Genome Sequence of Salmonella enterica Serovar Typhimurium Phage SAP12.

Here, we report the genome of phage SAP012, which was isolated against Salmonella enterica serovar Typhimurium. The SAP012 genome is 59,618 bp, with a G+C content of 56.2% and with no antibiotic resistance or virulence genes, and is quite similar at the nucleotide level to a number of previously sequenced Salmonella phage genomes, e.g., GenBank accession numbers KM366098.1 and KC139515.1.

Clinical and experimental bacteriophage studies: Recommendations for possible approaches for standing against SARS-CoV-2.

In 2019, the world faced a serious health challenge, the rapid spreading of a life-threatening viral pneumonia, coronavirus disease 2019 (COVID-19) caused by a betacoronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of January 2022 WHO statistics shows more than 5.6 million death and about 350 million infection by SARS-CoV-2. One of the life threatening aspects of COVID-19 is secondary infections and reduced efficacy of antibiotics against them. Since the beginning of COVID-19 many researches have been done on identification, treatment, and vaccine development. Bacterial viruses (bacteriophages) could offer novel approaches to detect, treat and control COVID-19. Phage therapy and in particular using phage cocktails can be used to control or eliminate the bacterial pathogen as an alternative or complementary therapeutic agent. At the same time, phage interaction with the host immune system can regulate the inflammatory response. In addition, phage display and engineered synthetic phages can be utilized to develop new vaccines and antibodies, stimulate the immune system, and elicit a rapid and well-appropriate defense response. The emergence of SARS-CoV-2 new variants like delta and omicron has proved the urgent need for precise, efficient and novel approaches for vaccine development and virus detection techniques in which bacteriophages may be one of the plausible solutions. Therefore, phages with similar morphology and/or genetic content to that of coronaviruses can be used for ecological and epidemiological modeling of SARS-CoV-2 behavior and future generations of coronavirus, and in general new viral pathogens. This article is a comprehensive review/perspective of potential applications of bacteriophages in the fight against the present pandemic and the post-COVID era.

Biodiversity of New Lytic Bacteriophages Infecting Shigella spp. in Freshwater Environment.

Bacteriophages, viruses that infect and replicate within prokaryotic cells are the most abundant life forms in the environment, yet the vast majority of them have not been properly reported or even discovered. Almost all reported bacteriophages infecting the Enterobacteriaceae family, with Escherichia coli being the major subject of studies, have been isolated from wastewater, sewage, and effluent resources. In the present study, we focused on the distribution and biodiversity of Shigella phages in an aquatic ecosystem. While no Shigella bacteria was recovered from the Yangtze River, three lytic phages were isolated from this ecosystem and were subjected to biological, morphological, and genomic characteristics. Comparative genomics and phylogenetic analyses demonstrated that vB _SflM_004 isolate belongs to Myoviridae family, Felixounavirus genus of Ounavirinae subfamily, vB_SdyM_006 was classified under the same family, however, it is suggested to be in a new genus under Tevenvirinae subfamily with some other related bacteriophages. vB_SsoS_008 phage belongs to the Siphoviridae family, Tunavirus genus, Tunavirinae subfamily. The phages did not harbor any genes involved in the lysogenic cycles and showed a high temperature and pH stability. The biodiversity of the isolated phages highly suggests that continued isolation on non-model members of Enterobacteriaceae family is necessary to fully understand bacteriophage diversity in aquatic environments.

Characterization of a novel bullet-shaped lytic bacteriophage against extensively drug-resistant Pseudomonas aeruginosa isolated from human and domestic sources.

Global spread and emergence of the extensively drug-resistant (XDR) strains of P. aeruginosa have become a concern, thus, searching for new alternative treatment approaches are required. This study was aimed to isolate and characterize a novel lytic phage against P. aeruginosa. Seventy XDR isolates of P. aeruginosa were collected from May to September 2018. Wastewater samples were used for isolation of lytic phage against XDR P. aeruginosa isolates. Host range, thermal and pH stability, adsorption rate, latent period, burst size and morphology of phage were determined following the standard protocols. Morphological characteristics of the phage revealed that it belonged to Podoviridae family and it was named vB-PaeP-007. Although the phage had a narrow host range, 47 out of 70 XDR isolates were susceptible to it. The adsorption rate, latent period and burst size of vB-PaeP-007 were approximately 89.80% in 8 min, 10 min and 93 phages per cell, respectively. Its lysis activity remained at a wide range of pH (4 up to 12) and temperature (- 20.00 up to 70.00 ˚C). Regarding the physiological features and host range of the vB-PaeP-007 phage, it could be a promising candidate for phage therapy and bio-controlling of infections from XDR isolates of P. aeruginosa in human and livestock storage centers.

