SAYAK DAS - Academia.edu (original) (raw)

Papers by SAYAK DAS

Meta Gene

Abstract Parageobacillus sp. strain SY1 was isolated from the Yumthang hot spring of the North Si... more Abstract Parageobacillus sp. strain SY1 was isolated from the Yumthang hot spring of the North Sikkim, Himalayan region of India. A detailed study was carried out on this strain as these strains are thermophilic and are very important due to the thermostable nature of their enzymes. In the present study we are reporting the draft genome sequence of Parageobacillus sp. strain SY1. The genome possesses the size of 3,216,693 bps, with an average G + C content of 42.5%. The genome assembly has 1407 contigs (with Protein Encoding Genes PEGs). The genome contains 4360 coding sequences with 19 tRNA and 22 rRNA predicted genes. Based on COG classification, the predicted proteins were divided into 27 functional categories. Parageobacillus sp. strain SY1 genome have genes for sulfur, nitrogen, and phosphorous metabolism. The strain possesses various nitrate and nitrite ammonification genes. Carbohydrate metabolism constitutes lactate fermentation and mixed acid fermentation. Analysis of the genome also suggested the presence of ATP-dependent proteases which help in the bacterial degradation of peptides during the damage caused at the time of its invasion. Moreover, the genome also harbors genes for various other proteases which might also be responsible for extracellular proteolysis. The genome information of Parageobacillus sp. strain SY1 might help in better understanding of its functional properties and can be used as thermostable protease producer.

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms

Journal of Medical Virology

The aim of the study was to trace and understand the origin of Severe acute respiratory syndrome ... more The aim of the study was to trace and understand the origin of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through various available literatures and accessible databases. Although the world enters the third year of the coronavirus disease 2019 pandemic, health and socioeconomic impacts continue to mount, the origin and mechanisms of spill-over of the SARS-CoV-2 into humans remain elusive. Therefore, a systematic review of the literature was performed that showcased the integrated information obtained through manual searches, digital databases (PubMed, CINAHL, and MEDLINE) searches, and searches from legitimate publications (1966-2022), followed by meta-analysis. Our systematic analysis data proposed three postulated hypotheses concerning the origin of the SARS-CoV-2, which include zoonotic origin (Z), laboratory origin (L), and obscure origin (O). Despite the fact that the zoonotic origin for SARS-CoV-2 has not been conclusively identified to date, our data suggest a zoonotic origin, in contrast to some alternative concepts, including the probability of a laboratory incident or leak. Our data exhibit that zoonotic origin (Z) has higher evidence-based support as compared to laboratory origin (L). Importantly, based on all the studies included, we generated the forest plot with 95% confidence intervals (CIs) of the risk ratio estimates. Our meta-analysis further supports the zoonotic origin of SARS/SARS-CoV-2 in the included studies.

Zenodo (CERN European Organization for Nuclear Research), 2014

Faalgee is an ethno traditional dish of Sherpa community. It is predominantly prepared and consum... more Faalgee is an ethno traditional dish of Sherpa community. It is predominantly prepared and consumed by the traditionally enriched people residing in the Himalayan region of Sikkim. Thus only few members of the old tribes of Sherpa community residing in this Himalayan region have this traditional knowledge to prepare this cereal based non-fermented dish, Faalgee. Our emphasis in this paper is to document this indigenous knowledge of preparation of this ethnic dish of Sherpa communities. It is basically prepared from maize seeds during August to October as it is grown abundantly during this period. Partially ripe maize cones are placed in a perforated container called Jaygha (copper pot) with water and boiled in a chula until maize is properly cooked. The cooked maize is removed from container and the seeds of maize are separated from the cones. The separated seeds are sun dried in Gundrey (mat) for 2-3 days. These dried seeds of maize are called Faalgee. Faalgee dish is prepared by grinding these dried seeds of maize, in Gatay (grinder). This grinded maize seeds are cooked in a container with water until it gets swollen and this swollen Faalgee is cooked in edible oil or ghee. A Faalgee dish is generally prepared during winter seasons by the Sherpa community. It’s generally believed that Faalgee soup keeps the body warm during the extreme cold winter at the higher altitudes.

