Yogesh Shouche

Yogesh Shouche
National Centre For Cell Science, Pune | NCCS · MicrobialCultureCollection (MCC)

About

759
Publications
134,067
Reads
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12,693
Citations
Citations since 2017
149 Research Items
7440 Citations
201720182019202020212022202302004006008001,0001,2001,400
201720182019202020212022202302004006008001,0001,2001,400
201720182019202020212022202302004006008001,0001,2001,400
201720182019202020212022202302004006008001,0001,2001,400
Additional affiliations
April 1991 - present
National Centre For Cell Science, Pune
Position
  • Researcher

Publications

Publications (759)
Article
Full-text available
Indian lotus (Nelumbo nucifera) is one of the dominant aquatic plants cultivated in Dal Lake, situated at 1586 m above mean sea level (MSL) in the northeast of Srinagar, Kashmir. Despite their economic and ecological role, the microbial communities associated with the lotus plant are still unexplored. In this study, we investigated the prokaryotic...
Article
Studies of the human microbiome are providing a deeper understanding of its significance to human health {AuQ: Edit OK?}, and increasing evidence links the microbiota with several diseases. Nevertheless, the exact mechanisms involved in human–microbe interactions are mostly undefined. The genomic potential of the human microbiome to biosynthesize d...
Article
In the present study, the microbial community residing at different depths of the landfill was characterized to assess their roles in serving as a methane sink. Physico-chemical characterization revealed the characteristic signatures of anaerobic degradation of organic matter in the bottom soil (50–60 cm) and, active process of aerobic denitrificat...
Article
Introduction. Vaginal colonization of Group B Streptococcus (GBS) is associated with preterm births and neonatal sepsis. Thus routine screening of GBS in prenatal care is recommended. Hypothesis. Chromogenic media (carrot broth) aids in specific and rapid detection of GBS. Aim. To investigate the efficiency of Strep B Carrot Broth for detection of...
Article
Full-text available
The microbial diversity in the Indian caves is inadequately characterized. This study reports on the culturable microbial communities in caves from the Indian sub-continent. This study aims to expand the current understanding of bacterial diversity in the speleothems and wall deposits from Krem Soitan, Krem Lawbah, Krem Mawpun in Khasi Hills, Megha...
Article
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Breakthrough infections with SARS-CoV-2 Delta variant have been reported in doubly-vaccinated recipients and as re-infections. Studies of viral spread within hospital settings have highlighted the potential for transmission between doubly-vaccinated patients and health care workers and have highlighted the benefits of high-grade respiratory protect...
Preprint
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Cellophane, a bio-based fibrous film is considered sustainable, biodegradable and potential substitute for petrochemical based plastic films. However, addition of extra coating agents are making them recalcitrant in nature and therefore, their persistence after disposal is becoming a serious environmental concern. In this study, previously defined...
Article
The human oral cavity harbours complex microbial communities with various commensal microorganisms that play pivotal roles in maintaining host health and immunity but can elicit local and systemic diseases. The role of commensal microorganisms in SARS-CoV-2 infection and disease susceptibility and enrichment of opportunistic pathobionts in the oral...
Article
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Culture-independent sequence data from various environmental samples have revealed an immense microbial diversity of environmental, clinical, and industrial importance that has not yet been cultured. Cultivation is imperative to validate findings emerging from cultivation-independent molecular data and exploit the isolated organisms for biotechnolo...
Article
The bacterial composition of naturally fermented Indian food, Idli was studied by high-throughput Illumina amplicon sequencing at different taxonomic levels. Metagenomic investigation revealed fold change with respect to some of the phylotypes in 06th to 12th h of fermentation, suggesting the synergistic mode of nutrition. After 12th h fermentation...
Article
Full-text available
Honeybees are eusocial insects with close interaction with their surrounding environment. Gut microbiota in honeybees play a significant role in host health, biology, and interaction behavior with the surrounding environment. Apis florea, a wild bee, is the most primitive among all honeybees and is indigenous to the Indian subcontinent. Previous re...
Article
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Growing evidence suggests an altered gut microbiome in patients with heart failure (HF). However, the exact interrelationship between microbiota, HF, and its consequences on the metabolome are still unknown. We thus aimed here to decipher the association between the severity and progression of HF and the gut microbiome composition and circulating m...
Article
Background It is known that anti-oxidant defense is compromised in diabetic individuals. In our study, we indeed found decreased catalase activity in diabetic individuals compared to non-diabetic controls. Therefore, we analyzed the single nucleotide polymorphisms (SNPs) in the promoter region of catalase in diabetic individuals. To investigate cat...
