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Method report How nb1 reads your gut Reviewed by the Science Board · 2026

Method report · Gut sequencing

Most gut tests read one gene. We read all of them.

Stop buying supplements blindly. Until your gut has been read at this resolution, every formula is a guess.

Start your gut reading

You see your results before you pay. Nothing is charged until you decide.

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NB1FIRST

Valid on 4 and 12 month plans only. Not available on the monthly rolling plan.

nb1 partner laboratory bench
Weighing an active ingredient on a precision balance
Sorting botanical raw material by hand
Resolution
Species and strain
Per sample
200 to 400 species read
Reference set
8,069 metagenomes · 26 countries
Sign off
Human reviewed, EU labs

Your genome, to scale

You are more microbe than human.

Your genome holds about 20,000 genes. The microbes you carry hold roughly 3.3 million more. Two people share 99.9% of their DNA and almost none of their gut. That is the part worth reading, and the part a one gene test cannot.

Your genome 20,000 genes
Your gut microbiome 3.3 million genes

165 : 1. Unlike your genome, this is the part that can change over time.

The method

Most gut tests read who is there. We read what they can do.

16S rRNA reads one marker gene and matches it to a database. Fast and cheap, which is why most gut tests use it. It stops at genus and cannot see what microbes do.

Shotgun metagenomics reads all the DNA in the sample. Every organism, every gene. Species, strains and the jobs they do. This is the only method nb1 uses.

Laboratory scientist pipetting samples into a tube rack

Taxonomic and functional depth by method

16S rRNA Shotgun metagenomics

Level16S rRNAShotgun
Phylum Resolved Resolved
Family Resolved Resolved
Genus Resolved Resolved
Species Partial, often ambiguous Resolved
Strain Not resolved Resolved
Gene content Not measured Measured directly
Metabolic pathways Inferred only Measured directly
Fungi, archaea, viruses Not detected Detected

Worked example

One genus. Four species. Four different jobs.

16S reports one number for Bifidobacterium. Shotgun splits the same sample into four species with four different jobs. A formula aimed at the genus hits all four, including the ones you do not need.

16S rRNA reading 1 row
Bifidobacterium (genus) 5.1%
Shotgun reading 4 rows, same sample
Bifidobacterium adolescentis 2.9% Ferments resistant starch. Contributes acetate that cross feeds butyrate producers.
Bifidobacterium longum 1.4% Uses plant oligosaccharides. Commonly associated with reduced gut permeability markers.
Bifidobacterium bifidum 0.6% Adheres to and degrades mucin. Occupies the mucus layer rather than the lumen.
Bifidobacterium breve 0.2% Degrades a narrow range of oligosaccharides. Low abundance in most adults.

Five reasons

Why the nb1 reading sits in a different category of precision

Five measurable properties of the method. No claims about outcomes.

  1. 16S rRNA 1 result

    One name: Bifidobacterium. Which species is unknown.

    Shotgun 4 results

    Four species named, each with its own role and abundance.

    01

    Species and strain resolution, not genus

    Marker gene: ~1,500 bp · Whole genome: 2 to 6 million bp per organism

    The 16S gene is nearly identical across species in a genus, so most results stop at the genus label.

    Shotgun reads whole genomes and names the species. A formula cannot target what the test cannot name.

  2. 16S rRNA names only

    A list of names. What they do is guessed from the name.

    Shotgun genes read

    The genes are read, so the jobs are measured: fibre, butyrate, bile.

    02

    Function is measured, not guessed

    Output: gene families and metabolic pathways per sample

    Bloating and energy depend on what your microbes do: which fibres they ferment, which acids they make. 16S cannot see genes, so function is inferred.

    Shotgun reads the genes directly. The pathways in your reading are observed in your sample, not borrowed from an average.

  3. 16S rRNA bacteria only

    Fungi and viruses carry no 16S gene. They are invisible.

    Shotgun all DNA

    Bacteria, archaea, fungi and viruses in one run.

    03

    The whole community, including non bacterial life

    Domains covered: bacteria, archaea, fungi, DNA viruses

    Fungi, viruses and phages carry no 16S gene. To that test they do not exist, even though they shape the bacteria around them.

    Shotgun reads all DNA, so they appear in the same run, at the same resolution.

  4. 16S rRNA distorted

    Four organisms at equal amounts, reported unevenly.

    Shotgun in proportion

    The same four, reported as they are.

    04

    Abundance without amplification bias

    16S copy number varies 1 to 15 per genome

    16S primers bind some organisms better than others, and the gene appears 1 to 15 times per genome. Both distort how much of each organism is reported.

    Shotgun samples DNA in proportion to what is there. That is the number a dose is calculated from.

  5. 16S rRNA reading 1 → 2

    Same genus both times. A strain swap does not register.

