Phylogenetic microbial genes bacterial. Medical search. Frequent questions

However, metagenomic approaches may not be well-suited to focused studies of microbial diversity and community structure that involve a large number of samples. (frontiersin.org)
Aiming to exploit the genetic potential of soils microorganisms from extreme environments to retrieve salinity tolerance genes, the diversity of saline soil was examined and soil metagenomic DNA was used. (conicet.gov.ar)
Since the estimated size of the cultivable bacterial population ranges between 0.1 and 1%, limited information about the population diversity is available. (conicet.gov.ar)
The application of next-generation sequencing technology in microbial community analysis increased our knowledge and understanding of the complexity and diversity of a variety of ecosystems. (frontiersin.org)
The by far most often used marker for prokaryotic diversity studies is the 16S rRNA or its corresponding gene. (frontiersin.org)
Schabereiter-Gurtner C , Saiz-Jimenez C , Piñar G , Lubitz W , Rölleke S . Phylogenetic diversity of bacteria associated with Paleolithic paintings and surrounding rock walls in two Spanish caves (Llonín and La Garma). (microbiologyresearch.org)
Highly specialized microbial diversity in hyper-arid polar desert. (microbiologyresearch.org)
Investigation of the microbial ecology of intertidal hot springs by using diversity analysis of 16S rRNA and chitinase genes. (microbiologyresearch.org)
rRNA-genes are used to explore microbial diversity as well as a method for bacterial annotation. (edu.ba)
The phylogenetic diversity of soil microbial communities in hydrocarbon contaminated and non-contaminated sites was compared to the diversity of hydrocarbon-degrading genes and soil physicochemical characteristics. (edu.au)
Terminal restriction fragment length polymorphism analysis of the 16S rRNA and alkB genes found that the patterns of diversity of these two genes were only correlated with each other where measurable levels of hydrocarbons were detected. (edu.au)
The functional gene diversity found in different soils did not group the sites accordingly to land management. (hindawi.com)
Recent studies have revealed a great diversity within the genes encoding these key enzymatic processes [ 6 - 10 ], providing an expanding database representing the known diversity of genes encoding key enzymatic steps involved in nutrient cycling. (hindawi.com)
In this way, the total metagenome of an environmental sample can be examined for the presence, diversity, and activity of genes critical to the major nutrient cycles. (hindawi.com)
Although sequence databases are becoming rather extensive, we clearly have yet to detect the full expanse of the diversity of key enzyme functions, and such microarray-based analyses still necessarily fail to cover all gene families that may be critical to nutrient cycling. (hindawi.com)
Thus, as our knowledge of gene diversity increases, so too will our ability to design probes to monitor a broader range of genes and activities, and such functional microarrays will continue to improve and become more complete as research progresses. (hindawi.com)
2018. "Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. (berscience.org)
We verify previously identified novel lineages and identify new phylogenetic diversity at lower taxonomic levels, for example, thousands of operational taxonomic units at the family-genus levels differ considerably from known sequences. (nau.edu)
The new sequences populate parts of the bacterial phylogenetic tree that previously were poorly described, but indicate that any comprehensive survey of GN diversity has only begun. (nau.edu)
Today, rRNA-based analysis remains a central method in microbiology, used not only to explore microbial diversity but also as a day-to-day method for bacterial identification. (asm.org)
Several investigations on the microbial diversity and functional properties of the International Space Station (ISS) environment were carried out to understand the influence of spaceflight conditions on the microbial population. (biomedcentral.com)
Microbial Diversity in the Genomic Era, pp. 37-46 Elsevier, ISBN:9780128148495. (unifi.it)
This balance is maintained by microbial diversity, genetic factors, and complex molecular-cellular interactions between host and microbiome. (uni-ulm.de)
We determined the phylogenetic diversity of the faecal microbiota of the only two cheetahs housed in an EAZA associated zoo in Flanders, Belgium, to gain first insights in the relative distribution, identity and potential role of the major community members. (biomedcentral.com)
The use of molecular phylogenetic approaches in microbial ecology has revolutionized our view of microbial diversity at high temperatures and led to the proposal of a new kingdom within the Archaea, namely, the "Korarchaeota. (montana.edu)
Of all the environmental factors, temperature-driven microbial diversity has attracted more attention (Inskeep, Rusch et al. (nature.com)
Therefore, temperature was of particular interest in its effect on microbial diversity and efforts to understand the mechanisms by which temperature regulates diversity have yielded two perspectives. (nature.com)
Firstly, high temperatures could act as a selective force, leading to environmental filtering, wherein species not adapted to the extreme conditions are eliminated, thus reducing microbial diversity (Guo, Wang et al. (nature.com)
2006). As organisms are exposed to challenging thermal conditions, genetic mutations and adaptations may occur, giving rise to novel traits and specialized thermal adaptations, which ultimately contribute to increased microbial diversity. (nature.com)

