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1.
Appl Microbiol Biotechnol ; 108(1): 438, 2024 Aug 12.
Article in English | MEDLINE | ID: mdl-39133323

ABSTRACT

This study investigated the impact of feeding 17% moringa leaf meal (MLM) on the ruminal and fecal microbial composition and body weight gain (BWG) performance of lambs (Ovis aries) and kids (Capra hircus). A total of n = 28 lambs (n = 14, no-moringa, n = 14, 17% moringa) and 24 kids (n = 12, no-moringa, n = 12, 17% moringa) were involved in the experiment and body weight was recorded fortnightly. Metagenomic shotgun sequencing was performed on 28, 22, and 26 ruminal solid, liquid fraction, and fecal samples from lambs, and 23, 22, and 23 samples from kids. Moringa supplementation significantly increased BWG in lambs (21.09 ± 0.78 to 26.12 ± 0.81 kg) and kids (14.60 ± 1.29 to 18.28 ± 1.09 kg) (p-value ≤ 0.01). Microbiome analysis revealed an elevated Firmicutes:Bacteroidetes ratio in the moringa diet group. Moringa-fed animals exhibited increased microbial genera associated with volatile fatty acids (VFAs) production (Prevotella, Anaerovibrio, Lachnospiraceae, Butyrivibrio, Christensenella) and starch and fiber digesters (Proteobacteria, Ruminococcus). The increase in the bacterial genus Sharpea suggested possible methane reduction and decreased proportion of pathogens, Aliarcobacter_ID28198, Campylobacter_ID194 and Campylobacter_ID1660076 suggest health benefits. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated significant alterations in microbial gene pool and metabolic pathways related to carbohydrate, protein, lipid and energy metabolism, indicating potential improvements in animal health. Overall, moringa feeding showed higher energy recovery, improved growth, and potential benefits in methane reduction and reduced pathogenic bacteria.


Subject(s)
Animal Feed , Feces , Gastrointestinal Microbiome , Goats , Moringa , Plant Leaves , Animals , Gastrointestinal Microbiome/drug effects , Animal Feed/analysis , Moringa/chemistry , Sheep , Feces/microbiology , Dietary Supplements , Fatty Acids, Volatile/metabolism , Rumen/microbiology , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , Bacteria/metabolism , Weight Gain/drug effects , Diet/veterinary , Metagenomics
2.
Mol Biol Rep ; 50(9): 7605-7618, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37532919

ABSTRACT

BACKGROUND: Brahmi is one of the important nootropic botanicals, widely sold in the market, with the name "Brahmi'' being used to describe both Bacopa monnieri and Centella asiatica species. The Brahmi herbal products market is expanding; hence, economically motivated adulteration is highly prevalent. METHODS AND RESULTS: This study aimed to develop DNA-based methods, including SCAR marker-based PCR and metabarcoding, to authenticate Brahmi herbal products and compare these methods with HPLC. These methods have been validated using mock controls (in-house blended formulations). All targeted plant species in mock controls were detected successfully with all three methods, whereas, in market samples, only 22.2%, 55.6%, and 50.0% were found positive for Brahmi by PCR assay, DNA metabarcoding, and HPLC, respectively. Metabarcoding can detect the presence of non-labeled plants together with targeted species, which is an advantage over PCR assay or HPLC. CONCLUSION: SCAR marker-based PCR is a rapid and cost-effective method for detecting the presence of B. monnieri and C. asiatica. However, in this study, the success rate of PCR amplification was relatively low because the primers targeted either RAPD or ITS-based SCAR markers. HPLC assay, although an alternative, was unable to detect the presence of other botanicals, just like the SCAR marker-based PCR assay. On the other hand, metabarcoding can be utilized to identify the target plants, even in very small quantities, while also providing simulated identification of other botanicals. This study successfully addressed the need for quality control of Brahmi herbal products and provided the first-time report of DNA metabarcoding for such products.


