scholarly journals Gut microbial ecology of Xenopus tadpoles across life stages

2020 ◽  
Author(s):  
Thibault Scalvenzi ◽  
Isabelle Clavereau ◽  
Mickaël Bourge ◽  
Nicolas Pollet
Keyword(s):  
Gut Microbiome ◽  
Essential Amino Acids ◽  
Biological Processes ◽  
Nitrogen Recycling ◽  
16S Rdna Gene ◽  
Microbiome Composition ◽  
Metabolic Interactions ◽  
Molecular Components ◽  
The Impact ◽  
Shed Light

AbstractBackgroundThe microorganism world living in amphibians is still largely under-represented and under-studied in the literature. Among anuran amphibians, African clawed frogs of the Xenopus genus stand as well-characterized models with an in-depth knowledge of their developmental biological processes including their metamorphosis. We used different approaches including flow cytometry and 16s rDNA gene metabarcoding to analyze the succession of microbial communities and their activities across different body habitats of Xenopus tropicalis. We used metagenomic and metatranscriptomic sequencing to evaluate the metabolic capacity of the premetamorphic tadpole’s gut microbiome.ResultsWe analyzed the bacterial components of the Xenopus gut microbiota, the adult gut biogeography, the succession of communities during ontogeny, the impact of the alimentation in shaping the tadpole’s gut bacterial communities, the transmission of skin and fecal bacteria to the eggs. We also identified the most active gut bacteria and their metabolic contribution to tadpole physiology including carbohydrate breakdown, nitrogen recycling, essential amino-acids and vitamin biosynthesis.ConclusionsWe present a comprehensive new microbiome dataset of a laboratory amphibian model. Our data provide evidences that studies on the Xenopus tadpole model can shed light on the interactions between a vertebrate host and its microbiome. We interpret our findings in light of bile acids being key molecular components regulating the gut microbiome composition during amphibian development and metamorphosis. Further studies into the metabolic interactions between amphibian tadpoles and their microbiota during early development and metamorphosis should provide useful information on the evolution of host-microbiota interactions in vertebrates.

scholarly journals Gut microbiome signatures of risk and prodromal markers of Parkinson’s disease

2019 ◽  
Author(s):  
Sebastian Heinzel ◽  
Velma T. E. Aho ◽  
Ulrike Suenkel ◽  
Anna-Katharina von Thaler ◽  
Claudia Schulte ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Gut Microbiome ◽  
Physical Inactivity ◽  
Disease Onset ◽  
Rem Sleep Behavior Disorder ◽  
Sleep Behavior ◽  
Microbiome Composition ◽  
Β Diversity ◽  
The Impact

AbstractObjectivesAlterations of the gut microbiome in Parkinson’s disease (PD) have been repeatedly demonstrated. However, little is known about whether such alterations precede disease onset and how they may be related to risk and prodromal markers of PD. We investigated associations of these features with gut microbiome composition.MethodsEstablished risk and prodromal markers of PD as well as factors related to diet/lifestyle, bowel function and medication were studied in relation to bacterial α-/β-diversity, enterotypes, and taxonomic composition in stool samples of 666 elderly TREND study participants.ResultsAmong risk and prodromal markers, physical inactivity, constipation and age showed associations with α- and β-diversity, and for both measures subthreshold parkinsonism and physical inactivity showed interaction effects. Moreover, male sex, possible REM-sleep behavior disorder (RBD), smoking as well as body-mass-index, antidiabetic and urate-lowering medication were associated with β-diversity. Physical inactivity and constipation severity were increased in individuals with the Firmicutes-enriched enterotype. Subthreshold parkinsonism was least frequently observed in individuals with the Prevotella-enriched enterotype. Differentially abundant taxa were linked to constipation, physical inactivity, possible RBD, and subthreshold parkinsonism. Substantia nigra hyperechogenicity, olfactory loss, depression, orthostatic hypotension, urinary/erectile dysfunction, PD family history and the overall prodromal PD probability showed no significant microbiome associations.InterpretationSeveral risk and prodromal markers of PD are associated with changes in gut microbiome composition. However, the impact of the gut microbiome on PD risk and potential microbiome-dependent subtypes in the prodrome of PD need further investigation based on prospective clinical and (multi)omics data in incident PD cases.

