Biology Commons^™

Comparative Genomic Analysis Of 31 Phytophthora Genomes Reveals Genome Plasticity And Horizontal Gene Transfer, Brent A. Kronmiller, Nicolas Feau, Danyu Shen, Javier F. Tabima, Shahin S. Ali, Andrew D. Armitage, Felipe Arredondo, Bryan A. Bailey, Stephanie R. Bollmann, Angela Dale, Richard J. Harrison, Kelly Hrywkiw, Takao Kasuga, Rebecca Mcdougal, Charlotte F. Nellist, Preeti Panda, Sucheta Tripathy, Nari M. Williams, Wenwu Ye, Yuanchao Wang, Richard C. Hamelin, Niklaus Grünwald

Biology

Phytophthora species are oomycete plant pathogens that cause great economic and ecological impacts. The Phytophthora genus includes over 180 known species, infecting a wide range of plant hosts, including crops, trees, and ornamentals. We sequenced the genomes of 31 individual Phytophthora species and 24 individual transcriptomes to study genetic relationships across the genus. De novo genome assemblies revealed variation in genome sizes, numbers of predicted genes, and in repetitive element content across the Phytophthora genus. A genus-wide comparison evaluated orthologous groups of genes. Predicted effector gene counts varied across Phytophthora species by effector family, genome size, and plant host range. …

Genetic Evaluation Of The Current Distribution And Possible Diffrentations Between Lasiurus Borealis And Lasiurus Frantzii In Southwestern North America, Zeinab M. Haidar

Cal Poly Humboldt theses and projects

Several recent accounts of overlap and historic misidentifications regarding two species of the genus Lasiurus, Western red bat (Lasiurus frantzii) and Eastern red bat (Lasiurus borealis), have cast doubt on our understanding of their distribution, assumed spatial allopatry, and interactions in the United States Southwest. With the use of morphometrics and genetic sequencing, utilizing tissue collected from specimens throughout California and adjoining states, we have reassessed the current distribution, best practices for field identification, and genetic differentiation between both species. Appropriate species classification by region was achieved utilizing mitochondrial DNA, targeting the cytochrome c oxidase …

Ngly1 Deficiency Affects Glycosaminoglycan Biosynthesis And Wnt Signaling Pathway In Mice, Amy Batten

PANDION: The Osprey Journal of Research and Ideas

Individuals affected by NGLY1 Deficiency cannot properly deglycosylate and recycle certain proteins. Even though less than 100 people worldwide have been diagnosed with this rare autosomal recessive condition, thousands are affected by similar glycosylation disorders. Common phenotypic manifestations of NGLY1 Deficiency include severe neural and intellectual delay, impaired muscle and liver function, and seizures that may become intractable. Very little is currently known about the various mechanisms through which NGLY1 deficiency affects the body and this has led to a lack of viable treatment options for those afflicted. This experiment uses a loss-of-function (LOF) mouse model of NGLY1 Deficiency homologous …

Diversity Of Reptile Sex Chromosome Evolution Revealed By Cytogenetic And Linked-Read Sequencing, Ze-Xian Zhu, Kazumi Matsubara, Foyez Shams, Jason Dobry, Erik Wapstra, Tony Gamble, Stephen D. Sarre, Arthur Georges, Jennifer A. Marshall Graves, Qi Zhou, Tariq Ezaz

Biological Sciences Faculty Research and Publications

Reptile sex determination is attracting much attention because the great diversity of sex-determination and dosage compensation mechanisms permits us to approach fundamental questions about mechanisms of sex chromosome turnover. Recent studies have made significant progress in better understanding diversity and conservation of reptile sex chromosomes, with however no reptile master sex determination genes identified. Here we describe an integrated genomics and cytogenetics pipeline, combining probes generated from the microdissected sex chromosomes with transcriptome and genome sequencing to explore the sex chromosome diversity in non-model Australian reptiles. We tested our pipeline on a turtle, two species of geckos, and a monitor …

