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Members of the bacterial genusBifidobacterium generally dominate the fecal microbiota of infants. The speciesBifidobacterium longum is prevalent, but theB. longum subsp.longum andB. longum subsp.infantis strains that are known to colonize the infant bowel are not usually differentiated in microbiota investigations. These subspecies differ in their capacities to metabolize human milk oligosaccharides (HMO) and may have different ecological and symbiotic roles in humans. Quantitative PCR provides a quick analytical method by which to accurately ascertain the abundances of target species in microbiotas and microcosms. However, amplification targets in DNA extracted from samples need to be dependably differential. We evaluated thetuf gene sequence as a molecular target for quantitative PCR measurements of the abundances ofB. longum subsp.infantis andB. longum subsp.longum in fecal microbiotas. This approach resulted in the detection of atuf gene variant (operational taxonomic unit 49 [OTU49]) in Chinese infants that has sequence similarities to bothB. longum subsp.infantis andB. longum subsp.longum . We compared the genome sequence and growth and transcriptional characteristics of an OTU49 isolate cultured in HMO medium to those of otherB. longum subsp.infantis cultures. We concluded from these studies that OTU49 belongs toB. longum subsp.infantis , that dependable quantitative PCR (qPCR) differentiation between theB. longum subspecies cannot be achieved by targetingtuf gene sequences, and that functional genes involved in carbohydrate metabolism might be better targets because they delineate ecological functions.IMPORTANCE High-throughput DNA sequencing methods and advanced bioinformatics analysis have revealed the composition and biochemical capacities of microbial communities (microbiota and microbiome), including those that inhabit the gut of human infants. However, the microbiology and function of natural ecosystems have received little attention in recent decades, so an appreciation of the dynamics of gut microbiota interactions is lacking. With respect to infants, rapid methodologies, such as quantitative PCR, are needed to determine the prevalences and proportions of different bifidobacterial species in observational and microcosm studies in order to obtain a better understanding of the dynamics of bifidobacterial nutrition and syntrophy, knowledge that might be used to manipulate the microbiota and perhaps ensure the better health of infants.

tuf Gene Sequence Variation in Bifidobacterium longum subsp. infantis Detected in the Fecal Microbiota of Chinese Infants