Publications by authors named "Yigang Tong"

217 Publications

Recent Advances and Perspectives on Expanding the Chemical Diversity of Lasso Peptides.

Front Bioeng Biotechnol 2021 24;9:741364. Epub 2021 Sep 24.

College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing family of natural products that exhibit a range of structures and bioactivities. Initially assembled from the twenty proteinogenic amino acids in a ribosome-dependent manner, RiPPs assume their peculiar bioactive structures through various post-translational modifications. The essential modifications representative of each subfamily of RiPP are performed on a precursor peptide by the so-called processing enzymes; however, various tailoring enzymes can also embellish the precursor peptide or processed peptide with additional functional groups. Lasso peptides are an interesting subfamily of RiPPs characterized by their unique lariat knot-like structure, wherein the C-terminal tail is inserted through a macrolactam ring fused by an isopeptide bond between the N-terminal amino group and an acidic side chain. Until recently, relatively few lasso peptides were found to be tailored with extra functional groups. Nevertheless, the development of new routes to diversify lasso peptides and thus introduce novel or enhanced biological, medicinally relevant, or catalytic properties is appealing. In this review, we highlight several strategies through which lasso peptides have been successfully modified and provide a brief overview of the latest findings on the tailoring of these peptides. We also propose future directions for lasso peptide tailoring as well as potential applications for these peptides in hybrid catalyst design.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fbioe.2021.741364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8498205PMC
September 2021

The origins of viruses: discovery takes time, international resources, and cooperation.

Lancet 2021 Oct 30;398(10309):1401-1402. Epub 2021 Sep 30.

National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. Electronic address:

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/S0140-6736(21)02180-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8483647PMC
October 2021

Outbreaks of Acute Respiratory Disease Associated with Human Adenovirus Infection in Closed Camps, China, December 2011-March 2014.

China CDC Wkly 2021 Sep;3(38):793-798

State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.

What Is Already Known On This Topic?: Human adenovirus (HAdV) was frequently associated with acute respiratory disease (ARD) outbreaks in military camps.

What Is Added By This Report?: HAdV-B7, HAdV-B14, and HAdV-B55 were determined to be responsible for 3, 2, and 4 ARD outbreaks in military camps, China, respectively, with a total attack rate of 28.0% during 2011 to 2014.

What Are The Implications For Public Health Practice?: The findings suggest that vaccine development and administration in military camps must be prioritized. Quarantining among new recruits before entering into the military and the identification of the major responsible genotypes at the current stage is warranted.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.46234/ccdcw2021.197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8477058PMC
September 2021

Tracing the origins of SARS-CoV-2: lessons learned from the past.

Cell Res 2021 Sep 29. Epub 2021 Sep 29.

Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41422-021-00575-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8480455PMC
September 2021

The Benefits of Breastfeeding Still Outweigh the Risks of COVID-19 Transmission.

Front Med (Lausanne) 2021 8;8:703950. Epub 2021 Sep 8.

Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmed.2021.703950DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8455845PMC
September 2021

Characteristics and genome analysis of a novel bacteriophage IME1323_01, the first temperate bacteriophage induced from Staphylococcus caprae.

Virus Res 2021 Nov 20;305:198569. Epub 2021 Sep 20.

College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China. Electronic address: Electronic address:

Temperate phages play an important role in the evolution of bacteria. So far, lytic phages have been wildly reported, but there is still limited knowledge regarding temperate phages in the genome of pathogenic Staphylococcus caprae. Here we present the characteristics and genome analysis of a novel bacteriophage IME1323_01, which is the first isolated bacteriophage of S. caprae. The phage genome is a 44282-bp linear dsDNA molecule with a GC content of 34.18%, which is similar to its host. The genome of IME1323_01 is most closely related with that of temperate phage IME1318_01, whereas the homology coverage is just 34%. Genome and proteome analyses confirmed the lysogenic nature of phage IME1323_01, which encodes the typical lysogen-related proteins integrase, CI, Cro, and anti-repressor proteins. Genomic and phylogenetic analysis revealed that phage IME1323_01 is a newly discovered phage, which belongs to subfamily Azeredovirinae in the family Siphoviridae. The goal of this study is to increase our knowledge about the phages of S. caprae and expand our armamentarium against the escalating threat of pathogenic bacteria.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.virusres.2021.198569DOI Listing
November 2021

Influence of oral nutritional agents rich in soluble dietary fiber on intestinal flora of elderly men with malnutrition.