Student Attitudes Contribute To The Effectiveness Of A Genomics Cure, David Lopatto, Anne G. Rosenwald, Rebecca C. Burgess, Catherine Silver Key, Melanie Van Stry, Matthew Wawersik, Justin R. Diangelo, Amy T. Hark, Matthew Skerritt, Anna K. Allen, Consuelo Alvarez, Sara Anderson, Cindy Arrigo, Andrew Arsham, Daron Barnard, James E.J. Bedard, Indrani Bose, John M. Braverman, Martin G. Burg, Paula Croonquist, Chunguang Du, Sondra Dubowsky, Heather Eisler, Matthew A. Escobar, Michael Foulk, Thomas Giarla, Rivka L. Glaser, Anya L. Goodman, Yuying Gosser, Adam Haberman, Charles Hauser, Shan Hays, Justin Thackeray

Biology

The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit. We found, in general, that the attitudes students bring with them into the classroom contribute to two outcome measures, namely, learning as assessed by a pre- and postquiz and perceived self-reported benefits. While the GEP CURE produces positive outcomes overall, the students with more positive attitudes toward science, particularly with respect …

The Presence And Distribution Of Crotoxin In The Rock Rattlesnake (Crotalus Lepidus), Jade Mellor

All Theses

Crotoxin and its homologs (hereafter all referred to as CTx) is a highly lethal heterodimeric beta-neurotoxin found in pitvipers (Crotalinae) and is the main driver of neurotoxic venom phenotypes (Type II). In contrast, hemorrhagic venom phenotypes (Type I) are characterized by high snake venom metalloproteinase expression and low toxicity. Although many rattlesnake species have been classified as either Type I or Type II, population level variation in venom phenotype has also been documented in several species. The presence or absence of CTx is the main component of this variation in venom phenotype and has been most widely studied in large-bodied …

Student Attitudes Contribute To The Effectiveness Of A Genomics Cure, Adam Haberman, Et Al.

Biology: Faculty Scholarship

The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit. We found, in general, that the attitudes students bring with them into the classroom contribute to two outcome measures, namely, learning as assessed by a pre- and postquiz and perceived self-reported benefits. While the GEP CURE produces positive outcomes overall, the students with more positive attitudes toward science, particularly with respect …

Clock-Linked Genes Underlie Seasonal Migratory Timing In A Diurnal Raptor, Christen M. Bossu, Julie A. Heath, Gregory S. Kaltenecker, Barbara Helm, Kristen C. Ruegg

Biology Faculty Publications and Presentations

Seasonal migration is a dynamic natural phenomenon that allows organisms to exploit favourable habitats across the annual cycle. While the morphological, physiological and behavioural changes associated with migratory behaviour are well characterized, the genetic basis of migration and its link to endogenous biological time-keeping pathways are poorly understood. Historically, genome-wide research has focused on genes of large effect, whereas many genes of small effect may work together to regulate complex traits like migratory behaviour. Here, we explicitly relax stringent outlier detection thresholds and, as a result, discover how multiple biological time-keeping genes are important to migratory timing in an iconic …

Understanding The Genomic Influence And Virulence Capabilities Of Environmentally Isolated Vibrios, Shannon Elizabeth Pipes

Theses and Dissertations

The genus Vibrio consists of Gram-negative bacteria that possess a curved rod shape and are routinely isolated from estuarine and coastal salt water. Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus are the major three species that contribute to human disease worldwide, and a variety of other Vibrio species contribute to persistent problems in the aquaculture and fishing industries. The CDC estimates that vibrios cause 80,000 cases of disease each year in the United States alone, however, this number is thought to be underestimated, since some disease is only self-limiting, meaning patients may not seek medical treatment and have …

Examining The Relationship Between The Testate Amoeba Hyalosphenia Papilio (Arcellinida, Amoebozoa) And Its Associated Intracellular Microalgae Using Molecular And Microscopic Methods, Agnes K.M. Weiner, Billie Cullison, Shailesh V. Date, Tomáš Tyml, Jean Marie Volland, Tanja Woyke, Laura A. Katz, Robin S. Sleith

