Characterization of gtf, a Glucosyltransferase Gene in the Genomes of Pediococcus parvulus and Oenococcus oeni, Two Bacterial Species Commonly Found in Wine

ABSTRACT “Ropiness” is a bacterial alteration in wines, beers, and ciders, caused by β-glucan-synthesizing pediococci. A single glucosyltransferase, Gtf, controls ropy polysaccharide synthesis. In this study, we show that the corresponding gtf gene is also present on the chromosomes of several strains of Oenococcus oeni isolated from nonropy wines. gtf is surrounded by mobile elements that may be implicated in its integration into the chromosome of O. oeni. gtf is expressed in all the gtf + strains, and β-glucan is detected in the majority of these strains. Part of this β-glucan accumulates around the cells forming a capsule, while the other part is liberated into the medium together with heteropolysaccharides. Most of the time, this polymer excretion does not lead to ropiness in a model medium. In addition, we show that wild or recombinant bacterial strains harboring a functional gtf gene (gtf +) are more resistant to several stresses occurring in wine (alcohol, pH, and SO2) and exhibit increased adhesion capacities compared to their gtf mutant variants.

Download Full-text

β-Lactamase inhibition profile of new amidine-substituted diazabicyclooctanes

Beilstein Journal of Organic Chemistry ◽

10.3762/bjoc.17.60 ◽

2021 ◽

Vol 17 ◽

pp. 711-718

Author(s):

Zafar Iqbal ◽

Lijuan Zhai ◽

Yuanyu Gao ◽

Dong Tang ◽

Xueqin Ma ◽

...

Keyword(s):

Antibacterial Activity ◽

Second Generation ◽

Bacterial Species ◽

The Other ◽

Inhibition Activity ◽

Bacterial Strains ◽

E Coli ◽

Mic Value

The diazabicyclooctane (DBO) scaffold is the backbone of non-β-lactam-based second generation β-lactamase inhibitors. As part of our efforts, we have synthesized a series of DBO derivatives A1–23 containing amidine substituents at the C2 position of the bicyclic ring. These compounds, alone and in combination with meropenem, were tested against ten bacterial strains for their antibacterial activity in vitro. All compounds did not show antibacterial activity when tested alone (MIC >64 mg/L), however, they exhibited a moderate inhibition activity in the presence of meropenem by lowering its MIC values. The compound A12 proved most potent among the other counterparts against all bacterial species with MIC from <0.125 mg/L to 2 mg/L, and is comparable to avibactam against both E. coli strains with a MIC value of <0.125 mg/L.

Download Full-text

The Expanded Universe of Prokaryotic Argonaute Proteins

mBio ◽

10.1128/mbio.01935-18 ◽

2018 ◽

Vol 9 (6) ◽

Cited By ~ 10

Author(s):

Sergei Ryazansky ◽

Andrey Kulbachinskiy ◽

Alexei A. Aravin

Keyword(s):

Rna Interference ◽

Nucleic Acid ◽

Genome Engineering ◽

Bacterial Species ◽

Host Cells ◽

Bacterial Strains ◽

Domains Of Life ◽

Genomic Studies ◽

Basic Biology

ABSTRACT Members of the ancient family of Argonaute (Ago) proteins are present in all domains of life. The common feature of Ago proteins is the ability to bind small nucleic acid guides and use them for sequence-specific recognition—and sometimes cleavage—of complementary targets. While eukaryotic Ago (eAgo) proteins are key players in RNA interference and related pathways, the properties and functions of these proteins in archaeal and bacterial species have just started to emerge. We undertook comprehensive exploration of prokaryotic Ago (pAgo) proteins in sequenced genomes and revealed their striking diversity in comparison with eAgos. Many pAgos contain divergent variants of the conserved domains involved in interactions with nucleic acids, while having extra domains that are absent in eAgos, suggesting that they might have unusual specificities in the nucleic acid recognition and cleavage. Many pAgos are associated with putative nucleases, helicases, and DNA binding proteins in the same gene or operon, suggesting that they are involved in target processing. The great variability of pAgos revealed by our analysis opens new ways for exploration of their functions in host cells and for their use as potential tools in genome editing. IMPORTANCE The eukaryotic Ago proteins and the RNA interference pathways they are involved in are widely used as a powerful tool in research and as potential therapeutics. In contrast, the properties and functions of prokaryotic Ago (pAgo) proteins have remained poorly understood. Understanding the diversity and functions of pAgos holds a huge potential for discovery of new cellular pathways and novel tools for genome manipulations. Only few pAgos have been characterized by structural or biochemical approaches, while previous genomic studies discovered about 300 proteins in archaeal and eubacterial genomes. Since that time the number of bacterial strains with sequenced genomes has greatly expanded, and many previously sequenced genomes have been revised. We undertook comprehensive analysis of pAgo proteins in sequenced genomes and almost tripled the number of known genes of this family. Our research thus forms a foundation for further experimental characterization of pAgo functions that will be important for understanding of the basic biology of these proteins and their adoption as a potential tool for genome engineering in the future.

