High Diversity of Myocyanophage in Various Aquatic Environments Revealed by High-Throughput Sequencing of Major Capsid Protein Gene With a New Set of Primers.

Abstract:

:Myocyanophages, a group of viruses infecting cyanobacteria, are abundant and play important roles in elemental cycling. Here we investigated the particle-associated viral communities retained on 0.2 μm filters and in sediment samples (representing ancient cyanophage communities) from four ocean and three lake locations, using high-throughput sequencing and a newly designed primer pair targeting a gene fragment (∼145-bp in length) encoding the cyanophage gp23 major capsid protein (MCP). Diverse viral communities were detected in all samples. The fragments of 142-, 145-, and 148-bp in length were most abundant in the amplicons, and most sequences (>92%) belonged to cyanophages. Additionally, different sequencing depths resulted in different diversity estimates of the viral community. Operational taxonomic units obtained from deep sequencing of the MCP gene covered the majority of those obtained from shallow sequencing, suggesting that deep sequencing exhibited a more complete picture of cyanophage community than shallow sequencing. Our results also revealed a wide geographic distribution of marine myocyanophages, i.e., higher dissimilarities of the myocyanophage communities corresponded with the larger distances between the sampling sites. Collectively, this study suggests that the newly designed primer pair can be effectively used to study the community and diversity of myocyanophage from different environments, and the high-throughput sequencing represents a good method to understand viral diversity.

journal_name

Front Microbiol

authors

Hou W,Wang S,Briggs BR,Li G,Xie W,Dong H

doi

10.3389/fmicb.2018.00887

subject

Has Abstract

pub_date

2018-05-03 00:00:00

pages

887

issn

1664-302X

journal_volume

9

pub_type

杂志文章
  • Anaerobic Degradation of the Plant Sugar Sulfoquinovose Concomitant With H2S Production: Escherichia coli K-12 and Desulfovibrio sp. Strain DF1 as Co-culture Model.

    abstract::Sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) is produced by plants and other phototrophs and its biodegradation is a relevant component of the biogeochemical carbon and sulfur cycles. SQ is known to be degraded by aerobic bacterial consortia in two tiers via C3-organosulfonates as transient intermediates to CO2, water ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.02792

    authors: Burrichter A,Denger K,Franchini P,Huhn T,Müller N,Spiteller D,Schleheck D

    更新日期:2018-11-27 00:00:00

  • Diet, Microbiota and Gut-Lung Connection.

    abstract::The gut microbial community (Gut microbiota) is known to impact metabolic functions as well as immune responses in our body. Diet plays an important role in determining the composition of the gut microbiota. Gut microbes help in assimilating dietary nutrients which are indigestible by humans. The metabolites produced ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2018.02147

    authors: Anand S,Mande SS

    更新日期:2018-09-19 00:00:00

  • Deciphering the Role of a SLOG Superfamily Protein YpsA in Gram-Positive Bacteria.

    abstract::Bacteria adapt to different environments by regulating cell division and several conditions that modulate cell division have been documented. Understanding how bacteria transduce environmental signals to control cell division is critical in understanding the global network of cell division regulation. In this article ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.00623

    authors: Brzozowski RS,Huber M,Burroughs AM,Graham G,Walker M,Alva SS,Aravind L,Eswara PJ

    更新日期:2019-04-05 00:00:00

  • Comparative Functional Genomic Analysis of Two Vibrio Phages Reveals Complex Metabolic Interactions with the Host Cell.

    abstract::Sequencing and annotation was performed for two large double stranded DNA bacteriophages, φGrn1 and φSt2 of the Myoviridae family, considered to be of great interest for phage therapy against Vibrios in aquaculture live feeds. In addition, phage-host metabolic interactions and exploitation was studied by transcript pr...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.01807

    authors: Skliros D,Kalatzis PG,Katharios P,Flemetakis E

    更新日期:2016-11-14 00:00:00

  • A Novel Microbial Culture Chamber Co-cultivation System to Study Algal-Bacteria Interactions Using Emiliania huxleyi and Phaeobacter inhibens as Model Organisms.