Biological Sciences: Faculty Publications

Symbiotic relationships between heterotrophic and phototrophic partners are common in microbial eukaryotes. Among Arcellinida (Amoebozoa) several species are associated with microalgae of the genus Chlorella (Archaeplastida). So far, these symbioses were assumed to be stable and mutualistic, yet details of the interactions are limited. Here, we analyzed 22 single-cell transcriptomes and 36 partially-sequenced genomes of the Arcellinida morphospecies Hyalosphenia papilio, which contains Chlorella algae, to shed light on the amoeba-algae association. By characterizing the genetic diversity of associated Chlorella, we detected two distinct clades that can be linked to host genetic diversity, yet at the same time show a biogeographic …

Standards Recommendations For The Earth Biogenome Project, Mara K. Lawniczak, Richard Durbin, Paul Flicek, Kerstin Lindblad-Toh, Xiaofeng Wei, John M. Archibald, William J. Baker, Katherine Belov, Mark L. Blaxter, Tomas Marques-Bonet, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Andrew J. Crawford, Robert P. Davey, Federica Di Palma, Qi Fang, Wilfried Haerty, Neil Hall, Katherine J. Hoff, Kerstin Howe, Erich D. Jarvis, Warren E. Johnson, Rebecca N. Johnson, Paul J. Kersey, Xin Liu, Jose V. Lopez, Eugene W. Myers, Olga Vinnere Pettersson, Adam M. Phillippy, Monica F. Poelchau, Kim D. Pruitt, Arang Rhie, Juan Carlos Castilla-Rubio, Sunil Kumar Sahu, Nicholas A. Salmon, Pamela S. Soltis, David Swarbreck, Françoise Thibaud-Nissen, Sibo Wang, Jill L. Wegrzyn, Guojie Zhang, He Zhang, Harris A. Lewin, Stephen Richards

Biology Faculty Articles

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. …

Genomic Epidemiology Of Clinical Salmonella Enterica In New Hampshire, 2017-2020, Madison R. Turcotte

Legacy Theses & Dissertations (2009 - 2024)

Antimicrobial resistance in Salmonella enterica remains a challenging public health threat. We aim to characterize the population structure and evolutionary history of 394 genomes of S. enterica isolates recovered from human clinical cases in New Hampshire, USA from 2017 to 2020. The population is phylogenetically diverse, consisting of 78 STs and 67 serotypes. We detected 61 genes associated with resistance to14 different antimicrobial classes. Rather than a single multidrug resistant clone expanding in the state, we found multiple lineages carrying different combinations of independently acquired resistance determinants. New or emerging lineages can therefore rapidly spread over relatively short timeframes. In …

Triophaser: Using Mendelian Inheritance Logic To Improve Genomic Phasing Of Trios, Dustin B. Miller, Stephen R. Piccolo

Faculty Publications

Background: When analyzing DNA sequence data of an individual, knowing which nucleotide was inherited from each parent can be benefcial when trying to identify certain types of DNA variants. Mendelian inheritance logic can be used to accurately phase (haplotype) the majority (67–83%) of an individual’s heterozygous nucleotide positions when genotypes are available for both parents (trio). However, when all members of a trio are heterozygous at a position, Mendelian inheritance logic cannot be used to phase. For such positions, a computational phasing algorithm can be used. Existing phasing algorithms use a haplotype reference panel, sequencing reads, and/or parental genotypes …

A Chromosome-Level Genome Assembly Of The Parasitoid Wasp, Cotesia Glomerata (Hymenoptera: Braconidae), Brendan J. Pinto, Jerome J. Weis, Tony Gamble, Paul J. Ode, Ryan Paul, Jennifer M. Zaspel

Biological Sciences Faculty Research and Publications

Hymenopterans make up about 20% of all animal species, but most are poorly known and lack high-quality genomic resources. One group of important, yet understudied hymenopterans are parasitoid wasps in the family Braconidae. Among this understudied group is the genus Cotesia, a clade of ~1,000 species routinely used in studies of physiology, ecology, biological control, and genetics. However, our ability to understand these organisms has been hindered by a lack of genomic resources. We helped bridge this gap by generating a high-quality genome assembly for the parasitoid wasp, Cotesia glomerata (Braconidae; Microgastrinae). We generated this assembly using multiple sequencing …

