Publications by authors named "Bhabatosh Das"

65 Publications

TLR22-mediated activation of TNF-α-caspase-1/IL-1β inflammatory axis leads to apoptosis of Aeromonas hydrophila-infected macrophages.

Mol Immunol 2021 Jul 6;137:114-123. Epub 2021 Jul 6.

Immunobiology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India; Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India. Electronic address:

Toll-like receptors (TLRs) represent first line of host defence against microbes. Amongst different TLRs, TLR22 is exclusively expressed in non-mammalian vertebrates, including fish. The precise role of TLR22 in fish-immunity remains abstruse. Herein, we used headkidney macrophages (HKM) from Clarias gariepinus and deciphered its role in fish-immunity. Highest tlr22 expression was observed in the immunocompetent organ - headkidney; nonetheless expression in other tissues suggests its possible involvement in non-immune sites also. Aeromonas hydrophila infection up-regulates tlr22 expression in HKM. Our RNAi based study suggested TLR22 restricts intracellular survival of A. hydrophila. Inhibitor and RNAi studies further implicated TLR22 induces pro-inflammatory cytokines TNF-α and IL-1β. We observed heightened caspase-1 activity and our results suggest the role of TLR22 in activating TNF-α/caspase-1/IL-1β cascade leading to caspase-3 mediated apoptosis of A. hydrophila-infected HKM. We conclude, TLR22 plays critical role in immune-surveillance and triggers pro-inflammatory cytokines leading to caspase mediated HKM apoptosis and pathogen clearance.
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http://dx.doi.org/10.1016/j.molimm.2021.06.025DOI Listing
July 2021

Laboratory evaluation of the rapid diagnostic tests for the detection of Vibrio cholerae O1 using diarrheal samples.

PLoS Negl Trop Dis 2021 Jun 15;15(6):e0009521. Epub 2021 Jun 15.

Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India.

Background: Cholera, an acute diarrheal disease is a major public health problem in many developing countries. Several rapid diagnostic tests (RDT) are available for the detection of cholera, but their efficacies are not compared in an endemic setting. In this study, we have compared the specificity and sensitivity of three RDT kits for the detection of Vibrio cholerae O1 and compared their efficiency with culture and polymerase chain reaction (PCR) methods.

Methods: Five hundred six diarrheal stool samples collected from patients from two different hospitals in Kolkata, India were tested using SD Bioline Cholera, SMART-II Cholera O1 and Crystal-VC RDT kits. All the stool samples were screened for the presence of V. cholerae by direct and enrichment culture methods. Stool DNA-based PCR assay was made to target the cholera toxin (ctxAB) and O1 somatic antigen (rfb) encoding genes. Statistical evaluation of the RDTs has been made using STATA software with stool culture and PCR results as the gold standards. The Bayesian latent class model (LCM) was used to evaluate the diagnostic tests in the absence of the gold standard.

Results: Involving culture technique as gold standard, the sensitivity and specificity of the cholera RDT kits in the direct testing of stools was highest with SAMRT-II (86.1%) and SD-Cholera (94.4%), respectively. The DNA based PCR assays gave very high sensitivity (98.4%) but the specificity was comparatively low (75.3%). After enrichment, the high sensitivity and specificity was detected with SAMRT-II (78.8%) and SD-Cholera (99.1%), respectively. Considering PCR as the gold standard, the sensitivity and specificity of the RDTs remained between 52.3-58.2% and 92.3-96.8%, respectively. In the LCM, the sensitivity of direct and enrichment testing was high in SAMRT-II (88% and 92%, respectively), but the specificity was high in SD cholera for both the methods (97% and 100%, respectively). The sensitivity/specificity of RDTs and direct culture have also been analyzed considering the age, gender and diarrheal disease severity of the patients.

Conclusion: Overall, the performance of the RDT kits remained almost similar in terms of specificity and sensitivity. Performance of PCR was superior to the antibody-based RDTs. The RTDs are very useful in identifying cholera cases during outbreak/epidemic situations and for making them as a point-of-care (POC) testing tool needs more improvement.
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http://dx.doi.org/10.1371/journal.pntd.0009521DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8232436PMC
June 2021

The Vaginal Microbial Signatures of Preterm Birth Delivery in Indian Women.

Front Cell Infect Microbiol 2021 13;11:622474. Epub 2021 May 13.

Molecular Genetics Laboratory, Translational Health Science and Technology Institute, National Capital Region (NCR) Biotech Science Cluster, Faridabad, India.

Background: The incidence of preterm birth (PTB) in India is around 13%. Specific bacterial communities or individual taxon living in the vaginal milieu of pregnant women is a potential risk factor for PTB and may play an important role in its pathophysiology. Besides, bacterial taxa associated with PTB vary across populations.

Objective: Conduct a comparative analysis of vaginal microbiome composition and microbial genomic repertoires of women who enrolled in the Interdisciplinary Group for Advanced Research on Birth Outcomes - A DBT India Initiative (GARBH-Ini) pregnancy cohort to identify bacterial taxa associated with term birth (TB) and PTB in Indian women.

Methods: Vaginal swabs were collected during all three trimesters from 38 pregnant Indian women who delivered spontaneous term (n=20) and preterm (n=18) neonates. Paired-end sequencing of V3-V4 region of 16S rRNA gene was performed using the metagenomic DNA isolated from vaginal swabs (n=115). Whole genome sequencing of bacterial species associated with birth outcomes was carried out by shotgun method. species were grown anaerobically in the De Man, Rogosa and Sharpe (MRS) agar culture medium for isolation of genomic DNA and whole genome sequencing.

Results: Vaginal microbiome of both term and preterm samples reveals similar alpha diversity indices. However, significantly higher abundance of (p-value <0.02), sp (p-value0.05), (p-value= 0.01) and (p-value0.0001) were identified in preterm samples whereas higher abundance of (p-value =0.010) was observed in term samples by Wilcoxon rank-sum test. The relative abundance of , and sp. were found to be significantly different over time between term and preterm mothers. Analyses of the representative genomes of and indicate presence of secretory transcriptional regulator and several ribosomally synthesized antimicrobial peptides correlated with anti-inflammatory condition in the vagina. These findings indicate protective role of and in reducing the risk of PTB.

