Production of Bacteriocin by Various Strains of Pediococcus acidilacti during Batch Fermentation and Identification of the Pediocin Structural Genes

2021 ◽  
Vol 37 (4) ◽  
pp. 20-31
Author(s):  
R. Vafadoost ◽  
F.B. Elegado ◽  
D. Aghajani ◽  
M.T.M. Perez
Keyword(s):  
Structural Gene ◽  
Metabolic Pathways ◽  
Batch Fermentation ◽  
Large Scale ◽  
Gene Sequence ◽  
Bacteriocin Production ◽  
Pediococcus Acidilactici ◽  
Structural Genes ◽  
Bacterial Strains ◽  
Grant Support

Bacteriocins are antimicrobial peptides produced by certain bacteria that can be alternatives to traditional antibiotics. This study aimed at evaluating large-scale bacteriocin production by the Pediococcus acidilactici strains in batch fermentation and to analyze the pediocin structural gene (papA) by bioinformatic methods. The fermentation using bacterial strains was carried out in Sartorius Biostat A-Plus Bioreactor, and the bacteriocin production was tested on Listeria innocua as a result of 24 h fermentation. The pediocin structural gene papA was amplified, and the amplicons of each strain were sequenced and analyzed to assess the secondary structure of pediocin and related metabolic pathways. It was shown that the papA structural gene sequence is a conserved region. All strains with a papA amplicon synthesis exhibited active bacteriocin synthesis Keywords: fermentation, Pediococcus acidilactici, purified bacteriocin, pediocin structural gene Funding - The authors acknowledge the grant support by the National Institutes of Molecular Biology and Biotechnology (BIOTECH), Laguna, Philippines.

Phyto-fabrication of Iron Nanoparticles: Characterization and Antibacterial Capacity

2020 ◽  
Vol 16 ◽  
Author(s):  
Asma S. Algebaly ◽  
Afrah E. Mohammed ◽  
Mudawi M. Elobeid
Keyword(s):  
Electron Microscopy ◽  
Plant Extracts ◽  
Large Scale ◽  
Iron Nanoparticles ◽  
Ethanolic Extract ◽  
Green Technology ◽  
Resistant Bacteria ◽  
Scale Production ◽  
Bacterial Strains ◽  
Plant Sources

Introduction: Fabrication of iron nanoparticles (FeNPs) has recently gained a great concern for their varied applications in remediation technologies of the environment. Objective: The current study aimed to fabricate iron nanoparticles by green technology approach using different plant sources, Azadirachta indica leaf and Calligonum comosum root following two extraction methods. Methods: Currently, a mixture of FeCl2 and FeCl3 was used to react with the plant extracts which are considered as reducing and stabilizing agents for the generation of FeNPs in one step. Different techniques were used for FeNPs identification. Results: Immediately after mixing of the two reaction components, the color changed to dark brown as an indication of safe conversion of Fe ions to FeNPs, that later confirmed by zeta sizer, transmission electron microscopy (TEM) and scanning electron microscopy (SEM). FeNPs fabricated by C. comosum showed smaller size when compared by those fabricated by A. indica. Using both plant sources, FeNPs fabricated by the aqueous extract had smaller size in relation to those fabricated by ethanolic extract. Furthermore, antibacterial ability against two bacterial strains was approved. Conclusion: The current results indicated that, at room temperature plant extracts fabricated Fe ion to Fe nanoparticles, suggesting its probable usage for large scale production as well as its suitability against bacteria. It could also be recommended for antibiotic resistant bacteria.

scholarly journals General Unified Microbiome Profiling Pipeline (GUMPP) for Large Scale, Streamlined and Reproducible Analysis of Bacterial 16S rRNA Data to Predicted Microbial Metagenomes, Enzymatic Reactions and Metabolic Pathways

Metabolites ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 336
Author(s):  
Boštjan Murovec ◽  
Leon Deutsch ◽  
Blaž Stres
Keyword(s):  
16S Rrna ◽  
Metabolic Pathways ◽  
Large Scale ◽  
Enzymatic Reactions ◽  
Operational Taxonomic Units ◽  
Biochemical Pathways ◽  
Meaningful Information ◽  
Novel Biomarkers ◽  
Reproducible Analysis ◽  
Microbiome Profiling

General Unified Microbiome Profiling Pipeline (GUMPP) was developed for large scale, streamlined and reproducible analysis of bacterial 16S rRNA data and prediction of microbial metagenomes, enzymatic reactions and metabolic pathways from amplicon data. GUMPP workflow introduces reproducible data analyses at each of the three levels of resolution (genus; operational taxonomic units (OTUs); amplicon sequence variants (ASVs)). The ability to support reproducible analyses enables production of datasets that ultimately identify the biochemical pathways characteristic of disease pathology. These datasets coupled to biostatistics and mathematical approaches of machine learning can play a significant role in extraction of truly significant and meaningful information from a wide set of 16S rRNA datasets. The adoption of GUMPP in the gut-microbiota related research enables focusing on the generation of novel biomarkers that can lead to the development of mechanistic hypotheses applicable to the development of novel therapies in personalized medicine.

