pime: A package for discovery of novel differences among microbial communities.

The data used for profiling microbial communities is usually sparse with some microbes having high abundance in a few samples and being nearly absent in others. However, current bioinformatics tools able to deal with this sparsity are lacking. pime (Prevalence Interval for Microbiome Evaluation) was designed to remove those taxa that may be high in relative abundance in just a few samples but have a low prevalence overall. The reliability and robustness of pime were compared against existing methods and tested using 16S rRNA independent data sets. pime filters microbial taxa not shared in a per treatment prevalence interval started at 5% prevalence with increasing increments of 5% at each filtering step. For each prevalence interval, hundreds of decision trees were calculated to predict the likelihood of detecting differences in treatments. The best prevalence-filtered data set was user-selected by choosing the prevalence interval that kept a large portion of the 16S rRNA sequences in the data set while also showing the lowest error rate. To obtain the likelihood of introducing type I error while building prevalence-filtered data sets, an error detection step based was also included. A pime reanalysis of published data sets uncovered other expected microbial associations than previously reported, which may be masked when only relative abundance was considered.

Influence of own mother's milk and different proportions of formula on intestinal microbiota of very preterm newborns.

OBJECTIVE: To determine the differences in preterm infants' stool microbiota considering the use of exclusive own mother's milk and formula in different proportions in the first 28 days of life. METHODS: The study included newborns with GA ≤ 32 weeks divided in 5 group according the feeding regimen: 7 exclusive own mother's milk, 8 exclusive preterm formula, 16 mixed feeding with >70% own mother's milk, 16 mixed feeding with >70% preterm formula, and 15 mixed 50% own mother's milk and preterm formula. Exclusion criteria: congenital infections, congenital malformations and newborns of drug addicted mothers. Stools were collected weekly during the first 28 days. Microbial DNA extraction, 16S rRNA amplification and sequencing were performed. RESULTS: All groups were similar in perinatal and neonatal data. There were significant differences in microbial community among treatments. Approximately 37% of the variation in distance between microbial communities was explained by use of exclusive own mother´s milk only compared to other diets. The diet composed by exclusive own mother´s milk allowed for greater microbial richness (average of 85 OTUs) while diets based on preferably formula, exclusive formula, preferably maternal milk, and mixed of formula and maternal milk presented an average of 9, 29, 23, and 25 OTUs respectively. The mean proportion of the genus Escherichia and Clostridium was always greater in those containing formula than in the those with maternal milk only. CONCLUSIONS: Fecal microbiota in the neonatal period of preterm infants fed with exclusive own mother's milk presented increased richness and differences in microbial composition from those fed with different proportions of formula.

Low Microbial Diversity and Abnormal Microbial Succession Is Associated with Necrotizing Enterocolitis in Preterm Infants.

Despite increased efforts, the diverse etiologies of Necrotizing Enterocolitis (NEC) have remained largely elusive. Clinical predictors of NEC remain ill-defined and currently lack sufficient specificity. The development of a thorough understanding of initial gut microbiota colonization pattern in preterm infants might help to improve early detection or prediction of NEC and its associated morbidities. Here we compared the fecal microbiota successions, microbial diversity, abundance and structure of newborns that developed NEC with preterm controls. A 16S rRNA based microbiota analysis was conducted in a total of 132 fecal samples that included the first stool (meconium) up until the 5th week of life or NEC diagnosis from 40 preterm babies (29 controls and 11 NEC cases). A single phylotype matching closest to the Enterobacteriaceae family correlated strongly with NEC. In DNA from the sample with the greatest abundance of this phylotype additional shotgun metagenomic sequencing revealed Citrobacter koseri and Klebsiella pneumoniae as the dominating taxa. These two taxa might represent suitable microbial biomarker targets for early diagnosis of NEC. In NEC cases, we further detected lower microbial diversity and an abnormal succession of the microbial community before NEC diagnosis. Finally, we also detected a disruption in anaerobic microorganisms in the co-occurrence network of meconium samples from NEC cases. Our data suggest that a strong dominance of Citrobacter koseri and/or Klebsiella pneumoniae, low diversity, low abundance of Lactobacillus, as well as an altered microbial-network structure during the first days of life, correlate with NEC risk in preterm infants. Confirmation of these findings in other hospitals might facilitate the development of a microbiota based screening approach for early detection of NEC.

Draft Genome of Rhodococcus rhodochrous TRN7, Isolated from the Coast of Trindade Island, Brazil.

Here, we present a draft genome and annotation of Rhodococcus rhodochrous TRN7, isolated from Trindade Island, Brazil, which will provide genetic data to benefit the understanding of its metabolism.