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1.
Nanomedicine ; 54: 102711, 2023 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-37813236

RESUMO

For the past decades, gene editing demonstrated the potential to attenuate each of the root causes of genetic, infectious, immune, cancerous, and degenerative disorders. More recently, Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated protein 9 (CRISPR-Cas9) editing proved effective for editing genomic, cancerous, or microbial DNA to limit disease onset or spread. However, the strategies to deliver CRISPR-Cas9 cargos and elicit protective immune responses requires safe delivery to disease targeted cells and tissues. While viral vector-based systems and viral particles demonstrate high efficiency and stable transgene expression, each are limited in their packaging capacities and secondary untoward immune responses. In contrast, the nonviral vector lipid nanoparticles were successfully used for as vaccine and therapeutic deliverables. Herein, we highlight each available gene delivery systems for treating and preventing a broad range of infectious, inflammatory, genetic, and degenerative diseases. STATEMENT OF SIGNIFICANCE: CRISPR-Cas9 gene editing for disease treatment and prevention is an emerging field that can change the outcome of many chronic debilitating disorders.


Assuntos
Sistemas CRISPR-Cas , Edição de Genes , Sistemas CRISPR-Cas/genética , Proteína 9 Associada à CRISPR/genética , Proteína 9 Associada à CRISPR/metabolismo , Técnicas de Transferência de Genes , Terapia Genética
2.
Arch Microbiol ; 204(8): 515, 2022 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-35867172

RESUMO

Textile wastewater contains dyes mixed with other contaminants in various concentrations. Bacteria-mediated decolorization and degradation of azo dyes have achieved momentum as a method of treatment attributed to their inexpensive, eco-friendly, and application to a wide range of azo dyes. However, a single species of bacteria is inefficient in decolorizing diverse groups of dyes which is one of the most significant challenges for environmental technologists working in bioremediation. In the present study, an aerobic bacterial consortium AUJ consisting of six different bacterial strains (Pseudomonas stutzeri AK1, Pseudomonas stutzeri AK2, Pseudomonas stutzeri AK3, Bacillus spp. AK4, Pseudomonas stutzeri AK5, and Pseudomonas stutzeri AK6) removed the individual azo dyes in the 24-94% range when used in more than 200 ppm concentration within 72-96 h. In addition, the consortium was able to decolorize 52.19% mixed dyes (100 ppm) and 44.55% Acid blue 113 when used at a concentration as high as 1100 ppm within 96 h. Optimization of various nutritional and environmental parameters revealed that glucose and yeast extract were the preferred carbon and nitrogen source, respectively, and analysis of treated dye products using high-performance liquid chromatography (HPLC), Fourier-transform infrared spectroscopy (FTIR), and gas chromatography-mass spectrometry (GC-MS) confirmed the breakdown of dye. In all, we present a bacterial consortium with a good ability of dye decolorization that can be used for degrading a wide variety of azo dyes.


Assuntos
Compostos Azo , Corantes , Compostos Azo/metabolismo , Bactérias/metabolismo , Biodegradação Ambiental , Corantes/química , Águas Residuárias/microbiologia
3.
BMC Genomics ; 16: 1116, 2015 Dec 29.
Artigo em Inglês | MEDLINE | ID: mdl-26714477

