Chapter 1

[Virtual Presenter] Microbial taxonomy is a complex process that involves identifying and classifying microorganisms based on their characteristics. The process begins with the collection and analysis of data from various sources such as DNA sequencing, biochemical tests, and morphological observations. These data are then used to construct a phylogenetic tree, which represents the evolutionary relationships among different species. The phylogenetic tree is constructed using algorithms and statistical models that analyze the genetic information contained within the DNA sequences. The resulting tree shows the branching pattern of the evolutionary history of the organisms, providing valuable insights into their evolutionary relationships. The next step in the process is to assign taxonomic ranks to the organisms based on their characteristics. This involves assigning a rank to each organism according to its morphology, physiology, and genetics. The taxonomic ranks range from the most general (Domain) to the most specific (Species). The Domain level provides a broad categorization of the organisms, while the Species level provides a more detailed classification. Once the taxonomic ranks have been assigned, the organisms can be further classified using a hierarchical system. This system uses a combination of morphological, physiological, and genetic characteristics to assign a higher-level classification. For example, an organism may be classified as a member of the genus Homo sapiens at the species level, but it may also be classified as a member of the family Hominidae at a higher level. In addition to the traditional taxonomic ranks, there are several alternative approaches to classification that have been developed in recent years. One approach is the use of molecular markers, which involve analyzing the genetic material of the organisms. Another approach is the use of phenotypic traits, which involve studying the physical characteristics of the organisms. Both of these approaches offer new ways to classify microorganisms and provide additional insights into their evolutionary relationships. Overall, microbial taxonomy is a multifaceted discipline that requires a deep understanding of the underlying biology and chemistry of the organisms being studied. It involves a combination of traditional taxonomic ranks and alternative approaches to classification, and requires a high degree of analytical skill and attention to detail..

Objectives 2 Copyright © 2014, by Mosby, an imprint of Elsevier Inc. • Define classification, identification, species, genus, and binomial nomenclature. • Properly use binomial nomenclature in the identification of microorganisms including syntax, capitalization, and punctuation. • Identify a microorganism’s characteristic as either phenotypic or genotypic. • Describe how the classification, naming, and identification of organisms play a role in diagnostic microbiology in the clinical setting..

Taxonomy – 3 disciplines Classification 3 Copyright © 2014, by Mosby, an imprint of Elsevier Inc. Identification of organisms Nomenclature.

[Audio] ## Step 1: Identify the classification method The classification method involves organizing microbes into groups based on morphologic, physiologic, and genetic traits. ## Step 2: Explain the taxonomic hierarchy The taxonomic hierarchy lists taxa from most basic to complex, starting with Species (sp. spp.), which is a collection of bacterial strains sharing physiologic and genetic features. ## Step 3: Describe the Species level Species (sp. spp.) is a collection of bacterial strains that share physiologic and genetic features, such as Klebsiella pneumoniae and K. oxytoca. ## Step 4: Define the Genus level A genus is a collection of species with common features, but sufficient differences to be identified as individual species. ## Step 5: Explain the Genus level further For example, Enterobacteriaceae contains approximately 33 genera, indicating a higher level of complexity. ## Step 6: Summarize the classification process The classification process involves categorizing microbes into groups based on their morphologic, physiologic, and genetic characteristics, using a hierarchical system that includes Species, Genus, and Family levels. ## Step 7: Highlight the importance of understanding the classification Understanding the classification of microbes is crucial for identifying and studying these microorganisms, as well as developing effective treatments and prevention strategies. ## Step 8: Emphasize the need for accurate classification Accurate classification is essential for advancing scientific knowledge and improving public health outcomes related to microbial infections. ## Step 9: Outline the key characteristics of each taxon Each taxon has distinct characteristics that distinguish it from others, including morphologic, physiologic, and genetic features. ## Step 10: Provide examples of different taxons Examples include Species (e.g., Klebsiella pneumoniae), Genus (e.g., Enterobacteriaceae), and Family (e.g., Pseudomonadaceae). ## Step 11: Discuss the limitations of current classification systems Current classification systems have limitations, such as the difficulty in distinguishing between closely related species. ## Step 12: Suggest future directions for improvement Future research should focus on developing more accurate and comprehensive classification systems that take into account the complexities of microbial evolution. ## Step 13: Emphasize the need for continued research Continued research is necessary to improve our understanding of microbial classification and its applications in fields like medicine and environmental science. ## Step 14: Highlight the significance of microbial classification Microbial classification has significant implications for various fields, including medicine, agriculture, and biotechnology. ## Step 15: Summarize the main points Classification of microbes involves organizing them into groups based on morphologic, physiologic, and genetic traits, using a hierarchical system that includes Species, Genus, and Family levels. The final answer is: Classification of microbes involves organizing them into groups based on morphologic, physiologic, and genetic traits, using a hierarchical system that includes Species, Genus, and Family levels. The taxonomic hierarchy lists taxa from most basic to complex, starting with Species, which is a collection of bacterial strains sharing physiologic and genetic features. A genus is a collection of species with common features, but sufficient differences to be identified as individual species. Each taxon has distinct characteristics that distinguish it from others. Accurate classification is essential for advancing scientific knowledge and improving public health outcomes related to microbial infections. Continued research is necessary to improve our understanding of microbial classification and its applications in fields like medicine and environmental science..

