Journal of Microbiology

Review

The “Cins” of Our Fathers: Rejuvenated Interest in Colicins to Combat Drug Resistance: Sumudu Upatissa , Robert J. Mitchell; J. Microbiol. 2023;61(2):145-158. Published online February 8, 2023; DOI: https://doi.org/10.1007/s12275-023-00023-x

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With the growing threat of antibiotic resistance, researchers around the globe are seeking alternatives to stem bacterial pathogenesis. One such alternative is bacteriocins, proteins produced by bacterial species to inhibit the growth and viability of related bacterial species. With their diverse mechanisms, which include pore formation and nuclease activities, and narrow spectrum of activities, which limit their impact to only certain bacterial species, unlike many chemical antibiotics, bacteriocins offer intriguing possibilities to selectively control individual bacterial populations. Within this review, therefore, we highlight current research exploring the application of colicins and microcins, a subset of bacteriocins, with an emphasis on their activities against drug-resistant pathogens, both in in vitro and in vivo settings.

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Isolation, Genomics-Based and Biochemical Characterization of Bacteriocinogenic Bacteria and Their Bacteriocins, Sourced from the Gastrointestinal Tract of Meat-Producing Pigs
Ester Sevillano, Irene Lafuente, Nuria Peña, Luis M. Cintas, Estefanía Muñoz-Atienza, Pablo E. Hernández, Juan Borrero
International Journal of Molecular Sciences.2024; 25(22): 12210. CrossRef
Intelligent Biological Networks: Improving Anti-Microbial Resistance Resilience through Nutritional Interventions to Understand Protozoal Gut Infections
Avinash V. Karpe, David J. Beale, Cuong D. Tran
Microorganisms.2023; 11(7): 1800. CrossRef
Pairing Colicins B and E5 with Bdellovibrio bacteriovorus To Eradicate Carbapenem- and Colistin-Resistant Strains of Escherichia coli
Sumudu Upatissa, Wonsik Mun, Robert J. Mitchell, Minsu Kim
Microbiology Spectrum.2023;[Epub] CrossRef
Bacteriocin-Producing Escherichia coli Q5 and C41 with Potential Probiotic Properties: In Silico, In Vitro, and In Vivo Studies
Veronika S. Mihailovskaya, Dmitry A. Sutormin, Marina O. Karipova, Anna B. Trofimova, Victor A. Mamontov, Konstantin Severinov, Marina V. Kuznetsova
International Journal of Molecular Sciences.2023; 24(16): 12636. CrossRef

Journal Articles

Monthly distribution of ammonia-oxidizing microbes in a tropical bay: Tie-Qiang Mao , Yan-Qun Li , Hong-Po Dong , Wen-Na Yang , Li-Jun Hou; J. Microbiol. 2021;59(1):10-19. Published online November 17, 2020; DOI: https://doi.org/10.1007/s12275-021-0287-5

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Abstract: Ammonia oxidation, performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), plays a critical role in the cycle of nitrogen in the ocean. For now, environmental variables controlling distribution of ammonia-oxidizing microbes are still largely unknown in oceanic environments. In this study, we used real-time quantitative PCR and high-throughput sequencing
methods
to investigate the abundance and diversity of AOA and AOB from sediment and water in Zhanjiang Bay. Phylogenic analysis revealed that the majority of AOA amoA sequences in water and sediment were affiliated with the genus Nitrosopumilus, whereas the Nitrosotalea cluster was only detected with low abundance in water. Nitrosomonas and Nitrosospira dominated AOB amoA sequences in water and sediment, respectively. The amoA copy numbers of both AOA and AOB varied significantly with month for both sediment and water. When water and sediment temperature dropped to 17– 20°C in December and February, respectively, the copy number of AOB amoA genes increased markedly and was much higher than for AOA amoA genes. Also, AOA abundance in water peaked in December when water temperature was lowest (17–20°C). Stepwise multiple regression analyses revealed that temperature was the most key factor driving monthly changes of AOA or AOB abundance. It is inferred that low water temperature may inhibit growth of phytoplankton and other microbes and so reduce competition for a common substrate, ammonium.

Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov., isolated from the rhizosphere of tomato (Solanum lycopersicum): Shin Ae Lee , Tae-Wan Kim , Mee-Kyung Sang , Jaekyeong Song , Soon-Wo Kwon , Hang-Yeon Weon; J. Microbiol. 2020;58(10):832-840. Published online September 29, 2020; DOI: https://doi.org/10.1007/s12275-020-0258-2

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Abstract

Two Gram-stain-positive, rod-shaped, endospore-forming bacteria, designated 12200R-189T and 14171R-81T were isolated from the rhizosphere of tomato plants. The 16S rRNA gene sequence similarity between strains 12200R-189T and 14171R-81T were 97.2%. Both strains showed the highest 16S rRNA gene sequence similarities to Paenibacillus sacheonensis SY01T (96.3% and 98.0%, respectively). The genome of strain 12200R-189T was approximately 6.7 Mb in size with 5,750 protein-coding genes (CDSs) and the G + C content was 58.1 mol%, whereas that of strain 14171R-81T comprised one chromosome of 7.0 Mb and two plasmids (0.2 Mb each) with 6,595 CDSs and the G + C content was 54.5 mol%. Comparative genome analysis revealed that average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among 12200R-189T, 14171R-81T, and other closely related species were below the cut-off levels 95% and 70%, respectively. Strain 12200R-189T grew at a temperature range of 15–40°C, pH 6.0–9.0, and 0–3% NaCl (w/v), whereas strain 14171R-81T grew at a temperature range of 10–37°C, pH 6.0– 8.0, and 0–1% NaCl (w/v). Menaquinone-7 (MK-7) was the only isoprenoid quinone detected in both strains. The predominant cellular fatty acids (> 10%) were iso-C15:0, anteiso- C15:0, and iso-C16:0. The polar lipids of strain 12200R- 189T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), aminophospholipid (APL), phospholipid (PL), phosphatidylglycolipid (PGL), and four aminophosphoglycolipids (APGLs) and those of strain 14171R-81T were DPG, PG, PE, APL, three PLs, two PGLs, and three APGLs. Based on phylogenetic, genomic, phenotypic, and chemotaxonomic analyses, strains 12200R- 189T and 14171R-81T represent two novel species of the genus Paenibacillus, for which the names Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov. are proposed. The type strains are 12200R-189T (= KACC 19916T = CCTCC AB 2020027T) and 14171R-81T (= KACC 19915T = CCTCC AB 2020026T).

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Description and genomic characterization of Jiella flava sp. nov., isolated from Acrostichum aureum
Ming-Sheng Chen, Xiu-Long Pu, Ming-Dan Weng, Li Chen, Lan-Ying Zhu, Li Tuo
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Jiella sonneratiae sp. nov., a novel endophytic bacterium isolated from bark of Sonneratia apetala
Ming-Sheng Chen, Hai-Bo Yi, Zi-Hao Huang, Xiao-Rui Yan, Xiao-Hui Chen, Xiao Ma, Zhou-Qing Zheng, Li Tuo
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Paenibacillus vietnamensis sp. nov., isolated from the rhizosphere soil of Arachis hypogaea
Minh Hong Nguyen, Mai Thi Ngoc Dinh, Keun Chul Lee, Ji-Sun Kim, Thao Kim Nu Nguyen, Jung-Sook Lee
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Effect of exopolysaccharides of Paenibacillus polymyxa rhizobacteria on physiological and morphological variables of wheat seedlings
Irina V. Yegorenkova, Kristina V. Tregubova, Alexander I. Krasov, Nina V. Evseeva, Larisa Yu. Matora
Journal of Microbiology.2021; 59(8): 729. CrossRef

Research Support, Non-U.S. Gov'ts

Identification of a New Bacillus licheniformis Strain Producing a Bacteriocin-Like Substance: Yaoqi Guo , Zhanqiao Yu , Jianhua Xie , Rijun Zhang; J. Microbiol. 2012;50(3):452-458. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2051-3

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Abstract: The emergence of antibiotic resistance has spurred a great number of studies for development of new antimicrobials in the past decade. The purpose of this study was to screen environmental samples for Bacillus strains producing potent antimicrobial agents. A new strain, which showed strong antimicrobial activity against Staphylococcus aureus and Salmonella enterica ser. Pullorum, was isolated from soil and designated as B116. This new isolate was identified as Bacillus licheniformis by morphological, biochemical and genetic analyses. The production of bacteriocin-like substance (BLS) started at early exponential phase and achieved highest level at early stationary phase. The BLS was precipitated by ammonium sulfate and its molecular mass was determined as ~4 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Culture supernatant of the new isolate exhibited antimicrobial activity against both Gram-positive and Gram-negative bacteria, including Bacillus cereus, Staphylococcus aureus, Listeria monocytogenes, Micrococcus luteus, Escherichia coli, and Salmonella spp. The BLS was resistant to heat, acid and alkaline treatment. Activity of the BLS was totally lost after digestion by pronase and partially lost after digestion by papain and lipase. The new isolate and relevant BLS are potentially useful in food and feed applications.

