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. 2023 Jan 31;8(1):e01239-22. doi: 10.1128/msystems.01239-22

TABLE 7.

Differentially abundant genera in the jejunal, ileal, cecal, and colonic chicken microbiota between the Control group and the BBR group that received a diet supplemented with 1 g berberine/kg feed for 12 days posthatcha

Phylum Class Order Family Genus Mean relative abundance (%)
 Log2 fold change Adjusted P value
Control BBR
Jejunum
 Firmicutes Clostridia Clostridiales Lachnospiraceae Fusicatenibacter 0.151 0.005 −4.67 <0.001
 Firmicutes Clostridia Clostridiales Peptostreptococcaceae Unculturedb 1.421 0.036 −5.11 0.002
 Firmicutes Clostridia Clostridiales Ruminococcaceae Negativibacillus 0.031 0.000 −2.76 0.002
 Firmicutes Clostridia Clostridiales Ruminococcaceae Uncultured 0.036 0.270 1.78 0.019
Ileum
 Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia- Shigella 0.150 2.410 3.79 0.002
 Firmicutes Clostridia Clostridiales Lachnospiraceae Shuttleworthia 0.033 0.017 −2.75 <0.001
 Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnospiraceae NK4A136 group 0.000 0.000 −1.72 0.002
 Firmicutes Clostridia Clostridiales Peptostreptococcaceae Unculturedb 7.341 0.005 −8.66 <0.001
 Firmicutes Clostridia Clostridiales Peptostreptococcaceae Romboutsia 0.487 0.000 −6.78 <0.001
 Firmicutes Clostridia Clostridiales Peptostreptococcaceae Family_Peptostreptococcaceae 0.167 0.000 −4.68 <0.001
 Firmicutes Clostridia Clostridiales Ruminococcaceae Negativibacillus 0.017 0.000 −2.46 <0.001
Cecum
 Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella 0.157 10.586 7.85 0.016
 Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Salmonella 0.074 0.205 4.03 0.031
 Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Family_Enterobacteriaceae 0.002 0.236 6.91 0.014
 Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia -Shigella 2.517 14.188 4.00 <0.001
 Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Proteus 0.105 1.919 7.55 0.026
 Firmicutes Clostridia Clostridiales Lachnospiraceae Shuttleworthia 0.610 0.000 −6.44 0.031
 Firmicutes Clostridia Clostridiales Lachnospiraceae Anaerostipes 0.619 0.010 −7.89 0.015
 Firmicutes Clostridia Enterobacteriales Lachnospiraceae [Eubacterium] hallii group 0.860 0.064 −6.42 0.001
 Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnospiraceae UCG−010 0.193 0.000 −5.61 <0.001
 Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnoclostridium 0.867 6.364 3.91 <0.001
 Firmicutes Clostridia Clostridiales Peptostreptococcaceae Unculturedb 1.419 0.000 −9.25 0.001
 Firmicutes Clostridia Clostridiales Peptostreptococcaceae Romboutsia 0.079 0.000 −5.14 0.005
 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium 8.050 0.002 −9.30 0.023
 Firmicutes Clostridia Clostridiales Ruminococcaceae Flavonifractor 0.843 4.538 4.87 0.001
Colon
 Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella 0.042 1.894 4.91 <0.001
 Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia -Shigella 0.658 15.184 4.80 <0.001
 Firmicutes Erysipelotrichia Erysipelotrichales Erysipelotrichaceae Merdibacter 0.062 0.000 −2.76 0.008
 Firmicutes Clostridia Clostridiales Lachnospiraceae Shuttleworthia 0.249 0.002 −5.10 <0.001
 Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnoclostridium 0.561 3.037 3.49 0.005
 Firmicutes Clostridia Clostridiales Peptostreptococcaceae Unculturedb 18.300 0.012 −11.36 <0.001
 Firmicutes Clostridia Clostridiales Peptostreptococcaceae Romboutsia 1.023 0.000 −9.24 <0.001
 Firmicutes Clostridia Clostridiales Peptostreptococcaceae Terrisporobacter 0.319 0.000 −3.06 0.044
 Firmicutes Clostridia Clostridiales Ruminococcaceae Subdoligranulum 1.079 0.002 −3.32 0.045
 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium 3.980 0.002 −5.79 0.005
 Firmicutes Clostridia Clostridiales Ruminococcaceae Flavonifractor 0.101 0.679 3.78 0.006
a

The taxonomic classification, the mean relative abundance, and the log2 fold change (BBR/Control) of the LinDA normalized abundance of each genus are shown. Only genera with P < 0.05 and |log2 fold change| >1.5 were considered biologically relevant and included.

b

The uncultured bacterium belongs to the OTU4409730, the sequence of which could either be identified as Romboutsia, Paraclostridium, or Terrisporobacter (97% ID NCBI BLAST).