Microbiology Commons^™

The Detection And Molecular Evolution Of Francisella Tularensis Subspecies, Mark K. Gunnell

Theses and Dissertations

Francisella tularensis is the etiological agent of tularemia, a zoonotic disease with worldwide prevalence. F. tularensis is a highly pathogenic organism and has been designated as a potential biothreat agent. Currently there are four recognized subspecies of F. tularensis: tularensis (type A), holarctica (type B), mediasiatica, and novicida. In addition, genomic studies have further subdivided type A tularensis into two subclassifications, type A.I and type A.II. These two subclassifications differ in geographic distribution with type A.I appearing mainly in the Eastern United States and type A.II appearing mainly in the Western United States. Because of differences of virulence among the …

Detection Methods And Intestinal Adherence Of Non-O157 Shiga Toxin-Producing Escherichia Coli, Zachary R. Stromberg

School of Veterinary and Biomedical Sciences: Dissertations, Theses, and Student Research

Shiga toxin-producing Escherichia coli (STEC) are enteric pathogens of humans. Cattle serve as a reservoir and harbor STEC in their intestines. Intimin-positive STEC are referred to as enterohemorrhagic E.coli (EHEC). Seven serogroups (O26, O45, O103, O111, O121, O145, and O157) account for the majority of illness due to STEC and are hereafter referred to as STEC/EHEC-7. To improve detection, enrichment broths were compared for supporting growth of STEC-7 and STEC O104:H4 (STEC-8). In pure culture, STEC enriched in trypticase soy broth (TSB) had significantly greater growth compared to TSB containing antimicrobials. In fecal samples, E. coli broth enrichment yielded …

Spectrum Of Histopathological Findings In Postmenopausal Bleeding, Muhammad Usman Tariq, Romana Idress, Ahmed Raheem, Naila Kayani

Department of Pathology and Laboratory Medicine

Objective:To determine the frequencies of histopathological findings in endometrial and endocervical biopsy samples with clinical history of Postmenopausal Bleeding (PMB). Study Design:Descriptive cross-sectional study. Place and Duration of Study:Section of Histopathology, Department of Pathology and Laboratory Medicine, The Aga Khan University Hospital, Karachi, from February 2012 to January 2013. Methodology:Atotal of 157 consecutive endometrial and endocervical biopsy specimens with history of postmenopausal bleeding were included. After microscopic examination, frequencies of histological findings in different age groups were generated. Chi-square and independent sample t-tests were applied to see whether the difference was significant which was set at p < 0.05. Results:One hundred and twenty-one (77.1%) specimens showed benign pathologies while 36 (22.9%) were malignant. Endometrial polyp was seen in 67 (42.7%) cases followed by endometrial carcinomas in 25 (15.9%), endometrial hyperplasia in 21 (13.4%), cervical carcinoma in 12 (7.6%) and cervical polyps in 9 (5.7%) cases. Ahighly significant increase in the percentage of malignant and pre-malignant lesions was seen with increasing age group (p < 0.001). Mean age of patients with type-2 endometrial carcinoma was higher than type-1 endometrial carcinoma but statistical significance was not observed (70.2 ±6.5 vs. 61.8 ±9.1 years respectively, p=0.069). Conclusion:Although benign pathologies were more common in postmenopausal bleeding but the collective proportion of endometrial and cervical malignancies and pre-malignant conditions was quite high. Therefore, PMB should be urgently evaluated for cause and early commencement of treatment

Degradation Of The Cancer Genomic Dna Deaminase Apobec3b By Siv Vif, Allison M. Land, Jiayi Wang, Emily K. Law, Ryan Aberle, Andrea Kirmaier, Annabel Krupp, Welkin E. Johnson, Reuben S. Harris

Biological Sciences Department Publications

APOBEC3B is a newly identified source of mutation in many cancers, including breast, head/neck, lung, bladder, cervical, and ovarian. APOBEC3B is a member of the APOBEC3 family of enzymes that deaminate DNA cytosine to produce the promutagenic lesion, uracil. Several APOBEC3 family members function to restrict virus replication. For instance, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H combine to restrict HIV-1 in human lymphocytes. HIV-1 counteracts these APOBEC3s with the viral protein Vif, which targets the relevant APOBEC3s for proteasomal degradation. While APOBEC3B does not restrict HIV-1 and is not targeted by HIV-1 Vif in CD4-positive T cells, we asked whether related …

