other:
Concentration Assay:Article Title: Functional characterisation of a new halotolerant seawater active glycoside hydrolase family 6 cellobiohydrolase from a salt marsh
Article Snippet: .. The polysaccharides utilized and their final concentration (w/v) in reaction mixtures included; 0.5% AvicelTM (m/v; Sigma), 1% (m/v) phosphoric acid swollen cellulose (PASC), 0.5% carboxy-methyl cellulose sodium salt (m/v; Sigma), 0.5% (m/v; Megazyme) beechwood xylan (1–4-ß-xylose), 0.1% (m/v; Megazyme) barley glucan (1–4-ß-glucan), 0.1% (m/v; Megazyme) lichenan (1,3:1,4-ß-glucan, 0.1% (m/v; Megazyme) pachyman (1,3-ß-glucan), 0.1% (m/v; Megazyme) arabinoxylan, 0.1% (m/v; Megazyme) arabinogalactan, 0.1% (m/v; Megazyme) xyloglucan, 0.1% (m/v; Megazyme) Lupin galactan, 0.1% (m/v; Megazyme) glucomannan, 0.1% (m/v; Megazyme) galactomannan, 0.1% (m/v; Megazyme) mannan (1–4-ß-mannan). ..
Virus:Article Title: The RNA landscape of the human commensal Segatella copri reveals a small RNA essential for gut colonization.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacterial strain used in this study This study Table S5 Biological samples Human stool samples (donors A-D) This study N/A Chemicals, peptides, and recombinant proteins Levan Sigma-Aldrich Cat#L8647 Arabinan Megazyme Cat#P-ARAB Arabinoxylan Megazyme Cat#P-WAXYRS Inulin Carbosynth Cat#YI01274 Pectic Galactan Megazyme Cat#P-PGAPT Xylan Carbosynth Cat#YC05381 Mucin Sigma-Aldrich Cat# M2378 Glycogen Sigma-Aldrich Cat#G0885 Pectin Fluka Cat#76282 Fructooligosaccharides Biosynth Cat# OF05207 Fructose Sigma-Aldrich Cat# F0127 DynaMarker, Prestain Marker for Small RNA Plus Biotrend DM253S Terminator Exonuclease Vertis Biotechnologie AG N/A T4 Polynucleotide Kinase New England Biolabs Cat#M0201 Critical commercial assays MEGAscript T7 Transcription kit Thermo Fisher Scientific Cat# AMB13345 Dig Luminescent Detection Kit Sigma-Aldrich Cat#11363514910 DIG RNA Labeling Mix Sigma-Aldrich Cat#11277073910 PCR DIG Labeling Mix Sigma-Aldrich Cat#11585550910 KAPA SYBR FAST Merck Cat#KK4602 NEBNext Ultra DNA Library Prep Kit for Illumina New England Biolabs Cat#E7370S Agencourt AMPure XP Beads Beckman Coulter, Inc. Cat#A63880 Pan-prokaryote riboPOOL Kit siTOOLs Biotech Cat#dp-K096-3 Ribo-Zero Plus Microbiome rRNA Depletion Kit Illumina Cat# 20072062 Illumina Stranded Total RNA Prep Illumina Cat# 20040534 NEBNext Ultra Directional RNA Library Prep Kit for Illumina New England Biolabs Cat#E7420S Deposited data Original blot images This study Mendeley Data: https://doi.org/10.17632/ skr3snz3ry.1 Raw sequencing data This study PRJNA1082502 Experimental models: Organisms/strains Segatella copri HDD04 Human isolates Li et al.21 Segatella copri HDA03 Human isolates Li et al.21 Segatella copri HDB01 Human isolates Li et al.21 Segatella copri HDC01 Human isolates Li et al.21 Segatella copri DSM18205 Human isolates Hayashi et al.24 Segatella brunsvicensis Ni025 Human isolates Blanco-Miguez et al.34 (Continued on next page) e1 Cell Host & Microbe 32, 1–17.e1–e6, November 13, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Segatella sinensis HDE04 Human isolates Li et al.21 Segatella brasiliensis HDD05 Human isolates Li et al.21 Segatella hominis HDD12 Human isolates Li et al.21 Oligo-MM12 WT C57BL/6NTac mice 8- 12 weeks, raised in gnotobiotic isolaters in germ-free facility at the Helmholtz Centre for Infection research, Germany Bred in house Brugiroux et al.39 Oligonucleotides DNA oligonucleotides used in this study This study Table S5 Recombinant