Isolation and Detection of Bacteriocin-Like Inhibitory Substances-Producing Bacteria from Fermented Mare’s Milk Sumbawa

Bacteriocin-like inhibitory substances (BLIS) produced by bacteria is a promising future food preservative agent. This study aimed to obtain bacterial strains that can produce broad-spectrum antibacterial agents and identify the best BLIS producer species based on 16S rDNA sequences. The bacterial strains were isolated from fer-mented mare’s milk using MRS and M17 agar medium. The isolates then were initially screened based on its antibacterial activity of crude cells against Staphylococcus aureus ATCC 6538. The selected strains were cultured and harvested for its cell-free supernatant (CFS). The pH of CFS was adjusted to 6.5 then used for antibacterial activity as-says against ten pathogenic bacteria. Also, the proteinaceous nature of BLIS compound was confirmed by testing with proteinase K. The gDNA of selected isolates was extracted and the 16S rDNA was am-plified using the polymerase chain reaction method then sequenced. The 16S rDNA sequences of the selected strains were used to identify the species using BLAST nucleotides from NCBI then the phylogenetic trees were constructed. 32 isolates was obtained, but only three iso-lates (BC9, SB7, and DC12) were selected as a result of antibacterial screening for further assays. The neutralized-CFS (N-CFS) of these isolates exhibited broad-spectrum antibacterial activity. The N-CFS could be assumed as BLIS. The isolate of BC9 was identified as Ba-cillus amyloliquefaciens strain BC9 that has 99.99 % similarity with B. amyloliquefaciens KC-1, SB7 was Lactobacillus plantarum strain SB7 that has 99.99 % similarity with Lb. plantarum JMC 1149T, and DC12 was Lactobacillus rhamnosus strain DC12 that has 100 % sim-ilarity with Lb. rhamnosus DSM 20021T. Thus, the BLIS produced by those strains is potential for future food and beverages preservations.

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Systematic position of Dinidoridae within the superfamily Pentatomoidea (Hemiptera: Heteroptera) revealed by the Bayesian phylogenetic analysis of the mitochondrial 12S and 16S rDNA sequences

Zootaxa ◽

10.11646/zootaxa.3423.1.5 ◽

2012 ◽

Vol 3423 (1) ◽

pp. 61 ◽

Cited By ~ 4

Author(s):

JERZY A. LIS ◽

PAWEŁ LIS ◽

DARIUSZ J. ZIAJA ◽

ANNA KOCOREK

Keyword(s):

16S Rdna ◽

Phylogenetic Trees ◽

Taxonomic Status ◽

Sister Group ◽

Systematic Position ◽

Bayesian Phylogenetic Analysis ◽

Rdna Sequences ◽

16S Rdna Sequences ◽

Molecular Affinity ◽

The Moment

Mitochondrial 12S and 16S rDNA sequences of five species of Dinidoridae Stål, 1868, a largely Paleotropical family, and 16 other shield bugs (Pentatomoidea) were studied. This was the first molecular examination of the systematic position of this family within the superfamily Pentatomoidea using more than a single dinidorid species. Phylogenetic trees obtained from the Bayesian inference of 12S and 16S sequences of these mitochondrial DNA, identified Dinidoridae as the monophylum and a sister group to the Tessaratomidae. Moreover, results of the study suggested a close molecular affinity of the genus Eumenotes to representatives of the subfamily Dinidorinae, which contradicts all previous morphological analyses that placed it within the subfamily Megymeninae. We suggest restoring taxonomic status of the tribe Eumenotini and removing it from the synonymy of Megymenini, leaving the genus with no subfamilial assignment for the moment.

