Elina Säde

Background: Leuconostoc gelidum and Leuconostoc gasicomitatum have dual roles in foods. They may spoil cold-stored packaged foods but can also be beneficial in kimchi fermentation. The impact in food science as well as the limited number of publicly available genomes prompted us to create pangenomes and perform genomic taxonomy analyses starting from de novo sequencing of the genomes of 37 L. gelidum/L. gasicomitatum strains from our culture collection. Our aim was also to evaluate the recently proposed change in taxonomy as well as to study the genomes of strains with different lifestyles in foods. Methods: We selected as diverse a set of strains as possible in terms of sources, previous genotyping results and geographical distribution, and included also 10 publicly available genomes in our analyses. We studied genomic taxonomy using pairwise average nucleotide identity (ANI) and calculation of digital DNA-DNA hybridisation (dDDH) scores. Phylogeny analyses were done using the core gene set of 1141 single-copy genes and a set of housekeeping genes commonly used for lactic acid bacteria. In addition, the pangenome and core genome sizes as well as some properties, such as acquired antimicrobial resistance (AMR), important due to the growth in foods, were analysed. Results: Genome relatedness indices and phylogenetic analyses supported the recently suggested classification that restores the taxonomic position of L. gelidum subsp. gasicomitatum back to the species level as L. gasicomitatum. Genome properties, such as size and coding potential, revealed limited intraspecies variation and showed no attribution to the source of isolation. The distribution of the unique genes between species and subspecies was not associated with the previously documented lifestyle in foods. None of the strains carried any acquired AMR genes or genes associated with any known form of virulence. Conclusion: Genome-wide examination of strains confirms that the proposition to restore the taxonomic position of L. gasicomitatum is justified. It further confirms that the distribution and lifestyle of L. gelidum and L. gasicomitatum in foods have not been driven by the evolution of functional and phylogenetic diversification detectable at the genome level.

Although Enterococcus, Lactococcus, Lactobacillus, and Streptococcus have been in the core of lactic acid bacteria (LAB) studies, they do not cover the broad taxonomic and functional diversity known to date. This chapter deals with four LAB genera that are less well known because of one or several reasons: (i) they are relatively young genera among LAB, (ii) some species are rarely isolated because they require specific culture conditions, (iii) they are difficult to identify or distinguish from other LAB genera phenotypically, and/or (iv) they reside in underexplored habitats. However, these four genera have relevance to the food and health area. The description of the first genus, Pediococcus, is followed by the genus Leuconostoc. We continue the Leuconostocaceae family with Weissella and close the chapter with a description of Carnobacterium, the type genus of the Carnobacteriaceae.

Yersinia enterocolitica is currently divided into two subspecies: subsp. enterocolitica including highly pathogenic strains of biotype 1B and subsp. palearctica including nonpathogenic strains of biotype 1A and moderately pathogenic strains of biotypes 2–5. In this work, we characterized 162 Y. enterocolitica strains of biotype 1A and 50 strains of biotypes 2–4 isolated from human, animal and food samples by restriction fragment length polymorphism using the HindIII restriction enzyme. Phylogenetic relatedness of 20 representative Y. enterocolitica strains including 15 biotype 1A strains was further studied by the multilocus sequence analysis of four housekeeping genes (glnA, gyrB, recA and HSP60). In all the analyses, biotype 1A strains formed a separate genomic group, which differed from Y. enterocolitica subsp. enterocolitica and from the strains of biotypes 2–4 of Y. enterocolitica subsp. palearctica. Based on these results, biotype 1A strains considered nonpathogenic should not be included in subspecies palearctica containing pathogenic strains of biotypes 2–5. Significance and Impact of the Study Yersinia enterocolitica strains are currently divided into six biotypes and two subspecies. Strains of biotype 1A, which are phenotypically and genotypically very heterogeneous, are classified as subspecies palearctica. In this study, European Y. enterocolitica 1A strains isolated from both human and nonhuman sources were characterized using restriction fragment length polymorphism and multilocus sequence analysis. The European biotype 1A strains formed a separate group, which differed from strains belonging to subspecies enterocolitica and palearctica. This may indicate that the current division between the two subspecies is not sufficient considering the strain diversity within Y. enterocolitica.

Microorganisms associated with the roots of plants have an important function in plant growth and in carbon sequestration in soil. Rice cultivation is the second largest anthropogenic source of atmospheric CH₄, which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of which as root exudates that is consumed by microorganisms. A stable isotope probing (SIP) approach was used to differentiate between microorganisms using plant photosynthate or soil carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with ¹³CO₂ for ten days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with ¹³C. 30 OTUs were labeled and mostly corresponded to Proteobacteria (13 OTUs) and Verrucomicrobia (8 OTUs). These OTUs were affiliated with the α, β and δ classes of Proteobacteria, and the Spartobacteria and Opitutae classes of Verrucomicrobia. In general, different bacterial groups were labeled in the root and rhizosphere reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (∼20%) compared with rhizosphere (∼4%), indicating that a greater proportion of the active microbial community on the roots incorporated plant-derived carbon within the time frame of the experiment.