Preprint
Full-text available
Indian lotus ( Nelumbo nucifera ) is one of the dominant aquatic plants cultivated in Dal Lake, situated at 1586 m above MSL in the northeast of Srinagar, Kashmir. Despite their economic and ecological role, the microbial communities associated with the lotus plant are still unexplored. In this study, we investigated prokaryotic communities harbour...
Article
Full-text available
Two aerobic, Gram-stain variable, catalase-positive and oxidase-negative rods named strain UniB2T and UniB3T, were isolated from digestive syrup containing fungal diastase (10 mg/ml), pepsin (2 mg/ml) and sugar base containing polyethylene glycol. Based on 16S rRNA gene sequence analysis, strain UniB2T has the highest sequence similarity with Paeni...
Article
The landfill is an inexpensive way of municipal solid waste (MSW) management and contributes extensively to the total carbon budget and global climate change. Three landfills from two geographically distinct metro- cities of India were taken as model systems to create microcosms and study their physiochemistry, microbiology, and carbon emission. Th...
Article
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Deadly surge in Delhi In the spring of 2021, Delhi, India experienced a wave of coronavirus cases that overwhelmed healthcare services despite the population showing a high level of immune positivity. Dhar et al . collated a mixture of serosurveillance, quantitative polymerase chain reaction, and genomic data, finding that waves of variants had pas...
Article
Objective To evaluate the effect of rectal administration of buttermilk processed with medicinal plants on gut microbial composition and thereby on weight in obese individuals.Methods With ethics committee approval, 16 obese individuals in the age group 20–50 years (BMI ≥30 kg/m2) were recruited who received a course of 15-enemas over 15-days. Of t...
Article
The 16S rRNA gene amplicon sequencing is a popular technique that provides accurate characterization of microbial taxonomic abundances but does not provide any functional information. Several tools are available to predict functional profiles based on 16S rRNA gene sequence data that use different genome databases and approaches. As variable region...
Article
Full-text available
Chronic exposures to tobacco and biomass smoke are the most prevalent risk factors for COPD development. Although microbial diversity in tobacco smoke-associated COPD (TSCOPD) has been investigated, microbiota in biomass smoke-associated COPD (BMSCOPD) is still unexplored. We aimed to compare the nasal and oral microbiota between healthy, TSCOPD, a...
Article
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For decades, bacterial natural products have served as valuable resources for developing novel drugs to treat several human diseases. Recent advancements in the integrative approach of using genomic and functional tools have proved beneficial in obtaining a comprehensive understanding of these biomolecules. This study presents an in-depth character...
Article
Facultative anaerobes are the most common cause of infections in anoxic parts of the human body, including deep wound, vagina, periodontal pockets, gastrointestinal tract, genitourinary tract and lungs. Generally, antibiotic susceptibility tests (AST) for facultative anaerobes are performed under aerobic conditions due to ease of handling and rapid...
Preprint
Full-text available
This study reports on the culturable microbial communities in caves from the Indian sub-continent. A high bacterial diversity and a greater bacterial taxonomic diversity is reported using MALDI-TOF spectrometry and 16S rRNA gene sequencing. This approach helped to detect a number bacterial strains from the Indian caves. The microbial diversity in t...
Article
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Invasive plants are known to alter the soil microbial communities; however, the effects of co-occurring native and invasive congeners on the soil bacterial diversity and their predictive metabolic profiles are not known. Here, we compared the rhizosphere bacterial communities of invasive Prosopis juliflora and its native congener Prosopis cineraria...
Preprint
Full-text available
Honey bees are complex social system, which are highly dynamic having close interactions with their surrounding environment. Gut microbiota of honey bees has a major role in interaction behavior with its environment and health. Apis florea is the primitive among all the honey bees and are indigenous to Indian subcontinent. The study reports the ide...
Article
Full-text available
Although skin is the primary affected organ in Leprosy, the role of the skin microbiome in its pathogenesis is not well understood. Recent reports have shown that skin of leprosy patients (LP) harbours perturbed microbiota which grants inflammation and disease progression. Herein, we present the results of nested Polymerase Chain Reaction-Denaturin...
Chapter
To understand the structural and functional relationships between microorganisms within a complex microbial community and/or with their host, it is important to study them as one rather than studying them separately. Next Generation Sequencing (NGS) based approaches evolved in last decades like 16S rRNA gene amplicon and metagenome sequencing revol...
Article
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Background: With virtually dried out new antibiotic discovery pipeline, emergence and spread of antimicrobial resistance is a cause for global concern. Colistin, a cyclic polypeptide antibiotic, often regarded as last resort for multi drug resistance gram-negative bacteria, is also rendered ineffective by horizontal transfer of resistance genes. Su...
