Browsing by Subject "bacteria"

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  • Harrison, Jesse P.; Chronopoulou, Panagiota-Myrsini; Salonen, Iines S.; Jilbert, Tom; Koho, Karoliina A. (2021)
    Metabarcoding analyses of bacterial and eukaryotic communities have been proposed as efficient tools for environmental impact assessment. It has been unclear, however, to which extent these analyses can provide similar or differing information on the ecological status of the environment. Here, we used 16S and 18S rRNA gene metabarcoding to compare eutrophication-induced shifts in sediment bacterial and eukaryotic community structure in relation to a range of porewater, sediment and bottom-water geochemical variables, using data obtained from six stations near a former rainbow trout farm in the Archipelago Sea (Baltic Sea). Shifts in the structure of both community types were correlated with a shared set of variables, including porewater ammonium concentrations and the sediment depth-integrated oxygen consumption rate. Distance-based redundancy analyses showed that variables typically employed in impact assessments, such as bottom water nutrient concentrations, explained less of the variance in community structure than alternative variables (e.g., porewater NH4+ inventories and sediment depth-integrated O2 consumption rates) selected due to their low collinearity (up to 40 vs. 58% of the variance explained, respectively). In monitoring surveys where analyses of both bacterial and eukaryotic communities may be impossible, either 16S or 18S rRNA gene metabarcoding can serve as reliable indicators of wider ecological impacts of eutrophication.
  • Keto-Timonen, R; Tolvanen, R; Lunden, J; Korkeala, H (2007)
    Contamination routes of Listeria monocytogenes were examined in a chilled food processing plant that produced ready-to-eat and ready-to-reheat meals during an 8-year period by amplified fragment length polymorphism (AFLP) analysis. A total of 319 L. monocytogenes isolates were recovered from raw materials (n=18), the environment (n=77), equipment (n=193), and products (n=31), and 18 different AFLP types were identified, five of which were repeatedly found to be persistent types. The three compartments (I to III) of the plant showed markedly different contamination statuses. Compartment I, which produced cooked meals, was heavily contaminated with three persistent AFLP types. AFLP type A1 dominated, and it comprised 93% of the isolates of the compartment. Compartment II, which produced uncooked chilled food, was contaminated with four persistent and five nonpersistent AFLP types. The equipment of compartment III, which produced cooked ready-to-reheat meals, was free of contamination. In compartments that produced cooked meals, the cleaning routines, product types, and lack of compartmentalization seemed to predispose production lines to persistent contamination. The most contaminated lines harbored L. monocytogenes in coolers, conveyors, and packing machines. Good compartmentalization limited the flow of L. monocytogenes into the postheat -treatment area and prevented the undesired movement of equipment and personnel, thus protecting the production lines from contamination. In compartment II, grated cheese was shown to cause product contamination. Therefore, special attention should be paid to continuous quality control of raw ingredients when uncooked ready-to-eat foods are produced. In compartment II, reconstruction of the production line resulted in reduced prevalence rates of L. monocytogenes and elimination of two persistent AFLP types.
  • Rinta-Kanto, J. M.; Pehkonen, K.; Sinkko, H.; Tamminen, M. V.; Timonen, S. (2018)
    In this study, the abundance and composition of prokaryotic communities associated with the inner tissue of fruiting bodies of Suillus bovinus, Boletus pinophilus, Cantharellus cibarius, Agaricus arvensis, Lycoperdon perlatum, and Piptoporus betulinus were analyzed using culture-independent methods. Our findings indicate that archaea and bacteria colonize the internal tissues of all investigated specimens and that archaea are prominent members of the prokaryotic community. The ratio of archaeal 16S rRNA gene copy numbers to those of bacteria was >1 in the fruiting bodies of four out of six fungal species included in the study. The largest proportion of archaeal 16S rRNA gene sequences belonged to thaumarchaeotal classes Terrestrial group, Miscellaneous Crenar-chaeotic Group (MCG), and Thermoplasmata. Bacterial communities showed characteristic compositions in each fungal species. Bacterial classes Gammaproteobacteria, Actinobacteria, Bacilli, and Clostridia were prominent among communities in fruiting body tissues. Bacterial populations in each fungal species had different characteristics. The results of this study imply that fruiting body tissues are an important habitat for abundant and diverse populations of archaea and bacteria.
