Fall 2025
Mondays in AgSci 204 at 11:30 am
“Surveillance of Paramyxoviruses in Chiropteran Hosts of American Samoa”
Date: 11/10
Speaker: Therese Cook
Microbiology Graduate Student
In-Person Only
Bats (order Chiroptera) represents one of the most ecologically and evolutionary diverse group of mammals, comprising more than 1,400 recognized species across all continents except Antarctica. Their unique immunological and physiological traits, including flight associated metabolic adaptations and tolerance to viral infections, makes them an exceptional natural reservoir for many pathogens. Among these, viruses within the Paramyxoviridae are a particular concern due to their host range, zoonotic potential, and their capacity to cause significant outbreaks in human and animal populations. Paramyxoviridae are enveloped, negative sense, single stranded RNA viruses encompassing over 75 species across multiple genera, including Morbillivirus, Pararubulavirus, Henipavirus, and Respirovirus. Some members of this family, such as Nipah and Hendra viruses (genus Henipavirus), canine distemper virus, and feline morbillivirus, have demonstrated the ability to cross species and cause significant disease. The Pacific region, there has been limited research on the viral ecology of bats, despite their potential role as reservoirs for emerging infectious diseases. American Samoa hosts two native fruit bats species – Pteropus samoensis and Pteropus tonganus – both of which are integral to the local ecosystem yet poorly studied in terms of their virological profiles. Given the global emergence of zoonotic Paramyxoviridae, investigating their viral diversity is important in understanding regional risks and establishing effective surveillance.
“Feral Swine as Reservoirs of Leptospirosis in Hawaiʻi: Integrating Spatial Epidemiology and Serological/Molecular Diagnostics to Assess Zoonotic Risk”
Date: 11/10
Speaker: Liam Fressie
Microbiology Graduate Student
In-Person Only
Leptospirosis, a zoonotic disease caused by Leptospira spp., is endemic in the Hawaiian islands, where case rates are up to 100 times higher than the United States National average. Feral swine are suspected to be major environmental reservoirs for Leptospira transmission to humans, yet their role across Hawai’iʻs diverse land management areas remains poorly characterized. This study will integrate serological, molecular, and spatial epidemiological approaches to clarify the contributions of feral swine to Leptospirosis exposure and risk across the Hawaiian islands. Historical (2012-2025) and newly collected feral swine serum samples will be screened by ELISA and confirmed via microscopic agglutination tests (MAT) to determine serovar specific exposures. Concurrently, Leptospira presence in feral swine urine, kidney tissues, and associated freshwater sources will be assessed using qPCR and Long read genomic sequencing. These data points will be combined with GIS based risk mapping to identify spatial “hot spots” of infection and overlap with reported human cases. Early findings suggest that feral swine harbor Leptospira serogroups that mirror those causing human infection, highlighting their epidemiological significance. This work will advance the understanding of how wildlife reservoirs sustain zoonotic disease cycles in tropical island ecosystems and provides actionable data for targeted feral swine management and public health interventions in Hawaiʻi
“Bacterial Alternative Ribosomal Proteins”
Date: 11/03
Speaker: Stevan Stojanović
Microbiology MS Student
In-Person Only
Ribosomes are an integral part of cell biology, seeing as they are the hub of protein synthesis. Proper function of ribosomes is essential for cell homeostasis. Ribosomes are comprised of two subunits, each containing rRNAs and ribosomal proteins. Ribosomal proteins are small, basic proteins that can effectively bind to many types of RNA. Conserved structure of these proteins allows for a proper assembly of the ribosomal complex, as well as adequate binding of rRNA, mRNA and tRNA. Some of these proteins have paralogs that, although are effectively the same structure, have differing sequences. These alternative ribosomal proteins are expressed when the cell is facing environmental stress due to lack of nutrients, i.e. zinc. These proteins are present in many bacteria, and may have functions outside of ribosome formation. Exploration of these functions may help in understanding bacterial stress responses and metabolic regulation.
“Harnessing the foliar mycobiome as a method to “rewild” endangered Hawaiian mints”
Date: 10/27
Speaker: Fabiola Suciu Zamora
Microbiology Graduate Student
In-Person Only
Hawai’i holds a dual title as both the endangered species and the biological invasion capital of the world; the latter serving as the primary driver of native ecosystem degradation. Native Hawaiian flora are particularly vulnerable to alien pathogens, and for many, survival requires heavy applications of synthetic fungicides. However, application of such fungicides eliminates the commensal members of the phyllosphere, increasing disease susceptibility upon reintroduction. The fate of the plant is dually unfavorable: left untreated, the plant is susceptible to pathogens that will likely kill it, but if treated, the immunocompromised plant, although alive, is not equipped to reestablish itself in its ancestral environment. Preliminary laboratory trials demonstrate that foliar mycobiome transplants, using the congener Phyllostegia hirsuta as a reservoir of donor microbes, can reduce disease severity and increase survival through metabolite mediated destruction of mildew hyphae. M. aphidis, a well-described mycoparasite, has emerged as a key contributor to disease reduction. This research aims to leverage the success of preliminary laboratory biocontrols into a field setting. Outplants will be placed across suitable habitats in the Waianae Mountain range on the West side of O’ahu. Surviving plants will be re-inoculated during quarterly monitoring periods. Foliar mycobiome assembly has the potential to shift restoration ecology toward microbiome-based solutions, reducing the reliance on synthetic fungicides while enabling long-term resilience of native flora.