All bacteria have ribosomal genes, but the exact sequence is unique to each species, serving as a genetic fingerprint. (wikipedia.org)
As central microbiota functions are determined by bacterial community networks, it is important to gain insight into the principles that govern bacteria-bacteria interactions. (nature.com)
To be able to predict, preserve and manipulate microbial community function, it is important to identify functionally important members and understand relevant interaction mechanisms between individual bacteria. (nature.com)
Christofer Osbecks 2019 "Exploring gene expression responses of marine bacteria to environmental factors" Linnaeus University (Sweden). (plymouth.ac.uk)
Anna Chiara Trano 2021 "Exploring marine bacterial communities with a focus on bacteria attached to particles" Based at Stazione Zoologica Anton Dohrn (Italy), PhD registered at Open University. (plymouth.ac.uk)
The first session of the research project was focused on functional-based screening method to screen a collection of 100 marine bacteria isolated from Svalbard and Lofoten islands for their ability to produce a broad spectrum of cold-active enzymes.The isolated bacteria were classified by 16S rRNA sequencing and the phylogenetic distribution of the detected activities was evaluated with the interest for finding new cold-active biocatalysts. (unina.it)
By analysing the overall microbial community composition (bacteria, fungi, archaea) across a terrestrial-freshwater gradient, the aim of this study was to understand the spatial distribution patterns of populations and identify taxa capable of crossing biome borders. (nature.com)
biodegradable enzymes present in the genes of some bacteria degrade HCH in soil. (ispub.com)
Bioinformatics strategies were used to find other homologous genes and proteins, which can also degrade HCH present in various bacteria for controlling of pollution and offer clue to prevent its entry in the food chain. (ispub.com)
On the basis of 16S rDNA phylogenetic analysis of bacteria was done. (ispub.com)
These ribosomal sequences was functional for the phylogenetic analysis and molecular taxonomic of any bacteria. (ispub.com)
PCR using the new primer pair on a set of template DNAs of different bacterial genera showed that the method was selective for bacteria belonging to the family Sphingomonadaceae . (ispub.com)
This pathway, called "natural transformation," is a major mechanism of gene transfer across bacteria and has a profound effect on genome evolution, including spreading antibiotic resistances and other virulence determinants. (drexel.edu)
We have developed a novel method for mapping genes in bacteria, exploiting natural transformation in combination with genome-wide deep sequencing. (drexel.edu)
Metagenomic DNA from both soil samples was extracted and used to amplify the 16S rRNA gene by using primers deduced from the division bacteria. (conicet.gov.ar)
In contrast to Bacteria, the archaeal domain was often not particularly addressed in the analysis of microbial communities. (frontiersin.org)
Streamlining Regulon Identification in Bacteria Regulons are a group of genes that can be turned on or off by the same regulatory protein. (doe.gov)
Dedysh SN , Pankratov TA , Belova SE , Kulichevskaya IS , Liesack W . Phylogenetic analysis and in situ identification of bacteria community composition in an acidic Sphagnum peat bog. (microbiologyresearch.org)
In this study, V1-V3 hyper variable regions from 16S rRNA genes of some known bacteria is taken from the work of A. Cosic. (edu.ba)
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. (debian.net)
however, little is known about their impact on arsenic-reducing bacteria and genes during arsenic transformation in flooded paddy soils. (researchwithrutgers.com)
In this study, microcosm experiments were established to profile transcriptional activity of As(V)-respiring gene (arrA) and arsenic resistance gene (arsC) as well as the associated bacteria regulated by lactate and/or biochar in anaerobic arsenic-contaminated paddy soils. (researchwithrutgers.com)
Chemical analyses revealed that lactate as the organic substrate stimulated microbial reduction of As(V) and Fe(III), which was simultaneously promoted by lactate+biochar, due to biochar's electron shuttle function that facilitates electron transfer from bacteria to As(V)/Fe(III). (researchwithrutgers.com)
Moreover, although the abundance of most protein groups reflected that of related bacterial populations, we found a specific independent regulation of bacteria-derived cell envelope proteins. (bmj.com)
Additional findings include some of the earliest-evolved sulfite reductases in bacteria, identification of a novel protein unique to sulfate-reducing bacteria, and a key sulfite reductase gene in putatively symbiotic candidate phyla radiation (CPR) bacteria. (berscience.org)
The microbial mats of Guerrero Negro (GN), Baja California Sur, Mexico historically were considered a simple environment, dominated by cyanobacteria and sulfate-reducing bacteria. (nau.edu)
We are also providing whole genome sequencing (WGS) that is the most discriminatory method for bacteria typing and can give us different type of genetic information like bacterial virulence genes, antimicrobial resistance genes and phylogenetic relationship between bacterial strains. (bior.lv)
In 2014, the MetaHIT consortium by bacteria of the genera Lacto- alytical method used: 66 from 16S published an integrated catalogue bacillus , Prevotella , and Sneathia , rDNA sequencing [11] or 57 from of 10 million bacterial genes de- whereas for infants delivered by whole-metagenome sequencing [5]. (who.int)

