scholarly journals Evaluation of Anti-biofilm Potential of Biosurfactant Extracted from Nocardia Species

Folia Medica ◽  
2021 ◽  
Vol 63 (3) ◽  
pp. 392-399
Author(s):  
Ali Javadi ◽  
Mohamad Reza Pourmand ◽  
Javad Hamedi ◽  
Fatemeh Gharebaghi ◽  
Zohre Baseri ◽  
...  
Keyword(s):  
Agar Plate ◽  
Compositional Analysis ◽  
16S Rrna Gene Sequencing ◽  
Hydrocarbon Chain ◽  
Laboratory Method ◽  
Rrna Gene ◽  
Surface Active Agents ◽  
Rrna Gene Sequencing ◽  
The Stability ◽  
Spreading Test

Introduction: Bacterial natural products such as biosurfactants and surface-active agents are important compounds which exhibit many applications in the fields of medicine.Aim: The aim of the present study was to isolate and identify Nocardia strains with high biosurfactant production and antibiofilm ability.Materials and methods: In the present study, a biosurfactant producing Nocardia species was isolated and identified by a laboratory method. Nocardia species were initially screened and then tested for their ability to produce biosurfactant. The oil spreading test and the surface tension measurements showed that one strain was a biosurfactant producer. The strain with the best surface activity results was selected for further studies and identified by 16S rRNA gene sequencing method. Fourier transform infrared spectroscopy (FTIR) and compositional analysis proved a biosurfactant structure.Results: Oil spreading test and blue agar plate test confirmed biosurfactants and extracellular anionic glycolipids. E24% assay using olive oil revealed strong emulsifying characteristic of the extracted biosurfactant with 100% emulsifying strength. FTIR spectrum indicated the presence of aliphatic hydrocarbon chain (lipid) along with the polysaccharide portion, confirming the glycolipid nature of the biosurfactant. The stability of the biosurfactant produced in different conditions was significant. Increasing concentration of BS significantly inhibited Pseudomonas aeruginosa biofilm.Conclusions: N. coubleae can be a representative of the genus Nocardia for the production of biosurfactants with beneficial physicochemical properties.

Production and Characterization of Biosurfactant by Nocardia Species Isolated Form Soil Samples in Tehran

2021 ◽  
Vol 58 (1) ◽  
pp. 74-80
Author(s):  
Ali Javadi ◽  
Mohamad Reza Pourmand ◽  
Javad Hamedi ◽  
Fatemeh Gharebaghi ◽  
Zohre Baseri ◽  
...  
Keyword(s):  
Agar Plate ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Producer Strain ◽  
Nocardia Species ◽  
Surface Tension Reduction ◽  
Sequencing Method ◽  
Rrna Gene Sequencing ◽  
The Stability

Abstract In this work, we report the Nocardia species were initially screened and then tested for their ability to produce biosurfactant. The biosurfactant production from the Nocardia species was determined by qualitative standard methods. The selected bacterial strain had better oil spreading and emulsifying activity and surface tension reduction. The biosurfactant producer strain was identified by 16S rRNA gene sequencing method. Using Fourier transform infrared spectroscopy and comparative analysis, the biosurfactant structure could be detected. Oil spreading tests and blue agar plate tests confirmed the presence of biosurfactant and extracellular anionic glycolipids. The E24% assay using olive oil showed strong emulsifying characteristic of extracted biosurfactant with a 100%. The stability of the biosurfactant produced in different conditions was significant. Nocardia coubleae was identified by biochemical methods and molecular methods.

scholarly journals Age-Related Colonic Mucosal Microbiome Community Shifts in Monkeys

2020 ◽  
Author(s):  
Ravichandra Vemuri ◽  
Chrissy Sherrill ◽  
Matthew A Davis ◽  
Kylie Kavanagh
Keyword(s):  
Microbial Community ◽  
Systemic Inflammation ◽  
16S Rrna Gene Sequencing ◽  
Microbial Interactions ◽  
Rrna Gene ◽  
Vervet Monkeys ◽  
Fecal Samples ◽  
Age Related ◽  
Rrna Gene Sequencing ◽  
The Stability