“Distribution of Pathogenic Leptospira in Watersheds of American Samoa.”
Date: 10/27
Speaker: Maria Karameli Telea
Microbiology Graduate Student
In-Person Only
Leptospirosis is a neglected but growing global public health concern, responsible for an estimated 1.03 million cases and 58,900 deaths annually (Costa et al., 2015). The disease, caused by pathogenic species of the genus Leptospira, is transmitted primarily through contact with water or soil contaminated by the urine of infected animals (Haake & Levett, 2015). In American Samoa, leptospirosis is endemic, with seroprevalence studies indicating that 15-17% of the population has been exposed to Leptospira (Lau et al., 2012). This study aims to assess the prevalence and distribution of pathogenic Leptospira in stream water across selected watersheds in American Samoa. Quantification and detection of pathogenic Leptospira will be performed using qPCR for the lipL32 gene, complemented by species-specific assays that resolve veterinary- relevant taxa, including L. interrogans, L. borgpetersenii, L. kirschneri, and L. noguchii, each with distinct ecology. Relationships between the leptospires concentrations, land use, population density, and physicochemical water parameters will be evaluated alongside microbial sources of tracking markers (human, dog, and pig-associated) to identify potential transmission pathways and associated risk factors. Understanding the environmental reservoirs and transmission pathways of Leptospira in water sources willsupport targeted public health interventions and improve water safety management strategies to reduce leptospirosis risk in American Samoa and, likely, similar Pacific Island communities.
“Investigating Novel Roles of PA0535 in Pseudomonas aeruginosa Biofilm Formation and Virulence”
Date: 10/20
Speaker: Selena Lu
Microbiology Graduate Student
In-Person Only
Biofilms produced by Pseudomonas aeruginosa (Pa), a notorious opportunistic pathogen, represent a significant clinical challenge due to their intrinsic resistance to antibiotics. This resistance poses a significant threat in patients with cystic fibrosis, where biofilms colonize the lungs and contribute to chronic, difficult-to-treat infections. In our previous spatial transcriptomic analysis of distinct biofilm regions (surface, middle, interior), the gene PA0535 was identified as a potential contributor to biofilm formation. Although PA0535 encodes a transcriptional inhibitor of the pauB1 gene, which encodes an oxidoreductase, its specific role in biofilm production has not been characterized. We investigated PA0535 using crystal violet biofilm assays and found that the PA0535 mutant exhibited significantly reduced biofilm production in comparison to wild-type and complement strains. Additionally, the competition assays in the Drosophila melanogaster feeding model and BALB/c mouse lung infection model revealed that the PA0535 mutant displayed reduced fitness compared to the wild type, underscoring its role in bacterial virulence. To further elucidate the molecular mechanisms of PA0535 regulation, we performed RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq). These results reveal a more broad and significant role for PA0535 in the regulation of Pa virulence than previously understood. Together, these results highlight PA0535 as a key regulator of genes involved in biofilm formation and virulence in Pa, offering a promising target for developing novel therapeutic strategies to combat biofilm-associated infections.
Literature Review:
“Biodegradation of hydrophobic pesticides by microalgae: Transformation products and impact on algae biochemical methane potential”
by Romina Avila, Andrea Peris, Ethel Eljarrat, Teresa Vicent, and Paqui Blánquez.
Date: 10/13
Speaker: Rylie Leffingwell
Microbiology PhD Student
In-Person Only
Intensive and extensive use of pesticides has contributed to their wide distribution in soil, air, and water. Due to their detrimental effects on non-target organisms, different technologies have been considered for their removal. In this work, three hydrophobic pesticide active compounds, namely, chlorpyrifos, cypermethrin, and oxadiazon, were selected to study the potential for their removal from aqueous media by a microalgae consortium. An abiotic and a killed control (thermally inactivated dead microalgae biomass) were employed to clarify their removal pathways, and pesticide content was quantified in liquid and biomass phases for 7 days. At the final time, total degradation (biodegradation plus photodegradation) contributed to the removal of 55% of oxadiazon, 35% of chlorpyrifos, and 14% of cypermethrin. Furthermore, more than 60% of chlorpyrifos and cypermethrin were removed by sorption onto microalgae biomass. Overall, the three pesticides showed high removal from the liquid phase. O,O-diethyl thiophosphate was identified in the liquid phase as a transformation product of chlorpyrifos formed by microalgae degradation. Phycoremediation was coupled with anaerobic degradation of the microalgae biomass containing the retained pesticides by sorption through biochemical methane potential tests. Anaerobic digestion was not inhibited by the pesticides as verified by methane production yields. The removal efficiency of the pesticides in the digestate was as follows: chlorpyrifos > cypermethrin > oxadiazon. These results highlight the potential of low-cost algal-based systems for the treatment of wastewater or effluents from agrochemical industries. The integration of wastewater treatment with biogas production through anaerobic digestion is a biorefinery approach that facilitates the economic feasibility of the process.