Subject(s)
DNA Barcoding, Taxonomic , DNA , Chromatography, High Pressure Liquid , Random Amplified Polymorphic DNA Technique , Polymerase Chain Reaction
3.
Genomics ; 114(4): 110399, 2022 07.
Article in English | MEDLINE | ID: mdl-35680011

ABSTRACT

Different human races across the globe responded in a different way to the SARS-CoV-2 infection leading to different disease severity. Therefore, it is anticipated that host genetic factors have a straight association with the COVID-19. We identified a total 6, 7, and 6 genomic loci for deceased-recovered, asymptomatic-recovered, and deceased-asymptomatic group comparison, respectively. Unfavourable alleles of the markers nearby the genes which are associated with lung and heart diseases such as Tumor necrosis factor superfamily (TNFSF4&18), showed noteworthy association with the disease severity and outcome for the COVID-19 patients in the western Indian population. The markers found with significant association with disease prognosis or recovery are of value in determining the individual's response to SARS-CoV-2 infection and can be used for the risk prediction in COVID-19. Besides, GWAS study in other populations from India may help to strengthen the outcome of this study.


Subject(s)
COVID-19 , Genome-Wide Association Study , Alleles , Asian People , COVID-19/diagnosis , COVID-19/genetics , Humans , India , OX40 Ligand/genetics , SARS-CoV-2 , Tumor Necrosis Factors/genetics
4.
Emerg Infect Dis ; 28(4): 751-758, 2022 04.
Article in English | MEDLINE | ID: mdl-35203112

ABSTRACT

Limited genomic sampling in many high-incidence countries has impeded studies of severe respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic epidemiology. Consequently, critical questions remain about the generation and global distribution of virus genetic diversity. We investigated SARS-CoV-2 transmission dynamics in Gujarat, India, during the state's first epidemic wave to shed light on spread of the virus in one of the regions hardest hit by the pandemic. By integrating case data and 434 whole-genome sequences sampled across 20 districts, we reconstructed the epidemic dynamics and spatial spread of SARS-CoV-2 in Gujarat. Our findings indicate global and regional connectivity and population density were major drivers of the Gujarat outbreak. We detected >100 virus lineage introductions, most of which appear to be associated with international travel. Within Gujarat, virus dissemination occurred predominantly from densely populated regions to geographically proximate locations that had low population density, suggesting that urban centers contributed disproportionately to virus spread.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Genome, Viral , Genomics , Humans , India/epidemiology , Phylogeny , SARS-CoV-2/genetics
5.
Microb Pathog ; 173(Pt A): 105829, 2022 Dec.
Article in English | MEDLINE | ID: mdl-36252893

ABSTRACT

The bacterial co-infections in SARS-CoV-2 patients remained the least explored subject of clinical manifestations that may also determine the disease severity. Nasopharyngeal microbial community structure within SARS-CoV-2 infected patients could reveal interesting microbiome dynamics that may influence the disease outcomes. Here, in this research study, we analyzed distinct nasopharyngeal microbiome profile in the deceased (n = 48) and recovered (n = 29) COVID-19 patients and compared it with control SARS-CoV-2 negative individuals (control) (n = 33). The nasal microbiome composition of the three groups varies significantly (PERMANOVA, p-value <0.001), where deceased patients showed higher species richness compared to the recovered and control groups. Pathogenic genera, including Corynebacterium (LDA score 5.51), Staphylococcus, Serratia, Klebsiella and their corresponding species were determined as biomarkers (p-value <0.05, LDA cutoff 4.0) in the deceased COVID-19 patients. Ochrobactrum (LDA score 5.79), and Burkholderia (LDA 5.29), were found in the recovered group which harbors ordinal bacteria (p-value <0.05, LDA-4.0) as biomarkers. Similarly, Pseudomonas (LDA score 6.19), and several healthy nasal cavity commensals including Veillonella, and Porphyromonas, were biomarkers for the control individuals. Healthy commensal bacteria may trigger the immune response and alter the viral infection susceptibility and thus, may play important role and possible recovery that needs to be further explored. This research finding provide vital information and have significant implications for understanding the microbial diversity of COVID-19 patients. However, additional studies are needed to address the microbiome-based therapeutics and diagnostics interventions.