RESUMO

BACKGROUND: The rumen microbiota functions as an effective system for conversion of dietary feed to microbial proteins and volatile fatty acids. In the present study, metagenomic approach was applied to elucidate the buffalo rumen microbiome of Jaffrabadi buffalo adapted to varied dietary treatments with the hypothesis that the microbial diversity and subsequent in the functional capacity will alter with diet change and enhance our knowledge of effect of microbe on host physiology. Eight adult animals were gradually adapted to an increasing roughage diet (4 animals each with green and dry roughage) containing 50:50 (J1), 75:25 (J2) and 100:0 (J3) roughage to concentrate proportion for 6 weeks. Metagenomic sequences of solid (fiber adherent microbiota) and liquid (fiber free microbiota) fractions obtained using Ion Torrent PGM platform were analyzed using MG-RAST server and CAZymes approach. RESULTS: Taxonomic analysis revealed that Bacteroidetes was the most abundant phylum followed by Firmicutes, Fibrobacter and Proteobacteria. Functional analysis revealed protein (25-30 %) and carbohydrate (15-20 %) metabolism as the dominant categories. Principal component analysis demonstrated that roughage proportion, fraction of rumen and type of forage affected rumen microbiome at taxonomic as well as functional level. Rumen metabolite study revealed that rumen fluid nitrogen content reduced in high roughage diet fed animals and pathway analysis showed reduction in the genes coding enzymes involved in methanogenesis pathway. CAZyme annotation revealed the abundance of genes encoding glycoside hydrolases (GH), with the GH3 family most abundant followed by GH2 and GH13 in all samples. CONCLUSIONS: Results reveals that high roughage diet feed improved microbial protein synthesis and reduces methane emission. CAZyme analysis indicated the importance of microbiome in feed component digestion for fulfilling energy requirements of the host. The findings help determine the role of rumen microbes in plant polysaccharide breakdown and in developing strategies to maximize productivity in ruminants.


Assuntos
Búfalos/metabolismo , Fibras na Dieta/microbiologia , Microbiota/genética , Animais , Búfalos/genética , Glicosídeo Hidrolases/genética , Metagenoma/genética , Metagenômica , Rúmen
4.
BMC Cancer ; 14: 925, 2014 Dec 08.
Artigo em Inglês | MEDLINE | ID: mdl-25487856

RESUMO

BACKGROUND: FUSE binding protein1 (FBP1) is a transactivator of transcription of human c-myc proto-oncogene and expressed mainly in undifferentiated cells. It is also present in differentiated normal cells albeit with very low background. FBP1 is abundantly expressed in the majority of hepatocellular carcinoma tumors and has been implicated in tumor development. Although it down-regulates the expression of proapoptotic p21 protein, it is not known whether FBP1 also interacts and antagonizes the function of tumor suppressor protein p53. METHODS: Western blotting was carried out to detect the expression level of FBP1, p21 and p53, and also p53 regulatory factors, BCCIP and TCTP; real-time quantitative PCR was done to determine the fold change in mRNA levels of target proteins; immunoprecipitation was carried out to determine the interaction of FBP1 with p53, BCCIP and TCTP. Cells stably knockdown for either FBP1; p53 or BCCIP were examined for p53 reporter activity under normal and radiation-induced stress. RESULTS: FBP1 physically interacted with p53, impairing its transcription activity and reducing p53-mediated sensitivity to cellular stress. Knockdown of FBP1 expression activated p53-mediated response to cellular stress while transient expression of FBP1 in FBP-knockdown cells restored the inhibition of p53 activity. FBP1 not only interacted with both BCCIP and TCTP, which, respectively, function as positive and negative regulators of p53, but also regulated their expression under cellular stress. In FBP knockdown cells, TCTP expression was down-regulated under radiation-induced stress whereas expression of BCCIP and p21 were significantly up-regulated suggesting FBP1 as a potential regulator of these proteins. We hypothesize that the FBP1-mediated suppression of p53 activity may occur via preventing the interaction of p53 with BCCIP as well as by FBP1-mediated regulation of p53 regulatory proteins, TCTP and BCCIP. Since FBP1 suppresses p53 activity and is overexpressed in most HCC tumors, it may have a possible role in tumorigenesis. CONCLUSION: FBP1 physically interacts with p53, functions as a regulator of p53-regulatory proteins (TCTP and BCCIP), and suppresses p53 transactivation activity under radiation-induced cellular stress. Since it is abundantly expressed in most HCC tumors, it may have implication in tumorigenesis and thus may be a possible target for drug development.