To obtain a better understanding of metabolically active microbial communities, we tested a molecular ecological approach using poly(A) tailing of environmental 16S rRNA, followed by full-length complementary DNA (cDNA) synthesis and sequencing to eliminate potential biases caused by mismatching of polymerase chain reaction (PCR) primer sequences. (frontiersin.org)
Considering the current limitations of NGS technology, full-length 16S rRNA gene sequences are better suited to downstream analytical methods such as fluorescence in situ hybridization. (frontiersin.org)
The original designs of most of the PCR primers used for the analysis of 16S rRNA genes were based on known sequences deposited in public databases. (frontiersin.org)
For example, a complete 16S rRNA gene sequence can be obtained by analyzing the sequences of genomes or large genome fragments, providing taxonomic information along with information on other functional genes. (frontiersin.org)
The HMP in particular includes, for each sample, both 16S rRNA gene surveys and shotgun metagenomic sequences, from a subset of the subjects recruited at two geographically distant locations in the United States. (biomedcentral.com)
Consequently, established primers specifically amplifying the archaeal 16S ribosomal gene region are scarce compared to the variety of primers targeting bacterial sequences. (frontiersin.org)
However, a disadvantage of this primer pair was its low specificity for the archaeal domain in the experimental application leading to high amounts of bacterial sequences within the dataset. (frontiersin.org)
Methods Total murine RNA was isolated from the small intestine of a 4-week-old BALB/c mouse (♂).Gene-specific primers were designed and synthesized according to the cDNA sequences of lactase-phlorizin hydrolase (LPH) in human, rat, and rabbit. (besjournal.com)
It has been shown by the author in previous articles that the Greengenes Classiﬁer can be successfully used as a bioinformatics program that performs taxonomic classiﬁcation of 16S rRNA gene sequences. (edu.ba)
Hence, analysis of phylogenetic marker gene sequences would provide a more reliable characterisation of the composition of microbial communities in the AD process. (cxcrinhibitor.com)
A preliminary molecular survey of the GN mat based on only 1500 small subunit rRNA gene sequences discovered several new phylum-level groups in the bacterial phylogenetic domain and many previously undetected lower-level taxa. (nau.edu)
Previous shotgun metagenomic data from the same depth profile show the same stratified pattern and suggest that metagenome properties may be predictable from rRNA gene sequences. (nau.edu)
The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). (asm.org)
Since microbial virulence increases in microgravity, AMR gene sequences of MAGs were compared with genomes of respective ISS isolates and corresponding type strains. (biomedcentral.com)
Comparative analyses of MAGs and whole-genome sequences of related ISS isolates and their type strains were characterized to understand the variation related to the microbial evolution under microgravity. (biomedcentral.com)
The new method circumvents the ambiguity of choosing the genes for phylogenetic reconstruction and avoids the necessity of aligning sequences of essentially different length and gene content. (scienceopen.com)
The DNA of a mixed community growing at 83°C, pH 7.6, was extracted and the small subunit ribosomal RNA gene (16S rDNA) sequences were obtained using the polymerase chain reaction. (montana.edu)

All microbial members (bacterial, archaeal, bacteriophage, viral, and fungal) have been included in this baseline dataset and both phylogenetic marker gene sequence [e.g. 16S rRNA, 18S rRNA, and internal transcribed spacer region (ITS)] and metagenomic whole genome shotgun sequence data were generated. (nih.gov)
Average microbial (bacterial and archaeal) community composition of groundwater sampled in Wellington. (auckland.ac.nz)
These results were determined by sequencing bacterial and archaeal 16S rRNA phylogenetic marker genes. (auckland.ac.nz)
Three archaeal 16S primer pairs as well as two bacterial and one general microbial 16S primer pairs were comprehensively tested by in-silico evaluation and performing an experimental analysis of a complex microbial community of a biogas reactor. (frontiersin.org)
Furthermore, in-silico evaluation of primers, especially those for amplification of archaeal 16S rRNA gene regions, does not necessarily reflect the results obtained in experimental approaches. (frontiersin.org)
Our aim in this study was to reveal the molecular phylogenetic structure of bacterial and archaeal and also the fungal communities in AD process operating at different temperatures and organic loads using 454-pyrosequencing. (cxcrinhibitor.com)
Sulfate reduction, an important anaerobic metabolism, impacts carbon, nitrogen, and hydrogen transformations in numerous environments across the planet and is known to be restricted to organisms from selected bacterial and archaeal phyla. (berscience.org)
We report here the occurrence of another member of this archaeal group and a deeply rooted bacterial sequence from a thermal spring in Yellowstone National Park (USA). (montana.edu)
The products were cloned and five different phylogenetic types ("phylotypes") were identified: four archaeal phylotypes, designated pBA1, pBA2, pBA3, and pBA5, and only one bacterial phylotype, designated pBB. (montana.edu)

This resource is the world's most comprehensive reference host/microbiome dataset as it includes the microbial community composition from five major body regions (nasal, oral, skin, gastrointestinal tract, and urogenital tract) of these subjects, and the predicted metabolic pathways of the microbial communities in these body regions. (nih.gov)
Additional attention has been paid to the gut microbiome in this cohort and the research community has used the HMP reference dataset to analyze the mobile gene content, the antibiotic resistome, the bacteriophage composition and the presence of putative pathogens in this key subset of the human microbiome reference dataset. (nih.gov)
We describe the bacterial community composition of ten digestive tract sites from more than 200 normal adults enrolled in the Human Microbiome Project, and metagenomically determined metabolic potentials of four representative sites. (biomedcentral.com)
Barcoded 454 pyrosequencing of taxonomic gene markers was used to describe the microbial communities in adjacent soil, freshwater and sediment samples and study the role of biotic and spatial factors in shaping their composition. (nature.com)
Few habitat generalists but a high number of specialists were detected indicating that microbial community composition was mainly regulated by species sorting and niche partitioning. (nature.com)
Microbial community composition seems to be governed by both deterministic and stochastic processes 30 . (nature.com)
The correlation between dysbiosis and IBD is not completely understood, and human studies involve confounding variables on bacterial composition, such as antibiotic use [ 10 ]. (biomedcentral.com)
Host species identity and host evolutionary history were both highly predictive of moss microbiome composition, highlighting strong phylogenetic coherence in these microbial communities. (biomedcentral.com)
Likewise, although moss microbial communities appear to be strongly influenced by host identity, it is unclear whether the differences in microbial community composition can be predicted from host phylogenetic relationships, the role of host species effects relative to geographic effects, and importantly, whether the composition of the microbial communities found in a given host species is stable across broad environmental gradients. (biomedcentral.com)
Land use change alters the structure and composition of microbial communities. (hindawi.com)
Most of the studies related to the impact of land use change on microbes have focused on the phylogenetic composition of the soil microbial community. (hindawi.com)
The CVTree web server (http://tlife.fudan.edu.cn/cvtree) presented here is a new implementation of the whole genome-based, alignment-free composition vector (CV) method for phylogenetic analysis. (scienceopen.com)
In domestic cats, taxonomic and functional studies of the intestinal microbial communities have shown that different sources of dietary fibre ( i.e. , cellulose, pectin, fructooligosaccharide) modified the composition of bacterial phyla in the faeces. (biomedcentral.com)