Download Full-text

Regulation of Hypercompetence in Legionella pneumophila

Journal of Bacteriology ◽

10.1128/jb.186.12.3814-3825.2004 ◽

2004 ◽

Vol 186 (12) ◽

pp. 3814-3825 ◽

Cited By ~ 57

Author(s):

Jessica A. Sexton ◽

Joseph P. Vogel

Keyword(s):

Legionella Pneumophila ◽

Bacterial Species ◽

Single Species ◽

Great Promise ◽

Dna Uptake ◽

Bacterial Strains ◽

Aerobic Growth ◽

Laboratory Conditions ◽

Normal Laboratory

ABSTRACT Although many bacteria are known to be naturally competent for DNA uptake, this ability varies dramatically between species and even within a single species, some isolates display high levels of competence while others seem to be completely nontransformable. Surprisingly, many nontransformable bacterial strains appear to encode components necessary for DNA uptake. We believe that many such strains are actually competent but that this ability has been overlooked because standard laboratory conditions are inappropriate for competence induction. For example, most strains of the gram-negative bacterium Legionella pneumophila are not competent under normal laboratory conditions of aerobic growth at 37°C. However, it was previously reported that microaerophilic growth at 37°C allows L. pneumophila serogroup 1 strain AA100 to be naturally transformed. Here we report that another L. pneumophila serogroup 1 strain, Lp02, can also be transformed under these conditions. Moreover, Lp02 can be induced to high levels of competence by a second set of conditions, aerobic growth at 30°C. In contrast to Lp02, AA100 is only minimally transformable at 30°C, indicating that Lp02 is hypercompetent under these conditions. To identify potential causes of hypercompetence, we isolated mutants of AA100 that exhibited enhanced DNA uptake. Characterization of these mutants revealed two genes, proQ and comR, that are involved in regulating competence in L. pneumophila. This approach, involving the isolation of hypercompetent mutants, shows great promise as a method for identifying natural transformation in bacterial species previously thought to be nontransformable.

Download Full-text

Characterization of Phascolarctobacterium succinatutens sp. nov., an Asaccharolytic, Succinate-Utilizing Bacterium Isolated from Human Feces

Applied and Environmental Microbiology ◽

10.1128/aem.06035-11 ◽

2011 ◽

Vol 78 (2) ◽

pp. 511-518 ◽

Cited By ~ 95

Author(s):

Yohei Watanabe ◽

Fumiko Nagai ◽

Masami Morotomi

Keyword(s):

Bacterial Species ◽

Short Chain Fatty Acids ◽

Pcr Analysis ◽

Rrna Gene ◽

Gi Tract ◽

Bacterial Strains ◽

High Sequence Identity ◽

Healthy Human ◽

Content Type

ABSTRACTIsolation, cultivation, and characterization of the intestinal microorganisms are important for understanding the comprehensive physiology of the human gastrointestinal (GI) tract microbiota. Here, we isolated two novel bacterial strains, YIT 12067Tand YIT 12068, from the feces of healthy human adults. Phylogenetic analysis indicated that they belonged to the same species and were most closely related toPhascolarctobacterium faeciumACM 3679T, with 91.4% to 91.5% 16S rRNA gene sequence similarities, respectively. Substrate availability tests revealed that the isolates used only succinate; they did not ferment any other short-chain fatty acids or carbohydrates tested. When these strains were cocultured with the xylan-utilizing and succinate-producing bacteriumParaprevotella xylaniphilaYIT 11841T, in medium supplemented with xylan but not succinate, their cell numbers became 2 to 3 orders of magnitude higher than those of the monoculture; succinate became undetectable, and propionate was formed. Database analysis revealed that over 200 uncultured bacterial clones from the feces of humans and other mammals showed high sequence identity (>98.7%) to YIT 12067T. Real-time PCR analysis also revealed that YIT 12067T-like bacteria were present in 21% of human fecal samples, at an average level of 3.34 × 108cells/g feces. These results indicate that YIT 12067T-like bacteria are distributed broadly in the GI tract as subdominant members that may adapt to the intestinal environment by specializing to utilize the succinate generated by other bacterial species. The phylogenetic and physiological properties of YIT 12067Tand YIT 12068 suggest that these strains represent a novel species, which we have designatedPhascolarctobacterium succinatutenssp. nov.

