scholarly journals Natural and after colon washing fecal samples: the two sides of the coin for investigating the human gut microbiome

2021 ◽  
Author(s):  
Elisabetta Piancone ◽  
Bruno Fosso ◽  
Mariangela De Robertis ◽  
Elisabetta Notario ◽  
Annarita Oranger ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Digital Pcr ◽  
Shannon Index ◽  
Individual Variability ◽  
Rrna Gene ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Taxonomic Analysis ◽  
Paired Samples

To date there are several studies focusing on the importance of gut microbiome for human health, however the selection of a universal sampling matrix representative of the microbial biodiversity associated to the gastrointestinal (GI) tract, still represents a challenge. Here we present a study in which, through a deep metabarcoding analysis of the 16S rRNA gene, we compared two sampling matrices, feces (F) and colonic lavage liquid (LL), in order to evaluate their accuracy to represent the complexity of the human gut microbiome. A training set of 37 volunteers was attained and paired F and LL samples were collected from each subject. A preliminary absolute quantification of total 16S rDNA, performed by droplet digital PCR (ddPCR), confirmed that sequencing and taxonomic analysis were performed on same total bacterial abundance obtained from the two sampling methods. The taxonomic analysis of paired samples revealed that, although specific taxa were predominantly or exclusively observed in LL samples, as well as other taxa were detectable only or were predominant in stool, the microbiomes of the paired samples F and LL in the same subject hold overlapping taxonomic composition. Moreover, LL samples revealed a higher biodiversity than stool at all taxonomic ranks, as demonstrated by the Shannon Index and the Inverse Simpson's Index. We also found greater inter-individual variability than intra-individual variability in both sample matrices. Finally, functional differences were unveiled in the gut microbiome detected in the F and LL samples. A significant overrepresentation of 22 and 13 metabolic pathways, mainly occurring in Firmicutes and Proteobacteria, was observed in gut microbiota detected in feces and LL samples, respectively. This suggests that LL samples may allow for the detection of microbes adhering to the intestinal mucosal surface as members of the resident flora that are not easily detectable in stool, most likely representative of a diet-influenced transient microbiota. This first comparative study on feces and LL samples for the study of the human gut microbiome demonstrates that the use of both types of sample matrices may represent a possible choice to obtain a more complete view of the human gut microbiota in response to different biological and clinical questions.

scholarly journals Impact of Different Exercise Modalities on the Human Gut Microbiome

Sports ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 14
Author(s):  
Dierdra Bycura ◽  
Anthony C. Santos ◽  
Arron Shiffer ◽  
Shari Kyman ◽  
Kyle Winfree ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Sequence Data ◽  
Exercise Program ◽  
Rrna Gene ◽  
Human Gut ◽  
Post Intervention ◽  
Cross Sectional ◽  
Intervention Phase ◽  
Human Gut Microbiome

In this study we examined changes to the human gut microbiome resulting from an eight-week intervention of either cardiorespiratory exercise (CRE) or resistance training exercise (RTE). Twenty-eight subjects (21 F; aged 18–26) were recruited for our CRE study and 28 subjects (17 F; aged 18–33) were recruited for our RTE study. Fecal samples for gut microbiome profiling were collected twice weekly during the pre-intervention phase (three weeks), intervention phase (eight weeks), and post-intervention phase (three weeks). Pre/post VO2max, three repetition maximum (3RM), and body composition measurements were conducted. Heart rate ranges for CRE were determined by subjects’ initial VO2max test. RTE weight ranges were established by subjects’ initial 3RM testing for squat, bench press, and bent-over row. Gut microbiota were profiled using 16S rRNA gene sequencing. Microbiome sequence data were analyzed with QIIME 2. CRE resulted in initial changes to the gut microbiome which were not sustained through or after the intervention period, while RTE resulted in no detectable changes to the gut microbiota. For both CRE and RTE, we observe some evidence that the baseline microbiome composition may be predictive of exercise gains. This work suggests that the human gut microbiome can change in response to a new exercise program, but the type of exercise likely impacts whether a change occurs. The changes observed in our CRE intervention resemble a disturbance to the microbiome, where an initial shift is observed followed by a return to the baseline state. More work is needed to understand how sustained changes to the microbiome occur, resulting in differences that have been reported in cross sectional studies of athletes and non-athletes.

