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.

Phylogenetic position of Chitinophaga pinensis in the Flexibacter-Bacteroides-Cytophaga phylum. (1/434)

Comparison of the 16S rRNA gene sequence determined for Chitinophaga pinensis showed that this species is most closely related to Flexibacter filiformis in the Flexibacter-Bacteroides-Cytophaga phylum. These two chitinolytic bacteria, which are characterized by transformation into spherical bodies on ageing, belong to a strongly supported lineage that also includes Cytophaga arvensicola, Flavobacterium ferrugineum and Flexibacter sancti. The lineage is distinct from the microcyst-forming species Sporocytophaga myxococcoides.  (+info)

Coenonia anatina gen. nov., sp. nov., a novel bacterium associated with respiratory disease in ducks and geese. (2/434)

Taxon 1502 was originally described as a Riemerella anatipestifer-like bacterium causing exudative septicaemia in ducks and geese. In the present study, an integrated genotypic and phenotypic approach was used to elucidate the phylogenetic affiliation and taxonomic relationships of 12 strains of taxon 1502. Whole-cell protein and fatty acid analyses and an extensive biochemical examination by using conventional tests and several API microtest systems indicated that all isolates formed a homogeneous taxon, which was confirmed by DNA-DNA hybridizations. 16S rDNA sequence analysis of a representative strain (LMG 14382T) indicated that this taxon belongs to the Cytophaga-Flavobacterium-Bacteroides phylum and revealed a moderate but distinct relationship to species of the genus Capnocytophaga (overall 16S rDNA sequence identities were 88.8-90.2%). Taxon 1502 is concluded to represent a single species that should be allocated to a novel genus, and the name Coenonia anatina gen. nov., sp. nov. is proposed. The DNA G + C content of representative strains was 35-36 mol% and the type strain is LMG 14382T.  (+info)

Physicochemical parameters for growth of the sea ice bacteria Glaciecola punicea ACAM 611(T) and Gelidibacter sp. strain IC158. (3/434)

The water activity and pH ranges for growth of Glaciecola punicea (a psychrophile) were extended when this organism was grown at suboptimal rather than optimal temperatures. No such extension was observed for Gelidibacter sp. strain IC158 (a psychrotolerant bacterium) at analogous temperatures. Salinity and pH may be primary physicochemical parameters controlling bacterial community development in sea ice.  (+info)

Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. (4/434)

Bacterial community composition, enzymatic activities, and carbon dynamics were examined during diatom blooms in four 200-liter laboratory seawater mesocosms. The objective was to determine whether the dramatic shifts in growth rates and ectoenzyme activities, which are commonly observed during the course of phytoplankton blooms and their subsequent demise, could result from shifts in bacterial community composition. Nutrient enrichment of metazoan-free seawater resulted in diatom blooms dominated by a Thalassiosira sp., which peaked 9 days after enrichment ( approximately 24 microg of chlorophyll a liter(-1)). At this time bacterial abundance abruptly decreased from 2.8 x 10(6) to 0.75 x 10(6) ml(-1), and an analysis of bacterial community composition, by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments, revealed the disappearance of three dominant phylotypes. Increased viral and flagellate abundances suggested that both lysis and grazing could have played a role in the observed phylotype-specific mortality. Subsequently, new phylotypes appeared and bacterial production, abundance, and enzyme activities shifted from being predominantly associated with the <1.0-microm size fraction towards the >1.0-microm size fraction, indicating a pronounced microbial colonization of particles. Sequencing of DGGE bands suggested that the observed rapid and extensive colonization of particulate matter was mainly by specialized alpha-Proteobacteria- and Cytophagales-related phylotypes. These particle-associated bacteria had high growth rates as well as high cell-specific aminopeptidase, beta-glucosidase, and lipase activities. Rate measurements as well as bacterial population dynamics were almost identical among the mesocosms indicating that the observed bacterial community dynamics were systematic and repeatable responses to the manipulated conditions.  (+info)

Increase in bacterial community diversity in subsurface aquifers receiving livestock wastewater input. (5/434)

Despite intensive studies of microbial-community diversity, the questions of which kinds of microbial populations are associated with changes in community diversity have not yet been fully solved by molecular approaches. In this study, to investigate the impact of livestock wastewater on changes in the bacterial communities in groundwater, bacterial communities in subsurface aquifers were analyzed by characterizing their 16S rDNA sequences. The similarity coefficients of restriction fragment length polymorphism (RFLP) patterns of the cloned 16S ribosomal DNAs showed that the bacterial communities in livestock wastewater samples were more closely related to those in contaminated aquifer samples. In addition, calculations of community diversity clearly showed that bacterial communities in the livestock wastewater and the contaminated aquifer were much more diverse than those in the uncontaminated aquifer. Thus, the increase in bacterial-community diversity in the contaminated aquifer was assumed to be due to the infiltration of livestock wastewater, containing high concentrations of diverse microbial flora, into the aquifer. Phylogenetic analysis of the sequences from a subset of the RFLP patterns showed that the Cytophaga-Flexibacter-Bacteroides and low-G+C gram-positive groups originating from livestock wastewater were responsible for the change in the bacterial community in groundwater. This was evidenced by the occurrence of rumen-related sequences not only in the livestock wastewater samples but also in the contaminated-groundwater samples. Rumen-related sequences, therefore, can be used as indicator sequences for fecal contamination of groundwater, particularly from livestock.  (+info)

Dyadobacter fermentans gen. nov., sp. nov., a novel gram-negative bacterium isolated from surface-sterilized Zea mays stems. (6/434)

A Gram-negative bacterium, designated NS114T, was isolated from duplicate treatments of surface-sterilized Zea mays stems. The plants were grown in synthetic soil under greenhouse conditions and watered with fertilizer containing no nitrogen. Strain NS114T could not be isolated from plants watered with the standard level or 20% (w/v) of the standard level of nitrogen. Cells occurred as pairs in young cultures that attached to form angled arrangements in R2A broth and occasionally formed rounded, horseshoe arrangements in YM broth. Cell variation resulted in flocculent chains of coccoid cells in old cultures. Strain NS114T fermented glucose and sucrose. The G + C content was 48 mol%. Phylogenetic analysis of the 16S rRNA gene showed that the strain was a member of the domain Bacteria and branched from a point equidistant from an aquatic organism, Runella slithyformis and a marine isolate, 'Microscilla furvescens'. Phenotypic and genotypic analyses indicated that strain NS114T could not be assigned to any recognized genus; therefore a new genus and species, Dyadobacter fermentans gen. nov., sp. nov., is proposed, for which NS114T is the type strain.  (+info)

Bacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom. (7/434)

The bacteria associated with oceanic algal blooms are acknowledged to play important roles in carbon, nitrogen, and sulfur cycling, yet little information is available on their identities or phylogenetic affiliations. Three culture-independent methods were used to characterize bacteria from a dimethylsulfoniopropionate (DMSP)-producing algal bloom in the North Atlantic. Group-specific 16S rRNA-targeted oligonucleotides, 16S ribosomal DNA (rDNA) clone libraries, and terminal restriction fragment length polymorphism analysis all indicated that the marine Roseobacter lineage was numerically important in the heterotrophic bacterial community, averaging >20% of the 16S rDNA sampled. Two other groups of heterotrophic bacteria, the SAR86 and SAR11 clades, were also shown by the three 16S rRNA-based methods to be abundant in the bloom community. In surface waters, the Roseobacter, SAR86, and SAR11 lineages together accounted for over 50% of the bacterial rDNA and showed little spatial variability in abundance despite variations in the dominant algal species. Depth profiles indicated that Roseobacter phylotype abundance decreased with depth and was positively correlated with chlorophyll a, DMSP, and total organic sulfur (dimethyl sulfide plus DMSP plus dimethyl sulfoxide) concentrations. Based on these data and previous physiological studies of cultured Roseobacter strains, we hypothesize that this lineage plays a role in cycling organic sulfur compounds produced within the bloom. Three other abundant bacterial phylotypes (representing a cyanobacterium and two members of the alpha Proteobacteria) were primarily associated with chlorophyll-rich surface waters of the bloom (0 to 50 m), while two others (representing Cytophagales and delta Proteobacteria) were primarily found in deeper waters (200 to 500 m).  (+info)

Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. (8/434)

A group of strains with potent extracellular enzymic activity were isolated from the surfaces of the chain-forming sea-ice diatom Melosira and from an unidentified macrophyte collected from the Eastern Antarctic coastal zone. 16S rDNA sequence analysis indicated that the strains belonged to the genus Cellulophaga and showed greatest similarity to the species Cellulophaga baltica (sequence similarity 97%). Phenotypic characteristics, DNA base composition and DNA-DNA hybridization values clearly separate the Antarctic strains from Cellulophaga baltica and other Cellulophaga species. Thus, the strains form a distinct and novel species and have the proposed name Cellulophaga algicola sp. nov. (type strain IC166T = ACAM 630T). In addition, it was recognized that the species Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989, a species phylogenetically remote from the type species of the genus Cytophaga, possessed 16S rDNA sequences and phenotypic and chemotaxonomic traits similar to those of other Cellulophaga species. Thus, it was proposed that the species Cytophaga uliginosa be renamed as Cellulophaga uliginosa comb. nov.  (+info)

*Bacteroidetes

... spp. are part of normal, healthy placental microbiome. By far, the ones in the Bacteroidia class are the most ... The phylum Bacteroidetes is composed of three large classes of Gram-negative, nonsporeforming, anaerobic or aerobic, and rod- ... Species from the Bacteroidetes and Chlorobi phyla branch very closely together in phylogenetic trees, indicating a close ... The class Bacteroidia was formerly called Bacteroidetes; as it was until recently the only class in the phylum, the name was ...

*Flavobacterium akiainvivens

Lineage( full ) cellular organisms; Bacteria; FCB group; Bacteroidetes/Chlorobi group; Bacteroidetes; Flavobacteriia; ...

*Pedo-repair RNA motif

BAL39, within the phylum Bacteroidetes. The motif might be in the 5' untranslated regions of operons containing genes predicted ...

*Fulvivirga

nov., a novel member of the phylum Bacteroidetes isolated from seawater in a mussel farm". International Journal of Systematic ... nov., a member of the phylum Bacteroidetes". International Journal of Systematic and Evolutionary Microbiology. 62 (Pt 9): 2213 ...

*Fulvivirga imtechensis

nov., a member of the phylum Bacteroidetes". International Journal of Systematic and Evolutionary Microbiology. 62 (Pt 9): 2213 ...

*Sphingobacterium thermophilum

nov., of the phylum Bacteroidetes, isolated from compost". International Journal of Systematic and Evolutionary Microbiology. ...

*Licancabur Lake

The proteobacteria and bacteroidetes-cytophaga-flavobacteria dominate the community of Licancabur Lake bacteria, something that ... bacteroidetes and betaproteobacteria. Overall, at such high lakes only a limited amount of bacterial taxa can be found. ...

*Alkaliflexus

... is a genus in the phylum Bacteroidetes (Bacteria). The name Alkaliflexus derives from: New Latin noun alkali (from ...

*Sediminitomix

nov., of the phylum Bacteroidetes, isolated from marine sediment". International Journal of Systematic and Evolutionary ...

*Adhaeribacter

... is a genus in the phylum Bacteroidetes (Bacteria). The name Adhaeribacter derives from: Latin v. adhaereo -ere, ...

*Aestuariicola

... is a genus in the phylum Bacteroidetes (Bacteria). The name Aestuariicola derives from: Latin noun aestuarium, ...

*Tamlana

... is a genus in the phylum Bacteroidetes (Bacteria). Two species have been described so far: T. agarivorans and T. ... As all members of the Bacteroidetes they are Gram negative.' They are non-flaggelate rod shaped, produced non-diffusible ...

*Algoriphagus

... is a genus in the phylum Bacteroidetes (Bacteria). The name Algoriphagus derives from: Latin masculine gender noun ...

*Croceibacter

... is a genus in the phylum Bacteroidetes (Bacteria). The name Croceibacter derives from: Latin adjective croceus, ...

*Acetomicrobium

... is a genus in the phylum Bacteroidetes (Bacteria). The name Acetomicrobium derives from: Latin noun acetum, ...

*Cryomorpha

... is a genus in the phylum Bacteroidetes (Bacteria). The name Cryomorpha derives from: Greek noun kruos, icy cold, ...

*Alistipes

... is a genus in the phylum Bacteroidetes (Bacteria). The name Alistipes derives from: Latin adjective alius, other; ...

*Actibacter

A. sediminis, like other members of the phylum Bacteroidetes, is Gram-negative and its major respiratory quinone is MK-6. ... Actibacter is a genus in the phylum Bacteroidetes (Bacteria). The genus contains a single species, namely A. sediminis. ...

*Crocinitomix

... is a genus in the phylum Bacteroidetes (Bacteria). The name Crocinitomix derives from: Latin adjective crocinus, ...

*Algibacter

... is a genus in the phylum Bacteroidetes (Bacteria). The name Algibacter derives from: Latin feminine gender noun alga ...

