scholarly journals Into the wild: microbiome transplant studies need broader ecological reality

2020 ◽  
Vol 287 (1921) ◽  
pp. 20192834 ◽  
Author(s):  
Christopher J. Greyson-Gaito ◽  
Timothy J. Bartley ◽  
Karl Cottenie ◽  
Will M. C. Jarvis ◽  
Amy E. M. Newman ◽  
...  
Keyword(s):  
Conceptual Framework ◽  
Microbial Communities ◽  
Gut Microbiome ◽  
Ecological Processes ◽  
Experimental Conditions ◽  
Host Environment ◽  
Host Taxon ◽  
Transplantation Experiments ◽  
Over Time ◽  
Transplant Experiments

Gut microbial communities (microbiomes) profoundly shape the ecology and evolution of multicellular life. Interactions between host and microbiome appear to be reciprocal, and ecological theory is now being applied to better understand how hosts and their microbiome influence each other. However, some ecological processes that underlie reciprocal host–microbiome interactions may be obscured by the current convention of highly controlled transplantation experiments. Although these approaches have yielded invaluable insights, there is a need for a broader array of approaches to fully understand host–microbiome reciprocity. Using a directed review, we surveyed the breadth of ecological reality in the current literature on gut microbiome transplants with non-human recipients. For 55 studies, we categorized nine key experimental conditions that impact the ecological reality (EcoReality) of the transplant, including host taxon match and donor environment. Using these categories, we rated the EcoReality of each transplant. Encouragingly, the breadth of EcoReality has increased over time, but some components of EcoReality are still relatively unexplored, including recipient host environment and microbiome state. The conceptual framework we develop here maps the landscape of possible EcoReality to highlight where fundamental ecological processes can be considered in future transplant experiments.

scholarly journals Into the wild: microbiome transplant studies need broader ecological reality

2019 ◽  
Author(s):  
Christopher J. Greyson-Gaito ◽  
Timothy John Bartley ◽  
Karl Cottenie ◽  
Will M.C. Jarvis ◽  
Amy E.M. Newman ◽  
...  
Keyword(s):  
Conceptual Framework ◽  
Microbial Communities ◽  
Gut Microbiome ◽  
Ecological Processes ◽  
Experimental Conditions ◽  
Host Environment ◽  
Host Taxon ◽  
Transplantation Experiments ◽  
Over Time ◽  
Transplant Experiments

Gut microbial communities (microbiomes) profoundly shape the ecology and evolution of multicellular life. Interactions between host and microbiome appear to be reciprocal, and ecological theory is now being applied to better understand how hosts and their microbiome influence each other. However, some ecological processes that underlie reciprocal host-microbiome interactions may be obscured by the current convention of highly-controlled transplantation experiments. Although these approaches have yielded invaluable insights, there is a need for a broader array of approaches to fully understand host-microbiome reciprocity. Using a directed review, we surveyed the breadth of ecological reality in the current literature on gut microbiome transplants with non-human recipients. For 55 studies, we categorized 9 key experimental conditions that impact the ecological reality (EcoReality) of the transplant, including host taxon match and donor environment. Using these categories, we rated the EcoReality of each transplant. Encouragingly, the breadth of EcoReality has increased over time, but some components of EcoReality are still relatively unexplored, including recipient host environment and microbiome state. The conceptual framework we develop here maps the landscape of possible EcoReality to highlight where fundamental ecological processes can be considered in future transplant experiments.

scholarly journals The meta-gut: Hippo inputs lead to community coalescence of animal and environmental microbiomes.

2021 ◽  
Author(s):  
Christopher Lee Dutton ◽  
Amanda L. Subalusky ◽  
Alvaro Sanchez Sanchez ◽  
Sylvie Lee Estrela ◽  
Nanxi Lu ◽  
...  
Keyword(s):  
Conceptual Framework ◽  
Microbial Communities ◽  
Gut Microbiome ◽  
Strong Influence ◽  
Ecosystem Processes ◽  
Aquatic Environments ◽  
Field Sampling ◽  
Pool Water ◽  
16S Rna

All animals carry specialized microbiomes, and their gut microbiotas in particular are continuously released into the environment through excretion of waste. Here we propose the meta-gut as a novel conceptual framework that addresses the ability of the gut microbiome released from an animal to function outside the host and potentially alter ecosystem processes mediated by microbes. An example considered here is the hippopotamus (hippo) and the pools they inhabit. Hippo pool biogeochemistry and fecal and pool water microbial communities were examined through field sampling and an experiment. Sequencing using 16S RNA methods revealed that the active microbial communities in hippo pools that received high inputs of hippo feces are more similar to the hippo gut microbiome than other nearby aquatic environments. The overlap between the microbiomes of the hippo gut and the waters into which they excrete therefore constitutes a meta-gut system with potentially strong influence on the biogeochemistry of pools and downstream waters. We propose that the meta-gut may be present where other species congregate in high densities, particularly in aquatic environments.

