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The Dynamics of Microbial Transfer and Persistence on Human SkinBateman, Ashley 06 September 2017 (has links)
The skin microbiome is a critical component of human health, however, little is understood about the daily dynamics of skin microbiome community assembly and the skin’s potential to acquire microorganisms from the external environment. I performed a series of microbial transfers using three skin habitat types (dry, moist, sebaceous) on human subject volunteers. Microbial communities were transferred to recipient skin using a sterile swab 1) from other skin sites on the same individual, 2) from other skin sites on a different individual, 3) and from two environmental donor sources (plant leaf surfaces and farm soil). With these experiments I was able to test for the presence of initial transfer effects and for the persistence of those effects over the time period sampled (2-, 4-, 8-, and 24-hours post-transfer). The sebaceous skin community was associated with the strongest initial effect of transfer and persistence on the moist recipient skin site, and to a lesser extent the dry skin site. The soil donor community when transferred to dry skin resulted in the strongest initial transfer effect and was persistent over 8- and even 24-hours post-transfer. These experiments are the first in scope and scale to directly demonstrate that dispersal from other human or environmental microbial communities are plausible drivers of community dynamics in the skin microbiome.
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Investigating the Role of the Human Microbiome in the Pathogenesis of Atopic Dermatitis in the Mechanisms of the Progression of Atopic Dermatitis to Asthma in Children (MPAACH) CohortGonzalez, Tammy 15 October 2020 (has links)
No description available.
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Studium vlivu kosmetických přípravků na mikrobiom lidské kůže pomocí molekulárních technik / Study of the effect of cosmetics on the human skin microbiome using molecular techniquesAlexová, Adéla January 2021 (has links)
The theoretical part of the thesis is focused on the basic description of the physiology of the skin, human microbiome and a brief summary of where individual microorganisms occur. Furthermore, there is a list of analytical and microbiological methods that are used in this thesis. In the beginning, the practical part is focused on determination of antimicrobial effects of the chosen cosmetic products using microbial tests. Then, the inhibiton and microbial effect of the chosen cosmetic products on examined microorganisms has been measured using ELISA method. The second part of the thesis is focused on the isolation of bacterial DNA in quality that would be high enough to be used for amplification in PCR. There has been an optimalization of isolation of microbial DNA that was to be found on tested subjects’ skin. The presence of chosen microorganisms on skin before and after the usage of cosmetic products was measured using a PCR method. PCR products were then detected using gel electrophoresis. From the gathered data it is clear that the number of observed microorganisms has changed significantly after the application of cosmetic products.
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Vliv různých kosmetických polysacharidů jako prebiotik na mikrobiom kůže / Influence of various cosmetic polysaccharides as prebiotics on skin microbiomePelánová, Lenka January 2021 (has links)
The presented master thesis deals with the monitoring of the influence of polysaccharides which are used as an additive in the cosmetic products, on the monitored types of bacteria which are part of the skin microbiome. And it also deals with the study the effect of polysaccharides as prebiotics on selected species of bacteria that are part of the skin microbiome. Two polysaccharides were selected to determine the effects on the skin microbiome: Nanomoist and PoLevan S. The first part of the thesis focuses on the literature search which deals with skin anatomy, skin diseases and skin microbiome and its function. The experimental part is focused on monitoring changes in the quantity of selected microorganisms of the skin microbiome, before and after application of polysaccharides to the skin using qPCR. Staphylococcus epidermidis, Cutibacterium acnes, Escherichia coli and Micrococcus luteus were monitored. The PCR products were detected by agarose gel electrophoresis. The bacterium Staphylococcus epidermidis was detected on the skin to the greatest extent, especially after the application of the polysaccharides Nanomoist and PoLevan S. Thus, a positive effect of both polysaccharides on the growth of this bacterium was found.