Cyclic Di-Gmp-Mediated Repression Of Swarming Motility By Pseudomonas Aeruginosa Pa14 Requires The Motab Stator, S. L. Kuchma, N. J. Delalez, L. M. Filkins, E. A. Snavely, J. P. Armitage, G. A. O'Toole

Dartmouth Scholarship

The second messenger cyclic diguanylate (c-di-GMP) plays a critical role in the regulation of motility. In Pseudomonas aeruginosa PA14, c-di-GMP inversely controls biofilm formation and surface swarming motility, with high levels of this dinucleotide signal stimulating biofilm formation and repressing swarming. P. aeruginosa encodes two stator complexes, MotAB and MotCD, that participate in the function of its single polar flagellum. Here we show that the repression of swarming motility requires a functional MotAB stator complex. Mutating the motAB genes restores swarming motility to a strain with artificially elevated levels of c-di-GMP as well as stimulates swarming in the wild-type strain, …

Steroid Receptor Isoform Expression In Drosophila Nociceptor Neurons Is Required For Normal Dendritic Arbor And Sensitivity, Aidan L. Mcparland, Taylor L. Follansbee, Gwendolyn D. Vesenka, Alexandra E. Panaitiu, Geoffrey K. Ganter

Biology Student Publications

Steroid hormones organize many aspects of development, including that of the nervous system. Steroids also play neuromodulatory and other activational roles, including regulation of sensitivity to painful stimuli in mammals. In Drosophila, ecdysteroids are the only steroid hormones, and therefore the fly represents a simplified model system in which to explore mechanisms of steroid neuromodulation of nociception. In this report, we present evidence that ecdysteroids, acting through two isoforms of their nuclear ecdysone receptor (EcR), modulate sensitivity to noxious thermal and mechanical stimuli in the fly larva. We show that EcRA and EcRB1 are expressed by third instar larvae in …

Loss Of Glycosaminoglycan Receptor Binding After Mosquito Cell Passage Reduces Chikungunya Virus Infectivity, Amber M. Paul, Dhiraj Acharya, John F. Anderson, Faqing Huang, Fengwei Bai

Publications

Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that can cause fever and chronic arthritis in humans. CHIKV that is generated in mosquito or mammalian cells differs in glycosylation patterns of viral proteins, which may affect its replication and virulence. Herein, we compare replication, pathogenicity, and receptor binding of CHIKV generated in Vero cells (mammal) or C6/36 cells (mosquito) through a single passage. We demonstrate that mosquito cell derived CHIKV (CHIKVmos) has slower replication than mammalian cell derived CHIKV (CHIKVvero), when tested in both human and murine cell lines. Consistent with this, CHIKVmos infection in both cell lines produce less cytopathic …

Seeps And Springs At A Platteville “Observatory” On The River Bluffs, Bj Bonin, Greg Brick, Julia R. Steenberg

Sinkhole Conference 2015

Residential building construction along the Mississippi River bluffs in the 1970s created a unique enclosed outcrop of the Late Ordovician Platteville Formation at Lilydale, Minnesota. This outcrop was examined in early 2013 after a newly-formed spring flooded an elevator shaft the previous year, drawing attention to the foundation conditions. The Lexington Riverside property is a six story condominium complex constructed within the top of the bluff. A two-level underground parking garage was built into the bluff. Bedrock was mechanically excavated to accommodate the construction of the building, creating an unweathered rock surface. The space between the structure and the excavated …

A Tail Of Two Phages: Genomic And Functional Analysis Of Listeria Monocytogenes Phages Vb_Lmos_188 And Vb_Lmos_293 Reveal The Receptor-Binding Proteins Involved In Host Specificity, Aidan Casey, Kieran Jordan, Horst Neve, Aidan Coffey, Olivia Mcauliffe

Department of Biological Sciences Publications

The physical characteristics of bacteriophages establish them as viable candidates for downstream development of pathogen detection assays and biocontrol measures. To utilize phages for such purposes, a detailed knowledge of their host interaction mechanisms is a prerequisite. There is currently a wealth of knowledge available concerning Gram-negative phage-host interaction, but little by comparison for Gram-positive phages and Listeria phages in particular. In this research, the lytic spectrum of two recently isolated Listeria monocytogenes phages (vB_LmoS_188 and vB_LmoS_293) was determined, and the genomic basis for their observed serotype 4b/4e host-specificity was investigated using comparative genomics. The late tail genes of these …

