Microbiology Commons^™

Genome-Guided Isolation Of The Hyperthermophilic Aerobe Fervidibacter Sacchari Reveals Conserved Polysaccharide Metabolism In The Armatimonadota, Nancy O. Nou, Jonathan K. Covington, Dengxun Lai, Xavier Mayali, Cale O. Seymour, Juliet Johnston, Jian-Yu Jiao, Steffen Buessecker, Damon Mosier, Alise R. Muok, Nicole Torosian, Allison M. Cook, Ariane Briegel, Tanja Woyke, Emiley Eloe-Fadrosh, Nicole Shapiro, Scott G. Bryan, Savannah Sleezer, Joshua Dimapilis, Cristina Gonzalez, Lizett Gonzalez, Marlene Noriega, Matthias Hess, Ross P. Carlson, Lan Liu, Meng-Meng Li, Zheng-Han Lian, Siqii Zhu, Fan Liu, Xian Sun, Beile Gao, Ritesh Mewalal, Miranda Harmon-Smith, Ian K. Blaby, Jan-Fang Cheng, Peter K. Weber, Gabriela Grigorean, Wen-Jun Li, Anne E. Dekas, Jennifer E. Pett-Ridge, Jeremy A. Dodsworth, Marike Palmer, Brian P. Hedlund

Life Sciences Faculty Research

Few aerobic hyperthermophilic microorganisms degrade polysaccharides. Here, we describe the genome-enabled enrichment and optical tweezer-based isolation of an aerobic polysaccharide-degrading hyperthermophile, Fervidibacter sacchari, previously ascribed to candidate phylum Fervidibacteria. F. sacchari uses polysaccharides and monosaccharides for growth at 65–87.5 °C and expresses 191 carbohydrate-active enzymes (CAZymes) according to RNA-Seq and proteomics, including 31 with unusual glycoside hydrolase domains (GH109, GH177, GH179). Fluorescence in-situ hybridization and nanoscale secondary ion mass spectrometry confirmed rapid assimilation of 13C-starch in spring sediments. Purified GHs were optimally active at 80–100 °C on ten different polysaccharides. Finally, we propose reassigning Fervidibacteria as a class …

Multiomics Of Yaks Reveals Significant Contribution Of Microbiome Into Host Metabolism, Shuli Yang, Jeiyi Zheng, Huaming Mao, Paramintra Vinitchaikul, Dongwang Wu, Jianmin Chai

Animal Science Faculty Publications and Presentations

An intensive feeding system might improve the production cycle of yaks. However, how intensive feeding system contributes to yak growth is unclear. Here, multi-omics, including rumen metagenomics, rumen and plasma metabolomics, were performed to classify the regulatory mechanisms of intensive feeding system on yaks. Increased growth performance were observed. Rumen metagenomics revealed that Clostridium, Methanobrevibacter, Piromyces and Anaeromyces increased in the intensively fed yaks, contributing to amino acid and carbohydrate metabolism. The grazing yaks had more cellulolytic microbes. These microbiomes were correlated with the pathways of "Alanine aspartate and glutamate metabolism" and "Pyruvate metabolism". Intensive feeding increased methane degradation functions, …

Natural Panola Mountain Ehrlichia Infections In Cattle In A Longitudinal Study Of Angus Beef Calves, Cierra Briggs, Drew Casey, Anna Grace Deakins, Jeremy G. Powell, Kelly Loftin, Emily G. Mcdermott

Entomology and Plant Pathology Faculty Publications and Presentations

Panola Mountain Ehrlichia (PME) is an emerging zoonotic pathogen, transmitted by Amblyomma americanum ticks in the southeastern United States. It is closely related to Ehrlichia ruminantium, the causative agent of heartwater disease. Heartwater disease is an often-fatal illness of ruminant livestock present in Africa and the Caribbean. The taxonomic relationship between PME and E. ruminantium has raised concerns about the pathogenicity of PME in livestock. To determine whether cattle could be naturally infected with PME in an endemic area, we conducted a one-year longitudinal study of Angus-breed beef calves in Fayetteville, Arkansas. One hundred seventy-seven calves born between September …

