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.Metagenome: A collective genome representative of the many organisms, primarily microorganisms, existing in a community.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).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.Intestines: The section of the alimentary canal from the STOMACH to the ANAL CANAL. It includes the LARGE INTESTINE and SMALL INTESTINE.Feces: Excrement from the INTESTINES, containing unabsorbed solids, waste products, secretions, and BACTERIA of the DIGESTIVE SYSTEM.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Prebiotics: Non-digestible food ingredients mostly of a carbohydrate base that improve human health by selectively stimulating the growth and/or activity of existing BACTERIA in the COLON.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.Biota: The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.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.Germ-Free Life: Animals not contaminated by or associated with any foreign organisms.Probiotics: Live microbial DIETARY SUPPLEMENTS which beneficially affect the host animal by improving its intestinal microbial balance. Antibiotics and other related compounds are not included in this definition. In humans, lactobacilli are commonly used as probiotics, either as single species or in mixed culture with other bacteria. Other genera that have been used are bifidobacteria and streptococci. (J. Nutr. 1995;125:1401-12)Dysbiosis: Changes in quantitative and qualitative composition of MICROBIOTA. The changes may lead to altered host microbial interaction or homeostatic imbalance that can contribute to a disease state often with inflammation.Biodiversity: The variety of all native living organisms and their various forms and interrelationships.Bacteroidetes: A phylum of bacteria comprised of three classes: Bacteroides, Flavobacteria, and Sphingobacteria.Lactobacillus: A genus of gram-positive, microaerophilic, rod-shaped bacteria occurring widely in nature. Its species are also part of the many normal flora of the mouth, intestinal tract, and vagina of many mammals, including humans. Pathogenicity from this genus is rare.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.Cecum: The blind sac or outpouching area of the LARGE INTESTINE that is below the entrance of the SMALL INTESTINE. It has a worm-like extension, the vermiform APPENDIX.Bacterial Load: Measurable quantity of bacteria in an object, organism, or organism compartment.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Metagenomics: The genomic analysis of assemblages of organisms.Intestinal Mucosa: Lining of the INTESTINES, consisting of an inner EPITHELIUM, a middle LAMINA PROPRIA, and an outer MUSCULARIS MUCOSAE. In the SMALL INTESTINE, the mucosa is characterized by a series of folds and abundance of absorptive cells (ENTEROCYTES) with MICROVILLI.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.Colon: The segment of LARGE INTESTINE between the CECUM and the RECTUM. It includes the ASCENDING COLON; the TRANSVERSE COLON; the DESCENDING COLON; and the SIGMOID COLON.Colony Count, Microbial: Enumeration by direct count of viable, isolated bacterial, archaeal, or fungal CELLS or SPORES capable of growth on solid CULTURE MEDIA. The method is used routinely by environmental microbiologists for quantifying organisms in AIR; FOOD; and WATER; by clinicians for measuring patients' microbial load; and in antimicrobial drug testing.Verrucomicrobia: A phylum of gram-negative bacteria containing seven class-level groups from a wide variety of environments. Most members are chemoheterotrophs.Bacterial Physiological Phenomena: Physiological processes and properties of BACTERIA.Microbial Interactions: The inter- and intra-relationships between various microorganisms. This can include both positive (like SYMBIOSIS) and negative (like ANTIBIOSIS) interactions. Examples include virus - bacteria and bacteria - bacteria.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.Synbiotics: Nutritional supplements combining PROBIOTICS (bacteria) and PREBIOTICS (sugars).Vagina: The genital canal in the female, extending from the UTERUS to the VULVA. (Stedman, 25th ed)Clostridium: A genus of motile or nonmotile gram-positive bacteria of the family Clostridiaceae. Many species have been identified with some being pathogenic. They occur in water, soil, and in the intestinal tract of humans and lower animals.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.Ruminococcus: A genus of gram-positive bacteria in the family Lachnospiraceae that inhabits the RUMEN; LARGE INTESTINE; and CECUM of MAMMALS.Mouth: The oval-shaped oral cavity located at the apex of the digestive tract and consisting of two parts: the vestibule and the oral cavity proper.