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Phylogenetic placement of unculturedCeanothusmicrosymbionts using 16S rRNA gene sequences

Canadian Journal of Botany ◽

10.1139/b99-080 ◽

1999 ◽

Vol 77 (9) ◽

pp. 1208-1213 ◽

Cited By ~ 1

Author(s):

Nancy J Ritchie ◽

David D Myrold

Keyword(s):

16S Rdna ◽

Phylogenetic Trees ◽

Full Length ◽

Likelihood Method ◽

Rrna Gene ◽

Consensus Sequences ◽

Rdna Sequences ◽

16S Rdna Sequences ◽

Polymerase Chain ◽

Ceanothus Americanus

Full-length 16S rDNA sequences were amplified directly from the nodules of Ceanothus americanus L. and Ceanothus thyrsiflorus Eschsch. using the polymerase chain reaction. Sequences were determined using an automated sequencer, compared against those in GenBank, and assembled into consensus sequences. The sequences were aligned with other full-length Frankia 16S rDNA sequences available from the data base. Phylogenetic trees were obtained using three different algorithms: neighbor joining, parsimony, and the maximum-likelihood method. All three methods showed that these Ceanothus L. microsymbionts were most closely related to the microsymbiont associated with Dryas drummondii Richardson ex Hook. Lvs. rather than Frankia isolated from the Elaeagnaceae.Key words: Frankia, Ceanothus, 16S rDNA.

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Partial and complete 16S rDNA sequences, their use in generation of 16S rDNA phylogenetic trees and their implications in molecular ecological studies

Molecular Microbial Ecology Manual ◽

10.1007/978-94-011-0351-0_18 ◽

1995 ◽

pp. 259-275 ◽

Cited By ~ 14

Author(s):

Erko Stackebrandt ◽

Fred A. Rainey

Keyword(s):

16S Rdna ◽

Phylogenetic Trees ◽

Ecological Studies ◽

Rdna Sequences ◽

16S Rdna Sequences

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Iron-reducing - and -proteobacteria isolated from laboratory-scaled heterotrophic feammox bioreactor

Vietnam Journal of Biotechnology ◽

10.15625/1811-4989/16333 ◽

2021 ◽

Vol 19 (2) ◽

pp. 359-369

Author(s):

Le Phuong Chung ◽

Nguyen Thi Hai ◽

Nguyen Huynh Minh Quyen ◽

Pham The Hai ◽

Dinh Thuy Hang

Keyword(s):

16S Rdna ◽

Iron Reduction ◽

Ferric Iron ◽

Nitrogen Loss ◽

Pseudomonas Stutzeri ◽

Ammonium Oxidation ◽

Bacterial Strains ◽

Ammonium Removal ◽

Rdna Sequences ◽

16S Rdna Sequences

Ammonium removal from wastewater is a crucial step in wastewater treatment. Presently employed technologies based on nitrification/denitrification and partial nitritation/anammox principles require oxygen for the nitrification step, and are therefore still not yet fully satisfied with the application practice. In recent years, biological ammonium oxidation coupled with ferric iron reduction (feammox) has been proposed to be responsible for the nitrogen loss in different ecological habitats. Related to the wastewater aspect, the feammox principle has been discussed as an alternative approach for ammonium removal without dependency on oxygen. From a laboratory-scaled feammox bioreactor operated under neutral pH, two bacterial strains FN7 and FN9 were isolated by using the anaerobic Hungate technique. Comparative analyses of 16S rDNA sequences showed that these strains were most closely related to the b-proteobacterium Aciclyphilus denitrificans and the g-proteobacterium Pseudomonas stutzeri, respectively. Although being phylogenetically apart, strains FN7 and FN9 shared several common physiological characteristics that are considered meaningful for the feammox process, i.e. (i) heteroptrophic ammonium oxidation, (ii) denitrification, and (iii) ferric iron reduction. These isolates are proposed to play certain roles in the studied feammox system, contributing to the ammonium removal under heterotrophic feammox condition. The 16S rDNA sequences of strains FN7 and FN9 were available in GenBank under the accession numbers LC474369 and MT568614, respectively.

