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BMC Bioinformatics Jan 2023Bacteriocins are defined as thermolabile peptides produced by bacteria with biological activity against taxonomically related species. These antimicrobial peptides have...
BACKGROUND
Bacteriocins are defined as thermolabile peptides produced by bacteria with biological activity against taxonomically related species. These antimicrobial peptides have a wide application including disease treatment, food conservation, and probiotics. However, even with a large industrial and biotechnological application potential, these peptides are still poorly studied and explored. BADASS is software with a user-friendly graphical interface applied to the search and analysis of bacteriocin diversity in whole-metagenome shotgun sequencing data.
RESULTS
The search for bacteriocin sequences is performed with tools such as BLAST or DIAMOND using the BAGEL4 database as a reference. The putative bacteriocin sequences identified are used to determine the abundance and richness of the three classes of bacteriocins. Abundance is calculated by comparing the reads identified as bacteriocins to the reads identified as 16S rRNA gene using SILVA database as a reference. BADASS has a complete pipeline that starts with the quality assessment of the raw data. At the end of the analysis, BADASS generates several plots of richness and abundance automatically as well as tabular files containing information about the main bacteriocins detected. The user is able to change the main parameters of the analysis in the graphical interface. To demonstrate how the software works, we used four datasets from WMS studies using default parameters. Lantibiotics were the most abundant bacteriocins in the four datasets. This class of bacteriocin is commonly produced by Streptomyces sp.
CONCLUSIONS
With a user-friendly graphical interface and a complete pipeline, BADASS proved to be a powerful tool for prospecting bacteriocin sequences in Whole-Metagenome Shotgun Sequencing (WMS) data. This tool is publicly available at https://sourceforge.net/projects/badass/ .
Topics: Bacteriocins; RNA, Ribosomal, 16S; Software; Bacteria; Metagenome; Anti-Bacterial Agents
PubMed: 36670373
DOI: 10.1186/s12859-022-05106-x -
Nature Reviews. Microbiology Nov 2021The microbiomes on human body surfaces affect health in multiple ways. They include not only commensal or mutualistic bacteria but also potentially pathogenic bacteria,... (Review)
Review
The microbiomes on human body surfaces affect health in multiple ways. They include not only commensal or mutualistic bacteria but also potentially pathogenic bacteria, which can enter sterile tissues to cause invasive infection. Many commensal bacteria produce small antibacterial molecules termed bacteriocins that have the capacity to eliminate specific colonizing pathogens; as such, bacteriocins have attracted increased attention as potential microbiome-editing tools. Metagenome-based and activity-based screening approaches have strongly expanded our knowledge of the abundance and diversity of bacteriocin biosynthetic gene clusters and the properties of a continuously growing list of bacteriocin classes. The dynamic acquisition, diversification or loss of bacteriocin genes can shape the fitness of a bacterial strain that is in competition with bacteriocin-susceptible bacteria. However, a bacteriocin can only provide a competitive advantage if its fitness benefit exceeds the metabolic cost of production, if it spares crucial mutualistic partner strains and if major competitors cannot develop resistance. In contrast to most currently available antibiotics, many bacteriocins have only narrow activity ranges and could be attractive agents for precision therapy and prevention of infections. A common scientific strategy involving multiple disciplines is needed to uncover the immense potential of microbiome-shaping bacteriocins.
Topics: Bacteria; Bacteriocins; Microbiota
PubMed: 34075213
DOI: 10.1038/s41579-021-00569-w -
Biotechnology Advances 2013Bacteriocins are ribosomally-synthesized antibacterial peptides. These compounds are produced by a broad variety of different bacteria belonging mainly to the genus... (Review)
Review
Bacteriocins are ribosomally-synthesized antibacterial peptides. These compounds are produced by a broad variety of different bacteria belonging mainly to the genus Bifidobacterium, to which health promoting properties have frequently been attributed. However, despite the fact that the identification of Bifidobacterium-associated bacteriocins was first reported in 1980 and that they exhibit antimicrobial activity against pathogenic microorganisms such as Listeria monocytogenes, Clostridium perfringens, and Escherichia coli, relatively little information is still available about the antimicrobial compounds produced by strains of this genus. More detailed understanding of the action mechanisms of these antimicrobials could allow us to determine the extent to which their production contributes to the probiotic properties of specific bifidobacteria strains and, potentially, be of crucial significance for ultimate preservation of functional foods or pharmaceutical applications. Here we review what is already known about their structure, classification, mode of action, functionality, immunity, production and purification.
