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Darra A, Singh V, Jena A, Popli P, Nada R, Gupta P, Bhadada SK, Singh AK, Sharma V, Bhattacharya A, Agrawal A, Dutta U. Hyperglycemia is associated with duodenal dysbiosis and altered duodenal microenvironment. Sci Rep 2023; 13:11038. [PMID: 37419941 PMCID: PMC10329043 DOI: 10.1038/s41598-023-37720-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 06/26/2023] [Indexed: 07/09/2023] Open
Abstract
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.
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Affiliation(s)
- Aarti Darra
- CSIR- Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vandana Singh
- CSIR- Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anuraag Jena
- Department of Gastroenterology, Post Graduate Institute of Medical Education and Research, Sector-12, Chandigarh, 160012, India
| | - Priyanka Popli
- Department of Gastroenterology, Post Graduate Institute of Medical Education and Research, Sector-12, Chandigarh, 160012, India
| | - Ritambhra Nada
- Department of Histopathology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Pankaj Gupta
- Department of Radiodiagnosis, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Sanjay Kumar Bhadada
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Anupam Kumar Singh
- Department of Gastroenterology, Post Graduate Institute of Medical Education and Research, Sector-12, Chandigarh, 160012, India
| | - Vishal Sharma
- Department of Gastroenterology, Post Graduate Institute of Medical Education and Research, Sector-12, Chandigarh, 160012, India
| | - Anish Bhattacharya
- Department of Nuclear Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Anurag Agrawal
- CSIR- Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Usha Dutta
- Department of Gastroenterology, Post Graduate Institute of Medical Education and Research, Sector-12, Chandigarh, 160012, India.
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D'Aloisio LD, Shetty V, Ballal M, Gibson DL. Following the Indian Immigrant: adoption of westernization results in a western gut microbiome and an increased risk of inflammatory bowel diseases. FEMS Microbiol Ecol 2022; 98:6825449. [PMID: 36370451 DOI: 10.1093/femsec/fiac133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/01/2022] [Accepted: 11/10/2022] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- Leah D D'Aloisio
- Department of Biology, University of British Columbia- Okanagan Campus, V1V 1V7 Kelowna, Canada
| | - Vignesh Shetty
- Enteric Disease Division, Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, 576104 Manipal, India.,Department of Medicine, University of Cambridge, CB2 2QQ Cambridge, United Kingdom
| | - Mamatha Ballal
- Enteric Disease Division, Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, 576104 Manipal, India
| | - Deanna L Gibson
- Department of Biology, University of British Columbia- Okanagan Campus, V1V 1V7 Kelowna, Canada.,Department of Medicine, University of British Columbia- Okanagan Campus, V1V 1V7 Kelowna, Canada
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3
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Hazarika P, Chattopadhyay I, Umpo M, Choudhury Y, Sharma I. Elucidating the gut microbiome alterations of tribal community of Arunachal Pradesh: perspectives on their lifestyle or food habits. Sci Rep 2022; 12:18296. [PMID: 36316382 PMCID: PMC9622709 DOI: 10.1038/s41598-022-23124-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 10/25/2022] [Indexed: 11/07/2022] Open
Abstract
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.
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Affiliation(s)
- Parijat Hazarika
- grid.411460.60000 0004 1767 4538Department of Microbiology, Assam University, Silchar, 788011 India
| | - Indranil Chattopadhyay
- grid.448768.10000 0004 1772 7660Department of Life Sciences, Central University of Tamil Nadu, 610 101, Thiruvarur, India
| | - Mika Umpo
- Department of Microbiology, Tomo Riba Institute of Health and Medical Sciences, Nahrlagun, 791110 India
| | - Yashmin Choudhury
- grid.411460.60000 0004 1767 4538Department of Biotechnology, Assam University, Silchar, 788011 India
| | - Indu Sharma
- grid.411460.60000 0004 1767 4538Department of Microbiology, Assam University, Silchar, 788011 India
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4
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Nadiger N, Anantharamu S, Priyanka CN, Vidal-Puig A, Mukhopadhyay A. Unique attributes of obesity in India: A narrative review. OBESITY MEDICINE 2022; 35:100454. [PMID: 38572212 PMCID: PMC7615800 DOI: 10.1016/j.obmed.2022.100454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
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.
