SEARCH · PubMed Health

Results for “Bacteroidetes”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 109 records · Page 6Linked to original sources

PubMed2006

Diversity of bacteria contaminating paper machines.

Formation of microbial biofilms and slimes is a general and serious problem in the operation of paper machines. Studies of microbial populations in paper machine-derived biofilms have been conducted using standard microbiological procedures; however, the bacterial genera present in this type of samples as well as their diversity are quite poorly known. Here, the bacterial diversity of 38 process water and 22 biofilm samples from four different Finnish paper machines were analyzed by length heterogeneity analysis of PCR-amplified 16S ribosomal DNA (LH-PCR). In addition, sequencing of the amplified 16S rRNA gene from 69 clones was conducted for characterization of the bacterial genera present in biofilm and slime samples. The LH-PCR profiles of both the free-living (process waters) and immobilized (biofilms) bacteria were diverse at all stages of the papermaking process. Out of the 69 sequenced clones, 44 belonged to alpha-Proteobacteria, most of which were close to the nitrogen-fixing root nodule genera Sinorhizobium, Rhizobium and Azorhizobium. Other clones were assigned to beta- and gamma-Proteobacteria and the phylum Bacteroidetes. In addition, eight of the clones were assigned to a yet uncultivated phylum, TM7. Finally, epifluorescence microscopy revealed that Gram-negative bacteria were predominant in both the biofilm (65%) and process water (54%) samples and a small coccoid cell morphology was most common in all samples. Together, our results show that the analysis of microbial samples from paper machines using modern molecular biology techniques adds valuable information and should, therefore, be useful as a more specific and sensitive microbiological method for the paper industry. This information could further be applied, e.g., in the development of more specific and environmental friendly antimicrobial agents for paper mills.

Bacteria↗

PubMed2006

Biodegradation of petroleum hydrocarbons in seawater at low temperatures (0-5 degrees C) and bacterial communities associated with degradation.

In this study biodegradation of hydrocarbons in thin oil films was investigated in seawater at low temperatures, 0 and 5 degrees C. Heterotrophic (HM) or oil-degrading (ODM) microorganisms enriched at the two temperatures showed 16S rRNA sequence similarities to several bacteria of Arctic or Antarctic origin. Biodegradation experiments were conducted with a crude mineral oil immobilized as thin films on hydrophobic Fluortex adsorbents in nutrient-enriched or sterile seawater. Chemical and respirometric analysis of hydrocarbon depletion showed that naphthalene and other small aromatic hydrocarbons (HCs) were primarily biodegraded after dissolution to the water phase, while biodegradation of larger polyaromatic hydrocarbons (PAH) and C(10)-C(36) n-alkanes, including n-hexadecane, was associated primarily with the oil films. Biodegradation of PAH and n-alkanes was significant at both 0 and 5 degrees C, but was decreased for several compounds at the lower temperature. n-Hexadecane biodegradation at the two temperatures was comparable at the end of the experiments, but was delayed at 0 degree C. Investigations of bacterial communities in seawater and on adsorbents by PCR amplification of 16S rRNA gene fragments and DGGE analysis indicated that predominant bacteria in the seawater gradually adhered to the oil-coated adsorbents during biodegradation at both temperatures. Sequence analysis of most DGGE bands aligned to members of the phyla Proteobacteria (Gammaproteobacteria) or Bacteroidetes. Most sequences from experiments at 0 degree C revealed affiliations to members of Arctic or Antarctic consortia, while no such homology was detected for sequences from degradation experiment run at 5 degrees C. In conclusion, marine microbial communities from cold seawater have potentials for oil film HC degradation at temperatures < or =5 degrees C, and psychrotrophic or psychrophilic bacteria may play an important role during oil HC biodegradation in seawater close to freezing point.

Arctic Regions↗

PubMed2006

Microbial succession in a compost-packed biofilter treating benzene-contaminated air.

