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Bioprospecção de genes biossintéticos de policetídeos em DNA metagenômico de solo de Mata Atlântica.; Polyketide biosynthetic gene bioprospection in metagenomic DNA from Atlantic Forest soil.

Massini, Karen Cristina
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 16/12/2009 PT
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36.05%
A Mata Atlântica brasileira é apontada como um dos mais importantes refúgios da biodiversidade em todo o planeta. Este bioma é extremamente importante sob o aspecto da riqueza de espécies vegetais e animais na sua composição e interações, porém ainda pouco conhecido e explorado sob o ponto de vista microbiológico. Um grama de solo pode conter cerca de 10 bilhões de micro-organismos de diferentes espécies. A maioria dos micro-organismos presentes nos solos não é de fácil cultivo em laboratório (somente 0.1-10% são recuperados), sendo necessária à utilização de novas técnicas para superar este problema. Muitos micro-organismos presentes no solo tem grande importância biotecnológica por produzirem compostos bioativos. O filo Actinobacteria é abundante em solos e de grande importância econômica, tendo em vista que a maioria dos antibióticos comercializados é produzido por membros deste grupo. Porém a biodiversidade microbiana da Mata Atlântica, bem como, o seu potencial biotecnológico não tem sido plenamente estudado. Poucos trabalhos mostram produtos do metabolismo microbiano com potencial em uso em indústrias e mostram menos ainda antimicrobianos produzidos por isolados bacterianos desta região. Dentro deste contexto...

Diversidade genética de microrganismos presentes em utrículos da planta carnívora Utricularia foliosa (Lentibulariaceae).; Microbial diversity inside the utricles of carnivorous plant Utricularia foliosa (Lentibulariaceae).

Silva, Carolina Bertini da
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 22/10/2013 PT
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O conhecimento da associação entre plantas carnívoras e a comunidade bacteriana pode mostrar uma diversidade ainda não conhecida, além de proporcionar um melhor entendimento dos mecanismos envolvidos na interação de ambas. O objetivo deste trabalho foi avaliar a diversidade microbiana presente em utrículos de Utricularia foliosa através da análise de bibliotecas do gene 16S rRNA obtida por pirosequenciamento. Os resultados indicam que no ponto 1, Proteobacteria (58%), Firmicutes (11%), Cyanobacteria (11%), Acidobacteria (7%), Verrucomicrobia (5%), Actinobacteria (3%) Chlamidiae (2%) e Bacteroidetes (1%) foram os grupos dominantes. Já no ponto 2 houve uma maior presença de Eukaryota (51%), sendo que os grupos mais presentes foram Streptophyta (88%), Bacillariophyta (7%) e Chlorophyta (2%). A grande presença de algas encontradas pode estar relacionada à disponibilidade de nutrientes nos utrículos e gerar um acréscimo de carbono e nitrogênio à cadeia alimentar no interior da armadilha.; Knowledge of the association between carnivorous plants and the bacterial community can show a diversity not yet known, and provide a better understanding of the mechanisms involved in the interaction of both.The aim of this study was to evaluate the microbial diversity present in utricles of Utricularia foliosa and evaluate the effect of plant growth site in this diversity. For this the 16S rRNA gene library was sequenced by pyrosequencing (454-Roche). The results indicate that in point 1...

The post-transcriptional gene silencing pathway in Eucalyptus

Sassaki, Flávio Tetsuo; Campos-Pereira, Tiago; de Godoy Maia, Ivan
Fonte: Universidade Estadual Paulista Publicador: Universidade Estadual Paulista
Tipo: Artigo de Revista Científica Formato: 496-500
ENG
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Post-transcriptional gene silencing (PTGS) is a conserved surveillance mechanism that identifies and cleaves double-stranded RNA molecules and their cellular cognate transcripts. The RNA silencing response is actually used as a powerful technique (named RNA interference) for potent and specific inhibition of gene expression in several organisms. To identify gene products in Eucalyptus sharing similarities with enzymes involved in the PTGS pathway, we queried the expressed sequence tag database of the Brazilian Eucalyptus Genome Sequence Project Consortium (FORESTs) with the amino acid sequences of known PTGS-related proteins. Among twenty-six prospected genes, our search detected fifteen assembled sequences encoding products presenting high level of similarity (E value < 10 -40) to proteins involved in PTGS in plants and other organisms. We conclude that most of the genes known to be involved in the PTGS pathway are represented in the FORESTs database. Copyright by the Brazilian Society of Genetics.