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Affiliation(s)
- Nikhil Nadiger
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, Koramangala, Bangalore, India
| | - Sahana Anantharamu
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, Koramangala, Bangalore, India
| | - CN Priyanka
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, Koramangala, Bangalore, India
| | - Antonio Vidal-Puig
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, MDU MRC, Addenbrooke's Hospital, Cambridge, UK
| | - Arpita Mukhopadhyay
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, Koramangala, Bangalore, India
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Kalia VC, Gong C, Shanmugam R, Lin H, Zhang L, Lee JK. The Emerging Biotherapeutic Agent: Akkermansia. Indian J Microbiol 2021; 62:1-10. [PMID: 34931096 PMCID: PMC8674859 DOI: 10.1007/s12088-021-00993-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/02/2021] [Indexed: 12/17/2022] Open
Abstract
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.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Chunjie Gong
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, 430068 People’s Republic of China
| | - Ramasamy Shanmugam
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Hui Lin
- College of Life Sciences, Gutian Edible Fungi Research Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002 People’s Republic of China
| | - Liaoyuan Zhang
- College of Life Sciences, Gutian Edible Fungi Research Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002 People’s Republic of China
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
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6
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Rishi P, Thakur K, Vij S, Rishi L, Singh A, Kaur IP, Patel SKS, Lee JK, Kalia VC. Diet, Gut Microbiota and COVID-19. Indian J Microbiol 2020; 60:420-429. [PMID: 33012868 PMCID: PMC7521193 DOI: 10.1007/s12088-020-00908-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022] Open
Abstract
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.
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Affiliation(s)
- Praveen Rishi
- Department of Microbiology, Panjab University, BMS Block I, South Campus, Chandigarh, India
| | - Khemraj Thakur
- Department of Microbiology, Panjab University, BMS Block I, South Campus, Chandigarh, India
| | - Shania Vij
- Department of Microbiology, Panjab University, BMS Block I, South Campus, Chandigarh, India
| | | | - Aagamjit Singh
- All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Indu Pal Kaur
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Sanjay K. S. Patel
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Vipin C. Kalia
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
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7
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Blackwell JM, Fakiola M, Singh OP. Genetics, Transcriptomics and Meta-Taxonomics in Visceral Leishmaniasis. Front Cell Infect Microbiol 2020; 10:590888. [PMID: 33324576 PMCID: PMC7723821 DOI: 10.3389/fcimb.2020.590888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/20/2020] [Indexed: 12/26/2022] Open
Abstract
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.
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Affiliation(s)
- Jenefer M. Blackwell
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
| | | | - Om Prakash Singh
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
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8
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Monaghan TM, Sloan TJ, Stockdale SR, Blanchard AM, Emes RD, Wilcox M, Biswas R, Nashine R, Manke S, Gandhi J, Jain P, Bhotmange S, Ambalkar S, Satav A, Draper LA, Hill C, Kashyap RS. Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome. Gut Microbes 2020; 12:1752605. [PMID: 32459982 PMCID: PMC7781581 DOI: 10.1080/19490976.2020.1752605] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
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 3rd 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.
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Affiliation(s)
- Tanya M. Monaghan
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK,Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK,CONTACT Tanya M. Monaghan NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Tim J. Sloan
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Adam M. Blanchard
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Richard D. Emes
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK,Advanced Data Analysis Centre, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Mark Wilcox
- Leeds Teaching Hospitals NHS Trust and University of Leeds, UK
| | - Rima Biswas
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Rupam Nashine
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Sonali Manke
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Jinal Gandhi
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Pratishtha Jain
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Shrejal Bhotmange
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Shrikant Ambalkar
- Department of Clinical Microbiology and Infection, King’s Mill Hospital, Sherwood Forest Hospitals NHS Trust, Sutton in Ashfield, UK
| | | | | | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Rajpal Singh Kashyap
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India,Rajpal Singh Kashyap Biochemistry Research Centre, Central India Institute of Medical Sciences, 88/2 Bajaj Nagar, Nagpur, Maharashtra, India
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9
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De R, Mukhopadhyay AK, Dutta S. 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. Gut Pathog 2020; 12:32. [PMID: 32655699 PMCID: PMC7339541 DOI: 10.1186/s13099-020-00371-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
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.