*Flavobacteriales

"Bacteroidetes". List of Prokaryotic names with Standing in Nomenclature (LPSN). Archived from the original on 2013-01-27. ... The order Flavobacteriales is of one of the four orders from the phylum Bacteroidetes. Comparative genomic studies have ... Gupta, R. S. (2004). The phylogeny and signature sequences characteristics of Fibrobacteres, Chlorobi, and Bacteroidetes. ... indicating the species from these two orders shared a common ancestor exclusive of other Bacteroidetes. Bergey's Manual of ...

*Echinicola vietnamensis

nov., a member of the phylum Bacteroidetes isolated from seawater". International Journal of Systematic and Evolutionary ...

*Nafulsella turpanensis

nov., a member of the phylum Bacteroidetes isolated from soil". International Journal of Systematic and Evolutionary ...

*Emticicia

nov., a new member of the family 'Flexibacteraceae', phylum Bacteroidetes". International Journal of Systematic and ...

*Methanobrevibacter smithii

The human gut microbiota is dominated by Bacteroidetes and Firmicutes. Archaea are most prominently represented by the ...
Glycobiology is important for the periodontal pathogen Tannerella forsythia, affecting the bacteriums cellular integrity, its life-style, and virulence potential. The bacterium possesses a unique Gram-negative cell envelope with a glycosylated surface (S-) layer as outermost decoration that is proposed to be anchored via a rough lipopolysaccharide. The S-layer glycan has the structure 4‑MeO-b-ManpNAcCONH2-(1→3)-[Pse5Am7Gc-(2→4)-]-b-ManpNAcA-(1→4)-[4-MeO-a-Galp-(1→2)-]-a-Fucp-(1→4)-[-a-Xylp-(1→3)-]-b-GlcpA-(1→3)-[-b-Digp-(1→2)-]-a-Galp and is linked to distinct serine and threonine residues within the D(S/T)(A/I/L/M/T/V) amino acid motif. Also several other Tannerella proteins are modified with the S‑layer oligosaccharide, indicating the presence of a general O‑glycosylation system. Protein O‑glycosylation impacts the life-style of T. forsythia since truncated S-layer glycans present in a defined mutant favor biofilm formation. While the S‑layer has also been shown to be a
Tannerella forsythia, a Gram-negative member of the Bacteroidetes has evolved to harvest and utilize sialic acid.. The most common sialic acid in humans is a mono-N-acetylated version termed Neu5Ac. Many bacteria are known to access sialic acid using sialidase enzymes. However, in humans a high proportion of sialic acid contains a second acetyl group attached via an O- group i.e. chiefly O-acetylated Neu5,9Ac2 or Neu5,4Ac2. This diacetylated sialic acid is not cleaved efficiently by many sialidases and in order to access diacetylated sialic acid, some organisms produce sialate-O-acetylesterases that catalyse removal of the second acetyl group. In this study we performed bioinformatic and biochemical characterization of a putative sialate-O-acetylesterase from T. forsythia (NanS), which contains two putative SGNH-hydrolase domains related to sialate-O-acetylesterases from a range of organisms. Purification of recombinant NanS revealed an esterase that has activity against Neu5,9Ac2 and its ...
Ubiquinone (UQ), also called coenzyme Q, and plastoquinone (PQ) are electron carriers in oxidative phosphorylation and photosynthesis, respectively. The quinoid nucleus of ubiquinone is derived from the shikimate pathway; 4-hydroxybenzoate is directly formed from chorismate in bacteria, while it can be formed from either chorismate or tyrosine in yeast. The following biosynthesis of terpenoid moiety involves reactions of prenylation, decarboxylation, and three hydroxylations alternating with three methylations. The order of these reactions are somewhat different between bacteria and yeast. Phylloquinone (vitamin K1), menaquinone (vitamin K2), and tocopherol (vitamin E) are fat-soluble vitamins. Phylloquinone is a compound present in all photosynthetic plants serving as a cofactor for photosystem I-mediated electron transport. Menaquinone is an obligatory component of the electron-transfer pathway in bacteria ...
Metagenomic studies confirm that obesity is associated with a composition of gut microbiota. There are some controversies, however, about the composition of gut microbial communities in obese individuals in different populations. To examine the association between body mass index and microbiota composition in Ukrainian population, fecal concentrations of Bacteroidetes, Firmicutes, Actinobacteria and Firmicutes/Bacteroidetes (F/B) ratio were analyzed in 61 adult individuals. The relative abundance of Actinobacteria was small (5-7%) and comparable in different BMI categories. The content of Firmicutes was gradually increased while the content of Bacteroidetes was decreased with increasing body mass index (BMI). The F/B ratio also raised with increasing BMI. In an unadjusted logistic regression model, F/B ratio was significantly associated with BMI (OR = 1.23, 95% CI 1,09-1,38). This association continued to be significant after adjusting for confounders such as age, sex, tobacco smoking and physical
Microbial source tracking to distinguish between human, livestock and wildlife fecal pollution using molecular techniques is a rapidly evolving approach in many developed countries, but has not previously been applied on the African continent. DNA extracts from cow, donkey, and human fecal specimens and raw domestic sewage samples collected in Kenya were tested against five existing quantitative PCR assays designed to detect universal (2), human-specific (2), and cow-specific (1) fecal Bacteroidales genetic markers. Water samples from the River Njoro in Kenya were evaluated using the five tested Bacteroidales markers and a multi-species assay for Cryptosporidium in a preliminary exploration of fecal pollution sources and health risks in this watershed. Diagnostic sensitivity on the validation set varied from 18 to 100% for the five assays while diagnostic specificity was 100%. Of the 2 universal assays, Total Bacteroidales [Dick, L.K, Field, K.G., 2004. Rapid estimation of numbers of fecal ...
Sheridan , P O , Martin , J C , Lawley , T D , Browne , H P , Harris , H M B , Bernalier-Donadille , A , Duncan , S H , OToole , P W , Scott , K P & Flint , H J 2016 , Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes Microbial Genomics , vol 2 , no. 2 , 43 , pp. 1-16 . DOI: 10.1099/mgen. ...
TY - JOUR. T1 - Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis. AU - Bahl,Martin Iain. AU - Bergström,Anders. AU - Licht,Tine Rask. PY - 2012. Y1 - 2012. N2 - Freezing stool samples prior to DNA extraction and downstream analysis is widely used in metagenomic studies of the human microbiota but may affect the inferred community composition. In this study, DNA was extracted either directly or following freeze storage of three homogenized human fecal samples using three different extraction methods. No consistent differences were observed in DNA yields between extractions on fresh and frozen samples; however, differences were observed between extraction methods. Quantitative PCRanalysis was subsequently performed on all DNA samples using six different primer pairs targeting 16S rRNA genes of significant bacterial groups, and the community composition was evaluated by comparing specific ratios of the ...
