Scientific evidence on the infant microbiome
The studies, bibliography, and methodology underlying Novabiomica's indicators, gathered in a single reference space.
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From literature to the platform
Scientific research on the infant gut microbiome is the foundation of the Novabiomica approach.
The selection of indicators is based on international scientific literature, including publications contributed to by researchers Giorgio Casaburi and Steven A. Frese.
In this section, we present the most relevant studies, their connection to the analyzed areas, and the methodology used, distinguishing biological evidence from the interpretative limits of the analyses.
Persistence of Supplemented Bifidobacterium longum subsp. infantis EVC001 in Breastfed Infants
Frese SA et al. · mSphere · 2017
The study documents the persistent colonization of B. infantis EVC001 in the breastfed infants studied and the associated changes in microbial composition and fecal biochemistry.
Read the study →Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria
Casaburi G et al. · Antimicrobial Resistance & Infection Control · 2019
The study analyzed the gut resistome of 60 breastfed infants, observing a lower abundance of genes associated with antibiotic resistance in the EVC001 group compared to controls.
Read the study →
Giorgio Casaburi presents the study in a plenary session at the 51st ESPGHAN Congress, Geneva, May 2018.
From research to international scientific discussion
Giorgio Casaburi, lead author of the study and co-founder of Novabiomica, presented the research in May 2018 at the 51st annual congress of ESPGHAN, the European Society for Paediatric Gastroenterology, Hepatology and Nutrition, in Geneva. The contribution was selected among the Top Abstracts in the Nutrition area and among the ten best abstracts of the entire congress, with a presentation in the plenary session.
The results on the infant gut resistome were also the subject of a congress press release, distributed through EurekAlert, bringing the research to the attention of the international pediatric scientific community.
A recognition that highlights the contribution to research on the infant microbiome and its relationship with antibiotic resistance.
Read the release on EurekAlert →Colonization of breastfed infants by Bifidobacterium longum subsp. infantis EVC001 reduces virulence gene abundance
Casaburi G, Frese SA · Human Microbiome Journal · 2018
The study observed a reduction in the abundance of genes associated with virulence factors in the gut microbiome of infants colonized with EVC001.
Read the study →Colonization by B. infantis EVC001 modulates enteric inflammation in exclusively breastfed infants
Henrick BM et al. · Pediatric Research · 2019
The study examined the associations between B. infantis colonization, microbial composition, and fecal inflammatory biomarkers measured directly in infants.
Read the study →Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States
Casaburi G et al. · Scientific Reports (Nature Portfolio) · 2021
The study, coordinated by Giorgio Casaburi as lead author, analyzed the gut microbiome of 227 infants between 0 and 6 months using shotgun metagenomics, recruited across seven research centers in five American states.
The analysis highlighted a reduced presence of Bifidobacterium, a limited genetic capacity to utilize human milk oligosaccharides (HMOs), and a frequent presence of potentially pathogenic bacteria and genes associated with antibiotic resistance.
These results helped highlight the importance of evaluating the infant microbiome not only through bacterial composition but also by considering its functional capabilities.
Read the study →Extended bibliography
Consult other scientific publications
O'Brien et al. (2026) — Randomized, placebo-controlled trial reveals the impact of dose and timing of B. infantis probiotic supplementation
Dose and timing of colonization · DOI 10.1128/msphere.00518-25
Casaburi et al. (2022) — Metabolic model of necrotizing enterocolitis in the premature newborn gut resulting from enteric dysbiosis
Metagenomics and metabolites in premature newborns · DOI 10.3389/fped.2022.893059
Lueschow et al. (2022) — B. longum subsp. infantis EVC001 Decreases Neonatal Murine Necrotizing Enterocolitis
O'Brien et al. (2022) — Early probiotic supplementation with B. infantis in breastfed infants leads to persistent colonization at 1 year
Persistence of colonization · DOI 10.1038/s41390-020-01350-0
Nguyen et al. (2021) — Impact of Probiotic B. infantis EVC001 Feeding in Premature Infants
Prematurity, resistome, and HMO · DOI 10.3389/fped.2021.618009
Duar et al. (2020) — Comparative Genome Analysis of B. infantis Strains Reveals Variation in HMO Utilization Genes
Duar et al. (2020) — Integrating the Ecosystem Services Framework to Define Dysbiosis of the Breastfed Infant Gut
The infant microbiome as an ecosystem · DOI 10.3389/fnut.2020.00033
Duar, Kyle & Casaburi (2020) — Colonization Resistance in the Infant Gut
Karav, Casaburi & Frese (2018) — Reduced colonic mucin degradation in breastfed infants
Mucin and the intestinal barrier · DOI 10.1002/2211-5463.12516
Henrick et al. (2018) — Elevated fecal pH indicates a profound change in the breastfed infant gut microbiome
From scientific evidence to microbiome indicators
Each area considers specific characteristics of the gut ecosystem, interpreted in light of available scientific knowledge and, where applicable, reference populations.
The goal is to offer a detailed representation of the microbiome, distinguishing the presence of microorganisms, their functional potential, and the developmental trajectories associated with the child's age.
1. Gut microbiome maturation
Analyzes microbial composition in relation to chronological age and the developmental trajectories observed in reference populations. Through microbial maturation models, it describes the sample's position relative to the expected trend for that age.
Indicators analyzed: estimated microbial age, chronological age, difference from the expected trajectory, maturation percentile, and comparison with available references.
2. Bifidobacteria and HMO utilization capacity
Examines the presence and abundance of gut bifidobacteria, with a particular focus on Bifidobacterium longum subsp. infantis, and identifies genes associated with the ability to utilize human milk oligosaccharides (HMOs).