Subject(s)
COVID-19 , Microbiota , Humans , SARS-CoV-2 , Nasopharynx/microbiology , Bacteria
6.
Environ Res ; 212(Pt B): 113288, 2022 09.
Article in English | MEDLINE | ID: mdl-35427588

ABSTRACT

An upsurge in textile dye pollution has demanded immediate efforts to develop an optimum technology for their bioremediation. However, the molecular mechanism underpinning aerobic decolorization of dyes is still in its infancy. Thus, in the current work, the intricacies of aerobic remediation of textile dyes by Pseudomonas aeruginosa D6 were understood via a transcriptomic approach. The bacterium isolated from the sludge sample of a common effluent treatment plant was able to decolorize 54.42, 57.66, 50.84 and 65.86% of 100 mg L-1 of four different dyes i.e., TD01, TD04, TD05, and TD06, respectively. The maximum decolorization was achieved within six days and thus, the first and sixth day of incubation were selected for transcriptome analysis at the early and late phase of the decolorization, respectively. The expression profiles of all samples were compared to gain insight into the dye-specific response of bacterium and it was found that it behaved most uniquely in the presence of the dye TD01. Several genes critical to core metabolic processes like the TCA cycle, glycolysis, pentose phosphate pathway, translation, cell motility etc. Were found to be overexpressed in the presence of dyes. Interestingly, in response to dyes, the benzoate degradation pathway was significantly upregulated in the bacterium as compared to control (i.e., bacterium without dye). Thus, seven genes contributing to the induction of the same were further studied by RT-qPCR analysis. Overall, the involvement of the benzoate pathway implies the appearance of aromatic intermediates during decolorization, which in turn infers dye degradation.


Subject(s)
Pseudomonas aeruginosa , Textile Industry , Azo Compounds , Benzoates , Biodegradation, Environmental , Coloring Agents/analysis , Gene Expression Profiling , Pseudomonas aeruginosa/genetics , Textiles , Up-Regulation
7.
BMC Womens Health ; 22(1): 113, 2022 04 12.
Article in English | MEDLINE | ID: mdl-35413875

ABSTRACT

BACKGROUND: Female reproductive tract dysbiosis impacts implantation. However, whether gut dysbiosis influences implantation failure and whether it accompanies reproductive tract dysbiosis remains scantly explored. Herein, we examined the gut-vaginal microbiota axis in infertile women. METHODS: We recruited 11 fertile women as the controls, and a cohort of 20 infertile women, 10 of whom had recurrent implantation failure (RIF), and another 10 had unexplained infertility (UE). Using amplicon sequencing, which employs PCR to create sequences of DNA called amplicon, we compared the diversity, structure, and composition of faecal and vaginal bacteria of the controls with that of the infertile cohort. Of note, we could only sequence 8 vaginal samples in each group (n = 24/31). RESULT: Compared with the controls, α-diversity and ß-diversity of the gut bacteria among the infertile groups differed significantly (p < 0.05). Taxa analysis revealed enrichment of Gram-positive bacteria in the RIF group, whereas Gram-negative bacteria were relatively abundant in the UE group. Strikingly, mucus-producing genera declined in the infertile cohort (p < 0.05). Hungatella, associated with trimethylamine N-oxide (TMAO) production, were enriched in the infertile cohort (p < 0.05). Vaginal microbiota was dominated by the genus Lactobacillus, with Lactobacillus iners AB-1 being the most abundant species across the groups. Compared with the infertile cohort, overgrowth of anaerobic bacteria, associated with vaginal dysbiosis, such as Leptotrichia and Snethia, occurred in the controls. CONCLUSION: The gut microbiota had little influence on the vaginal microbiota. Gut dysbiosis and vaginal eubiosis occurred in the infertile women, whereas the opposite trend occurred in the controls.


