scholarly journals Dynamic age-associated changes and their driver microbes in healthy gut microbiota of captive crab-eating macaques

2020 ◽  
Author(s):  
Zhi-Yuan Wei ◽  
Jun-Hua Rao ◽  
Ming-Tian Tang ◽  
Guo-An Zhao ◽  
Qi-Chun Li ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Alpha Diversity ◽  
Active Role ◽  
Antibiotic Use ◽  
Microbial Interactions ◽  
Topology Analysis ◽  
Show Evidence ◽  
Gut Mucosa ◽  
Metabolite Synthesis

Abstract Background: Previous population studies have indicated age-associated changes in the gut microbiota. However, the actual age effects on microbiota are inevitably confounded by varying environmental factors such as diets and antibiotic use in the populations. Captive crab-eating macaques reared in a well-controlled environment can provide a useful model to recapitulate dynamic age-associated changes in the healthy primate gut microbiota.Results: We show evidence supporting lifelong age-associated changes in the healthy gut microbiota of captive macaques. The Firmicutes to Bacteroidetes ratio and beta diversity but not alpha diversity changed significantly with age. The most significantly age-associated genera were mainly composed of commensals, such as Faecalibacterium . Unexpectedly, a subset of the age-associated microbes were suspicious pathogens such as Helicobacter and Campylobacter , which were enriched in infant macaques, and possibly associated with gut mucosa development. These age-associated microbes were main contributors to the gut microbiota networks. Importantly, topology analysis showed that connectivity of these networks changed with age, and its rapid decrease in elderly macaques might indicate altered microbial interactions associated with host aging. Prevotella 9 , one of the most abundant age-associated genera, was the driver responsible for the gut microbiota maturation from infants to young adults. In adults, Rikenellaceae RC9 gut group and Megasphaera were two key drivers that continuously played an active role in driving microbial community changes of across different stages of adulthood. We also showed evidence of age-associated changes in gut microbial phenotypes and functions, in particular pathways of immunomodulatory metabolite synthesis, and metabolism of lipids and carbohydrates. The driver microbes were key players involved in these functions.Conclusions: Our current study in captive macaques demonstrate evident age-associated changes during the lifelong process of healthy gut microbiota development. The enrichment of suspicious pathogens in healthy infant macaques might indicate the importance of appropriate exposure to these microbes for the developing immune system. The current study provides new insights into the pivotal role of driver microbes and microbial interactions in gut microbiota, and further underlines the importance of network analysis in microbiome studies. Our findings also provide a baseline for better understanding of disease-related changes in the primate gut microbiota.

scholarly journals Faecal Microbiota in Patients with Neurogenic Bowel Dysfunction and Spinal Cord Injury or Multiple Sclerosis—A Systematic Review

2021 ◽  
Vol 10 (8) ◽  
pp. 1598
Author(s):  
Willemijn Faber ◽  
Janneke Stolwijk-Swuste ◽  
Florian van Ginkel ◽  
Janneke Nachtegaal ◽  
Erwin Zoetendal ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Methodological Quality ◽  
Alpha Diversity ◽  
Bowel Function ◽  
Antibiotic Use ◽  
Bowel Dysfunction ◽  
Healthy Controls ◽  
Cord Injury ◽  
Neurogenic Bowel

Background: Neurogenic bowel dysfunction (NBD) frequently occurs in patients with spinal cord injury (SCI) and multiple sclerosis (MS) with comparable symptoms and is often difficult to treat. It has been suggested the gut microbiota might influence the course of NBD. We systematically reviewed the literature on the composition of the gut microbiota in SCI and MS, and the possible role of neurogenic bowel function, diet and antibiotic use. Methods: A systematic search was conducted in PubMed and Embase, which retrieved studies on the gut microbiota in SCI and MS. The Newcastle–Ottawa Quality Assessment Scale (NOS) was used to assess methodological quality. Results: We retrieved fourteen papers (four on SCI, ten on MS), describing the results of a total of 479 patients. The number of patients per study varied from 13 to 89 with an average of 34. Thirteen papers were observational studies and one study was an intervention study. The studies were case control studies in which the gut microbiota composition was determined by 16S rRNA gene sequencing. The methodological quality of the studies was mostly rated to be moderate. Results of two studies suggested that alpha diversity in chronic SCI patients is lower compared to healthy controls (HC), whereas results from five studies suggest that the alpha diversity of MS patients is similar compared to healthy subjects. The taxonomic changes in MS and SCI studies are diverse. Most studies did not account for possible confounding by diet, antibiotic use and bowel function. Conclusion: Based on these 14 papers, we cannot draw strong conclusions on the composition of the gut microbiota in SCI and MS patients. Putatively, alpha diversity in chronic SCI patients may be lower compared to healthy controls, while in MS patients, alpha diversity may be similar or lower compared to healthy controls. Future studies should provide a more detailed description of clinical characteristics of participants and of diet, antibiotic use and bowel function in order to make valid inferences on changes in gut microbiota and the possible role of diet, antibiotic use and bowel function in those changes.

