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A comprehensive automated pipeline for human microbiome sampling, 16S rRNA gene sequencing and bioinformatics processing

https://doi.org/10.1101/286526
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What this work says

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

inferredcites →https://doi.org/10.1002/bies.201400075openalex-snapshot
Altered brain‐gut axis in autism: Comorbidity or causative mechanisms?
inferredcites →https://doi.org/10.1016/b978-0-12-800100-4.00003-9openalex-snapshot
The Role of Short-Chain Fatty Acids in Health and Disease
inferredcites →https://doi.org/10.1016/j.ajog.2014.12.041openalex-snapshot
The preterm placental microbiome varies in association with excess maternal gestational weight gain
inferredcites →https://doi.org/10.1016/j.annepidem.2016.03.009openalex-snapshot
Challenges for case-control studies with microbiome data
inferredcites →https://doi.org/10.1016/j.bbi.2013.12.015openalex-snapshot
The role of microbiome in central nervous system disorders
inferredcites →https://doi.org/10.1016/j.chom.2017.03.010openalex-snapshot
The Gut Microbiome: Connecting Spatial Organization to Function
inferredcites →https://doi.org/10.1016/j.clim.2015.05.014openalex-snapshot
Immune–microbiota interactions in health and disease
inferredcites →https://doi.org/10.1016/j.cll.2014.08.006openalex-snapshot
The Changing Landscape of the Vaginal Microbiome
inferredcites →https://doi.org/10.1016/s0140-6736(02)07500-1openalex-snapshot
Cohort studies: marching towards outcomes
inferredcites →https://doi.org/10.1016/s0140-6736(02)07605-5openalex-snapshot
Case-control studies: research in reverse
inferredcites →https://doi.org/10.1016/s0378-1097(02)00895-9openalex-snapshot
A PCR-based method for identification of lactobacilli at the genus level
inferredcites →https://doi.org/10.1038/ismej.2014.195openalex-snapshot
Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences
inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot
DADA2: High-resolution sample inference from Illumina amplicon data
inferredcites →https://doi.org/10.1053/j.gastro.2014.02.009openalex-snapshot
The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead
inferredcites →https://doi.org/10.1093/bioinformatics/btq461openalex-snapshot
Search and clustering orders of magnitude faster than BLAST
inferredcites →https://doi.org/10.1093/bioinformatics/bts252openalex-snapshot
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
inferredcites →https://doi.org/10.1093/nar/gks808openalex-snapshot
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
inferredcites →https://doi.org/10.1093/nar/gkt1244openalex-snapshot
Ribosomal Database Project: data and tools for high throughput rRNA analysis
inferredcites →https://doi.org/10.1093/nar/gkt241openalex-snapshot
Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units
inferredcites →https://doi.org/10.1093/nar/gku1341openalex-snapshot
Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform
inferredcites →https://doi.org/10.1096/fj.12-220806openalex-snapshot
The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters
inferredcites →https://doi.org/10.1101/081257openalex-snapshot
UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing
inferredcites →https://doi.org/10.1111/1462-2920.12610openalex-snapshot
Limits to robustness and reproducibility in the demarcation of operational taxonomic units
inferredcites →https://doi.org/10.1111/cei.12321openalex-snapshot
The intestinal microbiome in type 1 diabetes
inferredcites →https://doi.org/10.1126/scitranslmed.3003605openalex-snapshot
Temporal Dynamics of the Human Vaginal Microbiota
inferredcites →https://doi.org/10.1128/aem.01403-14openalex-snapshot
DegePrime, a Program for Degenerate Primer Design for Broad-Taxonomic-Range PCR in Microbial Ecology Studies
inferredcites →https://doi.org/10.1128/aem.64.10.3724-3730.1998openalex-snapshot
Bias in Template-to-Product Ratios in Multitemplate PCR
inferredcites →https://doi.org/10.1186/s40168-015-0081-xopenalex-snapshot
Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity
inferredcites →https://doi.org/10.1186/s40168-015-0087-4openalex-snapshot
16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice
inferredcites →https://doi.org/10.1371/journal.pcbi.1003594openalex-snapshot
Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale
inferredcites →https://doi.org/10.1371/journal.pone.0049334openalex-snapshot
CREST – Classification Resources for Environmental Sequence Tags
inferredcites →https://doi.org/10.1371/journal.pone.0151990openalex-snapshot
Body Site Is a More Determinant Factor than Human Population Diversity in the Healthy Skin Microbiome
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.2337/dc14-0769openalex-snapshot
Insights Into the Role of the Microbiome in Obesity and Type 2 Diabetes
inferredcites →https://doi.org/10.3389/fmicb.2016.00679openalex-snapshot
Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea
inferredcites →https://doi.org/10.3389/fmicb.2017.00738openalex-snapshot
Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life
inferredcites →https://doi.org/10.3389/fmicb.2017.01561openalex-snapshot
Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing
inferredcites →https://doi.org/10.7717/peerj.1487openalex-snapshot
De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

