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. 2019 Nov 26;14(11):e0225448. doi: 10.1371/journal.pone.0225448

Table 5. Relative abundances and taxonomic classification of core operational taxonomic units (OTU; shared by all samples) in Japanese Black beef cattle during the Early, Middle, and Late fattening stages.

OTU Stage SEM
Early Middle Late RDP1 classification (genus level) BLASTn2 classification Percent to BLASTn identity3 Accession no.
OTU1 11.7 6.73 6.84 3.05 Unclassified Ruminococcaceae Ruminococcus bromii strain ATCC 27255 97.8 NR_025930.1
OTU2 6.85 6.47 6.46 2.31 Unclassified Lachnospiraceae Faecalimonas umbilicata strain EGH7 95.2 NR_156907.1
OTU4 2.89 3.46 2.86 1.42 Succiniclasticum Succiniclasticum ruminis strain SE10 95.9 NR_026205.1
OTU5 5.14a 1.85b 2.14ab 0.77 Unclassified Firmicutes Thermotalea metallivorans strain B2-1 88.6 NR_044503.1
OTU6 2.31 3.16 1.40 0.84 Prevotella Prevotella ruminicola strain Bryant 23 98.9 NR_102887.1
OTU8 4.62a 1.37b 1.91b 0.45 Unclassified Ruminococcaceae Pseudoflavonifractor phocaeensis strain Marseille-P3064 92.2 NR_147370.1
OTU10 2.10 2.04 0.80 0.57 Unclassified Ruminococcaceae Ruminococcus bromii strain ATCC 27255 95.6 NR_025930.1
OTU13 1.66 2.01 1.48 0.42 Mogibacterium Mogibacterium neglectum strain P9a-h 94.8 NR_027203.1
OTU15 1.77 0.69 2.26 0.66 Unclassified Ruminococcaceae Ruminococcus bromii strain ATCC 27255 94.5 NR_025930.1
OTU24 0.98 0.53 0.72 0.27 Unclassified Lachnospiraceae Faecalicatena orotica strain JCM 1429 93.3 NR_114392.1
OTU26 0.97a 0.17b 0.20b 0.14 Butyrivibrio Butyrivibrio proteoclasticus strain B316 99.3 NR_102893.1
OTU30 1.13a 0.13b 0.35c 0.11 Unclassified Firmicutes Novibacillus thermophilus strain SG-1 87.4 NR_136797.1
OTU34 0.65 0.28 0.71 0.17 Unclassified Firmicutes Monoglobus pectinilyticus strain 14 90.0 NR_159227.1
OTU35 0.56 0.62 0.77 0.29 Olsenella Olsenella profusa DSM 13989 98.5 NR_116938.1
OTU37 0.70a 0.14b 0.34b 0.10 Unclassified Clostridiales Incertae Sedis XIII Emergencia timonensis strain SN18 93.3 NR_144737.1
OTU43 0.38a 0.48b 0.20b 0.13 Unclassified Lachnospiraceae Acetatifactor muris strain CT-m2 91.5 NR_117905.1
OTU54 0.26 0.38 0.19 0.10 Schwartzia Schwartzia succinivorans strain S1-1 99.3 NR_029325.1
OTU55 0.12a 0.59b 0.57b 0.17 Unclassified Firmicutes Salinithrix halophila strain R4S8 87.0 NR_134171.1
OTU58 0.20 0.46 0.21 0.12 Unclassified Firmicutes Gracilibacter thermotolerans JW/YJL-S1 89.6 NR_115693.1
OTU62 0.09a 0.45b 0.12a 0.06 Ruminococcus Ruminococcus flavefaciens strain C94 98.9 NR_025931.1
OTU64 0.19 0.41 0.36 0.15 Unclassified Planctomycetaceae Thermostilla marina strain SVX8 84.8 NR_148598.1
OTU68 0.23 0.24 0.89 0.19 Unclassified Lachnospiraceae Blautia glucerasea strain JCM 17039 93.0 NR_113231.1
OTU79 0.21 0.27 0.30 0.09 Unclassified Clostridiales Ihubacter massiliensis strain Marseille-P2843 93.7 NR_144749.1
OTU80 0.24 0.28 0.12 0.07 Unclassified Firmicutes Geosporobacter ferrireducens strain IRF9 88.6 NR_148302.1
OTU86 0.14 0.21 0.23 0.08 Unclassified Clostridiales Vallitalea pronyensis strain FatNI3 90.4 NR_125677.1
OTU90 0.27 0.13 0.24 0.07 Atopobium Atopobium parvulum DSM 20469 95.5 NR_102936.1
OTU103 0.14 0.12 0.22 0.07 Unclassified Ruminococcaceae Sporobacter termitidis strain SYR 93.0 NR_044972.1
OTU110 0.23a 0.04b 0.10ab 0.05 Unclassified Clostridiales Anaerobacterium chartisolvens strain T-1-35 89.3 NR_125464.1
OTU125 0.09 0.12 0.23 0.05 Unclassified Ruminococcaceae Ruminococcus flavefaciens strain C94 94.1 NR_025931.1
OTU167 0.08a 0.06a 0.17b 0.02 Intestinimonas Intestinimonas butyriciproducens strain SRB-521-5-I 96.7 NR_118554.1
OTU183 0.09 0.04 0.07 0.02 Unclassified Clostridiales Eubacterium nodatum ATCC 33099 91.8 NR_118781.1
OTU184 0.03 0.09 0.08 0.02 Ruminococcus Ruminococcus albus 7 = DSM 20455 98.5 NR_074399.1
OTU189 0.09a 0.04b 0.09ab 0.02 Unclassified Firmicutes Caloramator fervidus strain RT4. B1 89.6 NR_025899.1
OTU199 0.07a 0.06a 0.02b 0.01 Unclassified Lachnospiraceae [Clostridium] aminophilum strain F 93.3 NR_118651.1
OTU238 0.07a 0.02b 0.08a 0.02 Unclassified Lachnospiraceae Merdimonas faecis strain BR31 91.1 NR_157642.1

a,b,cMean within a row, different superscripts significantly differ (P < 0.05)

1Ribosomal Database Project tools training set version 16 in the MiSeq standard operating procedure (MiSeq SOP) in Mothur (https://mothur.org/wiki/MiSeq_SOP; [19])

2Basic Local Alignment Search Tool

3Percent identity