Download Full-text

Combining Culture-Dependent and Independent Approaches for the Optimization of Epoxiconazole and Fludioxonil-Degrading Bacterial Consortia

Microorganisms ◽

10.3390/microorganisms9102109 ◽

2021 ◽

Vol 9 (10) ◽

pp. 2109

Author(s):

Diogo Alexandrino ◽

Ana Mucha ◽

Maria Paola Tomasino ◽

C. Marisa R. Almeida ◽

Maria Carvalho

Keyword(s):

Agricultural Soil ◽

Enrichment Culture ◽

Bacterial Species ◽

The Other ◽

Microbial Consortia ◽

Bacterial Isolates ◽

Bacterial Strains ◽

Bacterial Consortia ◽

First Time ◽

Culture Dependent

Epoxiconazole (EPO) and fludioxonil (FLU) are two widely used fluorinated pesticides known to be highly persistent and with high ecotoxicological potential, turning them into pollutants of concern. This work aimed to optimize two degrading bacterial consortia, previously obtained from an agricultural soil through enrichment with EPO and FLU, by characterizing the contribution of their corresponding bacterial isolates to the biodegradation of these pesticides using both culture-dependent and independent methodologies. Results showed that a co-culture of the strains Hydrogenophaga eletricum 5AE and Methylobacillus sp. 8AE was the most efficient in biodegrading EPO, being able to defluorinate ca. 80% of this pesticide in 28 days. This catabolic performance is likely the result of a commensalistic cooperation, in which H. eletricum may be the defluorinating strain and Methylobacillus sp. may assume an accessory, yet pivotal, catabolic role. Furthermore, 16S rRNA metabarcoding analysis revealed that these strains represent a minority in their original consortium, showing that the biodegradation of EPO can be driven by less abundant phylotypes in the community. On the other hand, none of the tested combinations of bacterial strains showed potential to biodegrade FLU, indicating that the key degrading strains were not successfully isolated from the original enrichment culture. Overall, this work shows, for the first time, the direct involvement of two bacterial species, namely H. eletricum and Methylobacillus sp., in the biodegradation of EPO, while also offering insight on how they might cooperate to accomplish this process. Moreover, the importance of adequate culture-dependent approaches in the engineering of microbial consortia for bioremediation purposes is also emphasized.

Download Full-text

THE IDENTIFICATION, PRODUCTION AND CHARACTERIZATION OF NATTOKINASE, BACTERIOCIN FROM BACTERIAL SPECIES

Bacterial Empire ◽

10.36547/be.2019.2.4.91-95 ◽

2019 ◽

Vol 2 (4) ◽

pp. 91

Author(s):

Lal Krishna

Keyword(s):

Enzyme Activity ◽

Bacillus Subtilis ◽

Pathogenic Bacteria ◽

Blood Clot ◽

Bacterial Species ◽

Antagonistic Activity ◽

Bacterial Strains ◽

Wide Range

The study was aimed at identification, production and characterization of nattokinase, bacteriocin from bacterial species. Nattokinase and bacteriocins finds a wide range of applications in Pharmaceutical industry, health care and medicine. Nattokinase is a highly active fibrinolytic enzyme secreted by Bacillus subtilis and bacteriocins are proteinaceous toxins produced by Lactobacillus to inhibit the growth of closely related bacterial strains. Bacillus subtilis and Lactobacillus isolates shown positive results to microscopic, biochemical analysis. The nattokinase and bacteriocins were produced by optimizing the media. The enzymes were purified by ammonium sulfate precipitation and HPLC. The enzyme activity for nattokinase was found at 7 mg/ml, pH 8.0 and temperature 48 ºC and the enzyme activity for bacteriocin was found at 3.9 mg/ml, pH 6.5 and temperature 30 °C. Bacteriocins from Lactobacillus showed good antagonistic activity against pathogenic bacteria. Nattokinase from Bacillus subtilis played a significant role in thrombolytic and anti-coagulation at in vitro. The results indicated that the pure enzyme has a potential in dissolving blood clot.

