ArticlePDF Available

Complete genome sequence of Streptococcus hyointestinalis B19, a strain producing bacteriocin, isolated from chicken feces

Authors:
Ju-Eun Lee at Chung-Ang University
Ju-Eun Lee
Sunhak Heo
Sunhak Heo
Sunhak Heo
  • This person is not on ResearchGate, or hasn't claimed this research yet.
Geun-Bae Kim at Chung-Ang University
Geun-Bae Kim
Download full-text PDF
Read full-text
Download citation

Abstract

Streptococcus hyointestinalis B19 was isolated from chicken feces collected from local farm in Anseong, Korea. S. hyointestinalis B19 was shown to produce bacteriocin-like compounds exhibiting inhibitory activities against several pathogens including strains of Clostridium perfringens and Listeria monocytogenes. The whole genome of S. hyointestinalis B19 strain was sequenced using PacBio RS II platform. The genome comprised four contigs with a size of 2,217,061 bp. The DNA G + C content was found to be 42.95 mol%. Annotation results revealed 2,266 coding sequences (CDSs), 18 rRNAs, and 61 tRNA genes. Based on genome analysis, we found that the strain B19 possessed various genes associated with bacteriocin synthesis, modification, and transport.
Available via license: CC BY-NC 4.0
Content may be subject to copyright.
420 https://www.ejast.org
Journal of Animal Science and Technology
RESEARCH ARTICLE
J Anim Sci Technol 2020;62(3):420-422
https://doi.org/10.5187/jast.2020.62.3.420 pISSN 2672-0191 eISSN 2055-0391
Complete genome sequence of
Streptococcus hyointestinalis B19,
a strain producing bacteriocin, iso-
lated from chicken feces
Ju-Eun Lee, Sunhak Heo and Geun-Bae Kim*
Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea
Abstract
Streptococcus hyointestinalis B19 was isolated from chicken feces collected from local farm
in Anseong, Korea. S. hyointestinalis B19 was shown to produce bacteriocin-like compounds
exhibiting inhibitory activities against several pathogens including strains of Clostridium per-
fringens and Listeria monocytogenes. The whole genome of S. hyointestinalis B19 strain was
sequenced using PacBio RS II platform. The genome comprised four contigs with a size of
2,217,061 bp. The DNA G + C content was found to be 42.95 mol%. Annotation results re-
vealed 2,266 coding sequences (CDSs), 18 rRNAs, and 61 tRNA genes. Based on genome
analysis, we found that the strain B19 possessed various genes associated with bacteriocin
synthesis, modication, and transport.
Keywords: Streptococcus hyointestinalis B19, Whole genome, Chicken feces, Bacteriocin
In recent years, there have been increasing studies to nd alternatives to antibiotics, such as antibodies,
probiotics, bacteriophages, and bacteriocins because of the increase in antibiotic resistance [1,2]. In our
previous study, we reported that S. hyointestinalis B19 has potential to be used in similar applications [3].
S. hyointestinalis B19 strain was found to produce antimicrobial protein molecules, which possess char-
acteristics similar to those of bacteriocin (heat stability). e selected strains of Clostridium perfringens
and Listeria monocytogenes were strongly inhibited by the strain B19. To conrm whether the antimicro-
bial substance is bacteriocin and to better understand the characteristics of the molecule, we carried out
whole genome sequencing of the strain B19.
S. hyointestinalis B19 was isolated from chicken fecal samples collected from local farm in Anseong,
Korea. e genomic DNA was extracted from the strain B19 cultured to stationary phase in M17 me-
dium supplemented with 0.5% (w/v) glucose using QIAamp PowerFecal DNA Kit (Qiagen) according
to the manufacturer’s instructions. e whole genome of strain B19 was sequenced using Pacic Biosci-
ences (PacBio) RS II Single Molecule Real Time (SMRT) platform with a 20 kb SMRTbellTM tem-
plate library at ChunLab. e reads were assembled on PacBio SMAR Analysis 2.3.0. Genome analy-
sis and annotation were performed by CLgenomicsTM v. 1.55 software. Transfer RNAs (tRNAs) were
identied using tRNAscan-SE v. 1.3.1. Ribosomal RNAs (rRNAs) and non-coding RNAs (ncRNAs)
were identied using INFERNAL v. 1.0.2 with Rfam 12.0 database. For CRISPR, PilerCR v. 1.06 and
CRT v. 1.2 were used. Protein-coding sequences (CDSs) were identied by using PRODIGAL v. 2.6.2
[4] and compared to protein databases (SwissProt, KEGG, SEED, EggNOG) using USEARCH v. 8.1
Received: Mar 4, 2020
Accepted: Mar 19, 2020
*Corresponding author
Geun-Bae Kim
Department of Animal Science and
Technology, Chung-Ang University,
Anseong 17546, Korea.
