Menu

Auto Tag: Microbial

July 7, 2019

Myxobacteria: Unraveling the potential of a unique microbiome niche

Natural products obtained from microorganisms have been playing an imperative role in drug discovery for decades. Hence, rightfully, microorganisms are considered as the richest source of biochemical remedies. In this review, we represent an unexplored family of bacteria considered to be prolific producers of diverse metabolites. Myxobacteria are gram-negative bacteria which have been reported to produce large families of secondary metabolites with prominent antimicrobial, antifungal, and antitumor activities. Klaus Gerth, Norbert Bedorf, Herbert Irschik, and Hans Reichenbach observed the antifungal activity of Sorangium cellulosum against Mucor hiemalis. In 2006, Hans Reichenbach and his team obtained a novel macrolide cruentaren A from Byssovorax cruenta (myxobacteria). Cruentaren A showed inhibitory activity against yeast and filamentous fungi. It also showed selective inhibitory activity against mitochondrial F-type ATPase. Cruentaren A has been found to be cytotoxic against various human cancer cell lines. In 2007, Reichenbach and his colleagues named an antibiotic produced by Sorangium cellulosum strain Soce895 as thuggacin. This antibiotic acts on the respiration of some bacteria. Other antibiotics from myxobacteria, myxovirescin, and megovalicin show broad-spectrum bactericidal activity. The College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China, evaluated the antitumor property of epothilone, which has shown promise for breast cancer treatment. The study determined high potential and versatile antimicrobial and antitumor secondary metabolites of myxobacteria. In yet another study, Ratjadone A, that exhibited strong antiviral activity against HIV, was obtained from Sorangium cellulosum strain. This compound shows antiviral activity in vitro but has low selectivity. Further search on the derivatives of this compound might help in the future. This is rationale enough to pre-empt that every strain of myxobacteria might be endowed to produce secondary metabolites with novel mechanisms of action which are rarely produced by other microbes. The available data establishes the impact of myxobacterial studies in search for novel metabolites as a front runner in microbiological research and worthy enough to be a thrust area of research in pharmacology.

Read more
July 7, 2019

Fe-S cluster assembly in oxymonads and related protists.

The oxymonad Monocercomonoides exilis was recently reported to be the first eukaryote that has completely lost the mitochondrial compartment. It was proposed that an important prerequisite for such a radical evolutionary step was the acquisition of the SUF Fe-S cluster assembly pathway from prokaryotes, making the mitochondrial ISC pathway dispensable. We have investigated genomic and transcriptomic data from six oxymonad species and their relatives, composing the group Preaxostyla (Metamonada, Excavata), for the presence and absence of enzymes involved in Fe-S cluster biosynthesis. None possesses enzymes of mitochondrial ISC pathway and all apparently possess the SUF pathway, composed of SufB, C, D, S, and U proteins, altogether suggesting that the transition from ISC to SUF preceded their last common ancestor. Interestingly, we observed that SufDSU were fused in all three oxymonad genomes, and in the genome of Paratrimastix pyriformis. The donor of the SUF genes is not clear from phylogenetic analyses, but the enzyme composition of the pathway and the presence of SufDSU fusion suggests Firmicutes, Thermotogae, Spirochaetes, Proteobacteria, or Chloroflexi as donors. The inventory of the downstream CIA pathway enzymes is consistent with that of closely related species that retain ISC, indicating that the switch from ISC to SUF did not markedly affect the downstream process of maturation of cytosolic and nuclear Fe-S proteins.

Read more
July 7, 2019

The molecular basis for the intramolecular migration (NIH shift) of the carboxyl group during para-hydroxybenzoate catabolism.