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)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.Inflammatory Bowel Diseases: Chronic, non-specific inflammation of the GASTROINTESTINAL TRACT. Etiology may be genetic or environmental. This term includes CROHN DISEASE and ULCERATIVE COLITIS.Vaginosis, Bacterial: Polymicrobial, nonspecific vaginitis associated with positive cultures of Gardnerella vaginalis and other anaerobic organisms and a decrease in lactobacilli. It remains unclear whether the initial pathogenic event is caused by the growth of anaerobes or a primary decrease in lactobacilli.Microbial Consortia: A group of different species of microorganisms that act together as a community.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Colitis: Inflammation of the COLON section of the large intestine (INTESTINE, LARGE), usually with symptoms such as DIARRHEA (often with blood and mucus), ABDOMINAL PAIN, and FEVER.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.Lactobacillales: An order of gram-positive bacteria in the class Bacilli, that have the ability to ferment sugars to lactic acid. They are widespread in nature and commonly used to produce fermented foods.Digestive System: A group of organs stretching from the MOUTH to the ANUS, serving to breakdown foods, assimilate nutrients, and eliminate waste. In humans, the digestive system includes the GASTROINTESTINAL TRACT and the accessory glands (LIVER; BILIARY TRACT; PANCREAS).Fusobacteria: A phylum of anaerobic, gram-negative bacteria with a chemoorganotrophic heterotrophic metabolism. They are resident flora of the OROPHARYNX.Biological Therapy: Treatment of diseases with biological materials or biological response modifiers, such as the use of GENES; CELLS; TISSUES; organs; SERUM; VACCINES; and humoral agents.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.Bacterial Translocation: The passage of viable bacteria from the GASTROINTESTINAL TRACT to extra-intestinal sites, such as the mesenteric lymph node complex, liver, spleen, kidney, and blood. Factors that promote bacterial translocation include overgrowth with gram-negative enteric bacilli, impaired host immune defenses, and injury to the INTESTINAL MUCOSA resulting in increased intestinal permeability. Bacterial translocation from the lung to the circulation is also possible and sometimes accompanies MECHANICAL VENTILATION.Fatty Acids, Volatile: Short-chain fatty acids of up to six carbon atoms in length. They are the major end products of microbial fermentation in the ruminant digestive tract and have also been implicated in the causation of neurological diseases in humans.Diet: Regular course of eating and drinking adopted by a person or animal.Infant Formula: Liquid formulations for the nutrition of infants that can substitute for BREAST MILK.High-Throughput Nucleotide Sequencing: 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.Fermentation: Anaerobic degradation of GLUCOSE or other organic nutrients to gain energy in the form of ATP. End products vary depending on organisms, substrates, and enzymatic pathways. Common fermentation products include ETHANOL and LACTIC ACID.Anti-Bacterial Agents: Substances that reduce the growth or reproduction of BACTERIA.Dental Plaque: A film that attaches to teeth, often causing DENTAL CARIES and GINGIVITIS. It is composed of MUCINS, secreted from salivary glands, and microorganisms.Gram-Positive Bacteria: Bacteria which retain the crystal violet stain when treated by Gram's method.Host-Pathogen Interactions: The interactions between a host and a pathogen, usually resulting in disease.Principal Component Analysis: Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.Immunity, Mucosal: Nonsusceptibility to the pathogenic effects of foreign microorganisms or antigenic substances as a result of antibody secretions of the mucous membranes. Mucosal epithelia in the gastrointestinal, respiratory, and reproductive tracts produce a form of IgA (IMMUNOGLOBULIN A, SECRETORY) that serves to protect these ports of entry into the body.Isoptera: An order of insects, restricted mostly to the tropics, containing at least eight families. A few species occur in temperate regions of North America.Lactobacillus acidophilus: A species of gram-positive, rod-shaped bacteria isolated from the intestinal tract of humans and animals, the human mouth, and vagina. This organism produces the fermented product, acidophilus milk.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.