Journal of Microbiology

Volume 57(7); July 2019

Review

MINIREVIEW] EAST1 toxin: An enigmatic molecule associated with sporadic episodes of diarrhea in humans and animals: J. Daniel Dubreuil; J. Microbiol. 2019;57(7):541-549. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8651-4

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EAST1 is produced by a subset of enteroaggregative Escherichia coli strains. This toxin is a 38-amino acid peptide of 4100 Da. It shares 50% homology with the enterotoxic domain of STa and interacts with the same receptor. The mechanism of action of EAST1is proposed to be identical to that of STa eliciting a cGMP increase. EAST1 is associated with diarrheal disease in Man and various animal species including cattle and swine. Nevertheless, as EAST1-positive strains as well as culture supernatants did not provoke unequivocally diarrhea either in animal models or in human volunteers, the role of this toxin in disease is today still debated. This review intent is to examine the role of EAST1 toxin in diarrheal illnesses.

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Survey in ruminants from Rwanda revealed high diversity and prevalence of extended-spectrum cephalosporin-resistant Enterobacterales
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Journal Articles

Rhizocompartments and environmental factors affect microbial composition and variation in native plants: Myung-Suk Kang , Moonsuk Hur , Soo-Je Park; J. Microbiol. 2019;57(7):550-561. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8646-1

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Abstract

Molecular analysis based on large-scale sequencing of the plant microbiota has revealed complex relationships between plants and microbial communities, and environmental factors such as soil type can influence these relationships. However, most studies on root-associated microbial communities have focused on model plants such as Arabidopsis, rice or crops. Herein, we examined the microbiota of rhizocompartments of two native plants, Sedum takesimense Nakai and Campanula takesimana Nakai, using archaeal and bacterial 16S rRNA gene amplicon profiling, and assessed relationships between environmental factors and microbial community composition. We identified 390 bacterial genera, including known plant-associated genera such as Pseudomonas, Flavobacterium, Bradyrhizobium and Rhizobium, and uncharacterized clades such as DA101 that might be important in root-associated microbial communities in bulk soil. Unexpectedly, Nitrososphaera clade members were abundant, indicating functional association with roots. Soil texture/type has a greater impact on microbial community composition in rhizocompartments than chemical factors. Our results provide fundamental knowledge on microbial diversity, community and correlations with environmental factors, and expand our understanding of the microbiota in rhizocompartments of native plants.

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Isolation and characterization of a novel piezotolerant bacterium Lysinibacillus yapensis sp. nov., from deep-sea sediment of the Yap Trench, Pacific Ocean: Libo Yu , Xixiang Tang , Shiping Wei , Yinkun Qiu , Xiashutong Xu , Guangxin Xu , Qilin Wang , Qian Yang; J. Microbiol. 2019;57(7):562-568. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8709-3

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Abstract

A Gram-positive, aerobic, rod-shaped, spore-forming bacterium, designated YLB-03T, with peritrichous flagella was isolated from deep-sea sediment of the Yap Trench at a depth of 4435 m. The bacterium was found to be catalase-positive but oxidase-negative. Growth of this bacterium was observed at 15–50°C (optimum 37°C), pH 5–10.5 (optimum 7), 0–5% NaCl (optimum 1%, w/v) and 0.1–50 MPa (optimum 0.1 MPa). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YLB-03T was a member of the genus Lysinibacillus. Strain YLB-03T was closely related to Lysinibacillus sinduriensis BLB-1T and Lysinibacillus chungkukjangi 2RL3-2T (98.4%), Lysinibacillus halotolerans LAM- 612T (98.0%), Lysinibacillus telephonicus KT735049T (97.5%), Lysinibacillus endophyticus C9T (97.5%), Lysinibacillus composti NCCP-36T and Lysinibacillus massiliensis 4400831T (97.3%). The ANI and the GGDC DNA-DNA hybridization estimate values between strain YLB-03T and closely related type strains were 73.7–76.3% and 34.7–38.7%, respectively. The principal fatty acids were anteiso-C15:0 and iso-C15:0. The G+C content of the chromosomal DNA was 39.6 mol%. The respiratory quinone was determined to be MK-7. The diagnostic amino acids in the cell wall peptidoglycan contained Lys-Asp (type A4α) and the cell-wall sugars were glucose and xylose. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid. The combined genotypic and phenotypic data showed that strain YLB-03T represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus yapensis sp. nov. is proposed, with the type strain YLB-03T (= MCCC 1A12698T = JCM 32871T).

