Browsing by Subject "16S rRNA"
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(2015)The shelf life of ESL milks and pasteurized creams is limited by bacterial spoilage. The current state of knowledge with respect to the diversity and activities of the spoilage microflora in these products is still limited. To date, studies on this subject are yet to be carried out in Finland. The aim of this study was to characterize the spoilage microorganisms found in ESL milks and pasteurised creams mainly produced in Finland. 10 ESL milks and 8 pasteurised cream packages were obtained from the Finnish retail market and were stored at 8?C, 15?C, room temperature and 30?C, respectively, until expiration. Total bacterial counts were evaluated and 31 bacterial isolates were selected. An attempt was made to characterize the bacterial isolates using rpoB and 16S rRNA partial gene sequence analyses. Psychrotrophic, spore-forming and spoilage features were also determined. Strain diversity was determined by rep-PCR profiling. Five selected isolates were subjected to metabolic profiling using the API50 CHB test. When growth was detected, total bacterial counts ranged from 2.67 to 3.74 and 2.54 to 8.98 log units in cream and ESL milk samples, respectively. Both ESL milks and cream samples were dominated by heat-resistant, spore-forming species of the Bacillus genera: the isolates were related to B. licheniformis. B. weihenstephanensis, B. safensis, B. kochii, B. pumilus, B. subtilis and B. anthracis. Intraspecies and intrasample strain diversity was very high. Isolates mainly displayed proteolytic and lipolytic activity. Psychrotrophic activity was high in the cream samples while most ESL milk isolates were mostly mesophilic. Tested isolates were non-lactose fermenters and had varying metabolic profiles. The study revealed that Finnish ESL milks and pasteurized creams are prone to spoilage by species of the Bacillus genera that have potential for lipolytic and proteolytic spoilage and some of which are considered toxigenic. There is wide intraspecies strain diversity responsible for the wide variability in metabolic, psychrotrophic and spoilage features. Phenotypic tests based on API50 CHB cannot be relied upon to make conclusions on taxonomy. Combining various methods is important for the comprehensive characterization of the bacterial isolates. Strategies to eliminate bacterial species of the Bacillus genera are important to prolong shelf life. However, intervention should be strain-specific to be effective. Large scale studies are required to confirm findings from this study.
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(2022)Cyanobacteria are an important part of the phytoplankton community and aquatic ecosystems. Cyanobacteria can form large mass occurrences, i.e. blooms, which can be toxic or cause other harm. Research and monitoring of cyanobacteria has been based on microscopy analysis. However, molecular-based methods, such as 16S rRNA sequencing are replacing microscopy analyses in the near future. The Finnish Environment Institute has stated that molecular methods are part of environmental monitoring before 2030. In this Master’s thesis the aim was to determine whether conventional microscopy analyses and 16S rRNA sequencing differ when comparing nano- and micro-sized cyanobacteria. The material was collected from a laboratory experiment of the Finnish Environment Institute’s (SYKE) MiDAS project, which was conducted in the summer of 2020. The results of the microscopy and 16S rRNA analyses differed from each other. The relative abundances of the cyanobacteria genera differed between sample types. Microscopy analyses estimated that the alpha diversity was higher compared to the results of the sequencing analyses. The main reason for the difference between the types of analyses was due to the differences in cyanobacteria belonging to the order of Synechococcales. Some of the Synechococcales species were observed only by the sequencing analyses, e.g. Snowella and some of the Synechococcales species were only observed by the microscopy analyses, e.g. Romeria and Woronichinia. It was observed that both methods are prone to identification errors. The differences between the 16S rRNA sequencing and the microscopy analyses are vastly different. It may affect on the review of long-term data of the phytoplankton community. Therefore, it is important to examine the differences between the types of analyses. Studying the dissimilarities between the types of analyses should be focused on the research of the small cell-sized colonial cyanobacteria, i.e. the species of Chroococcales and Synechococcales.
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(2020)Nautojen (Bos taurus) sorkka-alueen ihotulehdus (DD) on ympäri maailman levinnyt sairaus, jota on myös havaittu muilla sorkkaeläimillä. Nykytiedon mukaan nautojen DD on bakteeri-, ei virus- tai sienitauti. Se aiheuttaa haavoja, vaurioita ja känsiä. DD leviää helposti ja aiheuttaa eläimelle myös kipua, heikentää sen yleiskuntoa ja hyvinvointia sekä aiheuttaa tuotantotappioita. Keski-Euroopassa ja Yhdysvalloissa DD:n on havaittu leviävän lähes epidemialuonteisesti, kun taas Pohjoismaissa sitä on tavattu yksittäisissä karjoissa. Taudin etiologiasta, esiintyvyydestä ja parhaasta mahdollisesta hoitomuodosta on eri teorioita. Nykytiedon ja tieteellisen kirjallisuuden mukaan merkittävimpinä DD:n aiheuttajabakteereina pidetään eri Treponema-bakteerilajeja. Uusimpien tutkimusten perusteella taudin vakavuuteen vaikuttaa eri Treponema-lajien yhteisvaikutus keskenään tai muiden bakteereiden kanssa. Tämän tutkielman tavoite oli pystyttää bakteerien 16S rRNA-geenin rinnakkaissekvensointiin perustuva metataksonomiatyövuo bakteereiden tunnistamiseksi. Tutkielmassa vertailtiin kahta eri DNA-eristysmenetelmää, kahta sekvensointityövuota ja kahta bioinformatiikan analyysimenetelmää. Näytemateriaalina oli suomalaisten nautojen sorkka-alueen ihosta otetut biopsianäytteet (n=10). Viisi näytteistä oli terveestä M0-naudasta ja viisi M2-naudasta. Tuloksena havaittiin pieniä määriä Spirochaetaceae-bakteeriperheen sekvenssejä kahdesta M0 -diagnosoduista naudasta. Kaikista M2 - diagnoosin naudoista havaittiin runsaasti Spirochaetaceae - sekvenssejä. Lisäselvityksiä Treponema-bakteerien luotettavasta lajitason tunnistamisesta sekä niiden roolista taudissa tarvitaan. Bovine (Bos taurus) digital dermatitis (DD) of the foot is a widespead disease around the world, and it has also been diagnosed with several other hoofed ruminants. According to current knowledge, bovine digital dermatitis is a bacterial disease, not a viral or fungal disease. It causes ulcers, lesions, and raised calluses. DD spreads easily, and it can cause pain to the animal, weaken its overall health and well-being, as well as cause loss of production. DD has been almost epidemic in Central Europe, as well as in the United States of America, whereas in Scandinavia it has only been encountered in individual herds. According to current knowledge and the scientific literature, the most important bacteria responsible for DD are Treponema species. Recent studies suggest that the severity of the disease is affected by the interaction of different Treponema species with each other or with other bacteria. The aim of this thesis was to set up a metataxonomic pipeline for the parallel sequencing of the 16S rRNA bacterial gene, in order to identify the bacteria. Two different DNA extraction methods, two different sequencing pipelines, and two different bioinformatics pipelines were evaluated in this thesis. Sample material was biopsy samples of the skin of the Finnish bovine hoof (n=10). Five of the samples were from healthy M0 cattle and five from M2 cattle (acute active ulcerative lesions). As a result, small amounts of Spirochaetaceae bacterial family sequences were detected in two M0 diagnostic cattle . Abundant Spirochaetaceae sequences were found in all bovine diagnosed with M2. Further studies on the reliable species identification of Treponema bacteria and their role in the disease are needed.
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