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Vliv tenzidů a kosmetických polysacharidů na parametry pleti a její mikrobiom / Influence of surfactants and cosmetic polysaccharides on skin parameters and human skin microbiomePilipenco, Alina January 2020 (has links)
The aim of this diploma thesis was to investigate the effect of surfactants and cosmetic polysaccharides on skin parameters and its microbiome. Three surfactants were tested to determine their effect: Sodium Dodecyl Sulfate (SDS), Cocamidopropyl Betaine (CAPB), Decylglucoside (DG). Distilled water was also used for comparison. For the next part of the experimental work were selected 6 polysaccharides: high molecular weight Hyaluronic Acid (HMW HA), very low molecular weight Hyaluronic Acid (VLMW HA), Sodium Caproyl Hyaluronate (CaproylHA), Sodium Carboxymethyl -Glucan (NaCMG), Schizophyllan and Glucomannan. For comparison, placebo and untreated control (only CAPB treatment) were also included in the tests. The first part of the work is a literature search on the assigned topic, which contains the following parts: skin anatomy and its biophysical properties, skin microbiome and its functions, description of used surfactants and polysaccharides. The experimental part is mainly focused on bioengineering methods for evaluation of skin parameters and qRT-PCR to determine the relative proportion of main bacterial species of skin microbiome. First, the effect on the CT gene of 16S rDNA was analysed, and Propionibacterium acnes and Staphylococcus epidermidis strains were selected for further analysis. In conclusion are presented an overview of all properties of selected substances and assessment of their application in cosmetics.
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Bacteriophages in the honey bee gut and amphibian skin microbiomes: investigating the interactions between phages and their bacterial hostsBueren, Emma Kathryn Rose 14 June 2024 (has links)
The bacteria in host-associated microbial communities influence host health through various mechanisms, such as immune stimulation or the release of metabolites. However, viruses that target bacteria, called bacteriophages (phages), may also shape the animal microbiome. Most phage lifecycles can be classified as either lytic or temperate. Lytic phages infect and directly kill bacterial hosts and can directly regulate bacterial population size. Temperate phages, in contrast, have the potential to undergo either a lytic cycle or integrate into the bacterial genome as a prophage. As a prophage, the phage may alter bacterial host phenotypes by carrying novel genes associated with auxiliary metabolic functions, virulence-enhancing toxins, or resistance to other phage infections. Lytic phages may also carry certain auxiliary metabolic genes, which are instead used to takeover bacterial host functions to better accommodate the lytic lifecycle. In either case, the ability to alter bacterial phenotypes may have important ramifications on host-associated communities. This dissertation focused on the genetic contributions that phages, and particularly prophages, provide to the bacterial members of two separate host-associated communities: the honey bee (Apis mellifera) gut microbiome and the amphibian skin microbiome. My second chapter surveyed publicly available whole genome sequences of common honey bee gut bacterial species for prophages. It revealed that prophage distribution varied by bacterial host, and that the most common auxiliary metabolic genes were associated with carbohydrate metabolism. In chapter three, this bioinformatic pipeline was applied to the amphibian skin microbiome. Prophages were identified in whole genome bacterial sequences of bacteria isolated from the skin of American bullfrogs (Lithobates catesbeianus), eastern newts (Notophthalmus viridescens), Spring peepers (Pseudacris crucifer) and American toads (Anaxyrus americanus). Prophages were additionally identified in publicly available genomes of non-amphibian isolates of Janthinobacterium lividum, a bacteria found both on amphibian skin and broadly in the environment. In addition to a diverse set of predicted prophages across amphibian bacterial isolates, several Janthinobacterium lividum prophages from both amphibian and environmental isolates appear to encode a chitinase-like gene undergoing strong purifying selection within the bacterial host. While identifying the specific function of this gene would require in vitro isolation and testing, its high homology to chitinase and endolysins suggest it may be involved in the breakdown of either fungal or bacterial cellular wall components. Finally, my fourth chapter revisits the honey bee gut system by investigating the role of geographic distance in bacteriophage community similarity. A total of 12 apiaries across a transect of the United States, from Virginia to Washington, were sampled and honey bee viromes were sequenced, focusing