scholarly journals Genomic Insight into Pediococcus acidilactici HN9, a Potential Probiotic Strain Isolated from the Traditional Thai-Style Fermented Beef Nhang

2020 ◽  
Vol 9 (1) ◽  
pp. 50
Author(s):  
Komwit Surachat ◽  
Duangporn Kantachote ◽  
Panchalika Deachamag ◽  
Monwadee Wonglapsuwan
Keyword(s):  
Genome Analysis ◽  
Genome Stability ◽  
Starter Culture ◽  
Probiotic Strain ◽  
Pediococcus Acidilactici ◽  
Bacterial Strains ◽  
Circular Chromosome ◽  
Antimicrobial Resistance Genes ◽  
Depth Analysis ◽  
Food Applications

Pediococcus acidilactici HN9 is a beneficial lactic acid bacterium isolated from Nhang, a traditional Thai-style fermented beef. In this study, the molecular properties of P. acidilactici HN9 were characterized to provide insights into its potential probiotic activity. Specifically, this work sought to report the complete genome of P. acidilactici HN9 and perform a comparative genome analysis with other bacterial strains belonging to the genus Pediococcus. Genomic features of HN9 were compared with those of all other bacterial Pediococcus strains to examine the adaptation, evolutionary relationships, and diversity within this genus. Additionally, several bioinformatic approaches were used to investigate phylogenetic relationships, genome stability, virulence factors, bacteriocin production, and antimicrobial resistance genes of the HN9 strain, as well as to ensure its safety as a potential starter culture in food applications. A 2,034,522 bp circular chromosome and two circular plasmids, designated pHN9-1 (42,239-bp) and pHN9-2 (30,711-bp), were detected, and used for pan-genome analysis, as well as for identification of bacteriocin-encoding genes in 129 strains belonging to all Pediococcus species. Two CRISPR regions were identified in P. acidilactici HN9, including type II-A CRISPR/CRISPR-associated (Cas). This study provides an in-depth analysis on P. acidilactici HN9, facilitating a better understanding of its adaptability to different environments and its mechanism to maintain genome stability over time.

Whole-genome analysis of the potentially zoonotic Elizabethkingia miricola FL160902 with two new chromosomal MBL gene variants

2019 ◽  
Vol 75 (3) ◽  
pp. 526-530 ◽  
Author(s):  
Ruixue Hu ◽  
Qi Zhang ◽  
Zemao Gu
Keyword(s):  
Phylogenetic Analysis ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Genome Analysis ◽  
Snp Analysis ◽  
Gene Variants ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Circular Chromosome ◽  
Antimicrobial Resistance Genes

Abstract Objectives Elizabethkingia is an emerging life-threatening pathogen in both humans and animals. We describe the whole-genome analysis of an Elizabethkingia miricola strain isolated from a diseased frog in China and investigate the molecular mechanism of carbapenem resistance in this pathogen. Methods WGS of E. miricola FL160902 was performed using single-molecule, real-time technology. A phylogenetic tree was generated by SNP analysis, comparing the genome of our strain with other E. miricola isolates of amphibian and human origins. Antimicrobial resistance genes and virulence-related genes were identified using the Comprehensive Antibiotic Resistance Database (CARD) and the Virulence Factor Database (VFDB). Two putative carbapenemase genes were expressed in Escherichia coli to evaluate their contribution to antimicrobial resistance. Results The genome of E. miricola FL160902 consists of a 4 249 586 bp circular chromosome with 27 putative resistance genes and 38 predicted virulence-associated genes. Comparative genomic analysis demonstrated that the E. miricola strains of human and amphibian origins have similar virulence-associated gene profiles. In addition, all the amphibian isolates clustered together with one of the human isolates in the phylogenetic analysis. WGS revealed the presence of two novel MBL genes, designated blaBlaB-16 and blaGOB-19. Cloning of blaBlaB-16 and blaGOB-19 into E. coli DH5α resulted in increased MICs of most β-lactams, including imipenem, meropenem and ampicillin. Conclusions We identified two chromosomal MBL gene variants, named blaBlaB-16 and blaGOB-19 in an amphibian E. miricola isolate, which was considered potentially zoonotic based on phylogenetic analysis and virulence-associated gene comparison. This study highlights the importance of E. miricola as a potential zoonotic pathogen and a reservoir of MDR genes.

