Phylogenetic identification and in situ detection of individual microbial cells without cultivation

RI Amann, W Ludwig, KH Schleifer - Microbiological reviews, 1995 - Am Soc Microbiol
The frequent discrepancy between direct microscopic counts and numbers of culturable
bacteria from environmental samples is just one of several indications that we currently …

The uncultured microbial majority

MS Rappé, SJ Giovannoni - Annual Reviews in Microbiology, 2003 - annualreviews.org
▪ Abstract Since the delineation of 12 bacterial phyla by comparative phylogenetic analyses
of 16S ribosomal RNA in 1987 knowledge of microbial diversity has expanded dramatically …

Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products

J Handelsman, MR Rondon, SF Brady, J Clardy… - Chemistry & biology, 1998 - cell.com
Cultured soil microorganisms have provided a rich source of natural-product chemistry.
Because only a tiny fraction of soil microbes from soil are readily cultured, soil might be the …

DNA recovery from soils of diverse composition

J Zhou, MA Bruns, JM Tiedje - Applied and environmental …, 1996 - Am Soc Microbiol
A simple, rapid method for bacterial lysis and direct extraction of DNA from soils with minimal
shearing was developed to address the risk of chimera formation from small template DNA …

Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes

PH Janssen - Applied and environmental microbiology, 2006 - Am Soc Microbiol
In 1909, H. Joel Conn (25) expressed the hope that methods would soon be at hand by
which the significance of the different bacteria present in any soil could be determined …

The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set

H Daims, A Brühl, R Amann, KH Schleifer… - Systematic and applied …, 1999 - Elsevier
In situ hybridization with rRNA-targeted oligonucleotide probes has become a widely
applied tool for direct analysis of microbial population structures of complex natural and …

Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology

G Muyzer, K Smalla - Antonie van Leeuwenhoek, 1998 - Springer
Here, the state of the art of the application of denaturing gradient gel electrophoresis
(DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology will be …

Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis

F v. Wintzingerode, UB Göbel… - FEMS microbiology …, 1997 - academic.oup.com
After nearly 10 years of PCR-based analysis of prokaryotic small-subunit ribosomal RNAs
for ecological studies it seems necessary to summarize reported pitfalls of this approach …

The metagenomics of soil

R Daniel - Nature reviews microbiology, 2005 - nature.com
Phylogenetic surveys of soil ecosystems have shown that the number of prokaryotic species
found in a single sample exceeds that of known cultured prokaryotes. Soil metagenomics …

Sequence-based identification of microbial pathogens: a reconsideration of Koch's postulates

DN Fredericks, DA Relman - Clinical microbiology reviews, 1996 - Am Soc Microbiol
Over 100 years ago, Robert Koch introduced his ideas about how to prove a causal
relationship between a microorganism and a disease. Koch's postulates created a scientific …