scholarly journals Metabolic phenotyping for understanding the gut microbiome and host metabolic interplay

2017 ◽  
Vol 1 (4) ◽  
pp. 325-332 ◽  
Author(s):  
Abigail R. Basson ◽  
Anisha Wijeyesekera
Keyword(s):  
Gut Microbiome ◽  
Skin Diseases ◽  
Compositional Analysis ◽  
Exciting Field ◽  
Inflammatory Skin Diseases ◽  
Metabolic Phenotyping ◽  
Microbiome Composition ◽  
Host Health ◽  
The Impact ◽  
Analytical Approaches

There is growing interest in the role of the gut microbiome in human health and disease. This unique complex ecosystem has been implicated in many health conditions, including intestinal disorders, inflammatory skin diseases and metabolic syndrome. However, there is still much to learn regarding its capacity to affect host health. Many gut microbiome research studies focus on compositional analysis to better understand the causal relationships between microbial communities and disease phenotypes. Yet, microbial diversity and complexity is such that community structure alone does not provide full understanding of microbial function. Metabolic phenotyping is an exciting field in systems biology that provides information on metabolic outputs taking place in the system at a given moment in time. These readouts provide information relating to by-products of endogenous metabolic pathways, exogenous signals arising from diet, drugs and other lifestyle and environmental stimuli, as well as products of microbe–host co-metabolism. Thus, better understanding of the gut microbiome and host metabolic interplay can be gleaned using such analytical approaches. In this review, we describe research findings focussed on gut microbiota–host interactions, for functional insights into the impact of microbiome composition on host health. We evaluate different analytical approaches for capturing metabolic activity and discuss analytical methodological advancements that have made a contribution to the field. This information will aid in developing novel approaches to improve host health in the future, and therapeutic modulation of the microbiome may soon augment conventional clinical strategies.

scholarly journals A Microbiome-Driven Approach to Combating Depression During the COVID-19 Pandemic

2021 ◽  
Vol 8 ◽  
Author(s):  
Mahmoud A. Ghannoum ◽  
MaryKate Ford ◽  
Robert A. Bonomo ◽  
Ahmed Gamal ◽  
Thomas S. McCormick
Keyword(s):  
Gut Microbiome ◽  
Depressive Disorders ◽  
Emotional Health ◽  
Holistic Approach ◽  
Lifestyle Changes ◽  
Current Evidence ◽  
Complementary Approach ◽  
Huge Impact ◽  
The Impact ◽  
Shed Light

The significant stressors brought about and exacerbated by COVID-19 are associated with startling surges in mental health illnesses, specifically those related to depressive disorders. Given the huge impact of depression on society, and an incomplete understanding of impactful therapeutics, we have examined the current literature surrounding the microbiome and gut-brain axis to advance a potential complementary approach to address depression and depressive disorders that have increased during the COVID-19 pandemic. While we understand that the impact of the human gut microbiome on emotional health is a newly emerging field and more research needs to be conducted, the current evidence is extremely promising and suggests at least part of the answer to understanding depression in more depth may lie within the microbiome. As a result of these findings, we propose that a microbiome-based holistic approach, which involves carefully annotating the microbiome and potential modification through diet, probiotics, and lifestyle changes, may address depression. This paper's primary purpose is to shed light on the link between the gut microbiome and depression, including the gut-brain axis and propose a holistic approach to microbiome modification, with the ultimate goal of assisting individuals to manage their battle with depression through diet, probiotics, and lifestyle changes, in addition to offering a semblance of hope during these challenging times.

scholarly journals Association between Apolipoprotein E genotype and the gut microbiome composition in humans and mice

2018 ◽  
Author(s):  
Tam T.T. Tran ◽  
Simone Corsini ◽  
Lee Kellingray ◽  
Claire Hegarty ◽  
Gwénaëlle Le Gall ◽  
...  
Keyword(s):  
Apolipoprotein E ◽  
Gut Microbiome ◽  
Amplicon Sequencing ◽  
Short Chain Fatty Acids ◽  
Faecal Microbiota ◽  
Potential Therapeutic Target ◽  
Microbiome Composition ◽  
The Impact ◽  
Microbiota Diversity ◽  
Apolipoprotein E Genotype

