Microbiome Analysis Solutions

Why Gut Microbiota Matters

The human gut microbiota is a complex, dynamic ecosystem inhabited by bacteria, fungi, archaea, and viruses. The total number of microbial cells can exceed the body's own cells by an order of magnitude. The gut microbiota is involved in carbohydrate and protein metabolism, lipid exchange, and produces important metabolites such as short-chain fatty acids (SCFAs), secondary bile acids, vitamins and lipopolysaccharides that regulate appetite, intestinal motility, energy consumption, and immune system maturation.

Childhood Microbiome Formation

The establishment of the infant's gut microbiota is a long and dynamic process with four successive phases:

• Birth: Initial colonization by Streptococcus spp. and Enterobacterales
• 14 days: Lactobacillaceae, Bifidobacterium spp., Clostridium, Bacteroidota
• Complementary foods: Bacteroidota, Bacillota, Verrucomicrobiota, Actinomycetota, Pseudomonadota
• Weaning: Stabilization of microbiota composition

Factors Affecting Microbiota Formation

• Type of birth: Naturally born infants have stable composition from mother's vaginal, skin, and fecal microbiota. Caesarean section delays formation and increases opportunistic microorganisms (C. difficile, Enterococcus, Klebsiella, Streptococcus, Veillonella)
• Type of feeding: Breastfed infants are dominated by Bifidobacterium spp. (B. breve, B. bifidum, B. longum). Formula-fed children have more Bacteroides and Clostridium with reduced bifidobacteria
• Gestational age: Premature infants have delayed anaerobic colonization with higher Enterobacteriaceae and opportunistic microorganisms
• Antibiotics: Reduces overall diversity, increases drug-resistant bacteria from Enterobacteriaceae and Clostridium, decreases Bifidobacteriaceae, Bacilli and Lactobacillales

Technology

Detects microbial taxa that make up at least 99.9% of the total prokaryotic mass of a child's feces. The taxa are detailed to the level of clinical significance, taking into account the age of the child. Real-Time PCR is currently the most optimal approach - accurate and fast quantitative determination using species-specific or group-specific primers.

Normal Microbiota Detection

• Actinomycetota (Actinobacteria): Bifidobacterium spp. (B. bifidum, B. longum, B. breve, B. infantis, B. adolescentis) - among the first colonizers, dominant in first months, ferment breast milk oligosaccharides, activate cellular immunity
• Bacillota (Firmicutes): Clostridium leptum gr., Lachnospiraceae, Faecalibacterium prausnitzii (anti-inflammatory biomarker), Lactobacillaceae (probiotic, barrier function), Streptococcus spp.
• Bacteroidota (Bacteroidetes): Bacteroides spp. (vitamin K producers), Prevotella spp. (fiber degradation), Parabacteroides spp. (antimicrobial, bile acid conversion), Alistipes spp.
• Other bacteria: Akkermansia muciniphila (mucosal barrier function), Methanobacteriaceae (hydrogen oxidation), Desulfovibrio spp., Blautia spp.

Opportunistic Microbiota & Pathogenicity Markers

• Clostridioides difficile (tcdA, tcdB markers): Produces enterotoxins A and B, causes nosocomial infectious diarrhea, symptoms range from mild diarrhea to severe colitis
• Clostridium perfringens gr.: Associated with necrotizing enterocolitis in preterm infants, capable of producing multiple toxins
• Enterobacterales: Inflammation markers, associated with irritable bowel syndrome, inflammatory bowel disease, necrotizing enterocolitis
• Staphylococcus aureus (mecA marker): Slows normal microbiota formation, mecA gene indicates methicillin resistance
• Streptococcus agalactiae (srr2 marker): Strains with srr2 gene have increased virulence, can cause meningitis
• Candida spp. / Candida albicans: Present in 30-60% of healthy people, antibiotic treatment promotes colonization, can cause invasive infections

Comprehensive Detection Panel

• 43 Specific Markers: Comprehensive quantification of all clinically relevant taxa simultaneously
• Normobiota quantification: Actinomycetota, Bacillota, Bacteroidota, Pseudomonadota, Fusobacteriota, Verrucomicrobiota, Euryarchaeota
• Opportunistic microbiota: Complete pathobiont profiling and yeast fungi from genus Candida
• Bifidobacteria species: Detailed species-level determination including child and adult metabolic types
• Pathogenicity markers: mecA (methicillin resistance), srr2 (S. agalactiae virulence), tcdA/tcdB (C. difficile toxins)
• Ratio calculations: Bacillota/Bacteroidota ratio for inflammation assessment

Clinical Applications

Recommended when it is necessary to determine the qualitative composition and quantitative assessment of the microbiota of the large intestine in the context of medical and diagnostic procedures. A species-rich gut ecosystem is more resilient to adverse environmental stresses - reduced diversity is associated with disease presence.

Key Features

• 99.9% Coverage: Detects microbial taxa comprising the total prokaryotic mass of feces
• Age-Specific Norms: Results interpreted based on children's age-specific reference values
• Fast Analysis: Results in just a few hours, enabling quick clinical decisions
• Multiplex Format: Several DNA targets detected simultaneously in one test tube
• Internal Control: Assessment of DNA extraction and PCR quality for reliable results
• Automated Generation: Automatic results form creation with preset templates
• Dysbiosis Assessment: Normocenosis/dysbiosis status by relative abundance in total bacterial mass

Biomaterial

Feces (including meconium)