Characterisation of aerobically grown non-spore-forming bacteria from paper mill pulps containing recycled fibres.

A total of 179 non-spore-forming bacteria aerobically growing on Nutrient Agar, Plate Count Agar or in specific enrichment conditions for salmonella, campylobacteria, listeria, yersinia or staphylococci, were isolated from 16 untreated paper mill pulps. After phenotypical screening the isolates were characterised by automated ribotyping and partial sequencing of the 16S rRNA gene. They could be divided into seven taxonomical classes representing 63 taxa (species): actinobacteria (11 species), bacilli (7), flavobacteria (3) alphaproteobacteria (10), betaproteobacteria (5), gammaproteobacteria (25) and sphingobacteria (2). Most of the gammaproteobacteria were enterobacteria, mainly species of the genera Enterobacter (7 species, 7 samples/3 mills) and Klebsiella (5 species, 6 samples/3 mills). Other commonly occurring bacteria were most closely related to Microbacterium barkeri (7 samples/3 mills), Cloacibacterium normanense (6 samples/2 mills), Pseudoxanthomonas taiwanensis (5 samples/2 mills) and Sphingobacterium composti (5 samples/1 mill). Sporadic isolates of Listeria innocua, L. monocytogenes, Enterococcus casseliflavus and Staphylococcus warneri were detected, from which only L. monocytogenes is considered to be a food pathogen. No isolates of the genera Campylobacter, Salmonella or Yersinia were detected. The detected bacteria may be harmful in process control, but the load of food pathogens with recycled fibres to paper machines is insignificant. Faecal contamination of the pulp samples was not indicated.

Intra-individual diversity and similarity of salivary and faecal microbiota.

In the present study, polyphasic analysis [cultivation, combined with the fingerprinting of individual isolates, and denaturing gradient gel electrophoresis (DGGE)] was applied to study whether similar features concerning the diversity and temporal stability of selected bacterial groups could be detected intra-individually in two different niches - the oral cavity and the colon - from ten adult volunteers consuming probiotics. The predominant bacterial microbiota, Clostridium coccoides-Eubacterium rectale group and bifidobacterial populations, were generally stable in salivary and faecal samples, with the greater diversity seen in faeces. Furthermore, different species predominated at the two different sites. Lactobacillus group DGGE profiles were unstable, yet the intra-individual profiles from faecal and salivary samples collected at the same time resembled each other. The ingested probiotic product did not affect the stability of the bacterial groups studied. The culture-based analysis showed that most subjects harboured identical indigenous Lactobacillus genotypes in saliva and faeces (Lactobacillus rhamnosus, Lactobacillus gasseri, Lactobacillus paracasei and Lactobacillus plantarum group). Thus, identical indigenous lactobacilli were able to inhabit both ends of the orogastrointestinal tract, whereas the composition of the other bacterial groups studied varied between the two sites.

Use of results of microbiological analyses for risk-based control of Listeria monocytogenes in marinated broiler legs.

Microbial risk assessment provides a means of estimating consumer risks associated with food products. The methods can also be applied at the plant level. In this study results of microbiological analyses were used to develop a robust single plant level risk assessment. Furthermore, the prevalence and numbers of Listeria monocytogenes in marinated broiler legs in Finland were estimated. These estimates were based on information on the prevalence, numbers and genotypes of L. monocytogenes in 186 marinated broiler legs from 41 retail stores. The products were from three main Finnish producers, which produce 90% of all marinated broiler legs sold in Finland. The prevalence and numbers of L. monocytogenes were estimated by Monte Carlo simulation using WinBUGS, but the model is applicable to any software featuring standard probability distributions. The estimated mean annual number of L. monocytogenes-positive broiler legs sold in Finland was 7.2x10(6) with a 95% credible interval (CI) 6.7x10(6)-7.7x10(6). That would be 34%+/-1% of the marinated broiler legs sold in Finland. The mean number of L. monocytogenes in marinated broiler legs estimated at the sell-by-date was 2 CFU/g, with a 95% CI of 0-14 CFU/g. Producer-specific L. monocytogenes strains were recovered from the products throughout the year, which emphasizes the importance of characterizing the isolates and identifying strains that may cause problems as part of risk assessment studies. As the levels of L. monocytogenes were low, the risk of acquiring listeriosis from these products proved to be insignificant. Consequently there was no need for a thorough national level risk assessment. However, an approach using worst-case and average point estimates was applied to produce an example of single producer level risk assessment based on limited data. This assessment also indicated that the risk from these products was low. The risk-based approach presented in this work can provide estimation of public health risk on which control measures at the plant level can be based.