Assuntos
Biomarcadores Tumorais/metabolismo , Proteínas de Ligação ao Cálcio/metabolismo , Carcinoma Hepatocelular/metabolismo , Proteínas de Ciclo Celular/metabolismo , Inibidor de Quinase Dependente de Ciclina p21/metabolismo , DNA Helicases/metabolismo , Proteínas de Ligação a DNA/metabolismo , Neoplasias Hepáticas/metabolismo , Proteínas Nucleares/metabolismo , Transcrição Gênica , Proteína Supressora de Tumor p53/metabolismo , Proteínas de Ligação ao Cálcio/genética , Carcinoma Hepatocelular/genética , Proteínas de Ciclo Celular/genética , Linhagem Celular Tumoral , DNA Helicases/genética , Proteínas de Ligação a DNA/genética , Técnicas de Silenciamento de Genes , Humanos , Neoplasias Hepáticas/genética , Proteínas Nucleares/genética , Proto-Oncogene Mas , Proteínas de Ligação a RNA , Estresse Fisiológico , Proteína Tumoral 1 Controlada por Tradução , Proteína Supressora de Tumor p53/genética
5.
Sci Rep ; 14(1): 10525, 2024 05 08.
Artigo em Inglês | MEDLINE | ID: mdl-38720057

RESUMO

The narrow zone of soil around the plant roots with maximum microbial activity termed as rhizosphere. Rhizospheric bacteria promote the plant growth directly or indirectly by providing the nutrients and producing antimicrobial compounds. In this study, the rhizospheric microbiota of peanut plants was characterized from different farms using an Illumina-based partial 16S rRNA gene sequencing to evaluate microbial diversity and identify the core microbiome through culture-independent (CI) approach. Further, all rhizospheric bacteria that could grow on various nutrient media were identified, and the diversity of those microbes through culture-dependent method (CD) was then directly compared with their CI counterparts. The microbial population profiles showed a significant correlation with organic carbon and concentration of phosphate, manganese, and potassium in the rhizospheric soil. Genera like Sphingomicrobium, Actinoplanes, Aureimonas _A, Chryseobacterium, members from Sphingomonadaceae, Burkholderiaceae, Pseudomonadaceae, Enterobacteriaceae family, and Bacilli class were found in the core microbiome of peanut plants. As expected, the current study demonstrated more bacterial diversity in the CI method. However, a higher number of sequence variants were exclusively present in the CD approach compared to the number of sequence variants shared between both approaches. These CD-exclusive variants belonged to organisms that are more typically found in soil. Overall, this study portrayed the changes in the rhizospheric microbiota of peanuts in different rhizospheric soil and environmental conditions and gave an idea about core microbiome of peanut plant and comparative bacterial diversity identified through both approaches.


Assuntos
Arachis , Bactérias , Metagenômica , Microbiota , RNA Ribossômico 16S , Rizosfera , Microbiologia do Solo , Arachis/microbiologia , Índia , Microbiota/genética , RNA Ribossômico 16S/genética , Metagenômica/métodos , Bactérias/genética , Bactérias/classificação , Bactérias/isolamento & purificação , Fazendas , Raízes de Plantas/microbiologia , Filogenia , Metagenoma , Biodiversidade
6.
Front Microbiol ; 15: 1383989, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38694800

RESUMO

We investigated antibiotic resistance pattern in clinical bacterial pathogens isolated from in-patients and out-patients, and compared it with non-clinical bacterial isolates. 475 bacterial strains isolated from patients were examined for antibiotic resistance. Staphylococcus spp. (148; 31.1%) were found to be the most prevalent, followed by Klebsiella pneumoniae (135; 28.4%), Escherichia coli (74; 15.5%), Pseudomonas aeruginosa (65; 13.6%), Enterobacter spp. (28; 5.8%), and Acinetobacter spp. (25; 5.2%). Drug-resistant bacteria isolated were extended spectrum-ß-lactamase K. pneumoniae (8.8%), E. coli (20%), metallo-ß-lactamase P. aeruginosa (14; 2.9%), erythromycin-inducing clindamycin resistant (7.4%), and methicillin-resistant Staphylococcus species (21.6%). Pathogens belonging to the Enterobacteriaceae family were observed to undergo directional selection developing resistance against antibiotics ciprofloxacin, piperacillin-tazobactam, cefepime, and cefuroxime. Pathogens in the surgical ward exhibited higher levels of antibiotic resistance, while non-clinical P. aeruginosa and K. pneumoniae strains were more antibiotic-susceptible. Our research assisted in identifying the drugs that can be used to control infections caused by antimicrobial resistant bacteria in the population and in monitoring the prevalence of drug-resistant bacterial pathogens.

