Vagococcus proximus sp. nov. and Vagococcus intermedius sp. nov., originating from modified atmosphere packaged broiler meat.

During our studies on spoilage microbiomes of modified atmosphere packaged broiler meat, we isolated three strains (PNs007T, STAA11T and STAA25) of unknown identity. In this present polyphasic taxonomy study, including genome-based analyses, we discovered that these isolates represent two novel species belonging to the genus Vagococcus. In all phylogenetic analyses, PNs007T was positioned very close to Vagococcus fessus but both the average nucleotide identity (ANI; 89.5 %) and digital DNA-DNA hybridization (dDDH; 38.3 %) values distinguished it as a novel vagococcal species. STAA11T and STAA25 were genetically highly similar (16S rRNA, ANI and dDDH 100 %). The phylogenetic position of STAA11T was adjacent to but out of the cluster containing V. fessus, Vagococcus coleopterorum and PNs007T. According to the ANI (76.2-76.4 %) and dDDH (<22.6 %) values it also represented a novel vagococcal species. Phenotypic characteristics and chemotaxonomic properties of both novel species were typical for vagococci and they contained C16 : 0 (25.5-30.1 %) and C18 : 1 ω9c (67.3-73.0 %) as the major cellular fatty acids. The streptomycin-resistant genotype of STAA11T and STAA25 allowing the growth on streptomycin thallous acetate actidione medium was considered to result from a modification in codon 104 of the rpsL gene leading to P104A substitution. The ability of STAA11T and STAA25 to produce ammonia from arginine separated them from PNs007T, which did not show arginine deiminase activity. We propose the names Vagococcus proximus sp. nov. (type strain PNs007T=DSM 115185T=CCUG 76696T) and Vagococcus intermedius sp. nov. (type strain STAA11T=DSM 115183T=CCUG 76697T) for these novel species.

Marination increased tyramine levels in rainbow trout fillet strips packaged under modified atmosphere.

Marinades are increasingly used to manufacture raw fish products. In corresponding meats, marinating is known to have a major effect on the composition of the microbiome, but the effect of marinating on fish is not known as well. This knowledge gap prompted our study of the microbial ecology and amine formation in marinated and unmarinated modified atmosphere commercially packaged rainbow trout fillet strips. According to our findings, marination increased the maximum concentrations (7-8 log CFU/g) of psychrotrophic bacteria by one logarithmic unit and led to 5 times higher average tyramine concentrations than the corresponding unmarinated product. Instead, trimethylamine concentrations were 30 times higher in the unmarinated product than those in the marinated one. According to the 16 S rRNA sequence analyses, lactic acid bacteria (LAB) predominated in the marinated strips one day after the use-by date, whereas in the unmarinated strips Fusobacteriaceae and LAB were the dominating taxa. Based on the culture-dependent analysis, Latilactobacillus fuchuensis was the prevailing LAB in both products. Since the subset of L. fuchuensis strains tested was able to produce tyramine in vitro, we hypothesise that the use of the acidic marinade activated the production of tyrosine-decarboxylating enzymes in L. fuchuensis and led to the increased tyramine concentrations.

Metabolomics and bacterial diversity of packaged yellowfin tuna (Thunnus albacares) and salmon (Salmo salar) show fish species-specific spoilage development during chilled storage.

Microbial (colony counts, 16S rRNA gene amplification), chemical (pH, 1H NMR spectroscopy) and sensory changes in raw Atlantic Salmon (Salmo salar) and tuna (Thunnus albacares) fillets stored under vacuum at 3 °C were evaluated over a period of 12 days. Both species of fish are globally important and among the ten most consumed fishes in the world. Although the sensory analyses showed a decrease in the quality of both fish species, only the salmon fillets were considered spoiled at the end of the storage period. In salmon, trimethylamine was the main spoilage product and bacterial colony counts reached an average of 7.3 log10 cfu/g. The concentration of glucose decreased and the concentration of organic acids increased during storage revealing glucose fermentation. Photobacterium was the dominating genus in the salmon studied. In the tuna studied, the bacterial colony counts reached only an average of 4.6 log10 cfu/g. The dominating bacteria in tuna were Pseudomonas spp. Glucose levels did not decrease, suggesting that amino acids and lactate most likely acted as carbon sources for bacteria in tuna. In conclusion, the study revealed that salmon was clearly a more perishable fish than tuna.

Food Spoilage-Associated Leuconostoc, Lactococcus, and Lactobacillus Species Display Different Survival Strategies in Response to Competition.

