scholarly journals Accelerating Gut Microbiome Research with Robust Sample Collection

2021 ◽  
Author(s):  
Zoe J. Zreloff ◽  
Danielle Lange ◽  
Suzanne D. Vernon ◽  
Martha R. Carlin ◽  
Raul de Jesus Cano
Keyword(s):  
Microbial Diversity ◽  
Stool Sample ◽  
Gut Microbiome ◽  
Critical Role ◽  
Sample Collection ◽  
Fresh Sample ◽  
Microbiome Composition ◽  
Microbiome Profile ◽  
Health And Disease ◽  
Diversity Profiles

Background. Inferior quality of biological material compromises data, slows discovery, and wastes research funds. The gut microbiome plays a critical role in human health and disease, yet little attention has been given to optimizing collection and processing methods of human stool. Methods. We collected the entire bowel movement from 2 healthy volunteers: one to examine stool sample heterogeneity and one to test stool sample handling parameters. Sequencing and bi-oinformatic analyses were used to examine the microbiome composition. Results. The microbiome profile varied depending on where the subsample was obtained from the stool. The exterior cortex of the stool was rich in specific phyla and deficient in others while the interior core of the stool revealed opposite microbiome profiles. Sample processing also re-sulted in varying microbiome profiles. Homogenization and stabilization at 4°C gave superior microbial diversity profiles compared to the fresh or frozen subsamples of the same stool sample. Bacterial proliferation continued in the fresh subsample when processed at ambient temperature. Bacteroidetes proliferated and Firmicutes diminished during the 30-minute processing of fresh sample. The frozen sample had good overall diversity but Proteobacteria diminished likely be-cause of the freeze/thaw. Conclusions. The microbiome profile is specific to the section of the stool being sampled. Stool sample collection, homogenization, and stabilization at 4°C for 24 hours provides a “neat”, high-quality sample of sufficient quantity that can be banked into aliquots with nearly identical microbial diversity profiles. This collection pipeline is essential to accelerate our understanding of the gut microbiome in health and disease.

scholarly journals Accelerating Gut Microbiome Research with Robust Sample Collection

2020 ◽  
Author(s):  
Zoe J. Zreloff ◽  
Danielle Lange ◽  
Suzanne D. Vernon ◽  
Martha R. Carlin ◽  
Raul de Jesus Cano
Keyword(s):  
Microbial Diversity ◽  
Stool Sample ◽  
Gut Microbiome ◽  
Critical Role ◽  
Sample Collection ◽  
Fresh Sample ◽  
Microbiome Composition ◽  
Microbiome Profile ◽  
Health And Disease ◽  
Diversity Profiles

Abstract Background. Inferior quality of biological material compromises data, slows discovery, and wastes research funds. The gut microbiome plays a critical role in human health and disease, yet little attention has been given to optimizing collection and processing methods of human stool. Methods. We collected the entire bowel movement from 2 healthy volunteers: one to examine stool sample heterogeneity and one to test stool sample handling parameters. Sequencing and bioinformatic analyses were used to examine the microbiome composition. Results. The microbiome profile varied depending on where the subsample was obtained from the stool. The exterior cortex of the stool was rich in specific phyla and deficient in others while the interior core of the stool revealed opposite microbiome profiles. Sample processing also resulted in varying microbiome profiles. Homogenization and stabilization at 4°C gave superior microbial diversity profiles compared to the fresh or frozen subsamples of the same stool sample. Bacterial proliferation continued in the fresh subsample when processed at ambient temperature. Bacteroidetes proliferated and Firmicutes diminished during the 30-minute processing of fresh sample. The frozen sample had good overall diversity but Proteobacteria diminished likely because of the freeze/thaw. Conclusions. The microbiome profile is specific to the section of the stool being sampled. Stool sample collection, homogenization, and stabilization at 4°C for 24 hours provides a “neat”, high-quality sample of sufficient quantity that can be banked into aliquots with nearly identical microbial diversity profiles. This collection pipeline is essential to accelerate our understanding of the gut microbiome in health and disease

scholarly journals The sugar composition of the fibre in selected plant foods modulates weaning infants’ gut microbiome composition and fermentation metabolites in vitro