    abstract::Our understanding of microbial natural environments combines in situ experimentation with studies of specific interactions in laboratory-based setups. The purpose of this work was to develop, build and demonstrate the use of a microbial culture chamber enabling both in situ and laboratory-based studies. The design use...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.01705

    authors: Thøgersen MS,Melchiorsen J,Ingham C,Gram L

    更新日期:2018-07-30 00:00:00

  • Transposon Mutagenesis Identifies Novel Genes Associated with Staphylococcus aureus Persister Formation.

    abstract::Pathogenic bacterial persisters are responsible for the recalcitrance of chronic and persistent infections to antimicrobial therapy. Although the mechanisms of persister formation and survival have been widely studied in Escherichia coli, persistence mechanisms in Staphylococcus aureus remain largely unknown. Here, we...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2015.01437

    authors: Wang W,Chen J,Chen G,Du X,Cui P,Wu J,Zhao J,Wu N,Zhang W,Li M,Zhang Y

    更新日期:2015-12-23 00:00:00

  • Identification of XylR, the Activator of Arabinose/Xylose Inducible Regulon in Sulfolobus acidocaldarius and Its Application for Homologous Protein Expression.

    abstract::The thermophilic archaeon Sulfolobus acidocaldarius can use different carbon sources for growth, including the pentoses D-xylose and L-arabinose. In this study, we identified the activator XylR (saci_2116) responsible for the transcriptional regulation of the pentose transporter and pentose metabolizing genes in S. ac...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.01066

    authors: van der Kolk N,Wagner A,Wagner M,Waßmer B,Siebers B,Albers SV

    更新日期:2020-05-26 00:00:00

  • PnpM, a LysR-Type Transcriptional Regulator Activates the Hydroquinone Pathway in para-Nitrophenol Degradation in Pseudomonas sp. Strain WBC-3.

    abstract::A LysR-type transcriptional regulator (LTTR), PnpR, has previously been shown to activate the transcription of operons pnpA, pnpB, and pnpCDEFG for para-nitrophenol (PNP) degradation in Pseudomonas sp. strain WBC-3. Further preliminary evidence suggested the possible presence of an LTTR additional binding site in the ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.01714

    authors: Wang JP,Zhang WM,Chao HJ,Zhou NY

    更新日期:2017-09-14 00:00:00

  • Taisui TS-2007S, a Large Microbial Mat Discovered in Soil in China.

    abstract::In this study, Taisui TS-2007S, a previously unidentified biological object discovered in soil in China, was identified. TS-2007S was shown to contain abundant carbohydrates but a scarcity of protein, fat, and minerals. The exopolymers of TS-2007S showed FT-IR spectra that were similar to those of xanthan gum (XG) but...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.592034

    authors: Su T,Liu H,Zhang C,Shang D,Wang C,Qiu L

    更新日期:2020-11-11 00:00:00

  • Transcriptomic Analysis of Rhodococcus opacus R7 Grown on o-Xylene by RNA-Seq.

    abstract::Xylenes are considered one of the most common hazardous sources of environmental contamination. The biodegradation of these compounds has been often reported, rarer the ability to oxidize the ortho-isomer. Among few o-xylene-degrading bacteria, Rhodococcus opacus R7 is well known for its capability to degrade diverse ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.01808

    authors: Zampolli J,Di Canito A,Manconi A,Milanesi L,Di Gennaro P,Orro A

    更新日期:2020-08-12 00:00:00

  • Saccharomyces cerevisiae CNCM I-3856 as a New Therapeutic Agent Against Oropharyngeal Candidiasis.

    abstract::Oropharyngeal candidiasis is a common opportunistic mucosal infection of the oral cavity, mainly caused by an overgrowth of Candida albicans. This infection can inhibit nutritional intakes and strongly affect quality of life. To date, standard therapeutic strategies involving the administration of antifungal drugs can...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.01469

    authors: Roselletti E,Sabbatini S,Ballet N,Perito S,Pericolini E,Blasi E,Mosci P,Cayzeele Decherf A,Monari C,Vecchiarelli A