Genomic Gc Content Drifts Downward In Most Bacterial Genomes, Bert Ely

Faculty Publications

In every kingdom of life, GC->AT transitions occur more frequently than any other type of mutation due to the spontaneous deamination of cytidine. In eukaryotic genomes, this slow loss of GC base pairs is counteracted by biased gene conversion which increases genomic GC content as part of the recombination process. However, this type of biased gene conversion has not been observed in bacterial genomes, so we hypothesized that GC->AT transitions cause a reduction of genomic GC content in prokaryotic genomes on an evolutionary time scale. To test this hypothesis, we used a phylogenetic approach to analyze triplets of …

Analysis Of Structural Variation And Mtdna Copy Number In Finns, Liron Ganel

Arts & Sciences Graduate Student Theses and Dissertations

Cardiovascular disease (CVD) is a complex disease responsible for more deaths worldwide than any other cause according to the World Health Organization. Genetic association studies for CVD and related risk factors have successfully identified hundreds of loci associated with these complex diseases and traits, although much of their heritability remains unexplained. Structural variants (SVs) - including insertions, deletions, duplications, and inversions - are an understudied class of genomic variation that have the potential to explain much of the missing heritability of CVD and other complex traits. Here, we discuss advances emerging from the study of SVs in the context of …

The Impact Of Aquaculture On The Genetics And Distribution Of The Onuphid Annelid Diopatra Biscayensis, Matthew P. Galaska, David S. Wethey, Andrés Arias, Stanislas F. Dubios, Kenneth M. Halanych, Sarah A. Woodin

Faculty Publications

Aim

Evolutionary history of natural populations can be confounded by human intervention such as the case of decorator worm species Diopatra (Onuphidae), which have a history of being transported through anthropogenic activities. Because they build tubes and act as ecosystem engineers, they can have a large impact on the overall ecosystem in which they occur. One conspicuous member, Diopatra biscayensis, which was only described in 2012, has a fragmented distribution that includes the Bay of Biscay and the Normanno-Breton Gulf in the English Channel. This study explores the origin of these worms in the Normanno-Breton region, which has been …

Functional Genomics Reveals The Mechanisms And Evolution Of Extreme Physiological Adaptations In Snakes, Blair William Perry

Biology Dissertations - Archive

Previous studies examining post-feeding organ regeneration in the Burmese python (Python molurusbivittatus) have identified thousands of genes that are significantly differentially regulated during this process. However, substantial gaps remain in our understanding of coherent mechanisms and specific growth pathways that underlie these rapid and extensive shifts in organ form and function. Here we addressed these gaps by comparing gene expression in the Burmese python heart, liver, kidney, and small intestine across pre- and post-feeding time points (fasted, one day post-feeding, and four days post-feeding),and by conducting detailed analyses of molecular pathways and predictions of upstream regulatory molecules across these organ …

Involvement Of The Ino80 Chromatin Remodeling Complex In Cell Division And Genomic Stability, Ethan Chen

Biomedical Engineering Undergraduate Honors Theses

Cell division is a vital biological process for growth and development in both single and multi-cellular organisms—whereby the cell must duplicate its organelles and genome in entirety and appropriately distribute the copied contents to the daughter cells. Cells undergo a cycle of two distinct phases: interphase and mitosis. During interphase, the cell replicates its genomic DNA (in the form of chromosomes) located within the nucleus. DNA replication is carried out in a euchromatin state, where the chromosome structure is loose and easily accessible by DNA polymerase and other replication enzymes. Upon the completion of replication, chromatin is condensed into highly …

Omicsvolcano: Software For Intuitive Visualization And Interactive Exploration Of High-Throughput Biological Data, Irina Kuznetsova, Artur Lugmayr, Oliver Rackham, Aleksandra Filipovska

Research outputs 2014 to 2021

Advances in omics technologies have generated exponentially larger volumes of biological data; however, their analyses and interpretation are limited to computationally proficient scientists. We created OmicsVolcano, an interactive open-source software tool to enable visualization and exploration of high-throughput biological data, while highlighting features of interest using a volcano plot interface. In contrast to existing tools, our software and user-interface design allow it to be used without requiring any programming skills to generate high-quality and presentation-ready images.

