Analysis of fecal samples from 412 infants across the US shows that 19% of vaginally-born babies, and 35% of those born via C-section completely lack Bifidobacterium species in their gut microbiomes.

A shocking 92% of the infants, regardless of birth mode, lack B. infantis, a predominant beneficial bacterium found in children living in rural non-industrial regions.

The findings, from the ongoing My Baby Biome study, are alarming because a strong proportion of Bifidobacterium species in an infant’s microbiome is protective against many non-communicable disorders. Epidemiological studies indicate that absence of these organisms correlates with increased risk of eczema, atopic dermatitis, asthma, chronic allergies, and gut disorders.

The My Baby Biome study is a joint effort between a San Diego-based microbiome therapeutics company called Persephone Biosciences, and researchers at the Department of Pediatrics, University of Rochester School of Medicine & Dentistry. It is the first comprehensive analysis of the infant microbiome in the US. The seven-year project, which began in August 2022, is the largest cross-sectional assessment of infant microbiomics and metabolomics to date.

The initial report was published in late June, in the Nature online journal, Communications Biology.

Widespread Deficit

“The data demonstrates that infants one to three months of age have a widespread deficit of certain Bifidobacterium strains that heretofore predominated in the infant gut and are critical for healthy development,” the authors state. “Lack of key Bifidobacterium can be defined as a true dysbiosis of the infant gut.”

The researchers collected fecal samples from 412 infants aged one to three months—the immediate post-partum period which is a critical window for establishing the microbiome and for immune system development. The babies were from the 48 continental states, and the cohort was composed to reflect the overall racial/ ethnic demographics of the US.

Controlling for antibiotic use, the researchers found that infants lacking robust Bifidobacterium levels were 3 times more likely to develop allergies, eczema, or asthma by age two.

Birth modes (66% vaginal, 34% C-section) and feeding modes (54% exclusively breastfed, 13% exclusively formula-fed, 33% mixed) were comparable to Centers for Disease Control data for the US as a whole.

The investigators limited the sampling to the first 3 months of life, as this eliminates the complicating microbial variables inevitable with introduction of solid food.

Across the sample set they identified 559 distinct microbial species, each of which showing a relative abundance above the pre-determined 0.5% “noise” threshold. The per-infant average waw 12 species, with a standard deviation of 5.5.

It is important to stress that overall, the metagenomic analysis showed Bifidobacterium species were prevalent across the cohort. And when they were present, Bifidobacterium tended to be highly abundant. However, there was a very distinct 24% sub-cohort of kids who entirely lacked these important organisms. 

Impact of Birth Mode & Breastfeeding

The presence and prevalence of Bifidobacterium was not necessarily linked with birth mode: 65% of the infants born via C-section had normal or even robust Bifidobacterialcounts, while as noted previously, 19% of those born vaginally had no meaningful levels of these bugs.

This suggests “that the acquisition of Bifidobacterium is not limited to vaginal birth, and can occur through the environment,” say the authors.

Breastfeeding had a complex and variable impact on Bifidobacterium levels, and it was different depending on birth mode.

In vaginal birth babies, breastfeeding correlated with high Bifidobacterium levels. But in those born via C-section, the curve trended in the opposite direction. Breastfed C-section infants had decreased Bifidobacterium levels.

What would account for this?

John Jarman, the study’s lead author, and his colleagues posit that among C-section babies, breastfeeding promotes colonization of the gut by other non-Bifido organisms that are capable of consuming human milk oligosaccharides (HMOs). These non-Bifido HMO-loving bugs out-compete the Bifidobacteria that a baby might acquire via post-birth environmental exposures.

The My Baby Biome analysis does provide some objective evidence to bolster this speculation. The researchers found notable levels of several known HMO-consuming organisms in the subgroup of kids that lacked Bifidobacterium. Some of those HMO-philes are potentially pathogenic, including Klebsiella pnemoniae and Clostridium perfringens.

In vaginal birth babies, breastfeeding correlated with high Bifidobacterium levels. But in those born via C-section, the curve trended in the opposite direction. Breastfed C-section infants had decreased Bifidobacterium levels.

The latter organism, which was the most statistically significant of the HMO-consuming non-Bifido bugs, had a particularly high abundance in the subgroup of babies that were both breastfed and born by C-section.