Bacteriophages Isolated From Lake Michigan Demonstrate Broad Host-Range Across Several Bacterial Phyla, Kema Malki, Alex Kula, Katherine Bruder, Emily Sible, Thomas Hatzopoulos, Stephanie Steidel, Siobhan C. Watkins, Catherine Putonti

Biology: Faculty Publications and Other Works

BACKGROUND:

The study of bacteriophages continues to generate key information about microbial interactions in the environment. Many phenotypic characteristics of bacteriophages cannot be examined by sequencing alone, further highlighting the necessity for isolation and examination of phages from environmental samples. While much of our current knowledge base has been generated by the study of marine phages, freshwater viruses are understudied in comparison. Our group has previously conducted metagenomics-based studies samples collected from Lake Michigan - the data presented in this study relate to four phages that were extracted from the same samples.

FINDINGS:

Four phages were extracted from Lake Michigan …

Variation In Microbiome Composition And Stability For A Vancomycin Treated Primary Sclerosing Cholangitis Patient With Ulcerative Colitis Compared With Controls, Alanna Dubrovsky

Symposium

The bacterial composition of the human intestines contributes to much more than just digestion. In the inflammatory, autoimmune conditions primary sclerosing cholangitis (PSC) and ulcerative colitis (UC), the microbiome may be, in some cases, a factor. To gain a better understanding of the composition and stability of the microbiome in a patient treated with vancomycin for PSC, terminal restriction fragment (TRF) analysis was performed on 13 controls and 1 patient, and 16s rRNA microbiome composition analysis was performed on 1 patient and 3 controls. Results showed similar levels of stability, with surprising differences in composition.

Isolation & Characterization Of Bacteria In The Built Environment: Measuring The Effect Of Pharmaceuticals On Growth, Amanda V. Finck, Kelly J. Digeronimo, Nene S. Sy, Zakiya Whatley

Student Publications

This work reports the isolation and characterization of bacteria from the built environment at Gettysburg College in Gettysburg, PA. Surfaces of a water fountain on campus were swabbed and serially streaked to isolate multiple bacteria on R2A agar. Following multiple rounds of growth, the unknown microbial candidates were narrowed to two visibly­distinct organisms. Morphological characterization and phylogenetic identification based on 16S rDNA sequencing revealed that the isolates were Chryseobactierum hispalense and Microbacterium maritypicum. We report synergistic biofilm formation between Chryseobactierum hispalense and Microbacterium maritypicum. The contamination of drinking water with varying levels of personal care products and pharmaceuticals (PCPPs) is …

The Contribution Of Syntrophic Fatty-Acid Degrading Microbial Communities To Anaerobic Digester Function And Stability, Prince Peter Mathai

Dissertations (1934 -)

Anaerobic digestion (AD), the conversion of complex organic matter to methane, occurs through a series of reactions mediated by different guilds of microorganisms. AD process imbalances, such as organic overload or high organic loading rates (OLR), can result in the accumulation of volatile fatty acids (VFA) e.g., propionate, which must be degraded to maintain stable reactor function. VFAs are metabolized by syntrophic fatty-acid degrading bacteria (SFAB) in association with methanogenic archaea (collectively, syntrophic microbial communities, SMC). Despite their indispensable role in AD, little is known about the ecology of SFAB, especially under stressed conditions. To facilitate ecological studies, four quantitative …

Establishing Quality Control Values For Hematology Parameters: An Insight, Muhammad Shariq Shaikh

Department of Pathology and Laboratory Medicine

No abstract provided.

Biophysical Properties Of Cellular Membranes In Gram-Positive Bacterial Pathogens And Their Impact On Major Physiological Attributes And Virulence Determinants, Suranjana Sen

Theses and Dissertations

The cytoplasmic membrane of bacterial cells, forming an essential barrier from the surroundings, is a critical component of cellular physiology ensuring proper survival and maintenance of major cellular functions. The integrity of the membrane is an important feature that plays an essential role in the transport of solutes and nutrients through active and passive pathways, functions of membrane-associated proteins, electron transport and ATP synthesis, maintaining turgor pressure and combating environmental stresses, and thus is a crucial factor of a majority of cellular adaptations. The various biophysical properties affecting the integrity of this membrane are mainly determined by the composition and …

