Taxonomic Guide to Infectious Diseases

Understanding the Biologic Classes of Pathogenic Organisms

Jules J. Berman

• Publisher: Academic Press
• Year: 2019
• eBook ISBN: 9780128175774
• Edition: 2
• Topic: Sciences biologiques
• Subtopic: Maladies infectieuses

Taxonomic Guide to Infectious Diseases: Understanding the Biologic Classes of Pathogenic Organisms, Second Edition tackles the complexity of clinical microbiology by assigning every infectious organism to one of 40+ taxonomic classes and providing a description of the defining traits that apply to all the organisms within each class. This edition is an updated, revised and greatly expanded guide to the classes of organisms that infect humans. This book will provide students and clinicians alike with a simplified way to understand the complex fields of clinical microbiology and parasitology.- Focuses on human disease processes and includes numerous clinical tips for healthcare providers- Describes the principles of classification and explains why the science of taxonomy is vital to the fields of bioinformatics and modern disease research- Provides images of prototypical organisms for taxonomic classes- Includes a section that lists common taxonomic pitfalls and how they can be avoided

Chapter 1

Principles of taxonomy

Abstract

In a sense, this book is largely concerned with how scientists deal with the diversity of life forms that live on planet earth. We will show that the key to simplifying and understanding the diversity of life is through the process of classification. For modern biologists, the key to the classification of living organisms is evolutionary descent (i.e., phylogeny). The hierarchy of classes corresponds to the succession of organisms that evolved from the earliest living organism to the current set of extant species. Pre-Darwinian biologists, who knew nothing about evolution, somehow produced a classification that looks much like the classification we use today. How did they do it? In this chapter, we will introduce the scientific principles of classification, wherein organisms are placed into classes based on their relationships with other organisms. We will also discuss the difference between a relationship and a similarity, and why classifications cannot be built solely on the basis of shared similarities among organisms.

Keywords

Phylogeny; Tree of life; Species diversity; Classes; Subclasses; Ancestral lineage

Section 1.1 The consequence of evolution is diversity

There can be only one

Motto of the immortals in the fictional Highlander epic

Most readers are familiar with the premise of the “Highlander” movies and television shows, which depict a “survival-of-the-fittest” struggle among a population of immortal humans. In the end, there must be only one surviving immortal. Of course, the most casual glance at our surroundings informs us that we live in an “Anti-Highlander” world wherein evolution pushes us to ever-increasing species diversity [Glossary Survival of the fittest].

Introductory courses in evolution stress the notion that evolution leads to improved species, through natural selection [1]. If evolution served the single purpose of improving species, then we would live in a Highlander world, where a small number of the most successful species would prevail, and the others would perish. One of the recurring themes discussed in this book is that the primary consequence of evolution is speciation, the biological process that accounts for the enormous diversity of species that inhabit our planet. When we understand speciation, we can fully grasp the phylogenetic classification of organisms (i.e., the classification of species by their ancestral lineages). When we understand classification, we can simplify the task of understanding the biological properties of the thousands of species that are potential pathogens in humans. Furthermore, we can discover general methods of prevention or treatment that apply to whole classes of related organisms [Glossary Human ancestral lineage, Organism].

How many species live on earth today? A large number of species comes from the prokaryotes (i.e., cells with no nuclei, consisting of Class Bacteria plus Class Archaea), which are estimated to have between 100 thousand and 10 million species. These numbers almost certainly underestimate the true number of prokaryotic species, as they are based on molecular techniques that would exclude valid species that happen to have sequence similarities with other species [2]. As an example of how methodology impacts numbers, samples of soil yield a few hundred different species per gram, based on culturing. If the species are counted on the basis of 16s RNA gene sequencing, we find a few thousand different species of bacteria in each gram of soil. If we base the count on DNA-DNA reassociation kinetics, the number of different bacterial species, per gram of soil, rises to several million [3].

The eukaryotes (i.e., organisms whose cells contain a nucleus) are estimated to have about 9 million species [4]. As for the viruses, we really don't have any good estimate for the number of their species, although it is claimed that viruses account for the greatest number of organisms, species, and classes of species on the planet [5–7]. If we confine ourselves to counting just those viruses that infect mammals, we have an estimate of about 320,000 [8]. Adding up the estimates for prokaryotes, eukaryotes, and viruses, we get a rough and conservative 10-20 million living species.

In addition to the individual species of organisms that live on earth, there are numerous combinations of organisms whose lives are entangled with one another. Perhaps the best known examples of which are the lichens. Formerly known as the Mycophycophyta, lichens are now recognized to be aggregate organisms wherein each component has its own phylogenetic lineage. Lichens independently emerged from fungi associating with algae and cyanobacteria multiple times throughout history [9].