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.Molecular Typing: Using MOLECULAR BIOLOGY techniques, such as DNA SEQUENCE ANALYSIS; PULSED-FIELD GEL ELECTROPHORESIS; and DNA FINGERPRINTING, to identify, classify, and compare organisms and their subtypes.Lactobacillus reuteri: A species of gram-positive, rod-shaped LACTIC ACID bacteria found naturally in the human intestinal flora and BREAST MILK.Eubacterium: A genus of gram-positive, rod-shaped bacteria found in cavities of man and animals, animal and plant products, infections of soft tissue, and soil. Some species may be pathogenic. No endospores are produced. The genus Eubacterium should not be confused with EUBACTERIA, one of the three domains of life.Antibiosis: A natural association between organisms that is detrimental to at least one of them. This often refers to the production of chemicals by one microorganism that is harmful to another.Intestinal Diseases: Pathological processes in any segment of the INTESTINE from DUODENUM to RECTUM.Metabolome: The dynamic collection of metabolites which represent a cell's or organism's net metabolic response to current conditions.Intestine, Large: A segment of the LOWER GASTROINTESTINAL TRACT that includes the CECUM; the COLON; and the RECTUM.Mice, Inbred C57BLEcosystem: 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)Specific Pathogen-Free Organisms: Animals or humans raised in the absence of a particular disease-causing virus or other microorganism. Less frequently plants are cultivated pathogen-free.Gardnerella vaginalis: A species in the genus GARDNERELLA previously classified as Haemophilus vaginalis. This bacterium, also isolated from the female genital tract of healthy women, is implicated in the cause of bacterial vaginosis (VAGINOSIS, BACTERIAL).Irritable Bowel Syndrome: A disorder with chronic or recurrent colonic symptoms without a clearcut etiology. This condition is characterized by chronic or recurrent ABDOMINAL PAIN, bloating, MUCUS in FECES, and an erratic disturbance of DEFECATION.Enterobacteriaceae: A family of gram-negative, facultatively anaerobic, rod-shaped bacteria that do not form endospores. Its organisms are distributed worldwide with some being saprophytes and others being plant and animal parasites. Many species are of considerable economic importance due to their pathogenic effects on agriculture and livestock.Veillonellaceae: A family of gram-negative bacteria, in the phylum FIRMICUTES.Bacteria, AnaerobicEnterocolitis: Inflammation of the MUCOSA of both the SMALL INTESTINE and the LARGE INTESTINE. Etiology includes ISCHEMIA, infections, allergic, and immune responses.Ileum: The distal and narrowest portion of the SMALL INTESTINE, between the JEJUNUM and the ILEOCECAL VALVE of the LARGE INTESTINE.Lactobacillus fermentum: A species of gram-positive, rod-shaped bacteria associated with DENTAL CARIES.Gastrointestinal Contents: The contents included in all or any segment of the GASTROINTESTINAL TRACT.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.Lactobacillus rhamnosus: A species of gram-positive, rod-shaped bacteria used in PROBIOTICS.Health: The state of the organism when it functions optimally without evidence of disease.Oligosaccharides: Carbohydrates consisting of between two (DISACCHARIDES) and ten MONOSACCHARIDES connected by either an alpha- or beta-glycosidic link. They are found throughout nature in both the free and bound form.Helicobacter hepaticus: A species of HELICOBACTER that colonizes the CECUM and COLON of several strains of MICE, and is associated with HEPATITIS and carcinogenesis.Clostridium Infections: Infections with bacteria of the genus CLOSTRIDIUM.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.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.Polymorphism, Restriction Fragment Length: Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.Clostridium difficile: A common inhabitant of the colon flora in human infants and sometimes in adults. It produces a toxin that causes pseudomembranous enterocolitis (ENTEROCOLITIS, PSEUDOMEMBRANOUS) in patients receiving antibiotic therapy.Enteritis: Inflammation of any segment of the SMALL INTESTINE.DNA Fingerprinting: A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.Cedrus: A plant genus in the family PINACEAE, order Pinales, class Pinopsida, division Coniferophyta. It is the source of cedarwood oil. Cedar ordinarily refers to this but also forms part of the name of plants in other genera.Inulin: A starch found in the tubers and roots of many plants. Since it is hydrolyzable to FRUCTOSE, it is classified as a fructosan. It has been used in physiologic investigation for determination of the rate of glomerular function.Periodontitis: Inflammation and loss of connective tissues supporting or surrounding the teeth. This may involve any part of the PERIODONTIUM. Periodontitis is currently classified by disease progression (CHRONIC PERIODONTITIS; AGGRESSIVE PERIODONTITIS) instead of age of onset. (From 1999 International Workshop for a Classification of