Aging Med (Milton) 2021 Sep 31;4(3):162-168. Epub 2021 Aug 31.

Department of Endocrinology/Department of Health Care The Key Laboratory of Geriatrics Beijing Institution of Geriatrics Beijing Hospital National Center of Gerontology Institute of Geriatric Medicine Chinese Academy of Medical Sciences Beijing China.

Objective: Observe the influence of oral nutritional agents rich in soluble dietary (enteral nutritional suspension [TPF-DM]) on intestinal flora of elderly male subjects with malnutrition.

Method: Seventy-eight subjects with good nutrition were considered as the healthy control group. Twenty-eight male subjects who had malnutrition and were older than 70 years were included and randomly divided into the short-term (3 months) intervention group (n = 20) and the long-term (12 months) group (n = 8). They were provided with enteral nutritional suspension (TPF-DM) 500 mL/day or maximum tolerance dose, so as to observe the changes in nutrition-related indexes and intestinal flora after the elderly take enteral nutritional suspension (TPF-DM).

Results: (1) For elderly male subjects with malnutrition, their body weight, body mass index, hemoglobin, total protein, and albumin were significantly lower than the control group with favorable nutrition. (2) There were obvious differences in intestinal flora between healthy elderly male subjects and those with malnutrition. After the treatment of enteral nutritional suspension (TPF-DM), intestinal flora of the malnourished elderly subjects showed recovery toward the healthy elderly subjects. The obvious gradient changes of the flora were mainly in the bacteroidetes, firmicutes, and proteobacteria phyla, and the relative abundance of CAG2 clusters in the malnourished group was higher than that in the healthy control group, and the relative abundance decreased after long-term treatment, and the change approached the healthy control group. The relative abundance of CAG3 and CAG6 clusters in the malnourished group was lower than that in the healthy control group, and the relative abundance increased after long-term treatment, and the change approached the healthy control group.

Conclusion: Malnutrition has obvious impact on intestinal flora of the elderly. Enteral nutritional suspension (TPF-DM) not only prevents the further decline in the state of nutrition but also helps the recovery in intestinal flora of the elderly. Long-term application can produce better effects.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/agm2.12174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8444960PMC
September 2021

Artemether, Artesunate, Arteannuin B, Echinatin, Licochalcone B and Andrographolide Effectively Inhibit SARS-CoV-2 and Related Viruses .

Front Cell Infect Microbiol 2021 30;11:680127. Epub 2021 Aug 30.

Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.

Since the first reported case caused by the novel coronavirus SARS-CoV-2 infection in Wuhan, COVID-19 has caused serious deaths and an ongoing global pandemic, and it is still raging in more than 200 countries and regions around the world and many new variants have appeared in the process of continuous transmission. In the early stage of the epidemic prevention and control and clinical treatment, traditional Chinese medicine played a huge role in China. Here, we screened out six monomer compounds, including artemether, artesunate, arteannuin B, echinatin, licochalcone B and andrographolide, with excellent anti-SARS-CoV-2 and anti-GX_P2V activity from Anti-COVID-19 Traditional Chinese Medicine Compound Library containing 389 monomer compounds extracted from traditional Chinese medicine prescriptions "three formulas and three drugs". Our discovery preliminary proved the stage of action of those compounds against SARS-CoV-2 and provided inspiration for further research and clinical applications.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fcimb.2021.680127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8435859PMC
September 2021

All-in-one colorimetric RT-LAMP assay for point-of-care testing of SARS-CoV-2.

Analyst 2021 Sep 27;146(19):6026-6034. Epub 2021 Sep 27.

Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China.

The ongoing outbreaks of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have resulted in unprecedented challenges to global health. To effectively contain the COVID-19 transmission, rapid tests for detecting existing SARS-CoV-2 infections and assessing virus spread are critical. To address the huge need for ever-increasing tests, we developed a facile all-in-one nucleic acid testing assay by combining Si-OH activated glass bead (aGB)-based viral RNA fast extraction and colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) detection in a single tube. aGBs demonstrate a strong ability to capture viral RNA in a guanidinium-based lysis buffer, and the purified aGBs/RNA composite, without RNA elution step, could be directly used to perform RT-LAMP assay. The assay was well characterized by using a novel SARS-CoV-2-like coronavirus GX/P2V, and showed a limit of detection (LOD) of 15 copies per μL in simulated clinical samples within 50 min. We further demonstrated our assay by testing simulated SARS-CoV-2 pseudovirus samples, showing an LOD of 32 copies per μL and high specificity without cross-reactivity with the most closely related GX/P2V or host DNA/RNA. The all-in-one approach developed in this study has the potential as a simple, scalable, and time-saving alternative for point-of-care testing of SARS-CoV-2 in low-income regions, as well as a promising tool for at-home testing.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1039/d1an01043cDOI Listing
September 2021

Difference of Intrahost Dynamics of the Second Human Pegivirus and Hepatitis C Virus in HPgV-2/HCV-Coinfected Patients.