Subject(s)
Infertility, Female , Microbiota , Dysbiosis/complications , Dysbiosis/microbiology , Female , Humans , RNA, Ribosomal, 16S/genetics , Vagina/microbiology
8.
Anaerobe ; 73: 102508, 2022 Feb.
Article in English | MEDLINE | ID: mdl-34974183

ABSTRACT

Coconut coir (a lignin-rich, organic material) is widely used for its commercial and economic benefits. In this study, crossbred (exotic) and Kankrej (indigenous) breeds of cattle were fed diets containing 7 or 14% coconut coir. Metagenomic analyses (16S rRNA gene amplicon and shotgun sequencing) were used to characterize the microbial community in the rumen and fecal samples along with their functional capabilities. Both amplicon and shotgun analyses revealed the predominance of bacterial phyla, Bacteroidetes, Firmicutes, Actinobacteria and Fibrobacter in ruminal liquid, ruminal solid and fecal samples. 16S rRNA gene amplicon sequencing revealed a total of 18 different bacterial taxa were found to be enriched exclusively in the animals fed with 14% coir. The shotgun analysis revealed abundance of bacterial genera, Fibrobacter, Clostridium, Prevotella, Butyrivibrio, and Ruminococcus in both liquid and solid fractions of ruminal contents, while in the fecal sample, Bacteroides, Alistipes, Plaudibacter, Parabacteroides, Porphyromonas, and Victivallis and archaeal genus, Methanocorpusculum were abundant. The functional analysis based on dbCAN database suggested that among the Glycoside hydrolase family, genes that encode oligosaccharide degrading enzymes, GH3, GH13 (p-value < 0.05), and GH43 were abundant in the feces. In ruminal solid, cellulase encoding the GH5 family was abundant. Also, lignocellulosic binding modules encoded by the CBM family, including cellulose (CBM3) and hemicellulose binding modules (CBM32 and CBM67) were abundant. Thus, the study indicated the enrichment of lignocellulosic enzymes in ruminal contents in response to feeding the coconut coir, which could be mined for potential biofuel production and other biotechnological applications.


Subject(s)
Metagenome , Rumen , Animals , Cattle , Diet/veterinary , Feces , Lignin , RNA, Ribosomal, 16S/genetics , Rumen/microbiology
9.
Phytochem Anal ; 32(5): 804-810, 2021 Sep.
Article in English | MEDLINE | ID: mdl-33527609

ABSTRACT

INTRODUCTION: Ayurveda takes advantage of the beneficial properties of medicinal plants. High demands in combination with inadequate availability of botanicals and a lack of knowledge with respect to their precise identification lead to adulterations in herbal products. Identification becomes more difficult in complex herbal formulations. Four different polyherbal formulations have been analyzed for the present paper. The targeted plants have different pharmacological properties for various ailments. OBJECTIVE: We aimed to examine the rbcL gene based plant DNA mini-barcode to identify target and non-target plants in polyherbal formulations by using high-throughput next generation sequencing. METHODS: Degenerate primers of the selected mini-barcode region have been identified from the literature. A blend of 30 authentic medicinal plant species was used to examine the species resolution capacity of the mini-barcode. DNA was isolated from herbal formulations, an amplicon library was prepared, and sequencing was performed on an IonS5 system. Data were analyzed using various bioinformatics tools. RESULTS: Analysis of control pooled samples revealed the optimum resolving power of the DNA mini-barcode. Data analysis of the commercial samples revealed that only one herbal formulation contained all plants and matched with listed contents. In two formulations, only 10 out of 21 and 11 out of 20 plants were detected, respectively. Additionally, several non-listed plants were also detected in these formulations. Two formulations contained >20% reads assigned to non-target plants. Overall, 21.98% of the reads were assigned to non-target plants. CONCLUSION: The present study clearly demonstrated the successful application and potential of meta-barcoding in the quality control of complex herbal matrices. The results strongly suggest that this approach can be used in pharmacovigilance of processed herbal products.


Subject(s)
DNA Barcoding, Taxonomic , Plants, Medicinal , DNA, Plant/genetics , Medicine, Ayurvedic , Plants, Medicinal/genetics , Quality Control
10.
Mol Biol Rep ; 47(7): 5101-5114, 2020 Jul.
Article in English | MEDLINE | ID: mdl-32557173