    Shotgun reading 1 → 2

    Strain replaced. The change is visible and measurable.

    05

    Change can be tracked, reading to reading

    Advanced retests at the end of cycle 1, then every second cycle. Core retests on demand.

    At genus level, a strain replaced by another strain of the same genus looks like no change at all.

    At strain resolution the change is visible. That is what makes a retest meaningful and lets the formula be rebuilt on evidence.

The protocol, step by step

From sample to reformulation, in order

Data first. Formula second. Payment after you have seen the data.

Open laboratory floor with sequencing benches
  1. Day 0

    Kit ships

    Gut sampling kit arrives. Blood panel kit on Advanced. Return postage included.

  2. Day 1

    Sample at home

    A short intake and one gut sample, about ten minutes. Finger prick blood sample on Advanced.

  3. Weeks 1 to 2

    Shotgun sequencing

    All DNA in your sample is read and benchmarked against 8,069 reference metagenomes.

  4. Week 3 You decide and pay here

    You review your reading

    Your report is released to you. A nutritionist drafts your protocol and the science team signs it off.

  5. Week 4

    Formula ships

    Made only after your decision. Arrives pre packed by dose.

  6. End of cycle 1 · Advanced

    Retest and recalibrate

    Same markers, re measured. The formula is rebuilt from what moved. Core retests on demand.

What is in the protocol

Four components. None of them optional.

  • Sequencing included

    Species and strain resolution. The analysis is the product, not an add on.

  • Blood panel included on Advanced

    Omega 3, magnesium, vitamin D measured, not guessed. Doses adjusted to them.

  • Nutritionist protocol

    Written by a qualified nutritionist from your reading. Reviewed before release.

  • Reformulation every cycle

    On Advanced the formula is rebuilt from every analysis. Nothing is repeated on habit.

Morning blister pack

Morning · Activate

Live cultures and daily cofactors, dosed to your reading. Pre packed capsules.

Evening blister pack

Evening · Restore

Recovery and sleep support, included only when your biology calls for it.

nb1 prebiotics jar

Anytime · Nourish

Precision prebiotics, matched to the fibres your gut can ferment. One scoop.

The nb1 protocol kit with morning and evening doses

Three parts, one protocol. The kit is what arrives once the reading has been made and reviewed. It is built to the protocol, dose by dose, and on Advanced is remade from a new reading every cycle.

Start the process

You decide based on your actual results before paying. Nothing is charged until you have seen your reading.

Your reading

A species level inventory, benchmarked against 8,069 gut metagenomes from 26 countries

Your sample comes back as 200 to 400 species. We sort them into teams by the job they do, weigh the ratios between teams, and settle the picture into one balance score. The nutritionist protocol and the formula are derived from this document, and on Advanced a new reading replaces it from month 3.

  1. 01 Taxonomic profile to species and strain
  2. 02 Six functional teams, each checked against its healthy range
  3. 03 Blood panel markers integrated alongside the gut data on Advanced
  4. 04 One balance score, re measured at every retest. Average at first retest: 68.3 → 80.2

Gut reading · Sample 0421

Shotgun metagenomics · Reading 1

Reviewed

58/100

Balance score · Needs work

396

Species detected

6

Functional teams scored

Top species · relative abundance

  • Faecalibacterium prausnitzii
    11.2%
  • Bacteroides uniformis
    8.6%
  • Bifidobacterium adolescentis
    5.1%
  • Roseburia intestinalis
    3.4%
  • Akkermansia muciniphila
    0.9%

Six teams, sorted by job · vs healthy range

  • Fibre · break down fibre · 30.0% In range
  • Butyrate · make butyrate · 16.0% In range
  • Cross feeders · pass nutrients along · 9.0% In range
  • Bifido · feed the acetate base · 3.0% Low
  • Mucus · turn over the mucus layer · 3.0% In range
  • Protein · ferment protein · 11.0% High

From reading to ingredient

Every ingredient in your formula traces back to a line in your reading

The library holds 140 plus ingredients and named strains. Your reading decides which go in, at what dose, and which stay out. From the sample reading above:

Reading result

Protein fermentation team

High
Ingredient decision

Competitive and antimicrobial strains

Named, trademarked strains · Live cultures

Rationale

Crowd the protein fermenters back out and tip fermentation toward fibre.

Reading result

Bifido team

Low
Ingredient decision

B. animalis lactis BB-12

Anchor strain · Rebuild the bifido base

Rationale

Bifido reads below range. The most studied bifido strain, and the best at feeding the chain.

Reading result

Fibre fermentation

In range
Ingredient decision

GOS and PHGG, dosed to tolerance

Precision prebiotics · Inulin and beta glucans left out

Rationale

A strain is only worth adding if it is fed. Two fibres this gut can use, dosed to what it handles.

