High throughput DNA extraction of legume root nodules for rhizobial metagenomics

Johnson, Gabriel

doi:10.1186/s13568-019-0771-z

Cited by 12 publications

(7 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Gene and genome sequencing technics, in combinations with electrophoresis and polymerase chain reaction (PCR), allow faster and more efficient distinguishments of even closely related species [ 126 ]. Moreover, metagenomics and third-generation gene sequencing methods are more reliable, sensitive, and faster than traditional methods [ 127 , 128 ].…”

Section: Methods Used In Rhizobia Characterization In Africamentioning

confidence: 99%

Distribution, Characterization and the Commercialization of Elite Rhizobia Strains in Africa

Wekesa

Jalloh

John

et al. 2022

IJMS

View full text Add to dashboard Cite

Grain legumes play a significant role in smallholder farming systems in Africa because of their contribution to nutrition and income security and their role in fixing nitrogen. Biological Nitrogen Fixation (BNF) serves a critical role in improving soil fertility for legumes. Although much research has been conducted on rhizobia in nitrogen fixation and their contribution to soil fertility, much less is known about the distribution and diversity of the bacteria strains in different areas of the world and which of the strains achieve optimal benefits for the host plants under specific soil and environmental conditions. This paper reviews the distribution, characterization, and commercialization of elite rhizobia strains in Africa.

show abstract

Section: Methods Used In Rhizobia Characterization In Africamentioning

confidence: 99%

Distribution, Characterization and the Commercialization of Elite Rhizobia Strains in Africa

Wekesa

Jalloh

John

et al. 2022

IJMS

View full text Add to dashboard Cite

show abstract

“…In recent years, the progress of high-throughput sequencing technologies has allowed fundamental advancements in DNA sequencing (Shui et al 2020 ). With the declining expense of DNA sequencing, metagenomics has been rapidly developing (Johnson 2019 ). Metagenomics techniques are commonly used to sequence and analyse the whole genomes of microbes from a sample without the need for cell culture.…”

Section: Introductionmentioning

confidence: 99%

Harnessing the strategy of metagenomics for exploring the intestinal microecology of sable (Martes zibellina), the national first-level protected animal

Yan

Yao

et al. 2020

AMB Expr

View full text Add to dashboard Cite

Sable (Martes zibellina), a member of family Mustelidae, order Carnivora, is primarily distributed in the cold northern zone of Eurasia. The purpose of this study was to explore the intestinal flora of the sable by metagenomic library-based techniques. Libraries were sequenced on an Illumina HiSeq 4000 instrument. The effective sequencing data of each sample was above 6000 M, and the ratio of clean reads to raw reads was over 98%. The total ORF length was approximately 603,031, equivalent to 347.36 Mbp. We investigated gene functions with the KEGG database and identified 7140 KEGG ortholog (KO) groups comprising 129,788 genes across all of the samples. We selected a subset of genes with the highest abundances to construct cluster heat maps. From the results of the KEGG metabolic pathway annotations, we acquired information on gene functions, as represented by the categories of metabolism, environmental information processing, genetic information processing, cellular processes and organismal systems. We then investigated gene function with the CAZy database and identified functional carbohydrate hydrolases corresponding to genes in the intestinal microorganisms of sable. This finding is consistent with the fact that the sable is adapted to cold environments and requires a large amount of energy to maintain its metabolic activity. We also investigated gene functions with the eggNOG database; the main functions of genes included gene duplication, recombination and repair, transport and metabolism of amino acids, and transport and metabolism of carbohydrates. In this study, we attempted to identify the complex structure of the microbial population of sable based on metagenomic sequencing methods, which use whole metagenomic data, and to map the obtained sequences to known genes or pathways in existing databases, such as CAZy, KEGG, and eggNOG. We then explored the genetic composition and functional diversity of the microbial community based on the mapped functional categories.

show abstract

“…In recent years, the progress of high-throughput sequencing technologies has been a fundamental advancement in DNA sequencing (Shui et al 2020). With the declined expense of DNA sequencing, metagenomics has been in the stage of rapid development (Johnson 2019). The technique is usually used to sequence and analyze the whole genome of microbes in an entire sample, without the necessity for cell cultures, it is widely applied to probe environmental microbial diversity from the all levels, in consequence further study of the microbial community structure and ecosystem function is possible (Martin et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Harnessing the strategy of metagenomics for exploring the intestinal microecology of sable (Martes zibellina), the national first-level protected animal

Yan

Chen

et al. 2020

Preprint

View full text Add to dashboard Cite

Sable (Martes zibellina), belongs to Carnivora, Mustelidae and Maretes, was mainly distributed among the cold northern zone of Eurasia. The purpose of this study is to explore the intestinal flora of the sable by the method of the metagenomic library-based technique, libraries were sequenced on an Illumina HiSeq 4000 instrument. Effective Data volume of each sample is above 6000M, the ratio of the Effective Data (the Clean Data) to original Data (Raw Data) is over 98%. According to the analysis of statistical data, the Total length of ORF is about 603,031, which is 347.36 Mbp. We contrast the unique function of genes with KEGG database, we acquire 7140 genes (KO), a total of all the samples KO is 129788. We selected higher abundance genes to draw cluster heat maps, and according to the results of the KEGG metabolic pathway annotations, we acquire the gene function，including metabolism, environmental information processing, genetic information processing, cellular process and organismal systems. We contrast the unique function of genes with CAZy database, the functional carbohydrate hydrolases have corresponding genes in the intestinal microorganisms of the sable. This is closely related to the fact that the sable is adapted to cold environments and requires a large amount of energy to maintain its metabolic activity. We contrast the unique function of genes with eggNOG database，the main functions of genes included gene duplication, recombination and repair, transport and metabolism of amino acids, transport and metabolism of carbohydrates, etc. In this study, we intended to identify the complex microbial population structure of sables based on metagenomic sequencing method, which uses the whole metagenomic data, mapping the sequences to the known genes or the pathways in the existing databases, such as CAZy, KEGG, or eggNOG, and then exploring the genetic composition and functional diversity of microbial community based on the mapped functional categories.

show abstract

High throughput DNA extraction of legume root nodules for rhizobial metagenomics

Cited by 12 publications

References 27 publications

Distribution, Characterization and the Commercialization of Elite Rhizobia Strains in Africa

Distribution, Characterization and the Commercialization of Elite Rhizobia Strains in Africa

Harnessing the strategy of metagenomics for exploring the intestinal microecology of sable (Martes zibellina), the national first-level protected animal

Harnessing the strategy of metagenomics for exploring the intestinal microecology of sable (Martes zibellina), the national first-level protected animal

Contact Info

Product

Resources

About