Microbiomes and Host Associations

Plants and animals host complex microbial communities, their microbiomes, and these host-microbe associations range from mutually beneficial symbioses to relationships that shape host biology in subtle ways.

Definition

A microbiome is the community of microorganisms associated with a particular host or habitat, and host associations are the symbiotic relationships, ranging from mutualism to commensalism, between microbes and their plant or animal hosts.

Scope

This topic covers the concept of the microbiome as the community of microbes associated with a host or environment; the diversity and functions of host-associated communities; classic symbioses such as nitrogen-fixing root nodules and ruminant gut communities; the methods used to characterize microbiomes by sequencing; and the general principles of how microbial partners influence host nutrition, development, and defense.

Core questions

• What is a microbiome, and how is it characterized?
• How do microbial communities associate with plant and animal hosts?
• What functions do host-associated microbes provide?
• How do sequencing methods reveal microbiome composition?

Key concepts

• The microbiome concept
• Mutualism, commensalism, and symbiosis
• Nitrogen-fixing and gut symbioses
• Sequence-based community profiling
• Microbial contributions to host function

Key theories

Culture-independent microbiome analysis

Sequencing of marker genes and whole communities directly from host or environmental samples revealed the composition of microbiomes without cultivation, transforming the study of host-microbe associations.

Mechanisms

Host-associated microbes colonize specific tissues and surfaces, where they interact with the host and with one another. In many symbioses microbes provide functions the host cannot perform, such as fixing nitrogen for legumes or digesting plant material in herbivore guts, while the host supplies nutrients and habitat. Microbiomes are characterized by extracting community DNA and sequencing marker genes or whole genomes to reveal composition and functional potential.

Clinical relevance

Host-associated microbial communities contribute to plant and animal nutrition, development, and resistance to colonization by harmful microbes, and the study of microbiomes informs agriculture, environmental science, and research into how microbial communities relate to host biology.

History

Classic studies of symbioses such as nitrogen fixation in legume nodules, investigated by Beijerinck and others, established that microbes form essential partnerships with hosts. The later development of culture-independent sequencing, building on approaches like those of Pace, opened the systematic study of complex microbiomes.

Key figures

• Norman Pace
• Martinus Beijerinck

Seminal works

• pace1997
• madigan2018

Frequently asked questions

What is the difference between a microbiome and a microbial community?

A microbial community is any assemblage of interacting microbes in a shared environment. A microbiome usually refers to the community associated with a specific host or habitat, often considered together with its collective genes and functions.