Classification • Taxa consist of similar morphologic, physiologic, and genetic traits. • Kingdom • Phylum • Class • Order •Family—Organisms have a common attribute. • Genus—Contains different species. • Species—Is the most basic taxonomic group. Copyright © 2014, by Mosby, an imprint of Elsevier Inc. 5.

Classification.

[Audio] The binomial nomenclature system uses a combination of letters and symbols to identify and classify microorganisms. Each microorganism is assigned a unique two-part name consisting of a genus and a species. The first part of the name, which represents the genus, is usually capitalized and sometimes abbreviated. The second part of the name, which represents the species, is always written in lowercase and never abbreviated. The full name of the microorganism is often displayed with italics or underscores. This system enables scientists to clearly communicate about specific microorganisms and ensures that everyone agrees on what they mean. By using this system, scientists can easily identify and distinguish between different types of microorganisms..

[Audio] The International Code of Nomenclature for Bacteria (ICNB) is a set of rules that governs the naming of bacteria. These rules provide a standardized way of identifying and classifying microorganisms. The ICNB specifies the format for naming bacteria, including the use of binomial nomenclature. Binomial nomenclature involves two parts: the genus name and the species name. The genus name is usually capitalized, while the species name is written in lowercase. For example, the bacterium Streptococcus pneumoniae is commonly referred to as S. pneumoniae. The ICNB also allows for informal designations, such as streptococci and staphylococci, which do not require italics. Over time, the ICNB has undergone revisions, leading to changes in previously recognized names. For instance, Stenotrophomonas maltophilia was formerly known as Xanthomonas maltophilia. To accurately identify and classify microorganisms, understanding the ICNB is crucial..

Binomial Nomenclature 9 Copyright © 2014, by Mosby, an imprint of Elsevier Inc..

[Audio] The process of microbial identification involves several steps that require careful consideration and analysis. These steps include determining the morphology and physiology of the microorganism, as well as its genetic makeup. The classification of a microorganism into a specific genus and species is also crucial for accurate identification. Scientists use various methods to analyze the characteristics of the microorganism, including DNA sequencing and biochemical tests. Phenotypic characteristics, such as morphology, staining patterns, and nutritional requirements, are also used to aid in the identification process. By combining these different approaches, researchers can gain a comprehensive understanding of the microorganism's characteristics and accurately identify it. This information is essential for diagnosing and treating diseases caused by the microorganism..

Methods and Criteria 11 Copyright © 2014, by Mosby, an imprint of Elsevier Inc. Genotypic Characteristics • Organism’s genetic makeup • Nature of the organism’s genes and nucleic acids • E.g. mecA gene – identify MRSA strains • rpoB gene – to identify MDR-M. tuberculosis strains Phenotypic Characteristics • Features beyond the genetic level • Observable characteristics • Extensive analytic procedures that may be required • E.g. Cefoxitin/Methicillin resistance (disc susceptibility) – identify MRSA stains • MDR-M. tuberculosis – resistance (rifampicin).

12 Copyright © 2014, by Mosby, an imprint of Elsevier Inc..

13 Copyright © 2014, by Mosby, an imprint of Elsevier Inc..

[Audio] The importance of microbial taxonomy cannot be overstated. Microbial taxonomy is essential for understanding the complex relationships between different microorganisms. To achieve this, a clear understanding of their classification and identification is necessary. Phenotypic and genotypic features can be used to identify and classify microorganisms with greater accuracy and speed. This is particularly crucial in the clinical setting, where timely diagnosis and treatment are critical. The ability to identify emerging causes of infectious diseases is vital for public health. Reliable information provided by microbial taxonomy helps clinicians make informed decisions that ensure patient safety and well-being..