Tel: +82-31-670-3027
E-mail: kimgeun@cau.ac.kr
Copyright © 2020 Korean Society of
Animal Sciences and Technology.
This is an Open Access article
distributed under the terms of the
Creative Commons Attribution
Non-Commercial License (http://
creativecommons.org/licenses/by-
nc/4.0/) which permits unrestricted
non-commercial use, distribution, and
reproduction in any medium, provided
the original work is properly cited.
ORCID
Ju-Eun Lee
https://orcid.org/0000-0002-6467-1562
Sunhak Heo
https://orcid.org/0000-0002-2133-8540
Geun-Bae Kim
https://orcid.org/0000-0001-8531-1104
Competing interests
No potential conict of interest relevant
to this article was reported.
Funding sources
This manuscript has not received any
funding.
Acknowledgements
Not applicable.
Availability of data and material
Upon reasonable request, the datasets
of this study can be available from the
corresponding author.
https://doi.org/10.5187/jast.2020.62.3.420 https://www.ejast.org | 421
Lee et al.
[5] for functional annotation. e draft genome of S. hyointestinalis B19 consisted of a 2,217,061
bp chromosome with a G + C content of 42.95% (Table 1). e genome contained 2,266 coding
sequences (CDSs), 18 rRNAs, and 61 tRNA genes (Fig. 1).
e mining of the bacteriocinogenic gene clusters was performed by using the BAGEL4 plat-
form [6]. e genome possessed thmA-, thmB-like genes, and bovicin 255-like genes. e former
genes encode peptides mA and mB, respectively, that form ermophilin 13, the bacteriocin
Authors’ contributions
Conceptualization: Kim GB.
Data curation: Lee JE.
Formal analysis: Heo S.
Investigation: Lee JE, Heo S, Kim GB.
Writing - original draft: Lee JE.
Writing - review & editing: Lee JE, Kim GB.
Ethics approval and consent to participate
This manuscript does not require IRB/IACUC
approval because there are no human and
animal participants. Table 1. Genome features of Streptococcus hyointestinalis B19
Property Value
Genome assembly
Assemble method SMAR analysis version 2.3.0
Genome coverage 438.91x
Genome features
Genome size (bp) 2,217,061
No. of contigs 4
G + C content (%) 42.95
Protein-coding genes (CDSs) 2,266
rRNA genes 18
tRNA genes 61
Plasmids 0
Genbank accession No. JAAKGB000000000
Fig. 1. Circular genome map of Streptococcus hyointestinalis B19. From the outermost circle to the center,
each circle indicates information about tRNA/rRNA, forward and reverse coding sequences (CDSs), GC ratio,
and GC skew.
Streptococcus hyointestinalis B19 genome
422 | https://www.ejast.org https://doi.org/10.5187/jast.2020.62.3.420
rst isolated from S. thermophilus [7]. Strain 19 also contains the genes associated with ABC-trans-
porter and bacteriocin immunity for bacteriocin export and self-immunity to bacteriocin, respec-
tively. ese two genes are common members of the lantibiotic gene clusters [8].
Nucleotide sequence accession number
e GenBank/EMBL/DDBJ accession number for the genome sequence of S. hyointestinalis B19
is JAAKGB000000000.
REFERENCES
1. Czaplewski L, Bax R, Clokie M, Dawson M, Fairhead H, Fischetti VA, et al. Alternatives to
antibiotics-a pipeline portfolio review. Lancet Infect Dis. 2016;16:239-51.