Physical Mapping Of The Anopheles (Nyssorhynchus) Darlingi Genomic Scaffolds, Míriam Silva Rafael, Leticia Cegatti Bridi, Igor V. Sharakhov, Osvaldo Marinotti, Maria V. Sharakhova, Vladimir A. Timoshevskiy, Giselle Moura Guimarães-Marques, Valéria Silva Santos, Carlos Gustavo Nunes Da Silva, Spartaco Astolfi-Filho, Wanderli Pedro Tadei

Biology Faculty Publications

The genome assembly of Anopheles darlingi consists of 2221 scaffolds (N50 = 115,072 bp) and has a size spanning 136.94 Mbp. This assembly represents one of the smallest genomes among Anopheles species. Anopheles darlingi genomic DNA fragments of ~37 Kb were cloned, end-sequenced, and used as probes for fluorescence in situ hybridization (FISH) with salivary gland polytene chromosomes. In total, we mapped nine DNA probes to scaffolds and autosomal arms. Comparative analysis of the An. darlingi scaffolds with homologous sequences of the Anopheles albimanus and Anopheles gambiae genomes identified chromosomal rearrangements among these species. Our results confirmed that physical mapping …

Genetics Of Pediatric Musculoskeletal Disorders, Lilian Antunes

Arts & Sciences Graduate Student Theses and Dissertations

Pediatric musculoskeletal disorders are an extremely broad category of diseases that are often inherited. While individually rare, collectively these disorders are common, affecting around 3% of live births in the US. Despite the mounting clinical and molecular evidence for a genetic etiology, the cause for many patients with pediatric musculoskeletal disorders remain largely unknown. Major challenges in rare pediatric diseases include recruiting large numbers of patients and determining the significance and functional impacts of variants associated with disease within individuals or families. Whole exome sequencing (WES) is a powerful tool to identify coding variants that are associated with rare pediatric …

Chloroplast Genome Evolution In The Klebsormidiophyceae And Streptofilum, Sarah Glass

Theses and Dissertations

The Klebsormidiophyceae are a class of green microalgae found globally in both freshwater and terrestrial habitats. Morphology-based classification schemes of this class have been shown to be insufficient, particularly due to the simple morphology of these algae, the tendency of morphology to vary in culture versus in field conditions, and rampant morphological homoplasy. Molecular studies revealing cryptic diversity have renewed interest in this group. We sequenced the complete chloroplast genomes of taxa in the Klebsormidiophyceae representing the known taxonomic breadth of this class, as well as the chloroplast genomes of three strains of Streptofilum, a recently discovered algal lineage …

The Impacts Of External Patient Variables On Gene Expression Profiles Of Lung Adenocarcinomas, Michael Madsen

CMC Senior Theses

The search for improvements to detection and treatment of cancers is a paramount goal for all of medicine. The most important step for oncological research is to expand the knowledge base of the genetic characteristics and abnormalities that give rise to cancer. In our present day, one of the most pressing and deadly forms of cancer is that of the lung, with lung adenocarcinomas being the most prevalent variation of the disease. Improving our cancer genomic insight can provide the seedings for improved cancer detection, novel cancer treatment, and serve as a guide for avenues to explore with future oncological …

Composition And Homology In The Taxonomic Classification Of Escherichia Coli, Tanya Irani

Theses and Dissertations (Comprehensive)

As new techniques have been introduced, specifically the possibility of complete genome sequencing, better methods of defining bacterial species have also been proposed. One of the most recently proposed methods, using bioinformatic techniques, is to calculate the average nucleotide identity (ANI) between the homologous genome segments of different isolates. Another method for species discrimination that has been tested successfully is the similarity of DNA compositional signatures. However, in a recent update, DNA signatures split the available Escherichia coli complete genomes into three groups. To check if this result was consistent with such genomes belonging to different species, we tested methods …

