Journal articles: 'Eubacterial isolates'

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Sahm, Kerstin, Christian Knoblauch, and Rudolf Amann. "Phylogenetic Affiliation and Quantification of Psychrophilic Sulfate-Reducing Isolates in Marine Arctic Sediments." Applied and Environmental Microbiology 65, no. 9 (September 1, 1999): 3976–81. http://dx.doi.org/10.1128/aem.65.9.3976-3981.1999.

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ABSTRACT Thirteen psychrophilic sulfate-reducing isolates from two permanently cold fjords of the Arctic island Spitsbergen (Hornsund and Storfjord) were phylogenetically analyzed. They all belonged to the δ subclass of Proteobacteria and were widely distributed within this group, indicating that psychrophily is a polyphyletic property. A new 16S rRNA-directed oligonucleotide probe was designed against the largest coherent cluster of these isolates. The new probe, as well as a set of available probes, was applied in rRNA slot blot hybridization to investigate the composition of the sulfate-reducing bacterial community in the sediments. rRNA related to the new cluster of incompletely oxidizing, psychrophilic isolates made up 1.4 to 20.9% of eubacterial rRNA at Storfjord and 0.6 to 3.5% of eubacterial rRNA at Hornsund. This group was the second-most-abundant group of sulfate reducers at these sites. Denaturing gradient gel electrophoresis and hybridization analysis showed bands identical to those produced by our isolates. The data indicate that the psychrophilic isolates are quantitatively important in Svalbard sediments.

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Teigell-Perez, Gonzalez-Martin, Valladares, Smith, and Griffin. "Virus-Like Particle Production in Atmospheric Eubacteria Isolates." Atmosphere 10, no. 7 (July 19, 2019): 417. http://dx.doi.org/10.3390/atmos10070417.

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Culturable eubacterial isolates were collected at various altitudes in Earth’s atmosphere, including ~1.5 m above ground in Tallahassee, FL, USA; ~10.0 m above sea level over the mid-Atlantic ridge (~15° N); ~ 20 km above ground over the continental United States; ~20 km above sea level over the Pacific Ocean near southern California; and from the atmosphere of Carlsbad Cavern, Carlsbad Cavern National Park, NM, USA. Isolates were screened for the presence of inducible virus-like particles (VLP) through the use of mitomycin C and epifluorescent direct counts. We determined that 92.7% of the isolates carried inducible VLP counts in exposed versus non-exposed culture controls and that the relationship was statistically significant. Further statistical analyses revealed that the number of isolates that demonstrated VLP production did not vary among collection sites. These data demonstrate a high prevalence of VLP generation in isolates collected in the lower atmosphere and at extreme altitudes. They also show that species of eubacteria that are resistant to the rigors of atmospheric transport play a significant role in long-range atmospheric inter- and intra-continental dispersion of VLP and that long-range atmospheric transport of VLP may enhance rates of evolution at the microbial scale in receiving environments.

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Ventura, Marco, Roberto Reniero, and Ralf Zink. "Specific Identification and Targeted Characterization ofBifidobacterium lactis from Different Environmental Isolates by a Combined Multiplex-PCR Approach." Applied and Environmental Microbiology 67, no. 6 (June 1, 2001): 2760–65. http://dx.doi.org/10.1128/aem.67.6.2760-2765.2001.

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ABSTRACT The species Bifidobacterium lactis, with its main representative strain Bb12 (DSM 10140), is a yoghurt isolate used as a probiotic strain and is commercially applied in different types of yoghurts and infant formulas. In order to ensure the genetic identity and safety of this bacterial isolate, species- and strain-specific molecular tools for genetic fingerprinting must be available to identify isolated bifidobacteria or lactic acid bacteria from, e.g., various clinical environments of relevance in medical microbiology. Two opposing rRNA gene-targeted primers have been developed for specific detection of this microorganism by PCR. The specificity of this approach was evaluated and verified with DNA samples isolated from single and mixed cultures of bifidobacteria and lactobacilli (48 isolates, including the type strains of 29Bifidobacterium and 9 Lactobacillusspecies). Furthermore, we performed a Multiplex-PCR using oligonucleotide primers targeting a specific region of the 16S rRNA gene for the genus Bifidobacterium and a conserved eubacterial 16S rDNA sequence. The specificity and sensitivity of this detection with a pure culture of B. lactis were, respectively, 100 bacteria/ml after 25 cycles of PCR and 1 to 10 bacteria/ml after a 50-cycle nested-PCR approach.

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Karahan, Z. Ceren, Ipek Mumcuoglu, Haluk Guriz, Deniz Tamer, Neriman Balaban, Derya Aysev, and Nejat Akar. "PCR evaluation of false-positive signals from two automated blood-culture systems." Journal of Medical Microbiology 55, no. 1 (January 1, 2006): 53–57. http://dx.doi.org/10.1099/jmm.0.46196-0.

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Rapid detection of micro-organisms from blood is one of the most critical functions of a diagnostic microbiology laboratory. Automated blood-culture systems reduce the time needed to detect positive cultures, and reduce specimen handling. The false-positive rate of such systems is 1–10 %. In this study, the presence of pathogens in ‘false-positive’ bottles obtained from BACTEC 9050 (Becton Dickinson) and BacT/Alert (Biomérieux) systems was investigated by eubacterial and fungal PCR. A total of 169 subculture-negative aerobic blood-culture bottles (104 BacT/Alert and 65 BACTEC) were evaluated. Both fungal and eubacterial PCRs were negative for all BACTEC bottles. Fungal PCR was also negative for the BacT/Alert system, but 10 bottles (9·6 %) gave positive results by eubacterial PCR. Sequence analysis of the positive PCR amplicons indicated the presence of the following bacteria (number of isolates in parentheses): Pasteurella multocida (1), Staphylococcus epidermidis (2), Staphylococcus hominis (1), Micrococcus sp. (1), Streptococcus pneumoniae (1), Corynebacterium spp. (2), Brachibacterium sp. (1) and Arthrobacter/Rothia sp. (1). Antibiotic usage by the patients may be responsible for the inability of the laboratory to grow these bacteria on subcultures. For patients with more than one false-positive bottle, molecular methods can be used to evaluate the microbial DNA in these bottles. False positives from the BACTEC system may be due to elevated patient leukocyte counts or the high sensitivity of the system to background increases in CO2 concentration.

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Wood, Jacqueline, Karen P. Scott, Gorazd Avguštin, C. James Newbold, and Harry J. Flint. "Estimation of the Relative Abundance of DifferentBacteroides and Prevotella Ribotypes in Gut Samples by Restriction Enzyme Profiling of PCR-Amplified 16S rRNA Gene Sequences." Applied and Environmental Microbiology 64, no. 10 (October 1, 1998): 3683–89. http://dx.doi.org/10.1128/aem.64.10.3683-3689.1998.

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ABSTRACT We describe an approach for determining the genetic composition ofBacteroides and Prevotellapopulations in gut contents based on selective amplification of 16S rRNA gene sequences (rDNA) followed by cleavage of the amplified material with restriction enzymes. The relative contributions of different ribotypes to total Bacteroides andPrevotella 16S rDNA are estimated after end labelling of one of the PCR primers, and the contribution ofBacteroides and Prevotellasequences to total eubacterial 16S rDNA is estimated by measuring the binding of oligonucleotide probes to amplified DNA.Bacteroides and Prevotella 16S rDNA accounted for between 12 and 62% of total eubacterial 16S rDNA in samples of ruminal contents from six sheep and a cow. Ribotypes 4, 5, 6, and 7, which include most cultivated rumen Prevotellastrains, together accounted for between 20 and 86% of the total amplified Bacteroides andPrevotella rDNA in these samples. The most abundantBacteroides or Prevotella ribotype in four animals, however, was ribotype 8, for which there is only one known cultured isolate, while ribotypes 1 and 2, which include many colonic Bacteroides spp., were the most abundant in two animals. This indicates that some abundantBacteroides and Prevotella groups in the rumen are underrepresented among cultured rumenPrevotella isolates. The approach described here provides a rapid, convenient, and widely applicable method for comparing the genotypic composition of bacterial populations in gut samples.

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Pryde, Susan E., Anthony J. Richardson, Colin S. Stewart, and Harry J. Flint. "Molecular Analysis of the Microbial Diversity Present in the Colonic Wall, Colonic Lumen, and Cecal Lumen of a Pig." Applied and Environmental Microbiology 65, no. 12 (December 1, 1999): 5372–77. http://dx.doi.org/10.1128/aem.65.12.5372-5377.1999.

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ABSTRACT Random clones of 16S ribosomal DNA gene sequences were isolated after PCR amplification with eubacterial primers from total genomic DNA recovered from samples of the colonic lumen, colonic wall, and cecal lumen from a pig. Sequences were also obtained for cultures isolated anaerobically from the same colonic-wall sample. Phylogenetic analysis showed that many sequences were related to those ofLactobacillus or Streptococcus spp. or fell into clusters IX, XIVa, and XI of gram-positive bacteria. In addition, 59% of randomly cloned sequences showed less than 95% similarity to database entries or sequences from cultivated organisms. Cultivation bias is also suggested by the fact that the majority of isolates (54%) recovered from the colon wall by culturing were related toLactobacillus and Streptococcus, whereas this group accounted for only one-third of the sequence variation for the same sample from random cloning. The remaining cultured isolates were mainly Selenomonas related. A higher proportion ofLactobacillus reuteri-related sequences than ofLactobacillus acidophilus- and Lactobacillus amylovorus-related sequences were present in the colonic-wall sample. Since the majority of bacterial ribosomal sequences recovered from the colon wall are less than 95% related to known organisms, the roles of many of the predominant wall-associated bacteria remain to be defined.

