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Bacterial Groups (bacterial + groups)
Selected AbstractsDetection of activity among uncultured Actinobacteria in a drinking water reservoirFEMS MICROBIOLOGY ECOLOGY, Issue 3 2006Jeppe L. Nielsen Abstract The abundance, identity and activity of uncultured Bacteria and Actinobacteria present in a drinking water reservoir (North Pine Dam, Brisbane, Australia) were determined using a combination of fluorescence in situ hybridization (FISH) alone or with catalysed reporter deposition (CARD-FISH) with microautoradiography. The CARD-FISH technique was modified relative to previous described procedures and performed directly on gelatine cover slips in order to allow simultaneous combination with microautoradiography. Almost twofold higher numbers of microorganisms could be identified as either Bacteria or Actinobacteria using the CARD-FISH technique as compared with the traditional FISH technique. A combination of FISH or CARD-FISH with microautoradiography showed generally higher activity among the Actinobacteria than among all Bacteria. Another important observation was that many cells within the FISH-negative populations of both Actinobacteria and Bacteria were actively assimilating thymidine. Thus, great care should be taken when extrapolating the active fraction of a prokaryotic community to be equivalent to the FISH-detectable population in such environments. Bacterial groups within Actinobacteria produce the odours geosmin and 2-methylisoborneol, which lower the quality of surface water when used for drinking. The results indicate that combined microautoradiography and CARD-FISH may serve as an effective tool when studying identity and activity of microorganisms within freshwater environments. [source] The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genesENVIRONMENTAL MICROBIOLOGY, Issue 5 2010David L. Kirchman Summary Bacterial communities in the surface layer of the oceans consist of a few abundant phylotypes and many rare ones, most with unknown ecological functions and unclear roles in biogeochemical processes. To test hypotheses about relationships between abundant and rare phylotypes, we examined bacterial communities in the western Arctic Ocean using pyrosequence data of the V6 region of the 16S rRNA gene. Samples were collected from various locations in the Chukchi Sea, the Beaufort Sea and Franklin Bay in summer and winter. We found that bacterial communities differed between summer and winter at a few locations, but overall there was no significant difference between the two seasons in spite of large differences in biogeochemical properties. The sequence data suggested that abundant phylotypes remained abundant while rare phylotypes remained rare between the two seasons and among the Arctic regions examined here, arguing against the ,seed bank' hypothesis. Phylotype richness was calculated for various bacterial groups defined by sequence similarity or by phylogeny (phyla and proteobacterial classes). Abundant bacterial groups had higher within-group diversity than rare groups, suggesting that the ecological success of a bacterial lineage depends on diversity rather than on the dominance of a few phylotypes. In these Arctic waters, in spite of dramatic variation in several biogeochemical properties, bacterial community structure was remarkably stable over time and among regions, and any variation was due to the abundant phylotypes rather than rare ones. [source] Universal and species-specific bacterial ,fungiphiles' in the mycospheres of different basidiomycetous fungiENVIRONMENTAL MICROBIOLOGY, Issue 2 2009J. A. Warmink Summary In previous work, several bacterial groups that show a response to fruiting bodies (the mycosphere) of the ectomycorrhizal fungus Laccaria proxima were identified. We here extend this work to a broader range of fungal fruiting bodies sampled at two occasions. PCR-DGGE analyses showed clear effects of the mycosphere of diverse fungi on the total bacterial and Pseudomonas communities in comparison with those in the corresponding bulk soil. The diversities of the Pseudomonas communities increased dramatically in most of the mycospheres tested, which contrasted with a decrease of the diversity of the total bacterial communities in these habitats. The data also indicated the existence of universal (i.e. Pseudomonas poae, P. lini, P. umsongensis, P. corrugata, P. antarctica and Rahnella aquatilis) as well as specific (i.e. P. viridiflava and candidatus Xiphinematobacter americani) fungiphiles, defined as bacteria adapted to the mycospheres of, respectively, three or more or just one fungal species. The selection of such fungiphiles was shown to be strongly related to their capacities to use particular carbonaceous compounds, as evidenced using principal components analyses of BIOLOG-based substrate utilization tests. The differentiating compounds, i.e. l -arabinose, l -leucine, m-inositol, m-arabitol, d -mannitol and d -trehalose, were tentatively linked to compounds known to occur in mycosphere exudates. [source] Microbial community structure of ethanol type fermentation in bio-hydrogen productionENVIRONMENTAL MICROBIOLOGY, Issue 5 2007Nanqi Ren Summary Three continuous stirred-tank reactors (CSTRs) were used for H2 production from molasses wastewater at influent pH of 6.0,6.5 (reactor A), 5.5,6.0 (reactor B), or 4.0,4.5 (reactor C). After operation for 28 days, the microbial community formed ethanol type (C), propionate type (A) and ethanol-butyrate-mixed type (B) fermentation. The H2 production rate was the highest for ethanol type fermentation, 0.40 l (g VSS),1 day,1 or 0.45 l H2 (g COD removed),1. Microbial community dynamics and diversity were analysed using double-gradient denaturing gradient gel electrophoresis (DG-DGGE). Denaturing gradient gel electrophoresis profiles indicated that the community structures changed quickly in the first 14 days. Phylogenetic analysis indicated that the dominant bacterial groups were low G+C Gram-positive bacteria, Bacteroides, ,-Proteobacteria and Actinobacteria; ,-Proteobacteria, ,-Proteobacteria, ,-Proteobacteria and Spirochaetes were also presented as minor groups in the three reactors. H2 -producing bacteria were affiliated with Ethanoligenens, Acetanaerobacterium, Clostridium, Megasphaera, Citrobacter and Bacteroides. An ethanol-based H2 -producing bacterium, Ethanoligenens harbinense CGMCC1152, was isolated from reactor C and visualized using fluorescence in situ hybridization (FISH) to be 19% of the eubacteria in reactor C. In addition, isoenzyme activity staining for alcohol dehydrogenase (ADH) supported that the majority of ethanol-producing bacteria were affiliated with Ethanoligenens in the microbial community. [source] Grazer and virus-induced mortality of bacterioplankton accelerates development of Flectobacillus populations in a freshwater communityENVIRONMENTAL MICROBIOLOGY, Issue 3 2007Karel, imek Summary We present a detailed analysis of the effects of distinct bacterial mortality factors, viral lysis and heterotrophic nanoflagellates (HNF) bacterivory, associated with the development of filamentous Flectobacillus populations. Reservoir bacterioplankton communities were subjected to additions of both HNF and viruses together, or HNF alone, and then incubated in situ in dialyses bags. For distinct bacterial groups, mortality or growth stimulation was analysed by examining bacterial prey ingested in HNF food vacuoles with fluorescence in situ hybridization (FISH) and via FISH with microautoradiography (MAR-FISH). We also developed a semi-quantitative MAR-FISH-based estimation of relative activities of Flectobacillus populations (targeted by the R-FL615 probe). Bacterial groups vulnerable to HNF predation (mainly clusters of Betaproteobacteria), or discriminated against (Actinobacteria), were detected. Bacterial lineages most vulnerable to virus-lysis (mainly the Betaproteobacteria not targeted by the R-BT065 probe, of the Polynucleobacter cluster) were identified by comparing treatments with HNF alone to HNF and viruses together. Filaments affiliated with the Flectobacillus cluster appeared in both treatments, but were about twice as abundant, long and active as in incubations with viruses and HNF as compared with HNF alone. Viruses appeared to selectively suppress several bacterial groups, perhaps enhancing substrate availability thus stimulating growth and activity of filamentous Flectobacillus. [source] Key role of selective viral-induced mortality in determining marine bacterial community compositionENVIRONMENTAL MICROBIOLOGY, Issue 2 2007T. Bouvier Summary Viral infection is thought to play an important role in shaping bacterial community composition and diversity in aquatic ecosystems, but the strength of this interaction and the mechanisms underlying this regulation are still not well understood. The consensus is that viruses may impact the dominant bacterial strains, but there is little information as to how viruses may affect the less abundant taxa, which often comprise the bulk of the total bacterial diversity. The potential effect of viruses on the phylogenetic composition of marine bacterioplankton was assessed by incubating marine bacteria collected along a North Pacific coastal-open ocean transect in seawater that was greatly depleted of ambient viruses. The ambient communities were dominated by typical marine groups, including alphaproteobacteria and the Bacteroidetes. Incubation of these communities in virus-depleted ambient water yielded an unexpected and dramatic increase in the relative abundance of bacterial groups that are generally undetectable in the in situ assemblages, such as betaproteobacteria and Actinobacteria. Our results suggest that host susceptibility is not necessarily only proportional to its density but to other characteristics of the host, that rare marine bacterial groups may be more susceptible to