2. Joerger RD. Alternatives to antibiotics: bacteriocins, antimicrobial peptides and bacteriophages.
Poult Sci. 2003;82:640-7.
3. Heo S, Kim MG, Kwon M, Lee HS, Kim GB. Inhibition of Clostridium perfringens using
bacteriophages and bacteriocin producing strains. Korean J Food Sci Anim Resour. 2018;38:88-
98.
4. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokary-
otic gene recognition and translation initiation site identification. BMC Bioinformatics.
2010;11:119.
5. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics.
2010;26:2460-1.
6. van Heel AJ, de Jong A, Song C, Viel JH, Kok J, Kuipers OP. BAGEL4: a user–friendly web
server to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Res. 2018;46:W278-81.
7. Marciset O, Jeronimus-Stratingh MC, Mollet B, Poolman B. Thermophilin 13, a nontypi-
cal antilisterial poration complex bacteriocin, that functions without a receptor. J Biol Chem.
1997;272:14277-84.
8. McAulie O, Ross RP, Hill C. Lactibiotics: structure, biosynthesis and mode of action. FEMS
Microbiol Rev. 2001;25:285-308.
... continue to be a growing concern as it threatens the effectivity of traditional antimicrobial compounds against its target pathogens [1,2]. This evolutionary arms race demands the identification and development of novel antimicrobial compounds that have the potential to substitute antibiotic use and other similar applications. ...
... This evolutionary arms race demands the identification and development of novel antimicrobial compounds that have the potential to substitute antibiotic use and other similar applications. Bacteriocins, which are ribosomal-synthesized peptides produced by bacteria to inhibit the growth of closely related strains [2,3], are potential alternatives to traditional antibiotics [4]. Enterococcus faecalis CAUM157, a Gram-positive, facultatively anaerobic, non-spore-forming cocci [5], was observed to produce an antimicrobial protein with potent activity against a wide range of bacteria including periodontal disease-causing pathogens, Prevotella intermedia and Fusobacterium nucleatum [6], and Listeria monocytogenes, and Staphylococcus aureus (unpublished data). ...
Complete Genome Sequence of Enterococcus faecalis CAUM157 Isolated from Raw Cow’s Milk
Article
Full-text available
  • Aug 2020
Enterococcus faecalis CAUM157, isolated from raw cow’s milk, is a Gram-positive, facultatively anaerobic, and non-spore-forming bacterium capable of inhabiting a wide range of environmental niches. E. faecalis CAUM157 was observed to produce a two-peptide bacteriocin that had a wide range of activity against several pathogens, including Listeria monocytogenes, Staphylococcus aureus, and periodontitis-causing bacteria. The whole genome of E. faecalis CAUM157 was sequenced using the PacBio RS II platform, revealing a genome size of 2,972,812 bp with a G+C ratio of 37.44%, assembled into two contigs. Annotation analysis revealed 2,830 coding sequences, 12 rRNAs, and 61 tRNAs. Further, in silico analysis of the genome identified a single bacteriocin gene cluster.
View
... The two species identified include Streptococcus hyointestinalis and Streptococcus macedonicus. S. hyointestinalis was first isolated in the intestine of pigs [79] and has shown potential in producing anti-pathogen compounds similar to bacteriocin [80]. S. macedonicus, on the other hand, is known to participate in the fermentation of dairy and dairy-derived products. ...