Pseudomonas Bacteriophage Phi6 As A Model For Virus Emergence, Brian Elwood Ford

Dissertations, Theses, and Capstone Projects

The Pseudomonas bacteriophage Φ6 has a long and well-established history as a model organism. Here we describe a set of experiments to extend this model system to concepts previously unclaimed. Chapter 1 presents a brief background of the ecology of viruses that infect microorganisms. Chapter 2 examines genetic mutations allowing for host range expansion. Chapter 3 presents a novel paired strain assay to study how a non genetic host-acquired factor affects fitness of these enveloped viruses on subsequent hosts. Chapter 4 is an extension of this system to include how the bacteria host is affected in virus-host coevolution.

Modeling Radiation Effectiveness For Inactivation Of Bacillus Spores, Emily A. Knight

Theses and Dissertations

This research models and analyzes the inactivation of Bacillus spores following a radiation exposure and the process enacted by the Bacillus spore to repair the resulting damage. Irradiation of a spore and the medium surrounding the spore induces chemical reactions that produce reactive oxygen species (ROS). This research will consider the reaction- diffusion of these ROS throughout the spore. These ROS can react with the spore's DNA and enzymes to degrade them to such an extent that the DNA cannot be repaired or replicated, thus causing spore death. In order to survive a dose of radiation, a spore must repair …

Metalloregulation Of Helicobacter Pylori Physiology And Pathogenesis, Kathryn P. Haley, Jennifer A. Gaddy

Peer Reviewed Articles

Helicobacter pylori is a Gram-negative spiral-shaped bacterium that colonizes over half of the world's population. Chronic H. pylori infection is associated with increased risk for numerous disease outcomes including gastritis, dysplasia, neoplasia, B-cell lymphoma of mucosal-associated lymphoid tissue (MALT lymphoma), and invasive adenocarcinoma. The complex interactions that occur between pathogen and host are dynamic and exquisitely regulated, and the relationship between H. pylori and its human host are no exception. To successfully colonize, and subsequently persist, within the human stomach H. pylori must temporally regulate numerous genes to ensure localization to the gastric lumen and coordinated expression of virulence factors …

Flavodoxin-Like Proteins Protect Candida Albicans From Oxidative Stress And Promote Virulence, Lifang Li, Shamoon Naseem, Sahil Sharma, James B. Konopka

Department of Molecular Genetics and Microbiology Faculty Publications

The fungal pathogen Candida albicans causes lethal systemic infections in humans. To better define how pathogens resist oxidative attack by the immune system, we examined a family of four Flavodoxin-Like Proteins (FLPs) in C. albicans. In agreement with previous studies showing that FLPs in bacteria and plants act as NAD(P)H quinone oxidoreductases, a C.albicans quadruple mutant lacking all four FLPs (pst1Δ, pst2Δ, pst3Δ, ycp4Δ) was more sensitive to benzoquinone. Interestingly, the quadruple mutant was also more sensitive to a variety of oxidants. Quinone reductase activity confers important antioxidant effects because resistance …

Identification Of The Regulators Binding To The Upstream Region Of Glxr Of Corynebacterium Glutamicum, Bindu Subhadra, Durga Ray, Jong Yun Han, Kwang-Hee Bae, Jung-Kee Lee

Faculty Publications - Biological Sciences

GlxR is considered as a global transcriptional regulator controlling a large number of genes having broad physiological aspects in Corynebacterium glutamicum. However, the expression profile revealing the transcriptional control of glxR has not yet been studied in detail. DNA affinity chromatography experiments revealed the binding of transcriptional regulators SucR, RamB, GlxR, and a GntR-type protein (hereafter denoted as GntR3) to the upstream region of glxR. The binding of different regulators to the glxR promoter was confirmed by EMSA experiments. The expression of glxR was analyzed in detail under various carbon sources in the wild-type and different mutant strains. The sucR …

Meningeal Infiltration Of The Spinal Cord By Non-Classically Activated B Cells Is Associated With Chronic Disease Course In A Spontaneous B Cell-Dependent Model Of Cns Autoimmune Disease, Amy K. Dang, Yodit Tesfagiorgis, Rajiv W. Jain, Heather C. Craig, Steven M. Kerfoot

