The Human Microbiome Project

 At 2013-09-28 04:05:12 AM  |   173

In a healthy human adult, bacterial cells outnumber human cells, but the identity and degree of diversity of these bacteria in a single individual, their variability from person to person, and their role in disease and disease susceptibility has been largely unknown. The goal of the Human Microbiome Project is to characterize the human microbiome and analyze its role in human health and disease.  Read more

An environmental bacterial taxon with a large and distinct metabolic repertoire

 At 2014-03-06 11:04:16 AM  |   76

Cultivated bacteria such as actinomycetes are a highly useful source of biomedically important natural products. However, such ‘talented’ producers represent only a minute fraction of the entire, mostly uncultivated, prokaryotic diversity. The uncultured majority is generally perceived as a large, untapped resource of new drug candidates, but so far it is unknown whether taxa containing talented bacteria indeed exist. Read more

Biogenesis and functions of bacterial S-layers

 At 2014-03-01 08:20:03 PM  |   156

The outer surface of many archaea and bacteria is coated with a proteinaceous surface layer (known as an S-layer), which is formed by the self-assembly of monomeric proteins into a regularly spaced, two-dimensional array. Bacteria possess dedicated pathways for the secretion and anchoring of the S-layer to the cell wall, and some Gram-positive species have large S-layer-associated gene families. Read more

Ragout—a reference-assisted assembly tool for bacterial genomes

 At 2014-06-16 01:38:04 PM  |   152

Bacterial genomes are simpler than mammalian ones, and yet assembling the former from the data currently generated by high-throughput short-read sequencing machines still results in hundreds of contigs. To improve assembly quality, recent studies have utilized longer Pacific Biosciences (PacBio) reads or jumping libraries to connect contigs into larger scaffolds or help assemblers resolve ambiguities in repetitive regions of the genome. Read more

Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions

 At 2013-11-26 11:55:14 AM  |   152

The potential of bacterial whole-genome sequencing (WGS) to complement existing diagnostic infrastructures in clinical microbiology has been shown in proof-of-principle examples and extensively discussed. However, less attention has been drawn to bioinformatic challenges that are associated with the clinical adoption of WGS-based molecular diagnostics. This Perspective article discusses questions that are related to standard operating procedures, computational resource management, and data storage and integration in the context of recent developments in the sequencing and bioinformatics service markets.  Read more

Modern clinical microbiology

 At 2013-09-28 04:27:25 AM  |   176

In the twenty-first century, the clinical microbiology laboratory plays a central part in optimizing the management of infectious diseases and surveying local and global epidemiology. Modern clinical microbiology: new challenges and solutions. Read more

Sequencing Study Suggests Range of C. difficile Infection Sources

 At 2013-09-28 04:07:30 AM  |   209

It has been thought that Clostridium difficile infection is transmitted predominantly within health care settings. However, endemic spread has hampered identification of precise sources of infection and the assessment of the efficacy of interventions.  Read more

Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column

 At 2014-02-22 01:35:00 AM  |   229

Microbial gene expression in the environment has recently been assessed via pyrosequencing of total RNA extracted directly from natural microbial assemblages. Several such 'metatranscriptomic' studies have reported that many complementary DNA sequences shared no significant homology with known peptide sequences, and so might represent transcripts from uncharacterized proteins.  Read more