Genetic markers for beer-spoilage by lactobacilli and pediococci

The brewing industry has considerable economic impact worldwide; therefore, demand exists for a better understanding of the organisms that cause beer-spoilage. Low nutrient levels, depleted oxygen levels, high alcohol levels, and the presence of antimicrobial hop compounds all play a role in making beer an inhospitable environment for most microorganisms. Nonetheless, there are bacteria that are resistant to all of these selective pressures. The most common beer-spoilage bacteria are the Gram-positive lactic acid bacteria Lactobacillus and Pediococcus. It is currently believed that hop-resistance is the key factor(s) permitting Lactobacillus and Pediococcus bacteria to grow in beer. However, it is likely that in addition, ethanol-tolerance and the ability to acquire nutrients also play roles in the beer-spoilage ability of Lactobacillus and Pediococcus isolates. The ability of Lactobacillus and Pediococcus to grow in beer was assessed and correlated to the presence of previously described beer-spoilage related genes, as well as with the presence of novel genes identified in this study. Molecular and culture-based techniques for detection and differentiation between Lactobacillus and Pediococcus isolates that can and cannot grow in beer were established and described in detail. Interestingly, beer-spoilage related proteins were often found to share homology with multi-drug transporters. As such, the presence of these beer-spoilage associated genes was also compared to the ability of isolates to grow in the presence of a variety of antibiotics and, unexpectedly, beer-spoiling bacteria were found to be more susceptible to antibiotics than were non beer-spoiling isolates of the same genus. Additionally, it was found that isolates of Lactobacillus and Pediococcus that can grow in beer do not group phylogenetically. In order to fully appreciate the relationship of speciation with beer-spoilage, phylogenetic and whole genome/proteome studies were conducted to clarify the taxonomy of the Lactobacillus and Pediococcus genera. Through the research in this thesis, a greater understanding of the mechanism(s) enabling bacteria to grow in beer has been gained and taxonomy of the genera Lactobacillus and Pediococcus has been clarified

Susceptibility of Pediococcus isolates to antimicrobial compounds in relation to hop-resistance and beer-spoilage

<p>Abstract</p> <p>Background</p> <p>Though important in the context of food microbiology and as potential pathogens in immuno-compromised humans, bacterial isolates belonging to the genus <it>Pediococcus </it>are best known for their association with contamination of ethanol fermentation processes (beer, wine, or fuel ethanol). Use of antimicrobial compounds (e.g., hop-compounds, Penicillin) by some industries to combat <it>Pediococcus </it>contaminants is long-standing, yet knowledge about the resistance of pediococci to antimicrobial agents is minimal. Here we examined <it>Pediococcus </it>isolates to determine whether antibiotic resistance is associated with resistance to hops, presence of genes known to correlate with beer spoilage, or with ability to grow in beer.</p> <p>Results</p> <p>Lactic acid bacteria susceptibility test broth medium (LSM) used in combination with commercially available GPN3F antimicrobial susceptibility plates was an effective method for assessing antimicrobial susceptibility of <it>Pediococcus </it>isolates. We report the finding of Vancomycin-susceptible <it>Pediococcus </it>isolates from four species. Interestingly, we found that hop-resistant, beer-spoilage, and beer-spoilage gene-harbouring isolates had a tendency to be more susceptible, rather than more resistant, to antimicrobial compounds.</p> <p>Conclusion</p> <p>Our findings indicate that the mechanisms involved in conferring hop-resistance or ability to spoil beer by <it>Pediococcus </it>isolates are not associated with resistance to antibiotics commonly used for treatment of human infections. Also, Vancomycin-resistance was found to be isolate-specific and not intrinsic to the genus as previously believed.</p

The Characterization of Helicobacter pylori DNA Associated with Ancient Human Remains Recovered from a Canadian Glacier

Helicobacter pylori is a gram-negative bacterium that colonizes the stomach of nearly half of the world's population. Genotypic characterization of H. pylori strains involves the analysis of virulence-associated genes, such as vacA, which has multiple alleles. Previous phylogenetic analyses have revealed a connection between modern H. pylori strains and the movement of ancient human populations. In this study, H. pylori DNA was amplified from the stomach tissue of the Kwäday Dän Ts'ìnchi individual. This ancient individual was recovered from the Samuel Glacier in Tatshenshini-Alsek Park, British Columbia, Canada on the traditional territory of the Champagne and Aishihik First Nations and radiocarbon dated to a timeframe of approximately AD 1670 to 1850. This is the first ancient H. pylori strain to be characterized with vacA sequence data. The Tatshenshini H. pylori strain has a potential hybrid vacA m2a/m1d middle (m) region allele and a vacA s2 signal (s) region allele. A vacA s2 allele is more commonly identified with Western strains, and this suggests that European strains were present in northwestern Canada during the ancient individual's time. Phylogenetic analysis indicated that the vacA m1d region of the ancient strain clusters with previously published novel Native American strains that are closely related to Asian strains. This indicates a past connection between the Kwäday Dän Ts'ìnchi individual and the ancestors who arrived in the New World thousands of years ago

