scholarly journals Characterization of the first vaginal Lactobacillus crispatus genomes isolated in Brazil

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11079
Author(s):  
Marcelle Oliveira de Almeida ◽  
Rodrigo Carvalho ◽  
Flavia Figueira Aburjaile ◽  
Fabio Malcher Miranda ◽  
Janaína Canário Cerqueira ◽  
...  
Keyword(s):  
Positive Selection ◽  
Functional Characterization ◽  
Genomic Feature ◽  
Evolutionary Analysis ◽  
Vaginal Microbiome ◽  
Lactobacillus Crispatus ◽  
Antimicrobial Resistance Genes ◽  
Probiotic Strains ◽  
Genetic Mechanisms

Background Lactobacillus crispatus is the dominant species in the vaginal microbiota associated with health and considered a homeostasis biomarker. Interestingly, some strains are even used as probiotics. However, the genetic mechanisms of L. crispatus involved in the control of the vaginal microbiome and protection against bacterial vaginosis (BV) are not entirely known. To further investigate these mechanisms, we sequenced and characterized the first four L. crispatus genomes from vaginal samples from Brazilian women and used genome-wide association study (GWAS) and comparative analyses to identify genetic mechanisms involved in healthy or BV conditions and selective pressures acting in the vaginal microbiome. Methods The four genomes were sequenced, assembled using ten different strategies and automatically annotated. The functional characterization was performed by bioinformatics tools comparing with known probiotic strains. Moreover, it was selected one representative strain (L. crispatus CRI4) for in vitro detection of phages by electron microscopy. Evolutionary analysis, including phylogeny, GWAS and positive selection were performed using 46 public genomes strains representing health and BV conditions. Results Genes involved in probiotic effects such as lactic acid production, hydrogen peroxide, bacteriocins, and adhesin were identified. Three hemolysins and putrescine production were predicted, although these features are also present in other probiotic strains. The four genomes presented no plasmids, but 14 known families insertion sequences and several prophages were detected. However, none of the mobile genetic elements contained antimicrobial resistance genes. The genomes harbor a CRISPR-Cas subtype II-A system that is probably inactivated due to fragmentation of the genes csn2 and cas9. No genomic feature was associated with a health condition, perhaps due to its multifactorial characteristic. Five genes were identified as under positive selection, but the selective pressure remains to be discovered. In conclusion, the Brazilian strains investigated in this study present potential protective properties, although in vitro and in vivo studies are required to confirm their efficacy and safety to be considered for human use.

Insights into the biochemical and functional characterization of sortase E transpeptidase of Corynebacterium glutamicum

2019 ◽  
Vol 476 (24) ◽  
pp. 3835-3847 ◽  
Author(s):  
Aliyath Susmitha ◽  
Kesavan Madhavan Nampoothiri ◽  
Harsha Bajaj
Keyword(s):  
Protein Engineering ◽  
Cell Attachment ◽  
Functional Characterization ◽  
Protein Structures ◽  
Structural Similarity ◽  
Surface Proteins ◽  
Sortase A ◽  
Peptide Cleavage ◽  
New Findings

Most Gram-positive bacteria contain a membrane-bound transpeptidase known as sortase which covalently incorporates the surface proteins on to the cell wall. The sortase-displayed protein structures are involved in cell attachment, nutrient uptake and aerial hyphae formation. Among the six classes of sortase (A–F), sortase A of S. aureus is the well-characterized housekeeping enzyme considered as an ideal drug target and a valuable biochemical reagent for protein engineering. Similar to SrtA, class E sortase in GC rich bacteria plays a housekeeping role which is not studied extensively. However, C. glutamicum ATCC 13032, an industrially important organism known for amino acid production, carries a single putative sortase (NCgl2838) gene but neither in vitro peptide cleavage activity nor biochemical characterizations have been investigated. Here, we identified that the gene is having a sortase activity and analyzed its structural similarity with Cd-SrtF. The purified enzyme showed a greater affinity toward LAXTG substrate with a calculated KM of 12 ± 1 µM, one of the highest affinities reported for this class of enzyme. Moreover, site-directed mutation studies were carried to ascertain the structure functional relationship of Cg-SrtE and all these are new findings which will enable us to perceive exciting protein engineering applications with this class of enzyme from a non-pathogenic microbe.