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Effects of 16S rDNA sampling on estimates of endosymbiont lineages in sucking lice

10.7287/peerj.preprints.1457v1 ◽

2015 ◽

Author(s):

Julie M Allen ◽

J Gordon Burleigh ◽

Jessica E Light ◽

David L Reed

Keyword(s):

16S Rdna ◽

Phylogenetic Trees ◽

Sampling Strategies ◽

Host Group ◽

Rdna Sequences ◽

Endosymbiotic Bacteria ◽

16S Rdna Sequences ◽

Evolutionary Inference ◽

Sucking Lice ◽

Diversity Sampling

Co-evolution between insects and their endosymbiotic bacteria can be detected by constructing and comparing their phylogenetic trees. Even though taxon sampling can greatly affect phylogenetic and co-evolutionary inference, most hypotheses of endosymbiont relationships and estimates of the number of endosymbiont lineages within a host group have used only a small percentage of available bacterial sequences. Here we examined how different sampling strategies of Gammaproteobacteria sequences affect estimates of the number of endosymbiont lineages in parasitic sucking lice (Insecta: Phthirapatera: Anoplura). We estimated the number of louse endosymbiont lineages using both newly obtained and previously sequenced 16S rDNA bacterial sequences and more than 42,000 16S rDNA sequences from other Gammaproteobacteria. We also performed parametric and nonparametric bootstrapping experiments to examine the effects of phylogenetic error and uncertainty on these estimates. We found that sampling of 16S rDNA sequences affected the estimates of endosymbiont diversity in sucking lice until we reached a threshold of genetic diversity. Sampling by maximizing the diversity of 16S rDNA sequences was more efficient than simply randomly sampling available 16S rDNA sequences. Although simulation results support the finding of multiple endosymbiont lineages in sucking lice, the bootstrap results suggest that there is still uncertainty in estimates of the number of endosymbiont origins inferred from 16S rDNA alone.

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Degradation of morpholine, piperidine, and pyrrolidine by mycobacteria: evidences for the involvement of a cytochrome P450

Canadian Journal of Microbiology ◽

10.1139/w99-002 ◽

1999 ◽

Vol 45 (3) ◽

pp. 209-216 ◽

Cited By ~ 22

Author(s):

P Poupin ◽

J J Godon ◽

E Zumstein ◽

N Truffaut

Keyword(s):

Phylogenetic Analysis ◽

Cytochrome P450 ◽

16S Rdna ◽

Mycobacterium Smegmatis ◽

Energy Sources ◽

Mycobacterium Fortuitum ◽

Bacterial Strains ◽

Cyclic Amines ◽

Rdna Sequences ◽

16S Rdna Sequences

Nine bacterial strains that grew on morpholine and pyrrolidine as sole carbon, nitrogen, and energy sources were isolated from three different environments with no known morpholine contamination. One of these strains could also degrade piperidine. These bacteria were identified as Mycobacterium strains. A phylogenetic analysis based on the partial 16S rDNA sequences indicated that the isolated strains clustered within the fast growing group of mycobacteria. When the above-mentioned cyclic amines were used as growth substrates, the synthesis of a soluble cytochrome P450 was induced in all these bacteria. Other laboratory strains, Mycobacterium fortuitum and Mycobacterium smegmatis mc2155, were tested for their abilities to degrade morpholine. Neither of them degraded morpholine but could use pyrrolidine and piperidine. The growth of M. fortuitum and M. smegmatis mc2155 on these compounds involved a soluble cytochrome P450, suggesting that mycobacterial strains are naturally able to use pyrrolidine and have developed a similar enzymatic pathway to metabolize this amine.Key words: mycobacteria, morpholine, piperidine, pyrrolidine, cytochrome P450.