Conclusion: Our findings indicate that the dominance of specific species and few other facultative anaerobes are associated with birth outcomes.
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http://dx.doi.org/10.3389/fcimb.2021.622474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8169982PMC
July 2021

Low Abundance in the Lower Gut Microbiota Is Associated With -Related Gastric Ulcer and Gastric Cancer.

Front Microbiol 2021 26;12:631140. Epub 2021 Feb 26.

Rajiv Gandhi Centre for Biotechnology, Trivandrum, India.

infection in stomach leads to gastric cancer, gastric ulcer, and duodenal ulcer. More than 1 million people die each year due to these diseases, but why most -infected individuals remain asymptomatic while a certain proportion develops such severe gastric diseases remained an enigma. Several studies indicated that gastric and intestinal microbiota may play a critical role in the development of the -associated diseases. However, no specific microbe in the gastric or intestinal microbiota has been clearly linked to infection and related gastric diseases. Here, we studied infection, its virulence genes, the intestinal microbiota, and the clinical status of Trivandrum residents ( = 375) in southwestern India by standard culture, PCR genotype, Sanger sequencing, and microbiome analyses using Illumina Miseq and Nanopore GridION. Our analyses revealed that gastric colonization by virulent strains (+) is necessary but not sufficient for developing these diseases. Conversely, distinct microbial pools exist in the lower gut of the -infected vs. -non-infected individuals. (belonging to the phylum Actinobacteria) and (belonging to the phylum Bacteroidetes) were present in lower relative abundance for the + group than the - group ( < 0.05). On the contrary, for the + group, genus (bacteria belonging to the phylum Firmicutes) and genus (bacteria belonging to the phylum Bacteroidetes) were present in higher abundance compared to the group ( < 0.05). Notably, those who carried in the stomach and had developed aggressive gastric diseases also had extremely low relative abundance ( < 0.05) of several species (e.g., , ) in the lower gut suggesting a protective role of . Our results show the link between lower gastrointestinal microbes and upper gastrointestinal diseases. Moreover, the results are important for developing effective probiotic and early prognosis of severe gastric diseases.
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http://dx.doi.org/10.3389/fmicb.2021.631140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953064PMC
February 2021

Spatiotemporal persistence of multiple, diverse clades and toxins of Corynebacterium diphtheriae.

Nat Commun 2021 03 8;12(1):1500. Epub 2021 Mar 8.

Department of Medicine, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK.

Diphtheria is a respiratory disease caused by the bacterium Corynebacterium diphtheriae. Although the development of a toxin-based vaccine in the 1930s has allowed a high level of control over the disease, cases have increased in recent years. Here, we describe the genomic variation of 502 C. diphtheriae isolates across 16 countries and territories over 122 years. We generate a core gene phylogeny and determine the presence of antimicrobial resistance genes and variation within the tox gene of 291 tox isolates. Numerous, highly diverse clusters of C. diphtheriae are observed across the phylogeny, each containing isolates from multiple countries, regions and time of isolation. The number of antimicrobial resistance genes, as well as the breadth of antibiotic resistance, is substantially greater in the last decade than ever before. We identified and analysed 18 tox gene variants, with mutations estimated to be of medium to high structural impact.
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http://dx.doi.org/10.1038/s41467-021-21870-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7940655PMC
March 2021

Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark.

Genome Med 2021 Mar 3;13(1):36. Epub 2021 Mar 3.

TCS Research, Tata Consultancy Services Limited, 54B Hadapsar Industrial Estate, Pune, 411013, India.

Background: Recent studies have indicated an association of gut microbiota and microbial metabolites with type 2 diabetes mellitus (T2D). However, large-scale investigation of the gut microbiota of "prediabetic" (PD) subjects has not been reported. Identifying robust gut microbiome signatures of prediabetes and characterizing early prediabetic stages is important for the understanding of disease development and could be crucial in early diagnosis and prevention.

Methods: The current study performed amplification and sequencing on the variable regions (V1-V5) of the 16S rRNA genes to profile and compare gut microbiota of prediabetic individuals (N = 262) with normoglycemic individuals (N = 275) from two cohorts in India and Denmark. Similarly, fasting serum inflammatory biomarkers were profiled from the study participants.

Results: After correcting for strong country-specific cohort effect, 16 operational taxonomic units (OTUs) including members from the genera Prevotella9, Phascolarctobacterium, Barnesiella, Flavonifractor, Tyzzerella_4, Bacteroides, Faecalibacterium, and Agathobacter were identified as enriched in normoglycaemic subjects with respect to the subjects with prediabetes using a negative binomial Wald test. We also identified 144 OTUs enriched in the prediabetic subjects, which included members from the genera Megasphaera, Streptococcus, Prevotella9, Alistipes, Mitsuokella, Escherichia/Shigella, Prevotella2, Vibrio, Lactobacillus, Alloprevotella, Rhodococcus, and Klebsiella. Comparative analyses of relative abundance of bacterial taxa revealed that the Streptococcus, Escherichia/Shigella, Prevotella2, Vibrio, and Alloprevotella OTUs exhibited more than fourfold enrichment in the gut microbiota of prediabetic subjects. When considering subjects from the two geographies separately, we were able to identify additional gut microbiome signatures of prediabetes. The study reports a probable association of Megasphaera OTU(s) with impaired glucose tolerance, which is significantly pronounced in Indian subjects. While the overall results confirm a state of proinflammation as early as in prediabetes, the Indian cohort exhibited a characteristic pattern of abundance of inflammatory markers indicating low-grade intestinal inflammation at an overall population level, irrespective of glycemic status.

Conclusions: The results present trans-ethnic gut microbiome and inflammation signatures associated with prediabetes, in Indian and Danish populations. The identified associations may be explored further as potential early indicators for individuals at risk of dysglycemia.
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http://dx.doi.org/10.1186/s13073-021-00851-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7931552PMC
March 2021

Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India.

Genome Med 2021 Mar 3;13(1):37. Epub 2021 Mar 3.

Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen N, Denmark.

Background: Type 2 diabetes (T2D), a multifactorial disease influenced by host genetics and environmental factors, is the most common endocrine disease. Several studies have shown that the gut microbiota as a close-up environmental mediator influences host physiology including metabolism. The aim of the present study is to examine the compositional and functional potential of the gut microbiota across individuals from Denmark and South India with a focus on T2D. Many earlier studies have investigated the microbiome aspects of T2D, and it has also been anticipated that such microbial associations would be dependent on diet and ethnic origin. However, there has been no large scale trans-ethnic microbiome study earlier in this direction aimed at evaluating any "universal" microbiome signature of T2D.

