Rectal Swabs for Analysis of the Intestinal Microbiota

Budding, Andries E.; Grasman, Matthijs E.; Eck, Anat; Bogaards, Johannes A.; Vandenbroucke-Grauls, Christina M. J. E.; Bodegraven, Adriaan A. van; Savelkoul, Paul H. M.

doi:10.1371/journal.pone.0101344

Cited by 127 publications

(141 citation statements)

References 16 publications

(25 reference statements)

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“…Outcome of comparison between VOCs deriving from rectal swabs and fecal samples in the present study differ from a similar experiment on microbiota profiling [46]. Microbiota composition on fecal samples and rectal swabs profiles seemed to be comparable [46], whereas we observed significant differences in VOC profiles between the two niches.…”

Section: Discussioncontrasting

confidence: 85%

“…Microbiota composition on fecal samples and rectal swabs profiles seemed to be comparable [46], whereas we observed significant differences in VOC profiles between the two niches. Possibly, VOCs deriving from the swab itself may interact with the eNose sensors, influencing the measured VOC profile, thereby explaining the observed differences [47].…”

Section: Discussionmentioning

confidence: 66%

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Effects of Sampling Conditions and Environmental Factors on Fecal Volatile Organic Compound Analysis by an Electronic Nose Device

Berkhout

Benninga

Stein

et al. 2016

Sensors

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Prior to implementation of volatile organic compound (VOC) analysis in clinical practice, substantial challenges, including methodological, biological and analytical difficulties are faced. The aim of this study was to evaluate the influence of several sampling conditions and environmental factors on fecal VOC profiles, analyzed by an electronic nose (eNose). Effects of fecal sample mass, water content, duration of storage at room temperature, fecal sample temperature, number of freeze–thaw cycles and effect of sampling method (rectal swabs vs. fecal samples) on VOC profiles were assessed by analysis of totally 725 fecal samples by means of an eNose (Cyranose320®). Furthermore, fecal VOC profiles of totally 1285 fecal samples from 71 infants born at three different hospitals were compared to assess the influence of center of origin on VOC outcome. We observed that all analyzed variables significantly influenced fecal VOC composition. It was feasible to capture a VOC profile using rectal swabs, although this differed significantly from fecal VOC profiles of similar subjects. In addition, 1285 fecal VOC-profiles could significantly be discriminated based on center of birth. In conclusion, standardization of methodology is necessary before fecal VOC analysis can live up to its potential as diagnostic tool in clinical practice.

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Section: Discussioncontrasting

confidence: 85%

Section: Discussionmentioning

confidence: 66%

Effects of Sampling Conditions and Environmental Factors on Fecal Volatile Organic Compound Analysis by an Electronic Nose Device

Berkhout

Benninga

Stein

et al. 2016

Sensors

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“…We analyzed 16S rRNA gene pyrosequencing data from 71 tongue swabs, 50 skin swabs, and 77 GI samples (37 fecal samples, 40 rectal swabs) collected from 37 patients over 39 pediatric ICU (PICU) admissions [27]. Samples with below 200 reads following clustering were removed from downstream analysis.…”

Section: Resultsmentioning

confidence: 99%

Disruption of the microbiota across multiple body sites in critically ill children

et al. 2016

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BackgroundDespite intense interest in the links between the microbiome and human health, little has been written about dysbiosis among ICU patients. We characterized microbial diversity in samples from 37 children in a pediatric ICU (PICU). Standard measures of alpha and beta diversity were calculated, and results were compared with data from adult and pediatric reference datasets.ResultsBacterial 16S rRNA gene sequences were analyzed from 71 total tongue swabs, 50 skin swabs, and 77 stool samples or rectal swabs. The mean age of the PICU patients was 2.9 years (range 1–9 years), and many were chronically ill children that had previously been hospitalized in the PICU. Relative to healthy adults and children, alpha diversity was decreased in PICU GI and tongue but not skin samples. Measures of beta diversity indicated differences in community membership at each body site between PICU, adult, and pediatric groups. Taxonomic alterations in the PICU included enrichment of gut pathogens such as Enterococcus and Staphylococcus at multiple body sites and depletion of commensals such as Faecalibacterium and Ruminococcus from GI samples. Alpha and beta diversity were unstable over time in patients followed longitudinally. We observed the frequent presence of “dominant” pathogens in PICU samples at relative abundance >50%. PICU samples were characterized by loss of site specificity, with individual taxa commonly present simultaneously at three sample sites on a single individual. Some pathogens identified by culture of tracheal aspirates were commonly observed in skin samples from the same patient.ConclusionsWe conclude that the microbiota in critically ill children differs sharply from the microbiota of healthy children and adults. Acknowledgement of dysbiosis associated with critical illness could provide opportunities to modulate the microbiota with precision and thereby improve patient outcomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-016-0211-0) contains supplementary material, which is available to authorized users.

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“…In studies with other animal species, the microbiota in one or more parts of the gastrointestinal tract have been investigated through, for example, excreta, fecal or fistula samples (Harmoinen et al, 2001;De Filippo et al, 2010;Budding et al, 2014). In rabbits, bacteria in the caecotrophes were shown by denaturing gradient gel electrophoresis to be 71% similar to cecal microbiota (Rodriguez-Romero et al, 2009).…”

Section: Introductionmentioning

confidence: 99%