on the lytic and actively lysing temperate community of phages. Although each apiary possessed many unique bacteriophages, apiaries that were closer together did have more similar communities. Each bacteriophage community also carried auxiliary carbohydrate genes, especially those associated with sucrose degradation, and antimicrobial resistance genes. Combined, the results of these three studies suggest that bacteriophages, and particularly prophages, may be contributing to the genetic diversity of the bacterial community through nuanced relationships with their bacterial hosts. / Doctor of Philosophy / The microbial communities of animals, called "microbiomes", play important roles in the health of animals. The bacteria in these microbiomes can help strengthen the immune system, provide resistance to dangerous pathogens, and break down nutrients. However, bacteria are not alone in the microbiome; viruses are also present. Surprisingly, the vast majority of the world's viruses, even those living inside animals, infect bacteria. These viruses, called "bacteriophages" or "phages", can impact the bacterial communities in a microbiome. Phages can be grouped in to two broad categories based on lifecycle. Lytic phages kill the bacterial host directly after infection. Temperate phages, on the other hand, can either immediately kill the host like lytic phages or alternatively, become a part of the bacterial genome and live as prophages. Phages with both lifecycles can sometimes carry genes that, although not essential to the phage, may change the traits of the bacteria during infection. For example, some phages carry toxin genes, which bacteria use to cause disease in animals. Other phages might carry genes that provide antibiotic resistance or alter the metabolism of the infected bacteria. If a phage gene benefits the infected bacteria, the bacteria may begin interacting with its environment in a new way or may even become more abundant. Alternatively, phages that directly kill infected bacteria may have a negative effect on bacterial population sizes. To begin unraveling how phages influence bacterial species in microbiomes, I investigated two different animal systems: the Western honey bee (Apis mellifera) gut microbiome and the amphibian skin microbiome. I first identified prophages of several common bacterial species that reside in the honey bee gut (Chapter 2). Prophages were more common in certain bacterial species than others, and some possessed genes associated with the breakdown of sugars or pollen, suggesting they help honey bees process their food. Using similar techniques, I then identified prophages in bacteria isolated from the skin microbiomes of several amphibian species common in the eastern United States (American bullfrogs, Eastern newts, Spring peepers, and American toads) (Chapter 3). Most notably, the bacteria Janthinobacterium lividum may benefit from prophages that carry genes for potentially antifungal chitinase enzymes that destroy the fungal cell wall. Finally, I returned to the honey bee gut microbiome system by investigating how honey bee bacteriophage communities change over large geographic distances (Chapter 4). This study, which examined honey bees from 12 apiaries sampled from the east to west coast of the United States, looks primarily at lytic phage and temperate phage that are not integrated as prophage, but are instead seeking a bacterial host to infect. I found that nearby apiaries tended to have more similar communities of bacteriophages, compared to apiaries far away. Additionally, most bacteriophage communities carry genes associated with the breakdown of sugars like sucrose. Overall, these three studies show that phages, and especially prophages, contribute to the genetic landscape of the microbiome by broadly providing bacterial hosts with access to a diverse set of genes.
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Microbiome cutané et maladie fongique émergente du syndrome du museau blanc chez les chauves-souris d’Amérique du NordLemieux-Labonté, Virginie 09 1900 (has links)
Le syndrome du museau blanc (SMB), causé par le champignon Pseudogymnoascus destructans
(Pd), a mis en péril les populations de chauves-souris hibernantes en Amérique du
Nord. Certaines espèces sont hautement vulnérables à la maladie alors que d’autres espèces
semblent être résistantes ou tolérantes à l’infection. Plusieurs facteurs physiologiques et
environnementaux peuvent expliquer ces différences. Or avant 2015, peu d’études avaient
porté sur le microbiome de la peau en relation avec cette maladie. La présente thèse vise
à caractériser le microbiome cutané de chiroptères affectés par le SMB afin d’identifier les
facteurs de vulnérabilité ou de résistance à la maladie. L’objectif principal est de déterminer
comment le microbiome est affecté par la maladie ainsi que de déterminer si celui-ci à un
rôle dans la protection face à l’infection fongique.
