scholarly journals The Methods of Digging for “Gold” within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1756
Author(s):  
Jakub Lach ◽  
Paulina Jęcz ◽  
Dominik Strapagiel ◽  
Agnieszka Matera-Witkiewicz ◽  
Paweł Stączek
Keyword(s):  
In Silico ◽  
Genome Mining ◽  
Multidrug Resistant ◽  
Industrial Applications ◽  
Metagenomic Data ◽  
Resistant Bacteria ◽  
Low Oxygen ◽  
Domains Of Life ◽  
Low Oxygen Concentration

Halophiles, the salt-loving organisms, have been investigated for at least a hundred years. They are found in all three domains of life, namely Archaea, Bacteria, and Eukarya, and occur in saline and hypersaline environments worldwide. They are already a valuable source of various biomolecules for biotechnological, pharmaceutical, cosmetological and industrial applications. In the present era of multidrug-resistant bacteria, cancer expansion, and extreme environmental pollution, the demand for new, effective compounds is higher and more urgent than ever before. Thus, the unique metabolism of halophilic microorganisms, their low nutritional requirements and their ability to adapt to harsh conditions (high salinity, high pressure and UV radiation, low oxygen concentration, hydrophobic conditions, extreme temperatures and pH, toxic compounds and heavy metals) make them promising candidates as a fruitful source of bioactive compounds. The main aim of this review is to highlight the nucleic acid sequencing experimental strategies used in halophile studies in concert with the presentation of recent examples of bioproducts and functions discovered in silico in the halophile’s genomes. We point out methodological gaps and solutions based on in silico methods that are helpful in the identification of valuable bioproducts synthesized by halophiles. We also show the potential of an increasing number of publicly available genomic and metagenomic data for halophilic organisms that can be analysed to identify such new bioproducts and their producers.

scholarly journals Identification of a New Antimicrobial, Desertomycin H, Utilizing a Modified Crowded Plate Technique

Marine Drugs ◽  
2021 ◽  
Vol 19 (8) ◽  
pp. 424
Author(s):  
Osama G. Mohamed ◽  
Sadaf Dorandish ◽  
Rebecca Lindow ◽  
Megan Steltz ◽  
Ifrah Shoukat ◽  
...  
Keyword(s):  
Antibiotic Production ◽  
Gene Clusters ◽  
Multidrug Resistant ◽  
Microbial Interactions ◽  
Mass Spectrometry Data ◽  
Metagenomic Data ◽  
Resistant Bacteria ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Plate Technique

The antibiotic-resistant bacteria-associated infections are a major global healthcare threat. New classes of antimicrobial compounds are urgently needed as the frequency of infections caused by multidrug-resistant microbes continues to rise. Recent metagenomic data have demonstrated that there is still biosynthetic potential encoded in but transcriptionally silent in cultivatable bacterial genomes. However, the culture conditions required to identify and express silent biosynthetic gene clusters that yield natural products with antimicrobial activity are largely unknown. Here, we describe a new antibiotic discovery scheme, dubbed the modified crowded plate technique (mCPT), that utilizes complex microbial interactions to elicit antimicrobial production from otherwise silent biosynthetic gene clusters. Using the mCPT as part of the antibiotic crowdsourcing educational program Tiny Earth®, we isolated over 1400 antibiotic-producing microbes, including 62, showing activity against multidrug-resistant pathogens. The natural product extracts generated from six microbial isolates showed potent activity against vancomycin-intermediate resistant Staphylococcus aureus. We utilized a targeted approach that coupled mass spectrometry data with bioactivity, yielding a new macrolactone class of metabolite, desertomycin H. In this study, we successfully demonstrate a concept that significantly increased our ability to quickly and efficiently identify microbes capable of the silent antibiotic production.

scholarly journals Isolation and Characterization of Two Klebsiella pneumoniae Phages Encoding Divergent Depolymerases

2020 ◽  
Vol 21 (9) ◽  
pp. 3160 ◽  
Author(s):  
Pilar Domingo-Calap ◽  
Beatriz Beamud ◽  
Lucas Mora-Quilis ◽  
Fernando González-Candelas ◽  
Rafael Sanjuán
Keyword(s):  
Klebsiella Pneumoniae ◽  
Multidrug Resistant ◽  
Health Concern ◽  
Resistant Bacteria ◽  
Isolation And Characterization ◽  
The Family ◽  
Important Challenge ◽  
Tail Spike ◽  
Reference Strains

The emergence of multidrug-resistant bacteria is a major global health concern. The search for new therapies has brought bacteriophages into the spotlight, and new phages are being described as possible therapeutic agents. Among the bacteria that are most extensively resistant to current antibiotics is Klebsiella pneumoniae, whose hypervariable extracellular capsule makes treatment particularly difficult. Here, we describe two new K. pneumoniae phages, πVLC5 and πVLC6, isolated from environmental samples. These phages belong to the genus Drulisvirus within the family Podoviridae. Both phages encode a similar tail spike protein with putative depolymerase activity, which is shared among other related phages and probably determines their ability to specifically infect K. pneumoniae capsular types K22 and K37. In addition, we found that phage πVLC6 also infects capsular type K13 and is capable of striping the capsules of K. pneumoniae KL2 and KL3, although the phage was not infectious in these two strains. Genome sequence analysis suggested that the extended tropism of phage πVLC6 is conferred by a second, divergent depolymerase. Phage πVLC5 encodes yet another putative depolymerase, but we found no activity of this phage against capsular types other than K22 and K37, after testing a panel of 77 reference strains. Overall, our results confirm that most phages productively infected one or few Klebsiella capsular types. This constitutes an important challenge for clinical applications.