scholarly journals Correction: 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome

PLoS ONE ◽  
2019 ◽  
Vol 14 (2) ◽  
pp. e0212474 ◽  
Author(s):  
Daniel E. Almonacid ◽  
Laurens Kraal ◽  
Francisco J. Ossandon ◽  
Yelena V. Budovskaya ◽  
Juan Pablo Cardenas ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gut Microbiome ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Reference Ranges ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Rrna Gene Sequencing

scholarly journals Alterations in human gut microbiome composition and metabolism after exposure to glyphosate and Roundup and/or a spore-based formulation using the SHIME® technology

2021 ◽  
Author(s):  
Robin Mesnage ◽  
Marta Calatayud ◽  
Cindy Duysburgh ◽  
Massimo Marzorati ◽  
Michael Antoniou
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Large Scale ◽  
Epidemiological Studies ◽  
Human Gut ◽  
Microbiome Composition ◽  
Human Gut Microbiome ◽  
Ammonium Production ◽  
Profiling Techniques ◽  
Microbial Environment

Despite extensive research into the toxicology of the herbicide glyphosate, there are still major unknowns regarding its effects on the human gut microbiome. As a step in addressing this knowledge gap, we describe for the first time the effects of glyphosate and a Roundup glyphosate-based herbicide on infant gut microbiota using SHIME technology, which mimics the entire gastrointestinal tract. SHIME microbiota culture was undertaken in the presence of a concentration of 100 mg/L (corresponding to a dose of 1.6 mg/kg/day) glyphosate and the same glyphosate equivalent concentration of Roundup, which is in the range of the US chronic reference dose, and subjected to molecular profiling techniques to assess outcomes. Roundup and to a lesser extent glyphosate caused an increase in fermentation activity, resulting in acidification of the microbial environment. This was also reflected by an increase in lactate and acetate production concomitant to a decrease in the levels of propionate, valerate, caproate and butyrate. Ammonium production reflecting proteolytic activities was increased by Roundup exposure. Global metabolomics revealed large scale disturbances in metabolite profiles, including an increased abundance of long chain polyunsaturated fatty acids (n3 and n6). Although changes in bacterial composition measured by qPCR and 16S rRNA sequencing were less clear, our results suggested that lactobacilli had their growth stimulated as a result of microenvironment acidification. Co-treatment with the spore-based probiotic formulation MegaSporeBiotic reverted some of the changes in short-chain fatty acid levels. Altogether, our results suggest that glyphosate can exert effects on human gut microbiota at permitted regulatory levels of exposure, highlighting the need for epidemiological studies aimed at evaluating the effects of glyphosate herbicides on human gut microbiome function.

scholarly journals Captivity humanizes the primate microbiome

2016 ◽  
Vol 113 (37) ◽  
pp. 10376-10381 ◽  
Author(s):  
Jonathan B. Clayton ◽  
Pajau Vangay ◽  
Hu Huang ◽  
Tonya Ward ◽  
Benjamin M. Hillmann ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Meta Analysis ◽  
Human Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Modern Human ◽  
Primate Species ◽  
Rrna Gene ◽  
Human Gut ◽  
Dietary Analysis ◽  
Human Gut Microbiome

