scholarly journals Prediction of cellulolytic and hemicellulolytic bacterial diversity in the gut of Coptotermes gestroi in the Southern Vietnam

2020 ◽  
Vol 17 (3) ◽  
pp. 537-544
Author(s):  
Nguyen Thi Thao ◽  
Do Thi Huyen ◽  
Truong Nam Hai
Keyword(s):  
Bacterial Species ◽  
Abundant Species ◽  
Open Reading Frames ◽  
Metagenomic Dna ◽  
Free Living ◽  
Southern Vietnam ◽  
Degrading Bacteria ◽  
Coptotermes Gestroi ◽  
Reading Frames ◽  
Living Bacteria

In lower termite such as Coptotermes gestroi, cellulose and hemicellulose are hydrolysed by cellulases and hemicellulases secreted from bacteria, archaea, protozoa and fungy in the hindgut. In which, majority of the enzymes are contributed by protozoa. From the metagenomic DNA data (125,423 open reading frames -ORFs) of free-living bacteria in the gut of C. gestroi harvested in Southern Vietnam and by MEGA 4.0 software, 100.340 ORFs were classified into 1,368 species, 628 genera, 217 families, 97 orders, 41 classes and 22 phyla (Do et al., 2014). Among these, 2,131 ORFs (2,12%) belong to 24 bacterial species (account 1,75% bacterial species), 11 families, 9 orders, 8 classes and 5 phyla were predicted have ability to produce cellulases; 679 ORFs belong to 18 bacterial species 8 families, 6 orders, 5 classes, 4 phyla were predicted have ability to produce hemicellulase. Majority of cellulase producers were species which of Firmicutes (15/24 species), accumulated in class Clostridia, order Clostridiales. The most abundant cellulase producer was Pseudomonas fluorescens (1,258 ORFs) of order Pseudomonadaceae. Out of the 18 hemicellulase producers, the most abundant species was Clostridium thermocellum (113 ORFs) in the phylum Firmicutes, followed by 3 species belonging to the phylum Bacteroidetes. The species predicted to produce both cellulase, hemicellulase were C. thermocellum, Ruminococcusns flavefaciens and Bacillus subtilis. Our study provides  a data of gut cellulose and hemicellulose - degrading bacteria composition of C. gestroi

scholarly journals MINTIA: a metagenomic INserT integrated assembly and annotation tool

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11885
Author(s):  
Philippe Bardou ◽  
Sandrine Laguerre ◽  
Sarah Maman Haddad ◽  
Sabrina Legoueix Rodriguez ◽  
Elisabeth Laville ◽  
...  
Keyword(s):  
Software Package ◽  
Bacterial Species ◽  
Open Reading Frames ◽  
Functional Metagenomics ◽  
Metagenomic Dna ◽  
Metagenomic Sequence ◽  
Uncultured Bacteria ◽  
Activity Screening ◽  
User Friendly ◽  
Reading Frames

The earth harbors trillions of bacterial species adapted to very diverse ecosystems thanks to specific metabolic function acquisition. Most of the genes responsible for these functions belong to uncultured bacteria and are still to be discovered. Functional metagenomics based on activity screening is a classical way to retrieve these genes from microbiomes. This approach is based on the insertion of large metagenomic DNA fragments into a vector and transformation of a host to express heterologous genes. Metagenomic libraries are then screened for activities of interest, and the metagenomic DNA inserts of active clones are extracted to be sequenced and analysed to identify genes that are responsible for the detected activity. Hundreds of metagenomics sequences found using this strategy have already been published in public databases. Here we present the MINTIA software package enabling biologists to easily generate and analyze large metagenomic sequence sets, retrieved after activity-based screening. It filters reads, performs assembly, removes cloning vector, annotates open reading frames and generates user friendly reports as well as files ready for submission to international sequence repositories. The software package can be downloaded from https://github.com/Bios4Biol/MINTIA.

scholarly journals Whole Genome Sequencing and Analysis of Chlorimuron-Ethyl Degrading Bacteria Klebsiella pneumoniae 2N3

2019 ◽  
Vol 20 (12) ◽  
pp. 3053 ◽  
Author(s):  
Cheng Zhang ◽  
Qingkai Hao ◽  
Zhengyi Zhang ◽  
Xianghui Zhang ◽  
Hongyu Pan ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Gene Knockout ◽  
Scientific Evidence ◽  
Gc Content ◽  
Open Reading Frames ◽  
Degradation Rates ◽  
Degrading Bacteria ◽  
High Throughput Dna Sequencing ◽  
Chlorimuron Ethyl ◽  
Reading Frames