scholarly journals Superior Dispersal Ability Can Lead to Persistent Ecological Dominance throughout Succession

2019 ◽  
Vol 85 (6) ◽  
Author(s):  
Primrose J. Boynton ◽  
Celeste N. Peterson ◽  
Anne Pringle
Keyword(s):  
Microbial Communities ◽  
Carnivorous Plant ◽  
Dispersal Ability ◽  
Aquatic Communities ◽  
Ecological Processes ◽  
Microbial World ◽  
Content Type ◽  
Ecological Dominance ◽  
Changes Over Time ◽  
Over Time

ABSTRACTA large number of descriptive surveys have shown that microbial communities experience successional changes over time and that ecological dominance is common in the microbial world. However, direct evidence for the ecological processes mediating succession or causing ecological dominance remains rare. Different dispersal abilities among species may be a key mechanism. We surveyed fungal diversity within a metacommunity of pitchers of the model carnivorous plantSarracenia purpureaand discovered that the yeastCandida pseudoglaebosawas ecologically dominant. Its frequency in the metacommunity increased during the growing season, and it was not replaced by other taxa. We next measured its competitive ability in a manipulative laboratory experiment and tracked its dispersal over time in nature. Despite its dominance,C. pseudoglaebosais not a superior competitor. Instead, it is a superior disperser: it arrives in pitchers earlier, and disperses into more pitchers, than other fungi. Differential dispersal across the spatially structured metacommunity of individual pitchers emerges as a key driver of the continuous dominance ofC. pseudoglaebosaduring succession.IMPORTANCEMicrobial communities are ubiquitous and occupy nearly every imaginable habitat and resource, including human-influenced habitats (e.g., fermenting food and hospital surfaces) and habitats with little human influence (e.g., aquatic communities living in carnivorous plant pitchers). We studied yeast communities living in pitchers of the carnivorous purple pitcher plant to understand how and why microbial communities change over time. We found that dispersal ability is not only important for fungal communities early in their existence, it can also determine which species is dominant (here, the yeastCandida pseudoglaebosa) long after the species and its competitors have arrived. These results contrast with observations from many human-influenced habitats, in which a good competitor eventually outcompetes good dispersers, since humans often design these habitats to favor a specific competitor. This study will help microbiologists understand the qualities of microbial species that enable takeover of new habitats in both natural and human-influenced environments.

scholarly journals The Gut Microbiome of Exudivorous Wild and Captive Marmosets

2019 ◽  
Author(s):  
Joanna Malukiewicz ◽  
Reed A. Cartwright ◽  
Jorge A. Dergam ◽  
Claudia S. Igayara ◽  
Sharon Kessler ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Pathogenic Bacteria ◽  
Ribosomal Subunit ◽  
Gastrointestinal Diseases ◽  
Host Environment ◽  
Microbiome Composition ◽  
Distress Symptoms ◽  
Microbiome Diversity ◽  
Gastrointestinal Distress ◽  
Host Taxon

AbstractAmong mammals, captive dietary specialists like primate folivores are prone to gastrointestinal distress and suffer the greatest gut microbiome diversity losses relative to wild individuals. Less is known about the gut microbiome of mammalian exudivores, which exploit tree gums and sap, and increased knowledge could improve management of wild exudivores and facilitate captive exudivore welfare. A number of primates, including Callithrix marmosets, represent key mammalian exudivores. Captive marmosets commonly develop gastrointestinal distress symptoms that in human diseases are linked to microbiome dysbiosis. Thus, we studied wild and captive Callithrix gut microbiome composition and predictive function through 16S V4 ribosomal subunit sequencing of 59 wild, translocated, and captive pure and hybrid Callithrix. We found that host environment had a stronger effect on the gut microbiome than host taxon. Captive marmosets showed relatively reduced gut microbiome diversity. Wild Callithrix gut microbiomes were enriched for carbohydrate function and Bifidobacterium, which process host-indigestible carbohydrates. Captive marmosets had the highest relative abundance of Enterobacteriaceae, a family containing several pathogenic bacteria. Captive marmosets also showed gut microbiome composition aspects seen in human gastrointestinal diseases. Thus, captivity may perturb the exudivore gut microbiome, which raises implications for captive exudivore welfare and calls for modified husbandry practices.