AbstractApolipoprotein E (APOE) genotype is the strongest prevalent genetic risk factor for Alzheimer’s disease. Numerous studies have provided insights into the pathological mechanisms. However, a comprehensive understanding of the impact ofAPOEgenotype on microflora speciation and metabolism is completely lacking. The aim of this study was to investigate the association betweenAPOEgenotype and the gut microbiome composition in human andAPOE-targeted replacement (TR,APOE3andAPOE4) transgenic mice. Faecal microbiota amplicon sequencing from matched individuals with differentAPOEgenotypes revealed no significant differences in overall microbiota diversity (alpha or beta diversity) in group-aggregated humanAPOEgenotypes. However, several bacterial taxa showed significantly different relative abundance betweenAPOEgenotypes. Notably, we detected an association ofPrevotellaceaeandRuminococcaceaeand several butyrate-producing genera abundances withAPOEgenotypes. These findings were confirmed by comparing the gut microbiota ofAPOE-TR mice. Furthermore, metabolomic analysis of faecal water from murine samples detected significant differences in microbe-associated amino acids and short-chain fatty acids betweenAPOEgenotypes. Together, the findings indicate thatAPOEgenotype associated with specific gut microbiome profiles in both humans and inAPOE-TR mice. This suggests that the gut microbiome is worth further investigation as a potential therapeutic target to mitigate the deleterious impact of theAPOE4allele on cognitive decline and the prevention and treatment of AD.

scholarly journals Changes in the Gut Microbiome Community of nonhuman primate following radiation injury

2020 ◽  
Author(s):  
Raj Kalkeri ◽  
Kevin Walters ◽  
William Van Der Pol ◽  
Braden C. McFarland ◽  
Nathan Fisher ◽  
...  
Keyword(s):  
Radiation Exposure ◽  
Gut Microbiome ◽  
Radiation Injury ◽  
Lactobacillus Reuteri ◽  
Whole Body ◽  
High Dose ◽  
Microbiome Composition ◽  
Post Irradiation ◽  
High Doses ◽  
The Impact

Abstract Background Composition and maintenance of the microbiome is vital to gut homeostasis. However, there is limited knowledge regarding the impact of high doses of radiation, which can occur as a result of cancer radiation therapy, nuclear accidents or intentional release of a nuclear or radioactive weapon, on the composition of the gut microbiome. Therefore, we sought to analyze alterations to the gut microbiome of nonhuman primates (NHPs) exposed to high doses of radiation. Methods Fecal samples were collected from 19 NHPs (Chinese rhesus macaques, Macaca mulatta) one day prior and one and four days after exposure to 7.4 Gy cobalt-60 gamma-radiation (LD70 − 80/60). The 16S V4 rRNA sequences were extracted from each sample, followed by bioinformatics analysis using the QIIME platform. Results Alpha Diversity (Shannon Diversity Index), revealed no major difference between pre- and post-irradiation, whereas Beta diversity analysis showed significant differences in the microbiome after irradiation (day + 4) compared to baseline (pre-irradiation). The Firmicutes/Bacteriodetes ratio, a factor known to be associated with disruption of metabolic homeostasis, decreased from 1.2 to less than 1 post-radiation exposure. Actinobacillus, Bacteroides, Prevotella (Paraprevotellaceae family) and Veillonella genera were significantly increased by more than 2-fold and Acinetobacter and Aerococcus genus were decreased by more than 10-fold post-irradiation. Fifty-two percent (10/19) of animals exposed to radiation demonstrated diarrhea at day 4 post-irradiation. Comparison of microbiome composition of feces from animals with and without diarrhea at day 4 post-irradiation revealed an increase in Lactobacillus reuteri associated with diarrhea and a decrease of Lentisphaerae and Verrucomicrobioa phyla and Bacteroides in animals exhibiting diarrhea. Conclusion Our findings demonstrate that substantial alterations in the microbiome composition of NHPs occur following radiation injury and provide insight into early changes with high-dose, whole-body radiation exposure. Future studies will help identify microbiome biomarkers of radiation exposure and develop effective therapeutic intervention to mitigate the radiation injury.

scholarly journals Differences in Gut Microbiota as a Potential Factor in Alzheimer’s Disease Development