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Peters, Sabine, Stefanie Koschinsky, Frank Schwieger, and Christoph C. Tebbe. "Succession of Microbial Communities during Hot Composting as Detected by PCR–Single-Strand-Conformation Polymorphism-Based Genetic Profiles of Small-Subunit rRNA Genes." Applied and Environmental Microbiology 66, no. 3 (March 1, 2000): 930–36. http://dx.doi.org/10.1128/aem.66.3.930-936.2000.

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ABSTRACT A cultivation-independent technique for genetic profiling of PCR-amplified small-subunit rRNA genes (SSU rDNA) was chosen to characterize the diversity and succession of microbial communities during composting of an organic agricultural substrate. PCR amplifications were performed with DNA directly extracted from compost samples and with primers targeting either (i) the V4–V5 region of eubacterial 16S rRNA genes, (ii) the V3 region in the 16S rRNA genes of actinomycetes, or (iii) the V8–V9 region of fungal 18S rRNA genes. Homologous PCR products were converted to single-stranded DNA molecules by exonuclease digestion and were subsequently electrophoretically separated by their single-strand-conformation polymorphism (SSCP). Genetic profiles obtained by this technique showed a succession and increasing diversity of microbial populations with all primers. A total of 19 single products were isolated from the profiles by PCR reamplification and cloning. DNA sequencing of these molecular isolates showed similarities in the range of 92.3 to 100% to known gram-positive bacteria with a low or high G+C DNA content and to the SSU rDNA of γ-Proteobacteria. The amplified 18S rRNA gene sequences were related to the respective gene regions of Candida krusei and Candida tropicalis. Specific molecular isolates could be attributed to different composting stages. The diversity of cultivated bacteria isolated from samples taken at the end of the composting process was low. A total of 290 isolates were related to only 6 different species. Two or three of these species were also detectable in the SSCP community profiles. Our study indicates that community SSCP profiles can be highly useful for the monitoring of bacterial diversity and community successions in a biotechnologically relevant process.

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Navrátilová, Lucie, Magdalena Chromá, Vojtěch Hanulík, and Vladislav Raclavský. "Possibilities in Identification of Genomic Species of Burkholderia cepacia Complex by PCR and RFLP." Polish Journal of Microbiology 62, no. 4 (2013): 373–76. http://dx.doi.org/10.33073/pjm-2013-051.

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The strains belonging to Burkholderia cepacia complex are important opportunistic pathogens in immunocompromised patients and cause serious diseases. It is possible to obtain isolates from soil, water, plants and human samples. Taxonomy of this group is difficult. Burkholderia cepacia complex consists of seventeen genomic species and the genetic scheme is based on recA gene. Commonly, first five genomovars occurre in humans, mostly genomovars II and III, subdivision IIIA. Within this study we tested identification of first five genomovars by PCR with following melting analysis and RFLP. The experiments were targeted on eubacterial 16S rDNA and specific gene recA, which allowed identification of all five genomovars. RecA gene appeared as more suitable than 16S rDNA, which enabled direct identification of only genomovars II and V; genomovars I, III and IV were similar within 16S rDNA sequence.

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Kukkurainen, S., A. Leino, S. Vähämiko, H. R. Kärkkäinen, K. Ahanen, S. Sorvari, R. Rugienius, and O. Toldi. "Occurrence and Location of Endophytic Bacteria in Garden and Wild Strawberry." HortScience 40, no. 2 (April 2005): 348–52. http://dx.doi.org/10.21273/hortsci.40.2.348.

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The occurrence of bacteria in different tissues was studied using field-grown strawberries, in vitro-grown strawberries, wild strawberries, and aseptically germinated strawberry seedlings. Strawberry has a number of endophytic bacteria in its the internal tissue, most of which appear to be nonpathogenic. In the in vitro-grown strawberries, all identified isolates were in the genus Pantoea. In field-grown garden and wild strawberries the most common genera were Pantoea and Pseudomonas. Location of eubacterial inhabitants within strawberry tissue sections was studied by in situ hybridization. Bacteria were detected in flower stalks, leaf stalks, leaves, stolons, berries and aseptically germinated seedlings. The existence of bacteria in seeds and seedlings suggests that bacteria are able to move up to the generative tissue and, ultimately, to the next generation, forming a symbiosis-like chain of plant-bacteria coexistence.

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Babb, Kelly, Tomasz Bykowski, Sean P. Riley, M. Clarke Miller, Edward DeMoll, and Brian Stevenson. "Borrelia burgdorferi EbfC, a Novel, Chromosomally Encoded Protein, Binds Specific DNA Sequences Adjacent to erp Loci on the Spirochete's Resident cp32 Prophages." Journal of Bacteriology 188, no. 12 (June 15, 2006): 4331–39. http://dx.doi.org/10.1128/jb.00005-06.

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ABSTRACT All examined isolates of the Lyme disease spirochete, Borrelia burgdorferi, naturally maintain numerous variants of a prophage family as circular cp32 episomes. Each cp32 carries a locus encoding one or two different Erp outer membrane, surface-exposed lipoproteins. Many of the Erp proteins bind a host complement regulator, factor H, which is hypothesized to protect the spirochete from complement-mediated killing. We now describe the isolation and characterization of a novel, chromosomally encoded protein, EbfC, that binds specific DNA sequences located immediately 5′ of all erp loci. This is one of the first site-specific DNA-binding proteins to be identified in any spirochete. The location of the ebfC gene on the B. burgdorferi chromosome suggests that the cp32 prophages have evolved to use this bacterial host protein for their own benefit and that EbfC probably plays additional roles in the bacterium. A wide range of other bacteria encode homologs of EbfC, none of which have been well characterized, so demonstration that B. burgdorferi EbfC is a site-specific DNA-binding protein has broad implications across the eubacterial kingdom.

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Rickard, Alexander H., Andrew J. McBain, Amy T. Stead, and Peter Gilbert. "Shear Rate Moderates Community Diversity in Freshwater Biofilms." Applied and Environmental Microbiology 70, no. 12 (December 2004): 7426–35. http://dx.doi.org/10.1128/aem.70.12.7426-7435.2004.

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ABSTRACT The development of freshwater multispecies biofilms at solid-liquid interfaces occurs both in quiescent waters and under conditions of high shear rates. However, the influence of hydrodynamic shear rates on bacterial biofilm diversity is poorly understood. We hypothesized that different shear rates would significantly influence biofilm diversity and alter the relative proportions of coaggregating and autoaggregating community isolates. In order to study this hypothesis, freshwater biofilms were developed at five shear rates (<0.1 to 305 S−1) in a rotating concentric cylinder reactor fed with untreated potable water. Eubacterial diversity was assessed by denaturing gradient gel electrophoresis (DGGE) and culturing on R2A agar. Fifty morphologically distinct biofilm strains and 16 planktonic strains were isolated by culturing and identified by partial 16S rRNA gene sequencing, and their relatedness was determined by the construction of a neighbor-joining phylogenetic tree. Phylogenetic and DGGE analyses showed an inverse relationship between shear rate and bacterial diversity. An in vitro aggregation assay was used to assess the relative proportions of coaggregating and autoaggregating species from each biofilm. The highest proportion of autoaggregating bacteria was present at high shear rates (198 to 305 S−1). The intermediate shear rate (122 S−1) selected for the highest proportion of coaggregating bacteria (47%, or 17 of a possible 36 coaggregation interactions). Under static conditions (<0.1 S−1), 41 (33%) of a possible 125 coaggregation interactions were positive. Few coaggregation (3.3%) or autoaggregation (25%) interactions occurred between the 16 planktonic strains. In conclusion, these data show that shear rates affect biofilm diversity as well as the relative proportions of aggregating bacteria.

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Simpson, Kenneth W., Belgin Dogan, Mark Rishniw, Richard E. Goldstein, Suzanne Klaessig, Patrick L. McDonough, Alex J. German, et al. "Adherent and Invasive Escherichia coli Is Associated with Granulomatous Colitis in Boxer Dogs." Infection and Immunity 74, no. 8 (August 2006): 4778–92. http://dx.doi.org/10.1128/iai.00067-06.

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ABSTRACT The mucosa-associated microflora is increasingly considered to play a pivotal role in the pathogenesis of inflammatory bowel disease. This study explored the possibility that an abnormal mucosal flora is involved in the etiopathogenesis of granulomatous colitis of Boxer dogs (GCB). Colonic biopsy samples from affected dogs (n = 13) and controls (n = 38) were examined by fluorescent in situ hybridization (FISH) with a eubacterial 16S rRNA probe. Culture, 16S ribosomal DNA sequencing, and histochemistry were used to guide subsequent FISH. GCB-associated Escherichia coli isolates were evaluated for their ability to invade and persist in cultured epithelial cells and macrophages as well as for serotype, phylogenetic group, genome size, overall genotype, and presence of virulence genes. Intramucosal gram-negative coccobacilli were present in 100% of GCB samples but not controls. Invasive bacteria hybridized with FISH probes to E. coli. Three of four GCB-associated E. coli isolates adhered to, invaded, and replicated within cultured epithelial cells. Invasion triggered a“ splash”-type response, was decreased by cytochalasin D, genistein, colchicine, and wortmannin, and paralleled the behavior of the Crohn's disease-associated strain E. coli LF 82. GCB E. coli and LF 82 were diverse in serotype and overall genotype but similar in phylogeny (B2 and D), in virulence gene profiles (fyuA, irp1, irp2, chuA, fepC, ibeA, kpsMII, iss), in having a larger genome size than commensal E. coli, and in the presence of novel multilocus sequence types. We conclude that GCB is associated with selective intramucosal colonization by E. coli. E. coli strains associated with GCB and Crohn's disease have an adherent and invasive phenotype and novel multilocus sequence types and resemble E. coli associated with extraintestinal disease in phylogeny and virulence gene profile.