scholarly journals A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Adrienn Gréta Tóth ◽  
István Csabai ◽  
Gergely Maróti ◽  
Ákos Jerzsele ◽  
Attila Dubecz ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Pathogenic Bacteria ◽  
Gene Diversity ◽  
Fermented Food ◽  
Practical Significance ◽  
Fermented Foods ◽  
Bacterial Strains ◽  
Genetic Components ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene

AbstractAntimicrobial resistance (AMR) is a global threat gaining more and more practical significance every year. The main determinants of AMR are the antimicrobial resistance genes (ARGs). Since bacteria can share genetic components via horizontal gene transfer, even non-pathogenic bacteria may provide ARG to any pathogens which they become physically close to (e.g. in the human gut). In addition, fermented food naturally contains bacteria in high amounts. In this study, we examined the diversity of ARG content in various kefir and yoghurt samples (products, grains, bacterial strains) using a unified metagenomic approach. We found numerous ARGs of commonly used fermenting bacteria. Even with the strictest filter restrictions, we identified ARGs undermining the efficacy of aminocoumarins, aminoglycosides, carbapenems, cephalosporins, cephamycins, diaminopyrimidines, elfamycins, fluoroquinolones, fosfomycins, glycylcyclines, lincosamides, macrolides, monobactams, nitrofurans, nitroimidazoles, penams, penems, peptides, phenicols, rifamycins, tetracyclines and triclosan. In the case of gene lmrD, we detected genetic environment providing mobility of this ARG. Our findings support the theory that during the fermentation process, the ARG content of foods can grow due to bacterial multiplication. The results presented suggest that the starting culture strains of fermented foods should be monitored and selected in order to decrease the intake of ARGs via foods.

Characterization, Pathogenicity, Phylogeny, and Comparative Genomic Analysis of Pseudomonas tolaasii Strains Isolated from Various Mushrooms in China

2021 ◽  
Author(s):  
Zhenghui Liu ◽  
Yitong Zhao ◽  
Frederick Leo Sossah ◽  
Benjamin Azu Okorley ◽  
Daniel G. Amoako ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Genomic Analysis ◽  
Gene Families ◽  
Effective Control ◽  
Economic Losses ◽  
Comparative Genomic ◽  
Bacterial Strains ◽  
Secretion Systems ◽  
Pseudomonas Tolaasii ◽  
Antimicrobial Resistance Genes

Since 2016, devastating bacterial blotch affecting the fruiting bodies of Agaricus bisporus, Cordyceps militaris, Flammulina filiformis, and Pleurotus ostreatus in China has caused severe economic losses. We isolated 102 bacterial strains and characterized them polyphasically. We identified the causal agent as Pseudomonas tolaasii and confirmed the pathogenicity of the strains. A host range test further confirmed the pathogen’s ability to infect multiple hosts. This is the first report in China of bacterial blotch in C. militaris caused by P. tolaasii. Whole-genome sequences were generated for three strains: Pt11 (6.48 Mb), Pt51 (6.63 Mb), and Pt53 (6.80 Mb), and pangenome analysis was performed with 13 other publicly accessible P. tolaasii genomes to determine their genetic diversity, virulence, antibiotic resistance, and mobile genetic elements. The pangenome of P. tolaasii is open, and many more gene families are likely to emerge with further genome sequencing. Multilocus sequence analysis using the sequences of four common housekeeping genes (glns, gyrB, rpoB, and rpoD) showed high genetic variability among the P. tolaasii strains, with 115 strains clustered into a monophyletic group. The P. tolaasii strains possess various genes for secretion systems, virulence factors, carbohydrate-active enzymes, toxins, secondary metabolites, and antimicrobial resistance genes that are associated with pathogenesis and adapted to different environments. The myriad of insertion sequences, integrons, prophages, and genome islands encoded in the strains may contribute to genome plasticity, virulence, and antibiotic resistance. These findings advance understanding of the determinants of virulence, which can be targeted for the effective control of bacterial blotch disease.