Klebsiella pneumoniae 2N3 is a strain of gram-negative bacteria that can degrade chlorimuron-ethyl and grow with chlorimuron-ethyl as the sole nitrogen source. The complete genome of Klebsiella pneumoniae 2N3 was sequenced using third generation high-throughput DNA sequencing technology. The genomic size of strain 2N3 was 5.32 Mb with a GC content of 57.33% and a total of 5156 coding genes and 112 non-coding RNAs predicted. Two hydrolases expressed by open reading frames (ORFs) 0934 and 0492 were predicted and experimentally confirmed by gene knockout to be involved in the degradation of chlorimuron-ethyl. Strains of ΔORF 0934, ΔORF 0492, and wild type (WT) reached their highest growth rates after 8–10 hours in incubation. The degradation rates of chlorimuron-ethyl by both ΔORF 0934 and ΔORF 0492 decreased in comparison to the WT during the first 8 hours in culture by 25.60% and 24.74%, respectively, while strains ΔORF 0934, ΔORF 0492, and the WT reached the highest degradation rates of chlorimuron-ethyl in 36 hours of 74.56%, 90.53%, and 95.06%, respectively. This study provides scientific evidence to support the application of Klebsiella pneumoniae 2N3 in bioremediation to control environmental pollution.

scholarly journals Hydrolase CehA and Monooxygenase CfdC Are Responsible for Carbofuran Degradation inSphingomonassp. Strain CDS-1

2018 ◽  
Vol 84 (16) ◽  
Author(s):  
Xin Yan ◽  
Wen Jin ◽  
Guang Wu ◽  
Wankui Jiang ◽  
Zhangong Yang ◽  
...  
Keyword(s):  
Benzene Ring ◽  
Gene Knockout ◽  
Degradation Mechanism ◽  
Draft Genome ◽  
Open Reading Frames ◽  
Flavin Mononucleotide ◽  
Genetic Determinants ◽  
Content Type ◽  
Degrading Bacteria ◽  
Reading Frames

ABSTRACTCarbofuran, a broad-spectrum systemic insecticide, has been extensively used for approximately 50 years. Diverse carbofuran-degrading bacteria have been described, among which sphingomonads have exhibited an extraordinary ability to catabolize carbofuran; other bacteria can only convert carbofuran to carbofuran phenol, while all carbofuran-degrading sphingomonads can degrade both carbofuran and carbofuran phenol. However, the genetic basis of carbofuran catabolism in sphingomonads has not been well elucidated. In this work, we sequenced the draft genome ofSphingomonassp. strain CDS-1 that can transform both carbofuran and carbofuran phenol but fails to grow on them. On the basis of the hypothesis that the genes involved in carbofuran catabolism are highly conserved among carbofuran-degrading sphingomonads, two such genes,cehACDS-1andcfdCCDS-1, were predicted from the 84 open reading frames (ORFs) that share ≥95% nucleic acid similarities between strain CDS-1 and another sphingomonadNovosphingobiumsp. strain KN65.2 that is able to mineralize the benzene ring of carbofuran. The results of the gene knockout, genetic complementation, heterologous expression, and enzymatic experiments reveal thatcehACDS-1andcfdCCDS-1are responsible for the conversion of carbofuran and carbofuran phenol, respectively, in strain CDS-1. CehACDS-1hydrolyzes carbofuran to carbofuran phenol. CfdCCDS-1, a reduced flavin mononucleotide (FMNH2)- or reduced flavin adenine dinucleotide (FADH2)-dependent monooxygenase, hydroxylates carbofuran phenol at the benzene ring in the presence of NADH, FMN/FAD, and the reductase CfdX. It is worth noting that we found that carbaryl hydrolase CehAAC100, which was previously demonstrated to have no activity toward carbofuran, can actually convert carbofuran to carbofuran phenol, albeit with very low activity.IMPORTANCEDue to the extensive use of carbofuran over the past 50 years, bacteria have evolved catabolic pathways to mineralize this insecticide, which plays an important role in eliminating carbofuran residue in the environment. This study revealed the genetic determinants of carbofuran degradation inSphingomonassp. strain CDS-1. We speculate that the close homologuescehAandcfdCare highly conserved among other carbofuran-degrading sphingomonads and play the same roles as those described here. These findings deepen our understanding of the microbial degradation mechanism of carbofuran and lay a foundation for the better use of microbes to remediate carbofuran contamination.

scholarly journals Dynamics of Free-Living and Attached Bacterial Assemblages in Skeletonema sp. Diatom Cultures at Elevated Temperatures

