Table 1 Principal OTUs changed (FDR < 0.05) in faeces, ileum content and ileum mucosa samples between control pigs (Day 0) and Salmonella infected pigs (Day 2 post-infection).

From: Early Salmonella Typhimurium infection in pigs disrupts Microbiome composition and functionality principally at the ileum mucosa

	Phylum	Class	Family	Genus	Counts Control group^a	Counts Infected group^a	Scaling factor	Adjusted p-value^b
FAECES	Firmicutes	Clostridiales	Lachnospiraceae	Unclassified	1055	153	5.59	0.027
	Firmicutes	Clostridiales	Ruminococcaceae	Unclassified	8601	821	4.26	0.033
	Firmicutes	Erysipelotrichales	Erysipelotrichaceae	p-75-a5	3874	141	2.28	0.018
	Chlamydiae	Chlamydiales	Chlamydiaceae	Chlamydia	1	1580	2.23	0.008
	Firmicutes	Clostridiales	Ruminococcaceae	Unclassified	3273	22	1.69	0.008
	Firmicutes	Clostridiales	Ruminococcaceae	Unclassified	22	2529	0.39	0.008
	Firmicutes	Clostridiales	Mogibacteriaceae	Unclassified	0	344	0.25	0.025
	Proteobacteria	Tremblayales	Unclassified	Unclassified	9	570	−0.52	0.040
ILEUM CONTENT	Firmicutes	Lactobacillales	Lactobacillaceae	Lactobacillus mucosae	474	24	9.46	0.042
	Proteobacteria	Campylobacterales	Campylobacteraceae	Campylobacter	267	2	9.14	0.036
	Firmicutes	Lactobacillales	Streptococcaceae	Streptococcus	707	3	8.53	0.020
	Firmicutes	Clostridiales	Veillonellaceae	Megasphaera	312	0	7.35	0.017
	Firmicutes	Clostridiales	Veillonellaceae	Mitsuokella	1210	66	5.96	0.035
	Proteobacteria	Enterobacteriales	Enterobacteriaceae	Unclassified	0	690	−2.93	0.027
ILEUM MUCOSA	Firmicutes	Clostridiales	Lachnospiraceae	Clostridium	688	74	3.93	0.041
	Firmicutes	Clostridiales	Lachnospiraceae	Clostridium	802	83	3.71	0.037
	Firmicutes	Clostridiales	Veillonellaceae	Dialister	764	0	3.35	0.002
	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium	6456	4	3.05	1.081E-06
	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium	3132	1	3.04	1.022E-05
	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium	1767	3	3.02	1.565E-04
	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium	669	2	2.86	0.002
	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium	45161	38	2.67	1.695E-09
	Firmicutes	Lactobacillales	Lactobacillaceae	Lactobacillus	445	0	2.59	0.007
	Verrucomicrobia	Verrucomicrobiales	Verrucomicrobiaceae	Akkermansia	103	1691	−2.39	0.016
	Firmicutes	Clostridiales	Ruminococcaceae	Oscillospira	13	300	−2.84	0.032
	Bacteroidetes	Bacteroidales	Odoribacteraceae	Odoribacter	30	367	−4.51	0.035
	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium	4	537	−5.00	0.002
	Firmicutes	Lactobacillales	Streptococcaceae	Streptococcus	154	22415	−6.43	0.011
	Firmicutes	Clostridiales	Clostridiaceae	Candidatus Arthromitus	1	62633	−11.07	2.991E-08

^aNormalised counts of OTUs.
^bAdjusted p-value by false discovery rate.

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Table 1 Principal OTUs changed (FDR < 0.05) in faeces, ileum content and ileum mucosa samples between control pigs (Day 0) and Salmonella infected pigs (Day 2 post-infection).

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