scholarly journals Quantifying the impact of treatment history on plasmid-mediated resistance evolution in human gut microbiota

2019 ◽  
Vol 116 (46) ◽  
pp. 23106-23116 ◽  
Author(s):  
Burcu Tepekule ◽  
Pia Abel zur Wiesch ◽  
Roger D. Kouyos ◽  
Sebastian Bonhoeffer
Keyword(s):  
Antibiotic Resistance ◽  
Gut Microbiota ◽  
Drug Exposure ◽  
Center Of Mass ◽  
Antibiotic Use ◽  
Resistance Evolution ◽  
Treatment History ◽  
Resistant Infection ◽  
The Impact

To understand how antibiotic use affects the risk of a resistant infection, we present a computational model of the population dynamics of gut microbiota including antibiotic resistance-conferring plasmids. We then describe how this model is parameterized based on published microbiota data. Finally, we investigate how treatment history affects the prevalence of resistance among opportunistic enterobacterial pathogens. We simulate treatment histories and identify which properties of prior antibiotic exposure are most influential in determining the prevalence of resistance. We find that resistance prevalence can be predicted by 3 properties, namely the total days of drug exposure, the duration of the drug-free period after last treatment, and the center of mass of the treatment pattern. Overall this work provides a framework for capturing the role of the microbiome in the selection of antibiotic resistance and highlights the role of treatment history for the prevalence of resistance.

The Role of Biology in the Fossilization of Embryos and Other Soft-Bodied Organisms: Microbial Biofilms and Lagerstätten

2014 ◽  
Vol 20 ◽  
pp. 83-100
Author(s):  
Rudolf A. Raff ◽  
Elizabeth C. Raff
Keyword(s):  
Soft Tissue ◽  
Soft Tissues ◽  
Active Role ◽  
Microbial Interactions ◽  
Skin Texture ◽  
Microbial Biofilms ◽  
Insect Wings ◽  
Large Animals ◽  
Simple Systems

Soft-tissue fossils are among the most striking and informative remains of extinct organisms. Although relatively rare, they are diverse, ranging from single microbial cells to nuclei and chromosomes; algae; metazoan embryos and larvae; flowers; complete, small, soft-bodied metazoans, metazoan tissues; integumentary structures such as melanosomes; skin texture, vertebrate feathers and hair, insect wings with color patterns, and sometimes even the entire bodies of large animals. The susceptibility of newly dead soft tissues to physical destruction, consumption, and microbial decay makes their preservation unlikely under most taphonomic conditions. In addition, their vulnerability to rapid autolysis, bioturbation, and destructive physical processes requires that rapid biological events must occur as the critical first steps of fossilization. An understanding of the processes by which biological remains enter the fossil record is important in inferring what non-microbial and microbial processes were operative in Lagerstätten. Paleontologists have recognized that microbial biofilms often accompany soft-tissue fossils, and have suggested that bacteria play an active role in soft tissue fossilization, but that role must be determined experimentally with living bacteria and dead tissue.Marine embryos and marine bacteria are used to investigate the processes that mediate early steps in soft-tissue preservation because they offer simple systems for laboratory investigation of the roles of autolysis-blocking environments, microbial interactions, biofilm formation, and authigenic mineralization in taphonomy. Understanding microbially mediated preservation of embryos may supply new insights into a more general biology of fossilization.

scholarly journals The Role of Housing Environment and Dietary Protein Source on the Gut Microbiota of Chicken

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1085 ◽  
Author(s):  
Shawna Marie Hubert ◽  
Morouj Al-Ajeeli ◽  
Christopher A. Bailey ◽  
Giridhar Athrey
Keyword(s):  
Food Safety ◽  
Gut Microbiota ◽  
Production Systems ◽  
Alpha Diversity ◽  
The United States ◽  
Health Food ◽  
Feed Composition ◽  
Industry Standard ◽  
And Performance

