Rectal swabs are a reliable proxy for faecal samples in infant gut microbiota research based on 16S-rRNA sequencing

Reyman, Marta; Houten, Marlies A. van; Arp, Kayleigh; Sanders, Elisabeth A. M.; Bogaert, Debby

doi:10.1038/s41598-019-52549-z

Cited by 39 publications

(39 citation statements)

References 30 publications

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“…Currently, feces or mucosal biopsy specimens are the biological samples most commonly used for standard 16S analysis [ 33 ]. However, as shown in several studies, stool and rectal swab are highly similar, indicating that these sampling methods could be used interchangeably to assess the community structure of the distal GI tract [ 34 , 35 ]. Finally, no data on the molecular detection of SARS-CoV-2 in rectal swabs are presented in our patients.…”

Section: Discussionmentioning

confidence: 99%

16S rRNA gene sequencing of rectal swab in patients affected by COVID-19

et al. 2021

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COronaVIrus Disease-2019 (COVID-19) is a pandemic respiratory infection caused by a new betacoronavirus, the Severe Acute Respiratory Syndrome-CoronaVirus-2 (SARS-CoV-2). Few data are reported on the gut microbiota in COVID-19 patients. 16S rRNA gene sequencing was performed to reveal an altered composition of the gut microbiota in patients with COVID-19 pneumonia admitted in intensive care unit (ICU) (i-COVID19), or in infectious disease wards (w-COVID19) as compared to controls (CTRL). i-COVID19 patients showed a decrease of Chao1 index as compared to CTRL and w-COVID19 patients indicating that patients in ICU displayed a lower microbial richness while no change was observed as for Shannon Index. At the phylum level, an increase of Proteobacteria was detected in w-COVID19 patients as compared to CTRL. A decrease of Fusobacteria and Spirochetes has been found, with the latter decreased in i-COVID19 patients as compared to CTRL. Significant changes in gut microbial communities in patients with COVID-19 pneumonia with different disease severity compared to CTRL have been identified. Our preliminary data may provide valuable information and promising biomarkers for the diagnosis of the disease and, when validated in larger cohort, it could facilitate the stratification of patients based on the microbial signature.

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Section: Discussionmentioning

confidence: 99%

16S rRNA gene sequencing of rectal swab in patients affected by COVID-19

et al. 2021

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“…However, previous studies showed that bacterial communities defined from endorectal swabbing and stool specimens are similar. 37,38 In addition, we used an enrichment step that allows the recovery of Kp isolates even when the amount of starting material is low, which could potentially be the case when using rectal swabs.…”

Section: Discussionmentioning

confidence: 99%

Klebsiella pneumoniae carriage in low-income countries: antimicrobial resistance, genomic diversity and risk factors

et al. 2020

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Background: Klebsiella pneumoniae (hereafter, Kp) is a major public health threat responsible for high levels of multidrug resistant (MDR) human infections. Besides, Kp also causes severe infections in the community, especially in Asia and Africa. Although most Kp infections are caused by endogenous intestinal carriage, little is known about the prevalence and microbiological characteristics of Kp in asymptomatic human carriage, and attached risk factors including environmental sources exposure. Methods: Here, 911 pregnant women from communities in Madagascar, Cambodia, and Senegal were screened for gut colonization by Kp. Characteristics of Kp strains (antimicrobial susceptibility, genomic diversity, virulence, and resistance genes) were defined, and associated risk factors were investigated. Results: Kp carriage rate was 55.9%, and Kp populations were highly heterogeneous (6 phylogroups, 325 sequence types, Simpson index 99.6%). One third of Kp isolates had acquired antimicrobial resistance genes. MDR-Kp (11.7% to 39.7%) and extended spectrum beta-lactamase (ESBL)-producing Kp (0.7% to 14.7%) varied among countries. Isolates with virulence genes were detected (14.5%). Environmental exposure factors including food, animal contacts, or hospitalization of household members were associated with carriage of Kp, antimicrobial resistance and hypervirulence. However, risk factors were countryspecific and Kp subpopulation-specific. Conclusion: This large-scale multicenter study uncovers the huge diversity of Kp in human gut carriage, demonstrates that antimicrobial resistance is widespread in communities of three lowincome countries, and underlines the challenges posed by Kp colonization to the control of antimicrobial resistance.

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“…We used rectal swabs rather than fecal samples as a proxy for the gut microbiome, because rectal swabs could be more reliably collected from all of the individuals in our study. Rectal swabs and fecal samples from the same individual have been shown to be very similar and even interchangeable for inferring gut microbial composition with 16S sequencing [ 101 – 103 ].…”

Section: Methodsmentioning

confidence: 99%

Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques

et al. 2021

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Background An individual’s microbiome changes over the course of its lifetime, especially during infancy, and again in old age. Confounding factors such as diet and healthcare make it difficult to disentangle the interactions between age, health, and microbial changes in humans. Animal models present an excellent opportunity to study age- and sex-linked variation in the microbiome, but captivity is known to influence animal microbial abundance and composition, while studies of free-ranging animals are typically limited to studies of the fecal microbiome using samples collected non-invasively. Here, we analyze a large dataset of oral, rectal, and genital swabs collected from 105 free-ranging rhesus macaques (Macaca mulatta, aged 1 month-26 years), comprising one entire social group, from the island of Cayo Santiago, Puerto Rico. We sequenced 16S V4 rRNA amplicons for all samples. Results Infant gut microbial communities had significantly higher relative abundances of Bifidobacterium and Bacteroides and lower abundances of Ruminococcus, Fibrobacter, and Treponema compared to older age groups, consistent with a diet high in milk rather than solid foods. The genital microbiome varied widely between males and females in beta-diversity, taxonomic composition, and predicted functional profiles. Interestingly, only penile, but not vaginal, microbiomes exhibited distinct age-related changes in microbial beta-diversity, taxonomic composition, and predicted functions. Oral microbiome composition was associated with age, and was most distinctive between infants and other age classes. Conclusions Across all three body regions, with notable exceptions in the penile microbiome, while infants were distinctly different from other age groups, microbiomes of adults were relatively invariant, even in advanced age. While vaginal microbiomes were exceptionally stable, penile microbiomes were quite variable, especially at the onset of reproductive age. Relative invariance among adults, including elderly individuals, is contrary to findings in humans and mice. We discuss potential explanations for this observation, including that age-related microbiome variation seen in humans may be related to changes in diet and lifestyle.

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Rectal swabs are a reliable proxy for faecal samples in infant gut microbiota research based on 16S-rRNA sequencing

Cited by 39 publications

References 30 publications

16S rRNA gene sequencing of rectal swab in patients affected by COVID-19

16S rRNA gene sequencing of rectal swab in patients affected by COVID-19

Klebsiella pneumoniae carriage in low-income countries: antimicrobial resistance, genomic diversity and risk factors

Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques

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