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shanthi G. Parkar ◽  
Jovyn K. T. Frost ◽  
Doug Rosendale ◽  
Halina M. Stoklosinski ◽  
Carel M. H. Jobsis ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Gas Production ◽  
Sugar Composition ◽  
Microbiome Composition ◽  
Fibre Concentration ◽  
Microbiome Profile ◽  
Infant Gut Microbiome ◽  
Immune Health ◽  
Faecal Bacteria

AbstractEight plant-based foods: oat flour and pureed apple, blackcurrant, carrot, gold- and green-fleshed kiwifruit, pumpkin, sweetcorn, were pre-digested and fermented with pooled inocula of weaning infants’ faecal bacteria in an in vitro hindgut model. Inulin and water were included as controls. The pre-digested foods were analysed for digestion-resistant fibre-derived sugar composition and standardised to the same total fibre concentration prior to fermentation. The food-microbiome interactions were then characterised by measuring microbial acid and gas metabolites, microbial glycosidase activity and determining microbiome structure. At the physiologically relevant time of 10 h of fermentation, the xyloglucan-rich apple and blackcurrant favoured a propiogenic metabolic and microbiome profile with no measurable gas production. Glucose-rich, xyloglucan-poor pumpkin caused the greatest increases in lactate and acetate (indicative of high fermentability) commensurate with increased bifidobacteria. Glucose-rich, xyloglucan-poor oats and sweetcorn, and arabinogalactan-rich carrot also increased lactate and acetate, and were more stimulatory of clostridial families, which are indicative of increased microbial diversity and gut and immune health. Inulin favoured a probiotic-driven consortium, while water supported a proteolytic microbiome. This study shows that the fibre-derived sugar composition of complementary foods may shape infant gut microbiome structure and metabolic activity, at least in vitro.

scholarly journals The Microbiome and p-Inulin in Hemodialysis: A Feasibility Study

Kidney360 ◽  
2021 ◽  
pp. 10.34067/KID.0006132020
Author(s):  
Dominic S. Raj ◽  
Michael B. Sohn ◽  
David M. Charytan ◽  
Jonathan Himmelfarb ◽  
T. Alp Ikizler ◽  
...  
Keyword(s):  
Feasibility Study ◽  
Gut Microbiome ◽  
Post Treatment ◽  
Intestinal Microbiome ◽  
Maintenance Hemodialysis ◽  
Sample Collection ◽  
Microbiome Composition ◽  
Stool Samples ◽  
Pre Treatment ◽  
End Stage

Background: The intestinal microbiome is an appealing target for interventions in end-stage kidney disease (ESKD) because of its likely contribution to uremic toxicity. Before conducting clinical trials of microbiome-altering treatments, it is necessary to understand the within-person and between-person variability in the composition and function of the gut microbiome in patients with ESKD. Methods: Multi-center, non-randomized, crossover feasibility study of maintenance hemodialysis patients consisting of 3 phases: pre-treatment (8 weeks), treatment during which the prebiotic, p-inulin (Prebiotin®), was administered at a dose of 8 gm twice daily (12 weeks), and post-treatment (8 weeks). Stool samples were collected 1-2 times/week and blood was collected weekly for 28 weeks. The gut microbiome was characterized using 16S ribosomal RNA sequencing and metabolomic profiling. Results: Eleven of the 13 participants completed the 28-week study. Inter-participant variability was greater than intra-participant variability for microbiome composition (p<0.001 by UniFrac distances), and metabolomic composition (p<0.001 by Euclidean distances). p-Inulin was well-tolerated by 12 of 13 participants. Adherence to the frequent sample collection and self-aliquoting of stool samples were both 96%. A change in the microbiome composition from pre-treatment to post-treatment was evident by the overall shifts in weighted UniFrac distances (p=0.004) and a progressive decrease in prevalence of high intra-class correlations indicating an increase in intra-participant microbiome diversity during and after p-inulin treatment. An effect of p-inulin on the metabolomic profile was not evident. Conclusions: The intra-participant stability of the gut microbiome under no-treatment conditions, the tolerability of p-inulin, the signals of increased diversity of the microbiome with p-inulin treatment, and the willingness of participants to provide stool samples all support the feasibility of a larger trial to investigate interventions targeting the gut microbiome in patients with ESKD. Whether p-inulin has sufficient efficacy as an intervention requires evaluation in larger studies.

scholarly journals Fecal genomic DNA extraction method impacts outcome of MinION based metagenome profile of tuberculosis patients.

