A core gut microbiome in obese and lean twins
The faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers are characterized to address how host genotype, environmental exposure and host adiposity influence the gut microbiome.
Microbial diversity in the deep sea and the underexplored “rare biosphere”
- M. Sogin, H. Morrison, G. Herndl
- Environmental ScienceProceedings of the National Academy of Sciences
- 8 August 2006
It is shown that bacterial communities of deep water masses of the North Atlantic and diffuse flow hydrothermal vents are one to two orders of magnitude more complex than previously reported for any microbial environment.
The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions.
Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses.
- D. Lane, B. Pace, G. Olsen, D. Stahl, M. Sogin, N. Pace
- BiologyProceedings of the National Academy of Sciences…
- 1 October 1985
A protocol is described for rapidly generating large blocks of 16S rRNA sequence data without isolation of the 16 S rRNA or cloning of its gene, and its phylogenetic usefulness is evaluated by examination of several 17S rRNAs whose gene sequences are known.
Microbial Diversity of Hydrothermal Sediments in the Guaymas Basin: Evidence for Anaerobic Methanotrophic Communities
- A. Teske, K. Hinrichs, H. Jannasch
- Biology, Environmental ScienceApplied and Environmental Microbiology
- 1 April 2002
The combined evidence from bacterial phylogeny and molecular-isotopic data indicates an important role of some novel deeply branching bacteria in anaerobic methanotrophy in the trophic ecology of methane-rich hydrothermal vents.
Anvi’o: an advanced analysis and visualization platform for ‘omics data
Using anvi’o, this work re-analyzed publicly available datasets and explored temporal genomic changes within naturally occurring microbial populations through de novo characterization of single nucleotide variations, and linked cultivar and single-cell genomes with metagenomic and metatranscriptomic data.
Accuracy and quality of massively parallel DNA pyrosequencing
By using objective criteria to eliminate low quality data, the quality of individual GS20 sequence reads in molecular ecological applications can surpass the accuracy of traditional capillary methods.
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
It is shown that a 2% single- linkage preclustering methodology followed by an average-linkage clustering based on pairwise alignments more accurately predicts expected OTUs in both single and pooled template preparations of known taxonomic composition.
IDENTIFICATION OF GROUP‐ AND STRAIN‐SPECIFIC GENETIC MARKERS FOR GLOBALLY DISTRIBUTED ALEXANDRIUM (DINOPHYCEAE). II. SEQUENCE ANALYSIS OF A FRAGMENT OF THE LSU rRNA GENE 1
Results of this study are in complete agreement with conclusions from previous work using restriction fragment‐length polymorphism analysis of small subunit rRNA genes, but the LSU rDNA sequences provided finer‐scale species and population resolution.
The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing
Ciprofloxacin treatment influenced the abundance of about a third of the bacterial taxa in the gut, decreasing the taxonomic richness, diversity, and evenness of the community, and support the hypothesis of functional redundancy in the human gut microbiota.