Exploring prokaryotic diversity in the genomic era

By Philip Hugenholtz. Genome Biology, 2002

862 citations recorded by the source corpus.

Our understanding of prokaryote biology from study of pure cultures and genome sequencing has been limited by a pronounced sampling bias towards four bacterial phyla - Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes - out of 35 bacterial and 18 archaeal phylum-level lineages. This bias is beginning to be rectified by the use of phylogenetically directed isolation strategies and by directly accessing microbial genomes from environmental samples.

Subfields: Ecology, Food Science, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c246ff46223984d0196590194681a1243f5b5215

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Citations in the corpus

Large-scale machine learning for metagenomics sequence classification (2015, neutral): “It gives access to all organisms present in the sample even if they do not grow on culture media (Hugenholtz et al., 2002) and allows us to characterize with an unprecedented level of resolution the diversity of the microbial realm (Peterson et al., 2009). The raw output of a metagenomics experiment”
Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. (2006, neutral): “…the basis of 16S rRNA gene sequences, the domains Bacteria and Archaea were both suggested to contain a number of clone clusters at the phylum and subphylum levels that are composed solely of environmental 16S rRNA gene clones (Hugenholtz, 2002; Hugenholtz et al., 1998; Rappé & Giovannoni, 2003).”
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods (2007, background): “Unfortunately, because of the cultivation bias, the phylogenetic representation of naturally occurring microbial species is very poo”
Marine bacterial microdiversity as revealed by internal transcribed spacer analysis (2005, methodology): “The within-cluster similarity for the marine cyanobacteria subgroups is generally around 98%, whilst the between-cluster mean similarity values are at or below 93%, the similarity between the low-B/A clades I and II.”
Community structure and metabolism through reconstruction of microbial genomes from the environment (2004, background): “However, isolates have been the main source of sequence data, and only a small fraction of microorganisms have been cultivate”
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes (2006, methodology): “Once aligned, the entire batch can be classiﬁed by Greengenes using taxonomic nomenclature proposed by independent curators [NCBI, RDP/Bergey’s (19) Ludwig (20) Hugenholtz (21) and Pace (22)].”
Accurate phylogenetic classification of variable-length DNA fragments (2007, background): “Such insights could not have been obtained otherwise as the vast majority of microbes cannot be cultivated using standard technique”
Strategies for culture of 'unculturable' bacteria. (2010, methodology): “Even members of the TM7 Division, which have yet to be cultivated in isolation, were able to form colonies visible to the naked eye when incubation times of 50 days were used [unpublished observation reported in a review by Hugenholtz (2002)].”
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers (2008, methodology): “We then applied the mask Lane MaskPH ( 24 ) to the alignment, and used Clearcut 1.0.7’s relaxed neighbor joining method (25) to build the tree.”
MetaGene: prokaryotic gene finding from environmental genome shotgun sequences (2006, methodology): “The estimations based on 16S ribosomal RNA suggest that 99% of microbial species cannot be easily cultivated (1,2).”
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities (2005, background): “Ribosomal Database Project II (29) by Phil Hugenholtz (15).”
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes (2013, methodology): “Our phylogeny supports deep-branching of Candidatus acetothermum autotrophum (OP1), in agreement with 16S and protein-based studies, but between Thermotoga and Archaea rather than Deinococcus-Thermus 34,44 .”
Microbial Communities of Deep Marine Subsurface Sediments: Molecular and Cultivation Surveys (2006, background): “Recent reviews of microbial diversity on the basis of 16S rRNA sequences listed up to 52 phylum-level bacterial and ca. 20 phylum-level archaeal phylogenetic lineages, most of them with no or very few cultured representatives (Hugenholtz et al. 1998; Hugenholtz 2002; Rappe and Giovannoni 2003).”
Molecular Techniques to Assess Microbial Community Structure, Function, and Dynamics in the Environment (2011, background): “The major limitation of culture-based techniques is that >99% of the microorganisms in any environment observed through a microscope are not culti vable by standard culturing techniques (Hugenholtz 2002).”
Metagenomics: genomic analysis of microbial communities. (2004, background): “∗ Indicates phyla that Hugenholtz et al. (54) or Rappé & Giovannoni (90) noted as particularly abundant in environmental samples but underrepresented in culture.”
Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities (2005, neutral): “species that cannot currently be cultivated [8,9].”