“Antibacterial Activity and Proposed Mode of Action of Extracts from Selected Zimbabwean Medicinal Plants against Acinetobacter baumannii“
Date: 10/13
Speaker: Diksha Poojari
Microbiology PhD Student
In-Person Only
Acinetobacter baumannii was identified by the WHO as a priority pathogen in which the research and development of new antibiotics is urgently needed. Plant phytochemicals have potential as sources of new antimicrobials. The objective of this study was to determine the antibacterial activity of extracts of selected Zimbabwean medicinal plants against A. baumannii and to determine their possible mode of action. Extracts were prepared from the leaves of the eight plants, including the bark of Erythrina abyssinica, using solvents of different polarities. Antibacterial activity was evaluated using the micro broth dilution method coupled with the in vitro iodonitrotetrazolium colorimetric assay. Effects of the extracts on membrane integrity were determined by quantifying the amount of protein and nucleic acid leaked from the cells after exposure to the extracts. Effects of the extracts on biofilms were investigated. Toxicity studies were carried out using sheep erythrocytes and murine peritoneal cells. Seven out of eight evaluated plant extracts were found to have antibacterial activity. The Combretum apiculatum acetonide (CAA) extract showed the highest inhibitory activity against A. baumannii with a minimal inhibitory concentration of 125 μg/mL. The minimum inhibitory concentration (MIC) of the CAA extract caused a protein leakage of 32 μg/mL from A. baumannii. The Combretum apiculatum acetone (CAA), C. apiculatum methanolic (CAM), Combretum zeyheri methanolic (CZM), and Erythrina abyssinica methanolic (EAM) Extracts inhibited A. baumannii biofilm formation. The EAM extract was shown to disrupt mature biofilms. The potent extracts were non-toxic to sheep erythrocytes and mouse peritoneal cells. The activities shown by the extracts indicate that the plants have potential as sources of effective antibacterial and antibiofilm formation agents against A. baumannii.
“Modification of outer membrane modulates Burkholderia pseudomallei membrane permeability and innate immune responses”
Date: 10/06
Speaker: Thi Hai Au La
Microbiology PhD Student
In-Person Only
Burkholderia pseudomallei is a Gram-negative bacterial pathogen that causes the tropical disease melioidosis. Host mortality primarily results from sepsis related complications and associated cytokine release. Lipopolysaccharide (LPS) is major virulence factor and mediator of sepsis can be modified by B. pseudomallei to enhance bacterial adaptation and pathogenesis. lpxE, lpxO and pagL are three structural proteins that play role in dephosphorylation, hydroxylation and de- acylation of lipid A. However, their contribution to outer membrane permeability and host innate immune response has not been clearly understood. In this work, a panel of defined lipid A modification strains were generated in biosafe B. pseudomallei Bp82 strain to study effects on bacterial outer membrane physiology and cytokine regulation in human macrophages. Dephosphorylation, hydroxylation and de-acylation by lpxE, lpxO and pagL, respectively, caused changes to lipid A structure and membrane permeability of B. pseudomallei. Outer membrane vesicles (OMVs) were isolated from the mutant strains to study immunomodulatory effect on human monocyte-derived macrophages. Significant differences in expression dynamics of various cytokines were observed upon treatment with lpxE-expressing OMVs, compared to those treated with wildtype Bp82 OMVs. These results show significance of lipid A modifiers, LpxO and PagL, for B. pseudomallei pathophysiology, and highlight the immunomodulatory effect of lpxE-expressing OMVs which could enhance vaccine efficacy.
“Distribution and Diversity of Bartonella spp. in Small Mammal Communities from Montana and Idaho“
Date: 09/29
Speaker: Emily Greenman
Microbiology PhD Student
In-Person Only
Bartonella bacteria are widespread zoonotic pathogens that infect a diverse range of small mammals, yet their prevalence and distribution remain understudied in many host species. In this study, Bartonella infection was assessed across multiple small mammal species, revealing an overall prevalence of approximately 37% based on droplet digital PCR (ddPCR) screening. Following ddPCR screening, individuals that yielded positive results were selected for further analysis including genetic sequencing of the RNA polymerase beta-subunit (rpoB) gene. While 116 individuals of 313 tested positive, only 63 samples were successfully sequenced, likely due to low infection loads. BLAST analysis suggested the presence of several Bartonella species among the infected samples, with B. grahamii and B. washoensis being the most frequently detected. Phylogenetic analyses using both Bayesian inference (MrBayes) and maximum likelihood (IQ-TREE) approaches demonstrated strong host-associated clustering of known Bartonella species. These findings provide important insights into Bartonella prevalence, distribution, diversity, and host specificity.
