Bacteroidetes: A phylum of bacteria comprised of three classes: Bacteroides, Flavobacteria, and Sphingobacteria.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Metagenome: A collective genome representative of the many organisms, primarily microorganisms, existing in a community.Bacteria: 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.Proteobacteria: A phylum of bacteria consisting of the purple bacteria and their relatives which form a branch of the eubacterial tree. This group of predominantly gram-negative bacteria is classified based on homology of equivalent nucleotide sequences of 16S ribosomal RNA or by hybridization of ribosomal RNA or DNA with 16S and 23S ribosomal RNA.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.Biodiversity: The variety of all native living organisms and their various forms and interrelationships.Cytophagaceae: A family of gram-negative, gliding bacteria in the order Cytophagales, class Cytophagia. They are found in SOIL and SEA WATER.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Fusobacteria: A phylum of anaerobic, gram-negative bacteria with a chemoorganotrophic heterotrophic metabolism. They are resident flora of the OROPHARYNX.Gastrointestinal Tract: Generally refers to the digestive structures stretching from the MOUTH to ANUS, but does not include the accessory glandular organs (LIVER; BILIARY TRACT; PANCREAS).Biota: The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.Seawater: The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.Microbiota: 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.Genes, rRNA: Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.Denaturing Gradient Gel Electrophoresis: Electrophoresis in which various denaturant gradients are used to induce nucleic acids to melt at various stages resulting in separation of molecules based on small sequence differences including SNPs. The denaturants used include heat, formamide, and urea.Acidobacteria: A physiologically diverse phylum of acidophilic, gram-negative bacteria found in a wide variety of habitats, but particularly abundant in soils and sediments.Geologic Sediments: 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)Verrucomicrobia: A phylum of gram-negative bacteria containing seven class-level groups from a wide variety of environments. Most members are chemoheterotrophs.Microbial Consortia: A group of different species of microorganisms that act together as a community.Prevotella: A genus of gram-negative, anaerobic, nonsporeforming, nonmotile rods. Organisms of this genus had originally been classified as members of the BACTEROIDES genus but overwhelming biochemical and chemical findings in 1990 indicated the need to separate them from other Bacteroides species, and hence, this new genus was established.Molecular Sequence Data: 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.Bacteroides: A genus of gram-negative, anaerobic, rod-shaped bacteria. Its organisms are normal inhabitants of the oral, respiratory, intestinal, and urogenital cavities of humans, animals, and insects. Some species may be pathogenic.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.Actinobacteria: 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)Methanobrevibacter: A genus of gram-positive, anaerobic, cocci to short rod-shaped ARCHAEA, in the family METHANOBACTERIACEAE, order METHANOBACTERIALES. They are found in the GASTROINTESTINAL TRACT or other anoxic environments.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Metagenomics: The genomic analysis of assemblages of organisms.Flexibacter: A genus of gram-negative, chemoorganotrophic bacteria in the family CYTOPHAGACEAE. In some species there is a cyclic change in cell morphology.Feces: Excrement from the INTESTINES, containing unabsorbed solids, waste products, secretions, and BACTERIA of the DIGESTIVE SYSTEM.Plankton: 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.Mediterranean SeaFlavobacteriaceae: A family of bacteria in the order Sphingobacteriales, class Sphingobacteria. They are gram-negative rods, mostly saprophytic in terrestrial and aquatic habitats.Fresh Water: Water containing no significant amounts of salts, such as water from RIVERS and LAKES.Heterotrophic Processes: The processes by which organisms utilize organic substances as their nutrient sources. Contrasts with AUTOTROPHIC PROCESSES which make use of simple inorganic substances as the nutrient supply source. Heterotrophs can be either chemoheterotrophs (or chemoorganotrophs) which also require organic substances such as glucose for their primary metabolic energy requirements, or photoheterotrophs (or photoorganotrophs) which derive their primary energy requirements from light. Depending on environmental conditions some organisms can switch between different nutritional modes (AUTOTROPHY; heterotrophy; chemotrophy; or PHOTOTROPHY) to utilize different sources to meet their nutrients and energy requirements.Gammaproteobacteria: A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.Water Microbiology: The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.Archaea: 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.Fatty Acids: Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)Cluster Analysis: 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.Sewage: Refuse liquid or waste matter carried off by sewers.Bacteroidaceae: A family of gram-negative bacteria found primarily in the intestinal tracts and mucous membranes of warm-blooded animals. Its organisms are sometimes pathogenic.Bacterial Typing Techniques: Procedures for identifying types and strains of bacteria. The most frequently employed typing systems are BACTERIOPHAGE TYPING and SEROTYPING as well as bacteriocin typing and biotyping.Ecosystem: 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)Alphaproteobacteria: A class in the phylum PROTEOBACTERIA comprised mostly of two major phenotypes: purple non-sulfur bacteria and aerobic bacteriochlorophyll-containing bacteria.Lakes: Inland bodies of still or slowly moving FRESH WATER or salt water, larger than a pond, and supplied by RIVERS and streams.Rhizosphere: The immediate physical zone surrounding plant roots that include the plant roots. It is an area of intense and complex biological activity involving plants, microorganisms, other soil organisms, and the soil.Symbiosis: 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.