viral-induced mortality, and that these rare groups may actually be the winners of competition for resources. These observations are not inconsistent with the ,phage kills the winner' hypothesis but represent an extreme and yet undocumented case of this paradigm, where the potential winners apparently never actually develop beyond a very low abundance threshold in situ. We further suggest that this mode of regulation may influence not just the distribution of single strains but of entire phylogenetic groups. [source] Maximum growth rates and possible life strategies of different bacterioplankton groups in relation to phosphorus availability in a freshwater reservoirENVIRONMENTAL MICROBIOLOGY, Issue 9 2006Karel, imek Summary We investigated net growth rates of distinct bacterioplankton groups and heterotrophic nanoflagellate (HNF) communities in relation to phosphorus availability by analysing eight in situ manipulation experiments, conducted between 1997 and 2003, in the canyon-shaped ,ímov reservoir (Czech Republic). Water samples were size-fractionated and incubated in dialysis bags at the sampling site or transplanted into an area of the reservoir, which differed in phosphorus limitation (range of soluble reactive phosphorus concentrations , SRP, 0.7,96 µg l,1). Using five different rRNA-targeted oligonucleotide probes, net growth rates of the probe-defined bacterial groups and HNF assemblages were estimated and related to SRP using Monod kinetics, yielding growth rate constants specific for each bacterial group. We found highly significant differences among their maximum growth rates while insignificant differences were detected in the saturation constants. However, the latter constants represent only tentative estimates mainly due to insufficient sensitivity of the method used at low in situ SRP concentrations. Interestingly, in these same experiments HNF assemblages grew significantly faster than any bacterial group studied except for a small, but abundant cluster of Betaproteobacteria (targeted by the R-BT065 probe). Potential ecological implications of different growth capabilities for possible life strategies of different bacterial phylogenetic lineages are discussed. [source] Combined bromodeoxyuridine immunocapture and terminal-restriction fragment length polymorphism analysis highlights differences in the active soil bacterial metagenome due to Glomus mosseae inoculation or plant speciesENVIRONMENTAL MICROBIOLOGY, Issue 12 2005Veronica Artursson Summary High numbers of bacteria are associated with arbuscular mycorrhizal (AM) fungi, but their functions and in situ activities are largely unknown and most have never been characterized. The aim of the present study was to study the impact of Glomus mosseae inoculation and plant type on the active bacterial communities in soil by using a molecular approach, bromodeoxyuridine (BrdU) immunocapture in combination with terminal-restriction fragment length polymorphism (T-RFLP). This approach combined with sequence information from clone libraries, enabled the identification of actively growing populations, within the total bacterial community. Distinct differences in active bacterial community compositions were found according to G. mosseae inoculation, treatment with an antifungal compound (Benomyl) and plant type. The putative identities of the dominant bacterial species that were activated as a result of G. mosseae inoculation were found to be mostly uncultured bacteria and Paenibacillus species. These populations may represent novel bacterial groups that are able to influence the AM relationship and its subsequent effect on plant growth. [source] Contrasting bacterioplankton community composition and seasonal dynamics in two neighbouring hypertrophic freshwater lakesENVIRONMENTAL MICROBIOLOGY, Issue 11 2001K. Van der Gucht We characterized the bacterioplankton community and its seasonal dynamics in two neighbouring hypertrophic lakes by denaturing gradient gel electrophoresis (DGGE) analysis of short (193 bp) 16S ribosomal DNA polymerase chain reaction (PCR) products obtained with primers specific for the domain Bacteria. Lake Blankaart is turbid and has a high phytoplankton biomass and episodic cyanobacterial blooms, whereas biomanipulated Lake Visvijver is characterized by clearwater conditions and the establishment of a dense charophyte vegetation. Both lakes were dominated by bacterial groups commonly found in freshwater habitats (e.g. ACK4 cluster of Actinomycetes; ACK stands for clones isolated from the Adirondack mountain lakes). Yet, cluster analysis and principal components analysis (PCA) revealed that taxon composition of the bacterioplankton community of the two lakes differs substantially and consistently throughout the season. During the study year (1998), the bacterioplankton community of both lakes showed a distinct seasonal pattern. Lake Blankaart showed a clear differentiation between winter, spring, summer and autumn. In Lake