    更新日期:2019-07-11 00:00:00

  • Inhibition of Influenza Virus Infection by Lentinus edodes Mycelia Extract Through Its Direct Action and Immunopotentiating Activity.

    abstract::Lentinula edodes mycelia (LEM) solid culture extracts contain many bioactive compounds with diverse pharmacological activities such as antitumor, antiviral, and immunopotentiating effects. In this study, we examined the anti-influenza virus activity of LEM in vitro and in vivo. LEM directly inhibited influenza virus g...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.01164

    authors: Kuroki T,Lee S,Hirohama M,Taku T,Kumakura M,Haruyama T,Nagata K,Kawaguchi A

    更新日期:2018-05-29 00:00:00

  • Fic Proteins Inhibit the Activity of Topoisomerase IV by AMPylation in Diverse Bacteria.

    abstract::The Fic (filamentation induced by cyclic AMP) domain is a widely distributed motif with a conserved sequence of HPFx[D/E]GN[G/K]R, some of which regulate cellular activity by catalyzing the transfer of the AMP moiety from ATP to protein substrates. Some Fic proteins, including Fic-1 from the soil bacterium Pseudomonas...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.02084

    authors: Lu CH,McCloskey A,Chen FR,Nakayasu ES,Zhang LQ,Luo ZQ

    更新日期:2020-08-26 00:00:00

  • Adaptation to Blue Light in Marine Synechococcus Requires MpeU, an Enzyme with Similarity to Phycoerythrobilin Lyase Isomerases.

    abstract::Marine Synechococcus has successfully adapted to environments with different light colors, which likely contributes to this genus being the second most abundant group of microorganisms worldwide. Populations of Synechococcus that grow in deep, blue ocean waters contain large amounts of the blue-light absorbing chromop...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.00243

    authors: Mahmoud RM,Sanfilippo JE,Nguyen AA,Strnat JA,Partensky F,Garczarek L,Abo El Kassem N,Kehoe DM,Schluchter WM

    更新日期:2017-02-21 00:00:00

  • Role of Dilution Rate and Nutrient Availability in the Formation of Microbial Biofilms.

    abstract::We revisited the mathematical model of the chemostat and examined consequences of considerably decreasing the concentration of limiting nutrient in the inflow for the growth of both the planktonic and biofilm cells in the chemostat tank (fermenter). The model predicts a substantially lower steady-state biomass of plan...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.00916

    authors: Legner M,McMillen DR,Cvitkovitch DG

    更新日期:2019-04-30 00:00:00

  • Two Populations of Mites (Tyrophagus putrescentiae) Differ in Response to Feeding on Feces-Containing Diets.

    abstract::Background:Tyrophagus putrescentiae is a ubiquitous mite species in soil, stored products and house dust and infests food and causes allergies in people. T. putrescentiae populations harbor different bacterial communities, including intracellular symbionts and gut bacteria. The spread of microorganisms via the fecal p...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.02590

    authors: Hubert J,Nesvorna M,Sopko B,Smrz J,Klimov P,Erban T

    更新日期:2018-10-30 00:00:00

  • Antifungal Effect of Novel 2-Bromo-2-Chloro-2-(4-Chlorophenylsulfonyl)-1-Phenylethanone against Candida Strains.

    abstract::We investigated the antifungal activity of novel a 2-bromo-2-chloro-2-(4-chlorophenylsulfonyl)-1-phenylethanone (compound 4). The synthesis of compound 4 was commenced from sodium 4-chlorobenzene sulfinate and the final product was obtained by treatment of α-chloro-β-keto-sulfone with sodium hypobromite. The sensitivi...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.01309

    authors: Staniszewska M,Bondaryk M,Wieczorek M,Estrada-Mata E,Mora-Montes HM,Ochal Z

