Organelle 16S rRNA amplicon sequencing enables profiling of active gut microbiota in murine model

[1] Aßhauer KP(2015)Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data Bioinformatics 31 2882-2884

[2] Wemheuer B(2000)The ENZYME database in 2000 Nucleic Acids Res 28 304-305

[3] Daniel R(2019)EPA-ng: massively parallel evolutionary placement of genetic sequences Syst Biol 68 365-369

[4] Meinicke P(2020)Assessing similarities and disparities in the skin microbiota between wild and laboratory populations of house mice ISME J 14 2367-2380

[5] Bairoch A(2018)Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin Microbiome 6 1-17

[6] Barbera P(2019)Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 Nat Biotechnol 37 852-857

[7] Kozlov AM(2015)How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization The FEBS J 282 2029-2044

[8] Czech L(2016)DADA2: high-resolution sample inference from Illumina amplicon data Nat Methods 13 581-583

[9] Morel B(2017)Exact sequence variants should replace operational taxonomic units in marker-gene data analysis ISME J 11 2639-2643

[10] Darriba D(2012)Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice Cell Host Microbe 12 139-152

[1] Aßhauer KP(2015)Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data Bioinformatics 31 2882-2884

[2] Wemheuer B(2000)The ENZYME database in 2000 Nucleic Acids Res 28 304-305

[3] Daniel R(2019)EPA-ng: massively parallel evolutionary placement of genetic sequences Syst Biol 68 365-369

[4] Meinicke P(2020)Assessing similarities and disparities in the skin microbiota between wild and laboratory populations of house mice ISME J 14 2367-2380

[5] Bairoch A(2018)Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin Microbiome 6 1-17

[6] Barbera P(2019)Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 Nat Biotechnol 37 852-857

[7] Kozlov AM(2015)How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization The FEBS J 282 2029-2044

[8] Czech L(2016)DADA2: high-resolution sample inference from Illumina amplicon data Nat Methods 13 581-583

[9] Morel B(2017)Exact sequence variants should replace operational taxonomic units in marker-gene data analysis ISME J 11 2639-2643

[10] Darriba D(2012)Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice Cell Host Microbe 12 139-152