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Ureibacillus aquaedulcis sp. nov., isolated from freshwater well and reclassification of Lysinibacillus yapensis and Lysinibacillus antri as Ureibacillus yapensis comb. nov. and Ureibacillus antri comb. nov.
Amit Yadav, Ruchi Teware, Agrima Bhatt, Yash Bhavsar, Akanksha Maurya, Vipool Thorat, Venkata Ramana Vemuluri, Kiran Kirdat
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Lysinibacillus piscis sp. nov. isolated from the gut of mottled spinefoot Siganus fuscescens
Hiyu Kanbe, Yuki Sano, Kazumori Mise, Shusei Kanie, Natsumi Ushijima, Keisuke Kawano, Minoru Kihara, Hideomi Itoh
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A taxonomic note on the order Caryophanales: description of 12 novel families and emended description of 21 families
Yangjie Li, Dechao Zhang, Dexin Bo, Donghai Peng, Ming Sun, Jinshui Zheng
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Genomic insights into versatile lifestyle of three new bacterial candidate phyla
Xinxu Zhang, Zongbao Liu, Wei Xu, Jie Pan, Yuhan Huang, Mingwei Cai, Zhuhua Luo, Meng Li
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List of new names and new combinations previously effectively, but not validly, published
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Paenibacillus psychroresistens sp. nov., isolated from the soil of an Arctic glacial retreat: In-Tae Cha , Eui-Sang Cho , Yoo Kyung Lee , Seong Woon Roh , Myung-Ji Seo; J. Microbiol. 2019;57(7):569-574. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8666-x

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Abstract

Strain ML311-T8T was isolated from a glacial retreat area in Svalbard, Norway, and was taxonomically characterized by a polyphasic approach. Upon phylogenetic analysis, strain ML311-T8T was clustered with Paenibacillus arcticus MME2_ R6T and P. contaminans CKOBP-6T with 98.3–98.6 and 93.5– 93.9% 16S rRNA gene sequence similarities, respectively. DNA-DNA hybridization values between strain ML311-T8T and P. arcticus MME2_R6T was 19.9%. The genomic DNA G+C content was 41.1 mol%. The isolated strain was Gramstain- positive, strictly aerobic and rod-shaped, and grew in 0–0.5% (w/v) NaCl, at 4–23°C and pH 6.0–10.0, with optimal growth in 0% (w/v) NaCl, at 20°C and pH 7.0–8.0. The predominant respiratory quinone of strain ML311-T8T was MK- 7 and the major fatty acids were anteiso-C15:0 and C16:0. The polar lipids of strain ML311-T8T were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, three unidentified amino lipids, and three unidentified lipids. On the basis of polyphasic taxonomic analysis, the strain ML311-T8T is proposed to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus psychroresistens sp. nov. is proposed. The type strain is ML311-T8T (= KCCM 43190T = JCM 31243T).

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Microbiodiversity Landscape Present in the Mine-Tailings of the “Sierra de Huautla” Biosphere Reserve, Mexico
Maikel Gilberto Fernández-López, Ayixon Sánchez-Reyes, Marcos Eduardo Rosas-Ramírez, Edgar Balcázar-López
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Paenibacillus dendrobii sp. nov., an indole-3-acetic acid-producing endophytic bacterium isolated from Dendrobium nobile
Yadong Hu, Hongjie Li, Yaoyi Chen, Qiling Zhang, Shigang Zheng, Dan Rao, Ze Chun, Ruoxi Zhao
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Validation List no. 206. Valid publication of new names and new combinations effectively published outside the IJSEM
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Carbohydrate metabolism genes dominant in a subtropical marine mangrove ecosystem revealed by metagenomics analysis: Huaxian Zhao , Bing Yan , Shuming Mo , Shiqing Nie , Quanwen Li , Qian Ou , Bo Wu , Gonglingxia Jiang , Jinli Tang , Nan Li , Chengjian Jiang; J. Microbiol. 2019;57(7):575-586. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8679-5

