scholarly journals Intestinal TM7 bacterial phylogenies in active inflammatory bowel disease

2008 ◽  
Vol 57 (12) ◽  
pp. 1569-1576 ◽  
Author(s):  
Tanja Kuehbacher ◽  
Ateequr Rehman ◽  
Patricia Lepage ◽  
Stephan Hellmig ◽  
Ulrich R. Fölsch ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
16S Rrna ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Base Substitution ◽  
Clone Libraries ◽  
Bowel Diseases ◽  
Inflammatory Bowel ◽  
Almost All

TM7 is a recently described subgroup of Gram-positive uncultivable bacteria originally found in natural environmental habitats. An association of the TM7 bacterial division with the inflammatory pathogenesis of periodontitis has been previously shown. This study investigated TM7 phylogenies in patients with inflammatory bowel diseases (IBDs). The mucosal microbiota of patients with active Crohn's disease (CD; n=42) and ulcerative colitis (UC; n=31) was compared with that of controls (n=33). TM7 consortia were examined using molecular techniques based on 16S rRNA genes, including clone libraries, sequencing and in situ hybridization. TM7 molecular signatures could be cloned from mucosal samples of both IBD patients and controls, but the composition of the clone libraries differed significantly. Taxonomic analysis of the sequences revealed a higher diversity of TM7 phylotypes in CD (23 different phylotypes) than in UC (10) and non-IBD controls (12). All clone libraries showed a high number of novel sequences (21 for controls, 34 for CD and 29 for UC). A highly atypical base substitution for bacterial 16S rRNA genes associated with antibiotic resistance was detected in almost all sequences from CD (97.3 %) and UC (100 %) patients compared to only 65.1 % in the controls. TM7 bacteria might play an important role in IBD similar to that previously described in oral inflammation. The alterations of TM7 bacteria and the genetically determined antibiotic resistance of TM7 species in IBD could be a relevant part of a more general alteration of bacterial microbiota in IBD as recently found, e.g. as a promoter of inflammation at early stages of disease.

scholarly journals 1358. A Novel Rapidly Growing Mycobacteria (RGM) Species Causing Soft Tissue and Orthopedic Hardware Infection After Trauma

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S492-S492
Author(s):  
David C Nguyen ◽  
Michelle Lisgaris ◽  
Sruthi Vasireddy ◽  
Richard J Wallace ◽  
Federico Perez ◽  
...  
Keyword(s):  
Soft Tissue ◽  
16S Rrna ◽  
Antibiotic Susceptibility ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Mycobacterium Fortuitum ◽  
Rapidly Growing Mycobacteria ◽  
Maldi Tof

Abstract Background The widespread use of molecular techniques has resulted in increasing numbers of newly characterized rapidly growing mycobacteria (RGM). Many RGM cause soft tissue and orthopedic hardware infection, particularly after trauma. RGM species identification remains challenging with few genetic differences between species. Methods We describe a case involving RGM. We report results of matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry (Bruker Biotyper), sequencing of rpoB, erm(39), and 16S rRNA genes, and antibiotic susceptibility testing (AST). We review previous reports describing similar RGM infections. Results A 58-year-old male sustained multiple fractures and right thigh compartment syndrome after a motorcycle accident. He underwent fasciotomy and multi-stage surgical fixations. 3 months later, he had wound dehiscence, purulence and multiple fluid collections of his right leg and knee requiring surgical drainage and removal of orthopedic hardware. After 4 days, acid-fast bacilli grew on routine bacterial culture media. MALDI-TOF identified the isolate as Mycobacterium mageritense. In contrast, sequencing of 16S rRNA (100% identity) and erm(39) (> 99% identity) identified the isolate as Mycobacterium houstonense; erm(39) only had 80% similarity with Mycobacterium fortuitum. Sequencing of rpoB showed a 19 bp difference with the M. houstonense type strain, and showed similarity to M. fortuitum (97.64%) than M. houstonense (97.45%). AST demonstrated resistance to clarithromycin only. After initial treatment with imipenem, ciprofloxacin, and doxycycline, definite therapy with ciprofloxacin and doxycycline was successful. In the literature, we found one case each of M. mageritense and M. houstonense infection after trauma. Conclusion This case highlights the importance of RGM other than M. fortuitum as a cause of soft tissue and orthopedic hardware infections, and illustrates the difficulty of identifying them to the species level. Sequencing of erm(39) and 16S rRNA gene identified the isolate as M. houstonense, but the larger difference (>2.5%) in rpoB sequence suggests a novel species. Further characterization is underway. Efforts to determine RGM species and antibiotic susceptibility give important insight into diagnosis and management. Disclosures All authors: No reported disclosures.