Of special note are 2 chapters that are often missing in traditional medical microbiology books: 1 describes how long-term experimental evolutionary studies in the laboratory can contribute to our understanding of microbial pathogen evolution in the environment and clinics, and the other describes how gene inactivation and gene loss can be creative forces during the evolution of many microorganisms, especially obligate intracellular pathogens. (cdc.gov)
Such a macro-evolutionary framework would showcase the nonrandom patterns of the distribution of human pathogens among major phylogenetic groups of microorganisms. (cdc.gov)
Most studies on distribution of microorganisms, as well as structure and turn-over of microbial communities focus on one biome and little is known about the processes mediating and controlling transfers across a landscape gradient involving terrestrial and aquatic biomes, and the resulting biogeographical patterns of microbial community distribution. (nature.com)
Taken these results altogether, we conclude that, microbial community in that environment were found to be represented by highly diverse microorganisms, interestingly most of them seems to be uncultured. (conicet.gov.ar)
Colonization of the gut starts just after birth when pioneering species interact, through surface receptors, with gut cells to promote the expression of a specific set of host genes and favour the colonization of commensal microorganisms [6]. (deepdyve.com)
Despite the widespread availability of microbial genome data-close to 2,000 microbes have been and are being decoded to date-a vast unknown realm awaits scientists intent on exploring microorganisms that inhabit this "undiscovered country. (doe.gov)
Variations in the antimicrobial-resistant (AMR) and virulence genes of the selected 20 MAGs were characterized to predict the ecology and evolution of biosafety level (BSL) 2 microorganisms in space. (biomedcentral.com)

Ribotyping is a molecular technique for bacterial identification and characterization that uses information from rRNA-based phylogenetic analyses. (wikipedia.org)
In the first section, the 5 chapters introduce the basic processes affecting microbial evolution, from the individual molecular level to the genomic, cellular, and population levels. (cdc.gov)
These results clearly demonstrate that poly(A) tailing followed by cDNA sequencing is a powerful and less biased molecular ecological approach for the study of metabolically active microbial communities. (frontiersin.org)
The ribosomal operons mainly 16S rDNA has proven to be a stable and specific molecular marker for bacterial identification. (ispub.com)
The second approach uses molecular biology techniques to study microbial communities. (southalabama.edu)
Molecular tools such as PCR, gene probing, mRNA transcript analysis, and DNA sequencing can aid in this endeavour. (southalabama.edu)
Objective No Crohn's disease (CD) molecular maker has advanced to clinical use, and independent lines of evidence support a central role of the gut microbial community in CD. (bmj.com)
Conclusions This study provides the first evidence that quantifiable bacterial protein signals are associated with CD, which can have a profound impact on future molecular diagnosis. (bmj.com)
Identification methods are conceptually easier to interpret than molecular phylogenetic analyses and are often preferred when the groups are well understood. (asm.org)
The laboratory also performs molecular genetic analysis of microbial pollution in food products and environment. (bior.lv)

3. How do bacterial genomes change during the course of chronic infections? (drexel.edu)
Moreover, genetic and simple obesity share similar structural and functional features of dysbiosis, such as higher production of toxins with known potential to induce metabolic deteriorations (e.g. trimethylamine-N-oxide and indoxyl sulphate), higher abundance of genomes containing genes coding enzymes involved in the production of these toxic co-metabolites and higher abundance of pathways for biosynthesis of bacterial antigens (such as endotoxin) [13-15]. (deepdyve.com)
The HGT creates widespread discordance between evolutionary histories of different genes as genomes become mosaics of gene histories. (blogspot.com)
However, metagenome-assembled genomes (MAGs) of ISS samples are yet to be generated and subjected to various genomic analyses, including phylogenetic affiliation, predicted functional pathways, antimicrobial resistance, and virulence characteristics. (biomedcentral.com)
Since the first bacterial genomes were sequenced in 1995 there have been several attempts to infer prokaryote phylogeny from complete genomes. (scienceopen.com)
A catalogue of 178 reference bacterial birth, and the delivery type is the first core of species has been identified genomes distributed among different factor that has an impact. (who.int)

