High-resolution metagenomics targets specific functional types in complex microbial communities

2008 ◽  
Vol 26 (9) ◽  
pp. 1029-1034 ◽  
Author(s):  
Marina G Kalyuzhnaya ◽  
Alla Lapidus ◽  
Natalia Ivanova ◽  
Alex C Copeland ◽  
Alice C McHardy ◽  
...  
Keyword(s):  
High Resolution ◽  
Microbial Communities ◽  
Functional Types

High-Resolution Dynamics of Microbial Communities during Dissimilatory Selenate Reduction in Anoxic Soil

2015 ◽  
Vol 49 (13) ◽  
pp. 7684-7691 ◽  
Author(s):  
Ronald R. Navarro ◽  
Tomo Aoyagi ◽  
Makoto Kimura ◽  
Hideomi Itoh ◽  
Yuya Sato ◽  
...  
Keyword(s):  
High Resolution ◽  
Microbial Communities

scholarly journals Systems biology approach to elucidation of contaminant biodegradation in complex samples – integration of high-resolution analytical and molecular tools

2019 ◽  
Vol 218 ◽  
pp. 481-504 ◽  
Author(s):  
Caroline Gauchotte-Lindsay ◽  
Thomas J. Aspray ◽  
Mara Knapp ◽  
Umer Z. Ijaz
Keyword(s):  
Systems Biology ◽  
High Resolution ◽  
Microbial Communities ◽  
Contaminated Soils ◽  
Rational Design ◽  
Data Driven ◽  
Molecular Tools ◽  
Complex Samples ◽  
Driven Systems

We present here a data-driven systems biology framework for the rational design of biotechnological solutions for contaminated environments with the aim of understanding the interactions and mechanisms underpinning the role of microbial communities in the biodegradation of contaminated soils.

scholarly journals Two-target quantitative PCR to predict library composition for shallow shotgun sequencing

2020 ◽  
Author(s):  
Matthew Y. Cho ◽  
Marc Oliva ◽  
Anna Spreafico ◽  
Bo Chen ◽  
Xu Wei ◽  
...  
Keyword(s):  
High Resolution ◽  
Microbial Communities ◽  
Quantitative Pcr ◽  
Shotgun Sequencing ◽  
Accurate Prediction ◽  
Missing Information ◽  
Bacterial Genes

AbstractShotgun sequencing enables retrieving high resolution information 40 from complex microbial communities. However, the technique is limited by missing information about host-to-microbe ratios observed in different sample types. This makes it challenging to plan sequencing experiments, especially in the context of high sample multiplexing and/or limited sequencing output. We evaluated a qPCR-based assay to predict host-to microbe ratio prior to sequencing. Using a two-target assay aimed at conserved human and bacterial genes, we predicted human-to-microbe ratios in two sample types and validated it on independently collected samples. The assay enabled accurate prediction for a broad range of sample compositions.

scholarly journals Bottom-up ecology of the human microbiome: from metagenomes to metabolomes

2016 ◽  
Author(s):  
Daniel R. Garza ◽  
Marcel C. Van Verk ◽  
Martijn A. Huynen ◽  
Bas E. Dutilh
Keyword(s):  
High Resolution ◽  
Microbial Communities ◽  
Human Skin ◽  
Human Microbiome ◽  
Skin Microbiome ◽  
Body Site ◽  
Essential Factor ◽  
Metabolomics Data ◽  
Bottom Up ◽  
Site Specific

AbstractThe environmental metabolome is a dominant and essential factor shaping microbial communities. Thus, we hypothesized that metagenomic datasets could reveal the quantitative metabolic status of a given sample. Using a newly developed bottom-up ecology algorithm, we predicted high-resolution metabolomes of hundreds of metagenomic datasets from the human microbiome, revealing body-site specific metabolomes consistent with known metabolomics data, and suggesting that common cosmetics ingredients are some of the major metabolites shaping the human skin microbiome.

