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Applied and Environmental Microbiology Jun 2019The genus comprises a group of marine-dwelling species with worldwide distribution. Several species are regarded as causative agents of food spoilage and opportunistic...
Multilocus Sequence Analysis, a Rapid and Accurate Tool for Taxonomic Classification, Evolutionary Relationship Determination, and Population Biology Studies of the Genus .
The genus comprises a group of marine-dwelling species with worldwide distribution. Several species are regarded as causative agents of food spoilage and opportunistic pathogens of human diseases. In this study, a standard multilocus sequence analysis (MLSA) based on six protein-coding genes (, , , , , and ) was established as a rapid and accurate identification tool in 59 type strains. This method yielded sufficient resolving power in regard to enough informative sites, adequate sequence divergences, and distinct interspecies branches. The stability of phylogenetic topology was supported by high bootstrap values and concordance with different methods. The reliability of the MLSA scheme was further validated by identical phylogenies and high correlations of genomes. The MLSA approach provided a robust system to exhibit evolutionary relationships in the genus. The split network tree proposed twelve distinct monophyletic clades with identical G+C contents and high genetic similarities. A total of 86 tested strains were investigated to explore the population biology of the genus in China. The most prevalent species was , followed by , , , , and The strains frequently isolated from clinical and food samples highlighted the importance of increasing the surveillance of species. Based on the combined genetic, genomic, and phenotypic analyses, should be considered a synonym of , and should be reclassified as a synonym of The MLSA scheme based on six housekeeping genes (HKGs) (, , , , , and ) is well established as a reliable tool for taxonomic, evolutionary, and population diversity analyses of the genus in this study. The standard MLSA method allows researchers to make rapid, economical, and precise identification of strains. The robust phylogenetic network of MLSA provides profound insight into the evolutionary structure of the genus The population genetics of species determined by the MLSA approach plays a pivotal role in clinical diagnosis and routine monitoring. Further studies on remaining species and genomic analysis will enhance a more comprehensive understanding of the microbial systematics, phylogenetic relationships, and ecological status of the genus .
Topics: Bacterial Typing Techniques; Base Composition; Biological Evolution; China; DNA, Bacterial; Food Microbiology; Genes, Bacterial; Genes, Essential; Humans; Multilocus Sequence Typing; Phenotype; Phylogeny; RNA, Ribosomal, 16S; Reproducibility of Results; Sequence Analysis, DNA; Shewanella
PubMed: 30902862
DOI: 10.1128/AEM.03126-18 -
Sheng Wu Gong Cheng Xue Bao = Chinese... Mar 2023Facing the increasingly severe energy shortage and environmental pollution, electrocatalytic processes using electroactive microorganisms provide a new alternative for... (Review)
Review
Facing the increasingly severe energy shortage and environmental pollution, electrocatalytic processes using electroactive microorganisms provide a new alternative for achieving environmental-friendly production. Because of its unique respiratory mode and electron transfer ability, MR-1 has been widely used in the fields of microbial fuel cell, bioelectrosynthesis of value-added chemicals, metal waste treatment and environmental remediation system. The electrochemically active biofilm of . MR-1 is an excellent carrier for transferring the electrons of the electroactive microorganisms. The formation of electrochemically active biofilm is a dynamic and complex process, which is affected by many factors, such as electrode materials, culture conditions, strains and their metabolism. The electrochemically active biofilm plays a very important role in enhancing bacterial environmental stress resistance, improving nutrient uptake and electron transfer efficiency. This paper reviewed the formation process, influencing factors and applications of . MR-1 biofilm in bio-energy, bioremediation and biosensing, with the aim to facilitate and expand its further application.
Topics: Bioelectric Energy Sources; Biofilms; Electrodes; Electron Transport; Shewanella
PubMed: 36994560
DOI: 10.13345/j.cjb.220468 -
BMC Microbiology Nov 2020Infections caused by Shewanella spp. have been increasingly reported worldwide. The advances in genomic sciences have enabled better understanding about the taxonomy and...
BACKGROUND
Infections caused by Shewanella spp. have been increasingly reported worldwide. The advances in genomic sciences have enabled better understanding about the taxonomy and epidemiology of this agent. However, the scarcity of DNA sequencing data is still an obstacle for understanding the genus and its association with infections in humans and animals.
RESULTS
In this study, we report the first isolation and whole-genome sequencing of a Shewanella algae strain from a swine farm in Brazil using the boot sock method, as well as the resistance profile of this strain to antimicrobials. The isolate was first identified as Shewanella putrefaciens, but after whole-genome sequencing it showed greater similarity with Shewanella algae. The strain showed resistance to 46.7% of the antimicrobials tested, and 26 resistance genes were identified in the genome.
CONCLUSIONS
This report supports research made with Shewanella spp. and gives a step forward for understanding its taxonomy and epidemiology. It also highlights the risk of emerging pathogens with high resistance to antimicrobial formulas that are important to public health.