    更新日期:2016-08-25 00:00:00

  • Total Arsenic, pH, and Sulfate Are the Main Environmental Factors Affecting the Microbial Ecology of the Water and Sediments in Hulun Lake, China.

    abstract::Bacteria have the metabolic potential to produce a diverse array of secondary metabolites, which have important roles in biogeochemical cycling processes. However, for Hulun Lake and the rivers that enter into it, the bacterial community structures and their effects have not previously been widely studied, limiting ou...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.548607

    authors: Shang Y,Wu X,Wei Q,Dou H,Wang X,Chen J,Zhang H,Ma S,Zhang H

    更新日期:2020-09-24 00:00:00

  • Correlation of rpoB Mutations with Minimal Inhibitory Concentration of Rifampin and Rifabutin in Mycobacterium tuberculosis in an HIV/AIDS Endemic Setting, South Africa.

    abstract::Treatment of tuberculosis (TB) and HIV co-infections is often complicated by drug-to-drug interactions between anti-mycobacterial and anti-retroviral agents. Rifabutin (RFB) is an alternative to rifampin (RIF) for TB regimens and is recommended for HIV patients concurrently receiving protease inhibitors because of red...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.01947

    authors: Rukasha I,Said HM,Omar SV,Koornhof H,Dreyer AW,Musekiwa A,Moultrie H,Hoosen AA,Kaplan G,Fallows D,Ismail N

    更新日期:2016-12-05 00:00:00

  • Metagenomic Analysis of Bacteria, Fungi, Bacteriophages, and Helminths in the Gut of Giant Pandas.

    abstract::To obtain full details of gut microbiota, including bacteria, fungi, bacteriophages, and helminths, in giant pandas (GPs), we created a comprehensive microbial genome database and used metagenomic sequences to align against the database. We delineated a detailed and different gut microbiota structures of GPs. A total ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.01717

    authors: Yang S,Gao X,Meng J,Zhang A,Zhou Y,Long M,Li B,Deng W,Jin L,Zhao S,Wu D,He Y,Li C,Liu S,Huang Y,Zhang H,Zou L

    更新日期:2018-07-31 00:00:00

  • A Novel Antimicrobial Coating Represses Biofilm and Virulence-Related Genes in Methicillin-Resistant Staphylococcus aureus.

    abstract::Methicillin-resistant Staphylococcus aureus (MRSA) has become an important cause of hospital-acquired infections worldwide. It is one of the most threatening pathogens due to its multi-drug resistance and strong biofilm-forming capacity. Thus, there is an urgent need for novel alternative strategies to combat bacteria...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.00221

    authors: Vaishampayan A,de Jong A,Wight DJ,Kok J,Grohmann E

    更新日期:2018-02-15 00:00:00

  • Comparative Proteomics of Meat Spoilage Bacteria Predicts Drivers for Their Coexistence on Modified Atmosphere Packaged Meat.

    abstract::Besides intrinsic and extrinsic factors such as antagonism for organic substrates or temperature, the storage atmosphere of meat has a high influence on the development of its initial microbiota. Specific modified atmospheres (MAs) selectively suppress growth of aerobic and anaerobic bacteria, thus reshaping the initi...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.00209

    authors: Kolbeck S,Ludwig C,Meng C,Hilgarth M,Vogel RF

    更新日期:2020-02-14 00:00:00

  • A Cross-Protective Vaccine Against 4b and 1/2b Listeria monocytogenes.

    abstract::Listeria monocytogenes (Lm) is a foodborne zoonotic pathogen that causes listeriosis with a mortality rate of 20-30%. Serovar 4b and 1/2b isolates account for most of listeriosis outbreaks, however, no listeriosis vaccine is available for either prophylactic or therapeutic use. Here, we developed a triple-virulence-ge...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.569544

    authors: Meng F,Zhu T,Yao H,Ling Z,Feng Y,Li G,Li J,Sun X,Chen J,Meng C,Jiao X,Yin Y

