ArticlemSystems
Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research.
Article in mSystems. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 304 papers, 1 of them a synthesis that pooled it.
What it found
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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
304 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Breast cancer and microbiome: a systematic review highlighting challenges for clinical translation.BMC women's health · 2025Pooled it
- Dive surveys and eDNA detect contrasting macroalgal community composition in Nova Scotia, Canada.Journal of phycology · 2026Article
- Low determinism in community assembly of transient and resident pelagic fungi across climate zones in Scandinavian lakes.mSystems · 2026Article
- Microbial transmission and ecology of human and environmental microbial communities in childcare centers.Research square · 2026Article
- Age-related changes in the gut microbiota of a long-lived seabird suggest divergence from mammalian models.Royal Society open science · 2026Article
- Article
- Distinct benthic and planktonic microbial communities within the stratified water column of the perennially ice-covered Lake Joyce, Antarctica.FEMS microbiology ecology · 2026Article
- Microbial predictors of sustained clinical remission following the Crohn's disease exclusion diet in adults and microbiome shifts toward healthy pediatric controls.Crohn's & colitis 360 · 2026Article
- Population-based characterisation of child and adolescent oral bacterial microbiomes.Microbiome · 2026Article
- Stool microbial composition is associated with recent and future diarrhea and fever events in breastfed Danish infants.mSystems · 2026Observational
- Desiccation, but not shading, substantially shifts the microbial community composition of benthic microbial mats in meltwater ponds near Bratina Island, Antarctica.FEMS microbiology ecology · 2026Article
- Dietary sulfur amino acids enhance anti-tumor immunity in colon cancer via an NKT cell-XCL1-cDC1 circuit.Immunity · 2026Article
- Microbial fingerprinting of marine water masses in an Antarctic and hydrographically complex area.BMC biology · 2026Article
- Microbiota characterization ofMicrobiology resource announcements · 2026Article
- Personalized AZithromycin/metronidAZole + dietary therapy in pediatric Crohn disease: Results of a pilot study.Journal of pediatric gastroenterology and nutrition · 2026Article
- Dietary Vitamin B-9 and B-12 Deficiencies Alter Gut Homeostasis in Sprague-Dawley Rats.The Journal of nutrition · 2026Article
- Pseudomonas plecoglossicida disrupts intestinal homeostasis through manipulation of palmitoleic acid microbial metabolism.NPJ biofilms and microbiomes · 2026Article
- Short-term caloric restriction partially reprograms immune and microbial networks during acute DSS-induced colitis.Genes & nutrition · 2026Article
- Immobilization of a biostimulator microbial consortium on bacterial cellulose and its effect on onion growth, soil nutrient status and the microbial community.World journal of microbiology & biotechnology · 2026Article
- Study of Microbial Communities in the Soda Lake of Isabel Island: Identification of Polyhydroxybutyrate (PHB) Degrading Enzymes.Environmental microbiology reports · 2026Article
244 more citing papers are in PubMed but not listed here.
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
No grant is acknowledged in the PubMed record.
Abstract
Sequence-based approaches to study microbiomes, such as 16S rRNA gene sequencing and metagenomics, are uncovering associations between microbial taxa and a myriad of factors. A drawback of these approaches is that the necessary sequencing library preparation and bioinformatic analyses are complicated and continuously changing, which can be a barrier for researchers new to the field. We present three essential components to conducting a microbiome experiment from start to finish: first, a simplified and step-by-step custom gene sequencing protocol that requires limited lab equipment, is cost-effective, and has been thoroughly tested and utilized on various sample types; second, a series of scripts to integrate various commonly used bioinformatic tools that is available as a standalone installation or as a single downloadable virtual image; and third, a set of bioinformatic workflows and tutorials to provide step-by-step guidance and education for those new to the microbiome field. This resource will provide the foundations for those newly entering the microbiome field and will provide much-needed guidance and best practices to ensure that quality microbiome research is undertaken. All protocols, scripts, workflows, tutorials, and virtual images are freely available through the Microbiome Helper website (https://github.com/mlangill/microbiome_helper/wiki).
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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.