Characterization of aerobic bacterial and fungal microbiota on surfaces of historic Scottish monuments.

Twenty samples were taken from the inner or outer surfaces of stone monuments of six historic Scottish buildings and ruins. Biofilms developing on mineral substrates were analysed by in situ scanning electron microscopy and cultivation. Various methods were used to characterize the isolates including automated ribotyping, RAPD and sequencing of the 16S rRNA gene for bacteria, and stereomicroscopy and sequencing of the Internal Transcribed Spacers (ITS) for fungi. Most samples contained microbes between 10(5) and 10(7)cfug(-1) substrate. Actinobacteria belonging to the genus Streptomyces (17 samples/5 monuments) or Arthrobacter (12/3) and Pseudomonas (9/3) were frequently detected. Most streptomycetes were in terms of their 16S rRNA gene sequence most closely related to S. microflavus (10/3) or to the undescribed species S. "vulgaris" (8/3). Indoor and outdoor biofilms exhibited significant differences in their microbiota, as shown by both microscopy and isolation studies. Pigmented coccoid Arthrobacter species were typical for the outdoor samples, whereas Pseudomonas species were common in the indoor samples. Based on the low phylogenetic relationship to a known species (type strain), potential novel pigmented bacterial species belonging to the genera Arthrobacter, Brevundimonas, Cryseobacterium, Deinococcus and Dyadobacter were detected from the outdoor samples and to Pseudomonas from the indoor samples. Hyaline fungal species of Acremonium (10/4) mainly occurred in indoor samples, whereas pigmented species of Cladosporium (8/3), Penicillium (6/3) and Phialophora (6/2) were found outdoors. Using in situ microscopy diatom algae were also detected.

Megasphaera paucivorans sp. nov., Megasphaera sueciensis sp. nov. and Pectinatus haikarae sp. nov., isolated from brewery samples, and emended description of the genus Pectinatus.

Seven unidentified strictly anaerobic, Gram-negative, non-spore-forming bacteria from spoiled beer or the brewery environment were characterized. Based on 16S rRNA gene sequence analyses, all strains were affiliated to the Sporomusa sub-branch of the class 'Clostridia'. Three of the strains were non-motile cocci, on average 1.5 x 1.2 microm or 1.2 x 1.0 microm, occurring mainly singly or in pairs. They shared nearly identical (>99 %) 16S rRNA gene sequences, being most closely related to the species of the Megasphaera-Anaeroglobus group (< or =93.9 % similarity). According to DNA-DNA hybridization results, the coccoid strains represented two genospecies, neither of which was related to any of the recognized Megasphaera species. Several phenotypic characteristics and/or DNA G+C content also differentiated the strains from each other and from their closest relatives. The other four novel strains were motile, slightly curved to helical rods, 0.6-0.8 x 3-50 microm or more in size. They shared identical 16S rRNA gene sequences and ribofragment patterns. The highest 16S rRNA gene similarity was found between these isolates and Pectinatus cerevisiiphilus ATCC 29359T (95.6 %) and Pectinatus frisingensis ATCC 33332T (93.6 %). The novel strains also differed from recognized Pectinatus species in their sugar utilization, proteolytic activity, catalase activity, antibiotic resistance and temperature tolerance. The results suggest that the bacteria belong to three novel species, for which the names Megasphaera paucivorans sp. nov. (type strain VTT E-032341T = DSM 16981T), Megasphaera sueciensis sp. nov. (type strain VTT E-97791T = DSM 17042T) and Pectinatus haikarae sp. nov. (type strain VTT E-88329T = DSM 16980T) are proposed.

Myceligenerans crystallogenes sp. nov., isolated from Roman catacombs.

Three xylan-degrading actinobacterial strains were isolated from different sampling sites in the Roman catacombs of Domitilla and San Callisto. The organisms showed morphological and chemotaxonomic properties such as peptidoglycan type A4alpha, L-lys-L-thr-D-Glu; whole-cell sugars (glucose, mannose and galactose); octa-, hexa- and tetrahydrogenated menaquinones with nine isoprene units; phosphatidylglycerol and diphosphatidylglycerol as the major phospholipids; anteiso-C(15 : 0), iso-C(15 : 0) and iso-C(16 : 0) as the predominant fatty acids; and a DNA G+C content of 72 mol%. These features are consistent with affiliation of these isolates to the genus Myceligenerans. The three isolates shared a 16S rRNA gene similarity of 99.9 % and were most closely related to Myceligenerans xiligouense DSM 15700T (97.9 % sequence similarity). The low level of DNA-DNA relatedness (about 14 %) and the differences in phenotypic characteristics between the novel strains and M. xiligouense DSM 15700T justify the proposal of a novel species of the genus Myceligenerans, Myceligenerans crystallogenes sp. nov., with CD12E2-27T (= HKI 0369T = DSM 17134T = NCIMB 14061T = VTT E-032285T) as the type strain.

