Metagenomics: Genomic Analysis of Microbial Communities

Riesenfeld, Christian S.; Schloss, Patrick D.; Handelsman, Jo

doi:10.1146/annurev.genet.38.072902.091216

Cited by 941 publications

(609 citation statements)

References 126 publications

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“…Analyses of metagenomes, or composite genomes of microbial assemblages in particular habitats, (72,73) provide a new way at looking at in situ microbial communities and the relationships between genomes, organisms, populations and environments. (74,75,76,77,78,79,80) Although metagenomics is still at an early stage of constructing massive sequence inventories or gathering functional information, (81,82,83,84) the field could potentially lead to radical reappraisals of the nature of boundaries between biological entities and the organization of life itself. At the very least, it challenges highly individualistic assumptions of biological and molecular interaction.…”

Section: Applications To a Proposed Systemmentioning

confidence: 99%

Fundamental issues in systems biology

O’Malley¹,

Dupré²

2005

BioEssays

177

104

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FUNDAMENTAL ISSUES IN SYSTEMS BIOLOGY SummaryIn the context of scientists' reflections on genomics, we examine some fundamental issues in the emerging postgenomic discipline of systems biology.Systems biology is best understood as consisting of two streams. One, which we shall call 'pragmatic systems biology', emphasizes large-scale molecular interactions; the other, which we shall refer to as 'systems-theoretic biology', emphasizes system principles. Both are committed to mathematical modelling, and both lack a clear account of what biological systems are. We discuss the underlying issues in identifying systems and how causality operates at different levels of organization. We suggest that resolving such basic problems is a key task for successful systems biology, and that philosophers could contribute to its realization. We conclude with an argument for more sociologically informed collaboration between scientists and philosophers. KeywordsGenomics, systems biology, systems theory, philosophy of biology 3 FUNDAMENTAL ISSUES IN SYSTEMS BIOLOGYAs genomics matures from a data-collecting enterprise to an explanatory science, and as those scientific endeavours take on disciplinary contours, a range of underlying issues are being explicitly and implicitly addressed by the scientists involved. These reflections are an important part of the way a discipline constitutes itself as a field by setting out central problems and achievements alongside a history of conceptual and empirical precursors. One of the most widely discussed fields in emergent genomics is systems biology, and it raises several important questions that need to be resolved if the science is to advance.The issues that are most fundamental are how the systems that are the focus of systems biology are defined, and how those definitions affect the research agendas that arise from earlier scientific legacies. Preceding interpretations of genomicsThe early days of genomics began with fairly simple conceptualizations that emphasized the shift from identifying genes to sequencing and mapping entire genomes. (1) As the data poured in and the field achieved wide recognition, these definitions were expanded to give greater emphasis to functional analyses. (2,3) Although much of the discussion of the status of genomes has been conducted via evaluations of the evolving metaphors in genomic discourse -from the ineptness of the blueprint metaphor to analogies with jazz scores and Theseus's 4 ship - (4,5,6) there are also some excellent systematic discussions of genome conceptualizations. (7) Two issues concerning the status of knowledge in genomics are frequently discussed. The first is that early genomics shared the reductionist aspirations of genetics, which led to a preoccupation with sequence structure and deterministic accounts of function. (3, 8) Persistent (and prescient) demands for a more hierarchical and less simplistically deterministic understanding of molecular processes were voiced even in the early years of genomics. (9,10) These calls increased with ...

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Section: Applications To a Proposed Systemmentioning

confidence: 99%

Fundamental issues in systems biology

O’Malley¹,

Dupré²

2005

BioEssays

177

104

View full text Add to dashboard Cite

show abstract

“…At present there are thousands of complete bacterial genomes, 20,000 draft bacterial genomes, and 80,000 full or partial virus genomes in the public GenBank archive (Benson et al, 2015). This rich resource of sequenced genomes now makes it possible to sequence uncultured, unprocessed microbial DNA from almost any environment, ranging from soil to the deep ocean to the human body, and use computational sequence comparisons to identify many of the formerly hidden species in these environments (Riesenfeld, Schloss & Handelsman, 2004). Several accurate methods have appeared that can align a sequence ''read'' to a database of microbial genomes rapidly and accurately (see below), but this step alone is not sufficient to estimate how much of a species is present.…”

Section: Introductionmentioning

confidence: 99%

Bracken: estimating species abundance in metagenomics data

Breitwieser²,

Thielen

et al. 2017

PeerJ Computer Science

1,122

745

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Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within an environment. Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively sequenced the 16S ribosomal RNA gene that is present in bacterial species. As the cost of sequencing has fallen, though, metagenomics experiments have increasingly used unbiased shotgun sequencing to capture all the organisms in a sample. This approach requires a method for estimating abundance directly from the raw read data. Here we describe a fast, accurate new method that computes the abundance at the species level using the reads collected in a metagenomics experiment. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN) uses the taxonomic assignments made by Kraken, a very fast read-level classifier, along with information about the genomes themselves to estimate abundance at the species level, the genus level, or above. We demonstrate that Bracken can produce accurate species-and genus-level abundance estimates even when a sample contains multiple near-identical species.

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“…As a majority of fungi are not readily cultured (Pace, 1997;Rappé and Giovannoni, 2003;Fröhlich-Nowoisky et al, 2009) or easily identified by spores alone (Burge, 1985), these results are expected to be an underestimation of airborne fungal diversity (Wu et al, 2004). Metagenomics, a new field in biology, uses new DNA sequencing technologies (e.g., pyrosequencing) to directly sequence and identify environmental microbes (Riesenfeld et al, 2004). Such methods are expected to vastly improve our ability to identify and study the full spectrum of fungal diversity in the air.…”

Section: Introductionmentioning

confidence: 99%

Identifying airborne fungi in Seoul, Korea using metagenomics

Fong

Park

et al. 2014

J Microbiol.

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Fungal spores are widespread and common in the atmosphere. In this study, we use a metagenomic approach to study the fungal diversity in six total air samples collected from April to May 2012 in Seoul, Korea. This springtime period is important in Korea because of the peak in fungal spore concentration and Asian dust storms, although the year of this study (2012) was unique in that were no major Asian dust events. Clustering sequences for operational taxonomic unit (OTU) identification recovered 1,266 unique OTUs in the combined dataset, with between 223-396 OTUs present in individual samples. OTUs from three fungal phyla were identified. For Ascomycota, Davidiella (anamorph: Cladosporium) was the most common genus in all samples, often accounting for more than 50% of all sequences in a sample. Other common Ascomycota genera identified were Alternaria, Didymella, Khuskia, Geosmitha, Penicillium, and Aspergillus. While several Basidiomycota genera were observed, Chytridiomycota OTUs were only present in one sample. Consistency was observed within sampling days, but there was a large shift in species composition from Ascomycota dominant to Basidiomycota dominant in the middle of the sampling period. This marked change may have been caused by meteorological events. A potential set of 40 allergyinducing genera were identified, accounting for a large proportion of the diversity present (22.5-77.2%). Our study identifies high fungal diversity and potentially high levels of fungal allergens in springtime air of Korea, and provides a good baseline for future comparisons with Asian dust storms.

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Metagenomics: Genomic Analysis of Microbial Communities

Cited by 941 publications

References 126 publications

Fundamental issues in systems biology

Fundamental issues in systems biology

Bracken: estimating species abundance in metagenomics data

Identifying airborne fungi in Seoul, Korea using metagenomics

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