scholarly journals A high-throughput method to characterize the gut bacteria growth upon engineered nanomaterial treatment

2020 ◽  
Vol 7 (10) ◽  
pp. 3155-3166
Author(s):  
Qin Yang ◽  
Tharushi Prabha Keerthisinghe ◽  
Tiffany Rou Jie Tan ◽  
Xiaoqiong Cao ◽  
Magdiel Inggrid Setyawati ◽  
...  
Keyword(s):  
High Throughput ◽  
Gut Microbiome ◽  
Bacterial Culture ◽  
Human Gut ◽  
Bacteria Growth ◽  
Human Gut Microbiome ◽  
Engineered Nanomaterial ◽  
High Throughput Method ◽  
Pure Bacterial Culture

We developed a DNA-based quantification (DBQ) method in a 96-well plate format. The applicability of this method for several types of ENMs was proved in both pure bacterial culture and in vitro human gut microbiome community.

scholarly journals Lacticaseibacillus rhamnosus GG and Saccharomyces cerevisiae boulardii supplementation exert protective effects on human gut microbiome following antibiotic administration in vitro

2021 ◽  
pp. 1-16
Author(s):  
C. Duysburgh ◽  
P. Van den Abbeele ◽  
M. Morera ◽  
M. Marzorati
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Gut Microbiome ◽  
Gastrointestinal Symptoms ◽  
Lactobacillus Rhamnosus ◽  
Antibiotic Administration ◽  
Protective Effects ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
The Impact

Antibiotic-induced dysbiosis of the microbial community has been associated with several gastrointestinal symptoms. The impact of repeated administration of Lacticaseibacillus rhamnosus GG (CNCM-I-4798) (formerly known as Lactobacillus rhamnosus GG), Saccharomyces cerevisiae boulardii (CNCM-I-1079) and their combination (associated in Smebiocta/Smectaflora Protect®) in supporting recovery of gut microbiota functionality and composition during and following amoxicillin:clavulanic acid administration was evaluated in vitro. Antibiotic dosage negatively affected SCFA production, coinciding with detrimental effects on Bacteroidetes, Firmicutes and Bifidobacterium spp. in the simulated proximal colon, while Akkermansia muciniphila was significantly reduced in the distal colon. L. rhamnosus GG and S. boulardii were able to thrive in both colon regions upon dosing, with S. boulardii even showing protective effects on the survival of L. rhamnosus GG during antibiotic administration. The impact of the probiotic strains on microbiome recovery revealed that supplementation with L. rhamnosus GG and/or S. boulardii resulted in a stimulating effect on the most abundant bacterial groups within the bacterial community of each donor. For one of the donors tested, co-dosing of L. rhamnosus GG and S. boulardii resulted in superior short-chain fatty acid recovery accompanied by a stronger increase in abundance of Bifidobacteriaceae. Overall, the current study provides first evidence that combined supplementation of L. rhamnosus GG and S. boulardii might be an interesting candidate in limiting detrimental effects of amoxicillin:clavulanic acid on the human gut microbiome, though further studies are warranted to confirm these findings.

scholarly journals An in vitro intestinal platform with a self-sustaining oxygen gradient to study the human gut/microbiome interface

2019 ◽  
Vol 12 (1) ◽  
pp. 015006 ◽  
Author(s):  
Raehyun Kim ◽  
Peter J Attayek ◽  
Yuli Wang ◽  
Kathleen L Furtado ◽  
Rita Tamayo ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Human Gut ◽  
Oxygen Gradient ◽  
Human Gut Microbiome

scholarly journals Concentrated Raw Fibers Enhance the Fiber-Degrading Capacity of a Synthetic Human Gut Microbiome

2021 ◽  
Author(s):  
Alexander Steimle ◽  
Mareike Neumann ◽  
Erica Grant ◽  
Jonathan D Turner ◽  
Mahesh S Desai
Keyword(s):  
Gut Microbiome ◽  
A Priori ◽  
Human Gut ◽  
In Vivo Models ◽  
Human Gut Microbiome ◽  
Different Strains ◽  
Alpha Glucosidase ◽  
Prebiotic Fibers

