence in the fecal biota, and compared probiotic-mediated changes in vitro and in vivo. As expected, microbiomes of two enterotypes were identified in the feces of 21 animals, and it turned out that even a single dose of the probiotic altered the microbial composition. Upon repeated administration, the E1 biota temporarily acquired properties of the E2 type. Being highly sensitive to the intervention of probiotic bacteria at the phylum and genus levels, the fecal microbiomes retained the identity of their enterotypes when transferred to a medium optimized for gut bacteria. For the E2 biota, even similarities between probiotic-mediated reactions in vitro and in vivo were detected. Therefore, fecal-derived microbial communities are proposed as model consortia to optimize the response of resident bacteria to various agents.

Structural characteristics of gut microbiota in longevity from Changshou town, Hubei, China

The gut microbiota (GM) and its potential functions play a crucial role in maintaining host health and longevity. The aim of this study was to investigate the potential relationship between GM and longevity. We collected fecal samples from 92 healthy volunteers (middle-aged and elderly: 43-79 years old; longevity: ≥ 90 years old) from Changshou Town, Zhongxiang City, Hubei, China. In addition, we collected samples from 30 healthy middle-aged and elderly controls (aged 51-70 years) from Wuhan, Hubei. The 16S rDNA V3 + V4 region of the fecal samples was sequenced using high-throughput sequencing technology. Diversity analysis results showed that the elderly group with longevity and the elderly group with low body mass index (BMI) exhibited higher α diversity. However, no significant difference was observed in β diversity. The results of the microbiome composition indicate that Firmicutes, Proteobacteria, and Bacteroidota are the core phyla in all groups. Compared to younger elderly individuals, Akkermansia and Lactobacillus are significantly enriched in the long-lived elderly group, while Megamonas is significantly reduced. In addition, a high abundance of Akkermansia is a significant characteristic of elderly populations with low BMI values. Furthermore, the functional prediction results showed that the elderly longevity group had higher abilities in short-chain fatty acid metabolism, amino acid metabolism, and xenobiotic biodegradation. Taken together, our study provides characteristic information on GM in the long-lived elderly population in Changshou Town. This study can serve as a valuable addition to the current research on age-related GM. KEY POINTS: • The gut microbiota of elderly individuals with longevity and low BMI exhibit higher alpha diversity • Gut microbiota diversity did not differ significantly between genders in the elderly population • Several potentially beneficial bacteria (e.g., Akkermansia and Lactobacillus) are enriched in long-lived individuals.

Dimension reduction of microbiome data linked Bifidobacterium and Prevotella to allergic rhinitis

Dimension reduction has been used to visualise the distribution of multidimensional microbiome data, but the composite variables calculated by the dimension reduction methods have not been widely used to investigate the relationship of the human gut microbiome with lifestyle and disease. In the present study, we applied several dimension reduction methods, including principal component analysis, principal coordinate analysis (PCoA), non-metric multidimensional scaling (NMDS), and non-negative matrix factorization, to a microbiome dataset from 186 subjects with symptoms of  allergic rhinitis (AR) and 106 controls. All the dimension reduction methods supported that the distribution of microbial data points appeared to be continuous rather than discrete. Comparison of the composite variables calculated from the different dimension reduction methods showed that the characteristics of the composite variables differed depending on the distance matrices and the dimension reduction methods. The first composite variables calculated from PCoA and NMDS with the UniFrac distance were strongly associated with AR (FDR adjusted P = 2.4 × 10-4 for PCoA and P = 2.8 × 10-4 for NMDS), and also with the relative abundance of Bifidobacterium and Prevotella. The abundance of Bifidobacterium was also linked to intake of several nutrients, including carbohydrate, saturated fat, and alcohol via composite variables. Notably, the association between the composite variables and AR was much stronger than the association between the relative abundance of individual genera and AR. Our results highlight the usefulness of the dimension reduction methods for investigating the association of microbial composition with lifestyle and disease in clinical research.

Unveiling microbial biomarkers of ruminant methane emission through machine learning

Background

Enteric methane from cow burps, which results from microbial fermentation of high-fiber feed in the rumen, is a significant contributor to greenhouse gas emissions. A promising strategy to address this problem is microbiome-based precision feed, which involves identifying key microorganisms for methane production. While machine learning algorithms have shown success in associating human gut microbiome with various human diseases, there have been limited efforts to employ these algorithms to establish microbial biomarkers for methane emissions in ruminants.

Methods

In this study, we aim to identify potential methane biomarkers for methane emission from ruminants by employing regression algorithms commonly used in human microbiome studies, coupled with different feature selection methods. To achieve this, we analyzed the microbiome compositions and identified possible confounding metadata variables in two large public datasets of Holstein cows. Using both the microbiome features and identified metadata variables, we trained different regressors to predict methane emission. With the optimized models, permutation tests were used to determine feature importance to find informative microbial features.

Results

Among the regression algorithms tested, random forest regression outperformed others and allowed the identification of several crucial microbial taxa for methane emission as members of the native rumen microbiome, including the genera Piromyces, Succinivibrionaceae UCG-002, and Acetobacter. Additionally, our results revealed that certain herd locations and feed composition markers, such as the lipid intake and neutral-detergent fiber intake, are also predictive features for methane emissions.

Conclusion

We demonstrated that machine learning, particularly regression algorithms, can effectively predict cow methane emissions and identify relevant rumen microorganisms. Our findings offer valuable insights for the development of microbiome-based precision feed strategies aiming at reducing methane emissions.

The association between gut microbiome and growth in infants with cystic fibrosis

BACKGROUND

In cystic fibrosis (CF), pathophysiologic changes in the gastrointestinal tract lead to malnutrition and altered gut microbiome. Microbiome alterations have been linked to linear growth, gut inflammation and respiratory manifestations. Elucidating these gut microbiome alterations may provide insight into future nutritional management in CF.

METHODS

Infants were followed for 12-months at four sites in the United States (US-CF) and Australia (AUS-CF). 16S rRNA gene sequencing was performed on longitudinal stool samples. Associations between microbial abundance and age, antibiotic prophylaxis, malnutrition, and breast feeding were evaluated using generalized linear mixed models. Taxonomic and predictive functional features were compared between groups.

RESULTS

Infants with CF (N = 78) were enrolled as part of a larger study. AUS-CF infants had higher mean weight-for-age z-scores than US-CF infants (p = 0.02). A subset of participants (CF N = 40, non-CF disease controls N = 10) provided stool samples for microbiome analysis. AUS-CF infants had lower stool alpha diversity compared to US-CF infants (p < 0.001). AUS-CF infants had higher relative abundance of stool Proteobacteria compared to US-CF infants which was associated with antibiotic prophylaxis (p < 0.001). Malnutrition (weight-for-age <10th percentile) was associated with depleted Lactococcus (p < 0.001). Antibiotic prophylaxis (p = 0.002) and malnutrition (p = 0.012) were linked with predicted decreased activity of metabolic pathways responsible for short chain fatty acid processing.

CONCLUSIONS

In infants with CF, gut microbiome composition and diversity differed between the two continents. Gut microbial diversity was not linked to growth. The relationship between malnutrition and antibiotic prophylaxis with reduced SCFA fermentation could have implications for gut health and function and warrants additional investigation.

The Intestinal Microbiota in the Development of Chronic Liver Disease: Current Status

Chronic liver disease (CLD) is a significant global health burden, leading to millions of deaths annually. The gut-liver axis plays a pivotal role in this context, allowing the transport of gut-derived products directly to the liver, as well as biological compounds from the liver to the intestine. The gut microbiota plays a significant role in maintaining the health of the digestive system. A change in gut microbiome composition as seen in dysbiosis is associated with immune dysregulation, altered energy and gut hormone regulation, and increased intestinal permeability, contributing to inflammatory mechanisms and damage to the liver, irrespective of the underlying etiology of CLD. The aim of this review is to present the current knowledge about the composition of the intestinal microbiome in healthy individuals and those with CLD, including the factors that affect this composition, the impact of the altered microbiome on the liver, and the mechanisms by which it occurs. Furthermore, this review analyzes the effects of gut microbiome modulation on the course of CLD, by using pharmacotherapy, nutrition, fecal microbiota transplantation, supplements, and probiotics. This review opens avenues for the translation of knowledge about gut-liver interplay into clinical practice as an additional tool to fight CLD and its complications.