“Investigating the Role of Algal-Bacterial Community Interactions in Improving Health
and Sustainability of Hawaiian Fish Ponds”
Date: 09/29
Speaker: Alejandra Jacquez
Microbiology PhD Student
In-Person Only
In Hawai’i, fishponds called loko i’a have historically served important cultural and economic roles in the local community. In these ponds the prized ‘ama’ama grew, a food source to the locals. On the south side of Oahu, springs fed through lava tubes have dried due to land development, consequently cutting off freshwater flow to the ponds they once fed. Kānewai Spring is one of the few springs that has been restored with the help of the community and now serves as an educational center, giving insight into local ancient sustainability practices. Our goal is to identify microbial communities that contribute to the health of these habitats and apply that knowledge to future pond restorations.
Literature Review of
“Unraveling the Gut Microbiome of the Genus Herichthys (Pisces: Cichlidae): What Can We Learn from Museum Specimens?”
Date: 09/22
Author: Omar Mejía, Andrés Sánchez-Quinto, Elizabeth S. Gómez-Acata, Fabian Pérez-Miranda and Luisa I. Falcón
Speaker: Brianna Correa
Microbiology MS Student
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The use of museum preserved specimens to know microbiome in extinct and threatened species has been explored recently. The fishes of the genus Herichthys are distributed mainly in the Pánuco-Tamesí system in Northeastern Mexico, one of the most polluted basins in the country leading to near half of the species be considering as threatened. In this paper we used the hypervariable V4 region of the 16S rRNA gene from the 11 species of the genus Herichthys obtained from museum collections to evaluate the potential use of fixed preserved vouchers in the knowledge of gut microbiota diversity and the potential role of sympatric and allopatric speciation of the hosts in the gut microbiome evolution. The 100% of the samples were successfully amplified where the number of amplicons ranged from 4500 from a formaldehyde fixed specimen up to 55,000 in ethanol preserved specimens. Differences in gut microbiota were found between sympatric species and among the comparison of some trophic guilds. A non-random association between the gut host and their microbiome was found allow to suggest a potential phylosymbiosis relationship. In conclusion, the most abundant phyla recovered from the gut microbiota in this study were similar to those previously reported in other cichlids supporting the idea that a gut microbial core is conserved in this group of fishes despite millions of years of evolution and leading to support the potential use of museum specimens in microbiome studies.
“Anthrose, Iron, and Virulence: How a Spore Sugar Shapes Bacillus anthracis During Vegetative Growth“
Date: 09/15
Speaker: Prashant Dahal
Microbiology PhD Student
In-Person Only
Anthrax is a zoonotic disease caused by Bacillus anthracis and it remains a persistent global threat due to its spore-forming nature and capacity for genetic adaptation. Despite its slow evolutionary rate, mutations can significantly alter bacterial physiology and virulence. Globally, a unique pattern of evolution, evolution towards anthrose negativity, is being reported. In this study, we investigated anthrose-deficient B. anthracis strains emerging across diverse geographies, including Central Asia and Sub-Saharan Africa. Comparative genomic analysis and phylogenetics revealed distinct nucleic acid signatures associated with anthrose loss. Using bioluminescent reporter strains and RNA-seq, we observed that anthrose-negative mutants exhibited reduced expression of iron acquisition operons, including siderophore biosynthesis pathways, while simultaneously upregulating toxin and capsule production. This iron-starvation phenotype was confirmed through sensitivity to iron chelators and restored by exogenous anthrose or genetic complementation. In vivo characterization using wax worm and guinea pig models demonstrated enhanced virulence in anthrose-deficient strains, suggesting a compensatory pathogenic strategy under iron-limited conditions. These findings underscore the dual role of anthrose in spore structure and iron-responsive virulence regulation, and highlight the need to reassess current anthrax vaccination strategies to account for emerging pathogen variants with altered iron metabolism and immune evasion profiles.
“Influence of Water Quality on the Biodiversity and Distribution of Microalgae and Bacteria in Coastal Wastewater Treatment Plants“
Date: 09/08
Speaker: Abigail Lin
Microbiology MS Student
In-Person Only
The microalgae have increasingly gained attention as an effective and sustainable strategy to remove excess nutrients from wastewater. Wastewater studies on microalgae tend to focus on optimizing environmental conditions and interactions with bacteria to enhance nutrient removal efficiency. Furthermore, taxonomic studies typically use wastewater or sludge samples to characterize community diversities, resulting in an underrepresentation of non-suspended microbes. This study addresses knowledge gaps in the biodiversity and distribution of wastewater biofilm communities with samples from East Honolulu, Honouliuli, Wahiawā, Wai‘anae, and Sand Island wastewater treatment plants. The treatment processes are grouped into three phases: Phase I (influent, primary clarifier), Phase II (aeration tank, anoxic tank, return activated sludge), and Phase III (secondary clarifier, effluent). We analyzed water quality parameters and used Illumina MiSeq to sequence the amplified V4 region of 16S rRNA and the V9 region of 18S rRNA. Data was processed through QIIME2 and visualized using R. Diversity analyses suggested that eukaryotes were more susceptible to changes in water quality than bacteria. More specifically, based on redundancy analysis (RDA) plots, Neochloris, Characiopodium, Cladophora, and Ulva were strongly influenced by nitrogen and phosphorus. Results from this study can provide insight into dominant microalgae genera that are key bioremediators in coastal wastewater systems.