Identification of prevalent microbial communities in a municipal solid waste landfill

2006 ◽  
Vol 53 (8) ◽  
pp. 139-147 ◽  
Author(s):  
B. Calli ◽  
S. Durmaz ◽  
B. Mertoglu
Keyword(s):  
16S Rrna ◽  
Municipal Solid Waste ◽  
Microbial Communities ◽  
Solid Waste ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Fish Analysis ◽  
Municipal Solid Waste Landfill ◽  
Waste Landfill

To identify the microbial communities in Istanbul, Odayeri Municipal Solid Waste Landfill, leachate samples were collected from different sections at different stabilization phases. In identification of microbial communities in leachate samples, molecular techniques such as FISH, DGGE and cloning based on 16S rRNA and mcrA genes were used. As the chemical and microbiological compositions of the samples were compared, obvious correlations were found between the stability of the landfill section and abundance of active methanogens. On the other hand, there were considerable differences between acidogenic and mature leachate samples in DGGE profiles of archaeal and bacterial 16S rRNA genes. Moreover, in acidogenic leachate samples having BOD5/COD ratio of about 0.5 acetate utilizing Methanosarcina and Methanosaeta species were intensively detected in FISH. Although only very few H2-utilizing methanogens were identified with FISH analysis, most of the clones isolated from mature leachate samples clustered within H2-utilizing Methanobacteriales and Methanomicrobiales according to phylogenetic analysis of 16S rRNA and mcrA clones, respectively.

scholarly journals Phylogenetic Comparison of the Methanogenic Communities from an Acidic, Oligotrophic Fen and an Anaerobic Digester Treating Municipal Wastewater Sludge

2008 ◽  
Vol 74 (21) ◽  
pp. 6663-6671 ◽  
Author(s):  
Lisa M. Steinberg ◽  
John M. Regan
Keyword(s):  
16S Rrna ◽  
Municipal Wastewater ◽  
Anaerobic Digester ◽  
Wastewater Sludge ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Large Temperature ◽  
Clone Libraries ◽  
Average Sequence ◽  
Sequence Similarities

ABSTRACT Methanogens play a critical role in the decomposition of organics under anaerobic conditions. The methanogenic consortia in saturated wetland soils are often subjected to large temperature fluctuations and acidic conditions, imposing a selective pressure for psychro- and acidotolerant community members; however, methanogenic communities in engineered digesters are frequently maintained within a narrow range of mesophilic and circumneutral conditions to retain system stability. To investigate the hypothesis that these two disparate environments have distinct methanogenic communities, the methanogens in an oligotrophic acidic fen and a mesophilic anaerobic digester treating municipal wastewater sludge were characterized by creating clone libraries for the 16S rRNA and methyl coenzyme M reductase alpha subunit (mcrA) genes. A quantitative framework was developed to assess the differences between these two communities by calculating the average sequence similarity for 16S rRNA genes and mcrA within a genus and family using sequences of isolated and characterized methanogens within the approved methanogen taxonomy. The average sequence similarities for 16S rRNA genes within a genus and family were 96.0 and 93.5%, respectively, and the average sequence similarities for mcrA within a genus and family were 88.9 and 79%, respectively. The clone libraries of the bog and digester environments showed no overlap at the species level and almost no overlap at the family level. Both libraries were dominated by clones related to uncultured methanogen groups within the Methanomicrobiales, although members of the Methanosarcinales and Methanobacteriales were also found in both libraries. Diversity indices for the 16S rRNA gene library of the bog and both mcrA libraries were similar, but these indices indicated much lower diversity in the 16S digester library than in the other three libraries.

scholarly journals A Comparative Study: Taxonomic Grouping of Alkaline Protease Producing Bacilli

2017 ◽  
Vol 66 (1) ◽  
pp. 39-56
Author(s):  
Nilgun Tekin ◽  
Arzu Coleri Cihan ◽  
Basar Karaca ◽  
Cumhur Cokmus
Keyword(s):  
16S Rrna ◽  
Alkaline Protease ◽  
Phylogenetic Analyses ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Protease Production ◽  
Rrna Gene ◽  
Wide Range ◽  
Its Pcr