Lifestyle patterns influence the composition of the gut microbiome in a healthy Chinese population

High-throughput sequencing allows for the comprehensive analysis of the human intestinal microbiota. However, extensive association analyses between the microbiome and lifestyle differences in the Chinese population are limited. Here, we carried out an independent cohort study-the Chinese Healthy Gut Project (n = 483)-where correlations between the gut microbiota and dietary and lifestyle variables in a healthy Chinese population are defined. We collected both questionnaire data, including basic information and lifestyle and dietary variables, and fecal stools from the enrolled volunteers. We then performed 16S rRNA sequencing on the microbial DNA isolated from the stools to assess the composition of the intestinal microbiota. We found that Prevotella and Bacteroides were the most abundant genera in the healthy Chinese gut microbiome. Additionally, 9 out of 29 clinical and questionnaire-based phenotype covariates were found to be associated with the variation in the composition of the gut microbiota. Among these lifestyle phenotypes, sleep procrastination, negative mood, and drinking habits had the largest effect size. Additionally, an appreciable effect of urbanization was observed, resulting in decreased intra-individual diversity, increased inter-individual diversity, and an increased abundance of the Bacteroides enterotype. The results of this study provide a foundation for assessing the healthy Chinese gut microbiota community structure at baseline in a healthy Chinese population. Furthermore, this study also provides insights into understanding how distinctive living habits influence the relationships between the Chinese gut microbiome and systemic health state.

Bacterial dysbiosis and epithelial status of the California sea lion (Zalophus californianus) in the Gulf of California

Despite the high incidence of urogenital carcinoma (UGC) in California sea lions stranded along California, no UGC has been reported in other areas of their distribution; however, cell morphologies typical of premalignant states have been found. Risk factors for UGC include high of organochlorines and infection with a gammaherpesvirus, OtHV-1, but the importance of the bacteriome for epithelial status remains unknown. We characterized the genital bacteriome of adult female California sea lions along their distribution in the Gulf of California and examined whether the diversity and abundance of the bacteriome varied spatially, whether there were detectable differences in the bacteriome between healthy and altered epithelia, and whether the bacteriome was different in California sea lions infected with OtHV-1 or papillomavirus. We detected 2270 ASVs in the genital samples, of which 35 met the criteria for inclusion in the core bacteriome. Fusobacteriia and Clostridia were present in all samples, at high abundances, and Actinobacteria, Alphaproteobacteria, and Campylobacteria were also well-represented. Alpha diversity and abundance of the California sea lion genital bacteriome varied geographically. The abundance of bacterial ASVs varied depending on the genital epithelial status and inflammation, with differences driven by classes Fusobacteriia, Clostridia, Campylobacteria and Alphaproteobacteria. Alpha diversity and abundance were lowest in samples in which OtHV-1 was detected, and highest those with papillomavirus. Our study is the first investigation of how the bacteriome is related to epithelial status in a wild marine species prone to developing cancer.

Recent progress in plant-derived polysaccharides with prebiotic potential for intestinal health by targeting gut microbiota: a review

Natural products of plant origin are of high interest and widely used, especially in the food industry, due to their low toxicity and wide range of bioactive properties. Compared to other plant components, the safety of polysaccharides has been generally recognized. As dietary fibers, plant-derived polysaccharides are mostly degraded in the intestine by polysaccharide-degrading enzymes secreted by gut microbiota, and have potential prebiotic activity in both non-disease and disease states, which should not be overlooked, especially in terms of their involvement in the treatment of intestinal diseases and the promotion of intestinal health. This review elucidates the regulatory effects of plant-derived polysaccharides on gut microbiota and summarizes the mechanisms involved in targeting gut microbiota for the treatment of intestinal diseases. Further, the structure-activity relationships between different structural types of plant-derived polysaccharides and the occurrence of their prebiotic activity are further explored. Finally, the practical applications of plant-derived polysaccharides in food production and food packaging are summarized and discussed, providing important references for expanding the application of plant-derived polysaccharides in the food industry or developing functional dietary supplements.

Enterotypes of the human gut mycobiome

BACKGROUND

The fungal component of the human gut microbiome, also known as the mycobiome, plays a vital role in intestinal ecology and human health. However, the overall structure of the gut mycobiome as well as the inter-individual variations in fungal composition remains largely unknown. In this study, we collected a total of 3363 fungal sequencing samples from 16 cohorts across three continents, including 572 newly profiled samples from China.

RESULTS

We identify and characterize four mycobiome enterotypes using ITS profiling of 3363 samples from 16 cohorts. These enterotypes exhibit stability across populations and geographical locations and significant correlation with bacterial enterotypes. Particularly, we notice that fungal enterotypes have a strong age preference, where the enterotype dominated by Candida (i.e., Can_type enterotype) is enriched in the elderly population and confers an increased risk of multiple diseases associated with a compromised intestinal barrier. In addition, bidirectional mediation analysis reveals that the fungi-contributed aerobic respiration pathway associated with the Can_type enterotype might mediate the association between the compromised intestinal barrier and aging.

CONCLUSIONS

We show that the human gut mycobiome has stable compositional patterns across individuals and significantly correlates with multiple host factors, such as diseases and host age. Video Abstract.

Diarrheal-associated gut dysbiosis in cancer and inflammatory bowel disease patients is exacerbated by Clostridioides difficile infection

Introduction

Low diversity gut dysbiosis can take different forms depending on the disease context. In this study, we used shotgun metagenomic sequencing and gas chromatography-mass spectrometry (GC-MS) to compared the metagenomic and metabolomic profiles of Clostridioides (Clostridium) difficile diarrheal cancer and inflammatory bowel disease (IBD) patients and defined the additive effect of C. difficile infection (CDI) on intestinal dysbiosis.

Results

The study cohort consisted of 138 case-mix cancer patients, 43 IBD patients, and 45 healthy control individuals. Thirty-three patients were also infected with C. difficile. In the control group, three well-known enterotypes were identified, while the other groups presented with an additional Escherichia-driven enterotype. Bacterial diversity was significantly lower in all groups than in healthy controls, while the highest level of bacterial species richness was observed in cancer patients. Fifty-six bacterial species had abundance levels that differentiated diarrheal patient groups from the control group. Of these species, 52 and 4 (Bacteroides fragilis, Escherichia coli, Klebsiella pneumoniae, and Ruminococcus gnavus) were under-represented and over-represented, respectively, in all diarrheal patient groups. The relative abundances of propionate and butyrate were significantly lower in fecal samples from IBD and CDI patients than in control samples. Isobutyrate, propanate, and butyrate concentrations were lower in cancer, IBD, and CDI samples, respectively. Glycine and valine amino acids were over- represented in diarrheal patients.

Conclusion

Our data indicate that different external and internal factors drive comparable profiles of low diversity dysbiosis. While diarrheal-related low diversity dysbiosis may be a consequence of systemic cancer therapy, a similar phenotype is observed in cases of moderate to severe IBD, and in both cases, dysbiosis is exacerbated by incidence of CDI.

Microbiome-Gut-Mucosal-Immune-Brain Axis and Autism Spectrum Disorder (ASD): A Novel Proposal of the Role of the Gut Microbiome in ASD Aetiology

Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder characterised by deficits in social interaction and communication, as well as restricted and stereotyped interests. Due of the high prevalence of gastrointestinal disorders in individuals with ASD, researchers have investigated the gut microbiota as a potential contributor to its aetiology. The relationship between the microbiome, gut, and brain (microbiome-gut-brain axis) has been acknowledged as a key factor in modulating brain function and social behaviour, but its connection to the aetiology of ASD is not well understood. Recently, there has been increasing attention on the relationship between the immune system, gastrointestinal disorders and neurological issues in ASD, particularly in relation to the loss of specific species or a decrease in microbial diversity. It focuses on how gut microbiota dysbiosis can affect gut permeability, immune function and microbiota metabolites in ASD. However, a very complete study suggests that dysbiosis is a consequence of the disease and that it has practically no effect on autistic manifestations. This is a review of the relationship between the immune system, microbial diversity and the microbiome-gut-brain axis in the development of autistic symptoms severity and a proposal of a novel role of gut microbiome in ASD, where dysbiosis is a consequence of ASD-related behaviour and where dysbiosis in turn accentuates the autistic manifestations of the patients via the microbiome-gut-brain axis in a feedback circuit.

Metabolic pathway prediction of core microbiome based on enterotype and orotype

Introduction

Identification of key microbiome components has been suggested to help address the maintenance of oral and intestinal health in humans. The core microbiome is similar in all individuals, whereas the diverse microbiome varies across individuals, based on their unique lifestyles and phenotypic and genotypic determinants. In this study, we aimed to predict the metabolism of core microorganisms in the gut and oral environment based on enterotyping and orotyping.

Materials and methods

Gut and oral samples were collected from 83 Korean women aged 50 years or older. The extracted DNA was subjected to next-generation sequencing analysis of 16S rRNA hypervariable regions V3-V4.

