Browsing by master's degree program "Master's Programme in Microbiology and Microbial Biotechnology"

Mycosporines and mycosporine-like amino acids (MAAs) are small-molecules that provide UV protection in a broad range of organisms. Cyanobacteria produce a diverse set of MAA chemical variants, many of which are glycosylated. Even though the biosynthetic pathway for the production of a common cyanobacterial MAA, shinorine, is known, the biosynthetic origins of the glycosylated variants remains unclear. In this work, bioinformatics analyses were performed to catalogue the genetic diversity encoded in the MAA gene clusters in cyanobacterial genomes and identify a set of enzymes that might be involved in MAA biosynthesis. A total of 211 cyanobacterial genomes were found to contain the MAA gene cluster, with six containing glycosyltransferase genes within the gene cluster. Afterwards, 38 strains from the University of Helsinki Culture Collection were tested for the production of MAAs using QTOF-LC/MS analyses. This resulted in the identification of several novel glycosylated MAA chemical variants from Nostoc sp. UHCC 0302, which contained a 7.4 kb MAA biosynthetic gene cluster consisting of 7 genes, including two for glycosyltransferases and one for dioxygenase. Heterologous expression of this gene cluster in Escherichia coli TOP10 resulted in the production of a glycosylated porphyra-334 variant of 509 m/z by the transformant cells, showing that colanic acid biosynthesis glycosyltransferases can catalyse the addition of hexose to MAAs. These results suggested a biosynthetic route for the production of glycosylated MAAs in cyanobacteria and allowed to propose a putative role for dioxygenases in MAA biosynthesis. Further characterization of additional glycosyltransferases is necessary to improve our understanding of glycosylated MAA biosynthesis and functionality, which could be applied to large scale processes and be used in industrial applications.

Inflammatory bowel disease (IBD) is a globally increasing chronic disease, for which the pathogenesis still is unclear. The most common subtypes of IBD are Crohn’s disease (CD) and ulcerative colitis (UC). It is widely known that, in addition to the genetics, an altered immune response against the gut microbiome plays an important role in the development of the disease. For the IBD patients, to whom conventional medication is not sufficient, the TNF-α blocker infliximab, is given. However, about one third of the patients receiving infliximab treatment, do not respond to the drug, or lose response over time. Since there to this day are no reliable diagnostic markers available, the finding of such is of great importance. The goal of this study was to investigate possible markers for drug response in the gut mycobiota composition of IBD patients. The gut mycobiota composition of 72 IBD patients receiving infliximab was studied by MiSeq sequencing of fungal DNA from fecal samples, collected during one year. The sequencing data was analyzed using the mare package in R. In addition, anti-Saccharomyces cerevisiae antibody (ASCA) concentrations were measured from baseline serum samples by ELISA. Finally, calprotectin concentrations were measured from baseline and twelve weeks post infliximab serum samples by ELISA to study whether serum samples could be used instead of fecal samples for measuring calprotectin values. Results show an increase of the Candida and Spiromyces genera in the gut mycobiota of non-responding patients at baseline. At all timepoints, the Spiromyces genus was observed at a higher abundance, compared to the group of patients responding well or partially to the medication. Interestingly, the increase of Candida was seen only in Crohn’s disease patients, when looking at the composition at all timepoints. ASCA values did not differ between the response groups. The serum calprotectin values did not correlate with fecal calprotectin, and serum calprotectin can thus not be used as a marker of gut inflammation. In conclusion, the gut mycobiota can offer predictive markers for drug response prediction to infliximab in IBD patients, which can with further studies offer a clinical diagnostic tool for prediction of drug response.