It is worth noting that species counts, even among the most closely scrutinized classes of organisms, are always subject to revision. In the past, the rational basis for splitting a group of organisms into differently named species required, at the very least, heritable functional or morphologic differences among the members of the group. Gene sequencing has changed the rules for assigning new species. For example, various organisms with subtle differences from Bacteroides fragilis have been elevated to the level of species based on DNA homology studies. These include Bacteroides distasonis, Bacteroides ovatus, Bacteroides thetaiotaomicron, and Bacteroides vulgatus [10]. Accounting for underestimation, it should come as no surprise that one study has suggested that there are at least a trillion species of organisms on earth [11].

Of course, the number of living species is a tiny fraction of all the species that have lived and died through the course of earth's history. It is estimated that 5–50 billion species have lived on earth, and more than 99% of them have met with extinction, leaving a relatively scant 10–100 million living species [12]. If the purpose of every species were to ensure its own survival, then they are all doing a very bad job of it, insofar as nearly all species become extinct. In Section 2.2, “The Biological Process of Speciation,” we shall see that the determinant of biological success, for any species, is to produce new species. It is the production of descendant classes of species that confers inherited cellular properties that we observe in all living organisms, and that we now use to construct classifications of organisms.

Although there are millions of species on this planet, we should be grateful that only a tiny fraction is infectious to humans. Nobody knows the exact number of living species, but for the sake of discussion, let us accept that there are 50 million species of organisms on earth (a gross underestimate by some accounts). There have been about 1400 pathogenic organisms reported in the medical literature. This means that if you should stumble randomly upon a member of one of the species of life on earth, the probability that it is an infectious pathogen is about 0.000028 [Glossary Burden of infectious diseases, Incidence, Infectious disease].

With the all the different species of organisms on earth today, numbering perhaps in the hundreds of millions, how can we hope to understand the biosphere? It's all done with classification. Infectious agents fall into a scant 40 biological classes (32 classes of living organisms plus 7 classes of viruses plus 1 current class of prions). When we have learned the basic biology of the major taxonomic divisions that contain the infectious organisms, we will understand the fundamental biological features that characterize every clinically relevant organism.

Section 1.2 What is a classification?

Deus creavit, Linnaeus disposuit, Latin for “God Creates, Linnaeus organizes.”

Carolus Linnaeus

The human brain is constantly processing visual and other sensory information collected from the environment. When we walk down the street, we see images of concrete, asphalt, grass, other persons, birds, and so on. Every step we take conveys another world of sensory input. How can we process it all? The mathematician and philosopher Karl Pearson (1857–1936) has likened the human mind to a “sorting machine” [13]. We take a stream of sensory information and sort it into objects, and then we collectively put the individual objects into general classes. The green stuff on the ground is classified as “grass,” and the grass is subclassified under some larger groups such as “plants.” Flat stretches of asphalt and concrete may be classified under “road” and the road might be subclassified under “man-made constructions.” If we did not have a culturally determined classification of objects in the world, we would have no languages, no ability to communicate ideas, no way to remember what we see, and no way to draw general inferences about anything at all. Simply put, without classification, we would not be human.

Every culture has some particular way to impose a uniform perception of the environment. In English-speaking cultures, the term “hat” denotes a universally recognized object. Hats may be composed of many different types of materials, and they may vary greatly in size, weight, and shape. Nonetheless, we can almost always identify a hat when we see one, and we have no trouble distinguishing a hat from all other types of objects. An object is not classified as a hat simply because it shares a few structural similarities with other hats. A hat is classified as a hat because it has a relationship with every other hat, as an item of clothing that fits over the head.

Taxonomists search for relationships, not similarities, among different species and classes of organisms [14]. But isn't a similarity a type of relationship? Actually, no. To better understand the difference, imagine the following scenario. You look up at the clouds, and you begin to see the shape of a lion. The cloud has a tail, like a lion's tale, and a fluffy head, like a lion's mane. With a little imagination, the mouth of the lion seems to roar down from the sky. You have succeeded in finding similarities between the cloud and a lion. When you look at a cloud and you im...

Table of contents

• Cover image
• Title page
• Table of Contents
• Copyright
• Other books by the author
• About the author
• Preface to second edition
• Preface to first edition
• Chapter 1: Principles of taxonomy
• Chapter 2: Species and speciation
• Chapter 3: Bacteria
• Chapter 4: Eukaryotes
• Chapter 5: Animals
• Chapter 6: Fungi
• Chapter 7: Viruses
• Chapter 8: Changing how we think about infectious diseases
• Index