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Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities

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What this work says

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

inferredcites →https://doi.org/10.1016/j.yexcr.2014.01.008openalex-snapshot

Library preparation methods for next-generation sequencing: Tone down the bias

inferredcites →https://doi.org/10.1038/ismej.2011.41openalex-snapshot

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea

inferredcites →https://doi.org/10.1038/nature11053openalex-snapshot

Human gut microbiome viewed across age and geography

inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot

DADA2: High-resolution sample inference from Illumina amplicon data

inferredcites →https://doi.org/10.1038/s41587-019-0209-9openalex-snapshot

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

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Comparison of DNA Quantification Methods for Next Generation Sequencing

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Correction: Corrigendum: NPNT is Expressed by Osteoblasts and Mediates Angiogenesis via the Activation of Extracellular Signal-regulated Kinase

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Microbial diversity in the deep sea and the underexplored “rare biosphere”

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Marine Benthic Diversity: A Comparative Study

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Properties of the Rarefaction Diversity Measurement

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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

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Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

inferredcites →https://doi.org/10.1111/1758-2229.12438openalex-snapshot

Fungal identification biases in microbiome projects

inferredcites →https://doi.org/10.1128/aem.01043-13openalex-snapshot

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

inferredcites →https://doi.org/10.1186/1742-9994-10-45openalex-snapshot

Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species

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A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome

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The Earth Microbiome project: successes and aspirations

inferredcites →https://doi.org/10.1186/s40168-017-0237-yopenalex-snapshot

Normalization and microbial differential abundance strategies depend upon data characteristics

inferredcites →https://doi.org/10.1371/journal.pcbi.1003531openalex-snapshot

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

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Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Benthos

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Next-Generation Sequencing of Aquatic Oligochaetes: Comparison of Experimental Communities

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Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions

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Species Identification in Malaise Trap Samples by DNA Barcoding Based on NGS Technologies and a Scoring Matrix

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R: A Language and Environment for Statistical Computing

inferredcites →https://doi.org/10.3389/fmicb.2018.03010openalex-snapshot

Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences

inferredcites →https://doi.org/10.3389/fmicb.2019.02407openalex-snapshot

Rarefaction, Alpha Diversity, and Statistics

inferredcites →https://doi.org/10.3390/microorganisms7100393openalex-snapshot

The Impact of Bioinformatics Pipelines on Microbiota Studies: Does the Analytical “Microscope” Affect the Biological Interpretation?

inferredcites →https://doi.org/10.4172/jpb.1000381openalex-snapshot

A Comparison of Three Bioinformatics Pipelines for the Analysis of Preterm Gut Microbiota using 16S rRNA Gene Sequencing Data

inferredcites →https://doi.org/10.7717/peerj.2584openalex-snapshot

VSEARCH: a versatile open source tool for metagenomics

What points at this work

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

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Microbial communities in Phragmites australis biofilms from Masurian lakes (Poland) with varying trophic states

inferred← citeshttps://doi.org/10.1109/ic3ina72033.2026.11714834openalex-snapshot

Spatiotemporal Environmental Monitoring of Butterfly Diversity in Indonesia Using Citizen Science Data

inferred← citeshttps://doi.org/10.1111/1365-2745.70346openalex-snapshot

Beech decline reshapes fine root traits, microbial composition and soil carbon–nutrient cycling

inferred← citeshttps://doi.org/10.1111/1462-2920.15950openalex-snapshot

Temporal variations of Microsporidia diversity and discovery of new host–parasite interactions in a lake ecosystem

inferred← citeshttps://doi.org/10.1111/1462-2920.16563openalex-snapshot

Microbes and microplastics: Community shifts along an urban coastal contaminant gradient

inferred← citeshttps://doi.org/10.1111/1462-2920.16664openalex-snapshot

Local environment shapes milk microbiomes while evolutionary history constrains milk macronutrients in captive cercopithecine primates

