Evolution of the Human Microbiome and Impacts on Human Health, Infectious Disease, and Hominid Evolution

Abstract

Because the diverse microbial communities on and in the body (microbiome) are tightly coevolved with human cells, it is vital to explore the evolutionary history of the human microbiome. With the advent of new methodologies and sequencing technologies, researchers can now explore different factors that influence the bacterial community structure and colonization of specific species in the human microbiome. Using distant out-groups, such as chimpanzees, and human populations with unique lifestyles, such as Amerindians, the history and formation of the modern human microbiome in Westernized societies can be elucidated, providing vital information into how to these microbial communities were impacted by past events. Large cultural and dietary revolutions, such as the Neolithic Revolution (~7500 years ago) and the Industrial Revolution (~200 years ago), largely impacted these microbial communities. Ancient events, such as interbreeding and admixture with our closest ancient relatives, such as Neanderthals or Denisovans, could also have impacted the microbiome that modern humans carry today. Reconstructing the evolutionary history of the human microbiome has proven to be an intricate tale, with impacts on modern health and disease, as well as the evolutionary fate of modern humans.

Glossary

Allopatric

A descriptive term of processes, such as evolution, that happen to two different populations of organisms separated into different geographical locations

Amerindians

Indigenous populations that are currently living in North or South America, which are typically living without contact with Westernized civilizations

Anatomically modern humans

Hominids that are morphologically similar to modern Homo sapiens sapiens, i.e. modern humans, and likely originated from Africa around 200,000 years ago

Archaic humans

Hominids that share a lineage with Homo sapiens after the evolutionary split from chimpanzees, including Neandertals and Denisovans

Bacterial ‘fingerprints’ or fingerprinting

This is a technique that sequences a single gene conserved across all bacterial species, typically the gene encoding the 16S ribosomal RNA subunit, which provides a picture of all the bacterial species present and their abundances. These sequences can be highly specific to an individual, acting the same way a fingerprint does in forensics

Biofilm

This is a diverse bacterial community that forms works together as a single organism and can form on surfaces of hot springs, pipes, or even human teeth

Convergent evolution

An evolutionary process that results in similar outcomes, i.e. function, even though the species that are evolving are in different locations or are unrelated

Enterotypes

A simple way of classifying gut microbiomes based on the largest proportions of dominant bacterial phyla present in a sample

Hygiene hypothesis

The theory that a lack of exposure to microbes (or an increased exposure to sterile environments) increases one’s susceptibility to disease by failing to stimulate the immune system during development

Indigenous

A modern human population that is native to a specific place over a long time span, usually prior to European colonization during the colonial period

Industrial Revolution

A cultural change that occurred the eighteenth and nineteenth centuries, following the invention of the machine, and lead to numerous social and economic changes

Isotope analysis

The identification of chemical elements within compounds that are present in material to determine differences in composition, variation, or change, i.e. using carbon isotopes to track the diet of humans

Linear Pottery culture (LBK)

Linearbandkermik (LBK) is a culture existing about ~7500 years before present, which were Europe’s first farmers and are demarcated by a distinct banding pattern on the pottery

Microbiome

Any microbial community that exists in one space, i.e. the human body

Metagenome

The defining term of all of the genomes that exist in the human body, which includes the human genome and the bacterial or microbial genomes present

Metabarcoding

A technique that sequences one ‘barcoding’ or identifying gene conserved across a wide array of species as a means of surveying biodiversity

Next-generation DNA sequencing techniques

DNA sequencing by any diverse means to sequencing full genomes or millions of different sequencings in one experiment

Neolithic Revolution

A cultural and revolutionary process in which humans adopt farming techniques, leading to a whole host of social and economic changes

Oral caries (cavities)

An oral disease caused primarily by S. mutans, which deteriorates the enamel on the tooth surface and exposes nervous tissue

Post-depositional bias

Alterations to microbial communities after the sample is deposited or collected that occur due to environmental or decompositional factors

Periodontal disease

An oral disease of the gingiva or gums, in which diverse bacterial communities stimulate inflammation and destroy gingival tissue

Sanger DNA sequencing techniques

Chain termination DNA sequencing invented by Peter Sanger in 1977, which was a common method to determine the sequencing of deoxynucleotides in a single strand of only one DNA molecule

Scanning electron microscopy

A form of visualization that identifies the shapes of objects via a focused beam of electrons, illuminating the size and shape of many microorganisms

Sedentary lifestyles

Modern human habits that revolve around activities that do not involve physical movement (walking or running), resulting in the majority of a person’s time spent sitting or not moving

Sympatric

A descriptive term of processes, such as evolution, that happen to organisms located in the same location

Taphonomy

A process of degradation that ancient samples undergo, where DNA is enzymatically broken down and degraded, limiting the genetic information that can be obtained from a material. The process is highly dynamic and is dependent upon a vast array of variables, including temperature, water content, and soil chemistry