Anoplocephala perfoliata, an equine tapeworm, is an intestinal parasite of horses. Tapeworms colonize and live attached to the mucosal surfaces of ileum, caecum, and colon. The lifecycle of an equine tapeworm is indirect which means it requires an intermediate host in addition to its definitive host (a horse). The intermediate host is a mite (Oribatidae) which lives in pastures. The infection occurs when the horse digests the mites containing the infective larval forms while grazing. Infection is usually asymptomatic but can cause lesions in the intestines, and colic. The current coprological techniques often fail to recognise the infection, as they are based on observing the helminth eggs in faeces. Unlike many other intestinal parasites equine tapeworms do not release their eggs into the faecal matter. Instead, they are carried into the environment within the segments of the worm. This causes issues with diagnostics. In general, anthelmintics are recommended to be used only on horses that are diagnosed as having the need for a medication in order to prevent anthelmintic resistance from spreading. Problems in diagnosing the infections lead to decisions about medication having to be made without a proper diagnosis of a tapeworm infection. A reliable coprological test would identify the horses in need of medical care. Because of difficulties in detecting tapeworm eggs, antigens secreted by the worm could be used as a basis for test development. The aim of this study was to characterise secreted and somatic antigens and to localise them in the structures of the tapeworm, in order to obtain more information concerning the mechanisms of infection and to recognise potential antigen candidates for diagnostic purposes. Antigenic proteins were characterised using immunoblotting. Proteins were first separated based on their molecular weights and then treated with horse serum antibodies to indicate antigenic proteins. Immunohistochemical staining was used to localise the antigenic proteins in the structures of the tapeworm. Serum and worms collected from previously euthanised or slaughtered horses were used as material for this study. None of the horses were euthanised or slaughtered because of this study. Several of the secreted or somatic proteins were characterised as antigenic. The molecular weights of the observed characterised antigens ranged from 10 to 150 kDa (kilodaltons). Although these antigens were not specifically localised in the structures of the worm, the eggs and surface structures of the worm seemed to be antigenic. Exact locations could not be confirmed due to unspecific binding. Antigenic proteins characterised in this study by using immunoblotting will be identified using mass spectrometry in further studies. The end goal is to find a suitable antigen that can be used as a base for developing a diagnostic ELISA-test.

Tuberculosis (TB) still ranks as one of the most dangerous infectious diseases around the world and it is accountable for over 1.5 million deaths every year. World Health Organization has estimated that one fourth of the world’s population is infected with Mycobacterium tuberculosis. The current treatment against TB has drawbacks and the only available vaccine against TB does not provide sufficient protection against the disease and therefore new treatments are much needed. There has also been a lack of good animal models, but the zebrafish (Danio rerio) have been recently found to be a good model to study especially granuloma formation, latency, and reactivation of TB. Their natural pathogen, Mycobacterium marinum causes similar infection in the fish than M. tuberculosis in humans. One characteristic of TB is the formation of granulomas, which are aggregates of immune cells that contain the bacteria. However, M. tuberculosis can escape the granuloma and in such a way spread in the host. The inflammasome is an innate immune system mechanism that activates the immunological response in an infection and has a role in the formation of granulomas. PYCARD is an adaptor protein that has a role in inflammasome activation, which makes it an interesting target when studying the immunological response against M. tuberculosis infection. In this study, granuloma formation in pycard-/- and pycard+/+ zebrafish were compared. The granulomas were studied for their size, location, structure and hypoxicity, and the number of granulomas in each fish was counted. Also, the number of free bacteria was assessed. No significant differences were found in any of these aspects between pycard-/- and pycard+/+ fish. Variation between individual fish was great in both groups.

Human norovirus (HuNoV) is the leading cause of foodborne illness globally. Especially minimally processed goods such as berries and shellfish are common sources of HuNoV outbreaks. High pressure processing (HPP) is a relatively novel food processing technology that can both inactivate foodborne pathogens and extend the shelf-life of food items in cold temperatures. HPP is especially suitable for fresh purees, juices and sauces. In this study, we used murine norovirus strain MNV-1 to model the inactivation of HuNoV by HPP in three berry puree matrices and phosphate-buffered saline (PBS). We assessed the effect of HPP by cell-based TCID50 infectivity assay and real-time reverse transcription quantitative PCR (RT-qPCR) with RNase and porcine gastric mucin (PGM) binding assay. We strived to find if there were differences between distinct pressures (4500 and 6000 bars) and hold times (3, 6, and 9 minutes) to efficiently inactivate MNV-1 in berry purees. We observed that the matrix type affected the survival of MNV-1 significantly both during HPP and transportation. During transportation, MNV-1 survived better in PBS than in berry purees. MNV-1 was efficiently inactivated in PBS leading to >3-log10 reductions in the number of infectious particles (TCID50/ml) at both 4500 and 6000 bars. In berry puree matrices, MNV-1 was most efficiently inactivated in blackcurrant puree resulting in ≈3-log10 reductions in genome equivalents. The efficacy of pressures and hold-times could not be differentiated in any of the used matrices. MNV-1 in raspberry puree showed no infectivity in RAW 264.7 cells but displayed ≈2-log10 reductions in genome equivalents. MNV-1 in strawberry puree displayed <1-log10 reductions in RAW 264.7 cells. Our results imply that PGM binding assay and RNase as pre-RT-qPCR treatments have problems in selecting infectious MNV-1 particles for amplification. Hence when using these pre-treatments, concluding on MNV-1 infectivity should be done cautiously.