Alkaline proteases have biotechnological importance due to their activity and stability at alkaline pH. 56 bacteria, capable of growing under alkaline conditions were isolated and their alkaline protease activities were carried out at different parameters to determine their optimum alkaline protease production conditions. Seven isolates were showed higher alkaline protease production capacity than the reference strains. The highest alkaline protease producing isolates (103125 U/g), E114 and C265, were identified as Bacillus licheniformis with 99.4% and Bacillus mojavensis 99.8% based on 16S rRNA gene sequence similarities, respectively. Interestingly, the isolates identified as Bacillus safensis were also found to be high alkaline protease producing strains. Genotypic characterizations of the isolates were also determined by using a wide range of molecular techniques (ARDRA, ITS-PCR, (GTG)5-PCR, BOX-PCR). These different techniques allowed us to differentiate the alkaliphilic isolates and the results were in concurrence with phylogenetic analyses of the 16S rRNA genes. While ITS-PCR provided the highest correlation with 16S rRNA groups, (GTG)5-PCR showed the highest differentiation at species and intra-species level. In this study, each of the biotechnologically valuable alkaline protease producing isolates was grouped into their taxonomic positions with multi-genotypic analyses.

scholarly journals Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria

2015 ◽  
Vol 15 (1) ◽  
Author(s):  
Marketa Sagova-Mareckova ◽  
Dana Ulanova ◽  
Petra Sanderova ◽  
Marek Omelka ◽  
Zdenek Kamenik ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Phylogenetic Relatedness

scholarly journals Diversity and Structure of Bacterial Communities in Arctic versus Antarctic Pack Ice

2003 ◽  
Vol 69 (11) ◽  
pp. 6610-6619 ◽  
Author(s):  
Robin Brinkmeyer ◽  
Katrin Knittel ◽  
Jutta Jürgens ◽  
Horst Weyland ◽  
Rudolf Amann ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
The Arctic ◽  
Rrna Genes ◽  
Gene Clone ◽  
Rrna Gene ◽  
Antarctic Species ◽  
Pack Ice

ABSTRACT A comprehensive assessment of bacterial diversity and community composition in arctic and antarctic pack ice was conducted through cultivation and cultivation-independent molecular techniques. We sequenced 16S rRNA genes from 115 and 87 pure cultures of bacteria isolated from arctic and antarctic pack ice, respectively. Most of the 33 arctic phylotypes were >97% identical to previously described antarctic species or to our own antarctic isolates. At both poles, the α- and γ-proteobacteria and the Cytophaga-Flavobacterium group were the dominant taxonomic bacterial groups identified by cultivation as well as by molecular methods. The analysis of 16S rRNA gene clone libraries from multiple arctic and antarctic pack ice samples revealed a high incidence of closely overlapping 16S rRNA gene clone and isolate sequences. Simultaneous analysis of environmental samples with fluorescence in situ hybridization (FISH) showed that∼ 95% of 4′,6′-diamidino-2-phenylindole (DAPI)-stained cells hybridized with the general bacterial probe EUB338. More than 90% of those were further assignable. Approximately 50 and 36% were identified asγ -proteobacteria in arctic and antarctic samples,respectively. Approximately 25% were identified asα -proteobacteria, and 25% were identified as belonging to the Cytophaga-Flavobacterium group. For the quantification of specific members of the sea ice community, new oligonucleotide probes were developed which target the genera Octadecabacter, Glaciecola, Psychrobacter, Marinobacter, Shewanella, and Polaribacter. High FISH detection rates of these groups as well as high viable counts corroborated the overlap of clone and isolate sequences. A terrestrial influence on the arctic pack ice community was suggested by the presence of limnic phylotypes.

scholarly journals Assessment of Microbial Diversity in Four Southwestern United States Soils by 16S rRNA Gene Terminal Restriction Fragment Analysis

2000 ◽  
Vol 66 (7) ◽  
pp. 2943-2950 ◽  
Author(s):  
John Dunbar ◽  
Lawrence O. Ticknor ◽  
Cheryl R. Kuske
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rdna ◽  
Restriction Fragment ◽  
Community Diversity ◽  
Detection Sensitivity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Clone Libraries

