TABLE 2.
RFI-associated statistically significant microbial composition differences in the feces of pigs at three geographic locationsa
| Time point | Phylumb | Family | Genus | Location(s)c | Significanced | Differencee |
|---|---|---|---|---|---|---|
| Day 70 of age | Bacteroidetes | S24.7 | Uncultured | NI | F, G | ↓ |
| AT | G | ↑ | ||||
| Deferribacteres | Deferribacteraceae | Mucispirillum schaedleri | AT | P, G | ↑ | |
| Mucispirillum | NI | F, G | ↑ | |||
| AT | G | ↑ | ||||
| Day 134 of age | Firmicutes | Family XIII | Mogibacterium | NI | G | ↓ |
| Lachnospiraceae | Roseburia | NI | G | ↑ | ||
| Ruminococcaceae | Incertae sedis | ROI1 | G | ↓ | ||
| Uncultured | NI | G | ↓ | |||
| Erysipelotrichaceae | Uncultured | NI | G | ↓ | ||
| Planctomycetes | Planctomycetaceae | ROI2 | F | ↑ | ||
| SHA.109 | Uncultured | Uncultured | ROI2 | P, F, G | ↑ | |
| Spirochaetes | Spirochaetaceae | Treponema brennaborense | AT | G | ↑ | |
| Verrucomicrobia | ROI1 | P | ↓ | |||
| ROI1 | P | ↑ | ||||
| Euryarchaeota | Methanobacteriaceae | AT | F | ↑ | ||
| Methanobrevibacter | ROI1, ROI2 | G | ↑ | |||
| BS11.gut.group | Uncultured | ROI2 | F, G | ↑ | ||
| Prevotellaceae | Alloprevotella | ROI2 | G | ↓ | ||
| Bacteroidetes | RF16 | Uncultured | ROI1 | F, G | ↑ | |
| AT | G | ↑ | ||||
| Rikenellaceae | Alistipes | ROI2 | G | ↑ | ||
| Uncultured | Uncultured | ROI1 | F, G | ↓ | ||
| Candidate division TM7 | Unknown family | “Candidatus Saccharimonas” | ROI2 | P, F, G | ↓ | |
| Cyanobacteria | Uncultured | Uncultured | ROI1 | F, G | ↑ | |
| Firmicutes | Defluviitaleaceae | Uncultured | ROI1 | P, F, G | ↓ | |
| Family XI | Sedimentibacter | ROI2 | F, G | ↑ | ||
| Family XIII | Uncultured | ROI2 | F, G | ↑ | ||
| Lachnospiraceae | Lachnospira | ROI1 | G | ↓ | ||
| Marvinbryantia | ROI2 | G | ↓ | |||
| Oribacterium | NI | G | ↑ | |||
| ROI1 | G | ↓ | ||||
| Pseudobutyrivibrio | NI | G | ↑ | |||
| Ruminococcaceae | Faecalibacterium | ROI2 | G | ↓ | ||
| Papillibacter | ROI2 | G | ↑ | |||
| Ruminococcus | NI | G | ↓ | |||
| Subdoligranulum | ROI2 | G | ↓ | |||
| vadinBB60 | Unidentified | ROI2 | F, G | ↑ | ||
| Uncultured | Unidentified | AT | G | ↑ | ||
| Erysipelotrichaceae | Asteroleplasma | ROI2 | G | ↓ | ||
| Incertae sedis | ROI1 | G | ↓ | |||
| Veillonellaceae | Allisonella | ROI1 | G | ↓ | ||
| Mitsuokella | ROI1 | G | ↓ | |||
| Selenomonas | ROI2 | G | ↓ | |||
| Uncultured | ROI2 | G | ↓ | |||
| ROI1, ROI2 | P | ↑ | ||||
| Lentisphaerae | RF12 gut group, uncultured | Uncultured | ROI1 | F, G | ↑ | |
| Uncultured rumen bacterium | ROI1 | F, G | ↑ | |||
| RF12 gut group, unidentified | Uncultured | ROI1 | F, G | ↑ | ||
| WCHB1.25, uncultured | Uncultured | ROI1 | F, G | ↑ | ||
| Proteobacteria | Neisseriaceae | Leeia | ROI1 | F, G | ↑ | |
| Succinivibrionaceae | Uncultured | ROI1 | G | ↑ | ||
| TA18, uncultured | Uncultured | ROI2 | F, G | ↑ | ||
| Desulfovibrionaceae | Desulfovibrio | AT | F, G | ↑ | ||
| Tenericutes | RF9, uncultured | Uncultured | AT | F, G | ↑ | |
| Verrucomicrobia | Verrucomicrobiaceae | Akkermansia | ROI1 | P, F, G | ↑ | |
A total of 84 RFI-associated microbial composition differences were observed in the feces across the three geographic locations: 9 phyla, 23 families, and 52 genera.
All phylum-level differences between high- and low-RFI pigs are shown in Fig. S2 in the supplemental material.
AT, Austria; NI, Northern Ireland; ROI, Republic of Ireland (batches 1 and 2).
Significantly different (P < 0.05) at the phylum (P), family (F), and/or genus (G) level.
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).