Temporal dynamics of the very premature infant gut dominant microbiota

Abstract

BackgroundThe very-preterm infant gut microbiota is increasingly explored due to its probable role in the development of life threatening diseases. Results of high-throughput studies validate and renew the interest in approaches with lower resolution such as PCR-Temporal Temperature Gel Electrophoresis (TTGE) for the follow-up of dominant microbiota dynamics. We report here an extensive longitudinal study of gut colonization in very preterm infants. We explored by 16S rDNA-based PCR-TTGE a total of 354 stool specimens sampled during routine monitoring from the 1st to the 8th week of life in 30 very pre-term infants born before 30 weeks of gestational age.ResultsCombining comparison with a diversity ladder and sequencing allowed affiliation of 50 Species-Level Operational Taxonomic Units (SLOTUs) as well as semi-quantitative estimation of Operational Taxonomic Units (OTUs). Coagulase-negative staphylococci, mainly the Staphylococcus epidermidis, was found in all the infants during the study period and was the most represented (75.7% of the SLOTUs) from the first days of life. Enterococci, present in 60% of the infants were early, highly represented and persistent colonizers of the premature gut. Later Enterobacteriaceae and the genus Clostridium appeared and were found in 10 (33%) and 21 infants (70%), respectively. We showed a high representation of Veillonella in more than a quarter of the infants and being able to persistently colonize premature gut. The genera Anaerococcus, Aquabacterium, Bacillus, Bifidobacterium, Corynebacterium, Micrococcus, Oceanobacillus, Propionibacterium, Pseudomonas, Rothia, Sarcina, Sneathia and Streptococcus were observed as transient or persistent colonizers, each genus being found in a minority of infants.ConclusionsDespite low resolution, PCR-TTGE remains complementary to high-throughput sequencing-based approaches because it allows the follow-up of dominant bacteria in gut microbiota in a large longitudinal cohorts of preterm neonates. We described the development of pre-term gut microbiota that should be now replaced regarding the functional role of major OTUs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-014-0325-0) contains supplementary material, which is available to authorized users.

Loss of cutaneous microbial diversity during first 3 weeks of life in very low birthweight infants

“…It will be important to determine in a larger patient cohort whether environmental factors such as cutaneous and genital microbiome of the mother, colonization of the intensive care ward among others, have an effect on the skin microbiome of VLBW infants. Similar to reported longitudinal differences in the faecal microbiome, it would be interesting to further investigate how the cutaneous microbiome will change during the early life of VLBW neonates and whether such possible changes are linked to developmental or other clinical complications.…”

Microbiota network and mathematic microbe mutualism in colostrum and mature milk collected in two different geographic areas: Italy versus Burundi

“…The bacterial genus Aquabacterium , which seems to have a central role in Burundian colostrum, has been described as a colonizer of the very premature infant gut dominant microbiota (Aujoulat et al , 2014). Not surprisingly, this specific genus does not have a further role in the mature milk from Burundian mothers.…”

The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota

“…Preterm neonates exhibit delayed gut colonization with commensal anaerobic microbes, such as Bifidobacterium or Bacteroides, where instead their stools contain significantly higher levels of Enterobacteriaceae, Enterococcus, and other (opportunistic) pathogenic microorganisms than fecal material from full-term neonates (79,(90)(91)(92)(93)(94). Gram-positive bacteria, such as Staphylococcus, Enterococcus, and clostridia, dominate the gut microbiota of very premature infants during the first month of life, while Gram-negative microorganisms such as Enterobacteriaceae and Veillonella may be variably present in such cases (95). A pattern of colonization and succession of bacterial classes from Bacilli to Gammaproteobacteria to Clostridia was observed in a very-lowbirth-weight (VLBW) premature population (96).…”