Escherichia coli phenylalanyl-tRNA synthetase operon: transcription studies of wild-type and mutated operons on multicopy plasmids

1982 ◽  
Vol 152 (2) ◽  
pp. 661-668
Author(s):  
J A Plumbridge ◽  
M Springer
Keyword(s):  
Structural Gene ◽  
Trna Synthetase ◽  
Mrna Levels ◽  
Structural Genes ◽  
Cis Acting ◽  
Trna Synthetases ◽  
Hybridization Probes ◽  
Steady State Levels ◽  
Derivatives Of

The construction of three lambda bacteriophages containing parts of the structural gene for threonyl-tRNA synthetase, thrS, and those for the two subunits of phenylalanyl-tRNA synthetases, pheS and pheT, is described. These phages were used as hybridization probes to measure the in vivo levels of mRNA specific to these three genes. Plasmid pB1 carries the three genes thrS, pheS, and pheT, and strains carrying the plasmid show enhanced levels of mRNA corresponding to these genes. Although the steady-state levels of threonyl-tRNA synthetase and phenylalanyl-tRNA synthetase produced by the presence of the plasmid differed by a factor of 10, their pulse-labeled mRNA levels were about the same. Mutant derivatives of pB1 were also analyzed. Firstly, a cis-acting insertion located before the structural genes for phenylalanyl-tRNA synthetase caused a major decrease in both pheS and pheT mRNA. Secondly, mutations affecting either structural gene pheS or pheT caused a reduction in the mRNA levels for both pheS and pheT. This observation suggests that autoregulation plays a role in the expression of phenylalanyl-tRNA synthetase.

Detection of Biogenic Amine Producer Bacteria in a Typical Italian Goat Cheese

2008 ◽  
Vol 71 (1) ◽  
pp. 205-209 ◽  
Author(s):  
SILVIA BONETTA ◽  
SARA BONETTA ◽  
ELISABETTA CARRARO ◽  
JEAN DANIEL COÏSSON ◽  
FABIANO TRAVAGLIA ◽  
...  
Keyword(s):  
Biogenic Amines ◽  
Enterococcus Faecalis ◽  
Biogenic Amine ◽  
Pediococcus Acidilactici ◽  
Bacterial Strains ◽  
Goat Cheese ◽  
Low Concentrations ◽  
Amine Content ◽  
High Concentrations ◽  
Almost All

The aim of this study was to research decarboxylating bacterial strains and biogenic amine content in a typical Italian goat cheese (Robiola di Roccaverano). The study was performed on fresh and ripened samples of goat cheese manufactured from industrial and artisanal producers. Sixty-seven bacterial strains isolated showed decarboxylating activity, and Enterococcus faecalis was the most widespread decarboxylating species in all artisanal and industrial products. Pediococcus acidilactici and Enterococcus malodoratus were also identified as biogenic amine producers in Robiola di Roccaverano cheese. All the E. faecalis strains isolated in this study were able to decarboxylate tyrosine. Tyramine was the most abundant biogenic amine in cheese samples, while histamine was the most widespread. High amounts of these two biogenic amines were found in ripened samples (up to 2,067 mg/kg for tyramine and 1,786 mg/kg for histamine), whereas 2-phenylethylamine and tryptamine were present in almost all ripened cheeses at low concentrations. The detection of strains producing biogenic amines and the high concentrations of tyramine and histamine found in ripened Robiola di Roccaverano could represent a potential risk to the consumer.

scholarly journals Phoenix 2: A locally installable large-scale 16S rRNA gene sequence analysis pipeline with Web interface

2013 ◽  
Vol 167 (4) ◽  
pp. 393-403 ◽  
Author(s):  
Jung Soh ◽  
Xiaoli Dong ◽  
Sean M. Caffrey ◽  
Gerrit Voordouw ◽  
Christoph W. Sensen
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Large Scale ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Web Interface ◽  
Rrna Gene Sequence ◽  
Analysis Pipeline ◽  
Gene Sequence Analysis

scholarly journals Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea

2007 ◽  
Vol 57 (3) ◽  
pp. 548-551 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Min-Kyeong Kim ◽  
Seung-Hee Yoo ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Bacterial Strains ◽  
Lysobacter Enzymogenes ◽  
Gene Sequence Analysis ◽  
Greenhouse Soils

