Gut and vaginal microbiome

The microbiota is the set of bacteria, fungi, viruses and archaea that live in a site of the body; the microbiome is that community plus its genetic material and the environment it lives in. In everyday use the terms are used interchangeably, and when someone talks about getting their microbiome tested, they mean sequencing the DNA present in a sample to estimate which microorganisms are there and in what proportion.

These communities are not silent passengers. In the gut, they ferment fiber and produce short-chain fatty acids, synthesize vitamins, compete with pathogens and train the immune system. In the vagina, lactobacilli produce lactic acid, which keeps the pH low and unfavorable for many microorganisms. Antibiotics, diet, infections, the menstrual cycle, sexual activity and menopause change their composition.

The gut and the vagina are opposite ecosystems, and the logic of one should not be applied to the other. In the gut, high diversity is usually read as favorable. In the vagina, the most stable situation during the reproductive years is a low-diversity community dominated by lactobacilli. That is why each report is interpreted using criteria specific to its site.

We extract DNA from the sample and amplify the V3–V4 region of the 16S rRNA gene, a gene present in all bacteria that works like a barcode. The sequences are obtained on an Illumina sequencer at a specialized service center, in batches, and the bioinformatic analysis and interpretation are done in our laboratory following a standardized, documented procedure.

Processing identifies exact sequence variants (ASVs) with the DADA2 algorithm, assigns them taxonomy against the SILVA database and, when the region allows it, refines the species by alignment against NCBI type strains. A species is only named when identity is 99% or higher; if several species cannot be told apart in V3–V4, the report says so instead of guessing. Interpretation follows fixed rules: the same composition always produces the same text.

16S sequencing has limits that the report states explicitly: it reports relative abundances of bacteria, does not detect fungi, parasites or viruses, does not distinguish strains or toxins, and does not replace a culture or a PCR when the question is a specific infection. A reproducible result also requires care in how the sample is collected and stored, which is why the preparation instructions matter.

The report describes the bacterial composition of the stool at the phylum, family and genus level, with the species when the method allows it, and the diversity of the community (richness and the Shannon and Simpson indices). It highlights genera of clinical interest, such as Faecalibacterium and Roseburia (butyrate producers), Akkermansia, Bifidobacterium, Bacteroides and Prevotella, with a note on what the evidence associates with each one and on what is not yet established.

It also includes an explicit panel of potentially pathogenic bacteria (Clostridioides, Salmonella, Campylobacter, Escherichia/Shigella, Yersinia, Vibrio, Klebsiella and Helicobacter) that is always reported, as detected or not detected. Detection by 16S is not diagnostic: it does not identify toxigenic strains or distinguish colonization from infection, and a not-detected result does not rule out an infection. If an infection is clinically suspected, the appropriate test is a stool culture or a targeted molecular test.

Following the international consensus on microbiome testing published in 2025, the report does not include the Firmicutes/Bacteroidetes ratio, dysbiosis indices or diet or supplement recommendations: there is currently no reference gut microbiome against which to compare a person, and conclusions of that kind do not have sufficient support. In addition, a stool sample does not necessarily reflect the microbiota attached to the intestinal mucosa. What the report does provide is a detailed, reproducible description for a healthcare professional to interpret in context.

The report classifies the community into a community state type (CST I to V) using the VALENCIA algorithm, the reference method derived from the work of Ravel and colleagues, who described the usual patterns in asymptomatic women. Four of those patterns are dominated by a single Lactobacillus species (L. crispatus, L. gasseri, L. iners or L. jensenii), and the fifth is more diverse, with fewer lactobacilli and more anaerobes, which does not in itself mean disease.

In addition to the CST, the report details lactobacilli by species and a panel of microorganisms of interest that is always reported: bacteria associated with bacterial vaginosis (Gardnerella, Fannyhessea, Prevotella, Sneathia, Megasphaera, BVAB1, BVAB2, BVAB3, Mobiluncus, Mycoplasma hominis), bacteria associated with aerobic vaginitis (Streptococcus agalactiae, Enterococcus, Escherichia, Klebsiella, Staphylococcus) and genital mycoplasmas. For sexually transmitted bacteria, the sensitivity of the method has not been validated: a not-detected result does not rule out infection.

Sequencing is not the recommended method for diagnosing bacterial vaginosis or candidiasis. Current guidelines maintain established diagnostic criteria (Amsel criteria, Nugent score, vaginal discharge culture and molecular tests validated for that purpose). That is why the test is provided as a descriptive, complementary tool, for your gynecologist to integrate with your symptoms and the rest of your tests.

It makes sense when you and your healthcare professional want to know the composition of the bacterial community as a complement to the clinical evaluation: for example, to document the baseline before a change in diet, a long-term treatment or the use of probiotics, and to measure again afterward; or when the gynecologist wants to know whether L. crispatus or L. iners predominates in a patient with recurrent discomfort and no clear diagnosis.

It is not the right test when the question is an acute infection. For diarrhea, the appropriate tests are a stool culture, a stool parasite exam, Clostridioides difficile toxin testing or a gastrointestinal molecular panel. For vaginal discharge with symptoms, a wet mount, a vaginal discharge culture and vaginal pH. For a sexually transmitted infection, the specific PCR. We also perform all of those tests, and they provide answers based on established diagnostic criteria.

Nor is it useful for choosing diets or supplements on your own: a microbiome profile does not tell you which foods are right for you. The measures that support the microbiota (fiber and plant variety, fermented foods, prudent use of antibiotics, no vaginal douching) are well established and do not require any prior test.

Vaginal microbiome: the sample is a vaginal swab taken by laboratory staff at an appointment; it takes less than a minute and does not hurt. It is collected outside your menstrual period, after 72 hours without sexual intercourse, vaginal suppositories, creams, vaginal douches or antiseptics. No fasting is required.

Gut microbiome: before your appointment, you pick up the kit at the laboratory, which contains a sterile container and instructions. You collect the sample at home, keep it in the refrigerator and drop it off within 24 hours, at your appointment time. No fasting or dietary changes are required.

Samples are sequenced in batches, and the report is delivered in 20 to 30 business days through the online results portal. If you have taken antibiotics, antifungals, laxatives, enemas, probiotics or omeprazole (and similar drugs) in the previous weeks, let us know: the test is still performed, but this is recorded because they change the microbiota and it is information your healthcare professional needs to interpret the results.