Vermicompost Core Microbiome

Updated: Apr 24

We are going to dig into the vermicompost samples a lot more and look at who most commonly there among all the samples. One way we can do this is a core microbiome analysis. Basically, we are just looking for organisms that are found in the most samples, kind of like the center of a Venn Diagram if each circle is a sample.

At the center would be the organisms that are found in all 3 samples. This gets a little more complicated when you have tons of samples but, it also gets more powerful. Dr. Vanzin has done an excellent job of using this analysis to highlight what organisms are broadly found in vermicompost.

Genus Level Core Microbiome

Let's zoom in as far as we can and look one level above species - the genus level. This would be similar to grouping all ~100 species of roses under the genus Rosa. Horses and Zebras would also be under the same genus.

Quick Figure Overview:

  • The names going down on the left are the organism groups.

  • The bottom x-axis is relative abundance (%) of each group.

  • The colors (red-yellow-blue) indicate prevalence (what percent of samples they were found) at that relative abundance.

That probably doesn't make tons of sense so lets look at an example.

Chryseolinea- contain known plant growth promoting organisms

The most common and abundant organisms, Chryseolinea is seen in nearly every vermicompost sample with at least 1% relative abundance as indicated by the 4 red bars. About half of the vermicompost samples have at least 3.5% of Chryseolinea as indicated by the last yellow blue bar.

A recent study on tomatoes, showed that Chryseolinea were the defining organism of the root microbiome of tomato plants amended with vermicompost. In this study vermicompost amended tomatoes performed just as well as synthetic fertilized tomatoes hinting that that this genus of organism could in part be responsible. Species of this genus have also been shown to suppress plant diseases such as Fusarium, and was found to be promoted by the application of bio-stimulants. A species of this organism has also been patented for the use of promoting cabbage growth in China.

Other prevalent organisms

This "Pirellula-related" genus, Pir4 lineage, is the second most common genus and unfortunately contains no cultured members. This means we do not know much about it because it has never been isolated and grown in pure culture. However, it has been seen associated with rice roots.

Flavobacterium is a broad and common collection of soil and aquatic microorganisms so it isn't surprising to see them as the third most common genus. Another one that jumps out is Devosia, which is also known to contain plant growth promoting species such as Devosia rhizoryzae.


Based on this analysis, we can start to understand that while all vermicompost samples might be different, they also contain a core group of organisms. As we have seen, potentially this group of organisms has been shown to promote plant growth and colonize roots. This finding is really exciting and hopefully can start to help explain why vermicompost of all types is so beneficial to plants.

Please feel free to read on or stop here and ask any questions. Thanks!

Bonus: Family Level Core Microbiome


If we look at Microscillaceae, it was the most prevalent and by far the most abundant family of organisms found in vermicompost. It was found in 94% of all samples with at least 1% relative abundance (bright red first box). In 40% of samples this family was found to be at least 10% of all sequences in the sample indicated by the last box. In my mind, this is pretty incredible because 10% seems quite high for such diverse samples at the family level.

This family was one I highlighted in the last post (if you made it that far) and previously seen in vermicompost used for bioremediation. it has been noted to degrade chemicals like atrazine, a widely used pesticide. Other than that there is just not much other information out there which highlights the amount of work scientists have left to explore.


The second most abundant family in our core microbiome is the Pirellulaceae that was found in >90% of all vermicompost samples. 40% of samples had at least 7% relative abundance so very similar to Microscillaceae . This family contains the Pir4 Lineage above. Interesting, the only study I could find highlighting this family had to do with earth worms, arbuscular mycorrhizal fungi (AMF), and how they help with antibiotic degradation. The key finding of the paper was that worms and AMF promote the growth of Pirellulaceae which increase antibiotic degradation.


The final family I will talk about is Chitinophagaceae, the third most common family which. It contains many species that are known plant growth promoting organisms such as Arachidicoccus rhizosphaerae. It is also associated with organic matter degradation which helps explain why it might be common in vermicompost.

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