Characterization of the bacterial gut microbiota of piglets suffering from new neonatal porcine diarrhoea

Hermann-Bank, Marie Louise; Skovgaard, Kerstin; Stockmarr, Anders; Strube, Mikael Lenz; Larsen, Niels; Kongsted, Hanne; Ingerslev, Hans-Christian; Mølbak, Lars; Boye, Mette

doi:10.1186/s12917-015-0419-4

BMC Veterinary Research

Table 2 Significant findings from the Gut Microbiotassay and 454 sequencing results displaying similar trends

From: Characterization of the bacterial gut microbiota of piglets suffering from new neonatal porcine diarrhoea

Primer set and respective 454 sequencing findings	Gut section estimate (ileum vs. colon)	Gut section p- value	Status estimate (diarrhoeic vs. healthy)	Status p -value	Gilt estimate (gilt vs. multiparous sow)	Gilt p -value	Percentage of diarrhoea estimate ^#	Percentage of diarrhoea p -value	Age estimate	Age p -value	Antibiotics estimate (treated vs. untreated)	Antibiotics p -value
Domain Bacteria B ²⁶⁸	0.12 [0.08,0.17]	<0.0001		NS		NS		NS	1.21 [1.01,1.44]	0.04		NS
Phylum Firmicutes ¹⁸³	2.37 [1.63,3.33]	<0.0001	0.58 [0.36,0.89]	0.02	0.55 [0.33,0.87]	0.01		NS	1.34 [1.13,1.59]	0.001		NS
Class Bacilli ¹²⁵	3.31 [1.98,5.20]	<0.0001	0.29 [0.18,0.46]	<0.0001		NS		NS	1.62 [1.27,2.03]	0.0001		NS
Genus *Enterococcus* ²⁷	3.51 [1.25,7.91]	0.02	24.15 [8.50,54.73]	<0.0001		NS		NS		NS		NS
species E. hirae (3.36/11.11)
species E. faecium (9.87/129.60)
species E. durans (15.57/255.00)
species E. mundtii (113.00/179.00)
Genus *Streptococcus* ⁴⁷	2.49 [1.53,3.82]	0.0002	0.09 [0.02,0.27]	0.0002	0.55 [0.29,0.93]	0.03	1.03 [1.01,1.05]	0.008	0.75 [0.62,0.90]	0.003		NS
species S. gallolyticus subsp. gallolyticus (0.29/0.22)
species S. alactolyticus (0.27/0.18)
species S. uberis (0.68/0.33)
Genus *Lactobacillus* ⁷⁹	4.97 [2.91,7.94]	<0.0001	0.29 [0.17,0.46]	<0.0001		NS		NS	1.75 [1.36,2.20]	<0.0001		NS
species L. acidophilus (0.35/0.06)
Family Clostridium cluster I ¹⁷	3.32 [1.37,6.79]	-	0.36 [0.04,1.39]	-		NS	1.03 [1.00,1.05]	0.04		NS		NS
species Cl. perfringens; ATCC 13124 (1.18/0.47)
Species *Cl. perfringens*	9.31 [3.40,20.66]	-	1.41 [0.51,3.16]	-		NS		NS	0.67 [0.49,0.90]	0.009		NS
Family Clostridium cluster IV ⁶⁴	0.12 [0.05,0.25]	<0.0001	0.13 [0.06,0.25]	<0.0001		NS		NS	1.41 [1.02,1.91]	0.04		NS
species Ruminococcus bromii (0.00/0.26)
Family Clostridium cluster XIV ⁸¹	0.08 [0.05,0.14]	<0.0001		NS		NS	0.99 [0.98,0.99]	0.001		NS		NS
species Roseburia inulinivorans (1.59/0.02)
Phylum Bacteroidetes ¹²⁶	0.02 [0.01,0.05]	-	0.12 [0.05,0.26]	-		NS		NS		NS		NS
Genus *Bacteroides* ⁶⁵	0.03 [0.01,0.07]	-	0.20 [0.08,0.43]	-		NS		NS		NS		NS
species Bacteroides pyogenes (0.02/0.33)^†
species Bacteroides rodentium (0.46/0.00)^†
species Bacteroides xylanisolvens (0.94/0.43)^†
species Porphyromonadaceae bacterium C941 (0.00/0.01)^†
Phylum Actinobacteria ⁷⁴	2.84 [1.64,4.60]	<0.0001	0.29 [0.17,0.46]	<0.0001		NS		NS	0.80 [0.65,0.99]	0.04		NS
species Bifidobacterium boum (0.41/0.06)
species Corynebacterium kutscheri (0.39/0.34)
Family Bifidobacteriaceae ¹²	2.56 [1.28,4.61]	0.007		NS		NS		NS		NS		NS
Phylum Fusobacteria ¹⁶	0.20 [0.10,0.34]	<0.0001	2.24 [1.11,4.05]	0.02		NS		NS	0.69 [0.53,0.88]	0.004	0.20 [0.05,0.52]	0.002
species F. mortiferum (2.25/1.21)
Class Beta- and Gammaproteobacteria ¹⁰⁹	2.54 [1.63,3.79]	<0.0001	0.72 [0.12,2.55]	-		NS		NS	0.69 [0.52,0.88]	-		NS
Family Enterobacteriaceae ⁸⁹	4.03 [2.50,6.16]	<0.0001	0.27 [0.04,1.02]	-	2.12 [1.09,3.75]	0.03		NS	0.54 [0.40,0.71]	-		NS
species Escherichia coli (8.61/6.22)
species E.coli; HQ219945.1.1457 (11.46/5.00)
species E. coli DEC8A (6.22/5.16)
Species *E. coli*	3.56 [2.05,5.76]	<0.0001	0.29 [0.02,1.26]	-	2.96 [1.39,5.56]	0.004		NS	0.58 [0.41,0.80]	-		NS
Class Deltaproteobacteria ¹		NS		NS		NS	0.98 [0.97,1.00]	0.04		NS	0.08 [0.00,0.48]	0.02
species Desulfovibrio piger (0.00/0.00)^†

Estimated fold changes as the estimates of the exponentiated effect parameter, corresponding 95% confidence intervals [], and p-values. Superscripted numbers equal the total number of OTUs belonging to the respective taxonomic group identified by sequencing amplicons generated by the Gut Microbiotassay. OTU-ratio between diarrhoeic and healthy piglets for ileum and colon, respectively, listed in parenthesis. ^†indicate a significant effect of interaction (Table 3). Species mark with † are not consistent findings. ^#Estimated fold changes for this category are calculated as: γ ^{percentage points}, where the parameter y from column 8 is the estimate of the exponential eβ of the estimated effect parameter β for diarrhoea in formula (1). The diarrhoeic percentage points range from 0 to 100.

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