A collective genome representative of the many organisms, primarily microorganisms, existing in a community.
A order of gram-negative bacteria whose members are found in a variety of aquatic habitats as well as animal hosts.
The genetic complement of a BACTERIA as represented in its DNA.
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
The relationships of groups of organisms as reflected by their genetic makeup.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.
The study of microorganisms living in a variety of environments (air, soil, water, etc.) and their pathogenic relationship to other organisms including man.
The variety of all native living organisms and their various forms and interrelationships.
The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.
Generally refers to the digestive structures stretching from the MOUTH to ANUS, but does not include the accessory glandular organs (LIVER; BILIARY TRACT; PANCREAS).
A group of different species of microorganisms that act together as a community.
An order of photosynthetic bacteria representing a physiological community of predominantly aquatic bacteria.
Devices for generating biological products that use light as the energy source. They are used for controlled BIOMASS production such as growing cyanobacteria, mosses, or algae.
A genus of PROCHLOROPHYTES containing unicellular, spherical bacteria without a mucilaginous sheath. They are found almost exclusively as extracellular symbionts of colonial ASCIDIANS on subtropical or tropical marine shores.
A great expanse of continuous bodies of salt water which together cover more than 70 percent of the earth's surface. Seas may be partially or entirely enclosed by land, and are smaller than the five oceans (Atlantic, Pacific, Indian, Arctic, and Antarctic).
The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.
One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.
The study of the origin, structure, development, growth, function, genetics, and reproduction of organisms which inhabit the OCEANS AND SEAS.
The systematic study of the complete DNA sequences (GENOME) of organisms.
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
Refuse liquid or waste matter carried off by sewers.
A genus of SPONGES in the family Chalinidae characterized by unispicular secondary lines in the choanosomal skeleton.
A genus of shallow-cupped SPONGES with a broad base in the family Theonellidae. They are characterized by ectosomal spicules dominated by phyllotriaenes.
A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The full collection of microbes (bacteria, fungi, virus, etc.) that naturally exist within a particular biological niche such as an organism, soil, a body of water, etc.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
Organisms that live in water.
Databases devoted to knowledge about specific genes and gene products.
Class of BACTERIA with diverse morphological properties. Strains of Actinobacteria show greater than 80% 16S rDNA/rRNA sequence similarity among each other and also the presence of certain signature nucleotides. (Stackebrandt E. et al, Int. J. Syst. Bacteriol. (1997) 47:479-491)
Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells.
A phylum of bacteria comprised of three classes: Bacteroides, Flavobacteria, and Sphingobacteria.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
The discarding or destroying of liquid waste products or their transformation into something useful or innocuous.
The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.
I'm sorry for any confusion, but the term "Pacific Ocean" is a geographical term referring to the largest ocean in the world, covering an area of about 63,800,000 square miles (165,200,000 square kilometers), and it is not a medical term.
Enzymes which catalyze the endohydrolysis of 1,4-beta-D-xylosidic linkages in XYLANS.
One of the three domains of life (the others being BACTERIA and ARCHAEA), also called Eukarya. These are organisms whose cells are enclosed in membranes and possess a nucleus. They comprise almost all multicellular and many unicellular organisms, and are traditionally divided into groups (sometimes called kingdoms) including ANIMALS; PLANTS; FUNGI; and various algae and other taxa that were previously part of the old kingdom Protista.
Habitat of hot water naturally heated by underlying geologic processes. Surface hot springs have been used for BALNEOLOGY. Underwater hot springs are called HYDROTHERMAL VENTS.
Physiological processes and properties of BACTERIA.
Community of tiny aquatic PLANTS and ANIMALS, and photosynthetic BACTERIA, that are either free-floating or suspended in the water, with little or no power of locomotion. They are divided into PHYTOPLANKTON and ZOOPLANKTON.
The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
Body of knowledge related to the use of organisms, cells or cell-derived constituents for the purpose of developing products which are technically, scientifically and clinically useful. Alteration of biologic function at the molecular level (i.e., GENETIC ENGINEERING) is a central focus; laboratory methods used include TRANSFECTION and CLONING technologies, sequence and structure analysis algorithms, computer databases, and gene and protein structure function analysis and prediction.
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
A mass of organic or inorganic solid fragmented material, or the solid fragment itself, that comes from the weathering of rock and is carried by, suspended in, or dropped by air, water, or ice. It refers also to a mass that is accumulated by any other natural agent and that forms in layers on the earth's surface, such as sand, gravel, silt, mud, fill, or loess. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1689)
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
Sequential operating programs and data which instruct the functioning of a digital computer.
A functional system which includes the organisms of a natural community together with their environment. (McGraw Hill Dictionary of Scientific and Technical Terms, 4th ed)
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
Esterases are hydrolase enzymes that catalyze the hydrolysis of ester bonds, converting esters into alcohols and acids, playing crucial roles in various biological processes including metabolism and detoxification.
The unconsolidated mineral or organic matter on the surface of the earth that serves as a natural medium for the growth of land plants.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.
Software designed to store, manipulate, manage, and control data for specific uses.
An enzyme of the hydrolase class that catalyzes the reaction of triacylglycerol and water to yield diacylglycerol and a fatty acid anion. It is produced by glands on the tongue and by the pancreas and initiates the digestion of dietary fats. (From Dorland, 27th ed) EC 3.1.1.3.
The first stomach of ruminants. It lies on the left side of the body, occupying the whole of the left side of the abdomen and even stretching across the median plane of the body to the right side. It is capacious, divided into an upper and a lower sac, each of which has a blind sac at its posterior extremity. The rumen is lined by mucous membrane containing no digestive glands, but mucus-secreting glands are present in large numbers. Coarse, partially chewed food is stored and churned in the rumen until the animal finds circumstances convenient for rumination. When this occurs, little balls of food are regurgitated through the esophagus into the mouth, and are subjected to a second more thorough mastication, swallowed, and passed on into other parts of the compound stomach. (From Black's Veterinary Dictionary, 17th ed)
Viruses whose hosts are bacterial cells.
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
Proteins found in any species of bacterium.
The naturally occurring transmission of genetic information between organisms, related or unrelated, circumventing parent-to-offspring transmission. Horizontal gene transfer may occur via a variety of naturally occurring processes such as GENETIC CONJUGATION; GENETIC TRANSDUCTION; and TRANSFECTION. It may result in a change of the recipient organism's genetic composition (TRANSFORMATION, GENETIC).
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
Genotypic differences observed among individuals in a population.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Excrement from the INTESTINES, containing unabsorbed solids, waste products, secretions, and BACTERIA of the DIGESTIVE SYSTEM.
The portion of an interactive computer program that issues messages to and receives commands from a user.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.

Multilocus sequence typing breathes life into a microbial metagenome. (1/1707)

Shot-gun sequencing of DNA isolated from the environment and the assembly of metagenomes from the resulting data has considerably advanced the study of microbial diversity. However, the subsequent matching of these hypothetical metagenomes to cultivable microorganisms is a limitation of such cultivation-independent methods of population analysis. Using a nucleotide sequence-based genetic typing method, multilocus sequence typing, we were able for the first time to match clonal cultivable isolates to a published and controversial bacterial metagenome, Burkholderia SAR-1, which derived from analysis of the Sargasso Sea. The matching cultivable isolates were all associated with infection and geographically widely distributed; taxonomic analysis demonstrated they were members of Burkholderia cepacia complex Group K. Comparison of the Burkholderia SAR-1 metagenome to closely related B. cepacia complex genomes indicated that it was greater than 98% intact in terms of conserved genes, and it also shared complete sequence identity with the cultivable isolates at random loci beyond the genes sampled by the multilocus sequence typing. Two features of the extant cultivable clones support the argument that the Burkholderia SAR-1 sequence may have been a contaminant in the original metagenomic survey: (i) their growth in conditions reflective of sea water was poor, suggesting the ocean was not their preferred habitat, and (ii) several of the matching isolates were epidemiologically linked to outbreaks of infection that resulted from contaminated medical devices or products, indicating an adaptive fitness of this bacterial strain towards contamination-associated environments. The ability to match identical cultivable strains of bacteria to a hypothetical metagenome is a unique feature of nucleotide sequence-based microbial typing methods; such matching would not have been possible with more traditional methods of genetic typing, such as those based on pattern matching of genomic restriction fragments or amplified DNA fragments. Overall, we have taken the first steps in moving the status of the Burkholderia SAR-1 metagenome from a hypothetical entity towards the basis for life of cultivable strains that may now be analysed in conjunction with the assembled metagenomic sequence data by the wider scientific community.  (+info)

Development of the human infant intestinal microbiota. (2/1707)

Almost immediately after a human being is born, so too is a new microbial ecosystem, one that resides in that person's gastrointestinal tract. Although it is a universal and integral part of human biology, the temporal progression of this process, the sources of the microbes that make up the ecosystem, how and why it varies from one infant to another, and how the composition of this ecosystem influences human physiology, development, and disease are still poorly understood. As a step toward systematically investigating these questions, we designed a microarray to detect and quantitate the small subunit ribosomal RNA (SSU rRNA) gene sequences of most currently recognized species and taxonomic groups of bacteria. We used this microarray, along with sequencing of cloned libraries of PCR-amplified SSU rDNA, to profile the microbial communities in an average of 26 stool samples each from 14 healthy, full-term human infants, including a pair of dizygotic twins, beginning with the first stool after birth and continuing at defined intervals throughout the first year of life. To investigate possible origins of the infant microbiota, we also profiled vaginal and milk samples from most of the mothers, and stool samples from all of the mothers, most of the fathers, and two siblings. The composition and temporal patterns of the microbial communities varied widely from baby to baby. Despite considerable temporal variation, the distinct features of each baby's microbial community were recognizable for intervals of weeks to months. The strikingly parallel temporal patterns of the twins suggested that incidental environmental exposures play a major role in determining the distinctive characteristics of the microbial community in each baby. By the end of the first year of life, the idiosyncratic microbial ecosystems in each baby, although still distinct, had converged toward a profile characteristic of the adult gastrointestinal tract.  (+info)

Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. (3/1707)