7.
Pol J Microbiol ; 62(2): 195-200, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-24053023

RESUMO

In the milk industry in India, buffalo breeds are most commonly used for milk production. Efficiency of fiber digestion in ruminants is critical for animal productivity. Bacteria play an important role in fiber digestion and utilization. Absolute quantification real-time PCR was used to quantify ten bacterial species in rumen fluid of Surti buffalo fed green fodder, dry roughage and compound concentrate mixture. Abundance of each target taxon was calculated as a fraction of the total 16S rRNA gene copies in the samples, using taxon-specific primers. Bacterial populations showed a clear predominance of Ruminococcus albus, which comprised 5.66% of the bacterial rRNA gene copies in the samples. However, only 0.9% to 4.24% of the bacterial rRNA gene copies were represented by the ruminal Fibrobacter succinogenes, Ruminococcus flavefaciens and Prevotella species. The proportion of rRNA gene copies attributable to Selenomonas ruminantium, Streptococcus bovis, Ruminobacter amylophilus, Treponema bryantii and Anaerovibrio lipolytica was even less abundant, each comprising < 0.11% of the bacterial rRNA gene copies. The data suggest that the aggregate abundance of the most intensively studied ruminal bacterial species is relatively low and that a large fraction of the uncultured population represents a single bacterial genus.


Assuntos
Líquidos Corporais/microbiologia , Búfalos/microbiologia , Reação em Cadeia da Polimerase em Tempo Real/veterinária , Rúmen/microbiologia , Animais , DNA Bacteriano/genética , Dieta/veterinária , Fibras na Dieta/metabolismo , Índia , RNA Bacteriano/genética , RNA Ribossômico 16S/genética
8.
Mol Biol Rep ; 39(4): 4841-8, 2012 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-21947953

RESUMO

The complex microbiome of the rumen functions as an effective system for the conversion of plant cell wall biomass to microbial proteins, short chain fatty acids and gases. In this study, metagenomic approaches were used to study the microbial populations and metabolic potential of the microbial community. DNA was extracted from Surti Buffalo rumen samples (four treatments diet) and sequenced separately using a 454 GS FLX Titanium system. We used comparative metagenomics to examine metabolic potential and phylogenetic composition from pyrosequence data generated in four samples, considering phylogenetic composition and metabolic potentials in the rumen may remarkably be different with respect to nutrient utilization. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of fermentation of carbohydrates in a high roughage diet. The distribution of phylotypes and environmental gene tags (EGTs) detected within each rumen sample were dominated by Bacteroidetes/Chlorobi, Firmicutes and Proteobacteria in all the samples. The results of this study could help to determine the role of rumen microbes and their enzymes in plant polysaccharide breakdown is fundamental to understanding digestion and maximising productivity in ruminant animals.