It is a rapid and specific method widely used in clinical diagnostics and analysis of microbial communities in food, water, and beverages. (wikipedia.org)
A key challenge in microbiome research is to predict the functionality of microbial communities based on community membership and (meta)-genomic data. (nature.com)
A multitude of different approaches has been used to characterize the ecological networks of microbial communities. (nature.com)
To experimentally verify the key ecological, structural, and functional role of certain species in driving community structure and function, synthetic microbial consortia provide several advantages over native communities. (nature.com)
Numerous studies on natural microbial communities from a variety of environments have been undertaken using 16S rRNA gene sequencing mediated by polymerase chain reaction (PCR) with oligonucleotide primers. (frontiersin.org)
Despite the fact that the latest NGS technologies enable reading only of relatively short sequence fragments (~500 bp), these so-called "deep sequencing" methods are still powerful tools that ultimately may enable researchers to obtain a more holistic understanding of microbial communities in their natural environments ( Fuhrman, 2009 ). (frontiersin.org)
This unique dataset permits novel studies of the human digestive tract within a large number of subjects, allows for comparisons of microbial communities between habitats, and enables the definition of distinct metabolic niches within and among individuals. (biomedcentral.com)
In finding few broadly distributed populations, our study points to biome specialization within microbial communities with limited potential for dispersal and colonization of new habitats along the terrestrial-freshwater continuum. (nature.com)
On the other hand, a metagenomic approach allows to access to knowledge of a broader range, and to be more representative of the microbial communities. (conicet.gov.ar)
Genome Insider: Methane Makers in Yosemite's Lakes Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work. (doe.gov)
In contrast, culture-independent analysis of microbial communities worldwide revealed that sd6 Acidobacteria prevail in soils with neutral pH. (microbiologyresearch.org)
Phylogenetic analysis of bacterial communities in mesophilic and thermophilic bioreactors treating pharmaceutical wastewater. (microbiologyresearch.org)
Yet the relative importance of moss host species, and environmental factors, in structuring these microbial communities and their N 2 -fixing potential remains unclear. (biomedcentral.com)
We studied 26 boreal and tundra moss species across 24 sites in Alaska, USA, from 61 to 69° N. We used cultivation-independent approaches to characterize the variation in moss-associated bacterial communities as a function of host species identity and site characteristics. (biomedcentral.com)
The strong effect of host identity on moss-associated bacterial communities demonstrates mosses' utility for understanding plant-microbe interactions in non-leguminous systems. (biomedcentral.com)
Like all plants, mosses associate with microbes and these microbial communities have key roles in multiple ecosystem-level processes. (biomedcentral.com)
It is likely that over a larger geographic area, spanning broader environmental gradients (i.e., latitudinal climate shifts and forest versus tundra ecosystem types), site conditions could play a more prominent role in structuring microbial communities. (biomedcentral.com)
To address these issues, we examined the bloom-associated microbial communities in single samples from Lake Erie (North America), Lake Tai (Taihu, China), and Grand Lakes St. Marys (OH, USA) using comparative metagenomics. (tennessee.edu)
Our observations build on an emerging body of metagenomic surveys describing the functional potential of microbial communities as more highly conserved than that of their phylogenetic makeup within natural systems. (tennessee.edu)
This level of complexity in the microbial community dynamics suggests that it is unlikely that one single environmental factor is responsible for structuring microbial communities. (edu.au)
Design We first developed and validated a workflow-including extraction of microbial communities, two-dimensional difference gel electrophoresis (2D-DIGE), and LC-MS/MS-to discover protein signals from CD-associated gut microbial communities. (bmj.com)
Here we interrogated the functional structure of soil microbial communities across different land uses. (hindawi.com)
Humans, animals and plants are closely related to complex microbial communities, the so-called microbiome. (uni-ulm.de)
Enteric viruses can disturb the balance of the microbial communities, which can lead to secondary infections and to shifts towards higher number of pathogenic microbe species. (uni-ulm.de)
2021) and these conditions provide numerous niches to support phylogenetically and functionally specialized microbial communities. (nature.com)
Understanding how microbial communities are assembled and how the presence or absence of species is related to that of others are central goals of microbial ecology. (peerj.com)

Here, we focused on the growth and metabolic interactions of the Oligo-Mouse-Microbiota (OMM 12 ) synthetic bacterial community, which is increasingly used as a model system in gut microbiome research. (nature.com)
To understand the relationship between our bacterial microbiome and health, it is essential to define the microbiome in the absence of disease. (biomedcentral.com)
The bacterial microbiome of the human digestive tract contributes to both health and disease. (biomedcentral.com)
human gut microbiome, data repositories, large-scale and integrative computational tools, modelling, immunomodulation, drug screening Background The human gastrointestinal tract is a complex ecosystem in which eukaryotic cells continuously interact with nutrients and with the complex microbial population of the gut microbiota [1]. (deepdyve.com)
These questions are not unique to the study of moss microbiomes, but the important role of bacterial N 2 -fixation makes the moss microbiome a useful model system for simultaneously studying plant-microbe associations and how these associations influence N cycling in high-latitude systems. (biomedcentral.com)
rRNA-genes for phylogenetic classifications started to be used in 1980s first time by Carl Woese which made a ground breaking contribution to microbiome science. (edu.ba)
Genes for antibiotic resistance and production of natural antimicrobial peptides, so-called bacteriocins, are used here as parameters for the function of a microbiome. (uni-ulm.de)
The colonic microbiome view is controversial, some people Metagenomics of the Human Intes- is the most diverse and also the best consider the gut microbiota to be tinal Tract (MetaHIT) consortium re- characterized microbial community. (who.int)