Detection of Biogenic Amine Producer Bacteria in a Typical Italian Goat Cheese

2008 ◽  
Vol 71 (1) ◽  
pp. 205-209 ◽  
Author(s):  
SILVIA BONETTA ◽  
SARA BONETTA ◽  
ELISABETTA CARRARO ◽  
JEAN DANIEL COÏSSON ◽  
FABIANO TRAVAGLIA ◽  
...  
Keyword(s):  
Biogenic Amines ◽  
Enterococcus Faecalis ◽  
Biogenic Amine ◽  
Pediococcus Acidilactici ◽  
Bacterial Strains ◽  
Goat Cheese ◽  
Low Concentrations ◽  
Amine Content ◽  
High Concentrations ◽  
Almost All

The aim of this study was to research decarboxylating bacterial strains and biogenic amine content in a typical Italian goat cheese (Robiola di Roccaverano). The study was performed on fresh and ripened samples of goat cheese manufactured from industrial and artisanal producers. Sixty-seven bacterial strains isolated showed decarboxylating activity, and Enterococcus faecalis was the most widespread decarboxylating species in all artisanal and industrial products. Pediococcus acidilactici and Enterococcus malodoratus were also identified as biogenic amine producers in Robiola di Roccaverano cheese. All the E. faecalis strains isolated in this study were able to decarboxylate tyrosine. Tyramine was the most abundant biogenic amine in cheese samples, while histamine was the most widespread. High amounts of these two biogenic amines were found in ripened samples (up to 2,067 mg/kg for tyramine and 1,786 mg/kg for histamine), whereas 2-phenylethylamine and tryptamine were present in almost all ripened cheeses at low concentrations. The detection of strains producing biogenic amines and the high concentrations of tyramine and histamine found in ripened Robiola di Roccaverano could represent a potential risk to the consumer.

scholarly journals Whole-Genome Sequence of Lactobacillus salivarius DJ-sa-01, Isolated from Chicken Small Intestine

2018 ◽  
Vol 7 (14) ◽  
Author(s):  
Dongjun Kim ◽  
Mun-Ju Cho ◽  
Seungchan Cho ◽  
Yongjun Lee ◽  
Sung June Byun ◽  
...  
Keyword(s):  
Small Intestine ◽  
Genome Sequence ◽  
Probiotic Strain ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Lactobacillus Salivarius ◽  
Circular Chromosome ◽  
Content Type ◽  
Single Circular Chromosome

We have identified the whole-genome sequence of Lactobacillus salivarius DJ-sa-01, a potential probiotic strain for poultry, isolated from a chicken small intestine. We used the PacBio and Illumina platforms to obtain the sequence of the entire single circular chromosome.

scholarly journals Probiotic and Antioxidant Potential of Lactobacillus reuteriLR12 and Lactobacillus lactisLL10 Isolated from Pineapple Puree and Quality Analysis of Pineapple-Flavored Goat Milk Yoghurt during Storage

2020 ◽  
Vol 8 (10) ◽  
pp. 1461 ◽  
Author(s):  
Naif Abdullah Al-Dhabi ◽  
Mariadhas Valan Arasu ◽  
Ponnuswamy Vijayaraghavan ◽  
Galal Ali Esmail ◽  
Veeramuthu Duraipandiyan ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Radical Scavenging Activity ◽  
Starter Culture ◽  
Radical Scavenging ◽  
Reducing Power ◽  
Goat Milk ◽  
Quality Analysis ◽  
Scavenging Activity ◽  
Bacterial Strains ◽  
Adhesion Properties