Periodontal Diseases and Conditions, American Academy of Periodontology)Citrobacter rodentium: A species of gram-negative bacteria in the genus CITROBACTER, family ENTEROBACTERIACEAE. As an important pathogen of laboratory mice, it serves as a model for investigating epithelial hyperproliferation and tumor promotion. It was previously considered a strain of CITROBACTER FREUNDII.Animal Feed: Foodstuff used especially for domestic and laboratory animals, or livestock.Lactobacillus plantarum: A species of rod-shaped, LACTIC ACID bacteria used in PROBIOTICS and SILAGE production.Inflammation: A pathological process characterized by injury or destruction of tissues caused by a variety of cytologic and chemical reactions. It is usually manifested by typical signs of pain, heat, redness, swelling, and loss of function.Bacteria, AerobicObesity: A status with BODY WEIGHT that is grossly above the acceptable or desirable weight, usually due to accumulation of excess FATS in the body. The standards may vary with age, sex, genetic or cultural background. In the BODY MASS INDEX, a BMI greater than 30.0 kg/m2 is considered obese, and a BMI greater than 40.0 kg/m2 is considered morbidly obese (MORBID OBESITY).Real-Time Polymerase Chain Reaction: Methods used for detecting the amplified DNA products from the polymerase chain reaction as they accumulate instead of at the end of the reaction.Immunity, Innate: The capacity of a normal organism to remain unaffected by microorganisms and their toxins. It results from the presence of naturally occurring ANTI-INFECTIVE AGENTS, constitutional factors such as BODY TEMPERATURE and immediate acting immune cells such as NATURAL KILLER CELLS.Megasphaera: A genus of gram-negative bacteria in the family ACIDAMINOCOCCACEAE, found in the RUMEN of SHEEP and CATTLE, and also in humans.Diet, High-Fat: Consumption of excessive DIETARY FATS.Gingiva: Oral tissue surrounding and attached to TEETH.Butyrates: Derivatives of BUTYRIC ACID. Included under this heading are a broad variety of acid forms, salts, esters, and amides that contain the carboxypropane structure.Periapical Abscess: Acute or chronic inflammation of tissues surrounding the apical portion of a tooth, associated with the collection of pus, resulting from infection following pulp infection through a carious lesion or as a result of an injury causing pulp necrosis. (Dorland, 27th ed)Intestine, Small: The portion of the GASTROINTESTINAL TRACT between the PYLORUS of the STOMACH and the ILEOCECAL VALVE of the LARGE INTESTINE. It is divisible into three portions: the DUODENUM, the JEJUNUM, and the ILEUM.Veillonella: A genus of gram-negative, anaerobic cocci parasitic in the mouth and in the intestinal and respiratory tracts of man and other animals.Tetrathionic Acid: A sulfuric acid dimer, formed by disulfide linkage. This compound has been used to prolong coagulation time and as an antidote in cyanide poisoning.Immune System: The body's defense mechanism against foreign organisms or substances and deviant native cells. It includes the humoral immune response and the cell-mediated response and consists of a complex of interrelated cellular, molecular, and genetic components.Bacteroides fragilis: Gram-negative bacteria occurring in the lower intestinal tracts of man and other animals. It is the most common species of anaerobic bacteria isolated from human soft tissue infections.Genetic Variation: Genotypic differences observed among individuals in a population.Immunoglobulin A, Secretory: The principle immunoglobulin in exocrine secretions such as milk, respiratory and intestinal mucin, saliva and tears. The complete molecule (around 400 kD) is composed of two four-chain units of IMMUNOGLOBULIN A, one SECRETORY COMPONENT and one J chain (IMMUNOGLOBULIN J-CHAINS).Crambe Sponge: A genus of SPONGES in the family Crambeidae characterized by desmoid spicules. The type species is Crambe crambe.Acetobacter: A species of gram-negative bacteria of the family ACETOBACTERACEAE found in FLOWERS and FRUIT. Cells are ellipsoidal to rod-shaped and straight or slightly curved.Geological Phenomena: The inanimate matter of Earth, the structures and properties of this matter, and the processes that affect it.Saliva: The clear, viscous fluid secreted by the SALIVARY GLANDS and mucous glands of the mouth. It contains MUCINS, water, organic salts, and ptylin.Homeostasis: The processes whereby the internal environment of an organism tends to remain balanced and stable.Fungi: A kingdom of eukaryotic, heterotrophic organisms that live parasitically as saprobes, including MUSHROOMS; YEASTS; smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi, commonly known as molds, refer to those that grow as multicellular colonies.