Air artificially contaminated with increasing concentrations of benzene was treated in a laboratory scale compost-packed biofilter for 240 days with a removal efficiency of 81-100%. The bacterial community in the packing material (PM) at different heights of the biofilter was analysed every 60 days. Bacterial plate counts and ribosomal intergenic spacer analysis (RISA) of the isolated strains showed that the number of cultivable aerobic heterotrophic bacteria and the species diversity increased with benzene availability. Identification of the isolated species and the main bands in denaturing gradient gel electrophoresis (DGGE) profiles from total compost DNA during the treatment revealed that, at a relatively low volumetric benzene load (1.2< or =VBL< or =6.4 g m(-3) (PM) h(-1)), besides low G+C Gram positive bacteria, originally present in the packing compost, bacteroidetes and beta- and gamma-proteobacteria became detectable in the colonising population. At the VBL value (24.8 g m(-3) (PM) h(-1)) ensuring the maximum elimination capacity of the biofilter (20.1 g m(-3) (PM) h(-1)), strains affiliated to the genus Rhodococcus dominated the microflora, followed by beta-proteobacteria comprising the genera Bordetella and Neisseria. Under these conditions, more than 35% of the isolated strains were able to grow on benzene as the sole carbon source. Comparison of DGGE and automated RISA profiles of the total community and isolated strains showed that a complex bacterial succession occurred in the reactor in response to the increasing concentrations of the pollutant and that cultivable bacteria played a major role in benzene degradation under the adopted conditions.

Air Pollutants↗

PubMed2024

Metagenomic Analysis of Gut Microbiome of Persistent Pulmonary Hypertension of the Newborn.

Persistent pulmonary hypertension of the newborn (PPHN) is one of the most common diseases in the neonatal intensive care unit which severely affects neonatal survival. Gut microbes play an increasingly important role in human health, but there are rarely reported how gut microbiota contribute to PPHN. In our study, the metagenomic sequencing of feces from 12 PPHN's neonates and 8 controls were performed to expose the relation between neonatal gut microbes and PPHN disease. Firstly, we found that the abundance of Actinobacteria, Proteobacteria, Bacteroidetes were significantly increased in PPHN compared with controls, but the Firmicutes components was reduced. And some pathogenic strains (like Vibrio metschnikovii) were significantly enriched in the PPHN compared with controls. Secondly, functional annotation of genes found that PPHN up-regulated transmembrane transport, but down-regulated ribosome and ATP binding. Lastly, microbial metabolic pathway enrichment analysis indicated that some metabolic pathway in PPHN were conflicting and contradictory, showed that an abnormally increased metabolism, disturbed protein synthesis and genomic instability in the PPHN neonate. Our results contribute to understanding the changes in the species and function of gut microbiota in PPHN, thus providing a theoretical basis for the explanation and treatment of PPHN.

Gastrointestinal Microbiome↗

PubMed2026

Comparative analysis of gut microbiota in yaks under different feeding management strategies during cold seasons.

Yaks (Bos grunniens) are crucial for the livelihoods of pastoral communities in cold regions, where feed scarcity during the cold season poses challenges to their health and productivity, underscoring the necessity of understanding how dietary management influences the gut microbiota. In this study, 24 yak steers matched for body weight and health status were randomly allocated to four groups: natural grazing or indoor feeding with roughage-to-concentrate ratios of 50:50, 70:30, or 90:10. Fecal samples were collected for 16S rDNA sequencing and subsequent functional prediction of the microbiota. The results showed that Firmicutes and Bacteroidetes were the dominant phyla across all groups, and UCG-005 and Rikenellaceae_RC9_gut_group were the predominant genera. Concentrate supplementation during the cold season significantly enhanced microbial richness and diversity, with the 70:30 ratio exerting the most pronounced beneficial effects on microbiota structure and key taxa enrichment. These findings highlight the critical role of dietary management in shaping the yak gut microbiota during cold seasons and suggest that the 70:30 ratio optimally improves microbial community structure, thereby promoting yak health and productivity under harsh climatic conditions. Future research should explore the long-term implications of such dietary strategies.