Article
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Pangong Tso is a long and narrow lake situated at an altitude of ~ 4266 m amsl in the Himalayan Plateau on the side of the India/China border. Biofilm has been observed in a small area near the shore of Pangong Tso. Bacterial communities of the lake sediment, water and biofilms were studied using amplicon sequencing of V3-V4 region of the 16S rRNA...
Article
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The taxonomy of the Asian tree frog genus Feihyla has been in a state of flux ever since its proposal in 2006. Allocation of species to Feihyla remains confusing, particularly with respect to the closely related genus Chirixalus (formerly Chiromantis sensu lato). At the same time, several Chirixalus species are known only from cursory descriptions...
Article
Bioactive metabolites derived from the phylum Actinobacteria represent many of the existing antimicrobial drugs. Compared with other bacterial pathogens, direct preliminary screening by diffusion assays is a limiting factor against Mycobacterium tuberculosis (Mtb) and different methodologies have been used to improve the search for new molecules. H...
Article
Microbes are providers of raw materials for green, red, blue and white or grey biotechnology. Recent data from DNA-based culture-independent research revealed that huge microbial diversity of immense biotechnological potential is not yet cultured. Cultivation, characterization and biobanking of microbial resources are imperative for academic as wel...
Preprint
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The PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Consortium has achieved its initial goal of completing the sequencing of 1000 SARS-CoV-2 genomes from nasopharyngeal and oropharyngeal swabs collected from individuals testing positive for COVID-19 by Real Time PCR. The samples were collected across 10 states covering different zones within India....
Preprint
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India has become the third worst-hit nation by the COVID-19 pandemic caused by the SARS-CoV-2 virus. Here, we investigated the molecular, phylogenomic, and evolutionary dynamics of SARS-CoV-2 in western India, the most affected region of the country. A total of 90 genomes were sequenced. Four nucleotide variants, namely C241T, C3037T, C14408T (Pro4...
Preprint
Full-text available
A novel bacterial strain designated ADMK78T was isolated from the saline desert soil. The cells were rod-shaped, Gram-negative, and non-motile. The strain ADMK78T grows best at 28 C and pH 7.0 and can tolerate up to 2% (w/v) NaCl. Based on 16S rRNA gene phylogeny, the strain ADMK78T belongs to the genus Rhizobium, with the highest similarity to Rhi...
Article
The human intestinal tract is colonized by a large number of diverse microorganisms that play various important physiologic functions. In inflammatory gut diseases including celiac disease (CeD), a dysbiotic state of microbiome has been observed. Interestingly, this perturbed microbiome is normalized towards eubiosis in patients showing recovery af...
Article
Full-text available
The Sambhar Salt Lake is a halite rich athalassohaline basin, provides a unique opportunity for microbial ecologists to study halophiles. The lake has a high proportion of Na+ and Cl- ions making it a hypersaline ecosystem. In the current study, archaea and bacteria from Sambhar Lake were isolated using two cultivation approaches. A total of 449 is...
Article
Abiotic stress factors hugely affect the agricultural productivity worldwide out of which the most hazardous factor is soil salinization. Most of the crops species are susceptible to increased soil salinity; there is a great interest in developing new strategies to ameliorate salt stress as well as to make robust crop species. In this study we have...
Article
Full-text available
Introduction: Species of genus Candida are part of the common microbiota of humans; however, some of the Candida species are known opportunistic pathogens. Formation of biofilms, resistance to antifungal drugs, and increase in asymptomatic infections demands more studies on isolation, identification and characterization of Candida from clinical sa...
Article
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Gut microbiota is considered to play a role in disease progression, and previous studies have reported an association of microbiome dysbiosis with T2D. In this study, we have attempted to investigate gut microbiota of ND, PreDMs, NewDMs, and KnownDMs. We found that the genera Akkermansia and Blautia decreased significantly ( P < 0.05) in treatment-...
Article
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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 thi...
Article
The gut microbial community is known to influence the human health and disease state and is shaped by various factors since birth. It is now evident that understanding the alterations in these commensal microbes during crucial stages of life is of utmost importance to determine and predict the health status of an individual. To study the gut microb...
Article
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Extensive survey was carried out in the state of Maharashtra, India, as part of a 3-year project to explore keratinophilic fungal diversity for conservation and biotechnological potential. A total of 578 soil samples were collected from keratin-rich habitats across 24 districts of Maharashtra State. Hair-baiting technique and micro-dilution drop-tr...