“Alternative ribosomal protein S18-2 acts as a transcriptional autoregulator in Mycobacterium smegmatis“
Date: 08/25
Speaker: Jayna Wong
Microbiology PhD Student
In-Person Only
Zinc ion is an essential micronutrient used in a plethora of cellular processes. Both environmental and pathogenic bacteria encounter zinc limitation; hence, bacteria have evolved diverse mechanisms to survive zinc limitation, including the expression of alternative ribosomal proteins (AltRPs). The AltRPs express during zinc limitation and replace zinc-binding paralogs in the ribosome. Mycobacteria share the conserved altRP operon, encoding genes for four AltRPs, but contributions of these individual AltRPs to bacterial physiology are unknown. Here, we investigate the specific function of one conserved AltRP, the S18-2 ribosomal protein in Mycobacterium smegmatis. Transcriptomics and quantitative PCR showed that deletion of the gene encoding S18-2(Δs18-2) resulted in reduced expression of the three other genes in the altRP operon, when compared to wild-type (WT) strain. In agreement with these results, we demonstrated that the activity of the altRP operon promoter was reduced in the Δs18-2 mutant vs. WT using a fluorescent reporter. To validate this autoregulation of the altRP operon by S18-2, chromatin immunoprecipitation sequencing (ChIP-seq) and protein pulldown experiments were done using FLAG-tagged and His-tagged S18-2 protein, respectively. ChIP-seq demonstrated enriched reads upstream of the altRP operon, indicating a possible binding site for S18-2. To further validate this finding, we designed protein pulldown experiments using a biotinylated DNA segment containing the upstream region of the altRP operon and streptavidin-conjugated magnetic beads. Quantification of pulled-down protein using ELISA verified that S18-2 was specifically bound to the upstream region of the altRP operon. Altogether, these data suggest that S18-2 can autoregulate expression of the altRP operon. To our knowledge, this is the first instance of a bacterial ribosomal protein conferring positive autoregulation on the transcriptional level, and provides new insights into the role of alternative ribosomal protein function in mycobacteria.
Fall 2025
Mondays at 11:30 am – 12:20 pm BIOMD T211
“Identifying the microbial origins of black spot disease in sea urchin Lytechinus pictus“
Date: 12/09
Speaker: Jenna Luc
Microbiology PhD Student
In-Person Only
“Black spot” or “bald” sea urchin disease (BSD) is a spectrum of pathogenic infections that adversely affects adult sea urchins, a keystone species in every marine ecosystem. Literature is sparse on the specific microbial source of the infection with the causative agent not known. The overarching goal of this research is to identify microbes unique to black spot disease in the sea urchin species, Lytechinus pictus. A disease severity scoring system was developed to observe progression of BSD for L. pictus. Fractionation of microbes by size isolated from diseased urchins and consequent exposure to healthy urchins point to a bacterial origin for BSD. 16S and shotgun metagenomic analyses uncovered BSD associated microbes in infected urchins compared to healthy urchins. These techniques lay a key foundation for future efforts in identifying specific pathogen(s) of BSD.
“Assessment of Microalgal and Bacterial Species Diversity in Wastewater Treatment Plants Using 16S and 18S rRNA Sequencing“
Date: 12/09
Speaker: Abigail Lin
Microbiology M.S. Student
In-Person Only
Hawaii’s groundwater is at risk from the estimated 87,900 cesspools distributed across the islands which pump 53 million gallons of raw sewage into the ground on a daily basis. Excess nutrients from untreated wastewater leads to eutrophication. Subsequent depletion of oxygen from bodies of water and heavy metal accumulation has severe consequences on the safety of public drinking water. Microalgae offers a natural and cost-effective solution to cesspools by absorbing nutrients and converting it to biomass that can be converted into biofuels. Previous research has shown that microalgal-bacterial relationships can promote nutrient removal. Bacteria produces carbon and breaks down ammonium and phosphorus to be more readily absorbed by microalgae while microalgae supplies bacteria with oxygen. Depending on environmental conditions, one species of bacteria or microalgae may outcompete another. Bacteria and microalgae coexistence is yet to be explored in wastewater systems. In this study, environmental DNA was collected from various wastewater treatment sites found in East Honolulu, Honouliuli, Wahima, Waianae, and Sand Island including the influent, primary clarifier, primary settler, screening bag, recycled activated sludge, aeration tank, anoxic tank, aerobic granular sludge reactor, secondary clarifier, and effluent tank. We will use 16S and 18S rRNA sequencing with Illumina to amplify the V4 region of bacteria and the V4 and V9 regions of eukarya. The resulting data will be used to construct a phylogeny of the microbial biodiversity in wastewater treatment plants. In doing so, we can describe species diversity of microalgae and bacteria found under different nutrient conditions. The results from this study can be used to determine the best species of microalgae and bacteria to be used to treat wastewater from cesspools.
