Mining the Core Gut Microbiome from a Sample Indian Population

Hyperglycemia is associated with duodenal dysbiosis and altered duodenal microenvironment

The gut microbiome influences the pathogenesis and course of metabolic disorders such as diabetes. While it is likely that duodenal mucosa associated microbiota contributes to the genesis and progression of increased blood sugar, including the pre-diabetic stage, it is much less studied than stool. We investigated paired stool and duodenal microbiota in subjects with hyperglycemia (HbA1c ≥ 5.7% and fasting plasma glucose > 100 mg/dl) compared to normoglycemic. We found patients with hyperglycemia (n = 33) had higher duodenal bacterial count (p = 0.008), increased pathobionts and reduction in beneficial flora compared to normoglycemic (n = 21). The microenvironment of duodenum was assessed by measuring oxygen saturation using T-Stat, serum inflammatory markers and zonulin for gut permeability. We observed that bacterial overload was correlated with increased serum zonulin (p = 0.061) and higher TNF-α (p = 0.054). Moreover, reduced oxygen saturation (p = 0.021) and a systemic proinflammatory state [increased total leukocyte count (p = 0.031) and reduced IL-10 (p = 0.015)] characterized the duodenum of hyperglycemic. Unlike stool flora, the variability in duodenal bacterial profile was associated with glycemic status and was predicted by bioinformatic analysis to adversely affect nutrient metabolism. Our findings offer new understanding of the compositional changes in the small intestine bacteria by identifying duodenal dysbiosis and altered local metabolism as potentially early events in hyperglycemia.

Following the Indian Immigrant: adoption of westernization results in a western gut microbiome and an increased risk of inflammatory bowel diseases

Indians who migrate to westernized countries such as Canada, the USA, and the UK are at an increased risk of developing inflammatory bowel disease (IBD). While the underlying aetiology of IBD remains unclear, a gut microbiome, i.e. no longer symbiotic with its host, is a major player. Increasing IBD incidence in Indian immigrants may be due to the adoption of western practices that result in loss of tolerance of a symbiotic community in the gut and its underlying immune responses. However, little is known about the microbial changes in the Indian gut, including shifts in the microbiome when they migrate to westernized countries. In this Current Opinion, we discuss what is known about the Indian gut microbiome and how living in a westernized environment may be impeding what was once a symbiotic relationship with their gut microbiome and intestinal mucosae, which may be the driving factor in their increased risk of IBD.

Elucidating the gut microbiome alterations of tribal community of Arunachal Pradesh: perspectives on their lifestyle or food habits

Gut microbiota studies of ethnic populations reveal gut microbial biomarkers for therapeutic options and detection of the disease state. The present study aimed to analyze the gut microbiome signatures in thirty individuals from the Adi, Apatani and Nyshi tribes of Arunachal Pradesh (ten in each cohort) by sequencing the V3 and V4 regions of 16S rRNA on the Illumina MiSeq Platform. The gut microbiome was highly predominated by Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidates in the three studied tribal groups. At the genus level, significant abundance of Bifidobacterium, Collinsella, Bacteroides, Prevotella, Lactobacillus, Streptococcus, Clostridium, Coprococcus, Dorea, Lachnospira, Roseburia, Ruminococcus, Faecalibacterium, Catenibacterium, Eubacterium, Citrobacter and Enterobacter were observed amongst the three tribes. The tribal communities residing in remote areas and following traditional lifestyle had higher gut microbiome diversity with a high prevalence of Prevotella and Collinsella in the Adi and Nyshi tribes, and Bifidobacterium and Catenibacterium in the Apatani tribe. Elucidating the gut microbiome of the tribal community of Arunachal Pradesh will add to the knowledge on relationships between microbial communities, dietary food factors, and the overall state of health of humans worldwide.

Unique attributes of obesity in India: A narrative review

Obesity has become a burgeoning epidemic in India, even though the country is still dealing with undernutrition. As a significant determinant of the Metabolic Syndrome (MetS) and non-communicable diseases (NCDs) such as type 2 diabetes mellitus (T2DM) and cardiovascular disease (CVD), understanding the Indian context of the problem and learning how to deal with the obesity epidemic in this country has gained paramount importance. This narrative review points to the unique features of the obesity epidemic in India and its associated contributing factors, including the evolving nature of the Indian diet, the peculiarity of the increased adiposity at lower BMIs, unique obesity-associated genetic variants in Indians, the contribution of the gut microbiome, the impact of chronic inflammation and the role of ambient air pollution, and the contribution of decreased physical activity levels concerning the rapid urbanisation and the built environment. We believe that disseminating our insights into these unique features influencing the development of obesity in India will help increase global awareness and pave the way for better control and management of this obesity epidemic.