In recent years, studies have focused on the therapeutic properties of probiotics to eliminate pathogenic microorganisms associated with various diseases. Lactobacilli are important probiotics groups that have been found to possess many health-promoting activities. This study was carried out to isolate LactobacillusreuteriLR12 and L. lactisLL10 from pineapple puree. The invitro analysis to evaluate probiotic characteristics of the isolated bacteria included survival in bile and acid tolerance. The cell-free supernatant of L. reuteri LR12 was effective against various pathogenic bacteria and fungi compared with L. lactisLL10. These two bacterial strains have strong anti-biofilm activity (100%) against Enterococcus faecalis, Staphylococcus aureus, and Bacillus cereus. The bacterial strains exhibited adhesion properties to HT-29 cells (human colorectal adenocarcinoma). These bacteria showed DPPH- (2,2-diphenyl-1-picryl-hydrazyl-hydrate) free radical scavenging activity, scavenging of hydroxyl radical activity, superoxide radical scavenging activity, and reducing power activity in the range of 72% ± 3%to 89.3% ± 1.7%, 64% ± 2.7%to 66.8% ± 1.5%, 59.8% ± 4.1% to 63.8% ± 2.1%, and 60.4% ± 1.8%to 66.1% ± 3.3%, respectively. Pineapple puree was used as the starter culture with milk for 2 days for yogurt preparation. Pineapple puree increased flavor and showed the physicochemical properties of yogurt. The finding of the sensory evaluation revealed no significant change compared with the control, except the appearance of yogurt. These findings show that Lactobacilli and pineapple puree have potential use in various probiotic preparations for the fermentation industry.

Influence of NaCl and NaNO3 on Sinigrin Hydrolysis by Foodborne Bacteria

2011 ◽  
Vol 74 (12) ◽  
pp. 2162-2168 ◽  
Author(s):  
S. HERZALLAH ◽  
M. LARA LLEDÓ ◽  
R. HOLLEY
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Fluorescens ◽  
Starter Culture ◽  
Allyl Isothiocyanate ◽  
Escherichia Coli O157 ◽  
Bacterial Strains ◽  
Natural Antimicrobial ◽  
Staphylococcus Carnosus ◽  
Factors Influencing ◽  
Endogenous Plant

The glucosinolate sinigrin (SNG) is converted by endogenous plant myrosinase or by bacterial myrosinase-like activity to form the potent antimicrobial allyl isothiocyanate. In order to use SNG as a natural antimicrobial precursor in food, it became important to better understand the ability of bacteria to synthesize the enzyme(s) and understand factors influencing this synthesis at a constant SNG concentration. Eight spoilage, pathogenic, or starter culture bacteria were grown separately in medium containing individual or combined salts with SNG. SNG degradation by the bacteria and the formation of its major degradation product, allyl isothiocyanate, were followed for 12 days at 30 or 35°C. The bacterial strains varied in their ability to metabolize SNG, and this was enhanced by NaCl and/or NaNO3. SNG hydrolysis took place after 4 days, and the greatest amount occurred by day 12. At 12 days, Escherichia coli O157:H7 showed the greatest capacity to hydrolyze SNG (45.3% degradation), followed by Staphylococcus carnosus (44.57%), while Pseudomonas fluorescens was not active against SNG. The ability of tested strains to metabolize SNG, in decreasing order, was as follows: Escherichia coli O157:H7 > Staphylococcus carnosus > Staphylococcus aureus > Pediococcus pentosaceus > Salmonella Typhimurium > Listeria monocytogenes > Enterococcus faecalis > Pseudomonas fluorescens.

scholarly journals Comparative genome analysis of Salmonella enterica serovar Gallinarum biovars Pullorum and Gallinarum decodes strain specific genes