Results

Gut bacteria were clustered into three enterotypes, while oral bacteria were clustered into three orotypes. Sixty-three of the core microbiome between the gut and oral population were correlated, and different metabolic pathways were predicted for each type. Eubacterium_g11, Actinomyces, Atopobium, and Enterococcus were significantly positively correlated between the gut and oral abundance. The four bacteria were classified as type 3 in orotype and type 2 in enterotype.

Conclusion

Overall, the study suggested that collapsing the human body's multidimensional microbiome into a few categories may help characterize the microbiomes better and address health issues more deeply.

The Diagnostic Potential of the Human Blood Microbiome: Are We Dreaming or Awake?

Human blood has historically been considered a sterile environment. Recently, a thriving microbiome dominated by Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes phyla was detected in healthy blood. The localization of these microbes is restricted to some blood cell populations, particularly the peripheral blood mononuclear cells and erythrocytes. It was hypothesized that the blood microbiome originates from the skin-oral-gut axis. In addition, many studies have evaluated the potential of blood microbiome dysbiosis as a prognostic marker in cardiovascular diseases, cirrhosis, severe liver fibrosis, severe acute pancreatitis, type 2 diabetes, and chronic kidney diseases. The present review aims to summarize current findings and most recent evidence in the field.

Effects of probiotics administration on lactose intolerance in adulthood: A meta-analysis

This meta-analysis aimed to investigate the effect of probiotic administration on adults with lactose intolerance. Twelve studies were identified from databases such as PubMed, Cochrane Library, and Web of Knowledge based on the inclusion and exclusion criteria. The effect size was estimated using the standardized mean difference (SMD), and Cochrane's Q test was used to evaluate the statistical heterogeneity of the effect size. Moderator analysis, including meta-ANOVA and meta-regression, were performed to determine the cause of heterogeneity in the effect size using a mixed-effect model. Egger's linear regression test was conducted to evaluate publication bias. The results showed that probiotic administration alleviated the symptoms of lactose intolerance, including abdominal pain, diarrhea, and flatulence. Among them, the area under the curve (AUC) showed the greatest decrease following probiotic administration (SMD, -4.96; 95% confidence interval, -6.92 to -3.00). In the meta-ANOVA test, abdominal pain and total symptoms decreased with monostrain probiotic administration. This combination was also effective for flatulence. The dosage of probiotics or lactose was significantly associated with a reduction in the total symptom score, and the linear regression models between the dosage and SMD were found to be Y = 2.3342 × dosage - 25.0400 (R² = 79.68%) and Y = 0.2345 × dosage - 7.6618 (R² = 34.03%), respectively. Publication bias was detected for most items. However, even after effect size correction, the probiotic administration effect for all items remained valid. The administration of probiotics was effective at improving adult lactose intolerance, and it is expected that the results of this study could help improve the nutritional status of adults by increasing their consumption of milk and dairy products in the future.

Increased intestinal-fatty acid binding protein in obesity-associated type 2 diabetes mellitus

BACKGROUND

Obesity is a traditional risk factor for type 2 diabetes mellitus (T2DM). However, recent studies reported that metabolically unhealthy obesity (MUO) exerts a higher risk of developing T2DM than metabolically healthy obesity (MHO) because of its higher state of insulin resistance. This may happen due to metabolic endotoxemia through gut dysbiosis and increased intestinal permeability. Our study aimed to know the association of intestinal permeability using intestinal fatty acid-binding protein (I-FABP) with obesity-related T2DM patients in Indonesia.

METHODS

This was a cross-sectional study that recruited 63 participants with obesity defined using body mass index (BMI) classification for the Asia-Pacific population (BMI ≥25 kg/m2). All participants were then grouped into T2DM and non-T2DM based on American Diabetes Association (ADA) diagnostic criteria. The I-FABP levels were measured using the enzyme-linked immunosorbent assay method.

RESULTS

The I-FABP level of T2DM group was higher compared to non-T2DM group, namely 2.82 (1.23) ng/mL vs. 1.78 (0.81) ng/mL (p<0.001; mean difference 1.033 with 95% CI 0.51-1.55). This difference was not attenuated even after adjustment for age. The fitted regression model using linear regression was: i-FABP = 1.787+1.034*(DM) (R2 = 18.20%, standardized ß = 0.442, p<0.001).

CONCLUSIONS

This study underscores the association of intestinal permeability with T2DM in people with obesity and supports the evidence of the potential role of intestinal permeability in the pathogenesis of obesity-related T2DM.

Characterisation of human milk bacterial DNA profiles in a small cohort of Australian women in relation to infant and maternal factors

Human milk is composed of complex microbial and non-microbial components that shape the infant gut microbiome. Although several maternal and infant factors have been associated with human milk microbiota, no study has investigated this in an Australian population. Therefore, we aimed to investigate associations between human milk bacterial composition of Australian women and maternal factors (body mass index (BMI), mode of delivery, breast pump use, allergy, parity) and infant factors (sex, mode of feeding, pacifier use, and introduction of solids). Full-length 16S rRNA gene sequencing was used to characterise milk bacterial DNA profiles. Milk from mothers with a normal BMI had a higher relative abundance of Streptococcus australis than that of underweight mothers, while milk from overweight mothers had a higher relative abundance of Streptococcus salivarius compared with underweight and obese mothers. Mothers who delivered vaginally had a higher relative abundance of Streptococcus mitis in their milk compared to those who delivered via emergency caesarean section. Milk of mothers who used a breast pump had a higher relative abundance of Staphylococcus epidermidis and Streptococcus parasanguinis. Milk of mothers whose infants used a pacifier had a higher relative abundance of S. australis and Streptococcus gwangjuense. Maternal BMI, mode of delivery, breast pump use, and infant pacifier use are associated with the bacterial composition of human milk in an Australian cohort. The data from this pilot study suggests that both mother and infant can contribute to the human milk microbiome.

Personalized Diets based on the Gut Microbiome as a Target for Health Maintenance: from Current Evidence to Future Possibilities

Recently, the concept of personalized nutrition has been developed, which states that food components do not always lead to the same metabolic responses, but vary from person to person. Although this concept has been studied based on individual genetic backgrounds, researchers have recently explored its potential role in the gut microbiome. The gut microbiota physiologically communicates with humans by forming a bidirectional relationship with the micronutrients, macronutrients, and phytochemicals consumed by the host. Furthermore, the gut microbiota can vary from person to person and can be easily shifted by diet. Therefore, several recent studies have reported the application of personalized nutrition to intestinal microflora. This review provides an overview of the interaction of diet with the gut microbiome and the latest evidence in understanding the inter-individual differences in dietary responsiveness according to individual baseline gut microbiota and microbiome-associated dietary intervention in diseases. The diversity of the gut microbiota and the presence of specific microorganisms can be attributed to physiological differences following dietary intervention. The difference in individual responsiveness based on the gut microbiota has the potential to become an important research approach for personalized nutrition and health management, although further well-designed large-scale studies are warranted.

Stochastic variational variable selection for high-dimensional microbiome data

BACKGROUND

The rapid and accurate identification of a minimal-size core set of representative microbial species plays an important role in the clustering of microbial community data and interpretation of clustering results. However, the huge dimensionality of microbial metagenomics datasets is a major challenge for the existing methods such as Dirichlet multinomial mixture (DMM) models. In the approach of the existing methods, the computational burden of identifying a small number of representative species from a large number of observed species remains a challenge.

RESULTS

We propose a novel approach to improve the performance of the widely used DMM approach by combining three ideas: (i) we propose an indicator variable to identify representative operational taxonomic units that substantially contribute to the differentiation among clusters; (ii) to address the computational burden of high-dimensional microbiome data, we propose a stochastic variational inference, which approximates the posterior distribution using a controllable distribution called variational distribution, and stochastic optimization algorithms for fast computation; and (iii) we extend the finite DMM model to an infinite case by considering Dirichlet process mixtures and estimating the number of clusters as a variational parameter. Using the proposed method, stochastic variational variable selection (SVVS), we analyzed the root microbiome data collected in our soybean field experiment, the human gut microbiome data from three published datasets of large-scale case-control studies and the healthy human microbiome data from the Human Microbiome Project.

CONCLUSIONS

SVVS demonstrates a better performance and significantly faster computation than those of the existing methods in all cases of testing datasets. In particular, SVVS is the only method that can analyze massive high-dimensional microbial data with more than 50,000 microbial species and 1000 samples. Furthermore, a core set of representative microbial species is identified using SVVS that can improve the interpretability of Bayesian mixture models for a wide range of microbiome studies. Video Abstract.

Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes

Studies of human microbiomes using new sequencing techniques have increasingly demonstrated that their ecologies are partly determined by the lifestyle and habits of individuals. As such, significant forensic information could be obtained from high throughput sequencing of the human microbiome. This approach, combined with multiple analytical techniques demonstrates that bacterial DNA can be used to uniquely identify an individual and to provide information about their life and behavioral patterns. However, the transformation of these findings into actionable forensic information, including the geolocation of the samples, remains limited by incomplete understanding of the effects of confounding factors and the paucity of diverse sequences. We obtained 16S rRNA sequences of stool and oral microbiomes collected from 206 young and healthy females from four globally diverse populations, in addition to supporting metadata, including dietary and medical information. Analysis of these microbiomes revealed detectable geolocation signals between the populations, even for populations living within the same city. Accounting for other lifestyle variables, such as diet and smoking, lessened but does not remove the geolocation signal.

Gut Microbiota in Nutrition and Health with a Special Focus on Specific Bacterial Clusters

Health is influenced by how the gut microbiome develops as a result of external and internal factors, such as nutrition, the environment, medication use, age, sex, and genetics. Alpha and beta diversity metrics and (enterotype) clustering methods are commonly employed to perform population studies and to analyse the effects of various treatments, yet, with the continuous development of (new) sequencing technologies, and as various omics fields as a result become more accessible for investigation, increasingly sophisticated methodologies are needed and indeed being developed in order to disentangle the complex ways in which the gut microbiome and health are intertwined. Diseases of affluence, such as type 2 diabetes (T2D) and cardiovascular diseases (CVD), are commonly linked to species associated with the Bacteroides enterotype(s) and a decline of various (beneficial) complex microbial trophic networks, which are in turn linked to the aforementioned factors. In this review, we (1) explore the effects that some of the most common internal and external factors have on the gut microbiome composition and how these in turn relate to T2D and CVD, and (2) discuss research opportunities enabled by and the limitations of some of the latest technical developments in the microbiome sector, including the use of artificial intelligence (AI), strain tracking, and peak to trough ratios.

Computational approach to modeling microbiome landscapes associated with chronic human disease progression

A microbial community is a dynamic system undergoing constant change in response to internal and external stimuli. These changes can have significant implications for human health. However, due to the difficulty in obtaining longitudinal samples, the study of the dynamic relationship between the microbiome and human health remains a challenge. Here, we introduce a novel computational strategy that uses massive cross-sectional sample data to model microbiome landscapes associated with chronic disease development. The strategy is based on the rationale that each static sample provides a snapshot of the disease process, and if the number of samples is sufficiently large, the footprints of individual samples populate progression trajectories, which enables us to recover disease progression paths along a microbiome landscape by using computational approaches. To demonstrate the validity of the proposed strategy, we developed a bioinformatics pipeline and applied it to a gut microbiome dataset available from a Crohn’s disease study. Our analysis resulted in one of the first working models of microbial progression for Crohn’s disease. We performed a series of interrogations to validate the constructed model. Our analysis suggested that the model recapitulated the longitudinal progression of microbial dysbiosis during the known clinical trajectory of Crohn’s disease. By overcoming restrictions associated with complex longitudinal sampling, the proposed strategy can provide valuable insights into the role of the microbiome in the pathogenesis of chronic disease and facilitate the shift of the field from descriptive research to mechanistic studies.

The delineation of system dynamics of a microbial community can provide a wealth of insights into the roles of the microbiome in the pathogenesis of chronic disease. However, due to the difficulty in obtaining longitudinal samples, most existing microbiome studies have been cross-sectional and largely descriptive. Here, we present a novel computational strategy that leverages massive static sample data to model microbiome landscapes associated with chronic disease development. To demonstrate the validity of the proposed strategy, we applied it to a gut microbiome dataset available from a Crohn’s disease study and constructed one of the first microbial progression models of the disease. We performed a series of interrogations on the constructed model. Our analysis suggested that the constructed model recapitulated the longitudinal progression of microbial dysbiosis during the known clinical trajectory of Crohn’s disease. By overcoming the sampling restrictions inherent to slowly progressive diseases, our approach is potentially widely applicable in many different studies across body sites, diseases, and other conditions.

Examining the association between the gastrointestinal microbiota and Gulf War illness: A prospective cohort study

Gulf War Illness (GWI) affects 25–35% of the 1991 Gulf War Veteran (GWV) population. Patients with GWI experience pain, fatigue, cognitive impairments, gastrointestinal dysfunction, skin disorders, and respiratory issues. In longitudinal studies, many patients with GWI have shown little to no improvement in symptoms since diagnosis. The gut microbiome and diet play an important role in human health and disease, and preliminary studies suggest it may play a role in GWI. To examine the relationship between the gut microbiota, diet, and GWI, we conducted an eight-week prospective cohort study collecting stool samples, medications, health history, and dietary data. Sixty-nine participants were enrolled into the study, 36 of which met the case definition for GWI. The gut microbiota of participants, determined by 16S rRNA sequencing of stool samples, was stable over the duration of the study and showed no within person (alpha diversity) differences. Between group analyses (beta diversity) identified statistically significant different between those with and without GWI. Several taxonomic lineages were identified as differentially abundant between those with and without GWI (n = 9) including a greater abundance of Lachnospiraceae and Ruminococcaceae in those without GWI. Additionally, there were taxonomic differences between those with high and low healthy eating index (HEI) scores including a greater abundance of Ruminococcaceae in those with higher HEI scores. This longitudinal cohort study of GWVs found that participants with GWI had significantly different microbiomes from those without GWI. Further studies are needed to determine the role these differences may play in the development and treatment of GWI.

Gut Microbiota in Psoriasis

Psoriasis is a chronic inflammatory skin disease with autoimmune pathogenic characteristics and is caused by chronic inflammation, which results in uncontrolled keratinocyte growth and defective differentiation. The link between the gut microbiota and immune system regulation opened a novel angle to understand the pathogenesis of many chronic multifactorial diseases, including psoriasis. Current evidence suggests that modulation of the gut microbiota, both through dietary approaches and through supplementation with probiotics and prebiotics, could represent a novel therapeutic approach. The present work aims to highlight the latest scientific evidence regarding the microbiome alterations of psoriatic patients, as well as state of the art insights in terms of microbiome-targeted therapies as promising preventive and therapeutic tools for psoriasis.

Valuing the Diversity of Research Methods to Advance Nutrition Science

The ASN Board of Directors appointed the Nutrition Research Task Force to develop a report on scientific methods used in nutrition science to advance discovery, interpretation, and application of knowledge in the field. The genesis of this report was growing concern about the tone of discourse among nutrition professionals and the implications of acrimony on the productive study and translation of nutrition science. Too often, honest differences of opinion are cast as conflicts instead of areas of needed collaboration. Recognition of the value (and limitations) of contributions from well-executed nutrition science derived from the various approaches used in the discipline, as well as appreciation of how their layering will yield the strongest evidence base, will provide a basis for greater productivity and impact. Greater collaborative efforts within the field of nutrition science will require an understanding that each method or approach has a place and function that should be valued and used together to create the nutrition evidence base. Precision nutrition was identified as an important emerging nutrition topic by the preponderance of task force members, and this theme was adopted for the report because it lent itself to integration of many approaches in nutrition science. Although the primary audience for this report is nutrition researchers and other nutrition professionals, a secondary aim is to develop a document useful for the various audiences that translate nutrition research, including journalists, clinicians, and policymakers. The intent is to promote accurate, transparent, verifiable evidence-based communication about nutrition science. This will facilitate reasoned interpretation and application of emerging findings and, thereby, improve understanding and trust in nutrition science and appropriate characterization, development, and adoption of recommendations.