Animals↗

PubMed2004

Microbial community dynamics based on 16S rRNA gene profiles in a Pacific Northwest estuary and its tributaries.

We analyzed bacterioplankton community structure in Tillamook Bay, Oregon and its tributaries to evaluate phylogenetic variability and its relation to changes in environmental conditions along an estuarine gradient. Using eubacterial primers, we amplified 16S rRNA genes from environmental DNA and analyzed the PCR products by length heterogeneity polymerase chain reaction (LH-PCR), which discriminates products based on naturally occurring length differences. Analysis of LH-PCR profiles by multivariate ordination methods revealed differences in community composition along the estuarine gradient that were correlated with changes in environmental variables. Microbial community differences were also detected among different rivers. Using partial 16S rRNA sequences, we identified members of dominant or unique gene fragment size classes distributed along the estuarine gradient. Gammaproteobacteria and Betaproteobacteria and members of the Bacteroidetes dominated in freshwater samples, while Alphaproteobacteria, Cyanobacteria and chloroplast genes dominated in marine samples. Changes in the microbial communities correlated most strongly with salinity and dissolved silicon, but were also strongly correlated with precipitation. We also identified specific gene fragments that were correlated with inorganic nutrients. Our data suggest that there is a significant and predictable change in microbial species composition along an estuarine gradient, shifting from a more complex community structure in freshwater habitats to a community more typical of open ocean samples in the marine-influenced sites. We also demonstrate the resolution and power of LH-PCR and multivariate analyses to provide a rapid assessment of major community shifts, and show how these shifts correlate with environmental variables.

Bacteria↗

PubMed2005

Characterization of bacterial communities in four freshwater lakes differing in nutrient load and food web structure.

The phylogenetic composition of bacterioplankton communities in the water column of four shallow eutrophic lakes was analyzed by partially sequencing cloned 16S rRNA genes and by PCR-DGGE analysis. The four lakes differed in nutrient load and food web structure: two were in a clearwater state and had dense stands of submerged macrophytes, while two others were in a turbid state characterized by the occurrence of phytoplankton blooms. One turbid and one clearwater lake had very high nutrient levels (total phosphorus > 100 microg/l), while the other lakes were less nutrient rich (total phosphorus < 100 microg/l). Cluster analysis, multidimensional scaling and ANOSIM (analysis of similarity) were used to investigate differences among the bacterial community composition in the four lakes. Our results show that each lake has its own distinct bacterioplankton community. The samples of lake Blankaart differed substantially from those of the other lakes; this pattern was consistent throughout the year of study. The bacterioplankton community composition in lake Blankaart seems to be less diverse and less stable than in the other three lakes. Clone library results reveal that Actinobacteria strongly dominated the bacterial community in lake Blankaart. The relative abundance of Betaproteobacteria was low, whereas this group was dominant in the other three lakes. Turbid lakes had a higher representation of Cyanobacteria, while clearwater lakes were characterized by more representatives of the Bacteroidetes. Correlating our DGGE data with environmental parameters, using the BIOENV procedure, suggests that differences are partly related to the equilibrium state of the lake.

Bacteria↗

PubMed2005

Impact of chromium-contaminated wastewaters on the microbial community of a river.

The influence of chromium on the microbial community structure was analyzed in a river system subjected to long-term chromium contamination, by plating and by sequencing 16S rRNA genes cloned from DNA extracted from the river sediments. We also analyzed the influence of chromium on the ability of the microbial community to resist and reduce Cr(VI) and on its resistance to antibiotics. Shifts in the microbial community structure were analyzed by amplified ribosomal DNA restriction analysis fingerprinting. The isolates obtained were phylogenetically related to Actinobacteria, Firmicutes, Bacteroidetes and Proteobacteria, whereas Acidobacteria and Deltaproteobacteria were only revealed by clone analyses. Cr(VI)-resistant and Cr(VI)-reducing strains were isolated in all sites examined. However, each sample site had a microbial community with a different antibiotic resistance pattern. Our study seems to indicate that in this river ecosystem chromium influenced the microbial communities, altering some of their functional characteristics, such as the percentage of the microbial community able to resist or to reduce Cr(VI) and the phylogenetic groups isolated, but it did not affect the structural diversity. Furthermore, the concentration of Cr(VI) in the sediments could not be correlated with a lower number of bacteria or lower index of generic diversity, neither with the ability of the microbial community to resist or to reduce higher Cr(VI) concentrations.