Psychrotrophic lactic acid bacteria (LAB) are the prevailing spoilage organisms in packaged cold-stored meat products. Species composition and metabolic activities of such LAB spoilage communities are determined by the nature of the meat product, storage conditions, and interspecies interactions. Our knowledge of system level responses of LAB during such interactions is very limited. To expand it, we studied interactions between three common psychrotrophic spoilage LAB (Leuconostoc gelidum, Lactococcus piscium, and Lactobacillus oligofermentans) by comparing their time course transcriptome profiles obtained during their growth in individual, pairwise, and triple cultures. The study revealed how these LAB employed different strategies to cope with the consequences of interspecies competition. The fastest-growing bacterium, Le. gelidum, attempted to enhance its nutrient-scavenging and growth capabilities in the presence of other LAB through upregulation of carbohydrate catabolic pathways, pyruvate fermentation enzymes, and ribosomal proteins, whereas the slower-growing Lc. piscium and Lb. oligofermentans downregulated these functions. These findings may explain the competitive success and predominance of Le. gelidum in a variety of spoiled foods. Peculiarly, interspecies interactions induced overexpression of prophage genes and restriction modification systems (mechanisms of DNA exchange and protection against it) in Lc. piscium and Lb. oligofermentans but not in Le. gelidum Cocultivation induced also overexpression of the numerous putative adhesins in Lb. oligofermentans These adhesins might contribute to the survival of this slowly growing bacterium in actively growing meat spoilage communities.IMPORTANCE Despite the apparent relevance of LAB for biotechnology and human health, interactions between members of LAB communities are not well known. Knowledge of such interactions is crucial for understanding how these communities function and, consequently, whether there is any possibility to develop new strategies to interfere with their growth and to postpone spoilage of packaged and refrigerated foods. With the help of controlled experiments, detailed regulation events can be observed. This study gives an insight into the system level interactions and the different competition-induced survival strategies related to enhanced uptake and catabolism of carbon sources, overexpression of adhesins and putative bacteriocins, and the induction of exchange of genetic material. Even though this experiment dealt with only three LAB strains in vitro, these findings agreed well with the relative abundance patterns typically reported for these species in natural food microbial communities.

Lactobacillus oligofermentans glucose, ribose and xylose transcriptomes show higher similarity between glucose and xylose catabolism-induced responses in the early exponential growth phase.

BACKGROUND: Lactobacillus oligofermentans has been mostly isolated from cold-stored packaged meat products in connection with their spoilage, but its precise role in meat spoilage is unknown. It belongs to the L. vaccinostercus group of obligate heterofermentative lactobacilli that generally ferment pentoses (e.g. xylose and ribose) more efficiently than hexoses (e.g. glucose). However, more efficient hexose utilization can be induced. The regulation mechanisms of the carbohydrate catabolism in such bacteria have been scarcely studied. To address this question, we provided the complete genome sequence of L. oligofermentans LMG 22743(T) and generated time course transcriptomes during its growth on glucose, ribose and xylose. RESULTS: The genome was manually annotated and its main functional features were examined. L. oligofermentans was confirmed to be able to efficiently utilize several hexoses and maltose, which is, presumably, induced by its repeated cultivation with glucose in vitro. Unexpectedly, in the beginning of the exponential growth phase, glucose- and xylose-induced transcriptome responses were more similar, whereas toward the end of the growth phase xylose and ribose transcriptomes became more alike. The promoter regions of genes simultaneously upregulated both on glucose and xylose in comparison with ribose (particularly, hexose and xylose utilization genes) were found to be enriched in the CcpA- binding site. Transcriptionally, no glucose-induced carbon catabolite repression was detected. The catabolism of glucose, which requires initial oxidation, led to significant overexpression of the NAD(P)H re-oxidation genes, the upstream regions of which were found to contain a motif, which was highly similar to a Rex repressor binding site. CONCLUSIONS: This paper presents the second complete genome and the first study of carbohydrate catabolism-dependent transcriptome response for a member of the L. vaccinostercus group. The transcriptomic changes detected in L. oligofermentans for growth with different carbohydrates differ significantly from those of facultative heterofermentative lactobacilli. The mechanism of CcpA regulation, putatively contributing to the observed similarities between glucose- and xylose-induced transcriptome responses and the absence of stringent carbon catabolite control, requires further studies. Finally, the cell redox balance maintenance, in terms of the NAD(P)+/NAD(P)H ratio, was predicted to be regulated by the Rex transcriptional regulator, supporting the previously made inference of Rex-regulons for members of the Lactobacillaceae family.