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Abstract

Mangrove sediment microorganisms play a vital role in the energy transformation and element cycling in marine wetland ecosystems. Using metagenomics analysis strategy, we compared the taxonomic structure and gene profile of the mangrove and non-mangrove sediment samples at the subtropical estuary in Beibu Gulf, South China Sea. Proteobacteria, Bacteroidetes, and Firmicutes were the most abundant bacterial phyla. Archaeal family Methanosarcinaceae and bacterial genera Vibrio and Dehalococcoides were significantly higher in the mangrove sediments than in the nonmangrove sediments. Functional analysis showed that “Carbohydrate metabolism” was the most abundant metabolic category. The feature of carbohydrate-active enzymes (CZs) was analyzed using the Carbohydrate-Active EnZymes Database. The significant differences of CZs between mangrove and non-mangrove sediments, were attributed to the amounts of polyphenol oxidase (EC 1.10.3.-), hexosyltransferase (EC 2.4.1.-), and β-N-acetylhexosaminidase (EC 3.2.1.52), which were higher in the mangrove sediment samples. Principal component analysis indicated that the microbial community and gene profile between mangrove and non-mangrove sediments were distinct. Redundancy analysis showed that total organic carbon is a significant factor that affects the microbial community and gene distribution. The results indicated that the mangrove ecosystem with massive amounts of organic carbon may promote the richness of carbohydrate metabolism genes and enhance the degradation and utilization of carbohydrates in the mangrove sediments.

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Kit-Ling Lam, Nora Fung-Yee Tam, Steven Jing-Liang Xu, Wing-Yin Mo, Yuet-Tung Tse, Kaze King-Yip Lai, Ping-Lung Chan, Fred Wang-Fat Lee
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Evolution of a major bovine mastitic genotype (rpoB sequence type 10-2) of Staphylococcus aureus in cows: Dae-Sung Ko , Danil Kim , Eun-Kyung Kim , Jae-Hong Kim , Hyuk-Joon Kwon; J. Microbiol. 2019;57(7):587-596. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8699-1

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Abstract

Staphylococcus aureus is the major pathogen leading to bovine mastitis globally while livestock-associated methicillin resistant S. aureus (LA-MRSA) has become a potential threat to public health. MRSA from bovine mastitis is not common but a methicillin susceptible S. aureus (MSSA) genotype, rpoB sequence type (RST)10-2 (RST10-2), is prevalent in Korea. To date, many genomic sequences from S. aureus have been elucidated, but the complete genome sequences of RST10-2 MSSA from bovine mastitis has never been reported. In this study, we determined the complete genome sequence of two RST10-2 MSSA that differ from each other in staphylococcal protein A and molecular prophage types [PMB64-1 (t2489/ mPPT0) and PMB81-4 (t127/mPPT1-2-3)] and conducted a comparative genomics study. The genomic sequences of PMB64-1 and PMB81-4 were more homologous to the representative human RST10-2 strains (MSSA476, MW2 etc.) compared to other RSTs. Most of them shared five common pseudogenes, along with high amino acid identity of four variable virulence genes that were identified in this study. However, PMB64-1 and PMB81-4 acquired different strainspecific pseudogenes and mobile genetic elements than the human strains. The unique pseudogene profile and high identity of the virulence genes were verified in RST10-2 field strains from bovine mastitis. Thus, bovine mastitic RST10-2 MSSA may have an evolutionary relationship with the human RST10- 2 community-associated (CA) MSSA and CA-MRSA strains but may have adapted to cows.

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Screening and identification of Aspergillus activity against Xanthomonas oryzae pv. oryzae and analysis of antimicrobial components: Bei Jiang , Zhiying Wang , Chuxuan Xu , Weijia Liu , Donghua Jiang; J. Microbiol. 2019;57(7):597-605. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8330-5

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Abstract

To screen for Aspergillus activity against Xanthomonas oryzae pv. oryzae and analyse the antimicrobial components involved, 60 Aspergillus spp. were isolated and purified from fruits, soil and other habitats. As-75, an Aspergillus strain that can antagonize Xanthomonas oryzae pv. oryzae, was identified based on the zone of inhibition formed during co-culture. According to morphological, ITS rDNA gene sequencing and phylogenetic tree results, the strain showed close homology to Aspergillus sclerotiorum. The biochemical characterization tests showed that the fermentation broth of strain As-75 exhibited a high capacity for environmental adaptation. The results of the antimicrobial spectrum experiments demonstrated that As-75 exhibited fairly strong antagonistic activity against five plant pathogenic fungi and six plant pathogenic bacteria in vitro. The fermentation broth of strain As-75 displayed maximum stability under fluorescent illumination at temperatures below 60°C at pH 6.5. A substance with antagonistic activity was obtained from strain As-75 via fractional extraction, silica gel column chromatography and thinlayer chromatography. Through mass spectrometry, nuclear magnetic resonance and electrospray ionization mass spectrometry (ESI-MS) analyses, the target compound was identified as (2Z)-2-butenedioic acid-2-(1-methylethenyl)-4-methyl ester; its molecular weight of 170.06 daltons and formula of C8H10O4 identify it as a novel compound. Trials of the preventative and curative effects demonstrated that compound S1 exhibited a better control efficiency than the control against rice bacterial blight. Additionally, the M1 processing
method
was better, and the efficiency of compound S1 in preventing rice bacterial blight in six rice varieties, TN1, IR24, ZF802, Zhonghua 11, Wuyunjing 21, and Nipponbare, was 78.3%, 77.5%, 74.2%, 75.3%, 70.9%, and 72.1%, respectively.