Microbial Populations Involved in Cycling of Dimethyl Sulfide and Methanethiol in Freshwater Sediments

Lomans, Bart P.; Luderer, Rianne; Steenbakkers, Peter; Pol, Arjan; van der Drift, Chris; Vogels, Godfried D.; Op den Camp, Huub J. M.
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /03/2001 EN
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35.89%
Although several microorganisms that produce and degrade methanethiol (MT) and dimethyl sulfide (DMS) have been isolated from various habitats, little is known about the numbers of these microorganisms in situ. This study reports on the identification and quantification of microorganisms involved in the cycling of MT and DMS in freshwater sediments. Sediment incubation studies revealed that the formation of MT and DMS is well balanced with their degradation. MT formation depends on the concentrations of both sulfide and methyl group-donating compounds. A most-probable number (MPN) dilution series with syringate as the growth substrate showed that methylation of sulfide with methyl groups derived from syringate is a commonly occurring process in situ. MT appeared to be primarily degraded by obligately methylotrophic methanogens, which were found in the highest positive dilutions on DMS and mixed substrates (methanol, trimethylamine [TMA], and DMS). Amplified ribosomal DNA restriction analysis (ARDRA) and 16S rRNA gene sequence analysis of the total DNA isolated from the sediments and of the DNA isolated from the highest positive dilutions of the MPN series (mixed substrates) revealed that the methanogens that are responsible for the degradation of MT...

Transcriptional Expression of the tceA Gene in a Dehalococcoides-Containing Microbial Enrichment

Johnson, David R.; Lee, Patrick K. H.; Holmes, Victor F.; Fortin, Alexander C.; Alvarez-Cohen, Lisa
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /11/2005 EN
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35.89%
Dynamic changes in the transcriptional expression of the tceA gene, which encodes a trichloroethene reductive dehalogenase, were characterized in a Dehalococcoides-containing microbial enrichment culture. Expression was quantified by real-time PCR as the number of tceA transcripts per tceA gene. Expression of tceA increased 40-fold after chlorinated ethene-starved cells were exposed to trichloroethene (TCE), cis-dichloroethene (DCE), or 1,1-DCE but did not increase after exposure to tetrachloroethene or vinyl chloride. Surprisingly, tceA expression also increased 30-fold after cellular exposure to the nonmetabolic substrate trans-DCE, indicating that expression of tceA is induced by both growth-supporting and non-growth-supporting chlorinated ethenes. Additional experiments revealed that the level of tceA expression was independent of the concentration of chlorinated ethenes (sum concentrations of TCE and DCEs of 2.2 to 333 μM), the concentration of the electron donor hydrogen (concentrations of 12 nM to 17 μM), and the presence of alternate bacterial electron acceptors (5 mM concentrations of fumarate, sulfate, sulfite, thiosulfate, nitrate, or nitrite) but was highly dependent on incubation temperature.

Introducing TreeClimber, a Test To Compare Microbial Community Structures

Schloss, Patrick D.; Handelsman, Jo
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /04/2006 EN
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The phylogenetic and ecological complexity of microbial communities necessitates the development of new methods to determine whether two or more communities have the same structure even though it is not possible to sample the communities exhaustively. To address this need, we adapted a method used in population genetics, the parsimony test, to determine the relatedness of communities. Here we describe our implementation of the parsimony test, TreeClimber, in which we reanalyzed six previously published studies and compared the results of the analysis to those obtained using ∫-LIBSHUFF.