Expression and Purification of Lacticin Q by Small Ubiquitin-Related Modifier Fusion in Escherichia coli: Qingshan Ma , Zhanqiao Yu , Bing Han , Qing Wang , Rijun Zhang; J. Microbiol. 2012;50(2):326-331. Published online April 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1425-x

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Abstract: Lacticin Q is a broad-spectrum class II bacteriocin with potential as an alternative to conventional antibiotics. The objective of this study was to produce recombinant lacticin Q using a small ubiquitin-related modifier (SUMO) fusion protein expression system. The 168-bp lacticin Q gene was cloned into the expression vector pET SUMO and transformed into Escherichia coli BL21(DE3). The soluble fusion protein was recovered with a Ni-NTA Sepharose column (95% purity); 130 mg protein was obtained per liter of fermentation culture. The SUMO tag was then proteolytically cleaved from the protein, which was re-applied to the column. Finally, about 32 mg lacticin Q (≥96% purity) was obtained. The recombinant protein exhibited antimicrobial properties similar to that of the native protein, demonstrating that lacticin Q had been successfully expressed by the SUMO fusion system.

Isolation and Characterization of Antifungal Peptides Produced by Bacillus amyloliquefaciens LBM5006: Lisianne Brittes Benitez , Renata Voltolini Velho , Marcia Pagno Lisboa , Luis Fernando da Costa Medina , Adriano Brandelli; J. Microbiol. 2010;48(6):791-797. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0164-0

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Abstract: Bacillus amyloliquefaciens LBM 5006 produces antagonistic activity against pathogenic bacteria and phytopathogenic fungi, including Aspergillus spp., Fusarium spp., and Bipolaris sorokiniana. PCR analysis revealed the presence of ituD, but not sfp genes, coding for iturin and surfactin, respectively. The antimicrobial substance produced by this strain was isolated by ammonium sulfate precipitation, gel filtration chromatography and 1-butanol extraction. The ultraviolet spectrum was typical of a polypeptide and the infrared spectrum indicates the presence of peptide bonds and acyl group(s). The antimicrobial substance was resistant to proteolytic enzymes and heat treatment, and was reactive with ninhydrin. Mass spectroscopy analysis indicated that B. amyloliquefaciens LBM 5006 produces two antimicrobial peptides, with main peaks at m/z 1,058 Da and 1,464 Da, corresponding to iturin-like and fengycin-like peptides, respectively. B. amyloliquefaciens LBM 5006 showed significant activity against phytopatogenic fungi, showing potential for use as a biocontrol agent or production of antifungal preparations.

Enterococcus faecium Isolated from Honey Synthesized Bacteriocin-Like Substances Active against Different Listeria monocytogenes Strains: Carolina Ibarguren , Raúl R. Raya , María C. Apella , M. Carina Audisio; J. Microbiol. 2010;48(1):44-52. Published online March 11, 2010; DOI: https://doi.org/10.1007/s12275-009-0177-8

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Abstract: Four Enterococcus faecium strains, isolated from honeycombs (C1 and M2d strains) and feral combs (Mori1 and M1b strains) secreted antimicrobial substances active against fourteen different Listeria spp. strains. The antimicrobial compound(s) present in the cell free supernatant were highly thermostable (121°C for 15 min) and inactivated by proteolytic enzymes, but not by α-amylase and lipase, thus suggesting a peptidic nature. Since the structural bacteriocin gene determinants of enterocins A and B were PCR amplified from the four E. faecium isolates, only the bacteriocin produced by strain C1 was further characterized: it showed a broad band of approximately 4.0-7.0 kDa in SDS-PAGE and was bactericidal (4 log decrease) against L. monocytogenes 99/287. L. monocytogenes 99/287R, a clone spontaneously resistant to the enterocin produced by E. avium DSMZ17511 (ex PA1), was not inhibited by the enterocin-like compounds produced by strain C1. However, it was inhibited in mixed culture fermentations by E. faecium C1 and a bacteriostatic effect was observed. The bacteriocin-producer Enterococcus strains were not haemolytic; gelatinase negative and sensitive to vancomycin and other clinically relevant antibiotics.