inferred← citeshttps://doi.org/10.1111/1462-2920.70029openalex-snapshot

Comparative Analysis of Protist Communities in Oilsands Tailings Using Amplicon Sequencing and Metagenomics

inferred← citeshttps://doi.org/10.1111/1462-2920.70256openalex-snapshot

Warming Causes a Decline in Baltic Sea Coastal Sediment Microbial Abundance

inferred← citeshttps://doi.org/10.1111/1755-0998.13730openalex-snapshot

Pitfalls in the statistical analysis of microbiome amplicon sequencing data

inferred← citeshttps://doi.org/10.1111/1758-2229.13145openalex-snapshot

The use of different 16S rRNA gene variable regions in biogeographical studies

inferred← citeshttps://doi.org/10.1111/1758-2229.70332openalex-snapshot

Phosphorus Acquisition Strategies Among Phytoplankton and Free‐Living Bacterial Communities in the Baltic Proper

inferred← citeshttps://doi.org/10.1111/evj.13884openalex-snapshot

Equine sinusitis aetiology is linked to sinus microbiome by amplicon sequencing

inferred← citeshttps://doi.org/10.1111/fwb.70047openalex-snapshot

How Do Environmental and Spatial Factors Influence Beta Diversity and Composition of Abundant and Rare Bacterioplankton Communities in Lakes From the Patagonian Plateaus?

inferred← citeshttps://doi.org/10.1111/gcb.16871openalex-snapshot

Ecosystem type drives soil eukaryotic diversity and composition in Europe

inferred← citeshttps://doi.org/10.1111/gcb.70486openalex-snapshot

Impacts of Climate, Organic Management, and Degradation Status on Soil Biodiversity in Agroecosystems Worldwide

inferred← citeshttps://doi.org/10.1111/mec.16460openalex-snapshot

Best practices in metabarcoding of fungi: From experimental design to results

inferred← citeshttps://doi.org/10.1111/mec.17135openalex-snapshot

Gut microbiota parallelism and divergence associated with colonisation of novel habitats

inferred← citeshttps://doi.org/10.1111/mec.17571openalex-snapshot

Associations Between Gut Microbiota Diversity and a Host Fitness Proxy in a Naturalistic Experiment Using Threespine Stickleback Fish

inferred← citeshttps://doi.org/10.1111/mec.70428openalex-snapshot

Consistent, Scale‐Dependent Differences in the Biogeography of Host‐Associated and Free‐Living Microbiomes Across Systems

inferred← citeshttps://doi.org/10.1111/nph.18954openalex-snapshot

Peat loss collocates with a threshold in plant–mycorrhizal associations in drained peatlands encroached by trees

inferred← citeshttps://doi.org/10.1111/nph.19690openalex-snapshot

Responses of vascular plant fine roots and associated microbial communities to whole‐ecosystem warming and elevated CO2 in northern peatlands

inferred← citeshttps://doi.org/10.1126/sciadv.adj8016openalex-snapshot

Connecting the multiple dimensions of global soil fungal diversity

inferred← citeshttps://doi.org/10.1128/mra.00881-23openalex-snapshot

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert

inferred← citeshttps://doi.org/10.1128/msphere.00313-25openalex-snapshot

Effect of temperature on microbial communities in bentonite for use in engineered barrier systems

inferred← citeshttps://doi.org/10.1128/msphere.00354-23openalex-snapshot

Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses

inferred← citeshttps://doi.org/10.1128/msphere.00355-23openalex-snapshot

Waste not, want not: revisiting the analysis that called into question the practice of rarefaction

inferred← citeshttps://doi.org/10.1128/msystems.00466-25openalex-snapshot

DNA reference reagents isolate biases in microbiome profiling: a global multi-lab study

inferred← citeshttps://doi.org/10.1128/msystems.00575-21openalex-snapshot

Taxon-Specific Shifts in Bacterial and Archaeal Transcription of Dissolved Organic Matter Cycling Genes in a Stratified Fjord