“Identification of an AcrR family transcriptional regulator, PA1290, important
for biofilm formation and pyocyanin production of Pseudomonas aeruginosa“
Date: 12/02
Speaker: Hung Vo
Microbiology PhD Candidate
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Meeting ID: 890 2777 5989
Passcode: 664574
Pseudomonas aeruginosa (Pa) is the most common opportunistic pathogen that
poses a significant risk to immunocompromised patients especially for cystic
fibrosis (CF) patients. Pa promotes biofilm formation in the airway of CF patients
that lead to complications of treatment because of antibiotic resistance.
In this study, an AcrR family transcriptional regulator of Pa, PA1290, was identified
to be essential for Pa biofilm formation and virulence. We identified that the mutant
of this regulator significantly reduced biofilm formation and increased virulence in
D. melanogaster and BALB/c mouse infection model. The mutant of this regulator
increase motility (swarming and swimming), affect to c-di-GMP signaling, and
regulate Rhl-RhlR and PQS of quorum sensing system. Especially, the mutant of this
regulator alters pyocyanin production of Pa in in vitro condition and biofilm
condition. ChIP-seq and RNA-seq assay were used to determine direct and indirect
regulation mechanisms of genes and pathways regulated by PA1290. Differential
gene expression analysis revealed that this regulator up-regulates 64 genes and
down-regulates 95 genes in biofilm condition, many of them are involved in type VI
secreting systems, biosynthesis of pyocyanin (phzA2-G2 genes) and type IV pilus
assembly related protein. Direct binding of regulator PA1290 to the promoter
region of PA1288-PA1289 genes and PA3464-PA3465 genes were identified by
promoter-lacZ fusion assay. PA1288 (odsT) gene is outer membrane oxylipin
transporter responsible for importing oxylipin and promote establishment of Pa
biofilm. PA3465 is predicted as transmembrane secretion effector belongs to major
facilitator superfamily (MFS) transporter and is involved in Pa biofilm formation.
Altogether, we demonstrated that regulator PA1290 plays a critical role in Pa
biofilm formation and virulence. The knowledge gained in the functional
characterization of this regulator contributes to a further understanding biofilm
physiology and regulatory networks of Pa biofilm formation.
“Characterizing ribosomes containing alternative
ribosomal proteins in Mycobacterium smegmatis“
Date: 11/25
Speaker: Stevan Stojanović
Microbiology PhD Student
In person only
Zinc is a micronutrient that is required for optimal growth of bacteria, since it serves as a
cofactor in many proteins. It has been shown that zinc limitation in M. smegmatis
causes a switch in a select number of ribosomal proteins to paralogs that do not contain
zinc binding motifs. Since the processes of the ribosomal component synthesis and
assembly are tightly regulated, changes of the ribosome structure may influence
changes in cell metabolism. M. smegmatis cells grown in zinc limited conditions start
expressing alternative ribosomal proteins that are under an operon controlled by zinc
concentration. M. smegmatis experiencing zinc limitation has a distinct elongated
phenotype as well as alternative ribosomes. There has been evidence that ribosomes
containing alternative ribosomal proteins have different affinity towards mRNA but it is
still unclear whether that is due to ribosomal proteins, ribosome associated proteins or
some other factors. Our goal is to elucidate the translational effects of alternative
ribosomal proteins as well as whether there are specific proteins that may associate
themselves with alternative ribosomes. Cryo-electron microscopy is a method that
produces high resolution, 3D images of biomolecules. This method in tandem with
proteomics analysis of ribosomes and ribosome associated proteins could shine a light
onto what properties alternative ribosomes have when compared to the primary
ribosomes. In vitro translation assays will be used for the purpose of understanding
differences across zinc limited and zinc replete M. smegmatis ribosomes. The insights
gained from this research may be used as a stepping stone in understanding bacterial
ribosome remodeling. Since M. smegmatis is used as a model system for M.
tuberculosis research it could also aid in our understanding of tuberculosis as a disease
and give new potential targets for drug discovery.
“Modifying the Outer Membrane to Enhance Vaccine Efficacy”
Date: 11/18
Speaker: Thi Hai Au La
Microbiology PhD Student
In person only
No Abstract
“Two novel cyanobacteria from an Hawaiian lava cave, and investigation of their secondary metabolites”
Date: 11/04
Speaker: Taylor Onouye
Microbiology PhD Student
In person only
Bacteria produce two types of metabolites, namely primary metabolites, which are essential for
survival, and secondary metabolites, which are required for auxiliary purposes such as stress
responses, defense mechanisms, metal transport, and signaling. Secondary metabolites can
include compounds that act as hormones, antibiotics, allelochemicals, and toxins. Two
cyanobacteria cultivated from a lava cave in Kilauea Caldera represent new species in genera
whose members are known to produce toxins, antibiotics, or protease inhibitors. Screening these
two new species for production of secondary metabolites began with sequencing and annotation
of their genomes, and will soon progress to in vitro testing of extracts from live cells against
other bacteria, fungi, and Artemia salina.
