Do All Animals Have a Microbiome? A Research Guide

From the guts of elephants to the tissues of coral reefs, scientists are uncovering a hidden yet essential world: the animal microbiome. As research expands across disciplines like ecology, veterinary science, and evolutionary biology, the question arises: Do all animals have a microbiome? And if so, what does it mean for scientific discovery?

In this guide, we explore what a microbiome is, how scientists study it, and why sequencing services are crucial to animal microbiome research. Whether you're working with mice in the lab or marine invertebrates in the wild, understanding the microbiome opens doors to new insights in animal biology.

What Is a Microbiome and How Do Scientists Study It?

The microbiome refers to the community of microorganisms (including bacteria, fungi, archaea, and viruses) that live in and on animals. It plays a crucial role in everything from nutrient absorption to immune regulation. While “microbiota” refers specifically to the microbial organisms themselves, “microbiome” encompasses their genes, functions, and environmental interactions.

Studying these communities requires advanced techniques in DNA sequencing, most commonly:

• 16S rRNA gene sequencing for identifying bacterial taxa
• Shotgun metagenomic sequencing to capture broader microbial diversity and function
• Metatranscriptomics and metabolomics for understanding activity and metabolite production

Projects like the Earth Microbiome Project have made large-scale, cross-species comparisons possible, while researchers follow best practices outlined by Knight et al. (2018) to ensure consistency and accuracy.

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Do All Animals Have a Microbiome? What the Research Shows

In short: yes, or at least, probably. Virtually all animals studied to date host some form of microbiome. However, there are also some species that may have little to no reliance on microbial symbionts. Generally, from insects and nematodes to whales and humans, the presence of resident microbial communities appears to be a near-universal trait. 

These communities vary:

• In density (gut-packed mammals vs. surface-housed invertebrates)
• In complexity (single-species symbionts vs. diverse ecosystems)
• In function (mutualistic, commensal, or even pathogenic)

McFall-Ngai et al. (2013) famously proposed that animals must now be studied as "metaorganisms," acknowledging their microbial partners. Even simple organisms like Hydra have stable, inherited microbiomes. Recent reviews in Frontiers in Microbiology further confirm that even invertebrates play host to rich microbial ecosystems.

Animal Microbiome Ecosystem Diagram

Microbiomes in Vertebrates vs. Invertebrates

Microbiome complexity often mirrors the evolutionary and ecological niches of their hosts.

• Mammals, birds, and reptiles tend to have more complex gut microbiomes shaped by diet, genetics, and long co-evolutionary histories.
• Insects, nematodes, and marine invertebrates may have microbiomes that are more influenced by the surrounding environment than by host control.
• Sponges, corals, and Hydra maintain surprisingly stable microbiomes despite lacking complex organ systems.

Sanders et al. (2014) showed that gut microbiota stability could be phylogenetically linked, drawing parallels between ants and apes. Meanwhile, Bosch (2013) highlighted how ancient organisms like cnidarians helped lay the foundations for microbial interactions in immunity.

Comparative Overview of Animal Microbiomes

This table highlights the diversity and significance of microbiomes across major animal groups, emphasising the variability in presence, complexity, and scientific importance.

The Role of the Microbiome in Animal Health and Development

Across the animal kingdom, microbiomes are increasingly recognised as drivers of development and health. Microbes influence:

• Nutrient metabolism and digestion

• Immune system development

• Behaviour, via neuroactive compounds

Studies using germ-free animals (born and raised without any microbiota) have revealed the essential role microbes play. These animals often show impaired immune function, poor growth, and altered brain development.

Emerging theories like the hologenome concept of evolution (proposed by Rosenberg & Zilber-Rosenberg, 2018) suggest that evolution acts on the host and its microbiome together as a single unit. This shifts how we view inheritance, adaptation, and even species boundaries.

Microbiome-Free Animals: Are There Any Exceptions?

Could some animals truly live without a microbiome? It’s a topic of active scientific debate.

Microbiome-free animals are species that appear to live without a stable or detectable community of microbes in or on their bodies. While rare, some animals may actively limit microbial colonisation, and in certain environments, a microbe-free lifestyle could offer evolutionary advantages. A few distantly related animal lineages have shown evidence of this microbiome-independent strategy.

For example, through the research of Hammer et al. (2019) who challenged the assumption that all animals require microbiomes. A few extremophile species or deep-sea invertebrates may host minimal or no resident microbes, though this often reflects limitations in detection rather than genuine absence.

Additionally, germ-free models in laboratory settings are created artificially, and such states rarely (if ever) occur naturally. In most cases, “microbiome absence” is context-dependent, meaning that early life stages, harsh environments, or specialised diets might reduce microbial presence temporarily.

Why Microbiome Sequencing Matters in Animal Research and Beyond

At Cmbio, we provide precision microbiome sequencing services that empower researchers and organisations to explore the animal microbiome in meaningful ways. Our tools are used across a range of sectors:

• Veterinary science: Diagnosing microbial imbalances in domestic animals
• Agriculture: Studying the impact of feed and environment on livestock microbiomes
• Laboratory models: Understanding microbiome-linked variability in mice and other research animals
• Zoonotic disease surveillance: Tracing microbial shifts linked to pathogen transmission

As Dorrestein et al. (2014) emphasised, host-microbe interactions lie at the heart of modern biology. Whether you’re investigating soil-animal microbiome links or host immunity in lab models, sequencing services offer clarity in a complex microbial world.

Unlock the Animal Microbiome with Microbiome Sequencing

To answer the question: Yes, all animals appear to have a microbiome, though the form, function, and complexity vary widely. From evolutionary symbiosis to daily health, the microbiome is essential to understanding animal life.

With ongoing advances in sequencing technology and data interpretation, we’re only just beginning to uncover what these microbial worlds can tell us. Whether you’re working with lab mice, poultry or salmon, we help you extract insights from the unseen world inside every animal.

Learn more about our animal microbiome research services

Do all animals have gut microbiomes FAQs

Do all mammalian species have a microbiome?

Yes, the mammalian gut microbiome is considered a near-universal feature across mammalian species. Gut microbes play essential roles in digestion, immune development, and overall health of mammals.

Do wild and captive animals have gut microbiomes?

Yes, gut microbial communities are present in both wild and captive animals. However, their composition can vary significantly depending on diet, habitat, and environmental exposure.

Do vertebrates have a microbiome?

Yes, both wild and captive vertebrates host diverse microbiomes, particularly in the gut. These microbial ecosystems of gut bacteria help regulate nutrient absorption, immune response, and even behaviour.