Environmental Sustainability, 2020

Solfataric mud sediment samples were analyzed from two hot springs of North Sikkim district of th... more Solfataric mud sediment samples were analyzed from two hot springs of North Sikkim district of the Sikkim Himalayas, located at the northeastern region of Indian Himalayan Geothermal Belt. Old Yume Samdung hot spring (OYS) and New Yume Samdung hot spring (NYS) are located 4500m above the mean sea level and are one of the highest located hot springs of Sikkim. OYS hot spring had more abundance of archaea than the NYS hot spring. The solfataric mud sediments of NYS had 0.03% and OYS had 1.06% archaeal reads of the whole microbiome. Both the samples were dominated by Euryarchaeota (NYS~85%; OYS~95%) followed by few representatives from Crenarchaeota (NYS~12%; OYS~3%) and Thaumanarchaeota (NYS~2%; OYS~1%). Based on abundance, Methanocaldococcus, Pyrococcus, Archaeoglobus, Methanobacter, and Thermococcus were the predominant genera in both the hot springs. Functional protein reads for Crenarchaeota were found among the orders of Desulfurococcales, Sulfolobales and Thermoproteales; whereas reads for the order Nanoarchaeales belonging to Nanoarchaeota phylum and orders Cenarchaeales; Nitrosopumilales from phylum Thaumarchaeota were present in the samples. Functional metagenomics revealed the methanogens of the hot springs. There were no functional genes detected for methanogenesis in NYS, whereas in the case of OYS it was abundantly present in various orders of Euryarchaeota-Methanobacteriales, Methanococcales, Methanopyrales, and Methanosarcinales. Three types of methanogenesis were found-aceticlastic, methylotrophic and hydrogenotrophic in the OYS metaarchaeome. Methanopyrus kandleri, Methanosarcina acetivorans, Methanothermobacter marburgensis, Methanothermobacter thermautotrophicus, and Methanocaldococcus jannaschii were the dominant methanogens found in the metaarchaeome, based on their functional proteins for methanogenesis.

Current Research in Microbial Sciences, 2022

Journal of Water and Environment Technology, 2020

The major recreational hot springs of Sikkim which are famous tourist destinations were selected ... more The major recreational hot springs of Sikkim which are famous tourist destinations were selected for the current study. Physicochemical and microbial quality of all the seven hot spring water samples were examined to assess the seasonal variation for three months. Polok hot spring was the hottest among all, whose temperature reached up to 75°C. In all the other hot springs, temperature ranged from 40°C to 50°C. Piper diagram, durov plot and schoeller plot categorized these hot springs as calcium chloride type. Elemental analysis showed similar pattern of composition in all the hot springs. Various other parameters such as total hardness of water, total alkalinity, phenolic compounds, biochemical oxygen demand, chemical oxygen demand were analyzed and they were found to be within the permissible limits of American Public Health Association and Bureau of Indian Standards. There was no growth in any differential and selection media used for the detection of coli-aerogenes, enteric bacterial pathogens belonging to Enterobacteriaceae, Salmonella-Shigella sp., Vibrio sp. and Pseudomonas sp. Hence, the hot springs of Sikkim are safe for recreational purposes.

Folia Microbiologica, 2021

Fungi are considered to be the most resilient and economically important microbial community that... more Fungi are considered to be the most resilient and economically important microbial community that can easily survive and optimally grow under a wide range of growth conditions. Thermophilic fungi from the geothermal sources have been less pondered upon and lie unexplored. Here, a microbiome approach was conducted to understand the concealed world of the environmental mycobiota from the two hot springs of North Sikkim district located in Northeast India. The solfataric muds from the hot springs were analyzed. In both the samples, on the basis of genus level classification, genus Fusarium had the highest abundance followed by Colletotrichum, Pochonia, Pyricularia, Neurospora, etc. Analyzing the predicted genes, the functional proteins of New Yume Samdung mycobiome were found to be dominated by the genera Fusarium (22%), Trichoderma (12%), and Aspergillus (11%), whereas in the case of Old Yume Samdung, it was dominated by the genera Aspergillus (11%), Saccharomyces (6%), and Fusarium (5%). Interestingly, in the studied mycobiome, environmental yeasts were also detected. From the functional metagenomics, sulfate adenylatetransferase (SAT) proteins for sulfur assimilation were found in some of the fungal reads. Toxin protein reads such as AM-toxin biosynthesis proteins, AF-toxin biosynthesis proteins, Gliotoxin biosynthesis proteins, and aflatoxin biosynthesis proteins were detected in the mycobiomes.

Sikkim doctrines the aboriginal religious practices, culminates indigenous traditions associated ... more Sikkim doctrines the aboriginal religious practices, culminates indigenous traditions associated with religion and faith based healing therapies and is a natural hub of traditional medicine. Faith healers and occupational folk medicine therapeuticians acts as alchemists. In this unfathomed virgin and picturesque state of pulchritudinous blooming orchids, rural population are directly depended upon the traditional medicines prescribed by the faith healers and the traditional occupational folk medicine doctors for their basic health issues and amenities. The knowledge of herbs or plant based panacea is a part of indigenous knowledge which has been snowballed from generation and ages since primordial origin. On the basis of proper signs and symptoms of the diseases, these herbal medicines are chosen. Their choice of medicine also depends upon the availability, particular geography; faith associated belief and cost effectiveness. This practice is on the verge of extinction as The Himala...