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Suyan Wang, Yanxia Wang, Xinchi Shi, Daniela D. Herrera-Balandrano, Xin Chen, Fengquan Liu, Pedro Laborda, Irina S. Druzhinina
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Alcohol dehydrogenase 1 participates in the Crabtree effect and connects fermentative and oxidative metabolism in the Zygomycete Mucor circinelloides: Rosa Angélica Rangel-Porras , Sharel P. Díaz-Pérez , Juan Manuel Mendoza-Hernández , Pamela Romo-Rodríguez , Viridiana Alejandre-Castañeda , Marco I Valle-Maldonado , Juan Carlos Torres-Guzmán , Gloria Angélica González-Hernández , Jesús Campos-Garcia , José Arnau , Víctor Meza-Carmen , J. Félix Gutiérrez-Corona; J. Microbiol. 2019;57(7):606-617. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8680-z

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Abstract

Mucor circinelloides is a dimorphic Zygomycete fungus that produces ethanol under aerobic conditions in the presence of glucose, which indicates that it is a Crabtree-positive fungus. To determine the physiological role of the alcohol dehydrogenase (ADH) activity elicited under these conditions, we obtained and characterized an allyl alcohol-resistant mutant that was defective in ADH activity, and examined the effect of adh mutation on physiological parameters related to carbon and energy metabolism. Compared to the Adh+ strain R7B, the ADH-defective (Adh-) strain M5 was unable to grow under anaerobic conditions, exhibited a considerable reduction in ethanol production in aerobic cultures when incubated with glucose, had markedly reduced growth capacity in the presence of oxygen when ethanol was the sole carbon source, and exhibited very low levels of NAD+-dependent alcohol dehydrogenase activity in the cytosolic fraction. Further characterization of the M5 strain showed that it contains a 10-bp deletion that interrupts the coding region of the adh1 gene. Complementation with the wild-type allele adh1+ by transformation of M5 remedied all the defects caused by the adh1 mutation. These findings indicate that in M. circinelloides, the product of the adh1 gene mediates the Crabtree effect, and can act as either a fermentative or an oxidative enzyme, depending on the nutritional conditions, thereby participating in the association between fermentative and oxidative metabolism. It was found that the spores of M. circinelloides possess low mRNA levels of the ethanol assimilation genes (adl2 and acs2), which could explain their inability to grow in the alcohol.

