Microbes, like bacteria, viruses, and fungi, are microscopic organisms found everywhere. Each has a genome, the complete set of genetic instructions for its structure and function. A microbial genome is this full blueprint, encoded in DNA or, for some viruses, RNA. Understanding these blueprints is important because microbes influence health, the environment, and industry, and studying them reveals how they operate.
Decoding the Blueprint of Microbes
Microbial genomes are composed of DNA and show diversity in size and structure. For instance, the bacterium Escherichia coli’s genome has about 4.6 million DNA base pairs, while the human genome has approximately 3 billion. Despite being smaller, microbial genomes are information-dense, with a high proportion of DNA coding for proteins and other functional molecules.
The organization of microbial genomes differs from that of more complex organisms. Many bacteria house their genetic material in a single, circular chromosome within the cell’s cytoplasm. In addition to the main chromosome, many bacteria also possess plasmids, which are small, circular pieces of DNA that exist independently. These plasmids can carry a handful of genes and can be transferred between different bacteria, often providing specific advantages.
Genes within microbial genomes are organized into units called operons. An operon is a cluster of genes controlled by a single switch, allowing them to be turned on and off together. This arrangement enables a microbe to respond rapidly and efficiently to environmental changes, such as the sudden appearance of a new food source.
Sequencing: Reading the Microbial Code
To understand a microbial genome, scientists must read its genetic sequence. This process, genome sequencing, determines the precise order of the nucleotide bases—adenine (A), cytosine (C), guanine (G), and thymine (T)—that make up the microbe’s DNA. This information provides a list of the organism’s genes, offering insights into its potential capabilities, like how it metabolizes food or causes disease.
The method for sequencing a microbial genome involves several steps:
- The microbe’s DNA is extracted and purified.
- This long strand of DNA is broken down into numerous small, overlapping fragments.
- High-tech sequencing machines read the order of the bases for each of these millions of fragments simultaneously.
- Computer programs piece the sequence back together by finding the overlapping sections among the fragments to reconstruct the full genome.
What once took years for the first microbial genome project is now accomplished in hours or days. This acceleration in technology has made sequencing more affordable and accessible, fueling advances in microbiology.
Microbial Genomes and Our Well-being
The study of microbial genomes impacts human health and our understanding of disease. When a new infectious disease emerges, sequencing the pathogen’s genome is a primary step. This genetic information helps researchers identify the microbe and can reveal virulence factors—genes that code for molecules that enable the organism to cause illness. This knowledge is used to track the spread of specific strains during an outbreak, such as with foodborne pathogens like Salmonella.
Our bodies are home to trillions of microbes, collectively known as the human microbiome, which play a part in our daily health. Analyzing the collective genomes of these communities, a field called metagenomics, has shown that gut bacteria aid digestion, produce vitamins, and train our immune systems. Disruptions in this internal ecosystem have been linked to a range of health issues, from inflammatory bowel disease to allergies.
Genomic information is used to address antibiotic resistance. A bacterial genome can change through mutation or acquire new genes from other microbes, often through plasmids, which can render antibiotics ineffective. By sequencing the genomes of resistant bacteria, scientists can monitor the emergence and spread of resistance genes. This informs treatment strategies and the development of new drugs.
Harnessing Microbial Genomes for a Better World
Understanding microbial genomes has applications beyond medicine that benefit society and the environment. Many microbes are natural recyclers, with genomes containing instructions for breaking down complex substances. For example, the bacterium Alcanivorax borkumensis has genes that allow it to consume hydrocarbons, making it useful for cleaning up oil spills. Other microbes are important for agriculture, with genomes that enable them to perform nitrogen fixation, converting atmospheric nitrogen into a form plants can use as fertilizer.
The biotechnology industry “mines” microbial genomes to find genes that code for useful products. Enzymes from microbes in extreme environments, like hot springs, are used in laundry detergents for high temperatures. Similarly, the genomes of yeast and bacteria are engineered to optimize the production of biofuels, vaccines, and vitamins.
Genetic insight into microbes also extends to food production. The flavors and textures of fermented foods like cheese, yogurt, and beer result from microbial metabolism. Scientists study the genomes of organisms like Lactobacillus and Saccharomyces to understand which genes are responsible for these traits. This allows for the selection and improvement of microbial strains to create more consistent food products.