Beneficial Effects of a Low-Glycemic Diet on Serum Metabolites and Gut Microbiota in Obese Women With Prevotella and Bacteriodes Enterotypes: A Randomized Clinical Trial

Generalized healthy eating patterns may not benefit everyone due to different genetics and enterotypes. We aimed to compare the effects of a low-glycemic diet representing the Korean traditional balanced diet (Low-GID) and westernized diet as a control diet (CD) on anthropometry, serum metabolites, and fecal bacteria in a randomized clinical trial according to enterotypes. We recruited 52 obese women aged 30-50 years, and they consumed Low-GID and CD meals for 1 month, with a 1-month washout period, in a crossover randomized clinical trial. The Low-GID was mainly composed of whole grains with fish, vegetables, seaweeds, and perilla oil, whereas CD contained refined rice, bread, noodles, meats, and processed foods. Serum lipid profiles, metabolomics, serum short-chain fatty acids, and fecal bacteria were analyzed. The important variables influenced by Low-GID and CD were determined by SHAP value in the XGBoost algorithm according to Bacteroides (ET-B) and Prevotella (ET-P). Low-GID and CD interventions did not change the enterotypes, but they modified serum metabolites and some fecal bacterial species differently according to enterotypes. The 10-fold cross-validation of the XGBoost classifier in the ET-P and ET-B clusters was 0.91 ± 0.04 and 0.8 ± 0.07, respectively. In the ET-P cluster, serum L-homocysteine, glutamate, leucine concentrations, and muscle mass were higher in the CD group than in the Low-GID group, whereas serum 3-hydroxybutyric acid concentration was significantly higher in the Low-GID group than in the CD group (p < 0.05). In fecal bacteria, Gemmiger formicilis, Collinsella aerofaciens, and Escherichia coli were higher in the CD group than in the Low-GID group. In the ET-B cohort, serum tryptophan and total cholesterol concentrations were higher in the CD group than in the Low-GID group, whereas serum glutathione and 3-hydroxybutyric acid concentrations were significantly higher in the Low-GID group than in the CD group (p < 0.05). However, Bifidobacterium longum was higher in CD than Low-GID in the ET-B cluster, but serum butyric acid levels were higher in the Low-GID than in the CD group. In conclusion, Low-GID can be recommended in obese women with both ET-P and ET-B enterotypes, although its efficacy was more effective in ET-P.

Clinical Trial Registration

[https://cris.nih.go.kr/cris/search/detailSearch.do/17398], identifier [KCT0005340].

Gut microbiome of healthy people and patients with hematological malignancies in Belarus

Gut microbiota plays an important role in human health and the development of various diseases. We describe the intestinal microbiome of 31 healthy individuals and 29 patients who have hematological malignancies from Belarus. Bacteria that belong to Faecalibacterium, Blautia, Bacteroides, Ruminococcus, Bifidobacterium, Prevotella, Lactobacillus, and Alistipes genera were predominant in the gut of healthy people. Based on the dominant microbiota species, two enterotype-like clusters that are driven by Bacteroides and Blautia, respectively, were identified. A significant decrease in alpha diversity and alterations in the taxonomic composition of the intestinal microbiota were observed in patients with hematological malignancies compared to healthy people. The microbiome of these patients contained a high proportion of Bacteroides, Blautia, Faecalibacterium, Lactobacillus, Prevotella, Alistipes, Enterococcus, Escherichia-Shigella, Ruminococcus gnavus group, Streptococcus, and Roseburia. An increased relative abundance of Bacteroides vulgatus, Ruminococcus torques, Veillonella, Tuzzerella, Sellimonas, and a decreased number of Akkermansia, Coprococcus, Roseburia, Agathobacter, Lachnoclostridium, and Dorea were observed in individuals with hematological malignancies. Generally, the composition of the gut microbiome in patients was more variable than that of healthy individuals, and alterations in the abundance of certain microbial taxa were individually specific.

Modifying the diet and gut microbiota to prevent and manage neurodegenerative diseases

The global prevalence of Alzheimer's disease and Parkinson's disease is steadily increasing due to the aging population. The lack of effective drugs against these neurodegenerative disorders makes it imperative to identify new strategies for their prevention and treatment. Recent studies have revealed that harnessing the power of the gut microbiota through modification of diet may be a valuable approach for reducing the risk, modulating the symptoms, and ameliorating the pathophysiological aspects of neurodegenerative diseases. Consuming specific dietary components can alter the prevalence of bacterial communities within the gut to a healthy enterotype, which can influence the production of beneficial metabolites by microbiota. This article focuses on several dietary components, which have been demonstrated to affect the gut microbiota-brain axis and therefore could lead to attenuation of specific pathological processes in neurodegenerative diseases. Published evidence indicates that fermented foods, including kefir, and foods that are high in bioactive polyphenols and complex carbohydrates, such as grapes, pomegranates, and seaweed, may be effective at reducing neuroinflammation, oxidative stress, neurotransmitter dysfunction, and neuronal death associated with Alzheimer's and Parkinson's diseases. Even though experimental evidence supporting the protective properties of the above dietary components in these diseases is emerging, it is evident that further human clinical studies are required to conclusively establish the benefits of any suggested dietary interventions. The translational potential of such research is illustrated by the clinical success of the recently developed Alzheimer's drug, GV-971, which is a seaweed derivative that works by modulating the gut microbiota-brain axis.

Characterization of the Gut Microbiota in Individuals with Overweight or Obesity during a Real-World Weight Loss Dietary Program: A Focus on the Bacteroides 2 Enterotype

Background: Dietary intervention is a cornerstone of weight loss therapies. In obesity, a dysbiotic gut microbiota (GM) is characterized by high levels of Bacteroides lineages and low diversity. We examined the GM composition changes, including the Bacteroides 2 enterotype (Bact2), in a real-world weight loss study in subjects following a high-protein hypocaloric diet with or without a live microorganisms (LMP) supplement. Method: 263 volunteers were part of this real-world weight loss program. The first phase was a high-protein low-carbohydrate calorie restriction diet with or without LMP supplements. Fecal samples were obtained at baseline and after 10% weight loss for 163 subjects. Metagenomic profiling was obtained by shotgun sequencing. Results: At baseline, the Bact2 enterotype was more prevalent in subjects with aggravated obesity and metabolic alterations. After weight loss, diversity increased and Bact2 prevalence decreased in subjects with lower GM diversity at baseline, notably in LMP consumers. Significant increases in Akkermansia muciniphila and Parabacteroides distasonis and significant decreases of Eubacterium rectale, Streptococcus thermophilus and Bifidobacterial lineages were observed after weight loss. Conclusions: Baseline microbiome composition is associated with differential changes in GM diversity and Bact2 enterotype prevalence after weight loss. Examining these signatures could drive future personalized nutrition efforts towards more favorable microbiome compositions.

Distinctive Gut Microbiota in Patients with Overweight and Obesity with Dyslipidemia and its Responses to Long-term Orlistat and Ezetimibe Intervention: A Randomized Controlled Open-label Trial

This study investigated the gut microbiota and short chain fatty acids (SCFAs) characteristics of subjects with obesity from Xinjiang in northwestern China, a region with a multiethnic culture and characteristic lifestyle, and to explore the potential microbes that respond to a 12-wk medication of orlistat and ezetimibe with a randomized controlled open-label trial manner. The gut microbiota profile of patients with overweight and obesity with dyslipidemia in Xinjiang was distinctive and characterized by enrichment of Lactobacillus and the reduction of the diversity and the depletion of Actinobacteria, Bacteroides, Bifidobacterium, and Bacteroides fragilis. Prevotella-type, Gemmiger-type, and Escherichia/Shigella-type were the gut microbial patterns of the Xinjiang population. However, the fecal SCFAs levels and enterotypes were similar between healthy individuals and patients. These results indicated that the contribution of the gut microbiota to obesity was highly dependent on geography and dietary habits. Waist circumference, total triglyceride (TG), and fasting blood glucose (FBG) were significantly decreased after orlistat therapy, whereas TG, total cholesterol (TC), and low density lipoprotein cholesterol (LDL-C) were significantly decreased by ezetimibe. Overall, the gut microbiota and their SCFAs metabolites were relatively stable after treatment with the two drugs, with alteration of some low-abundant bacteria, i.e., significantly increased Proteobacteria and decreased Alloprevotella after orlistat, and increased Fusobacteria and Fusobacterium after ezetimibe therapy. These results indicated that intestinal malabsorption of dietary fat and cholesterol caused by orlistat and ezetimibe had a limited effect on the overall gut microbial community and their metabolites. Nevertheless, significant correlations between several core microbes that responded to the medications and biochemical data were found; in particular, Actinomyces and Bacteroides were positively correlated with FBG after orlistat intervention, while Clostridium XVIII and Lachnospiracea incertae sedis were negatively correlated with TC and LDL-C after ezetimibe intervention, thus indicating their roles in improving glucolipid metabolism in obesity by acting as potential microbial targets.