The gut microbiota of chicken has received much attention due to its importance for bird health, food safety, and performance. In the United States, the impending transition to cage-free housing environments has raised many questions about its consequences for poultry health, productivity, and welfare. Therefore, we investigated how housing environments and feed composition affect the poultry gut microbiome. Such data is necessary to inform the design of production systems that promote health and food safety. In this study, we investigated the cecal microbiome of both caged and cage-free laying hens that were fed either an industry-standard soy-based versus a soy-free diet. Caged hens were housed in standard industry-style layer cages with one bird per cage, and cage-free hens were housed in a poultry barn with an outdoor enclosed yard with multiple hens per pen. Our study showed significant differences in the gut microbiota between cage-free and caged environments. Cage free housing generated higher diversity compared to caged housing. Furthermore, we observed a synergistic interaction of soy-based feed in cage-free housing, as the cage-free soy group showed the highest alpha diversity, whereas the caged-soy group showed the lowest diversity overall.

scholarly journals Tephritid-microbial interactions to enhance fruit fly performance in sterile insect technique programs

2019 ◽  
Vol 19 (S1) ◽  
Author(s):  
Ania T. Deutscher ◽  
Toni A. Chapman ◽  
Lucas A. Shuttleworth ◽  
Markus Riegler ◽  
Olivia L. Reynolds
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Sterile Insect Technique ◽  
Fruit Fly ◽  
Mass Rearing ◽  
Fruit Flies ◽  
Microbial Interactions ◽  
Important Pest ◽  
Gut Microbial Community

Abstract Background The Sterile Insect Technique (SIT) is being applied for the management of economically important pest fruit flies (Diptera: Tephritidae) in a number of countries worldwide. The success and cost effectiveness of SIT depends upon the ability of mass-reared sterilized male insects to successfully copulate with conspecific wild fertile females when released in the field. Methods We conducted a critical analysis of the literature about the tephritid gut microbiome including the advancement of methods for the identification and characterization of microbiota, particularly next generation sequencing, the impacts of irradiation (to induce sterility of flies) and fruit fly rearing, and the use of probiotics to manipulate the fruit fly gut microbiota. Results Domestication, mass-rearing, irradiation and handling, as required in SIT, may change the structure of the fruit flies’ gut microbial community compared to that of wild flies under field conditions. Gut microbiota of tephritids are important in their hosts’ development, performance and physiology. Knowledge of how mass-rearing and associated changes of the microbial community impact the functional role of the bacteria and host biology is limited. Probiotics offer potential to encourage a gut microbial community that limits pathogens, and improves the quality of fruit flies. Conclusions Advances in technologies used to identify and characterize the gut microbiota will continue to expand our understanding of tephritid gut microbial diversity and community composition. Knowledge about the functions of gut microbes will increase through the use of gnotobiotic models, genome sequencing, metagenomics, metatranscriptomics, metabolomics and metaproteomics. The use of probiotics, or manipulation of the gut microbiota, offers significant opportunities to enhance the production of high quality, performing fruit flies in operational SIT programs.

scholarly journals A systematic review on the role of microbiota in the pathogenesis and treatment of eating disorders

2020 ◽  
Vol 64 (1) ◽  
Author(s):  
Elvira Anna Carbone ◽  
Pasquale D'Amato ◽  
Giuseppe Vicchio ◽  
Pasquale De Fazio ◽  
Cristina Segura-Garcia
Keyword(s):  
Systematic Review ◽  
Eating Disorders ◽  
Gut Microbiota ◽  
Intestinal Inflammation ◽  
Fecal Microbiota Transplantation ◽  
Alpha Diversity ◽  
Fecal Microbiota ◽  
Cochrane Library ◽  
Affective Symptoms