Assuntos
Búfalos/genética , Búfalos/microbiologia , Metagenômica/métodos , Rúmen/microbiologia , Animais , Metabolismo dos Carboidratos/genética , Microbiologia Ambiental , Metagenoma/genética , Anotação de Sequência Molecular , Filogenia , Análise de Sequência de DNA
9.
PeerJ ; 9: e12035, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34557347

RESUMO

BACKGROUND: Sequencing driven metagenomics studies have been instrumental in various aspects of microbiology including identification of newer taxa. While this culture-independent approach has its own merits and demerits, several studies have focussed on comparing it with traditional culture-dependent (CD) approach. However, most of these comparative studies rely on Sanger sequencing of complete 16S rRNA gene from pure culture colonies to determine the culturable bacterial diversity. This approach undercounts culturable diversity as only fewer isolates are selected, sequenced, and identified. METHODS: In this study, we have used an Illumina based partial 16S sequencing to identify all the microbes growing on the media and directly comparing with its culture-independent (CI) counterpart. Eight different media were used to target different organisms from soil. Diversity on these media were compared with their CI counterpart. The NGS data was analysed using DADA2 to provide more resolution to the data. RESULTS: In line with studies of similar nature, current study presented higher bacterial diversity in CI approach. However, the current study reflected that a greater number of sequence variants were missed out in CI approach as compared to number of sequence variants shared with CD approach. We observed around 322 (5.98%) ASVs (Amplicon Sequence Variants) exclusively present in CD samples while, 234 (4.35%) ASVs were shared between both approaches. Most of these 322 CD exclusive ASVs were classified as Enterobacteriaceae family and Bacillus genus, with several ASVs annotated at the species level as well, and these organisms are more commonly observed in soil and were also detected in CI approach. Furthermore, 22 genera were exclusively detected in CD samples, most of which were reported from soil and water.

10.
Mar Pollut Bull ; 167: 112293, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33799152

RESUMO

Marine ecosystem harbors diverse microbial diversity adapted to varied environmental conditions and stress. Gujarat possesses a wide coastline with unique and diverse niche in its two Gulfs. PAHs enter marine environments through various anthropogenic discharges and act as a threat to environment due to their xenobiotic nature. In the present study, sediment cores were collected across 4 coordinates, each from Gulf of Kutch and Khambhat; while one from Arabian sea. These samples were enriched for fungal growth in basal medium supplemented with naphthalene, pyrene, phenanthrene, anthracene and fluoranthene. Eight isolates were obtained from 3 samples and checked for tolerance against 5 PAHs followed by assessment of their biodegradation ability. Penicillium ilerdanum NPDF1239-K3-F21 and Aspergillus versicolor NPDF190-C1-26 showed >75% ability to degrade multiple PAHs. The results reveal the potential of fungal isolates from pelagic sediment for further in situ optimization and application in PAH removal from contaminated soil and sediment.


Assuntos
Hidrocarbonetos Policíclicos Aromáticos , Aspergillus , Biodegradação Ambiental , Ecossistema , Fungos , Sedimentos Geológicos , Penicillium
11.
Sci Rep ; 11(1): 17457, 2021 08 31.
Artigo em Inglês | MEDLINE | ID: mdl-34465845

RESUMO

The rhizosphere, a narrow zone of soil near plant roots, is a hot spot for microbial activity. Rhizosphere microbiota directly or indirectly benefit plants by supplementing nutrients, producing beneficial chemicals, or suppressing pathogens. Plants attract and modulate bacteria within the rhizosphere by releasing exudates. Plants also tend to select the rhizosphere microbiota based on their needs; a phenomenon termed as "rhizosphere effect". In this study, we characterized the rhizosphere microbiota of peanut plants across the crop development cycle from pre-sowing of seeds to post-harvest of crop under field conditions. The rhizosphere and bulk soil samples from different crop developmental stages were also compared. The composition of bulk soil microbiota resembled microbiota of pre-sowing and post-harvest soil and was markedly different from rhizosphere soil samples. Rhizosphere samples were enriched with multiple organisms mostly from the Proteobacteria, Firmicutes and Bacteroidota phyla. Differences in diversity were observed among the rhizosphere samples but not in bulk soil across different crop development stages. Pseudomonas_M indica was highly enriched during the germination of seeds. Furthermore, Plant Growth Promoting (PGP) bacteria like Bacillus were enriched during the middle stages of crop development but there was a decline in PGP organisms in the matured crop stage. We also observed a significant association of pH and Electrical Conductivity (EC) with the profiles of microbial community. Overall, this study portrayed the changes in rhizosphere microbiota of peanut during different developmental stages of crop and may help to design stage specific bio-strategies such as bio-fertilizer to improve crop yield.