Enterococcus Faecium: Evolution, Adaptation, Pathogenesis And Emerging Therapeutics, Yahan Wei, Dennise Palacios Araya, Kelli L. Palmer

School of Podiatric Medicine Publications

The opportunistic pathogen Enterococcus faecium colonizes humans and a wide range of animals, endures numerous stresses, resists antibiotic treatment and stubbornly persists in clinical environments. The widespread application of antibiotics in hospitals and agriculture has contributed to the emergence of vancomycin-resistant E. faecium, which causes many hospital-acquired infections. In this Review, we explore recent discoveries about the evolutionary history, the environmental adaptation and the colonization and dissemination mechanisms of E. faecium and vancomycin-resistant E. faecium. These studies provide critical insights necessary for developing novel preventive and therapeutic approaches against vancomycin-resistant E. faecium and also reveal the intricate interrelationships …

What Drives Gut Microbial Diversity And Community Structure Among Closely-Related Host Species?, Rylee Jensen

All NMU Master's Theses

The gut microbiome (GMB) of mammals hosts an important community of microbes that perform countless micro-ecosystem services for the host and are influenced by numerous factors including host physiology, environment, and phylogeny. Phylogeny may have a unique effect on GMB diversity and community structure (i.e., a GMB profile) via phylosymbiosis, a theory in which the evolution of hosts matches the evolution of their associated microbiota. Elucidating phylosymbiosis in mammals is difficult because multiple intrinsic and extrinsic factors collectively drive individual GMB variation. Thus, there is a need to simultaneously analyze the role of physiology, environment, and phylogeny on shaping host …

Bcl-Xl Is Translocated To The Nucleus Via Ctbp2 To Epigenetically Promote Metastasis, Tiantian Zhang, Sha Li, Yingcai Adrian Tan, Xiang Chen, Cheryl Zhang, Zhengming Chen, Bikash Mishra, Joseph Hyungjoon Na, Soyoung Choi, Sandra J Shin, Priyadarshan Damle, Kranthi Kumar Chougoni, Steven R Grossman, Dunrui Wang, Xuejun Jiang, Yi Li, Erika Hissong, Yao-Tseng Chen, Jenny Z Xiang, Yi-Chieh Nancy Du

Faculty, Staff and Students Publications

Nuclear Bcl-xL is found to promote cancer metastasis independently of its mitochondria-based anti-apoptotic activity. How Bcl-xL is translocated into the nucleus and how nuclear Bcl-xL regulates histone H3 trimethyl Lys4 (H3K4me3) modification have yet to be understood. Here, we report that C-terminal Binding Protein 2 (CtBP2) binds to Bcl-xL via its N-terminus and translocates Bcl-xL into the nucleus. Knockdown of CtBP2 by shRNA decreases the nuclear portion of Bcl-xL and reverses Bcl-xL-induced invasion and metastasis in mouse models. Furthermore, knockout of CtBP2 not only reduces the nuclear portion of Bcl-xL but also suppresses Bcl-xL transcription. The binding between Bcl-xL and …

Factors Associated With Head And Neck Cancer Postoperative Radiotherapy Delays: A Systematic Review And Meta-Analysis, Kelsey A Duckett, Mohamed Faisal Kassir, Shaun A Nguyen, Emily A Brennan, Bhisham S Chera, Katherine R Sterba, Chanita Hughes Halbert, Elizabeth G Hill, Jessica Mccay, Sidharth V Puram, Ryan S Jackson, Vlad C Sandulache, Russel Kahmke, Nosayaba Osazuwa-Peters, Salma Ramadan, Brian Nussenbaum, Anthony J Alberg, Evan M Graboyes

Faculty, Staff and Students Publications

Objective: Initiating postoperative radiotherapy (PORT) within 6 weeks of surgery for head and neck squamous cell carcinoma (HNSCC) is included in the National Comprehensive Cancer Network Clincal Practice Guidelines and is a Commission on Cancer quality metric. Factors associated with delays in starting PORT have not been systematically described nor synthesized.

Data sources: PubMed, Scopus, and CINAHL.