Numerous microbes inhabit the human intestine, many of which are uncharacterized or uncultivable. They form a complex microbial community that deeply affects human physiology. To identify the genomic features common to all human gut microbiomes as well as those variable among them, we performed a large-scale comparative metagenomic analysis of fecal samples from 13 healthy individuals of various ages, including unweaned infants. We found that, while the gut microbiota from unweaned infants were simple and showed a high inter-individual variation in taxonomic and gene composition, those from adults and weaned children were more complex but showed a high functional uniformity regardless of age or sex. In searching for the genes over-represented in gut microbiomes, we identified 237 gene families commonly enriched in adult-type and 136 families in infant-type microbiomes, with a small overlap. An analysis of their predicted functions revealed various strategies employed by each type of microbiota to adapt to its intestinal environment, suggesting that these gene sets encode the core functions of adult and infant-type gut microbiota. By analysing the orphan genes, 647 new gene families were identified to be exclusively present in human intestinal microbiomes. In addition, we discovered a conjugative transposon family explosively amplified in human gut microbiomes, which strongly suggests that the intestine is a 'hot spot' for horizontal gene transfer between microbes.  (+info)

The human microbiome project. (4/1707)

A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease.  (+info)

Probiotic modulation of symbiotic gut microbial-host metabolic interactions in a humanized microbiome mouse model. (5/1707)

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The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. (6/1707)

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Skin microbiota: a source of disease or defence? (7/1707)

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The microbiome of the cloacal openings of the urogenital and anal tracts of the tammar wallaby, Macropus eugenii. (8/1707)

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A metagenome is the collective genetic material contained within a sample taken from a specific environment, such as soil or water, or within a community of organisms, like the microbiota found in the human gut. It includes the genomes of all the microorganisms present in that environment or community, including bacteria, archaea, fungi, viruses, and other microbes, whether they can be cultured in the lab or not. By analyzing the metagenome, scientists can gain insights into the diversity, abundance, and functional potential of the microbial communities present in that environment.

Planctomycetales is an order of bacteria that are characterized by their unique cell structure and reproductive processes. Here is a medical definition of Planctomycetales:

"An order of primarily freshwater, gram-negative, aerobic or facultatively anaerobic bacteria, distinguished by the presence of unique cell structures such as crateriform dejections on the cell surface, and reproductive processes involving budding or the formation of membrane-bounded propagules. The order includes several genera with medical relevance, including some that are capable of causing opportunistic infections in humans."

It's worth noting that while some species of Planctomycetales have been found to be associated with human infections, they are not typically considered major pathogens and are not a primary focus of medical research.

A bacterial genome is the complete set of genetic material, including both DNA and RNA, found within a single bacterium. It contains all the hereditary information necessary for the bacterium to grow, reproduce, and survive in its environment. The bacterial genome typically includes circular chromosomes, as well as plasmids, which are smaller, circular DNA molecules that can carry additional genes. These genes encode various functional elements such as enzymes, structural proteins, and regulatory sequences that determine the bacterium's characteristics and behavior.

Bacterial genomes vary widely in size, ranging from around 130 kilobases (kb) in Mycoplasma genitalium to over 14 megabases (Mb) in Sorangium cellulosum. The complete sequencing and analysis of bacterial genomes have provided valuable insights into the biology, evolution, and pathogenicity of bacteria, enabling researchers to better understand their roles in various diseases and potential applications in biotechnology.

Bacteria are single-celled microorganisms that are among the earliest known life forms on Earth. They are typically characterized as having a cell wall and no membrane-bound organelles. The majority of bacteria have a prokaryotic organization, meaning they lack a nucleus and other membrane-bound organelles.

Bacteria exist in diverse environments and can be found in every habitat on Earth, including soil, water, and the bodies of plants and animals. Some bacteria are beneficial to their hosts, while others can cause disease. Beneficial bacteria play important roles in processes such as digestion, nitrogen fixation, and biogeochemical cycling.

Bacteria reproduce asexually through binary fission or budding, and some species can also exchange genetic material through conjugation. They have a wide range of metabolic capabilities, with many using organic compounds as their source of energy, while others are capable of photosynthesis or chemosynthesis.

Bacteria are highly adaptable and can evolve rapidly in response to environmental changes. This has led to the development of antibiotic resistance in some species, which poses a significant public health challenge. Understanding the biology and behavior of bacteria is essential for developing strategies to prevent and treat bacterial infections and diseases.

Phylogeny is the evolutionary history and relationship among biological entities, such as species or genes, based on their shared characteristics. In other words, it refers to the branching pattern of evolution that shows how various organisms have descended from a common ancestor over time. Phylogenetic analysis involves constructing a tree-like diagram called a phylogenetic tree, which depicts the inferred evolutionary relationships among organisms or genes based on molecular sequence data or other types of characters. This information is crucial for understanding the diversity and distribution of life on Earth, as well as for studying the emergence and spread of diseases.

DNA Sequence Analysis is the systematic determination of the order of nucleotides in a DNA molecule. It is a critical component of modern molecular biology, genetics, and genetic engineering. The process involves determining the exact order of the four nucleotide bases - adenine (A), guanine (G), cytosine (C), and thymine (T) - in a DNA molecule or fragment. This information is used in various applications such as identifying gene mutations, studying evolutionary relationships, developing molecular markers for breeding, and diagnosing genetic diseases.

The process of DNA Sequence Analysis typically involves several steps, including DNA extraction, PCR amplification (if necessary), purification, sequencing reaction, and electrophoresis. The resulting data is then analyzed using specialized software to determine the exact sequence of nucleotides.

In recent years, high-throughput DNA sequencing technologies have revolutionized the field of genomics, enabling the rapid and cost-effective sequencing of entire genomes. This has led to an explosion of genomic data and new insights into the genetic basis of many diseases and traits.

Seawater is not a medical term, but it is a type of water that covers more than 70% of the Earth's surface. Medically, seawater can be relevant in certain contexts, such as in discussions of marine biology, environmental health, or water safety. Seawater has a high salt content, with an average salinity of around 3.5%, which is much higher than that of freshwater. This makes it unsuitable for drinking or irrigation without desalination.

Exposure to seawater can also have medical implications, such as in cases of immersion injuries, marine envenomations, or waterborne illnesses. However, there is no single medical definition of seawater.

Environmental Microbiology is a branch of microbiology that deals with the study of microorganisms, including bacteria, fungi, viruses, and other microscopic entities, that are found in various environments such as water, soil, air, and organic matter. This field focuses on understanding how these microbes interact with their surroundings, their role in various ecological systems, and their impact on human health and the environment. It also involves studying the genetic and biochemical mechanisms that allow microorganisms to survive and thrive in different environmental conditions, as well as the potential uses of microbes for bioremediation, bioenergy, and other industrial applications.

Biodiversity is the variety of different species of plants, animals, and microorganisms that live in an ecosystem. It also includes the variety of genes within a species and the variety of ecosystems (such as forests, grasslands, deserts, and oceans) that exist in a region or on Earth as a whole. Biodiversity is important for maintaining the health and balance of ecosystems, providing resources and services such as food, clean water, and pollination, and contributing to the discovery of new medicines and other useful products. The loss of biodiversity can have negative impacts on the functioning of ecosystems and the services they provide, and can threaten the survival of species and the livelihoods of people who depend on them.

An archaeal genome refers to the complete set of genetic material or DNA present in an archaea, a single-celled microorganism that is found in some of the most extreme environments on Earth. The genome of an archaea contains all the information necessary for its survival, including the instructions for building proteins and other essential molecules, as well as the regulatory elements that control gene expression.

Archaeal genomes are typically circular in structure and range in size from about 0.5 to over 5 million base pairs. They contain genes that are similar to those found in bacteria and eukaryotes, as well as unique genes that are specific to archaea. The study of archaeal genomes has provided valuable insights into the evolutionary history of life on Earth and has helped scientists understand the adaptations that allow these organisms to thrive in such harsh environments.

The gastrointestinal (GI) tract, also known as the digestive tract, is a continuous tube that starts at the mouth and ends at the anus. It is responsible for ingesting, digesting, absorbing, and excreting food and waste materials. The GI tract includes the mouth, esophagus, stomach, small intestine (duodenum, jejunum, ileum), large intestine (cecum, colon, rectum, anus), and accessory organs such as the liver, gallbladder, and pancreas. The primary function of this system is to process and extract nutrients from food while also protecting the body from harmful substances, pathogens, and toxins.

Microbial consortia refer to a group or community of microorganisms, including bacteria, archaea, fungi, and viruses, that naturally exist together in a specific environment and interact with each other. These interactions can be synergistic, where the organisms benefit from each other's presence, or competitive, where they compete for resources.

Microbial consortia play important roles in various biological processes, such as biogeochemical cycling, plant growth promotion, and wastewater treatment. The study of microbial consortia is essential to understanding the complex interactions between microorganisms and their environment, and has implications for fields such as medicine, agriculture, and environmental science.

Rhodospirillales is an order of predominantly gram-negative, aerobic or anaerobic, motile bacteria that are found in various environments such as freshwater, marine habitats, and soil. Many species in this order are capable of photosynthesis, particularly those belonging to the family Rhodospirillaceae. These photosynthetic bacteria, called purple bacteria, use bacteriochlorophyll and can grow under anaerobic conditions using light as an energy source. The order Rhodospirillales belongs to the class Alphaproteobacteria within the phylum Proteobacteria.

It is important to note that medical definitions typically focus on bacteria, viruses, or other microorganisms of clinical relevance. While Rhodospirillales does include some species that can be pathogenic in certain circumstances, it is not primarily a medical term and is more commonly used in the context of environmental or general microbiology.

A photobioreactor is not a medical term, but rather a term used in the fields of biology, engineering, and environmental science. It refers to a device or system designed for the cultivation of photosynthetic organisms such as algae, cyanobacteria, and other microorganisms using light as an energy source.

In simple terms, a photobioreactor is a bioreactor that uses light to drive the growth of photosynthetic organisms. These systems are often used in research, biotechnology, and wastewater treatment applications to produce valuable products such as biofuels, nutraceuticals, pharmaceuticals, and other high-value compounds.

While photobioreactors may not have a direct medical application, they can contribute to medical research and healthcare through the production of biomass or specific compounds that can be used in medical treatments, diagnostics, or therapeutic interventions.

I'm sorry for any confusion, but "Prochloron" does not have a widely accepted medical definition in the context of human health or diseases. It is a genus name in prokaryotic taxonomy, referring to a group of cyanobacteria (blue-green algae) that are capable of photosynthesis and contain chlorophyll a and b, similar to plants. They are often found as symbionts in marine animals, particularly in certain species of ascidians (sea squirts). If you have any questions related to healthcare, medicine, or biology, please feel free to ask!