Methods: 16S ribosomal RNA gene amplicon sequencing was performed on stool samples from 279 Danish and 294 Indian study participants. Any differences between the gut microbiota of both populations were explored using diversity measures and negative binomial Wald tests. Study samples were stratified to discover global and country-specific microbial signatures for T2D and treatment with the anti-hyperglycemic drug, metformin. To identify taxonomical and functional signatures of the gut microbiota for T2D and metformin treatment, we used alpha and beta diversity measures and differential abundances analysis, comparing metformin-naive T2D patients, metformin-treated T2D patients, and normoglycemic individuals.

Results: Overall, the gut microbial communities of Danes and Indians are compositionally very different. By analyzing the combined study materials, we identify microbial taxonomic and functional signatures for T2D and metformin treatment. T2D patients have an increased relative abundance of two operational taxonomic units (OTUs) from the Lachnospiraceae family, and a decreased abundance of Subdoligranulum and Butyricicoccus. Studying each population per se, we identified T2D-related microbial changes at the taxonomic level within the Danish population only. Alpha diversity indices show that there is no significant difference between normoglycemic individuals and metformin-naive T2D patients, whereas microbial richness is significantly decreased in metformin-treated T2D patients compared to metformin-naive T2D patients and normoglycemic individuals. Enrichment of two OTUs from Bacteroides and depletion of Faecalibacterium constitute a trans-ethnic signature of metformin treatment.

Conclusions: We demonstrate major compositional differences of the gut microbiota between Danish and South Indian individuals, some of which may relate to differences in ethnicity, lifestyle, and demography. By comparing metformin-naive T2D patients and normoglycemic individuals, we identify T2D-related microbiota changes in the Danish and Indian study samples. In the present trans-ethnic study, we confirm that metformin changes the taxonomic profile and functional potential of the gut microbiota.
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http://dx.doi.org/10.1186/s13073-021-00856-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7931542PMC
March 2021

(p)ppGpp Metabolism and Antimicrobial Resistance in Bacterial Pathogens.

Front Microbiol 2020 9;11:563944. Epub 2020 Oct 9.

Infectious Diseases and Immunology Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India.

Single cell microorganisms including pathogens relentlessly face myriads of physicochemical stresses in their living environment. In order to survive and multiply under such unfavorable conditions, microbes have evolved with complex genetic networks, which allow them to sense and respond against these stresses. Stringent response is one such adaptive mechanism where bacteria can survive under nutrient starvation and other related stresses. The effector molecules for the stringent response are guanosine-5'-triphosphate 3'-diphosphate (pppGpp) and guanosine-3', 5'-bis(diphosphate) (ppGpp), together called (p)ppGpp. These effector molecules are now emerging as master regulators for several physiological processes of bacteria including virulence, persistence, and antimicrobial resistance. (p)ppGpp may work independently or along with its cofactor DksA to modulate the activities of its prime target RNA polymerase and other metabolic enzymes, which are involved in different biosynthetic pathways. Enzymes involved in (p)ppGpp metabolisms are ubiquitously present in bacteria and categorized them into three classes, i.e., canonical (p)ppGpp synthetase (RelA), (p)ppGpp hydrolase/synthetase (SpoT/Rel/RSH), and small alarmone synthetases (SAS). While RelA gets activated in response to amino acid starvation, enzymes belonging to SpoT/Rel/RSH and SAS family can synthesize (p)ppGpp in response to glucose starvation and several other stress conditions. In this review, we will discuss about the current status of the following aspects: (i) diversity of (p)ppGpp biosynthetic enzymes among different bacterial species including enteropathogens, (ii) signals that modulate the activity of (p)ppGpp synthetase and hydrolase, (iii) effect of (p)ppGpp in the production of antibiotics, and (iv) role of (p)ppGpp in the emergence of antibiotic resistant pathogens. Emphasis has been given to the cholera pathogen due to its sophisticated and complex (p)ppGpp metabolic pathways, rapid mutational rate, and acquisition of antimicrobial resistance determinants through horizontal gene transfer. Finally, we discuss the prospect of (p)ppGpp metabolic enzymes as potential targets for developing antibiotic adjuvants and tackling persistence of infections.
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http://dx.doi.org/10.3389/fmicb.2020.563944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7581866PMC
October 2020

Vibrio Pathogenicity Island-1: The Master Determinant of Cholera Pathogenesis.

Front Cell Infect Microbiol 2020 6;10:561296. Epub 2020 Oct 6.

Translational Health Science and Technology Institute, Faridabad, India.

Cholera is an acute secretory diarrhoeal disease caused by the bacterium . The key determinants of cholera pathogenicity, cholera toxin (CT), and toxin co-regulated pilus (TCP) are part of the genome of two horizontally acquired Mobile Genetic Elements (MGEs), CTXΦ, and Vibrio pathogenicity island 1 (VPI-1), respectively. Besides, genome harbors several others MGEs that provide antimicrobial resistance, metabolic functions, and other fitness traits. VPI-1, one of the most well characterized genomic island (GI), deserved a special attention, because (i) it encodes many of the virulence factors that facilitate development of cholera (ii) it is essential for the acquisition of CTXΦ and production of CT, and (iii) it is crucial for colonization of in the host intestine. Nevertheless, VPI-1 is ubiquitously present in all the epidemic strains. Therefore, to understand the role of MGEs in the evolution of cholera pathogen from a natural aquatic habitat, it is important to understand the VPI-1 encoded functions, their acquisition and possible mode of dissemination. In this review, we have therefore discussed our present understanding of the different functions of VPI-1 those are associated with virulence, important for toxin production and essential for the disease development.
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http://dx.doi.org/10.3389/fcimb.2020.561296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7574455PMC
June 2021

Functional Insights Into the Role of in (p)ppGpp Metabolism of .

Front Microbiol 2020 29;11:564644. Epub 2020 Sep 29.

Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.