Download Full-text

Isolation, Identification and Characterization of AZO Dye reactive Violet 5R Degrading Bacterial Strains from the Textile Sludge

Journal of Bangladesh Academy of Sciences ◽

10.3329/jbas.v41i2.35493 ◽

2018 ◽

Vol 41 (2) ◽

pp. 136-143 ◽

Cited By ~ 1

Author(s):

Romana Siddique ◽

Hasan Hasnaeen Ahmed

Keyword(s):

Textile Industry ◽

Azo Dye ◽

The Other ◽

Bacterial Strains ◽

Decolorization Rate ◽

Streptococcus Equi ◽

Textile Sludge ◽

Academy Of Sciences ◽

Identification And Characterization

Three bacterial strains, Streptococcus equi subsp. zooepidemicus, Brevibacillus centrosporus and Paenibacillus azoreducens, have been isolated from the sludge samples collected from Textile Industry, Bhaluka, Bangladesh, which have the abilities to degrade Reactive Violet 5R. The decolourization rate was different for the different concentrations of the same dye. Brevibacillus centrosporus displayed a decolorization rate of 94.55%, 90.79%, 91.17% when inoculated and incubated in an SM broth containing the azo dye reactive violet 5R at 1% (v/v), 3% (v/v) and 5% (v/v) concentrations respectively for a consecutive 5 days. Paenibacillus azoreducens showed a decolorization rate of 85.63%, 86.48%, 38.81% for the 1% (v/v), 3% (v/v), and 5% (v/v) of the azo dye reactive violet 5R respective concentrations. On the other hand Streptococcus equi subsp zooepidemicus produced intriguing results where the decolorization rates were 67.78%, 21.69%, 40.10% for 1% (v/v), 3% (v/v) and 5% (v/v) respectively of the azo dye reactive violet 5R.Journal of Bangladesh Academy of Sciences, Vol. 41, No. 2, 136-143, 2017

Download Full-text

Characterization of Two Unique Cold-Active Lipases Derived from a Novel Deep-Sea Cold Seep Bacterium

Microorganisms ◽

10.3390/microorganisms9040802 ◽

2021 ◽

Vol 9 (4) ◽

pp. 802

Author(s):

Chenchen Guo ◽

Rikuan Zheng ◽

Ruining Cai ◽

Chaomin Sun ◽

Shimei Wu

Keyword(s):

Deep Sea ◽

Bacterial Species ◽

Deep Ocean ◽

Cold Seep ◽

Bacterial Strains ◽

E Coli ◽

Cold Active ◽

Genes Encoding ◽

Potential Inhibitors

The deep ocean microbiota has unexplored potential to provide enzymes with unique characteristics. In order to obtain cold-active lipases, bacterial strains isolated from the sediment of the deep-sea cold seep were screened, and a novel strain gcc21 exhibited a high lipase catalytic activity, even at the low temperature of 4 °C. The strain gcc21 was identified and proposed to represent a new species of Pseudomonas according to its physiological, biochemical, and genomic characteristics; it was named Pseudomonas marinensis. Two novel encoding genes for cold-active lipases (Lipase 1 and Lipase 2) were identified in the genome of strain gcc21. Genes encoding Lipase 1 and Lipase 2 were respectively cloned and overexpressed in E. coli cells, and corresponding lipases were further purified and characterized. Both Lipase 1 and Lipase 2 showed an optimal catalytic temperature at 4 °C, which is much lower than those of most reported cold-active lipases, but the activity and stability of Lipase 2 were much higher than those of Lipase 1 under different tested pHs and temperatures. In addition, Lipase 2 was more stable than Lipase 1 when treated with different metal ions, detergents, potential inhibitors, and organic solvents. In a combination of mutation and activity assays, catalytic triads of Ser, Asp, and His in Lipase 1 and Lipase 2 were demonstrated to be essential for maintaining enzyme activity. Phylogenetic analysis showed that both Lipase 1 and Lipase 2 belonged to lipase family III. Overall, our results indicate that deep-sea cold seep is a rich source for novel bacterial species that produce potentially unique cold-active enzymes.