The Emerging Biotherapeutic Agent: Akkermansia

The human gastrointestinal tract (GIT) is a well-recognized hub of microbial activities. The microbiota harboring the mucus layer of the GIT act as a defense against noxious substances, and pathogens including Clostridium difficile, Enterococcus faecium, Escherichia coli, Salmonella Typhimurium. Toxins, pathogens, and antibiotics perturb the commensal floral composition within the GIT. Imbalanced gut microbiota leads to dysbiosis, manifested as diseases ranging from obesity, diabetes, and cancer to reduced lifespan. Among the bacteria present in the gut microbiome, the most beneficial are those representing Firmicutes and Bacteroidetes. Recent studies have revealed the emergence of a novel biotherapeutic agent, Akkermansia, which is instrumental in regaining eubiosis and conferring various health benefits.

Diet, Gut Microbiota and COVID-19

Worldwide, millions of individuals have been affected by the prevailing SARS-CoV-2. Therefore, a robust immune system remains indispensable, as an immunocompromised host status has proven to be fatal. In the absence of any specific antiviral drug/vaccine, COVID-19 related drug repurposing along with various other non-pharmacological measures coupled with lockdown have been employed to combat this infection. In this context, a plant based rich fiber diet, which happens to be consumed by a majority of the Indian population, appears to be advantageous, as it replenishes the host gut microbiota with beneficial microbes thereby leading to a symbiotic association conferring various health benefits to the host including enhanced immunity. Further, implementation of the lockdown which has proven to be a good non-pharmacological measure, seems to have resulted in consumption of home cooked healthy diet, thereby enriching the beneficial microflora in the gut, which might have resulted in better prognosis of COVID-19 patients in India in comparison to that observed in the western countries.

Genetics, Transcriptomics and Meta-Taxonomics in Visceral Leishmaniasis

Visceral leishmaniasis (VL) caused by parasites of the Leishmania donovani complex can be fatal in susceptible individuals. Understanding the interactions between host and pathogen is one way to obtain leads to develop better drugs and for vaccine development. In recent years multiple omics-based approaches have assisted researchers to gain a more global picture of this interaction in leishmaniasis. Here we review results from studies using three omics-based approaches to study VL caused by L. donovani in India: (i) chip-based analysis of single nucleotide variants in the first genome-wide association study of host genetic risk factors for VL, followed by analysis of epitope binding to HLA DRB1 risk versus protective alleles; (ii) transcriptional profiling demonstrating pathways important in Amphotericin B treated compared to active VL cases, including demonstration that anti-interleukin-10 unleashes a storm of chemokines and cytokines in whole blood responses to soluble leishmania antigen in active cases; and (iii) a meta-taxonomic approach based on sequencing amplicons derived from regions of 16S ribosomal RNA (16S rRNA) and 18S rRNA genes that allowed us to determine composition of both prokaryotic and eukaryotic gut microflora in VL cases compared to endemic controls. Overall, our omics-based approaches demonstrate that global analyses of genetic risk factors, host responses to infection, and the interaction between host, parasite and the microbiome can point to the most critical factors that determine the outcome of infection.

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.

Metagenomic analysis of gut microbiome and resistome of diarrheal fecal samples from Kolkata, India, reveals the core and variable microbiota including signatures of microbial dark matter

BACKGROUND

Metagenomic analysis of the gut microbiome and resistome is instrumental for understanding the dynamics of diarrheal pathogenesis and antimicrobial resistance transmission (AMR). Metagenomic sequencing of 20 diarrheal fecal samples from Kolkata was conducted to understand the core and variable gut microbiota. Five of these samples were used for resistome analysis. The pilot study was conducted to determine a microbiota signature and the source of antimicrobial resistance genes (ARGs) in the diarrheal gut.