inferred← citeshttps://doi.org/10.1128/msystems.00726-24openalex-snapshot

In-hospital areas with distinct maintenance and staff/patient traffic have specific microbiome profiles, functions, and resistomes

inferred← citeshttps://doi.org/10.1128/msystems.00886-23openalex-snapshot

Seasonality and longer-term development generate temporal dynamics in the Populus microbiome

inferred← citeshttps://doi.org/10.1128/msystems.00930-26openalex-snapshot

Rarefaction is better than robust Aitchison PCA and other compositional data analysis methods at controlling for uneven sequencing effort

inferred← citeshttps://doi.org/10.1128/msystems.01119-23openalex-snapshot

Co-occurrence network analysis reveals the alterations of the skin microbiome and metabolome in adults with mild to moderate atopic dermatitis

inferred← citeshttps://doi.org/10.1128/spectrum.00269-21openalex-snapshot

Structure and Long-Term Stability of the Microbiome in Diverse Diatom Cultures

inferred← citeshttps://doi.org/10.1128/spectrum.02426-22openalex-snapshot

Heavy Metal Pollution Impacts Soil Bacterial Community Structure and Antimicrobial Resistance at the Birmingham 35th Avenue Superfund Site

inferred← citeshttps://doi.org/10.1128/spectrum.02910-23openalex-snapshot

Longitudinal analysis at three oral sites links oral microbiota to clinical outcomes in allogeneic hematopoietic stem-cell transplant

inferred← citeshttps://doi.org/10.11606/t.46.2023.tde-11122023-201308openalex-snapshot

Association of the oral microbiota dynamics with complications and outcomes in allogeneic hematopoietic stem cell transplant

inferred← citeshttps://doi.org/10.1172/jci.insight.205379openalex-snapshot

Multi-omics links microbial dysbiosis, systemic inflammation, and metabolomic disruptions to SNAE risk in treated HIV

inferred← citeshttps://doi.org/10.1177/0958305x231225295openalex-snapshot

The N-shaped environmental Kuznets curve for biodiversity loss: A count data analysis

inferred← citeshttps://doi.org/10.1186/s12862-025-02489-2openalex-snapshot

Phylogenetic influence on gut microbiome diversity within an African herbivore community

inferred← citeshttps://doi.org/10.1186/s12866-025-03981-xopenalex-snapshot

Exploring fecal microbial activity in zoo felids of varying body mass on a similar diet

inferred← citeshttps://doi.org/10.1186/s12866-025-04279-8openalex-snapshot

Seasonal and spatial dynamics of the intestinal microbiome in tropical freshwater fish: insights from Astyanax aeneus and Brycon costaricensis in the Peñas Blancas river basin, Costa Rica

inferred← citeshttps://doi.org/10.1186/s12870-025-06747-9openalex-snapshot

Inoculation of apple plantlets with Rhodococcus pseudokoreensis R79T enhances diversity and modulates the structure of bacterial rhizosphere communities in soil affected by apple replant disease

inferred← citeshttps://doi.org/10.1186/s13195-025-01941-1openalex-snapshot

Dysbiotic shift in the oral microbiota of patients with Alzheimer's disease compared to their healthy life partners—a combinatorial approach and a paired study design

inferred← citeshttps://doi.org/10.1186/s40168-023-01719-3openalex-snapshot

Biogeographic survey of soil bacterial communities across Antarctica

inferred← citeshttps://doi.org/10.1186/s40168-024-01774-4openalex-snapshot

Interindividual differences in aronia juice tolerability linked to gut microbiome and metabolome changes—secondary analysis of a randomized placebo-controlled parallel intervention trial

inferred← citeshttps://doi.org/10.1186/s40168-026-02392-yopenalex-snapshot

Metagenomic insights into the global wild boar faecal microbiome reveal novel taxa and carbohydrate degraders distinguishing wild and domesticated Sus