2021 ◽  
Vol 10 (3) ◽  
Author(s):  
Briya Patel ◽  
Leya Joykutty
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Gut Microbiome ◽  
Disease Development ◽  
Gamma Aminobutyric Acid ◽  
Human Species ◽  
Microbiome Composition ◽  
Potential Factor ◽  
The Impact ◽  
The Brain

Considering that humans consist of more non-human species than cells, it is critical to understand the impact of the microbiome on diseases. As Alzheimer’s disease becomes a more and more pressing issue, it may be possible to combat it or slow its progress by understanding how alterations in the gut microbiome, which can influence functions in the brain in a variety of ways, affect its development.Gut bacteria can produce neurotransmitters such as melatonin, gamma-aminobutyric acid, histamine, and acetylcholine, which can contribute or antagonize neuroinflammation and neurofibrillary tangles. It is best to balance beneficial bacteria with harmful bacteria. Additionally, using probiotics and altered diets can serve to change gut microbiome composition and influence Alzheimer’s disease development. It is important to understand microbiome-cell interactions and utilize that information to create new therapeutic strategies for Alzheimer’s disease through forms like diets, probiotics, and interventional procedures.

scholarly journals Exploring the impact of Helicobacter pylori on gut microbiome composition

PLoS ONE ◽  
2019 ◽  
Vol 14 (6) ◽  
pp. e0218274 ◽  
Author(s):  
Nihar Ranjan Dash ◽  
Ghalia Khoder ◽  
Aml Mohamed Nada ◽  
Mohammad Tahseen Al Bataineh
Keyword(s):  
Helicobacter Pylori ◽  
Gut Microbiome ◽  
Microbiome Composition ◽  
The Impact

scholarly journals Imidacloprid Decreases Honey Bee Survival Rates but Does Not Affect the Gut Microbiome

2018 ◽  
Vol 84 (13) ◽  
Author(s):  
Kasie Raymann ◽  
Erick V. S. Motta ◽  
Catherine Girard ◽  
Ian M. Riddington ◽  
Jordan A. Dinser ◽  
...  
Keyword(s):  
Honey Bee ◽  
Gut Microbiome ◽  
Honey Bees ◽  
Microbiome Composition ◽  
Susceptibility To Infection ◽  
Bee Colony ◽  
Colony Loss ◽  
Honey Bee Colony ◽  
The Impact

ABSTRACT Accumulating evidence suggests that pesticides have played a role in the increased rate of honey bee colony loss. One of the most commonly used pesticides in the United States is the neonicotinoid imidacloprid. Although the primary mode of action of imidacloprid is on the insect nervous system, it has also been shown to cause changes in insects' digestive physiology and alter the microbiota of Drosophila melanogaster larvae. The honey bee gut microbiome plays a major role in bee health. Although many studies have shown that imidacloprid affects honey bee behavior, its impact on the microbiome has not been fully elucidated. Here, we investigated the impact of imidacloprid on the gut microbiome composition, survivorship, and susceptibility to pathogens of honey bees. Consistent with other studies, we show that imidacloprid exposure results in an elevated mortality of honey bees in the hive and increases the susceptibility to infection by pathogens. However, we did not find evidence that imidacloprid affects the gut bacterial community of honey bees. Our in vitro experiments demonstrated that honey bee gut bacteria can grow in the presence of imidacloprid, and we found some evidence that imidacloprid can be metabolized in the bee gut environment. However, none of the individual bee gut bacterial species tested could metabolize imidacloprid, suggesting that the observed metabolism of imidacloprid within in vitro bee gut cultures is not caused by the gut bacteria. Overall, our results indicate that imidacloprid causes increased mortality in honey bees, but this mortality does not appear to be linked to the microbiome. IMPORTANCE Growing evidence suggests that the extensive use of pesticides has played a large role in the increased rate of honey bee colony loss. Despite extensive research on the effects of imidacloprid on honey bees, it is still unknown whether it impacts the community structure of the gut microbiome. Here, we investigated the impact of imidacloprid on the gut microbiome composition, survivorship, and susceptibility to pathogens of honey bees. We found that the exposure to imidacloprid resulted in an elevated mortality of honey bees and increased the susceptibility to infection by opportunistic pathogens. However, we did not find evidence that imidacloprid affects the gut microbiome of honey bees. We found some evidence that imidacloprid can be metabolized in the bee gut environment in vitro , but because it is quickly eliminated from the bee, it is unlikely that this metabolism occurs in nature. Thus, imidacloprid causes increased mortality in honey bees, but this does not appear to be linked to the microbiome.

