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. 2017 Mar 9;12(3):e0173818. doi: 10.1371/journal.pone.0173818

Table 1. Relative abundance of all taxa detected at greater than 0.50% mean relative abundance in at least one sample site (feces, oropharyngeal swabs (OP), bronchoalveolar lavage (BAL) or blood), annotated to the level of phylum, family, and operational taxonomic unit (OTU).

Data presented as mean ± standard error of the mean (SEM).

Phylum Family OTUs Feces OP BAL Blood
Actinobacteria Corynebacteriaceae Corynebacterium sp. 0.75 ± 0.23 0.01 ± 0.00 0.06 ± 0.03 0.00 ± 0.00
Bacteroidetes [Paraprevotellaceae] [Prevotella] sp. 0.94 ± 0.37 5.46 ± 0.87 0.02 ± 0.02 0.05 ± 0.12
[Weeksellaceae] Chryseobacterium sp. 0.01 ± 0.00 1.38 ± 0.17 0.05 ± 0.02 0.00 ± 0.00
Family [Weeksellaceae] 0.00 ± 0.00 1.72 ± 0.28 0.01 ± 0.01 0.00 ± 0.00
Bacteroidaceae Bacteroides fragilis 2.37 ± 0.47 0.00 ± 0.00 0.07 ± 0.05 0.00 ± 0.00
Bacteroides ovatus 10.43 ± 2.10 0.02 ± 0.01 0.31 ± 0.07 0.17 ± 0.18
Bacteroides plebeius 2.54 ± 1.22 0.01 ± 0.00 0.10 ± 0.07 0.00 ± 0.00
Bacteroides sp. 14.44 ± 2.56 4.23 ± 0.81 0.89 ± 0.27 1.26 ± 1.58
Chitinophagaceae Sediminibacterium sp. 0.01 ± 0.00 0.03 ± 0.01 0.59 ± 0.26 0.06 ± 0.15
Flavobacteriaceae Capnocytophaga sp. 0.00 ± 0.00 0.66 ± 0.08 0.00 ± 0.00 0.00 ± 0.00
Family Flavobacteriaceae 0.00 ± 0.00 1.09 ± 0.44 0.21 ± 0.19 0.05 ± 0.12
Porphyromonadaceae Porphyromonas endodontalis 0.00 ± 0.00 2.15 ± 0.33 0.02 ± 0.02 0.00 ± 0.00
Porphyromonas sp. 1.15 ± 0.54 10.16 ± 1.14 0.09 ± 0.08 0.10 ± 0.25
Prevotellaceae Prevotella copri 0.57 ± 0.34 0.01 ± 0.00 0.04 ± 0.02 0.00 ± 0.00
Rikenellaceae Family Rikenellaceae 0.00 ± 0.00 0.03 ± 0.02 0.36 ± 0.18 0.75 ± 1.28
S24-7 Family S24-7 0.04 ± 0.01 0.02 ± 0.00 0.82 ± 0.28 0.79 ± 0.79
Sphingobacteriaceae Family Sphingobacteriaceae 0.01 ± 0.01 0.00 ± 0.00 22.43 ± 5.10 64.25 ± 5.84
Firmicutes [Tissierellaceae] Anaerococcus sp. 7.31 ± 3.90 0.01 ± 0.00 0.13 ± 0.07 0.00 ± 0.00
Peptoniphilus sp. 2.07 ± 0.59 0.00 ± 0.00 0.08 ± 0.06 0.00 ± 0.00
Bacillaceae Geobacillus sp. 0.00 ± 0.00 0.01 ± 0.01 0.14 ± 0.07 1.32 ± 2.50
Erysipelotrichaceae Family Erysipelotrichaceae 0.02 ± 0.01 0.54 ± 0.10 0.02 ± 0.02 0.00 ± 0.00
Lachnospiraceae [Ruminococcus] gnavus 0.62 ± 0.16 0.00 ± 0.00 0.01 ± 0.01 0.00 ± 0.00
[Ruminococcus] sp. 0.50 ± 0.16 0.00 ± 0.00 0.00 ± 0.00 0.00 ± 0.00
Dorea sp. 0.50 ± 0.19 0.00 ± 0.00 0.01 ± 0.01 0.00 ± 0.00
Family Lachnospiraceae 0.94 ± 0.21 1.56 ± 0.23 0.06 ± 0.02 0.22 ± 0.35
Roseburia sp. 6.86 ± 1.91 0.01 ± 0.00 0.00 ± 0.00 0.00 ± 0.00
Order Clostridiales Order Clostridiales 0.43 ± 0.12 0.13 ± 0.06 0.44 ± 0.15 0.70 ± 1.29