Front Cell Infect Microbiol 2021 12;11:728415. Epub 2021 Aug 12.

Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China.

Background: The second human pegivirus (HPgV-2) and hepatitis C virus (HCV) belong to the Flaviviridae family and share some common genome features. However, the two viruses exhibit significantly different genetic diversity. The comparison of intrahost dynamics of HPgV-2 and HCV that mainly reflect virus-host interactions is needed to elucidate their intrahost difference of genetic diversity and the possible mechanisms.

Methods: Intrahost single nucleotide variations (iSNVs) were identified by means of next-generation sequencing from both cross-sectional and longitudinal samples from HPgV-2- and HCV-coinfected patients. The levels of human cytokines were quantified in the patient before and after HCV elimination by the treatment of direct-acting antivirals (DAA).

Results: Unlike HCV, the viral sequences of HPgV-2 are highly conserved among HPgV-2-infected patients. However, iSNV analysis confirmed the intrahost variation or quasispecies of HPgV-2. Almost all iSNVs of HPgV-2 did not accumulate or transmit within host over time, which may explain the highly conserved HPgV-2 consensus sequence. Intrahost variation of HPgV-2 mainly causes nucleotide transition in particular at the 3rd codon position and synonymous substitutions, indicating purifying or negative selection posed by host immune system. Cytokine data further indicate that HPgV-2 infection alone may not efficiently stimulate innate immune responses since proinflammatory cytokine expression dramatically decreased with elimination of HCV.

Conclusion: This study provided new insights into the intrahost genomic variations and evolutionary dynamics of HPgV-2 as well as the impact of host immune selection and virus polymerase on virus evolution. The different genetic diversity of HPgV-2 and HCV makes HPgV-2 a potential new model to investigate RNA virus diversity and the mechanism of viral polymerase in modulating virus replication.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fcimb.2021.728415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8403064PMC
August 2021

The Influence of Formulation Components and Environmental Humidity on Spray-Dried Phage Powders for Treatment of Respiratory Infections Caused by .

Pharmaceutics 2021 Jul 28;13(8). Epub 2021 Jul 28.

School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Shatin, NewTerritories, Hong Kong, China.

The feasibility of using respirable bacteriophage (phage) powder to treat lung infections has been demonstrated in animal models and clinical studies. This work investigated the influence of formulation compositions and excipient concentrations on the aerosol performance and storage stability of phage powder. An anti- phage vB_AbaM-IME-AB406 was incorporated into dry powders consisting of trehalose, mannitol and L-leucine for the first time. The phage stability upon the spray-drying process, room temperature storage and powder dispersion under different humidity conditions were assessed. In general, powders prepared with higher mannitol content (40% of the total solids) showed a lower degree of particle merging and no sense of stickiness during sample handling. These formulations also provided better storage stability of phage with no further titer loss after 1 month and <1 log titer loss in 6 months at high excipient concentration. Mannitol improved the dispersibility of phage powders, but the in vitro lung dose dropped sharply after exposure to high-humidity condition (65% RH) for formulations with 20% mannitol. While previously collected knowledge on phage powder preparation could be largely extended to formulate phage into inhalable dry powders, the environmental humidity may have great impacts on the stability and dispersion of phage; therefore, specific attention is required when optimizing phage powder formulations for global distribution.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/pharmaceutics13081162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8401170PMC
July 2021

Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021.

Arch Virol 2021 Nov;166(11):3239-3244

Latvian Biomedical Research and Study Center, Riga, Latvia.

In this article, we - the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) - summarise the results of our activities for the period March 2020 - March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00705-021-05205-9DOI Listing
November 2021

First report of norovirus sequences isolated from raccoon dogs in mainland China.

Virus Res 2021 Nov 13;305:198546. Epub 2021 Aug 13.