Assuntos
Arachis/microbiologia , Bactérias/classificação , Produtos Agrícolas/microbiologia , Microbiota , Raízes de Plantas/microbiologia , Rizosfera , Sementes/química , Bactérias/genética , Bactérias/crescimento & desenvolvimento , Filogenia , Microbiologia do Solo
12.
Pol J Microbiol ; 59(3): 175-8, 2010.
Artigo em Inglês | MEDLINE | ID: mdl-21033580

RESUMO

Methane emissions from ruminant livestock are considered to be one of the more potent forms of greenhouse gases contributing to global warming. Many strategies to reduce emissions are targeting the methanogens that inhabit the rumen, but such an approach can only be successful if it targets all the major groups of ruminant methanogens. Therefore, basic knowledge of the diversity of these microbes in breeds of buffalo is required. Therefore, the methanogenic community in the rumen of Surti buffaloes was analyzed by PCR amplification, cloning, and sequencing of methyl coenzyme M reductase (mcrA) gene. A total of 76 clones were identified, revealing 14 different sequences (phylotypes). All 14 sequences were similar to methanogens belonging to the order Methanobacteriales. Within Methanobacteriales, 12 clones (6 OTUs) were similar to Methanosphaera stadtmanae and the remaining 8 phylotypes (64 clones) were similar to unclassified Methanobacteriales. Overall, members of the Methanobacteriales dominated the mcrA clone library in the rumen of Surti buffalo. Further studies and effective strategies can be made to inhibit the growth of Methanobacteriales to reduce methane emission from the rumen which would help in preventing global warming.


Assuntos
Búfalos/fisiologia , Metano/metabolismo , Methanobacteriales/enzimologia , Rúmen/microbiologia , Animais , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , Oxirredutases , Filogenia
13.
3 Biotech ; 10(5): 214, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32351872

RESUMO

Textile industry is one of the anthropogenic activities that consume a large amount of water and pollute water bodies. It uses a massive amount of dyes, which is one of the main constituents of polluting textile effluent. In the present research, biodegradation of Acid Blue 113 dye, a commonly used textile di-azo dye, has been studied exploiting Pseudomonas stutzeri, strain AK6. The dye (300 ppm) was decolorized up to 86.2% within 96 h. The metabolites of Acid Blue 113 obtained after biodegradation were identified by various analytical techniques viz. HPLC (high-performance liquid chromatography) and GC-MS (gas chromatography-mass spectrometry). Genome analysis of isolate AK6 using IMG/M (Integrated Microbial Genomes and Microbiomes) system supported the role of azoreductase and laccase for the decolorization and degradation of azo dye. The ability of P. stutzeri AK6 to tolerate high amount of dye makes it a potential candidate for bioremediation and pre-processing to remove dyes from textile effluents.