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Affiliation(s)
- Rituparna De
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Shanta Dutta
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India
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10
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Human Gut Microbiota and Mental Health: Advancements and Challenges in Microbe-Based Therapeutic Interventions. Indian J Microbiol 2020; 60:405-419. [PMID: 33087991 DOI: 10.1007/s12088-020-00898-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/26/2020] [Indexed: 02/07/2023] Open
Abstract
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.
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11
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Chaudhari DS, Dhotre DP, Agarwal DM, Gaike AH, Bhalerao D, Jadhav P, Mongad D, Lubree H, Sinkar VP, Patil UK, Salvi S, Bavdekar A, Juvekar SK, Shouche YS. Gut, oral and skin microbiome of Indian patrilineal families reveal perceptible association with age. Sci Rep 2020; 10:5685. [PMID: 32231240 PMCID: PMC7105498 DOI: 10.1038/s41598-020-62195-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 03/05/2020] [Indexed: 01/13/2023] Open
Abstract
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.
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Affiliation(s)
- Diptaraj S Chaudhari
- National Centre for Microbial Resource, National Centre for Cell Science, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan, Pune, India.,R. C. Patel ASC College, Shirpur, Dhule, India
| | - Dhiraj P Dhotre
- National Centre for Microbial Resource, National Centre for Cell Science, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan, Pune, India.
| | - Dhiraj M Agarwal
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune, India
| | - Akshay H Gaike
- National Centre for Microbial Resource, National Centre for Cell Science, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan, Pune, India.,Vadu Rural Health Program, KEM Hospital Research Centre, Pune, India
| | - Devika Bhalerao
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune, India
| | - Parmeshwar Jadhav
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune, India
| | - Dattatray Mongad
- National Centre for Microbial Resource, National Centre for Cell Science, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan, Pune, India
| | - Himangi Lubree
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune, India
| | - Vilas P Sinkar
- National Centre for Microbial Resource, National Centre for Cell Science, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan, Pune, India
| | - Ulhas K Patil
- R. C. Patel ASC College, Shirpur, Dhule, India.,Department of Microbiology, Government Institute of Science, Aurangabad, India
| | - Sundeep Salvi
- Chest Research Foundation, Marigold Premises, Survey no 15, Kalyaninagar, Pune, India
| | - Ashish Bavdekar
- KEM Hospital, Pediatrics Department, KEM Hospital, Rasta Peth, Pune, India
| | - Sanjay K Juvekar
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune, India
| | - Yogesh S Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan, Pune, India.
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12
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Singhvi N, Gupta V, Gaur M, Sharma V, Puri A, Singh Y, Dubey GP, Lal R. Interplay of Human Gut Microbiome in Health and Wellness. Indian J Microbiol 2020; 60:26-36. [PMID: 32089571 PMCID: PMC7000599 DOI: 10.1007/s12088-019-00825-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 08/30/2019] [Indexed: 12/19/2022] Open
Abstract
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.
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Affiliation(s)
- Nirjara Singhvi
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Vipin Gupta
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Mohita Gaur
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Vishal Sharma
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Akshita Puri
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Gyanendra P. Dubey
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 75015 Paris, France
| | - Rup Lal
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003 India
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Lappan R, Classon C, Kumar S, Singh OP, de Almeida RV, Chakravarty J, Kumari P, Kansal S, Sundar S, Blackwell JM. Meta-taxonomic analysis of prokaryotic and eukaryotic gut flora in stool samples from visceral leishmaniasis cases and endemic controls in Bihar State India. PLoS Negl Trop Dis 2019; 13:e0007444. [PMID: 31490933 PMCID: PMC6750594 DOI: 10.1371/journal.pntd.0007444] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/18/2019] [Accepted: 08/12/2019] [Indexed: 12/31/2022] Open
Abstract
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.
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Affiliation(s)
- Rachael Lappan
- Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Cajsa Classon
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Shashi Kumar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Om Prakash Singh
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Ricardo V. de Almeida
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Jaya Chakravarty
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Poonam Kumari
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Sangeeta Kansal
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Shyam Sundar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Jenefer M. Blackwell
- Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia, Australia
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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