Article
A haloarchaeal strain (ESP3B_9T) was isolated from the salt pan of Sambhar salt lake, Rajasthan, India. Cells were coccoid, non-motile, Gram-stain-negative and formed reddish-pink pigmented colonies. The strain was aerobic, able to grow at 35-55 °C (optimum, 40 °C), in 20-35 % (25 %) NaCl and pH 8-10 (pH 9). Mg2+ not required for growth. The cells...
Article
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Ayurveda is one of the ancient systems of medicine which is widely practised as a personalized scientific approach towards the general wellness. Ayurvedic prakriti is broadly defined as the phenotypes which are determined on the basis of physical, psychological and physiological traits irrespective of their social, ethnic, dietary and geographical...
Article
The Kumbh Mela is considered the world’s largest mass gathering event (MGE). It represents a unique anthropogenic burden on the river ecosystem and may confer antimicrobial resistance among microbial communities. The present study explains the characterization of microbial isolates associated with Godavari River under the advent of the mass bathing...
Article
A novel Gram-stain-negative bacterial strain designated as MEB193T was isolated from a sediment sample collected from Lonar Lake, India. The cells were motile, non-spore-forming and rod-shaped. The strain was oxidase- and catalase-positive. It grew optimally at pH 9.0 and at 1 % (w/v) NaCl concentration at 30 °C. Based on 16S rRNA gene sequence sim...
Article
Krishna Godavari (KG) basin, located in the eastern continental margin of India, is a geological region well known for the abundance of economically important minerals. However, less is known about the microbial ecology of its subsurface sediments. The present study is the first report on the comprehensive culture-independent census of bacterial co...
Preprint
Full-text available
A novel bacterial strain designated TOUT106T was isolated from the surface of a tomato collected from the local vegetable market in Pune, India. The cells were rod shaped, Gram-stain-negative, encapsulated and non-motile. The strain TOUT106T grows as mucoid and translucent colonies on blood agar medium and the best growth was observed at 28 C and a...
Chapter
Full-text available
Human microbiome is known to play a key role in human health along with the host genetic makeup and environmental factors. Research studies carried out in the past decade have now established a clear association of human microbiome with various metabolic and gastrointestinal diseases through the state of dysbiosis. Extensive efforts have been made...
Article
Red kidney bean (RKB) is an important cash crop of the Western Indian Himlayan (WIH) regions. Despite of having a long cultivation history, very little has known about its rhizospheric microbial diversity, which is becoming important for employing sustainable agricultural plans. In this perspective, the bacterial diversity and community structure o...
Article
A Gram-stain-negative, aerobic, yellow-pigmented, oxidase-positive and rod-shaped bacterium, designated PRB40T, was isolated from the Godavari River in India during the course of 'Kumbh Mela', the world's largest mass gathering event. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain PRB40T formed a lineage within the fami...
Article
Full-text available
The human microbiota plays a crucial role in educating the immune system and influencing host health right since birth. Various maternal factors along with the vertical microbial transfer from the mother, as well as the horizontal environmental transmission and internal factors relating to the infant, play a crucial role in modulating the gut micro...
Article
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A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Article
This is a comprehensive analysis of idli fermentation employing modern molecular tools which provided valuable information about the bacterial diversity enabling its fermentation. The study has demonstrated the relationship between the bacterial population and its functional role in the process. The nature of idli fermentation was found to be more...
Article
Full-text available
Altitude is the major factor affecting both biodiversity and soil physiochemical properties of soil ecosystems. In order to understand the effect of altitude on soil physiochemical properties and bacterial diversity across the Himalayan cold desert, high altitude Gangotri soil ecosystem was studied and compared with the moderate altitude Kandakhal...
Data
Soil sampling sites in Western Indian Garhwal Himalaya. (TIF)
Data
Comparative soil chemical properties of Gangotri and Kandakhal soil. (DOCX)
Data
Sequencing parameters for Gangotri soil DNA. (DOCX)
Data
Temperature growth profile of the selected diazotrophic bacteria isolated at 2°C. (JPG)
Article
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The Himalayan Mountains are placed among the globally recognized biodiversity hot spots. While the Indian Himalayan Region (IHR) has been subjected to extensive studies on plant and animal biodiversity, microbial diversity is now being studied for its bioprospection. The present paper deals with the evaluation of bacterial diversity in high-altitud...
Article
Full-text available
Recent studies on celiac disease (CeD) have reported alterations in the gut microbiome. Whether this alteration in the microbial community is the cause or effect of the disease is not well understood, especially in adult onset of disease. The first-degree relatives (FDRs) of CeD patients may provide an opportunity to study gut microbiome in pre-dis...