ABSTRACT

The present study describes rumen microbiota composition and their functional profiles in Indian Surti buffaloes by metagenomic (MG) and metatranscriptomic (MT) approaches. The study compares samples from buffaloes fed three different proportion of roughages; green and dry type of roughage; and different rumen liquor fractions. Irrespective of sample, Bacteroidetes and Firmicutes were the most predominant bacterial phyla, followed by Proteobacteria, Fibrobacteres and Actinobacteria while, Prevotella, Bacteroides, Ruminococcus and Clostridium were the most abundant genera. Different proportions of taxa were observed in both MG and MT approaches indicating the differences in organisms present and organisms active in the rumen. Higher proportions of fungal taxa were observed in MT while important organisms like Fibrobacter and Butyrivibrio and abundant organisms like Bacteroides and Prevotella were underrepresented in MT data. Functionally, higher proportions of genes involved in Carbohydrate metabolism, Amino acid metabolism and Translation were observed in both data. Genes involved in Metabolism were observed to be underrepresented in MT data while, those involved in Genetic information processing were overrepresented in MT data. Further, genes involved in Carbohydrate metabolism were overexpressed compared to genes involved in Amino acid metabolism in MT data compared to MG data which had higher proportion of genes involved in Amino acid metabolism than Carbohydrate metabolism. In all significant differences were observed between both approaches, different fractions of rumen liquor (liquid and solid) and different proportions of roughage in diet.


Subject(s)
Buffaloes/microbiology , Gastrointestinal Microbiome , Metagenome , Rumen/microbiology , Transcriptome , Animals , Buffaloes/genetics , Carbohydrate Metabolism , RNA-Seq , Rumen/metabolism
11.
Funct Integr Genomics ; 19(2): 237-247, 2019 Mar.
Article in English | MEDLINE | ID: mdl-30357583

ABSTRACT

Microbial colonisation in the forestomach of a ruminant is one of the most crucial factors in determining many of its physiological developments and digestive capabilities. The present study attempts to identify establishment pattern of microbes in relation to food, age and rumen development in the buffalo calves at every fortnight interval from birth to 6 months of age, followed by every month till animals became 1 year of age. Diversity study based on 16S rRNA gene sequencing identified rapidly changing bacterial population during initial 60 days of life, which got assemblage as rumen became physiologically mature with increasing age of animals. A lactate fermenting aerobic to facultative anaerobic genera found during initial 30 days of life were expeditiously replaced by strict anaerobic cellulolytic bacterial population with increasing age. The study confirms that initial colonisation mainly depends on the oral cavity and skin of the mother, followed by the surrounding environment and feed offered, which is reversed in order once animal gets older. Some of the well-described genera based on culture-dependent studies like Ruminococcus spp. were found to be in lesser proportion suggesting an additional role of other microbes or niche in cellulose degradation. We report the presence of Porphyromonas spp. and Mannheimia glucosidal for the first time in bovine infants.


Subject(s)
Buffaloes/microbiology , Gastrointestinal Microbiome , Metagenome , Rumen/microbiology , Animals , Male , RNA, Ribosomal, 16S/genetics , Rumen/growth & development
12.
Funct Integr Genomics ; 18(2): 211-223, 2018 Mar.
Article in English | MEDLINE | ID: mdl-29332190

ABSTRACT

Cotton (Gossypium spp.) is an imperative economic crop of the globe due to its natural textile fiber. Molecular mechanisms of fiber development have been greatly revealed in allotetraploid cotton but remained unexplored in Gossypium herbaceum. G. herbaceum can withstand the rigors of nature like drought and pests but produce coarse lint. This undesirable characteristic strongly needs the knowledge of fiber development at molecular basis. The present study reported the transcriptome sequence of the developing fiber of G. herbaceum on pyrosequencing and its analysis. About 1.38 million raw and 1.12 million quality trimmed reads were obtained followed by de novo assembly-generated 20,125 unigenes containing 14,882 coding sequences (CDs). BLASTx-based test of homology indicated that A1-derived transcripts shared a high similarity with Gossypium arboreum (A2). Functional annotation of the CDs using the UniProt categorized them into biological processes, cellular components, and molecular function, COG classification showed that a large number of CDs have significant homology in COG database (6215 CDs), and mapping of CDs with Kyoto Encyclopedia of Genes and Genomes (KEGG) database generated 200 pathways ultimately showing predominant engagement in the fiber development process. Transcription factors were predicted by comparison with Plant Transcription Factor Database, and their differential expression between stages exposed their important regulatory role in fiber development. Differential expression analysis based on reads per kilobase of transcript per million mapped reads (RPKM) value revealed activities of specific gene related to carbohydrate and lipid synthesis, carbon metabolism, energy metabolism, signal transduction, etc., at four stages of fiber development, and was validated by qPCR. Overall, this study will help as a valuable foundation for diploid cotton fiber improvement.