Journal Articles

Mobilization Functions of the Bacteriocinogenic Plasmid pRJ6 of Staphylococcus aureus: Marcus Livio Varella Coelho , Hilana Ceotto , Danielle Jannuzzi Madureira , Ingolf F. Nes , Maria do Carmo de Freire Bastos; J. Microbiol. 2009;47(3):327-336. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-009-0044-7

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Abstract: Plasmid pRJ6 is the first known bacteriocinogenic mobilizable (Mob) plasmid of Staphylococcus aureus. Its Mob region is composed of four mob genes (mobCDAB) arranged as an operon, a genetic organization uncommon among S. aureus Mob plasmids. oriTpRJ6 was detected in a region of 431 bp, positioned immediately upstream of mobC. This region, when cloned into pCN37, was able to confer mobilization to the recombinant plasmid only in the presence of pRJ6. The entire Mob region, including oriTpRJ6, is much more similar to Mob regions from several coagulase-negative staphylococci plasmids, although some remarkable similarities with S. aureus Mob plasmids can also be noted. These similarities include the presence within oriTpRJ6 of the three mcb (MobC binding sites), firstly described in pC221 and pC223, an identical nick site also found in these same plasmids, and a nearly identical srapC223 site (sequence recognized by MobA). pRJ6 was successfully transferred to S. epidermidis by conjugation in the presence of the conjugative plasmid pGO1. Altogether these findings suggest that pRJ6 might have been originally a coagulase-negative staphylococci plasmid that had been transferred successfully to S. aureus.

Optimization of Bacteriocin ST311LD Production by Enterococcus faecium ST311LD, Isolated from Spoiled Black Olives: Svetoslav D. Todorov , Leon M.T. Dicks; J. Microbiol. 2005;43(4):370-374.; DOI: https://doi.org/2251 [pii]

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Abstract: Bacteriocin ST311LD is approximately 2.3 kDa in size. Low levels of bacteriocin activity were recorded in BHI and M17 broth (800 AU/ml) and in 10% (w/v) soy milk (3,200 AU/ml). No bacteriocin production was recorded in 10% (w/v) molasses, despite good growth. Optimal levels (12,800 AU/ml) were detected in MRS broth which had been supplemented with tryptone (20.0 g/l), saccharose (5.0 or 10.0 g/l) or vitamin C (1 ppm). Increased potassium levels did not result in higher levels of activity, and glycerol (1.0 g/l) inhibited the production of bacteriocin ST311LD.

Antibacterial Activities of Lactobacillus crispatus ATCC 33820 and Lactobacillus gasseri ATCC 33323: Jin-Woo Kim , S.N. Rajagopal; J. Microbiol. 2001;39(2):146-148.

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Abstract: Lactobacillus crispatus ATCC 33820 and L. gasseri ATCC 33323 were grown in MRS broth (pH 6.5) at 37 C for 24 h and the antibacterial activities of cell free culture supernatants were determined by the agar well diffusion method. The culture supernatants were inhibitory to Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Bacillus subtilis, Staphylococcus aureus, Enterococcus faecalis, Pediococcus acidilacticii, and Lactobacillus helveticus. The supernatants did not show any lysozyme activity. Addition of catalase did not affect the antibacterial activities of the supernatants. The antibacterial substances were heat stable (100 C for 60 min) and sensitive to proteases.

Improvement in the Stability of Glycinecin A through Protein Fusion of the Two Structural Components: Youngmee Kim , Somi K. Cho , Moonjae Cho; J. Microbiol. 2001;39(3):177-180.

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Abstract: Glycinecin A, a bacteriocin produced by Xanthomonas campestris pv. glycines, inhibits the growth of X. c. pv. vesicatoria. We have reported that purified glycinecin A is composed of two polypeptides, is active over a wide range of pH (6 to 9), and is stable at temperatures up to 60 C. Glycinecin A is a heterodimer consisting of 39- and 14-kDa subunits; the two encoding genes, glyA and glyB, respectively, have been cloned (Heu et al. 2001. Appl. Environ. Microbiol. 67, 4105-4110). Co-expression of glyA and glyB in the same cell is essential for bacteriocin activity. We constructed and produced a chimeric glycinecin A connecting glyA and glyB in one open reading frame. The chimeric glycinecin A has the same bactericidal activity as the wild-type glycinecin A. However, the chimeric glycinecin A is more stable in a wider range of pH and temperature.

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