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Is microbiome manipulation a solution or a tool?

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By: Ph.D Stephen G. Newman*

Science is a powerful tool for understanding how the world we live in works. This knowledge, when used wisely, has had, and will continue to have dramatic impacts on human welfare. Unfortunately, it can be challenging for the layman and even for many scientists to sort out what is real from what is not.

It is estimated by some that 50% or more of the papers published in peer reviewed scientific journals are not reproducible. Vast amounts of published observations fail this true test of validity; they are not reproducible.

Publishing for the sake of publishing has become routine and it is unfortunately all too common that some with questionable ethics cite the results from studies of this nature to support technologies and ultimately sales of products that may have no cost benefit.

As some terms become increasingly visible, they are being used in ad and promotional campaigns with the inevitable result that they end up as a part of the puffery that has become the norm for many marketing campaigns.

The words ecology, green, and sustainable come to mind. A word under threat today is microbiome.

What is the Microbiome?

The term microbiome can be confusing as it is often used specifically in reference to what is present on or in an animal. The broadest definition acknowledges that it is not solely about animals but that it encompasses all aspects of the environment of which animals are but one component.

An all-encompassing definition of the term microbiome is “All microorganisms, consisting of bacteria, bacteriophages (viruses that infect bacteria), fungi, protozoa and viruses that are present in a specific environment”.

This can be in and on an animal or a plant or it can refer to any element of the environment including objects. An assemblage of microbes anywhere would be considered a microbiome.

“The term, as used in reference to aquaculture, typically refers to what is present in and on the external and internal surfaces of a given aquatic animal. It can also refer to the specific microbial composition of individual elements of a production environment, such as the sediments, the water column, biofilms, etc.”

Any given microbiome is just a subset of a much larger ecosystem (which is a much larger microbiome). It is often thought of as being what is in the gut of an animal when the microbiome in the gut is just a small piece, a subset, of a much larger microbiome.

The microbiome has been the subject of intense research accelerating rapidly over the last decade or so.

Interest continues to grow as research suggests that various iterations of microbiomes may have profound impacts on animal health and general well-being. The multitude of organisms that make up a microbiome produce a wealth of metabolites some of which appear to serve important functions.

“We are only just beginning to understand what these are and what role they play in immunity, health, etc.”

Since the early 1880s, microbiologists have been growing bacteria on agar. Until recently this was the only tool available for identifying what was present.

Figure 1 shows typical vibrio colonies growing on a selective media.


We know today that most bacteria cannot be cultured. Some estimates are over 99%, although this not widely appreciated until the development of gene detection tools focusing on 16sRNA were developed.

This is a highly conserved gene that is critical for the formation of proteins. It has allowed researchers to characterize what is present without being able to culture the organisms present. The conserved and variable components of this ribosomal component are powerful tools for identifying genera and with specific probes, species.

Typically, the development of specific probes requires the ability to culture the bacteria on bacteriological media making the tool useful for broadly identifying what genera are present as most bacteria do not grow on media.

Figure 2 shows an overview of penaeid shrimp microbiomes.


As the word microbiome falls into over usage much as the words eco, green, and sustainable have, there will be publications that leave the reader with impressions that are inaccurate.

Much as with other nucleic acidbased tools there are inherent limitations in what we can learn from their use. Microbiome testing focuses on generalities in the sense that groups of related bacteria are identified.

The probes that are used are not usually species specific. This means that when a change in the relative percent ages of given genus occurs it does not tell us what species have been impacted. This is nonetheless useful information but limited.

“Microbiomes are a dynamic and constantly evolving assemblage of organisms. They can consist of thousands of species of microbes. Microbiomes appear to be in a constant state of flux in response to inputs and outputs.”

Many researchers are reporting on the composition of specific microbiomes as if they are static and even in some cases claims are being made that certain products bring about changes that are not just beneficial, but that are largely unaffected by externalities.

This could be misleading. The ability to manipulate the microbiome to reduce stress the animals are under, inure them to the presence of pathogens, and in general to increase productivity is being offer up as a solution to compensate for poor biosecurity.

Those that are advocating this do not seem to be addressing the fact that the microbiome is not stable. The assemblages of the microbes that make up any given microbiome, by their very nature, are going to be in a constantly evolving state as most ecosystems are in a state of constant change.

