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Page 14 of 14                Kreuze et al. Microbiome Res Rep 2025;4:7    https://dx.doi.org/10.20517/mrr.2024.51

                    abundance species in metagenomic samples. Genome Biol 2022;23:11.  DOI  PubMed  PMC
               109.      Camargo AP, Roux S, Schulz F, et al. Identification of mobile genetic elements with geNomad. Nat Biotechnol 2024;42:1303-12.
                    DOI  PubMed  PMC
               110.      Guo J, Bolduc B, Zayed AA, et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses.
                    Microbiome 2021;9:37.  DOI  PubMed  PMC
               111.      Ren J, Ahlgren NA, Lu YY, Fuhrman JA, Sun F. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled
                    metagenomic data. Microbiome 2017;5:69.  DOI  PubMed  PMC
               112.      Kent AG, Vill AC, Shi Q, Satlin MJ, Brito IL. Widespread transfer of mobile antibiotic resistance genes within individual gut
                    microbiomes revealed through bacterial Hi-C. Nat Commun 2020;11:4379.  DOI  PubMed  PMC
               113.      Marbouty M, Thierry A, Millot GA, Koszul R. MetaHiC phage-bacteria infection network reveals active cycling phages of the
                    healthy human gut. Elife 2021;10:e60608.  DOI  PubMed  PMC
               114.      Lawrence D, Campbell DE, Schriefer LA, et al. Single-cell genomics for resolution of conserved bacterial genes and mobile genetic
                    elements of the human intestinal microbiota using flow cytometry. Gut Microbes 2022;14:2029673.  DOI  PubMed  PMC
               115.      Browne HP, Forster SC, Anonye BO, et al. Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive
                    sporulation. Nature 2016;533:543-6.  DOI  PubMed  PMC
               116.      Fitzgerald CB, Shkoporov AN, Upadrasta A, Khokhlova EV, Ross RP, Hill C. Probing the “dark matter” of the human gut
                    phageome: culture assisted metagenomics enables rapid discovery and host-linking for novel bacteriophages. Front Cell Infect
                    Microbiol 2021;11:616918.  DOI  PubMed  PMC
               117.      Jin Z, Ng A, Maurice CF, Juncker D. The mini colon model: a benchtop multi-bioreactor system to investigate the gut microbiome.
                    Gut Microbes 2022;14:2096993.  DOI  PubMed  PMC
               118.      Ares-Arroyo M, Coluzzi C, de Sousa JAM, Rocha EPC. Hijackers, hitchhikers, or co-drivers? The mysteries of microbial mobilizable
                    genetic elements. EcoEvoRxiv 2024.  DOI
               119.      Ibarra-Chávez R, Brady A, Chen J, Penadés JR, Haag AF. Phage-inducible chromosomal islands promote genetic variability by
                    blocking phage reproduction and protecting transductants from phage lysis. PLoS Genet 2022;18:e1010146.  DOI  PubMed  PMC
               120.      Rousset F, Depardieu F, Miele S, et al. Phages and their satellites encode hotspots of antiviral systems. Cell Host Microbe
                    2022;30:740-53.e5.  DOI  PubMed  PMC
               121.      Fillol-Salom A, Rostøl JT, Ojiogu AD, et al. Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems
                    against competitors. Cell 2022;185:3248-62.e20.  DOI  PubMed
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