Lineage: cellular organisms; Bacteria; FCB group; Bacteroidetes/Chlorobi group; Bacteroidetes; unclassified Bacteroidetes; unclassified Bacteroidetes (miscellaneous ...
Lineage: cellular organisms; Bacteria; FCB group; Bacteroidetes/Chlorobi group; Bacteroidetes; Bacteroidia; Bacteroidales; Porphyromonadaceae; Porphyromonas; Porphyromonas ...
ID A0A142HPY3_9SPHI Unreviewed; 914 AA. AC A0A142HPY3; DT 08-JUN-2016, integrated into UniProtKB/TrEMBL. DT 08-JUN-2016, sequence version 1. DT 07-JUN-2017, entry version 8. DE SubName: Full=DNA ligase {ECO:0000313,EMBL:AMR30941.1}; GN ORFNames=A0256_05625 {ECO:0000313,EMBL:AMR30941.1}; OS Mucilaginibacter sp. PAMC 26640. OC Bacteria; Bacteroidetes; Sphingobacteriia; Sphingobacteriales; OC Sphingobacteriaceae; Mucilaginibacter. OX NCBI_TaxID=1300914 {ECO:0000313,EMBL:AMR30941.1, ECO:0000313,Proteomes:UP000073092}; RN [1] {ECO:0000313,EMBL:AMR30941.1, ECO:0000313,Proteomes:UP000073092} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=PAMC 26640 {ECO:0000313,EMBL:AMR30941.1, RC ECO:0000313,Proteomes:UP000073092}; RA Park H.; RT "Mucilaginibacter sp. genome sequencing."; RL Submitted (MAR-2016) to the EMBL/GenBank/DDBJ databases. CC ----------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms CC ...
Dernières PublicationsDe novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads. (2018) Eccles D, Chandler J, (...)
Dernières PublicationsPULDB: the expanded database of Polysaccharide Utilization Loci. (2018) Terrapon N, Lombard V, Drula E , Lapebie P, (...)
anecdotal evidence exists that Elixa is increasing populations of Lactobacilli in the gut and decreases Firmicutes/Bacteroidetes ratio that has been directly related to weight loss (elevated in obese subjects). ...
RYU, H., T. TRAN, M. W. WARE, B. Iker, S. GRIFFIN, A. EGOROV, T. Edge, N. Newmann, E. N. VILLEGAS, AND J. W. SANTO-DOMINGO. Application of leftover sample material from waterborne protozoa monitoring for the molecular detection of ,I,Bacteroidales,/I, and fecal source tracking markers. JOURNAL OF MICROBIOLOGICAL METHODS. Elsevier Science Ltd, New York, NY, 86(3):337-343, (2011 ...
Salinibacter ruber ATCC ® BAA-605D-5™ Designation: Genomic DNA from Salinibacter ruber strain DSM 13855 TypeStrain=True Application:
The oral pathogen Tannerella forsythia possesses a unique surface (S-) layer with a complex O-glycan containing a bacterial sialic acid mimic in the form of either pseudaminic acid or legionaminic acid at its terminal position. We hypothesize that different T. forsythia strains employ these stereoisomeric sugar acids for interacting with the immune system and resident host tissues in the periodontium. Here, we show how T. forsythia strains ATCC 43037 and UB4, displaying pseudaminic acid and legionaminic acid, respectively, and selected cell surface mutants of these strains, modulate the immune response in monocytes and human oral keratinocytes (HOK) using a multiplex immunoassay ...
Significantly more reads were assigned to the Bacteroidetes phylum in the experimental sample (36%) as compared to the control sample (8.2%). At the class level, Bacteroidia (1.3% in the control sample vs. 24.4% in the experimental sample) and Sphingobacteria (1.1% in the control sample vs. 7.8% in the experimental sample) contributed to higher percentages of the microbiota in the experimental sample than in the control sample. The significant elevation of Bacteroidetes in the intestinal community of the starved seabass sample is in agreement with some other studies [2, 34, 35] on dietary shifts. For example, in mice [34], fasting was associated with a significant increase in the proportional representation of the Bacteroidetes [from 20.6% (fed) to 42.3% (fasted)]. Bacteroides with a much larger genome size (e.g., Bacteroides fragilis Strain NCTC9343: 5,205,140 bp) are normally mutualistic in the animal gastrointestinal flora. A large part of the proteins made by the Bacteroides genome are able ...
The human gut microbiome is a highly diverse microbial ecosystem of approximately 400 different species, with most of the species belonging to the phylum Bacteroidetes or Firmicutes. Each person has an unique composition of bacteria, and its also clear that subsets of the population have microbiomes that look more a like, as different diets promote the growth of certain species in the gut, and some health disorders are characterized by a specific microbial profile. By now its well established that obesity is associated with an "obese microbiota" that is quite different than the microbiota of a lean person (1,2).. The first studies looking into the microbiota in overweight and obesity found that obese individuals have a decreased Bacteroidetes/Firmicutes ratio, but recent findings show that this isnt always the case. Also, since both "good" and "bad" bugs belong to both of these major groups of bacteria, the ratio between Bacteroidetes and Firmicutes doesnt necessarily tell us much about the ...
Article A comparative study of culture-independent, library-independent genotypic methods of fecal source tracking. Untitled Document Culture-independent fecal source tracking methods have many potential advantages over library-depende...
additional source Nedashkovskaya, O.I., Kim, S.B., Kwon, K.K.,Shin, D.S., Xuseong, L., Kim, S.-J., and Mikhailov, V.V. "Proposal of Algoriphagus vanfongensis sp. nov., transfer of members of the genera Hongiella Yi and Chun 2004 emend. Nedashkovskaya et al. 2004 and Chimaereicella Tiago et al. 2006 to the genus Algoriphagus, and emended description of the genus Algoriphagus Bowman et al. 2003 emend. Nedashkovskaya et al. 2004." Int. J. Syst. Evol. Microbiol. (2007) 57:1988-1994. [details] ...
Tripos muelleri infected by Amoebophrya ceratii-like. Photo: Catharina Alves-de-Souza. Green: cytoplasm of the parasite stained by FISH. Red: nuclei stained by propidium iodide. Blue: Host theca stained by calcofluor. ...