  • Kaikkonen, Laura; Enberg, Sara; Blomster, Jaanika; Luhtanen, Anne-Mari; Autio, Riitta; Rintala, Janne-Markus (Springer Nature, 2020)
    Polar Biology 43 9 (2020)
    Marine microbial communities undergo drastic changes during the seasonal cycle in high latitude seas. Despite the dominance of microbial biomass in the oceans, comprehensive studies on the seasonal changes of microbial plankton during the complete winter period are lacking. To study the seasonal variation in abundance of the microbial community, water samples were collected weekly in the Northern Baltic Sea from October to May. During ice cover from mid-January to April, samples from the sea ice and the underlying water were taken in addition to the water column samples. Abundances of bacteria, virus-like particles, nanoflagellates, and chlorophyll a concentrations were measured from sea ice, under-ice water, and the water column, and examined in relation to environmental conditions. All studied organisms had clear seasonal changes in abundance, and the sea-ice microbial community had an independent wintertime development compared to the water column. Bacteria were observed to have a key role in the biotic interactions in both ice and the water column, and the dormant period during the cold-water months (October–May) was limited to before ice formation. Our results provide the first insights into the temporal dynamics of bacteria and viruses during the whole cold-water season (October–May) in coastal high latitude seas, and demonstrate that changes in the environmental conditions are likely to affect bacterial dynamics and have implications on trophic interactions.
  • Kallio, Tauno (Suomen metsätieteellinen seura, 1974)
  • Giaretta, Paula R.; Suchodolski, Jan S.; Jergens, Albert E.; Steiner, Jorg M.; Lidbury, Jonathan A.; Cook, Audrey K.; Hanifeh, Mohsen; Spillmann, Thomas; Kilpinen, Susanne; Syrja, Pernilla; Rech, Raquel R. (2020)
    The intestinal microbiota is believed to play a role in the pathogenesis of inflammatory bowel disease in humans and chronic inflammatory enteropathy (CIE) in dogs. While most previous studies have described the gut microbiota using sequencing methods, it is fundamental to assess the spatial distribution of the bacteria for a better understanding of their relationship with the host. The microbiota in the colonic mucosa of 22 dogs with CIE and 11 control dogs was investigated using fluorescence in situ hybridization (FISH) with a universal eubacterial probe (EUB338) and specific probes for select bacterial groups. The number of total bacteria labeled with EUB338 probe was lower within the colonic crypts of dogs with CIE compared to controls. Helicobacter spp. and Akkermansia spp. were decreased on the colonic surface and in the crypts of dogs with CIE. Dogs with CIE had increased number of Escherichia coli/Shigella spp. on the colonic surface and within the crypts compared to control dogs. In conclusion, the bacterial microbiota in the colonic mucosa differed between dogs with and without CIE, with depletion of the crypt bacteria in dogs with CIE. The crypt bacterial species that was intimately associated with the host mucosa in control dogs was composed mainly of Helicobacter spp.
  • Eronen-Rasimus, Eeva Liisa; Kaartokallio, Hermanni; Lyra, Christina; Autio, Riitta; Kuosa, Harri; Dieckmann, Gerhard S.; Thomas, David N. (2014)
  • Langenheder, Silke; Wang, Jianjun; Karjalainen, Satu Maaria; Laamanen, Tiina M.; Tolonen, Kimmo T.; Vilmi, Annika; Heino, Jani (2017)
    The spatial structure and underlying assembly mechanisms of bacterial communities have been studied widely across aquatic systems, focusing primarily on isolated sites, such as different lakes, ponds and streams. Here, our main aim was to determine the underlying mechanisms for bacterial biofilm assembly within a large, highly connected lake system in Northern Finland using associative methods based on taxonomic and phylogenetic alpha-and beta-diversity and a large number of abiotic and biotic variables. Furthermore, null model approaches were used to quantify the relative importance of different community assembly processes. We found that spatial variation in bacterial communities within the lake was structured by different assembly processes, including stochasticity, species sorting and potentially even dispersal limitation. Species sorting by abiotic environmental conditions explained more of the taxonomic and particularly phylogenetic turnover in community composition compared with that by biotic variables. Finally, we observed clear differences in alpha diversity (species richness and phylogenetic diversity), which were to a stronger extent determined by abiotic compared with biotic factors, but also by dispersal effects. In summary, our study shows that the biodiversity of bacterial biofilm communities within a lake ecosystem is driven by within-habitat gradients in abiotic conditions and by stochastic and deterministic dispersal processes.
