Modern lifestyles have caused many microbial species that were once common in humans to disappear almost completely from the Western gut microbiome. These lost species play essential roles in metabolism, immune balance, gut barrier integrity and even the gut–brain axis. Traditional populations still carry these microbes in abundance. In the industrialised world, however, they are often missing entirely.

Our starter cultures are therefore built around the strains that current research identifies as the most depleted and the most physiologically important for restoring a resilient, balanced microbiome.

Below you will find a clear overview of which of our strains qualify as true lost species and why they matter so much.

The Three Most Important Lost Species

Limosilactobacillus reuteri

• Common in traditional populations, almost absent in Western microbiomes
• Function: calms the gut lining, regulates inflammation, supports metabolic balance and influences oxytocin pathways
• Reuteri is one of the key microbial species needed to rebuild a modern gut ecosystem

Bifidobacterium infantis

• Severely reduced in Europe and North America
• Function: lowers inflammation, strengthens the gut barrier, reduces gas formation and plays a central role in immune modulation
• Considered one of the most important lost species

Bifidobacterium longum

• One of the most significantly depleted microbes worldwide
• Function: modulates the gut–brain axis, regulates inflammation and supports metabolic balance
• A core strain for a stable and regulated gut environment

Additional Valuable Lost Species

Lactobacillus gasseri

• Clearly reduced in many studies
• Supports fat metabolism, helps regulate the small intestine and reduces inflammatory signals

Lactobacillus rhamnosus

• Often diminished in Western populations
• Important for gut barrier function, mood regulation, stress resilience and immune health

Lactobacillus brevis

• Abundant in traditional fermented foods, now rarely consumed
• Known for GABA production and supporting stress regulation

Bacillus subtilis

• Historically obtained from soil, plants and traditional foods; now almost absent
• Contributes to microbial stability and a resilient gut flora

Functional Complementary Strains

These strains are not classic lost species but remain valuable in specialised formulations:

Lactobacillus helveticus

Supports mood, stress regulation and immune balance

Bacillus coagulans

Highly acid resistant, supports digestion and small intestinal balance

Bacillus clausii

A robust spore forming strain that supports immune resilience and overall stability

Why We Use These Specific Strains

Our starter cultures are formulated to directly replenish the microbial species most affected by modern living. The key lost species appear across several of our sets. Strains that are functionally important but not severely depleted complement more specialised formulas such as our complete 6 month programme.

This gives you a clear, scientifically grounded combination of microbes designed to rebuild the gut microbiome in a way that reflects how it naturally exists in populations with higher microbial diversity.

Which of Our Bacterial Strains Have Antimicrobial Effects and Why This Matters

Many of our starter cultures contain bacterial strains that naturally exhibit antimicrobial activity. This means they produce substances that inhibit the growth of unwanted or harmful microbes in the gut. This effect is not comparable to a conventional antibiotic, but it does support the natural balance of the microbiome and helps beneficial bacteria establish themselves more easily.

Below you will find a clear and accessible overview of the antimicrobial properties of the key strains included in our starter sets.

Strains with Strong Antimicrobial Activity

• Limosilactobacillus reuteri
  L. reuteri produces reuterin, a naturally occurring substance with a broad antimicrobial spectrum. Reuterin inhibits bacteria, yeasts and certain parasites. In addition, this strain produces lactic acid, which further reduces the growth of pathogenic microbes.

• Limosilactobacillus gasseri
  This strain produces several bacteriocins, which are small protein molecules that specifically inhibit unwanted bacteria. L. gasseri can suppress organisms such as Staphylococcus aureus, Listeria species and certain Clostridia.

• Bacillus subtilis
  B. subtilis is an exceptionally stable strain that produces a range of natural antimicrobial substances, including bacitracin and surfactin. These compounds act against various bacteria and, in some cases, against fungi as well.

• Bacillus clausii
  B. clausii produces antimicrobial peptides and also supports immune function. It is a robust strain often used to stabilise the gut environment during and after antibiotic treatment.

Strains with Moderate Antimicrobial Activity

• Lacticaseibacillus rhamnosus
  This strain produces lactic acid and bacteriocins that help inhibit the growth of pathogenic microbes. It also binds to the gut lining and displaces unwanted bacteria.

• Bacillus coagulans
  Acts primarily through lactic acid production and the formation of small antimicrobial peptides. It also supports the natural barrier function of the gut.

• Lactobacillus brevis
  This strain is capable of producing bacteriocins and antifungal substances, helping to inhibit certain bacteria and yeasts.

• Lacticaseibacillus helveticus
  Acts mainly through lactic acid production and competition for nutrients. Its antimicrobial effects are milder compared to other Lactobacillus strains.

Strains with Mainly Indirect Antimicrobial Effects

• Bifidobacterium infantis
• Bifidobacterium longum

These Bifidobacteria do not rely on strong antimicrobial substances. Instead, they produce short-chain fatty acids that gently acidify the gut environment. This creates conditions in which pathogenic microbes struggle to grow. At the same time, they strengthen the gut barrier and support a stable, healthy microbiome.

Why This Information Matters

The antimicrobial properties of many of our strains help promote a balanced gut microbiome.

By allowing beneficial bacteria to displace unwanted microbes, they support:
• stable digestive function
• a strong gut barrier
• a favourable environment for other beneficial bacteria
• the regeneration of the microbiome after stress or disruption