DNA Plasmids generated in this study This study Table S5 Software and algorithms ANNOgesic Yu et al.25 https://annogesic.readthedocs.io/en/ latest/ READemption Förstner et al.66 https://reademption.readthedocs.io/en/ latest/ MetaPhlAn 4 (v 4.0.0) Blanco-Miguez et al.67 https://github.com/biobakery/MetaPhlAn blastn (v2.5.0) Altschul et al.68 https://blast.ncbi.nlm.nih.gov/Blast.cgi GraphPad Prism v8.4.3 GraphPad Software, Inc. N/A Samtools (v1.3.1) Danecek et al.69 N/A Bowtie2 (version 2.4.2) Langmead and Salzberg70 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml
Recombinant:Article Title: The RNA landscape of the human commensal Segatella copri reveals a small RNA essential for gut colonization.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacterial strain used in this study This study Table S5 Biological samples Human stool samples (donors A-D) This study N/A Chemicals, peptides, and recombinant proteins Levan Sigma-Aldrich Cat#L8647 Arabinan Megazyme Cat#P-ARAB Arabinoxylan Megazyme Cat#P-WAXYRS Inulin Carbosynth Cat#YI01274 Pectic Galactan Megazyme Cat#P-PGAPT Xylan Carbosynth Cat#YC05381 Mucin Sigma-Aldrich Cat# M2378 Glycogen Sigma-Aldrich Cat#G0885 Pectin Fluka Cat#76282 Fructooligosaccharides Biosynth Cat# OF05207 Fructose Sigma-Aldrich Cat# F0127 DynaMarker, Prestain Marker for Small RNA Plus Biotrend DM253S Terminator Exonuclease Vertis Biotechnologie AG N/A T4 Polynucleotide Kinase New England Biolabs Cat#M0201 Critical commercial assays MEGAscript T7 Transcription kit Thermo Fisher Scientific Cat# AMB13345 Dig Luminescent Detection Kit Sigma-Aldrich Cat#11363514910 DIG RNA Labeling Mix Sigma-Aldrich Cat#11277073910 PCR DIG Labeling Mix Sigma-Aldrich Cat#11585550910 KAPA SYBR FAST Merck Cat#KK4602 NEBNext Ultra DNA Library Prep Kit for Illumina New England Biolabs Cat#E7370S Agencourt AMPure XP Beads Beckman Coulter, Inc. Cat#A63880 Pan-prokaryote riboPOOL Kit siTOOLs Biotech Cat#dp-K096-3 Ribo-Zero Plus Microbiome rRNA Depletion Kit Illumina Cat# 20072062 Illumina Stranded Total RNA Prep Illumina Cat# 20040534 NEBNext Ultra Directional RNA Library Prep Kit for Illumina New England Biolabs Cat#E7420S Deposited data Original blot images This study Mendeley Data: https://doi.org/10.17632/ skr3snz3ry.1 Raw sequencing data This study PRJNA1082502 Experimental models: Organisms/strains Segatella copri HDD04 Human isolates Li et al.21 Segatella copri HDA03 Human isolates Li et al.21 Segatella copri HDB01 Human isolates Li et al.21 Segatella copri HDC01 Human isolates Li et al.21 Segatella copri DSM18205 Human isolates Hayashi et al.24 Segatella brunsvicensis Ni025 Human isolates Blanco-Miguez et al.34 (Continued on next page) e1 Cell Host & Microbe 32, 1–17.e1–e6, November 13, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Segatella sinensis HDE04 Human isolates Li et al.21 Segatella brasiliensis HDD05 Human isolates Li et al.21 Segatella hominis HDD12 Human isolates Li et al.21 Oligo-MM12 WT C57BL/6NTac mice 8- 12 weeks, raised in gnotobiotic isolaters in germ-free facility at the Helmholtz Centre for Infection research, Germany Bred in house Brugiroux et al.39 Oligonucleotides DNA oligonucleotides used in this study This study Table S5 Recombinant DNA Plasmids generated in this study This study Table S5 Software and algorithms ANNOgesic Yu et al.25 https://annogesic.readthedocs.io/en/ latest/ READemption Förstner et al.66 https://reademption.readthedocs.io/en/ latest/ MetaPhlAn 4 (v 4.0.0) Blanco-Miguez et al.67 https://github.com/biobakery/MetaPhlAn blastn (v2.5.0) Altschul et al.68 https://blast.ncbi.nlm.nih.gov/Blast.cgi GraphPad Prism v8.4.3 GraphPad Software, Inc. N/A Samtools (v1.3.1) Danecek et al.69 N/A Bowtie2 (version 2.4.2) Langmead and Salzberg70 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml
Marker:Article Title: The RNA landscape of the human commensal Segatella copri reveals a small RNA essential for gut colonization.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacterial strain used in this study This study Table S5 Biological samples Human stool samples (donors A-D) This study N/A Chemicals, peptides, and recombinant proteins Levan Sigma-Aldrich Cat#L8647 Arabinan Megazyme Cat#P-ARAB Arabinoxylan Megazyme Cat#P-WAXYRS Inulin Carbosynth Cat#YI01274 Pectic Galactan Megazyme Cat#P-PGAPT Xylan Carbosynth Cat#YC05381 Mucin Sigma-Aldrich Cat# M2378 Glycogen Sigma-Aldrich Cat#G0885 Pectin Fluka Cat#76282 Fructooligosaccharides Biosynth Cat# OF05207 Fructose Sigma-Aldrich Cat# F0127 DynaMarker, Prestain Marker for Small RNA Plus Biotrend DM253S Terminator Exonuclease Vertis Biotechnologie AG N/A T4 Polynucleotide Kinase New England Biolabs Cat#M0201 Critical commercial assays MEGAscript T7 Transcription kit Thermo Fisher Scientific Cat# AMB13345 Dig Luminescent Detection Kit Sigma-Aldrich Cat#11363514910 DIG RNA Labeling Mix Sigma-Aldrich Cat#11277073910 PCR DIG Labeling Mix Sigma-Aldrich Cat#11585550910 KAPA SYBR FAST Merck Cat#KK4602 NEBNext Ultra DNA Library Prep Kit for Illumina New England Biolabs Cat#E7370S Agencourt AMPure XP Beads Beckman Coulter, Inc. Cat#A63880 Pan-prokaryote riboPOOL Kit siTOOLs Biotech Cat#dp-K096-3 Ribo-Zero Plus Microbiome rRNA Depletion Kit Illumina Cat# 20072062 Illumina Stranded Total RNA Prep Illumina Cat# 20040534 NEBNext Ultra Directional RNA Library Prep Kit for Illumina New England Biolabs Cat#E7420S Deposited data Original blot images This study Mendeley Data: https://doi.org/10.17632/ skr3snz3ry.1 Raw sequencing data This study PRJNA1082502 Experimental models: Organisms/strains Segatella copri HDD04 Human isolates Li et al.21 Segatella copri HDA03 Human isolates Li et al.21 Segatella copri HDB01 Human isolates Li et al.21 Segatella copri HDC01 Human isolates Li et al.21 Segatella copri DSM18205 Human isolates Hayashi et al.24 Segatella brunsvicensis Ni025 Human isolates Blanco-Miguez et al.34 (Continued on next page) e1 Cell Host & Microbe 32, 1–17.e1–e6, November 13, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Segatella sinensis HDE04 Human isolates Li et al.21 Segatella brasiliensis HDD05 Human isolates Li et al.21 Segatella hominis HDD12 Human isolates Li et al.21 Oligo-MM12 WT C57BL/6NTac mice 8- 12 weeks, raised in gnotobiotic isolaters in germ-free facility at the Helmholtz Centre for Infection research, Germany Bred in house Brugiroux et al.39 Oligonucleotides DNA oligonucleotides used in this study This study Table S5 Recombinant DNA Plasmids generated in this study This study Table S5 Software and algorithms ANNOgesic Yu et al.25 https://annogesic.readthedocs.io/en/ latest/ READemption Förstner et al.66 https://reademption.readthedocs.io/en/ latest/ MetaPhlAn 4 (v 4.0.0) Blanco-Miguez et al.67 https://github.com/biobakery/MetaPhlAn blastn (v2.5.0) Altschul et al.68 https://blast.ncbi.nlm.nih.gov/Blast.cgi GraphPad Prism v8.4.3 GraphPad Software, Inc. N/A Samtools (v1.3.1) Danecek et al.69 N/A Bowtie2 (version 2.4.2) Langmead and Salzberg70 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml
Labeling:Article Title: The RNA landscape of the human commensal Segatella copri reveals a small RNA essential for gut colonization.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacterial strain used in this study This study Table S5 Biological samples Human stool samples (donors A-D) This study N/A Chemicals, peptides, and recombinant proteins Levan Sigma-Aldrich Cat#L8647 Arabinan Megazyme Cat#P-ARAB Arabinoxylan Megazyme Cat#P-WAXYRS Inulin Carbosynth Cat#YI01274 Pectic Galactan Megazyme Cat#P-PGAPT Xylan Carbosynth Cat#YC05381 Mucin Sigma-Aldrich Cat# M2378 Glycogen Sigma-Aldrich Cat#G0885 Pectin Fluka Cat#76282 Fructooligosaccharides Biosynth Cat# OF05207 Fructose Sigma-Aldrich Cat# F0127 DynaMarker, Prestain Marker for Small RNA Plus Biotrend DM253S Terminator Exonuclease Vertis Biotechnologie AG N/A T4 Polynucleotide Kinase New England Biolabs Cat#M0201 Critical commercial assays MEGAscript T7 Transcription kit Thermo Fisher Scientific Cat# AMB13345 Dig Luminescent Detection Kit Sigma-Aldrich Cat#11363514910 DIG RNA Labeling Mix Sigma-Aldrich Cat#11277073910 PCR DIG Labeling Mix Sigma-Aldrich Cat#11585550910 KAPA SYBR FAST Merck Cat#KK4602 NEBNext Ultra DNA Library Prep Kit for Illumina New England Biolabs Cat#E7370S Agencourt AMPure XP Beads Beckman Coulter, Inc. Cat#A63880 Pan-prokaryote riboPOOL Kit siTOOLs Biotech Cat#dp-K096-3 Ribo-Zero Plus Microbiome rRNA Depletion Kit Illumina Cat# 20072062 Illumina Stranded Total RNA Prep Illumina Cat# 20040534 NEBNext Ultra Directional RNA Library Prep Kit for Illumina New England Biolabs Cat#E7420S Deposited data Original blot images This study Mendeley Data: https://doi.org/10.17632/ skr3snz3ry.1 Raw sequencing data This study PRJNA1082502 Experimental models: Organisms/strains Segatella copri HDD04 Human isolates Li et al.21 Segatella copri HDA03 Human isolates Li et al.21 Segatella copri HDB01 Human isolates Li et al.21 Segatella copri HDC01 Human isolates Li et al.21 Segatella copri DSM18205 Human isolates Hayashi et al.24 Segatella brunsvicensis Ni025 Human isolates Blanco-Miguez et al.34 (Continued on next page) e1 Cell Host & Microbe 32, 1–17.e1–e6, November 13, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Segatella sinensis HDE04 Human isolates Li et al.21 Segatella brasiliensis HDD05 Human isolates Li et al.21 Segatella hominis HDD12 Human isolates Li et al.21 Oligo-MM12 WT C57BL/6NTac mice 8- 12 weeks, raised in gnotobiotic isolaters in germ-free facility at the Helmholtz Centre for Infection research, Germany Bred in house Brugiroux et al.39 Oligonucleotides DNA oligonucleotides used in this study This study Table S5 Recombinant DNA Plasmids generated in this study This study Table S5 Software and algorithms ANNOgesic Yu et al.25 https://annogesic.readthedocs.io/en/ latest/ READemption Förstner et al.66 https://reademption.readthedocs.io/en/ latest/ MetaPhlAn 4 (v 4.0.0) Blanco-Miguez et al.67 https://github.com/biobakery/MetaPhlAn blastn (v2.5.0) Altschul et al.68 https://blast.ncbi.nlm.nih.gov/Blast.cgi GraphPad Prism v8.4.3 GraphPad Software, Inc. N/A Samtools (v1.3.1) Danecek et al.69 N/A Bowtie2 (version 2.4.2) Langmead and Salzberg70 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml
Polymerase Chain Reaction:Article Title: The RNA landscape of the human commensal Segatella copri reveals a small RNA essential for gut colonization.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacterial strain used in this study This study Table S5 Biological samples Human stool samples (donors A-D) This study N/A Chemicals, peptides, and recombinant proteins Levan Sigma-Aldrich Cat#L8647 Arabinan Megazyme Cat#P-ARAB Arabinoxylan Megazyme Cat#P-WAXYRS Inulin Carbosynth Cat#YI01274 Pectic Galactan Megazyme Cat#P-PGAPT Xylan Carbosynth Cat#YC05381 Mucin Sigma-Aldrich Cat# M2378 Glycogen Sigma-Aldrich Cat#G0885 Pectin Fluka Cat#76282 Fructooligosaccharides Biosynth Cat# OF05207 Fructose Sigma-Aldrich Cat# F0127 DynaMarker, Prestain Marker for Small RNA Plus Biotrend DM253S Terminator Exonuclease Vertis Biotechnologie AG N/A T4 Polynucleotide Kinase New England Biolabs Cat#M0201 Critical commercial assays MEGAscript T7 Transcription kit Thermo Fisher Scientific Cat# AMB13345 Dig Luminescent Detection Kit Sigma-Aldrich Cat#11363514910 DIG RNA Labeling Mix Sigma-Aldrich Cat#11277073910 PCR DIG Labeling Mix Sigma-Aldrich Cat#11585550910 KAPA SYBR FAST Merck Cat#KK4602 NEBNext Ultra DNA Library Prep Kit for Illumina New England Biolabs Cat#E7370S Agencourt AMPure XP Beads Beckman Coulter, Inc. Cat#A63880 Pan-prokaryote riboPOOL Kit siTOOLs Biotech Cat#dp-K096-3 Ribo-Zero Plus Microbiome rRNA Depletion Kit Illumina Cat# 20072062 Illumina Stranded Total RNA Prep Illumina Cat# 20040534 NEBNext Ultra Directional RNA Library Prep Kit for Illumina New England Biolabs Cat#E7420S Deposited data Original blot images This study Mendeley Data: https://doi.org/10.17632/ skr3snz3ry.1 Raw sequencing data This study PRJNA1082502 Experimental models: Organisms/strains Segatella copri HDD04 Human isolates Li et al.21 Segatella copri HDA03 Human isolates Li et al.21 Segatella copri HDB01 Human isolates Li et al.21 Segatella copri HDC01 Human isolates Li et al.21 Segatella copri DSM18205 Human isolates Hayashi et al.24 Segatella brunsvicensis Ni025 Human isolates Blanco-Miguez et al.34 (Continued on next page) e1 Cell Host & Microbe 32, 1–17.e1–e6, November 13, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Segatella sinensis HDE04 Human isolates Li et al.21 Segatella brasiliensis HDD05 Human isolates Li et al.21 Segatella hominis HDD12 Human isolates Li et al.21 Oligo-MM12 WT C57BL/6NTac mice 8- 12 weeks, raised in gnotobiotic isolaters in germ-free facility at the Helmholtz Centre for Infection research, Germany Bred in house Brugiroux et al.39 Oligonucleotides DNA oligonucleotides used in this study This study Table S5 Recombinant DNA Plasmids generated in this study This study Table S5 Software and algorithms ANNOgesic Yu et al.25 https://annogesic.readthedocs.io/en/ latest/ READemption Förstner et al.66 https://reademption.readthedocs.io/en/ latest/ MetaPhlAn 4 (v 4.0.0) Blanco-Miguez et al.67 https://github.com/biobakery/MetaPhlAn blastn (v2.5.0) Altschul et al.68 https://blast.ncbi.nlm.nih.gov/Blast.cgi GraphPad Prism v8.4.3 GraphPad Software, Inc. N/A Samtools (v1.3.1) Danecek et al.69 N/A Bowtie2 (version 2.4.2) Langmead and Salzberg70 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml
Sequencing:Article Title: The RNA landscape of the human commensal Segatella copri reveals a small RNA essential for gut colonization.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacterial strain used in this study This study Table S5 Biological samples Human stool samples (donors A-D) This study N/A Chemicals, peptides, and recombinant proteins Levan Sigma-Aldrich Cat#L8647 Arabinan Megazyme Cat#P-ARAB Arabinoxylan Megazyme Cat#P-WAXYRS Inulin Carbosynth Cat#YI01274 Pectic Galactan Megazyme Cat#P-PGAPT Xylan Carbosynth Cat#YC05381 Mucin Sigma-Aldrich Cat# M2378 Glycogen Sigma-Aldrich Cat#G0885 Pectin Fluka Cat#76282 Fructooligosaccharides Biosynth Cat# OF05207 Fructose Sigma-Aldrich Cat# F0127 DynaMarker, Prestain Marker for Small RNA Plus Biotrend DM253S Terminator Exonuclease Vertis Biotechnologie AG N/A T4 Polynucleotide Kinase New England Biolabs Cat#M0201 Critical commercial assays MEGAscript T7 Transcription kit Thermo Fisher Scientific Cat# AMB13345 Dig Luminescent Detection Kit Sigma-Aldrich Cat#11363514910 DIG RNA Labeling Mix Sigma-Aldrich Cat#11277073910 PCR DIG Labeling Mix Sigma-Aldrich Cat#11585550910 KAPA SYBR FAST Merck Cat#KK4602 NEBNext Ultra DNA Library Prep Kit for Illumina New England Biolabs Cat#E7370S Agencourt AMPure XP Beads Beckman Coulter, Inc. Cat#A63880 Pan-prokaryote riboPOOL Kit siTOOLs Biotech Cat#dp-K096-3 Ribo-Zero Plus Microbiome rRNA Depletion Kit Illumina Cat# 20072062 Illumina Stranded Total RNA Prep Illumina Cat# 20040534 NEBNext Ultra Directional RNA Library Prep Kit for Illumina New England Biolabs Cat#E7420S Deposited data Original blot images This study Mendeley Data: https://doi.org/10.17632/ skr3snz3ry.1 Raw sequencing data This study PRJNA1082502 Experimental models: Organisms/strains Segatella copri HDD04 Human isolates Li et al.21 Segatella copri HDA03 Human isolates Li et al.21 Segatella copri HDB01 Human isolates Li et al.21 Segatella copri HDC01 Human isolates Li et al.21 Segatella copri DSM18205 Human isolates Hayashi et al.24 Segatella brunsvicensis Ni025 Human isolates Blanco-Miguez et al.34 (Continued on next page) e1 Cell Host & Microbe 32, 1–17.e1–e6, November 13, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Segatella sinensis HDE04 Human isolates Li et al.21 Segatella brasiliensis HDD05 Human isolates Li et al.21 Segatella hominis HDD12 Human isolates Li et al.21 Oligo-MM12 WT C57BL/6NTac mice 8- 12 weeks, raised in gnotobiotic isolaters in germ-free facility at the Helmholtz Centre for Infection research, Germany Bred in house Brugiroux et al.39 Oligonucleotides DNA oligonucleotides used in this study This study Table S5 Recombinant DNA Plasmids generated in this study This study Table S5 Software and algorithms ANNOgesic Yu et al.25 https://annogesic.readthedocs.io/en/ latest/ READemption Förstner et al.66 https://reademption.readthedocs.io/en/ latest/ MetaPhlAn 4 (v 4.0.0) Blanco-Miguez et al.67 https://github.com/biobakery/MetaPhlAn blastn (v2.5.0) Altschul et al.68 https://blast.ncbi.nlm.nih.gov/Blast.cgi GraphPad Prism v8.4.3 GraphPad Software, Inc. N/A Samtools (v1.3.1) Danecek et al.69 N/A Bowtie2 (version 2.4.2) Langmead and Salzberg70 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml
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![(A) Gene loci of putative xylan degradation/assimilation-related enzymes induced in the presence of mixture of <t>arabinoxylan</t> and its derived oligosaccharides. Black arrows indicate genes encoding putative glycoside hydrolases. (B) Expression of genes encoding putative xylan degradation/assimilation-related enzymes in the absence (black bars) and presence (white bars) of a mixture of arabinoxylan and its derived oligosaccharides. Gray diamonds indicate fold changes of expression of each gene (transcripts per million value in the presence/absence of additive saccharides). (C) Expression levels [log2 fold change: log 2 (transcripts per million value in the presence/absence of additive saccharides)] of genes located on contig-149924.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_8896/pmc12678896/pmc12678896__JAG-72-7204201-g04.jpg)