  • Camarena‐Gómez, María Teresa; Ruiz‐González, Clara; Piiparinen, Jonna; Lipsewers, Tobias; Sobrino, Cristina; Logares, Ramiro; Spilling, Kristian (American Society of Limnology and Oceanography, 2021)
    Limnology and Oceanography 66: 1, 255-271
    In parts of the Baltic Sea, the phytoplankton spring bloom communities, commonly dominated by diatoms, are shifting toward the co-occurrence of diatoms and dinoflagellates. Although phytoplankton are known to shape the composition and function of associated bacterioplankton communities, the potential bacterial responses to such a decrease of diatoms are unknown. Here we explored the changes in bacterial communities and heterotrophic production during the spring bloom in four consecutive spring blooms across several sub-basins of the Baltic Sea and related them to changes in environmental variables and in phytoplankton community structure. The taxonomic structure of bacterioplankton assemblages was partially explained by salinity and temperature but also linked to the phytoplankton community. Higher carbon biomass of the diatoms Achnanthes taeniata, Skeletonema marinoi, Thalassiosira levanderi, and Chaetoceros spp. was associated with more diverse bacterial communities dominated by copiotrophic bacteria (Flavobacteriia, Gammaproteobacteria, and Betaproteobacteria) and higher bacterial production. During dinoflagellate dominance, bacterial production was low and bacterial communities were dominated by Alphaproteobacteria, mainly SAR11. Our results suggest that increases in dinoflagellate abundance during the spring bloom will largely affect the structuring and functioning of the associated bacterial communities. This could decrease pelagic remineralization of organic matter and possibly affect the bacterial grazers communities.
  • Pehkonen, Kati (Helsingfors universitet, 2013)
    Fungi play a crucial role in the ecosystem by recycling nutrients and forming mycorrhizal roots with plants. Many of the decomposer and mycorrhizal fungi are Bacidiomycetes. In the sexual reproduction stage, Bacidiomycetes produce fruiting bodies which enable them to produce and disseminate spores allowing fungi to spread to new growing sites. Fruiting bodies have been discovered to contain bacteria which may have a role in differentiation and maintenance of the fruiting body. They might also protect fruiting bodies against animals and diseases, and influence the nutritional value of the fruiting body. There is little knowledge about the amount of bacteria in the fruiting bodies. All previous research has been carried out entirely by cultivation-based methods and it shows that different fungal species contain very different amounts of bacteria. Some fruiting bodies have been shown not to contain easily cultivatable bacteria. The occurrence of archaea in fruiting bodies has not been previously studied and investigation into their function in fungi has only recently begun. In the present work significant amounts of bacterial and archaeal 16S rRNA -gene copies were discovered in the fruiting bodies of three ectomycorrhizal and three decomposer fungi species. This is the first time fruiting bodies have been shown to contain archaea. The occurrence of bacteria and archaea and the abundance of their 16S rRNA -genes in the fruiting bodies were determined using PCR ja quantitative PCR methods. Suillus bovinus and Boletus pinophilus fruiting bodies contained significantly more archaeal than bacterial gene copies. Cantharellus cibarius and Lycoperdon perlatum contained more bacterial than archaeal 16S rRNA -gene copies. In two decomposer fungi fruiting bodies, Agaricus arvensis and Piptoporus betulinus, the abundance of bacterial and archaeal gene copy numbers were equal. Suillus bovinus fruiting bodies had the largest copy number of archaeal 16S rRNA -genes from all species investigated. According to the results obtained in this work, the occurrence of bacteria and archaea might be common in fruiting bodies. The presence of bacteria and archaea in significant amounts in fruiting bodies may indicate their necessity for the development and sustainability of the fruiting body and hence to the whole life cycle of fungi.