1986. Ribosomal ribonucleic acid gene restriction patterns as potential taxonomic tools. (wikipedia.org)
In addition to standard phylogenetic trees, users can also choose to output trees whose monophyletic branches are collapsed to various taxonomic levels. (scienceopen.com)

Ribotyping involves the digestion of bacterial genomic DNA with specific restriction enzymes. (wikipedia.org)
This book is one of the first to provide an up-to-date view on a fundamental issue in medical microbiology research: how the accumulated genetic and genomic information is contributing to our understanding of virulence factors and the evolution of virulence in microbial pathogens. (cdc.gov)
The long-term goal of this research is to apply statistical genomic approaches developed by human geneticists to the identification of bacterial virulence factors that contribute to disease in natural populations. (drexel.edu)
We are applying a variety of genomic methods to identifying putative virulence genes, including machine learning and phylogenetic correlated evolution methods. (drexel.edu)
This pattern was particularly noticeable in the genomic contribution of nitrogen assimilation genes. (tennessee.edu)
Furthermore, two approaches were used for isolation and phylogenetic identification of anaerobic consortium TERI SA1 involving 16S rRNA sequencing of culturable bacterial isolates as well as meta-genomic approach (by making a 16S rRNA gene library of total community DNA). (caritulisan.com)
MGTdb: a web service and database for studying the global and local genomic epidemiology of bacterial pathogens. (cdc.gov)

Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. (microbiologyresearch.org)
Mosses in high-latitude ecosystems harbor diverse bacterial taxa, including N 2 -fixers which are key contributors to nitrogen dynamics in these systems. (biomedcentral.com)
Our work also highlights the likely importance of novel bacterial taxa to N 2 -fixation in high-latitude ecosystems. (biomedcentral.com)

I study a range of topics in microbial biology, ecology, and evolution. (plymouth.ac.uk)
His Ecology study frequently links to related topics such as Microbial population biology. (research.com)
His scientific interests lie mostly in Ecology, Ecosystem, Biogeochemical cycle, Microbial population biology and Estuary. (research.com)

Therefore, sequencing the particular 16S gene and comparing it to a database would yield identification of the particular species. (wikipedia.org)
The 14 chapters are grouped into 3 broad sections: general concepts in microbial evolution, environment and the evolution of microbial pathogens, and the evolution of selected pathogenic species and mechanisms. (cdc.gov)
Therefore, the spatial and temporal patterns of distribution of microbial pathogens within a species and at the species level across the globe are highly relevant to the evolution of microbial pathogens. (cdc.gov)
The predominant intestinal microbial community consisted of 130 species or phylotypes according to the sequence data in this study. (nih.gov)
In 2002, an ad hoc committee for the reevaluation of species definition in bacteriology ( 24 ) advised that all new bacterial species descriptions include an rRNA sequence from the type strain, and in 2001, Bergey's Trust published a revised higher-order taxonomy attempting to reconcile bacterial taxonomy with rRNA-based phylogeny ( 12 , 13 ). (asm.org)
Among 46 MAGs retrieved, 18 bacterial species were identified, including one novel genus/species combination ( Kalamiella piersonii ) and one novel bacterial species ( Methylobacterium ajmalii ). (biomedcentral.com)
Phylogenetic analyses of five bacterial species showed ISS-specific evolution. (biomedcentral.com)

Ahmed Nawaz 2020 "Microbial colonisation and degradation of plastic pollution in the marine environment" Open University. (plymouth.ac.uk)
Mainly, two genes linA and linB encode dehydrochlorinase and dehalogenase enzymes involved in degradation of HCH. (ispub.com)
The first involves isolating pure cultures involved in the degradation of specific chemical compounds and characterising the genes and enzymes involved in the degradation pathway. (southalabama.edu)
I use primers and probes to key genes in the degradation pathways of various environmental contaminants to determine how the microbial community as a whole responds to that contaminant. (southalabama.edu)
Genes involved in hydrocarbon degradation including alkane mono-oxygenase, catchecol-2,3-dioxygenase and naphthalene dioxygenase were found throughout the study sites. (edu.au)
Fields with low C : N ratio had an overrepresentation of genes for carbon degradation, carbon fixation, metal reductase, and organic remediation categories, while fields with high C : N ratio had an overrepresentation of genes encoding dissimilatory sulfate reductase, methane oxidation, nitrification, and nitrogen fixation. (hindawi.com)

In this article we used Longest Common Subsequence similarity measure to classify bacterial 16S rRNA gene sequence short reads against the Greengenes library. (edu.ba)
Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. (asm.org)

However, there are known aerobic microbial e.g. fungal groups present in anaerobic digesters originating from the substrate [1]. (cxcrinhibitor.com)
and bacterial, fungal, and oomycete polygalacturonases. (hindawi.com)