Anti-Bacterial Agents↗

PubMed2005

Spatial distribution of bacterial phylotypes in the gut of the termite Reticulitermes speratus and the bacterial community colonizing the gut epithelium.

The bacterial community colonizing the gut wall of the termite Reticulitermes speratus was characterized without cultivation. Analysis of 16S rRNA genes after fractionation of the gut revealed that the bacterial composition on the gut wall was diverse and significantly different from that able to move unconfined in the gut fluid or physically associated with the gut protists. Actinobacteria, Firmicutes and Bacteroidetes were dominant on the gut wall, but Spirochaetes and the Termite group 1 phylum, abundant in the gut lumen, were relatively rare. A sequence-specific probe enabled the in situ detection of a rod-shaped Actinobacteria member, abundantly colonizing the gut paunch epithelium.

Animals↗

PubMed2005

Performance and microbial communities of a continuous stirred tank anaerobic reactor treating two-phases olive mill solid wastes at low organic loading rates.

A study of the performance and microbial communities of a continuous stirred tank reactor (CSTR) treating two-phases olive mill solid wastes (OMSW) was carried out at laboratory-scale. The reactor operated at a mesophilic temperature (35 degrees C) and an influent substrate concentration of 162 g total chemical oxygen demand (COD)L(-1) and 126 g volatile solids (VS)L(-1). The data analyzed in this work corresponded to a range of organic loading rates (OLR) of between 0.75 and 3.00 g CODL(-1)d(-1), getting removal efficiencies in the range of 97.0-95.6%. Methane production rate increased from 0.164 to 0.659 L CH(4)L(reactor)(-1)d(-1) when the OLR increased within the tested range. Methane yield coefficients were 0.225 L CH(4)g(-1) COD removed and 0.290 L CH(4)g(-1) VS removed and were virtually independent of the OLR applied. A molecular characterization of the microbial communities involved in the process was also accomplished. Molecular identification of microbial species was performed by PCR amplification of 16S ribosomal RNA genes, denaturing gradient gel electrophoresis (DGGE), cloning and sequencing. Among the predominant microorganisms in the bioreactor, the Firmicutes (mainly represented by Clostridiales) were the most abundant group, followed by the Chloroflexi and the Gamma-Proteobacteria (Pseudomonas species as the major representative). Other bacterial groups detected in the bioreactor were the Actinobacteria, Bacteroidetes and Deferribacteres. Among the Archaea, the methanogen Methanosaeta concilii was the most representative species.

Anaerobiosis↗

PubMed2006

Evaluation of gas removal and bacterial community diversity in a biofilter developed to treat composting exhaust gases.

The performance of a new, but simply constructed, biofilter system, developed to purify composting exhaust air, was evaluated. The biofilter was packed with mature compost mixed with activated carbon and sludge sourced from a wastewater treatment plant. An alternating air flow system and a bioaerosol reduction device were designed to prevent pressure drop and reduce bioaerosol release. Experimental results demonstrated that satisfactory removal efficiencies of nitrogen-containing compounds, sulfur-containing compounds, fatty acids, total hydrocarbon and odor were achieved at an empty bed retention time (EBRT) of 30s. No significant acidification or alkalinity in the biofilter was observed, and the system was characterized by a small pressure drop and a low level of bioaerosol emission. Denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH) techniques were used to uncover the changes in the bacterial community of the biofilter during the deodorization processes. A minimum of 16 bands were observed in the DGGE profile. Phylogenetic analysis revealed the phylum of Proteobacteria to be predominant, followed by Actinobacteria, Bacteroidetes, and Firmicutes, in descending order. However, the occurrence and predominance of specific bacterial species varied with the environmental conditions of the biofilter. Our results demonstrate - from both an engineering and biological point of view - the feasibility of the biofilter system described herein in purifying the gases derived from composting food waste.

