scholarly journals Parallel signatures of mammalian domestication and human industrialization in the gut microbiota

2019 ◽  
Author(s):  
Aspen T. Reese ◽  
Katia S. Chadaideh ◽  
Caroline E. Diggins ◽  
Mark Beckel ◽  
Peggy Callahan ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
Dominant Role ◽  
Domestic Animals ◽  
Domestic Animal ◽  
Microbial Interactions ◽  
Laboratory Mice ◽  
Wild Mammals ◽  
Traditional Societies ◽  
Ecological Shifts

AbstractDomestication may have had convergent effects on the microbiota of domesticates and humans through analogous ecological shifts. Comparing the gut microbiota of domestic and related wild mammals plus humans and chimpanzees, we found consistent shifts in composition in domestic animals and in humans from industrialized but not traditional societies. Reciprocal diet switches in mice and canids demonstrated that diet played a dominant role in shaping the domestic gut microbiota, with stronger responses in the member of the wild-domestic pair with higher dietary and microbial diversity. Laboratory mice recovered wild-like microbial diversity and responsiveness with experimental colonization. We conclude that domestication and industrialization have similarly impacted the gut microbiota, emphasizing the utility of domestic animal models and diets for understanding host-microbial interactions in rapidly changing environments.

scholarly journals A Model System for Feralizing Laboratory Mice in Large Farmyard-Like Pens

2021 ◽  
Vol 11 ◽  
Author(s):  
Henriette Arnesen ◽  
Linn Emilie Knutsen ◽  
Bente Wabakken Hognestad ◽  
Grethe Marie Johansen ◽  
Mats Bemark ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Real Life ◽  
Domestic Animal ◽  
Microbial Colonization ◽  
Housing System ◽  
Laboratory Mice ◽  
Natural Behavior ◽  
Immunological Phenotype ◽  
Living Mouse ◽  
Microbial Environment

Laboratory mice are typically housed under extremely clean laboratory conditions, far removed from the natural lifestyle of a free-living mouse. There is a risk that this isolation from real-life conditions may lead to poor translatability and misinterpretation of results. We and others have shown that feral mice as well as laboratory mice exposed to naturalistic environments harbor a more diverse gut microbiota and display an activated immunological phenotype compared to hygienic laboratory mice. We here describe a naturalistic indoors housing system for mice, representing a farmyard-type habitat typical for house mice. Large open pens were installed with soil and domestic animal feces, creating a highly diverse microbial environment and providing space and complexity allowing for natural behavior. Laboratory C57BL/6 mice were co-housed in this system together with wild-caught feral mice, included as a source of murine microbionts. We found that mice feralized in this manner displayed a gut microbiota structure similar to their feral cohabitants, such as higher relative content of Firmicutes and enrichment of Proteobacteria. Furthermore, the immunophenotype of feralized mice approached that of feral mice, with elevated levels of memory T-cells and late-stage NK cells compared to laboratory-housed control mice, indicating antigenic experience and immune training. The dietary elements presented in the mouse pens could only moderately explain changes in microbial colonization, and none of the immunological changes. In conclusion, this system enables various types of studies using genetically controlled mice on the background of adaptation to a high diversity microbial environment and a lifestyle natural for the species.

scholarly journals The gut microbiome of laboratory mice: considerations and best practices for translational research

2021 ◽  
Author(s):  
Aaron C. Ericsson ◽  
Craig L. Franklin
Keyword(s):  
Human Physiology ◽  
Best Practices ◽  
Gut Microbiota ◽  
Translational Research ◽  
Mouse Models ◽  
Gut Microbiome ◽  
Predictive Power ◽  
Environmental Influences ◽  
Pharmacological Intervention ◽  
Laboratory Mice

AbstractJust as the gut microbiota (GM) is now recognized as an integral mediator of environmental influences on human physiology, susceptibility to disease, and response to pharmacological intervention, so too does the GM of laboratory mice affect the phenotype of research using mouse models. Multiple experimental factors have been shown to affect the composition of the GM in research mice, as well as the model phenotype, suggesting that the GM represents a major component in experimental reproducibility. Moreover, several recent studies suggest that manipulation of the GM of laboratory mice can substantially improve the predictive power or translatability of data generated in mouse models to the human conditions under investigation. This review provides readers with information related to these various factors and practices, and recommendations regarding methods by which issues with poor reproducibility or translatability can be transformed into discoveries.

