Evidence map›Paper›PMID 34809575›Full record

ArticleBMC microbiology2021

Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts.

Zeni Wu, Autumn G Hullings, Reza Ghanbari, Arash Etemadi, Yunhu Wan, Bin Zhu, Hossein Poustchi, Behnam Bagheri Fahraji, Mohammad Javad Zare Sakhvidi, Jianxin Shi and 4 more

Open access · goldAbstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
2.6field-weighted citation impact, top 9% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed, 34 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors at 6 institutions in 2 countries.

Zeni Wu *Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Autumn G Hullings *Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Reza GhanbariDigestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Science, Tehran, Iran.
Arash EtemadiMetabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Yunhu WanFrederick National Laboratory for Cancer Research/Leidos Biomedical Research Laboratory, Inc., Frederick, MD, USA.
Bin ZhuFrederick National Laboratory for Cancer Research/Leidos Biomedical Research Laboratory, Inc., Frederick, MD, USA.
Hossein PoustchiDigestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Science, Tehran, Iran.
Behnam Bagheri FahrajiDepartment of Epidemiology, School of Public Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
Mohammad Javad Zare SakhvidiDepartment of Occupational Health, School of Public Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
Jianxin ShiBiostatistics Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Rob KnightDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Reza MalekzadehDigestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Science, Tehran, Iran. malek@tums.ac.ir.
Rashmi SinhaMetabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA. sinhar@exchange.nih.gov.
Emily VogtmannMetabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
National Cancer Institute · USUniversity of Tehran · IRShahid Sadoughi University of Medical Sciences and Health Services · IRDepartment of Health and Human Services · USNational Institutes of Health · USUniversity of California, San Diego · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundTo initiate fecal and oral collections in prospective cohort studies for microbial analyses, it is essential to understand how field conditions and geographic differences may impact microbial communities. This study aimed to investigate the impact of fecal and oral sample collection methods and room temperature storage on collection samples for studies of the human microbiota.

resultsWe collected fecal and oral samples from participants in two Iranian cohorts located in rural Yazd (n = 46) and urban Gonbad (n = 38) and investigated room temperature stability over 4 days of fecal (RNAlater and fecal occult blood test [FOBT] cards) and comparability of fecal and oral (OMNIgene ORAL kits and Scope mouthwash) collection methods. We calculated interclass correlation coefficients (ICCs) based on 3 alpha and 4 beta diversity metrics and the relative abundance of 3 phyla. After 4 days at room temperature, fecal stability ICCs and ICCs for Scope mouthwash were generally high for all microbial metrics. Similarly, the fecal comparability ICCs for RNAlater and FOBT cards were high, ranging from 0.63 (95% CI: 0.46, 0.75) for the relative abundance of Firmicutes to 0.93 (95% CI: 0.89, 0.96) for unweighted Unifrac. Comparability ICCs for OMNIgene ORAL and Scope mouthwash were lower than fecal ICCs, ranging from 0.55 (95% CI: 0.36, 0.70) for the Shannon index to 0.79 (95% CI: 0.69, 0.86) for Bray-Curtis. Overall, RNAlater, FOBT cards and Scope mouthwash were stable up to 4 days at room temperature. Samples collected using FOBT cards were generally comparable to RNAlater while the OMNIgene ORAL were less similar to Scope mouthwash.

conclusionsAs microbiome measures for feces samples collected using RNAlater, FOBT cards and oral samples collected using Scope mouthwash were stable over four days at room temperature, these would be most appropriate for microbial analyses in these populations. However, one collection method should be consistently since each method may induce some differences.

Indexed as

MicrobiotaAdultBacteriaCetylpyridiniumDNA, BacterialDrug CombinationsFecesFemaleHumansIranMaleMiddle AgedMouthProspective StudiesQuaternary Ammonium CompoundsRNA, Ribosomal, 16SCetylpyridiniumDNA, BacterialDrug CombinationsQuaternary Ammonium CompoundsRNA, Ribosomal, 16SScope mouthwashComparabilityFecesIranMicrobiomeSalivaStability

Identifiers

PMID34809575
PMCPMC8607576
OpenAlexW3216964789

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.