TABLE 3.
RFI-associated statistically significant microbial composition differences in the ileal and cecal digesta of pigs slaughtered at 134 days of age at three geographic locationsa
| Sample type | Phylumb | Family | Genus | Location(s)c | Significanced | Differencee |
|---|---|---|---|---|---|---|
| Ileum | Actinobacteria | Dietziaceae | Dietzia | ROI2 | F, G | ↑ |
| Microbacteriaceae | Leucobacter | ROI2 | G | ↑ | ||
| Micrococcaceae | Rothia | ROI2 | G | ↑ | ||
| Pseudonocardiaceae | Saccharopolyspora | ROI2 | F, G | ↑ | ||
| Bacteroidetes | S24.7 | Uncultured | ROI2 | G | ↑ | |
| Cyanobacteria | Gastranaerophilales, uncultured | Uncultured | ROI2 | P, F, G | ↑ | |
| Firmicutes | ROI2 | P | ↓ | |||
| Bacillaceae | Oceanobacillus | ROI2 | G | ↑ | ||
| Paucisalibacillus | ROI2 | G | ↑ | |||
| Paenibacillaceae | ROI2 | F | ↑ | |||
| Aerococcaceae | ROI2 | F | ↑ | |||
| Dolosicoccus | ROI2 | G | ↑ | |||
| Globicatella | ROI2 | G | ↑ | |||
| Enterococcaceae | Enterococcus | ROI2 | F, G | ↑ | ||
| Clostridiaceae 1 | Clostridium sensu stricto 1 | ROI1 | F, G | ↑ | ||
| Lachnospiraceae | Blautia | ROI2 | G | ↑ | ||
| Pseudobutyrivibrio | ROI2 | G | ↑ | |||
| Subdoligranulum | ROI2 | G | ↑ | |||
| vadinBB60 | Uncultured | ROI1 | G | ↓ | ||
| ROI2 | G | ↑ | ||||
| Erysipelotrichaceae | Turicibacter | ROI1 | F, G | ↑ | ||
| Solobacterium | ROI2 | G | ↑ | |||
| Veillonellaceae | Dialister | ROI2 | G | ↑ | ||
| Mitsuokella | ROI2 | G | ↑ | |||
| Planctomycetes | Planctomycetaceae | p1088 a5 gut group | ROI2 | P, F, G | ↑ | |
| Proteobacteria | Desulfovibrionaceae | Desulfovibrio | ROI2 | F, G | ↑ | |
| Helicobacteraceae | Helicobacter | ROI1 | F, G | ↓ | ||
| Pasteurellaceae | Actinobacillus | ROI2 | F, G | ↑ | ||
| Spirochaetae | Spirochaetaceae | Spirochaeta | ROI2 | G | ↑ | |
| Cecum | Actinobacteria | Microbacteriaceae | Microbacterium | ROI2 | F, G | ↑ |
| Coriobacteriaceae | Uncultured | ROI2 | F, G | ↑ | ||
| Bacteroidetes | Porphyromonadaceae | Paludibacter | ROI2 | G | ↑ | |
| RF16 | Uncultured | ROI1, ROI2 | F, G | ↑ | ||
| Rikenellaceae | ROI2 | F | ↑ | |||
| dgA 11 gut group | ROI2 | G | ↑ | |||
| RC9 gut group | ROI2 | G | ↑ | |||
| Cyanobacteria | 4c0d, uncultured | Uncultured | AT | P, F, G | ↑ | |
| Gastranaerophilales, uncultured | Uncultured | ROI2 | F, G | ↑ | ||
| Firmicutes | ROI1 | P | ↓ | |||
| Erysipelotrichaceae | Uncultured | ROI2 | F, G | ↑ | ||
| Asteroleplasma | ROI2 | G | ↑ | |||
| Family XIII | Uncultured | ROI2 | G | ↑ | ||
| Lachnospiraceae | Butyrivibrio | ROI2 | G | ↓ | ||
| Peptococcaceae | Peptococcus | ROI2 | F, G | ↑ | ||
| Ruminococcaceae | ROI2, AT | F | ↑ | |||
| Incertae sedis | ROI2 | G | ↑ | |||
| Oscillospira | ROI1 | G | ↓ | |||
| Papillibacter | ROI2 | G | ↑ | |||
| vadinBB60 | Uncultured | ROI2 | G | ↑ | ||
| Streptococcaceae | Streptococcus | ROI2 | F, G | ↓ | ||
| Veillonellaceae | Uncultured | ROI1 | F, G | ↓ | ||
| Lentisphaerae | RF12 gut group, uncultured | Uncultured | ROI2 | F, G | ↑ | |
| Proteobacteria | ROI1 | P | ↑ | |||
| Rhodospirillaceae | ROI1 | F | ↑ | |||
| Alcaligenaceae | Sutterella | ROI1 | F, G | ↑ | ||
| Oxalobacteraceae | Noviherbaspirillum | ROI2 | F, G | ↑ | ||
| GR WP33 58 | Uncultured | ROI2 | F, G | ↑ | ||
| Helicobacteraceae | Helicobacter | ROI2 | F, G | ↑ | ||
| Succinivibrionaceae | Ruminobacter | ROI1 | F, G | ↑ | ||
| Spirochaetes | Spirochaetaceae | Treponema | AT | G | ↓ | |
| Synergistetes | Synergistaceae | Pyramidobacter | ROI2 | F, G | ↑ | |
| Tenericutes | Anaeroplasmataceae | Anaeroplasma | ROI1 | F, G | ↑ | |
| NB1 n, uncultured | Uncultured | ROI2 | F, G | ↑ | ||
| Verrucomicrobia | Puniceicoccaceae | Puniceicoccus | ROI2 | P, F, G | ↑ | |
| vadinHA64, uncultured | Uncultured | ROI2 | F, G | ↑ | ||
| Verrucomicrobiaceae | Akkermansia | ROI1 | F, G | ↑ |
a
A total of 104 RFI-associated microbial composition differences were observed across the three geographic locations.
b
All phylum-level differences between high- and low-RFI pigs are shown in Fig. S2 in the supplemental material.
c
AT, Austria; ROI, Republic of Ireland (batches 1 and 2).
d
Significantly different (P < 0.05) at the phylum (P), family (F), and/or genus (G) level.
e
Arrows indicate relative-abundance differences in low-RFI pigs compared to high-RFI pigs at the same geographic location (↓, lower relative abundance; ↑, higher relative abundance).