Metagenomics: novel enzymes from non-culturable microbes.

Abstract:

:In the transition to the post-petroleum economy, there is a growing demand for novel enzymes with high process performances to replace traditional chemistry with a more 'green' approach. To date, microorganisms encompass the richest source of industrial biocatalysts, but the Earth-living microbiota remains largely untapped by using traditional isolation and cultivation methods. Metagenomics, which is culture independent, represents a powerful tool for discovering novel enzymes from unculturable microorganisms. Herein, we summarize the variety of approaches adopted for mining environmental DNA and, based on a systematic literature review, we provide a comprehensive list of 332 industrially relevant enzymes discovered from metagenomes within the last three years.

journal_name

FEMS Microbiol Lett

authors

Berini F,Casciello C,Marcone GL,Marinelli F

doi

10.1093/femsle/fnx211

subject

Has Abstract

pub_date

2017-11-15 00:00:00

issue

21

eissn

0378-1097

issn

1574-6968

pii

4329276

journal_volume

364

pub_type

杂志文章,评审
  • Expression of the landomycin biosynthetic gene cluster in a PKS mutant of Streptomyces fradiae is dependent on the coexpression of a putative transcriptional activator gene.

    abstract::The formation of landomycin A or one of its derivatives (5,6-anhydrolandomycin A) in a heterologous strain has never been achieved. It has now been made possible by the coexpression of a cosmid containing all biosynthetic genes necessary to produce landomycin A together with a pathway-specific regulatory gene. As host...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1016/S0378-1097(03)00861-9

    authors: von Mulert U,Luzhetskyy A,Hofmann C,Mayer A,Bechthold A

    更新日期:2004-01-15 00:00:00

  • Antibiotic treatment disrupts bacterial communities in the colon and rectum of simian immunodeficiency virus-infected macaques.

    abstract::Antibiotic therapies are known to disrupt gastrointestinal (GI) bacterial communities. HIV and pathogenic simian immunodeficiency virus (SIV) infections have also been associated with disrupted GI bacterial communities. We administered a combination antibiotic therapy to six SIV-infected rhesus macaques and collected ...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1093/femsle/fnx228

    authors: Zevin AS,Hensley-McBain T,Miller C,Smith E,Langevin S,Klatt NR

    更新日期:2017-12-15 00:00:00

  • Cholesteryl-6-O-acyl-alpha-D-glucopyranoside of Helicobacter pylori relate to relative lysophospholipid content.

    abstract::The presence of cholesteryl glucosides and high levels of lysophospholipids are elements making the cell wall of Helicobacter pylori unique. In this study, we have investigated the relationship between lysophospholipid content and cholesteryl glucoside composition of variants of 6 clinical isolates. The samples were c...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1016/j.femsle.2005.01.030

    authors: Tannaes T,Bukholm G

    更新日期:2005-03-01 00:00:00

  • Characterization of ISR region and development of a PCR assay for rapid detection of the fish pathogen Tenacibaculum soleae.

    abstract::The aims of this work were to characterize the 16S-23S internal spacer region of the fish pathogen Tenacibaculum soleae and to develop a PCR assay for its identification and detection. All T. soleae strains tested displayed a single internal spacer region class, containing tRNA(I) (le) and tRNA(A) ...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/j.1574-6968.2011.02404.x

    authors: López JR,Hamman-Khalifa AM,Navas JI,de la Herran R

    更新日期:2011-11-01 00:00:00

  • The ligase chain reaction distinguishes hepatitis B virus S-gene variants.

    abstract::A novel method for the identification of hepatitis B virus (HBV) variants was developed. The ligase chain reaction (LCR) distinguished the sequences of two isolates from the Gambia showing a change at nucleotide 421 within the region coding for the surface protein a antigenic determinant. One sequence was derived from...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/j.1574-6968.1995.tb07766.x

    authors: Karthigesu VD,Mendy M,Fortuin M,Whittle HC,Howard CR,Allison LM

    更新日期:1995-09-01 00:00:00

  • Cell wall substrate specificity of six different lysozymes and lysozyme inhibitory activity of bacterial extracts.

    abstract::We have investigated the specificity of six different lysozymes for peptidoglycan substrates obtained by extraction of a number of gram-negative bacteria and Micrococcus lysodeikticus with chloroform/Tris-HCl buffer (chloroform/buffer). The lysozymes included two that are commercially available (hen egg white lysozyme...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/j.1574-6968.2006.00240.x

    authors: Nakimbugwe D,Masschalck B,Deckers D,Callewaert L,Aertsen A,Michiels CW

    更新日期:2006-06-01 00:00:00

  • Antifungal activity against plant pathogenic fungi of chaetoviridins isolated from Chaetomium globosum.

