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Metagenomics

About: Metagenomics is a(n) research topic. Over the lifetime, 6750 publication(s) have been published within this topic receiving 421852 citation(s).

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Journal ArticleDOI: 10.1038/NMETH.2604
01 Oct 2013-Nature Methods
Abstract: Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.

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Topics: Metagenomics (53%)

7,953 Citations


Open accessJournal ArticleDOI: 10.1038/NATURE08821
Junjie Qin1, Ruiqiang Li1, Jeroen Raes2, Manimozhiyan Arumugam  +49 moreInstitutions (5)
04 Mar 2010-Nature
Abstract: To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, ~150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively

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Topics: Metagenomics (60%), Bacterial genome size (53%), Genomics (52%) ...read more

7,873 Citations


Open accessJournal ArticleDOI: 10.1038/NATURE07540
22 Jan 2009-Nature
Abstract: The human distal gut harbours a vast ensemble of microbes (the microbiota) that provide important metabolic capabilities, including the ability to extract energy from otherwise indigestible dietary polysaccharides. Studies of a few unrelated, healthy adults have revealed substantial diversity in their gut communities, as measured by sequencing 16S rRNA genes, yet how this diversity relates to function and to the rest of the genes in the collective genomes of the microbiota (the gut microbiome) remains obscure. Studies of lean and obese mice suggest that the gut microbiota affects energy balance by influencing the efficiency of calorie harvest from the diet, and how this harvested energy is used and stored. Here we characterize the faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers, to address how host genotype, environmental exposure and host adiposity influence the gut microbiome. Analysis of 154 individuals yielded 9,920 near full-length and 1,937,461 partial bacterial 16S rRNA sequences, plus 2.14 gigabases from their microbiomes. The results reveal that the human gut microbiome is shared among family members, but that each person's gut microbial community varies in the specific bacterial lineages present, with a comparable degree of co-variation between adult monozygotic and dizygotic twin pairs. However, there was a wide array of shared microbial genes among sampled individuals, comprising an extensive, identifiable 'core microbiome' at the gene, rather than at the organismal lineage, level. Obesity is associated with phylum-level changes in the microbiota, reduced bacterial diversity and altered representation of bacterial genes and metabolic pathways. These results demonstrate that a diversity of organismal assemblages can nonetheless yield a core microbiome at a functional level, and that deviations from this core are associated with different physiological states (obese compared with lean).

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Topics: Microbiome (64%), Human Microbiome Project (63%), Human microbiome (58%) ...read more

6,178 Citations


Open accessJournal ArticleDOI: 10.1186/GB-2011-12-6-R60
Nicola Segata1, Jacques Izard2, Jacques Izard1, Levi Waldron1  +4 moreInstitutions (3)
24 Jun 2011-Genome Biology
Abstract: This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.

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Topics: Biomarker discovery (51%), Metagenomics (51%)

6,049 Citations


Open accessJournal ArticleDOI: 10.1038/NBT.2676
Abstract: Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community's functional capabilities. Here we describe PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this 'predictive metagenomic' approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.

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Topics: Metagenomics (54%), Marker gene (52%), Human Microbiome Project (50%)

5,291 Citations


Performance
Metrics
No. of papers in the topic in previous years
YearPapers
20228
2021786
2020785
2019717
2018645
2017628

Top Attributes

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Topic's top 5 most impactful authors

Curtis Huttenhower

50 papers, 25.3K citations

Jillian F. Banfield

47 papers, 5.1K citations

Nicola Segata

39 papers, 10.3K citations

Susannah G. Tringe

37 papers, 6.9K citations

Philip Hugenholtz

32 papers, 8.5K citations

Network Information
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