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Fungal Alcohol Dehydrogenases: Physiological Function, Molecular Properties, Regulation of Their Production, and Biotechnological Potential
J. Félix Gutiérrez-Corona, Gloria Angélica González-Hernández, Israel Enrique Padilla-Guerrero, Vianey Olmedo-Monfil, Ana Lilia Martínez-Rocha, J. Alberto Patiño-Medina, Víctor Meza-Carmen, Juan Carlos Torres-Guzmán
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Role of the nonribosomal peptide synthetase siderophore enzyme (Rfs) ofMucor lusitanicusin controlling the growth of fungal phytopathogens
Viridiana Alejandre-Castañeda, J. Alberto Patiño-Medina, Juan Bosco Guzmán-Pérez, Marco I. Valle-Maldonado, Javier Villegas, César R. Solorio-Alvarado, León Francisco Ruiz-Herrera, Rafael Ortiz-Alvarado, Karla Macías-Sánchez, Martha I. Ramírez-Díaz, Vícto
Canadian Journal of Microbiology.2023; 69(5): 185. CrossRef
Blood Serum Stimulates the Virulence Potential of Mucorales through Enhancement in Mitochondrial Oxidative Metabolism and Rhizoferrin Production
José Alberto Patiño-Medina, Viridiana Alejandre-Castañeda, Marco Iván Valle-Maldonado, Mauro Manuel Martínez-Pacheco, León Francisco Ruiz-Herrera, Joel Ramírez-Emiliano, Oscar Abelardo Ramírez-Marroquín, Karla Viridiana Castro-Cerritos, Jesús Campos-Garcí
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Secretion of the siderophore rhizoferrin is regulated by the cAMP-PKA pathway and is involved in the virulence of Mucor lusitanicus
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Investigating the Effect of Alcohol Dehydrogenase Gene Knockout on Lipid Accumulation in Mucor circinelloides WJ11
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Z. Zhang, Y. Chang, H. Tang, H. Zhao, X. Chen, G. Tian, G. Liu, J. Cai, G. Jia
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Mass spore production of Mucor circinelloides on rice
J. Alberto Patiño-Medina, Viridiana Alejandre-Castañeda, Marco I. Valle-Maldonado, Javier Villegas, Martha I. Ramírez-Díaz, Rafael Ortiz-Alvarado, Víctor Meza-Carmen
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The heterotrimeric G‐protein beta subunit Gpb1 controls hyphal growth under low oxygen conditions through the protein kinase A pathway and is essential for virulence in the fungusMucor circinelloides
Marco Iván Valle‐Maldonado, José Alberto Patiño‐Medina, Carlos Pérez‐Arques, Nancy Yadira Reyes‐Mares, Irvin Eduardo Jácome‐Galarza, Rafael Ortíz‐Alvarado, Sandeep Vellanki, Martha Isela Ramírez‐Díaz, Soo Chan Lee, Victoriano Garre, Víctor Meza‐Carmen
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Alteration of Fermentative Metabolism Enhances Mucor circinelloides Virulence
Sharel P. Díaz-Pérez, J. Alberto Patiño-Medina, Marco I. Valle-Maldonado, Adolfo López-Torres, Irvin E. Jácome-Galarza, Verónica Anaya-Martínez, Verónica Gómez-Ruiz, Jesús Campos-García, Rosa E. Nuñez-Anita, Rafael Ortiz-Alvarado, Martha I. Ramírez-Díaz,
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Two novel synthetic peptides inhibit quorum sensing-dependent biofilm formation and some virulence factors in Pseudomonas aeruginosa PAO1: Mostafa N. Taha , Amal E. Saafan , A. Ahmedy , Eman El Gebaly , Ahmed S. Khairalla; J. Microbiol. 2019;57(7):618-625. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8548-2

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Abstract

Quorum sensing (QS) regulates virulence factor expression in Pseudomonas aeruginosa. Inhibiting the QS-controlled virulence factors without inhibiting the growth of P. aeruginosa is a promising approach for overcoming the widespread resistance of P. aeruginosa. This study was proposed to investigate the effects of two novel synthetic peptides on the biofilm development and virulence factor production of P. aeruginosa. The tested strain was P. aeruginosa PAO1. The results indicated that both of the synthetic peptides (LIVRHK and LIVRRK) inhibited (P < 0.05) the formation of biofilms and the production of virulence factors, including pyocyanin, protease, and rhamnolipids, without inhibiting the growth of PAO1. Additionally, we detected transcriptional changes related to QS and found a significant reduction in the levels of gene expression of lasI, lasR, rhlI, and rhlR. This study demonstrates that LIVRRK and LIVRHK are novel synthetic peptides that can act as potent inhibitors of QS-regulated virulence factors in P. aeruginosa. Moreover, these synthetic peptides have potential applications in the treatment of biofilmrelated diseases. Both peptides may be able to control chronic infections and biofilm-associated problems of P. aeruginosa.

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Superantigen SpeA attenuates the biofilm forming capacity of Streptococcus pyogenes: Anshu Babbar , Israel Barrantes , Dietmar H. Pieper , Andreas Itzek; J. Microbiol. 2019;57(7):626-636. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8648-z

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Abstract

Beta haemolytic Group A streptococcus (GAS) or Streptococcus pyogenes are strict human pathogens responsible for mild to severe fatal invasive infections. Even with enormous number of reports exploring the role of S. pyogenes exotoxins in its pathogenesis, inadequate knowledge on the biofilm process and the potential role of exotoxins in bacterial dissemination from matured biofilms has been a hindrance in development of effective and targeted treatments. Therefore, the present study was aimed in investigating the uncharted role of these exotoxins in biofilm process. Through our study the putative role of ciaRH in the SpeA dependent ablation of biofilm formation could be speculated and thus helping in bacterial dissemination. The seed-dispersal effect of SpeA was time and concentration dependent and seen to be consistent within various streptococcal species. Transcriptome analysis of SpeA treated S. pyogenes biofilms revealed the involvement of many transcriptional regulators (ciaRH) and response genes (luxS, shr, shp, SPy_0572), hinting towards specific mechanisms underlying the dispersal effect by SpeA. This finding opens up a discussion towards understanding a new mechanism involved in the pathogenesis of Streptococcus pyogenes and might help in understanding the bacterial infections in a better way.

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