Visvijver, summer samples differed greatly from spring, autumn and winter samples. We hypothesize that the contrasting bacterioplankton in the two neighbouring shallow lakes is determined largely by the presence or absence of macrophytes. [source] Response of bacterioplankton community structures to hydrological conditions and anthropogenic pollution in contrasting subtropical environmentsFEMS MICROBIOLOGY ECOLOGY, Issue 3 2009Rui Zhang Abstract Bacterioplankton community structures under contrasting subtropical marine environments (Hong Kong waters) were analyzed using 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) and subsequent sequencing of predominant bands for samples collected bimonthly from 2004 to 2006 at five stations. Generally, bacterial abundance was significantly higher in the summer than in the winter. The general seasonal variations of the bacterial community structure, as indicated by cluster analysis of the DGGE pattern, were best correlated with temperature at most stations, except for the station close to a sewage discharge outfall, which was best explained by pollution-indicating parameters (e.g. biochemical oxygen demand). Anthropogenic pollutions appear to have affected the presence and the intensity of DGGE bands at the stations receiving discharge of primarily treated sewage. The relative abundance of major bacterial species, calculated by the relative intensity of DGGE bands after PCR amplification, also indicated the effects of hydrological or seasonal variations and sewage discharges. For the first time, a systematic molecular fingerprinting analysis of the bacterioplankton community composition was carried out along the environmental and pollution gradient in a subtropical marine environment, and it suggests that hydrological conditions and anthropogenic pollutions altered the total bacterial community as well as the dominant bacterial groups. [source] Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle's feed efficiencyFEMS MICROBIOLOGY LETTERS, Issue 1 2008Le Luo Guan Abstract Linkage of rumen microbial structure to host phenotypical traits may enhance the understanding of host,microbial interactions in livestock species. This study used culture-independent PCR-denaturing gradient gel electrophoresis (PCR-DGGE) to investigate the microbial profiles in the rumen of cattle differing in feed efficiency. The analysis of detectable bacterial PCR-DGGE profiles showed that the profiles generated from efficient steers clustered together and were clearly separated from those obtained from inefficient steers, indicating that specific bacterial groups may only inhabit in efficient steers. In addition, the bacterial profiles were more likely clustered within a certain breed, suggesting that host genetics may play an important role in rumen microbial structure. The correlations between the concentrations of volatile fatty acids and feed efficiency traits were also observed. Significantly higher concentrations of butyrate (P<0.001) and valerate (P=0.006) were detected in the efficient steers. Our results revealed potential associations between the detectable rumen microbiota and its fermentation parameters with the feed efficiency of cattle. [source] Biogeochemical changes induced in uranium mining waste pile samples by uranyl nitrate treatments under anaerobic conditionsGEOBIOLOGY, Issue 3 2009A. GEISSLER Response of the subsurface soil bacterial community of a uranium mining waste pile to treatments with uranyl nitrate over different periods of time was studied under anaerobic conditions. The fate of the added U(VI) without supplementation with electron donors was investigated as well. By using 16S rRNA gene retrieval, we demonstrated that incubation with uranyl nitrate for 4 weeks resulted in a strong reduction in and even disappearance of some of the most predominant bacterial groups of the original sample. Instead, a strong proliferation of denitrifying and uranium-resistant populations of Rahnella spp. from Gammaproteobacteria and of Firmicutes occurred. After longer incubations for 14 weeks with uranyl nitrate, bacterial diversity increased and populations intrinsic to the untreated samples such as Bacteroidetes and Deltaproteobacteria propagated and replaced the above-mentioned uranium-resistant groups. This indicated that U(VI) was immobilized. Mössbauer spectroscopic analysis revealed an increased Fe(III) reduction by increasing the incubation time from four to 14 weeks. This result signified that Fe(III) was used as an electron acceptor by the bacterial community established at the later stages of the treatment. X-ray absorption spectroscopic analysis demonstrated that no detectable amounts of U(VI) were reduced to U(IV) in the time frames of the performed experiments. The reason for this observation is possibly due to the low level of electron donors in the studied oligotrophic environment. Time-resolved laser-induced fluorescence spectroscopic analysis