TABLE 3

Genus level taxa that were significantly changed in relation to the patients' conditions in gastric mucosal samplesa

Taxon/biomarkerComparison of patients positive vs patients negative to the indicated condition, performed with:
Helicobacter sequences included in the analysisHelicobacter sequences excluded from the analysis
TrendLEfSe P valueTrendLEfSe P value
H. pylori infectionb
    p_Actinobacteria, g_PropionibacteriumIncreased0.003No
    p_Bacteroidetes, g_TannerellaDecreased0.001Decreased0.009
    p_Proteobacteria, g_CampylobacterIncreased0.006No
    p_Proteobacteria, g_EnhydrobacterDecreased0.030Decreased0.043
    p_Proteobacteria, g_HaemophilusIncreased0.029No
    p_Bacteroidetes, g_CapnocytophagaIncreased0.044No
    p_Bacteroidetes, g_PrevotellaIncreased0.013No
    p_Firmicutes, g_BulleidiaIncreased0.011No
    p_Proteobacteria, g_PseudomonasIncreased0.049No
    p_Proteobacteria, g_HelicobacterIncreased0.0001No
    p_Proteobacteria, g_AcinetobacterDecreased0.041No
    p_Firmicutes, g_StaphylococcusIncreased0.042No
    p_Actinobacteria, g_CorynebacteriumDecreased0.014No
    p_Firmicutes, g_MogibacteriumDecreased0.021Decreased0.040
    p_Firmicutes, g_DialisterDecreased0.012No
PPI treatmentc
    p_Bacteroidetes, g_CapnocytophagaIncreased0.048No
    p_Proteobacteria, g_ActinobacillusIncreased0.028No
    p_Firmicutes, g_GranulicatellaIncreased0.003No
    p_Firmicutes, g_VeillonellaNoIncreased0.024
    p_Firmicutes, g_StreptococcusIncreased0.003Increased0.037
  • a Bold denotes genera whose relative abundance was found to change significantly when the linear discriminant analysis (LDA) effect size (LEfSe) method was applied in order to detect differentially abundant taxa among the patients' stomach bacterial communities, regardless of whether Helicobacter sequences were included or not included in the analysis. p_, phylum; g_, genus.

  • b Patients were categorized as positive or negative for the indicated condition, i.e., H. pylori (HP) infection, according to the results of conventional (nonsequencing) HP testing methods as specified in the text. Trends of increase or decrease for each taxon were calculated using the HP-negative patients as the reference group. Of the genera found to significantly differ in relative abundance among these patients, two genera, Mogibacterium (family Mogibacteriaceae) and Dialister (family Veillonellaceae), are members of the order Clostridiales.

  • c Patients were categorized as positive or negative for the indicated condition, i.e., proton-pump inhibitor (PPI) treatment, depending on whether they were, respectively, PPI users and PPI nonusers as specified in the text. Trends of increase or decrease for each taxon were calculated using the untreated patients (PPI nonusers) as the reference group. Of the genera found to significantly differ in relative abundance among these patients, two genera, Granulicatella (family Carnobacteriaceae) and Streptococcus (family Streptococcaceae), are members of the order Lactobacillales.