Influence of Sex and a High-Fiber Diet on the Gut Microbiome of Alentejano Pigs Raised to Heavy Weights
Article
Full-text available
  • Nov 2023
Simple Summary The concept of modernization of pig production systems should not rely only on new technological inputs and opportunities, but should also address societal expectations regarding animal well-being while maintaining product quality. The Alentejano (AL) pig is a fatty breed from Portugal traditionally raised outdoors, surgically castrated, and slaughtered at heavy weights for its renowned high-quality meat and meat products. The gastrointestinal tract of pigs harbors a diverse ecosystem of microorganisms that play a major role in feed digestion, nutrient absorption, and in the synthesis and metabolism of skatole, one of the main sources of the unpleasant boar taint. Our study aimed to investigate gut microbiota changes in heavy AL pigs fed with a new high-fiber diet, aiming to reduce the skatole-producing microbiota, while also exploring the effects of surgical castration in that community. The pigs that were fed the new diet presented higher abundances of species responsible for breaking down complex carbohydrate substrates, while castrated pigs presented lower abundances of probiotic bacteria, normally associated with better gut health and lower body fat. Utilizing fiber-enriched diets remains a promising approach to address boar taint in intact animals, especially when sourced from locally produced legumes and agricultural by-products, which can also contribute to broader sustainability objectives. Abstract This study investigates the influence of sex and a dietary transition on the gut microbiota of a local Portuguese pig breed. Three groups of male Alentejano pigs (n = 10 each) were raised between ~40 and 160 kg LW. Group C included pigs that were surgically castrated, while the I group included intact ones; both were fed with commercial diets. The third group, IExp, included intact pigs that were fed commercial diets until ~130 kg, then replaced by an experimental diet based on legumes and agro-industrial by-products between ~130 and 160 kg. Fecal samples were collected two weeks before slaughter. The total DNA was extracted and used for 16S metabarcoding on a MiSeq® System. The dietary transition from a commercial diet to the experimental diet substantially increased and shifted the diversity observed. Complex carbohydrate fermenting bacteria, such as Ruminococcus spp. and Sphaerochaeta spp., were significantly more abundant in IExp (q < 0.05). On the other hand, castrated pigs presented a significantly lower abundance of the potential probiotic, Roseburia spp. and Lachnospiraceae NK4A136 group (q < 0.01), bacteria commonly associated with better gut health and lower body fat composition. Understanding the role of gut microbiota is paramount to ensure a low skatole deposition and consumers’ acceptance of pork products from non-castrated male pigs.
View
... The obtained 16S rRNA sequence was identified by the EzBioCloud (https://www.ezbiocloud.net/?bannerId=8) sever to calculate and compare levels of similarity. For strain RerS4, ISP 2, ISP 3, ISP 4, ISP 5, ISP 6, ISP 7 [24] and nutrient agar [26] media were used to observe aerial and substrate mycelium. Spore characteristics were observed by scanning electron microscopy (SEM) (Hitachi SU8010) using cultures grown on ISP 3 agar at 28 • C for 2 weeks. ...
Whole genome analysis of Streptomyces sp. RerS4, a Rehmannia glutinosa rhizosphere microbe producing a new lipopeptide
Article
Full-text available
  • Aug 2023
Rehmannia glutinosa, a valuable medicinal plant, is threatened by ring rot, a condition that greatly affects its yield and quality. Interactions between plant and the rhizosphere soil microbiome in the context of pathogen invasion are generally more specific, with recruitment of specialized microbes potentially antagonistic to a certain pathogen. Isolation of microorganisms from rhizosphere soil of healthy and ring rot-infected R. glutinosa was carried out to screen antifungal microbes. A strain designated RerS4 isolated from ring rot-infected R. glutinosa rhizosphere soil with strong antifungal activities was selected for further study. RerS4 was taxonomically characterized as the genus Streptomyces according to its morphology and 16S rRNA sequences that were most closely related to Streptomyces racemochromogenes NRRL B-5430T (99.72%) and Streptomyces polychromogenes NBRC 13072T (99.72%). A new lipopeptide isolated from RerS4 showed restrained proliferation, but was devoid of significant antibacterial and antioxidant activity with minimum inhibitory concentration (MIC) values of 20.3 ± 2.5 and 70.8 ± 3.7 μg/mL and half-maximal inhibitory concentration (IC50) values of 23.3 ± 0.8 and 58.8 ± 2.9 μg/mL, respectively. In addition, we report the complete genome sequence of Streptomyces sp. RerS4, which consists of a 7,301,482 bp linear chromosome and a 242,139 bp plasmid. Genome analysis revealed that Streptomyces sp. RerS4 contained 25 biosynthetic gene clusters (BGCs) for secondary metabolites, among which 68% had low similarities with known BGCs, leading us to believe that Streptomyces sp. RerS4 could produce valuable bioactive compounds.