Air Pollutants↗

PubMed2006

Molecular microbial diversity of a soil sample and detection of ammonia oxidizers from Cape Evans, Mcmurdo Dry Valley, Antarctica.

The aim of our study was to estimate the uncultured eubacterial diversity of a soil sample collected below a dead seal, Cape Evans, McMurdo, Antarctica by an SSU rDNA gene library approach. Our study by sequencing of clones from SSU rDNA gene library approach revealed high diversity in the soil sample from Antarctica. More than 50% of clones showed homology to Cytophaga-Flavobacterium-Bacteroides group; sequences also belonged to alpha, beta, gamma proteobacteria, Thermus-Deinococcus and high GC gram-positive group; Phylogenetic analysis of the SSU rDNA clones showed the presence of species belonging to Cytophaga spp., Vitellibacter vladivostokensis, Aequorivita lipolytica, Aequorivita crocea, Flavobacterium spp., Flexibacter sp., Subsaxibacter broadyi, Bacteroidetes, Roseobacter sp., Sphingomonas baekryungensis, Nitrosospira sp., Nitrosomonas cryotolerans, Psychrobacter spp., Chromohalobacter sp., Psychrobacter okhotskensis, Psychrobacter fozii, Psychrobacter urativorans, Rubrobacter radiotolerans, Marinobacter sp., Rubrobacteridae, Desulfotomaculum aeronauticum and Deinococcus sp. The presence of ammonia oxidizing bacteria in Antarctica soil was confirmed by the presence of the amoA gene. Phylogenetic analysis revealed grouping of clones with their respective groups.

Ammonia↗

PubMed2004

The filtration-acclimatization method for isolation of an important fraction of the not readily cultivable bacteria.

We developed a novel method, the filtration-acclimatization method (FAM), which enables the isolation and cultivation of an important fraction of the bacterial diversity, which is not cultivable by standard methods. The method consists of a filtration step, which removes most of the readily cultivable bacteria able to overgrow slowly growing bacteria, and an acclimatization procedure that provides a slow transition from the low environmental substrate concentrations to the high concentration of standard microbial media. So far, we isolated in total 65 strains from surface freshwater habitats by utilizing FAM. The isolates are affiliated with Actinobacteria, Alpha-, Betaproteobacteria, Bacteroidetes, and Spirochaeta. All isolates are pure cultures and form visible colonies on agar plates with high substrate concentrations. For further analysis, strains sharing more than a 97% 16S rRNA gene sequence similarity were grouped into one taxon. Based on sequence similarities, 88% of the obtained taxa can be considered to be undescribed species (<97% similarity to closest species). The highest similarity value of the taxa to the respective closest related species ranged from 87.7% to 99.8%, and was on average 94.5%. For comparison we isolated, by direct plating of water samples on a rich agar medium, a similar number of taxa. Amongst these taxa the percentage of taxa, which can be considered to be undescribed species, was only half of the percentage found for the taxa isolated by FAM. More importantly, it was amongst the taxa obtained by the standard method no taxon that was closer related to an uncultured bacterium than to an isolate, while 56% of the taxa isolated by FAM were closely related to uncultured bacteria.

Bacteria↗

PubMed2004

Broad diversity of viable bacteria in 'sterile' (0.2 microm) filtered water.

