Data_Sheet_1_Influence of dietary n-3 long-chain fatty acids on microbial diversity and composition of sows’ feces, colostrum, milk, and suckling piglets’ feces.docx

IntroductionVery little is known about the impact of n-3 long-chain fatty acids (n-3 LCFAs) on the microbiota of sows and their piglets. The aim of this study was to evaluate the effect of n-3 LCFA in sow diets on the microbiota composition of sows’ feces, colostrum, and milk as well as that of piglets’ feces.MethodsTwenty-two sows were randomly assigned to either a control or an n-3 LCFA diet from service to weaning. Sows’ and piglets’ performance was monitored. The gestating and lactating sows’ microbiomes in feces, colostrum, and milk were characterized by 16s ribosomal RNA gene sequencing. The fecal microbiome from the two lowest (>800 g) and the two highest birth weight piglets per litter was also characterized, and the LPS levels in plasma were analyzed at weaning.Results and Discussionn-3 LCFA increased microbiota alpha diversity in suckling piglets’ and gestating sows’ feces. However, no effects were observed in colostrum, milk, or lactating sows’ feces. Dietary n-3 LCFA modified the microbiota composition of gestating sows’ feces, milk, and suckling piglets’ feces, without affecting lactating sows’ feces or colostrum. In gestating sows’ feces and milk, the decrease in genus Succinivibrio and the increase of Proteobacteria phylum, due to the increased genera Brenneria and Escherichia, respectively, stand out. In the feces of suckling piglets, the higher abundance of the beneficial genus Akkermansia and Bacteroides, and different species of Lactobacillus are highlighted. In addition, positive correlations for families and genera were found between lactating sows’ feces and milk, milk and suckling piglets’ feces, and lactating sows’ feces and suckling piglets’ feces. To conclude, dietary n-3 LCFA had a positive impact on the microbiome of suckling piglet’s feces by increasing microbial diversity and some beneficial bacteria populations, had a few minor modifications on the microbiome of milk and gestating sows’ feces and did not change the microbiome in lactating sows’ feces or colostrum. Therefore, this study shows the effect of dietary n-3 LCFA on the microbiota of sows, colostrum, milk, and suckling piglets during the lactation period providing crucial information on the microbiota status at the early stages of life, which have an impact on the post-weaning.</p

Distribution of virulence-associated gene profiles, phylogeny, serotyping and MLST results among all 32 strains.

<p>Phylo, phylogroup; ST, sequence type; Cplx, clonal complex. Adhesins <i>fimH</i> (D-mannose-specific adhesin of type I fimbriae), <i>fimAvMT78</i> (FimA variant MT78 of type 1 fimbriae), <i>papEF</i> and <i>papG</i> (P fimbria subunits), and <i>sfa/focDE</i> (S fimbrial adhesin/putative F1C fimbrial adhesin); toxins <i>cdtB</i> (cytolethal distending toxin), <i>hlyF</i> (hemolysin F), and <i>astA</i> (EAST1, enteroaggregative E. coli heat-stable toxin); siderophores fyuA (yersiniabactin), <i>iutA</i> (aerobactin), <i>iroN</i> (novel catecholate siderophore receptor), and <i>irp-2</i> (iron repressible associated with yersiniabactin synthesis); protectins <i>kpsM</i> (groups II and III, specifically targeting the K1, K2 and K5 genes of group II capsules), <i>cvaC</i> (ColV, colicin V from serum resistance-associated plasmids), <i>iss</i> (surface exclusion serum survival protein), and <i>traT</i> (serum resistance); miscellaneous virulence genes <i>ompT</i> (protease), <i>ibeA</i> (invasion of brain endothelium), <i>malX</i> (PAI, pathogenicity island marker), and <i>usp</i> (uropathogenic-specific protein, bacteriocin).</p><p>^a Virulence-associated genes shown in boldface are the five genes characteristics of APEC strains.</p><p>Distribution of virulence-associated gene profiles, phylogeny, serotyping and MLST results among all 32 strains.</p

Distribution and characterization of virulence-associated genes and phylogroups of the 32 isolates.

<p>Adhesins <i>fimH</i> (D-mannose-specific adhesin of type I fimbriae), <i>fimAvMT78</i> (FimA variant MT78 of type 1 fimbriae), <i>papEF</i> and <i>papG</i> (P fimbria subunits), <i>sfa/focDE</i> (S fimbrial adhesin/putative F1C fimbrial adhesin), and <i>afa/draBC</i> (Dr antigen specific adhesin); toxins <i>cnf1</i> (cytotoxic necrotizing factor 1), <i>cdtB</i> (cytolethal distending toxin), <i>sat</i> (secreted autotransporter toxin), <i>hlyA</i> (α-hemolysin), <i>hlyF</i> (hemolysin F), and <i>astA</i> (EAST1, enteroaggregative E. coli heat-stable toxin); siderophores fyuA (yersiniabactin), <i>iutA</i> (aerobactin), <i>iroN</i> (novel catecholate siderophore receptor), and <i>irp-2</i> (iron repressible associated with yersiniabactin synthesis); protectins <i>kpsM</i> (groups II and III, specifically targeting the K1, K2 and K5 genes of group II capsules), <i>cvaC</i> (ColV, colicin V from serum resistance-associated plasmids), <i>iss</i> (surface exclusion serum survival protein), and <i>traT</i> (serum resistance); miscellaneous virulence genes <i>ompT</i> (protease), <i>ibeA</i> (invasion of brain endothelium), <i>malX</i> (PAI, pathogenicity island marker), and <i>usp</i> (uropathogenic-specific protein, bacteriocin).</p><p>^a Virulence-associated genes shown with asterisk are the five genes characteristics of APEC strains.</p><p>^b<i>P</i> values (by Fisher’s exact test) are shown where P<0.05.</p><p>^c The virulence score was the number of virulence genes detected, adjusted for multiple detection of the <i>pap</i>, <i>sfa</i> and <i>foc</i>, and <i>kpsM</i> II operons. Virulence scores were compared by use of the Mann-Whitney U test.</p><p>Distribution and characterization of virulence-associated genes and phylogroups of the 32 isolates.</p

Identification and characterisation of the location of <i>bla</i>_CTX-M-14, <i>bla</i>_SHV-2, <i>bla</i>_SHV-12, <i>bla</i>_CMY-2 and <i>bla</i>_TEM among 11 cephalosporin resistant <i>E</i>. <i>coli</i> isolates.

<p>p(ST number), plasmid location; Inc, identified replicon.</p><p>^a Isolates are divided in APEC (N) and AFEC (GN) strains.</p><p>^b Replicon identifications are based on positive amplifications from the PCR-based replicon typing method.</p><p>^c Plasmids were named based on the source strains sequence type and plasmid size.</p><p>^d In all <i>E</i>. <i>coli</i> isolates, replicons from plasmids containing the different <i>bla</i> genes were identified by PCR-positive amplification and by Southern hybridisation of the S1-digested fragments.</p><p>Identification and characterisation of the location of <i>bla</i>_CTX-M-14, <i>bla</i>_SHV-2, <i>bla</i>_SHV-12, <i>bla</i>_CMY-2 and <i>bla</i>_TEM among 11 cephalosporin resistant <i>E</i>. <i>coli</i> isolates.</p