Unveiling the Gut Microbiota and Resistome of Wild Cotton Mice, Peromyscus gossypinus, from Heavy Metal- and Radionuclide-Contaminated Sites in the Southeastern United States

The prevalence of antibiotic resistance genes (ARGs) can be driven by direct selection from antibiotic use and indirect selection from substances such as heavy metals (HMs). While significant progress has been made to characterize the influence of HMs on the enrichment and dissemination of ARGs in the environment, there is still much we do not know. To fill this knowledge gap, we present a comprehensive analysis of gut bacteria associated with wild cotton mice (Peromyscus gossypinus) trapped from several areas affected by legacies of HM and radionuclide contamination. We explore how these contaminants affect gut microbial community (GMC) composition and diversity and the enrichment of antibiotic, biocide, and metal resistance genes. Although we were able to identify that a myriad of co-occurring antimicrobial and HM resistance genes appear in mice from all areas, including those without a history of contamination, the proportions of co-occurring ARGs and metal resistance genes (MRGs) are higher in sites with radionuclide contamination. These results support those from several previous studies and enhance our understanding of the coselection process, while providing new insights into the ubiquity of antimicrobial resistance in the resistome of wild animals. IMPORTANCE Antimicrobial resistance is a serious global public health concern because of its prevalence and ubiquitous distribution. The rapid dissemination of antibiotic resistance genes is thought to be the result of the massive overuse of antibiotics in agriculture and therapeutics. However, previous studies have demonstrated that the spread of antibiotic resistance genes can also be influenced by heavy metal contamination. This coselection phenomenon, whereby different resistance determinants are genetically linked on the same genetic element (coresistance) or a single genetic element provides resistance to multiple antimicrobial agents (cross-resistance), has profound clinical and environmental implications. In contrast to antibiotics, heavy metals can persist in the environment as a selection pressure for long periods of time. Thus, it is important to understand how antibiotic resistance genes are distributed in the environment and to what extent heavy metal contaminants may be driving their selection, which we have done in one environmental setting.

Microbiome in Blood Samples From the General Population Recruited in the MARK-AGE Project: A Pilot Study

The presence of circulating microbiome in blood has been reported in both physiological and pathological conditions, although its origins, identities and function remain to be elucidated. This study aimed to investigate the presence of blood microbiome by quantitative real-time PCRs targeting the 16S rRNA gene. To our knowledge, this is the first study in which the circulating microbiome has been analyzed in such a large sample of individuals since the study was carried out on 1285 Randomly recruited Age-Stratified Individuals from the General population (RASIG). The samples came from several different European countries recruited within the EU Project MARK-AGE in which a series of clinical biochemical parameters were determined. The results obtained reveal an association between microbial DNA copy number and geographic origin. By contrast, no gender and age-related difference emerged, thus demonstrating the role of the environment in influencing the above levels independent of age and gender at least until the age of 75. In addition, a significant positive association was found with Free Fatty Acids (FFA) levels, leukocyte count, insulin, and glucose levels. Since these factors play an essential role in both health and disease conditions, their association with the extent of the blood microbiome leads us to consider the blood microbiome as a potential biomarker of human health.

Different Reactions in Each Enterotype Depending on the Intake of Probiotic Yogurt Powder

Probiotics can be used as a nutritional strategy to improve gut homeostasis. We aimed to evaluate the intestinal microbiota profile of 18 subjects after ingestion of probiotic yogurt powder (PYP) based on enterotype. The subjects were classified into three enterotypes according to their microbial community: Bacteroides (n = 9, type B), Prevotella (n = 3, type P), and Ruminococcus (n = 6, type R). We performed controlled termination in a transient series that included a control period of three weeks before probiotic intake, PYP intake for three weeks, and a three-week washout period. Fecal microbiota composition was analyzed by sequencing the V3-V4 super variable region of 16S rRNA. Based on the Bristol stool shape scale, abnormal stool shape improved with PYP intake, and bowel movements were activated. The abundance of Faecalibacterium, Eggerthella, and Leuconostoc, which ferment and metabolize glucose, showed a strong correlation with type B Bacteroides, and glucose metabolism improvement was observed in all type B subjects. Alkaline phosphatase was significantly improved only in type B. In addition, the abundance of type B Bacteroides showed a negative correlation with that of Lactobacillus. The abundance of Streptococcus, Agathobacter, and Christensenella, which are involved in lipid metabolism, showed a strong correlation with that of type P Prevotella, and triglyceride metabolism improvement was observed in all type P subjects. The gut microbiota showed only short-term changes after PYP intake and showed resilience by returning to its original state when PYP intake was interrupted. In summary, the different responses to PYP intake may result from the different enterotypes and associated strains; therefore, the probiotic composition should be adjusted based on the individual enterotype.

Drastic Effects on the Microbiome of a Young Rower Engaged in High-Endurance Exercise After a Month Usage of a Dietary Fiber Supplement

Food supplements are increasingly used worldwide. However, research on the efficacy of such supplements on athlete's well-being and optimal sports performance is very limited. This study performed in junior academic rowing explores the effects of nutritional supplements to aid to the high energy requirements at periods of intense exercise. Herein, the effects of prebiotic fibers on the intestinal microbiome composition of an 18-year-old athlete exercising at high loads during an 8-month period in a “real-life” setting were examined using next-generation sequencing analysis. Results demonstrated that although the alpha diversity of the subject's microbiome drastically decreased [from 2.11 precompetition to 1.67 (p < 0.05)] upon fiber consumption, the Firmicutes/Bacteroidetes ratio increased significantly [from 3.11 to 4.55, as compared with population average (p < 0.05)]. Underlying these macrolevel microbial alterations were demonstrable shifts from acetate- to butyrate-producing bacteria, although with stable effects on the Veillonella species. To our knowledge, this a unique study that shows pronounced changes in the gut microbiome of the young athlete at the competition season and their favorable compensation by the dietary fiber intake. The data here expand the overall understanding of how the high energy needs in high-intensity sports like academic rowing could be supported by dietary fiber supplement consumption.

Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) is a chronic relapsing-remitting systemic disease of the gastrointestinal tract. It is well established that the gut microbiome has a profound impact on IBD pathogenesis. Our aim was to systematically review the literature on the IBD gut microbiome and its usefulness to provide microbiome-based biomarkers. A systematic search of the online bibliographic database PubMed from inception to August 2020 with screening in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines was conducted. One-hundred and forty-four papers were eligible for inclusion. There was a wide heterogeneity in microbiome analysis methods or experimental design. The IBD intestinal microbiome was generally characterized by reduced species richness and diversity, and lower temporal stability, while changes in the gut microbiome seemed to play a pivotal role in determining the onset of IBD. Multiple studies have identified certain microbial taxa that are enriched or depleted in IBD, including bacteria, fungi, viruses, and archaea. The two main features in this sense are the decrease in beneficial bacteria and the increase in pathogenic bacteria. Significant differences were also present between remission and relapse IBD status. Shifts in gut microbial community composition and abundance have proven to be valuable as diagnostic biomarkers. The gut microbiome plays a major role in IBD, yet studies need to go from casualty to causality. Longitudinal designs including newly diagnosed treatment-naïve patients are needed to provide insights into the role of microbes in the onset of intestinal inflammation. A better understanding of the human gut microbiome could provide innovative targets for diagnosis, prognosis, treatment and even cure of this relevant disease.

Significance of African Diets in Biotherapeutic Modulation of the Gut Microbiome

Diet plays an essential role in human development and growth, contributing to health and well-being. The socio-economic values, cultural perspectives, and dietary formulation in sub-Saharan Africa can influence gut health and disease prevention. The vast microbial ecosystems in the human gut frequently interrelate to maintain a healthy, well-coordinated cellular and humoral immune signalling to prevent metabolic dysfunction, pathogen dominance, and induction of systemic diseases. The diverse indigenous diets could differentially act as biotherapeutics to modulate microbial abundance and population characteristics. Such modulation could prevent stunted growth, malnutrition, induction of bowel diseases, attenuated immune responses, and mortality, particularly among infants. Understanding the associations between specific indigenous African diets and the predictability of the dynamics of gut bacteria genera promises potential biotherapeutics towards improving the prevention, control, and treatment of microbiome-associated diseases such as cancer, inflammatory bowel disease, obesity, type 2 diabetes, and cardiovascular disease. The dietary influence of many African diets (especially grain-base such as millet, maize, brown rice, sorghum, soya, and tapioca) promotes gut lining integrity, immune tolerance towards the microbiota, and its associated immune and inflammatory responses. A fibre-rich diet is a promising biotherapeutic candidate that could effectively modulate inflammatory mediators' expression associated with immune cell migration, lymphoid tissue maturation, and signalling pathways. It could also modulate the stimulation of cytokines and chemokines involved in ensuring balance for long-term microbiome programming. The interplay between host and gut microbial digestion is complex; microbes using and competing for dietary and endogenous proteins are often attributable to variances in the comparative abundances of Enterobacteriaceae taxa. Many auto-inducers could initiate the process of quorum sensing and mammalian epinephrine host cell signalling system. It could also downregulate inflammatory signals with microbiota tumour taxa that could trigger colorectal cancer initiation, metabolic type 2 diabetes, and inflammatory bowel diseases. The exploitation of essential biotherapeutic molecules derived from fibre-rich indigenous diet promises food substances for the downregulation of inflammatory signalling that could be harmful to gut microbiota ecological balance and improved immune response modulation.

