Complete Genome Sequences of Fish Pathogenic Weissella ceti Strains WS74 and WS105

The Weissella and Periweissella genera: up-to-date taxonomy, ecology, safety, biotechnological, and probiotic potential

Bacteria belonging to the genera Weissella and Periweissella are lactic acid bacteria, which emerged in the last decades for their probiotic and biotechnological potential. In 2015, an article reviewing the scientific literature till that date on the taxonomy, ecology, and biotechnological potential of the Weissella genus was published. Since then, the number of studies on this genus has increased enormously, several novel species have been discovered, the taxonomy of the genus underwent changes and new insights into the safety, and biotechnological and probiotic potential of weissellas and periweissellas could be gained. Here, we provide an updated overview (from 2015 until today) of the taxonomy, ecology, safety, biotechnological, and probiotic potential of these lactic acid bacteria.

Comparative polyphasic characterization of Weissella strains isolated from beaked whale and rainbow trout (Oncorhynchus mykiss): confirmation of Weissella ceti sp. nov. and description of the novel Weissella tructae sp. nov. isolated from farmed rainbow trout

The weissellosis agent bacterium (WS08T = CBMAI 2730) was isolated from diseased rainbow trout (Oncorhynchus mykiss) in Brazil. The whole genome sequence of this strain was compared with the Mexican W-1 strain, also isolated from diseased rainbow trout, and with the Weissella ceti type strain CECT 7719 T (= 1119-1A-09 T = CCUG 59653 T), recovered from the beaked whale. Digital DNA-DNA hybridization pairwise analyses scored 98.7% between the Mexican W-1 and Brazilian WS08T but just 24.4% for both fish isolates compared to the W. ceti type strain CECT 7719 T. The 16S rRNA gene sequence comparisons with isolates of W. ceti, available at GenBank, were conducted. All rainbow trout-pathogenic isolates grouped close (97% bootstrap confirmation), but when this group was compared to the W. ceti type strain CECT 7719 T the similarity varied from 78.9 to 79.1%. Phenotypic assays were also conducted, and the W. ceti type strain diverged from WS08T and W-1 in the hydrolysis of aesculin, D-mannose, and potassium gluconate and in the hydrolysis of hippurate. Moreover, WS08T and W-1 showed weak growth at 5 °C whereas no growth was observed for W. ceti CECT 7719 T. The major fatty acids (> 10% total fatty acids) presented by WS08T and W-1 were summed feature 8 (C18:1 ω7c/C18:1 ω6c), summed feature 3 (C16:1 ω6c/C16:1ω7c), and C16:0. The results of phylogenetic and phenotypic analyses clearly differentiated the W. ceti CECT 7719 T type strain from the assessed pathogenic strains obtained from rainbow trout. Therefore, Weissella strains isolated from rainbow trout, here represented by strain WS08T (= CBMAI 2730), should be known as members of a novel species for which the name Weissella tructae sp. nov. is proposed.

Complete Genome Sequence of Weissella cibaria NH9449 and Comprehensive Comparative-Genomic Analysis: Genomic Diversity and Versatility Trait Revealed

Lactic acid bacteria (LAB) in the genus Weissella spp. contain traits in their genome that confer versatility. In particular, Weissella cibaria encodes several beneficial genes that are useful in biotechnological applications. The complete genome of W. cibaria NH9449 was sequenced and an in silico comparative analysis was performed to gain insight into the genomic diversity among members of the genus Weissella. A total of 219 Weissella genomes were used in a bioinformatics analysis of pan-genomes, phylogenetics, self-defense mechanisms, virulence factors, antimicrobial resistance, and carbohydrate-active enzymes. These investigations showed that the strain NH9449 encodes several restriction-modification-related genes and a CRISPR-Cas region in its genome. The identification of carbohydrate-active enzyme-encoding genes indicated that this strain could be beneficial in biotechnological applications. The comparative genomic analysis reveals the very high genomic diversity in this genus, and some marked differences in genetic variation and genes among Weissella species. The calculated average amino acid identity (AAI) and phylogenetic analysis of core and accessory genes shows the possible existence of three new species in this genus. These new genomic insights into Weissella species and their biological functions could be useful in the food industry and other applications.