  • Cairns, Johannes; Koskinen, Katariina; Penttinen, Reetta; Patinen, Tommi; Hartikainen, Anna; Jokela, Roosa; Ruusulehto, Liisa; Viitamäki, Sirja; Mattila, Sari; Hiltunen, Teppo; Jalasvuori, Matti (2018)
    Mobile genetic elements such as conjugative plasmids are responsible for antibiotic resistance phenotypes in many bacterial pathogens. The ability to conjugate, the presence of antibiotics, and ecological interactions all have a notable role in the persistence of plasmids in bacterial populations. Here, we set out to investigate the contribution of these factors when the conjugation network was disturbed by a plasmid-dependent bacteriophage. Phage alone effectively caused the population to lose plasmids, thus rendering them susceptible to antibiotics. Leakiness of the antibiotic resistance mechanism allowing Black Queen evolution (i.e. a "race to the bottom") was a more significant factor than the antibiotic concentration (lethal vs sublethal) in determining plasmid prevalence. Interestingly, plasmid loss was also prevented by protozoan predation. These results show that outcomes of attempts to resensitize bacterial communities by disrupting the conjugation network are highly dependent on ecological factors and resistance mechanisms. IMPORTANCE Bacterial antibiotic resistance is often a part of mobile genetic elements that move from one bacterium to another. By interfering with the horizontal movement and the maintenance of these elements, it is possible to remove the resistance from the population. Here, we show that a so-called plasmid-dependent bacteriophage causes the initially resistant bacterial population to become susceptible to antibiotics. However, this effect is efficiently countered when the system also contains a predator that feeds on bacteria. Moreover, when the environment contains antibiotics, the survival of resistance is dependent on the resistance mechanism. When bacteria can help their contemporaries to degrade antibiotics, resistance is maintained by only a fraction of the community. On the other hand, when bacteria cannot help others, then all bacteria remain resistant. The concentration of the antibiotic played a less notable role than the antibiotic used. This report shows that the survival of antibiotic resistance in bacterial communities represents a complex process where many factors present in real-life systems define whether or not resistance is actually lost.
  • Snellman, Marja (2007)
    Community-acquired pneumonia (CAP) is a severe disease and a major cause of death worldwide especially among the elderly. The most common causative pathogen is Streptococcus pneumoniae, pneumococcus. The diagnosis of pneumococcal pneumonia is difficult because there is no gold standard, a diagnostic test that would identify all cases and yet be definite. National Public Health Institute has launched a Finnish Community-Acquired Pneumonia study investigating the frequency and causes of CAP among the elderly aged 65 years and above. Sputum, urine, blood and nasopharyngeal swab samples are the collected from the subjects enrolled in the study and a large number of microbiological assays are performed on samples. One of the main objectives is to find a case definition for pneumococcal pneumonia in the elderly. For this purpose, the accuracy of diagnostic tests performed in the study need to be evaluated. In the absence of gold standard, the true disease status of the subjects is latent and the sensitivities and the specificities of the tests cannot be estimated using conventional methods. The aim of this thesis is to to estimate the sensitivities and the specificities of diagnostic tests and estimate the prevalence of pneumococcal pneumonia among the elderly population in Finland using latent class analysis. The method is applied to data collected in the Finnish Community-Acquired Pneumonia study. Methodological issues in latent class analysis are discussed. In addition, a function for estimating the model parameters using statistical program R is presented. The main sources are: Agresti, Alan 2002: Categorical Data Analysis. Wiley. New York. Hagenaars, Jacques A. 1990: Categorical Longitudinal Data. Sage Publication. London Formann, A. - Kohlmann, T. 1996: Latent class analysis in medical research. Statistical Methods in Medical Research, 5, 179-211.
  • Teittinen, Anette; Virta, Leena; Li, Mingjia; Wang, Jianjun (2021)
    Islands provide ideal model systems to examine the factors influencing biodiversity, yet knowledge of microbial biodiversity on islands remains scarce. We collected a dataset from 101 rock pools along a freshwater to brackish water transition on islands of the Baltic Sea and investigated the patterns and drivers of community composition and species richness of diatoms, cyanobacteria and non-cyanobacteria bacteria among islands. We also examined whether environmental heterogeneity increased beta diversity and species richness within islands. Among islands, the patterns in community composition were concordant among the microbial groups, with distinct changes along the freshwater-brackish gradient. The patterns in species richness were context-dependent for each microbial group. In general, richness patterns were most strongly associated with nutrient concentrations or the distances to potential sources of immigrants, whereas no positive relationships between ecosystem size and richness were found. Within islands, environmental heterogeneity was positively correlated with the beta diversity of each microbial group, but not species richness. Our findings provide novel insights into the factors influencing microbial biodiversity. The results suggest that island microbial biodiversity patterns are influenced by species sorting and dispersal-related mechanisms and highlight the importance of environmental heterogeneity for beta diversity.
