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Interplay between the human gut microbiome and host metabolism.
The human gut is inhabited by a complex and metabolically active microbial ecosystem. While many studies focused on the effect of individual microbial taxa on human health, their overall metabolic potential has been under-explored. Using whole-metagenome shotgun sequencing data in 1,004 twins, we first observed that unrelated subjects share, on average, almost double the number of metabolic pathways (82%) than species (43%). Then, using 673 blood and 713 faecal metabolites, we found...
Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease.
The presence of advanced fibrosis in nonalcoholic fatty liver disease (NAFLD) is the most important predictor of liver mortality. There are limited data on the diagnostic accuracy of gut microbiota-derived signature for predicting the presence of advanced fibrosis. In this prospective study, we characterized the gut microbiome compositions using whole-genome shotgun sequencing of DNA extracted from stool samples. This study included 86 uniquely well-characterized patients with...
Design and synthesis of a minimal bacterial genome.
We used whole-genome design and complete chemical synthesis to minimize the 1079-kilobase pair synthetic genome of Mycoplasma mycoides JCVI-syn1.0. An initial design, based on collective knowledge of molecular biology combined with limited transposon mutagenesis data, failed to produce a viable cell. Improved transposon mutagenesis methods revealed a class of quasi-essential genes that are needed for robust growth, explaining the failure of our initial design. Three cycles of design,...
Complete genome sequence of Treponema pallidum, the syphilis spirochete.
The complete genome sequence of Treponema pallidum was determined and shown to be 1,138,006 base pairs containing 1041 predicted coding sequences (open reading frames). Systems for DNA replication, transcription, translation, and repair are intact, but catabolic and biosynthetic activities are minimized. The number of identifiable transporters is small, and no phosphoenolpyruvate:phosphotransferase carbohydrate transporters were found. Potential virulence factors include a family of 12...
Complete Genomes of All Known Human Rhinoviruses Are Published
ROCKVILLE, MD — February 12, 2009 — A team of researchers from the J. Craig Venter Institute (JCVI); the University of Maryland School of Medicine and the University of Wisconsin, Madison; announced today they have sequenced and analyzed the genomes of all known human rhinoviruses (HRVs). David Spiro, Ph.D., JCVI, Steve Liggett, M.D., the University of Maryland School of Medicine, and Ann Palmenberg, Ph.D., University of Wisconsin, Madison led the team whose work was...
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence (1,830,137 base pairs) of the genome from the bacterium Haemophilus influenzae Rd. This approach eliminates the need for initial mapping efforts and is therefore applicable to the vast array of microbial species for which genome maps are unavailable. The H. influenzae Rd genome sequence (Genome Sequence DataBase...
Entamoeba histolytica research presented at the Molecular Parasitology Meeting
Entamoeba histolytica causes invasive intestinal and extraintestinal infections, known as amoebiasis, in about 50 million people and still remains a significant cause of human death in developing countries. However, for unknown reasons, fewer than 10% of E. histolytica infections are symptomatic (causing symptoms such as diarrhea, dysentery or liver abscess). The J. Craig Venter Institute is among the institutions awarded the NIAID Genome Sequencing Centers for Infectious Diseases...
JCVI Launches New Internship Partnership with Smithsonian Science Education Center
Are you passionate about science education? If so, we have a unique hands-on opportunity for you to be a part of real teams of scientists and educators. Open to undergraduate and graduate students with no previous lab experience required.
Antarctic Epiblog: Leaving McMurdo
Ice formation outside McMurdo Station After we took our samples out at the ice edge, we returned to McMurdo Station for several intense days of demobilization. We had to return all of the large drills, power equipment and camping gear, and spent a considerable time preparing our own gear for shipment back to the United States. Our samples and some of our critical gear will go by air transport to Port Huemene in California, and the rest will be shipped back to the US by...
Assembly of eukaryotic algal chromosomes in yeast.
Synthetic genomic approaches offer unique opportunities to use powerful yeast and Escherichia coli genetic systems to assemble and modify chromosome-sized molecules before returning the modified DNA to the target host. For example, the entire 1 Mb Mycoplasma mycoides chromosome can be stably maintained and manipulated in yeast before being transplanted back into recipient cells. We have previously demonstrated that cloning in yeast of large (> ~ 150 kb), high G + C (55%)...