demonstrated that most of the added U(VI) was bound by organic or inorganic phosphate phases both of biotic origin. [source] Temperature dependence of Fe(III) and sulfate reduction rates and its effect on growth and composition of bacterial enrichments from an acidic pit lake neutralization experimentGEOBIOLOGY, Issue 4 2005J. MEIER ABSTRACT Microbial Fe(III) and sulfate reduction are important electron transport processes in acidic pit lakes and stimulation by the addition of organic substrates is a strategy to remove acidity, iron and sulfate. This principle was applied in a pilot-scale enclosure in pit lake 111 (Brandenburg, Germany). Because seasonal and spatial variation of temperature may affect the performance of in situ experiments considerably, the influence of temperature on Fe(III) and sulfate reduction was investigated in surface sediments from the enclosure in the range of 4,28 °C. Potential Fe(III) reduction and sulfate reduction rates increased exponentially with temperature, and the effect was quantified in terms of the apparent activation energy Ea measuring 42,46 kJ mol,1 and 52 kJ mol,1, respectively. Relatively high respiration rates at 4 °C and relatively low Q10 values (,2) indicated that microbial communities were well adapted to low temperatures. In order to evaluate the effect of temperature on growth and enrichment of iron and sulfate-reducing bacterial populations, MPN (Most Probable Number) dilution series were performed in media selecting for the different bacterial groups. While the temperature response of specific growth rates of acidophilic iron reducers showed mesophilic characteristics, the relatively high specific growth rates of sulfate reducers at the lowest incubation temperature indicated the presence of moderate psychrophilic bacteria. In contrast, the low cell numbers and low specific growth rates of neutrophilic iron reducers obtained in dilution cultures suggest that these populations play a less significant role in Fe and S cycling in these sediments. SSCP (Single-Strand Conformation Polymorphism) or DGGE (Denaturing Gradient Gel Electrophoresis) fingerprinting based on 16S rRNA genes of Bacteria indicated different bacterial populations in the MPN dilution series exhibiting different temperature ranges for growth. [source] Linking microbial activity and soil organic matter transformations in forest soils under elevated CO2GLOBAL CHANGE BIOLOGY, Issue 2 2005S. A. Billings Abstract Soil organic matter (SOM) dynamics ultimately govern the ability of soil to provide long-term C sequestration and the nutrients required for ecosystem productivity. Predicting belowground responses to elevated CO2 requires an integrated understanding of SOM transformations and the microbial activity that governs them. It remains unclear how the microorganisms upon which these transformations depend will function in an elevated CO2 world. This study examines SOM transformations and microbial metabolism in soils from the Duke Free Air Carbon Enrichment site in North Carolina, USA. We assessed microbial respiration and net nitrogen (N) mineralization in soils with and without elevated CO2 exposure during a 100-day incubation. We also traced the depleted C isotopic signature of the supplemental CO2 into SOM and the soils' phospholipid fatty acids (PLFA), which serve as biomarkers for living cells. Cumulative net N mineralization in elevated CO2 soils was 50% that in control soils after a 100-day incubation. Respiration was not altered with elevated CO2. C : N ratios of bulk SOM did not change with elevated CO2, but incubation data suggest that the C : N ratios of mineralized organic matter increased with elevated CO2. Values of SOM ,13C were depleted with elevated CO2 (,26.7±0.2 vs. ,30.2±0.3,), reflecting the depleted signature of the supplemental CO2. We compared ,13C of individual PLFA with the ,13C of SOM to discern incorporation of the depleted C isotopic signature into soil microbial groups in elevated CO2 plots. PLFA i15:0, a15:0, and 10Met18:0 reflected significant incorporation of recently produced photosynthate, suggesting that the bacterial groups defined by these biomarkers are active metabolizers in elevated CO2 soils. At least one of these groups (actinomycetes, 10Met18:0) specializes in metabolizing less labile substrates. Because control plots did not receive an equivalent 13C tracer, we cannot determine from these data whether this group of organisms was stimulated by elevated CO2 compared with these organisms in control soils. Stimulation of this group, if it occurred in the elevated CO2 plot, would be consistent with a decline in the availability of mineralizable organic matter with elevated CO2, which incubation data suggest may be the case in these soils. [source] Active Crohn's disease and ulcerative colitis can be specifically diagnosed and monitored based on the biostructure of the fecal floraINFLAMMATORY BOWEL DISEASES, Issue 2 2008Alexander Swidsinski