  • Liu, Xinxin; Hui, Nan; Kontro, Merja H. (2020)
    The triazine herbicide atrazine easily leaches with water through soil layers into groundwater, where it is persistent. Its behavior during short-term transport is poorly understood, and there is no in situ remediation method for it. The aim of this study was to investigate whether water circulation, or circulation combined with bioaugmentation (Pseudomonassp. ADP, or four isolates from atrazine-contaminated sediments) alone or with biostimulation (Na-citrate), could enhance atrazine dissipation in subsurface sediment-water systems. Atrazine concentrations (100 mg L-1) in the liquid phase of sediment slurries and in the circulating water of sediment columns were followed for 10 days. Atrazine was rapidly degraded to 53-64 mg L(-1)in the slurries, and further to 10-18 mg L(-1)in the circulating water, by the inherent microbes of sediments collected from 13.6 m in an atrazine-contaminated aquifer. Bioaugmentation without or with biostimulation had minor effects on atrazine degradation. The microbial number simultaneously increased in the slurries from 1.0 x 10(3)to 0.8-1.0 x 10(8)cfu mL(-1), and in the circulating water from 0.1-1.0 x 10(2)to 0.24-8.8 x 10(4)cfu mL(-1). In sediments without added atrazine, the cultivable microbial numbers remained low at 0.82-8.0 x 10(4)cfu mL(-1)in the slurries, and at 0.1-2.8 x 10(3)cfu mL(-1)in the circulating water. The cultivated microorganisms belonged to the nine generaAcinetobacter,Burkholderia,Methylobacterium,Pseudomonas,Rhodococcus,Sphingomonas,Streptomyces,VariovoraxandWilliamsia; i.e., biodiversity was low. Water flow through the sediments released adsorbed and complex-bound atrazine for microbial degradation, though the residual concentration of 10-64 mg L(-1)was high and could contaminate large groundwater volumes from a point source, e.g., during heavy rain or flooding.
  • Lassila, Joose (Helsingin yliopisto, 2020)
    The aim of this study was to examine the leaf endophytic bacteria in Plantago lanceolata. The first aim was to get a comprehensive picture of the bacterial diversity, by screening for the different bacterial genera inside the leaves. Furthermore, I aimed to examine the effect of soil and maternal genotype on the endophytic community within P. lanceolata leaves and search for clues of vertical inheritance of endophytes from parent to offspring via seeds. I studied the endophytic bacteria by extracting DNA from the plant leaves and by trying to amplify any bacterial DNA present to get a view of the bacterial diversity in the leaves. My aim was to compare the bacterial community of the mother plants to that of their offspring and also to compare the bacterial communities of plants grown in different soil conditions. Furthermore, I tried to study how the soil conditions affect the growth of P. lanceolata seedlings. I collected seeds and leaf samples of P. lanceolata from Åland, Southwestern Finland, from a population that is part of the ongoing long-term metapopulation research started in Åland in the early 90’s. I marked 21 plant individuals (hereafter referred to as the “mother plants”) in the field in June, when collecting the first leaf samples. In August I collected all seeds from the same plant individuals and a second set of leaf samples. I also collected soil samples from the same location. With the seeds collected from the wild population I executed a growth experiment in Viikki, Helsinki. I grew one set of seeds in twice autoclaved sand (hereafter referred to as the “sterile soil”) and another set in twice autoclaved sand mixed with soil collected from the Åland population (hereafter referred to as the “environmental soil”). I surface sterilized all seeds and then sowed each in their own growth pot and placed them in a growth chamber. During the experiment I took measurements of the leaves. At end of the growth experiment, I took samples of the leaves and surface sterilized them to exclude any epiphytic microorganisms from the analysis. I also surface sterilized the leaf samples taken from the mother plants. I then extracted DNA from the leaf samples and run PCR to amplify certain regions of the bacterial 16S rDNA gene, that is widely used in bacterial taxonomy. The obtained DNA reads where then clustered into Operational Taxonomic Units (OTUs) and assigned taxonomy using SILVA reference database. Mitochondria and chloroplasts of eukaryotic organisms also harbour 16S rDNA regions, so the challenge of studies looking at endophytic bacteria is to exclude the 16S regions of mitochondria and chloroplasts. This proved to be a problem in my study also. More than 86% of all DNA reads obtained turned out to be from P. lanceolata mitochondria and more than 12% from P. lanceolata chloroplasts. Only a bit more than 1% of the reads were eubacterial. This effectively hindered reliable analysis of the endophyte community. I nevertheless analysed the observed eubacterial diversity although the results must be taken as only preliminary and with utmost caution. The eubacterial reads