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Cytophaga: A genus of gram-negative gliding bacteria found in SOIL; HUMUS; and FRESHWATER and marine habitats.Gram-Positive Bacteria: Bacteria which retain the crystal violet stain when treated by Gram's method.Bacterial Physiological Phenomena: Physiological processes and properties of BACTERIA.Bioreactors: Tools or devices for generating products using the synthetic or chemical conversion capacity of a biological system. They can be classical fermentors, cell culture perfusion systems, or enzyme bioreactors. For production of proteins or enzymes, recombinant microorganisms such as bacteria, mammalian cells, or insect or plant cells are usually chosen.North SeaFlavobacterium: A genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in SOIL and WATER. Its organisms are also found in raw meats, MILK and other FOOD, hospital environments, and human clinical specimens. Some species are pathogenic in humans.Groundwater: Liquid water present beneath the surface of the earth.Waste Water: Contaminated water generated as a waste product of human activity.Chlorobi: A phylum of anoxygenic, phototrophic bacteria including the family Chlorobiaceae. They occur in aquatic sediments, sulfur springs, and hot springs and utilize reduced sulfur compounds instead of oxygen.Eutrophication: The enrichment of a terrestrial or aquatic ECOSYSTEM by the addition of nutrients, especially nitrogen and phosphorus, that results in a superabundant growth of plants, ALGAE, or other primary producers. It can be a natural process or result from human activity such as agriculture runoff or sewage pollution. In aquatic ecosystems, an increase in the algae population is termed an algal bloom.Soil: The unconsolidated mineral or organic matter on the surface of the earth that serves as a natural medium for the growth of land plants.Intestines: The section of the alimentary canal from the STOMACH to the ANAL CANAL. It includes the LARGE INTESTINE and SMALL INTESTINE.Vitamin K 2: A group of substances similar to VITAMIN K 1 which contains a ring of 2-methyl-1,4-naphthoquinione and an isoprenoid side chain of varying number of isoprene units. In vitamin K 2, each isoprene unit contains a double bond. They are produced by bacteria including the normal intestinal flora.Bacterial Load: Measurable quantity of bacteria in an object, organism, or organism compartment.Pigments, Biological: Any normal or abnormal coloring matter in PLANTS; ANIMALS or micro-organisms.Salinity: Degree of saltiness, which is largely the OSMOLAR CONCENTRATION of SODIUM CHLORIDE plus any other SALTS present. It is an ecological factor of considerable importance, influencing the types of organisms that live in an ENVIRONMENT.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.DNA, Archaeal: Deoxyribonucleic acid that makes up the genetic material of archaea.Methane: The simplest saturated hydrocarbon. It is a colorless, flammable gas, slightly soluble in water. It is one of the chief constituents of natural gas and is formed in the decomposition of organic matter. (Grant & Hackh's Chemical Dictionary, 5th ed)Betaproteobacteria: A class in the phylum PROTEOBACTERIA comprised of chemoheterotrophs and chemoautotrophs which derive nutrients from decomposition of organic material.Ice Cover: A thick mass of ICE formed over large regions of land; RIVERS; LAKES; ponds; or SEAWATER.Arctic Regions: The Arctic Ocean and the lands in it and adjacent to it. It includes Point Barrow, Alaska, most of the Franklin District in Canada, two thirds of Greenland, Svalbard, Franz Josef Land, Lapland, Novaya Zemlya, and Northern Siberia. (Webster's New Geographical Dictionary, 1988, p66)Porifera: The phylum of sponges which are sessile, suspension-feeding, multicellular animals that utilize flagellated cells called choanocytes to circulate water. Most are hermaphroditic. They are probably an early evolutionary side branch that gave rise to no other group of animals. Except for about 150 freshwater species, sponges are marine animals. They are a source of ALKALOIDS; STEROLS; and other complex molecules useful in medicine and biological research.Locomotion: Movement or the ability to move from one place or another. It can refer to humans, vertebrate or invertebrate animals, and microorganisms.Chloroflexi: Phylum of green nonsulfur bacteria including the family Chloroflexaceae, among others.Gene Transfer, Horizontal: 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).Industrial Waste: Worthless, damaged, defective, superfluous or effluent material from industrial operations.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Hemiptera: A large order of insects characterized by having the mouth parts adapted to piercing or sucking. It is comprised of four suborders: HETEROPTERA, Auchenorrhyncha, Sternorrhyncha, and Coleorrhyncha.Phytoplankton: Free-floating minute organisms that are photosynthetic. The term is non-taxonomic and refers to a lifestyle (energy utilization and motility), rather than a particular type of organism. Most, but not all, are unicellular algae. Important groups include DIATOMS; DINOFLAGELLATES; CYANOBACTERIA; CHLOROPHYTA; HAPTOPHYTA; CRYPTOMONADS; and silicoflagellates.Bacteria, AnaerobicWaste Disposal, Fluid: The discarding or destroying of liquid waste products or their transformation into something useful or innocuous.In Situ Hybridization, Fluorescence: A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.Aerobiosis: Life or metabolic reactions occurring in an environment containing oxygen.Carbohydrate Metabolism: Cellular processes in biosynthesis (anabolism) and degradation (catabolism) of CARBOHYDRATES.Bifidobacterium: A rod-shaped, gram-positive, non-acid-fast, non-spore-forming, non-motile bacterium that is a genus of the family Bifidobacteriaceae, order Bifidobacteriales, class ACTINOBACTERIA. It inhabits the intestines and feces of humans as well as the human vagina.Rumen: 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)Anaerobiosis: The complete absence, or (loosely) the paucity, of gaseous or dissolved elemental oxygen in a given place or environment. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Chryseobacterium: A genus of aerobic, gram-negative bacteria in the family FLAVOBACTERIACEAE. Many of its species were formerly in the genus FLAVOBACTERIUM.Gene Library: 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.