Microbiology & Immunology Publications

We characterized B cell infiltration of the spinal cord in a B cell-dependent spontaneous model of central nervous system (CNS) autoimmunity that develops in a proportion of mice with mutant T and B cell receptors specific for myelin oligodendrocyte glycoprotein. We found that, while males are more likely to develop disease, females are more likely to have a chronic rather than monophasic disease course. B cell infiltration of the spinal cord was investigated by histology and FACs. CD4⁺ T cell infiltration was pervasive throughout the white and in some cases gray matter. B cells were almost exclusively restricted to …

Local Bacteria Affect The Efficacy Of Chemotherapeutic Drugs, Panos Lehouritis, Joanne Cummins, Michael Stanton, Carola T Murphy, Florence O Mccarthy, Gregor Reid, Camilla Urbaniak, William L Byrne, Mark Tangney

Microbiology & Immunology Publications

In this study, the potential effects of bacteria on the efficacy of frequently used chemotherapies was examined. Bacteria and cancer cell lines were examined in vitro and in vivo for changes in the efficacy of cancer cell killing mediated by chemotherapeutic agents. Of 30 drugs examined in vitro, the efficacy of 10 was found to be significantly inhibited by certain bacteria, while the same bacteria improved the efficacy of six others. HPLC and mass spectrometry analyses of sample drugs (gemcitabine, fludarabine, cladribine, CB1954) demonstrated modification of drug chemical structure. The chemoresistance or increased cytotoxicity observed in vitro with sample drugs …

A Multi-Platform Metabolomics Approach Identifies Highly Specific Biomarkers Of Bacterial Diversity In The Vagina Of Pregnant And Non-Pregnant Women, Amy Mcmillan, Stephen Rulisa, Mark Sumarah, Jean M Macklaim, Justin Renaud, Jordan E Bisanz, Gregory B Gloor, Gregor Reid

Microbiology & Immunology Publications

Bacterial vaginosis (BV) increases transmission of HIV, enhances the risk of preterm labour, and is associated with malodour. Clinical diagnosis often relies on microscopy, which may not reflect the microbiota composition accurately. We use an untargeted metabolomics approach, whereby we normalize the weight of samples prior to analysis, to obtained precise measurements of metabolites in vaginal fluid. We identify biomarkers for BV with high sensitivity and specificity (AUC = 0.99) in a cohort of 131 pregnant and non-pregnant Rwandan women, and demonstrate that the vaginal metabolome is strongly associated with bacterial diversity. Metabolites associated with high diversity and clinical BV …

Demographics And Transfer Of Escherichia Coli Within Bos Taurus Populations, Joshua Ryan Dillard

Master's Theses

In the United States, symptoms caused by pathogenic strains of Escherichia coli are on the rise. A major source of these pathogenic strains is the E. coli in the digestive tract of cattle. The purpose of this project was to determine if E. coli are transferred between individuals of the same species and if interspecies transmission is possible. Proximity of cattle was also studied as a contributing factor to the transfer of E. coli. To accomplish this goal, E. coli isolates from cattle and cohabitating ground squirrels were compared through a new method of bacterial strain typing called pyroprinting. …

Drosophila Eye Model To Study Neuroprotective Role Of Creb Binding Protein (Cbp) In Alzheimer’S Disease, Timothy Cutler, Ankita Sarkar, Michael Moran, Andrew Steffensmeier, Oorvashi Roy Puli, Greg Mancini, Meghana Tare

Biology Faculty Publications

Background: The progressive neurodegenerative disorder Alzheimer’s disease (AD) manifests as loss of cognitive functions, and finally leads to death of the affected individual. AD may result from accumulation of amyloid plaques. These amyloid plaques comprising of amyloid-beta 42 (Aβ42) polypeptides results from the improper cleavage of amyloid precursor protein (APP) in the brain. The Aβ42 plaques have been shown to disrupt the normal cellular processes and thereby trigger abnormal signaling which results in the death of neurons. However, the molecular-genetic mechanism(s) responsible for Aβ42 mediated neurodegeneration is yet to be fully understood.

