As infant gut develops, microbial strains form individualized patterns of stability: Study

05-Nov-2020 - Last updated on 05-Nov-2020 at 17:38 GMT

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Two researchers from the University of Alabama at Birmingham have spent the last three years using the microbiome ‘fingerprint’ technique -- a method that harnesses the power of genomic tools and supercomputers to identify individual strains within a single species of the gut microbiome.

Now, Casey Morrow, PhD, Hyunmin Koo, PhD, and colleagues are using their experience in analyzing microbial strain stability to study these individualized patterns in humans. Their latest research was recently publishers in Frontiers in Pediatrics.

Composition and stability

The UAB researchers examined infants and children, from about 6 months of age to 6 years old. They observed that over time, there were individualized patterns of microbial strain specificity as the infant gut microbiomes developed.

Infant gut microbial ecosystems begin with short-term changes in microbial composition that eventually end up stable. This stability is key for efficient digestion of food, healthy immune development and resistance to colonization with pathogens.

"In general, the early gut microbial community is dominated by microbes that can feed on the carbohydrates present in breast milk or formula, such as Bifidobacterium adolescentis," Morrow said. "As the infant grows, the transition to solid foods and physical growth result in changes in the spatial structure of the gut, which contributes to the variation in the physical and chemical environment that provides new ecological niche opportunities for growth of microbial strains. This ecosystem transition correlates with the appearance of Bacteroidetes—such as Bacteroides vulgatus—within the gut microbial community structure."

The study

The researchers applied their microbe fingerprint technique to two metagenomic DNA sequencing data sets of fecal samples of infants and young children collected as a time series. The data they used was pulled from previously published studies by other researchers.

The data was split into two groups. The first set of 31 infants had samples collected shortly after birth and at 1, 2 and 3 years of age. Fourteen of the 31 children had multiple antibiotic treatments and the other 17 did not. The second data set included nine infants who were sampled from 6 months of age up to 6 years; four of the nine had been given multiple antibiotics.

Findings

Of the 17 infants in the first dataset who had not received antibiotics during the three years after birth, an infant-specific pattern was observed for stable and unstable microbial strains. Just one infant had no stable strains was identified out of the 20 bacterial species analyzed. For the 14 infants who had multiple doses of antibiotics, 10 showed a unique pattern of transient strains that appeared for a short time after multiple antibiotic treatments.

The researchers analyzed the second set’s gut microbial strain stability of Bacteroides vulgatus and Bifidobacterium adolescentis up to age 6. They found individual specific patterns of varying dominant microbial strains that were independent of antibiotic exposure and birth mode. A key finding is that there was no obvious linkage between strain changes in B. vulgatus and B. adolescentis. For instance, one infant given multiple antibiotics had limited change in B. vulgatus strains as B. adolescentis strains changed extensively, while another infant given multiple antibiotics had the opposite pattern of strain changes.

The researchers also saw several examples of transient microbial strain change for short periods, without antibiotic treatments, followed by recovery to the dominant strain. Although the driving force for those changes is unknown, there were several instances where an infant-specific complete strain change for B. vulgatus and for B. adolescentis occurred. The metadata for those infants showed no obvious correlation of those changes with gender, country of origin, delivery mode or whether the infant would go on to develop diabetes.

"The results of our analysis using both data sets highlight that microbial strain change is inherent in the developing infant gut microbial ecosystem," noted the authors. "Furthermore, the results from our study support the use of the strain-tracking method to monitor the development of a stable and healthy microbial community."

Not their first microbial rodeo

Koo, Morrow and colleagues have used their microbe fingerprint technique in previous strain-tracking studies.

In 2017 they discovered that fecal donor microbes remained in recipients for months or years after fecal transplants.
In 2018, they illustrated how changes in the upper gastrointestinal tract from obesity surgery led to the emergence of new microbial strains.
In 2019, they analyzed the stability of new strains in individuals after antibiotic treatments.
In 2020, Koo and Morrow conducted the adult twin study, which found that twins shared a certain strain or strains between each pair for years and even decades, even after they began living apart from each other.
Also in 2020, they showed that an individualized mosaic of microbial strains was transmitted to the infant gut microbiome from a mother through vaginal delivery, as analyzed in mother-infant pairs, as well in animal models.

Source: Frontiers in Pediatrics

30 September 2020 doi.org/10.3389/fped.2020.549844

“Strain Tracking to Identify Individualized Patterns of Microbial Strain Stability in the Developing Infant Gut Ecosystem”

Authors: H. Koo et al.