    abstract::The Chaetomium globosum strain F0142, which was isolated from barnyard grass, showed potent disease control efficacy against rice blast (Magnaporthe grisea) and wheat leaf rust (Puccinia recondita). Two antifungal substances were purified from broth from this organism and identified as chaetoviridins A and B. Chaetovi...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1016/j.femsle.2005.09.013

    authors: Park JH,Choi GJ,Jang KS,Lim HK,Kim HT,Cho KY,Kim JC

    更新日期:2005-11-15 00:00:00

  • Sample sequencing of a Salmonella typhimurium LT2 lambda library: comparison to the Escherichia coli K12 genome.

    abstract::As part of the ongoing sequencing of the complete Salmonella typhimurium LT2 genome, a partly ordered set of 416 lambda clones has been developed, representing over 90% of the genome. The average insert size is 17 kb. Sequences were obtained from both ends of each clone in this set. A total of over 600 kb of sequence ...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/j.1574-6968.1999.tb13533.x

    authors: Wong RM,Wong KK,Benson NR,McClelland M

    更新日期:1999-04-15 00:00:00

  • Cloning and characterization of genes encoding an enzyme which oxidizes dimethyl sulfide in Acinetobacter sp. strain 20B.

    abstract::Acinetobacter sp. strain 20B was isolated based on the ability to utilize dimethyl sulfide as the sole sulfur source. Since strain 20B oxidized indole as well as dimethyl sulfide, indigo production by recombinant Escherichia coli clones carrying Acinetobacter DNA was used as a selection for cloning genes encoding dime...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/j.1574-6968.1997.tb12692.x

    authors: Horinouchi M,Kasuga K,Nojiri H,Yamane H,Omori T

    更新日期:1997-10-01 00:00:00

  • Sequencing and characterization of a novel serine metalloprotease from Burkholderia pseudomallei.

    abstract::Burkholderia pseudomallei, a Gram-negative bacterium is found in the soil and water, mainly in Southeast Asia and Northern Australia. It is responsible for melioidosis in human and animals. The bacteria produce several potential virulent factors such as extracellular protease, hemolysin, lipase and lecithinase. The is...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/j.1574-6968.2000.tb09360.x

    authors: Lee MA,Liu Y

    更新日期:2000-11-01 00:00:00

  • Delineation of species within the Trichoderma viride/atroviride/koningii complex by UP-PCR cross-blot hybridization.

    abstract::Sequences from the ribosomal DNA ITS regions have shown that there is limited variation among the species in the Trichoderma viride/atroviride/koningii species complex also known as Hypocrea rufa complex, and that infraspecies variation sometimes is larger than interspecies variation. Strains belonging to T. viride, T...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1016/j.femsle.2004.06.041

    authors: Lübeck M,Bulat S,Alekhina I,Lieckfeldt E

    更新日期:2004-08-15 00:00:00

  • Characterization of outer membrane vesicles from a neonatal meningitic strain of Cronobacter sakazakii.

    abstract::Cronobacter sakazakii is associated with severe and often fatal cases of infant meningitis and necrotizing enterocolitis. The form of meningitis differs from that due to Neisseria meningitidis and Streptococcus spp., in that it is highly invasive and destructive towards human brain cells. However, there is relatively ...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1093/femsle/fnv085

    authors: Alzahrani H,Winter J,Boocock D,De Girolamo L,Forsythe SJ

    更新日期:2015-06-01 00:00:00

  • Effect of Mg(2+) ion in protein secretion by magnesium-resistant strains of Pseudomonas aeruginosa and Vibrio parahaemolyticus isolated from the coastal water of Haldia port.

    abstract::A rapidly growing industrial complex including oil refineries and chemical industries has developed around the coastal area of Haldia port in the district of Midnapore, West Bengal, India. The coastal water is highly polluted with industrial wastes along with petroleum hydrocarbons. The bacteria isolated from the diff...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/j.1574-6968.2000.tb09054.x

    authors: Bhattacharya M,Roy SS,Biswas D,Kumar R

    更新日期:2000-04-15 00:00:00

  • Multicopy suppression of a gacA mutation by the infC operon in Pseudomonas fluorescens CHA0: competition with the global translational regulator RsmA.

    abstract::The gacA gene of the biocontrol strain Pseudomonas fluorescens CHA0 codes for a response regulator which, together with the sensor kinase GacS (=LemA), is required for the production of exoenzymes and secondary metabolites involved in biocontrol, including hydrogen cyanide (HCN). A gacA multicopy suppressor was isolat...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/j.1574-6968.2000.tb09136.x

    authors: Blumer C,Haas D

    更新日期:2000-06-01 00:00:00

  • Protein expression by Streptococcus uberis in co-culture with bovine mammary epithelial cells.