Review methods: We included studies describing demographic characteristics, clinical factors, or social determinants of health associated with PORT delay (>6 weeks) in patients with HNSCC treated in the United States after 2003. Meta-analysis of odds ratios (ORs) was performed on nonoverlapping datasets. …

Transcriptomic And Epigenomic Signatures Distinguish High- And Low-Risk Endotypes For Liver Tumor Development, Sandra L Grimm, Tia Talley, Rahul K Jangid, Amrit Koirala, Micah B Castillo, Preethi H Gunaratne, Cristian Coarfa, Cheryl L Walker

Faculty, Staff and Students Publications

The epigenome is a target for environmental exposures and a potential determinant of inter-individual differences in response. In genetically identical C57Bl/6 mice exposed from gestation to weaning to the endocrine-disrupting chemical (EDC) tributyltin (TBT), hepatic tumor development later in life varied across multiple cohorts over time and depending on sex and diet. In one cohort where approximately half of TBT-exposed male mice developed liver tumors at 10 months (Katz et al. Hepatic tumor formation in adult mice developmentally exposed to organotin, Environmental Health Perspectives, 128 (1), 17010, 2020), transcriptomic (RNA-seq) and epigenomic (ChIP-seq) profiling was performed on blood and liver …

A Cross-Systems Primer For Synthetic Microbial Communities, Elijah C Mehlferber, Gontran Arnault, Bishnu Joshi, Laila P Partida-Martinez, Kathryn A Patras, Marie Simonin, Britt Koskella

Faculty, Staff and Students Publications

The design and use of synthetic communities, or SynComs, is one of the most promising strategies for disentangling the complex interactions within microbial communities, and between these communities and their hosts. Compared to natural communities, these simplified consortia provide the opportunity to study ecological interactions at tractable scales, as well as facilitating reproducibility and fostering interdisciplinary science. However, the effective implementation of the SynCom approach requires several important considerations regarding the development and application of these model systems. There are also emerging ethical considerations when both designing and deploying SynComs in clinical, agricultural or environmental settings. Here we outline current …

Solid Tumour-Induced Systemic Immunosuppression Involves Dichotomous Myeloid-B Cell Interactions, Xiaoxin Hao, Yichao Shen, Jun Liu, Angela Alexander, Ling Wu, Zhan Xu, Liqun Yu, Yang Gao, Fengshuo Liu, Hilda L Chan, Che-Hsing Li, Yunfeng Ding, Weijie Zhang, David G Edwards, Nan Chen, Azadeh Nasrazadani, Naoto T Ueno, Bora Lim, Xiang H-F Zhang

Faculty, Staff and Students Publications

Solid tumours induce systemic immunosuppression that involves myeloid and T cells. B cell-related mechanisms remain relatively understudied. Here we discover two distinct patterns of tumour-induced B cell abnormality (TiBA; TiBA-1 and TiBA-2), both associated with abnormal myelopoiesis in the bone marrow. TiBA-1 probably results from the niche competition between pre-progenitor-B cells and myeloid progenitors, leading to a global reduction in downstream B cells. TiBA-2 is characterized by systemic accumulation of a unique early B cell population, driven by interaction with excessive neutrophils. Importantly, TiBA-2-associated early B cells foster the systemic accumulation of exhaustion-like T cells. Myeloid and B cells from …

Specialized Contact Sites Regulate The Fusion Of Chlamydial Inclusion Membranes, Christine Linton, Jordan Wesolowski, Anna Lobley, Toshiyuki Yamaji, Kentaro Hanada, Fabienne Paumet

Department of Microbiology and Immunology Faculty Papers

The intracellular bacterial pathogen Chlamydia trachomatis replicates within a membrane-bound compartment called the inclusion. Upon infection with several chlamydiae, each bacterium creates its own inclusion, resulting in multiple inclusions within each host cell. Ultimately, these inclusions fuse together in a process that requires the chlamydial protein IncA. Here, we show that inclusions form unique contact sites (inclusion contact sites, ICSs) prior to fusion, that serve as fusogenic platforms in which specific lipids and chlamydial proteins concentrate. Fusion depends on IncA clustering within ICSs and is regulated by PI(3,4)P₂ and sphingolipids. As IncA concentrates within ICSs, its C-terminus likely interacts …

Construction And Characterization Of Dna Libraries From Cultured Phages And Environmental Viromes, Carmen Gu Liu, Brianna E Thompson, James D Chang, Lorna Min, Anthony W Maresso

Faculty, Staff and Students Publications

Despite many efforts to understand and leverage the functional potential of environmental viromes, most bacteriophage genes are largely uncharacterized. To explore novel biology from uncultivated microbes like phages, metagenomics has emerged as a powerful tool to directly mine new genes without the need to culture the diverse microbiota and the viruses within. When a pure computational approach cannot infer gene function, it may be necessary to create a DNA library from environmental genomic DNA, followed by the screening of that library for a particular function. However, these screens are often initiated without a metagenomic analysis of the completed DNA library …

Sall4 And Gata4 Induce Cardiac Fibroblast Transition Towards A Partially Multipotent State With Cardiogenic Potential, Hong Gao, Saliha Pathan, Beverly R E A Dixon, Aarthi Pugazenthi, Megumi Mathison, Tamer M A Mohamed, Todd K Rosengart, Jianchang Yang

Faculty, Staff and Students Publications

Cardiac cellular fate transition holds remarkable promise for the treatment of ischemic heart disease. We report that overexpressing two transcription factors, Sall4 and Gata4, which play distinct and overlapping roles in both pluripotent stem cell reprogramming and embryonic heart development, induces a fraction of stem-like cells in rodent cardiac fibroblasts that exhibit unlimited ex vivo expandability with clonogenicity. Transcriptomic and phenotypic analyses reveal that around 32 ± 6.4% of the expanding cells express Nkx2.5, while 13 ± 3.6% express Oct4. Activated signaling pathways like PI3K/Akt, Hippo, Wnt, and multiple epigenetic modification enzymes are also detected. Under suitable conditions, these cells …

Electric Potential Energy Optimized 3d Radial Sampling Trajectories For Mri, Christopher Huynh, Datta Singh Goolaub, Christopher K Macgowan

Faculty, Staff and Students Publications

A novel method for creating “golden” 3D center-out radial MRI sampling trajectories was developed and analyzed. This method, called ELECTRO (ELECTRic potential energy Optimized), uses repulsive forces to minimize electric potential energy. An objective function , the electric potential energies of all subsets of consecutive readouts in a 3D radial trajectory, and its reduced form were minimized using a multi-stage optimization strategy. A metric called normalized mean nearest neighbor angular distance (NMNA) was proposed for describing distributions of points on a sphere. ELECTRO and other relevant golden trajectories were compared in silico using NMNA and point spread function analysis. Consecutive …

Water Quality Of Silver Creek, A Buried Urban Stream, Nick Bultje, Valerie Krause, Rebecca Nulty

Student Papers and Reports

There are many sources of pollution that can affect a watershed. These pollutants can impact the water's pH, temperature, conductivity, and dissolved solids. Escherichia coli is a specific pollutant that comes from waste products of humans and animals. High levels of E. coli cause serious health problems. This study examines Silver Creek, a tributary within the Plaster Creek watershed. Silver Creek runs mostly underground and has storm drainage systems that flow into the creek. The goal was to explore the effects of the underground section of Silver Creek on water quality and E. coli levels. The water quality and levels …

Limits Of Longwood's Electron Microscope: A Study In Biological Imaging, Rachel Danzitz, Bjoern Ch. Ludwar

Fall Showcase for Research and Creative Inquiry

This study evaluates the imaging capabilities and limitations of the Hitachi TM4000II Plus Scanning Electron Microscope (SEM) and its Scanning Transmission adapter in biological imaging. A variety of specimens, including protozoans (e.g., Volvox and nematodes), bacteria (e.g., Magnetospirillum gryphiswaldense, Bacillus cereus, and Escherichia coli), tissue samples, and blood, were analyzed. While the SEM effectively imaged protozoans and bacteria, its ability to visualize viruses was deemed impractical. Despite claims of magnification up to 100,000x, clarity significantly decreased beyond 5,000x. The transmission adapter proved functional but challenging to operate consistently. The study highlights the microscope's limitations in producing high-clarity, …