“Focusing on shrimp farming as an example, the typical paradigm is outdoor culture exposed to the elements.”

Controlled inputs are the shrimp themselves (when from nucleus breeding facilities), nutrients that are added such as feed but also includes carbohydrate additions and many “snake oil” products that farmers routinely use that may have little or no impact on the animals.

As the shrimp grow, they consume a variety of feeds, they molt, defecate and some die. This adds to the pool of nutrients. Water may or may not be exchanged. This also impacts nutrients loads and composition.

In most instances it is an illusion that the inputs are controlled, i.e. that we are fully aware of what we are adding and how it is altering the microbiome. Microbiomes appear to evolve in response to inputs and their very nature is such that there is a continual battle for dominance among the components.

These have broad ranging impacts on a given microbiome’s development. We are still in the early stages of having an in-depth understanding of how all these factors interact to impact this.

“There are some that would have you think that the microbiome is stable and unchanging and that their products change it in a way that is consistently favorable.”

We know that this is more than likely not the case. This is not to say that benefits may not occur. It is far from being this simple and while data does suggest that one can bring about localized changes in the microbiome, to tout these changes as being permanent or even for that matter anything more than tools to help potentially shift things in favor of the shrimp, is naive at best and intended to mislead at worst.

For aquatic animals it has repeatedly been documented that for the most part what is in the gut is what is in the environment. With the advent of tools that allow scientists to determine the composition of the microbiome, we can take snap shots but no motion pictures, yet. This is leading to a lot of conclusions being made that may not be as accurate as the claims suggest.

“Typically, these may be reflections of how the microbiome changes in response to inputs, the environment, the presence of other organisms, and likely other factors that we have yet to fathom.”

A snapshot might be useful, but it more than likely does not reflect what one would see if one were mapping changes on a constant basis.

Observations that are based on what is occurring at a given moment might lead to some ideas about how the presence of certain organisms can apparently impact any number of different aspects of the host.

The data to date strongly suggests, that, likely through the production of metabolites that act directly on the host, or indirectly that act on other members of the microbiome or the host as well, there will be a wide range of impacts, not all necessarily favorable.

We must not allow ourselves to be fooled into thinking though that any changes we can bring about in the short term will automatically bring about meaningful long-term benefits. The literature is full of observations of this nature, any number of which would have you believe that what they posit reflects reality.

“The constantly changing nature of these complex assemblages of microbes makes it likely that what we note in our snapshots is offering but a short-term perspective on what is occurring.”

Do not be surprised if you see some claims being made for some products for fish and shrimp, that claim that when fed to them, will alter the microbiome in a manner that they will show data for as being proof of some wild claims.

The evidence in human beings to date suggests that this may be a simplification of what is going on. We are still in the early stages of sorting out how the myriad of variables that are a common element in shrimp and fish farming impact the microbiome in the animal and the environment around them.

If we produced these animals indoors in totally biosecure environments from cradle to grave and were able to control the inputs and outputs, then we might be able to end up with a more or less stable microbiome.

However, I would question if this were needed in these systems unless it can be shown that animals grow quicker and are more likely to realize their genetic potential than not.

From an animal health standpoint, if these systems are run properly, pathogens are not going to be an issue and having a microbiome that impacts the animal’s ability to deal with the presence of specific pathogens would seem to be a waste of resources.

“My final words are “caveat emptor”. Do not look for magic bullets to solve problems that are inherent in what really are biosecurity and even in some instances structural deficiencies in production paradigms.”

For shrimp farming, buying animals from nucleus breeding centers with lengthy histories and endless testing of individual broodstock is the best (and maybe the only) way to keep pathogens out of your production systems.

Do not rely on fixes that do not take this into account. Also bear in mind that stress is often what leads to increased susceptibility. Weakened animals can be killed by opportunistic pathogens, many of which are not inherently virulent. It is not likely that microbiome manipulation will change this.


Stephen G. Newman has a bachelor’s degree from the University of Maryland in Conservation and Resource Management (ecology) and a Ph.D. from the University of Miami, in Marine Microbiology.
He has over 40 years of experience working within a range of topics and approaches on aquaculture such as water quality, animal health, biosecurity with special focus on shrimp and salmonids.
He founded Aquaintech in 1996 and continues to be CEO of this company to the present day. It is heavily focused on providing consulting services around the world on microbial technologies and biosecurity issues.

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