Abstract Background There is growing interest in new factors contributing to the genesis of eating disorders (EDs). Research recently focused on the study of microbiota. Dysbiosis, associated with a specific genetic susceptibility, may contribute to the development of anorexia nervosa (AN), bulimia nervosa, or binge eating disorder, and several putative mechanisms have already been identified. Diet seems to have an impact not only on modification of the gut microbiota, facilitating dysbiosis, but also on its recovery in patients with EDs. Methods This systematic review based on the PICO strategy searching into PubMed, EMBASE, PsychINFO, and Cochrane Library examined the literature on the role of altered microbiota in the pathogenesis and treatment of EDs. Results Sixteen studies were included, mostly regarding AN. Alpha diversity and short-chain fatty acid (SCFA) levels were lower in patients with AN, and affective symptoms and ED psychopathology seem related to changes in gut microbiota. Microbiota-derived proteins stimulated the autoimmune system, altering neuroendocrine control of mood and satiety in EDs. Microbial richness increased in AN after weight regain on fecal microbiota transplantation. Conclusions Microbiota homeostasis seems essential for a healthy communication network between gut and brain. Dysbiosis may promote intestinal inflammation, alter gut permeability, and trigger immune reactions in the hunger/satiety regulation center contributing to the pathophysiological development of EDs. A restored microbial balance may be a possible treatment target for EDs. A better and more in-depth characterization of gut microbiota and gut–brain crosstalk is required. Future studies may deepen the therapeutic and preventive role of microbiota in EDs.

scholarly journals From Intrauterine to Extrauterine Life—The Role of Endogenous and Exogenous Factors in the Regulation of the Intestinal Microbiota Community and Gut Maturation in Early Life

2021 ◽  
Vol 8 ◽  
Author(s):  
Anna Socha-Banasiak ◽  
Malwina Pawłowska ◽  
Elżbieta Czkwianianc ◽  
Kateryna Pierzynowska
Keyword(s):  
Immune System ◽  
Gut Microbiota ◽  
Human Life ◽  
Antibiotic Use ◽  
Lymphoid Cells ◽  
Microbial Colonization ◽  
Digestive Tube ◽  
The Impact ◽  
Gut Maturation

Differentiation of the digestive tube and formation of the gut unit as a whole, are regulated by environmental factors through epigenetic modifications which enhance cellular plasticity. The critical period of DNA imprinting lasts from conception until approximately the 1,000th day of human life. During pregnancy, besides agents that may directly promote epigenetic programming (e.g., folate, zinc, and choline supplementation), some factors (e.g., antibiotic use, dietary components) can affect the composition of the mother's microbiota, in turn affecting the fetal microbiome which interacts with the offspring's intestinal epithelial cells. According to available literature that confirms intrauterine microbial colonization, the impact of the microbiome and its metabolites on the genome seems to be key in fetal development, including functional gut maturation and the general health status of the offspring, as well as later on in life. Although the origin of the fetal microbiome is still not well-understood, the bacteria may originate from both the vagina, as the baby is born, as well as from the maternal oral cavity/gut, through the bloodstream. Moreover, the composition of the fetal gut microbiota varies depending on gestational age, which in turn possibly affects the regulation of the immune system at the barrier between mother and fetus, leading to differences in the ability of microorganisms to access and survive in the fetal environment. One of the most important local functions of the gut microbiota during the prenatal period is their exposure to foreign antigens which in turn contributes to immune system and tissue development, including fetal intestinal Innate Lymphoid Cells (ILCs). Additional factors that determine further infant microbiome development include whether the infant is born premature or at term, the method of delivery, maternal antibiotic use, and the composition of the mother's milk, among others. However, the latest findings highlight the fact that a more diverse infant gut microbiome at birth facilitates the proliferation of stem cells by microbial metabolites and accelerates infant development. This phenomenon confirms the unique role of microbiome. This review emphasizes the crucial perinatal and postnatal factors that may influence fetal and neonatal microbiota, and in turn gut maturation.

scholarly journals Fecal microbiota transplantation in HIV: A pilot placebo-controlled study

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sergio Serrano-Villar ◽  
Alba Talavera-Rodríguez ◽  
María José Gosalbes ◽  
Nadia Madrid ◽  
José A. Pérez-Molina ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Fecal Microbiota Transplantation ◽  
Alpha Diversity ◽  
Antibiotic Use ◽  
Fecal Microbiota ◽  
Controlled Study ◽  
Double Blind Study ◽  
Intestinal Damage ◽  
Double Blind ◽  
Fatty Acid Binding

AbstractChanges in the microbiota have been linked to persistent inflammation during treated HIV infection. In this pilot double-blind study, we study 30 HIV-infected subjects on antiretroviral therapy (ART) with a CD4/CD8 ratio < 1 randomized to either weekly fecal microbiota capsules or placebo for 8 weeks. Stool donors were rationally selected based on their microbiota signatures. We report that fecal microbiota transplantation (FMT) is safe, not related to severe adverse events, and attenuates HIV-associated dysbiosis. FMT elicits changes in gut microbiota structure, including significant increases in alpha diversity, and a mild and transient engraftment of donor’s microbiota during the treatment period. The greater engraftment seems to be achieved by recent antibiotic use before FMT. The Lachnospiraceae and Ruminococcaceae families, which are typically depleted in people with HIV, are the taxa more robustly engrafted across time-points. In exploratory analyses, we describe a significant amelioration in the FMT group in intestinal fatty acid-binding protein (IFABP), a biomarker of intestinal damage that independently predicts mortality. Gut microbiota manipulation using a non-invasive and safe strategy of FMT delivery is feasible and deserves further investigation. Trial number: NCT03008941.