scholarly journals Lipidomics of Environmental Microbial Communities. I: Visualization of Component Distributions Using Untargeted Analysis of High-Resolution Mass Spectrometry Data

2021 ◽  
Vol 12 ◽  
Author(s):  
Nicole J. Bale ◽  
Su Ding ◽  
Ellen C. Hopmans ◽  
Milou G. I. Arts ◽  
Laura Villanueva ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Mass Spectrum ◽  
High Resolution ◽  
Microbial Communities ◽  
Water Column ◽  
High Resolution Mass Spectrometry ◽  
Untargeted Analysis ◽  
High Resolution Mass ◽  
Resolution Mass

Lipids, as one of the main building blocks of cells, can provide valuable information on microorganisms in the environment. Traditionally, gas or liquid chromatography coupled to mass spectrometry (MS) has been used to analyze environmental lipids. The resulting spectra were then processed through individual peak identification and comparison with previously published mass spectra. Here, we present an untargeted analysis of MS1 spectral data generated by ultra-high-pressure liquid chromatography coupled with high-resolution mass spectrometry of environmental microbial communities. Rather than attempting to relate each mass spectrum to a specific compound, we have treated each mass spectrum as a component, which can be clustered together with other components based on similarity in their abundance depth profiles through the water column. We present this untargeted data visualization method on lipids of suspended particles from the water column of the Black Sea, which included >14,000 components. These components form clusters that correspond with distinct microbial communities driven by the highly stratified water column. The clusters include both known and unknown compounds, predominantly lipids, demonstrating the value of this rapid approach to visualize component distributions and identify novel lipid biomarkers.

scholarly journals High-resolution ISR amplicon sequencing reveals personalized oral microbiome

2018 ◽  
Author(s):  
Chiranjit Mukherjee ◽  
Clifford J. Beall ◽  
Ann L. Griffen ◽  
Eugene J. Leys
Keyword(s):  
High Resolution ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Cost Effective ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Community Fingerprinting

AbstractBackground:Sequencing of the 16S rRNA gene has been the standard for studying the composition of microbial communities. While it allows identification of bacteria at the level of species, it does not usually provide sufficient information to resolve at the sub-species level. Species-level resolution is not adequate for studies of transmission or stability, or for exploring subspecies variation in disease association. Current approaches using whole metagenome shotgun sequencing require very high coverage that can be cost-prohibitive and computationally challenging for diverse communities. Thus there is a need for high-resolution, yet cost-effective, high-throughput methods for characterizing microbial communities.Results:Significant improvement in resolution for amplicon-based bacterial community analysis was achieved by combining amplicon sequencing of a high-diversity marker gene, the ribosomal operon ISR, with a probabilistic error modeling algorithm, DADA2. The resolving power of this new approach was compared to that of both standard and high-resolution 16S-based approaches using a set of longitudinal subgingival plaque samples. The ISR strategy achieved a 5.2-fold increase in community richness compared to reference-based 16S rRNA gene analysis, and showed 100% accuracy in predicting the correct source of a clinical sample. Individuals’ microbial communities were highly personalized, and although they exhibited some drift in membership and levels over time, that difference was always smaller than the differences between any two subjects, even after one year. The construction of an ISR database from publicly available genomic sequences allowed us to explore genomic variationwithinspecies, resulting in the identification of multiple variants of the ISR for most species.Conclusions:The ISR approach resulted in significantly improved resolution of communities, and revealed a highly personalized, stable human oral microbiota. Multiple ISR types were observed for all species examined, demonstrating a high level of subspecies variation in the oral microbiota. The approach is high-throughput, high-resolution yet cost-effective, allowing subspecies-level community fingerprinting at a cost comparable to that of 16S rRNA gene amplicon sequencing. It will be useful for a range of applications that require high-resolution identification of organisms, including microbial tracking, community fingerprinting, and potentially for identification of virulence-associated strains.

Sign in / Sign up

Export Citation Format

Share Document