I'm sorry for any confusion, but "Oceans and Seas" are not medical terms. Generally speaking, an ocean is a large body of saltwater that covers a majority of the Earth's surface, and a sea is a smaller body of saltwater that may be partially enclosed by land. However, if you have any questions related to marine biology or environmental science, I would be happy to try and help answer those for you!

I apologize, but there seems to be a misunderstanding. "Soil microbiology" is not a medical term; rather, it is a branch of microbiology that deals with the study of microorganisms in soil. It involves understanding the diversity, ecology, and biochemistry of bacteria, fungi, algae, protozoa, and other microscopic life forms found in soil. This field has applications in agriculture, environmental science, and waste management but is not directly related to medical definitions or human health.

Archaea are a domain of single-celled microorganisms that lack membrane-bound nuclei and other organelles. They are characterized by the unique structure of their cell walls, membranes, and ribosomes. Archaea were originally classified as bacteria, but they differ from bacteria in several key ways, including their genetic material and metabolic processes.

Archaea can be found in a wide range of environments, including some of the most extreme habitats on Earth, such as hot springs, deep-sea vents, and highly saline lakes. Some species of Archaea are able to survive in the absence of oxygen, while others require oxygen to live.

Archaea play important roles in global nutrient cycles, including the nitrogen cycle and the carbon cycle. They are also being studied for their potential role in industrial processes, such as the production of biofuels and the treatment of wastewater.

Ribosomal RNA (rRNA) is a type of RNA that combines with proteins to form ribosomes, which are complex structures inside cells where protein synthesis occurs. The "16S" refers to the sedimentation coefficient of the rRNA molecule, which is a measure of its size and shape. In particular, 16S rRNA is a component of the smaller subunit of the prokaryotic ribosome (found in bacteria and archaea), and is often used as a molecular marker for identifying and classifying these organisms due to its relative stability and conservation among species. The sequence of 16S rRNA can be compared across different species to determine their evolutionary relationships and taxonomic positions.

'Biota' is a term that refers to the total collection of living organisms in a particular habitat, ecosystem, or region. It includes all forms of life such as plants, animals, fungi, bacteria, and other microorganisms. Biota can be used to describe the communities of living things in a specific area, like a forest biota or marine biota, and it can also refer to the study of these organisms and their interactions with each other and their environment. In medical contexts, 'biota' may specifically refer to the microorganisms that inhabit the human body, such as the gut microbiota.

I apologize for the confusion, but "Marine Biology" is not a medical term. Instead, it is a branch of biology that deals with the study of marine organisms, their behaviors, and their interactions with the marine environment. Marine biologists investigate various aspects of marine life, such as the ecology, physiology, and genetics of marine plants, animals, and microorganisms. They also study the impact of human activities on marine ecosystems and work towards conservation efforts to protect these environments.

Genomics is the scientific study of genes and their functions. It involves the sequencing and analysis of an organism's genome, which is its complete set of DNA, including all of its genes. Genomics also includes the study of how genes interact with each other and with the environment. This field of study can provide important insights into the genetic basis of diseases and can lead to the development of new diagnostic tools and treatments.

High-throughput nucleotide sequencing, also known as next-generation sequencing (NGS), refers to a group of technologies that allow for the rapid and parallel determination of nucleotide sequences of DNA or RNA molecules. These techniques enable the sequencing of large numbers of DNA or RNA fragments simultaneously, resulting in the generation of vast amounts of sequence data in a single run.

High-throughput sequencing has revolutionized genomics research by allowing for the rapid and cost-effective sequencing of entire genomes, transcriptomes, and epigenomes. It has numerous applications in basic research, including genome assembly, gene expression analysis, variant detection, and methylation profiling, as well as in clinical settings, such as diagnosis of genetic diseases, identification of pathogens, and monitoring of cancer progression and treatment response.

Some common high-throughput sequencing platforms include Illumina (sequencing by synthesis), Ion Torrent (semiconductor sequencing), Pacific Biosciences (single molecule real-time sequencing), and Oxford Nanopore Technologies (nanopore sequencing). Each platform has its strengths and limitations, and the choice of technology depends on the specific research question and experimental design.

Sewage is not typically considered a medical term, but it does have relevance to public health and medicine. Sewage is the wastewater that is produced by households and industries, which contains a variety of contaminants including human waste, chemicals, and other pollutants. It can contain various pathogens such as bacteria, viruses, and parasites, which can cause diseases in humans if they come into contact with it or consume contaminated food or water. Therefore, the proper treatment and disposal of sewage is essential to prevent the spread of infectious diseases and protect public health.

I apologize for any confusion, but "Haliclona" is not a medical term. It is actually the name of a genus of marine sponges, also known as sea sponges. These sponges are found in various parts of the world and are characterized by their porous structure and the way they filter water to obtain food. If you have any questions related to medical terminology or concepts, I would be happy to help with those instead.

I'm sorry for any confusion, but "Theonella" is not a term that has a widely accepted or specific medical definition in the context of human health or diseases. It is the name of a genus of marine sponges, and some species of Theonella contain compounds with potential medicinal properties. However, it is not a term commonly used in medical practice or research. If you have more context or information about why you are looking for a medical definition of "Theonella," I may be able to provide a more helpful response.

A genomic library is a collection of cloned DNA fragments that represent the entire genetic material of an organism. It serves as a valuable resource for studying the function, organization, and regulation of genes within a given genome. Genomic libraries can be created using different types of vectors, such as bacterial artificial chromosomes (BACs), yeast artificial chromosomes (YACs), or plasmids, to accommodate various sizes of DNA inserts. These libraries facilitate the isolation and manipulation of specific genes or genomic regions for further analysis, including sequencing, gene expression studies, and functional genomics research.

Molecular sequence data refers to the specific arrangement of molecules, most commonly nucleotides in DNA or RNA, or amino acids in proteins, that make up a biological macromolecule. This data is generated through laboratory techniques such as sequencing, and provides information about the exact order of the constituent molecules. This data is crucial in various fields of biology, including genetics, evolution, and molecular biology, allowing for comparisons between different organisms, identification of genetic variations, and studies of gene function and regulation.

Medical Definition of Microbiota:

The community of microorganisms, including bacteria, viruses, fungi, and other microscopic life forms, that inhabit a specific environment or body part. In the human body, microbiota can be found on the skin, in the mouth, gut, and other areas. The largest concentration of microbiota is located in the intestines, where it plays an essential role in digestion, immune function, and overall health.

The composition of the microbiota can vary depending on factors such as age, diet, lifestyle, genetics, and environmental exposures. Dysbiosis, or imbalance of the microbiota, has been linked to various health conditions, including gastrointestinal disorders, allergies, autoimmune diseases, and neurological disorders.

Therefore, maintaining a healthy and diverse microbiota is crucial for overall health and well-being. This can be achieved through a balanced diet, regular exercise, adequate sleep, stress management, and other lifestyle practices that support the growth and maintenance of beneficial microorganisms in the body.

Bacterial DNA refers to the genetic material found in bacteria. It is composed of a double-stranded helix containing four nucleotide bases - adenine (A), thymine (T), guanine (G), and cytosine (C) - that are linked together by phosphodiester bonds. The sequence of these bases in the DNA molecule carries the genetic information necessary for the growth, development, and reproduction of bacteria.

Bacterial DNA is circular in most bacterial species, although some have linear chromosomes. In addition to the main chromosome, many bacteria also contain small circular pieces of DNA called plasmids that can carry additional genes and provide resistance to antibiotics or other environmental stressors.

Unlike eukaryotic cells, which have their DNA enclosed within a nucleus, bacterial DNA is present in the cytoplasm of the cell, where it is in direct contact with the cell's metabolic machinery. This allows for rapid gene expression and regulation in response to changing environmental conditions.

'Aquatic organisms' are living beings that inhabit bodies of water, such as oceans, seas, lakes, rivers, and ponds. This group includes a wide variety of species, ranging from tiny microorganisms like plankton to large marine mammals like whales. Aquatic organisms can be divided into several categories based on their specific adaptations to their environment, including:

1. Plankton: small organisms that drift with the water currents and include both plants (phytoplankton) and animals (zooplankton).
2. Nekton: actively swimming aquatic organisms, such as fish, squid, and marine mammals.
3. Benthos: organisms that live on or in the bottom of bodies of water, including crustaceans, mollusks, worms, and some types of algae.
4. Neuston: organisms that live at the air-water interface, such as certain species of insects and small fish.

Aquatic organisms play a critical role in maintaining the health and balance of aquatic ecosystems, providing food and habitat for other species, and contributing to global nutrient cycling and climate regulation.

A genetic database is a type of biomedical or health informatics database that stores and organizes genetic data, such as DNA sequences, gene maps, genotypes, haplotypes, and phenotype information. These databases can be used for various purposes, including research, clinical diagnosis, and personalized medicine.

There are different types of genetic databases, including:

1. Genomic databases: These databases store whole genome sequences, gene expression data, and other genomic information. Examples include the National Center for Biotechnology Information's (NCBI) GenBank, the European Nucleotide Archive (ENA), and the DNA Data Bank of Japan (DDBJ).
2. Gene databases: These databases contain information about specific genes, including their location, function, regulation, and evolution. Examples include the Online Mendelian Inheritance in Man (OMIM) database, the Universal Protein Resource (UniProt), and the Gene Ontology (GO) database.
3. Variant databases: These databases store information about genetic variants, such as single nucleotide polymorphisms (SNPs), insertions/deletions (INDELs), and copy number variations (CNVs). Examples include the Database of Single Nucleotide Polymorphisms (dbSNP), the Catalogue of Somatic Mutations in Cancer (COSMIC), and the International HapMap Project.
4. Clinical databases: These databases contain genetic and clinical information about patients, such as their genotype, phenotype, family history, and response to treatments. Examples include the ClinVar database, the Pharmacogenomics Knowledgebase (PharmGKB), and the Genetic Testing Registry (GTR).
5. Population databases: These databases store genetic information about different populations, including their ancestry, demographics, and genetic diversity. Examples include the 1000 Genomes Project, the Human Genome Diversity Project (HGDP), and the Allele Frequency Net Database (AFND).

Genetic databases can be publicly accessible or restricted to authorized users, depending on their purpose and content. They play a crucial role in advancing our understanding of genetics and genomics, as well as improving healthcare and personalized medicine.

