Characterization of the non-glandular gastric region microbiota in Helicobacter suis-infected versus non-infected pigs identifies a potential role for Fusobacterium gastrosuis in gastric ulceration

De Witte, Chloë; Demeyere, Kristel; De Bruyckere, Sofie; Taminiau, Bernard; Daube, Georges; Ducatelle, Richard; Meyer, Evelyne; Haesebrouck, Freddy

doi:10.1186/s13567-019-0656-9

Veterinary Research

Table 1 Overview of the main differences in relative abundance of taxa at phylum, family, genus and species level in the Pars oesophagea of the H. suis -positive and -negative pigs

From: Characterization of the non-glandular gastric region microbiota in Helicobacter suis-infected versus non-infected pigs identifies a potential role for Fusobacterium gastrosuis in gastric ulceration

Level	Taxa	H. suis +	H. suis −	p-value	Corrected p-value
Phylum	Fusobacteria	4.20 ± 1.02	1.26 ± 0.51	0.018	0.190
Family	Fusobacteriaceae	3.50 ± 0.83	0.94 ± 0.36	0.015	0.060
	Porphyromonadaceae	3.25 ± 0.51	0.19 ± 0.08	0.002	0.059
	Bacteroidaceae	0.25 ± 0.09	0.03 ± 0.02	0.028	0.206
	Clostridiaceae_1	18.02 ± 7.23	3.51 ± 1.44	0.045	0.262
	Gammaproteobacteriaceae_unclassified	2.02 ± 0.73	0.35 ± 0.19	0.021	0.177
	Actinobacteria_unclassified	0.00 ± 0.00	0.03 ± 0.01	0.005	0.051
	Bifidobacteriaceae	0.00 ± 0.00	0.13 ± 0.06	0.005	0.054
	Corynebacteriaceae	0.02 ± 0.01	0.27 ± 0.18	0.060	0.285
	Coriobacteriaceae	0.01 ± 0.01	0.10 ± 0.05	0.049	0.283
	Streptococcaceae	1.62 ± 0.84	2.38 ± 0.98	0.137	0.475
Genus	Fusobacterium	3.49 ± 0.83	0.94 ± 0.36	0.009	0.075
	Porphyromonas	2.51 ± 1.24	0.17 ± 0.07	0.007	0.073
	Porphyromonadaceae_unclassified	0.67 ± 0.34	0.02 ± 0.01	0.042	0.246
	Bacteroides	0.25 ± 0.09	0.03 ± 0.02	0.021	0.154
	Alloprevotella	3.66 ± 1.58	0.70 ± 0.35	0.034	0.219
	Clostridium_sensu_stricto_1	16.93 ± 6.80	3.03 ± 1.19	0.035	0.221
	Leuconostoc	0.02 ± 0.01	0.00 ± 0.00	< 0.001	0.019
	Pasteurella	0.03 ± 0.01	0.00 ± 0.00	0.003	0.042
	Gammaproteobacteria_unclassified	2.02 ± 0.73	0.35 ± 0.19	0.029	0.199
	Actinobacteria_unclassified	0.00 ± 0.00	0.03 ± 0.01	0.003	0.040
	Bifidobacterium	0.00 ± 0.00	0.13 ± 0.06	0.008	0.072
	Corynebacteriaceae_unclassified	0.00 ± 0.00	0.01 ± 0.00	0.038	0.236
	Lachnospiraceae_UCG-007	0.00 ± 0.00	0.02 ± 0.01	< 0.001	0.015
	Lachnospiraceae_XPB1014_group	0.00 ± 0.00	0.03 ± 0.02	0.004	0.045
	Staphylococcus	0.00 ± 0.00	0.02 ± 0.01	< 0.001	0.054
	Aerococcus	0.00 ± 0.00	0.11 ± 0.06	0.009	0.078
	Selenomonas	0.00 ± 0.00	0.30 ± 0.15	< 0.001	0.036
	Megasphaera	0.02 ± 0.01	1.14 ± 0.70	0.014	0.113
	Mitsuokella	0.01 ± 0.01	0.20 ± 0.08	0.011	0.091
	Veillonellaceae_unclassified	0.01 ± 0.01	0.42 ± 0.32	0.048	0.272