The primate gastrointestinal tract is home to trillions of bacteria, whose composition is associated with numerous metabolic, autoimmune, and infectious human diseases. Although there is increasing evidence that modern and Westernized societies are associated with dramatic loss of natural human gut microbiome diversity, the causes and consequences of such loss are challenging to study. Here we use nonhuman primates (NHPs) as a model system for studying the effects of emigration and lifestyle disruption on the human gut microbiome. Using 16S rRNA gene sequencing in two model NHP species, we show that although different primate species have distinctive signature microbiota in the wild, in captivity they lose their native microbes and become colonized with Prevotella and Bacteroides, the dominant genera in the modern human gut microbiome. We confirm that captive individuals from eight other NHP species in a different zoo show the same pattern of convergence, and that semicaptive primates housed in a sanctuary represent an intermediate microbiome state between wild and captive. Using deep shotgun sequencing, chemical dietary analysis, and chloroplast relative abundance, we show that decreasing dietary fiber and plant content are associated with the captive primate microbiome. Finally, in a meta-analysis including published human data, we show that captivity has a parallel effect on the NHP gut microbiome to that of Westernization in humans. These results demonstrate that captivity and lifestyle disruption cause primates to lose native microbiota and converge along an axis toward the modern human microbiome.

scholarly journals Analysis of Human Gut Microbiome: Taxonomy and Metabolic Functions in Thai Adults

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 331
Author(s):  
Nachon Raethong ◽  
Massalin Nakphaichit ◽  
Narissara Suratannon ◽  
Witida Sathitkowitchai ◽  
Wanlapa Weerapakorn ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Asian Country ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Thai Population ◽  
Shotgun Metagenomics ◽  
Human Gut Microbiome ◽  
Metabolic Functions

The gut microbiome plays a major role in the maintenance of human health. Characterizing the taxonomy and metabolic functions of the human gut microbiome is necessary for enhancing health. Here, we analyzed the metagenomic sequencing, assembly and construction of a meta-gene catalogue of the human gut microbiome with the overall aim of investigating the taxonomy and metabolic functions of the gut microbiome in Thai adults. As a result, the integrative analysis of 16S rRNA gene and whole metagenome shotgun (WMGS) sequencing data revealed that the dominant gut bacterial families were Lachnospiraceae and Ruminococcaceae of the Firmicutes phylum. Consistently, across 3.8 million (M) genes annotated from 163.5 gigabases (Gb) of WMGS sequencing data, a significant number of genes associated with carbohydrate metabolism of the dominant bacterial families were identified. Further identification of bacterial community-wide metabolic functions promisingly highlighted the importance of Roseburia and Faecalibacterium involvement in central carbon metabolism, sugar utilization and metabolism towards butyrate biosynthesis. This work presents an initial study of shotgun metagenomics in a Thai population-based cohort in a developing Southeast Asian country.

scholarly journals Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiangning Bai ◽  
Aswathy Narayanan ◽  
Piotr Nowak ◽  
Shilpa Ray ◽  
Ujjwal Neogi ◽  
...  
Keyword(s):  
Antiretroviral Therapy ◽  
Gut Microbiome ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Taxonomic Resolution ◽  
Rrna Gene ◽  
Human Gut ◽  
Shotgun Metagenomics ◽  
Human Gut Microbiome ◽  
Hiv 1

Gut microbiome plays a significant role in HIV-1 immunopathogenesis and HIV-1-associated complications. Previous studies have mostly been based on 16S rRNA gene sequencing, which is limited in taxonomic resolution at the genus level and inferred functionality. Herein, we performed a deep shotgun metagenomics study with the aim to obtain a more precise landscape of gut microbiome dysbiosis in HIV-1 infection. A reduced tendency of alpha diversity and significantly higher beta diversity were found in HIV-1-infected individuals on antiretroviral therapy (ART) compared to HIV-1-negative controls. Several species, such as Streptococcus anginosus, Actinomyces odontolyticus, and Rothia mucilaginosa, were significantly enriched in the HIV-1-ART group. Correlations were observed between the degree of immunodeficiency and gut microbiome in terms of microbiota composition and metabolic pathways. Furthermore, microbial shift in HIV-1-infected individuals was found to be associated with changes in microbial virulome and resistome. From the perspective of methodological evaluations, our study showed that different DNA extraction protocols significantly affect the genomic DNA quantity and quality. Moreover, whole metagenome sequencing depth affects critically the recovery of microbial genes, including virulome and resistome, while less than 5 million reads per sample is sufficient for taxonomy profiling in human fecal metagenomic samples. These findings advance our understanding of human gut microbiome and their potential associations with HIV-1 infection. The methodological assessment assists in future study design to accurately assess human gut microbiome.