College of Life Science and Technology, Beijing University of Chemical Technology, China. Electronic address:

Noroviruses can infect humans and a wide variety of other mammalian hosts, causing varying degrees of diarrhea. In this study, two novel norovirus genomes were identified for the first time in farmed raccoon dogs, designated as raccoon dog noroviruses BUCT-K1 and BUCT-K4. Neither the farmers nor the raccoon dogs had symptoms (e.g., diarrhea) at the time of sample collection. We collected 14 stool samples from two farms, and 85.7% (12/14) of the samples were norovirus positive by RT-PCR. The two norovirus genomes have the highest identity to Dog/Z7/19/CH, suggesting that the norovirus might have been transmitted from dogs to raccoon dogs. Genomic and evolutionary analyses indicated that different directions of evolution occurred following the spread of the norovirus to the raccoon dogs. This study has increased knowledge of norovirus-infected animal species and has provided additional information on the norovirus family.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.virusres.2021.198546DOI Listing
November 2021

A theoretical simulation of SARS-CoV-2 pooled testing: Pooled sample collection outperforms pooled RNA extraction.

Clin Chim Acta 2021 Oct 16;521:155-157. Epub 2021 Jul 16.

Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China. Electronic address:

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cca.2021.07.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8282448PMC
October 2021

Characterization and genome analysis of novel Klebsiella phage BUCT556A with lytic activity against carbapenemase-producing Klebsiella pneumoniae.

Virus Res 2021 Oct 13;303:198506. Epub 2021 Jul 13.

College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China. Electronic address:

Carbapenem-resistant Klebsiella pneumoniae (CRKP) have spread globally and led to the limited choice of antimicrobial treatment of K. pneumoniae-induced infections. Bacteriophages are considered as an effective strategy against bacterial infections. In this study, we isolated a novel Klebsiella phage BUCT556A with lytic activity against KPC-producing K. pneumoniae, which was a multi-drug resistant isolate. Phage BUCT556A had a symmetrical head and a long, non-contractile tail, belonging to the family Siphoviridae, order Caudoviridae. Phage BUCT556A had a relatively narrow host range, and a medium burst size of 91 PFU/cell. It was stable at broad temperature/pH range, and exhibited good tolerance to chloroform. The genome of phage BUCT556A was a 49, 376-bp linear double-stranded DNA molecule with average G + C content of 50.2%, and contained 75 open reading frames. There was no tRNA, antibiotic resistance, toxin, virulence related genes or lysogen-formation gene clusters detected in the genome of phage BUCT556A. Phylogenetic analyses based on the major capsid protein Mcp suggested that this phage had a close relationship with Klebsiella phage KLPN1. Together, through phenotypic combined with genomic DNA sequencing and analyses, our study suggests that phage BUCT556A has the potential to be used as a bacterial treatment tool for multidrug-resistant strains K. pneumoniae.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.virusres.2021.198506DOI Listing
October 2021

Characterization and genome sequence of the genetically unique Escherichia bacteriophage vB_EcoM_IME392.

Arch Virol 2021 Sep 8;166(9):2505-2520. Epub 2021 Jul 8.

College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.

In this study, a novel Escherichia coli-specific bacteriophage, vB_EcoM_IME392, was isolated from chicken farm sewage in Qingdao, China. The genome of IME392 was found by next-generation sequencing to be 116,460 base pairs in length with a G+C content of 45.4% (GenBank accession number MH719082). BLASTn results revealed that only 2% of the genome sequence of IME392 shows sequence similarity to known phage sequences in the GenBank database, which indicates that IME392 is a novel bacteriophage. Transmission electron microscopy showed that IME392 belongs to the family Myoviridae. The host range, the multiplicity of infection, and a one-step growth curve were also determined.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00705-021-05160-5DOI Listing
September 2021

An engineered genetic circuit for lactose intolerance alleviation.

BMC Biol 2021 07 5;19(1):137. Epub 2021 Jul 5.

College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, People's Republic of China.

Background: Lactose malabsorption occurs in around 68% of the world's population, causing lactose intolerance (LI) symptoms, such as abdominal pain, bloating, and diarrhea. To alleviate LI, previous studies have mainly focused on strengthening intestinal β-galactosidase activity while neglecting the inconspicuous drop in the colon pH caused by the fermentation of non-hydrolyzed lactose by the gut microbes. A drop in colon pH will reduce the intestinal β-galactosidase activity and influence intestinal homeostasis.

Results: Here, we synthesized a tri-stable-switch circuit equipped with high β-galactosidase activity and pH rescue ability. This circuit can switch in functionality between the expression of β-galactosidase and expression of L-lactate dehydrogenase in response to an intestinal lactose signal and intestinal pH signal, respectively. We confirmed that the circuit functionality was efficient in bacterial cultures at a range of pH levels, and in preventing a drop in pH and β-galactosidase activity after lactose administration to mice. An impact of the circuit on gut microbiota composition was also indicated.

