OpenLB
Open Library of Bioscience
Advanced Search
Methods in molecular biology (Clifton, N.J.)
2023;2555 23-49.

Functional Metagenomics as a Tool to Tap into Natural Diversity of Valuable Biotechnological Compounds.

Nancy Weiland-Bräuer, Livía Saleh, Ruth A Schmitz
Author Information
  1. Nancy Weiland-Bräuer: Institute for General Microbiology, Christian Albrechts University Kiel, Kiel, Germany.
  2. Livía Saleh: Institute for General Microbiology, Christian Albrechts University Kiel, Kiel, Germany.
  3. Ruth A Schmitz: Institute for General Microbiology, Christian Albrechts University Kiel, Kiel, Germany. rschmitz@ifam.uni-kiel.de.
PMID: 36306077 DOI: 10.1007/978-1-0716-2795-2_3

Abstract

The marine ecosystem covers more than 70% of the world's surface, and oceans represent a source of varied types of organisms due to the diversified environment. Consequently, the marine environment is an exceptional depot of novel bioactive natural products, with structural and chemical features generally not found in terrestrial habitats. Here, in particular, microbes represent a vast source of unknown and probably new physiological characteristics. They have evolved during extended evolutionary processes of physiological adaptations under various environmental conditions and selection pressures. However, to date, the biodiversity of marine microbes and the versatility of their bioactive compounds and metabolites have not been fully explored. Thus, metagenomic tools are required to exploit the untapped marine microbial diversity and their bioactive compounds. This chapter focuses on function-based marine metagenomics to screen for bioactive molecules of value for biotechnology. Functional metagenomic strategies are described, including sampling in the marine environment, constructing marine metagenomic large-insert libraries, and examples on function-based screens for quorum quenching and anti-biofilm activities.

Keywords

Biofilm Construction of fosmid libraries Crystal violet assay Environmental DNA Functional screening Marine functional metagenomics Peptides Quorum quenching

