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The Natural Probiotic? PNSB Shown to be Part of Indigenous Fish Gut Microbiota

Updated: May 14, 2023

The word ‘probiotic’ can mean different things in different discussions. Most often, it refers to microbes that benefit a host organism by aiding digestion. These so-called ‘gut flora’ increase feed conversion–that is, digesting or partially digesting food within the animal gut. Much of the food processed by these probiotic microbes consists of material that the animal cannot digest itself (cellulose, or ‘fiber,’ for example). In return, the probiotic organisms produce protein, fatty acids, vitamins and other substances that promote the host’s health and growth. In other words, by ingesting probiotics, the host ultimately can utilize more of what it eats for metabolism and biomass. What’s more, the animal resultantly generates less waste.

Both of these features–increased growth, reduced waste–have put probiotics in the spotlight amongst commercial fish farmers over the last couple decades. Purple non-sulfur bacteria (PNSB) in particular have received a lot of attention here on account of their apparent ability to suppress disease and improve water quality. The PNSB species most studied for probiotic applications has been Rhodopseudomonas palustris.

One of the first concerns of researchers was whether or not R. palustris could actually survive the transit through the hostile environment of the animal gut. Using simulated gastric transit conditions (pH 2.0, pH 3.0 and pH 4.0 gastric juices) and small intestinal transit conditions (pH 8.0, with or without 0.3% bile salts), Zhou et al (2007) cleverly demonstrated the viability of R. palustris as well as the related Rhodobacter sphaeroides in the fish gut. The effects of these microbes on the viability and permeability of fish intestinal epithelial cells (using the tilapia Oreochromis nilotica as a model) was also observed. Results from this study suggested not only that these PNSB remained viable throughout transit, but also that they posed no damage to the host’s digestive system.

Subsequent investigations of actual, functional aquaculture systems carried out by Zhou and others with tilapia, grass carp and yellow catfish revealed that when used as a probiotic, R. palustris is capable of significantly improving growth performance as well as enhancing the immune response and generally improving water quality. It even appears to increase the relative abundance of other beneficial gut microbiota such as bifidobacteria and lactobacilli.

But, does R. palustris naturally occur among the gut flora of wild fish? And, if so, does this include marine fish species?

A recent study was carried out by the Aoi Koga Lab at the Department of Applied Life Science (Sojo University, Kumamoto, Japan) answers this question fairly conclusively.

Koga et al (2022) detail the very first isolation of PNSB from the feces of a wild fish (ayu Plecoglossus altivelis) harvested from the Kuma River, Japan and compared these isolates with the PNSB isolated from the soil in the same area. All the isolated gut PNSB strains belonged to the genus Rhodopseudomonas; soil samples collected along the Kuma River included five Rhodopseudomonas strains (one PNSB isolated from soil belonged to the genus Rhodobacter). As ayu are euryhaline fish that move between seawater and freshwater, they expected that any Rhodopseudomonas palustris from the gut (i.e., under the higher salinity condition) would grow better than those from soil.

As they expected, PNSB from ayu showed a bit more more growth at higher salt concentrations than those PNSB that originated from soil. In fact, PNSB isolated from ayu caught at the most downstream point of the river grew best under high NaCl conditions, suggesting that the intestinal tract environment of marine fish might be more suitable for halophilic microorganisms generally. Since each strain was subcultured for over a year prior to this trial, it’s reasonable to rule out the possibility that the different strains have different salt affinities only because of recent adaptations. That is, the different strains actually have slightly different genetics that make each most fit for a specific environment (e.g., soil, fish gut, etc.).

That being said, the researchers themselves point out, “The phylogenetic tree based on the partial sequence of pufLM gene indicated that the PNSB from ayu and soil were similar.” So any genetic differences were pretty minor. On top of that, PNSB are exceptionally adaptable organisms (famously so, amongst ecologists), so most strains of R. palustris could conceivably inhabit a wide variety of habitats, including soil, fish guts, and most other places on Earth. Most certainly, if they can inhabit the ayu fish gut at all, they likely can inhabit the gut of any fish species (fish are osmoregulators, meaning their internal salinity varies little, whether in saltwater, brackish or freshwater environments). As the researchers state, “PNSB most commonly inhabit various fish, and the isolation of PNSB (including marine strains) from several kinds of fish is in progress in our laboratory.”

It’s cool enough that we now know that PNSB (including the highly useful species R. palustris) are naturally found in the guts of wild fish–particularly after so many researchers have demonstrated the benefits of R. palustris when used as a probiotic for captive fish! But the authors of this awesome paper go further in posing the question, ‘Are so-called indigenous gut bacteria strains better adapted to the intestinal tracts of fish than other, closely related strains, and would that indicate that they thus have a greater potential as probiotics?’ Only more brilliant studies such as this can answer that; it could be that fish farmers and aquarium hobbyists alike may look forward to more and more highly specialized microbial products in the future!

To learn more about how live PNSB can be added to live and prepared aquarium fish foods, visit:

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