TABLE 3.

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

Taxon/biomarker	Comparison of patients positive vs patients negative to the indicated condition, performed with:
	Helicobacter sequences included in the analysis		Helicobacter sequences excluded from the analysis
	Trend	LEfSe P value	Trend	LEfSe P value
H. pylori infectionb
p_Actinobacteria, g_Propionibacterium	Increased	0.003	No
p_Bacteroidetes, g_Tannerella	Decreased	0.001	Decreased	0.009
p_Proteobacteria, g_Campylobacter	Increased	0.006	No
p_Proteobacteria, g_Enhydrobacter	Decreased	0.030	Decreased	0.043
p_Proteobacteria, g_Haemophilus	Increased	0.029	No
p_Bacteroidetes, g_Capnocytophaga	Increased	0.044	No
p_Bacteroidetes, g_Prevotella	Increased	0.013	No
p_Firmicutes, g_Bulleidia	Increased	0.011	No
p_Proteobacteria, g_Pseudomonas	Increased	0.049	No
p_Proteobacteria, g_Helicobacter	Increased	0.0001	No
p_Proteobacteria, g_Acinetobacter	Decreased	0.041	No
p_Firmicutes, g_Staphylococcus	Increased	0.042	No
p_Actinobacteria, g_Corynebacterium	Decreased	0.014	No
p_Firmicutes, g_Mogibacterium	Decreased	0.021	Decreased	0.040
p_Firmicutes, g_Dialister	Decreased	0.012	No
PPI treatmentc
p_Bacteroidetes, g_Capnocytophaga	Increased	0.048	No
p_Proteobacteria, g_Actinobacillus	Increased	0.028	No
p_Firmicutes, g_Granulicatella	Increased	0.003	No
p_Firmicutes, g_Veillonella	No		Increased	0.024
p_Firmicutes, g_Streptococcus	Increased	0.003	Increased	0.037

^aBold 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.

^bPatients 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.

^cPatients 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.