scholarly journals Effects of Psychotropics on the Microbiome in Patients With Depression and Anxiety: Considerations in a Naturalistic Clinical Setting

2020 ◽  
Author(s):  
Yoshihiro Tomizawa ◽  
Shunya Kurokawa ◽  
Daiki Ishii ◽  
Katsuma Miyaho ◽  
Chiharu Ishii ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
Depressive Disorders ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Shannon Index ◽  
Rrna Gene ◽  
Depression And Anxiety ◽  
The Impact ◽  
Whole Tree

Abstract Background The antibacterial effects of psychotropics may be part of their pharmacological effects when treating depression. However, limited studies have focused on gut microbiota in relation to prescribed medication. Method We longitudinally investigated the relationship between patients’ prescribed medications and intestinal bacterial diversity in a naturalistic treatment course for patients with major depressive disorders and anxiety disorders. Patients were recruited and their stool was collected at 3 time points during their usual psychiatric treatments. Gut microbiota were analyzed using 16S rRNA gene sequencing. We examined the impact of psychotropics (i.e., antidepressants, anxiolytics, antipsychotics) on their gut microbial diversity and functions. Results We collected 246 stool samples from 40 patients. Despite no differences in microbial diversity between medication groups at the baseline, over the course of treatment, phylogenic diversity whole-tree diversity decreased in patients on antipsychotics compared with patients without (P = .027), and beta diversity followed this trend. Based on a fixed-effect model, antipsychotics predicted microbial diversity; the higher doses correlated with less diversity based on the Shannon index and phylogenic diversity whole tree (estimate = −0.00254, SE = 0.000595, P < .0001; estimate = −0.02644, SE = 0.00833, P = .002, respectively). Conclusion Antipsychotics may play a role in decreasing the alpha diversity of the gut microbiome among patients with depression and anxiety, and our results indicate a relationship with medication dosage. Future studies are warranted and should consider patients’ types and doses of antipsychotics in order to further elucidate the mechanisms of gut-brain interactions in psychiatric disorders.

scholarly journals Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community

mBio ◽  
2013 ◽  
Vol 4 (2) ◽  
Author(s):  
Jizhong Zhou ◽  
Wenzong Liu ◽  
Ye Deng ◽  
Yi-Huei Jiang ◽  
Kai Xue ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Diversity ◽  
Microbial Community Structure ◽  
Community Assembly ◽  
Ecosystem Functioning ◽  
Dominant Role ◽  
Microbial Biodiversity ◽  
Stochastic Assembly

ABSTRACTThe processes and mechanisms of community assembly and its relationships to community functioning are central issues in ecology. Both deterministic and stochastic factors play important roles in shaping community composition and structure, but the connection between community assembly and ecosystem functioning remains elusive, especially in microbial communities. Here, we used microbial electrolysis cell reactors as a model system to examine the roles of stochastic assembly in determining microbial community structure and functions. Under identical environmental conditions with the same source community, ecological drift (i.e., initial stochastic colonization) and subsequent biotic interactions created dramatically different communities with little overlap among 14 identical reactors, indicating that stochastic assembly played dominant roles in determining microbial community structure. Neutral community modeling analysis revealed that deterministic factors also played significant roles in shaping microbial community structure in these reactors. Most importantly, the newly formed communities differed substantially in community functions (e.g., H2production), which showed strong linkages to community structure. This study is the first to demonstrate that stochastic assembly plays a dominant role in determining not only community structure but also ecosystem functions. Elucidating the links among community assembly, biodiversity, and ecosystem functioning is critical to understanding ecosystem functioning, biodiversity preservation, and ecosystem management.IMPORTANCEMicroorganisms are the most diverse group of life known on earth. Although it is well documented that microbial natural biodiversity is extremely high, it is not clear why such high diversity is generated and maintained. Numerous studies have established the roles of niche-based deterministic factors (e.g., pH, temperature, and salt) in shaping microbial biodiversity, the importance of stochastic processes in generating microbial biodiversity is rarely appreciated. Moreover, while microorganisms mediate many ecosystem processes, the relationship between microbial diversity and ecosystem functioning remains largely elusive. Using a well-controlled laboratory system, this study provides empirical support for the dominant role of stochastic assembly in creating variations of microbial diversity and the first explicit evidence for the critical role of community assembly in influencing ecosystem functioning. The results presented in this study represent important contributions to the understanding of the mechanisms, especially stochastic processes, involved in shaping microbial biodiversity.

scholarly journals Challenges and Opportunities Developing Mathematical Models of Shared Pathogens of Domestic and Wild Animals

2018 ◽  
Vol 5 (4) ◽  
pp. 92 ◽  
Author(s):  
Kathryn Huyvaert ◽  
Robin Russell ◽  
Kelly Patyk ◽  
Meggan Craft ◽  
Paul Cross ◽  
...  
Keyword(s):  
Mathematical Models ◽  
Domestic Animals ◽  
Domestic Animal ◽  
Pathogen Transmission ◽  
Management Actions ◽  
Animal Populations ◽  
Challenges And Opportunities ◽  
Conservation Concern ◽  
Transmission Pathways ◽  
And Control

Diseases that affect both wild and domestic animals can be particularly difficult to prevent, predict, mitigate, and control. Such multi-host diseases can have devastating economic impacts on domestic animal producers and can present significant challenges to wildlife populations, particularly for populations of conservation concern. Few mathematical models exist that capture the complexities of these multi-host pathogens, yet the development of such models would allow us to estimate and compare the potential effectiveness of management actions for mitigating or suppressing disease in wildlife and/or livestock host populations. We conducted a workshop in March 2014 to identify the challenges associated with developing models of pathogen transmission across the wildlife-livestock interface. The development of mathematical models of pathogen transmission at this interface is hampered by the difficulties associated with describing the host-pathogen systems, including: (1) the identity of wildlife hosts, their distributions, and movement patterns; (2) the pathogen transmission pathways between wildlife and domestic animals; (3) the effects of the disease and concomitant mitigation efforts on wild and domestic animal populations; and (4) barriers to communication between sectors. To promote the development of mathematical models of transmission at this interface, we recommend further integration of modern quantitative techniques and improvement of communication among wildlife biologists, mathematical modelers, veterinary medicine professionals, producers, and other stakeholders concerned with the consequences of pathogen transmission at this important, yet poorly understood, interface.

scholarly journals A Tutela do Animal Doméstico no Âmbito das Constituições Federais Brasileiras de 1824 a 1988

2020 ◽  
Vol 20 (1) ◽  
pp. 2-11
Author(s):  
Nilsen Aparecida Vieira Marcondes
Keyword(s):  
Human Life ◽  
Domestic Animals ◽  
Domestic Animal ◽  
Point Of View ◽  
Continuous Development ◽  
Exotic Animals ◽  
Socially Constructed ◽  
Federal Constitution ◽  
The Subject ◽  
The Way

Objetiva-se discutir neste breve intróito retrospectivo de revisão de normatizações constitucionais pátrias a tutela do animal doméstico. Esta síntese reflexiva sobre a tutela do animal doméstico brasileiro no âmbito constitucional se apresenta quanto à forma de abordagem do assunto, como qualitativo, no que tange a modalidade investigativa como básico, do ponto de vista de seus objetivos, como descritivo, com relação aos procedimentos técnicos, qualifica-se como documental e bibliográfico. Conclui-se que os delineamentos, os limites, bem como os avanços na conquista da tutela animal e consequentemente do animal doméstico demonstram o quanto o reconhecimento de tal questão é socialmente construído. Além disso, a expansão, a solidificação e o desenvolvimento contínuo também da vida humana e da sociedade implicam necessariamente na preservação e na ampliação de acesso um direito fundamental nominalmente reconhecido pela Constituição Federal de 1988 como direito ao ambiente ecologicamente equilibrado no qual se insere evidentemente a fauna, ou seja, os animais domésticos, domesticados, silvestres e exóticos. Palavras-chave: Animal Doméstico. Tutela. Constituições Federais. Brasil.  AbstractThe objective of this brief retrospective introjective review of constitutional norms is to discuss the protection of domestic animals. This reflexive synthesis about the protection of the Brazilian domestic animal in the constitutional scope presents itself as to the way of approaching the subject, as qualitative, in what refers to the research modality as basic, from the point of view of its objectives, as descriptive, with respect to the procedures technicians, qualifies as documentary and bibliographical. It is concluded that the delineations, the limits, as well as the advances in the conquest of the animal guardianship and consequently of the domestic animal demonstrate how much the recognition of such question is socially constructed. In addition, the expansion, solidification and continuous development of human life and society necessarily imply the preservation and expansion of access to a fundamental right nominally recognized by the Federal Constitution of 1988 as a right to an environmentally balanced environment in which the animal, domesticated, wild and exotic animals. Keywords: Domestic Animals. Guardianship. Federal Constitutions. Brasil.

scholarly journals Microbial Diversity Profiling of Gut Microbiota of Macropus giganteus Using Three Hypervariable Regions of the Bacterial 16S rRNA

2021 ◽  
Vol 9 (8) ◽  
pp. 1721
Author(s):  
Christian O’Dea ◽  
Roger Huerlimann ◽  
Nicole Masters ◽  
Anna Kuballa ◽  
Cameron Veal ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Microbial Diversity ◽  
Surface Waters ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Faecal Contamination ◽  
Hypervariable Regions ◽  
Geographical Regions ◽  
V3 Region

Animal faecal contamination of surface waters poses a human health risk, as they may contain pathogenic bacteria or viruses. Of the numerous animal species residing along surface waterways in Australia, macropod species are a top contributor to wild animals’ faecal pollution load. We characterised the gut microbiota of 30 native Australian Eastern Grey Kangaroos from six geographical regions (five kangaroos from each region) within South East Queensland in order to establish their bacterial diversity and identify potential novel species-specific bacteria for the rapid detection of faecal contamination of surface waters by these animals. Using three hypervariable regions (HVRs) of the 16S rRNA gene (i.e., V1–V3, V3–V4, and V5–V6), for their effectiveness in delineating the gut microbial diversity, faecal samples from each region were pooled and microbial genomic DNA was extracted, sequenced, and analysed. Results indicated that V1-V3 yielded a higher taxa richness due to its larger target region (~480 bp); however, higher levels of unassigned taxa were observed using the V1-V3 region. In contrast, the V3–V4 HVR (~569 bp) attained a higher likelihood of a taxonomic hit identity to the bacterial species level, with a 5-fold decrease in unassigned taxa. There were distinct dissimilarities in beta diversity between the regions, with the V1-V3 region displaying the highest number of unique taxa (n = 42), followed by V3–V4 (n = 11) and V5–V6 (n = 8). Variations in the gut microbial diversity profiles of kangaroos from different regions were also observed, which indicates that environmental factors may impact the microbial development and, thus, the composition of the gut microbiome of these animals.

scholarly journals Re-emergence of animal rabies in northern Greece and subsequent human exposure, October 2012 – March 2013

2013 ◽  
Vol 18 (18) ◽  
Author(s):  
S Tsiodras ◽  
G Dougas ◽  
A Baka ◽  
C Billinis ◽  
S Doudounakis ◽  
...  
Keyword(s):  
Domestic Animals ◽  
Domestic Animal ◽  
World Health ◽  
Post Exposure Prophylaxis ◽  
Rabies Case ◽  
Red Foxes ◽  
Northern Greece ◽  
The World ◽  
Health Organization ◽  
Exposure Prophylaxis

Greece has been rabies-free since 1987 with no human cases since 1970. During 2012 to 2013, rabies has re-emerged in wild and domestic animals in northern Greece. By end March 2013, rabies was diagnosed in 17 animals including 14 red foxes, two shepherd dogs and one cat; 104 subsequent human exposures required post-exposure prophylaxis according to the World Health Organization criteria. Human exposures occurred within 50 km radius of a confirmed rabies case in a wild or domestic animal, and most frequently stray dogs were involved.