The largest group of bacteria but somewhat less diverse than the proteobacteria. Firmicutes play an important role in beer, wine, and cider spoilage and are present in greater numbers in obese individuals (vs Bacteroidetes). The group is typically divided into the Clostridia, which are anaerobic, the Bacilli, which are obligate or facultative aerobes, and the Mollicutes. It contains approximately 2475 species, 40% of which are aggregated in just 6 genera; Lactobacillus - 100 sp., Mycoplasma - 110 sp., Bacillus - 114 sp, Clostridium 146 sp and Streptomyces 509. The Firmicutes are all gram-positive bacteria unlike the Proteobacteria which are gram-negative. The Firmicutes are further divided according to their GC ratios. This is the ratio of Guanine and Cytosine to Guanine, Cytosine, Adenine and Thymine in the cell, thus a GC ratio = G+C divided by G+C+A+T times 100. Fermicutes are either High GC or Low GC. Each of these categories contains 3 major groups. ...
A novel mineral-weathering bacterium was isolated from weathered rock (potassic trachyte) surfaces collected from Nanjing (Jiangsu, PR China). Cells of strain JN246T were Gram-stain-negative, rod-shaped and non-motile. Strain JN246T was aerobic, catalase- and oxidase-positive, and grew optimally at 28 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain JN246T belonged to the genus Chitinophaga and the closest phylogenetic relatives were Chitinophaga eiseniae YC6729T (98.5 % 16S rRNA gene sequence similarity), Chitinophaga terrae KP01T (96.8 %), and Chitinophaga jiangningensis JN53T (96.3 %). The major respiratory quinone was MK-7 and the major polyamine was homospermidine. The major fatty acids were iso-C15 : 0, C16 : 1ω5c, C16 : 0 and iso-C17 : 0 3-OH. The polar lipid profile of strain JN246T consisted of phosphatidylethanolamine, unknown aminolipids and unknown lipids. The genomic DNA G+C content of strain JN246T was 48.8 mol%. Based on the low level of DNA-DNA relatedness of
Article Population Dynamics, Biokinetics and Gaseous Nitrogen Production from Partial Nitrification Reactors Operated Under Oxygen Limited Conditions. Biological nitrogen removal based on partial nitrification and denitrification via nitrite is a cos...
Tannerella forsythia ATCC ® 43037D-5™ Designation: Genomic DNA from Tannerella forsythia strain FDC 338 TypeStrain=True Application:
Monoclonal antibody against Tannerella forsythia, strain FDC 331 (OMZ 348) expressed by for use in Western Blot against Tannerella forsythia
from male volunteers with hypercholesterolemia (HC) and normocholesterolemia (NC) were determined by 16S rDNA sequencing, HPLC, GC and NMR, respectively. HC subjects were characterized by having lower relative abundance of Anaeroplasma (0.002% vs 0.219%, p-value = 0.026) and Haemophilus (0.041% vs 0.078%, p-value = 0.049), and higher of Odoribacter (0.51% vs 0.16%; p-value = 0.044). Correlation analysis revealed that Anaeroplasma and Haemophilus were associated to an unfavourable lipid profile: they correlated negatively to cholesterol and triglycerides related biomarkers and the ratio total to high density lipoprotein (HDL) cholesterol, and positively to HDL size. Odoribacter displayed an opposite behaviour. Faecal SCFAs profile revealed higher abundance of isobutyric (2.76% vs 0.82%, p-value = 0.049) and isovaleric acid (1.32% vs 0.06%, p-value = 0.016) in HC. Isobutyric acid correlated positively with Odoribacter and lipid parameters indicative of an unfavourable profile. BA profile did not ...
Tenuipalpidae comprises mites that transmit viruses to agriculturally important plants. Several tenuipalpid species present parthenogenesis, and in Brevipalpus yothersi, the endosymbiont Cardinium has been associated with female-only colonies. It is unclear what the bacterial composition of B. yothersi is, and how common Cardinium is in those microbiomes. We performed a comparative analysis of the bacteriomes in three populations of B. yothersi and three additional Tetranychoidea species using sequences from V4-fragment of 16S DNA. The bacteriomes were dominated by Bacteroidetes (especially Cardinium) and Proteobacteria, showing a remarkably low alpha diversity. Cardinium was present in about 22% of all sequences; however, it was not present in R. indica and T. evansi. In B. yothersi, the proportion of Cardinium was higher in adults than eggs, suggesting that proliferation of the bacteria could be the result of selective pressures from the host. This hypothesis was further supported because colonies of
Starting around 2004, the hallmark studies of Gordon et al demonstrated a potential relationship between the gut microbiome and development of an obese phenotype. An increase in relative abundance of Firmicutes and a proportional decrease in Bacteroidetes were associated with the microbiota of obese mice,23 which was confirmed in a human dietary intervention study demonstrating that weight loss of obese individuals (body mass index, BMI,30) was accompanied by an increase in the relative abundance of Bacteroidetes.24 Nevertheless, based on most human studies, the obesity-associated decrease in the ratio of Bacteroidetes to Firmicutes (B:F) remains controversial.24 ,25 This is likely due to heterogeneity among human subjects with respect to genotype and lifestyle. Recent studies have identified diet, especially fat, as a strong modulator of the microbiota, particularly in inbred and age-standardised laboratory animals. The sources of variation in the microbiota are mainly limited to the ...
We have analyzed 5,088 bacterial 16S rRNA gene sequences from the distal intestinal (cecal) microbiota of genetically obese ob/ob mice, lean ob/+ and wild-type siblings, and their ob/+ mothers, all fed the same polysaccharide-rich diet. Although the majority of mouse gut species are unique, the mouse and human microbiota(s) are similar at the division (superkingdom) level, with Firmicutes and Bacteroidetes dominating. Microbial-community composition is inherited from mothers. However, compared with lean mice and regardless of kinship, ob/ob animals have a 50% reduction in the abundance of Bacteroidetes and a proportional increase in Firmicutes. These changes, which are division-wide, indicate that, in this model, obesity affects the diversity of the gut microbiota and suggest that intentional manipulation of community structure may be useful for regulating energy balance in obese individuals. The sequences reported in this paper have been deposited in the GenBank database [accession nos. DQ ...
Objective The early intestinal microbiota exerts important stimuli for immune development, and a reduced microbial exposure as well as caesarean section (CS) has been associated with the development of allergic disease. Here we address how microbiota development in infants is affected by mode of delivery, and relate differences in colonisation patterns to the maturation of a balanced Th1/Th2 immune response.. ...
RODERIC (Repositori dObjectes Digitals per a lEnsenyament la Recerca i la Cultura) es el repositorio institucional de la Universitat de València. Se concibe como una ventanilla única para el acceso y la difusión de la producción digital de la Universitat. RODERIC responde al compromiso de la Universitat con el movimiento de acceso abierto al conocimiento adquirido con su adhesión a la Declaración de Berlín (30 Septiembre de 2008).