Species	Fusobacterium gastrosuis	3.11 ± 0.78	0.91 ± 0.35	0.015	0.068
	Porphyromonas_16S_OTU40	0.96 ± 0.37	0.04 ± 0.02	< 0.001	0.037
	Porphyromonas_16S_OTU24	1.36 ± 0.86	0.09 ± 0.04	0.041	0.595
	Porphyromonas_16S_OTU293	0.05 ± 0.02	0.01 ± 0.00	0.068	0.817
	Porphyromonadaceae_unclassified_16S_OTU1254	0.02 ± 0.01	0.00 ± 0.00	< 0.001	0.349
	Porphyromonadaceae_unclassified_16S_OTU61	0.50 ± 0.27	0.01 ± 0.01	0.041	0.600
	Porphyromonadaceae_unclassified_16S_OTU212	0.10 ± 0.07	0.00 ± 0.00	0.082	0.930
	Bacteroides_16S_OTU103	0.19 ± 0.09	0.02 ± 0.01	0.041	0.598
Species	Bacteroidales_unclassified_16S_OTU977	0.01 ± 0.00	0.00 ± 0.00	0.016	0.335
	Alloprevotella_16S_OTU50	0.74 ± 0.37	0.02 ± 0.01	0.026	0.475
	Alloprevotella_16S_OTU1438	0.02 ± 0.01	0.00 ± 0.00	0.069	0.822
	Clostridium_sensu_stricto_1_GQ249583	7.32 ± 2.86	1.26 ± 0.50	0.045	0.651
	Leuconostoc_16S_OTU708	0.02 ± 0.01	0.00 ± 0.00	< 0.001	0.047
	Pasteurella multocida	0.03 ± 0.01	0.00 ± 0.00	0.004	0.114
	Gammaproteobacteria_unidentified_16S_OTU46	0.30 ± 0.17	1.93 ± 0.69	0.045	0.424
	Bifidobacterium AB034094	0.00 ± 0.00	0.07 ± 0.03	0.035	0.537
	Bifidobacterium thermophilum	0.00 ± 0.00	0.05 ± 0.03	0.005	0.141
	Streptococcus_16S_OTU295	0.01 ± 0.01	0.08 ± 0.04	0.083	0.936
	Lachnospiraceae_UCG-007_16S_OTU727	0.00 ± 0.00	0.02 ± 0.01	< 0.001	1.278
	Lachnospiraceae_XPB1014_group_AB506358	0.00 ± 0.00	0.03 ± 0.02	0.003	0.093
	Staphylococcus EU341210	0.00 ± 0.00	0.01 ± 0.00	0.016	0.304
	Aerococcus suis	0.00 ± 0.00	0.09 ± 0.05	0.003	0.092
	Selenomonas bovis	0.00 ± 0.00	0.30 ± 0.15	< 0.001	0.046
	Megasphaera KF842421	0.00 ± 0.00	0.15 ± 0.08	< 0.001	0.034
	Megasphaera_16S_OTU1576	0.00 ± 0.00	0.02 ± 0.01	< 0.001	0.051
	Megasphaera_16S_OTU1120	0.00 ± 0.00	0.04 ± 0.01	0.011	0.260
	Megasphaera elsdenii	0.01 ± 0.01	0.82 ± 0.53	0.027	0.491
	Mitsuokella_16S_OTU1562	0.00 ± 0.00	0.01 ± 0.00	0.031	0.521
	Mitsuokella AB506409	0.00 ± 0.00	0.03 ± 0.01	0.041	0.602
	Mitsuokella AM500804	0.00 ± 0.00	0.03 ± 0.02	< 0.001	0.060
	Mitsuokella DQ797043	0.00 ± 0.00	0.08 ± 0.04	0.033	0.510
	Veilonellaceae_unclassified_16S_OTU715	0.00 ± 0.00	0.03 ± 0.01	< 0.001	0.035
	Veilonellaceae_unclassfied_16S_OTU1085	0.00 ± 0.00	0.02 ± 0.01	0.049	0.717

The data are presented as the mean relative abundance of the taxa with the standard error of the mean. Statistical differences were calculated using the non-parametric Kruskal–Wallis tests with Tukey post hoc tests and Benjamini–Hochberg False Discovery Rate were performed using STAMP. A corrected p-value lower than 0.05 is considered to be significant.

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