Consumption of prebiotic fibers to modulate the human gut microbiome is a promising strategy to positively impact health. Nevertheless, given the compositional complexity of the microbiome and its inter-individual variances, generalized recommendations on the source or amount of fiber supplements remain vague. This problem is further compounded by availability of tractable in vitro and in vivo models to validate certain fibers. We employed a gnotobiotic mouse model containing an a priori characterized 14-member synthetic human gut microbiome (SM) for their ability to metabolize a suit of fibers in vitro; the SM contains 14 different strains belonging to five distinct phyla. Since soluble purified fibers have been a common subject of studies, we specifically investigated the effects of concentrated raw fibers (CRFs)—containing fibers from pea, oat, psyllium, wheat and apple—on the compositional and functional alterations in the SM. We demonstrate that, compared to a fiber-free diet, CRF supplementation increased the abundance of fiber-degraders namely Eubacterium rectale, Roseburia intestinalis and Bacteroides ovatus and decreased the abundance of the mucin-degrader Akkermansia muciniphila. These results were corroborated by a general increase of bacterial fiber-degrading α-glucosidase enzyme activity. Overall, our results highlight the ability of CRFs to enhance the microbial fiber-degrading capacity.

scholarly journals Feeding Bugs to Bugs: Edible Insects Modify the Human Gut Microbiome in an in vitro Fermentation Model

2020 ◽  
Vol 11 ◽  
Author(s):  
Wayne Young ◽  
Sai Krishna Arojju ◽  
Mark R. McNeill ◽  
Elizabeth Rettedal ◽  
Jessica Gathercole ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Edible Insects ◽  
Human Gut ◽  
In Vitro Fermentation ◽  
Human Gut Microbiome ◽  
Fermentation Model

scholarly journals Concentrated Raw Fibers Enhance the Fiber-Degrading Capacity of a Synthetic Human Gut Microbiome

2021 ◽  
Vol 22 (13) ◽  
pp. 6855
Author(s):  
Alex Steimle ◽  
Mareike Neumann ◽  
Erica T. Grant ◽  
Jonathan D. Turner ◽  
Mahesh S. Desai
Keyword(s):  
Gut Microbiome ◽  
A Priori ◽  
Human Gut ◽  
General Increase ◽  
In Vivo Models ◽  
Human Gut Microbiome ◽  
Different Strains ◽  
Prebiotic Fibers

The consumption of prebiotic fibers to modulate the human gut microbiome is a promising strategy to positively impact health. Nevertheless, given the compositional complexity of the microbiome and its inter-individual variances, generalized recommendations on the source or amount of fiber supplements remain vague. This problem is further compounded by availability of tractable in vitro and in vivo models to validate certain fibers. We employed a gnotobiotic mouse model containing a 14-member synthetic human gut microbiome (SM) in vivo, characterized a priori for their ability to metabolize a collection of fibers in vitro. This SM contains 14 different strains belonging to five distinct phyla. Since soluble purified fibers have been a common subject of studies, we specifically investigated the effects of dietary concentrated raw fibers (CRFs)—containing fibers from pea, oat, psyllium, wheat and apple—on the compositional and functional alterations in the SM. We demonstrate that, compared to a fiber-free diet, CRF supplementation increased the abundance of fiber-degraders, namely Eubacterium rectale, Roseburia intestinalis and Bacteroides ovatus and decreased the abundance of the mucin-degrader Akkermansia muciniphila. These results were corroborated by a general increase of bacterial fiber-degrading α-glucosidase enzyme activity. Overall, our results highlight the ability of CRFs to enhance the microbial fiber-degrading capacity.

scholarly journals Microbe-seq: high-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

2020 ◽  
Author(s):  
Wenshan Zheng ◽  
Shijie Zhao ◽  
Yehang Yin ◽  
Huidan Zhang ◽  
David M. Needham ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
Gut Microbiome ◽  
Bacterial Species ◽  
Microbial Interactions ◽  
Single Individual ◽  
Human Gut ◽  
Single Strain ◽  
Human Gut Microbiome

AbstractWe present Microbe-seq, a high-throughput single-microbe method that yields strain-resolved genomes from complex microbial communities. We encapsulate individual microbes into droplets with microfluidics and liberate their DNA, which we amplify, tag with droplet-specific barcodes, and sequence. We use Microbe-seq to explore the human gut microbiome; we collect stool samples from a single individual, sequence over 20,000 microbes, and reconstruct nearly-complete genomes of almost 100 bacterial species, including several with multiple subspecies strains. We use these genomes to probe genomic signatures of microbial interactions: we reconstruct the horizontal gene transfer (HGT) network within the individual and observe far greater exchange within the same bacterial phylum than between different phyla. We probe bacteria-virus interactions; unexpectedly, we identify a significant in vivo association between crAssphage, an abundant bacteriophage, and a single strain of Bacteroides vulgatus. Microbe-seq contributes high-throughput culture-free capabilities to investigate genomic blueprints of complex microbial communities with single-microbe resolution.

scholarly journals The Human Gut Microbiome’s Influence on Arsenic Toxicity

2019 ◽  
Vol 5 (6) ◽  
pp. 491-504 ◽  
Author(s):  
Michael Coryell ◽  
Barbara A. Roggenbeck ◽  
Seth T. Walk
Keyword(s):  
Gut Microbiome ◽  
Arsenic Speciation ◽  
Methylation Status ◽  
Arsenic Exposure ◽  
Health Concern ◽  
Current Evidence ◽  
Arsenic Toxicity ◽  
Human Gut ◽  
Human Gut Microbiome

