Faecal microbiota of healthy adults in south India: Comparison of a tribal & a rural population

Dangua Fang induces anti-glucolipid metabolism disorder effects similar to those of direct NFIL3 inhibition

Background

Dangua Fang (DGF) is a traditional Chinese herbal formula widely used to regulate glucolipid metabolism. Nuclear factor, interleukin-3 regulated (NFIL3) plays a regulatory role in intestinal fat absorption and energy metabolism. Gut microbiota can modulate NFIL3 expression and affect host metabolism.

Purpose

This study aimed to investigate the effects of DGF or NFIL3 inhibition on the gut microbiota and their metabolites in mice with glucolipid metabolism disorder (GLMD) and explore the relationship between DGF anti-GLMD effects and those of direct NFIL3 inhibition.

Methods

A GLMD mouse model was established by induction with a high-glucose and high-fat diet. The mice were divided into the control group (CG), model group (MG), DGF group (DFG), DGF + siRNA group (DFSG), and siRNA group (SG). The mice were administered sterile water, DGF, and/or intraperitoneal injections of siRNA-NFIL3 or normal saline for 15 weeks, following which glucolipid metabolic indicators, NFIL3 levels, and histopathological alterations in the liver and small intestinal tissues were evaluated. Additionally, the gut microbiota and differential metabolites were analysed, and linear regression analysis was conducted between gut microbial species and metabolic indicators to assess the role of the gut microbiota in metabolic regulation.

Results

Significant differences were observed between the CG and MG groups for various indicators. Compared with that in the MG group, the GLMD in the DFG, DFSG, and SG groups was significantly improved, and the pathological morphology of the liver and small intestine was altered. The NFIL3 mRNA and protein expression levels in the serum, liver, and small intestine were significantly decreased. The relative abundance of Bacteroidota decreased, whereas that of Firmicutes increased, and changes in the gut microbiota significantly correlated with serum total cholesterol (TC), triglyceride (TG), and free fatty acid (FFA) levels. Moreover, lipid metabolism-related pathways were significantly altered in all three intervention groups.

Conclusion

DGF reduced NFIL3 expression in GLMD mice, regulated the gut microbiota and their metabolites, and altered lipid metabolism-related pathways, with anti-GLMD effects similar to those of direct NFIL3 inhibition.

Establishment and perturbation of human gut microbiome: common trends and variations between Indian and global populations

Human gut microbial species are crucial for dietary metabolism and biosynthesis of micronutrients. Digested products are utilised by the host as well as several gut bacterial species. These species are influenced by various factors such as diet, age, geographical location, and ethnicity. India is home to the largest human population in the world. It is spread across diverse ecological and geographical locations. With variable dietary habits and lifestyles, Indians have unique gut microbial composition. This review captures contrasting and common trends of gut bacterial community establishment in infants (born through different modes of delivery), and how that bacterial community manifests itself along infancy, through old age between Indian and global populations. Because dysbiosis of the gut community structure is associated with various diseases, this review also highlights the common and unique bacterial species associated with various communicable as well as noncommunicable diseases such as diarrhoea, amoebiasis, malnutrition, type 2 diabetes, obesity, colorectal cancer, inflammatory bowel disease, and gut inflammation and damage to the brain in the global and Indian population.

Predictive association of gut microbiome and NLR in anemic low middle-income population of Odisha- a cross-sectional study

Background

Iron is abundant on earth but not readily available for colonizing bacteria due to its low solubility in the human body. Hosts and microbiota compete fiercely for iron. <15% Supplemented Iron is absorbed in the small bowel, and the remaining iron is a source of dysbiosis. The gut microbiome signatures to the level of predicting anemia among low-middle-income populations are unknown. The present study was conducted to identify gut microbiome signatures that have predictive potential in association with Neutrophil to lymphocytes ratio (NLR) and Mean corpuscular volume (MCV) in anemia.

Methods

One hundred and four participants between 10 and 70 years were recruited from Odisha's Low Middle-Income (LMI) rural population. Hematological parameters such as Hemoglobin (HGB), NLR, and MCV were measured, and NLR was categorized using percentiles. The microbiome signatures were analyzed from 61 anemic and 43 non-anemic participants using 16 s rRNA sequencing, followed by the Bioinformatics analysis performed to identify the diversity, correlations, and indicator species. The Multi-Layered Perceptron Neural Network (MLPNN) model were applied to predict anemia.

Results

Significant microbiome diversity among anemic participants was observed between the lower, middle, and upper Quartile NLR groups. For anemic participants with NLR in the lower quartile, alpha indices indicated bacterial overgrowth, and consistently, we identified R. faecis and B. uniformis were predominating. Using ROC analysis, R. faecis had better distinction (AUC = 0.803) to predict anemia with lower NLR. In contrast, E. biforme and H. parainfluenzae were indicators of the NLR in the middle and upper quartile, respectively. While in Non-anemic participants with low MCV, the bacterial alteration was inversely related to gender. Furthermore, our Multi-Layered Perceptron Neural Network (MLPNN) models also provided 89% accuracy in predicting Anemic or Non-Anemic from the top 20 OTUs, HGB level, NLR, MCV, and indicator species.