Subject(s)
Cotton Fiber/standards , Gossypium/genetics , Transcriptome , Genes, Plant , Gossypium/growth & development
13.
Anaerobe ; 44: 106-116, 2017 Apr.
Article in English | MEDLINE | ID: mdl-28246035

ABSTRACT

Recent advances in next generation sequencing technology have enabled analysis of complex microbial community from genome to transcriptome level. In the present study, metatranscriptomic approach was applied to elucidate functionally active bacteria and their biological processes in rumen of buffalo (Bubalus bubalis) adapted to different dietary treatments. Buffaloes were adapted to a diet containing 50:50, 75:25 and 100:0 forage to concentrate ratio, each for 6 weeks, before ruminal content sample collection. Metatranscriptomes from rumen fiber adherent and fiber-free active bacteria were sequenced using Ion Torrent PGM platform followed by annotation using MG-RAST server and CAZYmes (Carbohydrate active enzymes) analysis toolkit. In all the samples Bacteroidetes was the most abundant phylum followed by Firmicutes. Functional analysis using KEGG Orthology database revealed Metabolism as the most abundant category at level 1 within which Carbohydrate metabolism was dominating. Diet treatments also exerted significant differences in proportion of enzymes involved in metabolic pathways for VFA production. Carbohydrate Active Enzyme(CAZy) analysis revealed the abundance of genes encoding glycoside hydrolases with the highest representation of GH13 CAZy family in all the samples. The findings provide an overview of the activities occurring in the rumen as well as active bacterial population and the changes occurring through different dietary treatments.


Subject(s)
Buffaloes/microbiology , Diet/methods , Gastrointestinal Microbiome , Metagenomics , Rumen/microbiology , Animal Feed , Animals , Computational Biology , Gene Expression Profiling
14.
World J Microbiol Biotechnol ; 33(4): 65, 2017 Apr.
Article in English | MEDLINE | ID: mdl-28260194

ABSTRACT

Nematode-trapping fungi are well known for their inherent potential to trap and kill nematodes using specialized trapping devices. However, the molecular mechanisms underlying the trapping and subsequent processes are still unclear. Therefore, in this study, we examined differential genes expression in two nematode-trapping fungi after baiting with nematode extracts. In Arthrobotrys conoides, 809 transcripts associated with diverse functions such as signal transduction, morphogenesis, stress response and peroxisomal proteins, proteases, chitinases and genes involved in the host-pathogen interaction showed differential expression with fold change (>±1.5 fold) in the presence of nematode extract with FDR (p-value < 0.001). G-proteins and mitogen activated protein kinases are considered crucial for signal transduction mechanism. Results of qRT-PCR of 20 genes further validated the sequencing data. Further, variations in gene expression among Duddingtonia flagrans and A. conoides showed septicity of nematode-trapping fungi for its host. The findings illustrate the molecular mechanism of fungal parasitism in A. conoides which may be helpful in developing a potential biocontrol agent against parasitic nematodes.


Subject(s)
Ascomycota/physiology , Fungal Proteins/genetics , Nematoda/microbiology , Root Nodules, Plant/microbiology , Sequence Analysis, RNA/methods , Animals , Ascomycota/genetics , Ascomycota/isolation & purification , Gene Expression Regulation, Fungal , Host-Pathogen Interactions , Pest Control , RNA, Fungal/analysis
15.
Sci Total Environ ; 912: 168882, 2024 Feb 20.
Article in English | MEDLINE | ID: mdl-38040372