The stringent response, an adaptive response to nutrient limitation and exposure to xenobiotics in bacteria, is mediated by two intracellular signaling molecules, pppGpp and ppGpp, together called (p)ppGpp. The cellular level of (p)ppGpp in bacterial cells is controlled by the Rel/Spo family of proteins. In the cholera pathogen, , (p)ppGpp metabolism is regulated by the products of at least three genes , , and . In this study, we identify and characterize the function of the guanosine-5'-triphosphate 3'-diphosphate pyrophosphatase A (GppA) encoding gene of . Genomic analysis indicates that the locus is conserved in vibrios and organized as a bicistronic operon along with the gene. We engineered the genome of to develop different mutants devoid of GppA and/or other phosphate metabolic enzymes. Our findings indicate that in , GppA plays an important role in the conversion of pppGpp to ppGpp during amino acid deprivation but not during glucose starvation. Quantitative analyses of the transcript level reveal its differential expression pattern at different growth phases and starvation conditions. It has been observed that the GppA deficiency during amino acid starvation condition could be complemented by overexpressing the exopolyphosphatase coding gene of . By deletion analysis, we further demonstrate that the amino and carboxy terminal sequences flanking the Ppx-GppA motif of the GppA protein of are also important for its enzymatic function.
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http://dx.doi.org/10.3389/fmicb.2020.564644DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7552824PMC
September 2020

Molecular insights into the genome dynamics and interactions between core and acquired genomes of .

Proc Natl Acad Sci U S A 2020 09 1;117(38):23762-23773. Epub 2020 Sep 1.

Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad 121001, India;

Bacterial species are hosts to horizontally acquired mobile genetic elements (MGEs), which encode virulence, toxin, antimicrobial resistance, and other metabolic functions. The bipartite genome of harbors sporadic and conserved MGEs that contribute in the disease development and survival of the pathogens. For a comprehensive understanding of dynamics of MGEs in the bacterial genome, we engineered the genome of and examined in vitro and in vivo stability of genomic islands (GIs), integrative conjugative elements (ICEs), and prophages. Recombinant vectors carrying the integration module of these GIs, ICE and CTXΦ, helped us to understand the efficiency of integrations of MGEs in the chromosome. We have deleted more than 250 acquired genes from 6 different loci in the chromosome and showed contribution of CTX prophage in the essentiality of SOS response master regulator LexA, which is otherwise not essential for viability in other bacteria, including In addition, we observed that the core genome-encoded RecA helps CTXΦ to bypass immunity and allow it to replicate in the host bacterium in the presence of similar prophage in the chromosome. Finally, our proteomics analysis reveals the importance of MGEs in modulating the levels of cellular proteome. This study engineered the genome of to remove all of the GIs, ICEs, and prophages and revealed important interactions between core and acquired genomes.
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http://dx.doi.org/10.1073/pnas.2006283117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7519391PMC
September 2020

Gut microbiome diversity in acute severe colitis is distinct from mild to moderate ulcerative colitis.

J Gastroenterol Hepatol 2021 Mar 14;36(3):731-739. Epub 2020 Sep 14.

Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India.

Background And Aim: Although the gut microbiome of patients with ulcerative colitis (UC) has been characterized, no study has characterized the gut microbiome in acute severe colitis (ASC). We compared the gut microbiome of patients with UC, ASC, and healthy controls (HCs).

Methods: Patients with mild to moderate UC (n = 24), ASC (n = 19 with 21 episodes) and HCs (n = 50) were recruited prospectively. A 16SrDNA amplicon approach was used to explore gut microbial diversity and taxonomic repertoires. UC was diagnosed using European Crohn's and Colitis Organization guidelines, and ASC was diagnosed using Truelove and Witts' criteria.

Results: The normalized alpha diversity was significantly lower in ASC than mild-moderately active UC (P < 0.05) or HC (P < 0.001). The gut microbiome in ASC was highly unstable, as characterized by high intracohort variation (analyzed using J-divergence measure), which was significantly greater than in UC or HC. On principal coordinate analysis, the microbiome of HC and UC were similar, with the ASC cohort being distinct from both. Comparison of ranked abundances identified four distinct clusters of genera (G1, G2, G3, and G4), with specific trends in their abundance across three groups: G1/G2A clusters had the least, whereas G3 had the highest abundance in the ASC cohort.

Conclusions: Gut microbial diversity is lower in ASC than mild-moderate UC or HCs. Gut microbiome composition is increasingly unstable in ASC, with a distinct abundance of specific genera varying between HCs and ASC. Mild-moderate UC lies within the spectrum.
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http://dx.doi.org/10.1111/jgh.15232DOI Listing
March 2021

The 2019 novel coronavirus disease (COVID-19) pandemic: A review of the current evidence.

Indian J Med Res 2020 Feb & Mar;151(2 & 3):147-159

Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India.

A novel coronavirus (nCoV) spillover event, with its epicenter in Wuhan, People's Republic of China, has emerged as a public health emergency of international concern. This began as an outbreak in December 2019, and till February 28, 2020, there have been 83,704 confirmed cases of novel coronavirus disease 2019 (COVID-19) globally, with 2,859 deaths, resulting in an overall case fatality rate of 3.41 per cent (95% confidence interval 3.29-3.54%). By this time (February 28, 2020) 58 countries or territories and one international conveyance (Diamond Princess Cruise Ship) were affected. As a part of the global response to manage and contain the pandemic, major emphasis was placed on generating research intelligence to guide evidence-based responses to contain the virus, which was named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), owing to its genetic similarities with the SARS virus. This review summarizes the emerging evidence which can help guide the public health response, particularly in India. Key areas have been identified in which research needs to be conducted to generate critical intelligence for advising prevention and control efforts. The emergence of SARS-CoV-2 has once again exposed the weaknesses of global health systems preparedness, ability to respond to an infectious threat, the rapidity of transmission of infections across international borders and the ineffectiveness of knee-jerk policy responses to emerging/re-emerging infectious disease threats. The review concludes with the key learning points from the ongoing efforts to prevent and contain COVID-19 and identifies the need to invest in health systems, community-led response mechanisms and the need for preparedness and global health security.
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http://dx.doi.org/10.4103/ijmr.IJMR_519_20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7357405PMC
May 2020

Vaginal Microbiome of Pregnant Indian Women: Insights into the Genome of Dominant Lactobacillus Species.