scholarly journals Prevalence of Extended-Spectrum β-Lactamases in E. coli of Rats in the Region North East of Gabon

2020 ◽  
Vol 2020 ◽  
pp. 1-6
Author(s):  
Richard Onanga ◽  
Pierre Philippe Mbehang Nguema ◽  
Guy Roger Ndong Atome ◽  
Arsène Mabika Mabika ◽  
Berthelemy Ngoubangoye ◽  
...  
Keyword(s):  
Multidrug Resistant ◽  
Resistant Bacteria ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
North East ◽  
Molecular Tests ◽  
Extended Spectrum ◽  
Susceptibility Tests ◽  
Animal Feces

Antibiotic resistance occurs in the environment by multiplication and the spread of multidrug-resistant bacteria that would be due to an improper and incorrect use of antibiotics in human and veterinary medicine. The aim of this study was to establish the prevalence of E.coli producing Extended-Spectrum beta-Lactamase (ESBL) antibiotics from rats and gregarious animals in a semirural area of Gabon and to evaluate the origin of a resistance distribution in the environment from animal feces. The bacterial culture was carried out, and the identification of E. coli strains on a specific medium and the antibiotic susceptibility tests allowed establishing the prevalence. Characterization of resistance genes was performed by gene amplification after DNA extraction. On 161 feces collected in rats, 32 strains were isolated, and 11 strains of E. coli produced ESBL with a prevalence of 34.37%. Molecular tests showed that CTX-M genes 214 bp were identified in rats. The presence of CTX-M genes could have a human origin. So, the rats can carry ESBL-producing Enterobacteriaceae which poses a risk to human health and pets in this region of Gabon.

scholarly journals JD419, a Staphylococcus aureus Phage With a Unique Morphology and Broad Host Range

2021 ◽  
Vol 12 ◽  
Author(s):  
Tingting Feng ◽  
Sebastian Leptihn ◽  
Ke Dong ◽  
Belinda Loh ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Host Range ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Complete Characterization ◽  
Resistant Bacteria ◽  
Broad Host Range ◽  
Gene Engineering ◽  
Mrsa Strains

Phage therapy represents a possible treatment option to cure infections caused by multidrug-resistant bacteria, including methicillin and vancomycin-resistant Staphylococcus aureus, to which most antibiotics have become ineffective. In the present study, we report the isolation and complete characterization of a novel phage named JD219 exhibiting a broad host range able to infect 61 of 138 clinical strains of S. aureus tested, which included MRSA strains as well. The phage JD419 exhibits a unique morphology with an elongated capsid and a flexible tail. To evaluate the potential of JD419 to be used as a therapeutic phage, we tested the ability of the phage particles to remain infectious after treatment exceeding physiological pH or temperature. The activity was retained at pH values of 6.0–8.0 and below 50°C. As phages can contain virulence genes, JD419’s complete genome was sequenced. The 45509 bp genome is predicted to contain 65 ORFs, none of which show homology to any known virulence or antibiotic resistance genes. Genome analysis indicates that JD419 is a temperate phage, despite observing rapid replication and lysis of host strains. Following the recent advances in synthetic biology, JD419 can be modified by gene engineering to remove prophage-related genes, preventing potential lysogeny, in order to be deployed as a therapeutic phage.

scholarly journals Structural characterization of scorpion peptides and their bactericidal activity against clinical isolates of multidrug-resistant bacteria

PLoS ONE ◽  
2019 ◽  
Vol 14 (11) ◽  
pp. e0222438 ◽  
Author(s):  
Catherine Cesa-Luna ◽  
Jesús Muñoz-Rojas ◽  
Gloria Saab-Rincon ◽  
Antonino Baez ◽  
Yolanda Elizabeth Morales-García ◽  
...  
Keyword(s):  
Structural Characterization ◽  
Bactericidal Activity ◽  
Multidrug Resistant ◽  
Clinical Isolates ◽  
Resistant Bacteria ◽  
Multidrug Resistant Bacteria

scholarly journals Isolation and Characterization of Multidrug Resistant Enterobacteriaceae in Urine Sample of Patients Suffering from Urinary Tract Infection with Diabetes and Nephropathy

2021 ◽  
Vol 20 (1) ◽  
pp. 87-93
Author(s):  
Nazmul Ahsan ◽  
Monzilur Rahman ◽  
Md Nazrul Islam ◽  
Anwarul Azim Akhand
Keyword(s):  
Urinary Tract Infection ◽  
Urinary Tract ◽  
Tract Infection ◽  
Multidrug Resistant ◽  
Resistant Bacteria ◽  
Diabetic Patients ◽  
Isolation And Characterization ◽  
Alternative Drug ◽  
Enterobacter Asburiae

Multidrug-resistant (MDR) organisms are spreading widely and becoming an issue of utmost importance to deal with. In the current study, ten urine samples from diabetic patients suffering from multiple complications, including urinary tract infection (UTI) and nephropathy were investigated. Antibiogram assays of the bacterial isolates from collected samples demonstrated resistance against most of the antibiotics tested. Further studies were conducted to determine the types of resistant bacteria that caused UTI. Analyzing the 16S rDNA sequence and phylogenetic tree, 3 isolates were identified as Escherichia coli, 5 as Klebsiella pneumoniae and the rest 2 as Enterobacter asburiae. The findings of this research indicate the necessity of urgent attention to find an effective alternative drug for treating infections caused by these resistant isolates. Dhaka Univ. J. Pharm. Sci. 20(1): 87-93, 2021 (June)

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