Download Full-text

Comparison of Different Primer Sets for Use in Automated Ribosomal Intergenic Spacer Analysis of Complex Bacterial Communities

Applied and Environmental Microbiology ◽

10.1128/aem.70.10.6147-6156.2004 ◽

2004 ◽

Vol 70 (10) ◽

pp. 6147-6156 ◽

Cited By ~ 362

Author(s):

Massimiliano Cardinale ◽

Lorenzo Brusetti ◽

Paola Quatrini ◽

Sara Borin ◽

Anna Maria Puglia ◽

...

Keyword(s):

Bacterial Communities ◽

Bacterial Species ◽

Intergenic Spacer ◽

The Other ◽

23S Rrna ◽

Bacterial Strains ◽

Appl Environ ◽

Ribosomal Intergenic Spacer ◽

Primer Sets ◽

Dna Template

ABSTRACT ITSF and ITSReub, constituting a new primer set designed for the amplification of the 16S-23S rRNA intergenic transcribed spacers, have been compared with primer sets consisting of 1406F and 23Sr (M. M. Fisher and E. W. Triplett, Appl. Environ. Microbiol. 65:4630-4636, 1999) and S-D-Bact-1522-b-S-20 and L-D-Bact-132-a-A-18 (L. Ranjard et al., Appl. Environ. Microbiol. 67:4479-4487, 2001), previously proposed for automated ribosomal intergenic spacer analysis (ARISA) of complex bacterial communities. An agricultural soil and a polluted soil, maize silage, goat milk, a small marble sample from the façade of the Certosa of Pavia (Pavia, Italy), and brine from a deep hypersaline anoxic basin in the Mediterranean Sea were analyzed with the three primer sets. The number of peaks in the ARISA profiles, the range of peak size (width of the profile), and the reproducibility of results were used as indices to evaluate the efficiency of the three primer sets. The overall data showed that ITSF and ITSReub generated the most informative (in term of peak number) and reproducible profiles and yielded a wider range of spacer sizes (134 to 1,387) than the other primer sets, which were limited in detecting long fragments. The minimum amount of DNA template and sensitivity in detection of minor DNA populations were evaluated with artificial mixtures of defined bacterial species. ITSF and ITSReub amplified all the bacteria at DNA template concentrations from 280 to 0.14 ng μl−1, while the other primer sets failed to detect the spacers of one or more bacterial strains. Although the primer set consisting of ITSF and ITSReub and that of S-D-Bact-1522-b-S-20 and L-D-Bact-132-a-A-18 showed similar sensitivities for the DNA of Allorhizobium undicula mixed with the DNA of other species, the S-D-Bact-1522-b-S-20 and L-D-Bact-132-a-A-18 primer set failed to detect the DNA of Pseudomonas stutzeri.

Download Full-text

Glaciochemistry and pigment producing ability of bacteria from roof of the world, the glaciers of Karakoram, Pakistan

10.21203/rs.3.rs-271782/v1 ◽

2021 ◽

Author(s):

Noor Hassan ◽

Muhammad Rafiq ◽

Abdul Haleem ◽

Aamir Ali Shah ◽

Fariha Hasan

Keyword(s):

Bacterial Species ◽

Rpob Gene ◽

Mountain Range ◽

Bacterial Strains ◽

Mountain Ranges ◽

The World ◽

Alternative Sources ◽

Geochemical Analyses ◽

Pigmented Bacteria

Abstract The Karakoram Mountain Range (KMR) is one of the largest mountain ranges in the world, with ~ 37% of its area glaciated. Here, we present the geochemistry of ice, sediment and meltwaters sampled from Ghulmet, Ghulkin and Hopar glaciers of the Karakoram Range, Pakistan, in addition to the first information on the diversity of pigmented bacteria evaluated using culture-dependent techniques. Geochemical analyses revealed Ca2+ and SO42− to be the most abundant cation and anion species across all glacial samples, respectively. Total organic carbon (TOC), total nitrogen (TN) and total phosphorus (TP) were found in the sediments of all glaciers studied in current research. Bacterial species were capable of producing a variety of different pigments, including alloxanthin, astaxanthin, bacterioruberin, β-carotene, 19'-hexanoyloxyfucoxanthin, peridinin, violacein and zeaxanthin. Culturable bacterial diversity was studied using two molecular biomarkers, 16S rRNA and rpoB gene, with a total of 82 bacterial strains representing 25 genera identified across all glacial samples. This study provides the first characterization of glacier-associated, pigment-producing bacterial communities from the KMR. Findings are important for considerations of alternative sources of conventional pigment production in industrial fields.

Download Full-text