Table 3.
The relative abundances of each 16S rRNA gene sequence variant at 0 h (before treatment) and at 48 h (after treatment) were compiled for each steer.
| Base mean | log2 Fold change | p-value | padj | Phylum | Class | Order | Family | Genus | Sequence |
|---|---|---|---|---|---|---|---|---|---|
| 625.4 | 4.10 | 8.93E-08 | 2.38E-05 | Bacteroidetes | Bacteroidia | Bacteroidales | Prevotellaceae | Prevotellaceae_UCG-003 | TACGGAAGAT GCGAGCGTTA TCCGGATTTA TTGGGTTTAA AGGGAGCGTA GGCGGGCTGT TAAGTCAGCG GTAAAATGTC AAGGCCCAAC CTTGTCCTGC CGTTGAAACT GGCGGTCTTG AATGCACACA AGGGAGATGG AATTCGTCGT GTAGCGGTGA AATGCTTAGA TATGACGAAG AACTCCGATT GCGAAGGCAG TCTCCTGGGG TGTAATTGAC GCTGAGGCTC GAAAGTGCGG GTATCAAACA GG |
| 34.9 | −5.73 | 1.32E-06 | 0.000132 | Bacteroidetes | Bacteroidia | Bacteroidales | Rikenellaceae | Alistipes | TACGGAGGAT CCAAGCGTTA TCCGGATTTA TTGGGTTTAA AGGGTGCGTA GGCGGTTTGA TAAGTTAGAG GTTAAATGTC AGTGCTCAAC ACTGGCCTGC CTCTAATACT GTTGGACTAG AGAGTAGATG CGGTAGGCGG AATGTATGGT GTAGCGGTGA AATGCGTAGA GATCATACAG AACACCGATT GCGAAGGCAG CTTACCAAAC TATATCTGAC GTTGAGGCAC GAAAGCGTGG GTAGCAAACA GG |
| 17.26 | −6.21 | 1.65E-07 | 3.29E-05 | Bacteroidetes | Bacteroidia | Bacteroidales | Rikenellaceae | Alistipes | TACGGAGGAT CCAAGCGTTA TCCGGATTTA TTGGGTTTAA AGGGTGCGTA GGCGGTTTTA TAAGTTAGAG GTTAAATGTC AGGGCTCAAC TCTGGCCTGC CTCTAATACT GTAGGACTAG AGAGTAGATG CGGTAGGCGG AATGTATGGT GTAGCGGTGA AATGCGTAGA GATCATACAG AACACCGATT GCGAAGGCAG CTTACCAAAC TATATCTGAC GTTGAGGCAC GAAAGCGTGG GTAGCAAACA GG |
| 25.4 | −2.37 | 9.79E-05 | 0.006527 | Firmicutes | Clostridia | Clostridiales | Christensenellaceae | Christensenell aceae_R-7_group |
TACGTAGGGG GCGAGCGTTG TCCGGAATGA TTGGGCGTAA AGGGCGCGTA GGCGGCCTGG TAAGTCTGGA GTGAAAGTCC TGCTTTCAAG GTGGGAATTG CTTTGGATAC TGCTAGGCTC GAGTGCAGGA GAGGAAAGCG GAATTACCGG TGTAGCGGTG AAATGCGTAG AGATCGGTAG GAACACCAGT GGCGAAGGCG GCTTTCTGGA CTGAAACTGA CGCTGAGGCG CGAAAGCGTG GGGAGCAAA CAGG |
| 12.7 | −5.88 | 3.77E-07 | 5.02E-05 | Bacteroidetes | Bacteroidia | Bacteroidales | Rikenellaceae | Alistipes | TACGGAGGAT CCAAGCGTTA TCCGGATTTA TTGGGTTTAA AGGGTGCGTA GGCGGTTTGG TAAGTTAGAG GTGAAATTTC AGGGCTCAAC CTTGACATTG CCTCTGATAC TGCCGAGCTA GAGAGTAGTT GCTGTGGGCG GAATGTATGG TGTAGCGGTG AAATGCTTAG AGATCATACA GAACACCGAT TGCGAAGGCA GCTCACAAAA CTATATCTGA CGTTGAGGCA CGAAAGCGTG GGTAGCAAAC AGG |
| 13.0 | −3.64 | 8.99E-06 | 0.00072 | Firmicutes | Clostridia | Clostridiales | Christensenellaceae | Christensenell aceae_R-7_group |
TACGTAGGGG GCAAGCGTTG TCCGGAATGA CTGGGCGTAA AGGGCGTGTA GGCGGCTTTT TAAGTGTGAA GTGAAAGTCC TGCTTTCAAG GTGGGAATTG CTTTGCAAAC TGGAGAGCTT GAGTGCGGAA GAGGTAAGTG GAATTCCCAG TGTAGCGGTG AAATGCGTAG AGATTGGGAG GAACACCAGT GGCGAAGGCG ACTTACTGGG CCGCAACTGA CGCTGAGGCG CGAAAGCGTG GGGAGCGAAC AGG |
