TABLE 3

The OTUs that were common to 90% of individuals within each species; taxonomic assignments were made using RDP classifier (see text for more details)

PhylumClassOrderFamilyGenus or speciesOTU_idIAVa
PositiveNegative
ProteobacteriaGammaproteobacteriaPasteurellalesPasteurellaceaeNew.ReferenceOTU552+
ProteobacteriaEpsilonproteobacteriaCampylobacteralesCampylobacteraceaeCampylobacter284123+
ProteobacteriaEpsilonproteobacteriaCampylobacteralesCampylobacteraceaeCampylobacterNew.ReferenceOTU451+
FusobacteriaFusobacteriiaFusobacterialesLeptotrichiaceaeNew.ReferenceOTU81
FusobacteriaFusobacteriiaFusobacterialesFusobacteriaceaeFusobacterium4439398
FirmicutesClostridiaClostridialesVeillonellaceaeVeillonella disparNew.ReferenceOTU568
FirmicutesClostridiaClostridialesNew.ReferenceOTU701+
BacteroidetesFlavobacteriiaFlavobacterialesFlavobacteriaceae1122504+
BacteroidetesBacteroidiaBacteroidalesPorphyromonadaceaeParabacteroidesNew.ReferenceOTU712
  • a IAV, whether that OTU was also found in 90% of all IAV+ or IAV birds.