ABSTRACT

Plastic pollution increases globally due to the high volume of its production and inadequate mismanagement, leading to dumps in landfills affecting terrestrial and aquatic ecosystems. Landfills, as sink for plastics, leach various toxic chemicals and microplastics into the environment. We scrutinized the genetic expression for low-density polyethylene (LDPE) degradation via microorganisms to investigate cell viability and metabolic activities for biodegradation and genetic profiling. Samples were collected from the Pirana waste landfill at Ahmedabad, Gujarat, which is one of the largest and oldest municipal solid waste (MSW) dump sites in Asia. Results analyzed that isolated bacterial culture PN(A)1 (Bacillus cereus) is metabolically active on LDPE as carbon source during starvation conditions when incubated for up to 60 days, which was confirmed via 2,3,5-triphenyl-tetrazolium chloride (TTC) reduction test, reported cell viability and LDPE degradation. Abrasions, surface erosions, and cavity formations were analyzed via scanning electron microscopy (SEM), whereas the breakdown of high molecular polymers converted to low molecules, i.e., depolymerization, was also observed via Fourier-transform infrared (FTIR) spectroscopy over 90 days, along with changes in functional groups of carboxylic acids and aldehyde as well as the formation of polysulfide, aliphatic compounds, aromatic ethers, alcohols, and ether linkages. Further, transcriptomic analysis was performed via DESeq2 analysis to understand key gene expression patterns and pathways involved in LDPE degradation. During the initial phase of LDPE degradation, genes related to biological processes, like membrane transportation, ABC transporters, carbon and lipid metabolism, fatty acid degradation/oxidation, and TCA cycle, are likely to indicate pathways for stress response and molecular functions, like oxidoreductase, catalytic, lyase, transferase, and hydrolase activities were expressed. Interlinking between metabolic pathways indicates biodegradation process that mineralizes LDPE during subsequent incubation days. These pathways can be targeted for increasing the efficiency of LDPE degradation using microbes in future studies. Thus, considering microbial-mediated biodegradation as practical, eco-friendly, and low-cost alternatives, healthy biomes can degrade polymers in natural environments explored by understanding the genetic and enzymatic expression, connecting their role in the process to the likely metabolic pathways involved, thereby increasing the rate of their biodegradation.


Subject(s)
Plastics , Polyethylene , Polyethylene/metabolism , Plastics/metabolism , Ecosystem , Biodegradation, Environmental , Waste Disposal Facilities , Carbon
16.
J Air Waste Manag Assoc ; 74(5): 335-344, 2024 05.
Article in English | MEDLINE | ID: mdl-38407923

ABSTRACT

Azo dyes, when released untreated in the environment, cause detrimental effects on flora and fauna. Azoreductases are enzymes capable of cleaving commercially used azo dyes, sometimes in less toxic by-products which can be further degraded via synergistic microbial cometabolism. In this study, azoreductases encoded by FMN1 and FMN2 genes were screened from metagenome shotgun sequences generated from the samples of textile dye industries' effluents, cloned, expressed, and evaluated for their azo dye decolorization efficacy. At pH 7 and 45°C temperature, both recombinant enzymes FMN1 and FMN2 were able to decolorize methyl red at 20 and 100 ppm concentrations, respectively. FMN2 was found to be more efficient in decolorization/degradation of methyl red than FMN1. This study offers valuable insights into the possible application of azoreductases to reduce the environmental damage caused by azo dyes, with the hope of contributing to sustainable and eco-friendly practices for the environment management. This enzymatic approach offers a promising solution for the bioremediation of textile industrial effluents. However, the study acknowledges the need for further process optimization to enhance the efficacy of these enzymes in large-scale applications.Implications: The study underscores the environmental hazards associated with untreated release of azo dyes into the environment and emphasizes the potential of azoreductases, specifically those encoded by FMN1 and FMN2 genes, to mitigate the detrimental effects. The study emphasizes the ongoing commitment to refining and advancing the enzymatic approach for the bioremediation of azo dye-containing effluents, marking a positive stride toward more sustainable industrial practices.