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.Enterocolitis, Necrotizing: ENTEROCOLITIS with extensive ulceration (ULCER) and NECROSIS. It is observed primarily in LOW BIRTH WEIGHT INFANT.Swine: Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).Gastrointestinal Diseases: Diseases in any segment of the GASTROINTESTINAL TRACT from ESOPHAGUS to RECTUM.Philology: The study of literature in its widest sense, including grammar, etymology, criticism, literary history, language history, linguistic history, systems of writing, and anything else that is relevant to literature or language viewed as literature. Philology as a discipline has both philosophical and scientific overtones.Gingival Pocket: An abnormal extension of a gingival sulcus not accompanied by the apical migration of the epithelial attachment.Microarray Analysis: The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.Lower Gastrointestinal Tract: The segment of GASTROINTESTINAL TRACT that includes the small intestine below the DUODENUM, and the LARGE INTESTINE.Milk, HumanFructans: Polysaccharides composed of D-fructose units.Paneth Cells: Differentiated epithelial cells of the INTESTINAL MUCOSA, found in the basal part of the intestinal crypts of Lieberkuhn. Paneth cells secrete GROWTH FACTORS, digestive enzymes such as LYSOZYME and antimicrobial peptides such as cryptdins (ALPHA-DEFENSINS) into the crypt lumen.Gram-Negative Anaerobic Cocci: A group of anaerobic coccoid bacteria that show up as pink (negative) when treated by the gram-staining method.Cefoperazone: Semisynthetic broad-spectrum cephalosporin with a tetrazolyl moiety that is resistant to beta-lactamase. It has been proposed especially against Pseudomonas infections.Trichuris: A genus of nematode worms comprising the whipworms.Infant, Newborn: An infant during the first month after birth.Streptomycin: An antibiotic produced by the soil actinomycete Streptomyces griseus. It acts by inhibiting the initiation and elongation processes during protein synthesis.Dietary Fiber: The remnants of plant cell walls that are resistant to digestion by the alimentary enzymes of man. It comprises various polysaccharides and lignins.Gammaproteobacteria: A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.Dietary Supplements: Products in capsule, tablet or liquid form that provide dietary ingredients, and that are intended to be taken by mouth to increase the intake of nutrients. Dietary supplements can include macronutrients, such as proteins, carbohydrates, and fats; and/or MICRONUTRIENTS, such as VITAMINS; MINERALS; and PHYTOCHEMICALS.Halitosis: An offensive, foul breath odor resulting from a variety of causes such as poor oral hygiene, dental or oral infections, or the ingestion of certain foods.Volatile Organic Compounds: Organic compounds that have a relatively high VAPOR PRESSURE at room temperature.Cultured Milk Products: Milk modified with controlled FERMENTATION. This should not be confused with KAFFIR LIME or with KAFFIR CORN.Oropharynx: The middle portion of the pharynx that lies posterior to the mouth, inferior to the SOFT PALATE, and superior to the base of the tongue and EPIGLOTTIS. It has a digestive function as food passes from the mouth into the oropharynx before entering ESOPHAGUS.Enterococcus: A genus of gram-positive, coccoid bacteria consisting of organisms causing variable hemolysis that are normal flora of the intestinal tract. Previously thought to be a member of the genus STREPTOCOCCUS, it is now recognized as a separate genus.Amorphophallus: A plant genus of the family ARACEAE. Members contain konjac glucomannan (MANNANS) and SEROTONIN.Colic: A clinical syndrome with intermittent abdominal pain characterized by sudden onset and cessation that is commonly seen in infants. It is usually associated with obstruction of the INTESTINES; of the CYSTIC DUCT; or of the URINARY TRACT.Capnocytophaga: A gram-negative gliding bacterium isolated from the oral cavity. It is a pathogen often causing PERIODONTITIS.Lactobacillaceae: A family of gram-positive bacteria found regularly in the mouth and intestinal tract of man and other animals, in food and dairy products, and in fermenting vegetable juices. A few species are highly pathogenic.Porphyromonas: A genus of gram-negative, anaerobic, nonsporeforming, nonmotile rods or coccobacilli. Organisms in this genus had originally been classified as members of the BACTEROIDES genus but overwhelming biochemical and chemical findings indicated the need to separate them from other Bacteroides species, and hence, this new genus was created.Amish: An ethnic group with shared religious beliefs. Originating in Switzerland in the late 1600s, and first migrating to the mid-Atlantic, they now live throughout Eastern and Mid-Western United States and elsewhere. Communities are usually