Abstract Purpose of Review Arsenic exposure is a public health concern of global proportions with a high degree of interindividual variability in pathologic outcomes. Arsenic metabolism is a key factor underlying toxicity, and the primary purpose of this review is to summarize recent discoveries concerning the influence of the human gut microbiome on the metabolism, bioavailability, and toxicity of ingested arsenic. We review and discuss the current state of knowledge along with relevant methodologies for studying these phenomena. Recent Findings Bacteria in the human gut can biochemically transform arsenic-containing compounds (arsenicals). Recent publications utilizing culture-based approaches combined with analytical biochemistry and molecular genetics have helped identify several arsenical transformations by bacteria that are at least possible in the human gut and are likely to mediate arsenic toxicity to the host. Other studies that directly incubate stool samples in vitro also demonstrate the gut microbiome’s potential to alter arsenic speciation and bioavailability. In vivo disruption or elimination of the microbiome has been shown to influence toxicity and body burden of arsenic through altered excretion and biotransformation of arsenicals. Currently, few clinical or epidemiological studies have investigated relationships between the gut microbiome and arsenic-related health outcomes in humans, although current evidence provides strong rationale for this research in the future. Summary The human gut microbiome can metabolize arsenic and influence arsenical oxidation state, methylation status, thiolation status, bioavailability, and excretion. We discuss the strength of current evidence and propose that the microbiome be considered in future epidemiologic and toxicologic studies of human arsenic exposure.

scholarly journals Acquired interbacterial defense systems protect against interspecies antagonism in the human gut microbiome

2018 ◽  
Author(s):  
Benjamin D. Ross ◽  
Adrian J. Verster ◽  
Matthew C. Radey ◽  
Danica T. Schmidtke ◽  
Christopher E. Pope ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Gene Clusters ◽  
Protective Capacity ◽  
Human Gut ◽  
Microbiome Composition ◽  
Toxin Resistance ◽  
Human Gut Microbiome ◽  
Bacterial Antagonism ◽  
The Impact

AbstractThe impact of direct interactions between co-resident microbes on microbiome composition is not well understood. Here we report the occurrence of acquired interbacterial defense (AID) gene clusters in bacterial residents of the human gut microbiome. These clusters encode arrays of immunity genes that protect against type VI secretion toxin-mediated intra- and inter-species bacterial antagonism. Moreover, the clusters reside on mobile elements and we demonstrate that their transfer is sufficient to confer toxin resistance in vitro and in gnotobiotic mice. Finally, we identify and validate the protective capacity of a recombinase-associated AID subtype (rAID-1) present broadly in Bacteroidales genomes. These rAID-1 gene clusters have a structure suggestive of active gene acquisition and include predicted immunity factors of toxins deriving from diverse organisms. Our data suggest that neutralization of contact-dependent interbacterial antagonism via AID systems shapes human gut microbiome ecology.

scholarly journals SRS-FISH: High-Throughput Platform Linking Microbiome Function to Identity at the Single Cell Level

2021 ◽  
Author(s):  
Xiaowei Ge ◽  
Fátima C. Pereira ◽  
Matthias Mitteregger ◽  
David Berry ◽  
Meng Zhang ◽  
...  
Keyword(s):  
Single Cell ◽  
High Throughput ◽  
Gut Microbiome ◽  
Single Cells ◽  
Unexpected Finding ◽  
Single Cell Level ◽  
Cell Level ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Function Identity

One of the biggest challenges in microbiome research in environmental and medical samples is to better understand functional properties of microbial community members at a single cell level. Single cell isotope probing has become a key tool for this purpose, but the currently applied detection methods for measuring isotope incorporation into single cells do not allow high-throughput analyses. Here, we report on the development of an imaging-based approach termed stimulated Raman scattering - two-photon fluorescence in situ hybridization (SRS-FISH) for high-throughput function-identity analyses of microbial communities with single cell resolution. SRS-FISH has an imaging speed of 10 to 100 milliseconds per cell, which is two to three orders of magnitude faster than spontaneous Raman-FISH. Using this technique, we delineated metabolic responses of thirty thousand individual cells to various mucosal sugars in the human gut microbiome via incorporation of deuterium from heavy water as an activity marker. Application of SRS-FISH to investigate the utilization of host-derived nutrients by two major human gut microbiome taxa revealed that response to mucosal sugars tends to be dominated by Bacteroidales, with an unexpected finding that Clostridia can outperform Bacteroidales at foraging fucose.

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