Microb Ecol 2020 Aug 23;80(2):487-499. Epub 2020 Mar 23.

Molecular Genetics Laboratory, Translational Health Science and Technology Institute|, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO box #04, Faridabad, Haryana, 121001, India.

The trillions of microorganisms residing in the human body display varying degrees of compositional and functional diversities within and between individuals and contribute significantly to host physiology and susceptibility to disease. Microbial species present in the vaginal milieu of reproductive age women showed a large personal component and varies widely in different ethnic groups at the taxonomic, genomic, and functional levels. Lactobacillus iners, L. crispatus, L. gasseri, L. jensenii, and L. johnsonii are most frequently detected bacterial species in the vaginal milieu of reproductive age women. However, we currently lack (i) an understanding of the baseline vaginal microbiota of reproductive age Indian women, (ii) the extent of taxonomic and functional variations of vaginal microbiota between individuals and (iii) the genomic repertoires of the dominant vaginal microbiota associated with the Indian subjects. In our study, we analyzed the metagenome of high vaginal swab (HVS) samples collected from 40 pregnant Indian women enrolled in the GARBH-Ini cohort. Composition and abundance of bacterial species was characterized by pyrosequencing 16S rRNA gene. We identified 3067 OTUs with ≥ 10 reads from four different bacterial phyla. Several species of lactobacilli were clustered into three community state types (CSTs). L. iners, L. crispatus, L. gasseri, and L. jensenii are the most frequently detected Lactobacillus species in the vaginal environment of Indian women. Other than Lactobacillus, several species of Halomonas were also identified in the vaginal environment of most of the women sampled. To gain genomic and functional insights, we isolated several Lactobacillus species from the HVS samples and explored their whole genome sequences by shotgun sequencing. We analyzed the genome of dominant Lactobacillus species, L. iners, L. crispatus, L. gasseri, and L. paragesseri to represent the CSTs and identify functions that may influence the composition of complex vaginal microbial ecology. This study reports for the first time the vaginal microbial ecology of Indian women and genomic insights into L. iners, L. crispatus, L. gasseri, and L. paragesseri commonly found in the genital tract of reproductive age women.
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http://dx.doi.org/10.1007/s00248-020-01501-0DOI Listing
August 2020

Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi.

NPJ Biofilms Microbiomes 2019;5(1):37. Epub 2019 Dec 20.

1Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871 Japan.

The bacterial species living in the gut mediate many aspects of biological processes such as nutrition and activation of adaptive immunity. In addition, commensal fungi residing in the intestine also influence host health. Although the interaction of bacterium and fungus has been shown, its precise mechanism during colonization of the human intestine remains largely unknown. Here, we show interaction between bacterial and fungal species for utilization of dietary components driving their efficient growth in the intestine. Next generation sequencing of fecal samples from Japanese and Indian adults revealed differential patterns of bacterial and fungal composition. In particular, Indians, who consume more plant polysaccharides than Japanese, harbored increased numbers of and . spp. showed strong growth responses to the plant polysaccharide arabinoxylan in vitro. Furthermore, the culture supernatants of spp. grown with arabinoxylan promoted rapid proliferation of . Arabinose was identified as a potential growth-inducing factor in the culture supernatants. spp. exhibited a growth response to xylose, but not to arabinose, whereas proliferated in response to both xylose and arabinose. spp., but not , colonized the intestine of germ-free mice. However, successfully colonized mouse intestine already harboring . These findings demonstrate a proof of concept that fungal members of gut microbiota can facilitate a colonization of the intestine by their bacterial counterparts, potentially mediated by a dietary metabolite.
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http://dx.doi.org/10.1038/s41522-019-0110-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6925221PMC
June 2020

Diphtheria.

Nat Rev Dis Primers 2019 12 5;5(1):81. Epub 2019 Dec 5.

Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India.

Diphtheria is a potentially fatal infection mostly caused by toxigenic Corynebacterium diphtheriae strains and occasionally by toxigenic C. ulcerans and C. pseudotuberculosis strains. Diphtheria is generally an acute respiratory infection, characterized by the formation of a pseudomembrane in the throat, but cutaneous infections are possible. Systemic effects, such as myocarditis and neuropathy, which are associated with increased fatality risk, are due to diphtheria toxin, an exotoxin produced by the pathogen that inhibits protein synthesis and causes cell death. Clinical diagnosis is confirmed by the isolation and identification of the causative Corynebacterium spp., usually by bacterial culture followed by enzymatic and toxin detection tests. Diphtheria can be treated with the timely administration of diphtheria antitoxin and antimicrobial therapy. Although effective vaccines are available, this disease has the potential to re-emerge in countries where the recommended vaccination programmes are not sustained, and increasing proportions of adults are becoming susceptible to diphtheria. Thousands of diphtheria cases are still reported annually from several countries in Asia and Africa, along with many outbreaks. Changes in the epidemiology of diphtheria have been reported worldwide. The prevalence of toxigenic Corynebacterium spp. highlights the need for proper clinical and epidemiological investigations to quickly identify and treat affected individuals, along with public health measures to prevent and contain the spread of this disease.
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http://dx.doi.org/10.1038/s41572-019-0131-yDOI Listing
December 2019

Homeostasis and dysbiosis of the gut microbiome in health and disease.

J Biosci 2019 Oct;44(5)

Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad 121 001, India.

The human gastrointestinal tract (GIT) harbors taxonomically and functionally complex microbial ecosystem. The composition of the microbial species in the GIT ecosystem varies among individuals and throughout development. Both environmental factors as well as host genetics influence the composition and homeostasis of GIT microbiome. Intrinsic GIT microbiome can be characterized in terms of diversity, richness, dynamics and resilience. In healthy individual, microbial communities maintain homeostatic equilibrium and are resistant against perturbations. The resilience and resistance to perturbations of the GIT microbial ecosystem are robust but not absolute. Several factors can affect the homeostatic equilibrium of GIT microbiome and lead to dysbiotic microbiome configuration. Taxonomic and/or functional dysbiosis in the GIT microbiome is associated with numerous health disorders like inflammatory bowel disease (IBD), malnutrition, metabolic disorders, asthma and neurodegenerative diseases. In this review, we discuss our current understanding of homeostasis and dysbiosis of the microbial ecology in the human gut and health disorders that are associated with the microbiome dysbiosis.
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October 2019

Insights into the gastrointestinal tract microbiomes of Indian population.