Abstract Age-related changes in gut microbiome impact host health. The interactive relationship between the microbiome and physiological systems in an aged body system remains to be clearly defined, particularly in the context of inflammation. Therefore, we aimed to evaluate systemic inflammation, microbial translocation (MT), and differences between fecal and mucosal microbiomes. Ascending colon mucosal biopsies, fecal samples, and blood samples from healthy young and old female vervet monkeys were collected for 16S rRNA gene sequencing, MT, and cytokine analyses, respectively. To demonstrate microbial co-occurrence patterns, we used Kendall’s tau correlation measure of interactions between microbes. We found elevated levels of plasma LBP-1, MCP-1, and CRP in old monkeys, indicative of higher MT and systemic inflammation. Microbiome analysis revealed significant differences specific to age. At the phylum level, abundances of pathobionts such as Proteobacteria were increased in the mucosa of old monkeys. At the family level, Helicobacteriaceae was highly abundant in mucosal samples (old); in contrast, Ruminococcaceae were higher in the fecal samples of old monkeys. We found significantly lower Firmicutes:Bacteroidetes ratio and lower abundance of butyrate-producing microbes in old monkeys, consistent with less healthy profiles. Microbial community co-occurrence analysis on mucosal samples revealed 13 nodes and 41 associations in the young monkeys, but only 12 nodes and 21 associations in the old monkeys. Our findings provide novel insights into systemic inflammation and gut microbial interactions, highlight the importance of the mucosal niche, and facilitate further understanding of the decline in the stability of the microbial community with aging.

scholarly journals Age-Related Colonic Mucosal Microbiome Community Shifts in Monkeys

2020 ◽  
Author(s):  
Ravichandra Vemuri ◽  
Chrissy Sherrill ◽  
Matthew Davis ◽  
Kylie Kavanagh
Keyword(s):  
Microbial Community ◽  
Systemic Inflammation ◽  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Microbial Interactions ◽  
Rrna Gene ◽  
Vervet Monkeys ◽  
Age Related ◽  
Rrna Gene Sequencing ◽  
The Stability

AbstractRecent evidence suggests that gut microbiome changes that occur with age impact the health of the host. While it is known that the gut microbiome and physiological systems interact, the relationship between the microbiome in an aged body system remains to be clearly defined, particularly in the context of inflammation. Therefore, we aimed to evaluate systemic inflammation and the mucosal microbiome in young and old female vervet monkeys. Ascending colon mucosal biopsies and blood samples from healthy young and old monkeys were collected for 16S rRNA gene sequencing and cytokine analyses, respectively. To demonstrate microbial co-occurrence patterns, we used Kendall’s tau correlation measure of interactions between microbes. We found elevated levels of plasma MCP-1 and CRP in old monkeys, which are indicative of higher systemic inflammation. Microbiome analysis revealed increases in abundance of opportunistic pathobionts such as members of the Proteobacteria phylum in old monkeys. At the family level, abundances of Prevotellaceae and Helicobacteraceae were higher in old monkeys than in young. We also found significantly lower Firmicutes to Bacteroidetes ratio (P= 0.03) and lower abundance of butyrate-producing microbes in old monkeys, consistent with a less healthy profile. Microbial community co-occurrence analysis revealed 13 nodes and 41 associations in the young monkeys, but only 12 nodes and 21 associations in the old monkeys. Our findings provided novel insights into systemic inflammation and gut microbial interactions, highlights the importance of the mucosal niche changes with age, and may facilitate further understanding of the decline in the stability of the microbial community with aging.

scholarly journals Identification of Potentially active Methanogenic Population for Degradation of Organic Substances in UASFFR for Treating Sago Wastewater

2019 ◽  
Vol 8 (4) ◽  
pp. 5267-5269
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Research Work ◽  
Agar Plate ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Anaerobic Sludge ◽  
Rrna Gene ◽  
Microbial Decomposition ◽  
Rrna Gene Sequencing