Au Chapitre 1, nous avons tout d’abord exploré et comparé le microbiote cutané
de petites chauves-souris brunes (Myotis lucifugus) non affectées par le SMB avec celui
de chauves-souris survivantes au SMB pour tester l’hypothèse selon laquelle le microbiote
cutané est modifié par la maladie. Nos résultats montrent que le site d’hibernation influence
fortement la composition et la diversité du microbiote cutané. Les sites d’hibernations Pd
positifs et négatifs diffèrent significativement en termes de diversité, ainsi qu’en termes de
composition du microbiote. La diversité est réduite au sein du microbiote des chauves-souris
survivantes au SMB et enrichi en taxons tels que Janthinobacterium, Micrococcaceae,
Pseudomonas, Ralstonia et Rhodococcus. Certains de ces taxons sont reconnus pour leur
potentiel antifongique et des souches spécifiques de Rhodococcus et de Pseudomonas peuvent
inhiber la croissance de Pd. Nos résultats sont cohérents avec l’hypothèse selon laquelle
l’infection par Pd modifie le microbiote cutané des chauves-souris survivantes et suggèrent
que le microbiote peut jouer un rôle de protection face au SMB.
Au Chapitre 2, nous avons étudié le microbiote d’une espèce résistante au champignon
Pd en milieu contrôlé avant et après infection afin d’établir la réponse potentielle à la maladie.
L’espèce étudiée est la grande chauve-souris brune (Eptesicus fuscus) dont le microbiote
cutané pourrait jouer un rôle de protection contre l’infection. Nos résultats montrent que la
diversité du microbiote de la grande chauve-souris brune inoculée avec Pd est plus variable
dans le temps, tandis que la diversité du microbiote des chauves-souris du groupe contrôle
demeure stable. Parmi les taxons les plus abondants, Pseudomonas et Rhodococcus, deux
taxons connus pour leur potentiel antifongique contre Pd et d’autres champignons, sont
restés stables durant l’expérience. Ainsi, bien que l’inoculation par le champignon Pd ait
déstabilisé le microbiote cutané, les bactéries aux propriétés antifongiques n’ont pas été
affectées. Cette étude est la première à démontrer le potentiel du microbiote cutané d’une
espèce de chauves-souris pour la résistance au SMB.
Au Chapitre 3, le microbiome cutané de la petite chauve-souris brune a été évalué
en milieu naturel dans le contexte du SMB, à l’aide de la métagénomique, une approche
haute résolution pour observer le potentiel fonctionnel du microbiome (métagénome
fonctionnel). Nos résultats ont permis d’établir que le temps depuis l’infection a un effet
significatif sur le métagénome fonctionnel. En effet, les chauves-souris dans la première
année suivant l’infection ont un métagénome fonctionnel perturbé qui subit une perte de
diversité fonctionnelle importante. Toutefois, le métagénome fonctionnel revient à une
structure et composition similaire d’avant infection après 10 ans. Certaines fonctions
détectées suite à l’infection sont associées à des gènes reliés au transport et à l’assimilation
de métaux, des facteurs limitants pour la croissance du champignon. Ces gènes
pourraient donc avoir un rôle à jouer dans la résistance ou la vulnérabilité à la maladie.
Globalement, l’étude du métagénome chez la petite chauve-souris brune indique une
vulnérabilité du métagénome fonctionnel au champignon, mais que celui-ci semble se rétablir
après 10 ans. Une telle réponse pourrait avoir un impact sur la résilience de M. lucifugus.