Metabolic network reconstruction in combination with metabolomics analysis of bacterial culture supernatants provided insights into the metabolic potential and activity of the individual community members. (nature.com)
Exploring marine microbial community dynamics on natural and synthetic polymers" University of Warwick. (plymouth.ac.uk)
16S rRNA gene data derived from a shotgun metagenome of the same reactor sample added an additional perspective on the community structure. (frontiersin.org)
Overall our results indicate a rather limited comparability between community structures investigated and determined using different primer pairs as well as between metagenome and 16S rRNA gene amplicon based community structure analysis. (frontiersin.org)
I love this concept as they are able to control the microbial community and then test dynamics of how specific phage affect that community inside a living host. (blogspot.com)
Lauber CL , Hamady M , Knight R , Fierer N . Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. (microbiologyresearch.org)
Together the Cyanobacteria and Proteobacteria comprised >90% of each bloom bacterial community sample, although the dominant phylum varied between systems. (tennessee.edu)
2013. Microbial community analysis of Deepwater Horizon oil-spill impacted sites along the Gulf coast using functional and phylogenetic markers. (southalabama.edu)
An investigation of the influence of soil properties on microbial community dynamics in soil on sub-Antarctic Macquarie Island found that both carbon and nitrogen were important factors in determining soil microbial community structure. (edu.au)
We found that different sections of the microbial community are affected by different environmental factors depending on whether hydrocarbons were present. (edu.au)
The overall microbial community structure as measured by the 16S rRNA gene was most influenced by the presence of carbon both as total organic carbon and as petroleum hydrocarbons. (edu.au)
In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio. (hindawi.com)
In fact, this is the basis of currently used methods that link gene surveys to metabolic predictions of community function. (berscience.org)
Culture-independent rRNA community profiling instead revealed these microbial mats as among the most phylogenetically diverse environments known. (nau.edu)
To fulfil these roles, some stability and consistency within the gut microbial community is required. (uni-ulm.de)
In situ hybridization with bacterial-specific and Aquificales -specific fluorescent oligonucleotide probes indicated the bacterial population dominated the community and most likely contributed significantly to biogeochemical cycling within the community. (montana.edu)
2013). Similarly, temperature is one of the most important niche axis in shaping microbial community structure, carbon fixation rate and community assembly in Tengchong hot springs (Hou, Wang et al. (nature.com)
The recent success gut microbial genes, obtained after has fantastic potential, it has only of faecal microbiota transplantation, sequencing whole faecal microbiota been about 10 years since the sci- especially in the context of Clostridi- metagenomes from 124 European indi- entific community first realized its im- um difficile infection, argues for such viduals [4]. (who.int)
Under healthy conditions, the in- nomes obtained from individuals crobiota resembles the mother's skin testinal microbiota is considered to on three continents, including 760 microbial community, composed of be a stable community, influenced samples from Europe. (who.int)

Moreover, it is well recognized that the excessive use of broad-spectrum antibiotics can affect the relative proportions of gut microbial populations and foster bacterial resistance [24]. (deepdyve.com)
Therefore, the presence of S. mutans in individuals with low caries experiences could be explained by differences in bacterial virulence factors or endogenous factors within the host populations. (bvsalud.org)

Antimicrobial resistance occurs through different mechanisms, which include spontaneous (natural) genetic mutations and horizontal transfer of resistant genes through deoxyribonucleic acid (DNA). (who.int)

Several studies have demonstrated that the colonization and accumulation of Streptococcus mutans is associated with dental caries in humans, since they are influenced by various factors in the oral cavity, such as nutrition and hygiene conditions of the host, salivary components, cleaning power and salivary flow and characteristics related with microbial virulence factors 3 . (bvsalud.org)

In some part, this was due to the lack of a consistent, higher-level bacterial classification structure (taxonomy). (asm.org)
Agreement with taxonomy should be taken as a major criterion to estimate prokaryotic phylogenetic trees. (scienceopen.com)
In addition, IGS sequencing (e.g., sequencing of intergenic regions between the 16S and 23S rRNA genes) has been used to taxonomy studies, while partial sequencing of the gene gtfB , which encodes the enzyme glucosyltransferase B, has been used to investigate enzymatic activity and virulence 11-12 . (bvsalud.org)

Our primary model system is the human bacterial pathogen Haemophilus influenzae , an important agent of ear infections (otitis media) in children, as well as lung infections associated with chronic respiratory conditions. (drexel.edu)
Barrier agains t pathogen s gut bacterial genes in the MetaHIT ation when attempting to extrapolate [10], although Proteobacteria, Ver- catalogue were also well represent- results obtained in mouse models to rucomicrobia, and Fusobacteria are ed in the other metagenomes that the situation in humans. (who.int)

I have also used metagenomic approaches to identify novel genes from the environment. (southalabama.edu)

These processes are fundamental to the evolution of all groups of organisms, and the analysis of the unparalleled datasets in microbial pathogens can teach us much about the evolution of other groups of organisms. (cdc.gov)
They take action by transferring with microbial reactions in the target organisms. (ispub.com)
Moreover, despite variation in the phylogenetic assignments of bloom-associated organisms, the functional potential of bloom members remained relatively constant between systems. (tennessee.edu)
Until now, sulfate reduction was believed to be restricted to organisms from select bacterial and archael phyla. (berscience.org)
They used genome-resolved metagenomics to discover roles in sulfur cycling for organisms from 16 microbial phyla not previously associated with this process. (berscience.org)
A systematic way of inferring evolutionary relatedness of microbial organisms from the oligopeptide content, i.e., frequency of amino acid K-strings in their complete proteomes, is proposed. (scienceopen.com)

In the second section, the 5 chapters review how interactions between microbes and various natural biotic and abiotic factors can influence the origin and evolution of virulence in microbial pathogens. (cdc.gov)
The discovery of novel microbes connected to sulfur cycling is relevant in biogeochemistry, ecosystem science, and engineering, and can fundamentally reshape understanding of microbial function and capabilities associated with phylogenetic information. (berscience.org)
MAGs were further used to analyze if genes involved in AMR and biofilm formation of viable microbes in ISS have variation due to generational evolution in microgravity and radiation pressure. (biomedcentral.com)