Conclusions: Due to its ability to flexibly adapt to environmental variation, in particular to stabilize colon pH and maintain β-galactosidase activity after lactose influx, the tri-stable-switch circuit can serve as a promising prototype for the relief of lactose intolerance.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12915-021-01070-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8259030PMC
July 2021

Characterization and Genomic Analysis of BUCT549, a Novel Bacteriophage Infecting With Flagella as Receptor.

Front Microbiol 2021 17;12:668319. Epub 2021 Jun 17.

College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.

is one of the most important of pathogens that can infect humans and a variety of aquatic animals, and it can cause food poisoning and septicemia in humans. Widely used antibiotics are gradually losing their usefulness, and phages are gaining more attention as new antibacterial strategies. To have more potential strategies for controlling pathogenic bacteria, we isolated a novel phage BUCT549 from seafood market sewage. It was classified as a new member of the family by transmission electron microscopy and a phylogenetic tree. We propose creating a new genus for BUCT549 based on the intergenomic similarities (maximum is 56%) obtained from VIRIDIC calculations. Phage BUCT549 could be used for phage therapy due to its stability in a wide pH (3.0-11.0) range and high-temperature (up to 60°C) environment. It had a latent period of 30-40 min and a burst size of 141 PFU/infected bacterium. In the phylogenetic tree based on a terminase large subunit, BUCT549 was closely related to eight phages with different species of host. Meanwhile, our experiments proved that BUCT549 has the ability to infect a strain of . A coevolution experiment determined that three strains of tolerant evaded phage infestation by mutating the MSHA-related membrane protein expression genes, which caused the loss of flagellum. This research on novel phage identification and the mechanism of infestation will help phages to become an integral part of the strategy for biological control agents.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2021.668319DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8245777PMC
June 2021

Isolation, Characterization, and Genome Sequence Analysis of a Novel Lytic Phage, Xoo-sp15 Infecting Xanthomonas oryzae pv. oryzae.

Curr Microbiol 2021 Aug 2;78(8):3192-3200. Epub 2021 Jul 2.

State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.

Xanthomonas oryzae pv. oryzae (X. oryzae) is a bacterial pathovar of rice diseases all over the world. Owing to emerging antibacterial resistance, phage therapies have gained significant attention to treat various bacterial infections. Nevertheless, comprehensive research is needed for their use as a safe biocontrol agent. In this study, isolation and characterization of a novel phage Xoo-sp15, that infects X. oryzae was ascertained through experimental and bioinformatics analyses to determine its virulent potency and reliability. High throughput sequencing demonstrated that Xoo-sp15 has a dsDNA genome with a total size of 157,091 bp and 39.9% GC content lower than its host (63.6%). Morphological and phylogenetic analyses characterized it as a new member of the Bastille-like group within the family Herelleviridae. In silico analysis revealed that it contains 229 open reading frames and 16 tRNAs. Additionally, this novel phage does not contain any resistant determinants and can infect nine X. oryzae strains. Therefore, Xoo-sp15 has the potential to serve as a novel candidate for phage therapy.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00284-021-02556-zDOI Listing
August 2021

The zoonotic and natural foci characteristics of SARS-CoV-2.

J Biosaf Biosecur 2021 Jun 24;3(1):51-55. Epub 2021 Jun 24.

State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China.

The origin of SARS-CoV-2 is still an unresolved mystery. In this study, we systematically reviewed the main research progress of wild animals carrying virus highly homologous to SARS-CoV-2 and analyzed the natural foci characteristics of SARS-CoV-2. The complexity of SARS-CoV-2 origin in wild animals and the possibility of SARS-CoV-2 long-term existence in human populations are also discussed. The joint investigation of corona virus carried by wildlife, as well as the ecology and patho-ecology of bats and other wildlife, are key measures to further clarify the characteristics of natural foci of SARS-CoV-2 and actively defend against future outbreaks of emerging zoonotic diseases.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jobb.2021.06.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8221912PMC
June 2021

Cultivation of a Lytic Double-Stranded RNA Bacteriophage Infecting Microvirgula aerodenitrificans Reveals a Mutualistic Parasitic Lifestyle.

J Virol 2021 08 10;95(17):e0039921. Epub 2021 Aug 10.