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McBain, Andrew J., Robert G. Bartolo, Carl E. Catrenich, Duane Charbonneau, Ruth G. Ledder, and Peter Gilbert. "Effects of Triclosan-Containing Rinse on the Dynamics and Antimicrobial Susceptibility of In Vitro Plaque Ecosystems." Antimicrobial Agents and Chemotherapy 47, no. 11 (November 2003): 3531–38. http://dx.doi.org/10.1128/aac.47.11.3531-3538.2003.

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ABSTRACT Dental plaque microcosms were established under a feast-famine regimen within constant-depth film fermentors and exposed four times daily postfeeding to a triclosan (TR)-containing rinse (dentifrice) (TRD). This was diluted so that the antimicrobial content was 0.6 mg/ml. Microcosms were characterized by heterotrophic plate counts and PCR-denaturing gradient gel electrophoresis (DGGE) with primers specific for the V2-V3 region of the eubacterial 16S rRNA gene (rDNA). Dominant isolates and PCR amplicons were identified by partial sequencing of 16S rDNA. TRD caused considerable decreases in the counts of both gram-negative organisms and total anaerobic cells, transiently lowered the numbers of streptococci and actinomycetes, and markedly increased the proportion of lactobacilli. DGGE indicated the presence of putatively unculturable bacteria and showed that a Porphyromonas sp. and Selenomonas infelix had been inhibited by TRD. Pure culture studies of 10 oral bacteria (eight genera) showed that Neisseria subflava, Prevotella nigrescens, and Porphyromonas gingivalis were highly susceptible to TR, while the lactobacilli and streptococci were the least susceptible. Clonal expansion of the lactobacilli in the pulsed microcosm could be explained on the basis of TR activity. The mean MICs of TR, chlorhexidine, erythromycin, penicillin V, and vancomycin for the population before and after 5 days of exposure to TRD showed few significant changes. In conclusion, changes in plaque microcosm populations following repeated exposure to TRD showed inhibition of the most susceptible flora and clonal expansion of less susceptible species.

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Forterre, Patrick, Christiane Eue, Mouldy Sioud, and Abdellah Hamal. "Studies on DNA polymerases and topoisomerases in archaebacteria." Canadian Journal of Microbiology 35, no. 1 (January 1, 1989): 228–33. http://dx.doi.org/10.1139/m89-035.

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We have isolated DNA polymerases and topoisomerases from two thermoacidophilic archaebacteria: Sulfolobus acidocaldarius and Thermoplasma acidophilum. The DNA polymerases are composed of a single polypeptide with molecular masses of 100 and 85 kDa, respectively. Antibodies against Sulfolobus DNA polymerase did not cross react with Thermoplasma DNA polymerase. Whereas the major DNA topoisomerase activity in S. acidocaldarius is an ATP-dependent type I DNA topoisomerase with a reverse gyrase activity, the major DNA topoisomerase activity in T. acidophilum is a ATP-independent relaxing activity. Both enzymes resemble more the eubacterial than the eukaryotic type I DNA topoisomerase. We have found that small plasmids from halobacteria are negatively supercoiled and that DNA topoisomerase II inhibitors modify their topology. This suggests the existence of an archaebacterial type II DNA topoisomerase related to its eubacterial and eukaryotic counterparts. As in eubacteria, novobiocin induces positive supercoiling of halobacterial plasmids, indicating the absence of a eukaryotic-like type I DNA topoisomerase that relaxes positive superturns.Key words: archaebacteria, DNA topoisomerases, DNA polymerases, DNA topology, gyrase.

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You, Yaqi, Markus Hilpert, and Mandy J. Ward. "Detection of a Common and Persistenttet(L)-Carrying Plasmid in Chicken-Waste-Impacted Farm Soil." Applied and Environmental Microbiology 78, no. 9 (March 2, 2012): 3203–13. http://dx.doi.org/10.1128/aem.07763-11.

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ABSTRACTThe connection between farm-generated animal waste and the dissemination of antibiotic resistance in soil microbial communities, via mobile genetic elements, remains obscure. In this study, electromagnetic induction (EMI) surveying of a broiler chicken farm assisted soil sampling from a chicken-waste-impacted site and a marginally affected site. Consistent with the EMI survey, a disparity existed between the two sites with regard to soil pH, tetracycline resistance (Tcr) levels among culturable soil bacteria, and the incidence and prevalence of severaltetandermgenes in the soils. No significant difference was observed in these aspects between the marginally affected site and several sites in a relatively pristine regional forest. When the farm was in operation,tet(L),tet(M),tet(O),erm(A),erm(B), anderm(C) genes were detected in the waste-affected soil. Two years after all waste was removed from the farm,tet(L),tet(M),tet(O), anderm(C) genes were still detected. The abundances oftet(L),tet(O), anderm(B) were measured using quantitative PCR, and the copy numbers of each were normalized to eubacterial 16S rRNA gene copy numbers.tet(L) was the most prevalent gene, whereastet(O) was the most persistent, although all declined over the 2-year period. A mobilizable plasmid carryingtet(L) was identified in seven of 14 Tcrsoil isolates. The plasmid's hosts were identified as species ofBhargavaea,Sporosarcina, andBacillus. The plasmid's mobilization (mob) gene was quantified to estimate its prevalence in the soil, and the ratio oftet(L) tomobwas shown to have changed from 34:1 to 1:1 over the 2-year sampling period.

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Gich, Frederic, Karin Schubert, Alke Bruns, Herbert Hoffelner, and Jörg Overmann. "Specific Detection, Isolation, and Characterization of Selected, Previously Uncultured Members of the Freshwater Bacterioplankton Community." Applied and Environmental Microbiology 71, no. 10 (October 2005): 5908–19. http://dx.doi.org/10.1128/aem.71.10.5908-5919.2005.

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ABSTRACT High-throughput cultivation was combined with rapid and group-specific phylogenetic fingerprinting in order to recover representatives of three freshwater bacterioplankton communities. A total of 570 bacterial cultures were obtained by employing the most probable number and MicroDrop techniques. The majority of the cultured bacteria were closely related to previously uncultured bacteria and grouped with the α-Proteobacteria, β-Proteobacteria, Actinobacteria, Firmicutes, or Flavobacteria-Cytophaga lineage. Correspondingly, the natural bacterioplankton community was analyzed by high-resolution phylogenetic fingerprinting of these five bacterial lineages. 16S rRNA gene fragments were generated for each lineage and subsequently separated by denaturing gradient gel electrophoresis. By the combination of five group-specific PCR protocols, the total number of 16S rRNA gene fingerprints generated from the natural communities was increased sixfold compared to conventional (eubacterial) fingerprinting. Four of the environmental α-Proteobacteria 16S rRNA gene sequences obtained from the natural community were found to be identical to those of bacterial isolates. One of these phylotypes was detected in 14 different cultures and hence represented the most frequently cultured bacterium. Three of these 14 strains were characterized in detail. Their complete 16S rRNA gene sequences showed only 93% similarity to that of Sandaracinobacter sibiricus, the closest relative described so far. The novel phylotype of bacterium is a strict aerobe capable of using numerous organic carbon substrates and contains bacteriochlorophyll a bound to two different photosynthetic light-harvesting complexes. Dot blot hybridization revealed that the strains occur in lakes of different trophic status and constitute up to 2% of the microbial community.

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Mishra, Saroj K., Curt J. Whitenack, and Alan R. Putnam. "Herbicidal Properties of Metabolites from Several Genera of Soil Microorganisms." Weed Science 36, no. 1 (January 1988): 122–26. http://dx.doi.org/10.1017/s0043174500074555.

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Metabolites from 906 microbial isolates were evaluated for herbicidal properties. These included 266 isolates ofStreptomyces, 502 isolates of non-Streptomycesactinomycetes representing 18 genera, 28 unidentified aerobic actinomycetes, 70 fungi, and 40 isolates of eubacteria. Metabolites from 72 isolates significantly inhibited germination of cress seeds. In terms of generic specificity and frequency, about 18% of all theStreptomycesandNocardiopsisisolates and 13% ofActinoplanesisolates were toxic to cress (Lepidium sativumL.) seeds. Among other inhibitors were three isolates ofActinomaduraand one isolate each ofMicromonospora, Micropolyspora, Strep to sporangium, Streptoverticillium, andBacillus, and two isolates of unidentified actinomycetes. The toxigenic fungi included two isolates ofPenicilliumand one isolate each ofAspergillus, Scopulariopsis, andPaecilomycesspecies. About half the isolates toxic to cress were toxic to barnyardgrass (Echinochloa crus-galliL. Beauv. # ECHCG) seeds. of the isolates found effective in the secondary screening on the potted weeds, eight belonged to the genusStreptomycesand one was identified asScopulariopsis brumptii. None of the examined isolates ofRhodococcus, Nocardia, Oerskovia, Thermoactinomyces, Thermomonospora, andsix other genera of actinomycetes showed any appreciable toxicity to the seeds of either species.