References

  1. Chappell A (2020) Into the deep: new insights into integrated ocean mapping and habitat characterizations of the North Atlantic and Eastern Pacific basins. In: Ocean sciences meeting 2020, Agu
  2. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95(12):6578–6583 [PMID: 9618454]
  3. Flemming H-C, Wuertz S (2019) Bacteria and archaea on earth and their abundance in biofilms. Nat Rev Microbiol 17(4):247–260 [PMID: 30760902]
  4. Brander KM, Ottersen G, Bakker JP, Beaugrand G, Herr H et al (2016) Environmental impacts – marine ecosystems. In: North Sea region climate change assessment. Springer, Cham, pp 241–274
  5. Costello MJ, Chaudhary C (2017) Marine biodiversity, biogeography, deep-sea gradients, and conservation. Curr Biol 27(11):R511–R527 [PMID: 28586689]
  6. Decho AW, Gutierrez T (2017) Microbial extracellular polymeric substances (EPSs) in ocean systems. Front Microbiol 8:922 [PMID: 28603518]
  7. Malve H (2016) Exploring the ocean for new drug developments: marine pharmacology. J Pharm Bioallied Sci 8(2):83 [PMID: 27134458]
  8. Vignesh S, Raja A, James RA (2011) Marine drugs: implication and future studies. Int J Pharmacol 7:22–30
  9. Martins A, Vieira H, Gaspar H, Santos S (2014) Marketed marine natural products in the pharmaceutical and cosmeceutical industries: tips for success. Mar Drugs 12(2):1066–1101 [PMID: 24549205]
  10. Rao TE, Imchen M, Kumavath R (2017) Marine enzymes: production and applications for human health. In: Advances in food and nutrition research, vol 80. Elsevier, pp 149–163
  11. Rotter A, Bacu A, Barbier M, Bertoni F, Bones AM et al (2020) A new network for the advancement of marine biotechnology in Europe and beyond. Front Mar Sci 7:278
  12. Greco GR, Cinquegrani M (2016) Firms plunge into the sea. Marine biotechnology industry, a first investigation. Front Mar Sci 2:124
  13. Mayekar T, Salgaonkar A, Koli J, Patil P, Chaudhari A et al (2012) Marine biotechnology: bioactive natural products and their applications. Aquafind
  14. Lozada M, Dionisi HM (2015) Microbial bioprospecting in marine environments. In: Springer handbook of marine biotechnology. Springer, pp 307–326
  15. Pan SY, Pan S, Yu Z-L, Ma D-L, Chen S-B et al (2010) New perspectives on innovative drug discovery: an overview. J Pharm Pharm Sci 13(3):450–471 [PMID: 21092716]
  16. Khalifa SA, Elias N, Farag MA, Chen L, Saeed A et al (2019) Marine natural products: a source of novel anticancer drugs. Mar Drugs 17(9):491 [>PMCID: ]
  17. Joshi B, Panda SK, Jouneghani RS, Liu M, Parajuli N et al (2020) Antibacterial, antifungal, antiviral, and anthelmintic activities of medicinal plants of Nepal selected based on ethnobotanical evidence. Evid Based Complementary Altern Med 2020:1043471
  18. Dayanidhi DL, Thomas BC, Osterberg JS, Vuong M, Vargas G et al (2021) Exploring the diversity of the marine environment for new anti-cancer compounds. Front Mar Sci 7:1184
  19. Amann RI, Ludwig W, Schleifer K-H (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59(1):143–169 [PMID: 7535888]
  20. Vartoukian SR, Palmer RM, Wade WG (2010) Strategies for culture of ‘unculturable’ bacteria. FEMS Microbiol Lett 309(1):1–7 [PMID: 20487025]
  21. Steen AD, Crits-Christoph A, Carini P, DeAngelis KM, Fierer N et al (2019) High proportions of bacteria and archaea across most biomes remain uncultured. ISME J 13(12):3126–3130 [PMID: 31388130]
  22. Streit WR, Schmitz RA (2004) Metagenomics – the key to the uncultured microbes. Curr Opin Microbiol 7(5):492–498 [PMID: 15451504]
  23. Lorenz P, Eck J (2005) Metagenomics and industrial applications. Nat Rev Microbiol 3:510–516 [PMID: 15931168]
  24. Pham VD, Palden T, DeLong EF (2007) Large-scale screens of metagenomic libraries. J Vis Exp 4:201
  25. DeLong EF (2009) The microbial ocean from genomes to biomes. Nature 459(7244):200–206 [PMID: 19444206]
  26. Kirubakaran R, ArulJothi K, Revathi S, Shameem N, Parray JA (2020) Emerging priorities for microbial metagenome research. Bioresour Technol Rep 11:100485 [PMID: 32835181]
  27. Franco-Duarte R, Černáková L, Kadam S, Kaushik S, Salehi B et al (2019) Advances in chemical and biological methods to identify microorganisms – from past to present. Microorganisms 7(5):130 [>PMCID: ]
  28. Simon C, Daniel R (2011) Metagenomic analyses: past and future trends. Appl Environ Microbiol 77(4):1153–1161 [PMID: 21169428]
  29. Trindade M, van Zyl LJ, Navarro-Fernández J, Abd Elrazak A (2015) Targeted metagenomics as a tool to tap into marine natural product diversity for the discovery and production of drug candidates. Front Microbiol 6:890 [PMID: 26379658]