School of Biology & Engineering, Guizhou Medical University, Guiyang, Guizhou Province, People's Republic of China.

Bacteriophages are considered the most abundant entities on earth. However, there are merely seven sequenced double-stranded RNA (dsRNA) phages, compared to thousands of sequenced double-stranded DNA (dsDNA) phages. Interestingly, dsRNA viruses are quite common in fungi and usually have a lifestyle of commensalism or mutualism. Thus, the classical protocol of using double-layer agar plates to characterize phage plaques might be significantly biased in the isolation of dsRNA phages beyond strictly lytic lifestyles. Thus, we applied a protocol for isolating fungal viruses to identify RNA phages in bacteria and successfully isolated a novel dsRNA phage, phiNY, from Microvirgula aerodenitrificans. phiNY has a genome consisting of three dsRNA segments, and its genome sequence has no nucleotide sequence similarity with any other phage. Although phiNY encodes a lytic protein of glycoside hydrolase, and phage particles are consistently released during bacterial growth, phiNY replication did not block bacterial growth, nor did it form any plaques on agar plates. More strikingly, the phiNY-infected strain grew faster than the phiNY-negative strain, indicating a mutualistic parasitic lifestyle. Thus, this study not only reveals a new mutualistic parasitic dsRNA phage but also implies that other virus isolation methods would be valuable to identify phages with nonlytic lifestyles. Viruses with dsRNA genomes are quite diverse and infect organisms in all three domains of life. Although dsRNA viruses that infect humans, plants, and fungi are quite common, dsRNA viruses that infect bacteria, known as bacteriophages, are quite understudied, and only seven dsRNA phages have been sequenced so far. One possible explanation for the rare isolation of dsRNA phages might be the protocol of the double-layer agar plate assay. Phages without strictly lytic lifestyles might not form plaques. Thus, we applied the protocol of isolating fungal viruses to identify RNA phages inside bacteria and successfully isolated a novel dsRNA phage, phiNY, with a mutualistic parasitic lifestyle. This study implies that dsRNA phages without strictly lytic lifestyles might be common in nature and deserve more investigations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/JVI.00399-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8354237PMC
August 2021

Isolation and characterization of a podovirus infecting the opportunist pathogen Vibrio alginolyticus and Vibrio parahaemolyticus.

Virus Res 2021 Sep 11;302:198481. Epub 2021 Jun 11.

College of Life Science and Technology, Beijing University of Chemical Technology, China. Electronic address:

Bacterial infections have a negative impact on both animal husbandry industry and medicine, and increasing bacterial drug resistance exacerbates this adverse impact. Phages show promise as an alternative to drugs against drug-resistant bacteria. In this study, a novel virulent bacteriophage (phage) vB_ValP_IME234 against Vibrio alginolyticus and Vibrio parahaemolyticus was isolated from freshwater in Beijing, China. Phage vB_ValP_IME234 had an isometric head (59 nm in diameter) and a short tail (10 nm long), belonging to Podoviridae family. Its complete genome is liner double-stranded DNA (dsDNA) with a GC content of 41.6% while encoding 61 putative proteins. Three transfer RNA (tRNA) and no lysogenic gene was detected. vB_ValP_IME234 had a polyvalent infectivity, a burst of 390 PFU/cell, and is stable under different temperatures (4 °C to 50 °C) and pH (6.0 to 10.0) values. Host range test showed that vB_ValP_IME234 has the ability to infect seven strains of Vibrio in total. Phylogenetic analyses based on terminase and capsid suggested that this phage had a close relationship with Vibrio phages. These results indicate that vB_ValP_IME234 could be used as a potential biocontrol agent against V. alginolyticus strains.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.virusres.2021.198481DOI Listing
September 2021

Biochemical and genomic characterization of a novel bacteriophage BUCT555 lysing Stenotrophomonas maltophilia.

Virus Res 2021 Aug 28;301:198465. Epub 2021 May 28.