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255612
Author(s):  
Rajesh Kumar Vaid ◽  
Zoozeal Thakur ◽  
Taruna Anand ◽  
Sanjay Kumar ◽  
Bhupendra Nath Tripathi
Keyword(s):  
Genome Analysis ◽  
Salmonella Enterica ◽  
Core Genome ◽  
Genomic Islands ◽  
Economic Losses ◽  
Genotypic Differences ◽  
Comparative Genome Analysis ◽  
Comparative Genome ◽  
Genomic Features ◽  
Antimicrobial Resistance Genes

Salmonella enterica serovar Gallinarum biovar Pullorum (bvP) and biovar Gallinarum (bvG) are the etiological agents of pullorum disease (PD) and fowl typhoid (FT) respectively, which cause huge economic losses to poultry industry especially in developing countries including India. Vaccination and biosecurity measures are currently being employed to control and reduce the S. Gallinarum infections. High endemicity, poor implementation of hygiene and lack of effective vaccines pose challenges in prevention and control of disease in intensively maintained poultry flocks. Comparative genome analysis unravels similarities and dissimilarities thus facilitating identification of genomic features that aids in pathogenesis, niche adaptation and in tracing of evolutionary history. The present investigation was carried out to assess the genotypic differences amongst S.enterica serovar Gallinarum strains including Indian strain S. Gallinarum Sal40 VTCCBAA614. The comparative genome analysis revealed an open pan-genome consisting of 5091 coding sequence (CDS) with 3270 CDS belonging to core-genome, 1254 CDS to dispensable genome and strain specific genes i.e. singletons ranging from 3 to 102 amongst the analyzed strains. Moreover, the investigated strains exhibited diversity in genomic features such as virulence factors, genomic islands, prophage regions, toxin-antitoxin cassettes, and acquired antimicrobial resistance genes. Core genome identified in the study can give important leads in the direction of design of rapid and reliable diagnostics, and vaccine design for effective infection control as well as eradication. Additionally, the identified genetic differences among the S. enterica serovar Gallinarum strains could be used for bacterial typing, structure based inhibitor development by future experimental investigations on the data generated.

scholarly journals Gut Microbiota Manipulation in Foals—Naturopathic Diarrhea Management, or Unsubstantiated Folly?

Pathogens ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1137
Author(s):  
Rachel Goodman-Davis ◽  
Marianna Figurska ◽  
Anna Cywinska
Keyword(s):  
Quality Control ◽  
Clinical Trials ◽  
Fecal Microbiota Transplantation ◽  
Fecal Microbiota ◽  
Evidence Based ◽  
Economic Consequence ◽  
Bacterial Strains ◽  
Antimicrobial Resistance Genes ◽  
Health And Disease ◽  
Pros And Cons

Diarrhea in foals is a problem of significant clinical and economic consequence, and there are good reasons to believe microbiota manipulation can play an important role in its management. However, given the dynamic development of the foal microbiota and its importance in health and disease, any prophylactic or therapeutic efforts to alter its composition should be evidence based. The few clinical trials of probiotic preparations conducted in foals to date show underwhelming evidence of efficacy and a demonstrated potential to aggravate rather than mitigate diarrhea. Furthermore, recent studies have affirmed that variable but universally inadequate quality control of probiotics enables inadvertent administration of toxin-producing or otherwise pathogenic bacterial strains, as well as strains bearing transferrable antimicrobial resistance genes. Consequently, it seems advisable to approach probiotic therapy in particular with caution for the time being. While prebiotics show initial promise, an even greater scarcity of clinical trials makes it impossible to weigh the pros and cons of their use. Advancing technology will surely continue to enable more detailed and accurate mapping of the equine adult and juvenile microbiota and potentially elucidate the complexities of causation in dysbiosis and disease. In the meantime, fecal microbiota transplantation may be an attractive therapeutic shortcut, allowing practitioners to reconstruct a healthy microbiota even without fully understanding its constitution.

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