Abstract
Members of the genus Bifidobacterium are abundant in the stool of most human infants during the initial exclusively milk-fed period of life, especially at an age of 2–3 months (Harmsen et al., 2000; Favier et al., 2002; Mariat et al., 2009; Coppa et al., 2011; Turroni et al., 2012; Yatsunenko et al., 2012; Tannock et al., 2013; Barrett et al., 2015). Bifidobacteria dominate the stool microbiota regardless of whether the infants are fed human milk or formula based on ruminant milk (cow or goat). However, bifidobacteria have about 20% higher relative abundances in human milk-fed compared to formula-fed babies (Tannock et al., 2013). The greater abundance of bifidobacteria in human-milk-fed infants can, at least in part, be explained by the fact that bifidobacterial species that are enriched in the infant bowel can utilize Human Milk Oligosaccharides (HMO) or their components as growth substrates (Sela et al., 2008; LoCascio et al., 2010; Garrido et al., 2013). It could be anticipated, therefore, that bifidobacteria would be detectable in the stool microbiota of every child nourished at the breast because of the supply of appropriate growth substrates. This expectation is not borne out completely because a proportion of infants have very low abundance or undetectable bifidobacteria as members of the fecal microbiota regardless of breast milk or formula feeding (Young et al., 2004; Gore et al., 2008; Tannock et al., 2013). Antibiotics had not been administered to these infants. How then can the absence of bifidobacteria be explained?
Highlights
Specialty section: This article was submitted to Microbial Symbioses, a section of the journal Frontiers in Microbiology
Bifidobacteria dominate the stool microbiota regardless of whether the infants are fed human milk or formula based on ruminant milk
The greater abundance of bifidobacteria in human-milk-fed infants can, at least in part, be explained by the fact that bifidobacterial species that are enriched in the infant bowel can utilize Human Milk Oligosaccharides (HMO) or their components as growth substrates (Sela et al, 2008; LoCascio et al, 2010; Garrido et al, 2013)
Summary
An obvious reason for bifidobacteria-negative feces is that the detection methods lack sufficient sensitivity. Culture-based methods usually have a lower detection limit of 1 × 103 per gram, fluorescent in situ hybridization (FISH) 1 × 106 − 107 per gram (manual or digital counts respectively) or ∼4 × 104 by flow cytometry, and denaturing gradient gel electrophoresis of PCR. High throughput DNA sequencing methods, such as Illumina, generate tens of thousands of 16S rRNA gene sequences per DNA sample, but there may be several hundred OTU per sample. While lack of sufficient sensitivity of detection methods remains a possibility, it probably does not provide the total explanation
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