The analysis integrates taxonomic and functional information, distinguishing the presence of specific microorganisms from the availability of genetic pathways involved in HMO metabolism.
Indicators analyzed: bifidobacteria abundance, B. infantis identification, subspecies genetic markers, HMO clusters, glycosidase (GH) families, genetic capacity to utilize fucosylated, sialylated, and other HMO structures.
Scientific references: Frese et al. (2017); Duar et al. (2020); Casaburi et al. (2021).
3. Ecology, composition, and microbial diversity
Describes the structure of the gut microbial community, considering the distribution of bacterial families, genera, and species, as well as the physiological variations that characterize the first months of life.
The analysis includes indicators of richness, diversity, and evenness, useful for describing the complexity of the ecosystem. Their interpretation must be contextualized by age: higher diversity does not necessarily represent a more favorable condition in a newborn.
Indicators analyzed: taxonomic abundances, observed species, Shannon index, inverse Simpson index, and Pielou's evenness index.
Scientific references: Frese et al. (2017); Casaburi et al. (2021); Bottino et al. (2025).
4. Gut resistome and antibiotic resistance genes
Characterizes the repertoire of genes associated with antibiotic resistance present in the gut microbiome, distinguishing resistance classes and selected genetic markers of biological relevance.
This information describes the resistome detectable via metagenomics and is not equivalent to an antibiogram or proof of phenotypic resistance in a specific microorganism.
Indicators analyzed: ARG genes, antibiotic resistance classes, abundance of selected markers, and resistance gene diversity.
5. Virulence factors and pro-inflammatory potential
Examines selected genetic markers associated with bacterial virulence factors and microbial components of biological interest, including genes linked to the biosynthesis of specific lipopolysaccharide (LPS) structures.
The identification of these markers does not prove the actual production of the molecules, the activation of an inflammatory response, or the presence of a pathological condition.
Indicators analyzed: selected virulence genes, abundance of virulence markers, and genes associated with the biosynthesis of LPS structures.
Scientific references: Vatanen T et al. (2016), Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell; Casaburi & Frese (2018); Henrick et al. (2019).
6. Potential production of short-chain fatty acids (SCFAs)
Analyzes microbial genes associated with metabolic pathways involved in the production of short-chain fatty acids, including acetate, propionate, and butyrate.
These metabolites participate in various interactions between the microbiome and the gut environment. Their biological significance varies depending on age, available substrate, and the structure of the microbial community.
Indicators analyzed: genetic potential associated with the production of acetate, propionate, and butyrate.
Scientific reference: Frese et al. (2017).
7. Lactate metabolism
Evaluates microbial genes associated with the production of lactate, a relevant metabolite in the ecology of the infant gut microbiome and in metabolic interactions between different bacterial populations.
Lactate can represent an important fermentation product for some bacteria, including bifidobacteria. However, the presence of the genes does not allow for determining the concentration of the metabolite in the gut.
Indicator analyzed: genetic potential associated with lactate production.
8. Histamine metabolism
Examines microbial genetic markers associated with the production of histamine, a biologically active molecule involved in numerous physiological and signaling processes.
The presence of genes associated with this metabolism indicates functional potential and does not allow for establishing the amount of histamine actually produced or for attributing clinical symptoms.
Indicator analyzed: abundance of selected genes associated with histamine metabolism.
9. Sulfur metabolism and H₂S production potential
Identifies genes associated with selected microbial pathways involved in the production of hydrogen sulfide (H₂S), with particular reference to markers of sulfate-reducing bacteria.
H₂S is a molecule with biological effects that depend on context and concentration. Metagenomic analysis identifies genetic potential without directly measuring gas production.
Indicator analyzed: abundance of selected genetic markers associated with the potential for H₂S production by sulfate-reducing bacteria.
Associated module: Cautionary Load. The indicator contributes to the module by comparison with the distribution of the reference cohort, without attributing diagnostic significance to the result.
10. Potential for intestinal mucin degradation
Examines selected microbial genes associated with the degradation of mucins, fundamental components of the mucus layer that lines the intestinal epithelium.
The analysis allows for describing the genetic potential of the microbial community to utilize mucin-derived substrates, without directly measuring the integrity or thickness of the mucus barrier.
Indicator analyzed: curated genetic potential for mucin degradation.
How we analyze the microbiome
Novabiomica uses shotgun metagenomic sequencing to analyze the microbial DNA present in fecal samples.
Unlike methods based exclusively on the amplification of specific genetic regions, the shotgun approach allows for obtaining information on both the taxonomic composition of the microbiome and the genetic potential of selected microbial functions.
Sequencing data undergo quality controls, filtering of human-origin sequences, and bioinformatic analysis through dedicated pipelines. The results are then organized into indicators that facilitate the reading of infant gut microbiome characteristics.
Limits of the analysis
The detection of genetic sequences does not necessarily prove gene expression or corresponding metabolic activity. Results must be interpreted considering the child's age, diet, clinical history, and other characteristics.
The informational report is not a diagnosis or a therapeutic indication: for any doubts, consult your primary pediatrician.
Scientific experience
Novabiomica's scientific approach is developed from research experience in the fields of the infant gut microbiome, metagenomics, and bioinformatics.
Selected publications include contributions from Giorgio Casaburi and Steven A. Frese, who participated in studies dedicated to microbial colonization in the first months of life, human milk oligosaccharide metabolism, the resistome, and interactions between the microbiome and the gut environment.
Discover the Novabiomica scientific teamFrom evidence to the informational report
Discover how Novabiomica translates this evidence into readable indicators, from the fecal sample to the dashboard.
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