  30. Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68(4):669–685 [PMID: 15590779]
  31. Banik JJ, Brady SF (2010) Recent application of metagenomic approaches toward the discovery of antimicrobials and other bioactive small molecules. Curr Opin Microbiol 13(5):603–609 [PMID: 20884282]
  32. Ngara TR, Zhang H (2018) Recent advances in function-based metagenomic screening. Genomics Proteomics Bioinformatics 16(6):405–415. https://doi.org/10.1016/j.gpb.2018.01.002 [DOI: 10.1016/j.gpb.2018.01.002]
  33. Cao Y, Fanning S, Proos S, Jordan K, Srikumar S (2017) A review on the applications of next generation sequencing technologies as applied to food-related microbiome studies. Front Microbiol 8:1829 [PMID: 29033905]
  34. Quince C, Walker AW, Simpson JT, Loman NJ, Segata N (2017) Shotgun metagenomics, from sampling to analysis. Nat Biotechnol 35(9):833–844 [PMID: 28898207]
  35. Burks DJ, Azad RK (2020) Higher-order Markov models for metagenomic sequence classification. Bioinformatics 36(14):4130–4136 [PMID: 32516355]
  36. Bosi E, Bacci G, Mengoni A, Fondi M (2017) Perspectives and challenges in microbial communities metabolic modeling. Front Genet 8:88 [PMID: 28680442]
  37. Rocha-Martin J, Harrington C, Dobson AD, O’Gara F (2014) Emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds. Mar Drugs 12(6):3516–3559 [PMID: 24918453]
  38. Ferrer M, Beloqui A, Timmis KN, Golyshin PN (2009) Metagenomics for mining new genetic resources of microbial communities. J Mol Microbiol Biotechnol 16(1–2):109–123 [PMID: 18957866]
  39. Guazzaroni ME, Silva-Rocha R, Ward RJ (2015) Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening. Microb Biotechnol 8(1):52–64 [PMID: 25123225]
  40. Brady SF, Chao CJ, Handelsman J, Clardy J (2001) Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA. Org Lett 3(13):1981–1984 [PMID: 11418029]
  41. Lim HK, Chung EJ, Kim J-C, Choi GJ, Jang KS et al (2005) Characterization of a forest soil metagenome clone that confers indirubin and indigo production on Escherichia coli. Appl Environ Microbiol 71(12):7768–7777 [PMID: 16332749]
  42. Gillespie DE, Brady SF, Bettermann AD, Cianciotto NP, Liles MR et al (2002) Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Appl Environ Microbiol 68:4301–4306 [PMID: 12200279]
  43. Tiwari R, Nain L, Labrou NE, Shukla P (2018) Bioprospecting of functional cellulases from metagenome for second generation biofuel production: a review. Crit Rev Microbiol 44(2):244–257 [PMID: 28609211]
  44. Escuder-Rodríguez J-J, DeCastro M-E, Cerdán M-E, Rodríguez-Belmonte E et al (2018) Cellulases from thermophiles found by metagenomics. Microorganisms 6(3):66 [>PMCID: ]
  45. Devi SG, Fathima AA, Sanitha M, Iyappan S, Curtis WR, Ramya M (2016) Expression and characterization of alkaline protease from the metagenomic library of tannery activated sludge. J Biosci Bioeng 122(6):694–700 [PMID: 27323930]
  46. Pessoa TB, Rezende RP, Marques ELS, Pirovani CP, Dos Santos TF et al (2017) Metagenomic alkaline protease from mangrove sediment. J Basic Microbiol 57(11):962–973 [PMID: 28804942]
  47. López-López O, Cerdan ME, Gonzalez Siso MI (2014) New extremophilic lipases and esterases from metagenomics. Curr Protein Pept Sci 15(5):445–455 [PMID: 24588890]
  48. Kaur G, Singh A, Sharma R, Sharma V, Verma S, Sharma PK (2016) Cloning, expression, purification and characterization of lipase from Bacillus licheniformis, isolated from hot spring of Himachal Pradesh, India. 3 Biotech 6(1):49 [PMID: 28330118]
  49. Harzevili FD, Chen H (2018) Microbial biotechnology: Progress and trends. CRC Press
  50. Felczykowska A, Krajewska A, Zielińska S, Łoś JM, Bloch SK, Nejman-Faleńczyk B (2015) The most widespread problems in the function-based microbial metagenomics. Acta Biochim Pol 62(1):161–166 [PMID: 25680374]
  51. Robinson SL, Piel J, Sunagawa S (2021) A roadmap for metagenomic enzyme discovery. Nat Prod Rep 38(11):1994–2023 [PMID: 34821235]
  52. Katzke N, Knapp A, Loeschcke A, Drepper T, Jaeger K-E (2017) Novel tools for the functional expression of metagenomic DNA. In: Metagenomics. Springer, pp 159–196
  53. Gabor EM, Alkema WB, Janssen DB (2004) Quantifying the accessibility of the metagenome by random expression cloning techniques. Environ Microbiol 6(9):879–886. https://doi.org/10.1111/j.1462-2920.2004.00640.x [DOI: 10.1111/j.1462-2920.2004.00640.x]