close-knit and marriage is within the community.Mucin-2: A gel-forming mucin found predominantly in SMALL INTESTINE and variety of mucous membrane-containing organs. It provides a protective, lubricating barrier against particles and infectious agents.Human Experimentation: The use of humans as investigational subjects.Betaproteobacteria: A class in the phylum PROTEOBACTERIA comprised of chemoheterotrophs and chemoautotrophs which derive nutrients from decomposition of organic material.Mucous Membrane: An EPITHELIUM with MUCUS-secreting cells, such as GOBLET CELLS. It forms the lining of many body cavities, such as the DIGESTIVE TRACT, the RESPIRATORY TRACT, and the reproductive tract. Mucosa, rich in blood and lymph vessels, comprises an inner epithelium, a middle layer (lamina propria) of loose CONNECTIVE TISSUE, and an outer layer (muscularis mucosae) of SMOOTH MUSCLE CELLS that separates the mucosa from submucosa.Geology: The science of the earth and other celestial bodies and their history as recorded in the rocks. It includes the study of geologic processes of an area such as rock formations, weathering and erosion, and sedimentation. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Enterocolitis, Pseudomembranous: An acute inflammation of the INTESTINAL MUCOSA that is characterized by the presence of pseudomembranes or plaques in the SMALL INTESTINE (pseudomembranous enteritis) and the LARGE INTESTINE (pseudomembranous colitis). It is commonly associated with antibiotic therapy and CLOSTRIDIUM DIFFICILE colonization.Fusobacterium: A genus of gram-negative, anaerobic, rod-shaped bacteria found in cavities of humans and other animals. No endospores are formed. Some species are pathogenic and occur in various purulent or gangrenous infections.Dextran Sulfate: Long-chain polymer of glucose containing 17-20% sulfur. It has been used as an anticoagulant and also has been shown to inhibit the binding of HIV-1 to CD4-POSITIVE T-LYMPHOCYTES. It is commonly used as both an experimental and clinical laboratory reagent and has been investigated for use as an antiviral agent, in the treatment of hypolipidemia, and for the prevention of free radical damage, among other applications.Carbohydrate Metabolism: Cellular processes in biosynthesis (anabolism) and degradation (catabolism) of CARBOHYDRATES.Breast Feeding: The nursing of an infant at the breast.Peri-Implantitis: An inflammatory process with loss of supporting bone in the tissues surrounding functioning DENTAL IMPLANTS.Immunomodulation: Alteration of the immune system or of an immune response by agents that activate or suppress its function. This can include IMMUNIZATION or administration of immunomodulatory drugs. Immunomodulation can also encompass non-therapeutic alteration of the immune system effected by endogenous or exogenous substances.Colon, Transverse: The segment of LARGE INTESTINE between ASCENDING COLON and DESCENDING COLON. It passes from the RIGHT COLIC FLEXURE across the ABDOMEN, then turns sharply at the left colonic flexure into the descending colon.Gram-Negative Bacteria: Bacteria which lose crystal violet stain but are stained pink when treated by Gram's method.Mice, Knockout: Strains of mice in which certain GENES of their GENOMES have been disrupted, or "knocked-out". To produce knockouts, using RECOMBINANT DNA technology, the normal DNA sequence of the gene being studied is altered to prevent synthesis of a normal gene product. Cloned cells in which this DNA alteration is successful are then injected into mouse EMBRYOS to produce chimeric mice. The chimeric mice are then bred to yield a strain in which all the cells of the mouse contain the disrupted gene. Knockout mice are used as EXPERIMENTAL ANIMAL MODELS for diseases (DISEASE MODELS, ANIMAL) and to clarify the functions of the genes.Bread: Baked food product made of flour or meal that is moistened, kneaded, and sometimes fermented. A major food since prehistoric times, it has been made in various forms using a variety of ingredients and methods.Ribosome Subunits, Small: The small ribonucleoprotein component of RIBOSOMES. It contains the MESSENGER RNA binding site and two TRANSFER RNA binding sites - one for the incoming AMINO ACYL TRNA (A site) and the other (P site) for the peptidyl tRNA carrying the elongating peptide chain.