14.
Probiotics Antimicrob Proteins ; 12(3): 1126-1138, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-31942681

RESUMO

Weissella paramesenteroides has gained a considerable attention as bacteriocin and exopolysaccharide producers. However, potential of W. paramesenteroides to utilize different prebiotics is unexplored area of research. Fruits being vectors of various probiotics, five W. paramesenteroides strains, namely, FX1, FX2, FX5, FX9, and FX12, were isolated from different fruits. They were screened and selected based on their ability to survive at pH 2.5 and in 1.0% sodium taurocholate, high cell surface hydrophobicity, mucin adhesion, bile-induced biofilm formation, antimicrobial activity (AMA) against selected enteropathogens, and prebiotic utilization ability, implicating the functional properties of these strains. In vitro safety evaluation showed that strains were susceptible to antibiotics except vancomycin and did not harbor any virulent traits such as biogenic amine production, hemolysis, and DNase production. Based on their functionality, two strains FX5 and FX9 were selected for prebiotic utilization studies by thin layer chromatography (TLC) and short-chain fatty acids (SCFAs) production by high performance liquid chromatography. TLC profile evinced the ability of these two strains to utilize low molecular weight galactooligosaccharides (GOS) and fructooligosaccharides (FOS), as only the upper low molecular weight fractions were disappeared from cell-free-supernatants (CFS). Enhanced ß-galactosidase activity correlated with galactose accumulation in residual CFS of GOS displayed GOS utilization ability. Both the strains exhibited AMA against E. coli and Staph. aureus and high SCFAs production in the presence of prebiotic, suggesting their synbiotic potential. Thus, W. paramesenteroides strains FX5 and FX9 exhibit potential probiotic properties with prebiotic utilization and can be taken forward to evaluate synergistic synbiotic potential in detail.


Assuntos
Frutas/microbiologia , Prebióticos , Probióticos , Weissella , Aderência Bacteriana , Escherichia coli/efeitos dos fármacos , Probióticos/isolamento & purificação , Weissella/isolamento & purificação , Weissella/metabolismo
15.
Front Microbiol ; 8: 559, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28439260

RESUMO

Innovations in next-generation sequencing technology have introduced new avenues in microbial studies through "omics" approaches. This technology has considerably augmented the knowledge of the microbial world without isolation prior to their identification. With an enormous volume of bacterial "omics" data, considerable attempts have been recently invested to improve an insight into virosphere. The interplay between bacteriophages and their host has created a significant influence on the biogeochemical cycles, microbial diversity, and bacterial population regulation. This review highlights various concepts such as genomics, transcriptomics, proteomics, and metabolomics to infer the phylogenetic affiliation and function of bacteriophages and their impact on diverse microbial communities. Omics technologies illuminate the role of bacteriophage in an environment, the influences of phage proteins on the bacterial host and provide information about the genes important for interaction with bacteria. These investigations will reveal some of bio-molecules and biomarkers of the novel phage which demand to be unveiled.

16.
Genome Announc ; 4(2)2016 Mar 10.
Artigo em Inglês | MEDLINE | ID: mdl-26966205

RESUMO

Bacillus subtilis C3, a commercial textile dye-decolorizing and -degrading bacterium, was isolated from the common effluent treatment plant (CEPT) of the Jetpur textile dyeing and printing industrial sector situated in the district of Rajkot, Gujarat, India. Here, we present the annotated 4.18-Mb draft genome sequence of B. subtilis C3, providing information about the metabolic pathways involved in decolorization and degradation of several commercial textile azo dyes. Thus, we confirm B. subtilis C3 as a potential candidate for bioremediation of textile effluents.

17.
J Mol Microbiol Biotechnol ; 25(4): 292-9, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26304839

RESUMO

AIM: To reassemble Prevotella ruminicola genome from rumen metagenomic data of cattle and buffalo and compare with the published reference genome. METHOD: Rumen microbial communities from Mehsani buffaloes (n = 8) and Kankrej cattle (n = 8), each adapted to different proportions of a dry or green roughage diet, were subjected to metagenomic sequencing by Ion Torrent PGM, and subsequent reads were analyzed by MG-RAST. Using reference-guided assembly of the sequences against the published P. ruminicola strain 23, draft genomes of 2.56 and 2.46 Mb were reconstructed from Mehsani buffalo and Kankrej cows, respectively. The genomes were annotated using the RAST Server and carbohydrate active enzyme (CAZyme) analysis. RESULTS: Taxonomic analysis by MG-RAST revealed P. ruminicola to be the most abundant species present among the rumen microflora. Functional annotation of reconstructed genomes using the RAST Server depicted the maximum assignment of coding sequences involved in the subsystems amino acid and derivatives and carbohydrate metabolism. CAZyme profiling revealed the glycoside hydrolases (GH) family to be the most abundant. GH family subclassification revealed that the extracted genomes had more sequence hits for GH2, GH3, GH92 and GH97 as compared to the reference. CONCLUSION: The results reflect the metabolic significance of rumen-adapted P. ruminicola in utilizing a coarse diet for animals based on acquisition of novel genetic elements.