scholarly journals Serial Analysis of the Gut and Respiratory Microbiome in Cystic Fibrosis in Infancy: Interaction between Intestinal and Respiratory Tracts and Impact of Nutritional Exposures

mBio ◽  
2012 ◽  
Vol 3 (4) ◽  
Author(s):  
J. C. Madan ◽  
D. C. Koestler ◽  
B. A. Stanton ◽  
L. Davidson ◽  
L. A. Moulton ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Respiratory Tract ◽  
Microbial Communities ◽  
Effective Means ◽  
Significant Proportion ◽  
Gut Colonization ◽  
Pulmonary Damage ◽  
Chronic Colonization ◽  
High Degree ◽  
Over Time

ABSTRACT Pulmonary damage caused by chronic colonization of the cystic fibrosis (CF) lung by microbial communities is the proximal cause of respiratory failure. While there has been an effort to document the microbiome of the CF lung in pediatric and adult patients, little is known regarding the developing microflora in infants. We examined the respiratory and intestinal microbiota development in infants with CF from birth to 21 months. Distinct genera dominated in the gut compared to those in the respiratory tract, yet some bacteria overlapped, demonstrating a core microbiota dominated by Veillonella and Streptococcus. Bacterial diversity increased significantly over time, with evidence of more rapidly acquired diversity in the respiratory tract. There was a high degree of concordance between the bacteria that were increasing or decreasing over time in both compartments; in particular, a significant proportion (14/16 genera) increasing in the gut were also increasing in the respiratory tract. For 7 genera, gut colonization presages their appearance in the respiratory tract. Clustering analysis of respiratory samples indicated profiles of bacteria associated with breast-feeding, and for gut samples, introduction of solid foods even after adjustment for the time at which the sample was collected. Furthermore, changes in diet also result in altered respiratory microflora, suggesting a link between nutrition and development of microbial communities in the respiratory tract. Our findings suggest that nutritional factors and gut colonization patterns are determinants of the microbial development of respiratory tract microbiota in infants with CF and present opportunities for early intervention in CF with altered dietary or probiotic strategies. IMPORTANCE While efforts have been focused on assessing the microbiome of pediatric and adult cystic fibrosis (CF) patients to understand how chronic colonization by these microbes contributes to pulmonary damage, little is known regarding the earliest development of respiratory and gut microflora in infants with CF. Our findings suggest that colonization of the respiratory tract by microbes is presaged by colonization of the gut and demonstrated a role of nutrition in development of the respiratory microflora. Thus, targeted dietary or probiotic strategies may be an effective means to change the course of the colonization of the CF lung and thereby improve patient outcomes.

Gamifying the Media Classroom

2017 ◽  
Vol 7 (4) ◽  
pp. 22-49
Author(s):  
Katie Seaborn ◽  
Deborah I. Fels ◽  
Rob Bajko ◽  
Jaigris Hodson
Keyword(s):  
Social Media ◽  
Student Engagement ◽  
Conceptual Framework ◽  
Student Perspective ◽  
Educational Settings ◽  
The Media ◽  
Game Elements ◽  
The Impact ◽  
Over Time

Gamification, or the use of game elements in non-game contexts, has become a popular and increasingly accepted method of engaging learners in educational settings. However, there have been few comparisons of different kinds of courses and students, particularly in terms of discipline and content. Additionally, little work has reported on course instructor/designer perspectives. Finally, few studies on gamification have used a conceptual framework to assess the impact on student engagement. This paper reports on findings from evaluating two gamified multimedia and social media undergraduate courses over the course of one semester. Findings from applying a multidimensional framework suggest that the gamification approach taken was moderately effective for students overall, with some elements being more engaging than others in general and for each course over time." Post-term questionnaires posed to the instructors/course designers revealed congruence with the student perspective and several challenges pre- and post-implementation, despite the use of established rules for gamifying curricula.

scholarly journals Immune Gene Expression Covaries with Gut Microbiome Composition in Stickleback

mBio ◽  
2021 ◽  
Vol 12 (3) ◽  
Author(s):  
Lauren E. Fuess ◽  
Stijn den Haan ◽  
Fei Ling ◽  
Jesse N. Weber ◽  
Natalie C. Steinel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Microbial Communities ◽  
Gut Microbiome ◽  
Alpha Diversity ◽  
Host Immunity ◽  
Host Gene ◽  
Microbiota Composition ◽  
Host Gene Expression ◽  
Microbiome Composition ◽  
Immune Genes

