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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and R.K.P. and partial support was also provided by the following: grants NIH U54CA143925 and U54MD012388.
Structure, Function and Diversity of the Healthy Human Microbiome
The Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far, finding the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals.
Inferring Correlation Networks from Genomic Survey Data
It is shown that community diversity is the key factor that modulates the acuteness of such compositional effects, and a new approach is developed, called SparCC, which is capable of estimating correlation values from compositional data.
SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases
Wastewater surveillance at a major urban treatment facility in Massachusetts found the presence of SARS-CoV-2 at high titers in the period from March 18 - 25 using RT-qPCR, and the identity of the PCR product was confirmed by direct DNA sequencing.
Rapid evolutionary innovation during an Archaean genetic expansion
An explicit model of macroevolution including gene birth, transfer, duplication and loss events is used to map the evolutionary history of 3,983 gene families across the three domains of life onto a geological timeline and suggests a brief period of genetic innovation during the Archaean eon gave rise to 27% of major modern gene families.
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
QIIME 2 provides new features that will drive the next generation of microbiome research, including interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.
Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks
Bacterial response to nitric oxide (NO) is of major importance since NO is an obligatory intermediate of the nitrogen cycle. Transcriptional regulation of the dissimilatory nitric oxides metabolism…
Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton
- D. Hunt, L. David, D. Gevers, S. Preheim, E. Alm, M. Polz
- Biology, Environmental ScienceScience
- 23 May 2008
Spatial and temporal resource partitioning among Vibrionaceae strains coexisting in coastal bacterioplankton is described and environmental specialization may be an important correlate or even trigger of speciation among sympatric microbes.
A novel method for accurate operon predictions in all sequenced prokaryotes
This work combines comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes, and finds several surprises: H.pylori has many operons, contrary to previous reports; Bacillus anthracis has an unusual number of pseudogenes within conserved operons; and Synechocystis PCC 6803 has manyOperon structure across 124 genomes.
Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth
DNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South African gold mine was sequenced and assembled into a single, complete genome that indicates a motile, sporulating, sulfate-reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon by using machinery shared with archaea.