2021 ◽  
Author(s):  
Sukanya Sahu ◽  
Sandeep Kaushik ◽  
Bidhan Goswami ◽  
Arunabha Dasgupta ◽  
Hritusree Guha ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Dna Extraction ◽  
Gut Microbiome ◽  
Extraction Method ◽  
Critical Role ◽  
Isoamyl Alcohol ◽  
Fecal Samples ◽  
Sequencing Platform ◽  
Dna Extraction Method ◽  
Generation Sequencing

In the present era, emergence of next generation sequencing approaches has revolutionized the field of gut microbiome study. However, the adopted DNA extraction step used in metagenomics experiments and its efficiency may play a critical role in their reproducibility and outcome. In this study, fecal samples from active and non-tuberculosis subjects (ATB/NTB, n=7) were used. Fecal samples of a subgroup of these subjects were subjected to Mechanical enzymatic lysis (MEL) and Phenol: Chloroform: Isoamyl Alcohol (PCIA) methods of DNA extraction and a third-generation sequencing platform i.e., MinION was employed for microbiome profiling. Findings of this study demonstrated that DNA extraction method significantly impacts the DNA yield and microbial diversity. Irrespective of the adopted method of DNA extraction, ATB patients showed altered microbial diversity compared to NTB controls. Also, the fecal microbial diversity details are better captured in samples processed by MEL method and may be suitable to be adopted for high-throughput gut microbiome studies.

scholarly journals Dynamic Changes in Fecal Microbial Communities of Neonatal Dairy Calves by Aging and Diarrhea

Animals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 1113
Author(s):  
Eun-Tae Kim ◽  
Sang-Jin Lee ◽  
Tae-Yong Kim ◽  
Hyo-Gun Lee ◽  
Rahman M. Atikur ◽  
...  
Keyword(s):  
Health Status ◽  
Gut Microbiota ◽  
Growth Performance ◽  
Gut Microbiome ◽  
Environmental Changes ◽  
Critical Role ◽  
Dairy Calves ◽  
Sphingolipid Metabolism ◽  
Fecal Microbiome ◽  
Microbiome Composition

Microbiota plays a critical role in the overall growth performance and health status of dairy cows, especially during their early life. Several studies have reported that fecal microbiome of neonatal calves is shifted by various factors such as diarrhea, antibiotic treatment, or environmental changes. Despite the importance of gut microbiome, a lack of knowledge regarding the composition and functions of microbiota impedes the development of new strategies for improving growth performance and disease resistance during the neonatal calf period. In this study, we utilized next-generation sequencing to monitor the time-dependent dynamics of the gut microbiota of dairy calves before weaning (1–8 weeks of age) and further investigated the microbiome changes caused by diarrhea. Metagenomic analysis revealed that continuous changes, including increasing gut microbiome diversity, occurred from 1 to 5 weeks of age. However, the composition and diversity of the fecal microbiome did not change after 6 weeks of age. The most prominent changes in the fecal microbiome composition caused by aging at family level were a decreased abundance of Bacteroidaceae and Enterobacteriaceae and an increased abundance of Prevotellaceae. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis indicated that the abundance of microbial genes associated with various metabolic pathways changed with aging. All calves with diarrhea symptoms showed drastic microbiome changes and about a week later returned to the microbiome of pre-diarrheal stage regardless of age. At phylum level, abundance of Bacteroidetes was decreased (p = 0.09) and that of Proteobacteria increased (p = 0.07) during diarrhea. PICRUSt analysis indicated that microbial metabolism-related genes, such as starch and sucrose metabolism, sphingolipid metabolism, alanine aspartate, and glutamate metabolism were significantly altered in diarrheal calves. Together, these results highlight the important implications of gut microbiota in gut metabolism and health status of neonatal dairy calves.

scholarly journals A Pilot Correlation Study of Gut Microbiome between Children with Henoch-Schönlein Purpura and their Mothers