Recent Research in Science and Technology, 2013

Fenced by the geo-political features all around, Sikkim sits magnificently in the lap of The Hima... more Fenced by the geo-political features all around, Sikkim sits magnificently in the lap of The Himalayas with Mount Khanchengdzonga signifying the peaks of divinity and cultural proximity. Sikkim is the natural ecological host to many Hot springs of geothermal characteristics. Hot Springs of Sikkim are regarded as ethical and holistic elements having importance of locale panacea. Hot springs are any natural geothermal spring or a natural discharge of groundwater with elevated temperature with respect to the surrounding. The characteristics or the suitability of these hot springs for human use is determined by its chemical constituents. Most of the Hot Springs is rich in several kinds of chemicals and minerals. Presence of these chemicals and minerals along with higher temperature of these hot springs determine its balneotherapeutic properties. The average temperature of the studied Hot springs being 60°C according to Kent classification as “Scalding” can be regarded as the best ecolog...

The solfataric soil sediments of the hot springs of Sikkim located at Yume Samdung and Lachen val... more The solfataric soil sediments of the hot springs of Sikkim located at Yume Samdung and Lachen valley were studied for deciphering the uncultured bacterial diversity. The main aim here is to present a comparative study and generate a baseline data on the post-monsoon seasonal variation for the months of October and December, analysed through 16S rRNA V3-V4 amplicon sequencing. At phylum level, in the New Yume Samdung (NYS) hot spring soil sample, in the month of October it was dominated by Proteobacteria (21.03%) followed by Thermi (12.33%) and Bacteroidetes (9.95%) whereas in December it was dominated by Proteobacteria (23.61%) followed by Chloroflexi (19.15%) and Bacteroidetes (16.55%). For Old Yume Samdung (OYS) hot spring soil sample, in the month of October, it was dominated by Proteobacteria (25.22%) followed by Bacteroidetes (11.76%) and Thermi (8.11%) whereas in December it was dominated by Proteobacteria (20.58%) followed by Chloroflexi (18.88%) and Thermi (9.89%). And in th...

International Journal of Systematic and Evolutionary Microbiology, 2020

Members of the genus Geobacillus within the phylum Firmicutes are Gram-stain-positive, aerobic, e... more Members of the genus Geobacillus within the phylum Firmicutes are Gram-stain-positive, aerobic, endospore-forming, obligate thermophiles. In 2016, the genus Geobacillus was subdivided into two genera based on whole-genome approaches. The new genus, Parageobacillus , comprises five genomospecies. In this study, we recommend the reclassification of two Geobacillus species, Geobacillus galactosidasius and Geobacillus yumthangensis , into the genus Parageobacillus . We have applied whole genome approaches to estimate the phylogenetic relatedness among the 18 Geobacillus and Parageobacillus type strains for which genome sequences are currently publicly available. The phylogenomic metrics AAI (average amino acid identity), ANI (average nucleotide identity) and dDDH (digital DNA–DNA hybridization) denoted that the type strains of G. galactosidasius and G. yumthangensis belong to the genus Parageobacillus . Furthermore, a phylogeny based on comparison of the 16S rRNA gene sequences, recN ge...

Ecotoxicology and Environmental Safety, 2020

Glacier studies as of late have ruffled many eyeballs, exploring this frigid ecology to understan... more Glacier studies as of late have ruffled many eyeballs, exploring this frigid ecology to understand the impact of climate change. Mapquesting the glaciers led to the discovery of concealed world of "psychrophiles" harboring in it. In the present study, the antibiotic resistance genes (ARGs) and heavy metal resistance genes (MRGs) were evaluated through both the culture-dependent and culture-independent methods. Samples were collected from two different glaciers, i.e., debris-covered glacier (Changme Khangpu) and debris-free glacier (Changme Khang). Functional metagenomics of both the glacier samples, provided evidence of presence of resistant genes against various antibiotic groups. Bacitracin resistant gene (bacA) was the predominant ARG in both the glaciers. MRGs in both the glacier samples were diversified as the genes detected were resistant against various heavy metals such as arsenic, tungsten, mercury, zinc, chromium, copper, cobalt, and iron. Unique MRGs identified from Changme Khangpu glacier were resistant to copper (cutA, cutE, cutC, cutF, cueR, copC, and copB) and chromium (yelf, ruvB, nfsA, chrR, and chrA) whereas, from Changme Khang glacier they showed resistance against cobalt (mgtA, dmef, corD, corC, corB, and cnrA), and iron (yefD, yefC, yefB, and yefA) heavy metals. ARGs aligned maximum identity with Gram-negative psychrotolerant bacteria. The cultured bacterial isolates showed tolerance to high concentrations of tested heavy metal solutions. Interestingly, some of the antibiotic resistant bacterial isolates also showed tolerance towards the higher concentrations of heavy metals. Thus, an introspection of the hypothesis of co-occurrence and/co-selection of ARGs and MRGs in such environments has been highlighted here.