Development of spoilage bacterial community and volatile compounds in chilled beef under vacuum or high oxygen atmospheres.

Research into microbial community development and metabolism is essential to understand meat spoilage. Recent years have seen the emergence of powerful molecular techniques that are being used alongside conventional microbiology approaches. This enables more accurate studies on meat spoilage. The aim of this study was to investigate the influence of packaging (under vacuum and in high oxygen atmosphere) on the development of microbial communities and metabolic activities at 6 °C by using culture-dependent (cultivation, ribotyping) and culture-independent (amplicon sequencing) methods. At the beginning of shelf life, the microbial community mostly consisted of Carnobacterium and Lactobacillus. After two weeks of storage, Lactococcus and Lactobacillus were the dominant genera under vacuum and Leuconostoc in high oxygen meat packages. This indicates that oxygen favoured the genus Leuconostoc comprising only heterofermentative species and hence potential producers of undesirable compounds. Also the number of volatile compounds, such as diacetyl, 1-octen-3-ol and hexanoic acids, was higher in high oxygen packages than under vacuum packages. The beef in high oxygen atmosphere packaging was detected as spoiled in sensory evaluation over 10 days earlier than beef under vacuum packaging. Leuconostoc gelidum, Lactococcus piscium, Lactobacillus sakei and Lactobacillus algidus were the most common species of bacteria. The results obtained from identification of the isolates using ribotyping and amplicon sequencing correlated, except for L. algidus, which was detected in both types of packaging by amplicon sequencing, but only in vacuum packaged samples using the culture-based technique. This indicates that L. algidus grew, but was not cultivable in high oxygen beef using the Nordic Committee on Food Analysis standard method.

Genome Sequence and Transcriptome Analysis of Meat-Spoilage-Associated Lactic Acid Bacterium Lactococcus piscium MKFS47.

Lactococcus piscium is a psychrotrophic lactic acid bacterium and is known to be one of the predominant species within spoilage microbial communities in cold-stored packaged foods, particularly in meat products. Its presence in such products has been associated with the formation of buttery and sour off-odors. Nevertheless, the spoilage potential of L. piscium varies dramatically depending on the strain and growth conditions. Additional knowledge about the genome is required to explain such variation, understand its phylogeny, and study gene functions. Here, we present the complete and annotated genomic sequence of L. piscium MKFS47, combined with a time course analysis of the glucose catabolism-based transcriptome. In addition, a comparative analysis of gene contents was done for L. piscium MKFS47 and 29 other lactococci, revealing three distinct clades within the genus. The genome of L. piscium MKFS47 consists of one chromosome, carrying 2,289 genes, and two plasmids. A wide range of carbohydrates was predicted to be fermented, and growth on glycerol was observed. Both carbohydrate and glycerol catabolic pathways were significantly upregulated in the course of time as a result of glucose exhaustion. At the same time, differential expression of the pyruvate utilization pathways, implicated in the formation of spoilage substances, switched the metabolism toward a heterofermentative mode. In agreement with data from previous inoculation studies, L. piscium MKFS47 was identified as an efficient producer of buttery-odor compounds under aerobic conditions. Finally, genes and pathways that may contribute to increased survival in meat environments were considered.

Production of buttery-odor compounds and transcriptome response in Leuconostoc gelidum subsp. gasicomitatum LMG18811T during growth on various carbon sources.

Leuconostoc gelidum subsp. gasicomitatum is a common spoilage bacterium in meat products packaged under oxygen-containing modified atmospheres. Buttery off-odors related to diacetyl/acetoin formation are frequently associated with the spoilage of these products. A whole-genome microarray study, together with gas chromatography (GC)-mass spectrometry (MS) analyses of the pathway end products, was performed to investigate the transcriptome response of L. gelidum subsp. gasicomitatum LMG18811(T) growing on semidefined media containing glucose, ribose, or inosine, which are essential carbon sources in meat. Generally, the gene expression patterns with ribose and inosine were quite similar, indicating that catabolism of ribose and nucleosides is closely linked. Diacetyl/acetoin concentrations as high as 110 or 470 µM were measured when growth was based on inosine or ribose, respectively. The gene expression results for pyruvate metabolism (upregulation of α-acetolactate synthase, downregulation of l-lactate dehydrogenase and pyruvate dehydrogenase) were as expected when diacetyl and acetoin were the end products. No diacetyl production (<7.5 µM) was detected with the glucose-containing medium, even though the cell counts of LMG18811(T) was 6 or 10 times higher than that on inosine or ribose, respectively. Although glucose was the most effective carbon source for the growth of L. gelidum subsp. gasicomitatum, utilization of inosine and ribose resulted in the production of the unwanted buttery-odor compounds. These results increase our understanding of which compounds are likely to enhance the formation of buttery odors during meat spoilage caused by L. gelidum subsp. gasicomitatum.