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Barcenilla, Adela, Susan E. Pryde, Jennifer C. Martin, Sylvia H. Duncan, Colin S. Stewart, Colin Henderson, and Harry J. Flint. "Phylogenetic Relationships of Butyrate-Producing Bacteria from the Human Gut." Applied and Environmental Microbiology 66, no. 4 (April 1, 2000): 1654–61. http://dx.doi.org/10.1128/aem.66.4.1654-1661.2000.

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ABSTRACT Butyrate is a preferred energy source for colonic epithelial cells and is thought to play an important role in maintaining colonic health in humans. In order to investigate the diversity and stability of butyrate-producing organisms of the colonic flora, anaerobic butyrate-producing bacteria were isolated from freshly voided human fecal samples from three healthy individuals: an infant, an adult omnivore, and an adult vegetarian. A second isolation was performed on the same three individuals 1 year later. Of a total of 313 bacterial isolates, 74 produced more than 2 mM butyrate in vitro. Butyrate-producing isolates were grouped by 16S ribosomal DNA (rDNA) PCR-restriction fragment length polymorphism analysis. The results indicate very little overlap between the predominant ribotypes of the three subjects; furthermore, the flora of each individual changed significantly between the two isolations. Complete sequences of 16S rDNAs were determined for 24 representative strains and subjected to phylogenetic analysis. Eighty percent of the butyrate-producing isolates fell within the XIVa cluster of gram-positive bacteria as defined by M. D. Collins et al. (Int. J. Syst. Bacteriol. 44:812–826, 1994) and A. Willems et al. (Int. J. Syst. Bacteriol. 46:195–199, 1996), with the most abundant group (10 of 24 or 42%) clustering with Eubacterium rectale, Eubacterium ramulus, and Roseburia cecicola. Fifty percent of the butyrate-producing isolates were net acetate consumers during growth, suggesting that they employ the butyryl coenzyme A-acetyl coenzyme A transferase pathway for butyrate production. In contrast, only 1% of the 239 non-butyrate-producing isolates consumed acetate.

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Ikeyama, Nao, Atsushi Toyoda, Sho Morohoshi, Tadao Kunihiro, Takumi Murakami, Hiroshi Mori, Takao Iino, Moriya Ohkuma, and Mitsuo Sakamoto. "Amedibacterium intestinale gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium dolichum Moore et al. 1976 (Approved Lists 1980) as Amedibacillus dolichus gen. nov., comb. nov." International Journal of Systematic and Evolutionary Microbiology 70, no. 6 (June 1, 2020): 3656–64. http://dx.doi.org/10.1099/ijsem.0.004215.

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Four strains (9CBEGH2T, 9BBH35, 6BBH38 and 6EGH11) of Gram-stain-positive, obligately anaerobic, rod-shaped bacteria were isolated from faecal samples from healthy Japanese humans. The results of 16S rRNA gene sequence analysis indicated that the four strains represented members of the family Erysipelotrichaceae and formed a monophyletic cluster with ‘ Absiella argi ’ strain N6H1-5 (99.4% sequence similarity) and Eubacterium sp. Marseille-P5640 (99.3 %). Eubacterium dolichum JCM 10413T (94.2 %) and Eubacterium tortuosum ATCC 25548T (93.7 %) were located near this monophyletic cluster. The isolates, 9CBEGH2T, ‘ A. argi ’ JCM 30884 and Eubacterium sp. Marseille-P5640 shared 98.7–99.1% average nucleotide identity (ANI) with each other. Moreover, the in silico DNA–DNA hybridization (DDH) values among three strains were 88.4–90.6%, indicating that these strains represent the same species. Strain 9CBEGH2T showed 21.5–24.1 % in silico DDH values with other related taxa. In addition, the ANI values between strain 9CBEGH2T and other related taxa ranged from 71.2 % to 73.5 %, indicating that this strain should be considered as representing a novel species on the basis of whole-genome relatedness. Therefore, we formally propose a novel name for ‘ A. argi ’ strains identified because the name ‘ A. argi ’ has been effectively, but not validly, published since 2017. On the basis of the collected data, strain 9CBEGH2T represents a novel species of a novel genus, for which the name Amedibacterium intestinale gen. nov., sp. nov. is proposed. The type strain of A. intestinale is 9CBEGH2T (=JCM 33778T=DSM 110575T).

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Goel, Usha, Tiiu Kauri, Donn J. Kushner, and Hans-W. Ackermann. "A moderately halophilic Vibrio from a Spanish saltern and its lytic bacteriophage." Canadian Journal of Microbiology 42, no. 10 (October 1, 1996): 1015–23. http://dx.doi.org/10.1139/m96-130.

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A number of bacteria and their phages were isolated from a saltern near Alicante, Spain. One isolate, Vibrio B1, a moderate halophile that is probably a strain of Vibrio costicola, was host to a lytic phage, UTAK. Studies of the host bacterium included the effects of salt concentrations on the action of a number of inhibitory agents. Phage UTAK has a head, a tail, and a baseplate. It contains 80 kbp of double-stranded DNA with no unusual bases. It was stable for long periods in the absence of high salt concentrations and even in distilled water. Salt concentrations had little effect on adsorption of UTAK to its host but resulted in considerable changes in burst size. It appears that phages of halophilic and salt-tolerant eubacteria, and also of some marine bacteria, have much lower salt requirements for stability than the phages of halophilic archaebacteria. Our results suggest that ionic controls of phage replication in these eubacteria may differ from those of growth.Key words: halophiles, Vibrio sp., bacteriophage, salt responses.

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Oren, Aharon. "Intracellular salt concentrations of the anaerobic halophilic eubacteria Haloanaerobium praevalens and Halobacteroides halobius." Canadian Journal of Microbiology 32, no. 1 (January 1, 1986): 4–9. http://dx.doi.org/10.1139/m86-002.

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The obligately anaerobic, moderately halophilic eubacteria Haloanaerobium praevalens (isolated from Great Salt Lake, Utah) and Halobacteroides halobius (isolated from the Dead Sea) were found to contain high intracellular potassium concentrations (0.76–2.05 M, not well correlated with the external NaCl concentration), and high intracellular sodium concentrations (0.28–2.6 M, increasing with increasing extracellular NaCl concentration). The sum of intracellular potassium and sodium concentrations approximated the total cation concentration of the medium. Internal chloride concentrations in Haloanaerobium praevalens equalled the external chloride concentration. Organic solutes, such as betaine, glycerol, and different amino acids that have been shown to serve as compatible solutes in other halophilic eubacteria and eukaryotic organisms, were not found in significant concentrations. Analysis of the amino acids in the proteins of the anaerobic halophilic eubacteria showed an excess of acidic amino acids, similar to that reported in halophilic archaebacteria of the genus Halobacterium.

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Ficker, Monica, Kirsten Krastel, Stephen Orlicky, and Elizabeth Edwards. "Molecular Characterization of a Toluene-Degrading Methanogenic Consortium." Applied and Environmental Microbiology 65, no. 12 (December 1, 1999): 5576–85. http://dx.doi.org/10.1128/aem.65.12.5576-5585.1999.

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ABSTRACT A toluene-degrading methanogenic consortium enriched from creosote-contaminated aquifer material was maintained on toluene as the sole carbon and energy source for 10 years. The species in the consortium were characterized by using a molecular approach. Total genomic DNA was isolated, and 16S rRNA genes were amplified by using PCR performed with kingdom-specific primers that were specific for 16S rRNA genes from either members of the kingdom Bacteria or members of the kingdom Archaea. A total of 90 eubacterial clones and 75 archaeal clones were grouped by performing a restriction fragment length polymorphism (RFLP) analysis. Six eubacterial sequences and two archaeal sequences were found in the greatest abundance (in six or more clones) based on the RFLP analysis. The relative abundance of each putative species was estimated by using fluorescent in situ hybridization (FISH), and the presence of putative species was determined qualitatively by performing slot blot hybridization with consortium DNA. Both archaeal species and two of the six eubacterial species were detected in the DNA and FISH hybridization experiments. A phylogenetic analysis of these four dominant organisms suggested that the two archaeal species are related to the generaMethanosaeta and Methanospirillum. One of the eubacterial species is related to the genusDesulfotomaculum, while the other is not related to any previously described genus. By elimination, we propose that the last organism probably initiates the attack on toluene.

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Ramachandran, Kogeethavani, Uyub Abdul Manaf, and Latiffah Zakaria. "Molecular characterization and pathogenicity of Erwinia spp. associated with pineapple [Ananas comosus (L.) Merr.] and papaya (Carica papaya L.)." Journal of Plant Protection Research 55, no. 4 (December 1, 2015): 396–404. http://dx.doi.org/10.1515/jppr-2015-0053.

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AbstractThe Erwinia species are well-known pathogens of economic importance in Malaysia causing serious damage to high-value fruit crops that include pineapple [Ananas comosus (L.) Merr.] and papaya (Carica papaya L.).The 16S rRNA sequence using eubacteria fD1 and rP2 primers, identified two bacteria species; Dickeya zeae from pineapple heart rot, and Erwinia mallotivora from papaya dieback. Phylogenetic analysis based on the neighbor-joining method indicated that all the bacterial isolates clustered in their own taxa and formed monophyletic clades. From the pathogenicity test, all isolates of D. zeae and E. mallotivora showed pathogenic reactions on their respective host plants. Genetic variability of these isolates was assessed using repetitive sequence-based PCR (rep-PCR) fingerprinting. The results indicated interspecies, and intraspecies variation in both species’ isolates. There were more polymorphic bands shown by rep-PCR fingerprints than enterobacterial repetitive intergenic consensus (ERIC) and BOX- PCRs, however both species’ isolates produced distinguishable banding patterns. Unweighted pair-group method with arithmetic averages (UPGMA) cluster analysis indicated that all Dickeya and Erwinia isolates from the same species were grouped in the same main cluster. Similarity among the isolates ranged from 77 to 99%. Sequencing of 16S rRNA using eubacteria fD1 and rP2 primers, and rep-PCR fingerprinting revealed diversity among Dickeya and Erwinia isolates. But this method appears to be reliable for discriminating isolates from pineapple heart rot and papaya dieback.