RESULTS

16S rRNA amplicon sequencing was performed using Illumina MiSeq platform and analysed using the MGnify pipeline. The Genome Taxonomy Database (GTDB-Tk) was used for bacterial taxonomic identification. Diarrheal etiology was determined by culture method. Phylum Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria were consistently present in 20 samples. Firmicutes was the most abundant phylum in 11 samples. The Bacteroidetes/Firmicutes ratio was less than 1 in 18 samples. 584 genera were observed. 18 of these were present in all the 20 samples. Proteobacteria was the dominant phylum in 6 samples associated with Vibrio cholerae infection. Conservation of operational taxonomic units (OTUs) among all the samples indicated the existence of a core microbiome. Asymptomatic carriage of pathogens like Vibrio cholerae and Helicobacter pylori was found. Signature of Candidate phyla or "microbial dark matter" occurred. Significant correlation of relative abundance of bacterial families of commensals and pathogens were found. Whole-genome sequencing (WGS) on Illumina MiSeq system and assembly of raw reads using metaSPAdes v3.9.1 was performed to study the resistome of 5 samples. ABRicate was used to assign ARG function. 491 resistance determinants were identified. In 80% of the samples tetracycline resistance was the most abundant resistance determinant. High abundance of ARGs against β-lactams, aminoglycosides, quinolones and macrolides was found. Eschericia sp. was the major contributor of ARGs.

CONCLUSIONS

This is the first comparative study of the gut microbiome associated with different diarrheal pathogens. It presents the first catalogue of different bacterial taxa representing the core and variable microbiome in acute diarrheal patients. The study helped to define a trend in the gut microbiota signature associated with diarrhea and revealed which ARGs are abundantly present and the metagenome-assembled genomes (MAGs) contributing to AMR.

Human Gut Microbiota and Mental Health: Advancements and Challenges in Microbe-Based Therapeutic Interventions

Gut microbes play prime role in human health and have shown to exert their influence on various physiological responses including neurological functions. Growing evidences in recent years have indicated a key role of gut microbiota in contributing to mental health. The connection between gut and brain is modulated by microbes via neural, neuroendocrinal and metabolic pathways that are mediated through various neurotransmitters and their precursors, hormones, cytokines and bioactive metabolites. Impaired functioning of this connection can lead to manifestation of mental disorders. Around 1 billion of the world population is reported to suffer from emotional, psychological and neurological imbalances, substance use disorders and cognitive, psychosocial and intellectual disabilities. Thus, it becomes imperative to understand the role of gut microbes in mental disorders. Since variations occur in the conditions associated with different mental disorders and some of them have overlapping symptoms, it becomes important to have a holistic understanding of gut dysbiosis in these disorders. In this review, we consolidate the recent data on alterations in the gut microbes and its consequences in various neurological, psychological and neurodegenerative disorders. Further, considering these evidences, several studies have been undertaken to specifically target the gut microbiota through different therapeutic interventions including administration of live microbes (psychobiotics) to treat mental health disorders and/or their symptoms. We review these studies and propose that an integrative and personalized approach, where combinations of microbe-based therapeutic interventions to modulate gut microbes and in-use psychological treatment practices can be integrated and based on patient's gut microbiome can be potentially adopted for effective treatment of the mental disorders.

Gut, oral and skin microbiome of Indian patrilineal families reveal perceptible association with age

The human microbiome plays a key role in maintaining host homeostasis and is influenced by age, geography, diet, and other factors. Traditionally, India has an established convention of extended family arrangements wherein three or more generations, bound by genetic relatedness, stay in the same household. In the present study, we have utilized this unique family arrangement to understand the association of age with the microbiome. We characterized stool, oral and skin microbiome of 54 healthy individuals from six joint families by 16S rRNA gene-based metagenomics. In total, 69 (1.03%), 293 (2.68%) and 190 (8.66%) differentially abundant OTUs were detected across three generations in the gut, skin and oral microbiome, respectively. Age-associated changes in the gut and oral microbiome of patrilineal families showed positive correlations in the abundance of phyla Proteobacteria and Fusobacteria, respectively. Genera Treponema and Fusobacterium showed a positive correlation with age while Granulicatella and Streptococcus showed a negative correlation with age in the oral microbiome. Members of genus Prevotella illustrated high abundance and prevalence as a core OTUs in the gut and oral microbiome. In conclusion, this study highlights that precise and perceptible association of age with microbiome can be drawn when other causal factors are kept constant.

