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 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 Possibilities and limits for using the gut microbiome to improve captive animal health

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Jessica Diaz ◽  
Aspen T. Reese
Keyword(s):  
Gut Microbiome ◽  
Host Species ◽  
Animal Health ◽  
Health Impacts ◽  
Wide Range ◽  
Host Health ◽  
In Captivity ◽  
Outstanding Question ◽  
The Impact ◽  
Captive Animal

AbstractBecause of its potential to modulate host health, the gut microbiome of captive animals has become an increasingly important area of research. In this paper, we review the current literature comparing the gut microbiomes of wild and captive animals, as well as experiments tracking the microbiome when animals are moved between wild and captive environments. As a whole, these studies report highly idiosyncratic results with significant differences in the effect of captivity on the gut microbiome between host species. While a few studies have analyzed the functional capacity of captive microbiomes, there has been little research directly addressing the health consequences of captive microbiomes. Therefore, the current body of literature cannot broadly answer what costs, if any, arise from having a captive microbiome in captivity. Addressing this outstanding question will be critical to determining whether it is worth pursuing microbial manipulations as a conservation tool. To stimulate the next wave of research which can tie the captive microbiome to functional and health impacts, we outline a wide range of tools that can be used to manipulate the microbiome in captivity and suggest a variety of methods for measuring the impact of such manipulation preceding therapeutic use. Altogether, we caution researchers against generalizing results between host species given the variability in gut community responses to captivity and highlight the need to understand what role the gut microbiome plays in captive animal health before putting microbiome manipulations broadly into practice.

scholarly journals The Impact and Consequences of SARS-CoV-2 Pandemic on a Single University Dermatology Outpatient Clinic in Germany

2020 ◽  
Vol 17 (17) ◽  
pp. 6182
Author(s):  
Rosi Wang ◽  
Charlotte Helf ◽  
Linda Tizek ◽  
Ruth Neuhauser ◽  
Kilian Eyerich ◽  
...  
Keyword(s):  
Health Care ◽  
Outpatient Clinic ◽  
Skin Diseases ◽  
Health Care Systems ◽  
Age Groups ◽  
Peak Time ◽  
Malignant Diseases ◽  
Inflammatory Skin Diseases ◽  
Care Systems ◽  
The Impact

The pandemic outbreak of coronavirus disease 2019 (COVID-19) affects health care systems globally and leads to other challenges besides infection and its direct medical consequences. The aim of this study was to investigate the impact of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic on the university dermatology outpatient clinic (UDOC) of the Technical University of Munich, Germany. We analyzed datasets from 2015 until 2020 extracted from the hospital information system database and our documented outpatient files regarding patient numbers, gender, age, and diagnoses. In 2020, case numbers of outpatient care declined significantly (p = 0.021) compared to previous years and was related to the timing of political announcements answering SARS-CoV-2 pandemic. Additionally, during calendar week 10 to 15—the peak time of the spread of COVID-19 in Germany—the proportion of patients missing their consultation was significantly higher in 2020 than in 2019 (22.4% vs. 12.4%; p < 0.001). Gender-associated differences regarding absences were not detected, but patients aged 85 years or older were significantly more likely to miss their consultation compared to all other age groups (p = 0.002). Regarding different disease clusters, patients with chronic inflammatory skin diseases and infectious and malignant diseases were more likely to miss their consultation (p = 0.006). Noticeably, less patients with malignant diseases, and particularly malignant melanoma, were registered during this pandemic. Our data support the hypothesis that medically constructive prioritization might not be implemented properly by patients themselves. Identifying missed patients and catching up on their medical care apart from COVID-19 will pose an enormous challenge for health care systems globally.

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 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 Host phylogeny and life history stage shape the gut microbiome in dwarf (Kogia sima) and pygmy (Kogia breviceps) sperm whales

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Elizabeth R. Denison ◽  
Ryan G. Rhodes ◽  
William A. McLellan ◽  
D. Ann Pabst ◽  
Patrick M. Erwin
Keyword(s):  
Gut Microbiome ◽  
Life Stage ◽  
Life History Stage ◽  
Rrna Gene ◽  
Sperm Whales ◽  
Microbiome Composition ◽  
Host Health ◽  
Species Specific ◽  
Kogia Sima ◽  
Host Development

Abstract Gut microbiomes perform crucial roles in host health and development, but few studies have explored cetacean microbiomes especially deep divers. We characterized the gut microbiomes of stranded dwarf (Kogia sima) and pygmy (K. breviceps) sperm whales to examine the effects of phylogeny and life stage on microbiome composition and diversity. 16S rRNA gene sequence analysis revealed diverse gut communities (averaging 674 OTUs) dominated by a few symbiont taxa (25 OTUs accounted for 64% of total relative abundance). Both phylogeny and life stage shaped community composition and diversity, with species-specific microbiome differences present early in life. Further analysis showed evidence of microbiome convergence with host maturity, albeit through different processes: symbiont ‘accumulation’ in K. sima and ‘winnowing’ in K. breviceps, indicating different methods of community assembly during host development. Furthermore, culture-based analyses yielded 116 pure cultures matching 25 OTUs, including one isolate positive for chitin utilization. Our findings indicate that kogiid gut microbiomes are highly diverse and species-specific, undergo significant shifts with host development, and can be cultivated on specialized media under anaerobic conditions. These results enhance our understanding of the kogiid gut microbiome and may provide useful information for symbiont assessment in host health.

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.

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