Assessing and optimizing microbial processes impacting mine reclamation

Microbes influence a wide range of processes, acting as catalysts to accelerate reactions or enable them to occur in a wider range of conditions. In the context of mine reclamation, many aspects are impacted by microbes and understanding their role is critical to making informed decisions, optimizing processes, and improving reclamation success. Examples of microbes affecting mine reclamation processes will be presented, including: passive- and semi-passive water treatment (including metals, metalloids, ammonia, nitrate, acid-rock drainage, heap leach detoxification), soil bioremediation, and revegetation. An overview of the tools currently being used at mines for microbial community profiling will be discussed, spanning from traditional growth-based techniques, through to modern day standardized genetic community profiling based on DNA-sequencing. This information will be provided in the context of how they have been used to guide and optimize mine reclamation strategies.Non UBCUnreviewedOthe

Assessment of the Huckleberry Mine site for potential passive or semi-passive acid rock drainage treatment options

Passive water treatment is often sought as a component of long-term mine closure scenarios, as it promotes relatively self-sustaining beneficial conditions for impacted water management at low maintenance and operational costs. However, owing to the biogeochemical nature of these technologies, a site-specific phased approach is necessary for successful implementation. Huckleberry Mine was evaluated for the viability of passive water treatment technologies to address potential future acid rock drainage (ARD)-impacted waters containing constituents such as aluminum and copper. Natural wetlands, seepage collection ponds, and ARD-impacted areas were assessed using genetic microbial community profiling, paired with traditional growth-based microbial characterization and quantification. This information was evaluated in the context of water chemistry, treatment objectives, and biogeochemical processes to develop a conceptual treatment train to semi-passively treat water. A phased program was then developed to determine if each step of the treatment train could address its goals individually, or if it would be best implemented to reduce costs associated with an equivalent active water treatment step.Non UBCUnreviewedOthe

PCR primers for the amplification of <i>Helicobacter pylori vacA</i> and <i>cagA</i> regions.

a<p>R is A or G, W is A or T, and Y is C or T.</p

Phylogenetic tree of the <i>vacA</i> m region that indicates the <i>H. pylori</i> DNA associated with the ancient stomach tissue is type <i>vacA</i> m1d.

<p>All sequences identifiers in the analysis are as described by Yamazaki and colleagues <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016864#pone.0016864-Yamazaki1" target="_blank">[14]</a> and Yamaoka and colleagues <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016864#pone.0016864-Yamaoka1" target="_blank">[11]</a>. Numbers given at nodes indicate the bootstrap value as a percentage, and only values greater than 50% are displayed.</p

Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Characterization of Athabasca Oil Sand Process-Affected Waters Incubated in the Presence of Wetland Plants

Naphthenic acid fraction compounds (NAFCs) are naturally present in the oil sand. These compounds become integrated into the oil sands process-affected water (OSPW) during the bitumen extraction process. NAFCs have been identified as causing toxicity in the OSPW to aquatic organisms. Water treatment technologies that are largely passive, such as constructed treatment wetlands, are a sought-after technology for the degradation of NAFCs in aquatic environments, partly because of their low energy intensity. However, it can be challenging to accurately assess the performance regarding decreased NAFC concentration and biodegradation characteristics in water samples that have been exposed to such systems. This is due to interferences of biological products such as fatty acids and humic-like materials, which may give false-positive information on NAFCs estimation with conventional analytical sample cleanup methods such as liquid–liquid extraction (LLE). It is recognized that this same issue exists when attempting to characterize NAFCs in natural wetlands for environmental monitoring purposes and, therefore, an analytical method that can remove background interferences in water samples is desirable on several fronts. Studies were thus conducted to develop and compare methods for NAFC isolation in an experimental wetland setting. A controlled greenhouse experiment was conducted with sedge (Carex aquatilis), bulrush (Schoenoplectus acutus), and cattail (Typha latifolia) grown in OSPW. Two methodsthe Isolute Biotage ENV+ SPE method and a new weak anion exchange (WAX SPE)were assessed for their ability to isolate, clean up, and concentrate NAFCs in OSPW and municipal tap water (control) that were exposed to samples of plants and associated microbes. Negative-ion-electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS) data revealed that WAX SPE method has better relative enhancement (5%–50%) of O₂ classes in OSPW exposed to wetland plants, compared to ENV+ SPE method. The WAX SPE method is a good candidate for the isolation of organic compounds in complex environmental matrices and supports the development of analytical protocols for isolation and characterization of NAFCs. Compound classes from negative-ion ESI-FT-ICR-MS data were further probed using principal component analysis (PCA) to evaluate the NAFCs that are potential indicators of efficiency of engineered wetlands for monitoring in future wetland studies. Given the PCA results, future wetland NAFC degradation investigations should target O₂ classes for detailed evaluation of the performance of treatment systems, or measurement of the fate and distributions of NAFCs in natural wetlands exposed to OSPW