Occurrence and molecular characterization of cultivable mesophilic and thermophilic obligate anaerobic bacteria isolated from paper mills.

The aim of this work was to characterize the cultivable obligate anaerobic bacterial population in paper mill environments. A total of 177 anaerobically grown bacterial isolates were screened for aerotolerance, from which 67 obligate anaerobes were characterized by automated ribotyping and 41 were further identified by partial 16S rDNA sequencing. The mesophilic isolates indicated 11 different taxa (species) within the genus Clostridium and the thermophilic isolates four taxa within the genus Thermoanaerobacterium and one within Thermoanaerobacter (both formerly Clostridium). The most widespread mesophilic bacterium was closely related to C. magnum and occurred in three of four mills. One mill was contaminated with a novel mesophilic bacterium most closely related to C. thiosulfatireducens. The most common thermophile was T. thermosaccharolyticum, occurring in all four mills. The genetic relationships of the mill isolates to described species indicated that most of them are potential members of new species. On the basis of identical ribotypes clay could be identified to be the contamination source of thermophilic bacteria. Automated ribotyping can be a useful tool for the identification of clostridia as soon as comprehensive identification libraries are available.

Typing of Listeria monocytogenes isolates originating from the food processing industry with automated ribotyping and pulsed-field gel electrophoresis.

A total of 486 Listeria monocytogenes isolates originating from 17 Finnish food processing plants (representing meat, poultry, fish, and dairy production) were collected and typed by automated ribotyping using EcoRI as the restriction enzyme. The isolates were divided into 16 different ribotypes (RTs). Some of these isolates (121), representing all EcoRI types and 16 food plants, were subjected to ribotyping with the PvuII enzyme, to pulsed-field gel electrophoresis (PFGE) typing with AscI and SmaI restriction enzymes, and to serotyping with O-antigen antisera. Nineteen ribotypes were generated with PvuII, 42 macrorestriction patterns were generated with AscI and 24 with SmaI, and three serotypes were generated with antisera. When the results were combined, the overall number of RTs was 23, and that of the PFGE types was 46. Thus, the overall discrimination power of PFGE was higher (discrimination index [DI] 0.966) than that of ribotyping (DI 0.906). The most common serotype (90.1% of the isolates) was 1/2, and isolates of serotype 4 (3.3%) were rare. There was no connection between food sectors and RTs or PFGE types, but PFGE indicated the single plants (78.3% of the types) better than ribotyping (56.5%). On the basis of its automation and on the availability of identification databases, automated ribotyping had some advantages over PFGE. Overall, automated ribotyping can be considered a practical and rapid tool when Listeria contamination is suspected and when screening a large number of isolates is necessary, e.g., when tracing contamination sources. However, in cases of outbreaks, the identical patterns must be confirmed by PFGE, which is a more discriminatory method.

Characterization of Listeria monocytogenes isolates from the meat, poultry and seafood industries by automated ribotyping.

A total of 564 Listeria monocytogenes isolates were characterized by automated ribotyping. The samples were taken from equipment, personnel and the environment after cleaning procedures and during food processing, as well as from raw materials and products from six meat, two poultry and five seafood processing plants located in the Faroe Islands, Finland, Iceland, Norway and Sweden. Altogether, 25 different ribotypes (RTs) were generated. Two RTs occurred in the samples from all three food sectors--meat, poultry and seafood. Four RTs occurred in meat and poultry plant samples and other four RTs occurred in meat and seafood plant samples. Five RTs occurred only in meat plant samples, five only in poultry plant samples and five only in seafood plant samples. Eight of the thirteen plants had their own in-house L. monocytogenes ribotype. There was geographical differences between the RTs, but no correlation between RTs and food sectors was detected. The discrimination power of automated ribotyping was satisfactory to trace the contamination sources in the food processing plants clearly indicating the sites at which improved cleaning procedures were necessary. In addition, it was possible to screen a large number of isolates with two instruments located at different institutes and to make a reliable combination of the results.