Research on Neonatal Microbiomes: What Neonatologists Need to Know

Michael P. Sherman, John Minnerly, William Curtiss, Shaukat Rangwala, Scott T. Kelley
2014 Neonatology  
Introduction At birth, neonatal organs are either sterile or have low numbers of bacteria, but by adulthood, there are between 10 and 100 trillion microbes residing in the human body. Microbial environments in neonates and adults of interest include the skin, nose and oropharynx, the lower respiratory tract, the gastrointestinal tract with its regional differences, and the urogenital tract with special interest in the vagina [1] . Of these habitats, microbes living in the small and large
more » ... ne of prematurely born infants have received the most attention. Fecal specimens showing reduced gut-related bacterial diversity and the presence of potential pathogens are associated with late-onset neonatal sepsis [2] . Moreover, a shift in the fecal microbiota to a predominance of the phylum Proteobacteria and a reduction in the phylum Firmicutes has been seen 72 h before the onset of necrotizing enterocolitis [3] . Understanding how microbial diversity in infants relates to neonatal infections is an important aspect of this research. Presently, it is appreciated that the composition of intestinal microbiota is influenced by an infant's genetic background [4, 5] , vaginal or caesarean delivery [6] , residence at home versus in the hospital [7-9] , the adminis- Abstract The aim of this article is to educate neonatal caregivers about metagenomics. This scientific field uses novel and ever changing molecular methods to identify how infants become colonized with microbes after birth. Publications using metagenomics appear infrequently in the neonatal literature because clinicians are unaccustomed to the analytical techniques, data interpretation, and illustration of the results. This review covers those areas. After a brief introduction of neonatal citations forthcoming from metagenomic studies, the following topics are covered: (1) the history of metagenomics, (2) a description of current and emerging instruments used to define microbial populations in human organs, and (3) how extensive databases generated by genome analyzers are examined and presented to readers. Clinicians may feel like they are learning a new language; however, they will appreciate this task is essential to understanding and practicing neonatal medicine in the future.
doi:10.1159/000354944 pmid:24193200 pmcid:PMC3903415 fatcat:vn66vdqbmvhz7e6rjfygujobpi