    更新日期:2020-12-11 00:00:00

  • Analysis of Two Complementary Single-Gene Deletion Mutant Libraries of Salmonella Typhimurium in Intraperitoneal Infection of BALB/c Mice.

    abstract::Two pools of individual single gene deletion (SGD) mutants of S. Typhimurium 14028s encompassing deletions of 3,923 annotated non-essential ORFs and sRNAs were screened by intraperitoneal (IP) injection in BALB/c mice followed by recovery from spleen and liver 2 days post infection. The relative abundance of each muta...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2015.01455

    authors: Silva-Valenzuela CA,Molina-Quiroz RC,Desai P,Valenzuela C,Porwollik S,Zhao M,Hoffman RM,Andrews-Polymenis H,Contreras I,Santiviago CA,McClelland M

    更新日期:2016-01-05 00:00:00

  • Simulation Modeling to Compare High-Throughput, Low-Iteration Optimization Strategies for Metabolic Engineering.

    abstract::Increasing the final titer of a multi-gene metabolic pathway can be viewed as a multivariate optimization problem. While numerous multivariate optimization algorithms exist, few are specifically designed to accommodate the constraints posed by genetic engineering workflows. We present a strategy for optimizing express...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.00313

    authors: Heinsch SC,Das SR,Smanski MJ

    更新日期:2018-02-27 00:00:00

  • Effects of Wilting and Lactobacillus plantarum Addition on the Fermentation Quality and Microbial Community of Moringa oleifera Leaf Silage.

    abstract::The objective of this study was to evaluate the effects of wilting and Lactobacillus plantarum (LP) addition on the silage fermentation quality and microbial community of Moringa oleifera Lam. leaf silage. Unwilted (direct-cut) or wilted M. oleifera leaves were prepared either with or without LP (1.0 × 106 cfu/g) foll...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.01817

    authors: Wang Y,Wang C,Zhou W,Yang FY,Chen XY,Zhang Q

    更新日期:2018-08-06 00:00:00

  • Aspergillus fumigatus-Related Species in Clinical Practice.

    abstract::Aspergillus fumigatus is the main etiologic agent of invasive aspergillosis (IA). Other Aspergillus species belonging to the section Fumigati (A. fumigatus complex) may occasionally be the cause of IA. These strains are often misidentified, as they cannot be distinguished from A. fumigatus by conventional morphologica...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2016.00683

    authors: Lamoth F

    更新日期:2016-05-17 00:00:00

  • Stuck in the Middle: Fibronectin-Binding Proteins in Gram-Positive Bacteria.

    abstract::Fibronectin is a multidomain glycoprotein found ubiquitously in human body fluids and extracellular matrices of a variety of cell types from all human tissues and organs, including intestinal epithelial cells. Fibronectin plays a major role in the regulation of cell migration, tissue repair, and cell adhesion. Importa...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2016.01504

    authors: Hymes JP,Klaenhammer TR

    更新日期:2016-09-22 00:00:00

  • Analysis of Difference in Microbial Community and Physicochemical Indices Between Surface and Central Parts of Chinese Special-Flavor Baijiu Daqu.

    abstract::Special-flavor Baijiu is a unique Baijiu in Jiangxi Province, China, whose uniqueness mainly depends on the unique production process of special-flavor Baijiu Daqu. However, the microbial structure and physicochemical indices of different parts of the special-flavor Baijiu Daqu are still unknown. This greatly reduces ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.592421

    authors: Chen Y,Li K,Liu T,Li R,Fu G,Wan Y,Zheng F

    更新日期:2021-01-14 00:00:00

  • Rational and combinatorial tailoring of bioactive cyclic dipeptides.

    abstract::Modified cyclic dipeptides represent a diverse family of microbial secondary metabolites. They display a broad variety of biological and pharmacological activities and have long been recognized as privileged structures with the ability to bind to a wide range of receptors. This is due to their conformationally constra...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2015.00785

    authors: Giessen TW,Marahiel MA

    更新日期:2015-07-30 00:00:00