Interplay of Human Gut Microbiome in Health and Wellness

The gut microbiome analysis, with specific interest on their direct impact towards the human health, is currently revolutionizing the unexplored frontiers of the pathogenesis and wellness. Although in-depth investigations of gut microbiome, 'the Black Boxes', complexities and functionalities are yet at its infancy, profound evidences are being reported for their concurrent involvement in disease etiology and its treatment. Interestingly, studies from the 'minimal murine' (Oligo-MM12), 'humanized' microbiota gnotobiotic mice models and patient samples, combined with multi-omics and cell biology approaches, have been revealing the implications of these findings in the treatment of gut dysbiosis associated diseases. Nonetheless, due to the inherent heterogeneity of the gut commensals and their unified co-existence with opportunistic pathobionts, it is utmost essential to highlight their functionalities in 'good or bad' gut in human wellness. We have specifically reviewed dietary lifestyle and infectious diseases linked with the gut bacterial consortia to delineate the ecobiotic approaches towards their treatment. This notably includes gut mucosal immunity mediated diseases such as Tuberculosis, IBD, CDI, Type 2 Diabetes, etc. Alongside of each dysbiosis, we have described the current therapeutic advancements of the pre- and probiotics derived from human microbiome studies to restore gut microbial homeostasis. With a continuous running debate on the role of microbiota in above mentioned diseases, we have collected numerous scientific evidences highlighting a previously unanticipated complex involvement of gut microbiome in the potential of human health.

Meta-taxonomic analysis of prokaryotic and eukaryotic gut flora in stool samples from visceral leishmaniasis cases and endemic controls in Bihar State India

Visceral leishmaniasis (VL) caused by Leishmania donovani remains of public health concern in rural India. Those at risk of VL are also at risk of other neglected tropical diseases (NTDs) including soil transmitted helminths. Intestinal helminths are potent regulators of host immune responses sometimes mediated through cross-talk with gut microbiota. We evaluate a meta-taxonomic approach to determine the composition of prokaryotic and eukaryotic gut microflora using amplicon-based sequencing of 16S ribosomal RNA (16S rRNA) and 18S rRNA gene regions. The most abundant bacterial taxa identified in faecal samples from Bihar State India were Prevotella (37.1%), Faecalibacterium (11.3%), Escherichia-Shigella (9.1%), Alloprevotella (4.5%), Bacteroides (4.1%), Ruminococcaceae UCG-002 (1.6%), and Bifidobacterium (1.5%). Eukaryotic taxa identified (excluding plant genera) included Blastocystis (57.9%; Order: Stramenopiles), Dientamoeba (12.1%; Family: Tritrichomonadea), Pentatrichomonas (10.1%; Family: Trichomonodea), Entamoeba (3.5%; Family: Entamoebida), Ascaridida (0.8%; Family: Chromodorea; concordant with Ascaris by microscopy), Rhabditida (0.8%; Family: Chromodorea; concordant with Strongyloides), and Cyclophyllidea (0.2%; Order: Eucestoda; concordant with Hymenolepis). Overall alpha (Shannon's, Faith's and Pielou's indices) and beta (Bray-Curtis dissimilarity statistic; weighted UniFrac distances) diversity of taxa did not differ significantly by age, sex, geographic subdistrict, or VL case (N = 23) versus endemic control (EC; N = 23) status. However, taxon-specific associations occurred: (i) Ruminococcaceae UCG- 014 and Gastranaerophilales_uncultured bacterium were enriched in EC compared to VL cases; (ii) Pentatrichomonas was more abundant in VL cases than in EC, whereas the reverse occurred for Entamoeba. Across the cohort, high Escherichia-Shigella was associated with reduced bacterial diversity, while high Blastocystis was associated with high bacterial diversity and low Escherichia-Shigella. Individuals with high Blastocystis had low Bacteroidaceae and high Clostridiales vadin BB60 whereas the reverse held true for low Blastocystis. This scoping study provides useful baseline data upon which to develop a broader analysis of pathogenic enteric microflora and their influence on gut microbial health and NTDs generally.