J Biosci 2019 Oct;44(5)

Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad 121 001, India.

Trillions of microbes living in the gastrointestinal tract (GIT) of the human body finely tune homeostatic equilibrium in the GIT ecosystem and encode key functionalities that play crucial role in host metabolic functions, synthesis of macro- and micronutrients, xenobiotics metabolisms, development of innate and adaptive immune systems, tissue and organ developments and resistance against invasion of enteric pathogens. The microbial diversity and richness of GIT ecosystem varies greatly between individuals and over time. Extent of taxonomic and functional variations in GIT ecosystem is linked with dietary habit, pharmaceuticals usages, age, sex, body mass index, ethnicity, geography, altitude and civilization. Understanding a holistic picture of GIT microbiome of healthy people living across geography and identifying population specific 'keystone' taxa is of immense importance for identifying microbial species that may provide protection against chronic and metabolic diseases. Knowledge on geographic or ethnicity specific microbial signatures may also help us to understand the varied efficacy of different drugs and vaccines in different population. India is the home of more than 1.36 billion people belonging to 2000 human communities residing in well distinct geography. In the present review, we discuss the microbial signatures in health and diseases of the rural and urban Indians living in sea level and high altitude areas.
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October 2019

Corrigendum: Revisiting the Global Epidemiology of Cholera in Conjunction With the Genomics of .

Front Public Health 2019;7:237. Epub 2019 Aug 23.

Rajiv Gandhi Centre for Biotechnology, Trivandrum, India.

[This corrects the article DOI: 10.3389/fpubh.2019.00203.].
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http://dx.doi.org/10.3389/fpubh.2019.00237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6716542PMC
August 2019

Insights into TLCΦ lysogeny: A twist in the mechanism of IMEX integration.

Authors:
Bhabatosh Das

Proc Natl Acad Sci U S A 2019 09 22;116(37):18159-18161. Epub 2019 Aug 22.

Molecular Genetics Laboratory, Translational Health Science and Technology Institute, The National Capital Region Biotech Science Cluster, Faridabad-121001, India

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http://dx.doi.org/10.1073/pnas.1912633116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6744843PMC
September 2019

Diagnostic techniques for rapid detection of Vibrio cholerae O1/O139.

Vaccine 2020 02 16;38 Suppl 1:A73-A82. Epub 2019 Aug 16.

Department of International Health Program in Global Disease Epidemiology and Control, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.

Cholera caused by the toxigenic Vibrio cholerae is still a major public health problem in many countries. This disease is mainly due to poor sanitation, hygiene and consumption of unsafe water. Several recent epidemics of cholera showed its increasing intensity, duration and severity of the illness. This indicates an urgent need for effective management and preventive measures in controlling the outbreaks and epidemics. In preventing and spread of epidemic cholera, rapid diagnostic tests (RDTs) are useful in screening suspected stool specimens, water/food samples. Several RDTs developed recently are considered as investigative tools in confirming cholera cases, as the culture techniques are difficult to establish and/or maintain. The usefulness of RDTs will be more at the point-of-care facilities as it helps to make appropriate decisions in the management of outbreaks or epidemiological surveillance by the public health authorities. Apart from RDTs, several other tests are available for the direct detection of either V. cholerae or its cholera toxin. Viable but non-culturable (VBNC) state of V. cholerae poses a great challenge in developing RDTs. The aim of this article is to provide an overview of current knowledge about RDT and other techniques with reference to their status and future potentials in detecting cholera/V. cholerae.
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http://dx.doi.org/10.1016/j.vaccine.2019.07.099DOI Listing
February 2020

Revisiting the Global Epidemiology of Cholera in Conjuction With the Genomics of .

Front Public Health 2019 23;7:203. Epub 2019 Jul 23.

Rajiv Gandhi Centre for Biotechnology, Trivandrum, India.

Toxigenic is responsible for 1.4 to 4.3 million cases with about 21,000-143,000 deaths per year. Dominance of O1 and O139 serogroups, classical and El tor biotypes, alterations in CTX phages and the pathogenicity Islands are some of the major features of isolates that are responsible for cholera epidemics. Whole-genome sequencing (WGS) based analyses of single-nucleotide polymorphisms (SNPs) and other infrequent genetic variants provide a robust phylogenetic framework. Recent studies on the global transmission of pandemic O1 strains have shown the existence of eight different phyletic lineages. In these, the classical and El Tor biotype strains were separated as two distinctly evolved lineages. The frequency of SNP accumulation and the temporal and geographical distribution supports the perception that the seventh cholera pandemic (7CP) has spread from the Bay of Bengal region in three independent but overlapping waves. The 2010 Haitian outbreak shared a common ancestor with South-Asian wave-3 strains. In West Africa and East/Southern Africa, cholera epidemics are caused by single expanded lineage, which has been introduced several times since 1970. The Latin American epidemics that occurred in 1991 and 2010 were the result of introductions of two 7CP sublineages. Sublineages representing wave-3 have caused huge outbreaks in Haiti and Yemen. The Ogawa-Inaba serotype switchover in several cholera epidemics are believed to be due to the involvement of certain selection mechanism(s) rather than due to random events. O139 serogroup is phylogenetically related to the 7CP El Tor, and almost all these isolates belonged to the multilocus sequence type-69. Additional phenotypic and genotypic information have been generated to understand the pathogenicity of classical and El Tor vibrios. Presence of integrative conjugative elements (ICE) with antibiotic resistance gene cassettes, clustered regularly interspaced short palindromic repeats-associated protein system and promoter based ToxRS expression of cholera toxin (CT) separates classical and El Tor biotypes. With the availability of WGS information, several important applications including, molecular typing, antimicrobial resistance, new diagnostics, and vaccination strategies could be generated.
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http://dx.doi.org/10.3389/fpubh.2019.00203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6664003PMC
July 2019

Commentary: Functionality of Two Origins of Replication in Strains With a Single Chromosome.

Front Microbiol 2019 19;10:1314. Epub 2019 Jun 19.

Center of Cancer Research (CCR), National Cancer Institute (NCI) and National Institute Health (NIH), Bethesda, MD, United States.

