Template:Towson University

From MicrobeWiki, the student-edited microbiology resource

MicrobeWiki Page Assessment

Create a resource for other people to appreciate the amazing diversity of the microbial world! Demonstrate your knowledge of your microbe by creating a MicrobeWiki page using the scientific literature and reputable resources. Each section of your page must integrate course Learning Objectives (LO) to demonstrate your understanding of microbiology. Each section must have at least 2 references to the primary peer-reviewed literature and at least 1 reference to a reputable reference book. All references must be cited in the References section. Please remove the LO and the instructions from each section. You only need to put your text in the different sections.

Introduction

LO: “Microorganisms provide essential models that give us fundamental knowledge about life processes.”

LO: Because the true diversity of microbial life is largely unknown, its effects and potential benefits have not been fully explored.

LO: Mutations and horizontal gene transfer, with an immense variety of microenvironments, have selected for a huge diversity of microorganisms.

  • Tying the introduction to the learning objectives with detailed support, write a “hook” to convince the reader that YOUR microbe is interesting and make them want to read more!
  • In the introduction, briefly describe the habitat and the organism that is the topic of this page.
  • Include:
    • habitat
    • organism
    • organism’s ecological significance (what metabolic processes do they carry out?)
    • and the importance of the microbe in this environment (what ecological function does it perform?)
  • Image of the organism and description of the image.
    • Describe what kind of microscope took the image, the magnification, staining (if appropriate), the name of the organism, and highlight any key features illustrated in the image. Cite the source of the image and include the citation in the reference section.

If you have obtained permission - include a photo of the organism under a microscope and/or growing in culture with figure legend and properly cited! If you have NOT obtained permission for a photo, please include a link to a photo of the organism. Include the information that would normally be in the figure legend when linking to the photo.

Classification

LO: Organisms are classified using a standard taxonomic rank.

  • Give the taxonomic rank in descending order of your organism.
Domain; Phylum; Class; Order; Family; Genus; Species
  • Provide a link to the following pages specific to your organism
    • NCBI: Taxonomy
    • JGI:GOLD

Phylogenetic Relatedness

LO: The evolutionary relatedness of organisms is best reflected in phylogenetic trees.

  • Cite and link out to peer-reviewed scientific literature that constructs phylogenetic trees using either 16S rRNA, multiple housekeeping genes, or whole genomes.
  • Describe the genes and phylogenetic methods used to create the tree.
  • What is the closest relative of your identified isolate according to the phylogenetic tree you used?
  • Include a link to a figure of the most recently constructed phylogenetic tree with proper citation and a detailed description of the tree.
  • In the description include: the gene(s)/genomes used and the phylogenetic method used.

Ecological Habitat

LO: Microorganisms are ubiquitous and live in diverse and dynamic ecosystems.

LO: The survival and growth of any microorganism in a given environment depends on its metabolic characteristics.

  • Describe its habitat and contributions to the environment. Note that an organism’s environment might be in or on another organism (e.g. bacteria in insect digestive system)
  • Include a link to a photo of a representative habitat with a figure caption that explains what kind of habitat this is and where the habitat is found.
  • Where the genus is most commonly found
    • If it is found in the environment, what macroscopic “field marks” does it have (color, smell, etc…)
    • If found in clinical samples – what is a diagnostic test?
  • Describe the physical and chemical abiotic characteristics of the environment
    • Temperature, pH, oxygen, etc..

Significance to the Environment

LO: “Microbes are essential for life as we know it and the processes that support life” – how does your organism and your organisms’ metabolism support life on planet Earth?

LO: Human impact on the environment influences the evolution of microorganisms (e.g., emerging diseases and the selection of antibiotic resistance).

  • Describe how this microbe cycles nutrients in the environment. Note that an organism’s environment might be in or on another organism (e.g. bacteria in insect digestive system)
  • Include links to other MicrobeWiki pages on nutrient cycling or other reputable information on nutrient cycling geared toward the public (podcasts, blogs, gov or professional sites)
  • Are there human-induced changes to the environment that have influenced this microbe’s evolution, population numbers, or spread? (e.g. agriculture, clear-cutting/destruction of natural areas, greenhouse gasses, high nitrogen/phosphorous run-off, oil spills, overuse of antibiotics,...)

Ecological Lifestyle and Interactions

LO: “Microorganisms provide essential models that give us fundamental knowledge about life processes.”

LO: “Microorganisms are ubiquitious and live in diverse and dynamic ecosystems."

LO: “Microorganisms and their environment interact with and modify each other.”

LO: “Most bacterial in nature live in biofilm communities.”

  • Describe the organism’s lifestyle, the organisms it interacts with, and how these interactions influence their environment.
  • Name and describe the kind of lifestyle of the organism (free-living? host-associated? obligate? Facultative? Parasitic? Mutualistic? Saprophytic?)
    • If the organism is mutualistic or pathogenic, state what host it most commonly associates with
    • If parasitic – what disease does it cause and what are the symptoms?
    • If mutualistic – what cost/benefit does it receive from the host and what cost/benefit does it give the host?
    • If saprophytic, what kinds of organisms does it feed upon?
    • Does the lifestyle of the organism changes with the host or context? If so, you might select one type of lifestyle to focus on, but then mention the other associations in a few sentences.
  • Describe key groups of microbes that your microbe interacts or are associated with important processes found in this environment.
    • Link to other MicrobeWiki pages or other reputable resources where possible.
  • Describe biological interactions that might take place in this environment, using as many sections/subsections as you require.
    • Are there important biological interactions that are important in this environment?
    • Do these interactions influence microbial populations and their activities?
    • How do these interactions influence other organisms?

