Recognizing the reagent microbiome

Bacteria comprise the most diverse domain of life on Earth, where they occupy nearly every possible ecological niche and play key roles in biological and chemical processes. Studying the composition and ecology of bacterial ecosystems and understanding their function are of prime importance. High-throughput sequencing technologies enable nearly comprehensive descriptions of bacterial diversity through 16S ribosomal RNA gene amplicons. Analyses of these communities generally rely upon taxonomic assignments through reference data bases or clustering approaches using de facto sequence similarity thresholds to identify operational taxonomic units. However, these methods often fail to resolve ecologically meaningful differences between closely related organisms in complex microbial data sets. In this paper, we describe oligotyping, a novel supervised computational method that allows researchers to investigate the diversity of closely related but distinct bacterial organisms in final operational taxonomic units identified in environmental data sets through 16S ribosomal RNA gene data by the canonical approaches. Our analysis of two data sets from two different environments demonstrates the capacity of oligotyping at discriminating distinct microbial populations of ecological importance. Oligotyping can resolve the distribution of closely related organisms across environments and unveil previously overlooked ecological patterns for microbial communities. The URL http://oligotyping.org offers an open-source software pipeline for oligotyping.

In recent years, a greater appreciation for the microbes inhabiting human body sites has emerged. In the female mammary gland, milk has been shown to contain bacterial species, ostensibly reaching the ducts from the skin. We decided to investigate whether there is a microbiome within the mammary tissue. Using 16S rRNA sequencing and culture, we analyzed breast tissue from 81 women with and without cancer in Canada and Ireland. A diverse population of bacteria was detected within tissue collected from sites all around the breast in women aged 18 to 90, not all of whom had a history of lactation. The principal phylum was Proteobacteria. The most abundant taxa in the Canadian samples were Bacillus (11.4%), Acinetobacter (10.0%), Enterobacteriaceae (8.3%), Pseudomonas (6.5%), Staphylococcus (6.5%), Propionibacterium (5.8%), Comamonadaceae (5.7%), Gammaproteobacteria (5.0%), and Prevotella (5.0%). In the Irish samples the most abundant taxa were Enterobacteriaceae (30.8%), Staphylococcus (12.7%), Listeria welshimeri (12.1%), Propionibacterium (10.1%), and Pseudomonas (5.3%). None of the subjects had signs or symptoms of infection, but the presence of viable bacteria was confirmed in some samples by culture. The extent to which these organisms play a role in health or disease remains to be determined.

Initial neonatal gut colonisation is a crucial stage for developing a healthy physiology, beneficially influenced by breast-feeding. Breast milk has been shown not only to provide nutrients and bioactive/immunological compounds, but also commensal bacteria, including gut-associated anaerobic Bifidobacterium spp. The aim of the present study was to investigate bacterial diversity in breast milk, with emphasis on identifying gut-associated obligate anaerobes. Breast milk collected from seven mothers at three sampling points (days 3-6, 9-14 and 25-30 postpartum) was analysed by combined culture-dependent and state-of-the-art, culture-independent methods (Sanger sequencing and 454-pyrosequencing). In addition to the predominance of facultative anaerobes such as Staphylococcus, Streptococcus and Propionibacterium (>90% of isolated strains and 23·7% relative abundance using pyrosequencing), significant populations of obligate anaerobes, including Bifidobacterium and Veillonella, were detected using pyrosequencing and confirmed by the isolation of viable strains (3·4% of isolates and 1·4% relative abundance). Pyrosequencing also revealed the presence of DNA of multiple major gut-associated obligate anaerobes (6·2% relative abundance) such as Bacteroides and, for the first time, several members of the Clostridia, including butyrate producers, such as Faecalibacterium and Roseburia, which are important for colonic health. The present study suggests that breast milk may be a major source of bacterial diversity to the neonatal gut, including gut-associated obligate anaerobes, and may thus significantly influence gut colonisation and maturation of the immune system.