2021 ◽  
Vol 8 ◽  
Author(s):  
Zichao Deng ◽  
Shouchang Chen ◽  
Ping Zhang ◽  
Xu Zhang ◽  
Jonathan M. Adams ◽  
...  
Keyword(s):  
Community Structure ◽  
Elevated Temperature ◽  
Bacterial Communities ◽  
Elevated Temperatures ◽  
Bacterial Species ◽  
Positive Interactions ◽  
Growth Stages ◽  
Free Living ◽  
Attached Bacteria ◽  
Living Bacteria

In the context of global warming, changes in phytoplankton-associated bacterial communities have the potential to change biogeochemical cycling and food webs in marine ecosystems. Skeletonema is a cosmopolitan diatom genus in coastal waters worldwide. Here, we grew a Skeletonema strain with its native bacterial assemblage at different temperatures and examined cell concentrations of Skeletonema sp. and free-living bacteria, dissolved organic carbon (DOC) concentrations of cultures, and the community structure of both free-living and attached bacteria at different culture stages. The results showed that elevated temperature increased the specific growth rates of both Skeletonema and free-living bacteria. Different growth stages had a more pronounced effect on community structure compared with temperatures and different physical states of bacteria. The effects of temperature on the structure of the free-living bacterial community were more pronounced compared with diatom-attached bacteria. Carbon metabolism genes and those for some specific amino acid pathways were found to be positively correlated with elevated temperature, which may have profound implications on the oceanic carbon cycle and the marine microbial loop. Network analysis revealed evidence of enhanced cooperation with an increase in positive interactions among different bacteria at elevated temperature. This may help the whole community to overcome the stress of elevated temperature. We speculate that different bacterial species may build more integrated networks with a modified functional profile of the whole community to cope with elevated temperature. This study contributes to an improved understanding of the response of diatom-associated bacterial communities to elevated temperature.

scholarly journals Probe design for mining and selection of genes coding endo 1- 4 xylanase from dna metagenome data

2018 ◽  
Vol 40 (1) ◽  
pp. 39-50
Author(s):  
Do Thi Huyen ◽  
Nguyen Minh Giang ◽  
Nguyen Thu Nguyet ◽  
Truong Nam Hai
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Probe Design ◽  
Amino Acid Residues ◽  
High Similarity ◽  
Metagenomic Dna ◽  
Free Living ◽  
Conserved Residues ◽  
Living Bacteria ◽  
Selection Of

According to the CAZY classification, endo 1- 4 xylanase belongs to GH 5, 8, 10, 11, 30, 51, 98. However only 03 sequences of GH8, 27 sequences of GH10, 18 sequence of GH11, only one sequence of each GH30 and GH51 from CAZy and NCBI database were thouroughly experimentally studied for biological activity and characteristics of the enzyme. Through the collected sequences, two probes for endo 1- 4 xylanase of GH10 and GH11 were designed, based on the sequence homology. The GH10 probe was 338 amino acids lenghth contained all the conserved amino acid residues (16 conserved residues in all sequences, 13 residues similar in almost sequences, 14 residues conserved in many sequences) with the lowest maxscore of 189, coverage of 88% and identity of 39%. The GH11 probe was 204 amino acids contained all the conserved amino acid residues (54 conserved residues were identity in all sequences, 25 residues similar in almost sequences, 24 residues conserved in many sequences) with the lowest maxscore of 165, coverage of 84% and identity of 50%. Using the two probes, we mined only one sequence (GL0018509) for endo 1- 4 xylanase from metagenomic DNA data of free-living bacteria in Coptotermes termite gut. Prediction of three-dimention structure of GL0018509 sequence by Phyre2 and Swiss Prot showed that this sequence was high similarity (95% by Phyre2 and 93,4% by Swiss Prot) with endo 1- 4 xylanase with the 100% confidence.

scholarly journals Analysis of the pmsCEAB Gene Cluster Involved in Biosynthesis of Salicylic Acid and the Siderophore Pseudomonine in the Biocontrol Strain Pseudomonas fluorescensWCS374

2001 ◽  
Vol 183 (6) ◽  
pp. 1909-1920 ◽  
Author(s):  
Jesús Mercado-Blanco ◽  
Koen M. G. M. van der Drift ◽  
Per E. Olsson ◽  
Jane E. Thomas-Oates ◽  
Leendert C. van Loon ◽  
...  
Keyword(s):  
Salicylic Acid ◽  
Histidine Decarboxylase ◽  
Bacterial Species ◽  
Open Reading Frames ◽  
Putative Promoter Region ◽  
E Coli ◽  
Low Levels ◽  
Reading Frames ◽  
Siderophore Activity

ABSTRACT Mutants of Pseudomonas fluorescens WCS374 defective in biosynthesis of the fluorescent siderophore pseudobactin still display siderophore activity, indicating the production of a second siderophore. A recombinant cosmid clone (pMB374-07) of a WCS374 gene library harboring loci necessary for the biosynthesis of salicylic acid (SA) and this second siderophore pseudomonine was isolated. The salicylate biosynthesis region of WCS374 was localized in a 5-kb EcoRI fragment of pMB374-07. The SA and pseudomonine biosynthesis region was identified by transfer of cosmid pMB374-07 to a pseudobactin-deficient strain of P. putida. Sequence analysis of the 5-kb subclone revealed the presence of four open reading frames (ORFs). Products of two ORFs (pmsC andpmsB) showed homologies with chorismate-utilizing enzymes; a third ORF (pmsE) encoded a protein with strong similarity with enzymes involved in the biosynthesis of siderophores in other bacterial species. The region also contained a putative histidine decarboxylase gene (pmsA). A putative promoter region and two predicted iron boxes were localized upstream of pmsC. We determined by reverse transcriptase-mediated PCR that thepmsCEAB genes are cotranscribed and that expression is iron regulated. In vivo expression of SA genes was achieved in P. putida and Escherichia coli cells. In E. coli, deletions affecting the first ORF (pmsC) diminished SA production, whereas deletion of pmsBabolished it completely. The pmsB gene induced low levels of SA production in E. coli when expressed under control of the lacZ promoter. Several lines of evidence indicate that SA and pseudomonine biosynthesis are related. Moreover, we isolated a Tn5 mutant (374-05) that is simultaneously impaired in SA and pseudomonine production.

scholarly journals Identification of pBC218/pBC210 Genes of Bacillus cereus G9241 in Five Florida Soils Using qPCR

2014 ◽  
Vol 2014 ◽  
pp. 1-7
Author(s):  
Vicki Ann Luna ◽  
Kimmy Nguyen ◽  
Damian H. Gilling
Keyword(s):  
Public Health ◽  
Bacterial Species ◽  
Geographical Area ◽  
Soil Samples ◽  
Open Reading Frames ◽  
Public Health Importance ◽  
Potential Threat ◽  
Gram Negative ◽  
Positive Results ◽  
Reading Frames

The distribution of the virulent plasmid pBC210 of B. cereus that carries several B. anthracis genes and has been implicated in lethal anthrax-like pulmonary disease is unknown. We screened our collection of 103 B. cereus isolates and 256 soil samples using a quantitative PCR (qPCR) assay that targeted three open reading frames putatively unique to pBC210. When tested with DNA from 2 B. cereus strains carrying pBC210, and 64 Gram-positive and 55 Gram-negative bacterial species, the assay had 100% sensitivity and specificity. None of the DNA from the B. cereus isolates yielded positive amplicons but DNA extracted from five soils collected in Florida gave positive results for all three target sequences of pBC210. While screening confirms that pBC210 is uncommon in B. cereus, this study is the first to report that pBC210 is present in Florida soils. This study improves our knowledge of the distribution of pBC210 in soils and, of public health importance, the potential threat of B. cereus isolates carrying the toxin-carrying plasmid. We demonstrated that sequences of pBC210 can be found in a larger geographical area than previously thought and that finding more B. cereus carrying the virulent plasmid is a possibility in the future.

scholarly journals A Novel Integrative Conjugative Element Mediates Genetic Transfer from Group G Streptococcus to Other β-Hemolytic Streptococci

2009 ◽  
Vol 191 (7) ◽  
pp. 2257-2265 ◽  
Author(s):  
Mark R. Davies ◽  
Josephine Shera ◽  
Gary H. Van Domselaar ◽  
Kadaba S. Sriprakash ◽  
David J. McMillan
Keyword(s):  
Group A Streptococcus ◽  
Bacterial Species ◽  
Group B Streptococcus ◽  
Gene Clusters ◽  
Kanamycin Resistance ◽  
Open Reading Frames ◽  
Cadmium Resistance ◽  
Integrative Conjugative Element ◽  
Group B ◽  
Reading Frames