Changes in the population of Lactobacillus spp, Firmicutes and Bacteroidetes between the control and the experimental groups in chicks.Results were based on the
In this study, three polysaccharides including water-soluble polysaccharide (WSP), dilute alkali-soluble polysaccharide (DASP) and concentrated alkali-soluble polysaccharide (CASP) were extracted from purple sweet potatoes and then administered to normal and cyclophosphamide (CTX) treated mice by gavage. The results showed that WSP and CASP could restore the spleen index and immune cytokine (IL-2 and IL-6) levels in CTX treated mice, while DASP could enhance the levels of TNF-α, IL-2 and IL-6. As compared to the normal control group, WSP and CASP treatment groups exhibited increased levels of Bacteroidetes, Lachnospiraceae and Oscillospira, but decreased levels of Firmicutes, Alcaligenaceae and Sutterella in normal mice ...
Altschul S. F., W. Gish, W. Miller, E. W. Myers and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:3389-3402. [PubMED]. Anton J., E. Llobet-Brossa, F. Rodríguez-Valera and R. I. Amann. 1999. Fluorescence in situ hybridization analysis of the prokaryotic community inhabiting crystallizer ponds. Environ. Microbiol. 1:517-523. [PubMED]. Anton J., R. Rosselló-Mora, F. Rodríguez-Valera and R. Amann. 2000. Extremely halophilic Bacteria in crystallizer ponds from solar salterns. Appl. Environ. Microbiol. 66:3052-3057. [PubMED]. Anton J., A. Pena, F. Santos, M. Martinez-Garcia, P. Schmitt-Kopplin and R. Rossello-Mora. 2008. Distribution, abundance and diversity of the extremely halophilic bacterium. Salinibacter ruber. Saline Systems. 4:15. [PubMED]. Baati H., S. Guermazi, R. Amdouni, N. Gharsallah, A. Sghir and E. Ammar. 2008. Prokaryotic diversity of a Tunisian multipond solar saltern. Extremophiles. 12:505-518. [PubMED]. Benlloch S., A. López-López, E. O. Casamayor, L. ...
A vast majority of intestinal bacteria belong to one of two phylum of bacteria: Firmicutes and Bacteroidetes. Among these two phylum the bacteria in the intestinal with the largest populations are thought to be (in no particular order) genera Bacteroides (bact.), Clostridium (firm.), Bifidobacterium (bact.), Peptostreptococcus (firm.) and Ruminococcus (firm.) with minor populations of Escherichia (proteo), Lactobacillus (firm), Enterobacter (proteo) and Enterococcus (firm) with various methanogens.3,8,9. The parentheses identify the phylum type for the particular bacteria. It must be emphasized that specifics regarding exact populations are still far and few between relative to the specific genus which make up the Firmicutes and Bacteroidetes phylums for they contain 250 and 20 genera respectively;10 however, it is thought that Ruminococcus makes up a significant percentage of the Firmicutes phylum. On a side note Firmicutes bacteria are typically gram-positive (outside a very small few which ...
TY - JOUR. T1 - An alternative polysaccharide uptake mechanism of marine bacteria. AU - Reintjes,Greta. AU - Arnosti,Carol. AU - Fuchs,Bernhard M.. AU - Amann,Rudolf. PY - 2017/7/1. Y1 - 2017/7/1. N2 - Heterotrophic microbial communities process much of the carbon fixed by phytoplankton in the ocean, thus having a critical role in the global carbon cycle. A major fraction of the phytoplankton-derived substrates are high-molecular-weight (HMW) polysaccharides. For bacterial uptake, these substrates must initially be hydrolysed to smaller sizes by extracellular enzymes. We investigated polysaccharide hydrolysis by microbial communities during a transect of the Atlantic Ocean, and serendipitously discovered - using super-resolution structured illumination microscopy - that up to 26% of total cells showed uptake of fluorescently labelled polysaccharides (FLA-PS). Fluorescence in situ hybridisation identified these organisms as members of the bacterial phyla Bacteroidetes and Planctomycetes and the ...
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Catalyzes the phosphorylation of D-fructose 6-phosphate to fructose 1,6-bisphosphate by ATP, the first committing step of glycolysis.
Managing Inflammation Inflammation is present in all chronic diseases, but most particularly in those directly related to the gut like; ulcerative colitis, small intestine bacterial overgrowth (SIBO), Crohns and Celiac disease, and obesity. As more data accumulates on the Pathomechanism of these diseases, and as we learn more about the hidden world of our gut flora its becoming more obvious how big of a role the microbiota play in the pathogenesis of these diseases. For instance, a recent Dutch study examined the fecal microbiota of 28 individuals that were segregated into two groups, obese and non-obese. They found that the obese group lacked bacterial diversity, and the bacterial strains were of a pro-inflammatory nature compared to the non-obese group.[i] - keep in mind that adiposity is a state of chronic inflammation. An older study was able to show that there is a microbial component to obesity, which manifests in a decreased ratio of Bacteroidetes to Firmicutes, both of which are ...
TLR4 has been hypothesized to play a key role in the development of both chemotherapy-induced gut toxicity and pain (9, 15). Results from the current study support this newly proposed hypothesis, highlighting significant improvements in symptomatic parameters of gut toxicity and histopathologic markers in BALB/c-Tlr4−/−billy mice treated with irinotecan. This study is also the first to show paralleled improvements in in vivo pain markers and central glial reactivity following irinotecan.. The gut microbiota is critical in regulating the severity of gut toxicity, with increased levels of LPS-producing, gram-negative bacteria correlating with diarrhea severity (5, 29). Comparable levels of major phylogenies (fermicutes and bacteroidetes) were seen in WT and BALB/c-Tlr4−/−billy mice at baseline. However, small variations were seen in two relatively low-abundance microbes. These differences seen in the composition of the gut microbiome in WT and BALB/c-Tlr4−/−billy mice are not ...
Project "Biological removal of nitrogen from reject water by means of nitrification via nitrite and autotrophic denitrification". This project is leading to the development of a computerized control system that enables the autonomous operation of ammonium treatment systems by means of partial nitrification, much cheaper than the conventional nitrification to nitrate process. ...
The latest issue of Gut reported decreased gut microbiota diversity, delayed Bacteroidetes colonization and reduced Th1 responses in infants delivered by Cesarean section.. ...