Assuntos
Prevotella ruminicola/genética , Rúmen/microbiologia , Animais , Bactérias/classificação , Bactérias/enzimologia , Bactérias/genética , Bactérias/isolamento & purificação , Proteínas de Bactérias/genética , Búfalos , Bovinos , Microbioma Gastrointestinal , Genoma Bacteriano , Metagenômica , Fases de Leitura Aberta , Filogenia , Prevotella ruminicola/classificação , Prevotella ruminicola/enzimologia , Prevotella ruminicola/isolamento & purificação
18.
Genom Data ; 5: 109-11, 2015 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-26484236

RESUMO

Genomic analysis of Clostridium sp. NCR, an anaerobic Gram positive bacterium which was isolated from rumen fluid of Mehsani breed of buffalo revealed presence of various environmental gene tags (EGTs) involved in pathways for utilizing a wide range of substrates. Here we report the sequence of this rumen isolate, its whole genome sequence has been deposited in DDBJ/EMBL/GenBank under the accession number JQHY00000000. The genome comprises of a 3.62-Mb draft genome with a G + C content of 28.10%, which encodes a total of 3126 proteins. Functional analysis provides information about the microbe's role in maintaining host homeostasis and its fiber degradation potential.

19.
Genome Announc ; 2(1)2014 Feb 27.
Artigo em Inglês | MEDLINE | ID: mdl-24578273

RESUMO

Lactobacillus rhamnosus strain LR231 was isolated from the feces of healthy human subjects. It is observed to be a potential probiotic strain, having a broad spectrum of antimicrobial activity against a wide range of human pathogens and food pathogens. Here, we provide the 2.59-Mb draft genome sequence of L. rhamnosus LR231.

20.
Colloids Surf B Biointerfaces ; 122: 175-183, 2014 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-25033437

RESUMO

This work reports intercalation of a sparingly soluble antibiotic (ciprofloxacin) into layered nanostructure silicate, montmorillonite (MMT) and its reaction with bone derived polypeptide, gelatin that yields three-dimensional composite hydrogel. Drug intercalation results in changes in MMT layered space and drug loaded MMT and gelatin creates 3D morphology with biodegradable composite hydrogels. These changes can be correlated with electrostatic interactions between the drug, MMT and the gelatin polypeptides as confirmed by X-ray diffraction patterns, thermal, spectroscopic analyses, computational modeling and 3D morphology revealed by SEM and TEM analysis. No significant changes in structural and functional properties of drug was found after intercalation in MMT layers and composite hydrogels. In vitro drug release profiles showed controlled release up to 150h. The drug loaded composite hydrogels were tested on lung cancer cells (A549) by MTT assay. The results of in vitro cell migration and proliferation assay were promising as composite hydrogels induced wound healing progression. In vitro biodegradation was studied using proteolytic enzymes (lysozyme and protease K) at physiological conditions. This new approach of drug intercalation into the layered nanostructure silicate by ion-exchange may have significant applications in cost-effective wound dressing biomaterial with antimicrobial property.


Assuntos
Antibacterianos/administração & dosagem , Bandagens , Bentonita/administração & dosagem , Materiais Biocompatíveis , Ciprofloxacina/administração & dosagem , Sistemas de Liberação de Medicamentos , Gelatina/administração & dosagem , Hidrogéis , Ferimentos e Lesões/terapia , Linhagem Celular Tumoral , Humanos , Microscopia Eletrônica de Varredura , Microscopia Eletrônica de Transmissão , Difração de Pó , Espectroscopia de Infravermelho com Transformada de Fourier
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