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http://dx.doi.org/10.3389/fmicb.2019.01314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594386PMC
June 2019

CTX phage of Vibrio cholerae: Genomics and applications.

Vaccine 2020 02 1;38 Suppl 1:A7-A12. Epub 2019 Jul 1.

Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India. Electronic address:

The bipartite genome of Vibrio cholerae is divided into two circular non-homologous chromosomes, which harbor several genetic elements like phages, plasmids, transposons, integrative conjugative elements, and pathogenic islands that encode functions responsible for disease development, antimicrobial resistance, and subsistence in hostile environments. These elements are highly heterogeneous, mobile in nature, and encode their own mobility functions or exploit host-encoded enzymes for intra- and inter-cellular movements. The key toxin of V. cholerae responsible for the life-threatening diarrheal disease cholera, the cholera toxin, is coded by part of the genome of a filamentous phage, CTXϕ. The replicative genome of CTXϕ is divided into two distinct modular structures and has adopted a unique strategy for its irreversible integration into the V. cholerae chromosomes. CTXϕ exploits two host-encoded tyrosine recombinases, XerC and XerD, for its integration in the highly conserved dimer resolution site (dif) of V. cholerae chromosomes. CTXϕ can replicate only in the limited number of Vibrio species. In contrast, the phage integration into the bacterial chromosome does not rely on its replication and could integrate to the dif site of large numbers of gram-negative bacteria. Recent pangenomic analysis revealed that like CTXϕ, the bacterial dif site is the integration spot for several other mobile genetic elements such as plasmids and genomic islands. In this review we discuss about current molecular insights into CTXϕ genomics and its replication and integration mechanisms into hosts. Particular emphasis has been given on the exploitation of CTXϕ genomics knowledge in developing genetic tools and designing environmentally safe recombinant live oral cholera vaccine strains.
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http://dx.doi.org/10.1016/j.vaccine.2019.06.034DOI Listing
February 2020

Antibiotic resistance in Vibrio cholerae: Understanding the ecology of resistance genes and mechanisms.

Vaccine 2020 02 2;38 Suppl 1:A83-A92. Epub 2019 Jul 2.

Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad 121 001, India.

The unique genetic makeup and remarkable competency of Vibrio cholerae are the key factors that help the cholera pathogen adapt rapidly to adverse environmental conditions and resist the detrimental effect of antimicrobial agents. In the last few decades, V. cholerae that causes acute watery diarrhoeal disease cholera has emerged as a notorious multidrug resistant (MDR) enteric pathogen. Although chromosomal mutations can contribute to antimicrobial resistance (AMR), the frequent acquisition of extrachromosomal mobile genetic elements (MGEs) from closely/distantly related bacterial species are major players in V. cholerae drug resistance. Whole genome sequence analysis of clinical and environmental V. cholerae strains revealed that the genome of most of the recent isolates harbour integrating conjugative elements (ICEs), plasmids, superintegron, transposable elements and insertion sequences, which are the key carriers of genetic traits encoding antimicrobial resistance function. Different antimicrobial resistance genes identified in V. cholerae can contribute in antibiotic resistance by facilitating one of the following three mechanisms; (i) reduced permeability or active efflux of the antibiotics, (ii) alteration of the antibiotic targets by introducing post-transcriptional/translational modifications and (iii) hydrolysis or chemical modification of antibiotics. Here, we present an overview of the present insights on the emergence and mechanisms of AMR in V. cholerae.
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http://dx.doi.org/10.1016/j.vaccine.2019.06.031DOI Listing
February 2020

Genomic plasticity associated with antimicrobial resistance in .

Proc Natl Acad Sci U S A 2019 03 13;116(13):6226-6231. Epub 2019 Mar 13.

Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad 121001, India;

The Bay of Bengal is known as the epicenter for seeding several devastating cholera outbreaks across the globe. , the etiological agent of cholera, has extraordinary competency to acquire exogenous DNA by horizontal gene transfer (HGT) and adapt them into its genome for structuring metabolic processes, developing drug resistance, and colonizing the human intestine. Antimicrobial resistance (AMR) in has become a global concern. However, little is known about the identity of the resistance traits, source of AMR genes, acquisition process, and stability of the genetic elements linked with resistance genes in Here we present details of AMR profiles of 443 strains isolated from the stool samples of diarrheal patients from two regions of India. We sequenced the whole genome of multidrug-resistant (MDR) and extensively drug-resistant (XDR) to identify AMR genes and genomic elements that harbor the resistance traits. Our genomic findings were further confirmed by proteome analysis. We also engineered the genome of to monitor the importance of the autonomously replicating plasmid and core genome in the resistance profile. Our findings provided insights into the genomes of recent cholera isolates and identified several acquired traits including plasmids, transposons, integrative conjugative elements (ICEs), pathogenicity islands (PIs), prophages, and gene cassettes that confer fitness to the pathogen. The knowledge generated from this study would help in better understanding of evolution and management of cholera disease by providing clinical guidance on preferred treatment regimens.
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http://dx.doi.org/10.1073/pnas.1900141116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6442563PMC
March 2019

Serum protein signature of coronary artery disease in type 2 diabetes mellitus.

J Transl Med 2019 01 24;17(1):17. Epub 2019 Jan 24.

Drug Discovery Research Center, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, 121001, India.

Background: Coronary artery disease (CAD) is the leading cause of morbidity and mortality in patients with type 2 diabetes mellitus (T2DM). The purpose of the present study was to discriminate the Indian CAD patients with or without T2DM by using multiple pathophysiological biomarkers.

Methods: Using sensitive multiplex protein assays, we assessed 46 protein markers including cytokines/chemokines, metabolic hormones, adipokines and apolipoproteins for evaluating different pathophysiological conditions of control, T2DM, CAD and T2DM with CAD patients (T2DM_CAD). Network analysis was performed to create protein-protein interaction networks by using significantly (p < 0.05) altered protein markers in each disease using STRING 10.5 database. We used two supervised analysis methods i.e., between class analysis (BCA) and principal component analysis (PCA) to reveals distinct biomarkers profiles. Further, random forest classification (RF) was used to classify the diseases by the panel of markers.

