Page 48 - Read Online
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Page 18 of 18               Fabbrini et al. Microbiome Res Rep 2023;2:25  https://dx.doi.org/10.20517/mrr.2023.25

               58.      Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods
                   2010;7:335-6.  DOI  PubMed  PMC
               59.      Blanco-Míguez A, Beghini F, Cumbo F, et al. Extending and improving metagenomic taxonomic profiling with uncharacterized
                   species using MetaPhlAn 4. Nat Biotechnol 2023.  DOI
               60.      Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol 2019;20:257.  DOI  PubMed  PMC
               61.      Milani C, Lugli GA, Fontana F, et al. METAnnotatorX : a comprehensive tool for deep and shallow metagenomic data set analyses.
                                                       2
                   mSystems 2021;6:e0058321.  DOI  PubMed  PMC
               62.      Douglas GM, Maffei VJ, Zaneveld JR, et al. PICRUSt2 for prediction of metagenome functions. Nat Biotechnol 2020;38:685-8.  DOI
                   PubMed  PMC
               63.      Beghini F, McIver LJ, Blanco-Míguez A, et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial
                   communities with bioBakery 3. Elife 2021:10:e65088.  DOI  PubMed  PMC
               64.      Liu J, Wang H, Yang H, et al. Composition-based classification of short metagenomic sequences elucidates the landscapes of
                   taxonomic and functional enrichment of microorganisms. Nucleic Acids Res 2013;41:e3.  DOI  PubMed  PMC
               65.      Huerta-Cepas J, Szklarczyk D, Heller D, et al. EggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology
                   resource based on 5090 organisms and 2502 viruses. Nucleic Acids Re ;47:D309-14.  DOI  PubMed  PMC
               66.      Uritskiy GV, DiRuggiero J, Taylor J. MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome
                   2018;6:158.  DOI  PubMed  PMC
               67.      Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30:2068-9.  DOI  PubMed
               68.      Muller J, Szklarczyk D, Julien P, et al. EggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised
                   orthologous groups, species and functional annotations. Nucleic Acids Res 2010;38:D190-5.  DOI  PubMed  PMC
               69.      Cao Q, Sun X, Rajesh K, et al. Effects of rare microbiome taxa filtering on statistical analysis. Front Microbiol 2020;11:607325.  DOI
                   PubMed  PMC
               70.      Wang M, Tu Q. Effective data filtering is prerequisite for robust microbial association network construction. Front Microbiol
                   2022;13:1016947.  DOI  PubMed  PMC
               71.      Mokhtari EB, Ridenhour BJ. Filtering ASVs/OTUs via mutual information-based microbiome network analysis. BMC Bioinformatics
                   2022;23:380.  DOI  PubMed  PMC
               72.      Thomas AM, Manghi P, Asnicar F, et al. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial
                   diagnostic signatures and a link with choline degradation. Nat Med 2019;25:667-678.  DOI
               73.      Wang K, Wu W, Wang Q, et al. The negative effect of Akkermansia muciniphila-mediated post-antibiotic reconstitution of the gut
                   microbiota on the development of colitis-associated colorectal cancer in mice. Front Microbiol 2022;13:932047.  DOI  PubMed  PMC
               74.      Tilg H, Adolph TE, Gerner RR, Moschen AR. The intestinal microbiota in colorectal cancer. Cancer Cell 2018;33:954-64.  DOI
                   PubMed
               75.      Berry D, Widder S. Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Front Microbiol
                   2014;5:219.  DOI  PubMed  PMC
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