“Combating the threats of antimicrobial resistance and zoonotic diseases to achieve the GHSA in Bangladesh“
Date: 10/28
Speaker: Samun Sarker
Microbiology PhD Student
In person only
“Immunogenicity of Unique Mycobacterium leprae Proteins Expressed During Human Infection“
Date: 10/21
Speaker: Selena Lu
Microbiology PhD Student
In person only
Mycobacterium leprae is the causative agent of leprosy or Hansen’s Disease. This disease is known as one of the oldest infectious diseases in human history and affects the skin and peripheral nervous system causing skin lesions and nerve damage. Leprosy can lead to life-long deformities like the loss of digits or limbs. Despite its long history with humans, we still lack a comprehensive understanding of its pathogenesis and no vaccine is available. This lack of understanding stems from the limited availability of research tools and the fact that this bacteria remains unculturable. While leprosy is treatable with antibiotics, we lack a specific diagnostic test for leprosy and must rely on invasive biopsies and microscopy to diagnose people. Previously, the Hoang lab utilized single-cell transcriptomics to visualize the in vivo transcriptome of M. leprae in the human host. Gene expression analysis identified a set of genes encoding for hypothetical proteins that are unique to M. leprae. The goal of this study is to determine the immunogenicity of these unique hypothetical proteins of M. leprae which could potentially lead to the discovery of new diagnostic targets.
“A Microbial Community Analysis of Two Hawaiian Fishponds using 16S, 18S, and ITS Sequencing“
Date: 10/14
Speaker: Angeline Casale
Microbiology PhD Student
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Meeting ID: 779 8848 3105
Passcode: 2GxkYR
Hawaiian fishponds, or loko i`a, are an ancient form of aquaculture that consistently and sustainably ensured the sustenance of Native Hawaiians for hundreds of years. Through the utilization of natural ecological processes in conjunction with human intervention, early Hawaiians were able to create an aquatic environment that facilitated the growth of algal and microbial food sources for captured herbivorous fish. It is estimated that 488 loko i`a existed on Hawai`i prior to Western contact, but only a small percentage of these fishponds exist today and even less remain in use. In collaboration with the Maunalua Fishpond Heritage Center, we are interested in monitoring the aquatic microbial community of both Kānewai Spring/Fishpond and Kalauhaʻihaʻi Fishpond located in Kuli’ou’ou, Oahu. We will use 16S, 18S, and ITS sequencing to track the composition of microbes in the water column, sediment, and biofilms of these fishponds prior to and as they are restored. This data will provide more insight into how these natural aquaculture systems work and can aid in the restoration and management of future productive loko i`a.
“Iron acquisition and vaccine strategies against anthrose-negative Bacillus anthracis“
Date: 10/07
Speaker: Prashant Dahal
Microbiology PhD Student,
PATH Group, School of Life Sciences,
College of Natural Sciences, University of Hawaii at Manoa
In-Person only
No Abstract
“Assessing Vertebrate biodiversity in a kelp forest ecosystem using environmental DNA“
Date: 9/30
Speaker: Brianna Correa
Microbiology MS Student
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Meeting ID: 980 6753 4611
Passcode: 8Mmb0u
Preserving biodiversity is a global challenge requiring data on species’ distribution and abundance over large geographic and temporal scales. However, traditional methods to survey mobile species’ distribution and abundance in marine environments are often inefficient, environmentally destructive, or resource-intensive. Metabarcoding of environmental DNA (eDNA) offers a new means to assess biodiversity and on much larger scales, but adoption of this approach for surveying whole animal communities in large, dynamic aquatic systems has been slowed by significant unknowns surrounding error rates of detection and relevant spatial resolution of eDNA surveys. Here, we report the results of a 2.5km eDNA transect surveying the vertebrate fauna present along a gradation of diverse marine habitats associated with a kelp forest ecosystem. Using PCR primers that target the mitochondrial 12S rRNA gene of marine fishes and mammals, we generated eDNA sequence data and compared it to simultaneous visual dive surveys. We find spatial concordance between individual species’ eDNA and visual survey trends, and that eDNA is able to distinguish vertebrate community assemblages from habitats separated by as little as similar to 60m. eDNA reliably detected vertebrates with low false-negative error rates (1/12 taxa) when compared to the surveys, and revealed cryptic species known to occupy the habitats but overlooked by visual methods. This study also presents an explicit accounting of false negatives and positives in metabarcoding data, which illustrate the influence of gene marker selection, replication, contamination, biases impacting eDNA count data and ecology of target species on eDNA detection rates in an open ecosystem.
“Quantitative Microbial Risk Assessment in Hawaii: The Role of Dead-End Ultrafiltration
in Recreational Water Quality“
Date: 9/30
Speaker: Melissa Minato
Microbiology MS Student
In-Person only
Annually, there are an estimated 90 million recreational waterborne illnesses across the United States, primarily linked to enteric pathogens. To protect public health, the Environmental Protection Agency (EPA) uses fecal indicator bacteria (FIB) like enterococci and E. coli to detect and evaluate these risks. However, the review of a series of published research studies indicated that in Hawaii, these FIB may not effectively indicate water quality due to their growth in natural environments. This may lead to poor correlations with the concentrations of enteric pathogens and related health risks. To better protect the public and develop meaningful water quality standards and effective water quality management strategies, quantitative microbial risk assessment (QMRA) studies are required to link swimming-related risks from enteric pathogens to the current or alternative FIB concentrations. Previous efforts in Hawaii faced challenges due to low pathogen levels in streams and beaches. To detect enteric pathogens at levels relevant to risk estimates needed to develop water quality standards, analyses of large sample volumes are needed. This project intends to use dead-end ultrafiltration devices (PMACS or EPA Method 1642), to recover enteric pathogens (human adenoviruses, human noroviruses, Salmonella, Campylobacter) from the stream water. It aims to evaluate the relationship between current FIB (E. coli, enterococci) and potential alternative fecal indicators (Clostridium perfringens, F+ and somatic coliphages). The results of this study should enable the state to develop meaningful and protective, likely site-specific, water quality standards.