2020 ◽  
Author(s):  
Changying Zhao ◽  
Ying Wang ◽  
Junjie Yang ◽  
Jiaming Zhang ◽  
Xuemei Liu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Critical Role ◽  
Correlation Study ◽  
Healthy Children ◽  
Microbiome Composition ◽  
Preliminary Study ◽  
Schonlein Purpura ◽  
Gut Microbiota Dysbiosis ◽  
Gut Microbiota Composition

Abstract Background: Vertical microbiome transmission from mothers plays an important role inchildren with the establishment and development of gutmicrobiome.Our previous study has found that gut microbiota dysbiosis is associated with Henoch-Schönleinpurpura(HSP) in children,while it is unclear whether there is a correlation between the gut microbiome of the HSP children and their mothers. Methods: In this study, 50HSP child-mother pairs and 61 matched healthy child-mother pairs were enrolled and examined.Stool samples were collected for DNA extraction and 16S rRNA genesequencing, followed by analyses of the gut microbiota composition.Results: Significant differences were observed in the gut microbiome composition between HSP children and healthy children. Several unique biomarkers, such as Enterococcus, Fusobacterium,Veillonellaand Streptococcus were identified. A significant increase of the relative abundance of Prevotella and Megamonas were observed in HSP’s mothers (HSP-M) compared with mothers of the healthy children (H-M). HSP children’s gut microbiome is closely associated with that of their mothers, and the taxon of AcidaminococcusandRoseburiawere onlyfound in the gut microbiome of HSP children and their mothers (HSP-M+C).Conclusions: Our preliminary study revealed that the gut microbiome of HSP children are closely associated with that of their mothers, although children with HSP still possess unique bacterial biomarkers. Dysbiosis of the maternal gut microbiota may play a critical role in increasing the risk of HSP in children, which deserve further longitudinalinvestigations to uncover its mechanisms.

scholarly journals Dynamic Changes of Gut Microbiome and Immune Response During the Acute Stage of Stroke in a Pig Model (P14-012-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Julie Jeon ◽  
Jeferson Lourenco ◽  
Erin Kaiser ◽  
Elizabeth Waters ◽  
Kelly Scheulin ◽  
...  
Keyword(s):  
Immune Response ◽  
Ischemic Stroke ◽  
Gut Microbiome ◽  
Critical Role ◽  
The United States ◽  
Acute Stage ◽  
Pig Model ◽  
Stroke Recovery ◽  
Microbiome Composition ◽  
Α Diversity

Abstract Objectives Stroke is a leading cause of mortality and disability in the United States. Secondary injuries induced by inflammation plays a critical role in stroke recovery. This study investigates gut microbiome changes during the acute stage of ischemic stroke to better understand the role of gut microbiome in inflammation in an ischemic stroke pig model. Methods Ischemic stroke was induced by middle cerebral artery occlusion in pigs (n = 7). Fecal samples were collected at pre-stoke (PRE), 1 (1DPS), 3 (3DPS), and 5 days post-stroke (5DPS) to measure gut microbiome composition. Blood samples were collected at 1DPS for white blood cell analysis. Results Ischemic stroke was confirmed by magnetic resonance imaging at 1DPS. The dominant pre-stroke fecal bacterial phyla (>1% relative abundance) were Firmicutes (89.2%), Bacteroidetes (3.7%), Actinobacteria (2.0%) and Proteobacteria (1.3%). This composition significantly (P < 0.05) differed at 3DPS with a decreased Firmicutes (68.1%) and increased Actinobacteria (3.70%) and Proteobacteria (19.0%), and a trending (P = 0.06) increase among Bacteroidetes (7.6%). At 5DPS, Bacteroidetes (7.6%) remained elevated, but Firmicutes (86.6%), Actinobacteria (2.0%) and Proteobacteria (0.7%) returned to levels similar to PRE. At 1DPS, the α-diversity measured by Shannon index and species evenness were both decreased (P < 0.05), suggesting that overall bacterial diversity decreased immediately after the stroke. β-diversity analysis showed a trend for overall differences over time (P = 0.07), but no differences between specific days were found. Elevated inflammation and neutrophil-to-lymphocyte ratio (NLR) following stroke event have been related to negative functional outcome in stroke patients. At 1DPS, a significant increase in NLR was observed in the stroke pigs compared to those at PRE (P < 0.05), suggesting initiation of inflammatory response following stroke. Conclusions Ischemic stroke altered the gut microbiome composition, reduced microbiome diversity and increased immune response in pigs. Future studies are warranted to investigate systemic and neural inflammation mediated by the alteration of the gut microbiome following ischemic stroke. Funding Sources The study was funded by the National Institute of Health and University of Georgia (Faculty Research Grant).

