Current Sampling Methods for Gut Microbiota: A Call for More Precise Devices

Tang, Qiang; Jin, Ge; Wang, Gang; Li, Tianyu; Liu, Xiang; Wang, Bangmao; Cao, Hailong

doi:10.3389/fcimb.2020.00151

Cited by 263 publications

(180 citation statements)

References 90 publications

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“…Fresh stool specimens were taken at participants' homes using a sterile spoon or swab and were immediately preserved using chemical DNA stabilizers (OMNIgene Gut) to maintain DNA integrity. Previous analyses have demonstrated the ability for these stabilizers to preserve samples sufficiently at varying temperature conditions over multiple weeks with results comparable with immediate freezing [61][62][63] . Microbial DNA was then isolated from 250 μL of homogenized stool, using an automated protocol and MoBio's Power-Mag ® Soil DNA isolation kit (+ClearMag ® ) microbiome DNA isolation kit on the KingFisher TM Flex instrument.…”

Section: Discussionmentioning

confidence: 99%

Health and disease markers correlate with gut microbiome composition across thousands of people

et al. 2020

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Variation in the human gut microbiome can reflect host lifestyle and behaviors and influence disease biomarker levels in the blood. Understanding the relationships between gut microbes and host phenotypes are critical for understanding wellness and disease. Here, we examine associations between the gut microbiota and ~150 host phenotypic features across ~3,400 individuals. We identify major axes of taxonomic variance in the gut and a putative diversity maximum along the Firmicutes-to-Bacteroidetes axis. Our analyses reveal both known and unknown associations between microbiome composition and host clinical markers and lifestyle factors, including host-microbe associations that are composition-specific. These results suggest potential opportunities for targeted interventions that alter the composition of the microbiome to improve host health. By uncovering the interrelationships between host diet and lifestyle factors, clinical blood markers, and the human gut microbiome at the population-scale, our results serve as a roadmap for future studies on host-microbe interactions and interventions.

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Section: Discussionmentioning

confidence: 99%

Health and disease markers correlate with gut microbiome composition across thousands of people

et al. 2020

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“…Fecal profiling of the microbial populations is investigated most frequently because the sampling of feces is non-invasive and convenient for patients compared to performing an invasive biopsy or collecting luminal content of ilea or colons (130). However, there is increasing evidence that the observed microbial composition in feces is different from the content of mucosal samples of the GI tract (123,(131)(132)(133)(134)(135).…”

Section: The Gut Microbiome and The Intestinal Immune Systemmentioning

confidence: 99%

Resolving the Paradox of Colon Cancer Through the Integration of Genetics, Immunology, and the Microbiota

et al. 2020

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While colorectal cancers (CRC) are paradigmatic tumors invaded by effector memory lymphocytes, the mechanisms accounting for the relative resistance of MSI negative CRC to immunogenic cell death mediated by oxaliplatin and immune checkpoint inhibitors has remained an open conundrum. Here, we propose the viewpoint where its microenvironmental contexture could be explained -at least in part- by macroenvironmental cues constituted by the complex interplay between the epithelial barrier, its microbial ecosystem, and the local immune system. Taken together this dynamic ménage-à-trois offers novel coordinated actors of the humoral and cellular immune responses actionable to restore sensitivity to immune checkpoint inhibition. Solving this paradox involves breaking tolerance to crypt stem cells by inducing the immunogenic apoptosis of ileal cells in the context of an ileal microbiome shifted towards immunogenic bacteria using cytotoxicants. This manoeuver results in the elicitation of a productive Tfh and B cell dialogue in mesenteric lymph nodes culminating in tumor-specific memory CD8+ T cell responses sparing the normal epithelium.

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“…In the case of culture, there are many limitations. First, there is a need for validated techniques for sterile aspiration of small bowel fluid without contamination from oral microbiota [14,15]. Second, the ideal sampling location within the 20-foot length of the small bowel is subject to question [16].…”

Section: Introductionmentioning

confidence: 99%

The duodenal microbiome is altered in small intestinal bacterial overgrowth

et al. 2020

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Small intestinal bacterial overgrowth (SIBO) is highly prevalent and is associated with numerous gastrointestinal disorders, but the microbes involved remain poorly defined. Moreover, existing studies of microbiome alterations in SIBO have utilized stool samples, which are not representative of the entire gastrointestinal tract. Therefore, we aimed to determine and compare the duodenal microbiome composition in SIBO and non-SIBO subjects, using duodenal aspirates from subjects undergoing standard-of-care esophagogastroduodenoscopy without colon preparation. Using the recently-redefined cutoff for SIBO of >10 3 colony forming units per milliliter (CFU/mL), 42 SIBO and 98 non-SIBO subjects were identified. Duodenal samples from SIBO subjects had 4x10 3-fold higher counts than non-SIBO subjects when plated on MacConkey agar (P<0.0001), and 3.8-fold higher counts when plated on blood agar (P<0.0001). Twenty subjects had also undergone lactulose hydrogen breath tests (LHBTs), of whom 7/20 had SIBO. At the 90-minute timepoint, 4/7 SIBO subjects had positive LHBTs (rise in hydrogen (H 2) � 20 ppm above baseline), as compared to 2/13 non-SIBO subjects. 16S ribosomal RNA (rRNA) sequencing revealed that SIBO subjects had 4.31-fold higher relative abundance of Proteobacteria (FDR P<0.0001) and 1.64-fold lower Firmicutes (P<0.0003) than non-SIBO subjects. This increased relative abundance of Proteobacteria correlated with decreased α-diversity in SIBO subjects (Spearman R = 0.4866, P<0.0001) Specific increases in class Gammaproteobacteria correlated with the area-under-the-curve for H 2 for 0-90 mins during LHBT (R = 0.630, P = 0.002). Increases in Gammaproteobacteria resulted primarily from higher relative abundances of the family Enterobacteriaceae (FDR P<0.0001), which correlated with the symptom of bloating (Spearman R = 0.185, 2-tailed P = 0.028). Increases in family Aeromonadaceae correlated with urgency with bowel movement (Spearman R = 0.186, 2-tailed P = 0.028). These results validate the >10 3 CFU/mL cutoff for the definition of SIBO, and also reveal specific overgrowth of Proteobacteria in SIBO vs. non-SIBO subjects, coupled with an altered Proteobacterial profile that correlates with symptom severity. Future research may elucidate host-microbiome interactions underlying these symptoms in SIBO patients.

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Current Sampling Methods for Gut Microbiota: A Call for More Precise Devices

Cited by 263 publications

References 90 publications

Health and disease markers correlate with gut microbiome composition across thousands of people

Health and disease markers correlate with gut microbiome composition across thousands of people

Resolving the Paradox of Colon Cancer Through the Integration of Genetics, Immunology, and the Microbiota

The duodenal microbiome is altered in small intestinal bacterial overgrowth

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