Analysis of Fecal Indicator Bacteria, Microbial Source Tracking (MST) in American Samoa Watersheds“
Speaker: Nu Jahat Jabin
MS thesis proposal presentation,
Dr. Marek Kirs Lab, UHM
American Samoa (AS) watersheds support various ecosystem services. The rapidly growing island population and its needs can compromise the water quality in the watersheds, posing a risk to public health and ecosystem integrity. Currently, AS relies on standard fecal indicator bacteria (FIB), namely enterococci and Escherichia coli, for monitoring stream and beach water quality, much like the US. This study assessed 50 soil and 41 water samples across five watersheds (classified from pristine to extensive) for FIB (enterococci, E. coli, Clostridium perfringens) and MST markers (human-associated CrAssphage and HF183, dog-associated BacCan-UCD, and pig-associated Pig-2-Bac). STV-based water quality standards for enterococci (130 MPN/100ml) and E. coli (410 MPN/100ml), utilized in AS, were not met by 80.5 and 65.9% of the stream samples, respectively. At least one of the four MST markers was detected in 36.4% and 44.4% of the water samples that did not comply with the enterococci or E. coli standards, respectively. At least one of the two human-associated markers were detected in 27.3% and 33.3% of the water samples that did not comply with the enterococci or E. coli standard, respectively, therefore indicating that the source of elevated levels of indicator bacteria in the majority of the cases was not sewage or waste from animals common in AS. Concentrations of the markers in the samples positive for markers did not correlate with any of the FIB tested (P>0.05 on all tests). Detection of human-associated markers was limited to two out of the five watersheds classified as extensive. Our limited validation of MST markers based on the 37 fecal samples of animals common in AS (farm pigs, dogs, fruit bats, chickens, birds) and six wastewater samples collected from two treatment plants indicated 100% sensitivity for all four markers. Human-associated marker (HF183) was detected in a single dog fecal sample (97.3% specificity), and dog-associated markers (BacCan-UCD) were detected in two chicken and pig samples (89.2% specificity); no cross-reactivity of CrAssphage and Pig-2-Bac were detected. All soil samples were negative for the human-associated markers, but dog-associated and pig-associated markers were detected in two and one soil sample, respectively. Both enterococci and E. coli were detected in 92.0% of soil samples, averaging 954 and 1,375 MPN/g, respectively, likely implicating soils as the major source of elevated levels of FIB in AS watersheds.
“Evaluating the Salivary Microbiome as a Diagnostic Marker for a COVID-Associated Inflammatory Condition in Children“
Speaker: Brandon O’Sullivan
UHM School of Life Sciences
COVID-19 is a severe respiratory illness caused by the virus SARS-CoV-2. Although most pediatric COVID-19 cases are not serious, some children present more acutely and require inpatient treatment. Additionally, some children develop a distinct condition called Multisystem Inflammatory Syndrome in Children (MIS-C) 2-6 weeks after SARS-CoV-2 infection. MIS-C is characterized by severe whole-body inflammation and frequently is confused with Kawasaki disease, as both syndromes present with high inflammatory markers and similar physical exam findings. As such, correctly and rapidly diagnosing MIS-C can be a challenge for healthcare providers. Abnormalities in the salivary microbiome have previously been linked to endocarditis and diseases such as rheumatoid arthritis and diabetes (Willis et al., 2020). Consequently, we sought to compare the microbiomes of different cohorts, focusing on the bacteria present in saliva, to determine if any taxa differed in relative abundance with the goal of identifying diagnostic or prognostic markers. We compared children with MIS-C to those with Kawasaki disease, viral respiratory illnesses, cases with varying degrees of severity of COVID-19, and healthy controls. We recruited subjects from both the US and Colombia to reduce the impact of regional differences. We used Intus Biosciences’s Strain ID approach to amplify a ~2,500 bp region containing the entirety of the 16S rRNA gene and internal transcribed spacer region, and a portion of the 23S rRNA gene, which allows for greater taxonomic resolution. The amplicons were subjected to PacBio sequencing; we then used DADA2 to infer Amplicon Sequence Variants (ASVs), and QIIME2 and various R packages for the data analysis. Our results showed differences between the overall structure of the bacterial community in the saliva of children with MIS-C and other cohorts, as well as statistically significant shifts in the relative abundance of several taxa in the MIS-C cohort. Our results suggest that the salivary microbiome can serve as a biomarker to distinguish these unique clinical entities in children.