Actinobacteria are a group of gram-positive bacteria that are widely distributed in nature, including in soil, water, and various organic substrates. They are characterized by their high G+C content in their DNA and complex cell wall composition, which often contains mycolic acids. Some Actinobacteria are known to form branching filaments, giving them a characteristic "actinomycete" morphology. Many species of Actinobacteria have important roles in industry, agriculture, and medicine. For example, some produce antibiotics, enzymes, and other bioactive compounds, while others play key roles in biogeochemical cycles such as the decomposition of organic matter and the fixation of nitrogen. Additionally, some Actinobacteria are pathogenic and can cause diseases in humans, animals, and plants.

A virus is a small infectious agent that replicates inside the living cells of an organism. It is not considered to be a living organism itself, as it lacks the necessary components to independently maintain its own metabolic functions. Viruses are typically composed of genetic material, either DNA or RNA, surrounded by a protein coat called a capsid. Some viruses also have an outer lipid membrane known as an envelope.

Viruses can infect all types of organisms, from animals and plants to bacteria and archaea. They cause various diseases by invading the host cell, hijacking its machinery, and using it to produce numerous copies of themselves, which can then infect other cells. The resulting infection and the immune response it triggers can lead to a range of symptoms, depending on the virus and the host organism.

Viruses are transmitted through various means, such as respiratory droplets, bodily fluids, contaminated food or water, and vectors like insects. Prevention methods include vaccination, practicing good hygiene, using personal protective equipment, and implementing public health measures to control their spread.

Bacteroidetes is a large phylum of gram-negative, predominantly anaerobic bacteria that are commonly found in the gastrointestinal tract of animals, including humans. They play an important role in the breakdown and fermentation of complex carbohydrates in the gut, producing short-chain fatty acids as a byproduct. Some species of Bacteroidetes have also been identified as opportunistic pathogens and can cause infections in immunocompromised individuals or under certain conditions.

The medical relevance of Bacteroidetes lies in their role in maintaining gut homeostasis, modulating the immune system, and protecting against pathogenic bacteria. Dysbiosis of the gut microbiota, including changes in the abundance and diversity of Bacteroidetes, has been associated with various diseases such as inflammatory bowel disease, obesity, diabetes, and cardiovascular disease. Therefore, understanding the ecology and function of Bacteroidetes is important for developing novel therapeutic strategies to target these conditions.

Cluster analysis is a statistical method used to group similar objects or data points together based on their characteristics or features. In medical and healthcare research, cluster analysis can be used to identify patterns or relationships within complex datasets, such as patient records or genetic information. This technique can help researchers to classify patients into distinct subgroups based on their symptoms, diagnoses, or other variables, which can inform more personalized treatment plans or public health interventions.

Cluster analysis involves several steps, including:

1. Data preparation: The researcher must first collect and clean the data, ensuring that it is complete and free from errors. This may involve removing outlier values or missing data points.
2. Distance measurement: Next, the researcher must determine how to measure the distance between each pair of data points. Common methods include Euclidean distance (the straight-line distance between two points) or Manhattan distance (the distance between two points along a grid).
3. Clustering algorithm: The researcher then applies a clustering algorithm, which groups similar data points together based on their distances from one another. Common algorithms include hierarchical clustering (which creates a tree-like structure of clusters) or k-means clustering (which assigns each data point to the nearest centroid).
4. Validation: Finally, the researcher must validate the results of the cluster analysis by evaluating the stability and robustness of the clusters. This may involve re-running the analysis with different distance measures or clustering algorithms, or comparing the results to external criteria.

Cluster analysis is a powerful tool for identifying patterns and relationships within complex datasets, but it requires careful consideration of the data preparation, distance measurement, and validation steps to ensure accurate and meaningful results.

Fluid waste disposal in a medical context refers to the proper and safe management of liquid byproducts generated during medical procedures, patient care, or research. These fluids can include bodily excretions (such as urine, feces, or vomit), irrigation solutions, blood, or other biological fluids.

The process of fluid waste disposal involves several steps:

1. Collection: Fluid waste is collected in appropriate containers that are designed to prevent leakage and contamination.
2. Segregation: Different types of fluid waste may require separate collection and disposal methods based on their infectious or hazardous nature.
3. Treatment: Depending on the type and volume of fluid waste, various treatments can be applied, such as disinfection, sterilization, or chemical neutralization, to reduce the risk of infection or harm to the environment and personnel.
4. Disposal: Treated fluid waste is then disposed of according to local regulations, which may involve transporting it to a designated waste management facility for further processing or disposal in a safe and environmentally friendly manner (e.g., deep well injection, incineration, or landfilling).
5. Documentation and tracking: Proper records should be maintained to ensure compliance with regulatory requirements and to enable effective monitoring and auditing of the waste disposal process.

It is essential to handle fluid waste disposal carefully to minimize the risk of infection, protect the environment, and maintain regulatory compliance. Healthcare facilities must adhere to strict guidelines and regulations regarding fluid waste management to ensure the safety of patients, staff, and the community.

Water microbiology is not a formal medical term, but rather a branch of microbiology that deals with the study of microorganisms found in water. It involves the identification, enumeration, and characterization of bacteria, viruses, parasites, and other microscopic organisms present in water sources such as lakes, rivers, oceans, groundwater, drinking water, and wastewater.

In a medical context, water microbiology is relevant to public health because it helps to assess the safety of water supplies for human consumption and recreational activities. It also plays a critical role in understanding and preventing waterborne diseases caused by pathogenic microorganisms that can lead to illnesses such as diarrhea, skin infections, and respiratory problems.

Water microbiologists use various techniques to study water microorganisms, including culturing, microscopy, genetic analysis, and biochemical tests. They also investigate the ecology of these organisms, their interactions with other species, and their response to environmental factors such as temperature, pH, and nutrient availability.

Overall, water microbiology is a vital field that helps ensure the safety of our water resources and protects public health.

I'm sorry for any confusion, but the term "Pacific Ocean" is a geographical term referring to the largest single body of saltwater on Earth, extending from the Arctic in the north to the Antarctic in the south. It covers an area of about 63,800,000 square miles (165,200,000 square kilometers).

If you're looking for a medical term or definition, I'd be happy to help with that as well. Could you please provide more context?

Endo-1,4-beta Xylanases are a type of enzyme that catalyze the endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans, which are complex polysaccharides made up of beta-1,4-linked xylose residues. Xylan is a major hemicellulose component found in the cell walls of plants, and endo-1,4-beta Xylanases play an important role in the breakdown and digestion of plant material by various organisms, including bacteria, fungi, and animals. These enzymes are widely used in industrial applications, such as biofuel production, food processing, and pulp and paper manufacturing, to break down xylans and improve the efficiency of various processes.

Eukaryota is a domain that consists of organisms whose cells have a true nucleus and complex organelles. This domain includes animals, plants, fungi, and protists. The term "eukaryote" comes from the Greek words "eu," meaning true or good, and "karyon," meaning nut or kernel. In eukaryotic cells, the genetic material is housed within a membrane-bound nucleus, and the DNA is organized into chromosomes. This is in contrast to prokaryotic cells, which do not have a true nucleus and have their genetic material dispersed throughout the cytoplasm.

Eukaryotic cells are generally larger and more complex than prokaryotic cells. They have many different organelles, including mitochondria, chloroplasts, endoplasmic reticulum, and Golgi apparatus, that perform specific functions to support the cell's metabolism and survival. Eukaryotic cells also have a cytoskeleton made up of microtubules, actin filaments, and intermediate filaments, which provide structure and shape to the cell and allow for movement of organelles and other cellular components.

Eukaryotes are diverse and can be found in many different environments, ranging from single-celled organisms that live in water or soil to multicellular organisms that live on land or in aquatic habitats. Some eukaryotes are unicellular, meaning they consist of a single cell, while others are multicellular, meaning they consist of many cells that work together to form tissues and organs.

In summary, Eukaryota is a domain of organisms whose cells have a true nucleus and complex organelles. This domain includes animals, plants, fungi, and protists, and the eukaryotic cells are generally larger and more complex than prokaryotic cells.

'Hot Springs' are a type of geothermal feature where water is heated by the Earth's internal heat and emerges from the ground at temperatures greater than the surrounding air temperature. The water in hot springs can range in temperature from warm to extremely hot, and it is often rich in minerals such as calcium, magnesium, sulfur, and sodium.

People have been using hot springs for thousands of years for various purposes, including relaxation, recreation, and therapeutic benefits. The heat and mineral content of the water can help to soothe sore muscles, improve circulation, and promote healing in some cases. However, it is important to note that not all hot springs are safe for bathing, as some may contain harmful bacteria or pollutants. It is always recommended to check with local authorities before using a hot spring for therapeutic purposes.

Bacterial physiological phenomena refer to the various functional processes and activities that occur within bacteria, which are necessary for their survival, growth, and reproduction. These phenomena include:

1. Metabolism: This is the process by which bacteria convert nutrients into energy and cellular components. It involves a series of chemical reactions that break down organic compounds such as carbohydrates, lipids, and proteins to produce energy in the form of ATP (adenosine triphosphate).
2. Respiration: This is the process by which bacteria use oxygen to convert organic compounds into carbon dioxide and water, releasing energy in the form of ATP. Some bacteria can also perform anaerobic respiration, using alternative electron acceptors such as nitrate or sulfate instead of oxygen.
3. Fermentation: This is a type of anaerobic metabolism in which bacteria convert organic compounds into simpler molecules, releasing energy in the form of ATP. Unlike respiration, fermentation does not require an external electron acceptor.
4. Motility: Many bacteria are capable of moving independently, using various mechanisms such as flagella or twitching motility. This allows them to move towards favorable environments and away from harmful ones.
5. Chemotaxis: Bacteria can sense and respond to chemical gradients in their environment, allowing them to move towards attractants and away from repellents.
6. Quorum sensing: Bacteria can communicate with each other using signaling molecules called autoinducers. When the concentration of autoinducers reaches a certain threshold, the bacteria can coordinate their behavior, such as initiating biofilm formation or producing virulence factors.
7. Sporulation: Some bacteria can form spores, which are highly resistant to heat, radiation, and chemicals. Spores can remain dormant for long periods of time and germinate when conditions are favorable.
8. Biofilm formation: Bacteria can form complex communities called biofilms, which are composed of cells embedded in a matrix of extracellular polymeric substances (EPS). Biofilms can provide protection from environmental stressors and host immune responses.
9. Cell division: Bacteria reproduce by binary fission, where the cell divides into two identical daughter cells. This process is regulated by various cell cycle checkpoints and can be influenced by environmental factors such as nutrient availability.