Two bacterial strains, designated GH34-4T and GH41-7T, were isolated from greenhouse soil cultivated with cucumber. The bacteria were strictly aerobic, Gram-negative, rod-shaped and oxidase- and catalase-positive. 16S rRNA gene sequence analysis indicated that these strains belong to the genus Lysobacter within the Gammaproteobacteria. Strain GH34-4T showed highest sequence similarity to Lysobacter yangpyeongensis GH19-3T (97.5 %) and Lysobacter koreensis Dae16T (96.4 %), and strain GH41-7T showed highest sequence similarity to Lysobacter antibioticus DSM 2044T (97.5 %), Lysobacter enzymogenes DSM 2043T (97.5 %) and Lysobacter gummosus ATCC 29489T (97.4 %). Levels of DNA–DNA relatedness indicated that strains GH34-4T and GH41-7T represented species clearly different from L. yangpyeongensis, L. antibioticus, L. enzymogenes and L. gummosus. The major cellular fatty acids of strains GH34-4T and GH41-7T were iso-C16 : 0, iso-C15 : 0 and iso-C17 : 1 ω9c, and the major isoprenoid quinone was Q-8. The DNA G+C contents of GH34-4T and GH41-7T were 62.5 and 66.6 mol%, respectively. On the basis of the polyphasic taxonomic data presented, it is evident that each of these strains represents a novel species of the genus Lysobacter, for which the names Lysobacter niabensis sp. nov. (type strain GH34-4T=KACC 11587T=DSM 18244T) and Lysobacter niastensis sp. nov. (type strain GH41-7T=KACC 11588T=DSM 18481T) are proposed.

scholarly journals Proteomic responses of spores of Bacillus subtilis to thermosonication involve large-scale alterations in metabolic pathways

2020 ◽  
Vol 64 ◽  
pp. 104992
Author(s):  
Lihua Fan ◽  
Furong Hou ◽  
Aliyu Idris Muhammad ◽  
Balarabe Bilyaminu Ismail ◽  
Ruiling lv ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Metabolic Pathways ◽  
Large Scale ◽  
Proteomic Responses

scholarly journals MetaBMF: a scalable binning algorithm for large-scale reference-free metagenomic studies

2019 ◽  
Vol 36 (2) ◽  
pp. 356-363 ◽  
Author(s):  
Terry Ma ◽  
Di Xiao ◽  
Xin Xing
Keyword(s):  
Large Scale ◽  
Empirical Studies ◽  
Nonnegative Matrix ◽  
Rapid Identification ◽  
Strain Level ◽  
Bacterial Strains ◽  
Binary Matrix ◽  
Next Generation Sequencing Technology ◽  
Microbial Species ◽  
Reference Genomes

Abstract Motivation Metagenomics studies microbial genomes in an ecosystem such as the gastrointestinal tract of a human. Identification of novel microbial species and quantification of their distributional variations among different samples that are sequenced using next-generation-sequencing technology hold the key to the success of most metagenomic studies. To achieve these goals, we propose a simple yet powerful metagenomic binning method, MetaBMF. The method does not require prior knowledge of reference genomes and produces highly accurate results, even at a strain level. Thus, it can be broadly used to identify disease-related microbial organisms that are not well-studied. Results Mathematically, we count the number of mapped reads on each assembled genomic fragment cross different samples as our input matrix and propose a scalable stratified angle regression algorithm to factorize this count matrix into a product of a binary matrix and a nonnegative matrix. The binary matrix can be used to separate microbial species and the nonnegative matrix quantifies the species distributions in different samples. In simulation and empirical studies, we demonstrate that MetaBMF has a high binning accuracy. It can not only bin DNA fragments accurately at a species level but also at a strain level. As shown in our example, we can accurately identify the Shiga-toxigenic Escherichia coli O104: H4 strain which led to the 2011 German E.coli outbreak. Our efforts in these areas should lead to (i) fundamental advances in metagenomic binning, (ii) development and refinement of technology for the rapid identification and quantification of microbial distributions and (iii) finding of potential probiotics or reliable pathogenic bacterial strains. Availability and implementation The software is available at https://github.com/didi10384/MetaBMF.

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