A comparative study on adhesion and recovery of potential probiotic strains ofLactobacillusspp. by in vitro assay and analysis of human colon biopsies

2009 ◽  
Vol 21 (2) ◽  
Author(s):  
Nadja Larsen ◽  
Kim F. Michaelsen ◽  
Anders Pærregaard ◽  
Finn K. Vogensen ◽  
Mogens Jakobsen
Keyword(s):  
Comparative Study ◽  
Human Colon ◽  
In Vitro Assay ◽  
Vitro Assay ◽  
Probiotic Strains

Novel Toxin-antitoxin System Xn-mazEF from Xenorhabdus nematophi-la: Identification, Characterization and Functional Exploration

2020 ◽  
Vol 16 ◽  
Author(s):  
Jogendra Singh Nim ◽  
Mohit Yadav ◽  
Lalit Kumar Gautam ◽  
Chaitali Ghosh ◽  
Shakti Sahi ◽  
...  
Keyword(s):  
Interaction Analysis ◽  
Functional Characterization ◽  
Host Cells ◽  
System Control ◽  
Xenorhabdus Nematophila ◽  
Functional Features ◽  
Dynamics Simulations ◽  
Species Specific ◽  
Rna Interaction

Background: Xenorhabdus nematophila maintains species-specific mutual interaction with nematodes of Steinernema genus. Type II Toxin Antitoxin (TA) systems, the mazEF TA system controls stress and programmed cell death in bacteria. Objective: This study elucidates the functional characterization of Xn-mazEF, a mazEF homolog in X. nematophila by computational and in vitro approaches. Methods: 3 D- structural models for Xn-MazE toxin and Xn-MazF antitoxin were generated, validated and characterized for protein - RNA interaction analysis. Further biological and cellular functions of Xn-MazF toxin were also predicted. Molecular dynamics simulations of 50ns for Xn-MazF toxin complexed with nucleic acid units (DU, RU, RC, and RU) were performed. The MazF toxin and complete MazEF operon were endogenously expressed and monitored for the killing of Escherichia coli host cells under arabinose induced tightly regulated system. Results: Upon induction, E. coli expressing toxin showed rapid killing within four hours and attained up to 65% growth inhibition, while the expression of the entire operon did not show significant killing. The observation suggests that the Xn-mazEF TA system control transcriptional regulation in X. nematophila and helps to manage stress or cause toxicity leading to programmed death of cells. Conclusion: The study provides insights into structural and functional features of novel toxin, XnMazF and provides an initial inference on control of X. nematophila growth regulated by TA systems.

scholarly journals Functional identification of ygiP as a positive regulator of the ttdA-ttdB-ygjE operon

Microbiology ◽  
2006 ◽  
Vol 152 (7) ◽  
pp. 2129-2135 ◽  
Author(s):  
Taku Oshima ◽  
Francis Biville
Keyword(s):  
Functional Characterization ◽  
Anaerobic Growth ◽  
Functional Identification ◽  
New Members ◽  
E Coli ◽  
Inner Membrane Protein ◽  
Tartrate Dehydratase

Functional characterization of unknown genes is currently a major task in biology. The search for gene function involves a combination of various in silico, in vitro and in vivo approaches. Available knowledge from the study of more than 21 LysR-type regulators in Escherichia coli has facilitated the classification of new members of the family. From sequence similarities and its location on the E. coli chromosome, it is suggested that ygiP encodes a lysR regulator controlling the expression of a neighbouring operon; this operon encodes the two subunits of tartrate dehydratase (TtdA, TtdB) and YgiE, an integral inner-membrane protein possibly involved in tartrate uptake. Expression of tartrate dehydratase, which converts tartrate to oxaloacetate, is required for anaerobic growth on glycerol as carbon source in the presence of tartrate. Here, it has been demonstrated that disruption of ygiP, ttdA or ygjE abolishes tartrate-dependent anaerobic growth on glycerol. It has also been shown that tartrate-dependent induction of the ttdA-ttdB-ygjE operon requires a functional YgiP.

scholarly journals Functional Characterization of the mazEF Toxin-Antitoxin System in the Pathogenic Bacterium Agrobacterium tumefaciens

2021 ◽  
Vol 9 (5) ◽  
pp. 1107
Author(s):  
Wonho Choi ◽  
Yoshihiro Yamaguchi ◽  
Ji-Young Park ◽  
Sang-Hyun Park ◽  
Hyeok-Won Lee ◽  
...  
Keyword(s):  
Agrobacterium Tumefaciens ◽  
Physiological Function ◽  
Functional Characterization ◽  
Site Directed Mutagenesis ◽  
In Vitro Assays ◽  
Cell Growth Inhibition ◽  
The Right