The NIH shift is a chemical rearrangement in which a substituent on an aromatic ring undergoes an intramolecular migration, primarily during an enzymatic hydroxylation reaction. The molecular mechanism for the NIH shift of a carboxyl group has remained a mystery for 40 years. Here, we elucidate the molecular mechanism of the reaction in the conversion of para-hydroxybenzoate (PHB) to gentisate (GA, 2, 5-dihydroxybenzoate). Three genes (phgABC) from the PHB utilizer Brevibacillus laterosporus PHB-7a encode enzymes (p-hydroxybenzoyl-CoA ligase, p-hydroxybenzoyl-CoA hydroxylase and gentisyl-CoA thioesterase, respectively) catalyzing the conversion of PHB to GA via a route involving CoA thioester formation, hydroxylation concomitant with a 1, 2-shift of the acetyl CoA moiety and thioester hydrolysis. The shift of the carboxyl group was established rigorously by stable isotopic experiments with heterologously expressed phgABC, converting 2, 3, 5, 6-tetradeutero-PHB and [carboxyl-13 C]-PHB to 3, 4, 6-trideutero-GA and [carboxyl-13 C]-GA respectively. This is distinct from the NIH shifts of hydrogen and aceto substituents, where a single oxygenase catalyzes the reaction without the involvement of a thioester. The discovery of this three-step strategy for carboxyl group migration reveals a novel role of the CoA thioester in biochemistry and also illustrates the diversity and complexity of microbial catabolism in the carbon cycle.© 2018 John Wiley & Sons Ltd.

Read more
July 7, 2019

Genomic features of the Helicobacter pylori strain PMSS1 and its virulence attributes as deduced from its in vivo colonisation patterns.

The human gastric pathogen Helicobacter pylori occurs in two basic variants, either exhibiting a functional cagPAI-encoded type-4-secretion-system (T4SS) or not. Only a few cagPAI-positive strains have been successfully adapted for long-term infection of mice, including the pre-mouse Sydney strain 1 (PMSS1). Here we confirm that PMSS1 induces gastric inflammation and neutrophil infiltration in mice, progressing to intestinal metaplasia. Complete genome analysis of PMSS1 revealed 1,423 coding sequences, encompassing the cagPAI gene cluster and, unusually, the location of the cytotoxin-associated gene A (cagA) approximately 15 kb downstream of the island. PMSS1 harbours three genetically exchangeable loci that are occupied by the hopQ coding sequences. HopQ represents a critical co-factor required for the translocation of CagA into the host cell and activation of NF-?B via the T4SS. Long-term colonisation of mice led to an impairment of cagPAI functionality. One of the bacterial clones re-isolated at four months post-infection revealed a mutation in the cagPAI gene cagW, resulting in a frame shift mutation, which prevented CagA translocation, possibly due to an impairment of T4SS function. Rescue of the mutant cagW re-established CagA translocation. Our data reveal intriguing insights into the adaptive abilities of PMSS1, suggesting functional modulation of the H. pylori cagPAI virulence attribute.© 2018 The Authors. Molecular Microbiology Published by John Wiley & Sons Ltd.

Read more
July 7, 2019

The complete genomic sequence of a novel cold-adapted bacterium, Planococcus maritimus Y42, isolated from crude oil-contaminated soil.

Planococcus maritimus Y42, isolated from the petroleum-contaminated soil of the Qaidam Basin, can use crude oil as its sole source of carbon and energy at 20 °C. The genome of P. maritimus strain Y42 has been sequenced to provide information on its properties. Genomic analysis shows that the genome of strain Y42 contains one circular DNA chromosome with a size of 3,718,896 bp and a GC content of 48.8%, and three plasmids (329,482; 89,073; and 12,282 bp). Although the strain Y42 did not show a remarkably higher ability in degrading crude oil than other oil-degrading bacteria, the existence of strain Y42 played a significant role to reducing the overall environmental impact as an indigenous oil-degrading bacterium. In addition, genome annotation revealed that strain Y42 has many genes responsible for hydrocarbon degradation. Structural features of the genomes might provide a competitive edge for P. maritimus strain Y42 to survive in oil-polluted environments and be worthy of further study in oil degradation for the recovery of crude oil-polluted environments.

Read more
July 7, 2019

One complete and three draft genome sequences of four Brochothrix thermosphacta strains, CD 337, TAP 175, BSAS1 3 and EBP 3070.

Brochothrix thermosphacta is one of the dominant bacterial species associated with spoilage of chilled meat and seafood products through the production of various metabolites responsible for off-odors. However, metabolic pathways leading to meat and seafood spoilage are not all well known. The production of spoiling molecules seems to depend both on strains and on food matrix. Several B. thermosphacta genome sequences have been reported, all issued from meat isolates. Here, we report four genome sequences, one complete and three as drafts. The four B. thermosphacta strains CD 337, TAP 175, BSAS1 3, and EBP 3070 were isolated from different ecological niches (seafood or meat products either spoiled or not and bovine slaughterhouse). These strains known as phenotypically and genetically different were selected to represent intraspecies diversity. CD 337 genome is 2,594,337 bp long, complete and circular, containing 2593 protein coding sequences and 28 RNA genes. TAP 175, BSAS1 3, and EBP 3070 genomes are arranged in 57, 83, and 71 contigs, containing 2515, 2668, and 2611 protein-coding sequences, respectively. These genomes were compared with two other B. thermosphacta complete genome sequences. The main genome content differences between strains are phages, plasmids, restriction/modification systems, and cell surface functions, suggesting a similar metabolic potential but a different niche adaptation capacity.