ABSTRACT The ability of terminal restriction fragment (T-RFLP or TRF) profiles of 16S rRNA genes to provide useful information about the relative diversity of complex microbial communities was investigated by comparison with other methods. Four soil communities representing two pinyon rhizosphere and two between-tree (interspace) soil environments were compared by analysis of 16S rRNA gene clone libraries and culture collections (Dunbar et al., Appl. Environ. Microbiol. 65:1662–1669, 1998) and by analysis of 16S rDNA TRF profiles of community DNA. The TRF method was able to differentiate the four communities in a manner consistent with previous comparisons of the communities by analysis of 16S rDNA clone libraries. TRF profiles were not useful for calculating and comparing traditional community richness or evenness values among the four soil environments. Statistics calculated from RsaI, HhaI, HaeIII, and MspI profiles of each community were inconsistent, and the combined data were not significantly different between samples. The detection sensitivity of the method was tested. In standard PCRs, a seeded population comprising 0.1 to 1% of the total community could be detected. The combined results demonstrate that TRF analysis is an excellent method for rapidly comparing the relationships between bacterial communities in environmental samples. However, for highly complex communities, the method appears unable to provide classical measures of relative community diversity.

A survey of the composition and diversity of bacterial populations in bleached kraft pulp-mill wastewater secondary treatment systems

2004 ◽  
Vol 50 (8) ◽  
pp. 633-644 ◽  
Author(s):  
Kimberley A Gilbride ◽  
Roberta R Fulthorpe
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Pulp Mill ◽  
Paper Mill ◽  
Pulp And Paper ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Secondary Treatment ◽  
Pulp And Paper Mill

Bacterial community compositions from 10 pulp- and paper-mill treatment systems were compared using both traditional and molecular techniques. 16S-RFLP (Random Fragment Length Polymorphisms) analysis was used to examine the genotypic profiles of the whole bacterial community of each treatment system. Although all the communities shared approximately 60% of their DNA band pattern, as determined by computer-assisted cluster analysis, each community displayed a unique profile that was stable over time under normal operating parameters. Reverse Sample Genome Probing (RSGP) and 16S-RFLP were used to compare the culturable bacterial communities of several geographically separated pulp-mill biotreatment system communities. There was little overlap in the composition of the culturable community between mills at the genus level. Furthermore, RSGP variation was almost as high within a mill as between mills. Partial sequences of the 16S rRNA genes from culturable isolates identified Bacillus spp., Pseudomonas spp., and Xanthobacter as some of the dominant species. Finally, several 16S rRNA genes from two whole community 16S RNA gene libraries were partially sequenced and identified as similar to unknown α-, β-, and γ-Proteobacteria, Ralstonia, Alcaligenes, Nitrospira, Firmicutes, and clones representing the new Holophaga/Acidobacterium phylum. These findings suggest that although these pulp- and paper-mill biotreatment communities perform similar functions, they are populated by unique mixtures of species.Key words: biodiversity, 16S-RFLP, secondary treatment, pulp mills.

scholarly journals Relationship of Temporal and Spatial Variabilities of Ammonia-Oxidizing Bacteria to Nitrification Rates in Monterey Bay, California

2005 ◽  
Vol 71 (2) ◽  
pp. 697-705 ◽  
Author(s):  
G. D. O'Mullan ◽  
B. B. Ward
Keyword(s):  
16S Rrna ◽  
Spatial Dynamics ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ammonia Oxidizing Bacteria ◽  
Monterey Bay ◽  
Strong Positive Correlation ◽  
Clone Libraries ◽  
Bacterial Populations ◽  
Temporal And Spatial

ABSTRACT Temporal and spatial dynamics of ammonia-oxidizing bacteria (AOB) were examined using genes encoding 16S rRNA and ammonia monooxygenase subunit A (AmoA) in Monterey Bay, Calif. Samples were collected from three depths in the water column on four dates at one mid-bay station. Diversity estimators for the two genes showed a strong positive correlation, indicating that overlapping bacterial populations had been sampled by both sets of clone libraries. Some samples that were separated by only 15 m in depth had less genetic similarity than samples that were collected from the same depth months apart. Clone libraries from the Monterey Bay AOB community were dominated by Nitrosospira-like sequences and clearly differentiated from the adjacent AOB community in Elkhorn Slough. Many Monterey Bay clones clustered with previously identified 16S rRNA and amoA groups composed entirely of marine sequences, supporting the hypothesis that these groups are specific to the marine environment and are dominant marine AOB. In addition, novel, phylogenetically distinct groups of AOB sequences were identified and compared to sequences in the database. Only one cluster of gammaproteobacterial AOB was detected using 16S rRNA genes. Although significant genetic variation was detected in AOB populations from both vertical and temporal samples, no significant correlation was detected between diversity and environmental variables or the rate of nitrification.

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