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Kutty, Razia, Hemant J. Purohit, and Purushottam Khanna. "Isolation and characterization of aPseudomonassp. strain PH1 utilizing meta-aminophenol." Canadian Journal of Microbiology 46, no. 3 (March 1, 2000): 211–17. http://dx.doi.org/10.1139/w99-132.

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Pseudomonas sp. strain PH1 was isolated from soil contaminated with pharmaceutical and dye industry waste. The isolate PH1 could use m-aminophenol as a sole source of carbon, nitrogen, and energy to support the growth. PH1 could degrade up to 0.32 mM m-aminophenol in 120 h, when provided as nitrogen source at 0.4 mM concentration with citrate (0.5 mM) as a carbon source in the growth medium. The presence of ammonium chloride as an additional nitrogen source repressed the degradation of m-aminophenol by PH1. To identify strain PH1, the 16S rDNA sequence was amplified by PCR using conserved eubacterial primers. The FASTA program was used to analyze the 16S rDNA sequence and the resulting homology patterns suggested that PH1 is a Pseudomonas.Key words: m-aminophenol, resorcinol, DNA sequencing.

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Herles, Claudia, Annett Braune, and Michael Blaut. "First bacterial chalcone isomerase isolated from Eubacterium ramulus." Archives of Microbiology 181, no. 6 (June 1, 2004): 428–34. http://dx.doi.org/10.1007/s00203-004-0676-2.

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Davis, J. E., L. P. Jones, and J. E. Zajic. "Heterotrophic eubacteria isolated from cultures of the cyanobacterium, spirulina maxima." Acta Biotechnologica 10, no. 1 (1990): 99–104. http://dx.doi.org/10.1002/abio.370100124.

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Wang, Yu-Jen, Sung-Chou Li, Wei-Chen Lin, and Fu-Chin Huang. "Intracellular Microbiome Profiling of the Acanthamoeba Clinical Isolates from Lens Associated Keratitis." Pathogens 10, no. 3 (February 25, 2021): 266. http://dx.doi.org/10.3390/pathogens10030266.

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Acanthamoeba act as hosts for various microorganisms and pathogens, causing Acanthamoeba Keratitis (AK). To investigate the association between endosymbionts and AK progression, we performed a metagenomics study to characterize the intracellular microbiome from five lenses associated with AK isolates and standard strains to characterize the role of ocular flora in AK progression. The used clinical isolates were axenic cultured from lenses associated with AK patients. AK isolates and standard controls such as 16S ribosomal RNA sequencing techniques were used for analysis. The microbiome compositions and relative abundance values were compared. The orders of Clostridiales and Bacteroidales presented major populations of intracellular microbes belonging to all isolates. Comparison of the different source isolates showed that most of the abundance in keratitis isolates came from Ruminococcus gnavus (121.0 folds), Eubacterium dolichum (54.15 folds), Roseburia faecis (24.51 folds), and Blautia producta (3.15 folds). Further analysis of the relative abundance data from keratitis isolates showed that Blautia producta was positively correlated with the disease course. In contrast, Bacteroides ovatus was found to be abundant in early-stage keratitis isolates. This study reveals the abundant anaerobic Gram-positive rods present in severe keratitis isolate and characterize the association between Acanthamoeba and ocular flora in AK progression.

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DOWNES, JULIA, MARK A. MUNSON, DAVID A. SPRATT, EIJA KONONEN, EVELIINA TARKKA, HANNELE JOUSIMIES-SOMER, and WILLIAM G. WADE. "Characterisation of Eubacterium-like strains isolated from oral infections." Journal of Medical Microbiology 50, no. 11 (November 1, 2001): 947–51. http://dx.doi.org/10.1099/0022-1317-50-11-947.

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Uematsu, H., F. Nakazawa, T. Ikeda, and E. Hoshino. "Eubacterium saphenus sp. nov., Isolated from Human Periodontal Pockets." International Journal of Systematic Bacteriology 43, no. 2 (April 1, 1993): 302–4. http://dx.doi.org/10.1099/00207713-43-2-302.

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UEMATSU, H., F. NAKAZAWA, T. IKEDA, and E. HOSHINO. "Eubacterium saphenus sp. nov., Isolated from Human Periodontal Pockets." International Journal of Systematic Bacteriology 43, no. 4 (October 1, 1993): 867. http://dx.doi.org/10.1099/00207713-43-4-867a.

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POCO, S. E., F. NAKAZAWA, M. SATO, and E. HOSHINO. "Eubacterium minutum sp. nov., Isolated from Human Periodontal Pockets." International Journal of Systematic Bacteriology 46, no. 1 (January 1, 1996): 31–34. http://dx.doi.org/10.1099/00207713-46-1-31.

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POCO, S. E., F. NAKAZAWA, T. IKEDA, M. SATO, T. SATO, and E. HOSHINO. "Eubacterium exiguum sp. nov., Isolated from Human Oral Lesions." International Journal of Systematic Bacteriology 46, no. 4 (October 1, 1996): 1120–24. http://dx.doi.org/10.1099/00207713-46-4-1120.

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IRSCHIK, HERBERT, ROLF JANSEN, KLAUS GERTH, GERHARDT HÖFLE, and HANS REICHENBACH. "The sorangicins, novel and powerful inhibitors of eubacterial RNA polymerase isolated from myxobacteria." Journal of Antibiotics 40, no. 1 (1987): 7–13. http://dx.doi.org/10.7164/antibiotics.40.7.

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34

Hedberg, Maria E., Edward R. B. Moore, Liselott Svensson-Stadler, Per Hörstedt, Vladimir Baranov, Olle Hernell, Sun Nyunt Wai, Sten Hammarström, and Marie-Louise Hammarström. "Lachnoanaerobaculum gen. nov., a new genus in the Lachnospiraceae : characterization of Lachnoanaerobaculum umeaense gen. nov., sp. nov., isolated from the human small intestine, and Lachnoanaerobaculum orale sp. nov., isolated from saliva, and reclassification of Eubacterium saburreum (Prévot 1966) Holdeman and Moore 1970 as Lachnoanaerobaculum saburreum comb. nov." International Journal of Systematic and Evolutionary Microbiology 62, Pt_11 (November 1, 2012): 2685–90. http://dx.doi.org/10.1099/ijs.0.033613-0.

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Two novel obligately anaerobic, Gram-stain-positive, saccharolytic and non-proteolytic spore-forming bacilli (strains CD3 : 22T and N1T) are described. Strain CD3 : 22T was isolated from a biopsy of the small intestine of a child with coeliac disease, and strain N1T from the saliva of a healthy young man. The cells of both strains were observed to be filamentous, approximately 5 to >20 µm long, some of them curving and with swellings. The novel organisms produced H2S, NH3, butyric acid and acetic acid as major metabolic end products. Phylogenetic analyses, based on comparative 16S rRNA gene sequencing, revealed close relationships (98 % sequence similarity) between the two isolates, as well as the type strain of Eubacterium saburreum and four other Lachnospiraceae bacterium-/ E. saburreum -like organisms. This group of bacteria were clearly different from any of the 19 known genera in the family Lachnospiraceae . While Eubacterium species are reported to be non-spore-forming, reanalysis of E. saburreum CCUG 28089T confirmed that the bacterium is indeed able to form spores. Based on 16S rRNA gene sequencing, phenotypic and biochemical properties, strains CD3 : 22T and N1T represent novel species of a new and distinct genus, named Lachnoanaerobaculum gen. nov., in the family Lachnospiraceae [within the order Clostridiales , class Clostridia , phylum Firmicutes ]. Strain CD3 : 22T ( = CCUG 58757T = DSM 23576T) is the type strain of the type species, Lachnoanaerobaculum umeaense gen. nov., sp. nov., of the proposed new genus. Strain N1T ( = CCUG 60305T = DSM 24553T) is the type strain of Lachnoanaerobaculum orale sp. nov. Moreover, Eubacterium saburreum is reclassified as Lachnoanaerobaculum saburreum comb. nov. (type strain CCUG 28089T = ATCC 33271T = CIP 105341T = DSM 3986T = JCM 11021T = VPI 11763T).

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Olsen, M. A., A. S. Blix, THA Utsi, W. Sørmo, and S. D. Mathiesen. "Chitinolytic bacteria in the minke whale forestomach." Canadian Journal of Microbiology 46, no. 1 (December 17, 1999): 85–94. http://dx.doi.org/10.1139/w99-112.

