New Developments in Techniques Like Metagenomics and Metaproteomics for Isolation, Identification, and Characterization of Microbes from Varied Environment

  • Ashton PM, Nair S, Dallman T et al (2015) MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat Biotechnol 33:296–302

    CrossRef 
    CAS 
    PubMed 

    Google Scholar
     

  • Fenn JB, Mann M, Meng CK et al (1990) ChemInform abstract: electrospray ionization for mass spectrometry of large biomolecules. ChemInform 246(4926):64–71


    Google Scholar
     

  • Frith MC, Hamada M, Horton P (2010) Parameters for accurate genome alignment. BMC Bioinformatics 11(1):1–14


    Google Scholar
     

  • Geer LY, Markey SP, Kowalak JA et al (2004) Open mass spectrometry search algorithm. J Proteome Res 3:958–964

    CrossRef 
    CAS 
    PubMed 

    Google Scholar
     

  • Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17:333–351

    CrossRef 
    CAS 
    PubMed 

    Google Scholar
     

  • Graham C, McMullan G, Graham RLJ (2011) Proteomics in the microbial sciences. Bioeng Bugs 2:17–30

    CrossRef 
    PubMed 

    Google Scholar
     

  • Greninger AL, Naccache SN, Federman S et al (2015) Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med 7:1–13

    CrossRef 

    Google Scholar
     

  • Haft DH, DiCuccio M, Badretdin A et al (2018) RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 46:D851–D860

    CrossRef 
    CAS 
    PubMed 

    Google Scholar
     

  • Harris MA, Clark J, Ireland A et al (2004) The gene oncology (GO) database and informatics resource. Nucleic Acids Res 32:258–261

    CrossRef 

    Google Scholar
     

  • Heyer R, Schallert K, Zoun R et al (2017) Challenges and perspectives of metaproteomic data analysis. J Biotechnol 261:24–36

    CrossRef 
    CAS 
    PubMed 

    Google Scholar
     

  • Hillenkamp F, Karas M (1990) Mass spectrometry of peptides and proteins by matrix-assisted ultraviolet laser desorption/ionization. Methods Enzymol 193:280–295

    CrossRef 
    CAS 
    PubMed 

    Google Scholar
     

  • Huerta-Cepas J, Szklarczyk D, Heller D et al (2019) EggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 47:D309–D314

    CrossRef 
    CAS 
    PubMed 

    Google Scholar
     

  • Issa Isaac N, Philippe D, Nicholas A et al (2019) Metaproteomics of the human gut microbiota: challenges and contributions to other OMICS. Clin Mass Spectrom 14:18–30

    CrossRef 
    PubMed 

    Google Scholar
     

  • Josic D, Kovac S (2010) Reversed-phase high performance liquid chromatography of proteins. Curr Protoc Protein Sci 2010:1–22


    Google Scholar
     

  • Kleiner M (2019) Metaproteomics: much more than measuring gene expression in microbial communities. mSystems 4(3):e00115–e00119

    CrossRef 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kleiner M, Thorson E, Sharp CE et al (2017) Assessing species biomass contributions in microbial communities via metaproteomics. Nat Commun 8(1):1–14

    CrossRef 
    CAS 

    Google Scholar
     

  • Ko KKK, Chng KR, Nagarajan N (2022) Metagenomics-enabled microbial surveillance. Nat Microbiol 7:486–496

    CrossRef 
    CAS 
    PubMed 

    Google Scholar
     

  • Li N, Cai Q, Miao Q et al (2021) High-throughput metagenomics for identification of pathogens in the clinical settings. Small Methods 5:1–27


    Google Scholar
     

  • Liu S, Moon CD, Zheng N et al (2022) Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation. Microbiome 10:1–14

    CrossRef 

    Google Scholar
     

  • Moss EL, Maghini DG, Bhatt AS (2020) Complete, closed bacterial genomes from microbiomes using nanopore sequencing. Nat Biotechnol 38:701–707

    CrossRef 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Parks DH, Imelfort M, Skennerton CT et al (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055

    CrossRef 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Quick J, Ashton P, Calus S et al (2015) Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol 16(1):1–14

    CrossRef 
    CAS 

    Google Scholar
     

  • Raza S, Ameen A (2017) International journal of advances in scientific research metaproteomics approaches and techniques: a review. Int J Adv Sci Res 3:49–51

    CrossRef 

    Google Scholar
     

  • Sachsenberg T, Herbst FA, Taubert M et al (2015) MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics. J Proteome Res 14:619–627

    CrossRef 
    CAS 
    PubMed 

    Google Scholar
     

  • Tanca A, Palomba A, Pisanu S et al (2015) Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota. Proteomics 15:3474–3485

    CrossRef 
    CAS 
    PubMed 

    Google Scholar
     

  • Tyson GW, Chapman J, Hugenholtz P et al (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43

    CrossRef 
    CAS 
    PubMed 

    Google Scholar
     

  • Venter JC, Remington K, Heidelberg JF et al (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304(5667):66–74

    CrossRef 
    CAS 
    PubMed 

    Google Scholar
     

  • Vizca JA, Csordas A, Griss J et al (2016) Erratum: 2016 update of the PRIDE database and its related tools (Nucleic Acids Research (2016) 44:D1 D447-D456)


    Google Scholar
     

  • White RA, Bottos EM, Roy Chowdhury T et al (2016) Moleculo long-read sequencing facilitates assembly and genomic binning from complex soil metagenomes. mSystems 1:1–15

    CrossRef 

    Google Scholar
     

  • Yu X, Jiang W, Shi Y et al (2019) Applications of sequencing technology in clinical microbial infection. J Cell Mol Med 23:7143–7150

    CrossRef 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang L, Chen FX, Zeng Z et al (2021) Advances in metagenomics and its application in environmental microorganisms. Front Microbiol 12:1–15

    CrossRef 

    Google Scholar
     

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