Significance of heme-based respiration in meat spoilage caused by Leuconostoc gasicomitatum.

Leuconostoc gasicomitatum is a psychrotrophic lactic acid bacterium (LAB) which causes spoilage in cold-stored modified-atmosphere-packaged (MAP) meat products. In addition to the fermentative metabolism, L. gasicomitatum is able to respire when exogenous heme and oxygen are available. In this study, we investigated the respiration effects on growth rate, biomass, gene expression, and volatile organic compound (VOC) production in laboratory media and pork loin. The meat samples were evaluated by a sensory panel every second or third day for 29 days. We observed that functional respiration increased the growth (rate and yield) of L. gasicomitatum in laboratory media with added heme and in situ meat with endogenous heme. Respiration increased enormously (up to 2,600-fold) the accumulation of acetoin and diacetyl, which are buttery off-odor compounds in meat. Our transcriptome analyses showed that the gene expression patterns were quite similar, irrespective of whether respiration was turned off by excluding heme from the medium or mutating the cydB gene, which is essential in the respiratory chain. The respiration-based growth of L. gasicomitatum in meat was obtained in terms of population development and subsequent development of sensory characteristics. Respiration is thus a key factor explaining why L. gasicomitatum is so well adapted in high-oxygen packed meat.

Family portrait of Bacillus cereus and Bacillus weihenstephanensis cereulide-producing strains.

Two thousand Bacillus cereus sensu lato isolates from food and environmental matrices were screened by PCR for the presence of cereulide-producing strains. This survey identified 73 potential emetic strains, most of which originated from non-random food and clinical samplings. None of the 460 Bacillus thuringiensis, Bacillus mycoides and Bacillus pseudomycoides strains were PCR-positive for the cereulide genetic determinants. The chromosomal and extrachromosomal gene pool diversity of a subset of 30 cereulide-producing strains was then assessed using multilocus sequence typing, large plasmid gel electrophoresis and Southern blot hybridization. The strain toxicity on boar sperm and cereulide production were also analysed. The most striking observation was the identification of two distinct clusters of cereulide-producing strains, with members of the second group (cluster II) identified as psychrotolerant B. weihenstephanensis able to grow at 8°C. Moreover, the location of the cereulide genetic determinants was shown to vary depending on the strain, indicating a probable genomic mobility.

Influence of type of food on the kinetics and overall production of Bacillus cereus emetic toxin.

Potato puree and penne pasta were inoculated with cereulide producing B. cereus 5964a and B. cereus NS117. Static incubation at 28 degrees C proved these two foods to be a better substrate for higher cereulide production (4,080 ng/g in puree and 3,200 ng/g in penne were produced by B. cereus 5964a during 48 h of incubation) compared with boiled rice (2,000 ng/g). This difference occurred despite B. cereus counts of more than 10(8) CFU/g in all three products. Aeration of cultures had a negative effect on cereulide production, causing concentrations more than 10-fold lower than in some statically incubated samples. Cereulide production remained undetectable in shaken milk, whereas it reached 1,140 ng/ml in statically incubated milk. At 12 and 22 degrees C, presence of background flora was also a determinative factor. A total B. cereus count of more than 106 CFU/ml did not necessarily lead to uniform cereulide production and was also dependent on the B. cereus strain involved. In this study, we confirm that a number of factors play a crucial role in the determination of the extent to which, if at all, cereulide will be produced. Among those, type of the food, temperature, pH, and whether additional aeration (via incubation on an orbital shaker) is induced had an important role. An important effect was also induced by the cereulide-producing strain involved.

Cereulide-producing strains of Bacillus cereus show diversity.

Producers of cereulide, the emetic toxin of Bacillus cereus, are known to constitute a specific subset within this species. We investigated physiological and genetic properties of 24 strains of B. cereus including two high cereulide producers (600-1,800 ng cereulide mg(-1) wet weight biomass), seven average producers (180-600 ng cereulide mg(-1) wet weight biomass), four low cereulide producers (20-160 ng cereulide mg(-1) wet weight biomass) and 11 non-producers representing isolates from food, food poisoning, human gut and environment. The 13 cereulide producers possessed 16S rRNA gene sequences identical to each other and identical to that of B. anthracis strains Ames, Sterne from GenBank and strain NC 08234-02, but showed diversity in the adk gene (two sequence types), in ribopatterns obtained with EcoRI and PvuII (three types of patterns), in tyrosin decomposition, haemolysis and lecithin hydrolysis (two phenotypes). The cereulide-producing isolates from the human gut represented two ribopatterns of which one was novel to cereulide-producing B. cereus and two phenotypes. We conclude that the cereulide-producing B. cereus are genetically and biochemically more diverse than hitherto thought.