John R. S. Fincham (1926–2005): A Life in Microbial Genetics

Radford, Alan; Davis, R. H.
Fonte: Copyright © 2005 by the Genetics Society of America Publicador: Copyright © 2005 by the Genetics Society of America
Tipo: Artigo de Revista Científica
Publicado em /09/2005 EN
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35.89%

Drop-Size Soda Lakes: Transient Microbial Habitats on a Salt-Secreting Desert Tree

Qvit-Raz, Noga; Jurkevitch, Edouard; Belkin, Shimshon
Fonte: Genetics Society of America Publicador: Genetics Society of America
Tipo: Artigo de Revista Científica
Publicado em /03/2008 EN
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We describe a hitherto unrecognized bacterial community, inhabiting the leaf surfaces of the salt-excreting desert tree Tamarix. High temperatures, strong radiation, and very low humidity dictate a daytime existence in complete desiccation, but damp nights allow the microbial population to proliferate in a sugar-rich, alkaline, and hypersaline solution, before drying up again after sunrise. The exclusively bacterial population contains many undescribed species and genera, but nevertheless appears to be characterized by relatively limited species diversity. Sequences of 16S rRNA genes from either isolates or total community DNA place the identified members of the community in five bacterial groups (Actinobacteria, Bacteroidetes, Firmicutes, α-, and γ-Proteobacteria); in each of these, they concentrate in a very narrow branch that in most cases harbors organisms isolated from unrelated halophilic environments.

Surviving the Bottleneck: Transmission Mutants and the Evolution of Microbial Populations

Handel, Andreas; Bennett, Matthew R.
Fonte: Genetics Society of America Publicador: Genetics Society of America
Tipo: Artigo de Revista Científica
Publicado em /12/2008 EN
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The ability of microbial populations to increase fitness through fixation of mutants with an increased growth rate has been well described. In experimental studies, this is often the only way fitness can be increased. In natural settings, however, fitness can also be improved by increasing the ability of the microbe to transmit from one host to the next. For many pathogens, transmission includes a phase outside the host during which they need to survive before the chance of reinfecting a new host occurs. In such a situation, a reduced death rate during this phase will lead to improved fitness. Here, we compute the fixation probability of mutants that better survive the transmission bottleneck during the evolution of microbial populations. We derive analytical results that show that transmission mutants are often likely to occur and that their importance relative to growth mutants increases as the population decline during the transmission phase increases. We confirm our theoretical results with numerical simulations and suggest specific experiments that can be done to test our predictions.

Flipping DNA to Generate and Regulate Microbial Consortia

Ramadas, Rohini; Thattai, Mukund
Fonte: Genetics Society of America Publicador: Genetics Society of America
Tipo: Artigo de Revista Científica
Publicado em /01/2010 EN
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Communities of interdependent microbes, found in diverse natural contexts, have recently attracted the attention of bioengineers. Such consortia have potential applications in biosynthesis, with metabolic tasks distributed over several phenotypes, and in live-cell microbicide therapies where phenotypic diversity might aid in immune evasion. Here we investigate one route to generate synthetic microbial consortia and to regulate their phenotypic diversity, through programmed genetic interconversions. In our theoretical model, genotypes involve ordered combinations of DNA elements representing promoters, protein-coding genes, and transcription terminators; genotypic interconversions are driven by a recombinase enzyme that inverts DNA segments; and selectable phenotypes correspond to distinct patterns of gene expression. We analyze the microbial population as it evolves along a graph whose nodes are distinct genotypes and whose edges are interconversions. We show that the steady-state proportion of each genotype depends on its own growth advantage, as well as on its connectivity to other genotypes. Multiple phenotypes with identical or distinct growth rates can be indefinitely maintained in the population, while their proportion can be regulated by varying the rate of DNA flipping. Recombinase-based synthetic constructs have already been implemented; the graph-theoretic framework developed here will be useful in adapting them to generate microbial consortia.

What can microbial genetics teach sociobiology?