    abstract::Three strains of Streptococcus uberis isolated from dairy cows with mastitis were co-cultured with a bovine mammary epithelial cell line (MAC-T) in Dulbecco's modified Eagle's medium without fetal bovine serum. Protein profiles from culture supernatants and bacterial pellets among different treatments were compared by...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/j.1574-6968.1998.tb13896.x

    authors: Fang W,Luther DA,Oliver SP

    更新日期:1998-09-15 00:00:00

  • Evidence for a net-like organization of lipopolysaccharide particles in the Escherichia coli outer membrane.

    abstract::Cell wall LPS of Escherichia coli are organized as particles which are visible in the electron microscope, after treatment of the wall with alkali. We now describe alkali treated walls of three E. coli strains with differences in susceptibility to the T4 phage infection. Strain CR63, a usual host for the T4 phage, sho...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1016/0378-1097(89)90163-8

    authors: Zorzopulos J,de Long S,Chapman V,Kozloff LM

    更新日期:1989-10-01 00:00:00

  • Antibacterial effects of protruding and recessed shark skin micropatterned surfaces of polyacrylate plate with a shallow groove.

    abstract::Antibacterial effects in terms of biofilm formation and swarming motility were studied using polyacrylate plates having protruding or recessed shark skin micropatterned surfaces with a shallow groove (2 μm pattern width and spacing, 0.4 μm pattern height). It was found that biofilm formation and swarming motility of P...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/1574-6968.12604

    authors: Sakamoto A,Terui Y,Horie C,Fukui T,Masuzawa T,Sugawara S,Shigeta K,Shigeta T,Igarashi K,Kashiwagi K

    更新日期:2014-12-01 00:00:00

  • Characterization of lyso-galactolipids, C-2 and C-3 O-acyl trigalactosylglycerol isomers, obtained from the lichenized fungus Dictyonema glabratum.

    abstract::A mixture of two lyso isomers of a galactolipid was obtained from Dictyonema glabratum. Aqueous hydrolysis gave rise to galactose and glycerol in a 3:1 molar ratio. ESI-MS spectroscopy gave, in the positive-ion mode, a pseudomolecular ion at m/z 839 and daughter ions with m/z 677, 600, 515 and 353, suggesting three ga...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/j.1574-6968.2001.tb09461.x

    authors: Sassaki GL,Gorin PA,Iacomini M

    更新日期:2001-01-15 00:00:00

  • Structural studies on the Ebola virus matrix protein VP40 indicate that matrix proteins of enveloped RNA viruses are analogues but not homologues.

    abstract::Matrix proteins are the driving force of assembly of enveloped viruses. Their main function is to interact with and polymerize at cellular membranes and link other viral components to the matrix-membrane complex resulting in individual particle shapes and ensuring the integrity of the viral particle. Although matrix p...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章,评审

    doi:10.1016/j.femsle.2004.03.002

    authors: Timmins J,Ruigrok RW,Weissenhorn W

    更新日期:2004-04-15 00:00:00

  • Differentiation of enterococci from other group D streptococci by means of a specific monoclonal antibody.

    abstract::We report on the specificity of a monoclonal antibody which reacts with autoclaved extracts of four species of enterococci but does not react to the same extent with similar extracts from two non-enterococcal group D streptococci. The monoclonal antibody also reacts specifically with purified lipoteichoic acid from St...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1016/0378-1097(91)90426-b

    authors: Hammonds SJ,Easterbrook TJ,McIllmurray MB

    更新日期:1991-07-15 00:00:00

  • Transposon mutagenesis in Staphylococcus epidermidis using the Enterococcus faecalis transposon Tn917.

    abstract::We transformed a clinical Staphylococcus epidermidis isolate with the Enterococcus faecalis transposon Tn917-carrying plasmid pTV1. Loss of plasmid replication was observed at 47 degrees C. Tn917 transposes efficiently and apparently randomly. The transposition frequency could be stimulated by erythromycin. Transposon...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1016/0378-1097(91)90335-8

    authors: Grueter L,Koenig O,Laufs R

    更新日期:1991-08-01 00:00:00

  • Chitin degradation by cellulolytic anaerobes and facultative aerobes from soils and sediments.

    abstract::Species of strictly and facultatively anaerobic cellulolytic bacteria from soils and sediments were examined for the ability to degrade chitin. Of 22 species studied, 16 degraded insoluble chitin. Cellulomonas uda, which was selected for a comparative study of its cellulase and chitinase enzyme systems, produced diffe...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/j.1574-6968.2001.tb10912.x

    authors: Reguera G,Leschine SB

    更新日期:2001-11-13 00:00:00

  • Evidence for importance of the Staphylococcus hyicus lipase pro-peptide in lipase secretion, stability and activity.

    abstract::To investigate the function of the pro-peptide (PP) region of the Staphylococcus hyicus exolipase, restriction sites were created in the lipase gene to facilitate the construction of deletions in this region. Lipase gene expression was carried out in Staphylococcus carnosus. In the presence of the entire PP region, th...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/j.1574-6968.1994.tb07098.x

    authors: Demleitner G,Götz F

    更新日期:1994-08-15 00:00:00

  • Analysis of Cre1 binding sites in the Trichoderma reesei cbh1 upstream region.