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Minke whales consume large amounts of pelagic crustaceans. Digestion of the prey is initiated by indigenous bacteria in a rumen-like forestomach system. A major structural component of the crustacean exoskeleton is chitin, the β-1,4-linked polymer of N-acetyl-D-glucosamine. The exoskeletons appear to dissolve completely in the non-glandular forestomach. Bacteria in the forestomach fluid of six krill-eating minke whales were enumerated and isolated using an anaerobic habitat-simulating culture medium. Median viable population densities ranged between 6.0 × 106and 9.9 × 109bacterial cells per mL forestomach fluid. Bacterial isolates (n = 44) cultured from the forestomach fluid of one minke whale mainly resembled strains of Eubacterium (25%),Streptococcus (18%), Clostridium (14%), and Bacteroides (11%). As much as 12% of the bacterial isolates were chitinolytic, while β-N-acetylglucosaminidase activity was demonstrated in 54% of the isolates, and utilisation of N-acetyl-D-glucosamine was observed in 73%. The chitinolytic isolates resembled strains of Bacteroides, Bacteroidaceae, Clostridium, and Streptococcus. Scanning and transmission electron microscopy of partly digested krill from the minke whale forestomach revealed bacteria close to and inside the chitinous exoskeleton. The bacterial chitinase may act on the chitinous crustacean exoskeletons, thereby allowing other bacteria access to the nutritious soft inner tissues of the prey, and thus initiating its degradation and fermentation.Key words: chitinase, β-N-acetylglucosaminidase, cetacea, symbiotic microbial digestion.

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Sumarlin, La Ode, Farida Ariyanti, Megga Ratnasari Pikoli, Anna Muawanah, and Meyliana Wulandari. "Isolation and Characterization of Cellulolytic Bacteria During Natural Fermentation of Sweet Orange Peel Waste (Citrus sinensis)." Al-Kauniyah: Jurnal Biologi 15, no. 2 (October 31, 2022): 298–308. http://dx.doi.org/10.15408/kauniyah.v15i2.23357.

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Abstract Orange peel is one of organic waste which contains fibers, such as cellulose and hemicellulose utilized by cellulolytic microorganisms as growth media in the fermentation process. Cellulolytic microorganisms are widely used in many industries. This research will observe the profile of bacterial colonies, particularly cellulosic bacteria, during the fermentation of orange peels (Citrus sinensis). Fermentation was carried out during the research process; the bacteria were further isolated in Carboxymethyl Cellulose (CMC) media. The fermentation process was performed for 14 weeks where sampling on the first week was done every day for five days (H0–H4), while sampling from the 2nd to 14th weeks were conducted once a week (M2–M14). The isolation process was carried out in a Nutrient Agar medium with spreading method by calculating the Total Plate Count (TPC) of bacterial colonies and observing the macroscopic morphology of bacterial colonies. Bacterial counts are expressed in Colony Forming Units (CFU)/mL or viable count/mL. The identification of bacterial genus was based on the Bergey's Manual of Determinative Bacteriology. Bacterial isolation from the fermentation of sweet orange peel resulted in 20 isolates where 16 isolates were found to be cellulolytic bacteria through qualitative test in Carboxymethyl Cellulose (CMC) agar plate. The hypothetic genus of 16 bacterial isolates were Eubacterium, Cellulomonas, Microbacterium, Micrococcus, Planococcus, Pseudomonas, Azotobacter, Azomonas, Flavobacterium, Cytophaga, and Jonesia. Isolate F15 (Cytophaga and Azomonas) was found to dominate the growth, while other isolates grew alternately with lesser frequency. Hypothetic genus of bacteria actively involved in the process were cellulolytic bacteria, allowing the liquid of fermentation products to be possibly used in the application.AbstrakKulit jeruk merupakan salah satu limbah organik yang mengandung serat seperti selulosa dan hemiselulosa yang dapat dimanfaatkan oleh mikroorganisme selulolitik sebagai media pertumbuhan dalam proses fermentasi. Mikroorganisme selulolitik telah digunakan di banyak industri. Penelitian ini mengamati profil koloni bakteri selama proses fermentasi kulit jeruk terutama bakteri selulotik. Selama proses penelitian dilakukan proses fermentasi, lalu bakteri diisolasi menggunakan media Carboxyl Methyl Callulose (CMC). Proses fermentasi dilakukan selama 14 minggu dengan rincian sampling pada Minggu ke-1 dilakukan setiap hari selama 5 hari (H0–H4), sedangkan minggu ke-2 hingga 14 dilakukan setiap seminggu sekali (M2–M14). Proses isolasi dilakukan dalam medium Nutrient Agar dengan teknik sebar dengan perhitungan koloni Total Plate Count (TPC) dan pengamatan morfologi koloni bakteri secara makroskopis. Hasil perhitungan bakteri dinyatakan dalam Colony Forming Units (CFU)/mL atau viabel count/mL. Pendugaan genus bakteri berdasarkan Bergey's Manual of Determinative Bacteriology. Hasil isolasi bakteri dari fermentasi kulit jeruk manis adalah 20 isolat yang 16 di antaranya merupakan bakteri selulolitik melalui uji kualitatif pada media plat Carboxymethyl Cellulose (CMC). Genus hipotetik bakteri dari 16 isolat adalah Eubacterium, Cellulomonas, Microbacterium, Micrococcus, Planococcus, Pseudomonas, Azotobacter, Azomonas, Flavobacterium, Cytophaga, dan Jonesia. Isolat F15 (Cytophaga dan Azomonas) mendominasi pertumbuhan, sedangkan isolat lain tumbuh berselang seling dengan frekuensi yang lebih kecil. Genus bakteri hipotetik yang terlibat aktif adalah bakteri selulolitik sehingga cairan hasil fermentasi dapat digunakan dalam aplikasi.

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McBain, Andrew J., Robert G. Bartolo, Carl E. Catrenich, Duane Charbonneau, Ruth G. Ledder, Alexander H. Rickard, Sharon A. Symmons, and Peter Gilbert. "Microbial Characterization of Biofilms in Domestic Drains and the Establishment of Stable Biofilm Microcosms." Applied and Environmental Microbiology 69, no. 1 (January 2003): 177–85. http://dx.doi.org/10.1128/aem.69.1.177-185.2003.

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ABSTRACT We have used heterotrophic plate counts, together with live-dead direct staining and denaturing gradient gel electrophoresis (DGGE), to characterize the eubacterial communities that had formed as biofilms within domestic sink drain outlets. Laboratory microcosms of these environments were established using excised biofilms from two separate drain biofilm samples to inoculate constant-depth film fermentors (CDFFs). Drain biofilms harbored 9.8 to 11.3 log10 cells of viable enteric species and pseudomonads/g, while CDFF-grown biofilms harbored 10.6 to 11.4 log10 cells/g. Since live-dead direct staining revealed various efficiencies of recovery by culture, samples were analyzed by DGGE, utilizing primers specific for the V2-V3 region of eubacterial 16S rDNA. These analyses showed that the major PCR amplicons from in situ material were represented in the microcosms and maintained there over extended periods. Sequencing of amplicons resolved by DGGE revealed that the biofilms were dominated by a small number of genera, which were also isolated by culture. One drain sample harbored the protozoan Colpoda maupasi, together with rhabtidid nematodes and bdelloid rotifers. The microcosm enables the maintenance of stable drain-type bacterial communities and represents a useful tool for the modeling of this ecosystem.

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Begum, Ishrat, Sana Javed, Saima ,. Salman, Kashif Ali Channar, Zafar Iqbal, and Muhammad Muslim Khahro. "Common Microorganisms and Drug Sensitivity in Odontogenic Infection." Pakistan Journal of Medical and Health Sciences 16, no. 1 (January 30, 2022): 1044–46. http://dx.doi.org/10.53350/pjmhs221611044.

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Objective: To determine the frequency of causative microorganisms and drug sensitivity in odontogenic infection. Methodology: This cross-sectional study was done at the department of Oral and maxillofacial surgery of Liaquat University Hospital Hyderabad, during six months from August 2018 to January 2019). All subjects of 12 to 50 years of age, either gender with odontogenic infections were included. Pus was collected by transport media/swab stick and sent to the Hospital diagnostic laboratory for culture and antibiotic susceptibility, while the antibiotic sensitivity test for the isolates was performed, whereas the data was collected on pre-designed proforma and analyzed by SPSS version 26. Results: A total of 200 patients with odontogenic infection of either gender were studied. Mean age of these cases was 51.94±8.93 years and males were in majority 63.5%. The causative microorganism includes Staphylococcus species 24.5%, Streptococcus 22.0%, Pseudomonas aeruginosa 16.0%, eubacterium 13.5%, Porphyromonas 10.5%, Prevotella 6.5%, and Fusobacterium 7.0%, while drug sensitivity includes Ampicillin 33.5%, amikacin 24.5%, Gentamicin 17.0%, Cefotaxime 14.5% and ceftazidime 10.5%. Frequency of causative microorganisms was statistically significant according to gender (p <0.05), while insignificant according to age (P->0.05). Conclusion: As per study conclusion the staphylococcus species, streptococcus, Pseudomonas aeruginosa, eubacterium, Porphyromonas Prevotella and fusobacterium were observed to be the causative organisms in odontogenic infection. Ampicillin was the highly sensitive antibiotic drug followed by amikacin, gentamicin, cefotaxime and ceftazidime. Odontogenic infection cultures are necessary to isolate all pathogens and for successful management. Key words: Odontogenic infections, Microorganism, antibiotic sensitivity

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Duncan, Sylvia H., Petra Louis, and Harry J. Flint. "Lactate-Utilizing Bacteria, Isolated from Human Feces, That Produce Butyrate as a Major Fermentation Product." Applied and Environmental Microbiology 70, no. 10 (October 2004): 5810–17. http://dx.doi.org/10.1128/aem.70.10.5810-5817.2004.

