A Catalog of Reference Genomes from the Human Microbiome

By K. Nelson, George M. Weinstock, S. Highlander, K. Worley, H. Creasy, Jennifer R. Wortman, D. Rusch, M. Mitreva, Erica Sodergren, A. Chinwalla and 73 more. Science, 2010

715 citations recorded by the source corpus.

News from the Inner Tube of Life A major initiative by the U.S. National Institutes of Health to sequence 900 genomes of microorganisms that live on the surfaces and orifices of the human body has established standardized protocols and methods for such large-scale reference sequencing. By combining previously accumulated data with new data, Nelson et al. (p. 994) present an initial analysis of 178 bacterial genomes. The sampling so far barely scratches the surface of the microbial diversity found on humans, but the work provides an important baseline for future analyses. Standardized protocols and methods are being established for large-scale sequencing of the microorganisms living on humans. The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified (“novel”) polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (~97%) were unique. In addition, this set of microbial genomes allows for ~40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented.

Subfields: Food Science, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7ff55c2d97b590b19b7117448ef3be043dbc6e8f

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Citations in the corpus

Computational meta'omics for microbial community studies (2013, background): “For example, marine microbial communities are responsible for half of the oxygen produced on our planet (Rocap et al , 2003), and the complex human microbiome complements us with over 100 times more genes than those in our own genome (Qin et al , 2010; The Human Microbiome Project Consortium, 2012b)”
Microbes inside—from diversity to function: the case of Akkermansia (2012, methodology): “Moreover, the availability of genome sequences of intestinal isolates (Nelson et al., 2010) as well as new bioinformatic tools (Rooijers et al., 2011) will contribute to further expanding these approaches (see Figure 2).”
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products (2013, neutral): “For example, only a fraction of the > 10,000 bacterial species in the human microbiome have been sequenced (Nelson et al., 2010; Wylie et al., 2012).”
Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads (2013, background): “For example, only a fraction of the 10,000+ bacterial species in the human microbiome have been sequenced [3,4].”
Ribosomal Multi-Locus Sequence Typing: universal characterisation of bacteria from domain to strain (2012, methodology): “Sequence analysis of the 16S rRNA gene has also been used extensively in the examination of microbial communities, such as the human microbiome (Nelson et al., 2010) and environmental communities (Lim et al.”