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First Report of Bacterial Leaf Blight of Coriander Caused by Xanthomonas campestris pv. coriandri in Taiwan

Plant Disease ◽

10.1094/pdis.2004.88.8.910a ◽

2004 ◽

Vol 88 (8) ◽

pp. 910-910 ◽

Cited By ~ 2

Author(s):

Y.-A. Lee ◽

Y.-H. Liu ◽

H.-L. Liu

Keyword(s):

16S Rdna ◽

Xanthomonas Campestris ◽

Pathogenic Bacteria ◽

Leaf Blight ◽

Bacterial Leaf Blight ◽

Rdna Sequences ◽

16S Rdna Sequences ◽

First Occurrence ◽

Plastic Bag ◽

Agar Media

Leaf blight symptoms on coriander (Coriandrum sativum) were observed during the summers of 2000 to 2002 in fields at the Beidou and Sijhou townships, Changhua County, Taiwan. Symptoms first appeared as small spots on the lower sides of leaves and stems. The centers of the spots quickly turned brown and were surrounded by whitish yellow halos. The brown spots and halos enlarged rapidly and coalesced into irregular, yellowish or brownish dry dead areas on the leaf. V-shaped and chlorotic blotch symptoms were also found at the margins of leaves. Isolations from diseased leaves consistently yielded bacterial colonies that were yellow and glistening on nutrient and potato dextrose agar media. Five representative strains were chosen for further characterization. All strains were gram-negative rods, aerobic, and produced yellow, nonwater soluble, xanthomonadin pigments identified by thin-layer chromatography (1). The strains were positive for catalase and β-galactosidase and negative for oxidase, nitrate reductase, urease, and tryptophanase (indole production) and hydrolyzed starch, gelatin, and esculin. Hydrogen sulfide was produced from cysteine. L-asparagine was not sufficient as a sole carbon source for growth. In Dye's medium C, acids were produced from metabolizing arabinose, glucose, and sucrose but not from rhamnose, cellobiose, lactose, dulcitol, mannitol, and sorbitol. The bacterium was identified as Xanthomonas campestris. Almost complete 16S rDNA sequence of strain TC3 (1,502 bp; GenBank Accession No. AY604178) was determined and compared with available 16S rDNA sequences in GenBank. The sequence was highly identical (99%) to those of Xanthomonas campestris pathovars. Coriander plants were inoculated by spraying bacterial suspensions (108 CFU/ml) on leaves, enclosed in a plastic bag to maintain high humidity for 2 days, and kept in a growth chamber at 28°C. Typical symptoms were observed in 2 to 6 days in all four inoculated plants and appeared to be identical to those observed in the fields. Control plants were inoculated with sterile distilled water and showed no symptoms. The bacterium was readily reisolated from diseased leaves. Bacterial leaf blight of coriander was first reported in India, and the pathogen was identified as X. campestris pv. coriandri (2). To our knowledge, this is the first occurrence of this bacterium on coriander in Taiwan. References: (1) N. W. Schaad et al. Laboratory Guide for Identification of Plant Pathogenic Bacteria. 3rd ed. The American Phytopathological Society, St. Paul, MN, 2001. (2) M. C. Srinivasan et al. Proc. Indian Acad. Sci. Sect. B 53:298, 1961.

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Effects of 16S rDNA sampling on estimates of the number of endosymbiont lineages in sucking lice

PeerJ ◽

10.7717/peerj.2187 ◽

2016 ◽

Vol 4 ◽

pp. e2187 ◽

Cited By ~ 6

Author(s):

Julie M. Allen ◽

J. Gordon Burleigh ◽

Jessica E. Light ◽

David L. Reed

Keyword(s):

16S Rdna ◽

Phylogenetic Trees ◽

Sampling Strategy ◽

Taxon Sampling ◽

Sampling Strategies ◽

Rdna Sequences ◽

16S Rdna Sequences ◽

Evolutionary Inference ◽

Sucking Lice ◽

Simulation Results

Phylogenetic trees can reveal the origins of endosymbiotic lineages of bacteria and detect patterns of co-evolution with their hosts. Although taxon sampling can greatly affect phylogenetic and co-evolutionary inference, most hypotheses of endosymbiont relationships are based on few available bacterial sequences. Here we examined how different sampling strategies ofGammaproteobacteriasequences affect estimates of the number of endosymbiont lineages in parasitic sucking lice (Insecta: Phthirapatera: Anoplura). We estimated the number of louse endosymbiont lineages using both newly obtained and previously sequenced 16S rDNA bacterial sequences and more than 42,000 16S rDNA sequences from otherGammaproteobacteria. We also performed parametric and nonparametric bootstrapping experiments to examine the effects of phylogenetic error and uncertainty on these estimates. Sampling of 16S rDNA sequences affects the estimates of endosymbiont diversity in sucking lice until we reach a threshold of genetic diversity, the size of which depends on the sampling strategy. Sampling by maximizing the diversity of 16S rDNA sequences is more efficient than randomly sampling available 16S rDNA sequences. Although simulation results validate estimates of multiple endosymbiont lineages in sucking lice, the bootstrap results suggest that the precise number of endosymbiont origins is still uncertain.

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Bacterial Phylogenetic Clusters Revealed by Genome Structure

Journal of Bacteriology ◽

10.1128/jb.181.21.6747-6755.1999 ◽

1999 ◽

Vol 181 (21) ◽

pp. 6747-6755 ◽

Cited By ~ 42

Author(s):

Shu-Lin Liu ◽

Anthony B. Schryvers ◽

Kenneth E. Sanderson ◽

Randal N. Johnston

Keyword(s):

16S Rdna ◽

Pathogenic Bacteria ◽

Large Scale ◽

Pasteurella Multocida ◽

Bacterial Species ◽

Genome Structure ◽

Individual Species ◽

Accurate Identification ◽

Rdna Sequences ◽

16S Rdna Sequences

ABSTRACT Current bacterial taxonomy is mostly based on phenotypic criteria, which may yield misleading interpretations in classification and identification. As a result, bacteria not closely related may be grouped together as a genus or species. For pathogenic bacteria, incorrect classification or misidentification could be disastrous. There is therefore an urgent need for appropriate methodologies to classify bacteria according to phylogeny and corresponding new approaches that permit their rapid and accurate identification. For this purpose, we have devised a strategy enabling us to resolve phylogenetic clusters of bacteria by comparing their genome structures. These structures were revealed by cleaving genomic DNA with the endonuclease I-CeuI, which cuts within the 23S ribosomal DNA (rDNA) sequences, and by mapping the resulting large DNA fragments with pulsed-field gel electrophoresis. We tested this experimental system on two representative bacterial genera: Salmonellaand Pasteurella. Among Salmonella spp., I-CeuI mapping revealed virtually indistinguishable genome structures, demonstrating a high degree of structural conservation. Consistent with this, 16S rDNA sequences are also highly conserved among the Salmonella spp. In marked contrast, thePasteurella strains have very different genome structures among and even within individual species. The divergence ofPasteurella was also reflected in 16S rDNA sequences and far exceeded that seen between Escherichia andSalmonella. Based on this diversity, the Pasteurella haemolytica strains we analyzed could be divided into 14 phylogenetic groups and the Pasteurella multocida strains could be divided into 9 groups. If criteria for defining bacterial species or genera similar to those used for Salmonella andEscherichia coli were applied, the striking phylogenetic diversity would allow bacteria in the currently recognized species ofP. multocida and P. haemolytica to be divided into different species, genera, or even higher ranks. On the other hand, strains of Pasteurella ureae and Pasteurella pneumotropica are very similar to those of P. multocida in both genome structure and 16S rDNA sequence and should be regarded as strains within this species. We conclude that large-scale genome structure can be a sensitive indicator of phylogenetic relationships and that, therefore, I-CeuI-based genomic mapping is an efficient tool for probing the phylogenetic status of bacteria.

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