The technology behind BugSpeaks
Shotgun metagenomic sequencing: the science behind the test
Shotgun metagenomic sequencing — the technique that reads all the DNA in your microbiome, not just fragments of it.
How we look at the microbiome
Four things that make the analysis detailed
01 · Depth
We see the rare microbes too
Shotgun sequencing also recognises microbes with a low share in the sample; 16S usually gives a more general picture — down to genus level.
02 · Breadth
All the DNA, not just the bacteria
We do not read bacterial DNA alone. The shotgun approach analyses all the genetic material in the sample — bacteria, archaea, fungi, viruses, plus the genes for antibiotic resistance. One test, a broad picture.
03 · Function
Not only who lives in you, but what they do
Identifying the species answers which microbes live in you. Functional analysis answers what they can do — producing vitamins, short-chain fatty acids and neurotransmitters, and metabolising specific foods.
04 · Evidence
Recommendations grounded in your data
The data turns into concrete steps — a personalised 12-week plan matched to your profile. The approach was clinically tested in a pilot open-label randomised study with 30 adults (India, 90 days), carried out and funded by Leucine Rich Bio (PeerJ, 2024). The results have not been confirmed by independent studies and do not mean that the test or the plan treats any disease.
Methods compared
How does our technology compare?
Every method has its place. Here it is honestly, method against method — where BugSpeaks gives a broader picture.
vs16S tests16S sequencing reads a single gene and sees only bacteria — a good general overview, but without the depth needed for concrete decisions.
BugSpeaks16S tests
What you get
The technology turns into concrete answers
Sequencing turns into data you can use to change how you eat. Here is exactly what you learn.
- 01
100+ indicators
Potential for vitamins, metabolites and neurotransmitters, beneficial and opportunistic microbes, breakdown of lactose, fructose, gluten and histamine, resistance genes for 90 antibiotics, five health indicators and similarity to the microbiome in 8 common conditions.
- 02
90 antibiotics
The report shows which known resistance genes your gut bacteria carry — general information about the microbiome. It does not show whether a treatment will work, is not an antibiogram and is not for choosing an antibiotic.
- 03
Resolution down to species level
The gut report shows the share of 21 lactobacillus species separately, not just of the genus as a whole.
- 04
Functional pathways
An analysis of the metabolic capabilities of your microbiome — how it processes macronutrients and which short-chain fatty acids it produces.
- 05
Comparison with reference groups
Your results are compared with a reference group defined by the laboratory, so you can clearly see where you stand against it.
- 06
A personalised plan
Data becomes action: a 12-week nutrition plan with concrete recommendations based on your microbiome profile.
The process
From sample to report
Six clear steps between the moment you open the kit and the moment you receive your personalised report in your profile.
Step 01
Collecting the sample at home
A sterile kit with instructions. You take a stool sample with the device provided — it takes about 5 minutes. No fasting or special preparation is needed.
Step 02
Returning the sample
You place the sample in the sterile container with preservative and return it to us in Bulgaria free of charge, with the enclosed waybill. From there we send it to the laboratory under the test code only. The preservative stabilises the DNA for up to 30 days at room temperature.
Step 03
DNA extraction
In the laboratory, specialists extract all the genetic material from the sample through mechanical and chemical lysis. DNA quality is checked by fluorometric quantification and gel electrophoresis.
Step 04
Library preparation and sequencing
The DNA is sequenced by shotgun metagenomics on the Oxford Nanopore platform — a long-read technology that reads long DNA fragments (from thousands to over 100,000 bases). Long reads help identify microbes down to species level.
Step 05
Bioinformatic analysis
The reads go through quality control and alignment against reference databases (NCBI RefSeq, KEGG, ResFinder). Taxonomic classification, abundance estimation and functional annotation are applied.
Step 06
Interpretation and the report
The results are processed with the laboratory's bioinformatic algorithms. A 48-page report is generated with the Rych Index™, concrete indicators and a 12-week plan — in Bulgarian.
Laboratory and scientific basis
Where the analysis is done
and what it rests on
The laboratory
The analysis is performed in the Leucine Rich Bio laboratory in India — shotgun metagenomic sequencing on the Oxford Nanopore platform.
A scientific foundation
The technology is based on the research of Leucine Rich Bio Pvt Ltd, published in peer-reviewed journals.
GDPR protection
Your account and report are stored encrypted in the EU (Frankfurt). The laboratory in India receives the sample and the data for the analysis under the test code only — without your name or contact details — and keeps the raw data for up to 2 years. We do not sell data or use it for advertising.
Technical questions
Deep into the methodology
For readers who want to understand exactly how the technology behind the results works.
Sequencing is performed by shotgun metagenomics on the Oxford Nanopore platform (long-read). Shotgun sequencing also recognises microbes with a low share in the sample.
16S rRNA sequences only one conserved gene shared by all bacteria. It usually gives resolution at genus or family level and does not show a large part of the information — functional pathways, antibiotic resistance genes, non-bacterial microorganisms. For a more detailed analysis that is not enough. Shotgun metagenomics reads all the DNA in the sample — which is why it provides that information too.
Yes. Unlike 16S rRNA or qPCR-based methods, the shotgun metagenomic approach reads all the DNA in the sample. That includes bacteria, archaea, fungi (Candida, Saccharomyces and others), bacteriophages, and DNA viruses. The results include a profile of the microbial community.
The reads are aligned against reference genome databases (NCBI RefSeq, Genome Taxonomy Database). The algorithms look for specific marker genes that tell individual species apart — for example the different Lactobacillus or Bifidobacterium species.
The reads are compared against specialised databases such as CARD (Comprehensive Antibiotic Resistance Database) and ResFinder, which catalogue known resistance genes. The report shows which of those genes, linked to 90 antibiotics, your gut bacteria carry — general information about the microbiome. It does not show whether a treatment will work, is not an antibiogram and is not for choosing an antibiotic.
In addition to identifying the species, we also analyse what they do in biochemical terms. The reads are mapped against the metabolic pathways in KEGG (Kyoto Encyclopedia of Genes and Genomes). That tells us how capable your microbiome is of producing short-chain fatty acids, vitamins and neurotransmitters, or of metabolising specific molecules such as gluten or lactose.
1) DNA sequencing shows which microorganisms are present, but not which of them are metabolically active at that moment. That requires RNA sequencing, which is considerably more expensive. 2) The results reflect a snapshot at the moment of sampling — the microbiome changes with diet and stress. 3) The test is not intended to diagnose, prevent, monitor or predict disease — the results describe the microbes and nutrition, not your state of health.
Your results are compared with a reference group defined by the laboratory. The algorithm shows you where your result stands relative to that group, rather than against absolute “ideal” values — because the microbiome differs from person to person.
The microbiome changes from day to day, so two samples from the same person are never exactly the same. To track changes we recommend a repeat test after 10–12 weeks.