Topics: Amino Acid Sequence; Anti-Bacterial Agents; Bacteriocins; Bifidobacterium; Culture Media; Molecular Sequence Data
PubMed: 23384878
DOI: 10.1016/j.biotechadv.2013.01.010 -
Applied Microbiology and Biotechnology May 2018Bacteriocins are ribosomally synthesised small antimicrobial peptides produced from a wide range of bacteria, and also rich sources for potential alternatives to... (Review)
Review
Bacteriocins are ribosomally synthesised small antimicrobial peptides produced from a wide range of bacteria, and also rich sources for potential alternatives to traditional antibiotics. Many bacteriocins have highly specific antibacterial activity against target pathogens, even including drug-resistant bacteria such as methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus. As the final and essential step during biosynthesis, the leader sequence removal and exportation of matured bacteriocin are lacking of research and therefore the last to be understood. In respect of production, bacteriocin precursor peptides are processed and exported by a group of membrane proteins from the ATP-binding cassette transporter family. The main aims of this article are to summarise knowledge till now on the leader signal and correlated transporters for bacteriocin secretion in gram-positive bacteria in a review for the first time, to introduce different strategies for higher production, and to offer new insights into many essential but still unanswered questions above for the purpose of more efficient bacteriocin utilisation.
Topics: Anti-Bacterial Agents; Bacteriocins; Chemistry, Pharmaceutical; Gram-Positive Bacteria; Membrane Transport Proteins; Methicillin-Resistant Staphylococcus aureus
PubMed: 29560521
DOI: 10.1007/s00253-018-8917-5 -
Current Drug Metabolism 2017Bacteriocin have been tested as safe and effective alternative molecules over the currently used chemotherapeutic agents. Thus, being an important clinical significance,... (Review)
Review
BACKGROUND
Bacteriocin have been tested as safe and effective alternative molecules over the currently used chemotherapeutic agents. Thus, being an important clinical significance, its screening and recovery methods along with its application are poorly described. Therefore, their screening, purification strategies and utilities must me extended. Thus, in this review, we, summarize potential application, various screening and purification methods used for recovery of bacteriocins.
METHODS
To complete this review, many reviews and previously published reports were studied. We, concentrated on review question and exclusion and inclusion criteria. The quality of content was evaluated by the quality the quality contents evaluation method. The standard method is used to describe the useful contents of available resources and appraised.
RESULTS
One hundred twenty research and review reports were used to complete this report. Sixty reports were used to make a collective information on screening and production of Bacteriocin Eighty two papers were used to explore the antimicrobial, therapeutic, diagnostic etc potentialities of bacteriocin in diverse field. The summarize form of data also presented in the form of tables and figures. This review describes the various methods and parameters that must be considered during the screening and purification methods. Moreover, the useful information is collected in regard represent it therapeutic potentialities in various fields for the welfare of human being.
CONCLUSIONS
The conclusion of this review presented the significance of a fundamental framework for planning to understanding the basic requirement needed for fast, cost effective screening and purification of bacteriocins. The summered area of their utilities also helpful to extend the research field of bacteriocin. Thus, this report would be useful not only to scale up the screening and production strategies faster at economical rate, but also provides a platform to extend the research field of bacteriocin in many ways.
Topics: Animals; Anti-Bacterial Agents; Bacteriocins; Humans
PubMed: 28093993
DOI: 10.2174/1389200218666170116111309 -
Cellular and Molecular Life Sciences :... Sep 2011Bacteriocin AS-48 is an intriguing molecule because of its unique structural characteristics, genetic regulation, broad activity spectrum, and potential biotechnological... (Review)
Review
Bacteriocin AS-48 is an intriguing molecule because of its unique structural characteristics, genetic regulation, broad activity spectrum, and potential biotechnological applications. It was the first reported circular bacteriocin and has been undoubtedly the best characterized for the last 25 years. Thus, AS-48 is the prototype of circular bacteriocins (class IV), for which the structure and genetic regulation have been elucidated. This review discusses the state-of-the-art in genetic engineering with regard to this circular protein, with the use of site-directed mutagenesis and circular permutation. Mutagenesis studies have been used to unravel the role of (a) different residues in the biological activity, underlining the relevance of several residues involved in membrane interaction and the low correlation between stability and activity and (b) three amino acids involved in maturation, providing information on the specificity of the leader peptidase and the circularization process itself. To investigate the role of circularity in the stability and biological properties of the enterocin AS-48, two different ways of linearization have been attempted: in vitro by limited proteolysis experiments and in vivo by circular permutation in the structural gene as-48A. The results summarized here show the significance of circularization on the secondary structure, potency and, especially, the stability of AS-48 and point as well to a putative role of the leader peptide as a protecting moiety in the pre-proprotein. Taken all together, the data available on circular bacteriocins support the idea that AS-48 has been engineered by nature to make a remarkably active and stable protein with a broad spectrum of activity.