Anaerobic digestion process is the best method for treating industrial wastewater with dynamic relationship between microorganisms. The objective of this research work is to assess the microbial population that coordinates with anaerobic codigestion of biomass cultivated on sago wastewater. An upflow anaerobic sludge fixed film reactor was used to achieve high rates of microbial decomposition. The bacterial colonies were counted and predominant culture was streaked in newer sterile nutrient agar plate. The predominant culture was subjected to molecular identification using 16S rRNA gene sequencing and Gram’s staining. Isolated organism chryseomicrobium species and the organism are identified as Chryseomicrobium palamuruense by using the biochemical and 16S rRNA gene sequencing.

scholarly journals Comprehensive Compositional Analysis of the Slit Lamp Bacteriota

2021 ◽  
Vol 11 ◽  
Author(s):  
Birgit Fritz ◽  
Edita Paschko ◽  
Wayne Young ◽  
Daniel Böhringer ◽  
Siegfried Wahl ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Tertiary Care ◽  
Compositional Analysis ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Slit Lamp ◽  
Taxonomic Assignment ◽  
Coagulase Negative Staphylococci ◽  
Bacterial Phyla ◽  
Rrna Gene Sequencing

Slit lamps are routinely used to examine large numbers of patients every day due to high throughput. Previous, cultivation-based results suggested slit lamps to be contaminated with bacteria, mostly coagulase-negative staphylococci, followed by micrococci, bacilli, but also Staphylococcus aureus. Our study aimed at obtaining a much more comprehensive, cultivation-independent view of the slit lamp bacteriota and its hygienic relevance, as regularly touched surfaces usually represent fomites, particularly if used by different persons. We performed extensive 16S rRNA gene sequencing to analyse the bacteriota, of 46 slit lamps from two tertiary care centers at two sampling sites, respectively. 82 samples yielded enough sequences for downstream analyses and revealed contamination with bacteria of mostly human skin, mucosa and probably eye origin, predominantly cutibacteria, staphylococci and corynebacteria. The taxonomic assignment of 3369 ASVs (amplicon sequence variants) revealed 19 bacterial phyla and 468 genera across all samples. As antibiotic resistances are of major concern, we screened all samples for methicillin-resistant Staphylococcus aureus (MRSA) using qPCR, however, no signals above the detection limit were detected. Our study provides first comprehensive insight into the slit lamp microbiota. It underlines that slit lamps carry a highly diverse, skin-like bacterial microbiota and that thorough cleaning and disinfection after use is highly recommendable to prevent eye and skin infections.

Screening and Molecular Characterization of Cellulase Producing Actinobacteria from Litchi Orchard

2019 ◽  
Vol 13 (1) ◽  
pp. 90-101
Author(s):  
Sanju Kumari ◽  
Utkarshini Sharma ◽  
Rohit Krishna ◽  
Kanak Sinha ◽  
Santosh Kumar
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Biochemical Characterization ◽  
Evolutionary Relationship ◽  
Gene Sequencing ◽  
Cellulase Activity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Background: Cellulolysis is of considerable economic importance in laundry detergents, textile and pulp and paper industries and in fermentation of biomass into biofuels. Objective: The aim was to screen cellulase producing actinobacteria from the fruit orchard because of its requirement in several chemical reactions. Methods: Strains of actinobacteria were isolated on Sabouraud’s agar medium. Similarities in cultural and biochemical characterization by growing the strains on ISP medium and dissimilarities among them perpetuated to recognise nine groups of actinobacteria. Cellulase activity was measured by the diameter of clear zone around colonies on CMC agar and the amount of reducing sugar liberated from carboxymethyl cellulose in the supernatant of the CMC broth. Further, 16S rRNA gene sequencing and molecular characterization were placed before NCBI for obtaining recognition with accession numbers. Results: Prominent clear zones on spraying Congo Red were found around the cultures of strains of three groups SK703, SK706, SK708 on CMC agar plates. The enzyme assay for carboxymethylcellulase displayed extra cellulase activity in broth: 0.14, 0.82 and 0.66 µmol mL-1 min-1, respectively at optimum conditions of 35°C, pH 7.3 and 96 h of incubation. However, the specific cellulase activities per 1 mg of protein did not differ that way. It was 1.55, 1.71 and 1.83 μmol mL-1 min-1. The growing mycelia possessed short compact chains of 10-20 conidia on aerial branches. These morphological and biochemical characteristics, followed by their verification by Bergey’s Manual, categorically allowed the strains to be placed under actinobacteria. Further, 16S rRNA gene sequencing, molecular characterization and their evolutionary relationship through phylogenetics also confirmed the putative cellulase producing isolates of SK706 and SK708 subgroups to be the strains of Streptomyces. These strains on getting NCBI recognition were christened as Streptomyces glaucescens strain SK91L (KF527284) and Streptomyces rochei strain SK78L (KF515951), respectively. Conclusion: Conclusive evidence on the basis of different parameters established the presence of cellulase producing actinobacteria in the litchi orchard which can convert cellulose into fermentable sugar.