Read more
July 7, 2019

PacBio genome sequences of Escherichia coli serotype O157:H7, diffusely adherent E. coli, and Salmonella enterica strains, all carrying plasmids with an mcr-1 resistance gene.

We report here Illumina-corrected PacBio whole-genome sequences of an Escherichia coli serotype O157:H7 strain (2017C-4109), an E. coli serotype O[undetermined]:H2 strain (2017C-4173W12), and a Salmonella enterica subsp. enterica serovar Enteritidis strain (2017K-0021), all of which carried the mcr-1 resistance gene on an IncI2 or IncX4 plasmid. We also determined that pMCR-1-CTSe is identical to a previously published plasmid, pMCR-1-CT.

Read more
July 7, 2019

Salicibibacter kimchii gen. nov., sp. nov., a moderately halophilic and alkalitolerant bacterium in the family Bacillaceae, isolated from kimchi.

A moderately halophilic and alkalitolerant bacterial strain NKC1-1T was isolated from commercial kimchi in Korea. Strain NKC1-1T was Gram-stain-positive, aerobic, rod-shaped, non-motile, and contained diaminopimelic acid-type murein. Cell growth was observed in a medium containing 0-25% (w/v) NaCl (optimal at 10% [w/v]), at 20-40°C (optimal at 37°C) and pH 6.5-10.0 (optimal at pH 9.0). The major isoprenoid quinone of the isolate was menaquinone-7, and the major polar lipids were phosphatidylglycerol and unidentified phospholipids. Cell membrane of the strain contained iso-C17:0 and anteiso-C15:0 as the major fatty acids. Its DNA G + C content was 45.2 mol%. Phylogenetic analysis indicated the strain to be most closely related to Geomicrobium halophilum with 92.7-92.9% 16S rRNA gene sequence similarity. Based on polyphasic taxonomic evaluation with phenotypic, phylogenetic, and chemotaxonomic analyses, the strain represents a novel species in a new genus, for which the name Salicibibacter kimchii gen. nov., sp. nov. is proposed (= CECT 9537T; KCCM 43276T).

Read more
July 7, 2019

Identification and genome analysis of Deinococcus actinosclerus SJTR1, a novel 17ß-estradiol degradation bacterium.

Biodegradation with microorganisms is considered as an efficient strategy to remove the environmental pollutants. In this work, Deinococcus actinosclerus SJTR1 isolated from the wastewater was confirmed with great degradation capability to 17ß-estradiol, one typical estrogen chemical. It could degrade nearly 90% of 17ß-estradiol (10 mg/L) in 5 days and transform it into estrone; its degradation kinetics fitted for the first-order kinetic equation. The whole genome sequence of D. actinosclerus SJTR1 was obtained and annotated, containing one chromosome (3,315,586 bp) and four plasmids (ranging from 17,267 bp to 460,244 bp). A total of 3913 CDSs and 73 RNA genes (including 12 rRNA genes, 50 tRNA genes, and 11 ncRNA genes) were identified in its whole genome sequence. On this basis, a series of potential genes involved in steroid metabolism and stress responses of D. actinosclerus SJTR1 were predicted. It is the first report of Deinococcus strain with the degradation capability to estrogens. This work could enrich the genome sources of the estrogen-degrading strains and promote the degradation mechanism study of 17ß-estradiol in bacteria.

Read more
July 7, 2019

Complete genome sequence of Bordetella sp. HZ20 sheds light on the ecological role of bacterium without algal-polysaccharides degrading abilities in the brown seaweed-abundant environment

Bordetella sp. HZ20 was isolated from the surface of brown seaweed (Laminaria japonica) and absence of the abilities to decompose the brown seaweed. The genome of Bordetella sp. HZ20 was sequenced and comprised of one circular chromosome with the size of 4,227,194?bp and DNA G?+?C content of 55.5%. Genomic annotation showed that, Bordetella sp. HZ20 may have chitin degradation related enzymes, heparin-sulfate lyase-like protein and enzymes related to the synthase and utilization of polyhydroxyalkanoate for carbon utilization, nitrate and nitrite reductase, glutamate dehydrogenase, glutamate synthase and glutamine synthetase for nitrogen cycle, polyphosphate kinases (pkk1 and pkk2), the high-affinity phosphate-specific transport (Pst) system and the low-affinity inorganic phosphate transporter (pitA) for phosphorus cycle, cysteine synthase and type III acyl coenzyme A transferase (dddD) for sulfur cycle. These features indicated the metabolic patterns of Bordetella sp. HZ20 in C, N, P and S cycles. In addition, the predicted Pst system and cysteine synthase were also related to biofilm formation which showed the potential pathogenicity of Bordetella sp. HZ20 to the cells of animals or plants. This study provides evidences about the metabolic patterns of Bordetella sp. HZ20 and broadens our understandings about ecological roles of bacterium without algal-polysaccharides degrading abilities in the brown seaweed-abundant environment.

Read more
July 7, 2019

Lifestyle of Lactobacillus hordei isolated from water kefir based on genomic, proteomic and physiological characterization.

Water kefir is a traditional fermented beverage made from sucrose, water, kefir granules, dried or fresh fruits. In our water kefir granules, Lactobacillus (L.) hordei is one of the predominant lactic acid bacteria (LAB) species of this presumed symbiotic consortium. It faces abundant sucrose versus limitation of amino- and fatty acids in an acidic environment. Sequencing of the genome of L. hordei TMW 1.1822 revealed one chromosome plus three plasmids. The size of the chromosome was 2.42?Mbp with a GC content of 35% GC and 2461 predicted coding sequences. Furthermore, we identified 1474 proteins upon growth on water kefir medium. Metabolic prediction revealed all enzymes required for the glycolytic Embden-Meyerhof (EMP) and phosphoketolase (PKP) pathways. Genes encoding all enzymes involved in citrate, pyruvate and mannitol metabolism are present. Moreover, it was confirmed that L. hordei is prototrophic for 11 amino acids and auxotrophic for 6 amino acids when combining putative biosynthesis pathways for amino acids with physiological characterization. Still, for glycine, serine and methionine no sure auxotype could be determined. The OppABCDF peptide transport system is complete, and 13 genes encoding peptidases are present. The arginine deiminase system, was predicted to be complete except for carbamate kinase, thus enabling neutralization reactions via ammonium formation but no additional energy generation. Taken together our findings enable prediction of the L. hordei lifestyle in water kefir: Abundant sucrose is consumed directly via parallel EMP and PK pathways and is also extracellularly converted to dextran and fructose by a glucansucrase, leaving fructose as additional carbon source. Essential amino acids (in the form of peptides) and citrate are acquired from fruits. In the lack of FabB unsaturated fatty acids are synthesized by predicted alternative enzymes. Formation of acetoin and diacetyl as well as arginine conversion reactions enable acidification limitation. Other members of the water kefir consortium (yeasts, acetic acid bacteria) likely facilitate or support growth of L. hordei by delivering gluconate, mannitol, amino- and fatty acids and vitamins. Copyright © 2018 Elsevier B.V. All rights reserved.

Read more
July 7, 2019

Whole-genome sequence of purple non-sulfur bacteria, Rhodobacter sphaeroides strain MBTLJ-8 with improved CO2 reduction capacity.

Rhodobacter sphaeroides consists of two chromosomes and many plasmids and incorporates many environmentally important functional gene. Rhodobacter sphaeroides MBTLJ-8 was derived from R. sphaeroides 2.4.1 using chemical mutagenesis and is characterized by enhanced production of physiological active compounds as well as improved carbon dioxide reduction capacity. We reported the complete genome sequence and characteristics based on genomic information of this bacteria. Therefore, this genome sequence provides elucidation for improved CO2 fixation and enhanced physiological active compounds production, and will be used as the efficient photosynthetic bacteria for the biological CO2 reduction system. Copyright © 2018 Elsevier B.V. All rights reserved.

Read more

Subscribe for blog updates:

Talk with an expert

If you have a question, need to check the status of an order, or are interested in purchasing an instrument, we're here to help.