Publications

combined use of 16s ribosomal dna and 16s rrna to study the bacterial community of polychlorinated biphenyl-polluted soil.	the bacterial diversity assessed from clone libraries prepared from rrna (two libraries) and ribosomal dna (rdna) (one library) from polychlorinated biphenyl (pcb)-polluted soil has been analyzed. a good correspondence of the community composition found in the two types of library was observed. nearly 29% of the cloned sequences in the rdna library were identical to sequences in the rrna libraries. more than 60% of the total cloned sequence types analyzed were grouped in phylogenetic groups (a c ...	2001	11282645
improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions acidobacteria, actinobacteria, proteobacteria, and verrucomicrobia.	the culturability of bacteria in the bulk soil of an australian pasture was investigated by using nutrient broth at 1/100 of its normal concentration (dilute nutrient broth [dnb]) as the growth medium. three-tube most-probable-number serial dilution culture resulted in a mean viable count that was only 1.4% of the mean microscopically determined total cell count. plate counts with dnb solidified with agar and with gellan gum resulted in viable counts that were 5.2 and 7.5% of the mean microscopi ...	2002	11976113
molecular basis of bacterial outer membrane permeability revisited.	gram-negative bacteria characteristically are surrounded by an additional membrane layer, the outer membrane. although outer membrane components often play important roles in the interaction of symbiotic or pathogenic bacteria with their host organisms, the major role of this membrane must usually be to serve as a permeability barrier to prevent the entry of noxious compounds and at the same time to allow the influx of nutrient molecules. this review summarizes the development in the field since ...	2003	14665678
plasmid donor affects host range of promiscuous incp-1beta plasmid pb10 in an activated-sludge microbial community.	horizontal transfer of multiresistance plasmids in the environment contributes to the growing problem of drug-resistant pathogens. even though the plasmid host cell is the primary environment in which the plasmid functions, possible effects of the plasmid donor on the range of bacteria to which plasmids spread in microbial communities have not been investigated. in this study we show that the host range of a broad-host-range plasmid within an activated-sludge microbial community was influenced b ...	2005	16151119
cohesion group approach for evolutionary analysis of tyra, a protein family with wide-ranging substrate specificities.	many enzymes and other proteins are difficult subjects for bioinformatic analysis because they exhibit variant catalytic, structural, regulatory, and fusion mode features within a protein family whose sequences are not highly conserved. however, such features reflect dynamic and interesting scenarios of evolutionary importance. the value of experimental data obtained from individual organisms is instantly magnified to the extent that given features of the experimental organism can be projected u ...	2008	18322033
complete genome of phenylobacterium zucineum--a novel facultative intracellular bacterium isolated from human erythroleukemia cell line k562.	phenylobacterium zucineum is a recently identified facultative intracellular species isolated from the human leukemia cell line k562. unlike the known intracellular pathogens, p. zucineum maintains a stable association with its host cell without affecting the growth and morphology of the latter.	2008	18700039
biodegradation of a biocide (cu-n-cyclohexyldiazenium dioxide) component of a wood preservative by a defined soil bacterial community.	the wood protection industry has refined their products from chrome-, copper-, and arsenate-based wood preservatives toward solely copper-based preservatives in combination with organic biocides. one of these is cu-hdo, containing the chelation product of copper and n-cyclohexyldiazenium dioxide (hdo). in this study, the fate of isotope-labeled ((13)c) and nonlabeled ((12)c) cu-hdo incorporated in wood sawdust mixed with soil was investigated. hdo concentration was monitored by high-pressure liq ...	2010	20952650
biodegradation of ochratoxin a for food and feed decontamination.	ochratoxin a (ota) is one of the most important mycotoxins that is found in food and feed products. it has proven toxic properties, being primarily known for its nephrotoxicity and carcinogenicity to certain animal species. ota is produced by several species of aspergillus and penicillium that can be found in a wide variety of agricultural products, which makes the presence of ota in these products common. many countries have statutory limits for ota, and concentrations need to be reduced to as ...	2010	22069627