MD Abstract Background: The intestinal microflora is important in the pathogenesis of inflammatory bowel disease (IBD). The impact of its spatial organization on health and disease is unknown. Methods: We investigated sections of paraffin-embedded punched fecal cylinders. Fluctuations in spatial distribution of 11 bacterial groups were monitored in healthy subjects (n = 32), patients with IBD (n = 204), and other gastrointestinal diseases (n = 186) using fluorescence in situ hybridization (FISH). Results: The microbial structure differed in patients with Crohn's disease (CD), ulcerative colitis (UC), and healthy and disease controls. The profiles of CD and UC were distinctly opposite in 6 of 11 FISH probes used. Most prominent were a depletion of Faecalibacterium prausnitzii (Fprau<1 × 109/mL) with a normal leukocyte count in CD and a massive increase of leukocytes in the fecal-mucus transition zone (>30 leukocytes/104,m2) with high Fprau in patients with UC. These 2 features alone enabled the recognition of active CD (Crohn's Disease Activity Index [CDAI] >150) or UC (Clinical Activity Index [CAI] >3) with 79%/80% sensitivity and 98%/100% specificity. The mismatch in the sensitivity was mainly due to overlap between single IBD entities, and the specificity was exclusively due to the similarity of Crohn's and celiac disease. When inflammatory bowel disease (IBD) patients were pooled the sensitivity was 100% for severe disease, 84% for moderate activity, 72% for IBD with ,12 months remission, and 24% for IBD with >12 months remission. Conclusions: The fecal flora is highly structured and spatially organized. Diagnosing IBD and monitoring disease activity can be performed based on analysis of punched fecal cylinders independent from the patient's complaints. (Inflamm Bowel Dis 2007) [source] Hydrolysis and microbial community analyses in two-stage anaerobic digestion of energy cropsJOURNAL OF APPLIED MICROBIOLOGY, Issue 3 2007D.G. Cirne Abstract Aims:, The roles of the diverse populations of micro-organisms responsible for biodegradation of organic matter to form methane and carbon dioxide are rudimentarily understood. To expand the knowledge on links between microbial communities and the rate limiting, hydrolytic stage of two-stage biogas production from energy crops, this study was performed. Methods and Results:, The process performance and microbial communities (as determined by fluorescence in situ hybridization) in two separate two-stage batch digestions of sugar beets and grass/clover were studied. The microbial populations developed in the hydrolytic stage of anaerobic digestion of beets and grass/clover showed very few similarities, despite that the hydrolysis dynamics were similar. In both substrates, the solubilization of organic material was rapid for the first 10 days and accompanied by a build-up of volatile fatty acids (VFAs) and lactate. Between days 10 and 15, VFA and lactate concentrations decreased, as did the solubilization rates. For both substrates, Archaea started to appear in the hydrolytic stage between days 10 and 15, and the fraction of Bacteria decreased. The major bacterial group detected in the leachate fraction for beets was Alphaproteobacteria, whereas for grass/clover it was Firmicutes. The number of cells that bound to probes specifically targeting bacteria with cellulolytic activity was higher in the digestion of grass than in the digestion of beet. Conclusions:, This study allowed the identification of the general bacterial groups involved, and the identification of a clear shift in the microbial population when hydrolysis rate became limiting for each of the substrates investigated. Significance and Impact of the Study:, The findings from this study could be considered as a first step towards the development of strategies to stimulate hydrolysis further and ultimately increasing the methane production rates and yields from reactor-based digestion of these substrates. [source] Isolation and characterization of lactic acid bacteria from dochi (fermented black beans), a traditional fermented food in TaiwanLETTERS IN APPLIED MICROBIOLOGY, Issue 2 2006Y.-S. Chen Abstract Aims:, To isolate, characterize and identify lactic acid bacteria (LAB) in dochi (fermented black beans), a traditional fermented food in Taiwan. Methods and Results:, A total of 30 samples were collected from three different dochi producers and analysed after different periods of storage. Fifty-two cultures of LAB were isolated from dochi samples and the isolates were divided into classes by phenotype and then into groups by restriction fragment length polymorphism analysis and sequencing of 16S ribosomal DNA. Phenotypic and biochemical characteristics identified six different bacterial groups (A,F) and showed that the majority of the isolates were homofermentative LAB. Enterococcus faecium was the most abundant of the dochi -isolated LAB. All isolated LAB were able to grow in MRS broth containing 