Bacteriophages enhance microbiota analysis.

Serious bowel diseases are the major cause of death in neonates < 27 weeks of gestation. The microbiota of preterm neonates has been widely studied yet microbial disequilibrium remains an elusive concept. Here, we combine bacteriophages and bacterial community analyses that aid resolution of gut microbiota development.Preterm infant stool samples were collected from 5 patients, including 2 twin pairs, admitted to the neonatal intensive care unit. Sampling was conducted at 2 timepoints spanning the first 60 days of life. DNA sequencing was used to profile the bacterial, fungal, free and chemically induced phage populations in preterm infant stool. Microbial community structures were aligned with clinical metadata to investigate relationships between features of the microbiota and clinical presentation.Considerable overlap is observed when employing different methods to interrogate the gut microbiota. The community structure was more patient specific in bacterial than phage communities with less bacterial community dissimilarity between controls and patients with GI complications. The twin-pair described the majority of variance in both bacterial and phage communities. Balanced error rates of sample classification based on GI complications was lowest using free phage communities. Greatest discriminative resolution was obtained when combining bacterial and phage community data. Current regimes of antifungals limited the levels of fungal data meaning comparative studies could not be undertaken.We here demonstrate the potential importance of combining bacterial and phage community analysis when monitoring polymicrobial infection and community structure.