Jares E, Jarvis D, Jassem E, Jenko K, Jiméneracruz Uscanga RD, Johnston SL, Joos G, Jošt M, Julge K, Jung K, Just J, Jutel M, Kaidashev I, Kalayci O, Kalyoncu F, Kapsali J, Kardas P, Karjalainen J, Kasala CA, Katotomichelakis M, Kavaliukaite L, Kazi BS, Keil T, Keith P, Khaitov M, Khaltaev N, Kim Y, Kirenga B, Kleine‐Tebbe J, Klimek L, Koffi N’Goran B, Kompoti E, Kopač P, Koppelman G, KorenJeverica A, Koskinen S, Košnik M, Kostov KV, Kowalski ML, Kralimarkova T, Kramer Vrščaj K, Kraxner H, Kreft S, Kritikos V, Kudlay D, Kuitunen M, Kull I, Kuna P, Kupczyk M, Kvedariene V, Kyriakakou M, Lalek N, Landi M, Lane S, Larenas‐Linnemann D, Lau S, Laune D, Lavrut J, Le L, Lenzenhuber M, Lessa M, Levin M, Li J, Lieberman P, Liotta G, Lipworth B, Liu X, Lobo R, Lodrup Carlsen KC, Lombardi C, Louis R, Loukidis S, Lourenço O, Luna Pech JA, Madjar B, Maggi E, Magnan A, Mahboub B, Mair A, Mais Y, Maitland van der Zee A, Makela M, Makris M, Malling H, Mandajieva M, Manning P, Manousakis M, Maragoudakis P, Marseglia G, Marshall G, Reza Masjedi M, Máspero JF, Matta Campos JJ, Maurer M, Mavale‐Manuel S, Meço C, Melén E, Melioli G, Melo‐Gomes E, Meltzer EO, Menditto E, Menzies‐Gow A, Merk H, Michel J, Micheli Y, Miculinic N, Midão L, Mihaltan F, Mikos N, Milanese M, Milenkovic B, Mitsias D, Moalla B, Moda G, Mogica Martínez MD, Mohammad Y, Moin M, Molimard M, Momas I, Mommers M, Monaco A, Montefort S, Mora D, Morais‐Almeida M, Mösges R, Mostafa B, Mullol J, Münter L, Muraro A, Murray R, Musarra A, Mustakov T, Naclerio R, Nadeau KC, Nadif R, Nakonechna A, Namazova‐Baranova L, Navarro‐Locsin G, Neffen H, Nekam K, Neou A, Nettis E, Neuberger D, Nicod L, Nicola S, Niederberger‐Leppin V, Niedoszytko M, Nieto A, Novellino E, Nunes E, Nyembue D, O’Hehir R, Odjakova C, Ohta K, Okamoto Y, Okubo K, Oliver B, Onorato GL, Pia Orru M, Ouédraogo S, Ouoba K, Paggiaro PL, Pagkalos A, Pajno G, Pala G, Palaniappan S, Pali‐Schöll I, Palkonen S, Palmer S, Panaitescu Bunu C, Panzner P, Papadopoulos NG, Papanikolaou V, Papi A, Paralchev B, Paraskevopoulos G, Park H, Passalacqua G, Patella V, Pavord I, Pawankar R, Pedersen S, Peleve S, Pellegino S, Pereira A, Pérez T, Perna A, Peroni D, Pfaar O, Pham‐Thi N, Pigearias B, Pin I, Piskou K, Pitsios C, Plavec D, Poethig D, Pohl W, Poplas Susic A, Popov TA, Portejoie F, Potter P, Poulsen L, Prados‐Torres A, Prarros F, Price D, Prokopakis E, Puggioni F, Puig‐Domenech E, Puy R, Rabe K, Raciborski F, Ramos J, Recto MT, Reda SM, Regateiro FS, Reider N, Reitsma S, Repka‐Ramirez S, Ridolo E, Rimmer J, Rivero Yeverino D, Angelo Rizzo J, Robalo‐Cordeiro C, Roberts G, Roche N, Rodríguez González M, Rodríguez Zagal E, Rolla G, Rolland C, Roller‐Wirnsberger R, Roman Rodriguez M, Romano A, Romantowski J, Rombaux P, Romualdez J, Rosado‐Pinto J, Rosario N, Rosenwasser L, Rossi O, Rottem M, Rouadi P, Rovina N, Rozman Sinur I, Ruiz M, Ruiz Segura LT, Ryan D, Sagara H, Sakai D, Sakurai D, Saleh W, Salimaki J, Samitas K, Samolinski B, Sánchez Coronel MG, Sanchez‐Borges M, Sanchez‐Lopez J, Sarafoleanu C, Sarquis Serpa F, Sastre‐Dominguez J, Savi E, Sawaf B, Scadding GK, Scheire S, Schmid‐Grendelmeier P, Schuhl JF, Schunemann H, Schvalbová M, Schwarze J, Scichilone N, Senna G, Sepúlveda C, Serrano E, Shields M, Shishkov V, Siafakas N, Simeonov A, FER Simons E, Carlos Sisul J, Sitkauskiene B, Skrindo I, SokličKošak T, Solé D, Sooronbaev T, Soto‐Martinez M, Soto‐Quiros M, Sousa Pinto B, Sova M, Soyka M, Specjalski K, Spranger O, Stamataki S, Stefanaki L, Stellato C, Stelmach R, Strandberg T, Stute P, Subramaniam A, Suppli Ulrik C, Sutherland M, Sylvestre S, Syrigou A, Taborda Barata L, Takovska N, Tan R, Tan F, Tan V, Ping Tang I, Taniguchi M, Tannert L, Tantilipikorn P, Tattersall J, Tesi F, Thijs C, Thomas M, To T, Todo‐Bom A, Togias A, Tomazic P, Tomic‐Spiric V, Toppila‐Salmi S, Toskala E, Triggiani M, Triller N, Triller K, Tsiligianni I, Uberti M, Ulmeanu R, Urbancic J, Urrutia Pereira M, Vachova M, Valdés F, Valenta R, Valentin Rostan M, Valero A, Valiulis A, Vallianatou M, Valovirta E, Van Eerd M, Van Ganse E, Hage M, Vandenplas O, Vasankari T, Vassileva D, Velasco Munoz C, Ventura MT, Vera‐Munoz C, Vicheva D, Vichyanond P, Vidgren P, Viegi G, Vogelmeier C, Von Hertzen L, Vontetsianos T, Vourdas D, Tran Thien Quan V, Wagenmann M, Walker S, Wallace D, Wang DY, Waserman S, Wickman M, Williams S, Williams D, Wilson N, Wong G, Woo K, Wright J, Wroczynski P, Xepapadaki P, Yakovliev P, Yamaguchi M, Yan K, Yeow Yap Y, Yawn B, Yiallouros P, Yorgancioglu A, Yoshihara S, Young I, Yusuf OB, Zaidi A, Zaitoun F, Zar H, Zedda M, Zernotti ME, Zhang L, Zhong N, Zidarn M, Zubrinich C. Cabbage and fermented vegetables: From death rate heterogeneity in countries to candidates for mitigation strategies of severe COVID-19

Large differences in COVID‐19 death rates exist between countries and between regions of the same country. Some very low death rate countries such as Eastern Asia, Central Europe, or the Balkans have a common feature of eating large quantities of fermented foods. Although biases exist when examining ecological studies, fermented vegetables or cabbage have been associated with low death rates in European countries. SARS‐CoV‐2 binds to its receptor, the angiotensin‐converting enzyme 2 (ACE2). As a result of SARS‐CoV‐2 binding, ACE2 downregulation enhances the angiotensin II receptor type 1 (AT₁R) axis associated with oxidative stress. This leads to insulin resistance as well as lung and endothelial damage, two severe outcomes of COVID‐19. The nuclear factor (erythroid‐derived 2)‐like 2 (Nrf2) is the most potent antioxidant in humans and can block in particular the AT₁R axis. Cabbage contains precursors of sulforaphane, the most active natural activator of Nrf2. Fermented vegetables contain many lactobacilli, which are also potent Nrf2 activators. Three examples are: kimchi in Korea, westernized foods, and the slum paradox. It is proposed that fermented cabbage is a proof‐of‐concept of dietary manipulations that may enhance Nrf2‐associated antioxidant effects, helpful in mitigating COVID‐19 severity.

Gastrointestinal disturbance and effect of fecal microbiota transplantation in discharged COVID-19 patients

BACKGROUND

To investigate the potential beneficial effect of fecal microbiota transplantation (FMT) on gastrointestinal symptoms, gut dysbiosis and immune status in discharged COVID-19 patients.