Plankton is not a medical term, but it is a term used in the field of marine biology. Plankton are tiny organisms that live in water and are unable to move independently against the current or tide. They include both plants (phytoplankton) and animals (zooplankton). Phytoplankton are photosynthetic and serve as the base of the ocean food chain, while zooplankton consume phytoplankton and in turn serve as a food source for larger animals. Plankton are important for understanding the health and productivity of aquatic ecosystems.

In the context of medicine and biology, symbiosis is a type of close and long-term biological interaction between two different biological organisms. Generally, one organism, called the symbiont, lives inside or on another organism, called the host. This interaction can be mutually beneficial (mutualistic), harmful to the host organism (parasitic), or have no effect on either organism (commensal).

Examples of mutualistic symbiotic relationships in humans include the bacteria that live in our gut and help us digest food, as well as the algae that live inside corals and provide them with nutrients. Parasitic symbioses, on the other hand, involve organisms like viruses or parasitic worms that live inside a host and cause harm to it.

It's worth noting that while the term "symbiosis" is often used in popular culture to refer to any close relationship between two organisms, in scientific contexts it has a more specific meaning related to long-term biological interactions.

Computational biology is a branch of biology that uses mathematical and computational methods to study biological data, models, and processes. It involves the development and application of algorithms, statistical models, and computational approaches to analyze and interpret large-scale molecular and phenotypic data from genomics, transcriptomics, proteomics, metabolomics, and other high-throughput technologies. The goal is to gain insights into biological systems and processes, develop predictive models, and inform experimental design and hypothesis testing in the life sciences. Computational biology encompasses a wide range of disciplines, including bioinformatics, systems biology, computational genomics, network biology, and mathematical modeling of biological systems.

Biotechnology is defined in the medical field as a branch of technology that utilizes biological processes, organisms, or systems to create products that are technologically useful. This can include various methods and techniques such as genetic engineering, cell culture, fermentation, and others. The goal of biotechnology is to harness the power of biology to produce drugs, vaccines, diagnostic tests, biofuels, and other industrial products, as well as to advance our understanding of living systems for medical and scientific research.

The use of biotechnology has led to significant advances in medicine, including the development of new treatments for genetic diseases, improved methods for diagnosing illnesses, and the creation of vaccines to prevent infectious diseases. However, it also raises ethical and societal concerns related to issues such as genetic modification of organisms, cloning, and biosecurity.

Molecular sequence annotation is the process of identifying and describing the characteristics, functional elements, and relevant information of a DNA, RNA, or protein sequence at the molecular level. This process involves marking the location and function of various features such as genes, regulatory regions, coding and non-coding sequences, intron-exon boundaries, promoters, introns, untranslated regions (UTRs), binding sites for proteins or other molecules, and post-translational modifications in a given molecular sequence.

The annotation can be manual, where experts curate and analyze the data to predict features based on biological knowledge and experimental evidence. Alternatively, computational methods using various bioinformatics tools and algorithms can be employed for automated annotation. These tools often rely on comparative analysis, pattern recognition, and machine learning techniques to identify conserved sequence patterns, motifs, or domains that are associated with specific functions.

The annotated molecular sequences serve as valuable resources in genomic and proteomic studies, contributing to the understanding of gene function, evolutionary relationships, disease associations, and biotechnological applications.

A viral genome is the genetic material (DNA or RNA) that is present in a virus. It contains all the genetic information that a virus needs to replicate itself and infect its host. The size and complexity of viral genomes can vary greatly, ranging from a few thousand bases to hundreds of thousands of bases. Some viruses have linear genomes, while others have circular genomes. The genome of a virus also contains the information necessary for the virus to hijack the host cell's machinery and use it to produce new copies of the virus. Understanding the genetic makeup of viruses is important for developing vaccines and antiviral treatments.

I'm sorry for any confusion, but "geologic sediments" is not a term used in medical definitions. Geological sediments are deposits of material that accumulate over time, usually in layers, as a result of natural geological processes such as weathering, erosion, and deposition. These sediments can eventually become rock formations and provide important clues about the Earth's history, including information about past climates, environments, and life on Earth.

An open reading frame (ORF) is a continuous stretch of DNA or RNA sequence that has the potential to be translated into a protein. It begins with a start codon (usually "ATG" in DNA, which corresponds to "AUG" in RNA) and ends with a stop codon ("TAA", "TAG", or "TGA" in DNA; "UAA", "UAG", or "UGA" in RNA). The sequence between these two points is called a coding sequence (CDS), which, when transcribed into mRNA and translated into amino acids, forms a polypeptide chain.

In eukaryotic cells, ORFs can be located in either protein-coding genes or non-coding regions of the genome. In prokaryotic cells, multiple ORFs may be present on a single strand of DNA, often organized into operons that are transcribed together as a single mRNA molecule.

It's important to note that not all ORFs necessarily represent functional proteins; some may be pseudogenes or result from errors in genome annotation. Therefore, additional experimental evidence is typically required to confirm the expression and functionality of a given ORF.

I am not aware of a widely accepted medical definition for the term "software," as it is more commonly used in the context of computer science and technology. Software refers to programs, data, and instructions that are used by computers to perform various tasks. It does not have direct relevance to medical fields such as anatomy, physiology, or clinical practice. If you have any questions related to medicine or healthcare, I would be happy to try to help with those instead!

An "ecosystem" is not a term that has a specific medical definition, as it is a concept that is more commonly used in the fields of ecology and environmental science. However, I can provide you with the general ecological definition of an ecosystem:

An ecosystem is a community of living organisms interacting with each other and their non-living environment, including both biotic factors (plants, animals, microorganisms) and abiotic factors (climate, soil, water, and air). These interactions create a complex network of relationships that form the foundation of ecological processes, such as energy flow, nutrient cycling, and population dynamics.

While there is no direct medical definition for an ecosystem, understanding the principles of ecosystems can have important implications for human health. For example, healthy ecosystems can provide clean air and water, regulate climate, support food production, and offer opportunities for recreation and relaxation, all of which contribute to overall well-being. Conversely, degraded ecosystems can lead to increased exposure to environmental hazards, reduced access to natural resources, and heightened risks of infectious diseases. Therefore, maintaining the health and integrity of ecosystems is crucial for promoting human health and preventing disease.

In genetics, sequence alignment is the process of arranging two or more DNA, RNA, or protein sequences to identify regions of similarity or homology between them. This is often done using computational methods to compare the nucleotide or amino acid sequences and identify matching patterns, which can provide insight into evolutionary relationships, functional domains, or potential genetic disorders. The alignment process typically involves adjusting gaps and mismatches in the sequences to maximize the similarity between them, resulting in an aligned sequence that can be visually represented and analyzed.

A "gene library" is not a recognized term in medical genetics or molecular biology. However, the closest concept that might be referred to by this term is a "genomic library," which is a collection of DNA clones that represent the entire genetic material of an organism. These libraries are used for various research purposes, such as identifying and studying specific genes or gene functions.

Esterases are a group of enzymes that catalyze the hydrolysis of ester bonds in esters, producing alcohols and carboxylic acids. They are widely distributed in plants, animals, and microorganisms and play important roles in various biological processes, such as metabolism, digestion, and detoxification.

Esterases can be classified into several types based on their substrate specificity, including carboxylesterases, cholinesterases, lipases, and phosphatases. These enzymes have different structures and mechanisms of action but all share the ability to hydrolyze esters.

Carboxylesterases are the most abundant and diverse group of esterases, with a wide range of substrate specificity. They play important roles in the metabolism of drugs, xenobiotics, and lipids. Cholinesterases, on the other hand, specifically hydrolyze choline esters, such as acetylcholine, which is an important neurotransmitter in the nervous system. Lipases are a type of esterase that preferentially hydrolyzes triglycerides and plays a crucial role in fat digestion and metabolism. Phosphatases are enzymes that remove phosphate groups from various molecules, including esters, and have important functions in signal transduction and other cellular processes.

Esterases can also be used in industrial applications, such as in the production of biodiesel, detergents, and food additives. They are often produced by microbial fermentation or extracted from plants and animals. The use of esterases in biotechnology is an active area of research, with potential applications in biofuel production, bioremediation, and medical diagnostics.

I'm sorry for any confusion, but "soil" is not a term that has a medical definition. Soil is defined as the top layer of earth in which plants grow, a mixture of organic material, clay, sand, and silt. If you have any questions related to medicine or health, I would be happy to try to help answer them for you.

Molecular cloning is a laboratory technique used to create multiple copies of a specific DNA sequence. This process involves several steps:

1. Isolation: The first step in molecular cloning is to isolate the DNA sequence of interest from the rest of the genomic DNA. This can be done using various methods such as PCR (polymerase chain reaction), restriction enzymes, or hybridization.
2. Vector construction: Once the DNA sequence of interest has been isolated, it must be inserted into a vector, which is a small circular DNA molecule that can replicate independently in a host cell. Common vectors used in molecular cloning include plasmids and phages.
3. Transformation: The constructed vector is then introduced into a host cell, usually a bacterial or yeast cell, through a process called transformation. This can be done using various methods such as electroporation or chemical transformation.
4. Selection: After transformation, the host cells are grown in selective media that allow only those cells containing the vector to grow. This ensures that the DNA sequence of interest has been successfully cloned into the vector.
5. Amplification: Once the host cells have been selected, they can be grown in large quantities to amplify the number of copies of the cloned DNA sequence.

Molecular cloning is a powerful tool in molecular biology and has numerous applications, including the production of recombinant proteins, gene therapy, functional analysis of genes, and genetic engineering.

An algorithm is not a medical term, but rather a concept from computer science and mathematics. In the context of medicine, algorithms are often used to describe step-by-step procedures for diagnosing or managing medical conditions. These procedures typically involve a series of rules or decision points that help healthcare professionals make informed decisions about patient care.

For example, an algorithm for diagnosing a particular type of heart disease might involve taking a patient's medical history, performing a physical exam, ordering certain diagnostic tests, and interpreting the results in a specific way. By following this algorithm, healthcare professionals can ensure that they are using a consistent and evidence-based approach to making a diagnosis.

