ArticleFrontiers in microbiology2019
Among Live and Dead Bacteria, the Optimization of Sample Collection and Processing Remains Essential in Recovering Gut Microbiota Components.
Article in Frontiers in microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It has been retracted, and should not be counted. Cited by 45 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
45 citing papers in PubMed, 1 synthesis or guideline pooled it, 69 citations in OpenAlex.
- Pooled it
- Towards a Standard Protocol for Fecal Microbiota Transplantation in Irritable Bowel Syndrome.Journal of neurogastroenterology and motility · 2026Review
- The effects of filtration and centrifugation on the gut microbiota in fecal microbiota transplantation preparation.Frontiers in microbiology · 2026Article
- Effects of sweet chestnut (Frontiers in veterinary science · 2026Article
- Optimized Protocol for the Collection, Cryopreservation, and In Vitro Cultivation of Human Gut Microbiota for Toxicomicrobiomics Applications.Bio-protocol · 2025Article
- Do we need a standardized 16S rRNA gene amplicon sequencing analysis protocol for poultry microbiota research?Poultry science · 2025Review
- Recent Insights into the Evolving Role of the Gut Microbiome in Critical Care.Critical care clinics · 2025Review
- A decade of advances in human gut microbiome-derived biotherapeutics.Nature microbiology · 2025Review
- Retraction: Deciphering the urinary microbiota repertoire by culturomics reveals mostly anaerobic bacteria from the gut.Frontiers in microbiology · 2025Article
- Laboratory preparation methods for human-derived fecal microbial suspensions for fecal microbiota transplantation: a review and standardization perspectives.Frontiers in microbiology · 2025Review
- Article
- Retraction: Tobacco smoking affects the salivary gram-positive bacterial population.Frontiers in public health · 2025Article
- Diversity of bacteria within the human gut and its contribution to the functional unity of holobionts.NPJ biofilms and microbiomes · 2024Review
- Evaluating Bacterial Viability in Faecal Microbiota Transplantation: A Comparative Analysis of In Vitro Cultivation and Membrane Integrity Methods.Journal of clinical laboratory analysis · 2024Article
- Article
- Developing the Common Marmoset as a Translational Geroscience Model to Study the Microbiome and Healthy Aging.Microorganisms · 2024Review
- Vitamin B12 analogues from gut microbes and diet differentially impact commensal propionate producers of the human gut.Frontiers in nutrition · 2024Article
- Novel role of folate (vitamin B9) released by fermenting bacteria under Human Intestine like environment.Scientific reports · 2023Article
- Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples.Nature methods · 2023Article
- The Effects of Milk Replacer Supplemented withVeterinary sciences · 2023Article
Corrections and comments
- Retraction · 2025-07-07Investigation by Journal/Publisher · Lack of IRB/IACUC Approval and/or Compliance · Objections by Author(s) ·
- Retracted
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The human gut microbiota plays an important role in human health. Accessing and culturing the gut microbes remains critical in microbiology. The culturomics approach, combined with sequencing strategies, provides new insights in the study of gut microbiota components. However, we are still far from having described all the microbes. Many factors are involved in recovering as much bacteria as possible. One of the most important factors is sample preparation and conservation. The aim of the present work was to evaluate three different types of stool sample conditioning by mainly studying the effect of atmospheric oxygen on bacterial viability and culturability. Quantitative analysis of fecal samples from eight different healthy individuals was carried out using a culture-independent method (flow cytometry) and a culture-dependent method (plating technique). We found that the cultured bacteria reached a 50% yield when the samples were exposed to oxygen for 120 min without any protectant medium, while the percentage of culturability increased to 67% in the presence of antioxidants. More importantly, when samples were exposed to oxygen for less than 2 min, combined with the work under the anaerobic chamber, no discordance was found between the two counting techniques and the culturability increased to 87%. Our study confirmed the importance of sample conditioning to preserve the bacterial viability in samples, especially for oxygen-sensitive intestinal bacteria.
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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.