    abstract::A 1.5-kb XbaI-SacII fragment containing the upstream region of the Trichoderma reesei cellobiohydrolase I gene (cbh1) has been sequenced. The 1.5-kb fragment contains eight 6-bp sites having an identical or similar sequence to the consensus sequence for binding a catabolite repressor, Aspergillus nidulans CreA. Result...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/j.1574-6968.1996.tb08601.x

    authors: Takashima S,Iikura H,Nakamura A,Masaki H,Uozumi T

    更新日期:1996-12-15 00:00:00

  • Phylogenetic position of the menaquinone-containing acidophilic chemo-organotroph Acidobacterium capsulatum.

    abstract::The phylogenetic position of an acidophilic chemo-organotrophic menaquinone-containing bacterium, Acidobacterium capsulatum, was studied on the basis of 16S rRNA gene sequence information. A. capsulatum showed the highest level of sequence similarity to Heliobacterium chlorum, a member of the Gram-positive group, yet ...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/j.1574-6968.1995.tb07816.x

    authors: Hiraishi A,Kishimoto N,Kosako Y,Wakao N,Tano T

    更新日期:1995-10-01 00:00:00

  • Characterization of a replication locus and formation of a higher-order complex between RepA protein and two inverted repeats in Streptomyces plasmid pSV1.

    abstract::We identified the minimal locus of 163-kb plasmid pSV1 of Streptomyces violaceoruber for the replication in S. lividans. This locus comprised a repA gene and an upstream 407-bp sequence containing two inverted repeats (IR-III and IR-IV) within an iteron, an AT-rich region and a 300-bp noncoding sequence (NCS). RepA pr...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/1574-6968.12307

    authors: Chen Y,Tan H,Qin Z

    更新日期:2013-12-01 00:00:00

  • Genetic and antigenic comparison of Streptococcus mutans fructosyltransferase and glucan-binding protein.

    abstract::The genes for fructosyltransferase (ftf) and glucan-binding protein (gbp) of Streptococcus mutans strain Ingbritt have been cloned in E. coli using bacteriophage and plasmid vectors. A single ftf gene appears to be responsible for the appearance of several FTF of different electrophoretic mobilities. Despite the fact ...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1016/0378-1097(89)90432-1

    authors: Aduse-Opoku J,Gilpin ML,Russell RR

    更新日期:1989-06-01 00:00:00

  • Synthesis of poly(3-hydroxyalkanoates) in Escherichia coli expressing the PHA synthase gene phaC2 from Pseudomonas aeruginosa: comparison of PhaC1 and PhaC2.

    abstract::In order to obtain functional expression of PHA synthase gene phaC2 from Pseudomonas aeruginosa in Escherichia coli, the coding region of phaC2 was subcloned, including the ribosomal binding site, into pBluescript SK- collinear to the lac promoter. This plasmid pBHR71-C2 enabled functional expression of phaC2 in E. co...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/j.1574-6968.1997.tb12767.x

    authors: Qi Q,Rehm BH,Steinbüchel A

    更新日期:1997-12-01 00:00:00

  • Isolation of genes encoding beta-D-xylanase, beta-D-xylosidase and alpha-L-arabinofuranosidase activities from the rumen bacterium Prevotella ruminicola B1(4).

    abstract::Prevotella ruminicola B1(4) is a strictly anaerobic, Gram-negative, polysaccharide-degrading rumen bacterium. Xylanase activity in this strain was found to be inducible, the specific activity of cells grown on xylan being increased at least 20-fold by comparison with cells grown on glucose. Ten bacteriophage clones ex...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/j.1574-6968.1995.tb07349.x

    authors: Gasparic A,Marinsek-Logar R,Martin J,Wallace RJ,Nekrep FV,Flint HJ

    更新日期:1995-01-15 00:00:00

  • Cross-utilization and expression of outer membrane receptor proteins for siderophore uptake by Diamondback moth Plutella xylostella (Lepidoptera: Plutellidae) gut bacteria.

    abstract::Siderophore production by entomo- and phytopathogens, plus the cross-utilization of these siderophores and expression of outer membrane receptor proteins (OMRPs) by Diamondback moth (DBM) gut bacterial strains, were all examined. All the tested strains grew in the presence of 2, 2'-dipyridyl, and the Brachybacterium s...

    journal_title:FEMS microbiology letters

    pub_type: 杂志文章

    doi:10.1111/j.1574-6968.2008.01350.x

    authors: Indiragandhi P,Anandham R,Madhaiyan M,Kim GH,Sa T

    更新日期:2008-12-01 00:00:00