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 typePhylumbFamilyGenusLocation(s)cSignificancedDifferencee
IleumActinobacteriaDietziaceaeDietziaROI2F, G
MicrobacteriaceaeLeucobacterROI2G
MicrococcaceaeRothiaROI2G
PseudonocardiaceaeSaccharopolysporaROI2F, G
BacteroidetesS24.7UnculturedROI2G
CyanobacteriaGastranaerophilales, unculturedUnculturedROI2P, F, G
FirmicutesROI2P
BacillaceaeOceanobacillusROI2G
PaucisalibacillusROI2G
PaenibacillaceaeROI2F
AerococcaceaeROI2F
DolosicoccusROI2G
GlobicatellaROI2G
EnterococcaceaeEnterococcusROI2F, G
Clostridiaceae 1Clostridium sensu stricto 1ROI1F, G
LachnospiraceaeBlautiaROI2G
PseudobutyrivibrioROI2G
SubdoligranulumROI2G
vadinBB60UnculturedROI1G
ROI2G
ErysipelotrichaceaeTuricibacterROI1F, G
SolobacteriumROI2G
VeillonellaceaeDialisterROI2G
MitsuokellaROI2G
PlanctomycetesPlanctomycetaceaep1088 a5 gut groupROI2P, F, G
ProteobacteriaDesulfovibrionaceaeDesulfovibrioROI2F, G
HelicobacteraceaeHelicobacterROI1F, G
PasteurellaceaeActinobacillusROI2F, G
SpirochaetaeSpirochaetaceaeSpirochaetaROI2G
CecumActinobacteriaMicrobacteriaceaeMicrobacteriumROI2F, G
CoriobacteriaceaeUnculturedROI2F, G
BacteroidetesPorphyromonadaceaePaludibacterROI2G
RF16UnculturedROI1, ROI2F, G
RikenellaceaeROI2F
dgA 11 gut groupROI2G
RC9 gut groupROI2G
Cyanobacteria4c0d, unculturedUnculturedATP, F, G
Gastranaerophilales, unculturedUnculturedROI2F, G
FirmicutesROI1P
ErysipelotrichaceaeUnculturedROI2F, G
AsteroleplasmaROI2G
Family XIIIUnculturedROI2G
LachnospiraceaeButyrivibrioROI2G
PeptococcaceaePeptococcusROI2F, G
RuminococcaceaeROI2, ATF
Incertae sedisROI2G
OscillospiraROI1G
PapillibacterROI2G
vadinBB60UnculturedROI2G
StreptococcaceaeStreptococcusROI2F, G
VeillonellaceaeUnculturedROI1F, G
LentisphaeraeRF12 gut group, unculturedUnculturedROI2F, G
ProteobacteriaROI1P
RhodospirillaceaeROI1F
AlcaligenaceaeSutterellaROI1F, G
OxalobacteraceaeNoviherbaspirillumROI2F, G
GR WP33 58UnculturedROI2F, G
HelicobacteraceaeHelicobacterROI2F, G
SuccinivibrionaceaeRuminobacterROI1F, G
SpirochaetesSpirochaetaceaeTreponemaATG
SynergistetesSynergistaceaePyramidobacterROI2F, G
TenericutesAnaeroplasmataceaeAnaeroplasmaROI1F, G
NB1 n, unculturedUnculturedROI2F, G
VerrucomicrobiaPuniceicoccaceaePuniceicoccusROI2P, F, G
vadinHA64, unculturedUnculturedROI2F, G
VerrucomicrobiaceaeAkkermansiaROI1F, 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).