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Table 1 Mean relative abundance (%) of bacterial phyla calculated based on copies per million reads across feces, manure, lagoon and soil samples from both farm types

From: The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania

Phylum CF CL CM CS OF OL OM OS RS Overall
Proteobacteria 16.78 59.72 63.16 53.06 17.38 42.58 63.86 57.17 56.77 35.40
Actinobacteria 8.18 8.50 13.30 37.31 11.93 9.40 11.33 32.51 33.65 15.88
Bacteroidetes 34.36 19.40 12.07 2.24 27.67 19.27 12.29 4.05 2.27 21.04
Planctomycetes 0.17 0.19 0.36 2.09 0.22 0.37 0.13 1.90 2.25 0.67
Firmicutes 35.06 8.37 7.05 2.13 38.06 16.77 9.69 1.74 1.74 22.04
Acidobacteria 0.14 0.09 0.15 0.95 0.15 0.17 0.06 0.78 1.01 0.32
Gemmatimonadetes 0.02 0.03 0.11 0.52 0.03 0.06 0.04 0.36 0.50 0.14
Verrucomicrobia 0.30 0.10 0.44 0.35 0.39 0.64 0.09 0.33 0.53 0.35
Deinococcus-Thermus 0.14 0.11 0.20 0.31 0.19 0.21 0.25 0.30 0.29 0.20
Cyanobacteria 0.70 0.35 0.32 0.32 0.81 0.96 0.29 0.28 0.32 0.60
Chloroflexi 0.15 0.18 0.28 0.25 0.19 0.61 0.09 0.21 0.20 0.23
Nitrospirae 0.04 0.02 0.03 0.16 0.05 0.06 0.02 0.11 0.15 0.06
Kiritimatiellaeota 0.01 0.03 0.02 0.06 0.02 0.17 0.01 0.05 0.06 0.04
Spirochaetes 1.48 1.54 0.76 0.05 1.04 5.46 0.14 0.04 0.05 1.33
Chlorobi 0.12 0.08 0.06 0.04 0.14 0.21 0.04 0.04 0.05 0.11
Armatimonadetes 0.01 0.01 0.01 0.03 0.01 0.01 0.00 0.02 0.03 0.01
Synergistetes 0.08 0.13 0.05 0.03 0.09 0.32 0.02 0.03 0.02 0.09
Unclassfied 0.01 0.01 0.07 0.01 0.02 0.04 0.01 0.01 0.01 0.02
Thermotogae 0.13 0.08 0.12 0.01 0.14 0.23 0.04 0.01 0.01 0.10
Tenericutes 0.68 0.73 0.75 0.01 0.67 1.69 1.17 0.01 0.01 0.63
Fusobacteria 0.73 0.14 0.11 0.01 0.38 0.27 0.17 0.01 0.01 0.34
Candidatus Bipolaricaulota 0.00 0.00 0.00 0.01 0.00 0.01 0.00 0.01 0.00 0.00
Aquificae 0.06 0.02 0.01 0.01 0.08 0.04 0.01 0.01 0.01 0.04
Chrysiogenetes 0.01 0.00 0.01 0.01 0.01 0.01 0.00 0.01 0.01 0.01
Chlamydiae 0.07 0.03 0.03 0.01 0.08 0.04 0.03 0.00 0.01 0.05
Thermodesulfobacteria 0.03 0.01 0.01 0.00 0.03 0.03 0.01 0.00 0.00 0.02
Balneolaeota 0.01 0.01 0.01 0.00 0.01 0.02 0.01 0.00 0.00 0.01
Deferribacteres 0.04 0.02 0.03 0.00 0.04 0.04 0.01 0.00 0.00 0.03
Calditrichaeota 0.01 0.01 0.00 0.00 0.01 0.02 0.00 0.00 0.00 0.01
Ignavibacteriae 0.02 0.01 0.01 0.00 0.02 0.03 0.01 0.00 0.00 0.02
Elusimicrobia 0.03 0.01 0.00 0.00 0.04 0.03 0.00 0.00 0.00 0.02
Fibrobacteres 0.04 0.03 0.02 0.00 0.06 0.05 0.01 0.00 0.00 0.03
Caldiserica 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Coprothermobacterota 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Candidatus Saccharibacteria 0.01 0.00 0.00 0.00 0.01 0.02 0.01 0.00 0.00 0.01
Candidatus Cloacimonetes 0.38 0.03 0.42 0.00 0.01 0.15 0.15 0.00 0.00 0.14
Dictyoglomi 0.01 0.00 0.00 0.00 0.01 0.01 0.00 0.00 0.00 0.01
  1. CF conventional feces; OF organic feces; CL conventional lagoon; OL organic lagoon; CM conventional manure; OM organic manure; CS conventional soil; OS organic soil; RS reference soil