HMOs are the third most abundant solid component of human milk, following lipids and lactose. The degree to which particular organisms can use HMOs as fuel has a strong influence on infant microbiome composition. Further, HMOs have direct and indirect effects on infant immune system development.

Three Key Clusters

Based on patterns of microbiome composition, the researchers divided the cohort into three general clusters:

• C1 (24% of the total), is characterized by a high abundance of HMO-consuming Bifidobacterium (such as B. breve). Four species– Bifidobacterium breve, Bifidobacterium bifidum, Bifidobacterium longum subsp. longum, and Bifidobacterium longum subsp. Infantis were the most abundant in this cluster.  most abundant species
• C2 (37%) was characterized by a high abundance of B. longum, and a strong presence of organisms belonging to the Bacteroidota genus.
• C3 (39%) showed a markedly lower proportion of Bifidobacterium, but high abundance of Firmicutes and Proteobacteria. In this cluster, the most statistically abundant organism was the problematic C. perfringens.

The authors noted that relative to the other two clusters, Cluster 3 had large proportion of the babies born via C-section. Cluster 1 had a higher proportion of breastfed infants, compared with C2 and C3.

The My Baby Biome team looked at a host of genomic and metabolomic variables across the three clusters.

They found that the presence of genes for antimicrobial resistance (AMR), as well as virulence factor (VF) genes, were inversely correlated with abundance of Bifidobacterium. C3, the cluster with the lowest levels of Bifidobacterium, had the highest AMR and VF gene abundance. C1, the ‘healthy’ cluster with robust Bifidobacterium populations, had the lowest AMR and VF prevalence.  

This supports the notion that an infant gut microbiome rich in Bifidobacterium species is a healthier, less pathogenic ecosystem.

The investigators found several troubling anomalies in C3, including altered bile acid metabolism, reduced thiamine production, and a shift in short-chain fatty acid production tending toward higher butyrate production.

Cluster 3 as well as cluster 2 also showed a trend toward reduced production of aromatic lactic acids such as indole-3-lactate, which have important immune-system modulating properties. Notably, the fecal pH was highest in C3 and lowest in C1. The finding reflects differences in production of acetate and lactate.

Though the specific meaning of each observed variation is still to be determined, it is very clear that metabolically the three clusters were quite different.

Troubling Signs

What does all of this mean clinically?

My Baby Biome is an ongoing study that will track health and illness within the cohort for a total of seven years. But already, the researchers are seeing some troubling signs.

They’ve obtained health survey data on 210 of the participating infants who’ve reached age 2. Controlling for antibiotic use (and 54% of parents reported at least one course of antibiotics in the first 24 months of life), they found that compared with the C1 infants, those in C2 and C3 were 3 times more likely to develop allergies, eczema, or asthma.

In total, nearly one-third (30%) of all the kids followed-up so far, have at least one of these three “adverse immunological outcomes.”

Jarman and colleagues note that in the absence of robust Bifidobacterium levels, it is far easier for other HMO-consuming bacteria to rush in and fill the niche. In cluster C2, they found that the gap was often filled by Bacteroidaceae. These bugs have mucin-utilization genes that do let them use HMOs. Though not pathogenic per se, the Bacgeroidaceae fail to provide the same metabolic and immune system benefts as Bifidobacteria.

They point out that Western diet and lifestyle have promoted the proliferation of many HMO-consuming microbes not found in other less industrialized parts of the world.

Given that 79% of the total My Baby Biome cohort fall into clusters 2 and 3, and lack healthy levels of Bifidobacterium, this does not bode well for the future.

In the absence of Bifidobacterium, it is far easier for other HMO-consuming bacteria to rush in and fill the niche. Some of these, like Clostridium perfringens, may be pathogenic.

That said, the data gathered so far do support the notion that a strong prevalence and abundance of Bifidobacterium in an infant’s early-life microbiome could be protective against a number of common non-communicable chronic diseases. “Given the alarming rise in NCDs and their link to the infant gut microbiome, the gut microbiota offers an opportunity for early intervention with lifelong health impact.”

Persephone Biotherapeutics, the sponsor of the study, is developing new “symbiotic” products specifically for infants and toddlers. The goal is to re-equilibrate the developing gut microbiome toward a more healthful composition.

Company founder, Stephaine Culler, PhD, is a chemical engineer and microbiome scientist, committed to developing live biotherapeutics with specific health benefits. The company is located within Johnson & Johnson’s JLABS incubator in San Diego.

END