Methodology/Principal Findings: We have utilized Gal4/UAS system to …

The Cababc Operon Essential For Biofilm And Rugose Colony Development In Vibrio Vulnificus, Jin Hwan Park, Youmi Jo, Song Yee Jang, Haenaem Kwon, Yasuhiko Irie, Matthew R. Parsek, Myung Hee Kim, Sang Ho Choi

Biology Faculty Publications

A transcriptome analysis identified Vibrio vulnificus cabABC genes which were preferentially expressed in biofilms. The cabABC genes were transcribed as a single operon. The cabA gene was induced by elevated 3′,5′-cyclic diguanylic acid (c-di-GMP) and encoded a calcium-binding protein CabA. Comparison of the biofilms produced by the cabA mutant and its parent strain JN111 in microtiter plates using crystal-violet staining demonstrated that CabA contributed to biofilm formation in a calcium-dependent manner under elevated c-di-GMP conditions. Genetic and biochemical analyses revealed that CabA was secreted to the cell exterior through functional CabB and CabC, distributed throughout the biofilm matrix, and produced …

Lymphangioma Circumscriptum: Clinicopathological Spectrum Of 29 Cases, Saira Fatima, Nasir Uddin, Romana Idrees, Khurram Minhas, Zubair Ahmad, Rashida Ahmad, Naila Kayani, Muhammad Arif

Department of Pathology and Laboratory Medicine

Objective:
To describe the clinicopathological spectrum of Lymphangioma Circumscriptum (LC).
Study Design:
Observational case series.
Place and Duration of Study:
Department of Pathology and Microbiology, AKUH, Karachi, from 2002 to 2012.
Methodology:
All reported cases of LC were retrieved from medical record. Clinical and pathological features were noted. Frequency percentages were determined.
Results:
There were 29 cases of LC predominantly males (62%). The mean age was 27.17 ±15.5 years. The commonest sites was anal/perianal region (24%) followed by extremities (17%) and tongue, (14%). Vulval LC was seen in 3 patients. Two cases were described on scrotum. The lesions were most …

Pathogen-Specific Burdens Of Community Diarrhoea In Developing Countries: A Multisite Birth Cohort Study (Mal-Ed), Sadia Shakoor, Shahida Qureshi, Furqan Kabir, Anita K. M. Zaidi, Zulfiqar Ahmed Bhutta, Imran Ahmed, Didar Alam, Syed Asad Ali, Muneera Rasheed, Sajid Bashir Soofi, Ali Turab, Aisha Khizar Yousafzai

Department of Pathology and Laboratory Medicine

Background: Most studies of the causes of diarrhoea in low-income and middle-income countries have looked at severe disease in people presenting for care, and there are few estimates of pathogen-specific diarrhoea burdens in the community.
Methods: We undertook a birth cohort study with not only intensive community surveillance for diarrhoea but also routine collection of non-diarrhoeal stools from eight sites in South America, Africa, and Asia. We enrolled children within 17 days of birth, and diarrhoeal episodes (defined as maternal report of three or more loose stools in 24 h, or one loose stool with visible blood) were identified through …

Absence Of Soda Increases The Levels Of Oxidation Of Key Metabolic Determinants Of Borrelia Burgdorferi, Maria D. Esteve-Gassent, Trever C. Smith Ii, Christina M. Small, Derek P. Thomas, J Seshu

Peer Reviewed Articles

Borrelia burgdorferi, the causative agent of Lyme disease, alters its gene expression in response to environmental signals unique to its tick vector or vertebrate hosts. B. burgdorferi carries one superoxide dismutase gene (sodA) capable of controlling intracellular superoxide levels. Previously, sodA was shown to be essential for infection of B. burgdorferi in the C3H/HeN model of Lyme disease. We employed two-dimensional electrophoresis (2-DE) and immunoblot analysis with antibodies specific to carbonylated proteins to identify targets that were differentially oxidized in the soluble fractions of the sodA mutant compared to its isogenic parental control strain following …

An Exploration Of The Phylogenetic Placement Of Recently Discovered Ultrasmall Archaeal Lineages, Jeffrey M. O'Brien

Honors Scholar Theses

In recent years, several new clades within the domain Achaea have been discovered. This is due in part to microbiological sampling of novel environments, and the increasing ability to detect and sequence uncultivable organisms through metagenomic analysis. These organisms share certain features, such as small cell size and streamlined genomes. Reduction in genome size can present difficulties to phylogenetic reconstruction programs. Since there is less genetic data to work with, these organisms often have missing genes in concatenated multiple sequence alignments. Evolutionary Biologists have not reached a consensus on the placement of these lineages in the archaeal evolutionary tree. There …