Hansson, H.G. (2001). Echinodermata, in: Costello, M.J. et al. (Ed.) (2001). European register of marine species: a check-list of the marine species in Europe and a bibliography of guides to their identification. Collection Patrimoines Naturels, 50: pp. 336- ...
The gut microbiota plays an important role in health and development of infants and diet may be the most important environmental factor on gut bacterial composition. It is well known that the microbiota of breast-fed and formula-fed infants differ significantly [3]. Very little information about the relationship of diet, microbiota and immune system development and function is available for infants. We have used a pig model to study these effects. Previous reports showed that cecum from the sow-fed group was enriched with Prevotella, Oscillibacter, and Clostridium [21], while the formula group was enriched with Bacteroides, Parabacteroides, and Alistipes [25]. However, our study found that relative to sow-fed piglets, those fed with formula showed increased Streptococcus, Blautia, Citrobacter, Butrycimonas, Parabacteroides, Lactococcus. In addition, in milk-fed piglets, Anaerotruncus, Akkermansia, Enterococcus, Acinetobacter, Christensenella, and Holdemania were increased, while in soy-fed group ...
Dr. Phillip Gedalanga of California State University, Fullerton will present a one-hour seminar titled "Investigating the role of cell viability in genetic markers for microbial source tracking of fecal contamination in a southern California watershed". ...
Affiliation:九州大学,大学病院,研究員, Research Field:Morphological basic dentistry,Dental engineering/Regenerative dentistry,Periodontal dentistry,Social dentistry,Periodontology, Keywords:歯周病原細菌,Porphyromonas gingivalis,歯周炎,総頸動脈内膜中膜複合体,慢性辺縁性歯周炎,高次構造,安定型高次構造リポ多糖,歯周病,バイオフィルム,Tannerella forsythensis, # of Research Projects:5, # of Research Products:15, Ongoing Project:非熱的不可逆エレクトロポレーションによるインプラント周囲炎の低侵襲治療法
Table 3: The change of 7 types of strains numbers, Firmicutes/Bacteroidetes ratio in feces, and IPI value among 4 groups between 0 week and 8 weeks ...
Hahnke RL†, Meier-Kolthoff JP†, García-Lopez M, Mukherjee S, Huntemann M, Ivanova NN, Woyke T, Kyrpides NC, Klenk H-P, Göker M: Genome-based taxonomic classification of Bacteroidetes. Front Microbiol 2016, 7:2003. http://dx.doi.org/10.3389/fmicb.2016.02003. † contributed equally. Blanco-Míguez A, Meier-Kolthoff JP, Gutiérrez-Jácome A, Göker M, Fdez-Riverola F, Sánchez B, Lourenço A: Improving phylogeny reconstruction at the strain level using peptidome datasets. PLOS Comput Biol 2016, 12:e1005271. http://dx.doi.org/10.1371/JOURNAL.PCBI.1005271. Reau AJ La, Meier-Kolthoff JP, Suen G: A sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host-association. Microb Genomics 2016 (published ahead of print). http://dx.doi.org/10.1099/mgen.0.000099. Barka EA, Vatsa P, Sanchez L, Gaveau-vaillant N, Jacquard C, Meier-Kolthoff JP, Klenk H-P, Clément C, Ouhdouch Y, van Wezel GP: Correction for Barka et al., Taxonomy, Physiology, and Natural Products of ...
Early results are promising, but additional testing is required before an FDA-approved therapy would be available or recommended to the public
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For thousands of users around the world, density measurement means DMA™ 4500 M. These density meters are in use day in, day out, wherever reliable and accurate 5-digit density values are required. To achieve this, the patented repeated fade-out method applied by DMA™ 4500 M delivers the most stable density results based on comprehensive knowledge of the oscillation characteristics. This method results in viscosity correction which is twice as effective as anything else available on the market. The automatic bubble detection system gives you back control of your filling. With this unique method you also benefit from built-in intelligence: frequently changing users with differing filling approaches, humidity, air pressure, and instrument condition, all these have no effect on the operation and results.. Entre em contato ...
Buffalo dung is a low-cost substrate with plenty of carbohydrates, an optimal carbon/nitrogen ratio, and a rich microbial flora, and could become a valuable source of biogas. Therefore, in the present study we compared the type and amount of specific eubacteria to the different configurations of pH, temperature and thermal pretreatment after fermentation in batch reactors in order to understand the suitability of buffalo manure for hydrogen production. The phylogenetic structure of the microbial community in fermentation samples was studied using denaturing gradient gel electrophoresis to generate fingerprints of 16S rRNA genes. The sequences analysis revealed abundance of the phyla Bacteroidetes and Firmicutes, and in particular of the order Clostridiales. Very active hydrogen producing bacteria belonging to Clostridium cellulosi species were identified demonstrating the suitability of this substrate to produce hydrogen. Moreover, a large fraction of 16S-rDNA amplicons could not be assigned to ...
2017, Springer Science+Business Media B.V. Seagrasses are a diverse group of angiosperms that evolved to live in shallow coastal waters, an environment regularly subjected to changes in oxygen, carbon dioxide and irradiance. Zostera muelleri is the dominant species in south-eastern Australia, and is critical for healthy coastal ecosystems. Despite its ecological importance, little is known about the pathways of carbon fixation in Z. muelleri and their regulation in response to environmental changes. In this study, the response of Z. muelleri exposed to control and very low oxygen conditions was investigated by using (i) oxygen microsensors combined with a custom-made flow chamber to measure changes in photosynthesis and respiration, and (ii) reverse transcription quantitative real-time PCR to measure changes in expression levels of key genes involved in C4 metabolism. We found that very low levels of oxygen (i) altered the photophysiology of Z. muelleri, a characteristic of C3 mechanism of ...
WHAT: Your microbial diversity score just hit the 95th percentile! Nice job! When you started playing "gotta eat em all" you were only at 80%. An intestinal sensor transmits real-time information about your microbiome to the game, which then uses computer vision to identify foods--in your refrigerator, at the grocery store, or on a restaurant menu--that could help boost your gut health. The goal: maximize diversity. Every new microbe you "capture" in your gut adds to your score, and also helps build the worlds largest crowd-sourced database of microbiome data. This microbiome game craze has taken over cities around the world--kids in Singapore are begging to go hunt for rare microbiome-boosting foods at wet markets, and urban foraging teams in Seattle are mapping public fruit trees in search of polyphenols that help increase Bacteroidetes. Fermentation bars have opened up everywhere from Kyoto to Johannesburg with lines out the door for coveted krauts and misos. Prior to the launch of the ...