Algorithms can also be used to guide treatment decisions. For instance, an algorithm for managing diabetes might involve setting target blood sugar levels, recommending certain medications or lifestyle changes based on the patient's individual needs, and monitoring the patient's response to treatment over time.

Overall, algorithms are valuable tools in medicine because they help standardize clinical decision-making and ensure that patients receive high-quality care based on the latest scientific evidence.

Metabolic networks and pathways refer to the complex interconnected series of biochemical reactions that occur within cells to maintain life. These reactions are catalyzed by enzymes and are responsible for the conversion of nutrients into energy, as well as the synthesis and breakdown of various molecules required for cellular function.

A metabolic pathway is a series of chemical reactions that occur in a specific order, with each reaction being catalyzed by a different enzyme. These pathways are often interconnected, forming a larger network of interactions known as a metabolic network.

Metabolic networks can be represented as complex diagrams or models, which show the relationships between different pathways and the flow of matter and energy through the system. These networks can help researchers to understand how cells regulate their metabolism in response to changes in their environment, and how disruptions to these networks can lead to disease.

Some common examples of metabolic pathways include glycolysis, the citric acid cycle (also known as the Krebs cycle), and the pentose phosphate pathway. Each of these pathways plays a critical role in maintaining cellular homeostasis and providing energy for cellular functions.

A Database Management System (DBMS) is a software application that enables users to define, create, maintain, and manipulate databases. It provides a structured way to organize, store, retrieve, and manage data in a digital format. The DBMS serves as an interface between the database and the applications or users that access it, allowing for standardized interactions and data access methods. Common functions of a DBMS include data definition, data manipulation, data security, data recovery, and concurrent data access control. Examples of DBMS include MySQL, Oracle, Microsoft SQL Server, and MongoDB.

Lipase is an enzyme that is produced by the pancreas and found in the digestive system of most organisms. Its primary function is to catalyze the hydrolysis of fats (triglycerides) into smaller molecules, such as fatty acids and glycerol, which can then be absorbed by the intestines and utilized for energy or stored for later use.

In medical terms, lipase levels in the blood are often measured to diagnose or monitor conditions that affect the pancreas, such as pancreatitis (inflammation of the pancreas), pancreatic cancer, or cystic fibrosis. Elevated lipase levels may indicate damage to the pancreas and its ability to produce digestive enzymes.

The rumen is the largest compartment of the stomach in ruminant animals, such as cows, goats, and sheep. It is a specialized fermentation chamber where microbes break down tough plant material into nutrients that the animal can absorb and use for energy and growth. The rumen contains billions of microorganisms, including bacteria, protozoa, and fungi, which help to break down cellulose and other complex carbohydrates in the plant material through fermentation.

The rumen is characterized by its large size, muscular walls, and the presence of a thick mat of partially digested food and microbes called the rumen mat or cud. The animal regurgitates the rumen contents periodically to chew it again, which helps to break down the plant material further and mix it with saliva, creating a more favorable environment for fermentation.

The rumen plays an essential role in the digestion and nutrition of ruminant animals, allowing them to thrive on a diet of low-quality plant material that would be difficult for other animals to digest.

Bacteriophages, often simply called phages, are viruses that infect and replicate within bacteria. They consist of a protein coat, called the capsid, that encases the genetic material, which can be either DNA or RNA. Bacteriophages are highly specific, meaning they only infect certain types of bacteria, and they reproduce by hijacking the bacterial cell's machinery to produce more viruses.

Once a phage infects a bacterium, it can either replicate its genetic material and create new phages (lytic cycle), or integrate its genetic material into the bacterial chromosome and replicate along with the bacterium (lysogenic cycle). In the lytic cycle, the newly formed phages are released by lysing, or breaking open, the bacterial cell.

Bacteriophages play a crucial role in shaping microbial communities and have been studied as potential alternatives to antibiotics for treating bacterial infections.

Temperature, in a medical context, is a measure of the degree of hotness or coldness of a body or environment. It is usually measured using a thermometer and reported in degrees Celsius (°C), degrees Fahrenheit (°F), or kelvin (K). In the human body, normal core temperature ranges from about 36.5-37.5°C (97.7-99.5°F) when measured rectally, and can vary slightly depending on factors such as time of day, physical activity, and menstrual cycle. Elevated body temperature is a common sign of infection or inflammation, while abnormally low body temperature can indicate hypothermia or other medical conditions.

Bacterial proteins are a type of protein that are produced by bacteria as part of their structural or functional components. These proteins can be involved in various cellular processes, such as metabolism, DNA replication, transcription, and translation. They can also play a role in bacterial pathogenesis, helping the bacteria to evade the host's immune system, acquire nutrients, and multiply within the host.

Bacterial proteins can be classified into different categories based on their function, such as:

1. Enzymes: Proteins that catalyze chemical reactions in the bacterial cell.
2. Structural proteins: Proteins that provide structural support and maintain the shape of the bacterial cell.
3. Signaling proteins: Proteins that help bacteria to communicate with each other and coordinate their behavior.
4. Transport proteins: Proteins that facilitate the movement of molecules across the bacterial cell membrane.
5. Toxins: Proteins that are produced by pathogenic bacteria to damage host cells and promote infection.
6. Surface proteins: Proteins that are located on the surface of the bacterial cell and interact with the environment or host cells.

Understanding the structure and function of bacterial proteins is important for developing new antibiotics, vaccines, and other therapeutic strategies to combat bacterial infections.

Horizontal gene transfer (HGT), also known as lateral gene transfer, is the movement of genetic material between organisms in a manner other than from parent to offspring (vertical gene transfer). In horizontal gene transfer, an organism can take up genetic material directly from its environment and incorporate it into its own genome. This process is common in bacteria and archaea, but has also been observed in eukaryotes including plants and animals.

Horizontal gene transfer can occur through several mechanisms, including:

1. Transformation: the uptake of free DNA from the environment by a cell.
2. Transduction: the transfer of genetic material between cells by a virus (bacteriophage).
3. Conjugation: the direct transfer of genetic material between two cells in physical contact, often facilitated by a conjugative plasmid or other mobile genetic element.

Horizontal gene transfer can play an important role in the evolution and adaptation of organisms, allowing them to acquire new traits and functions rapidly. It is also of concern in the context of genetically modified organisms (GMOs) and antibiotic resistance, as it can facilitate the spread of genes that confer resistance or other undesirable traits.

A genome is the complete set of genetic material (DNA, or in some viruses, RNA) present in a single cell of an organism. It includes all of the genes, both coding and noncoding, as well as other regulatory elements that together determine the unique characteristics of that organism. The human genome, for example, contains approximately 3 billion base pairs and about 20,000-25,000 protein-coding genes.

The term "genome" was first coined by Hans Winkler in 1920, derived from the word "gene" and the suffix "-ome," which refers to a complete set of something. The study of genomes is known as genomics.

Understanding the genome can provide valuable insights into the genetic basis of diseases, evolution, and other biological processes. With advancements in sequencing technologies, it has become possible to determine the entire genomic sequence of many organisms, including humans, and use this information for various applications such as personalized medicine, gene therapy, and biotechnology.

I'm sorry for any confusion, but "Internet" is a term that pertains to the global network of interconnected computers and servers that enable the transmission and reception of data via the internet protocol (IP). It is not a medical term and does not have a specific medical definition. If you have any questions related to medicine or health, I'd be happy to try to help answer them for you!

Base composition in genetics refers to the relative proportion of the four nucleotide bases (adenine, thymine, guanine, and cytosine) in a DNA or RNA molecule. In DNA, adenine pairs with thymine, and guanine pairs with cytosine, so the base composition is often expressed in terms of the ratio of adenine + thymine (A-T) to guanine + cytosine (G-C). This ratio can vary between species and even between different regions of the same genome. The base composition can provide important clues about the function, evolution, and structure of genetic material.

Genetic variation refers to the differences in DNA sequences among individuals and populations. These variations can result from mutations, genetic recombination, or gene flow between populations. Genetic variation is essential for evolution by providing the raw material upon which natural selection acts. It can occur within a single gene, between different genes, or at larger scales, such as differences in the number of chromosomes or entire sets of chromosomes. The study of genetic variation is crucial in understanding the genetic basis of diseases and traits, as well as the evolutionary history and relationships among species.

A base sequence in the context of molecular biology refers to the specific order of nucleotides in a DNA or RNA molecule. In DNA, these nucleotides are adenine (A), guanine (G), cytosine (C), and thymine (T). In RNA, uracil (U) takes the place of thymine. The base sequence contains genetic information that is transcribed into RNA and ultimately translated into proteins. It is the exact order of these bases that determines the genetic code and thus the function of the DNA or RNA molecule.

Feces are the solid or semisolid remains of food that could not be digested or absorbed in the small intestine, along with bacteria and other waste products. After being stored in the colon, feces are eliminated from the body through the rectum and anus during defecation. Feces can vary in color, consistency, and odor depending on a person's diet, health status, and other factors.

A User-Computer Interface (also known as Human-Computer Interaction) refers to the point at which a person (user) interacts with a computer system. This can include both hardware and software components, such as keyboards, mice, touchscreens, and graphical user interfaces (GUIs). The design of the user-computer interface is crucial in determining the usability and accessibility of a computer system for the user. A well-designed interface should be intuitive, efficient, and easy to use, minimizing the cognitive load on the user and allowing them to effectively accomplish their tasks.

An amino acid sequence is the specific order of amino acids in a protein or peptide molecule, formed by the linking of the amino group (-NH2) of one amino acid to the carboxyl group (-COOH) of another amino acid through a peptide bond. The sequence is determined by the genetic code and is unique to each type of protein or peptide. It plays a crucial role in determining the three-dimensional structure and function of proteins.