Foster, Kevin R.; Parkinson, Katie; Thompson, Christopher R.L.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
EN
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Progress in our understanding of sociobiology has occurred with little knowledge of the genetic mechanisms that underlie social traits. However, several recent studies have described microbial genes that affect social traits, thereby bringing genetics to sociobiology. A key finding is that simple genetic changes can have marked social consequences, and mutations that affect cheating and recognition behaviors have been discovered. The study of these mutants confirms a central theoretical prediction of social evolution: that genetic relatedness promotes cooperation. Microbial genetics also provides an important new perspective: that the genome-to-phenome mapping of social organisms might be organized to constrain the evolution of social cheaters. This constraint can occur both through pleiotropic genes that link cheating to a personal cost and through the existence of phoenix genes, which rescue cooperative systems from selfish and destructive strategies. These new insights show the power of studying microorganisms to improve our understanding of the evolution of cooperation.

IFIM: a database of integrated fitness information for microbial genes

Wei, Wen; Ye, Yuan-Nong; Luo, Sen; Deng, Yan-Yan; Lin, Dan; Guo, Feng-Biao
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Publicado em 11/06/2014 EN
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Knowledge of an organism’s fitness for survival is important for a complete understanding of microbial genetics and effective drug design. Current essential gene databases provide only binary essentiality data from genome-wide experiments. We therefore developed a new database that Integrates quantitative Fitness Information for Microbial genes (IFIM). The IFIM database currently contains data from 16 experiments and 2186 theoretical predictions. The highly significant correlation between the experiment-derived fitness data and our computational simulations demonstrated that the computer-generated predictions were often as reliable as the experimental data. The data in IFIM can be accessed easily, and the interface allows users to browse through the gene fitness information that it contains. IFIM is the first resource that allows easy access to fitness data of microbial genes. We believe this database will contribute to a better understanding of microbial genetics and will be useful in designing drugs to resist microbial pathogens, especially when experimental data are unavailable.

Microbial quality of soil from the Pampa biome in response to different grazing pressures

Vargas, Rafael S.; Bataiolli, Renata; da Costa, Pedro B.; Lisboa, Bruno; Passaglia, Luciane Maria P.; Beneduzi, Anelise; Vargas, Luciano K.
Fonte: Sociedade Brasileira de Genética Publicador: Sociedade Brasileira de Genética
Tipo: Artigo de Revista Científica
EN
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35.97%
The aim of this study was to evaluate the impact of different grazing pressures on the activity and diversity of soil bacteria. We performed a long-term experiment in Eldorado do Sul, southern Brazil, that assessed three levels of grazing pressure: high pressure (HP), with 4% herbage allowance (HA), moderate pressure (MP), with 12% HA, and low pressure (LP), with 16% HA. Two reference areas were also assessed, one of never-grazed native vegetation (NG) and another of regenerated vegetation after two years of grazing (RG). Soil samples were evaluated for microbial biomass and enzymatic (β-glucosidase, arylsulfatase and urease) activities. The structure of the bacterial community and the population of diazotrophic bacteria were evaluated by RFLP of the 16S rRNA and nifH genes, respectively. The diversity of diazotrophic bacteria was assessed by partial sequencing of the 16S rDNA gene. The presence of grazing animals increased soil microbial biomass in MP and HP. The structures of the bacterial community and the populations of diazotrophic bacteria were altered by the different grazing managements, with a greater diversity of diazotrophic bacteria in the LP treatment. Based on the characteristics evaluated, the MP treatment was the most appropriate for animal production and conservation of the Pampa biome.

A Quantitative Test of Population Genetics Using Spatio-Genetic Patterns in Bacterial Colonies

Korolev, Kirill; Xavier, Joao; Foster, Kevin; Nelson, David R.
Fonte: University of Chicago Press Publicador: University of Chicago Press
Tipo: Artigo de Revista Científica
EN_US
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36.03%
It is widely accepted that population genetics theory is the cornerstone of evolutionary analyses. Empirical tests of the theory, however, are challenging because of the complex relationships between space, dispersal, and evolution. Critically, we lack quantitative validation of the spatial models of population genetics. Here we combine analytics, on and off-lattice simulations, and experiments with bacteria to perform quantitative tests of the theory. We study two bacterial species, the gut microbe Escherichia coli and the opportunistic pathogen Pseudomonas aeruginosa, and show that spatio-genetic patterns in colony biofilms of both species are accurately described by an extension of the one-dimensional stepping-stone model. We use one empirical measure, genetic diversity at the colony periphery, to parameterize our models and show that we can then accurately predict another key variable: the degree of short-range cell migration along an edge. Moreover, the model allows us to estimate other key parameters including effective population size (density) at the expansion frontier. While our experimental system is a simplification of natural microbial community, we argue it is a proof of principle that the spatial models of population genetics can quantitatively capture organismal evolution.; Physics

Deciphering microbial landscapes of fish eggs to mitigate emerging diseases.