  54. Alam K, Abbasi MN, Hao J, Zhang Y, Li A (2021) Strategies for natural products discovery from uncultured mMicroorganisms. Molecules (Basel, Switzerland) 26(10):2977
  55. Culligan EP, Sleator RD (2016) Editorial: from genes to species: novel insights from metagenomics. Front Microbiol 7:1181. https://doi.org/10.3389/fmicb.2016.01181 [DOI: 10.3389/fmicb.2016.01181]
  56. Schmidt EW (2008) Trading molecules and tracking targets in symbiotic interactions. Nat Chem Biol 4(8):466–473. https://doi.org/10.1038/nchembio.101 [DOI: 10.1038/nchembio.101]
  57. Brady SF, Simmons L, Kim JH, Schmidt EW (2009) Metagenomic approaches to natural products from free-living and symbiotic organisms. Nat Prod Rep 26(11):1488–1503. https://doi.org/10.1039/b817078a [DOI: 10.1039/b817078a]
  58. Adnani N, Rajski SR, Bugni TS (2017) Symbiosis-inspired approaches to antibiotic discovery. Nat Prod Rep 34(7):784–814. https://doi.org/10.1039/C7NP00009J [DOI: 10.1039/C7NP00009J]
  59. Rosano GL, Ceccarelli EA (2014) Recombinant protein expression in Escherichia coli: advances and challenges. Front Microbiol 5:172. https://doi.org/10.3389/fmicb.2014.00172 [DOI: 10.3389/fmicb.2014.00172]
  60. Atanasov AG, Zotchev SB, Dirsch VM, Orhan IE, Banach M et al (2021) Natural products in drug discovery: advances and opportunities. Nat Rev Drug Discov 20(3):200–216. https://doi.org/10.1038/s41573-020-00114-z [DOI: 10.1038/s41573-020-00114-z]
  61. Nora LC, Westmann CA, Martins-Santana L, Alves LF, Monteiro LMO et al (2019) The art of vector engineering: towards the construction of next-generation genetic tools. Microb Biotechnol 12(1):125–147. https://doi.org/10.1111/1751-7915.13318 [DOI: 10.1111/1751-7915.13318]
  62. Lam KN, Cheng J, Engel K, Neufeld JD, Charles TC (2015) Current and future resources for functional metagenomics. Front Microbiol 6:1196. https://doi.org/10.3389/fmicb.2015.01196 [DOI: 10.3389/fmicb.2015.01196]
  63. Harbers M (2008) The current status of cDNA cloning. Genomics 91(3):232–242 [PMID: 18222633]
  64. Cowan D, Meyer Q, Stafford W, Muyanga S, Cameron R, Wittwer P (2005) Metagenomic gene discovery: past, present and future. Trends Biotechnol 23(6):321–329 [PMID: 15922085]
  65. Beja O, Suzuki MT, Koonin EV, Aravind L, Hadd A et al (2000) Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol 2(5):516–529 [PMID: 11233160]
  66. Distaso MA, Tran H, Ferrer M, Golyshin PN (2017) Metagenomic mining of enzyme diversity. In: Lee SY (ed) Consequences of microbial interactions with hydrocarbons, oils, and lipids: production of fuels and chemicals. Springer, Cham, pp 245–269. https://doi.org/10.1007/978-3-319-50436-0_216 [DOI: 10.1007/978-3-319-50436-0_216]
  67. Weiland-Bräuer N, Pinnow N, Schmitz RA (2015) Novel reporter for identification of interference with acyl homoserine lactone and autoinducer-2 quorum sensing. Appl Environ Microbiol 81(4):1477–1489. https://doi.org/10.1128/AEM.03290-14 [DOI: 10.1128/AEM.03290-14]
  68. Gabor EM, de Vries eJ, Janssen DB (2003) Efficient recovery of environmental DNA for expression cloning by indirect extraction methods. FEMS Microbiol Ecol 44:153–163 [PMID: 19719633]
  69. Henne A, Daniel R, Schmitz RA, Gottschalk G (1999) Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4-hydroxybutyrate. Appl Environ Microbiol 65(9):3901–3907 [PMID: 10473393]
  70. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM et al (2006) Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc Natl Acad Sci U S A 103(32):12115–12120 [PMID: 16880384]
  71. De Corte D, Yokokawa T, Varela MM, Agogue H, Herndl GJ (2009) Spatial distribution of Bacteria and Archaea and amoA gene copy numbers throughout the water column of the Eastern Mediterranean Sea. ISME J 3:147–158 [PMID: 18818711]
  72. Borrel G, Brugere J-F, Gribaldo S, Schmitz RA, Moissl-Eichinger C (2020) The host-associated archaeome. Nat Rev Microbiol 18(11):622–636 [PMID: 32690877]
  73. Treusch AH, Kletzin A, Raddatz G, Ochsenreiter T, Quaiser A et al (2004) Characterization of large insert DNA libraries from soil for environmental genomic studies of Archaea. Environ Microbiol 6:970–980 [PMID: 15305922]
  74. Wild J, Hradecna Z, Posfai G, Szybalski W (1996) A broad-host-range in vivo pop-out and amplification system for generating large quantities of 50- to 100-kb genomic fragments for direct DNA sequencing. Gene 179:181–188 [PMID: 8955645]
  75. Wild J, Hradecna Z, Szybalski W (2002) Conditionally amplifiable BACs: switching from singel-cpy to high-copy vectors and genomic clones. Genome Res 12:1434–1444 [PMID: 12213781]