Results: Our two supervised analysis methods BCA and PCA revealed a distinct biomarker profiles and high degree of variability in the marker profiles for T2DM_CAD and CAD. Thereafter, the present study identified multiple potential biomarkers to differentiate T2DM, CAD, and T2DM_CAD patients based on their relative abundance in serum. RF classified T2DM based on the abundance patterns of nine markers i.e., IL-1β, GM-CSF, glucagon, PAI-I, rantes, IP-10, resistin, GIP and Apo-B; CAD by 14 markers i.e., resistin, PDGF-BB, PAI-1, lipocalin-2, leptin, IL-13, eotaxin, GM-CSF, Apo-E, ghrelin, adipsin, GIP, Apo-CII and IP-10; and T2DM _CAD by 12 markers i.e., insulin, resistin, PAI-1, adiponectin, lipocalin-2, GM-CSF, adipsin, leptin, Apo-AII, rantes, IL-6 and ghrelin with respect to the control subjects. Using network analysis, we have identified several cellular network proteins like PTPN1, AKT1, INSR, LEPR, IRS1, IRS2, IL1R2, IL6R, PCSK9 and MYD88, which are responsible for regulating inflammation, insulin resistance, and atherosclerosis.

Conclusion: We have identified three distinct sets of serum markers for diabetes, CAD and diabetes associated with CAD in Indian patients using nonparametric-based machine learning approach. These multiple marker classifiers may be useful for monitoring progression from a healthy person to T2DM and T2DM to T2DM_CAD. However, these findings need to be further confirmed in the future studies with large number of samples.
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http://dx.doi.org/10.1186/s12967-018-1755-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6345069PMC
January 2019

Molecular Insights into Antimicrobial Resistance Traits of Commensal Human Gut Microbiota.

Microb Ecol 2019 Feb 16;77(2):546-557. Epub 2018 Jul 16.

Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India.

Antimicrobial resistance (AMR) among bacterial species that resides in complex ecosystems is a natural phenomenon. Indiscriminate use of antimicrobials in healthcare, livestock, and agriculture provides an evolutionary advantage to the resistant variants to dominate the ecosystem. Ascendency of resistant variants threatens the efficacy of most, if not all, of the antimicrobial drugs commonly used to prevent and/or cure microbial infections. Resistant phenotype is very common in enteric bacteria. The most common mechanisms of AMR are enzymatic modifications to the antimicrobials or their target molecules. In enteric bacteria, most of the resistance traits are acquired by horizontal gene transfer from closely or distantly related bacterial population. AMR traits are generally linked with mobile genetic elements (MGEs) and could rapidly disseminate to the bacterial species through horizontal gene transfer (HGT) from a pool of resistance genes. Although prevalence of AMR genes among pathogenic bacteria is widely studied in the interest of infectious disease management, the resistance profile and the genetic traits that encode resistance to the commensal microbiota residing in the gut of healthy humans are not well-studied. In the present study, we have characterized AMR phenotypes and genotypes of five dominant commensal enteric bacteria isolated from the gut of healthy Indians. Our study revealed that like pathogenic bacteria, enteric commensals are also multidrug-resistant. The genes encoding antibiotic resistance are physically linked with MGEs and could disseminate vertically to the progeny and laterally to the distantly related microbial species. Consequently, the AMR genes present in the chromosome of commensal gut bacteria could be a potential source of resistance functions for other enteric pathogens.
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http://dx.doi.org/10.1007/s00248-018-1228-7DOI Listing
February 2019

Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas.

Sci Rep 2018 07 4;8(1):10104. Epub 2018 Jul 4.

Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India.

The diversity and basic functional attributes of the gut microbiome of healthy Indians is not well understood. This study investigated the gut microbiome of three Indian communities: individuals residing in rural and urban (n = 49) sea level Ballabhgarh areas and in rural high altitude areas of Leh, Ladakh in North India (n = 35). Our study revealed that the gut microbiome of Indian communities is dominated by Firmicutes followed by Bacteroidetes, Actinobateria and Proteobacteria. Although, 54 core bacterial genera were detected across the three distinct communities, the gut bacterial composition displayed specific signatures and was observed to be influenced by the topographical location and dietary intake of the individuals. The gut microbiome of individuals living in Leh was observed to be significantly similar with a high representation of Bacteroidetes and low abundance of Proteobacteria. In contrast, the gut microbiome of individuals living in Ballabhgarh areas harbored higher number of Firmicutes and Proteobacteria and is enriched with microbial xenobiotic degradation pathways. The rural community residing in sea level Ballabhgarh areas has unique microbiome characterized not only by a higher diversity, but also a higher degree of interindividual homogeneity.
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http://dx.doi.org/10.1038/s41598-018-28550-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031670PMC
July 2018

Novel Genetic Tool to Study the Stability of Genomic Islands.

Recent Pat Biotechnol 2018 ;12(3):200-207

Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India.

Background: Genomic islands (GIs) are discrete segments of mobile DNA with defined boundaries according to recent patents, acquired in the bacterial genome from another organism by horizontal gene transfer during the course of evolution. GIs contribute significantly to virulence, disease development, antimicrobial resistance and metabolic process.

Objective: The present study focuses on the development of a vector based genetic tool carrying selectable and counter-selectable markers, in order to flag the GIs in the bacterial chromosome and monitor their stability under in vitro and in vivo conditions.

Method: We engineered suicide vectors, pSB40 and pSB41, carrying single or tandem copies of chloramphenicol acetyltransferase (cat) and levansucrase (sacB) alleles, respectively. The sacB-cat allele in both the vectors is flanked by several restriction sites. To test the suitability of sacB-cat allele for monitoring GI loss, we introduced the allele in the Vibrio Pathogenicity Island-1 (VPI-1) in Vibrio cholerae genome.

Results: The V. cholerae strain carrying sacB-cat allele in VPI-1 element showed resistance to chloramphenicol and sensitivity to sucrose at optimal growth conditions. Loss of VPI-1 element from the V. cholerae genome was simply monitored by growing the cells on selection agar plates supplemented with sucrose. Our results showed that the genetic tool we developed is suitable for monitoring GI stability in the bacterial genome.

Conclusion: The present study indicates that pSB40 and pSB41are efficient and sensitive genetic tool that can be used for reverse genetics experiments and monitoring stability of mobile genetic elements in the bacterial genome.
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http://dx.doi.org/10.2174/1872208312666180223113618DOI Listing
November 2018