scholarly journals The varying effects of antibiotics on gut microbiota

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lulu Yang ◽  
Ousman Bajinka ◽  
Pa Omar Jarju ◽  
Yurong Tan ◽  
Aji Mary Taal ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Bacterial Communities ◽  
Antibiotic Use ◽  
Therapeutic Drugs ◽  
Antibiotic Drug ◽  
Drug Doses ◽  
Animal Feeding ◽  
The Common

AbstractAntibiotics are lifesaving therapeutic drugs that have been used by human for decades. They are used both in the fight against bacterial pathogens for both human and for animal feeding. However, of recent, their effects on the gut microbial compositions and diversities have attracted much attention. Existing literature have established the dysbiosis (reduced diversity) in the gut microbiota in association with antibiotic and antibiotic drug doses. In the light of spelling out the varying effects of antibiotic use on gut microbiota, this review aimed at given an account on the degree of gut microbial alteration caused by common antibiotics. While some common antibiotics are found to destroy the common phyla, other debilitating effects were observed. The effects can be attributed to the mode of mechanism, the class of antibiotic, the degree of resistance of the antibiotic used, the dosage used during the treatment, the route of administration, the pharmacokinetic and pharmacodynamics properties and the spectrum of the antibiotic agent. Health status, stress or the type of diet an individual feeds on could be a great proportion as confounding factors. While it is understood that only the bacterial communities are explored in the quest to establishing the role of gut in health, other gut microbial species are somehow contributing to the dysbiosis status of the gut microbiota. Until now, long term natural fluctuations like diseases outbreaks and mutations of the strain might as well rendered alteration to the gut independent of antibiotic treatments.

scholarly journals Role of the Aryl Hydrocarbon Receptor and Gut Microbiota-Derived Metabolites Indole-3-Acetic Acid in Sulforaphane Alleviates Hepatic Steatosis in Mice

2021 ◽  
Vol 8 ◽  
Author(s):  
Xiuxiu Xu ◽  
Siyuan Sun ◽  
Ling Liang ◽  
Chenxi Lou ◽  
Qijin He ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Gut Microbiota ◽  
Aryl Hydrocarbon Receptor ◽  
Hepatic Steatosis ◽  
Cholesterol Metabolism ◽  
Microbial Interactions ◽  
Aryl Hydrocarbon ◽  
Reduced Body ◽  
Indole 3 Acetic Acid

Scope: Gut microbiome-derived metabolites are the major mediators of diet-induced host-microbial interactions. Aryl hydrocarbon receptor (AHR) plays a crucial role in glucose, lipid, and cholesterol metabolism in the liver. In this study, we aimed to investigate the role of indole-3-acetic acid (IAA) and AHR in sulforaphane (SFN) alleviates hepatic steatosis in mice fed on a high-fat diet (HFD).Methods and Results: The HFD-fed male C57BL/6 mice were intervened with SFN for 6 weeks. HFD-mice showed classical pathophysiological characteristics of hepatic steatosis. The results showed that SFN significantly reduced body weight, liver inflammation and hepatic steatosis in HFD-fed mice. SFN reduced hepatic lipogenesis by activating AHR/SREBP-1C pathway, which was confirmed in HepG2 cell experiments. Moreover, SFN increased hepatic antioxidant activity by modulating Nrf-2/NQO1 expression. SFN increased serum and liver IAA level in HFD mice. Notably, SFN manipulated the gut microbiota, resulting in reducing Deferribacteres and proportions of the phylum Firmicutes/Bacteroidetes and increasing the abundance of specific bacteria that produce IAA. Furthermore, SFN upregulated Ahr expression and decreased the expression of inflammatory cytokines in Raw264.7 cells.Conclusions: SFN ameliorated hepatic steatosis not only by modulating lipid metabolism via AHR/SREBP-1C pathway but regulating IAA and gut microbiota in HFD-induced NAFLD mice.

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