The infant airway microbiome in health and disease impacts later asthma development

The infant airway microbiome in health and disease impacts later asthma development

Shu Mei Teo, Danny Mok, Kym Pham, Merci Kusel, Michael Serralha, Niamh Troy, Barbara J Holt, Belinda J Hales, Michael L Walker, Elysia Hollams, Yury H Bochkov, Kristine Grindle, Sebastian L Johnston, James E Gern, Peter D Sly, Patrick G Holt, Kathryn E Holt, Michael Inouye
doi: http://dx.doi.org/10.1101/012070

The nasopharynx (NP) is a reservoir for microbes associated with acute respiratory illnesses (ARI). The development of asthma is initiated during infancy, driven by airway inflammation associated with infections. Here, we report viral and bacterial community profiling of NP aspirates across a birth cohort, capturing all lower respiratory illnesses during their first year. Most infants were initially colonized with Staphylococcus or Corynebacterium before stable colonization with Alloiococcus or Moraxella, with transient incursions of Streptococcus, Moraxella or Haemophilus marking virus-associated ARIs. Our data identify the NP microbiome as a determinant for infection spread to the lower airways, severity of accompanying inflammatory symptoms, and risk for future asthma development. Early asymptomatic colonization with Streptococcus was a strong asthma predictor, and antibiotic usage disrupted asymptomatic colonization patterns.

A robust statistical framework for reconstructing genomes from metagenomic data

A robust statistical framework for reconstructing genomes from metagenomic data

Dongwan Don Kang, Jeff Froula, Rob Egan, Zhong Wang
doi: http://dx.doi.org/10.1101/011460

We present software that reconstructs genomes from shotgun metagenomic sequences using a reference-independent approach. This method permits the identification of OTUs in large complex communities where many species are unknown. Binning reduces the complexity of a metagenomic dataset enabling many downstream analyses previously unavailable. In this study we developed MetaBAT, a robust statistical framework that integrates probabilistic distances of genome abundance with sequence composition for automatic binning. Applying MetaBAT to a human gut microbiome dataset identified 173 highly specific genomes bins including many representing previously unidentified species.

Resolving microbial microdiversity with high accuracy full length 16S rRNA Illumina sequencing

Resolving microbial microdiversity with high accuracy full length 16S rRNA Illumina sequencing
Catherine Burke, Aaron E Darling
doi: http://dx.doi.org/10.1101/010967

We describe a method for sequencing full-length 16S rRNA gene amplicons using the high throughput Illumina MiSeq platform. The resulting sequences have about 100-fold higher accuracy than standard Illumina reads and are chimera filtered using information from a single molecule dual tagging scheme that boosts the signal available for chimera detection. We demonstrate that the data provides fine scale phylogenetic resolution not available from Illumina amplicon methods targeting smaller variable regions of the 16S rRNA gene.

Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment

Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment

Michael B Burns, Joshua Lynch, Timothy K Starr, Dan Knights, Ran Blekhman
doi: http://dx.doi.org/10.1101/009431

Background The human gut microbiome is associated with the development of colon cancer, and recent studies have found changes in the composition of the microbial communities in cancer patients compared to healthy controls. However, host-bacteria interactions are mainly expected to occur in the cancer microenvironment, whereas current studies primarily use stool samples to survey the microbiome. Here, we highlight the major shifts in the colorectal tumor microbiome relative to that of matched normal colon tissue from the same individual, allowing us to survey the microbial communities at the tumor microenvironment, and provides intrinsic control for environmental and host genetic effects on the microbiome. Results We characterized the microbiome in 44 primary tumor and 44 patient-matched normal colon tissues. We find that tumors harbor distinct microbial communities compared to nearby healthy tissue. Our results show increased microbial diversity at the tumor microenvironment, with changes in the abundances of commensal and pathogenic bacterial taxa, including Fusobacterium and Providencia. While Fusobacteria has previously been implicated in CRC, Providencia is a novel tumor- associated agent, and has several features that make it a potential cancer driver, including a strong immunogenic LPS and an ability to damage colorectal tissue. Additionally, we identified a significant enrichment of virulence-associated genes in the colorectal cancer microenvironment. Conclusions This work identifies bacterial taxa significantly correlated with colorectal cancer, including a novel finding of an elevated abundance of Providencia in the tumor microenvironment. We also describe several metabolic pathways and enzymes differentially present in the tumor associated microbiome, and show that the bacterial genes in the tumor microenvironment are enriched for virulence associated genes from the aggregate microbial community. This virulence enrichment indicates that the microbiome likely plays an active role in colorectal cancer development and/or progression. These reuslts provide a starting point for future prognostic and therapeutic research with the potential to improve patient outcomes.

Bayesian mixture analysis for metagenomic community profiling.

Bayesian mixture analysis for metagenomic community profiling.

Sofia Morfopoulou, Vincent Plagnol

Deep sequencing of clinical samples is now an established tool for the detection of infectious pathogens, with direct medical applications. The large amount of data generated provides an opportunity to detect species even at very low levels, provided that computational tools can effectively interpret potentially complex metagenomic mixtures. Data interpretation is complicated by the fact that short sequencing reads can match multiple organisms and by the lack of completeness of existing databases, in particular for viral pathogens. This interpretation problem can be formulated statistically as a mixture model, where the species of origin of each read is missing, but the complete knowledge of all species present in the mixture helps with the individual reads assignment. Several analytical tools have been proposed to approximately solve this computational problem. Here, we show that the use of parallel Monte Carlo Markov chains (MCMC) for the exploration of the species space enables the identification of the set of species most likely to contribute to the mixture. The added accuracy comes at a cost of increased computation time. Our approach is useful for solving complex mixtures involving several related species. We designed our method specifically for the analysis of deep transcriptome sequencing datasets and with a particular focus on viral pathogen detection, but the principles are applicable more generally to all types of metagenomics mixtures. The code is available on github (http://github.com/smorfopoulou/metaMix) and the process is currently being implemented in a user friendly R package (metaMix, to be submitted to CRAN).

Reagent contamination can critically impact sequence-based microbiome analyses


Reagent contamination can critically impact sequence-based microbiome analyses

Susannah Salter, Michael J Cox, Elena M Turek, Szymon T Calus, William O Cookson, Miriam F Moffatt, Paul Turner, Julian Parkhill, Nick Loman, Alan W Walker

The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents. In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. Contamination impacts both PCR-based 16S rRNA gene surveys and shotgun metagenomics. These results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination. Concurrent sequencing of negative control samples is strongly advised.

Phylogenetics and the human microbiome

Phylogenetics and the human microbiome
Frederick A Matsen IV
Comments: to appear in Systematic Biology
Subjects: Populations and Evolution (q-bio.PE); Genomics (q-bio.GN)

The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this paper I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work.