Antibiotic resistance is a growing threat to global health due to overuse and misuse of antibiotics leading to untreatable or difficult to treat infections. Natural environments are an important reservoir of antibiotic resistance. The release of antibiotics into the environment promotes the development of antibiotic resistant bacteria and environmental occurrence of antibiotic resistance genes (ARGs). ARGs are common in nature and prevalent in aquatic environments such as surface waters and effluent. Cyanobacteria are widely found in marine, freshwater, and terrestrial environments. Since their ubiquitous presence in water environments cyanobacteria are exposed to antibiotic pollution and are in contact with resistant bacteria. The role of cyanobacteria in the antimicrobial resistome and dissemination of ARGs has only been studied recently. This work aimed to evaluate the antibiotic susceptibilities of 51 cyanobacterial strains against different classes of antibiotics, using liquid batch cultures, antibiotic discs, and bioinformatics approaches. Cyanobacterial strains used in this work were sensitive to most of the tested antibiotics. However, majority of the strains also showed resistance against trimethoprim and novobiocin. Overall, there was little variation in the antibiotic resistances observed between strains but differences in sensitivity to different antibiotics was observed between species and strains with most differences seen with Nostoc spp. According to bioinformatic tools used (CARD database and BLASTp) FosA protein was found only in strains showing resistance against fosfomycin but not in any sensitive phenotypes and therefore fosA gene was selected as the most promising putative resistance gene for subsequent assays. To determine whether the fosA from cyanobacteria could confer resistance to fosfomycin, the fosA gene from Nostoc sp. XPORK 5A was cloned into pET28a(+) expression vector under the control of T7 promoter and subsequently native cyanobacterial promoter. The ability of Escherichia coli BL21 (DE3) carrying each plasmid constructs to grow in the presence of fosfomycin was determined with agar plates and growth curve assay. E. coli transformants containing the fosA gene and T7 promoter conferred high-level resistance to fosfomycin showing ability to grow at the highest concentrations tested (1mg/ml) on agar plates and (500 µg/ml) in growth curve assay. FosA protein expression from the native cyanobacterial promoter appeared to be weaker and conferred lower-level resistance to fosfomycin (≥ 10 µg/ml). The results of this study provide more information about the antibiotic susceptibility of cyanobacteria. In addition, replicating a horizontal transfer of the fosA gene from cyanobacteria to proteobacteria conferred resistance to fosfomycin and these results may indicate that also nonpathogenic cyanobacteria could act as a source of fosA antibiotic resistance genes.

Saprotrophic wood-decaying fungi access nutritional carbon by degrading lignocellulosic biomass with ligninolytic and carbohydrate active enzymes. Research of species-species level interactions of the fungi is crucial to understand ecosystem functions and carbon cycling. Furthermore, research results of wood-decaying fungi and interspecific fungal interactions can be beneficial for development of biotechnological applications. In this study, two brown rot species Fomitopsis pinicola and Fomitopsis betulina, two white rot species Phlebia radiata and Fomes fomentarius and one soft rot species Schizophyllum commune were studied in combination cultures on birch wood substrate for 12 weeks. Interactions of the fungi were studied by analysing laccase, manganese peroxidase, xylanase, and iron reduction activities, and by analysing the expression of genes coding for lignocellulose-degrading enzymes. pH of the cultures was measured to estimate the metabolic activity of the fungal species. Suppression of xylanase and iron reduction activities demonstrated dominance of the white rot species over the other decay type species in the co-cultures. In addition to the depressed enzyme activities, increase in white rot production of laccase and manganese peroxidase activities indicated combative interactions in the co-cultures. This study evidenced species and growth-time dependent changes in signature enzyme activities and in gene expression of wood-decaying fungi during interspecific fungal interactions.

Mycosporine-like Amino Acids (MAAs) are small, secondary metabolites, with the ability to absorb UV light. They are produced by cyanobacteria to act as a sunscreen. The aim of this study was to catalogue MAA genetic and chemical diversity in strains of the cyanobacterial genus Nostoc. MAAs were detected in 21 of the 68 Nostoc strains using LC/MS. Fifty four different MAAs were detected across the Nostoc strains. Glycosylated MAAs were detected in 17 of the 21 strains with hexose being the most commonly occurring sugar. Surprisingly, two structurally distinct MAAs were detected from a lichen symbiont strain, Nostoc sp. UHCC 0926. Chemical analysis detected a theoretical methylated and glycosylated variant (m/z 583, C23H39N2O15), and a suspected tri-core variant (m/z 757, C34H53N4O15) with three chromophore rings as opposed to one which is typically found. The glycosylated MAA was predicted to have a hexenimine core which was methylated and had two hexose moieties. The tri-core consisted of 2 aminohexenone cores, one on either side of a central aminohexenimine core. An 8.3 Mb draft genome sequence was obtained to identify the MAA biosynthetic gene cluster responsible for the biosynthesis of these two unusual MAAs. This resulted in the detection of two gene clusters mysA-B-C1 and mysD-C2-C3. This gene cluster organisation was compared with those of other Nostoc strains. The gene cluster organization in Nostoc sp. UHCC 0926 was unique because it was the only strain to have two gene clusters and three mysC genes despite one of the other Nostocs having the ability to produce a tri-core MAA. The strain was cultured and harvested to allow for the extraction and purification of the target MAAs. The tri-core MAA structure was confirmed by NMR. However only a putative structure for the glycosylated MAA was made. The UV absorption spectrum of the tri-core MAA had an absorption maximum at 312 nm while the glycosylated and methylated MAA had an absorption maximum at 336 nm. The investigation into the MAA production of UHCC strains expands the known chemical and genetic diversity of MAAs produced by strains of the Nostoc genus.