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ABSTRACT The microbial community of the human colon contains many bacteria that produce lactic acid, but lactate is normally detected only at low concentrations (<5 mM) in feces from healthy individuals. It is not clear, however, which bacteria are mainly responsible for lactate utilization in the human colon. Here, bacteria able to utilize lactate and produce butyrate were identified among isolates obtained from 10−8 dilutions of fecal samples from five different subjects. Out of nine such strains identified, four were found to be related to Eubacterium hallii and two to Anaerostipes caccae, while the remaining three represent a new species within clostridial cluster XIVa based on their 16S rRNA sequences. Significant ability to utilize lactate was not detected in the butyrate-producing species Roseburia intestinalis, Eubacterium rectale, or Faecalibacterium prausnitzii. Whereas E. hallii and A. caccae strains used both d- and l-lactate, the remaining strains used only the d form. Addition of glucose to batch cultures prevented lactate utilization until the glucose became exhausted. However, when two E. hallii strains and one A. caccae strain were grown in separate cocultures with a starch-utilizing Bifidobacterium adolescentis isolate, with starch as the carbohydrate energy source, the l-lactate produced by B. adolescentis became undetectable and butyrate was formed. Such cross-feeding may help to explain the reported butyrogenic effect of certain dietary substrates, including resistant starch. The abundance of E. hallii in particular in the colonic ecosystem suggests that these bacteria play important roles in preventing lactate accumulation.

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Abdulla, Dr Ahmad Hayder, Dr Lukmman F. Omar, and Dr Haween T. Hassan. "dentification and Antimicrobial Susceptibility of Bacterial Isolates from Odontogenic Abscesses." Mustansiria Dental Journal 5, no. 4 (January 25, 2018): 422–28. http://dx.doi.org/10.32828/mdj.v5i4.570.

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Objective: The purpose of the study was to identify the bacterial composition of the microbiota from odontogenic abscesses and their antimicrobial susceptibilities.Study Design: An aspirate of pus from 37 patients with odontogenic abscesses was obtained by needle aspiration and processed aerobically and under anaerobic conditions. Bacteria were isolated and identified by standard Laboratory methods. Then antimicrobial susceptibility of isolated bacteria was determined by using disc diffusion method.Results: Out of 37 aspirates, 100% yielded positive culture, 34 aspirates contained a mix of microorganisms. A total of 90 strains of bacteria were isolated.Out of 90 strains, 63 strains were anaerobes and 27 strains were aerobes and facultative anaerobes. The mean number of strains per sample was 2.4, two samples were purely anaerobes, 9 samples were mixed anaerobes, 2 samples were purely facultative anaerobes, no purely aerobic, 17 had mixed growth of anaerobes and facultative anaerobes, and 7 samples had mixed growth of aerobes and facultative anaerobic bacteria. Out of 90 isolates, 42 (46.67%) were Gram-positive cocci, 25 (27.78%) were Gram-positive bacilli, 21 (23.33%) were Gram-negative bacilli, and 2 (2.22%) were Candida albicans. The genera of bacteria most frequently isolated were viridans group streptococci, Peptostreptococcus spp., Eubacterium spp., and Prevotella spp. Invitro antibiotic sensitivity of isolated microorganisms were tested for Penicillin, Amoxillin, Ampicillin, Amoxicillin/Clavulanic acid, Erythromycin, and Metronidazole by disc diffusion method. All isolates were sensitive to Amoxillin+ clavulanic acid: 27/27(100%), followed by Ampicillin: 24/27(88.89%), Amoxillin: 23/27(85.19%), Penicillin: 22/27(81.48%), Erythromycin: 12/27(44.44%), and metronidazole: 10/27(37.04%).Conclusions: The present results confirm the existence of mixed infection with predominance of anaerobic and facultative anaerobic bacteria in odontogenic abscesses. Penicillin still possesses antimicrobial activity against the majority of bacteria isolated from odontogenic infections. However, if penicillin therapy has failed to be effective, the combination of penicillin with ampicillin or amoxillin with clavulanic acid is recommended.

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Stepanov, V. M., G. N. Rudenskaya, L. P. Revina, Y. B. Gryaznova, E. N. Lysogorskaya, Filippova IYu, and I. I. Ivanova. "A serine proteinase of an archaebacterium, Halobacterium mediterranei. A homologue of eubacterial subtilisins." Biochemical Journal 285, no. 1 (July 1, 1992): 281–86. http://dx.doi.org/10.1042/bj2850281.

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A homogeneous serine proteinase secreted by the extreme halophilic bacterium Halobacterium mediterranei 1538 was isolated by affinity chromatography on bacitracin-Sepharose with a yield of 48% (260-fold purification). The enzyme reveals an optimum for pyroglutamyl-Ala-Ala-Leu p-nitroanilide hydrolysis at pH 8.0-8.5 (Km 0.14 mM; k(cat). 36.9 s-1). Its activity increases linearly with NaCl concentration over the range 2-5 M. The substrate specificity of the enzyme is comparable with that of secretory subtilisins, the extent of protein degradation approaching that attained with proteinase K. The enzyme has a molecular mass of 41 kDa and a pI of 7.5. The N-terminal sequence of H. mediterranei serine proteinase reveals a 50% identity with that of Thermoactinomyces vulgaris serine proteinases, indicating that the enzyme belongs to the subtilisin family. Hence the serine proteinase secreted by the halophilic bacterium should be considered as a functional analogue, and a structural homologue, of eubacterial serine proteinases (subtilisins).

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HOFSTAD, TOR. "IMMUNOCHEMISTRY OF A CELL WALL POLYSACCHARIDE ISOLATED FROM EUBACTERIUM SABURREUM, STRAIN L49." Acta Pathologica Microbiologica Scandinavica Section B Microbiology 83B, no. 5 (August 15, 2009): 471–76. http://dx.doi.org/10.1111/j.1699-0463.1975.tb00127.x.

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Wells, James E., and Phillip B. Hylemon. "Identification and Characterization of a Bile Acid 7α-Dehydroxylation Operon in Clostridium sp. Strain TO-931, a Highly Active 7α-Dehydroxylating Strain Isolated from Human Feces." Applied and Environmental Microbiology 66, no. 3 (March 1, 2000): 1107–13. http://dx.doi.org/10.1128/aem.66.3.1107-1113.2000.

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ABSTRACT Clostridium sp. strain TO-931 can rapidly convert the primary bile acid cholic acid to a potentially toxic compound, deoxycholic acid. Mixed oligonucleotide probes were used to isolate a gene fragment encoding a putative bile acid transporter fromClostridium sp. strain TO-931. This DNA fragment had 60% nucleotide sequence identity to a known bile acid transporter gene fromEubacterium sp. strain VPI 12708, another bile acid-7α-dehydroxylating intestinal bacterium. The DNA (9.15 kb) surrounding the transporter gene was cloned fromClostridium sp. strain TO-931 and sequenced. Within this larger DNA fragment was a 7.9-kb region, containing six successive open reading frames (ORFs), that was encoded by a single 8.1-kb transcript, as determined by Northern blot analysis. The gene arrangement and DNA sequence of the Clostridium sp. strain TO-931 operon are similar to those of a Eubacterium sp. strain VPI 12708 bile acid-inducible operon containing nine ORFs. Several genes in theEubacterium sp. strain VPI 12708 operon have been shown to encode products required for bile acid 7α-dehydroxylation. InClostridium sp. strain TO-931, genes potentially encoding bile acid-coenzyme A (CoA) ligase, 3α-hydroxysteroid dehydrogenase, bile acid 7α-dehydratase, bile acid-CoA hydrolase, and a bile acid transporter were similar in size and exhibited amino acid homology to similar gene products from Eubacterium sp. strain VPI 12708 (encoded by baiB, baiA, baiE,baiF, and baiG, respectively). However, no genes similar to Eubacterium sp. strain VPI 12708biaH or baiI were found in theClostridium sp. strain TO-931 bai operon, and the two putative Eubacterium sp. strain VPI 12708 genes,baiC and baiD, were arranged in one continuous ORF in Clostridium sp. strain TO-931. Intergene regions showed no significant DNA sequence similarity, but primer extension analysis identified a region 115 bp upstream from the first ORF that exhibited 58% identity to a bai operator/promoter region identified in Eubacterium sp. strain VPI 12708. These results indicate that the gene organization, gene product amino acid sequences, and promoters of the bile acid-inducible operons ofClostridium sp. strain TO-931 and Eubacteriumsp. strain VPI 12708 are highly conserved.

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Jeong, Hyunyoung, Young Woon Lim, Hana Yi, Yuji Sekiguchi, Yoichi Kamagata, and Jongsik Chun. "Anaerosporobacter mobilis gen. nov., sp. nov., isolated from forest soil." International Journal of Systematic and Evolutionary Microbiology 57, no. 8 (August 1, 2007): 1784–87. http://dx.doi.org/10.1099/ijs.0.63283-0.