View
... Putative protein coding sequences were predicted using Glimmer v3.02 [4], rapid prokaryotic genome annotation (PROKKA) v1.14.5 [5] and Rapid Annotation using Subsystem Technology (RAST) v2.0 [6]. The results from the three prediction methods were confirmed by manual curation [7]. The genes of rRNA and tRNA were predicted using RNAmmer v1.2 and tRNAscan-SE v1.4, ...
Complete genome sequence of Lactococcus lactis strain K_LL005, a xylose-utilizing bacterium isolated from grasshopper (Oxya chinensis sinuosa)
Article
Full-text available
  • Dec 2020
Lactococcus lactis is a fermentative lactic acid bacterium that is used extensively in food fermentations. The L. lactis strain K_LL005 was isolated from the grasshopper (Oxya chinensis sinuosa) gut in Korea. In this study, we reported the complete genome sequence of Lactococcus lactis K_LL005. The final complete genome assembly consist of one circular chromosome (2,375,093 bp) with an overall guanine + cytosine (G + C) content of 35.0%. Annotation results revealed 2,281 protein-coding sequences (CDSs), 19 rRNAs, and 68 tRNA genes. Lactococcus lactis K_LL005 has a gene encoding xylose metabolism such as xylR, xylA, and xylB (xylRAB).
View
Dietary inclusion of High Amylose Cornstarch Increased Cecal digesta Lactobacillus and Terrisporobacter and Decreased Streptococcus Genera of Weanling Pigs
Preprint
Full-text available
  • Jan 2024
The study investigated the effect of dietary inclusion of high amylose cornstarch ( HA-starch ) on cecal microbiota composition and volatile fatty acid ( VFA ) concentrations in weanling pigs fed high levels of cold-pressed canola cake ( CPCC ). Weaned pigs (240 mixed sex; 7.1 ± 1.2 kg) were housed in 40 pens (6 pigs/pen) and fed a common commercial diet for 7 days, followed by the experimental diets for 28 d, which contained either 0% or 40% CPCC with either 0% or 40% HA-starch. At the end of the study, one pig from each pen (n = 8) was selected and euthanized to collect cecal digesta for microbial and VFA composition analyses. The HA-starch increased (p < 0.001) acetate, propionate, and butyrate concentrations, thereby increasing total VFA concentration (p < 0.001). There was a tendency for cecal butyrate and total VFA concentrations to decrease when pigs were fed the 40% CPCC diet without HA-starch but increase when fed the 40% CPCC diet containing 40% HA-starch (CPCC x HA-starch effect; p = 0.09), indicating HA-starch can increase cecal butyrate and total VFA concentrations in pigs fed a diet with high CPCC level. The proportions of Lactobacillus and Terrisporobacter were high, whereas low proportions of Streptococcus genus were observed in the cecal microbiota of pigs fed diets containing 40% HA-starch. Also, pathways consistent with carbohydrate digestion, absorption, and phosphate metabolism were enriched in pigs when the diet included 40% HA-starch. In summary, incorporating high amounts of HA-starch in a weanling pig diet containing high levels of CPCC may benefit gut health and digestive performance by enhancing the abundance of probiotic commensal bacteria, contributing to increased enzymatic activity and carbohydrate metabolism.
View
Complete genome sequence of Bacillus coagulans CACC834 isolated from canine
Article
Full-text available
  • Oct 2021
Bacillus coagulans CACC 834 was isolated from canine feces, and its potential probiotic properties were characterized by functional genome analysis. Whole-genome sequencing of B. coagulans CACC 834 was performed using the PacBio RSII platforms. The complete genome assembly consisted of one circular chromosome (3.1 Mb) with guanine (G) + cytosine (C) content of 47.1%. Annotation revealed 3,181 protein-coding sequences (CDSs), 30 rRNAs, and 83 tRNAs. Gene associated 11% of the genes were involved in replication, recombination, and repair. We also annotated various stress-related, acid resistance, bile salt resistance and adhesion-related domains in this strain, which likely provide support in exerting probiotic action by survival under gastrointestinal tract. These results add to our comprehensive understanding of B. coagulans and suggest potential mammal-related industrial applications.