inferred← citeshttps://doi.org/10.1186/s40793-023-00544-3openalex-snapshot

Phytoplankton ecology in the early years of a boreal oil sands end pit lake

inferred← citeshttps://doi.org/10.1186/s40793-025-00747-wopenalex-snapshot

Close encounters on a micro scale: microplastic sorption of polycyclic aromatic hydrocarbons and their potential effects on associated biofilm communities

inferred← citeshttps://doi.org/10.1186/s40793-025-00762-xopenalex-snapshot

Transient colonization by Priestia megaterium B1L5 alters the structure of the rhizosphere microbiome towards potential plant beneficial bacterial groups in apple plantlets

inferred← citeshttps://doi.org/10.1186/s42523-022-00204-wopenalex-snapshot

Influence of management practice on the microbiota of a critically endangered species: a longitudinal study of kākāpō chick faeces and associated nest litter

inferred← citeshttps://doi.org/10.1186/s42523-023-00226-yopenalex-snapshot

Bacterial topography of the upper and lower respiratory tract in pigs

inferred← citeshttps://doi.org/10.1186/s42523-025-00404-0openalex-snapshot

Host traits and environmental variation shape gut microbiota diversity in wild threespine stickleback

inferred← citeshttps://doi.org/10.1186/s42523-026-00553-wopenalex-snapshot

African carnivore gut bacterial diversity and composition are associated with sample condition but not storage technique

inferred← citeshttps://doi.org/10.1371/journal.pone.0246919openalex-snapshot

Tree rows in temperate agroforestry croplands alter the composition of soil bacterial communities

inferred← citeshttps://doi.org/10.1371/journal.pone.0266698openalex-snapshot

Intrinsic and extrinsic factors influence on an omnivore’s gut microbiome

inferred← citeshttps://doi.org/10.1371/journal.pone.0316101openalex-snapshot

Impacts of host phylogeny, diet, and geography on the gut microbiome of rodents

inferred← citeshttps://doi.org/10.1371/journal.pone.0333639openalex-snapshot

Interspecific variation in gut microbiome diversity across the Etosha National Park herbivore community

inferred← citeshttps://doi.org/10.1371/journal.pone.0335173openalex-snapshot

Cuts or carcasses? Diet form affects fecal microbial and animal fiber fractions in a large carnivore, the Asiatic lion

inferred← citeshttps://doi.org/10.1371/journal.pone.0345317openalex-snapshot

Gut site and sex-specific enrichment of bacterial taxa and predicted metabolic pathways in wild American black bear (Ursus americanus)

inferred← citeshttps://doi.org/10.15446/abc.v31n1.118251openalex-snapshot

Effect of the steroidal plant growth promoter SPGP4 on the microbial diversity of soils cultivated with maize and beans

inferred← citeshttps://doi.org/10.15446/acag.v72n3.112558openalex-snapshot

Exploración del microbioma intestinal de larvas de Zophobas morio (Coleoptera: Tenebrionidae) asociado a una dieta de poliestireno expandido

inferred← citeshttps://doi.org/10.21203/rs.3.rs-4824173/v1openalex-snapshot

Dental biofilm serves as an ecological reservoir of acid-producer pathogens in head and neck cancer patients with radiotherapy-related caries

inferred← citeshttps://doi.org/10.21203/rs.3.rs-7367951/v1openalex-snapshot

Assessment of Insect Communities with Metabarcoding

inferred← citeshttps://doi.org/10.2139/ssrn.5061653openalex-snapshot

Microbial Biomass – Not Diversity – Drives Soil Carbon and Nitrogen Dynamics in Spanish Holm Oak Ecosystems

inferred← citeshttps://doi.org/10.2139/ssrn.5220083openalex-snapshot

Molecular and Morphological Methods Show Contrasting Results on the Effects of Land-Use Intensity on Soil Faunal Diversity

inferred← citeshttps://doi.org/10.31390/gradschool_theses.5607openalex-snapshot

ANALYSIS OF GEOGRAPHIC VARIABILITY OF FECAL MICROBIOMES OF FRATERCULA ARCTICA AND CROSS-COMPARISON OF FECAL MICROBIOMES OF DIFFERENT AVIAN FEEDING TYPES

inferred← citeshttps://doi.org/10.32614/cran.package.coremicrobiomeropenalex-snapshot