Peptostreptococcaceae Family Peptostreptococcaceae 0.02 ± 0.01 1.28 ± 0.21 0.00 ± 0.00 0.00 ± 0.00
Peptostreptococcus sp. 0.98 ± 0.21 0.01 ± 0.01 0.01 ± 0.01 0.00 ± 0.00
Ruminococcaceae Faecalibacterium prausnitzii 0.55 ± 0.42 0.00 ± 0.00 0.04 ± 0.02 0.00 ± 0.00
Family Ruminococcaceae 0.83 ± 0.16 0.01 ± 0.00 0.08 ± 0.04 0.11 ± 0.27
Ruminococcus sp. 0.55 ± 0.07 0.00 ± 0.00 0.00 ± 0.00 0.00 ± 0.00
Staphylococcaceae Staphylococcus sp. 1.29 ± 0.59 0.92 ± 0.87 0.19 ± 0.08 0.30 ± 0.25
Streptococcaceae Streptococcus sp. 3.59 ± 1.02 0.27 ± 0.05 0.37 ± 0.11 0.29 ± 0.46
Veillonellaceae Megasphaera sp. 0.63 ± 0.26 0.00 ± 0.00 0.03 ± 0.02 0.00 ± 0.00
Fusobacteria Fusobacteriaceae Fusobacterium sp. 11.68 ± 2.40 2.04 ± 0.32 0.12 ± 0.05 0.15 ± 0.37
Proteobacteria Alcaligenaceae Kerstersia gyiorum 0.00 ± 0.00 2.96 ± 2.80 1.76 ± 1.37 0.00 ± 0.00
Sutterella sp. 0.78 ± 0.17 0.00 ± 0.00 0.01 ± 0.01 0.00 ± 0.00
Bradyrhizobiaceae Family Bradyrhizobiaceae 0.06 ± 0.02 0.40 ± 0.06 15.83 ± 2.18 19.71 ± 2.30
Burkholderiaceae Lautropia sp. 0.00 ± 0.00 0.78 ± 0.15 0.00 ± 0.00 0.00 ± 0.00
Campylobacteraceae Campylobacter sp. 8.87 ± 3.32 0.19 ± 0.03 0.09 ± 0.05 0.00 ± 0.00
Cardiobacteriaceae Family Cardiobacteriaceae 0.00 ± 0.00 1.55 ± 0.36 0.02 ± 0.02 0.00 ± 0.00
Comamonadaceae Delftia sp. 0.03 ± 0.01 0.16 ± 0.06 0.68 ± 0.16 0.00 ± 0.00
Enterobacteriaceae Family Enterobacteriaceae 7.09 ± 1.57 0.01 ± 0.00 0.11 ± 0.05 0.00 ± 0.00
Methylobacteriaceae Methylobacterium sp. 0.00 ± 0.00 0.00 ± 0.00 0.09 ± 0.03 0.99 ± 0.89
Moraxellaceae Acinetobacter johnsonii 0.11 ± 0.05 1.01 ± 0.35 3.48 ± 0.57 0.25 ± 0.28
Enhydrobacter sp. 0.00 ± 0.00 3.04 ± 0.77 0.06 ± 0.05 0.15 ± 0.37
Family Moraxellaceae 0.00 ± 0.00 0.99 ± 0.17 0.00 ± 0.00 0.00 ± 0.00
Moraxella sp. 0.01 ± 0.00 9.74 ± 1.42 0.28 ± 0.17 0.15 ± 0.37
Neisseriaceae Conchiformibius kuhniae 0.02 ± 0.01 8.61 ± 1.23 0.10 ± 0.08 0.10 ± 0.25
Family Neisseriaceae 0.00 ± 0.00 1.16 ± 0.14 0.03 ± 0.03 0.00 ± 0.00
Oxalobacteraceae Family Oxalobacteraceae 0.00 ± 0.00 0.00 ± 0.00 0.02 ± 0.01 0.00 ± 0.00
Pasteurellaceae Actinobacillus sp. 0.00 ± 0.00 0.77 ± 0.40 0.04 ± 0.02 0.00 ± 0.00
Family Pasteurellaceae 0.05 ± 0.03 11.77 ± 2.05 0.12 ± 0.10 0.05 ± 0.12
Pasteurella multocida 0.00 ± 0.00 3.45 ± 0.67 0.00 ± 0.00 0.10 ± 0.25
Pseudomonadaceae Pseudomonas sp. 1.18 ± 0.52 10.13 ± 3.67 33.90 ± 7.12 0.00 ± 0.00
Sphingomonadaceae Sphingobium sp. 0.09 ± 0.04 0.76 ± 0.29 2.51 ± 0.51 0.00 ± 0.00
Succinivibrionaceae Anaerobiospirillum sp. 2.87 ± 1.96 0.00 ± 0.00 0.01 ± 0.01 0.00 ± 0.00
Xanthomonadaceae Family Xanthomonadaceae 0.03 ± 0.01 0.36 ± 0.07 0.67 ± 0.14 0.00 ± 0.00
SR1 Phylum SR1 Phylum SR1 0.00 ± 0.00 1.03 ± 0.29 0.00 ± 0.00 0.00 ± 0.00