Reading result

Mucus team

In range
Ingredient decision

No mucus layer support added

Omitted by reading

Rationale

The mucus team is in range. No measured reason to add anything.

Leaving an ingredient out is a decision made from the same data as putting one in.

Browse the ingredient library

Reviews

Their own words

  • "They moved very quickly. I received the kit for the biological sample fast, and it was very easy to send back. The questionnaire I filled out was thorough and detailed."

    Eugen nb1 customer · Trustpilot

  • "Everything is prompt and they really take care of every aspect of the experience. It really is a helpful, prompt and reliable company I leave my gut health in the hands of with certainty."

    Ramona nb1 customer · Trustpilot

  • "The process was straightforward and professional throughout, with no friction anywhere. Given how much I travel internationally, recovery and sleep support matter enormously to me. The results speak for themselves."

    Sirko nb1 customer · Trustpilot

The science board

Every reading and every formula is signed off by a scientist

The nb1 scientific team runs the method and signs off every protocol. Two independent validators with no stake in nb1 challenge it.

  • 7 specialists
  • 3 universities
  • 290+ publications
  • 17,000+ citations
  • Dr. Polina Novikova

    Dr. Polina Novikova

    Chief Scientific Officer

    PhD Bioinformatics, University of Luxembourg

  • Dr. Monica S. Matchado

    Dr. Monica S. Matchado

    Bioinformatics

    Functional profiling, TU Munich

  • Dr. Marijn Lewis

    Dr. Marijn Lewis

    Immunology and Gut Health

    PhD, University of Zurich

  • Katia B. Otterstedt

    Katia B. Otterstedt

    Clinical Research

    Genomics, ECLIN

  • Dr. Irina Utkina

    Dr. Irina Utkina

    Bioinformatics

    University of Toronto

  • Prof. Dr. Dirk Haller Independent

    Prof. Dr. Dirk Haller

    Nutrition and Immunology

    ZIEL Director, TU Munich

  • Dr. Koen Venema Independent

    Dr. Koen Venema

    Gut Microbiology

    254 publications

Meet the whole science board

Questions

Method, process and payment, answered

What is the difference between shotgun metagenomics and 16S rRNA sequencing?

16S reads one marker gene and resolves to genus. Shotgun reads all DNA, resolves species and strains, and recovers the genes present. nb1 uses shotgun for every reading.

Why does resolution matter for a supplement?

Species in the same genus can have opposite effects. A formula can only target what the test can name.

When do I pay?

Only when your formula enters manufacture, around week 3, after you have seen your reading.

What is the checkout code for?

Enter NB1FIRST at checkout. Valid on 4 and 12 month plans, not on the monthly rolling plan.

What is in the blood panel?

On Advanced, blood biomarkers are measured in cycles that alternate with your gut reading. Nutrient levels are measured, not guessed, and the doses in your protocol are adjusted to them.

Is the nutritionist protocol a meal plan?

No. It is a written protocol from a qualified nutritionist on which inputs support or work against the organisms in your reading. Reviewed before release.

How often is the formula rebuilt?

On Advanced the formula rebuilds from every analysis: gut and blood cycles alternate, with the first retest at the end of your first cycle and then every second cycle. On Core you can add a retest whenever you want to see your change.

How is my sample handled?

Sealed in a stabilising buffer, sequenced in certified EU labs. Data stored under EU data protection rules and never sold.

What does the 8,069 reference metagenome set do?

Your DNA is benchmarked against 8,069 gut metagenomes from 26 countries, with 155 signature species tracked against peer reviewed references. The healthy baseline is not drawn from one population.

Who reviews the science?

The nb1 scientific team, led by Dr. Polina Novikova, designs and runs the method and signs off every protocol before manufacture. Two independent validators, Prof. Dr. Dirk Haller and Dr. Koen Venema, review and challenge the method with no stake in nb1.

Can I see my raw data?

Yes. Your report is released at week 3. Full data can be requested from your account.

What if my reading changes my mind?

You decide after seeing your results. If you stop, nothing is charged and your data can be deleted on request.

End of dossier

Read the gut first. Decide after.

Sequencing, nutritionist protocol, and on Advanced blood panel and reformulation every cycle. You see your results before you pay.

Start the process

Checkout code NB1FIRST · Valid on 4 and 12 month plans

Included in every protocol

  • Shotgun metagenomic sequencing Included
  • Blood panel Advanced
  • Nutritionist protocol Included
  • Retest and reformulation every cycle Advanced

Charged only after you have reviewed your reading.

  • You pay on production

    Charged only when your formula is made, never before your analysis completes.

  • Cancel anytime

    Start month to month, no minimum commitment.

  • Analysis included

    The analysis is the product. It is in your subscription, not an add on.