BRUIJN, I.; LIU, Y.; JACK, A. L. H.; DRYNAN, K.; BERG, A. H.; THOEN, E.; SANDOVAL-SIERRA, V.; SKAAR, I.; WEST, P.; VOORT, M. van der; MENDES, R.; MAZZOLA, M.; RAAIJMAKERS, J.
Fonte: In: INTERNATIONAL SYMPOSIUM ON MICROBIAL ECOLOGY, 15., 2014, Seoul. Proceedings... Wageningen: The International Society for Microbial Ecology (ISME), 2014. Publicador: In: INTERNATIONAL SYMPOSIUM ON MICROBIAL ECOLOGY, 15., 2014, Seoul. Proceedings... Wageningen: The International Society for Microbial Ecology (ISME), 2014.
Tipo: Resumo em anais de congresso (ALICE) Formato: p. 282.
EN
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2014

Reflections on Scientific Lives: A microbiologist/biochemist surveys the changing scene

Gest, Howard
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Artigo de Revista Científica
EN_US
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Current microbiology/biochemistry textbooks are encyclopedic tomes which include little information about the scientists in academia and non-profit research institutes who erected the extensive framework of our current knowledge. This essay discusses the dubious notion that a new major kind of “scientific life” is emerging in biotechnology…a blend of unfettered academic (“basic”) research and industrial (“applied”) research. Examples are given of outstanding academic scientists whose creativity in seeking new basic knowledge of cell (and virus) growth, biochemistry, and genetics led to the major tools of the applied biotechnology industry.

Predominant Effect of Host Genetics on Levels of Lactobacillus johnsonii Bacteria in the Mouse Gut▿†

Buhnik-Rosenblau, Keren; Danin-Poleg, Yael; Kashi, Yechezkel
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /09/2011 EN
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The gut microbiota is strongly associated with the well-being of the host. Its composition is affected by environmental factors, such as food and maternal inoculation, while the relative impact of the host's genetics have been recently uncovered. Here, we studied the effect of the host genetic background on the composition of intestinal bacteria in a murine model, focusing on lactic acid bacteria (LAB) as an important group that includes many probiotic strains. Based on 16S rRNA gene genotyping, variation was observed in fecal LAB populations of BALB/c and C57BL/6J mouse lines. Lactobacillus johnsonii, a potentially probiotic bacterium, appeared at significantly higher levels in C57BL/6J versus BALB/c mouse feces. In the BALB/c gut, the L. johnsonii level decreased rapidly after oral administration, suggesting that some selective force does not allow its persistence at higher levels. The genetic inheritance of L. johnsonii levels was further tested in reciprocal crosses between the two mouse lines. The resultant F1 offspring presented similar L. johnsonii levels, confirming that mouse genetics plays a major role in determining these levels compared to the smaller maternal effect. Our findings suggest that mouse genetics has a major effect on the composition of the LAB population in general and on the persistence of L. johnsonii in the gut in particular. Concentrating on a narrow spectrum of culturable LAB enables the isolation and characterization of such potentially probiotic bacterial strains...