6% NaCl, but only Enterococcus, Pediococcus and Tetragenococcus species could grow in MRS broth containing 10% NaCl. Furthermore, antibacterial activities of isolates were determined, and four isolates showed inhibitory activities against the indicator strain Lactobacillus sakei JCM 1157T. Conclusions:, These results suggest that Ent. faecium is the main LAB present during the fermentation of dochi. Significance and Impact of the Study:, This is the first report describing the distribution and varieties of LAB that exist in the dochi fermentation process. [source] Development of a quantitative tool for the comparison of the prebiotic effect of dietary oligosaccharidesLETTERS IN APPLIED MICROBIOLOGY, Issue 4 2003R. Palframan Abstract Aims: To develop a quantitative equation [prebiotic index (PI)] to aid the analysis of prebiotic fermentation of commercially available and novel prebiotic carbohydrates in vitro, using previously published fermentation data. Methods: The PI equation is based on the changes in key bacterial groups during fermentation. The bacterial groups incorporated into this PI equation were bifidobacteria, lactobacilli, clostridia and bacteroides. The changes in these bacterial groups from previous studies were entered into the PI equation in order to determine a quantitative PI score. PI scores were than compared with the qualitative conclusions made in these publications. In general the PI scores agreed with the qualitative conclusions drawn and provided a quantitative measure. Conclusions: The PI allows the magnitude of prebiotic effects to be quantified rather than evaluations being solely qualitative. Significance and Impact of the Study: The PI equation may be of great use in quantifying prebiotic effects in vitro. It is expected that this will facilitate more rational food product development and the development of more potent prebiotics with activity at lower doses. [source] Recognition of anaerobic bacterial isolates in vitro using electronic nose technologyLETTERS IN APPLIED MICROBIOLOGY, Issue 5 2002A. Pavlou Aims: Use of an electronic nose (e.nose) system to differentiation between anaerobic bacteria grown in vitro on agar media. Methods and Results: Cultures of Clostridium spp. (14 strains) and Bacteroides fragilis (12 strains) were grown on blood agar plates and incubated in sampling bags for 30 min before head space analysis of the volatiles. Qualitative analyses of the volatile production patterns was carried out using an e.nose system with 14 conducting polymer sensors. Using data analysis techniques such as principal components analysis (PCA), genetic algorithms and neural networks it was possible to differentiate between agar blanks and individual species which accounted for all the data. A total of eight unknowns were correctly discriminated into the bacterial groups. Conclusions: This is the first report of in vitro complex volatile pattern recognition and differentiation of anaerobic pathogens. Significance and Impact of the Study: These results suggest the potential for application of e.nose technology in early diagnosis of microbial pathogens of medical importance. [source] Treatment of sanitary-important bacteria by bacteriocin substance V24 in cattle dung waterLETTERS IN APPLIED MICROBIOLOGY, Issue 5 2000A. Lauková Quantification of sanitary-important bacteria (e.g. Enterobacteriaceae), as well as indicators of environmental contamination, was assessed in samples of cattle dung from 25 cattle farms in 15 north-eastern Slovakia districts. The inhibitory effect of crude bacteriocin extract CBE V24 from Enterococcus faecalis V24 against Listeria monocytogenes Ohio and Yersinia enterocolitica YE85 was examined in cattle dung water with the aim of finding a new way of eliminating the health risk of the animal slurry. The following bacterial groups were quantified: Salmonella spp., Shigella -like spp., Proteus spp., Enterobacter spp., Citrobacter spp., Pseudomonas spp., Escherichia coli, Listeria spp., staphylococci, streptococci and enterococci (the average count ranged from 102 up to 104 cfu ml,1). Antagonistic effect of the crude bacteriocin from Enterococcus faecalis V24 in the range of 100,600 Arbitrary units per ml (AU ml,1) was shown against the following bacteria: Enterobacter cloacae, Ent. asburiae, Proteus spp., Salmonella spp., Acinetobacter lwoffi, L. monocytogenes as well as Y. enterocolitica YE85. During tests performed to study the inhibitory effect of the crude bacteriocin CBE V24 (concentration 800, 1600 AU ml,1) against L. monocytogenes Ohio and Y. enterocolitica YE85 in experimentally contaminated cattle dung, a reduction of 2·03 and 1·44 log cfu ml,1, respectively, was already noted after 1 h after crude bacteriocin CBE V24 addition. [source] Lactobacillus strains stabilize intestinal microbiota in Japanese cedar pollinosis patientsMICROBIOLOGY AND IMMUNOLOGY, Issue 4 2009Akira Kubota ABSTRACT A randomized double-blind, placebo-controlled