scholarly journals Highly Reproducible 16S Sequencing Facilitates Measurement of Host Genetic Influences on the Stickleback Gut Microbiome

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Clayton M. Small ◽  
Mark Currey ◽  
Emily A. Beck ◽  
Susan Bassham ◽  
William A. Cresko
Keyword(s):  
Microbial Diversity ◽  
High Throughput ◽  
Gut Microbiome ◽  
Dna Isolation ◽  
Minor Effect ◽  
Tissue Preparation ◽  
Host Genotype ◽  
16S Sequencing ◽  
Microbiome Composition ◽  
Host Microbe Interactions

ABSTRACT Multicellular organisms interact with resident microbes in important ways, and a better understanding of host-microbe interactions is aided by tools such as high-throughput 16S sequencing. However, rigorous evaluation of the veracity of these tools in a different context from which they were developed has often lagged behind. Our goal was to perform one such critical test by examining how variation in tissue preparation and DNA isolation could affect inferences about gut microbiome variation between two genetically divergent lines of threespine stickleback fish maintained in the same laboratory environment. Using careful experimental design and intensive sampling of individuals, we addressed technical and biological sources of variation in 16S-based estimates of microbial diversity. After employing a two-tiered bead beating approach that comprised tissue homogenization followed by microbial lysis in subsamples, we found an extremely minor effect of DNA isolation protocol relative to among-host microbial diversity differences. Abundance estimates for rare operational taxonomic units (OTUs), however, showed much lower reproducibility. Gut microbiome composition was highly variable across fish—even among cohoused siblings—relative to technical replicates, but a subtle effect of host genotype (stickleback line) was nevertheless detected for some microbial taxa. IMPORTANCE Our findings demonstrate the importance of appropriately quantifying biological and technical variance components when attempting to understand major influences on high-throughput microbiome data. Our focus was on understanding among-host (biological) variance in community metrics and its magnitude in relation to within-host (technical) variance, because meaningful comparisons among individuals are necessary in addressing major questions in host-microbe ecology and evolution, such as heritability of the microbiome. Our study design and insights should provide a useful example for others desiring to quantify microbiome variation at biological levels in the face of various technical factors in a variety of systems.

scholarly journals Sex Differences in Intestinal Microbial Composition and Function of Hainan Special Wild Boar

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1553
Author(s):  
Xiaozhe Wang ◽  
Ying Zhang ◽  
Qiong Wen ◽  
Ying Wang ◽  
Zhixin Wang ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Wild Boar ◽  
Membrane Transport ◽  
Gut Microbiome ◽  
Disease Status ◽  
Fecal Microbiota ◽  
Female Group ◽  
Microbial Composition ◽  
Health And Disease ◽  
And Function

The gut microbiome plays an important role in the health and disease status of the host. Research on the effect of sex on animal intestinal microorganisms is still limited; and the effect of castration on the gut microbiome of male pigs has not been fully investigated. In this study, 30 Hainan special wild boars at the same growth stage were divided into three groups (10 entire males, 10 females, and 10 castrated males). High-throughput 16S rRNA sequencing was used to investigate the fecal microbiota of the Hainan special wild boar. Firmicutes, Bacteroidetes, Actinobacteria, Spirochaetes, and Proteobacteria were the five dominant phyla found in the specimens. The relative abundance of Bacteroidetes was higher in the microbiota of female pigs than in male pigs, while Firmicutes was on the contrary. The percentage of Streptococcus and Lactobacillus was higher in males than females. The microbial diversity of females was significantly higher compared to males; castration increased the intestinal microbial diversity of males. Functional prediction showed that male fecal microorganisms were rich in membrane transport and carbohydrate metabolism; energy metabolism, glycan biosynthesis, and metabolism of cofactors and vitamins were rich in the female group; the fecal microorganisms of castrated males had higher membrane transport abundance.

Sign in / Sign up

Export Citation Format

Share Document