Journal: Applied and Environmental Microbiology

Article Title: Quantitative metagenomics using a portable protocol

doi: 10.1128/aem.02179-25

Figure Lengend Snippet: Evaluation of DNA extraction methods on the microbial community in mixed liquor sludge samples (ML). ( A ) Purity and quantity and ( B ) DNA fragment size distribution for DNA extracted using different protocols. The line, bar, and bubble plots indicate the average purity, DNA yield, and fragment distribution, respectively. The star, circle, and filled triangle represent the mean, median, and peak of DNA fragments by molarity, respectively. ( C ) Alpha diversity (Chao1 index), ( D ) beta diversity, and ( E ) composition of the microbial community for prokaryotes using 16S rRNA gene amplicon sequencing. Beta diversity is measured using an NMDS2 plot based on Bray-Curtis distance.

Article Snippet: DNA extracted from ZymoBIOMICS Microbial Community Standard (Even Distribution) (Zymo Even Cell, ) and gut microbiome standard (Zymo Gut, ) (Zymo Research Corporation, CA, USA), ML, SE, and AL using the optimized DNA extraction protocol (see “A portable DNA extraction strategy was validated across varying microbial loads and sample types,” below) was used as the sample DNA.

Techniques: DNA Extraction, Amplification, Sequencing

Journal: Plant Biotechnology Journal

Article Title: Advancing Plant Microbiome Research Through Host DNA Depletion Techniques

doi: 10.1111/pbi.70379

Figure Lengend Snippet: Importance of host depletion methods in plant metagenomics. Understanding the complex interactions between plants and their associated microbial communities is pivotal for plant health and growth. Metagenomic analysis is a powerful tool to reveal the composition, structure and functional potential of microbial communities. As research focus has gradually expanded from rhizosphere soil to specific plant compartments such as roots, stems and leaves, and from high biomass to low biomass samples, the severe host contamination has become a significant issue. A high proportion of host DNA results in wasted sequencing resources, reduced sensitivity and obscured microbial signals, thereby impeding the effective application of metagenomics in plant microbiome research. The development and optimisation of host depletion approaches are therefore essential to improve microbial signal recovery, enhance sequencing efficiency and facilitate deeper insights into plant–microbe interactions.

Article Snippet: This principle underlies the NEBNext Microbiome DNA Enrichment Kit, which has been widely used.

Techniques: Metagenomics, Functional Assay, Sequencing

Journal: Plant Biotechnology Journal

Article Title: Advancing Plant Microbiome Research Through Host DNA Depletion Techniques

doi: 10.1111/pbi.70379

Figure Lengend Snippet: Host DNA depletion facilitates metagenomic analysis of the plant holobiont and enables microbiome‐based applications in sustainable agriculture. Effective host depletion methods enrich microbial DNA from plant‐associated samples, improving the resolution and accuracy of metagenomic analyses. This supports genome‐resolved metagenomics, functional profiling and integration with other omics (e.g., metatranscriptomics, metabolomics), thereby enabling a holistic understanding of plant microbiomes across compartments such as the rhizosphere, endosphere and phyllosphere. Insights gained can inform the development of targeted microbiome‐based agents for crop management, ultimately contributing to increased stress tolerance, improved yields and enhanced nutritional quality of crops.

Article Snippet: This principle underlies the NEBNext Microbiome DNA Enrichment Kit, which has been widely used.

Techniques: Metagenomics, Functional Assay

Journal: Animal Microbiome

Article Title: Multi-omics characterization of blood metabolites and cervical microbiota associated with estrus in simmental cattle

doi: 10.1186/s42523-026-00571-8

Figure Lengend Snippet: Bacterial community structure in the cervical microbiota. ( A ) OTU distribution. ( B ) α diversity indices. ( C ) PCoA clustering. ( D ) Dominant phyla ( Firmicutes , Bacteroidetes ). ( E ) Genus-level composition. ( F ) Clustered heatmap of the dominant genera. ( G ) LEfSe-identified bacterial biomarkers (LDA > 2). Data from 16 S rRNA sequencing ( n = 6/group)

Article Snippet: Genomic DNA was extracted from cervical swabs using the FastPure Microbiome DNA Isolation Kit (Vazyme, Nanjing, China) following the manufacturer’s instructions.

Techniques: Sequencing

Journal: Animal Microbiome

Article Title: Multi-omics characterization of blood metabolites and cervical microbiota associated with estrus in simmental cattle

doi: 10.1186/s42523-026-00571-8

Figure Lengend Snippet: Fungal community structure in the cervical microbiota. ( A ) OTU distribution. ( B ) α diversity indices. ( C ) PCoA clustering. ( D ) Dominant phyla ( Ascomycota , Basidiomycota ). ( E ) Genus-level composition. ( F ) Clustered heatmap of the dominant genera. ( G ) LEfSe-identified fungal biomarkers (LDA > 2). Data from ITS sequencing ( n = 6/group)

Article Snippet: Genomic DNA was extracted from cervical swabs using the FastPure Microbiome DNA Isolation Kit (Vazyme, Nanjing, China) following the manufacturer’s instructions.

Techniques: Sequencing

Journal: Animal Microbiome

Article Title: Multi-omics characterization of blood metabolites and cervical microbiota associated with estrus in simmental cattle

doi: 10.1186/s42523-026-00571-8

Figure Lengend Snippet: Correlations between reproductive hormones and cervical microbiota. ( A ) Heatmap showing Spearman correlations between serum hormone concentrations (E2, PROG) and relative abundances of bacterial phyla. ( B ) Correlations between hormones and fungal genera ( Bacteroides , Prevotellaceae _UCG-003, p < 0.05)

Article Snippet: Genomic DNA was extracted from cervical swabs using the FastPure Microbiome DNA Isolation Kit (Vazyme, Nanjing, China) following the manufacturer’s instructions.

Techniques: