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Bacteroidetes (5):
Recent article
Bacteroidetes
Abstract
We report a metagenomic analysis of a healthy human plaque sample using a combination of second-generation sequencing platforms. A total of 860 million base pairs of non-human sequences were generated. Various analysis tools revealed the presence of 12 well-characterized phyla, members of the TM-7 a...
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PMID: 21040513
PDF is available here.
PDF is available here.
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Abstract
We propose the names Mucilaginibacter gossypii sp. nov. (type strain Gh-67(T) =NCIMB 14470(T) =KCTC 22380(T)) and Mucilaginibacter gossypiicola sp. nov. (type strain Gh-48(T) =NCIMB 14471(T) =KCTC 22379(T))....
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PMID: 19946048
PDF is available here.
PDF is available here.
Abstract
I and/or anteiso-C₁₇ :₁ B), iso-C₁₅:₀ and C₁₆:₁ω5c. The fatty acid content of strain 6424S-61(T) mainly comprised iso-C₁₅ :₁ G and iso-C₁₅:₀. Comparative analysis of phenotypic and phylogenetic traits indicated that strains 6424S-25(T) and 6515J-31(T) represented t...
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PMID: 19946049
PDF is available here.
PDF is available here.
Abstract
A novel Gram-negative, rod-shaped, non-motile bacterium, designated strain LW7(T), was isolated from a water sample collected at a depth of 4.5 m from Lonar Lake in Buldhana district, Maharastra, India. The cell suspension was dark-reddish orange due to the presence of carotenoids. The fatty acids w...
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PMID: 19933591
PDF is available here.
PDF is available here.
Water Research (44)16 2010
Abstract
Quantitative assessment of multiple sources to short-term variations in recreational water quality, as indexed by faecal indicator organism (FIO) concentrations, is becoming increasingly important with adoption of modern water quality standards and catchment-based water quality management requiremen...
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PMID: 20630556
PDF is available here.
PDF is available here.
Proteomics (10)17 2010
Abstract
We have used iTRAQ proteomics to identify and quantify alterations in global protein expression of T. forsythia during growth in a biofilm. This is the first proteomic study concentrating on biofilm growth in this key periodontal pathogen, and this study has identified several changes in protein exp...
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PMID: 20806225
PDF is available here.
PDF is available here.
Annals of Surgery (252)1 2010
Abstract
UC pouch patients have a different, less diverse, gut microbiota than FAP patients. A further reduction in bacterial diversity but no significant dysbiosis occurs in those with pouchitis. The study suggests that a dysbiosis occurs in the ileal pouch of UC RPC patients which predisposes to, but may n...
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PMID: 20562611
PDF is available here.
PDF is available here.
Abstract
We conclude that assays for Bacteroidales 16S rRNA genes are not specific enough to discern fecal contamination of drinking water in the Netherlands....
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PMID: 20511431
PDF is available here.
PDF is available here.
Abstract
Leeches are widespread in the Great Lakes Basin, yet their potential to harbor disease-causing agents has not been investigated. The purpose of this study was to identify the bacterial community of the commonly occurring leech, Myzobdella lugubris, within the Lake Erie Watershed. Leech samples were...
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PMID: 20597437
PDF is available here.
PDF is available here.
Abstract
Porphyromonas gingivalis secretes strong proteases called gingipains that are implicated in periodontal pathogenesis. Protein secretion systems common to other Gram-negative bacteria are lacking in P. gingivalis, but several proteins, including PorT, have been linked to gingipain secretion. Comparat...
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PMID: 19966289
PDF is available here.
PDF is available here.
Abstract
Bacterial abundance and diversity in snow of East Rongbuk, Laohugou and Hailuogou glaciers on the Tibetan Plateau were investigated through epifluorescence microscope and denaturing gradient gel electrophoresis. Cell abundance ranged from 4.0 x 10(3) to 290.2 x 10(3) cells/mL. The phylogenetic trees...
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PMID: 21174974
PDF is available here.
PDF is available here.
Abstract
We provide evidence for the presence of additional proteins which are presumably presented extracellularly and should thus also be important for host cell interaction. Surprisingly, we did not find homologues of any of the well-known protein secretion systems required to translocate effector protein...
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PMID: 21178499
PDF is available here.
PDF is available here.
Biological Chemistry (391)1 2010
Abstract
We characterized a matrix metalloprotease (MMP)-like enzyme of T. forsythia referred to as karilysin. Full-length (without a signal peptide) recombinant karilysin (49.9 kDa) processed itself into the mature 18-kDa enzyme through sequential autoproteolytic cleavage at both N- and C-terminal profragme...
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PMID: 19919176
PDF is available here.
PDF is available here.
Abstract
We reported our discovery of Acanthamoeba contamination in domestic tap water; in that study, we determined that some Acanthamoeba strains harbor endosymbiotic bacteria, via our molecular characterization by mitochondrial DNA restriction fragment length polymorphism (Mt DNA RFLP). Five (29.4%) among...
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PMID: 19967080
PDF is available here.
PDF is available here.
Abstract
Bioaugmentation of bioreactors focuses on the removal of numerous organics, with little attention typically paid to the maintenance of high and stable nitrite accumulation in partial nitrification. In this study, a bioaugmented membrane bioreactor (MBR) inoculated with enriched ammonia-oxidizing bac...
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PMID: 20075634
PDF is available here.
PDF is available here.
Biochemistry (Washington) (48)46 2009
Abstract
We show that salinixanthin, the light-harvesting carotenoid antenna of xanthorhodopsin, can be reconstituted into the retinal protein from Gloeobacter violaceus expressed in Escherichia coli. Reconstitution of gloeobacter rhodopsin with the carotenoid is accompanied by characteristic absorption chan...
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PMID: 19842712
PDF is available here.
PDF is available here.
PLoS Genetics (5)11 2009
Abstract
We describe the genome sequence and inferred metabolism of Blattabacterium strain Bge, the primary Flavobacteria endosymbiont of the omnivorous German cockroach Blattella germanica. Through comparative genomics with other insect endosymbionts and free-living Flavobacteria we reveal that Blattabacter...
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PMID: 19911043
PDF is available here.
PDF is available here.
Abstract
More species were detected in patients with disease (GR or RP) than in those without disease (PH). Subjects with RP were distinguished from GRs or those with PH by a significantly higher frequency of putative periodontal pathogens, such as Parvimonas micra (previously Peptostreptococcus micros or Mi...
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PMID: 19722792
PDF is available here.
PDF is available here.
Abstract
We evaluated the specificity, distribution, and sensitivity of Prevotella strain-based (PF163 and PigBac1) and methanogen-based (P23-2) PCR assays proposed to detect swine fecal pollution in environmental waters. The assays were tested against 222 fecal DNA extracts derived from target and nontarget...
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PMID: 19633126
PDF is available here.
PDF is available here.
Abstract
These results suggest that specific phylotypes of bacteria were associated with the degradation of each hydrocarbon....
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PMID: 19652511
PDF is available here.
PDF is available here.
Abstract
This study investigated the endosymbiotic bacteria living inside the poultry red mite collected from five samples of one commercial farm from the UK and 16 farms from France using genus-specific PCR, PCR-TTGE and DNA sequencing. Endosymbiotic bacteria are intracellular obligate organisms that can ca...
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PMID: 19145467
PDF is available here.
PDF is available here.
Abstract
Hypersaline microbial mat communities have recently been shown to be more diverse than once thought. The variability in community composition of hypersaline mats, both in terms of spatial and temporal dimensions, is still poorly understood. Because this information is essential to understanding the...
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PMID: 19175677
PDF is available here.
PDF is available here.
Extremophiles (13)2 2009
Abstract
The microbial communities of freshwater hot spring mats from Boekleung (Western Thailand) were studied. Temperatures ranged from over 50 up to 57 degrees C. Green-, red-, and yellow colored mat layers were analyzed. In order to detect the major components of the microbial communities constituting th...
