Document Type

Thesis - Open Access

Award Date


Degree Name

Master of Science (MS)


Biology and Microbiology

First Advisor

Shin-Yi Lee Marzano

Second Advisor

Xiuqing Wang


16S, diet, gut microbiome, metatranscriptome, virome


The neonatal intestinal microbiome consists of all microorganisms in the gut. Although the microbiome is critical to human health and disease, its colonization remains incompletely understood, particularly in the preterm infant. We aimed to characterize the intestinal bacteria microbiome and virome in moderate-to-late preterm infants. We hypothesized that the bacteria microbiome and virome differs between breast milk and formula-fed infants. We collected stool samples from twenty infants born between 32 0/7 and 36 6/7 weeks gestation. Samples were collected after infants reached full volume enteral feedings. Ten infants were breast milk fed and ten received infant formula. DNA and RNA were extracted from fecal samples and sequenced using amplicon sequencing of 16S rRNA seq and RNAseq. 16S results showed that breast milk and formula-fed infants had similar bacterial diversity. Firmicutes were found in all samples and constituted the predominate phylum in most of infants regardless of nutrition. Breast milk-fed infants have 18% and 15% of Veillonella and Escherichia, respectively compared to 10% and 0.02% in formula-fed. 18% and 17% of Streptococcus and Klebsiella in formula group, but 9% and 8% in breast milk group. Overall, the abundant of Propionibacterium was significantly higher in breast milk-fed infants than formula fed. These results were basically consistent with metatranscriptome results except breast milk-fed group had more Streptococcus than formula group. For virome composition, we identified three different bacteriophages and discovered that the read counts of Siphoviridae were significantly higher in formula fed infants from metatranscriptome results (p-value = 0.002). Based on sample analysis from these twenty preterm infants, we concluded that the preterm intestinal microbiome is altered by diet. While microbial diversity was similar between breast milk- and formula-fed infants, the predominant bacteria differed. The abundance of Siphoviridae seems to be related to formula-fed. Our results provide new knowledge on diet affection of moderate to late preterm infants in both bacteria microbiome and virome aspect, and two different methods, 16S sequencing and RNAseq, commonly used to study intestinal microbes were compared to provide a reference for selection.

Library of Congress Subject Headings

Premature infants -- Nutrition.
Gastrointestinal system -- Microbiology.
Bacteria -- Health aspects.
Breast milk -- Physiological effect.
Infant formulas -- Physiological effect.



Number of Pages



South Dakota State University


In Copyright - Educational Use Permitted