ArticleFrontiers in microbiology2021
DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data.
Article in Frontiers in microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed.
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- Structure and Metabolic Potential of Microbial Communities in High-altitude Lake Enriched with Dissolved Organic Carbon.Current microbiology · 2026Article
- Trait-based signatures associated with persistence and thermal benefit in a genomically decayed coral probiotic.The ISME journal · 2026Article
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- A metagenomic exploration of microbial distribution among the pond sediment, shrimp (Penaeus monodon) tissue and pond water: A special focus on nutrient cycling and shrimp viral pathogens.Journal, genetic engineering & biotechnology · 2025Article
- CNPS.cycle: streamlining shotgun metagenomic data analysis for biogeochemical cycles.mSystems · 2025Article
- First Insight into the Natural Attenuation of Emerging Contaminants Using a Metagenomics Approach from Drinking Water Sources in the Free State.Microorganisms · 2025Article
- Plasticity of the gut microbiome of golden snub-nosed monkeys (Rhinopithecus roxellana) in response to seasonal variation in diet.NPJ biofilms and microbiomes · 2025Article
- MSFT-transformer: a multistage fusion tabular transformer for disease prediction using metagenomic data.Briefings in bioinformatics · 2025Article
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- Chemoautotrophic Thermodesulfobacteriota as a key genomic potential group in the hypoxic diazotrophic community of the Changjiang (Yangtze River) estuary.Frontiers in microbiology · 2025Article
- Adaptive characteristics of the gut microbiota of the scaly-sided merganser (Frontiers in microbiology · 2025Article
- Metabolic Potential and Microbial Diversity of Late Archean to Early Proterozoic Ocean Analog Hot Springs of Japan.Microbes and environments · 2025Article
- Factors influencing the spatial distributions of river microbial communities at the watershed scale: a case study involving the Wuding River Basin.Frontiers in microbiology · 2025Article
- Diversity of bacterial communities in wetlands of Calakmul Biosphere Reserve: a comparative analysis between conserved and semi-urbanized zones in pre-Mayan Train era.BMC microbiology · 2024Article
- Nitrite-driven anaerobic ethane oxidation.Environmental science and ecotechnology · 2024Article
- Structural and functional bacterial biodiversity in a copper, zinc and nickel amended bioreactor: shotgun metagenomic study.BMC microbiology · 2024Article
- Potential coupling of microbial methane, nitrogen, and sulphur cycling in the Okinawa Trough cold seep sediments.Microbiology spectrum · 2024Article
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Authors and funding
9 authors.
Funding
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Abstract
Metagenomics and metatranscriptomics are powerful methods to uncover key micro-organisms and processes driving biogeochemical cycling in natural ecosystems. Databases dedicated to depicting biogeochemical pathways (for example, metabolism of dimethylsulfoniopropionate (DMSP), which is an abundant organosulfur compound) from metagenomic/metatranscriptomic data are rarely seen. Additionally, a recognized normalization model to estimate the relative abundance and environmental importance of pathways from metagenomic and metatranscriptomic data has not been organized to date. These limitations impact the ability to accurately relate key microbial-driven biogeochemical processes to differences in environmental conditions. Thus, an easy-to-use, specialized tool that infers and visually compares the potential for biogeochemical processes, including DMSP cycling, is urgently required. To solve these issues, we developed DiTing, a tool wrapper to infer and compare biogeochemical pathways among a set of given metagenomic or metatranscriptomic reads in one step, based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) and a manually created DMSP cycling gene database. Accurate and specific formulae for over 100 pathways were developed to calculate their relative abundance. Output reports detail the relative abundance of biogeochemical pathways in both text and graphical format. DiTing was applied to simulated metagenomic data and resulted in consistent genetic features of simulated benchmark genomic data. Subsequently, when applied to natural metagenomic and metatranscriptomic data from hydrothermal vents and the
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