ABSTRACT Commensal microbial communities have immense effects on their vertebrate hosts, contributing to a number of physiological functions, as well as host fitness. In particular, host immunity is strongly linked to microbiota composition through poorly understood bi-directional links. Gene expression may be a potential mediator of these links between microbial communities and host function. However, few studies have investigated connections between microbiota composition and expression of host immune genes in complex systems. Here, we leverage a large study of laboratory-raised fish from the species Gasterosteus aculeatus (three-spined stickleback) to document correlations between gene expression and microbiome composition. First, we examined correlations between microbiome alpha diversity and gene expression. Our results demonstrate robust positive associations between microbial alpha diversity and expression of host immune genes. Next, we examined correlations between host gene expression and abundance of microbial taxa. We identified 15 microbial families that were highly correlated with host gene expression. These families were all tightly correlated with host expression of immune genes and processes, falling into one of three categories—those positively correlated, negatively correlated, and neutrally related to immune processes. Furthermore, we highlight several important immune processes that are commonly associated with the abundance of these taxa, including both macrophage and B cell functions. Further functional characterization of microbial taxa will help disentangle the mechanisms of the correlations described here. In sum, our study supports prevailing hypotheses of intimate links between host immunity and gut microbiome composition. IMPORTANCE Here, we document associations between host gene expression and gut microbiome composition in a nonmammalian vertebrate species. We highlight associations between expression of immune genes and both microbiome diversity and abundance of specific microbial taxa. These findings support other findings from model systems which have suggested that gut microbiome composition and host immunity are intimately linked. Furthermore, we demonstrate that these correlations are truly systemic; the gene expression detailed here was collected from an important fish immune organ (the head kidney) that is anatomically distant from the gut. This emphasizes the systemic impact of connections between gut microbiota and host immune function. Our work is a significant advancement in the understanding of immune-microbiome links in nonmodel, natural systems.

scholarly journals A Literature Review on Ubuntu Concept as a Panacea for African Ecclesiology: A Case Study of Harvest Revival Ministry Churches in Kenya

2021 ◽  
Vol 4 (2) ◽  
pp. 22-37
Author(s):  
Peter Lee Ochieng Oduor
Keyword(s):  
Latin America ◽  
Literature Review ◽  
Conceptual Framework ◽  
The Reformation ◽  
African Ecclesiology ◽  
Christian Thought ◽  
African Setting ◽  
Over Time

The study seeks to examine the approaches taken currently with regard to scholarship on ecclesiology from the patristic era, the medieval era to that of the reformation and beyond. The study evaluates the various ecclesiological approaches of various confessional traditions that have defined ecclesiology over time. In progression, the study examines contextual ecclesiologies with a focus on three specific cultural geographical environments of Africa, Asia, and Latin America. This is because of the significance that these regions play in the current global shift within Christendom. African ecclesiology has been the centre of focus in an attempt to link all the discussed ecclesiologies with the African Christian thought. The study intends to review the Ubuntu concept and to capture the concept of the humanness of people in the African setting. The study intends to expose the gap in the literature demonstrating that the African conceptual framework can indeed be of use in articulating theology relevant to the African world. The study was keen to evaluate the contribution towards the development and construction of an African ecclesiology using the Ubuntu concept as a remedy to solve ecclesiological problems witnessed in Africa.

scholarly journals Local versus site-level effects of algae on coral microbial communities

2021 ◽  
Vol 8 (9) ◽  
pp. 210035
Author(s):  
Amy A. Briggs ◽  
Anya L. Brown ◽  
Craig W. Osenberg
Keyword(s):  
Microbial Communities ◽  
Spatial Scales ◽  
French Polynesia ◽  
Negative Effects ◽  
Ecological Processes ◽  
Antagonistic Effects ◽  
Alpha And Beta Diversity ◽  
Macroalgal Cover ◽  
Coral Microbiome ◽  
Turf Algae

Microbes influence ecological processes, including the dynamics and health of macro-organisms and their interactions with other species. In coral reefs, microbes mediate negative effects of algae on corals when corals are in contact with algae. However, it is unknown whether these effects extend to larger spatial scales, such as at sites with high algal densities. We investigated how local algal contact and site-level macroalgal cover influenced coral microbial communities in a field study at two islands in French Polynesia, Mo'orea and Mangareva. At 5 sites at each island, we sampled prokaryotic microbial communities (microbiomes) associated with corals, macroalgae, turf algae and water, with coral samples taken from individuals that were isolated from or in contact with turf or macroalgae. Algal contact and macroalgal cover had antagonistic effects on coral microbiome alpha and beta diversity. Additionally, coral microbiomes shifted and became more similar to macroalgal microbiomes at sites with high macroalgal cover and with algal contact, although the microbial taxa that changed varied by island. Our results indicate that coral microbiomes can be affected by algae outside of the coral's immediate vicinity, and local- and site-level effects of algae can obscure each other's effects when both scales are not considered.

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