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PMID: 19109691
PDF is available here.
PDF is available here.
Mikrobiologiia (78)3 2009
Abstract
Mikrobiologiia (78)3 2009
Abstract
Abstract
The objective of this study was to investigate the culturable psychrotolerant microbial community in groundwater from Seabee Hook, Antarctica. Shallow groundwater can be present in coastal regions at higher latitudes during the Antarctic summer. Perched groundwater atop ice-cemented permafrost occur...
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PMID: 19190697
PDF is available here.
PDF is available here.
Environmental Science (30)1 2009
Abstract
The composition of bacterial community in the Alexandrium tamarense culture was determined by analyzing the 16S rDNA clone libraries. 16S rRNA gene was amplified by using the total DNA extracted from the A. tamarense culture at three growth stages as templates. 34 different restriction fragment leng...
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PMID: 19353893
PDF is available here.
PDF is available here.
Abstract
The diversity and spatial distribution of bacteria in a lab-scale biotrickling filter treating high loads of hydrogen sulfide (H(2)S) were investigated. Diversity and community structure were studied by terminal-restriction fragment length polymorphism (T-RFLP). A 16S rRNA gene clone library was est...
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PMID: 19380998
PDF is available here.
PDF is available here.
Microbial Ecology (57)1 2009
Abstract
Bacteria were identified from a large, seasonally flooded river (Paraná River, Brazil) and two floodplain habitats that were part of the same river system yet very different in nature: clearwater Garças Lagoon and the highly humic waters of Patos Lagoon. Bacterioplankton were collected during mid-...
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PMID: 18587611
PDF is available here.
PDF is available here.
Abstract
A marine bacterium, designated IMCC3223T, was isolated from Antarctic coastal seawater and subjected to a polyphasic taxonomic investigation. Cells of the strain were Gram-negative, short to elongated rods that were orange-coloured but negative for flexirubin-type pigments, obligately aerobic, chemo...
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PMID: 19126725
PDF is available here.
PDF is available here.
Abstract
A novel bacterial strain, designated Dae 13T, was isolated from sediment from a freshwater lake in Daejeon, South Korea, and was characterized taxonomically by using a polyphasic approach. The isolate was Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped. Phylogenetic analysis bas...
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PMID: 19126726
PDF is available here.
PDF is available here.
Abstract
Molecular phylogeny of 31 taxa of Bacteroidales symbionts from 17 protist genera in 10 families was examined based on 16S rRNA gene sequences. Their localization, morphology, and specificity were also examined by fluorescent in situ hybridizations. Although a monophyletic grouping of the ectosymbion...
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PMID: 19586555
PDF is available here.
PDF is available here.
Abstract
We characterized the bacterial diversity of newly produced steelmaking wastes (NPSW) and steelmaking wastes deposited (SWD) in a restricted land area, generated by the siderurgic industry, using the 16S rDNA clone library approach. A total of 212 partial-length sequences were analyzed, revealing 123...
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PMID: 19096454
PDF is available here.
PDF is available here.
Abstract
We outline an alternative cytogenetic mechanism for bacterial endosymbiont-induced parthenogenesis in Hymenoptera. During female gamete formation in Rickettsia-infected Neochrysocharis formosa (Westwood) parasitoids, meiotic cells undergo only a single equational division followed by the expulsion o...
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PMID: 18713719
PDF is available here.
PDF is available here.
Abstract
These results reinforce the idea of the role that lateral gene transfer plays in the configuration of bacterial genomes, thereby providing alternative metabolic pathways, even with the replacement of primary and essential cell functions, as exemplified by NAD biosynthesis....
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PMID: 19005186
PDF is available here.
PDF is available here.
Abstract
Tidal effects on the composition of free-living (FL) and particle-associated (PA) bacterial communities were studied in a tidal flat ecosystem in the southern North Sea. Denaturing gradient gel electrophoresis targeting the 16S rRNA gene and the 16S rRNA of Bacteria, Bacteroidetes, Alphaproteobacter...
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PMID: 18811653
PDF is available here.
PDF is available here.