Agrobacterium tumefaciens is a pathogen of various plants which transfers its own DNA (T-DNA) to the host plants. It is used for producing genetically modified plants with this ability. To control T-DNA transfer to the right place, toxin-antitoxin (TA) systems of A. tumefaciens were used to control the target site of transfer without any unintentional targeting. Here, we describe a toxin-antitoxin system, Atu0939 (mazE-at) and Atu0940 (mazF-at), in the chromosome of Agrobacterium tumefaciens. The toxin in the TA system has 33.3% identity and 45.5% similarity with MazF in Escherichia coli. The expression of MazF-at caused cell growth inhibition, while cells with MazF-at co-expressed with MazE-at grew normally. In vivo and in vitro assays revealed that MazF-at inhibited protein synthesis by decreasing the cellular mRNA stability. Moreover, the catalytic residue of MazF-at was determined to be the 24th glutamic acid using site-directed mutagenesis. From the results, we concluded that MazF-at is a type II toxin-antitoxin system and a ribosome-independent endoribonuclease. Here, we characterized a TA system in A. tumefaciens whose understanding might help to find its physiological function and to develop further applications.

scholarly journals In Vitro Bile Salt Hydrolase (BSH) Activity Screening of Different Probiotic Microorganisms

Foods ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 674
Author(s):  
Jimmy G. Hernández-Gómez ◽  
Argelia López-Bonilla ◽  
Gabriela Trejo-Tapia ◽  
Sandra V. Ávila-Reyes ◽  
Antonio R. Jiménez-Aparicio ◽  
...  
Keyword(s):  
Bile Salt ◽  
High Performance ◽  
Probiotic Strain ◽  
Saccharomyces Boulardii ◽  
Bile Salt Hydrolase ◽  
Sodium Glycocholate ◽  
Probiotic Yeast ◽  
Probiotic Strains ◽  
Bsh Activity

Bile salt hydrolase (BSH) activity in probiotic strains is usually correlated with the ability to lower serum cholesterol levels in hypercholesterolemic patients. The objective of this study was the evaluation of BSH in five probiotic strains of lactic acid bacteria (LAB) and a probiotic yeast. The activity was assessed using a qualitative direct plate test and a quantitative high-performance thin- layer chromatography assay. The six strains differed in their BSH substrate preference and activity. Lactobacillus plantarum DGIA1, a potentially probiotic strain isolated from a double cream cheese from Chiapas, Mexico, showed excellent deconjugation activities in the four tested bile acids (69, 100, 81, and 92% for sodium glycocholate, glycodeoxycholate, taurocholate, and taurodeoxycholate, respectively). In the case of the commercial probiotic yeast Saccharomyces boulardii, the deconjugation activities were good against sodium glycodeoxycholate, taurocholate, and taurodeoxycholate (100, 57, and 63%, respectively). These last two results are part of the novelty of the work. A weak deconjugative activity (5%) was observed in the case of sodium glycocholate. This is the first time that the BSH activity has been detected in this yeast.

scholarly journals Viable and Heat-Killed Probiotic Strains Improve Oral Immunity by Elevating the IgA Concentration in the Oral Mucosa

2021 ◽  
Author(s):  
Wen-Yang Lin ◽  
Yi-Wei Kuo ◽  
Ching-Wei Chen ◽  
Yu-Fen Huang ◽  
Chen-Hung Hsu ◽  
...  
Keyword(s):  
Streptococcus Mutans ◽  
The Body ◽  
Effective Dosage ◽  
Tgf Beta ◽  
Oral Tablet ◽  
Beneficial Effects ◽  
Bifidobacterium Animalis ◽  
Probiotic Strains ◽  
Oral Pathogens

AbstractOral-nasal mucosal immunity plays a crucial role in protecting the body against bacterial and viral invasion. Safe probiotic products have been used to enhance human immunity and oral health. In this study, we verified the beneficial effects of mixed viable probiotic tablets, consisting of Lactobacillus salivarius subsp. salicinius AP-32, Bifidobacterium animalis subsp. lactis CP-9, and Lactobacillus paracasei ET-66, and heat-killed probiotic tablets, consisting of L. salivarius subsp. salicinius AP-32 and L. paracasei ET-66, on oral immunity among 45 healthy participants. Participants were randomly divided into viable probiotic, heat-killed probiotic, and placebo groups. The administration of treatment lasted for 4 weeks. Saliva samples were collected at Weeks 0, 2, 4, and 6, and Lactobacillus, Bifidobacterium and Streptococcus mutans populations and IgA concentration were measured. IgA concentrations, levels of TGF-beta and IL-10 in PBMCs cells were quantified by ELISA method. Results showed that salivary IgA levels were significantly increased on administration of both the viable (119.30 ± 12.63%, ***P < 0.001) and heat-killed (116.78 ± 12.28%, ***P < 0.001) probiotics for 4 weeks. Among three probiotic strains, AP-32 would effectively increase the levels of TGF-beta and IL-10 in PBMCs. The oral pathogen Streptococcus mutans was significantly reduced on viable probiotic tablet administration (49.60 ± 31.01%, ***P < 0.001). The in vitro antibacterial test confirmed that viable probiotics effectively limited the survival rate of oral pathogens. Thus, this clinical pilot study demonstrated that oral probiotic tablets both in viable form or heat-killed form could exert beneficial effects on oral immunity via IL-10, TGB-beta mediated IgA secretion. The effective dosage of viable probiotic content in the oral tablet was 109 CFUs/g and the heat-killed oral tablet was 1 × 1010 cells/g.