Conclusion

These findings strongly associate anemic hematological parameters and microbiome. Such predictive association between the gut microbiome and NLR could be further evaluated and utilized to design precision nutrition models and to predict Iron supplementation and dietary intervention responses in both community and clinical settings.

Mapping microbiome-redox spectrum and evaluating Microbial-Redox Index in chronic gastritis

Peptic ulcer disease (PUD) and chronic gastritis are prevalent in developing countries. The role of oxidative stress in the pathogenesis of gastrointestinal mucosal disorders is well recognized. In PUD, the gastric mucosa and its associated microbiome are subject to diet and stress-induced oxidative perturbations. Tissue redox potential (ORP) measurement can quantify oxidative stress, reflecting the balance between prooxidants and antioxidants. This study hypothesizes that the oxidative stress quantified by tissue ORP will be associated with characteristic changes in the mucosa-associated microbiome in PUD and gastritis. In addition, we propose using relative microbial abundance as a quantitative marker of mucosal health. Endoscopy was performed to obtain gastric mucosal biopsies from ten PUD and ten non-ulcer dyspepsia (NUD) patients. The tissue ORP was measured directly with a microelectrode using a biopsy specimen. A second specimen from an adjacent site was subjected to 16s rRNA gene sequencing. From the OTUs, the relative abundance of the microbial taxon in each of the samples was derived. We analyzed the genome of the predominant species for genes encoding the utilization of oxygen as an electron acceptor in respiration and for the presence of antioxidant defense mechanisms. The organisms were then grouped based on their established and inferred redox traits. Shannon diversity index and Species richness were calculated on rarefied data. The relative abundance of organisms that prefer high ORP over those that favor low ORP is conceived as the “Microbial Redox Index (MRI),” an indicator of mucosal health. In the gastric mucosa, aerobic species predominate and are more diverse than the anaerobes. The predominant aerobes are Helicobacter pylori and Sphingobacterium mizutaii. The abundance of these two species had an inverse correlation with the abundance of low ORP preferring anaerobes. Their relative abundance ratio (Microbial Redox Index) correlated with the tissue oxidation–reduction potential (ORP), a direct measure of oxidative stress. Correlation analysis also revealed that the abundance of all anaerobes inversely correlated with the dominant aerobic taxa. In addition, Shannon and Species richness diversity indices, the probable indicators of mucosal health, were negatively correlated with Microbial Redox Index. Using PUD as a prototype mucosal disease, this article describes a generalized approach to infer and quantify mucosal oxidative stress by analyzing the relative abundance of microorganisms that preferentially grow at the extremes of the tissue redox potential. This ratiometric Microbial Redox Index can also be assessed using simple qPCR without the need for sequencing. The approach described herein may be helpful as a widely applicable quantitative measure of mucosal health with prognostic and therapeutic implications.

Reanalysis of the Mars500 experiment reveals common gut microbiome alterations in astronauts induced by long-duration confinement

Maintaining astronaut health throughout long-duration spaceflight is essential to the feasibility of a manned mission to Mars. The ground-based Mars500 experiment investigated long-duration health by isolating six astronauts for 520 days, the longest controlled human confinement study conducted to date. After 520 days, astronauts had uniform strength and lean body mass losses, and increased fasting plasma glucose, calprotectin, and neutrophil levels characteristic of intestinal inflammation but previous analyses revealed no common significant changes in gut microbiota. This study reanalysed data from early (days 7–45) and late (days 420–520) faecal samples and identified 408 exact sequence variants (ESVs), including 213 shared by all astronauts. Thirty-two ESVs were significantly differentially abundant over time, including depletion of keystone resistant starch degrading, anti-inflammatory and insulin sensitivity-associated species, such as Faecalibacterium prausnitzii, Ruminococcus bromii, Blautia luti, Anaerostipes hadrus, Roseburia faecis, and Lactobacillus rogosae, and enrichment of yet-to-be-cultured bacteria. Additionally, the extraordinary experimental confinement allowed observation of microbiota potentially shared between astronauts and their habitat. Forty-nine species were shared, representing 49% and 12% of the human and environmental microbiome diversity, respectively. These findings reveal the microbiota which significantly altered in relative abundance throughout confinement, including species known to influence inflammation and host glucose homeostasis consistent with astronaut symptoms. Identification of microbiome alterations after 520 days of isolation represents a missing piece connecting Mars500 astronaut physiological studies. Knowledge of the impact of long-term confinement upon the human microbiome helps to improve our understanding of how humans interact with their habitats and is a valuable step forward towards enabling long-duration spaceflight.

Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome

BACKGROUND

The Central Indian gut microbiome remains grossly understudied. Herein, we sought to investigate the burden of antimicrobial resistance and diarrheal diseases, particularly Clostridioides difficile, in rural-agricultural and urban populations in Central India, where there is widespread unregulated antibiotic use. We utilized shotgun metagenomics to comprehensively characterize the bacterial and viral fractions of the gut microbiome and their encoded functions in 105 participants.

RESULTS

We observed distinct rural-urban differences in bacterial and viral populations, with geography exhibiting a greater influence than diarrheal status. Clostridioides difficile disease was more commonly observed in urban subjects, and their microbiomes were enriched in metabolic pathways relating to the metabolism of industrial compounds and genes encoding resistance to 3^rd generation cephalosporins and carbapenems. By linking phages present in the microbiome to their bacterial hosts through CRISPR spacers, phage variation could be directly related to shifts in bacterial populations, with the auxiliary metabolic potential of rural-associated phages enriched for carbon and amino acid energy metabolism.

CONCLUSIONS

We report distinct differences in antimicrobial resistance gene profiles, enrichment of metabolic pathways and phage composition between rural and urban populations, as well as a higher burden of Clostridioides difficile disease in the urban population. Our results reveal that geography is the key driver of variation in urban and rural Indian microbiomes, with acute diarrheal disease, including C. difficile disease exerting a lesser impact. Future studies will be required to understand the potential role of dietary, cultural, and genetic factors in contributing to microbiome differences between rural and urban populations.

The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients?

The gut microbiota is emerging as a promising target for the management or prevention of inflammatory and metabolic disorders in humans. Many of the current research efforts are focused on the identification of specific microbial signatures, more particularly for those associated with obesity, type 2 diabetes, and cardiovascular diseases. Some studies have described that the gut microbiota of obese animals and humans exhibits a higher Firmicutes/Bacteroidetes ratio compared with normal-weight individuals, proposing this ratio as an eventual biomarker. Accordingly, the Firmicutes/Bacteroidetes ratio is frequently cited in the scientific literature as a hallmark of obesity. The aim of the present review was to discuss the validity of this potential marker, based on the great amount of contradictory results reported in the literature. Such discrepancies might be explained by the existence of interpretative bias generated by methodological differences in sample processing and DNA sequence analysis, or by the generally poor characterization of the recruited subjects and, more particularly, the lack of consideration of lifestyle-associated factors known to affect microbiota composition and/or diversity. For these reasons, it is currently difficult to associate the Firmicutes/Bacteroidetes ratio with a determined health status and more specifically to consider it as a hallmark of obesity.

Impact of a Nomadic Pastoral Lifestyle on the Gut Microbiome in the Fulani Living in Nigeria

The co-evolution of the gut microbiota with its human host has revolutionized our current scientific viewpoint about the contribution of diet and lifestyle on human health. Most studies so far have focused on populations living in the United States and Europe or compared those with communities from other geographic areas in the world. In order to determine the taxonomic and predicted functional profile of the gut microbiome of a hitherto unstudied human community, we investigated the phylogenetic diversity of the gut microbiota in a community of Fulani nomadic pastoralists, and their semi-urbanized neighbors - the Jarawa. The Jarawa reside in a city (Jos) in the north-central part of Nigeria, and are adapted in part to a westernized lifestyle. The nomadic Fulani lifestyle resembles a mix of Paleolithic and Neolithic lifestyle patterns with a greater predisposition to diseases. The fecal microbiota of the Fulani and the Jarawa were characterized by paired-end Illumina MiSeq sequencing of the 16S rRNA gene, followed by downstream bioinformatics analysis of the sequence reads. The Fulani harbored increased numbers of signatures of microbes that are known to be associated with a foraging lifestyle such as the Bacteroidetes, Spirochaetes, and Prevotellaceae, while the Jarawa were dominated by signatures of Firmicutes, Ruminococcaceae, Lachnospiraceae, and Christensenellaceae. Notably, the gut microbiota of the Fulani showed less taxonomic diversity than those of the Jarawa. Although they reside in the same geographical zone, microbial community composition was significantly different between the two groups. Pathogens were predicted to be more abundant in the gut microbiota of the Fulani than of the Jarawa. Predicted pathogenic pathways and pathways associated with the breakdown of fiber-rich diet were enriched in the Fulani, including glutathione metabolism, while pathways associated with the consumption of low-fiber diet and xenobiotics, including fructose and mannose metabolic pathways, and nitrotoluene degradation pathways, respectively, were enriched in the Jarawa. Significant differences in composition between both groups were likely due to differences in diet and lifestyle and exposure to pathogens. These results suggest that microbial diversity may not always be higher in non-industrialized societies than in westernized societies, as previously assumed.