  76. Wang W, Zheng G, Lu Y (2021) Recent advances in strategies for the cloning of natural product biosynthetic gene clusters. Front Bioeng Biotechnol 9:692797. https://doi.org/10.3389/fbioe.2021.692797 [DOI: 10.3389/fbioe.2021.692797]
  77. Westenberg M, Bamps S, Soedling H, Hope IA, Dolphin CT (2010) Escherichia coli MW005: lambda Red-mediated recombineering and copy-number induction of oriV-equipped constructs in a single host. BMC Biotechnol 10(1):27 [PMID: 20350301]
  78. Brady SF, Chao CJ, Clardy J (2002) New natural product families from an environmental DNA (eDNA) gene cluster. J Am Chem Soc 124:9968–9969 [PMID: 12188643]
  79. Al-Amoudi S, Razali R, Essack M, Amini MS, Bougouffa S, Archer JAC, Lafi FF, Bajic VB (2016) Metagenomics as a preliminary screen for antimicrobial bioprospecting. Gene 594(2):248–258. https://doi.org/10.1016/j.gene.2016.09.021 [DOI: 10.1016/j.gene.2016.09.021]
  80. Madalozzo AD, Martini VP, Kuniyoshi KK, de Souza EM, Pedrosa FBO et al (2015) Immobilization of LipC12, a new lipase obtained by metagenomics, and its application in the synthesis of biodiesel esters. J Mol Catal B Enzym 116:45–51
  81. Almeida JM, Martini VP, Iulek J, Alnoch RC, Moure VR et al (2019) Biochemical characterization and application of a new lipase and its cognate foldase obtained from a metagenomic library derived from fat-contaminated soil. Int J Biol Macromol 137:442–454. https://doi.org/10.1016/j.ijbiomac.2019.06.203 [DOI: 10.1016/j.ijbiomac.2019.06.203]
  82. Cretoiu MS, Kielak AM, Al-Soud WA, Sörensen SJ, van Elsas JD (2012) Mining of unexplored habitats for novel chitinases – chiA as a helper gene proxy in metagenomics. Appl Microbiol Biotechnol 94(5):1347–1358 [PMID: 22526805]
  83. Berini F, Presti I, Beltrametti F, Pedroli M, Vårum KM et al (2017) Production and characterization of a novel antifungal chitinase identified by functional screening of a suppressive-soil metagenome. Microb Cell Factories 16(1):16. https://doi.org/10.1186/s12934-017-0634-8 [DOI: 10.1186/s12934-017-0634-8]
  84. Majernik A, Gottschalk G, Daniel R (2001) Screening of environmental DNA libraries for the presence of genes conferring Na(Li)/H antiporter activity on Escherichia coli: characterization of the recovered genes and the corresponding gene products. J Bacteriol 183(22):6645–6653 [PMID: 11673435]
  85. Abisado RG, Benomar S, Klaus JR, Dandekar AA, Chandler JR (2018) Bacterial quorum sensing and microbial community interactions. MBio 9(3):e02331-02317. https://doi.org/10.1128/mBio.02331-17 [DOI: 10.1128/mBio.02331-17]
  86. Bassler BL (2002) Small talk. Cell-to-cell communication in bacteria. Cell 109(4):421–424 [PMID: 12086599]
  87. Castillo A (2015) How bacteria use Quorum sensing to communicate: how do bacteria talk to each other. Nat Educ 8(2):4
  88. Pereira CS, Thompson JA, Xavier KB (2013) AI-2-mediated signalling in bacteria. FEMS Microbiol Rev 37(2):156–181 [PMID: 22712853]
  89. Grandclâment C, Tannières M, Morâra S, Dessaux Y, Faure DD (2016) Quorum quenching: role in nature and applied developments. FEMS Microbiol Rev 40:fuv038
  90. Rutherford ST, Bassler BL (2012) Bacterial quorum sensing: its role in virulence and possibilities for its control. Cold Spring Harb Perspect Med 2(11):a012427. https://doi.org/10.1101/cshperspect.a012427 [DOI: 10.1101/cshperspect.a012427]
  91. Rémy B, Mion S, Plener L, Elias M, Chabrière E, Daudé D (2018) Interference in bacterial quorum sensing: a biopharmaceutical perspective. Front Pharmacol 9:203–203. https://doi.org/10.3389/fphar.2018.00203 [DOI: 10.3389/fphar.2018.00203]
  92. Krzyżek P (2019) Challenges and limitations of anti-quorum sensing therapies. Front Microbiol 10:2473–2473. https://doi.org/10.3389/fmicb.2019.02473 [DOI: 10.3389/fmicb.2019.02473]
  93. Jiang Q, Chen J, Yang C, Yin Y, Yao K (2019) Quorum sensing: a prospective therapeutic target for bacterial diseases. BioMed Res Intern 2019:2015978–2015978. https://doi.org/10.1155/2019/2015978 [DOI: 10.1155/2019/2015978]
  94. Bhardwaj A, Kittappa V, Rajpara N (2013) Bacterial quorum sensing inhibitors: attractive alternatives for control of infectious pathogens showing multiple drug resistance. Recent Pat Antiinfect Drug Discov 8:68–83. https://doi.org/10.2174/1574891X11308010012 [DOI: 10.2174/1574891X11308010012]
  95. Koo H, Allan RN, Howlin RP, Stoodley P, Hall-Stoodley L (2017) Targeting microbial biofilms: current and prospective therapeutic strategies. Nat Rev Microbiol 15(12):740–755. https://doi.org/10.1038/nrmicro.2017.99 [DOI: 10.1038/nrmicro.2017.99]