Consensus Guidelines For Advancing Coral Holobiont Genome And Specimen Voucher Deposition, Christian R. Voolstra, Kate M. Quigley, Sarah W. Davies, John Everett Parkinson, Raquel S. Peixoto, Manuel Aranda, Andrew C. Baker, Adam R. Barno, Daniel J. Barshis, Francesca Benzoni, Victor Bonito, David G. Bourne, Carol Buitrago-López, Tom C.L. Bridge, Cheong Xin Chan, David J. Combosch, Jamie Craggs, Jörg C. Frommlet, Santiago Herrera, Andrea M. Quattrini, Till Röthig, James D. Reimer, Esther Rubio-Portillo, David J. Suggett, Helena Villela, Maren Ziegler, Michael Sweet

Biological Sciences Faculty Publications

Coral research is being ushered into the genomic era. To fully capitalize on the potential discoveries from this genomic revolution, the rapidly increasing number of high-quality genomes requires effective pairing with rigorous taxonomic characterizations of specimens and the contextualization of their ecological relevance. However, to date there is no formal framework that genomicists, taxonomists, and coral scientists can collectively use to systematically acquire and link these data. Spurred by the recently announced “Coral symbiosis sensitivity to environmental change hub” under the “Aquatic Symbiosis Genomics Project” - a collaboration between the Wellcome Sanger Institute and the Gordon and Betty Moore Foundation …

Molecular Responses To Catastrophic Molting In A Wild Marine Mammal, Anna Keith

University of the Pacific Theses and Dissertations

While most mammals shed their hair and skin either continuously or seasonally, northern elephant seals (Mirounga angustirostris) undergo an annual catastrophic molt, in which they shed their entire fur and underlying skin layer in the span of just three weeks. Due to the energetic and thermoregulatory constraints of molting and the large distances between their coastal rookeries and foraging grounds, elephant seals must remain on land and fast for the duration of their molt. Previous studies of molting northern elephant seals have examined endocrine and metabolic adjustments to fasting, but not the molecular processes underlying molting. We examined changes in …

Evolution Of Green Blood In New Guinea Lizards: Phylogenomics, Biogeography, And Comparative Genomics, Zachary Rodriguez

LSU Doctoral Dissertations

Non-model organisms with evolutionary novelties and complex distributions can provide valuable insight into the mechanisms underlying biological diversity. Green blood is one of the most unusual vertebrate physiologies and has repeatedly evolved in lizards from the megadiverse island of New Guinea. An unusually high concentration of the toxic green bile pigment biliverdin causes the green coloration of these lizards' blood, muscles, and bones. This dissertation uncovered the complex history of this novel trait (Chapter 2), identified protein-coding sequences that underlie green blood in lizards (Chapter 3), and explored evolutionary processes that drive genetic diversity in high-elevation lizards. To accurately trace …

A Mechanistic And Genomic Analysis Of Molluscum Contagiosum Virus Immune Evasion, Ian Benjamin Harvey

Arts & Sciences Graduate Student Theses and Dissertations

Molluscum contagiosum virus (MCV) is a common human-specific poxvirus with a proclivity forinfecting children and the immune-compromised. A characteristic MCV infection is restricted tothe epidermal layers of the skin and can persist for weeks to years in an otherwise healthyindividual. The high clinical burden of MCV is at odds with our limited knowledge regarding howit successfully evades the human immune response, which is in part due to the lack of an animalmodel or cell line to propagate the virus. Through this dissertation, we have uncovered andcharacterized a novel mechanism by which MC80, a protein encoded by MCV, downregulateshost MHC-I surface …

Introducing Lu-1, A Novel Lactobacillus Jensenii Phage Abundant In The Urogenital Tract, Taylor Miller-Ensminger, Rita Mormando, Laura Maskeri, Jason W. Shapiro, Alan J. Wolfe, Catherine Putonti

Bioinformatics Faculty Publications

Bacteriophages (phages) play a key role in shaping microbial communities, including those of the human body. Phages are abundant members of the urogenital tract, most often persisting through the lysogenic life cycle as prophages integrated within the genomes of their bacterial hosts. While numerous studies of the urogenital microbiota have focused on the most abundant bacterial member of this niche–Lactobacillus species–very little is known about Lactobacillus phages. Focusing on Lactobacillus jensenii strains from the urinary tract, we identified numerous prophages related to the previously characterized Lv-1 phage from a vaginal L. jensenii strain. Furthermore, we identified a new L. jensenii …