scholarly journals The Western Dietary Pattern Combined with Vancomycin-Mediated Changes to the Gut Microbiome Exacerbates Colitis Severity and Colon Tumorigenesis

Nutrients ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 881
Author(s):  
Niklas D. Aardema ◽  
Daphne M. Rodriguez ◽  
Arnaud J. Van Wettere ◽  
Abby D. Benninghoff ◽  
Korry J. Hintze
Keyword(s):  
Colorectal Cancer ◽  
Gut Microbiome ◽  
Tumor Development ◽  
Alpha Diversity ◽  
Basal Diet ◽  
Plain Water ◽  
Microbiome Composition ◽  
Colon Tumorigenesis ◽  
Induced Changes ◽  
The Impact

Previous work by our group using a mouse model of inflammation-associated colorectal cancer (CAC) showed that the total Western diet (TWD) promoted colon tumor development. Others have also shown that vancomycin-mediated changes to the gut microbiome increased colorectal cancer (CRC). Therefore, the objective of this study was to determine the impact of vancomycin on colon tumorigenesis in the context of a standard mouse diet or the TWD. A 2 × 2 factorial design was used, in which C57Bl/6J mice were fed either the standard AIN93G diet or TWD and with vancomycin in the drinking water or not. While both the TWD and vancomycin treatments independently increased parameters associated with gut inflammation and tumorigenesis compared to AIN93G and plain water controls, mice fed the TWD and treated with vancomycin had significantly increased tumor multiplicity and burden relative to all other treatments. Vancomycin treatment significantly decreased alpha diversity and changed the abundance of several taxa at the phylum, family, and genus levels. Conversely, basal diet had relatively minor effects on the gut microbiome composition. These results support our previous research that the TWD promotes colon tumorigenesis and suggest that vancomycin-induced changes to the gut microbiome are associated with higher tumor rates.

scholarly journals Examining the Effects of an Anti-Salmonella Bacteriophage Preparation, BAFASAL®, on Ex-Vivo Human Gut Microbiome Composition and Function Using a Multi-Omics Approach

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1734
Author(s):  
Janice Mayne ◽  
Xu Zhang ◽  
James Butcher ◽  
Krystal Walker ◽  
Zhibin Ning ◽  
...  
Keyword(s):  
Food Chain ◽  
Gut Microbiome ◽  
Food Industry ◽  
Ex Vivo ◽  
Human Gut ◽  
Microbiome Composition ◽  
Human Gut Microbiome ◽  
And Function ◽  
The Impact

Salmonella infections (salmonellosis) pose serious health risks to humans, usually via food-chain contamination. This foodborne pathogen causes major food losses and human illnesses, with significant economic impacts. Overuse of antibiotics in the food industry has led to multidrug-resistant strains of bacteria, and governments are now restricting their use, leading the food industry to search for alternatives to secure food chains. Bacteriophages, viruses that infect and kill bacteria, are currently being investigated and used as replacement treatments and prophylactics due to their specificity and efficacy. They are generally regarded as safe alternatives to antibiotics, as they are natural components of the ecosystem. However, when specifically used in the industry, they can also make their way into humans through our food chain or exposure, as is the case for antibiotics. In particular, agricultural workers could be repeatedly exposed to bacteriophages supplemented to animal feeds. To our knowledge, no studies have investigated the effects of such exposure to bacteriophages on the human gut microbiome. In this study, we used a novel in-vitro assay called RapidAIM to investigate the effect of a bacteriophage mixture, BAFASAL®, used in poultry farming on five individual human gut microbiomes. Multi-omics analyses, including 16S rRNA gene sequencing and metaproteomic, revealed that ex-vivo human gut microbiota composition and function were unaffected by BAFASAL® treatment, providing an additional measure for its safety. Due to the critical role of the gut microbiome in human health and the known role of bacteriophages in regulation of microbiome composition and function, we suggest assaying the impact of bacteriophage-cocktails on the human gut microbiome as a part of their safety assessment.

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