  96. Donlan RM, Costerton JW (2002) Biofilms: survival mechanisms of clinically relevant microorganisms. Clin Microbiol Rev 15(2):167–193 [PMID: 11932229]
  97. Dong YH, Wang LY, Zhang LH (2007) Quorum-quenching microbial infections: mechanisms and implications. Philos Trans R Soc Lond A 362(1483):1201–1211
  98. Hoiby N, Bjarnsholt T, Givskov M, Molin S, Ciofu O (2010) Antibiotic resistance of bacterial biofilms. Int J Antimicrob Agents 35(4):322–332. https://doi.org/10.1016/j.ijantimicag.2009.12.011 [DOI: 10.1016/j.ijantimicag.2009.12.011]
  99. Romero M, Acuna L, Otero A (2012) Patents on quorum quenching: interfering with bacterial communication as a strategy to fight infections. Recent Pat Biotechnol 6(1):2–12 [PMID: 22420877]
  100. Inoue H, Nojima H, Okayama H (1990) High efficiency transformation of Escherichia coli with plasmids. Gene 96:23–28 [PMID: 2265755]
  101. Apostolopoulos V, Bojarska J, Chai T-T, Elnagdy S, Kaczmarek K et al (2021) A global review on short peptides: frontiers and perspectives. Molecules (Basel, Switzerland) 26(2):430
  102. Mor A (2001) Peptides: biological activities of small peptides. e LS
  103. Bosso M, Ständker L, Kirchhoff F, Münch J (2018) Exploiting the human peptidome for novel antimicrobial and anticancer agents. Bioorg Med Chem 26(10):2719–2726. https://doi.org/10.1016/j.bmc.2017.10.038 [DOI: 10.1016/j.bmc.2017.10.038]
  104. Hancock RE (2000) Cationic antimicrobial peptides: towards clinical applications. Expert Opin Investig Drugs 9(8):1723–1729 [PMID: 11060771]
  105. Mahlapuu M, Håkansson J, Ringstad L, Björn C (2016) Antimicrobial peptides: an emerging category of therapeutic agents. Front Cell Infect Microbiol 6:194 [PMID: 28083516]
  106. Nguyen B-N, Tieves F, Rohr T, Wobst H, Schöpf FS et al (2021) Numaswitch: an efficient high-titer expression platform to produce peptides and small proteins. AMB Express 11(1):1–7
  107. Rungpragayphan S, Yamane T, Nakano H (2007) SIMPLEX: single-molecule PCR-linked in vitro expression: a novel method for high-throughput construction and screening of protein libraries. Methods Mol Biol 375:79–94 [PMID: 17634597]
  108. Jaroszewicz W, Morcinek-Orłowska J, Pierzynowska K, Gaffke L, Węgrzyn G (2021) Phage display and other peptide display technologies. FEMS Microbiol Rev:fuab052. https://doi.org/10.1093/femsre/fuab052
  109. Failmezger J (2018) Understanding limitations to increased potential of cell-free protein synthesis
  110. He J, You H, Sandström E, Nittinger E, Bjerrum EJ et al (2021) Molecular optimization by capturing chemist’s intuition using deep neural networks. J Cheminform 13(1):1–17
  111. Gautam A, Chaudhary K, Kumar R, Sharma A, Kapoor P et al (2013) In silico approaches for designing highly effective cell penetrating peptides. J Transl Med 11(1):1–12
  112. Nongonierma AB, Dellafiora L, Paolella S, Galaverna G, Cozzini P, FitzGerald RJ (2018) In silico approaches applied to the study of peptide analogs of Ile-Pro-Ile in relation to their dipeptidyl peptidase IV inhibitory properties. Front Endocrinol 9:329
  113. Djordjevic D, Wiedmann M, McLandsborough L (2002) Microtiter plate assay for assessment of Listeria monocytogenes biofilm formation. Appl Environ Microbiol 68(6):2950–2958 [PMID: 12039754]
  114. Merritt JH, Kadouri DE, O’Toole GA (2005) Growing and analyzing static biofilms. Curr Protoc Microbiol Chapter 1:Unit-1B.1. https://doi.org/10.1002/9780471729259.mc01b01s00 [DOI: 10.1002/9780471729259.mc01b01s00]
  115. Mack DR, Blain-Nelson PL (1995) Disparate in vitro inhibition of adhesion of enteropathogenic Escherichia coli RDEC-1 by mucins isolated from various regions of the intestinal tract. Pediatr Res 37(1):75–80 [PMID: 7700737]
  116. Christensen GD, Simpson WA, Younger JJ, Baddour LM, Barrett FF et al (1985) Adherence of coagulase-negative staphylococci to plastic tissue culture plates: a quantitative model for the adherence of staphylococci to medical devices. J Clin Microbiol 22(6):996–1006. https://doi.org/10.1128/jcm.22.6.996-1006.1985 [DOI: 10.1128/jcm.22.6.996-1006.1985]
  117. Pitts B, Hamilton MA, Zelver N, Stewart PS (2003) A microtiter-plate screening method for biofilm disinfection and removal. J Microbiol Methods 54(2):269–276. https://doi.org/10.1016/s0167-7012(03)00034-4 [DOI: 10.1016/s0167-7012(03)00034-4]
  118. Azeredo J, Azevedo NF, Briandet R, Cerca N, Coenye T et al (2017) Critical review on biofilm methods. Crit Rev Microbiol 43(3):313–351 [PMID: 27868469]