CASE PRESENTATION

A total of 11 COVID-19 patients were recruited in April, 2020, about one month on average after they were discharged from the hospital. All subjects received FMT for 4 consecutive days by oral capsule administrations with 10 capsules for each day. In total, 5 out of 11 patients reported to be suffered from gastrointestinal symptoms, which were improved after FMT. After FMT, alterations of B cells were observed, which was characterized as decreased naive B cell (P = 0.012) and increased memory B cells (P = 0.001) and non-switched B cells (P = 0.012).The microbial community richness indicated by operational taxonomic units number, observed species and Chao1 estimator was marginally increased after FMT. Gut microbiome composition of discharged COVID-19 patients differed from that of the general population at both phylum and genera level, which was characterized with a lower proportion of Firmicutes (41.0%) and Actinobacteria (4.0%), higher proportion of Bacteroidetes (42.9%) and Proteobacteria (9.2%). FMT can partially restore the gut dysbiosis by increasing the relative abundance of Actinobacteria (15.0%) and reducing Proteobacteria (2.8%) at the phylum level. At the genera level, Bifidobacterium and Faecalibacterium had significantly increased after FMT.

CONCLUSIONS

After FMT, altered peripheral lymphocyte subset, restored gut microbiota and alleviated gastrointestinal disorders were observe, suggesting that FMT may serve as a potential therapeutic and rehabilitative intervention for the COVID-19.

Potential role of probiotic species in ameliorating oxidative stress, effect on liver profile and hormones in male albino rat model

Probiotics are living micro-organism preparations which can vigorously inhibit the probable pathogens colonization in the gut microbial ecology. Current experiment was designed to investigate the efficacy of imported probiotic species compared with the indigenous probiotics species on the oxidative stress, enzymes, and hormones in animal model. Thirty Albino rats were equally divided into three groups with 10 rats ( n = 10) in each group as Control (C), supplemented with imported probiotic species (IP), and supplemented with indigenous probiotics species (InP) for 21 days under controlled environment. The evaluation of treatments was done by testing the serum oxidative stress markers, liver enzymes (Aspartate transaminase and Alanine aminotransferase), lipid profile, and hormonal dynamics including Lutinizing hormone (LH), follicular stimulating hormone (FSH), and growth hormone (GH) in albino male rats. Results revealed that use of indigenous probiotic species significantly ( p < 0.05) reduces the oxidative stress and improves the antioxidant capacity; liver enzymes, total cholesterol, and LDL-Cholesterol were also reduced significantly ( p < 0.05) in InP as compared to IP group. Moreover, results of hormones including LH, FSH, and GH explored that indigenous probiotics have significant ( p < 0.05) potential to improve these hormones as compared to imported probiotics. Although, it could be concluded that InP have beneficial role in preventing the body from oxidative stress as well as in improving the blood parameters but comprehensive studies are required to investigate the detail gut ecology of the indigenous species which will definitely a strong support in preparing a more suitable local probiotic supplement.

Altered diversity and composition of gut microbiota in Wilson's disease

Wilson's disease (WD) is an autosomal recessive inherited disorder of chronic copper toxicosis with high mortality and disability. Recent evidence suggests a correlation between dysbiosis in gut microbiome and multiple diseases such as genetic and metabolic disease. However, the impact of intestinal microbiota polymorphism in WD have not been fully elaborated and need to be explore for seeking some microbiota benefit for WD patients. In this study, the 16S rRNA sequencing was performed on fecal samples from 14 patients with WD and was compared to the results from 16 healthy individuals. The diversity and composition of the gut microbiome in the WD group were significantly lower than those in healthy individuals. The WD group presented unique richness of Gemellaceae, Pseudomonadaceae and Spirochaetaceae at family level, which were hardly detected in healthy controls. The WD group had a markedly lower abundance of Actinobacteria, Firmicutes and Verrucomicrobia, and a higher abundance of Bacteroidetes, Proteobacteria, Cyanobacteria and Fusobacteria than that in healthy individuals. The Firmicutes to Bacteroidetes ratio in the WD group was significantly lower than that of healthy control. In addition, the functional profile of the gut microbiome from WD patients showed a lower abundance of bacterial groups involved in the host immune and metabolism associated systems pathways such as transcription factors and ABC-type transporters, compared to healthy individuals. These results implied dysbiosis of gut microbiota may be influenced by the host metabolic disorders of WD, which may provide a new understanding of the pathogenesis and new possible therapeutic targets for WD.

The Gut Microbiota and Inflammation: An Overview

The gut microbiota encompasses a diverse community of bacteria that carry out various functions influencing the overall health of the host. These comprise nutrient metabolism, immune system regulation and natural defence against infection. The presence of certain bacteria is associated with inflammatory molecules that may bring about inflammation in various body tissues. Inflammation underlies many chronic multisystem conditions including obesity, atherosclerosis, type 2 diabetes mellitus and inflammatory bowel disease. Inflammation may be triggered by structural components of the bacteria which can result in a cascade of inflammatory pathways involving interleukins and other cytokines. Similarly, by-products of metabolic processes in bacteria, including some short-chain fatty acids, can play a role in inhibiting inflammatory processes. In this review, we aimed to provide an overview of the relationship between the gut microbiota and inflammatory molecules and to highlight relevant knowledge gaps in this field. Based on the current literature, it appears that as the gut microbiota composition differs between individuals and is contingent on a variety of factors like diet and genetics, some individuals may possess bacteria associated with pro-inflammatory effects whilst others may harbour those with anti-inflammatory effects. Recent technological advancements have allowed for better methods of characterising the gut microbiota. Further research to continually improve our understanding of the inflammatory pathways that interact with bacteria may elucidate reasons behind varying presentations of the same disease and varied responses to the same treatment in different individuals. Furthermore, it can inform clinical practice as anti-inflammatory microbes can be employed in probiotic therapies or used to identify suitable prebiotic therapies.

Comparative gut microbiome analysis of the Prakriti and Sasang systems reveals functional level similarities in constitutionally similar classes

The traditional medicinal systems (TMS) of India (Prakriti) and Korea (Sasang) classify human individuals based on their constitution determined by the physiological and psychological traits of individuals. Similarities in the constitutions are already found between the classes of Prakriti (Vata, Pitta, and Kapha) and Sasang (TE: Taeeumin, SE: Soeumin, and SY: Soyangin) systems. Gut health is an important aspect of this constitution based classification in TMS. To determine the role of gut microbes in such classifications, we have analyzed the gut microbiome (taxa and imputed functions) in the constitutionally similar Prakriti and Sasang classes. An enrichment of Bacteroides and Prevotella enterotypes is observed in the Sasang and Prakriti samples, respectively. The impact of the constitution is found to be more prominent with respect to the taxa and predicted-functions within the Prakriti classes. Gut microbiome functional-level similarities are found to correlate well with the host phenotypes of the constitutionally similar Prakriti and Sasang classes. An enrichment of carbohydrate and amino-acid metabolism is observed in the Vata and SE classes which may be responsible for meeting with their high energy demands and lean phenotype. The Pitta and SY classes exhibit the high capacity to metabolize toxins. An enrichment of functions responsible for predisposition to obesity and high drug metabolism is observed in the Kapha and TE classes. The contribution of gut adaptive functions is found to correlate with the constitution-based classification in both Prakriti and Sasang systems. The TE class harboured the highest number of biofilm-forming and stress-tolerant microbes thus exhibiting the maximum tolerance of environmental stress. Similarities in the gut microbiota and the resulting disease predisposition patterns are found to exist between the constitutionally matching Prakriti and Sasang classes.

Enterotypes of the Gut Microbial Community and Their Response to Plant Secondary Compounds in Plateau Pikas

Animal gut microbiomes can be clustered into “enterotypes” characterized by an abundance of signature genera. The characteristic determinants, stability, and resilience of these community clusters remain poorly understood. We used plateau pika (Ochotona curzoniae) as a model and identified three enterotypes by 16S rDNA sequencing. Among the top 15 genera, 13 showed significantly different levels of abundance between the enterotypes combined with different microbial functions and distinct fecal short-chain fatty acids. We monitored changes in the microbial community associated with the transfer of plateau pikas from field to laboratory and observed that feeding them a single diet reduced microbial diversity, resulting in a single enterotype with an altered composition of the dominant bacteria. However, microbial diversity, an abundance of some changed dominant genera, and enterotypes were partially restored after adding swainsonine (a plant secondary compound found in the natural diet of plateau pikas) to the feed. These results provide strong evidence that gut microbial diversity and enterotypes are directly related to specific diet, thereby indicating that the formation of different enterotypes can help animals adapt to complex food conditions. Additionally, natural plant secondary compounds can maintain dominant bacteria and inter-individual differences of gut microbiota and promote the resilience of enterotypes in small herbivorous mammals.