The Promise Of The Optimal Gut Microbiome
I awoke to another paper in my feed promising to tell me what is the “optimal gut microbiome”.
Alas the paper
Asnicar, F., Manghi, P., Fackelmann, G. _et al._ Gut micro-organisms associated with health, nutrition and dietary interventions. _Nature_ (2025). https://doi.org/10.1038/s41586-025-09854-7
Another fascinating deep dive into the connection between diet , microbiome, and disease. A massive effort of tracking 48,000 adults in Western Society using the Zoe stool microbiome testing technology.
Before I was swallowed up by the massive paper; I wrote down the questions I wanted the paper to tell me so I could use it today for myself and my patients.
1. Which species in the microbiome are shown to improve disease such as reduce inflammation, oxidative stress, mitochondrial dysfunction?
2. Which species in the microbiome are shown to worsen disease such and increase inflammation, oxidative stress, mitochondrial dysfunction?
3. By which mechanisms do the gut microbiota shift disease states?
4. What prebiotics, fibers, and microbial accessible nutrients directly cause expansion in these optimized microbes?
5. What environmental such as arsenic, microplastics, or forever chemicals directly impacts influence the expansion or function of these optimal microbes?’
These five questions are my holy grail for microbiome science at this point.
I am not sitting in an ivory tower.
I have a patient in a few hours that needs this information to feel better.
Spoiler alert the paper continued to give me a lot of associative data and still leaves much speculation on mechanism and solid actionable data.
Here was my big take away.
When it comes to applying microbiome information to health:
- High fat diets....concerning
- Fiber rich diets...likely very helpful
- Low Fat. Diets....possibly helpful
- Exercise...As expected.
Favorable Microbiota
- Faecalibacterium prausnitzii
- Blautia glucerasea
- Roseburia hominis
All of the above are known to produce short-chain fatty acids (SCFAs) that improve glycemia, lipids, and inflammation.
You can extrapolate that to mean they are helpful in reducing most of the major maladies of Western Society.
Unfavorable Microbiota
- Ruminococcus gnavus
Flagged as Unfavorable....yet.
- Flavonifractor plautii (this was flagged as unfavorable but as you will see below it some settings it is seen as favorable)
The paper linked these unfavorable microbes to pro-inflammatory and endotoxin pathways.
Which one could extrapolate would contribute to most of the major western maladies.
My connections in my brain start working and I realize that I recently learned that Blautia species and Faecalibacterium prausnitzii are more on a abundant low fat diet
And a higher fat diet was associated with decreased Faecalibacterium prausnitzii.
This connection was mentioned in Wan,et. al, 2019
Now, it is understood that Faecalibacterium prausnitzii ( a strict anaerobe) is a key butyrate producer and we certainly see lower levels in disease states flaring IBD.
And we know Faecalibacterium prausnitzii thrives on foods rich in the prebiotics Fructooligosaccharides (FOS), Inulin, and Pectin found in a high fiber diet.
And, that butyrate maintains the oxygen gradient in the gut that prevents pathogen and pathobiont expansion. So it is understandable why that one showed up so strongly as a major player.
In addition, Roseburia hominis is also a butyrate producer.
Earlier we learned in Mailing, et. al 2019 that women who performed at least 3 hours of exercise per week had increased levels of Faecalibacterium prausnitzii, Roseburia hominis, and Akkermansia muciniphilia.
Ruminococcus Gnavus:
Ruminococcus gnavus is often implicated in gut barrier disruption, dysbiosis, and inflammatory disease . We have seen in studies where omega-3 consumption reduces Ruminococcus gnavus. (see Vallone, et.al 2019)
And I spoke about that in this post
Flavonifractor plautii
This flavonoid eating microbe does not have much research however, why would it be elevated in disease states? One hypothesis is that it is metabolizing polyphenols in a way that otherwise might be used for other health benefits. Yet, that is purely speculation. As we also have seen in human trials on patients with IBD , that Flavonifractor plautii elevations is associated with IBD remission for patients on biologics. ( see Tamburini FB, 2024)
Parting words that we can apply to any microbiome study
Don’t chase individual species but rather instead chase function.
Just because you heard Blautia glucerasea is good **–**don’t throw out the high fat bulletproof coffee with the bathwater.
Pause.
You must realize...
This is still associative/observational data and not mechanistic and is not even close to the standard of double-blinded-placebo controlled research.
It matters, but don’t get too excited.
Ask questions like?
1. How much butyrate am I producing?
2. How are my systemic inflammatory markers
3. Do I have dysbiosis?
4. Do I have oxidative stress.?
5. Is my intestinal barrier breached?
These are functional questions that put together a better handle on how to shift your microbiome.
If this resonated with you, please share it with clinicians or patients who are navigating microbiome confusion.
Also please consider joining The Gut Freedom Universe and our upcoming course The Gut Freedom Intensive.