Isolation, characterization, and PCR-based molecular identification of a siphoviridae phage infecting Shigella dysenteriae.

BACKGROUND: Shigella dysenteriae is one of the members of Shigella genus which was the main responsible of different Shigellosis outbreaks worldwide. The increasing consumption of antibiotics has led to the emergence and spreading of antibiotic-resistant strains. Therefore, finding new alternatives for infection control is essential, one of which is using bacteriophages. MATERIALS AND METHODS: Lytic bacteriophage against Shigella dysenteriae was isolated from petroleum refinery wastewater. Phage morphological and genetic characteristics were studied using TEM, and sequencing, respectively. In addition, the genome size was estimated, and phage resistance to different temperatures and pH, host range, adsorption rate, and one-step growth were investigated. RESULTS: According to the morphology and genetic results, this phage was named vB-SdyS-ISF003. Sequencing of the PCR products revealed that the vB-SdyS-ISF003 phage belongs to the species T1virus, subfamily Tunavirinae of family Siphoviridae. This was the first detected bacteriophage against S. dysenteriae, which belongs to the family Siphoviridae. In addition, its host range was limited to S. dysenteriae. The genome size was about 62 kb. vB-SdyS-ISF003 phage has a number of desirable characteristics including the limited host range to S. dysenteriae, very short connection time, a relatively wide range of temperature tolerance -20 to 50 °C, pH tolerance of 7-9 without significant reduction in the phage titer. CONCLUSION: vB-SdyS-ISF003 is a novel virulent T1virus phage and has the appropriate potential for being used in bio controlling of S. dysenteriae in different condition.

Bioremediation of chromium contaminated water by diatoms with concomitant lipid accumulation for biofuel production.

Hexavalent chromium compounds such as chromate and dichromate, commonly designated as Cr (VI) compounds, are widely used heavy metals in different industries and are considered highly toxic to most life forms. Unfortunately, they have become a major pollutant of groundwater and rivers around dichromate using industries. Bioremediation is widely used to decrease the amount of dichromate in wastewater but requires large amounts of precious fresh water. Here we tested two marine micro-algal species, Phaeodactylum tricornutum strain CCY0033 and Navicula pelliculosa strain CCMP543, for their ability of dichromate bioremediation and concomitantly producing lipids that can serve as biofuel. Dichromate tolerance of the strains was investigated under different growth conditions in order to obtain high biomass yields, high lipid accumulation and high dichromate removal from the medium. Both algal strains grew well and produced high biomass in media containing up to 1 mg of dichromate per liter. Variations in growth conditions revealed that dichromate removal from the medium correlated positively with biomass yield. Dichromate removal using living cells was in the same order of magnitude as with autoclaved dead cells or when using extracted extracellular polymeric substances (EPS). This suggests biosorption of dichromate to cell-associated polymeric substances as the major mechanism of the bioremediation process. For both strains, optimal dichromate removal and lipid production were achieved at a light intensity of 55 µmol m-2s-1 and at a sodium nitrate concentration of 3 mM. The optimal temperature for dichromate removal and lipid production was 23 °C for P. tricornutum and 27 °C for N. pelliculosa. Compared to P. tricornutum strain CCY0033, N. pelliculosa strain CCMP543 produced an overall higher lipid yield under these conditions.

Improvement of hydrolysis and fermentation of sugarcane bagasse by soaking in aqueous ammonia and methanolic ammonia.

Sugarcane bagasse was pretreated by soaking it in aqueous ammonia (SAA) and methanolic aqueous ammonia (SMAA) at 70 °C for 12 h. Then the pretreated as well as untreated bagasse was subjected to enzymatic hydrolysis at 50 °C for 72 h by 15 FPU cellulase and 30 CBU cellobiase per g of substrate. The hydrolysis of SAA-pretreated bagasse with a solid to liquid (S:L) ratio of 1:10 resulted in 95.9% of the maximum theoretical yield. The production yield for SMAA at an S:L ratio of 1:6 with 15% methanol was 88.6%, while it was only 21.3% for the untreated bagasse. Ethanol production by simultaneous saccharification and fermentation was conducted at 37 °C for 72 h. The results revealed that the ethanol production yield was improved from 12.7% for the untreated bagasse to 92.45% and 90.8% for the SAA and the SMAA pretreated bagasse, respectively. The compositional and chemical structural analysis suggested that lignin removal and crystallinity reduction were responsible for the hydrolysis and SSF improvements.