CoreMicrobiomeR: Identification of Core Microbiome

inferred← citeshttps://doi.org/10.32614/cran.package.srsopenalex-snapshot

SRS: Scaling with Ranked Subsampling

inferred← citeshttps://doi.org/10.3354/meps14974openalex-snapshot

Pan-Caribbean emergence and persistence of Durusdinium spp. driven by bleaching stress

inferred← citeshttps://doi.org/10.3389/fcimb.2022.862338openalex-snapshot

Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling

inferred← citeshttps://doi.org/10.3389/fcimb.2026.1930709openalex-snapshot

Gut microbial dynamics and antibiotic resistance during rifaximin therapy in severe cirrhosis: a ProPILA-Rifax ancillary study

inferred← citeshttps://doi.org/10.3389/fmicb.2021.659918openalex-snapshot

Phylogeny- and Abundance-Based Metrics Allow for the Consistent Comparison of Core Gut Microbiome Diversity Indices Across Host Species

inferred← citeshttps://doi.org/10.3389/fmicb.2022.1034138openalex-snapshot

Long-term mercury contamination does not affect the microbial gene potential for C and N cycling in soils but enhances detoxification gene abundance

inferred← citeshttps://doi.org/10.3389/fmicb.2022.1096186openalex-snapshot

Distribution and diversity of anaerobic thermophiles and putative anaerobic nickel-dependent carbon monoxide-oxidizing thermophiles in mesothermal soils and sediments

inferred← citeshttps://doi.org/10.3389/fmicb.2022.873281openalex-snapshot

Long-Term Warming of Baltic Sea Coastal Waters Affects Bacterial Communities in Bottom Water and Sediments Differently

inferred← citeshttps://doi.org/10.3389/fmicb.2022.949152openalex-snapshot

Microbiome and pathobiome analyses reveal changes in community structure by foliar pathogen infection in rice

inferred← citeshttps://doi.org/10.3389/fmicb.2023.1130969openalex-snapshot

Diversity and function of soybean rhizosphere microbiome under nature farming

inferred← citeshttps://doi.org/10.3389/fmicb.2023.1203216openalex-snapshot

Microbial diversity in Antarctic Dry Valley soils across an altitudinal gradient

inferred← citeshttps://doi.org/10.3389/fmicb.2023.1231832openalex-snapshot

Grapevines escaping trunk diseases in New Zealand vineyards have a distinct microbiome structure

inferred← citeshttps://doi.org/10.3389/fmicb.2024.1393538openalex-snapshot

Climate change induces shifts in coastal Baltic Sea surface water microorganism stress and photosynthesis gene expression

inferred← citeshttps://doi.org/10.3389/fmicb.2024.1428815openalex-snapshot

Asynchronous patterns in soil bacterial diversity and functional potentials along an alpine altitudinal gradient

inferred← citeshttps://doi.org/10.3389/fmicb.2026.1945124openalex-snapshot

Effects of a microbial treatment of Lactobacillus casei, Saccharomyces cerevisiae, and Lactobacillus plantarum on blueberry fruit quality, rhizosphere soil properties, and bacterial communities

inferred← citeshttps://doi.org/10.3390/app112311473openalex-snapshot

‘SRS’ R Package and ‘q2-srs’ QIIME 2 Plugin: Normalization of Microbiome Data Using Scaling with Ranked Subsampling (SRS)

inferred← citeshttps://doi.org/10.3390/ejihpe15030033openalex-snapshot

Enhancing Emotional Intelligence in Autism Spectrum Disorder Through Intervention: A Systematic Review

inferred← citeshttps://doi.org/10.3390/foods12203827openalex-snapshot

Characterization of the Bacterial Composition of 47 Fermented Foods in Sweden

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