Genetic elements of microbes: a comprehensive and integrated genomic database application

Benjamin, Ashlee
Fonte: Rochester Instituto de Tecnologia Publicador: Rochester Instituto de Tecnologia
Tipo: Tese de Doutorado
EN_US
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36.11%
The increasing abundance of genomic data has led to the creation of several databases containing the sequence data, metadata about the sequences and information about the organisms. These data are useful in many areas of biological research. Of the many available databases, few contain a significant amount of genome-associated data. In an effort to create a comprehensive microbial genomes database, the Genetic Elements of Microbes (GEM) database application was created. A K-mer analysis tool was also created and added the GEM application to provide an analysis of sequence composition and potential Lateral Gene Transfer (LGT) identification. The GEM application was designed to be convenient to maintain and extend. The K-mer analysis tool's ability to identify islands and to identify LGT events was tested with comparisons to published works. The GEM database application provides another source of genomic sequence and genome-associated data for the scientific community. The K-mer analysis addition provides an easy-to-customize tool to identify regions of dissimilarity and identify potential LGT events. The GEM application interface is publicly accessible at http://bucatini.bioinformatics.rit.edu/~amb4541/cgi-bin/GEMSearch.cgi. The standalone K-mer analysis interface is available at http://bucatini.bioinformatics.rit.edu/~amb4541/cgi-bin/KmerAnalysis.cgi.

The Vaginal Microbiome: Disease, Genetics and the Environment

Jennifer M. Fettweis; Joao P. Alves; Joseph F. Borzelleca; James P. Brooks; Christopher J. Friedline; Yuan Gao; Xi Gao; Philippe Girerd; Michael D. Harwich; Stephanie L. Hendricks; Kimberly K. Jefferson; Vladimir Lee; Huan Mo; Michael C. Neale; Federico
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Marker Paper / Data Plan
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The vagina is an interactive interface between the host and the environment. Its surface is covered by a protective epithelium colonized by bacteria and other microorganisms. The ectocervix is nonsterile, whereas the endocervix and the upper genital tract are assumed to be sterile in healthy women. Therefore, the cervix serves a pivotal role as a gatekeeper to protect the upper genital tract from microbial invasion and subsequent reproductive pathology. Microorganisms that cross this barrier can cause preterm labor, pelvic inflammatory disease, and other gynecologic and reproductive disorders. Homeostasis of the microbiome in the vagina and ectocervix plays a paramount role in reproductive health. Depending on its composition, the microbiome may protect the vagina from infectious or non-infectious diseases, or it may enhance its susceptibility to them. Because of the nature of this organ, and the fact that it is continuously colonized by bacteria from birth to death, it is virtually certain that this rich environment evolved in concert with its microbial flora. Specific interactions dictated by the genetics of both the host and microbes are likely responsible for maintaining both the environment and the microbiome. However, the genetic basis of these interactions in both the host and the bacterial colonizers is currently unknown. _Lactobacillus_ species are associated with vaginal health...

The Vaginal Microbiome: Disease, Genetics and the Environment

Jennifer M. Fettweis; Joao P. Alves; Joseph F. Borzelleca; James P. Brooks; Christopher J. Friedline; Yuan Gao; Xi Gao; Philippe Girerd; Michael D. Harwich; Stephanie L. Hendricks; Kimberly K. Jefferson; Vladimir Lee; Huan Mo; Michael C. Neale; Federico
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Marker Paper / Data Plan
Relevância na Pesquisa
36.18%
The vagina is an interactive interface between the host and the environment. Its surface is covered by a protective epithelium colonized by bacteria and other microorganisms. The ectocervix is nonsterile, whereas the endocervix and the upper genital tract are assumed to be sterile in healthy women. Therefore, the cervix serves a pivotal role as a gatekeeper to protect the upper genital tract from microbial invasion and subsequent reproductive pathology. Microorganisms that cross this barrier can cause preterm labor, pelvic inflammatory disease, and other gynecologic and reproductive disorders. Homeostasis of the microbiome in the vagina and ectocervix plays a paramount role in reproductive health. Depending on its composition, the microbiome may protect the vagina from infectious or non-infectious diseases, or it may enhance its susceptibility to them. Because of the nature of this organ, and the fact that it is continuously colonized by bacteria from birth to death, it is virtually certain that this rich environment evolved in concert with its microbial flora. Specific interactions dictated by the genetics of both the host and microbes are likely responsible for maintaining both the environment and the microbiome. However, the genetic basis of these interactions in both the host and the bacterial colonizers is currently unknown. Lactobacillus species are associated with vaginal health...