ABSTRACT Lateral gene transfer is a significant contributor to the ongoing evolution of many bacterial pathogens, including β-hemolytic streptococci. Here we provide the first characterization of a novel integrative conjugative element (ICE), ICESde3396, from Streptococcus dysgalactiae subsp. equisimilis (group G streptococcus [GGS]), a bacterium commonly found in the throat and skin of humans. ICESde3396 is 64 kb in size and encodes 66 putative open reading frames. ICESde3396 shares 38 open reading frames with a putative ICE from Streptococcus agalactiae (group B streptococcus [GBS]), ICESa2603. In addition to genes involves in conjugal processes, ICESde3396 also carries genes predicted to be involved in virulence and resistance to various metals. A major feature of ICESde3396 differentiating it from ICESa2603 is the presence of an 18-kb internal recombinogenic region containing four unique gene clusters, which appear to have been acquired from streptococcal and nonstreptococcal bacterial species. The four clusters include two cadmium resistance operons, an arsenic resistance operon, and genes with orthologues in a group A streptococcus (GAS) prophage. Streptococci that naturally harbor ICESde3396 have increased resistance to cadmium and arsenate, indicating the functionality of genes present in the 18-kb recombinogenic region. By marking ICESde3396 with a kanamycin resistance gene, we demonstrate that the ICE is transferable to other GGS isolates as well as GBS and GAS. To investigate the presence of the ICE in clinical streptococcal isolates, we screened 69 isolates (30 GGS, 19 GBS, and 20 GAS isolates) for the presence of three separate regions of ICESde3396. Eleven isolates possessed all three regions, suggesting they harbored ICESde3396-like elements. Another four isolates possessed ICESa2603-like elements. We propose that ICESde3396 is a mobile genetic element that is capable of acquiring DNA from multiple bacterial sources and is a vehicle for dissemination of this DNA through the wider β-hemolytic streptococcal population.

scholarly journals Vibrio natriegens, a new genomic powerhouse

2016 ◽  
Author(s):  
Henry H. Lee ◽  
Nili Ostrov ◽  
Brandon G. Wong ◽  
Michaela A. Gold ◽  
Ahmad S. Khalil ◽  
...  
Keyword(s):  
Recombinant Dna ◽  
Open Reading Frames ◽  
Host Organism ◽  
Recombinant Dna Technology ◽  
Free Living ◽  
Growth Properties ◽  
Culturing Conditions ◽  
Laboratory Culturing ◽  
Tools And Techniques ◽  
Reading Frames

Recombinant DNA technology has revolutionized biomedical research with continual innovations advancing the speed and throughput of molecular biology. Nearly all these tools, however, are reliant onEscherichia colias a host organism, and its lengthy growth rate increasingly dominates experimental time. Here we report the development ofVibrio natriegens, a free-living bacteria with the fastest generation time known, into a genetically tractable host organism. We systematically characterize its growth properties to establish basic laboratory culturing conditions. We provide the first completeVibrio natriegensgenome, consisting of two chromosomes of 3,248,023 bp and 1,927,310 bp that together encode 4,578 open reading frames. We reveal genetic tools and techniques for working withVibrio natriegens. These foundational resources will usher in an era of advanced genomics to accelerate biological, biotechnological, and medical discoveries.

Cellular Adaptations to Cytoplasmic Mg2+ Limitation

2021 ◽  
Vol 75 (1) ◽  
pp. 649-672
Author(s):  
Eduardo A. Groisman ◽  
Carissa Chan
Keyword(s):  
Protein Synthesis ◽  
Bacterial Species ◽  
Transcriptional Regulator ◽  
Living Cells ◽  
Open Reading Frames ◽  
Enzymatic Reactions ◽  
Leader Region ◽  
Coding Regions ◽  
Reading Frames ◽  
Do So

Mg2+ is the most abundant divalent cation in living cells. It is essential for charge neutralization, macromolecule stabilization, and the assembly and activity of ribosomes and as a cofactor for enzymatic reactions. When experiencing low cytoplasmic Mg2+, bacteria adopt two main strategies: They increase the abundance and activity of Mg2+ importers and decrease the abundance of Mg2+-chelating ATP and rRNA. These changes reduce regulated proteolysis by ATP-dependent proteases and protein synthesis in a systemic fashion. In many bacterial species, the transcriptional regulator PhoP controls expression of proteins mediating these changes. The 5′ leader region of some mRNAs responds to low cytoplasmic Mg2+ or to disruptions in translation of open reading frames in the leader regions by furthering expression of the associated coding regions, which specify proteins mediating survival when the cytoplasmic Mg2+ concentration is low. Microbial species often utilize similar adaptation strategies to cope with low cytoplasmic Mg2+ despite relying on different genes to do so.

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