MeSH Term

Ecosystem
Metagenomics
Metagenome
Biotechnology
Biodiversity
Journal Article
Article has an altmetric score of 4

Word Cloud

Created with Highcharts 10.0.0marinebioactiveenvironmentmetagenomicFunctionalrepresentsourcemicrobesphysiologicalcompoundsfunction-basedmetagenomicslibrariesquenchingecosystemcovers70%world'ssurfaceoceansvariedtypesorganismsduediversifiedConsequentlyexceptionaldepotnovelnaturalproductsstructuralchemicalfeaturesgenerallyfoundterrestrialhabitatsparticularvastunknownprobablynewcharacteristicsevolvedextendedevolutionaryprocessesadaptationsvariousenvironmentalconditionsselectionpressuresHoweverdatebiodiversityversatilitymetabolitesfullyexploredThustoolsrequiredexploituntappedmicrobialdiversitychapterfocusesscreenmoleculesvaluebiotechnologystrategiesdescribedincludingsamplingconstructinglarge-insertexamplesscreensquorumanti-biofilmactivitiesMetagenomicsToolTapNaturalDiversityValuableBiotechnologicalCompoundsBiofilmConstructionfosmidCrystalvioletassayEnvironmentalDNAscreeningMarinefunctionalPeptidesQuorum

Similar Articles

Cited By

No available data.