Shashank Gupta

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Verified

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• Doctor of Philosophy
• Researcher at Örebro University

Microbiome-directed dietary interventions such as microbiota-directed fibers (MDFs) have a proven track record in eliciting responses in beneficial gut microbes and are increasingly being promoted as an effective strategy to improve animal production systems. Here we used initial metataxonomic data on fish gut microbiomes as well as a wealth of a p...

To ensure sustainable aquaculture, it is essential to understand the path ‘from feed to fish’, whereby the gut microbiome plays an important role in digestion and metabolism, ultimately influencing host health and growth. Previous work has reported the taxonomic composition of the Atlantic salmon (Salmo salar) gut microbiome; however, functional in...

Microbiome-directed dietary interventions such as microbiota-directed fibers (MDFs) have a proven track record in eliciting responses in beneficial gut microbes and are increasingly being promoted as an effective strategy to improve animal production systems. Here we used initial metataxonomic data on fish gut microbiomes as well as a wealth of a p...

The essential role of the gut microbiota for host health and nutrition is well established for many terrestrial animals, while its importance for fish and particularly Atlantic salmon is unclear. Here, we present the Salmon Microbial Genome Atlas (SMGA) originating from wild and farmed fish both in freshwater and seawater, and consisting of 211 hig...

Introduction: Rural children have a lower risk of asthma and atopic diseases than urban children. However, whether indoor microbiota in non-farming rural homes provides protection is unclear. Methods: Here, we examine if microbes in the beds of rural and urban infants are associated with later development of atopic diseases. We studied fungi and...

Background Growing up with siblings has been linked to numerous health outcomes and is also an important determinant for the developing microbiota. Nonetheless, research into the role of having siblings on the developing microbiota has mainly been incidental. Results Here, we investigate the specific effects of having siblings on the developing ai...

Antibiotic-resistant pathogens constitute an escalating public health concern. Hence a better understanding of the underlying processes responsible for this expansion is urgently needed. Co-selection of heavy metal/biocide and antibiotic resistance genes (ARGs) has been suggested as one potential mechanism promoting the proliferation of antimicrobi...

Antimicrobial resistance (AMR) is an accelerating global threat, yet the nature of AMR in the gut microbiome and how AMR is acquired during early life remain largely unknown. In a cohort of 662 Danish children, we characterized the antibiotic resistance genes (ARGs) acquired during the first year of life and assessed the impacts of diverse environm...

Antimicrobial resistance (AMR) is an accelerating global threat to modern medicine, yet the nature of AMR in the gut microbiome and how AMR is acquired during early life remain largely unknown. In a cohort of 662 Danish children, we characterized the antibiotic resistance genes (ARGs) acquired during the first year of life and assessed the impacts...

Antibiotic-resistant pathogens constitute an escalating public health concern. Hence a better understanding of the underlying processes responsible for this expansion is urgently needed. Co-selection of heavy metals/biocides and antibiotic resistance genes (ARGs) has been suggested as one potential mechanism promoting the proliferation of antimicro...

Studying respiratory illness-specific microbial signatures and their interaction with other micro-residents could provide a better understanding of lung microbial ecology. Each respiratory illness has a specific disease etiology, however, so far no study has revealed disease—specific microbial markers. The present study was designed to determine di...

Pharmaceutical substances present at low concentrations in the environment may cause effects on biological systems such as microbial consortia living on solid riverbed substrates. These consortia are an important part of the river ecosystem as they form part of the food chain. This case study aims to contribute to an increased understanding of how...

Background: From early life, children are exposed to a multitude of environmental exposures, which may be of crucial importance for healthy development. Here, the environmental microbiota may be of particular interest as it represents the interface between environmental factors and the child. As infants in modern societies spend a considerable amo...

Background From early life, children are exposed to a multitude of environmental exposures, which may be of crucial importance for healthy development. Here, the environmental microbiota may be of particular interest as it represents the interface between environmental factors and the child. As infants in modern societies spend a considerable amoun...

Background From early life children are exposed to a multitude of environmental exposures, which may be of crucial importance for a healthy development. Here, the environmental microbiota may be of particular interest as it represents the interface between environmental factors and the child. As infants in modern societies spend a considerable amou...

Next-Generation Sequencing (NGS) of 16S rRNA gene is now one of the most widely used application to investigate the microbiota at any given body site in research. Since NGS is more sensitive than traditional culture methods (TCMs), many studies have argued for them to replace TCMs. However, are we really ready for this transition? Here we compare t...