scholarly journals Minimizing confounders and increasing data quality in murine models for studies of the gut microbiome

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5166 ◽  
Author(s):  
Jun Miyoshi ◽  
Vanessa Leone ◽  
Kentaro Nobutani ◽  
Mark W. Musch ◽  
Kristina Martinez-Guryn ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Standard Operating Procedure ◽  
Individual Variability ◽  
Rrna Gene ◽  
Murine Models ◽  
Single Room ◽  
Specific Pathogen ◽  
Microbe Interactions ◽  
Host Microbe Interactions

Murine models are widely used to explore host-microbe interactions because of the challenges and limitations inherent to human studies. However, microbiome studies in murine models are not without their nuances. Inter-individual variations in gut microbiota are frequent even in animals housed within the same room. We therefore sought to find an efficient and effective standard operating procedure (SOP) to minimize these effects to improve consistency and reproducibility in murine microbiota studies. Mice were housed in a single room under specific-pathogen free conditions. Soiled cage bedding was routinely mixed weekly and distributed among all cages from weaning (three weeks old) until the onset of the study. Females and males were separated by sex and group-housed (up to five mice/cage) at weaning. 16S rRNA gene analyses of fecal samples showed that this protocol significantly reduced pre-study variability of gut microbiota amongst animals compared to other conventional measures used to normalize microbiota when large experimental cohorts have been required. A significant and consistent effect size was observed in gut microbiota when mice were switched from regular chow to purified diet in both sexes. However, sex and aging appeared to be independent drivers of gut microbial assemblage and should be taken into account in studies of this nature. In summary, we report a practical and effective pre-study SOP for normalizing the gut microbiome of murine cohorts that minimizes inter-individual variability and resolves co-housing problems inherent to male mice. This SOP may increase quality, rigor, and reproducibility of data acquisition and analysis.

scholarly journals MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome

2021 ◽  
Vol 17 (1) ◽  
pp. e1008487
Author(s):  
Preecha Patumcharoenpol ◽  
Massalin Nakphaichit ◽  
Gianni Panagiotou ◽  
Anchalee Senavonge ◽  
Narissara Suratannon ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gut Microbiome ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Functional Capability ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Metabolic Functions ◽  
Scale Models

Investigating metabolic functional capability of a human gut microbiome enables the quantification of microbiome changes, which can cause a phenotypic change of host physiology and disease. One possible way to estimate the functional capability of a microbial community is through inferring metagenomic content from 16S rRNA gene sequences. Genome-scale models (GEMs) can be used as scaffold for functional estimation analysis at a systematic level, however up to date, there is no integrative toolbox based on GEMs for uncovering metabolic functions. Here, we developed the MetGEMs (metagenome-scale models) toolbox, an open-source application for inferring metabolic functions from 16S rRNA gene sequences to facilitate the study of the human gut microbiome by the wider scientific community. The developed toolbox was validated using shotgun metagenomic data and shown to be superior in predicting functional composition in human clinical samples compared to existing state-of-the-art tools. Therefore, the MetGEMs toolbox was subsequently applied for annotating putative enzyme functions and metabolic routes related in human disease using atopic dermatitis as a case study.

scholarly journals Consistent Prebiotic Effects of Carrot RG-I on the Gut Microbiota of Four Human Adult Donors in the SHIME® Model despite Baseline Individual Variability

2021 ◽  
Vol 9 (10) ◽  
pp. 2142
Author(s):  
Pieter Van den Abbeele ◽  
Cindy Duysburgh ◽  
Ilse Cleenwerck ◽  
Ruud Albers ◽  
Massimo Marzorati ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Bifidobacterium Longum ◽  
Health Benefit ◽  
Repeated Administration ◽  
Vital Role ◽  
Individual Variability ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Rhamnogalacturonan I ◽  
The Impact

