What is Microbial Taxonomy?

Taxonomy is the science of naming, classifying, and describing organisms. The taxonomy will include all the plants, microorganisms, and animals on this planet. Carl Linnaeus coined the taxonomy term. He is known as the father of taxonomy. Microbial taxonomy is a criterion of grouping microorganisms into groups based on their similarities and past relatedness. Microorganisms belonging to the same group are differentiated from the others via grouping into categories. This differentiation makes the study of microorganisms easy. There are different types of microbial taxonomies like Numerical and Molecular taxonomy. The study of microorganisms is known as microbiology. Microbiology is a broad term that takes into account microbial cultures, taxonomic studies, evolutionary relationships. Microbial interaction and diversity are huge data that needs to be compiled under the subject of microbiology. Microbiology covers various organisms like bacteria, fungi, algae, plants, animals, etc. 

Three Disciples of Taxonomy

Classification

It is the organization of the microorganisms into similar groups based on morphological, genetic, and phylogenetic traits. The microbial classification is performed based on how they look and their mode of action. This classification helps in the sectors like agriculture, industries, and food technology. Accurate identification will allow appropriate microbial, plant, and animal classification.

Nomenclature

Nomenclature is a system of naming species in biological taxonomy. Two terms represent the organism's species, the genus, and species names, which are Latinized words originating from numerous sources.

Identification

In biology, identification is the process of attributing a pre-existing taxon name to an individual organism. Individualistic natural body traits, experimentally generated individual markers, or natural individualistic molecular markers can identify organisms to individual scientific names.

Numerical Taxonomy

This method includes many different criteria to group the microorganisms into categories at once. If only one basis were considered, there would be a huge number of microorganisms in a category; hence it would be difficult to study them. The groups are formed based on microbial similarities and calculating the similarity coefficient. At a certain threshold value, the microorganisms will get placed in a category.

Molecular Microbial Taxonomy

This method includes the generation and inheritance of mutations. A mutation is a deletion, insertion, or replacement of a nucleotide or amino acid group in the genetic material. Sometimes mutation proves to be an advantage to the microorganism. Thus it is passed down to generations. But on the other hand, mutation can also cause harm to microbial growth. As mutations are very minute changes in the genetic material, they will form divergent microorganisms from the same genetic parent after millions of years. By targeting and sequencing the desired gene, one can find similarities and dissimilarities between the divergent microorganisms. When enough genomes from organisms have been sequenced, a dendrogram can be constructed to display the extent of similarities between them. The basic principle of molecular microbial taxonomy is to sequence the 16S RNA, usually in prokaryotes. The evolution in the 16s RNA is quite slow, and therefore the changes can be seen profoundly after millions of years, making it easy to generate a similarity. The polymerase chain reaction is a technique used to amplify the target sequence and make the evolutionary or phylogeny tree. According to updated information, microorganisms have three evolutionary branches - bacteria, archaea, and eukaryotes. 

Biological Classification

The study of biological classification is called taxonomy. The microbial classification, nomenclature, and identification form the microbial taxonomy. The biological classification was a system classified by scientists to categorize the organisms based on physical attributes and genetic analysis. There are seven taxonomic ranks which they described - kingdom, phylum, class, order, family, genus, and species. Every organism is placed under this hierarchical order as we go down the hierarchy, the specificities increase and the number of organism decrease. The taxonomic ranks are called taxon. The taxon kingdom is the most broadly classified, and the species taxon is the lowest and most specific taxon. In taxonomy, binomial nomenclature was a formal system used to name the species. Taxonomic diversity is the other term that defines the mean taxonomic path between randomly chosen organisms. It will take into account the taxonomic differences and species richness (heterogenicity). The taxonomic study is made easier by creating the taxon via the biological classification method.

Bacterial Identification and Taxonomy

The bacterial identification can be broadly classified into two groups - genotypic and phenotypic techniques. The genotype will include profiling based on similar genetic material, and the phenotype performs profiling based on the microorganism's chemical composition and metabolic aspects. Microbiology is the study of organisms. Thus, it is important to make this study flexible by categorizing the microorganisms. Phenotypic characters are more reliable as the information about the bacteria's survival, food habits, developmental and antibiotic resistance is considered. Both phenotypic and genotypic studies are complementary. Genotypic identification can be performed either by pattern-based technique or sequence-based techniques. FAME (fatty acid analysis) is used to classify bacteria based on their fatty acid composition. The prokaryotes fatty acids are quite different from eukaryotes regarding their length, double bonds, branched chains, and rings. 

Dendrogram

It is a diagram that depicts the evolutionary relationship between the organisms. It is a way to allocate the organisms into clusters. It shows the relatedness between merged classes of organisms. The distances between a species merging or diverging from the parents' characters help to plot the dendrogram. It will provide a detailed view of the similarity percentage.

Common Mistakes

• Taxonomy does not include the study of evolution. Evolution has its branch of science.
• There are both divergent and convergent species.
• The domain is a taxon included in the modern classification.

Context and Applications

This topic is significant in the professional exams for both undergraduate and graduate courses, especially for

• Bachelor of Science in Biology
• Master of Science in biotechnology
• Bioinformatics

Related Concepts

1. Phylogeny
2. Nomenclature
3. Genomic fingerprinting