ReviewThe ISME journal2017
Capturing the genetic makeup of the active microbiome in situ.
Review in The ISME journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
38 citing papers in PubMed.
- From dividing to dormant: embracing the full activity spectrum for environmental microorganisms.Microbiology and molecular biology reviews : MMBR · 2026Review
- Evidence for cable bacteria inhabiting deep in anoxic sediment reveals a novel ecological niche.Environmental microbiome · 2026Article
- Review
- Microbial dormancy as an ecological and biogeochemical regulator on Earth.Nature communications · 2025Review
- Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing.ISME communications · 2025Article
- Precision isolation and cultivation of single cells by vortex and flat-top laser ejection.Frontiers in microbiology · 2024Article
- Microbiomes of urban trees: unveiling contributions to atmospheric pollution mitigation.Frontiers in microbiology · 2024Article
- High concentrate diets altered the structure and function of rumen microbiome in goats.Frontiers in microbiology · 2024Article
- Metatranscriptomics-guided genome-scale metabolic modeling of microbial communities.Cell reports methods · 2023Article
- Functional microbial ecology in arctic soils: the need for a year-round perspective.FEMS microbiology ecology · 2022Article
- Active antibiotic resistome in soils unraveled by single-cell isotope probing and targeted metagenomics.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Organelle 16S rRNA amplicon sequencing enables profiling of active gut microbiota in murine model.Applied microbiology and biotechnology · 2022Article
- Microbial ecology of biofiltration used for producing safe drinking water.Applied microbiology and biotechnology · 2022Review
- Long-term patterns of an interconnected core marine microbiota.Environmental microbiome · 2022Article
- Isolation and Culture of Single Microbial Cells by Laser Ejection Sorting Technology.Applied and environmental microbiology · 2022Article
- Application of ecosystem-specific reference databases for increased taxonomic resolution in soil microbial profiling.Frontiers in microbiology · 2022Article
- Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses.The ISME journal · 2021Article
- Using Stable Isotope Probing and Raman Microspectroscopy To Measure Growth Rates of Heterotrophic Bacteria.Applied and environmental microbiology · 2021Article
- Article
- Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap.Molecular ecology · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.