Significance to Humans

LO: “Microorganisms can interact with both human and nonhuman hosts in beneficial, neutral, and detrimental ways.”

LO: “Humans utilize (note: this is the correct way to use utilize!) and harness microorganisms and their products.”

  • Describe how this microbe has influenced human society now or in the past.
    • If your microbe is a pathogen, does the ecology and metabolism of the pathogen suggest how we can interrupt its interactions with the host?
  • If there is technology or product that this microbe is part of or could be a part of:
    • describe the technology
    • how this technology or product influences human lives.

Cell Structure

LO: Microbes have unique cell structures that can be targets for antibiotic, immunity, and phage infection.

LO: Microbes have specialized structures (e.g. flagella, endospores, and pili) that often confer critical capabilities.

Provide a physical and metabolic description of the organism. Are there special diagnostic media or methods to distinguish this microbe from close relatives?

  • Colony morphology (size, shape, texture, pigmentation, smell?, etc…)
  • Cell morphology
  • Gram type, if applicable
  • Motility
  • Any other important structures

Cell Metabolism

LO: “Microbes are essential for life as we know it and the processes that support life.” LO: “Microorganisms provide essential models that give us fundamental knowledge about life processes.” LO: Because the true diversity of microbial life is largely unknown, its effects and potential benefits have not been fully explored.

Provide a physical and metabolic description of the organism. Are there special diagnostic media or methods to distinguish this microbe from close relatives?

  • Optimal abiotic growth conditions (temperature, salinity, oxygen, UV)
  • Carbon growth sources
  • Other metabolic abilities
  • Any other unique abilities (e.g toxin production, antibiotic resistance, etc...)

.

Genome Structure, Content, and/or Gene Expression

LO: Genome structure and content provide insight into a microbe's evolutionary history, ecological niche, and interactions with hosts and other microbes.

LO: Mutations and horizontal gene transfer, with an immense variety of microenvironments, have selected for a huge diversity of microorganisms.

LO: The regulation of gene expression is influenced by external and internal molecular cues and/or signals.

LO: Cell genomes can be manipulated to alter cell function.

LO: Genetic variations can impact microbial functions (e.g. in biofilm formation, pathogenicity, and drug resistance).

Metrics

  • Genome size
  • % GC
  • number of chromosomes and/or plasmids?
  • Circular or linear?
  • Other interesting features?

Relevance

  • Why was this organism sequenced?
  • Where was this organism sequenced?
  • Provide a direct link to the sequenced genome
  • What does the genome tell us about this organism? Ie. What new insights do we have after it is sequenced?
  • Give an example of an interesting feature found in the genome (LGT, mutations, plasmids, antibiotic resistance, toxins, etc...).
  • Explain why this feature is important for the microbes’ survival or success.

Interesting Feature

LO: Mutations and horizontal gene transfer, with an immense variety of microenvironments, have selected for a huge diversity of microorganisms.

LO: Human impact on the environment influences the evolution of microorganisms (e.g., emerging diseases and the selection of antibiotic resistance).

LO: Because the true diversity of microbial life is largely unknown, its effects and potential benefits have not been fully explored.

Describe in detail one particularly interesting aspect of your organism.

  • Why is this detail interesting?
  • How does it help the organism survive?
  • How does this interesting feature influence the larger environment or other microbes?
  • How can this interesting feature be helpful to humans?
  • In ~3 sentences propose WHY more research and WHAT kind of new research should be done on this organism and others like it. Connect this to the learning objective about the importance of microbial diversity
  • If you have created a graphical abstract, meme, image, etc... about this organism and its interesting feature, include it here. You can put a creative commons copywrite it to control how other people use it: https://creativecommons.org/about/cclicenses/

References

Each section must have at least 2 references to the primary peer-reviewed literature and at least 1 reference to a reference book like Bergey’s Manual or resources available on the NCBI bookshelf. Also, link out to reputable blogs like Small Things Considered (https://schaechter.asmblog.org/schaechter/), MostlyMicrobes (http://www.mostlymicrobes.com/), Sarah’s Little World (https://sarahs-world.blog/), professional websites American Society for Microbiology (https://asm.org/browse-asm), Microbiology Society (https://microbiologysociety.org/), and podcasts like the many by ASM (https://asm.org/podcasts), This Podcast Will Kill You (https://thispodcastwillkillyou.com/), etc… These should also be cited in the reference section.

Is this a peer-reviewed journal? Check this partial list: https://www.openacessjournal.com/peer-reviewed-journals

Convert your References section to Vancouver format: BibGuru (https://www.bibguru.com/), PMID2cite (https://www.pmid2cite.com/)

Example references: Vancouver citation

Journal

Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500. https://doi.org/10.1099/00207713-50-2-489

Book

Surname Initials. Book title. Edition - if available: Publisher, place of publication; Year .

Books with Editors

Beers MH, Porter RS, Jones TV, Kaplan JL, Berkwits M, editors. The Merck manual of diagnosis and therapy. 18th ed. Whitehouse Station (NJ): Merck Research Laboratories; 2006.

Authored chapter in edited publication;;

Glennon RA, Dukat M. Serotonin receptors and drugs affecting serotonergic neurotransmission. In: Williams DA, Lemke TL, editors. Foye's principles of medicinal chemistry. 5th ed. Philadelphia: Lippincott Williams & Wilkins; 2002.

Electronic

World Health Organization (WHO). Mortality country fact sheet 2006 [internet]. Geneva: WHO; 2006. Available from: www.who.int/whosis/mort_emro_pak_pakistan.pdf

Edited by <your name>, a @MicrobialTowson student of Dr. Anne M. Estes at Towson University. Template adapted from templates by Angela Kent, University of Illinois at Urbana-Champaign and James W. Brown, Microbiology, NC State University.

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