clustered into 218 OTUs, representing 71 different bacterial genera. Six most common genera constituted over 83% of eubacterial reads. Most of these bacteria, most notably Shewanella, Ralstonia and Halomonas, could be identified as being clearly contaminants and not real endophytes. For the 65 less common bacterial genera I performed community analysis using Bray-Curtis Dissimilarity index and Analysis of Similarities (ANOSIM). The results showed that there was a significant difference between the different soil treatments (P = 0.014, R = 0.3787) and also between the two growth chambers (P = 0.011, R = 0.5493). I found no effect of maternal genotype on the bacterial community. Therefore, I observed no sign of vertical inheritance of endophytes. The growth experiment results showed that germination percentage was significantly lower in the environmental soil than in the sterile soil for all genotypes (F = 10.78, P = 0.0012). However, seedling in the environmental soil grew bigger than the seedlings in the sterile soil (F = 10.91, P < 0.0001). For future studies on similar topics, validating molecular methods before large scale sequencing could yield more reliable results. Size fractionating the DNA products of the first PCR round could exclude most mitochondrial sequences and hence allow better analysis of endophytes. This would enable studying interesting questions on coevolution and ecology of host-endophyte interactions. Although I did find some differences in the bacterial communities of different treatments, these results must be considered with caution and as only preliminary.
  • Teittinen, Anette; Wang, Jianjun; Stromgard, Simon; Soininen, Janne (2017)
    Aim: Elevational biodiversity patterns are understudied in high-latitude aquatic systems, even though these systems are important for detecting very early impacts of climatic changes on Earth. The aim of this study was to examine the elevational trends in species richness and local contribution to beta diversity (LCBD) of three biofilm microbial groups in freshwater ponds and to identify the key mechanisms underlying these patterns. Location: One hundred and forty-six ponds in subarctic Finland and Norway distributed across the tree line along an elevational gradient of 10-1,038 m a.s.l., spanning from forested landscape to barren boulder fields. Time period: July-August 2015. Major taxa studied: Diatoms, cyanobacteria and non-cyanobacteria. Methods: Generalized linear models were used to identify the most important pond variables explaining richness and LCBD. Structural equation models were used to explore the direct and indirect effects of multiscale drivers on richness and LCBD. Results: Diatom and cyanobacteria richness showed unimodal elevational patterns, whereas non-cyanobacteria richness decreased with increasing elevation. The LCBD-elevation relationship was U-shaped for all three microbial groups. Diatom and cyanobacteria richness and LCBD were best explained by local pond variables, especially by pH. Non-cyanobacteria richness and LCBD were related to pond variables, elevation as a proxy for climatic conditions, and normalized difference vegetation index as a proxy for terrestrial productivity. Main conclusions: Aquatic autotrophs were primarily controlled by environmental filtering, whereas heterotrophic bacteria were also affected by terrestrial productivity and elevation. All studied aspects of microbial diversity were directly or indirectly linked to elevation; therefore, climatic changes may greatly alter aquatic microbial assemblages.
  • Valkonen, M.; Täubel, M.; Pekkanen, J.; Tischer, C.; Rintala, H.; Zock, J. -P.; Casas, L.; Probst-Hensch, N.; Forsberg, B.; Holm, M.; Janson, C.; Pin, I.; Gislason, T.; Jarvis, D.; Heinrich, J.; Hyvärinen, A. (2018)
    Microbial exposures in homes of asthmatic adults have been rarely investigated; specificities and implications for respiratory health are not well understood. The objectives of this study were to investigate associations of microbial levels with asthma status, asthma symptoms, bronchial hyperresponsiveness (BHR), and atopy. Mattress dust samples of 199 asthmatics and 198 control subjects from 7 European countries participating in the European Community Respiratory Health Survey II study were analyzed for fungal and bacterial cell wall components and individual taxa. We observed trends for protective associations of higher levels of mostly bacterial markers. Increased levels of muramic acid, a cell wall component predominant in Gram-positive bacteria, tended to be inversely associated with asthma (OR's for different quartiles: II 0.71 [0.39-1.30], III 0.44 [0.23-0.82], and IV 0.60 [0.31-1.18] P for trend .07) and with asthma score (P for trend .06) and with atopy (P for trend .02). These associations were more pronounced in northern Europe. This study among adults across Europe supports a potential protective effect of Gram-positive bacteria in mattress dust and points out that this may be more pronounced in areas where microbial exposure levels are generally lower.