Topics: Bacteriocins; Enterococcus faecalis; Mutagenesis, Site-Directed; Protein Engineering; Protein Structure, Secondary
PubMed: 21590312
DOI: 10.1007/s00018-011-0724-4 -
Probiotics and Antimicrobial Proteins Dec 2022Listeria monocytogenes is a well-known foodborne pathogen that usually lives as biofilm to cope with unfavorable surroundings. Bacteriocins have been reported as...
Listeria monocytogenes is a well-known foodborne pathogen that usually lives as biofilm to cope with unfavorable surroundings. Bacteriocins have been reported as antimicrobial compounds, and their bactericidal actions have been extensively studied, but their antibiofilm actions have rarely been studied. Previous study indicated that bacteriocin BMP32r has a broad-spectrum antibacterial activity. In this study, the efficacy of BMP32r against the planktonic bacteria, inhibition of forming biofilm, destruction of mature biofilm, and kill persisters of L. monocytogenes ATCC 15,313 was determined. BMP32r exhibited the bactericidal effect on L. monocytogenes planktonic bacteria. Crystal violet staining showed that sub-minimum inhibitory concentrations (SICs) of BMP32r (1/32 × MIC and 1/16 × MIC) significantly (p < 0.001) inhibit the biofilm formation. In addition, the results of CCK-8, plate count, ruthenium red staining, scanning electron microscopy, and real-time quantitative PCR assay showed that SICs of BMP32r reduced cell adhesion, exopolysaccharide production, quorum sensing, and virulence genes expression in biofilm formation. Moreover, higher concentrations of BMP32r (2 × MIC and 4 × MIC) disrupt the mature biofilm by killing the bacteria in the biofilm and kill L. monocytogenes persisters bacteria effectively. Therefore, BMP32r has promising potential as an antibiofilm agent to combat L. monocytogenes.
Topics: Listeria monocytogenes; Bacteriocins; Biofilms; Quorum Sensing; Microbial Sensitivity Tests; Anti-Bacterial Agents
PubMed: 34709598
DOI: 10.1007/s12602-021-09863-8 -
Methods in Molecular Biology (Clifton,... 1995
Topics: Bacteria; Bacterial Typing Techniques; Bacteriocins; Drug Resistance, Microbial
PubMed: 7550719
DOI: 10.1385/0-89603-297-3:5 -
Deutsche Medizinische Wochenschrift... Sep 1966
Review
Topics: Anti-Bacterial Agents; Bacteriocins; Chemical Phenomena; Chemistry; Colicins
PubMed: 5332126
DOI: 10.1055/s-0028-1111586 -
IET Nanobiotechnology May 2020Bacteriocins produced by lactic acid bacteria are safer alternatives to the more popularly used chemical preservatives which exhibit several adverse effects. The...
Bacteriocins produced by lactic acid bacteria are safer alternatives to the more popularly used chemical preservatives which exhibit several adverse effects. The bacteriocins have an advantage of being efficient in controlling food pathogens without possessing any side-effects. However, the bacteriocins have a limitation of exhibiting a narrow antimicrobial spectrum and having a high-dosage requirement. With an aim to combat these limitations, the present study involved the biosynthesis of bacteriocin-capped nanoparticles, using two bacteriocins (Bac4463 and Bac22) extracted and purified from strains. Nanoconjugates synthesised at optimum conditions were characterized using various physico-chemical techniques. The interaction of bacteriocin-capped silver nanoparticles with the pathogenic bacteria was observed using scanning electron microscopy, wherein the deformed and elongated cells were clearly visible. antimicrobial efficacy of both Bac4463-capped silver nanoparticles and Bac22-capped silver nanoparticles against different food pathogens was observed to be enhanced in comparison to the antimicrobial activity of bacteriocins alone. Minimum inhibitory concentration was observed to be as low as 8 μg/ml for Bac4463-capped silver nanoparticles against , and 2 μg/ml for Bac22-capped silver nanoparticles against . This study, therefore, recommends the use of bacteriocin-capped nanoparticles as food preservatives to control the growth of food spoiling bacteria.
Topics: Anti-Bacterial Agents; Bacteria; Bacteriocins; Metal Nanoparticles; Microbial Sensitivity Tests; Silver
PubMed: 32338634
DOI: 10.1049/iet-nbt.2019.0323