The human gut microbiome has a significant role in host physiology; however its role in gluten catabolism is debatable. Present study explores the role of human gut microbes in gluten catabolism and a native human gut microbe Cellulomonas sp. HM71 was identified. SSU rDNA analysis has described human gut microbiome structure and also confirmed the...

Heterogeneity amidst healthy individuals at genomic level is being widely acknowledged. This, in turn, is modulated by differential response to environmental cues and treatment regimens, necessitating the need for stratified/personalized therapy. We intend to understand the molecular determinants of Ayurvedic way (ancient Indian system of medicine)...

PCoA plot of beta diversity calculated using Bray-Curtis distance for (A) males and (B) female samples.

Diversity panel of Prakriti after removing two highly abundant phyla, viz., Firmicutes and Bacteroidetes. (A) Diversity (Shannon), (B) Richness, and (C) Evenness in male samples. (E) Diversity (Shannon), (F) Richness, and (G) Evenness in female samples. PCoA plot of beta diversity calculated using Bray-Curtis distance (D) in males and (H) in female...

Relative abundances of Prakriti specific signature taxons i.e., Roseburia inulinivorans (A) and Fusicatenibacter saccharivorans (B) in male subjects.

Details of volunteers enrolled in this study.

Relative abundances of Prakriti specific signature taxons Bacteroides vulgatus (A); Blautia obeum (B); Blautia stercoris (C); Blautia torques (D); Butyrivibrio crossotus (E); Clostridium indolis (F); Incertae Sedis Mahella (G); Lachnospira eligens (H); Oscillibacter valericigenes (I) in female subjects.

List of Primers used for qPCR analysis.

Core Microbiome in male and female groups.

qPCR analysis data to validate relative abundance of differentially abundant microbial enterotypes in Vata, Pitta, and Kapha.

Osmotolerance is one of the critical factors for successful survival and colonization of microbes in saline environments. Nonetheless, information about these osmotolerance mechanisms is still inadequate. Exploration of the saline soil microbiome for its community structure and novel genetic elements is likely to provide information on the mechanis...

Every niche in the biosphere is touched by the seemingly endless capacity of microbes to transform the world around them by adapting swiftly and flexibly to the environmental changes, likewise the gastrointestinal tract is no exception. The ability to cope with rapid changes in external osmolarity is an important aspect of gut microbes for their su...

Survival in a given environment requires specific functions, so genomic variation is anticipated within in individual taxonomic groups that exhibit a large diversity in lifestyles. In this study, we sequence and assemble the genome of Oceanobacillus faecalis strain HM6, a resident of the human gut. Using the genus Oceanobacillus and the HM6 draft g...

Survival in a given environment requires specific functions, so genomic variation is anticipated within in individual taxonomic groups that exhibit a large diversity in lifestyles. In this study, we sequence and assemble the genome of Oceanobacillus faecalis strain HM6, a resident of the human gut. Using the genus Oceanobacillus and the HM6 draft g...

Soil is a complex ecosystem with defined microbial community signatures, modulated by the interaction between biotic and abiotic factors. Amidst biotic factors, land usage have significant impact onto the soil microbial structure and ecosystem functioning. In the current study, metagenomic approach was used to decipher effect of hospital settings o...

Comparative analysis of the metagenomic DNA isolated under different microbial purification conditions

Gel electrophoresis of fresh and frozen human fecal metagenomic DNA Metagenomic DNA isolated from fresh human feces (lane 1) or one-month-old human feces stored at –86 °C (lane 2) using current method was separated on 0.8% agarose gel. NEX-GEN DNA ladder (EXL)(Puregene, Genetix Biotech, India) was used as DNA marker.

List of primers used in current study

Microbes are ubiquitously distributed in nature, and recent culture-independent studies have highlighted the significance of gut microbiota in human health and disease. Fecal DNA is the primary source for the majority of human gut microbiome studies. However, further improvement is needed to obtain fecal metagenomic DNA with sufficient amount and g...

Ureases are ubiquitous in nature having similar catalytic function yet sometimes different protein structures. Catalytic hydrolysis of urea results in the production of ammonia causing abrupt pH increase of the surrounding medium. This increase in pH has has been shown to have adverse effects on human health and agriculture. The efficiency of soil...