Sperm bioassay for rapid detection of cereulide-producing Bacillus cereus in food and related environments.

A novel in vitro method, sperm micro assay for rapidly distinguishing cereulide, the emetic toxin producing Bacillus cereus from non-producers is described and its use for quantitating cereulide and screening large numbers of B. cereus strains/colonies evaluated. The assay is non-laborious and can be executed with equipment present in most laboratories. Boar spermatozoa, purchased as standard semen from artificial insemination suppliers, are used to detect toxicity. Boar sperms respond within 5 min by cessation of motility when exposed at 37 degrees C to heat-treated (100 degrees C) extract prepared from a cereulide containing B. cereus. The assay can be done on individual colonies on the primary plate, with no need for pure culture and the qualitative result is obtained within 30 min. The assay is robust, not sensitive to age or storage of the culture plates. The use of the sperm micro assay for semiquantitative estimation of cereulide in B. cereus was validated with 14 different B. cereus strains using as reference the specific chemical assay for cereulide, based on liquid chromatography-ion trap mass spectrometry (LC-ion trap MS). The cereulide contents calculated from endpoint dilutions of the sperm micro assay matched the result of the chemical analysis closely. The detection threshold of the sperm micro assay was measured as 0.3 +/- 0.1 ng of cereulide per 5.4 x 10(6) sperm cells in 0.2 ml or 0.9 ng of cereulide per mg of B. cereus biomass (wet wt.). Food-related B. cereus strains contained 4-400 ng of cereulide per mg (wet wt.). When a large number of B. cereus of food, non-food, clinical and environmental origins were screened and 107 independent strains/isolates were identified as cereulide producers, it was observed that all of these had low or no haemolytic activity when cultivated on bovine blood agar. None of the strains/isolates with wide, clear zones of haemolysis, considered typical of B. cereus, produced cereulide.

Differentiated Paju cells have increased resistance to toxic effects of potassium ionophores.

In this study we have investigated the impact of differentiation of neuronal cells on their sensitivity to microbial toxins. We used the human neural crest-derived tumor cell line Paju, which can be induced to differentiation in vitro by treatment with phorbol 12-myristate 13-acetate. Addition of the highly toxic potassium ionophores cereulide (4.5 and 9.0 ng/ml) or valinomycin (20 ng/ml), to cultures of undifferentiated Paju cells caused collapse of the mitochondrial membrane potential - measured with the fluorescent probe 5,5',6,6'-tetrachloro-1,1',3,3'-tetrabenzimidazole carbocyanine iodide (JC-1) followed by detachment of the cells and their apoptotic death. After induced differentiation of the Paju cells, their mitochondria retained the membrane potential upon exposure to the toxins and the cells displayed increased resistance to apoptosis as compared with undifferentiated cells. This effect may be caused by an elevated expression of the anti-apoptotic protein Bcl-2 and of the neuroprotective factor, stanniocalcin, in differentiated cells.

Potential of Bacillus cereus for producing an emetic toxin, cereulide, in bakery products: quantitative analysis by chemical and biological methods.

A method for the direct quantitative analysis of cereulide, the emetic toxin of Bacillus cereus, in bakery products was developed. The analysis was based on robotized extraction followed by quantitation of cereulide by liquid chromatography-mass spectrometry and an assay of toxicity by the boar sperm motility inhibition test. The bioassay and the chemical assay gave comparable results, demonstrating that the extracted cereulide was in a biologically active form. Cereulide was formed when cereulide-producing B. cereus strains were present at > or = 10(6) CFU/g in products with water activity values of > 0.953 and pHs of > 5.6. Rice-containing pastries accumulated high contents of cereulide (0.3 to 5.5 microg/g [wet weight]) when stored at nonrefrigeration temperatures (21 to 23 degrees C). Cereulide was not formed in products stored at refrigeration temperatures (4 to 8 degrees C). Cereulide is not inactivated by heating during food processing. Therefore, direct analysis of this toxin in food is preferable to cultivating methods for assessing the risk of food poisoning by emetic B. cereus.