View
BAGEL4: A user-friendly web server to thoroughly mine RiPPs and bacteriocins
Article
Full-text available
  • May 2018
Interest in secondary metabolites such as RiPPs (ribosomally synthesized and posttranslationally modified peptides) is increasing worldwide. To facilitate the research in this field we have updated our mining web server. BAGEL4 is faster than its predecessor and is now fully independent from ORF-calling. Gene clusters of interest are discovered using the core-peptide database and/or through HMM motifs that are present in associated context genes. The databases used for mining have been updated and extended with literature references and links to UniProt and NCBI. Additionally, we have included automated promoter and terminator prediction and the option to upload RNA expression data, which can be displayed along with the identified clusters. Further improvements include the annotation of the context genes, which is now based on a fast blast against the prokaryote part of the UniRef90 database, and the improved web-BLAST feature that dynamically loads structural data such as internal cross-linking from UniProt. Overall BAGEL4 provides the user with more information through a user-friendly web-interface which simplifies data evaluation. BAGEL4 is freely accessible at http://bagel4.molgenrug.nl.
View
Inhibition of Clostridium perfringens using Bacteriophages and Bacteriocin Producing Strains
Article
Full-text available
  • Feb 2018
In this study, we isolated and characterized a bacteriocin-producing strain and two bacteriophages (P4, A3), showing antimicrobial effects against Clostridium perfringens, from chicken and swine feces by the spot-on-the lawn antagonism method. The selected strain was identified as Streptococcus hyointestinalis by 16S rRNA gene sequencing. The bacteriocin from the isolated strain exhibited strong inhibitory activity against four strains of C. perfringens and all the tested strains of Listeria monocytogenes, and the bacteriocin were highly heat- and pH-stable even at pH 2, pH 10 and 121°C for 15 min. We also evaluated the combined effects of the isolated bacteriocin and phages. Combining the phage treatments and bacteriocin resulted in a synergetic effect compared with the phage or the bacteriocin alone. In addition, during the probiotic test, the bacteriocin-producing S. hyointestinalis B19 strain reduced the population of C. perfringens significantly. Treatment with S. hyointestinalis B19 and a cocktail of lytic bacteriophages eradicated the C. perfringens KCTC 3269T, completely. Consequently, the isolated bacteriocin and bacteriophages represent candidates for effective biocontrol of C. perfringens, and bacteriocin-producing S. hyointestinalis B19 is a potential probiotic candidate for use in domestic animals.
View
Alternatives to antibiotics—a pipeline portfolio review
Article
Full-text available
  • Jan 2016
  • LANCET INFECT DIS
Antibiotics have saved countless lives and enabled the development of modern medicine over the past 70 years. However, it is clear that the success of antibiotics might only have been temporary and we now expect a long-term and perhaps never-ending challenge to find new therapies to combat antibiotic-resistant bacteria. A broader approach to address bacterial infection is needed. In this Review, we discuss alternatives to antibiotics, which we defined as non-compound approaches (products other than classic antibacterial agents) that target bacteria or any approaches that target the host. The most advanced approaches are antibodies, probiotics, and vaccines in phase 2 and phase 3 trials. This first wave of alternatives to antibiotics will probably best serve as adjunctive or preventive therapies, which suggests that conventional antibiotics are still needed. Funding of more than £1·5 billion is needed over 10 years to test and develop these alternatives to antibiotics. Investment needs to be partnered with translational expertise and targeted to support the validation of these approaches in phase 2 trials, which would be a catalyst for active engagement and investment by the pharmaceutical and biotechnology industry. Only a sustained, concerted, and coordinated international effort will provide the solutions needed for the future.
View
Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ.. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 11: 119
Article
Full-text available
  • Mar 2010
  • BMC BIOINFORMATICS
The quality of automated gene prediction in microbial organisms has improved steadily over the past decade, but there is still room for improvement. Increasing the number of correct identifications, both of genes and of the translation initiation sites for each gene, and reducing the overall number of false positives, are all desirable goals. With our years of experience in manually curating genomes for the Joint Genome Institute, we developed a new gene prediction algorithm called Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm). With Prodigal, we focused specifically on the three goals of improved gene structure prediction, improved translation initiation site recognition, and reduced false positives. We compared the results of Prodigal to existing gene-finding methods to demonstrate that it met each of these objectives. We built a fast, lightweight, open source gene prediction program called Prodigal http://compbio.ornl.gov/prodigal/. Prodigal achieved good results compared to existing methods, and we believe it will be a valuable asset to automated microbial annotation pipelines.