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Crohn Disease: A chronic transmural inflammation that may involve any part of the DIGESTIVE TRACT from MOUTH to ANUS, mostly found in the ILEUM, the CECUM, and the COLON. In Crohn disease, the inflammation, extending through the intestinal wall from the MUCOSA to the serosa, is characteristically asymmetric and segmental. Epithelioid GRANULOMAS may be seen in some patients.Chlortetracycline: A TETRACYCLINE with a 7-chloro substitution.Lactobacillus casei: A rod-shaped bacterium isolated from milk and cheese, dairy products and dairy environments, sour dough, cow dung, silage, and human mouth, human intestinal contents and stools, and the human vagina.Trichuriasis: Infection with nematodes of the genus TRICHURIS, formerly called Trichocephalus.Carnobacteriaceae: A family of gram-positive, lactic acid-producing bacteria in the order Lactobacillales. It includes both high-pressure-loving species (piezophiles) found in the deep ocean, and Antarctic species.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Rifamycins: A group of ANTI-BACTERIAL AGENTS characterized by a chromophoric naphthohydroquinone group spanned by an aliphatic bridge not previously found in other known ANTI-BACTERIAL AGENTS. They have been isolated from fermentation broths of Streptomyces mediterranei.Mucins: High molecular weight mucoproteins that protect the surface of EPITHELIAL CELLS by providing a barrier to particulate matter and microorganisms. Membrane-anchored mucins may have additional roles concerned with protein interactions at the cell surface.Oligochaeta: A class of annelid worms with few setae per segment. It includes the earthworms such as Lumbricus and Eisenia.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Streptococcaceae: A family of gram-positive non-sporing bacteria including many parasitic, pathogenic, and saprophytic forms.Disease Models, Animal: Naturally occurring or experimentally induced animal diseases with pathological processes sufficiently similar to those of human diseases. They are used as study models for human diseases.Ecology: The branch of science concerned with the interrelationship of organisms and their ENVIRONMENT, especially as manifested by natural cycles and rhythms, community development and structure, interactions between different kinds of organisms, geographic distributions, and population alterations. (Webster's, 3d ed)Clostridium butyricum: Type species of the genus CLOSTRIDIUM, a gram-positive bacteria in the family Clostridiaceae. It is used as a source of PROBIOTICS.Respiratory System: The tubular and cavernous organs and structures, by means of which pulmonary ventilation and gas exchange between ambient air and the blood are brought about.Diarrhea: An increased liquidity or decreased consistency of FECES, such as running stool. Fecal consistency is related to the ratio of water-holding capacity of insoluble solids to total water, rather than the amount of water present. Diarrhea is not hyperdefecation or increased fecal weight.Abiotrophia: A genus of gram-positive, facultatively anaerobic bacteria in the family Aerococcaceae.Bacterial Infections: Infections by bacteria, general or unspecified.Immunoglobulin A: Represents 15-20% of the human serum immunoglobulins, mostly as the 4-chain polymer in humans or dimer in other mammals. Secretory IgA (IMMUNOGLOBULIN A, SECRETORY) is the main immunoglobulin in secretions.Starch: Any of a group of polysaccharides of the general formula (C6-H10-O5)n, composed of a long-chain polymer of glucose in the form of amylose and amylopectin. It is the chief storage form of energy reserve (carbohydrates) in plants.Fibrobacter: A genus of gram-negative, anaerobic bacteria in the family Fibrobacteraceae, isolated from the human GASTROINTESTINAL TRACT.Myeloid Differentiation Factor 88: An intracellular signaling adaptor protein that plays a role in TOLL-LIKE RECEPTOR and INTERLEUKIN 1 RECEPTORS signal transduction. It forms a signaling complex with the activated cell surface receptors and members of the IRAK KINASES.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.Pediococcus: A genus of gram-positive, facultatively anaerobic bacteria whose growth is dependent on the presence of a fermentable carbohydrate. No endospores are produced. Its organisms are found in fermenting plant products and are nonpathogenic to plants and animals, including humans.Leukocyte L1 Antigen Complex: A member of the S-100 protein family that is present at high levels in the blood and interstitial fluid in several infectious, inflammatory, and malignant disorders, including rheumatoid arthritis, inflammatory bowel disease, and cystic fibrosis. It is a complex of a light chain (CALGRANULIN A) and a heavy chain (CALGRANULIN B). L1 binds calcium through an EF-hand motif, and has been shown to possess antimicrobial activity.Adaptive Immunity: Protection from an infectious disease agent that is mediated by B- and T- LYMPHOCYTES following exposure to specific antigen, and characterized by IMMUNOLOGIC MEMORY. It can result from either previous infection with that agent or vaccination (IMMUNITY, ACTIVE), or transfer of antibody or lymphocytes from an immune donor (IMMUNIZATION, PASSIVE).