scholarly journals Diversity, Composition and Functional Inference of Gut Microbiota in Indian Cabbage white Pieris canidia (Lepidoptera: Pieridae)

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 254
Author(s):  
Ying Wang ◽  
Jianqing Zhu ◽  
Jie Fang ◽  
Li Shen ◽  
Shuojia Ma ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Adult Survival ◽  
Rrna Gene ◽  
Life Stages ◽  
Microbial Composition ◽  
Significant Difference ◽  
Functional Inference ◽  
Rrna Gene Sequencing ◽  
Insect Fitness

We characterized the gut microbial composition and relative abundance of gut bacteria in the larvae and adults of Pieris canidia by 16S rRNA gene sequencing. The gut microbiota structure was similar across the life stages and sexes. The comparative functional analysis on P. canidia bacterial communities with PICRUSt showed the enrichment of several pathways including those for energy metabolism, immune system, digestive system, xenobiotics biodegradation, transport, cell growth and death. The parameters often used as a proxy of insect fitness (development time, pupation rate, emergence rate, adult survival rate and weight of 5th instars larvae) showed a significant difference between treatment group and untreated group and point to potential fitness advantages with the gut microbiomes in P. canidia. These data provide an overall view of the bacterial community across the life stages and sexes in P. canidia.

scholarly journals Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Janis R. Bedarf ◽  
Naiara Beraza ◽  
Hassan Khazneh ◽  
Ezgi Özkurt ◽  
David Baker ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
False Positive ◽  
Gene Sequencing ◽  
Bacterial Biomass ◽  
16S Rrna Gene Sequencing ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Abstract Background Recent studies suggested the existence of (poly-)microbial infections in human brains. These have been described either as putative pathogens linked to the neuro-inflammatory changes seen in Parkinson’s disease (PD) and Alzheimer’s disease (AD) or as a “brain microbiome” in the context of healthy patients’ brain samples. Methods Using 16S rRNA gene sequencing, we tested the hypothesis that there is a bacterial brain microbiome. We evaluated brain samples from healthy human subjects and individuals suffering from PD (olfactory bulb and pre-frontal cortex), as well as murine brains. In line with state-of-the-art recommendations, we included several negative and positive controls in our analysis and estimated total bacterial biomass by 16S rRNA gene qPCR. Results Amplicon sequencing did detect bacterial signals in both human and murine samples, but estimated bacterial biomass was extremely low in all samples. Stringent reanalyses implied bacterial signals being explained by a combination of exogenous DNA contamination (54.8%) and false positive amplification of host DNA (34.2%, off-target amplicons). Several seemingly brain-enriched microbes in our dataset turned out to be false-positive signals upon closer examination. We identified off-target amplification as a major confounding factor in low-bacterial/high-host-DNA scenarios. These amplified human or mouse DNA sequences were clustered and falsely assigned to bacterial taxa in the majority of tested amplicon sequencing pipelines. Off-target amplicons seemed to be related to the tissue’s sterility and could also be found in independent brain 16S rRNA gene sequences. Conclusions Taxonomic signals obtained from (extremely) low biomass samples by 16S rRNA gene sequencing must be scrutinized closely to exclude the possibility of off-target amplifications, amplicons that can only appear enriched in biological samples, but are sometimes assigned to bacterial taxa. Sequences must be explicitly matched against any possible background genomes present in large quantities (i.e., the host genome). Using close scrutiny in our approach, we find no evidence supporting the hypothetical presence of either a brain microbiome or a bacterial infection in PD brains.

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