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Randomized lasso associates freshwater lake-system specific bacterial taxa with heterotrophic production through flow cytometry

https://doi.org/10.1101/392852
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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FlowRepository: A resource of annotated flow cytometry datasets associated with peer‐reviewed publications
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Correlation detection strategies in microbial data sets vary widely in sensitivity and precision
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Bacterial community segmentation facilitates the prediction of ecosystem function along the coast of the western Antarctic Peninsula
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High-fat maternal diet during pregnancy persistently alters the offspring microbiome in a primate model
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Relic DNA is abundant in soil and obscures estimates of soil microbial diversity
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Phylogenetic clustering of small low nucleic acid-content bacteria across diverse freshwater ecosystems
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Best practices for analysing microbiomes
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Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls
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Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities
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Dormancy contributes to the maintenance of microbial diversity
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Flow cytometric monitoring of bacterioplankton phenotypic diversity predicts high population‐specific feeding rates by invasive dreissenid mussels
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Keystone taxa predict compositional change in microbial communities
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Diel dynamics and coupling of heterotrophic prokaryotes and dissolved organic matter in epipelagic and mesopelagic waters of the central Red Sea
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Stability Selection
inferredcites →https://doi.org/10.1111/j.1574-6976.2000.tb00549.xopenalex-snapshot
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phytools: an R package for phylogenetic comparative biology (and other things)
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Application of multivariate statistical techniques in microbial ecology
inferredcites →https://doi.org/10.1126/science.1122050openalex-snapshot
Genomic Islands and the Ecology and Evolution of Prochlorococcus
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Significance of Size and Nucleic Acid Content Heterogeneity as Measured by Flow Cytometry in Natural Planktonic Bacteria
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Direct and Indirect Effects of Protist Predation on Population Size Structure of a Bacterial Strain with High Phenotypic Plasticity
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Microbiome Data Distinguish Patients with Clostridium difficile Infection and Non-C. difficile-Associated Diarrhea from Healthy Controls
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A Guide to the Natural History of Freshwater Lake Bacteria
inferredcites →https://doi.org/10.1128/msphere.00327-18openalex-snapshot
TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution
inferredcites →https://doi.org/10.1146/annurev-statistics-010814-020351openalex-snapshot
Microbiome, Metagenomics, and High-Dimensional Compositional Data Analysis
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Structure of the gut microbiome following colonization with human feces determines colonic tumor burden
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Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem
inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
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phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
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Monitoring of Dynamic Microbiological Processes Using Real-Time Flow Cytometry
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RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition
inferredcites →https://doi.org/10.1371/journal.pone.0195112openalex-snapshot
Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats
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Feature Selection with the Boruta Package
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Statsmodels: Econometric and Statistical Modeling with Python
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R: A Language and Environment for Statistical Computing
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Dynamics of heterotrophic bacteria in temperate coastal waters: similar net growth but different controls in low and high nucleic acid cells
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Variations of bacterial-specific activity with cell size and nucleic acid content assessed by flow cytometry
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Activity and diversity of bacterial cells with high and low nucleic acid content
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Assessing the relevance of nucleic acid content as an indicator of marine bacterial activity
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Protein content and protein synthesis rates of planktonic marine bacteria
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Metacommunity dynamics of bacteria in an arctic lake: the impact of species sorting and mass effects on bacterial production and biogeography
inferredcites →https://doi.org/10.3389/fmicb.2016.00853openalex-snapshot
Bacterial Dormancy Is More Prevalent in Freshwater than Hypersaline Lakes
inferredcites →https://doi.org/10.3389/fmicb.2016.00903openalex-snapshot
Flow Cytometric Assessment of Bacterial Abundance in Soils, Sediments and Sludge
inferredcites →https://doi.org/10.3389/fmicb.2017.02224openalex-snapshot
Microbiome Datasets Are Compositional: And This Is Not Optional
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Using flow cytometry for counting natural planktonic bacteria and understanding the structure of planktonic bacterial communities
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Single‐cell physiological structure and growth rates of heterotrophic bacteria in a temperate estuary (Waquoit Bay, Massachusetts)

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1101/641464openalex-snapshot
PhenoGMM : Gaussian mixture modelling of microbial cytometry data enables efficient predictions of biodiversity
inferred← citeshttps://doi.org/10.3390/w18091059openalex-snapshot
Added Value of MBR and Ozonation for Advanced Wastewater Treatment Based on Antibiotic Resistance Genes and Bacteroidales as a Marker for Fecal Gene Load
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