scholarly journals Interstrain Variability of Human Vaginal Lactobacillus crispatus for Metabolism of Biogenic Amines and Antimicrobial Activity against Urogenital Pathogens

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4538
Author(s):  
Scarlett Puebla-Barragan ◽  
Emiley Watson ◽  
Charlotte van der Veer ◽  
John A. Chmiel ◽  
Charles Carr ◽  
...  
Keyword(s):  
Biogenic Amines ◽  
Metabolic Pathways ◽  
Vaginal Microbiota ◽  
Comparative Genome Analysis ◽  
Genetic Traits ◽  
Lactobacillus Crispatus ◽  
Vaginal Swabs ◽  
The Common ◽  
Synthesis And Degradation

Lactobacillus crispatus is the dominant species in the vagina of many women. With the potential for strains of this species to be used as a probiotic to help prevent and treat dysbiosis, we investigated isolates from vaginal swabs with Lactobacillus-dominated and a dysbiotic microbiota. A comparative genome analysis led to the identification of metabolic pathways for synthesis and degradation of three major biogenic amines in most strains. However, targeted metabolomic analysis of the production and degradation of biogenic amines showed that certain strains have either the ability to produce or to degrade these compounds. Notably, six strains produced cadaverine, one produced putrescine, and two produced tyramine. These biogenic amines are known to raise vaginal pH, cause malodour, and make the environment more favourable to vaginal pathogens. In vitro experiments confirmed that strains isolated from women with a dysbiotic vaginal microbiota have higher antimicrobial effects against the common urogenital pathogens Escherichia coli and Enterococcus faecium. The results indicate that not all L. crispatus vaginal strains appear suitable for probiotic application and the basis for selection should not be only the overall composition of the vaginal microbiota of the host from which they came, but specific biochemical and genetic traits.

scholarly journals Multifunctional Coatings for Robotic Implanted Device

2019 ◽  
Vol 20 (20) ◽  
pp. 5126 ◽  
Author(s):  
Caterina Cristallini ◽  
Serena Danti ◽  
Bahareh Azimi ◽  
Veronika Tempesti ◽  
Claudio Ricci ◽  
...  
Keyword(s):  
Acrylic Acid ◽  
Vinyl Alcohol ◽  
Soft Tissues ◽  
Functional Characterization ◽  
Titanium Substrate ◽  
Repair Process ◽  
Chemical Imaging ◽  
In Vitro Cytotoxicity ◽  
Poly Vinyl Alcohol

The objective of this study was the preparation and physico-chemical, mechanical, biological, and functional characterization of a multifunctional coating for an innovative, fully implantable device. The multifunctional coating was designed to have three fundamental properties: adhesion to device, close mechanical resemblance to human soft tissues, and control of the inflammatory response and tissue repair process. This aim was fulfilled by preparing a multilayered coating based on three components: a hydrophilic primer to allow device adhesion, a poly(vinyl alcohol) hydrogel layer to provide good mechanical compliance with the human tissue, and a layer of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) fibers. The use of biopolymer fibers offered the potential for a long-term interface able to modulate the release of an anti-inflammatory drug (dexamethasone), thus contrasting acute and chronic inflammation response following device implantation. Two copolymers, poly(vinyl acetate-acrylic acid) and poly(vinyl alcohol-acrylic acid), were synthetized and characterized using thermal analysis (DSC, TGA), Fourier transform infrared spectroscopy (FT-IR chemical imaging), in vitro cell viability, and an adhesion test. The resulting hydrogels were biocompatible, biostable, mechanically compatible with soft tissues, and able to incorporate and release the drug. Finally, the multifunctional coating showed a good adhesion to titanium substrate, no in vitro cytotoxicity, and a prolonged and controlled drug release.

Extended evolutionary theory makes human culture more amenable to evolutionary analysis

2007 ◽  
Vol 30 (4) ◽  
pp. 374-374 ◽  
Author(s):  
Alex Mesoudi
Keyword(s):  
Evolutionary Theory ◽  
Cultural Change ◽  
Evolutionary Analysis ◽  
Cognitive Mechanisms ◽  
Human Culture ◽  
Genetic Mechanisms

AbstractJablonka & Lamb's (J&L's) extended evolutionary theory is more amenable to being applied to human cultural change than standard neo-Darwinian evolutionary theory. However, the authors are too quick to dismiss past evolutionary approaches to human culture. They also overlook a potential parallel between evolved genetic mechanisms that enhance evolvability and learned cognitive mechanisms that enhance learnability.

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