MEGAN MEtaGenome ANalyzer. A stand-alone metagenome analysis tool. MetaGeneMark MetaGeneMark for MetaGenome Gene Finding ... GOLD Genomes OnLine Database (GOLD). IMG/M The Integrated Microbial Genomes system, for metagenome analysis by the DOE-JGI. ... "Fragmentation and coverage variation in viral metagenome assemblies, and their effect in diversity calculations". Frontiers in ... by metagenomic sequencing of viral nucleic acids and is frequently used to describe environmental shotgun metagenomes. Viral ...
The term was derived from "metagenome". Wilmes and Bond proposed the term "metaproteomics" for the large-scale characterization ... complement approaches that assess community composition based on gene copy counts such as 16S rRNA gene amplicon or metagenome ...
Metagenome analyses by Bäckström et al. showed in 2019 that there must be a whole series of previously unknown viruses known as ...
"Pfam alignment: PF03377 metagenome (auto-generated match)". Retrieved 28 May 2019. Bertonati C, Duchateau P, Juillerat A, Silva ... Similar sequences found in metagenomes include EBN19408 and ECR81667. Whilst repeats of MOrTL1 and 2 both conform structurally ...
"Info - Symbiochloris reticulata Africa extracted metagenome v1.0". genome.jgi.doe.gov. Retrieved 2018-07-31. Xu, Yan; Wang, ...
Jaenicke, S; Albaum, SP; Blumenkamp, P; Linke, B; Stoye, J; Goesmann, A (2018). "Flexible metagenome analysis using the MGX ... Metagenome analysis), ASA³P (automated WGS analysis of bacterial cohorts), Bakta (annotation of bacterial genomes and plasmids ...
Ward TL, Hosid S, Ioshikhes I, Altosaar I (May 2013). "Human milk metagenome: a functional capacity analysis". BMC Microbiology ...
"A catalog of the mouse gut metagenome". Nature Biotechnology. 33 (10): 1103-1108. doi:10.1038/nbt.3353. ISSN 1087-0156. PMID ...
Zhu, Zheng (2014). "Self-organizing approach for meta-genomes". Computational Biology and Chemistry. 53: 118-124. doi:10.1016/j ... Zhu, Jianfeng; Zheng, Wei-Mou (2014). "Self-organizing approach for meta-genomes". Computational Biology and Chemistry. 53: 118 ... Rosen, Gail; Garbarine, Elaine; Caseiro, Diamantino; Polikar, Robi; Sokhansanj, Bahrad (2008). "Metagenome Fragment ...
The term microbiome is also sometimes confused with the metagenome. Metagenome is, however, clearly defined as a collection of ... Based on metagenome data, microbial genomes can be reconstructed. While first metagenome-assembled genomes were reconstructed ... Metagenome data provides a playground for new predictions, yet much more data is needed to strengthen the links between ... Viral metagenomes can be suggested as a semantically and scientifically better term. Co-occurrence networks help visualising ...
2006) An Experimental Metagenome Data Management and Analysis System. Bioinformatics 22, e359-67. PMID 16873494 Markowitz VM, ... 2015) Ten years of maintaining and expanding a microbial genome and metagenome analysis system. Trends in Microbiology 23(11): ... 2017) Protein Structure Determination using Metagenome sequence data. Science 355:294-298. PMID 28104891. GSC Board Members ... 2017) Critical Assessment of Metagenome Interpretation - a benchmark of computational metagenomics software. Nature Methods 14( ...
Ghai, Rohit (2012). "Metagenomes of Mediterranean Coastal Lagoons". Scientific Reports. 2: 490. doi:10.1038/srep00490. PMC ...
"Assembling the Marine Metagenome, One Cell at a Time". PLOS ONE. 4 (4): e5299. Bibcode:2009PLoSO...4.5299W. doi:10.1371/journal ...
Karlsson FH, Tremaroli V, Nookaew I, Bergström G, Behre CJ, Fagerberg B, Nielsen J, Bäckhed F (2013). "Gut metagenome in ... He was involved in early studies on using metagenome sequencing for characterization of the gut microbiota and demonstrating ... "Symptomatic atherosclerosis is associated with an altered gut metagenome". Nat Commun. 3: 1245. Bibcode:2012NatCo...3.1245K. ...
"Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-659. Bibcode: ...
logDice is also used as part of the Mash Distance for genome and metagenome distance estimation Finally, Dice is used in image ... "Mash: fast genome and metagenome distance estimation using MinHash." Genome biology 17.1 (2016): 1-14. Bray, J. Roger; Curtis, ...
Ondov B, Treangen T, Melsted P, Mallonee A, Bergman N, Koren S, Phillippy A (2016). "Mash: fast genome and metagenome distance ...
"Scaling metagenome sequence assembly with probabilistic de Bruijn graphs". Proceedings of the National Academy of Sciences. 109 ...
"Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-659. doi:10.1038/ ...
Databases exist for each type of biological data, for example for biosynthetic gene clusters and metagenomes. The National ... Cao L, Shcherbin E, Mohimani H (August 2019). "A Metabolome- and Metagenome-Wide Association Network Reveals Microbial Natural ... fast genome and metagenome distance estimation using MinHash". Genome Biology. 17 (1): 132. doi:10.1186/s13059-016-0997-x. PMC ... an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine ...
A metagenome of Solorina crocea was reported in 2022. In addition to the fungal component of the lichen, the metagenome ... "Metagenomes of Lichens Solorina crocea and Peltigera canina". Microbiology Resource Announcements. 11 (1): e01000-21. doi: ...
March 2010). "Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes". Genome ... "Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-659. Bibcode: ...
Ondov B, Treangen T, Melsted P, Mallonee A, Bergman N, Koren S, Phillippy A (2016). "Mash: fast genome and metagenome distance ...
"Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-659. Bibcode: ...
... in addition to phages and cow rumen metagenomes, as mentioned above. Within the Bacillota, they are present in a few species of ... "Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-659. Bibcode: ...
"Effects of Dietary Fiber on the Feline Gastrointestinal Metagenome". Journal of Proteome Research. 11 (12): 5924-5933. doi: ...
... fast genome and metagenome distance estimation using MinHash". Genome Biology. 17 (1): 132. doi:10.1186/s13059-016-0997-x. ISSN ...
"Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-659. Bibcode: ...
"Relating the metatranscriptome and metagenome of the human gut". Proceedings of the National Academy of Sciences of the United ... "Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes". Briefings in ... "Species-level functional profiling of metagenomes and metatranscriptomes". Nature Methods. 15 (11): 962-968. doi:10.1038/s41592 ...
March 2010). "Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes". Genome ... "Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-659. Bibcode: ...
SRX5089181: A31_Kinneret_Metagenome. 1 ILLUMINA (NextSeq 500) run: 14.5M spots, 4.3G bases, 1.8Gb downloads ...
aquarium metagenome. Taxonomy ID: 3073560 (for references in articles please use NCBI:txid3073560). current name. aquarium ... NCBI BLAST name: metagenomes. Rank: species. Genetic code: Translation table 11 (Bacterial, Archaeal and Plant Plastid). ...
Our targeted metagenomics panels decrease background contamination, interrogate all 16S rRNA variable regions and allow low DNA input
Genes and Proteins Orthologs, modules and networks 00001 KEGG Orthology (KO) ...
start_date_time_utc"="2014-06-24T07:20:00+00 ...
In it Pascal Hingamp et al discuss an Open Source, Open Science system for metagenome annotation (see PLoS Biology - Metagenome ... They do this as part of a course on metagenome annotation. And the software for running this is all Open Source and available. ...
Cow rumen metagenome study on Scicasts. "The problem with second-generation biofuels is the problem of unlocking the soluble ...
Comparing the genomes with globally distributed metagenomes reveals significant fragment recruitment at high sequence identity ... temporal dynamics and biogeography of a large set of new bacterioplankton genomes assembled from metagenomes. We propose that ... Here, we used metagenome time-series data from a sampling station in the central Baltic Sea to generate metagenome-assembled ... Hugerth, L.W., Larsson, J., Alneberg, J. et al. Metagenome-assembled genomes uncover a global brackish microbiome. Genome Biol ...
data metagenome QIIME2 • 221 views ADD COMMENT • link 15 months ago by kocharovskayaj • 0 ...
"A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate" Frontiers in Bioengineering and ... Direct links to each metagenome are provided in Supplementary Table S6. Direct links to the MAGs are provided in Supplementary ... A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate. ... A metagenomic analysis was used to assess microbial community dynamics, construct metagenome-assembled genomes (MAGs), and ...
Draft Metagenome Sequences of the Sphagnum (Peat Moss) Microbiome from Ambient and Warmed Environments across Europe. Published ... We present 49 metagenome assemblies of the microbiome associated with Sphagnum (peat moss) collected from ambient, artificially ... Draft Metagenome Sequences of the Sphagnum (Peat Moss) Microbiome from Ambient and Warmed Environments across Europe ...
10 kb by 10 to 100-fold for low input metagenomes. Conclusions PCR-amplified metagenomes have enabled scientists to explore ... with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to ... Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds ... Methods Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified ...
Webinar공지] METAGENOME ASSEMBLY AND CHARACTERIZATION OF A POOLED HUMAN FECAL REFERENCE 페이지 정보. 작성자 Kyongshin 작성일23-03-10 14:27 ...
We also demonstrate the use of operons as a subset to represent the trends of secondary metabolites in whole-metagenome data ... 16), E. coli c20 draft genome extracted from chicken gut and finally on 145 whole-metagenome data samples from human gut. ... In this work, we identified whole-genome and metagenomic operons via MetaRon (Metagenome and whole-genome opeRon prediction ... Using operonic data from metagenome to study secondary metabolic trends will significantly reduce the data volume to more ...
Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes ... Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes ... 1. The rational of analyzing metagenomes from fecal samples in 5 individuals is not clear. In fact, for the purpose of this ... They also used this approach to analyze metagenomes from 5 fecal human samples. The results validate the new program and TAS ...
Three commands to start analyzing your metagenome data ... Metagenome-atlas is a easy-to-use metagenomic pipeline. It ... mamba install -y -c bioconda -c conda-forge metagenome-atlas atlas init --db-dir databases path/to/fastq/files atlas run all ...
Deep-sea hydrothermal vent samples metagenome sequencing Metagenome ...
Metagenomics is the study of microbial communities in their original habitats and helps identify individual species within microbial habitats.
But if the metagenome is too complicated, I agree with the previous post that both 25 M and 69 M reads are just to scratch the ... But if the metagenome is too complicated, I agree with the previous post that both 25 M and 69 M reads are just to scratch the ... For a metagenome, the complexity can vary depending on your sample. If you had a very complex sample, 25M reads (platform? ... I just started using meta-velvet to assemble high quality metagenome data. I tried running meta-velvet with a k-mer of 45, ...
Search "+Ecological network -Metagenome -Microbiome ...
Discussion of any scientific study related to high content or next generation genomics. Whole genome association, metagenomics, digital gene expression, etc.
MeGAMerge is a flexible method that generates improved metagenome assemblies, with the ability to accommodate upcoming ... Table 2 Metrics of quality of metagenome assembly. HMP project (SRS022071) and Oil spill sample were assembled using multiple ... such as available marine or soil metagenomes. When compared to a pelagic metagenome sample taken during the Horizon oil spill ... For metagenomes, contig N50 (size of contig where all contigs of equal or larger size add up to half the assembly size) and ...