scholarly journals Grazing Management Influences Gut Microbial Diversity of Livestock in the Same Area

2020 ◽  
Vol 12 (10) ◽  
pp. 4160
Author(s):  
Pengfei Song ◽  
Wen Qin ◽  
YanGan Huang ◽  
Lei Wang ◽  
Zhenyuan Cai ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
Qaidam Basin ◽  
Management Strategies ◽  
Grazing Management ◽  
Important Indicator ◽  
Sheep And Goats ◽  
Free Range ◽  
Significant Difference ◽  
Healthy Growth

The composition of gut microbiota is closely related to health and nutrition of livestock. Research on the interaction between gut microbiota in livestock and grazing management strategies is unfortunately sparse. By studying the compositions of gut microbiota in sheep and goats in a single, mixed grazing population under the control of herdsman, as well as those of free-range camels in the same area of Qaidam Basin, we found that the composition of gut microbiota between sheep and goats showed no significant difference. However, there were significant differences between mixed group and camels at α- and β-diversities. We speculate that grazing management can shape gut microbial diversity indirectly. Mixed grazing under the control of herdsman lead to similarities in the diversity of gut microbiota among different species and limit their diversities of gut microbiota, which is not conducive to healthy growth of the host. On the contrary, free-range grazing is better for the diversity of gut microbiota. In order to sustainably manage populations of livestock, gut microbiota analysis may prove to be an important indicator for evaluating the merits of different grazing management strategies. Our results lay a foundation to improve the health of livestock and grazing management.

scholarly journals Dynamic Changes in the Gut Microbiome at the Acute Stage of Ischemic Stroke in a Pig Model

2020 ◽  
Vol 14 ◽  
Author(s):  
Julie Jeon ◽  
Jeferson Lourenco ◽  
Erin E. Kaiser ◽  
Elizabeth S. Waters ◽  
Kelly M. Scheulin ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Gut Microbiota ◽  
Microbial Diversity ◽  
Gut Microbiome ◽  
Injury Severity ◽  
The United States ◽  
Acute Stage ◽  
Pig Model ◽  
Lesion Volume ◽  
Clinical Prognosis

Stroke is a major cause of death and long-term disability affecting seven million adults in the United States each year. Recently, it has been demonstrated that neurological diseases, associated pathology, and susceptibility changes correlated with changes in the gut microbiota. However, changes in the microbial community in stroke has not been well characterized. The acute stage of stroke is a critical period for assessing injury severity, therapeutic intervention, and clinical prognosis. We investigated the changes in the gut microbiota composition and diversity using a middle cerebral artery (MCA) occlusion ischemic stroke pig model. Ischemic stroke was induced by cauterization of the MCA in pigs. Blood samples were collected prestroke and 4 h, 12 h, 1 day, and 5 days poststroke to evaluate circulating proinflammatory cytokines. Fecal samples were collected prestroke and 1, 3, and 5 days poststroke to assess gut microbiome changes. Results showed elevated systemic inflammation with increased plasma levels of tumor necrosis factor alpha at 4 h and interleukin-6 at 12 h poststroke, relative to prestroke. Microbial diversity and evenness were reduced at 1 day poststroke compared to prestroke. Microbial diversity at 3 days poststroke was negatively correlated with lesion volume. Moreover, beta-diversity analysis revealed trending overall differences over time, with the most significant changes in microbial patterns observed between prestroke and 3 days poststroke. Abundance of the Proteobacteria was significantly increased, while Firmicutes decreased at 3 days poststroke, compared to prestroke populations. Abundance of the lactic acid bacteria Lactobacillus was reduced at 3 days poststroke. By day 5, the microbial pattern returned to similar values as prestroke, suggesting the plasticity of gut microbiome in an acute period of stroke in a pig model. These findings provide a basis for characterizing gut microbial changes during the acute stage of stroke, which can be used to assess stroke pathology and the potential development of therapeutic targets.

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