View
Thermophilin 13, a Nontypical Antilisterial Poration Complex Bacteriocin, That Functions without a Receptor
Article
Full-text available
  • Jun 1997
A novel broad host range antimicrobial substance, Thermophilin 13, has been isolated and purified from the growth medium of Streptococcus thermophilus. Thermophilin 13 is composed of the antibacterial peptide ThmA (M r of 5776) and the enhancing factor ThmB (M r of 3910); the latter peptide increased the activity of ThmA ∼40 ×. Both peptides are encoded by a single operon, and an equimolar ratio was optimal for Thermophilin 13 activity. Despite the antilisterial activity of Thermophilin 13, neither ThmA nor ThmB contain the YGNGV-C consensus sequence of Listeria-active peptides, and post-translational modifications comparable to that in the lantibiotics are also absent. Mass spectrometry did reveal the apparent oxidation of methionines in ThmA, which resulted in a peptide that could not be enhanced any longer by ThmB, whereas the intrinsic bactericidal activity was normal. Thermophilin 13 dissipated the membrane potential and the pH gradient in liposomes, and this activity was independent of membrane components from a sensitive strain (e.g. lipid or proteinaceous receptor). Models of possible poration complexes formed are proposed on the basis of sequence comparisons, structure predictions, and the functional analysis of Thermophilin 13.
View
Alternatives to Antibiotics: Bacteriocins, Antimicrobial Peptides and Bacteriophages
Article
Full-text available
  • May 2003
Bacteriocins, antimicrobial peptides, and bacteriophage have attracted attention as potential substitutes for, or as additions to, currently used antimicrobial compounds. This publication will review research on the potential application of these alternative antimicrobial agents to poultry production and processing. Bacteriocins are proteinaceous compounds of bacterial origin that are lethal to bacteria other than the producing strain. It is assumed that some of the bacteria in the intestinal tract produce bacteriocins as a means to achieve a competitive advantage, and bacteriocin-producing bacteria might be a desirable part of competitive exclusion preparations. Purified or partially purified bacteriocins could be used as preservatives or for the reduction or elimination of certain pathogens. Currently only nisin, produced by certain strains of Lactococcus lactis subsp. lactis, has regulatory approval for use in certain foods, and its use for poultry products has been studied extensively. Exploration of the application of antimicrobial peptides from sources other than bacteria to poultry has not yet commenced to a significant extent. Evidence for the ability of chickens to produce such antimicrobial peptides has been provided, and it is likely that these peptides play an important role in the defense against various pathogens. Bacteriophages have received renewed attention as possible agents against infecting bacteria. Evidence from several trials indicates that phage therapy can be effective under certain circumstances. Numerous obstacles for the use of phage as antimicrobials for poultry or poultry products remain. Chiefly among them are the narrow host range of many phages, the issue of phage resistance, and the possibility of phage-mediated transfer of genetic material to bacterial hosts. Regulatory issues and the high cost of producing such alternative antimicrobial agents are also factors that might prevent application of these agents in the near future.
View
Search and Clustering Orders of Magnitude Faster than BLAST
Article
  • Oct 2010
  • BIOINFORMATICS
Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets. Binaries are available at no charge for non-commercial use at http://www.drive5.com/usearch.
View
McAuliffe, O, Ross, RP & Hill, C. Lantibiotics: structure, biosynthesis and mode of action. FEMS Microbiol. Rev. 25, 285-308
Article
  • Jun 2001
The lantibiotics are a group of ribosomally synthesised, post-translationally modified peptides containing unusual amino acids, such as dehydrated and lanthionine residues. This group of bacteriocins has attracted much attention in recent years due to the success of the well characterised lantibiotic, nisin, as a food preservative. Numerous other lantibiotics have since been identified and can be divided into two groups on the basis of their structures, designated type-A and type-B. To date, many of these lantibiotics have undergone extensive characterisation resulting in an advanced understanding of them at both the structural and mechanistic level. This review outlines some of the more recent developments in the biochemistry, genetics and mechanism of action of these peptides.
View