  • Gilbert-Girard, Shella; Savijoki, Kirsi; Yli-Kauhaluoma, Jari; Fallarero, Adyary (2020)
    In recent years, bacterial infections have become a main concern following the spread of antimicrobial resistance. In addition, bacterial biofilms are known for their high tolerance to antimicrobials and they are regarded as a main cause of recalcitrant infections in humans. Many efforts have been deployed in order to find new antibacterial therapeutic options and the high-throughput screening (HTS) of large libraries of compounds is one of the utilized strategies. However, HTS efforts for anti-biofilm discovery remain uncommon. Here, we miniaturized a 96-well plate (96WP) screening platform, into a 384-well plate (384WP) format, based on a sequential viability and biomass measurements for the assessment of anti-biofilm activity. During the assay optimization process, different parameters were evaluated while using Staphylococcus aureus and Pseudomonas aeruginosa as the bacterial models. We compared the performance of the optimized 384WP platform to our previously established 96WP-based platform by carrying out a pilot screening of 100 compounds, followed by the screening of a library of 2000 compounds to identify new repurposed anti-biofilm agents. Our results show that the optimized 384WP platform is well-suited for screening purposes, allowing for the rapid screening of a higher number of compounds in a run in a reliable manner.
  • Donaldson, D.J.; Tervahattu, H.; Tuck, A.F. (Springer Science+Business Media B.V., 2004)
    Recent experimental work has verified the prediction that marine aerosols could have an exterior film of amphiphiles; palmitic, stearic and oleic acids were predominant. Thermodynamic analysis has revealed that such aerosols are energetically capable of asymmetric division. In a prebiotic terrestrial environment, one of the products of such aerosol fission would have been bacterially sized (microns), the other would have been virally sized (tens of nanometers). Plausible avenues for chemical differentiation between the two particles are discussed, and the probabilities for the transition from geochemistry to biochemistry updated in light of recent palaeo fossil studies.
  • Munsch-Alatossava, Patricia; Käkelä, Reijo; Ibarra, Dominique; Youbi-Idrissi, Mohammed; Alatossava, Tapani (2018)
    Cold storage aims to preserve the quality and safety of raw milk from farms to dairies; unfortunately, low temperatures also promote the growth of psychrotrophic bacteria, some of which produce heat-stable enzymes that cause spoilage of milk or dairy products. Previously, N-2 gas flushing of raw milk has demonstrated significant potential as a method to hinder bacterial growth at both laboratory and pilot plant scales. Using a mass spectrometry-based lipidomics approach, we examined the impact of cold storage [at 6 degrees C for up to 7 days, the control condition (C)], on the relative amounts of major phospholipids (phosphatidylethanolamine/PE, phosphatidylcholine/PC, phosphatidylserine/PS, phosphatidylinositol/PI, and sphingomyelin/SM) in three bovine raw milk samples, and compared it to the condition that received additional N-2 gas flushing (N). As expected, bacterial growth was hindered by the N-2-based treatment (over 4 log-units lower at day 7) compared to the non-treated control condition. At the end of the cold storage period, the control condition (C7) revealed higher hydrolysis of PC, SM, PE, and PS (the major species reached 27.2, 26.7, 34.6, and 9.9 mu M, respectively), compared to the N-2-flushed samples (N7) (the major species reached 55.6, 35.9, 54.0, and 18.8 mu M, respectively). C7 samples also exhibited a three-fold higher phosphatidic acid (PA) content (6.8 mu M) and a five-fold higher content (17.3 mu M) of lysophospholipids (LPE, LPC, LPS, and LPI) whereas both lysophospholipids and PA remained at their initial levels for 7 days in N7 samples. Taking into consideration the significant phospholipid losses in the controls, the lipid profiling results together with the microbiological data suggest a major role of phospholipase (PLase) C (PLC) in phospholipolysis during cold storage. However, the experimental data also indicate that bacterial sphingomyelinase C, together with PLases PLD and PLA contributed to the degradation of phospholipids present in raw milk as well, and potential contributions from PLB activity cannot be excluded. Altogether, this lipidomics study highlights the beneficial effects of N-2 flushing treatment on the quality and safety of raw milk through its ability to effectively hinder phospholipolysis during cold storage.