The human gut microbiome is currently recognized to play a vital role in human biology and development, with diet as a major modulator. Therefore, novel indigestible polysaccharides that confer a health benefit upon their fermentation by the microbiome are under investigation. Based on the recently demonstrated prebiotic potential of a carrot-derived pectin extract enriched for rhamnogalacturonan I (cRG-I), the current study aimed to assess the impact of cRG-I upon repeated administration using the M-SHIME technology (3 weeks at 3g cRG-I/d). Consistent effects across four simulated adult donors included enhanced levels of acetate (+21.1 mM), propionate (+17.6 mM), and to a lesser extent butyrate (+4.1 mM), coinciding with a marked increase of OTUs related to Bacteroides dorei and Prevotella species with versatile enzymatic potential likely allowing them to serve as primary degraders of cRG-I. These Bacteroidetes members are able to produce succinate, explaining the consistent increase of an OTU related to the succinate-converting Phascolarctobacterium faecium (+0.47 log10(cells/mL)). While the Bifidobacteriaceae family remained unaffected, a specific OTU related to Bifidobacterium longum increased significantly upon cRG-I treatment (+1.32 log10(cells/mL)). Additional monoculture experiments suggested that Bifidobacterium species are unable to ferment cRG-I structures as such and that B. longum probably feeds on arabinan and galactan side chains of cRG-I, released by aforementioned Bacteroidetes members. Overall, this study confirms the prebiotic potential of cRG-I and additionally highlights the marked consistency of the microbial changes observed across simulated subjects, suggesting the involvement of a specialized consortium in cRG-I fermentation by the human gut microbiome.

scholarly journals Acute Sleep-Wake Cycle Shift Results in Community Alteration of Human Gut Microbiome

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Zhi Liu ◽  
Zhi-Yuan Wei ◽  
Junyu Chen ◽  
Kun Chen ◽  
Xuhua Mao ◽  
...  
Keyword(s):  
Circadian Rhythm ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Cognitive Impairments ◽  
Modern Society ◽  
Human Diseases ◽  
Rrna Gene ◽  
Cardiovascular Disorders ◽  
Human Gut ◽  
Functional Profiles

ABSTRACT Disturbances of sleep and the underlying circadian rhythm are related to many human diseases, such as obesity, diabetes, cardiovascular disorders, and cognitive impairments. Dysbiosis of the gut microbiome has also been reported to be associated with the pathologies of these diseases. Therefore, we proposed that disturbed sleep may regulate gut microbiota homeostasis. In this study, we mimicked the sleep-wake cycle shift, one typical type of circadian rhythm disturbances in young people, in recruited subjects. We used 16S rRNA gene amplicon sequencing to define microbial taxa from their fecal samples. Although the relative abundances of the microbes were not significantly altered, the functional-profile analysis of gut microbiota revealed functions enriched during the sleep-wake cycle shift. In addition, the microbial networks were quite distinct among baseline, shift, and recovery stages. These results suggest that an acute sleep-wake cycle shift may exert a limited influence on the gut microbiome, mainly including the functional profiles of the microbes and the microbial relationships within the microbial community. IMPORTANCE Circadian rhythm misalignment due to social jet lag, shift work, early morning starts, and delayed bedtimes is becoming common in our modern society. Disturbances of sleep and the underlying circadian rhythms are related to multiple human diseases, such as obesity, diabetes, cardiovascular disorders, and cognitive impairments. Given the crucial role of microbiota in the same pathologies as are caused by sleep disturbance, how the gut microbiota is affected by sleep is of increasing interest. The results of this study indicate that the acute circadian rhythm disturbance caused by sleep-wake shifts affect the human gut microbiota, especially the functional profiles of gut microbes and interactions among them. Further experiments with a longer-time-scale intervention and larger sample size are needed to assess the effects of chronic circadian rhythm disruption on the gut microbiome and to guide possible microbial therapies for clinical intervention in the related diseases.

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