| 11.8 | −3.53 | 1.52E-06 | 0.000135 | Bacteroidetes | Bacteroidia | Bacteroidales | Rikenellaceae | Rikenellace ae_RC9_gut_group |
TACGGGGGAT GCAAGCGTTA TCCGGATTTA TTGGGTTTAA AGGGTGCGTA GGCTGTCCGG TAAGTCAGCG GTGAAATTTA GGGGCTCAAC CTCTACCGTG CCGTTGATAC TGTCGGGCTA GAATGCGGAT GCCGTGGGAG GAATGTGTGG TGTAGCGGTG AAATGCATAG ATATCACACA GAACACCGAT TGCGAAGGCA TCTCACGAAT CCGCAATTGA CGCTGATGCA CGAAAGCGTG GGGATCAAAC AGG |
| 20.8 | −5.91 | 2.73E-09 | 2.19E-06 | Firmicutes | Erysipelotrichia | Erysipelotrichales | Erysipelotrichaceae | Faecalitalea | TACGTAGGTG GCGAGCGTTA TCCGGAATCA TTGGGCGTAA AGGGTGCGTA GGTGGCAGAA TAAGTCTGAA GTAAAAGGCT GCAGCTCAAC TGCAGTATGC TTTGGAAACT GTTCAGCTAG AGTGCGGAAG AGGGCGATGG AATTCCATGT GTAGCGGTAA AATGCGTAGA TATATGGAGG AACACCAGTG GCGAAGGCGG TCGCCTGGTC CGTAACTGAC ACTGAGGCAC GAAAGCGTGG GGAGCAAATA GG |
| 12.9 | −4.43 | 2.96E-07 | 4.73E-05 | Firmicutes | Clostridia | Clostridiales | Christensenellaceae | Christensenellaceae_R-7_group | TACGTAGGGG GCAAGCGTTG TCCGGAATGA CTGGGCGTAA AGGGCGTGTA GGCGGCTCTT TAAGTCTGAA GTGAAAGTCC TGCTTTCAAG GTGGGAATTG CTTTGGAGAC TGGAGAGCTT GAGTGCGGAA GAGGTAAGTG GAATTCCCAG TGTAGCGGTG AAATGCGTAG AGATTGGGAG GAACACCAGT GGCGAAGGCG ACTTACTGGG CCGTAACTGA CGCTGAGGCG CGAAAGCGTG GGGAGCGAAC AGG |
| 11.9 | −3.84 | 2.08E-08 | 8.31E-06 | Bacteroidetes | Bacteroidia | Bacteroidales | Rikenellaceae | dgA-11_gut_group | TACGGAGGAT GCGAGCGTTA TCCGGATTTA TTGGGTTTAA AGGGTGCGTA GGCGGTTACT GTAAGTCAGT GGTGAAATTT TGATGCTTAA CATTAAAAGT GCCATAGATA CTGCAGAGCT GGAATGGGGA TGCTGTCAGC GGAATGTGTA GTGTAGCGGT GAAATGCATA GATATTACAC AGAACACCGA TTGCGAAGGC AGCTGACAAA TCCTTTATTG ACGCTGATGC ACGAAAGTGT GGGGATCAAA CAGG |
| 9.4 | −4.85 | 9.11E-07 | 0.000104 | Cyanobacteria | Melainabacteria | Gastranaerophilales | NA | NA | TACGGGGGAT GCAAGCGTTG TCCGGAATCA TTGGGCGTAA AGAGTTCGTA GGTGGCCTGT TAAGTCTGGT GTTAAATGCA GAGGCTCAAC TTCTGTTCGG CACTGGATAC TGGCAAGCTT GAATGCGGTA GAGGTAAAGG GAATTCCTGG TGTAGCGGTG AAATGCGTAG ATATCAGGAG GAACATCGGT GGCGAAAGCG CTTTACTGGG CCGTAATTGA CACTGAGGAA CGAAAGCCAG GGTAGCAAAT GGG |
| 4.72 | −5.03 | 4.84E-05 | 0.00352 | Proteobacteria | Gammaproteo bacteria |
Enterobacteriales | Enterobacteriaceae | Escherichia/Shigella | TACGGAGGGT GCAAGCGTTA ATCGGAATTA CTGGGCGTAA AGCGCACGCA GGCGGTTTGT TAAGTCAGAT GTGAAATCCC CGGGCTCAAC CTGGGAACTG CATCTGATAC TGGCAAGCTT GAGTCTCGTA GAGGGGGGTA GAATTCCAGG TGTAGCGGTG AAATGCGTAG AGATCTGGAG GAATACCGGT GGCGAAGGCG GCCCCCTGGA CGAAGACTGA CGCTCAGGTG CGAAAGCGTG GGGAGCAAAC AGG |
The DESeq2 method was used to test for significant changes in relative abundance, while controlling for the sampled steer. Sequence variants that were significant when controlling for an FDR of 0.01 using the Benjamini-Hochberg method are reported. The log2FoldChange indicates the fold change from 0 to 48 h and the baseMean indicates the average starting abundance at 0 h.