Filtration of liquids through 0.2-microm filters is a common and often-used method for the removal of microorganisms from heat-sensitive solutions. Such 0.2 microm filtrations are frequently referred to as 'sterile filtration', reflecting the general belief that all living organisms are excluded from the filtrate. However, it has been demonstrated that a few bacterial species can pass through 0.2-microm filters. Despite these observations, it is generally assumed that most bacteria are unable to pass through these filters. In contrast to this assumption, a wide diversity of 19 bacterial taxa was isolated by the acclimatization method from 0.2 microm-filtrated freshwater samples. All isolates were able to grow on substrate-rich agar plates. The size of the isolated strains ranged from <1 to >10 microm in cell length. The obtained isolates belong to the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Spirochaetes. Previous studies which did not use the acclimatization method reported that only two out of the 19 taxa passed through 0.2- or 0.45-microm filters. The majority of the obtained isolates were more closely related to uncultured than to previously cultured bacteria. It is assumed that the obtained taxa represent only a small fraction of the bacteria able to pass through 0.2-microm filters, and it is concluded that microbiologists may have dramatically underestimated the diversity of 0.2 microm-filterable bacteria.

Bacteria↗

PubMed2006

Molecular analyses of microbial diversity associated with the Lonar soda lake in India: an impact crater in a basalt area.

The prokaryotic diversity associated with an Indian soda lake (Lonar Crater Lake) located in a basaltic soil area was investigated using a culture-independent approach. Community DNA was extracted directly from four sediment samples obtained by coring to depths of 10-20 cm. Small subunit rRNA genes (16S rDNA) were amplified by PCR using primers specific to the domains Bacteria and Archaea. The PCR products were cloned and sequenced. For the bacterial rDNA clone library, 500 clones were randomly selected for further analysis. After restriction fragment length polymorphism (RFLP) analysis and subsequent sequencing, a total of 44 unique phylotypes were obtained. These phylotypes spanned a wide range within the domain Bacteria, occupying eight major lineages/phyla. 34% of the clones were classified as firmicutes. The other clones were grouped into proteobacteria (29.5%), actinobacteria (6.8%), deinococcus-thermus (4.5%), cytophages-flavobacterium-bacteroidetes (13.3%), planctomycetes (6.8%), cyanobacteria (4.5%) and spirochetes (2.27%). In the case of the archaeal 16S rDNA library, analysis of 250 randomly selected clones revealed the presence of 13 distinct phylotypes; 5 phylotypes were associated with Crenarchaeota and 8 with Euryarchaeota. Most of the euryarchaeota sequences were related to methanogens. Findings from this molecular study of a site investigated for the first time have revealed the presence of a highly diverse bacterial population and a comparatively less diverse archaeal population. The majority ( approximately 80%) of the cloned sequences show little affiliation with known taxa (<97% sequence similarity) and may represent novel taxa/sequences and organisms specifically adapted to this basaltic soda lake environment. Diversity analyses demonstrate greater diversity and evenness of bacterial species compared to a skewed representation of species for Archaea.

Archaea↗

PubMed2006

Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Rømø Basin, Wadden Sea.

Molecular biological methods were used to investigate the microbial diversity and community structure in intertidal sandy sediments near the island of Sylt (Wadden Sea) at a site which was characterized for transport and mineralization rates in a parallel study (D. de Beer, F. Wenzhöfer, T. Ferdelman, S.E. Boehme, M. Huettel, J.E.E. van Beusekom, M.E. Böttcher, N. Musat, N. Dubilier, Transport and mineralization rates in North Sea sandy intertidal sediments, Sylt-Romo Basin, Wadden Sea, Limnol. Oceanogr. 50 (2005) 113-127). Comparative 16S rRNA sequence analysis revealed a high bacterial diversity. Most sequences retrieved by PCR with a general bacterial primer set were affiliated with Bacteroidetes, Gammaproteobacteria, Deltaproteobacteria and the Pirellula cluster of Planctomycetales. Fluorescence in situ hybridization (FISH) and slot-blot hybridization with group-specific rRNA-targeted oligonucleotide probes were used to characterize the microbial community structure over depth (0-12 cm) and seasons (March, July, October). We found high abundances of bacteria with total cell numbers up to 3 x 10(9) cells ml(-1) and a clear seasonal variation, with higher values in July and October versus March. The microbial community was dominated by members of the Planctomycetes, the Cytophaga/Flavobacterium group, Gammaproteobacteria, and bacteria of the Desulfosarcina/Desulfococcus group. The high abundance (1.5 x 10(7)-1.8 x 10(8) cells ml(-1) accounting for 3-19% of all cells) of presumably aerobic heterotrophic polymer-degrading planctomycetes is in line with the high permeability, deep oxygen penetration, and the high rates of aerobic mineralization of algal biomass measured in the sandy sediments by de Beer et al. (2005). The high and stable abundance of members of the Desulfosarcina/Desulfococcus group, both over depth and season, suggests that these bacteria may play a more important role than previously assumed based on low sulfate reduction rates in parallel cores (de Beer et al., 2005).