The increase of antibiotic resistance is one of the major healthcare threats globally. One potential way to battle against antibiotic resistant bacterial infections is to treat them with the natural opponents of bacteria, bacteriophages, known as phage therapy. The aim of this thesis was to identify new bacteriophages against clinically notable bacterial species such as Escherichia coli, Burkholderia cepacia, Enterococcus faecalis and Enterococcus faecium. Bacteriophages were screened from various origins such as hospital sewage samples, soil samples and manure samples, collected in between 2019 and 2022. The isolated bacteriophages were then initially characterized to evaluate their potential use in phage therapy. In this thesis, two phages (fHo-Eco16, fHo-Eco17) against clinical E. coli isolate and one phage (fHo-Efa06) against clinical E. faecalis isolate were found from the recently collected Finnish hospital sewage sample pool. Both E. coli phages were classified as Felixounaviruses belonging to family of Ounavirinae and class of Caudoviricetes. Enterococcus phage fHo-Efa06 was characterized as Saphexavirus belonging to class of Caudoviricetes. Preliminary genome annotation did not reveal any characteristics of lysogenic lifecycle, or antibiotic resistance or bacterial toxin genes, which would prevent the use of phages in phage therapy. Both E. coli phages (fHo-Eco16, fHo-Eco17) showed narrow host range infecting only the primary host bacterial isolate but none of 29 other tested clinical E. coli isolates. Phage fHo-Efa06 showed relatively broad host range properties infecting nine tested E. faecalis isolates out of 20 tested E. faecalis isolates but no infection capabilities against six tested clinical E. faecium isolates. In conclusion, freshly collected hospital sewage seemed to be optimal environment to find bacteriophages against clinical bacterial isolates. Furthermore, phages fHo-Eco16, fHo-Eco17 and fHo-Efa06 did not display any strictly unsuitable properties which could prevent their use in phage therapy. In turn, to obtain the definitive certainty on the usability of the phages in therapeutic use, in-depth host range screening together with detailed functional and structural annotation for the phage genomes of fHo-Efa06, fHo-Eco16 and fHo-Eco17 should be completed.

Fecal microbiota transplantation (FMT) is used to treat recurrent Clostridioides difficile infection (rCDI), and its potential as a treatment for other inflammatory conditions, like inflammatory bowel diseases (IBD), or irritable bowel syndrome (IBS), has been extensively studied lately. It has been noticed that some bacteria in fecal transplants do not require physical contact with intestinal epithelium to alleviate inflammation, and extracellular vesicles (EVs) have been proposed to carry the anti-inflammatory properties of those beneficial bacteria. In this thesis project, an isolation protocol was set up to isolate EVs from two fecal-originated Bacteroides isolates, Bacteroides ovatus and Bacteroides vulgatus, which had shown anti-inflammatory potential in previous studies. Isolation of EVs succeeded, and both isolates were confirmed to produce EVs. To study the anti-inflammatory potential, human colon epithelial cells (HT-29) were treated with several dilutions of isolated EVs, and then challenged with lipopolysaccharide (LPS) to induce inflammation. Amount of produced interleukin (IL-) 8 was measured as a marker of inflammation. EVs of both Bacteroides isolates continuously showed anti-inflammatory potential, but statistically significant conclusions could not be made. EVs have a potential to be used as a treatment in different inflammatory conditions and as adjuvant factors in synthetic FMT. To study the immunomodulatory potential of EVs of Bacteroides species more, proteomic analysis of contents of EVs, as well as potential to improve intestinal barrier are suggested. Also, testing the ability to alleviate production of other inflammatory markers could reveal more anti-inflammatory potential.