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A strictly anaerobic, Gram-positive, endospore-forming bacterium, strain HY-37-4T, was isolated from a forest-soil sample collected in Jeju, Republic of Korea. The cells were motile rods with peritrichous flagella. Strain HY-37-4T fermented various carbohydrates and the end products from glucose were formate, acetate and H2. The major cellular fatty acids were C16 : 0, C16 : 0 3-OH and iso-C17 : 1 I/anteiso B. The G+C content of the DNA was 41 mol%. A phylogenetic analysis based on 16S rRNA sequence data indicated that the forest isolate was most closely related to Clostridium herbivorans, Clostridium populeti, Clostridium polysaccharolyticum and Eubacterium xylanophilum, which belong to Clostridium cluster XIVa. However, the low levels of 16S rRNA gene sequence similarity (92.3–93.9 %) with respect to these taxa indicate that strain HY-37-4T represents a novel species. Several phenotypic characteristics readily allowed the isolate to be distinguished from other phylogenetically related taxa. On the basis of the polyphasic evidence, strain HY-37-4T represents a novel taxon, for which the name Anaerosporobacter mobilis gen. nov., sp. nov. is proposed. The type strain is HY-37-4T (=IMSNU 40011T=KCTC 5027T=DSM 15930T).

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Darwis, Welly, Annisa Prastika Supriyanto, Risky Hadi Wibowo, Sipriyadi Sipriyadi, and Rochmah Supriati. "Endophytic Bacteria Identification of Red Ginger (Zingiber officinale var. Rubrum) From Enggano Island." Elkawnie 8, no. 1 (June 30, 2022): 119. http://dx.doi.org/10.22373/ekw.v8i1.11498.

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Abstract: Endophytic bacteria are bacteria associated with the tissues of healthy plants that are beneficial. Almost every higher plant has some endophytic bacteria, one of which is Red Ginger (Zingiber officinale var. Rubrum) from Enggano Island. This research aims to obtain endophytic bacteria and to identify the Red Ginger (Zingiber officinale var. Rubrum) endophytic bacteria collected from Enggano Island. Endophyte bacteria isolation was carried out by the paste method on medium Nutrient Agar (NA) after sterilizing the surface of plant organs using alcohol and sodium hypochlorite 5,25%. A total of 24 isolates of endophytic bacteria of Red Ginger (Zingiber officinale var. Rubrum) were isolated from rhizomes (stem modification), leaf sheath, and leaf sheet. Endophytic bacteria were identified based on morphological observation, biochemical tests, and Gram-staining. As a result, the diversity of bacteria consists of 7 genera, namely the genus Bacillus, Sporosarcina, Amphibacillus, Azotobacter, Eubacterium, Pimelobacter, and Micrococcus. The genus Bacillus consists of 4 species, the genus Sporosarcina consists of 6 species, the genus Amphibacillus consists of 1 species, the genus Azotobacter consists of 2 species, the genus Eubacterium consists of 1 species, the genus Pimelobacter consists of 1 species, and the genus Micrococcus which also consists of 1 species. Bacillus is the most common type of endophytic bacteria that was found in red ginger from Enggano Island.Abstrak: Bakteri endofit adalah bakteri yang berasosiasi dengan jaringan tanaman yang memiliki banyak manfaat, baik bagi manusia maupun tumbuhan itu sendiri. Hampir setiap tumbuhan tingkat tinggi memiliki beberapa bakteri endofit, salah satunya jahe merah (Zingiber officinale var. Rubrum) yang berasal dari Pulau Enggano. Penelitian ini bertujuan untuk mendapatkan bakteri endofit dan mengetahui keanekaragaman bakteri endofit yang diisolasi dari jahe merah (Zingiber officinale var. Rubrum) asal Pulau Enggano. Isolasi bakteri endofit dilakukan dengan metode tempel pada media Nutrient Agar (NA) setelah dilakukan sterilisasi permukaan organ tanaman menggunakan alkohol dan natrium hipoklorit 5,25%. Sebanyak 24 isolat bakteri endofit jahe merah (Zingiber officinale var. Rubrum) diisolasi dari rimpang (modifikasi batang), pelepah daun, dan helaian daun. Bakteri endofit diidentifikasi berdasarkan pengamatan morfologi, uji biokimia, dan pewarnaan Gram. Hasilnya, keanekaragaman bakteri terdiri dari 7 genus, yaitu Bacillus, Sporosarcina, Amphibacillus, Azotobacter, Eubacterium, Pimelobacter, dan Micrococcus. Genus Bacillus terdiri dari 4 spesies, genus Sporosarcina terdiri dari 6 spesies, genus Amphibacillus terdiri dari 1 spesies, genus Azotobacter terdiri dari 2 spesies, genus Eubacterium terdiri dari 1 spesies, genus Pimelobacter terdiri dari 1 spesies, dan genus Micrococcus yang juga terdiri dari 1 spesies. Bacillus merupakan genus yang mendominasi keanekaragaman bakteri endofit yang diisolasi dari jahe merah asal Pulau Enggano.

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IRSCHIK, HERBERT, HERMANN AUGUSTINIAK, KLAUS GERTH, GERHARD HÖFLE, and HANS REICHENBACH. "Antibiotics from gliding bacteria. No. 68. The Ripostatins, Novel Inhibitors of Eubacterial RNA Polymerase Isolated from Myxobacteria." Journal of Antibiotics 48, no. 8 (1995): 787–92. http://dx.doi.org/10.7164/antibiotics.48.787.

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Ehrenshaft, Marilyn, and Margaret E. Daub. "Isolation of PDX2, a Second Novel Gene in the Pyridoxine Biosynthesis Pathway of Eukaryotes, Archaebacteria, and a Subset of Eubacteria." Journal of Bacteriology 183, no. 11 (June 1, 2001): 3383–90. http://dx.doi.org/10.1128/jb.183.11.3383-3390.2001.

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ABSTRACT In this paper we describe the isolation of a second gene in the newly identified pyridoxine biosynthesis pathway of archaebacteria, some eubacteria, fungi, and plants. Although pyridoxine biosynthesis has been thoroughly examined in Escherichia coli, recent characterization of the Cercospora nicotianae biosynthesis gene PDX1 led to the discovery that most organisms contain a pyridoxine synthesis gene not found in E. coli. PDX2was isolated by a degenerate primer strategy based on conserved sequences of a gene specific to PDX1-containing organisms. The role of PDX2 in pyridoxine biosynthesis was confirmed by complementation of two C. nicotianae pyridoxine auxotrophs not mutant in PDX1. Also, targeted gene replacement of PDX2 in C. nicotianae results in pyridoxine auxotrophy. Comparable to PDX1, PDX2 homologues are not found in any of the organisms with homologues to theE. coli pyridoxine genes, but are found in the same archaebacteria, eubacteria, fungi, and plants that containPDX1 homologues. PDX2 proteins are less well conserved than their PDX1 counterparts but contain several protein motifs that are conserved throughout all PDX2 proteins.

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Millard, James, Alexander Agius, Ying Zhang, Philippe Soucaille, and Nigel Peter Minton. "Exploitation of a Type 1 Toxin–Antitoxin System as an Inducible Counter-Selective Marker for Genome Editing in the Acetogen Eubacterium limosum." Microorganisms 11, no. 5 (May 10, 2023): 1256. http://dx.doi.org/10.3390/microorganisms11051256.

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Targeted mutations in the anaerobic methylotroph Eubacterium limosum have previously been obtained using CRISPR-based mutagenesis methods. In this study, a RelB-family toxin from Eubacterium callanderi was placed under the control of an anhydrotetracycline-sensitive promoter, forming an inducible counter-selective system. This inducible system was coupled with a non-replicative integrating mutagenesis vector to create precise gene deletions in Eubacterium limosum B2. The genes targeted in this study were those encoding the histidine biosynthesis gene hisI, the methanol methyltransferase and corrinoid protein mtaA and mtaC, and mtcB, encoding an Mttb-family methyltransferase which has previously been shown to demethylate L-carnitine. A targeted deletion within hisI brought about the expected histidine auxotrophy, and deletions of mtaA and mtaC both abolished autotrophic growth on methanol. Deletion of mtcB was shown to abolish the growth of E. limosum on L-carnitine. After an initial selection step to isolate transformant colonies, only a single induction step was required to obtain mutant colonies for the desired targets. The combination of an inducible counter-selective marker and a non-replicating integrative plasmid allows for quick gene editing of E. limosum.

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Ambrožič Dolinšek, Jana, Maja Ravnikar, Jana Žel, Tina Demšar, Marjana Camloh, Katarina Cankar, and Taja Dreo. "Tissue culture of Pyrethrum (Tanacetum cinerariifolium) and associated microbial contamination." Acta Biologica Slovenica 53, no. 1 (July 1, 2010): 63–68. http://dx.doi.org/10.14720/abs.53.1.15369.

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Microbial contamination was observed on several subcultures of Pyrethrum (Tanacetum cinerariifolium) (Trevir.) Schultz-bip. callus lines. The presence of microorganisms- sms was detected by isolation of contaminants in pure culture from 7 out of 34 callus lines and direct ampliication of eubacterial 16S rDNA in the pyrethrum callus and plants and isolated bacteria. Altogether 16 contaminants were further analyzed, observing their morphology on several media and restriction of ampliied 16S rDNA. Analysis revealed presence and persistence of morphologically and genetically diverse bacteria in pyrethrum tissue culture. Due to cross-reactivity of 16S rDNA primers with DNA of plant origin, no conclusions could be drawn on the origin of contaminants.

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IRSCHIK, H., H. AUGUSTINIAK, K. GERTH, G. HOEFLE, and H. REICHENBACH. "ChemInform Abstract: Antibiotics from Gliding Bacteria. Part 68. Ripostatins, Novel Inhibitors of Eubacterial RNA Polymerase Isolated from Myxobacteria." ChemInform 27, no. 4 (August 12, 2010): no. http://dx.doi.org/10.1002/chin.199604271.

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Journal articles on the topic 'Eubacterial isolates'

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