Culture-independent study on the co-occurrence of L. monocytogenes with other bacterial genera and bacterial diversity on cleaned conveyor surfaces in a swine slaughterhouse

<p><strong>Figure 1. </strong>Violin box plot representation of alpha diversity of bacterial OTUs from meat conveyor surfaces in a cutting facility from a swine slaughterhouse. a) Diversity was measured by Shannon diversity index and Shannon evenness index according to sampling visit, with medians compared using the Kruskall-Walis test. b) Diversity was measured by Shannon diversity index and Shannon evenness index according to <em>Listeria monocytogenes</em> culture status, with medians compared using the Wilcoxon test. Statistical significance: n.s.,<em> p</em>&gt; 0.05; *, <em>p</em>&lt;0.05; **, <em>p</em>&lt;0.01; ***<em>p</em>&lt;0.001.</p> <p><strong>Figure 2</strong>: Non-metric multidimensional scaling (NMDS) of Bray-Curtis and Jaccard distances of bacteria community identified using 16S Miseq sequencing technology on samples isolated from cutting facility conveyor-surfaces according to sampling visit (a and b) and <em>Listeria monocytogenes</em> culture status (c and d). Pairwise PERMANOVA with 999 permutations (using pseudo-F ratios) was used for all comparisons.</p> <p>&nbsp;</p> <p><strong>Figure 3</strong>: Relative frequency of different taxonomic profiles identified from OTUs in cutting-facility conveyor surfaces. a) Relative abundance of the top sixteen genera according to the sampling periods. b) Relative abundance of the top sixteen genera according to <em>L. monocytogenes</em> culture results.</p> <p>&nbsp;</p> <p><strong>Figure 4:</strong> Network construction based on Spearman correlation, Bray-Curtis dissimilarities, andKulback-Leibler dissimilarities. a) General network of all associations between genera clustered according to constant Potts model (communities sharing most links between each other). The size of each node refers to the abundance of the genus, the thickness of the link refers to its weight (presented here by the Spearman correlation coefficient), and the color of each node refers to the community (nodes with the same color belong to the same community). b) Network construction based on the direct associations between <em>Listeri</em>a genus and the other genera and indirect associations between those genera and others. Links colored in red represent negative associations between the genera while green links represent positive associations. The node labelled &ldquo;none&rdquo; refers to the unidentified genus from the Elusimicrobia phylum.</p> <p><strong>Supplementary material</strong></p> <p><strong>Supplementary Table 1: </strong>Sample identification with number of sequences, OTUs, <em>Listeria monocytogenes</em> culture-base status and Shannon measure and its evenness.</p> <p><strong>Supplementary Table 2: </strong>Total number of nodes and links resulting from the network construction based on the Spearman correlation, Bray-Curtis, and Kullback-leibler dissimilarities.</p> <p><strong>Supplementary Figure S1:</strong> Rarefaction curve of OTUs for each sample collected from meat conveyor surfaces.</p> <p><strong>Supplementary Figure S2:</strong> Relative frequency of bacterial species identified from OTUs detected in cutting-facility conveyor surfaces according to positive samples to <em>Listeria monocytogenes </em>culture-based method.</p>