College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China. Electronic address:

Stenotrophomonas maltophilia is a common conditional pathogen, and it is naturally resistant to most commonly used clinical antibiotics. The bacteriophage is considered to be a potential antibiotic alternative for treating multi-drug-resistant bacteria. In this study, a bacteriophage BUCT555 was isolated from hospital sewage for lysing the clinical multi-drug resistant Stenotrophomonas maltophilia. Electron microscopy studies revealed this phage belongs to the Podoviridae family. The double-stranded DNA genome of bacteriophage BUCT555 is composed of 39,440 bp with a GC content of 61.43%. The genome contains 57 open reading frames, 14 of which had assigned functions, while no virulence related genes, antibiotic resistance genes or tRNA were identified. The burst size of BUCT555 was 204 pfu per infected cell. Structure proteins of bacteriophage BUCT555 generated by SDS-PAGE and HPLC-MS revealed that it contains seven proteins with molecular weight ranging from 19 to 89 kDa. BLASTn analysis showed that phage BUCT555 has 2% homology with other phages in NCBI database, suggesting BUCT555 is a new phage genus of Podoviridae that infects Stenotrophomonas maltophilia. Characterization of the bacteriophage BUCT555 enriches our knowledge about the diversity of Stenotrophomonas maltophilia bacteriophages.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.virusres.2021.198465DOI Listing
August 2021

Rapid and highly sensitive one-tube colorimetric RT-LAMP assay for visual detection of SARS-CoV-2 RNA.

Biosens Bioelectron 2021 Sep 13;187:113330. Epub 2021 May 13.

Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, PR China. Electronic address:

Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a highly contagious disease. To tame the continuously raging outbreak of COVID-19, developing a cheap, rapid and sensitive testing assay is absolutely imperative. Herein, we developed a one-tube colorimetric RT-LAMP assay for the visual detection of SARS-CoV-2 RNA. The assay integrates Si-OH magnetic beads (MBs)-based fast RNA extraction and rapid isothermal amplification in a single tube, thus bypassing the RNA elution step and directly amplifying on-beads RNA molecules with the visualized results. This one-tube assay has a limit of detection (LOD) as low as 200 copies/mL for sample input volumes of up to 600 μL, and can be performed in less than 1 h from sample collection to result readout. This assay demonstrated a 100% concordance with the gold standard test RT-qPCR test by using 29 clinical specimens and showed high specificity. This one-tube colorimetric RT-LAMP assay can serve as an alternative platform for a rapid and sensitive diagnostic test for COVID-19 and is particularly suitable for use at community clinics or township hospitals.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bios.2021.113330DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8117486PMC
September 2021

Ultrafast multiplexed detection of SARS-CoV-2 RNA using a rapid droplet digital PCR system.

Biosens Bioelectron 2021 Sep 4;188:113282. Epub 2021 May 4.

State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China. Electronic address:

We report the first combination of droplet digital and rapid PCR techniques for efficient, accurate, and quantitative detection of SARS-CoV-2 RNA. The presented rapid digital PCR system simultaneously detects two specific targets (ORF1ab and N genes) and one reference gene (RNase P) with a single PCR thermal cycling period around 7 s and the total running time less than 5 min. A clear positive signal could be identified within 115 s via the rapid digital RT-PCR, suggesting its efficiency for the end-point detection. In addition, benchmark tests with serial diluted reference samples of SARS-CoV-2 RNA reveal the excellent accuracy of our system (R>0.99). More importantly, the rapid digital PCR system gives consistent and accurate detection of low-concentration reference samples, whereas qPCR yields Ct values with significant variations that could lead to false-negative results. Finally, we apply the rapid digital PCR system to analyze clinical samples with both positive and control cases, where results are consistent with qPCR test outcomes. By providing similar accuracy with qPCR while minimizing the detection time-consuming and the false-negative tendency, the presented rapid digital PCR system represents a promising improvement on the rapid diagnosis of COVID-19.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bios.2021.113282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8093165PMC
September 2021

Metatranscriptomic analysis identifies different viral-like sequences in two neotropical Mansoniini mosquito species.

Virus Res 2021 Aug 17;301:198455. Epub 2021 May 17.

Departamento de Entomologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil; Programa de Pós-graduação em Biociências e Biotecnologia em Saúde, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil; Núcleo de Bioinformática, Fundação Oswaldo Cruz, Departamento de Entomologia, Recife, Pernambuco, Brazil. Electronic address:

Mosquitoes interact with a wide range of viruses including both arboviruses and insect-specific viruses. This study aimed to characterize the RNA viruses that are interacting with Mansonia wilsoni and Coquillettidia hermanoi mosquito species. The total RNA extracted from mosquito pools were sequenced on a Ion torrent platform. Viral contigs were identified against viral databases and their evolutionary relationship were reconstructed. We identified a total of 107 viral sequences, 11 of which were assigned as endogenous viral elements, and at least six known viral families were identified. Phylogenetic reconstructions were performed for 4 viral families. All Mansoniini viruses investigated through phylogenetic analysis are closely related to insect-specific viruses found in other mosquito species although with considerable divergence at the amino acid level, suggesting that we have detected new viral lineages. This study enhanced our understanding about the virome of two sylvatic Mansoniini mosquitoes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.virusres.2021.198455DOI Listing
August 2021

Ubiquitin-Modified Proteome of SARS-CoV-2-Infected Host Cells Reveals Insights into Virus-Host Interaction and Pathogenesis.