Ophidiomyces Ophidiicola And Texas Snakes: A Field To Bench Study Of Ophidiomycosis, Kenlynn L. Volz

Biology Theses

Ophidiomyces ophidiicola (Oo), the primary cause of Ophidiomycosis, is a fungal pathogen recently detected in Texas snakes. Prior to this study, there were major knowledge gaps regarding Oo growth, spread, and suitable environmental conditions. This study filled those gaps using a field to bench approach involving sampling snakes across Texas, in vitro fungal growth, and ecological niche modeling. 103 snakes were sampled across Texas in 2023 and 2024 and six cases of Oo infection were detected. Results of the growth experiment suggest that Oo prefers more stable temperatures and high humidity to a point and that there is a …

Corrigendum: Sars-Cov-2 Seroprevalence In Pregnant Women In Kilifi, Kenya From March 2020 To March 2022, Angela Koech, Geoffrey Omuse, Joseph Mutunga, Moses Mukhanya, Onesmus Wanje, Grace Mwashigadi, Geoffrey Katana, Rachel Craik, Alex Mugo, Marleen Temmerman

Pathology, East Africa

Background: Seroprevalence studies are an alternative approach to estimating the extent of transmission of SARS-CoV-2 and the evolution of the pandemic in different geographical settings. We aimed to determine the SARS-CoV-2 seroprevalence from March 2020 to March 2022 in a rural and urban setting in Kilifi County, Kenya.

Methods: We obtained representative random samples of stored serum from a pregnancy cohort study for the period March 2020 to March 2022 and tested for antibodies against the spike protein using a qualitative SARS-CoV-2 ELISA kit (Wantai, total antibodies). All positive samples were retested for anti-SARS-CoV-2 anti-nucleocapsid antibodies (Euroimmun, ELISA kits, NCP, …

The Absence Of Cxcl10 Activity Does Not Affect The Capability Of Cd8+ T Cells To Migrate And Eliminate The Tissue Cysts Of Toxoplasma Gondii From The Brains Of Chronically Infected Mice, Rajesh Mani, Yasuhiro Suzuki

Markey Cancer Center Faculty Publications

Toxoplasma gondii forms tissue cysts in neurons and astrocytes in the brain to establish chronic infection, and astrocytes express the CXCL10 chemokine in chronically infected mice. Since chemokines mediate the migration of T cells to attack their targets, and since CXCL10 plays key roles in T cell-mediated control of the proliferation of tachyzoites (the acute stage form) of T. gondii during the acute stage of infection, we examined whether CXCL10 is involved in recruiting anti-cyst CD8+ cytotoxic T cells to eliminate the cysts in their brains. We employed adoptive transfer of CD8+ immune T cells to infected, T cell-deficient SCID …

Influenza C Virus In Us Children With Acute Respiratory Infection 2016–2019, Bethany K Sederdahl, Geoffrey A Weinberg, Angela P Campbell, Rangaraj Selvarangan, Jennifer E Schuster, Joana Y Lively, Samantha M Olson, Julie A Boom, Pedro A Piedra, Natasha B Halasa, Laura Stewart, Peter G Szilagyi, G K Balasubramani, Theresa Sax, Judith M Martin, Robert W Hickey, Marian G Michaels, John V Williams, New Vaccine Surveillance Network

Faculty, Staff and Students Publications

Influenza C virus (ICV) is an orthomyxovirus related to influenza A and B, yet due to few commercial assays, epidemiologic studies may underestimate incidence of ICV infection and disease. We describe the epidemiology and characteristics of ICV within the New Vaccine Surveillance Network (NVSN), a Centers for Disease Control and Prevention (CDC)-led network that conducts population-based surveillance for pediatric acute respiratory illness (ARI). Nasal or/combined throat swabs were collected from emergency department (ED) or inpatient ARI cases, or healthy controls, between 12/05/2016-10/31/2019 and tested by molecular assays for ICV and other respiratory viruses. Parent surveys and chart review were used …