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Macrogenome sequencing

Product Description
Case Interpretation

Macrogenomic sequencing aims to sequence the genomes of microbial communities in specific environmental samples in order to analyse the genetic composition and function of microbial communities, to decipher the diversity and abundance of microbial communities, explore the relationship between microbes and their environment, microbes and hosts, and discover and study new genes with specific functions. Macrogenomics is a new approach to study microbial diversity, population structure, evolutionary relationships, functional activity, interactions and relationships with the environment, using the genome of the microbial community in environmental samples as the object of study and functional gene screening and/or sequencing as the means of study. This technique can be used to unravel the diversity and abundance of microbial populations, explore the relationships between microbes and their environment, microbes and their hosts, and discover and study new, functionally specific genes.

 

technology roadmap:

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technical parameter:

Sample requirements

Sequencing strategy Lead time

Sample type: Environmental microbial DNA samples

Sample concentration: ≥50 ng/μl

Total sample mass: ≥3 μg

Sequencing mode: Illumina/MGI/Double-end sequencing

Sequencing depth: 5-10G clean data

45 days

 

Product advantages.

a. Technical advantages: PCR-free library construction for more accurate species annotation, and new splicing methods to reduce the false positive rate of gene annotation;

b. Customised solutions: In addition to conventional analyses, a number of advanced analyses are available to provide the best solution for your project.

Case 1 Global Marine Microbial Structure and Function

Background

Microorganisms are the main drivers of biochemistry, but there are significant challenges in analysing their microbial population structure, functional diversity and ecological factors in general.

Study

243 samples were collected from 68 sampling sites in three layers (surface SRF, lowest photosynthetic layer DCM, mesopelagic MESO) of different seawater from major representative global ocean regions (except the Arctic). DNA was extracted, sequenced by Illumina PE100, and then OTU clustering and analysis as well as some functional gene prediction, colony structure and functional analysis was carried out. Ecology, systems biology and oceanography were combined to study plankton in the ocean.

Conclusions

Temperature was found to be the largest driver of microbial species diversity and the broad range of functions in marine microbes predicts their potential to influence global climate change.

 

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Figure 1. Research findings of global marine microbial diversity

 

Case 2 Accurate and sensitive identification of eukaryotic microorganisms from macro-genome sequencing data

Background

Eukaryotic microbes occur alongside bacteria and archaea in natural microbial systems, including host-associated microbiomes. Although eukaryotic microbes are critical to these communities, they are difficult to study using birdshot sequencing techniques and are therefore excluded.

Study

This study presents EukDetect, a novel strategy for macrogenomic detection of eukaryotes, applying EukDetect to human, plant and aquatic microbiome-related public datasets to infer the role of eukaryotes in these environments. The results show that the EukDetect approach to tagging genes greatly expands the number of detectable disease-associated eukaryotic species in host-associated and environmental microbiomes. The flow chart of the entire approach is shown below.

Conclusions

Eukaryotes can be effectively detected from whole macrogenome sequencing data through conserved eukaryotic gene databases. As more macro-genome sequencing data from host-associated and environmental microbiomes become available, tools like EukDetect will reveal the contribution of eukaryotic microbes to different environments.

 

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Figure 2 Macro genome analysis flow chart

 

Research conclusion:
Eukaryotes can be effectively detected from the whole genome sequencing data through the conservative eukaryotic gene database. With the emergence of more macro-genome sequencing data from host-related and environmental microbiomes, tools like EukDetect will reveal the contribution of eukaryotic microorganisms to different environments.
reference:

  1. Bäckhed F, Roswall J, Peng Y, et al. Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life[J]. Cell Host & Microbe, 2015, 17(5):690-703.

  2. Lind A L, Pollard K S. Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing[J]. Microbiome, 2021, 9(1): 1-18.

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