Draft Genome Sequence of Weissella confusa MBF8-1, a Glucansucrase- and Bacteriocin-Producing Strain Isolated from a Homemade Soy Product

We report here the draft genome sequence of Weissella confusa MBF8-1, an isolate from a homemade fermented soybean product that produces sucrases and exhibits antibacterial (bacteriocin) activity. The draft genome of W. confusa MBF8-1 comprises a 2.2-Mbp chromosome and a 17.8-kbp bacteriocin-encoding plasmid. Two putative glucansucrase genes were also identified.

Comparative genome analysis of Weissella ceti, an emerging pathogen of farm-raised rainbow trout

Background

The genus Weissella belongs to the lactic acid bacteria and includes 18 currently identified species, predominantly isolated from fermented food but rarely from cases of bacteremia in animals. Recently, a new species, designated Weissella ceti, has been correlated with hemorrhagic illness in farm-raised rainbow trout in China, Brazil, and the USA, with high transmission and mortality rates during outbreaks. Although W. ceti is an important emerging veterinary pathogen, little is known about its genomic features or virulence mechanisms. To better understand these and to characterize the species, we have previously sequenced the genomes of W. ceti strains WS08, WS74, and WS105, isolated from different rainbow trout farms in Brazil and displaying different pulsed-field gel electrophoresis patterns. Here, we present a comparative analysis of the three previously sequenced genomes of W. ceti strains from Brazil along with W. ceti NC36 from the USA and those of other Weissella species.

Results

Phylogenomic and orthology-based analyses both showed a high-similarity in the genetic structure of these W. ceti strains. This structure is corroborated by the highly syntenic order of their genes and the neutral evolution inferred from Tajima’s D. A whole-genome multilocus sequence typing analysis distinguished strains WS08 and NC36 from strains WS74 and WS105. We predicted 10 putative genomic islands (GEI), among which PAIs 3a and 3b are phage sequences that occur only in WS105 and WS74, respectively, whereas PAI 1 is species specific.

Conclusions

We identified several genes putatively involved in the basic processes of bacterial physiology and pathogenesis, including survival in aquatic environment, adherence in the host, spread inside the host, resistance to immune-system-mediated stresses, and antibiotic resistance. These data provide new insights in the molecular epidemiology and host adaptation for this emerging pathogen in aquaculture.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2324-4) contains supplementary material, which is available to authorized users.

The controversial nature of the Weissella genus: technological and functional aspects versus whole genome analysis-based pathogenic potential for their application in food and health

Despite the use of several Weissella (W.) strains for biotechnological and probiotic purposes, certain species of this genus were found to act as opportunistic pathogens, while strains of W. ceti were recognized to be pathogenic for farmed rainbow trout. Herein, we investigated the pathogenic potential of weissellas based on in silico analyses of the 13 whole genome sequences available to date in the NCBI database. Our screening allowed us to find several virulence determinants such as collagen adhesins, aggregation substances, mucus-binding proteins, and hemolysins in some species. Moreover, we detected several antibiotic resistance-encoding genes, whose presence could increase the potential pathogenicity of some strains, but should not be regarded as an excluding trait for beneficial weissellas, as long as these genes are not present on mobile genetic elements. Thus, selection of weissellas intended to be used as starters or for biotechnological or probiotic purposes should be investigated regarding their safety aspects on a strain to strain basis, preferably also by genome sequencing, since nucleotide sequence heterogeneity in virulence and antibiotic resistance genes makes PCR-based screening unreliable for safety assessments. In this sense, the application of W. confusa and W. cibaria strains as starter cultures or as probiotics should be approached with caution, by carefully selecting strains that lack pathogenic potential.