Cette thèse a permis d’acquérir des connaissances fondamentales sur le microbiome cutané
des chauves-souris en hibernation pour mieux comprendre les communautés microbiennes de
la peau dans le contexte du SMB. Le microbiome pourrait en effet jouer un rôle dans la
vulnérabilité et la résistance des chauves-souris à la maladie, et il est essentiel d’adapter
notre façon d’aborder la protection de ces espèces et de leur microbiome. Nous souhaitons
que les travaux de cette thèse permettent de sensibiliser les acteurs de la conservation à
l’existence et à l’importance potentielle du microbiome pour la santé de son hôte. Cette
thèse fait également état de l’avancement des méthodes d’analyses qui permettront d’être
de plus en plus précis et d’appliquer les connaissances du microbiome en biologie de la
conservation. / White-nose syndrome (WNS) caused by the fungus Pseudogymnoascus destructans (Pd)
has put hibernating bat populations at risk in North America. Some species are highly
vulnerable to the disease while other species appear to be resistant or tolerant. Several
physiological and environmental factors can explain these differences. However, before 2015,
few studies have focused on the skin microbiome in relation to this disease. The present
thesis aims to characterize the cutaneous microbiome of bats affected by WNS in order to
identify the factors of vulnerability or resistance to the disease. The main objective is to
determine how the microbiome can protect against the Pd fungus, or conversely how the
microbiome is altered by the fungal infection.
In Chapter 1, we first explored and compared the skin microbiota of little brown bats
(Myotis lucifugus) unaffected by WNS with that of WNS survivors to test the hypothesis
that the skin microbiota is modified by the disease. Our results show that the hibernation
site strongly influences the composition and diversity of the skin microbiota. The Pd
positive and negative sites differ significantly in terms of diversity, as well as in terms of the
composition of the microbiota. Diversity is reduced within the microbiota of bats surviving
WNS and enriched in taxa such as Janthinobacterium, Micrococcaceae, Pseudomonas,
Ralstonia, and Rhodococcus. Some of these taxa are recognized for their antifungal potential
and specific strains of Rhodococcus and Pseudomonas may inhibit the growth of Pd. Our
results are consistent with the hypothesis that Pd infection modifies the skin microbiota of
surviving bats and suggest that the microbiota may play a protective role against WNS.
In Chapter 2, we studied in a controlled environment the microbiota of a species that
exhibits evidence of resistance with mild WNS symptoms, before and after infection, to
establish the potential response to the disease. The species studied is the big brown bat
(Eptesicus fuscus), whose skin microbiota could play a protective role against infection.
Our results show that the diversity of the microbiota of big brown bats inoculated with
Pd is more variable over time, while the diversity of the microbiota of the control bats
remains stable. Among the most abundant taxa, Pseudomonas and Rhodococcus, two taxa known for their antifungal potential against Pd and other fungi, remained stable during
the experiment. Thus, although inoculation with the Pd fungus destabilized the skin
microbiota, bacteria with antifungal properties were not affected. This study is the first to
demonstrate the potential of the skin microbiota of a bat species for resistance to WNS.
In Chapter 3, the skin microbiome of the little brown bat was evaluated in the natural
environment in the context of WNS, using metagenomics, a higher-resolution approach to
observe the functional potential of the microbiome (functional metagenome). Our results established
that the time since infection has a significant effect on the functional metagenome.
Indeed, bats in the first year after infection have a disrupted functional metagenome that
undergoes a significant loss of functional diversity. However, the functional metagenome
returns to a similar structure and composition to that observed before infection after 10
years. Certain functions detected following infection are associated with genes linked to the
transport and assimilation of metals, known limiting factors for the growth of the fungus.
These genes could therefore have a role to play in resistance or vulnerability to the disease.
Overall, this metagenomics study indicates functional metagenome vulnerability to the
fungus, although the original functional metagenome is reestablished after 10 years. Such
diversified response could impact M. lucifugus resilence.
This thesis provides fundamental knowledge on the skin microbiome of hibernating bats
to better understand the microbial communities of the skin in the context of WNS. The
microbiome could indeed play a role in the vulnerability and resistance of bats to disease
and it is essential to adapt our way of approaching the protection of these species and their
microbiomes. We hope that the results of this thesis will raise awareness among conservation
stakeholders about the existence and potential importance of the microbiome for the health
of its host. This thesis also reports on the advancement of analytical methods that will
make it possible to be more and more precise and to apply knowledge of the microbiome in
conservation biology.
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