ID A4AWT5_MARSH Unreviewed; 358 AA. AC A4AWT5; DT 03-APR-2007, integrated into UniProtKB/TrEMBL. DT 03-APR-2007, sequence version 1. DT 08-MAY-2019, entry version 88. DE RecName: Full=Queuine tRNA-ribosyltransferase {ECO:0000256,HAMAP-Rule:MF_00168, ECO:0000256,RuleBase:RU003777, ECO:0000256,SAAS:SAAS00087750}; DE EC=2.4.2.29 {ECO:0000256,HAMAP-Rule:MF_00168, ECO:0000256,RuleBase:RU003777, ECO:0000256,SAAS:SAAS00087822}; DE AltName: Full=Guanine insertion enzyme {ECO:0000256,HAMAP-Rule:MF_00168}; DE AltName: Full=tRNA-guanine transglycosylase {ECO:0000256,HAMAP-Rule:MF_00168}; GN Name=tgt {ECO:0000256,HAMAP-Rule:MF_00168}; GN OrderedLocusNames=FB2170_00065 {ECO:0000313,EMBL:EAQ99602.1}; OS Maribacter sp. (strain HTCC2170 / KCCM 42371). OC Bacteria; Bacteroidetes; Flavobacteriia; Flavobacteriales; OC Flavobacteriaceae; Maribacter. OX NCBI_TaxID=313603 {ECO:0000313,EMBL:EAQ99602.1, ECO:0000313,Proteomes:UP000001602}; RN [1] {ECO:0000313,EMBL:EAQ99602.1, ECO:0000313,Proteomes:UP000001602} RP ...
Sponges dont deserve their reputation as amorphous, uniform creatures, unable to show any coordinated behaviours. For Sally Leys from the University of Alberta, there is a lot more to sponges: `they are multi-cellular animals, she says, `and all multi-cellular animals must be able to coordinate behaviour. When Leys and her colleague Glen Elliott looked at sponges expelling waste, they found that they coordinated contractions in their bodies to achieve this (p. 3736). `The intriguing thing is that they can do this without a nervous system, says Leys.. The team collected samples of the freshwater sponge Ephydatia muelleri and removed the asexual cysts, called gemmules, from their samples. They then placed the gemmules in growth medium so that they could grow small sponges for their experiments. Juvenile E. muelleri are small and see-through, so it is relatively easy to see what is going on. The small sponges `look like a garden tent, with a chimney coming out of the middle, Leys explains. The ...
Gastrointestinal disturbances are commonly reported in children with autism, complicate clinical management, and may contribute to behavioral impairment. Reports of deficiencies in disaccharidase enzymatic activity and of beneficial responses to probiotic and dietary therapies led us to survey gene expression and the mucoepithelial microbiota in intestinal biopsies from children with autism and gastrointestinal disease and children with gastrointestinal disease alone. Ileal transcripts encoding disaccharidases and hexose transporters were deficient in children with autism, indicating impairment of the primary pathway for carbohydrate digestion and transport in enterocytes. Deficient expression of these enzymes and transporters was associated with expression of the intestinal transcription factor, CDX2. Metagenomic analysis of intestinal bacteria revealed compositional dysbiosis manifest as decreases in Bacteroidetes, increases in the ratio of Firmicutes to Bacteroidetes, and increases in
The female can live longer than 30 days with adequate nutrition and displays good searching ability. A mated female lays a single diploid egg in any nymphal stage of the citrus blackfly, but prefers the second stage, and this egg will produce a female. Under laboratory conditions (24°C) the development from egg to adult requires 30 to 35 days. Virgin females lay haploid eggs in the fully developed larva of the E. perplexa female (their own species) and thereby produce males (adelpho-parasite). The sex ratio in the field is about 1:7 (male:female). Encarsia perplexa is hyperparasitized by E. smithi (Silvestri) which was accidentally introduced to Florida by 1979. In Florida, E. perplexa and Amitus hesperidum (Hymenoptera: Platygastidae) coexist. The latter has a high rate of reproduction, and can produce 60 to 70 progeny per female making this species very effective in suppressing high densities of the citrus blackfly. Encarsia perplexa reproduces very slowly, but effectively limits A. woglumi ...
Objective: The present study investigated whether CAP exerted its anti-obesity effect through changes in the composition of gut microbiota and SCFAs, and whether the TRPV1 contributes to CAPs effects against obesity in HFD-fed mice.. Design: C57BL/6J (TRPV1+/+) and B6.129X1-Trpv1tm1Jul/J (TRPV1-/-) mice were respectively divided into three groups (n = 6),that is SLD, HFD-fed, and CAP (2 mg/kg, po) +HFD fed and were administered respective treatment for 12 weeks.. Results: We observed significantly lower weight gain and food intake, triglyceride, cholesterol, glucose, and insulin levels in HFD+CAP-fed TRPV1knockout (KO) mice compared to the HFD-fed KO mice, though this effect was more obvious in wild-type (WT) mice. CAP increased the numbers of Akkermansia, Prevotella, Bacteroides, Odoribacter, Allobaculum, Coprococcus, and S24-7, and reduced the numbers of Desulfovibrio, Escherichia, Helicobacter, and Sutterella in the HFD+CAP-fed WT and KO mice compared with HFD-fed WT and KO mice. CAP ...
While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200-900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole
Forsythia x intermedia, commonly known as border forsythia, is a deciduous hybrid shrub with upright-arching to spreading, often square-stemmed branches clad with ovate to lanceolate medium to dark green leaves (to 3-5" long and to 1" wide) which have toothed margins in the upper 1/2. Most cultivars mature to 6-10 tall spreading to as much as 12 wide, but some compact cultivars rise to only 30" tall. Shrubs are primarily noted for their brilliant, 4-lobed, often abundant golden flowers (each to 1 1/2" long) which typically bloom in clusters of 2-6 along the branches in late winter to early spring (February-March in Atlanta but March-early April in St. Louis). Flowers bloom before, or in some cases simultaneous to, the emergence of the new foliage. This shrub is sometimes referred to as the harbinger of spring or the ultimate symbol of spring because the flowers brighten the landscape at a time when not much else is in bloom. These shrubs are hybrids between weeping forsythia (F. suspensa) and ...
Sophisticated genomic techniques now allow scientists to estimate the strains, not just the species, in samples of the human guts microbe collection. Differences in the strains of microorganisms present might account for the variable influence the guts microbe community has on human health and disease. Understanding the effects of various strain combinations on such functions as metabolism, immunity and drug reactions might suggest ways to manipulate the gut microbiome to improve health.