trial was conducted to ascertain the intestinal microbiota-altering properties of LGG and L. gasseri TMC0356 (TMC0356) in Japanese cedar Cryptomeria japonica pollinosis patients. Fecal bacteria communities were examined before and after fermented milk administration using culture, FISH and T-RFLP methods. Test group subjects showed the presence of LGG and TMC0356 along with a significant increase in fecal lactobacilli (P < 0.001) after giving LGG and TMC0356 fermented milk. Culture and FISH analysis revealed no significant changes in other intestinal bacterial groups. Each subject exhibited a characteristic T-RFLP profile pattern that varied quantitatively and qualitatively with JCP shedding. Profile changes were observed in 53% of placebo group subjects and in 21% of test group subject's post-administration, indicating that LGG and TMC0356 suppressed intestinal microbiota changes in JCPsis patients. The results suggest that intestinal microbiota might be more sensitive to exposure to environmental allergens than expected from the results of general culture method studies. Stabilization of intestinal microbiota by selected probiotic strains such as LGG and TMC0356 could be beneficial to homeostasis of the intestinal microbiota and useful in the management of JCPsis. [source] Ultraviolet Radiation Induces Filamentation in Bacterial Assemblages from North Andean Patagonian LakesPHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2010Beatriz Modenutti Through laboratory experiments, we tested whether UV radiation (UVR) induces filamentation in natural bacteria assemblages from North Andean Patagonian lakes. We incubated water from three different lakes for 72 h in four separate treatments: (1) UVR + PAR (photosynthetically active radiation), (2) 50% UVR + PAR, (3) PAR and (4) 50% PAR. The irradiance levels used in the experiments were equivalent to those registered at the epilimnion of the lakes. In the UVR treatments filamentation was induced after the first 24 h and the proportion continued to increase for the next 48,72 h. A comparison of the gross composition and diversity of the entire community (cells >0.2 ,m) with bacterial filaments alone (>5.0 ,m) showed that UVR-induced filamentation is not a feature of any particular cluster. By sequencing part of the 16S rRNA gene of the taxonomic units obtained using denaturing gels, we observed that strains in the ,-Proteobacteria group were of relatively high importance in filament formation, followed by Cytophaga,Flavobacterium,Bacteroides, ,-Proteobacteria and ,-Proteobacteria, whereas Actinobacteria were almost nonexistent in the filaments. We propose that UVR doses equivalent to those of Andean lakes produce bacterial morphological changes, and that all bacterial groups except Actinobacteria can potentially form filaments. [source] An electron-flow model can predict complex redox reactions in mixed-culture fermentative BioH2: Microbial ecology evidenceBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2009Hyung-Sool Lee Abstract We developed the first model for predicting community structure in mixed-culture fermentative biohydrogen production using electron flows and NADH2 balances. A key assumption of the model is that H2 is produced only via the pyruvate decarboxylation-ferredoxin-hydrogenase pathway, which is commonly the case for fermentation by Clostridium and Ethanoligenens species. We experimentally tested the model using clone libraries to gauge community structures with mixed cultures in which we did not pre-select for specific bacterial groups, such as spore-formers. For experiments having final pHs 3.5 and 4.0, where H2 yield and soluble end-product distribution were distinctly different, we established stoichiometric reactions for each condition by using experimentally determined electron equivalent balances. The error in electron balancing was only 3% at final pH 3.5, in which butyrate and acetate were dominant organic products and the H2 yield was 2.1,mol,H2/mol,glucose. Clone-library analysis showed that clones affiliated with Clostridium sp. BL-22 and Clostridium sp. HPB-16 were dominant at final pH 3.5. For final pH 4.0, the H2 yield was 0.9,mol,H2/mol,glucose, ethanol, and acetate were the dominant organic products, and the electron balance error was 13%. The significant error indicates that a second pathway for H2 generation was active. The most abundant clones were affiliated with Klebsiella pneumoniae, which uses the formate-cleavage pathway for H2 production. Thus, the clone-library analyses confirmed that the model predictions for when the pyruvate decarboxylation-ferredoxin-hydrogenase pathway was (final pH 3.5) or was not (final pH 4.0) dominant. With the electron-flow model, we can easily assess the main mechanisms for H2 formation and the dominant H2 -producing bacteria in mixed-culture fermentative bioH2. Biotechnol. Bioeng. 2009; 104: 687,697 © 2009 Wiley Periodicals, Inc. [source] | ||||||||||||||||||||||||||||