Current Research in Microbial Sciences, 2020

This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

Gene Reports, 2018

We are reporting the draft genome sequence of the Geobacillus yumthangensis AYN2 sp. nov. with th... more We are reporting the draft genome sequence of the Geobacillus yumthangensis AYN2 sp. nov. with the genome size of (~3.4 Mb) corresponding to 3712 predicted genes with (G + C) content of 42.28%. This bacterium possesses motility and chemotaxis genes, sulfur and denitrifying reductase gene clusters. This thermophilic bacterium was isolated from the Yumthang Hot Spring located in the North district of Sikkim, India.

Functional & Integrative Genomics, 2020

Sikkim is one of the bio-diverse states of India, which harbors diverse alkaline and sulfur rich ... more Sikkim is one of the bio-diverse states of India, which harbors diverse alkaline and sulfur rich hot springs in its vicinity. However, there is a dearth of data present in terms of microbial and its functional diversity as only a few hot springs have been studied in this area. Thus, in this regard, microbial and functional diversity of two hot springs by NGS, PLFA, and culture-independent approaches were carried out. PLFA and culture-dependent analysis was complementary as the Gram-positive bacteria were abundant in both the hot springs with the dominance of phylum Firmicutes with Geobacillus. Metagenomic analysis revealed the abundance of Proteobacteria, Actinobacteria, and Firmicutes in both hot springs. Functional metagenomics suggested that both Yumthang and Reshi hot spring possess a diverse set of genes analogous to stress such as genes allied to osmotic, heat shock, and acid stresses; defense analogies such as multidrug resistance efflux pump, multidrug transport system, and β-lactamase; and CRISPR analogues such as related to Cas1, Cas2, Cas3, cmr1-5 proteins, CT1972, and CT1133 gene families. The xenobiotic analogues were found against benzoate, nitrotolune, xylene, DDT, and chlorocyclohexane/chlorobenzene degradation. Thus, these defensive mechanisms against environmental and anthropogenic hiccups and hindrances provide the eco-efficiency to such thermal habitats. The higher enzymatic, degradation, defense, stress potential and the lower percentage identity (< 95%) of isolates encourage the further exploration and exploitation of these habitats for industrial and biotechnological purposes.

Mechanisms of occurrence and expressions of antibiotic resistance genes (ARGs) in thermophilic ba... more Mechanisms of occurrence and expressions of antibiotic resistance genes (ARGs) in thermophilic bacteria are still unknown owing to limited research and data. The evolution and proliferation of ARGs in the thermophilic bacteria is unclear and needs a comprehensive study. In this research, comparative profiling of antibiotic resistance genes and metal tolerance genes among the thermophilic bacteria has been done by culture-independent functional metagenomic methods. Metagenomic analysis showed the dominance of Proteobacteria, Actinobacteria. Firmicutes and Bacteroidetes in these hot springs. ARG analysis through shotgun gene sequencing was found to be negative in case of thermophilic bacteria. However, few of genes were detected but they were showing maximum similarity with mesophilic bacteria. Concurrently, metal resistance genes were also detected in the metagenome sequence of hot springs. Detection of metal resistance gene and absence of ARG’s investigated by whole genome sequencin...

Environmental Sustainability, 2019

Microbial communities at cryosphere are the cosmopolitan buffers of important biogeochemical proc... more Microbial communities at cryosphere are the cosmopolitan buffers of important biogeochemical processes stationed at extreme archaic and frigid conditions. In the present study microbial diversity analysis from accumulation zone of two glaciers of North Sikkim, India has been carried by two culture independent methods. The phospholipid fatty acids analysis of Changme Khang and Changme Khangpu glacier showed that both of these were dominated by Gram-positive bacteria followed by Gram-negative bacteria. Among the two glaciers, Changme Khang (54.04%) had higher percentage of Gram-positive bacteria than Changme Khangpu (24.84%), while Gram-negative bacteria were higher in Changme Khangpu (22.65%) than Changme Khang (4.41%). The metagenomic analysis shows the dominance of Proteobacteria followed by Firmicutes and Actinobacteria. Betaproteobacteria were the dominant class among Proteobacteria. Similar kind of bacterial diversity was also observed from other polar and non-polar glaciers.