Abstract
This study used a nested multiplex PCR method to detect three periodontal pathogens in subgingival plaque collected before treatment and at 2 and 6 months posttreatment from 107 patients with severe, generalized periodontitis. The proportions of the patients who harbored these bacteria before period...
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PMID: 18701660
PDF is available here.
PDF is available here.
Abstract
Members of the genera Bacteroides and Parabacteroides are important constituents of both human and animal intestinal microbiota, and are significant facultative pathogens. In this study, the ability of Bacteroides spp. and Parabacteroides distasonis isolated from both diarrhoeal and normal stools (n...
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PMID: 18828854
PDF is available here.
PDF is available here.
Environmental Microbiology (10)10 2008
Abstract
The impairment of water quality by faecal pollution is a global public health concern. Microbial source tracking methods help to identify faecal sources but the few recent quantitative microbial source tracking applications disregarded catchment hydrology and pollution dynamics. This quantitative mi...
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PMID: 18564182
PDF is available here.
PDF is available here.
Journal of Bacteriology (95)5 2008
Abstract
We show that energy transfer occurs from the excited singlet S(2) state of salinixanthin to the S(1) state of the retinal. Comparison of the absorption spectrum with the excitation spectrum for retinal emission yields 45 +/- 5% efficiency for the energy transfer. Such high efficiency would require c...
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PMID: 18515390
PDF is available here.
PDF is available here.
Abstract
Tuz Lake is an inland thalassohaline water body located in central Anatolia that contributes to 60% of the total salt production in Turkey per year. The microbiota inhabiting this lake has been studied by FISH, denaturing gradient gel electrophoresis of PCR-amplified fragments of 16S rRNA genes, and...
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PMID: 18537839
PDF is available here.
PDF is available here.
Abstract
Strain NJ-44(T), isolated from sediment of the eutrophic Guanting Reservoir in Beijing (China), was subjected to a taxonomic study using a polyphasic approach. The strain was aerobic, with salmon-pink-pigmented colonies on R2A agar. Cells were single, Gram-negative rods, motile by gliding. Phylogene...
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PMID: 18768628
PDF is available here.
PDF is available here.
Abstract
An extracellular polysaccharide-producing bacterium, strain SCK(T), was isolated from a soil sample taken from Kameino, Fujisawa, Japan. The isolate was Gram-negative and cells were non-motile, irregular-shaped rods that grew optimally at 25 degrees C and grew between pH 5 and 8. Strain SCK(T) conta...
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PMID: 18768602
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)35 2008
Abstract
We cloned and expressed them in Escherichia coli. One of them (SrSRI) was expressed well as a recombinant protein having all-trans retinal as a chromophore. UV-Vis, low-temperature UV-Vis, pH-titration, and flash photolysis experiments revealed that the photochemical properties of SrSRI are similar...
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PMID: 18566451
PDF is available here.
PDF is available here.
Abstract
Tissue & Cell (40)4 2008
Abstract
Scaphoideus titanus is the insect vector of flavescence dorée (FD), a yellow disease of grapevines. Observations on adult females and nymphs of S. titanus showed that this insect is associated with a complex microbial community. Ultrastructural analysis showed that the fat body, salivary glands and...
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PMID: 18272191
PDF is available here.
PDF is available here.
Abstract
Bacteria were present in all cases, confirming the infectious etiology of post-treatment disease. Seventy-four bacterial taxa belonging to six phyla were found in the nine cases investigated. Of these, 55% were identified as as-yet-uncultivated phylotypes, which also made up a significant proportion...
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PMID: 18582326
PDF is available here.
PDF is available here.
Abstract
We studied the effect of ectomycorrhizal fungi on bacterial communities colonizing roots of Douglas fir (Pseudotsuga menziesii). Mycorrhizal tips were cleaned of soil and separated based on gross morphological characteristics. Sequencing of the internal transcribed spacers of the nuclear rRNA gene c...
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PMID: 18459969
PDF is available here.
PDF is available here.