J Proteome Res 2021 05 5;20(5):2224-2239. Epub 2021 Mar 5.

Key Laboratory of Zoonotic of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, Liaoning Province, P. R. China.

The outbreak of coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has posed a serious threat to global public health. The mechanism of pathogenesis and the host immune response to SARS-CoV-2 infection are largely unknown. In the present study, we applied a quantitative proteomic technology to identify and quantify the ubiquitination changes that occur in both the virus and the Vero E6 cells during SARS-CoV-2 infection. By applying label-free, quantitative liquid chromatography with tandem mass spectrometry proteomics, 8943 lysine ubiquitination sites on 3086 proteins were identified, of which 138 sites on 104 proteins were quantified as significantly upregulated, while 828 sites on 447 proteins were downregulated at 72 h post-infection. Bioinformatics analysis suggested that SARS-CoV-2 infection might modulate host immune responses through the ubiquitination of important proteins, including USP5, IQGAP1, TRIM28, and Hsp90. Ubiquitination modification was also observed on 11 SAR-CoV-2 proteins, including proteins involved in virus replication and inhibition of the host innate immune response. Our study provides new insights into the interaction between SARS-CoV-2 and the host as well as potential targets for the prevention and treatment of COVID-19.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.0c00758DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7945586PMC
May 2021

Classification of the Gut Microbiota of Patients in Intensive Care Units During Development of Sepsis and Septic Shock.

Genomics Proteomics Bioinformatics 2020 Dec 17;18(6):696-707. Epub 2021 Feb 17.

Department of Critical Care Medicine, Peking Union Medical College Hospital, Beijing 100730, China. Electronic address:

The gut microbiota of intensive care unit (ICU) patients displays extreme dysbiosis associated with increased susceptibility to organ failure, sepsis, and septic shock. However, such dysbiosis is difficult to characterize owing to the high dimensional complexity of the gut microbiota. We tested whether the concept of enterotype can be applied to the gut microbiota of ICU patients to describe the dysbiosis. We collected 131 fecal samples from 64 ICU patients diagnosed with sepsis or septic shock and performed 16S rRNA gene sequencing to dissect their gut microbiota compositions. During the development of sepsis or septic shock and during various medical treatments, the ICU patients always exhibited two dysbiotic microbiota patterns, or ICU-enterotypes, which could not be explained by host properties such as age, sex, and body mass index, or external stressors such as infection site and antibiotic use. ICU-enterotype I (ICU E1) comprised predominantly Bacteroides and an unclassified genus of Enterobacteriaceae, while ICU-enterotype II (ICU E2) comprised predominantly Enterococcus. Among more critically ill patients with Acute Physiology and Chronic Health Evaluation II (APACHE II) scores > 18, septic shock was more likely to occur with ICU E1 (P = 0.041). Additionally, ICU E1 was correlated with high serum lactate levels (P = 0.007). Therefore, different patterns of dysbiosis were correlated with different clinical outcomes, suggesting that ICU-enterotypes should be diagnosed as independent clinical indices. Thus, the microbial-based human index classifier we propose is precise and effective for timely monitoring of ICU-enterotypes of individual patients. This work is a first step toward precision medicine for septic patients based on their gut microbiota profiles.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.gpb.2020.06.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8377022PMC
December 2020

Genomic analysis of bacteriophage Xoo-sp13 infecting Xanthomonas oryzae pv. oryzae.

Arch Virol 2021 Apr 14;166(4):1263-1265. Epub 2021 Feb 14.

State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China.

Xanthomonas oryzae pv. oryzae is a bacterial pathogen that gives rise to diseases in rice all over the world. A bacteriophage infecting this bacterium was isolated from rice fields in China. Here, we report the complete genome sequence of this phage, which has a linear dsDNA genome of 309,023 bp and a G + C content of 42.43%. It contains 401 open reading frames and encodes 28 tRNAs. It belongs to the family Myoviridae and has a broad host range, making it a possible candidate for phage therapy.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00705-021-04985-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7970823PMC
April 2021
-->