Subject(s)
Cloning, Molecular , Industrial Waste , Nitroreductases , Textile Industry , Nitroreductases/genetics , Nitroreductases/metabolism , NADH, NADPH Oxidoreductases/genetics , NADH, NADPH Oxidoreductases/metabolism , Flavin Mononucleotide/metabolism , Azo Compounds/metabolism , Biodegradation, Environmental , Water Pollutants, Chemical/metabolism , Coloring Agents/metabolism , Metagenomics/methods
17.
Mar Pollut Bull ; 201: 116172, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38394797

ABSTRACT

Corals harbour ~25 % of the marine diversity referring to biodiversity hotspots in marine ecosystems. Global efforts to find ways to restore the coral reef ecosystem from various threats can be complemented by studying coral-associated bacteria. Coral-associated bacteria are vital components of overall coral wellbeing. We explored the bacterial diversity associated with coral Dipsastraea favus (D. favus) collected from the Gulf of Kutch, India, using both culture-dependent and metagenomic approaches. In both approaches, phylum Proteobacteria, Firmicutes, and Actinobacteria predominated, comprising the genera Vibrio, Bacillus, Shewanella, Pseudoalteromonas, Exiguobacterium and Streptomyces. Moreover, the majority of culturable isolates showed multiple antibiotic resistance index ≥0.2. In this study, specific bacterial diversity associated with coral sp. D. favus and its possible role in managing coral health was established. Almost 43 strains from the samples were successfully cultured, creating a base for exploring these microbes for their potential use in coral conservation methods.


Subject(s)
Anthozoa , Tinea Favosa , Animals , Anthozoa/microbiology , Ecosystem , Phylogeny , RNA, Ribosomal, 16S , Bacteria/genetics , Coral Reefs , Biodiversity
18.
Pediatr Cardiol ; 34(6): 1508-10, 2013 Aug.
Article in English | MEDLINE | ID: mdl-22806711

ABSTRACT

Myriad electrocardiographic changes, such as ST-segment elevation/depression, altered T-wave morphology, and QT prolongation, have been described with hyperkalemia in the setting of diabetic ketoacidosis (DKA) [2, 3]. We present an adolescent with DKA in whom T-wave inversions was seen despite his having normal serum potassium level.


Subject(s)
Diabetic Ketoacidosis/physiopathology , Electrocardiography , Heart Conduction System/physiopathology , Myocardial Infarction/etiology , Potassium/blood , Adolescent , Diabetic Ketoacidosis/blood , Diabetic Ketoacidosis/complications , Diagnosis, Differential , Humans , Male , Myocardial Infarction/diagnosis , Myocardial Infarction/physiopathology
19.
Cureus ; 15(5): e39653, 2023 May.
Article in English | MEDLINE | ID: mdl-37388590

ABSTRACT

Acute cholecystitis, typically caused by gallstone obstruction of the cystic duct, is often complicated by infection. Mostly observed in immunocompromised patients with bacteremia Methicillin-resistant Staphylococcus aureus (MRSA) is not typically associated with this ailment. Here, we present a unique case of acute cholecystitis caused by MRSA in an immunocompetent patient without bacteremia or underlying disease. A male patient aged 59 years was admitted complaining of severe abdominal pain and nausea. Subsequent investigation confirmed acute calculous cholecystitis and thereafter, the patient underwent laparoscopic cholecystectomy. Gallbladder fluid culture indicated elevated quantities of MRSA growths, and suitable antimicrobial therapy was given as part of the treatment process. This exceptional case underlines the significance of recognizing MRSA as a potential pathogen in severe acute cholecystitis cases, particularly those with severe symptoms. Rapid identification and usage of anti-MRSA antibiotics play a crucial role in managing MRSA-related situations. Healthcare providers need to bear in mind the possibility of cholecystitis associated with MRSA particularly when conventional risk factors are not present. Timely intervention is essential for favorable patient outcomes.

20.
Cureus ; 15(9): e45564, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37868506

ABSTRACT

Symptoms of COVID-19 infection are usually mild in the healthy pediatric population. In some pediatric patients, COVID-19 infection can lead to multisystem inflammatory syndrome in children (MIS-C). We report two cases. Case 1 is a rare case of MIS-C symptoms, presenting with myalgia, chest pain, and fever three days after the second dose of the Pfizer-BioNTech COVID-19 vaccine, which is compared with Case 2, which is a case of MIS-C in an unvaccinated patient with COVID-19 infection who was noted to have acute kidney injury and fluid refractory hypotension. Although MIS-C was reported as a vaccine side effect, we conclude that COVID-19 infection led to the development of MIS-C in our case, not the COVID-19 vaccine. MIS-C symptoms were also noted to be less severe after the COVID-19 vaccine than in the unvaccinated patients.

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