Abstract
The Judicial Commission rules that the adjectival form is to be conserved in the specific epithet forsythia in Tannerella forsythia.
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PMID: 18676491
PDF is available here.
PDF is available here.
Effects of age and oral disease on systemic inflammatory and immune parameters in nonhuman primates.
Abstract
We hypothesized that the systemic host responses would be affected by the age, gender, and clinical oral presentation of the population, each contributing to inflammatory and immune responses that would reflect chronic oral infections. The results demonstrated that the prevalence and severity of per...
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PMID: 18448617
PDF is available here.
PDF is available here.
Abstract
A Gram-negative strain, PB92(T), which belongs to the family Sphingobacteriaceae, was isolated from soil (Daejeon, Korea). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PB92(T) was associated with the genus Pedobacter and was most closely related to the type strains Pedob...
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PMID: 18599709
PDF is available here.
PDF is available here.
Organic Letters (10)12 2008
Abstract
Ariakemicins A (1) and B (2), unusual linear hybrid polyketide-nonribosomal peptide antibiotics, were discovered from the fermentation extract of the marine gliding bacterium Rapidithrix sp. These metabolites were positional isomers with regard to a double bond and chromatographically inseparable, r...
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PMID: 18498148
PDF is available here.
PDF is available here.
Abstract
A novel aerobic, Gram-negative bacterium, designated strain CM41_14b(T), was isolated from surface waters in the coastal north-western Mediterranean Sea. Cells were non-motile, straight rods, 2.6 microm long and 0.7 microm wide and formed pale-orange colonies on marine agar medium. The G+C content o...
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PMID: 18523166
PDF is available here.
PDF is available here.
Abstract
The composition of 681 aerobic and heterotrophic strains that were isolated on two different media was assessed at four sampling points along a approximately 300 m stretch of a karst water rivulet. Based on partial sequence analysis of 16S rRNA genes, members of 35 genera were identified; however, o...
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PMID: 18645959
PDF is available here.
PDF is available here.
Abstract
Previously reported and redesigned primer and probe assays were evaluated for the quantitative analysis of the fecal indicator bacterial groups, Enterococcus and Bacteroidetes with three real-time PCR instrument and reagent systems. The efficiency and sensitivity of the original assays varied betwee...
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PMID: 18209285
PDF is available here.
PDF is available here.
Abstract
These results were comparable to those obtained by quantitative PCR and to those reported previously from studies using whole-cell fluorescence hybridization and 16S rRNA clone library methods, supporting the conclusion that HOPE can be a sensitive, specific, and rapid method to determine the relati...
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PMID: 18344347
PDF is available here.
PDF is available here.
Abstract
The structure and diversity of bacterial communities associated with the oxygen minimum zone (OMZ) of the eastern tropical South Pacific was studied through phylogenetic analysis. Clone libraries of 16S rRNA gene fragments were constructed using environmental DNA collected from the OMZ (60 m and 200...
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PMID: 18294206
PDF is available here.
PDF is available here.
Abstract
Three novel strains, designated Gsoil 034T, Gsoil 060T and Jip13T, isolated from soil from a ginseng field and compost in South Korea, were characterized using a polyphasic approach to clarify their taxonomic positions. These isolates were found to be Gram-negative, aerobic and heterotrophic, non-sp...
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PMID: 18450700
PDF is available here.
PDF is available here.
Abstract
We evaluated the characteristics of this microbe and its susceptibility to antimicrobial agents. In this study, D. capnocytophagoides was isolated by anaerobic blood cultures from a 78-year-old male with pancreatic cancer, ischemic heart disease, and diabetes mellitus, who also showed symptoms of ch...
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PMID: 18503172
PDF is available here.
PDF is available here.
Abstract
We isolated hundreds of soil bacteria with the capacity to grow on antibiotics as a sole carbon source. Of 18 antibiotics tested, representing eight major classes of natural and synthetic origin, 13 to 17 supported the growth of clonal bacteria from each of 11 diverse soils. Bacteria subsisting on a...
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PMID: 18388292
PDF is available here.
PDF is available here.