MeGAMerge is a flexible method that generates improved metagenome assemblies, with the ability to accommodate upcoming ... Table 2 Metrics of quality of metagenome assembly. HMP project (SRS022071) and Oil spill sample were assembled using multiple ... such as available marine or soil metagenomes. When compared to a pelagic metagenome sample taken during the Horizon oil spill ... For metagenomes, contig N50 (size of contig where all contigs of equal or larger size add up to half the assembly size) and ...
Genome Portal version:8.18.168 content:e3a5e14d1f portal-web-4.jgi.lbl.gov Release Date:03-Nov-2023 07:50:28.423 PST Current Date:30-Nov-2023 03:11:59.675 PST ...
PRJEB24517: Arctic microbiome along Svalbard Cross Shelf transects
Please confirm that you want to SAVE all your changes for Lobaria pulmonaria Scotland extracted metagenome v1.0. ... Please confirm that you want to DISCARD all your changes for Lobaria pulmonaria Scotland extracted metagenome v1.0. ...
What is a metagenome?. A metagenome is the collection of all genetic material present in an environmental sample and includes ...
... between community structures investigated and determined using different primer pairs as well as between metagenome and 16S ... 16S rRNA gene data derived from a shotgun metagenome of the same reactor sample added an additional perspective on the ... 16S rRNA gene data derived from a shotgun metagenome of the same reactor sample added an additional perspective on the ... In the metagenome derived 16S rRNA gene sequences, the classes Clostridia and Bacteroidia were highly abundant (18 and 16%) but ...
... De Simone G.;Pasquadibisceglie A.;Proietto R.; ... 2020). Contaminations in (meta)genome data: An open issue for the scientific community. IUBMB LIFE, 72(4), 698-705 [10.1002/iub ... 2020). Contaminations in (meta)genome data: An open issue for the scientific community. IUBMB LIFE, 72(4), 698-705 [10.1002/iub ...
However, metagenome-assembled genomes (MAGs) of ISS samples are yet to be generated and subjected to various genomic analyses, ... In total, 46 MAGs were assembled from 21 ISS environmental metagenomes, in which metaSPAdes yielded 20 MAGs and metaWRAP ... this is the first-time fungal genomes were assembled from ISS metagenomes. Phylogenetic analyses of five bacterial species ... Metagenome-assembled bacterial genomes. Out of the 42 ISS metagenomes submitted at NCBI, only PMA-treated metagenomes (n = 21) ...
  • We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥10 kb by 10 to 100-fold for low input metagenomes. (peerj.com)
  • Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes. (peerj.com)
  • In this work, we identified whole-genome and metagenomic operons via MetaRon (Metagenome and whole-genome opeRon prediction pipeline). (biomedcentral.com)
  • 16), E. coli c20 draft genome extracted from chicken gut and finally on 145 whole-metagenome data samples from human gut. (biomedcentral.com)
  • I tried to assembly a metagenome (plant endophyte, the plant genome is not avaiable now) uing ILLUMINA hiseq 2000 2*100 reads too, my data has 69 M paired end reads, 9.9 Billion bases. (seqanswers.com)
  • Due to the number, frequency, types and sizes of genomes present in highly diverse communities, additional sequencing of metagenome samples often captures novel genome fragments from increasingly rare members (or minor variants) of the community. (nature.com)
  • If you have a eukaryotic genome you're interested in, you could sketch it (sourmash sketch) and then use the branchwater tool to search most metagenomes in the SRA to see which ones have high containment with the genome your searched. (sciety.org)
  • Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. (mbl.edu)
  • We estimated the approximate locations of those reads on the CoV genome and their relative distances on the basis of alignment results exported with MEGAN 4-MetaGenome Analyzer ( http://ab.inf.uni-tuebingen.de/software/megan/ ). (cdc.gov)
  • Please confirm that you want to SAVE all your changes for 'Lobaria pulmonaria Scotland extracted metagenome v1.0' . (doe.gov)
  • Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. (peerj.com)
  • Multiple best practices are available to construct accurate and complete genomes from metagenomes, but high-quality MAGs are still relatively rare. (biomedcentral.com)
  • A metagenomic analysis was used to assess microbial community dynamics, construct metagenome-assembled genomes (MAGs), and evaluate the potential for lactose utilization and fermentation product synthesis of community members represented by the assembled MAGs. (glbrc.org)
  • We introduce the operational genomic unit (OGU) method , a metagenome analysis strategy that directly exploits sequence alignment hits to individual reference genomes as the minimum unit for assessing the diversity of microbial communities and their relevance to environmental factors. (bvsalud.org)
  • 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)
  • We also demonstrate the use of operons as a subset to represent the trends of secondary metabolites in whole-metagenome data and the role of secondary metabolites in the occurrence of disease condition. (biomedcentral.com)
  • 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)
  • Advancements in next-generation sequencing of bacterial genomes and metagenomes have expanded our ability to (1) identify species and track distinct strains, (2) comprehensively profile antibiotic resistance genes, and (3) resolve the mobile elements that facilitate intra- and intercellular gene transfer. (cdc.gov)
  • However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. (peerj.com)
  • MeGAMerge is a flexible method that generates improved metagenome assemblies, with the ability to accommodate upcoming sequencing platforms, as well as present and future assembly algorithms. (nature.com)
  • MetaQUAST: evaluation of metagenome assemblies. (cdc.gov)
  • Metagenome Annotation using massively parallel undergrads. (blogspot.com)
  • They do this as part of a course on metagenome annotation. (blogspot.com)
  • Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. (peerj.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)
  • 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)
  • Comparing the genomes with globally distributed metagenomes reveals significant fragment recruitment at high sequence identity from brackish waters in North America, but little from lakes or oceans. (biomedcentral.com)
  • We developed an ensemble approach that exploits k-mer and reference-based strategies to improve eukaryotic sequence identification from metagenomes and identified MetaBAT2 as the best performing binning approach for clustering of eukaryotic sequences. (sciety.org)
  • S23321 and photosynthetic B. oligotrophicum S58 T . Amplicon sequence and metagenome analysis revealed a relatively higher abundance (2.9-3.6%) of Bradyrhizobium in the roots. (elsevierpure.com)
  • yes my data is complex(animal rumen), my data set Illumina 25M HiSeq 2000 2x100, I just started using meta-velvet to assemble high quality metagenome data. (seqanswers.com)
  • If the purpose is just to recover genes from the metagenome, paired-end only Illumina data is useful to uncover genes except for those that suffer from strain variations. (seqanswers.com)
  • 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)
  • Nitrogenase structural gene sequences in the metagenome sequences were retrieved using two nitrogenase databases. (elsevierpure.com)
  • The term virome is also used to refer to viruses investigated by metagenomic sequencing of viral nucleic acids and is frequently used to describe environmental shotgun metagenomes. (wikipedia.org)
  • 16S rRNA gene data derived from a shotgun metagenome of the same reactor sample added an additional perspective on the community structure. (frontiersin.org)
  • We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. (peerj.com)
  • Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10 kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. (peerj.com)
  • How many contigs one can get after metagenome assembly? (seqanswers.com)
  • Many contigs can be assembled in a metagenome. (seqanswers.com)
  • PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes. (pacb.com)
  • The analysis of both the metagenome of the consortium and the reconstructed metagenome-assembled genomes show that the most abundant bacterial genus in the consortium, Acidocella , possess many of the genes required for the degradation of diesel fuel aromatic hydrocarbons, which are often the most toxic component. (springeropen.com)
  • Our software allows to analyze Gb-sized metagenomes with inexpensive hardware, and to recover species or genera-level bins with low error rates in a fully automated fashion. (pacb.com)
  • In total, 46 MAGs were assembled from 21 ISS environmental metagenomes, in which metaSPAdes yielded 20 MAGs and metaWRAP generated 26 MAGs. (biomedcentral.com)
  • Bacterial cells extracted from KM1 and KM2 roots were analyzed by metagenome, proteome, and isolation approaches and their DNA was isolated and sequenced. (elsevierpure.com)
  • 7468 /organism="Norovirus GII.6" /mol_type="genomic RNA" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:499193" /clone="V4B" /environmental_sample /country="Venezuela" /collection_date="2015" /metagenome_source="gut metagenome" /note="metagenomic" gene 5. (cdc.gov)
  • These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. (peerj.com)
  • Metagenome-atlas is a easy-to-use metagenomic pipeline. (github.io)
  • MeGAMerge pipeline for metagenomes. (nature.com)
  • Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy. (bvsalud.org)
  • Finally, we identified 1,232,407 unique operons from 145 paired-end human gut metagenome samples. (biomedcentral.com)
  • Due to the manual effort involved, this approach does not scale to multiple metagenome samples and requires substantial expertise, which researchers who are new to the area do not have. (pacb.com)
  • Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. (mbl.edu)
  • We describe the gene content, temporal dynamics and biogeography of a large set of new bacterioplankton genomes assembled from metagenomes. (biomedcentral.com)
  • PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. (peerj.com)
  • Using operonic data from metagenome to study secondary metabolic trends will significantly reduce the data volume to more precise data. (biomedcentral.com)
  • I just started using meta-velvet to assemble high quality metagenome data. (seqanswers.com)
  • This review provides a detailed overview of the approaches and bioinformatic tools available to study isolates and metagenomes of hospital-associated bacteria, and their multi-layered networks of transmission. (cdc.gov)
  • But if the metagenome is too complicated, I agree with the previous post that both 25 M and 69 M reads are just to scratch the surface. (seqanswers.com)
  • Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. (peerj.com)
  • A metagenome is the collection of all genetic material present in an environmental sample and includes the genomes of a diverse community of microbes. (cincinnatichildrens.org)
  • Metagenome assembly, in contrast, often has an unclear definition of assembly quality. (nature.com)
  • Furthermore, the identification of metabolic pathways associated with the occurrence of type 2 diabetes (T2D) also presents another dimension of analyzing the human gut metagenome. (biomedcentral.com)
  • Here, we present the biochemical characterization of a xylanase encoded by a Bacteroidetes strain isolated from the termite gut metagenome. (hal.science)