chemical, physical and biological approaches to prevent ochratoxin induced toxicoses in humans and animals.	ochratoxins are polyketide derived fungal secondary metabolites with nephrotoxic, immunosuppressive, teratogenic, and carcinogenic properties. ochratoxin-producing fungi may contaminate agricultural products in the field (preharvest spoilage), during storage (postharvest spoilage), or during processing. ochratoxin contamination of foods and feeds poses a serious health hazard to animals and humans. several strategies have been investigated for lowering the ochratoxin content in agricultural prod ...	2010	22069658
a systematic approach for discovering novel, clinically relevant bacteria.	sequencing of the 16s rrna gene (16s) is a reference method for bacterial identification. its expanded use has led to increased recognition of novel bacterial species. in most clinical laboratories, novel species are infrequently encountered, and their pathogenic potential is often difficult to assess. we reviewed partial 16s sequences from >26,000 clinical isolates, analyzed during february 2006-june 2010, and identified 673 that have <99% sequence identity with valid reference sequences and ar ...	2012	22377371
effect of antimicrobial growth promoter administration on the intestinal microbiota of beef cattle.	antimicrobial growth promoters (agps) are antimicrobial agents administered to livestock in feed for prolonged periods to enhance feed efficiency. beef cattle are primarily finished in confined feeding operations in canada and the usa, and the administration of agps such as chlortetracycline and sulfamethazine (aureo s-700 g) is the standard. the impacts of agps on the intestinal microbiota of beef cattle are currently uncertain; it is documented that agps administered to beef cattle pass throug ...	2013	23578222
isolation, screening and identification of swine gut microbiota with ochratoxin a biodegradation ability.	the potential for ochratoxin a (ota) degradation by swine intestinal microbiota was assessed in the current study. intestinal content that was collected aseptically from swine was spiked with 100 ppb ota and incubated for 6 and 12 h at 39°c. an ota assay was conducted using the incubated samples, and it was found that 20% of the ota toxin was detoxified, indicating the presence of microbes capable of ota degradation. twenty-eight bacterial species were isolated anaerobically in m 98-5 media and ...	2012	25049486
draft genome sequence of phenylobacterium immobile strain e (dsm 1986), isolated from uncontaminated soil in ecuador.	we report the draft genome sequence of 3.3 mb and the sequence (19.2 kb) of a natural plasmid isolated from phenylobacterium immobile strain e (dsm 1986), able to degrade xenobiotic compounds as the sole carbon source. the sequences reveal a large number of novel rieske nonheme iron aromatic ring-hydroxylating oxygenases (rhos).	2015	25977422
biodegradation of ochratoxin a by bacterial strains isolated from vineyard soils.	ochratoxin a (ota) is a mycotoxin with a main nephrotoxic activity contaminating several foodstuffs. in the present report, five soil samples collected from ota-contaminated vineyards were screened to isolate microorganisms able to biodegrade ota. when cultivated in ota-supplemented medium, ota was converted in otα by 225 bacterial isolates. to reveal clonal relationships between isolates, molecular typing by using an automated rep-pcr system was carried out, thus showing the presence of 27 diff ...	2015	26633497
metabolites of microbial origin with an impact on health: ochratoxin a and biogenic amines.	safety and quality are significant challenges for food; namely, safety represents a big threat all over the world and is one of the most important goal to be achieved in both western society and developing countries. wine safety mainly relies upon some metabolites and many of them are of microbial origin. the main goal of this review is a focus on two kinds of compounds (biogenic amines and mycotoxins, mainly ochratoxin a) for their deleterious effects on health. for each class of compounds, we ...	2016	27092133
biodegradation of mycotoxins: tales from known and unexplored worlds.	exposure to mycotoxins, secondary metabolites produced by fungi, may infer serious risks for animal and human health and lead to economic losses. several approaches to reduce these mycotoxins have been investigated such as chemical removal, physical binding, or microbial degradation. this review focuses on the microbial degradation or transformation of mycotoxins, with specific attention to the actual detoxification mechanisms of the mother compound. furthermore, based on the similarities in che ...	2016	27199907
hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments.	oil spills from pipeline ruptures are a major source of terrestrial petroleum pollution in cold regions. however, our knowledge of the bacterial response to crude oil contamination in cold regions remains to be further expanded, especially in terms of community shifts and potential development of hydrocarbon degraders. in this study we investigated changes of microbial diversity, population size and keystone taxa in permafrost soils at four different sites along the china-russia crude oil pipeli ...	2016	27886221