The epithelium function and the mucosal associated immune system are influenced by direct host-microbiota interactions and through modulation of the microbial metabolism [7]. (deepdyve.com)

Two of these are notable: the HMP Data Analysis and Coordination Center and the Qiita web-based microbial study management platform. (nih.gov)
In parallel, we used 16S rRNA gene sequencing for an integrated analysis of gut ecosystem structure and functions. (bmj.com)
The use of functional gene markers to monitor the presence and activity of genes responsible for key steps in terrestrial nutrient cycles may provide a much more directed approach to the analysis of the nutrient cycling properties of terrestrial ecosystems. (hindawi.com)
The development of whole genome-based alignment-free CV method has provided an independent verification to the traditional phylogenetic analysis based on a single gene or a few genes. (scienceopen.com)

Different patterns were observed in the two different soils.In addition, some clones from a library constructed with the 16S rRNA PCR product using primers for the genera Arquea were sequenced and a phylogenetic tree was built. (conicet.gov.ar)
With respect to microbial functions in soils, most studies have traditionally been based on enzyme activity screening, with relatively little attention paid to functional marker gene screening [ 5 ]. (hindawi.com)

The project consists of three parts: population structure and evolutionary history of 1) humans, 2) the human oral microbial flora, and 3) human pathogens. (eurac.edu)

Conclusions: The partial sequencing of the gtfB gene can be a useful tool for elucidating the colonization patterns of S. mutans . (bvsalud.org)
Caries is an infectious and transmissible disease associated with bacterial colonization of dental surfaces 1 . (bvsalud.org)

Newer work is using the same approach to map the genes responsible for natural variation in other pathogenesis traits, including resistance to human complement-mediated killing, as well as investigating the possibility of identifying genes involved in in vivo pathogenesis in an animal model of otitis media. (drexel.edu)
This report presents the status of AMR in Africa by analysing the main types of resistance and the underlying genes where possible. (who.int)
Gonococcal Antimicrobial Surveil ance Programme has antimicrobials representing four different classes, namely operated in the Western Pacific and South-East Asian penicil in (PEN), ciprofloxacin (CIP), tetracycline (TCY), regions since 1992, but surveil ance of gonococcal anti- ceftriaxone (CRO) and cefixime (CFX), by disc diffusion microbial resistance (AMR) remains limited in the Asia- and gradient diffusion (Etest, BioMerieux). (who.int)

Second, although base substitutions, insertions and deletions, homologous recombination, and lateral gene transfer are discussed throughout the book, a generalized quantitative review of the relative contributions of these processes during the evolution of certain groups of microbial pathogens (e.g. (cdc.gov)
Processes such as host-microbe crosstalk, immune activation and inflammation, microbe-microbe signalling, microbial metabolism and antimicrobial activity are bioactive in the human gut [3]. (deepdyve.com)
Moreover, it appears desirable to exploit non-tree-like evolutionary processes for the task of microbial classification. (blogspot.com)

Furthermore, DGGE (Denaturing Gradient Gel Electrophoresis) technique was used to separate the products of a nested amplification (the variable region of 16S rRNA gene) using bacterial primers, and primers specific for the genera Burkholderia. (conicet.gov.ar)

As relatively isolated ecosystems, terrestrial hot springs present a unique opportunity for microbial diversification and specialization. (nature.com)

While the bacterial fraction of many environments was extensively studied, the Archaea were often not specifically addressed. (frontiersin.org)

We are now using advanced optical mapping technology to reproduce these maps in the absence of genetic variation, in order to disentangle the role of chromosome structure from the potential for genetic incompatibilities ("speciation genes") skewing our results. (drexel.edu)
Based on the genetic similarity of the isolates and pattern of amino acid variations identified by partial sequencing of the gtfB gene, base-pair changes were identified and correlated with different virulence patterns among the isolates. (bvsalud.org)

In the second session of the project, a gene encoding for an esterase was amplified by PCR from a bacterial sequenced genome belonging to Thalassospira sp. (unina.it)
Selection for recombinants that acquired the trait, followed by genome-wide profiling of donor-specific allele frequencies, we can rapidly identify the relevant genes. (drexel.edu)

Biotic interactions within microbial groups based on an association network underlined the importance of Actinobacteria , Sordariomycetes , Agaricomycetes and Nitrososphaerales in connecting among biomes. (nature.com)

Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time. (research.com)

Rather, the soil factors, C : N ratio, phosphate, and total N, were the main factors driving the differences in functional genes across the fields examined. (hindawi.com)

Anatomy1

Organisms1

Chemicals and Drugs1

Phenomena and Processes6

Information Science2

Health Care1

Diversity29

Bacteria28

Sequences17

Archaeal9

Composition13

Microorganisms7

Molecular10

Genomes6

Communities26

Microbiome8

Taxonomic2

Genomic7

Taxa3

Ecology3

Species7

Degradation6

RRNA gene sequence2

Fungal2

Community19

Populations2

Antimicrobial resistance1

Virulence factors1

Taxonomy3

Pathogen2

Approaches1

Organisms6

Microbes3

Microbiota1

Analysis4

Soils2

Human pathogens1

Colonization2

Resistance3

Processes3

Primers1

Ecosystems1

Archaea1

Genetic2

Genome2

Interactions1

Biogeography1

Functional genes1