Bacteria↗

PubMed2006

Microbial community analysis of a biogas-producing completely stirred tank reactor fed continuously with fodder beet silage as mono-substrate.

The bioconversion of renewable raw material to biogas by anaerobic microbial fermentation processes in completely stirred tank reactors (CSTR) is a valuable alternative resource of energy especially for rural areas. However, knowledge about the microorganisms involved in the degradation of plant biomass is still poor. In this study, a first analysis of the biogas-forming process within a CSTR fed continuously with fodder beet silage as mono-substrate is presented in the context of molecular data on the microbial community composition. As indicated by the conventional process parameters like pH value, content of volatile fatty acids, N:P ratio and the biogas yield, the biogas-forming process within the CSTR occurred with a stable and efficient performance. The average biogas yield based on volatile solids was 0.87m(3)kg(-1) at an organic loading rate of 1.2-2.3kgm(-3)d(-1). This amounts to 94% of the theoretical maximum. In order to identify microorganisms within the CSTR, a 16S rDNA clone library was constructed by PCR amplification applying a prokaryote-specific primer set. One hundred and forty seven clones were obtained and subsequently characterized by amplified rDNA restriction analysis (ARDRA). The sequences of 60 unique ARDRA patterns were estimated in a length of approximately 800-900bp each. Four of them were assigned to the domain Archaea and 56 to the domain Bacteria. Within the domain Archaea, all clones showed a close relationship to methanogenic species. Major bacterial groups represented in the clone library were the class Clostridia of the phylum Firmicutes (22% of all 16S rDNA clones), the class Deltaproteobacteria of the phylum Proteobacteria (24%), the class Bacilli of the phylum Firmicutes (22%) and members of the phylum Bacteroidetes (21%). Within these major groups, the highest biodiversity was found within the class Clostridia (35% of all operational taxonomic units). Members of the phyla Actinobacteria and Spirochaetes were represented only by 5 and 2 clonal sequences, respectively.

Archaea↗

PubMed2006

Identification of bacteria associated with spreading odontogenic infections by 16S rRNA gene sequencing.

OBJECTIVE: To determine the bacterial species associated with spreading odontogenic infections (SOIs). STUDY DESIGN: Pus samples from 4 cases of SOI were analyzed by microbiological culture methods for the presence of bacteria, and by polymerase chain reaction (PCR) amplification, cloning, and sequencing of bacterial 16S rRNA genes. RESULTS: Culture methods identified species from the genera Prevotella, Streptococcus, and Fusobacterium, as well as anaerobic streptococci. Molecular detection methods identified a far more diverse microflora. The predominant genus detected was Prevotella, representing 102 (50.2%) of 203 clones analyzed. Prevotella oris was the most abundant species identified, representing 45 (22.2%) of 203 clones analyzed. Twelve clones (5.9%) represented uncultivable species, namely Prevotella PUS9.180, an uncultured Peptostreptococcus species, and an uncultured bacterium belonging to the Bacteroidetes phylum. CONCLUSIONS: Prevotella species may play an important role in SOIs, and further work to examine in more detail the pathogenicity determinants of these organisms and associated host responses is warranted.

Adolescent↗