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Environment & Microflora: Metagenomic sequencing for studying the microbial communities in their natural habitat

A big part of our environment is microbes. The air, soil, and aquatic microbiome both in normal and extreme conditions interact with the environment. The field that studies this interaction is called microbial ecology. There is a strong connection and interaction of the environmental microbiome with plants, crops, and other organisms. Understanding the genome of microorganisms is crucial for deepening knowledge in a variety of disciplines. For example, clinical data on pathogens (such as antibiotic resistance) or improvement of agricultural species through the addition of genes that improve resistance to pathogens and environmental stresses, or finding completely new potential enzymes for industrial production.

Recently, after sequencing became more accessible and became used more widely, scientists focused deeply on the microbial genome. Particularly, new sequencing methods have become available such as amplicon or shotgun metagenomic sequencing. The advantage of these methods is that there is no need for isolation and individual culturing of separate microbial species. Instead, a sample can be taken directly from the natural environment, and the sequencing analysis done directly. It is a perfect way to study the microorganisms in their natural habitat. For the amplicon metagenomic sequencing, the microbial intergenic regions or short hypervariable regions of conserved genes are PCR-amplified, and then sequenced by NGS methods. For shotgun metagenomic sequencing, the DNA is extracted and then subjected to rigorous QC and subsequent fragmentation, repair, phosphorylation to prepare for sequencing. Novogene performs sequencing using Illumina NovaSeq 6000. The simplicity of the approach is captivating – many microbial species are difficult or impossible to culture, and it takes tremendous time and effort. Microbial communities are closely interconnected and contain many species. Therefore, thanks to the novel sequencing approaches, unlike previous descriptive vector of microbial studies (looking at the variety of microbial species), we can now answer the questions on what are the functions of certain genes of these microorganisms and what metabolic pathways are involved.

The opportunities for exploration in the field of microbial ecology became extremely vast. Now, scientists can identify a multitude of species for an environmental sample. From there, the new term of environmental DNA (eDNA) arose. Instead of extracting DNA from each organism separately, it is collected from a variety of environmental samples such as seawater or soil. In general, eDNA is a main source of information on how the microorganisms are interacting within their environment. The knowledge can translate into agricultural and industrial fields as well. For example, wastewater plants are a perfect environment to study how humans interface with the environment. However, there is an insufficient study on contamination of the wastewater with antibiotic resistance genes (ARGs). Wastewater plants are of a public health concern and the knowledge on antibiotic resistance genes is crucial[1]. Previously, the researchers had to identify and isolate ARG hosts individually, with many limitations [1].

Thanks to the high-throughput metagenomics sequencing that Novogene provides on the Illumina platform, the samples can be collected directly from the source and processed immediately for sequencing. This presents another interesting angle of microbial ecology research is the target search for genes that have significance for the industry. For example, there was a need for a deeper understanding of agarose degradation and monosaccharides and oligosaccharides produced by this process, and the mangrove sediments create the special conditions to enrich the agarose degradation enzymes [2]. The mentioned monosaccharides and oligosaccharides are of interest for the bioenergy industry as well as for the chemical industry: drugs, cosmetics[2]. Thus, researches focused on mangrove sediments that are known to produce enzymes of interest. The scientists provided the most comprehensive research on analytic genes and related genomes in mangrove sediments by applying metagenomic sequencing. First, eDNA (environmental DNA) was extracted from sediment samples. This DNA was used to construct the library (400 bp and 6 Kb) [2]. The libraries were sequenced by Novogene using Illumina HiSeq. The sequencing method and the further metagenomic data analysis approaches enabled the researchers to get several important findings. First, the authors found 21 recombinant agarose-degrading enzymes. It was confirmed by heterologous expression studies. Then, out of 21 found candidates, Aga2 demonstrated the level of activity, which is promising for industrial production. Finally, the authors reported several genomes for the first time, including two potentially new species.

In sum, shotgun and amplicon metagenomic sequencing provide the opportunity to study the microbial communities in their natural habitat. The researchers can research the whole microbial community structure, as in the case of the wastewater study. Moreover, scientists may research functional genes and pathways, as we have seen in the case of mangrove sediments analysis research. Novogene can assist with the research on microbial ecology using shotgun and amplicon metagenomic sequencing. Novogene will help the scientist to answer the questions, which were unattainable until very recent times, providing excellent sequencing services, rigorous quality control, bioinformatics expertise, and thorough data analysis.


[1] Che Y, Xia Y, Liu L, et al. Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing[J]. Microbiome, 2019. doi: 10.1186/s40168-019-0663-0

[2] Wu Q, Lin D, Zhang Z, et al. Metagenomics Investigation of Agarlytic Genes and Genomes in Mangrove Sediments in China: A Potential Repertory for Carbohydrate-Active Enzymes[J]. Frontiers in Microbiology, 2018. doi: 10.3389/fmicb.2018.01864