What points at this work

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

inferred← citeshttps://doi.org/10.1002/ijc.32037openalex-snapshot
Colitis‐induced colorectal cancer and intestinal epithelial estrogen receptor beta impact gut microbiota diversity
inferred← citeshttps://doi.org/10.1016/j.isci.2025.112918openalex-snapshot
Immune development differs between preterm newborns fed mothers’ own milk and donor milk
inferred← citeshttps://doi.org/10.1016/j.jdsr.2022.05.002openalex-snapshot
Functional biomes beyond the bacteriome in the oral ecosystem
inferred← citeshttps://doi.org/10.1038/s41390-026-05290-zopenalex-snapshot
Supplementation with long-chain polyunsaturated fatty acids to extremely preterm infants associates with development of the intestinal microbiota
inferred← citeshttps://doi.org/10.1038/s41522-020-00146-8openalex-snapshot
Vaginal microbiota and human papillomavirus infection among young Swedish women
inferred← citeshttps://doi.org/10.1038/s41598-019-53599-zopenalex-snapshot
Effects of sampling strategy and DNA extraction on human skin microbiome investigations
inferred← citeshttps://doi.org/10.1038/s41598-020-57468-yopenalex-snapshot
Evidence of altered mucosa-associated and fecal microbiota composition in patients with Irritable Bowel Syndrome
inferred← citeshttps://doi.org/10.1080/19490976.2024.2416912openalex-snapshot
Fecal samples and rectal swabs adequately reflect the human colonic luminal microbiota
inferred← citeshttps://doi.org/10.1089/jmf.2021.0195openalex-snapshot
Effects of Consuming Fermented Fish (Surströmming) on the Fecal Microflora in Healthy Individuals
inferred← citeshttps://doi.org/10.1101/544502openalex-snapshot
Isolates from colonic spirochaetosis in humans show high genomic divergence and carry potential pathogenic features but are not detected by 16S amplicon sequencing using standard primers for the human microbiota
inferred← citeshttps://doi.org/10.1128/msystems.00119-18openalex-snapshot
Bacteriophages Synergize with the Gut Microbial Community To Combat Salmonella
inferred← citeshttps://doi.org/10.1128/msystems.01302-20openalex-snapshot
Tonsillar Microbiota: a Cross-Sectional Study of Patients with Chronic Tonsillitis or Tonsillar Hypertrophy
inferred← citeshttps://doi.org/10.1128/spectrum.05066-22openalex-snapshot
The Local Tumor Microbiome Is Associated with Survival in Late-Stage Colorectal Cancer Patients
inferred← citeshttps://doi.org/10.1136/bmjopen-2022-065825openalex-snapshot
Cohort profile: the Swedish Maternal Microbiome project (SweMaMi) – assessing the dynamic associations between the microbiome and maternal and neonatal adverse events
inferred← citeshttps://doi.org/10.1136/gutjnl-2019-318717openalex-snapshot
No distinct microbiome signature of irritable bowel syndrome found in a Swedish random population
inferred← citeshttps://doi.org/10.1186/s12969-021-00542-0openalex-snapshot
Fecal microbiota in children with juvenile idiopathic arthritis treated with methotrexate or etanercept
inferred← citeshttps://doi.org/10.1186/s13099-022-00518-9openalex-snapshot
Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort
inferred← citeshttps://doi.org/10.15698/mic2019.03.672openalex-snapshot
Simultaneous profiling of sexually transmitted bacterial pathogens, microbiome, and concordant host response in cervical samples using whole transcriptome sequencing analysis
inferred← citeshttps://doi.org/10.3389/fcimb.2019.00059openalex-snapshot
Changes in Cervical Human Papillomavirus (HPV) Prevalence at a Youth Clinic in Stockholm, Sweden, a Decade After the Introduction of the HPV Vaccine
inferred← citeshttps://doi.org/10.3389/fnut.2022.827182openalex-snapshot
Probiotic Mixture Containing Lactobacillus helveticus, Bifidobacterium longum and Lactiplantibacillus plantarum Affects Brain Responses Toward an Emotional Task in Healthy Subjects: A Randomized Clinical Trial
inferred← citeshttps://doi.org/10.3390/ijms21228634openalex-snapshot
Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes
inferred← citeshttps://doi.org/10.3390/microorganisms8040483openalex-snapshot
Beyond Just Bacteria: Functional Biomes in the Gut Ecosystem Including Virome, Mycobiome, Archaeome and Helminths
inferred← citeshttps://doi.org/10.3899/jrheum.200551openalex-snapshot
Fecal Microbiota in Untreated Children With Juvenile Idiopathic Arthritis: A Comparison With Healthy Children and Healthy Siblings
inferred← citeshttps://doi.org/10.6084/m9.figshare.26555174openalex-snapshot
Additional file 1 of Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort
inferred← citeshttps://doi.org/10.6084/m9.figshare.26555177openalex-snapshot
Additional file 2 of Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort
inferred← citeshttps://doi.org/10.6084/m9.figshare.26555180openalex-snapshot
Additional file 3 of Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort
inferred← citeshttps://doi.org/10.6084/m9.figshare.26555183openalex-snapshot
Additional file 4 of Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort
inferred← citeshttps://doi.org/10.6084/m9.figshare.26555186openalex-snapshot
Additional file 5 of Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort
inferred← citeshttps://doi.org/10.6084/m9.figshare.26555189openalex-snapshot
Additional file 6 of Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort
inferred← citeshttps://doi.org/10.6084/m9.figshare.26555192openalex-snapshot
Additional file 7 of Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort
inferred← citeshttps://doi.org/10.6084/m9.figshare.26555195openalex-snapshot
Additional file 8 of Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort
inferred← citeshttps://doi.org/10.6084/m9.figshare.26555198openalex-snapshot
Additional file 9 of Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort
inferred← citeshttps://doi.org/10.6084/m9.figshare.26555201openalex-snapshot
Additional file 10 of Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort
inferred← citeshttps://doi.org/10.6084/m9.figshare.26555204openalex-snapshot
Additional file 11 of Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort
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