Comparing the microbiota

of preterm infants

Published October 01 2017

Protein-based (A) and 16S-based (B) taxonomic profiles and protein-basedfunctional profiles (C) in extremely pretern (25-26 weeks), extremely preterm (27 weeks) and very preterm infants during postnatal weeks 3-6. Per time point, average relative abundances for each gestational age group are shown. Relative abundances were calculated using iBAQ intensities and read counts for protein and 16S-based profiles respectively. Mec: meconium.courtesy of Wageningen University

It has become increasingly apparent that the bacterial community of the gastrointestinal tract, termed the microbiota, plays an important role in health and disease. The development of the intestinal microbiota during early life coincides with the development of the GI tract and immune system. Multiple studies have aimed at understanding the development of the microbiota in newborns and its effect on early and later health outcomes.

Compared with full-term neonates, preterm infants are more frequently exposed to interventions during hospitalization, such as caesarean section delivery, antibiotics and respiratory support, which likely affect the development of their intestinal microbiota. Despite increasing knowledge about which bacteria are present in the GI tract of preterm infants, knowledge about the function of their gut bacteria is limited. A recent paper in Molecular & Cellular Proteomics reported the differences in microbiota composition and function in preterm infants.

Clara Belzer’s group at Wageningen University in the Netherlands focuses on the human microbiome and includes a special task force on early-life microbiota development. Together with Nutricia Research and clinicians from Isala Clinics, the group initiated a study on the microbiome of preterm infants. To determine if gestational age would influence the colonization by microbes, they studied how the bacterial community developed during the first six postnatal weeks in infants that were born extremely preterm (at less than 28 weeks of pregnancy, or EP) and very preterm (at less than 32 weeks, or VP).

To identify which bacteria were present, the researchers combined two techniques: 16S rRNA gene sequencing, to determine bacterial composition, and metaproteomics, a technique used less commonly in microbiome studies. The proteomics provided better insight into the activity of the microbes in the preterm intestine. They analyzed fecal samples collected from 10 preterm infants during the first six postnatal weeks. “Using a metaproteomics approach, we could identify the most abundant proteins present in the faeces of each infant over time,” Belzer and first author Romy Zwittink wrote in response to questions about this paper. Once the abundant proteins were identified, the authors used existing data to discover their function. “For many bacterial proteins, their function is known and stored in databases,” they wrote, “and we used this information to get insights in what the gut bacteria are doing.”

Zwittink and colleagues found significant differences between microbiota composition and function in EP versus VP infants. The authors suggest that the increase in respiratory support and antibiotic intervention seen in EP infants was associated with delayed colonization of the beneficial early-life colonizer Bifidobacterium. They observed a lower abundance of proteins involved in carbohydrate and energy metabolism, which are important for the degradation of milk, in EP infants. Proteins involved in membrane transport and translation were more abundant in EP infants than in VP infants, and this was likely a result of antibiotic pressure. These results indicate the importance of gestational age on microbiota development. VP infants had a better-established and more metabolically active microbiota compared with EP infants.

While the priority in preterm infant care is survival of the infant, clinicians are still interested in further improving care, and Zwittink’s research was developed through close collaboration with neonatologists. “In our opinion, the microbiota field should move from being mostly composition oriented to a more function-oriented field,” Zwittink and Belzer wrote. “Unravelling the activity and enzymatic capabilities of the intestinal microbiota might bring us closer to understanding its association with food digestion immune responses and thus health. These microbiota findings can be used to design food and microbiota-based therapies.”

The researchers were most surprised that duration of respiratory support was a major factor influencing the composition and function of preterm microbiota. “After discussion with neonatologists involved, we could put this into perspective, understanding that some methods of respiratory support allow for air to reach the gastrointestinal tract and can therefore greatly affect bacterial colonisation pattern,” Zwittink and Belzer wrote. “The microbial signature as we observed in extremely preterm infants with many potential pathogens has been previously associated with several negative health outcomes, including necrotising enterocolitis and late-onset sepsis. However, so far these are associations and no causal relationship has been shown. We can also speculate that a microbiota less active in milk degradation will be less favourable for the food digestion and energy harvest in a preterm infant.”

In the future, Zwittink and colleagues hope to confirm these findings in a larger cohort of preterm infants. They now are analysing microbiome data from a set of 120 infants. The researchers said that preterm birth is an increasing global problem, so they hope that these findings eventually will guide clinical practice and thereby improve the well-being and chance of survival of preterm infants.

Rachel Goldberg Rachel Goldberg is a molecular biologist and postdoctoral research fellow at the Johns Hopkins University School of Medicine.