Topics: Animals; Anti-Bacterial Agents; Brazil; DNA, Bacterial; Drug Resistance, Multiple, Bacterial; Environmental Microbiology; Farms; Genome, Bacterial; Microbial Sensitivity Tests; Phylogeny; RNA, Ribosomal, 16S; Shewanella; Swine; Virulence Factors
PubMed: 33234140
DOI: 10.1186/s12866-020-02040-x -
Molecular Microbiology Jul 2007Dissimilatory reduction of metal (e.g. Fe, Mn) (hydr)oxides represents a challenge for microorganisms, as their cell envelopes are impermeable to metal (hydr)oxides that... (Review)
Review
Dissimilatory reduction of metal (e.g. Fe, Mn) (hydr)oxides represents a challenge for microorganisms, as their cell envelopes are impermeable to metal (hydr)oxides that are poorly soluble in water. To overcome this physical barrier, the Gram-negative bacteria Shewanella oneidensis MR-1 and Geobacter sulfurreducens have developed electron transfer (ET) strategies that require multihaem c-type cytochromes (c-Cyts). In S. oneidensis MR-1, multihaem c-Cyts CymA and MtrA are believed to transfer electrons from the inner membrane quinone/quinol pool through the periplasm to the outer membrane. The type II secretion system of S. oneidensis MR-1 has been implicated in the reduction of metal (hydr)oxides, most likely by translocating decahaem c-Cyts MtrC and OmcA across outer membrane to the surface of bacterial cells where they form a protein complex. The extracellular MtrC and OmcA can directly reduce solid metal (hydr)oxides. Likewise, outer membrane multihaem c-Cyts OmcE and OmcS of G. sulfurreducens are suggested to transfer electrons from outer membrane to type IV pili that are hypothesized to relay the electrons to solid metal (hydr)oxides. Thus, multihaem c-Cyts play critical roles in S. oneidensis MR-1- and G. sulfurreducens-mediated dissimilatory reduction of solid metal (hydr)oxides by facilitating ET across the bacterial cell envelope.
Topics: Bacterial Outer Membrane Proteins; Cytochrome c Group; Electron Transport; Ferric Compounds; Geobacter; Heme; Manganese Compounds; Oxidation-Reduction; Oxides; Shewanella
PubMed: 17581116
DOI: 10.1111/j.1365-2958.2007.05783.x -
Journal of Food Protection Feb 2021Shewanella baltica, one of the dominant spoilers of seafoods, can synthesize putrescine from ornithine under acidic conditions, which could result in food spoilage and...
ABSTRACT
Shewanella baltica, one of the dominant spoilers of seafoods, can synthesize putrescine from ornithine under acidic conditions, which could result in food spoilage and health problems. We identified three regulatory enzymes (SpeC, SpeF, and PotE) in the ornithine decarboxylation (ODC) pathway of S. baltica by searching the NCBI database and exploring their functional roles through gene knock-out technology. The ornithine decarboxylase SpeC is an auxiliary adjustor of the ODC system, whereas the ornithine-putrescine transporter SpeE and ornithine decarboxylase SpeF participate in the production of extracellular putrescine. Exogenous addition of ornithine and putrescine promotes the extracellular secretion of putrescine by upregulating the expression of speF and potE. The putrescine biosynthesis and alkalization of cytoplasm is enhanced at weak acidic pH compared with neutral pH, especially at pH 6.0. The maximum upregulation of ODC genes and the optimum decarboxylation activity of SpeF are achieved in a weak acidic environment (pH 6.0), suggesting that the ODC pathway plays an important role in putrescine production and the cytoplasmic acid counteraction of S. baltica. This study contributes to a wider understanding of spoilage mechanisms in food systems and provides theoretical support for developing novel seafood preservation methods.
Topics: Decarboxylation; Ornithine; Putrescine; Shewanella
PubMed: 33003195
DOI: 10.4315/JFP-20-227 -
ELife Aug 2019bacteria use an abiotic reaction to help shuttle electrons outside of the cell.
bacteria use an abiotic reaction to help shuttle electrons outside of the cell.
Topics: Electrons; Shewanella
PubMed: 31393267
DOI: 10.7554/eLife.49831 -
MSphere Oct 2021Although spp. are most frequently isolated from marine environments; more rarely, they have been implicated in human infections. spp. are also recognized as the origin...
Although spp. are most frequently isolated from marine environments; more rarely, they have been implicated in human infections. spp. are also recognized as the origin of genes for carbapenem-hydrolyzing class D β-lactamases. Due to the spread globally among in recent years, risk assessments of both clinical and environmental strains are urgently needed. In this study, we analyzed the whole-genome sequences of 10 clinical isolates and 13 environmental isolates of spp. and compared them with those of species strains registered in public databases. In addition, the levels of transcription and β-lactamase activity of a carbapenem-resistant Shewanella algae isolate were compared with those of carbapenem-susceptible S. algae clade isolates. All clinical isolates were genetically identified as S. algae clade (S. algae, Shewanella chilikensis, and Shewanella carassii), whereas all but one of the environmental isolates were identified as various spp. outside the S. algae clade. Although all isolates of the S. algae clade commonly possessed an approximately 12,500-bp genetic region harboring , genetic structures outside this region were different among species. Among S. algae clade isolates, only one showed carbapenem resistance, and this isolate showed a high level of transcription and β-lactamase activity. Although this study documented the importance of the S. algae clade in human infections and the relationship between enhanced production of OXA-55-like and resistance to carbapenems in S. algae, further studies are needed to elucidate the generalizability of these findings. spp., which are known to carry chromosomally located genes, have mainly been isolated from marine environments; however, they can also cause infections in humans. In this study, we compared the molecular characteristics of clinical isolates of spp. with those originating from environmental sources. All 10 clinical isolates were genetically identified as members of the Shewanella algae clade (S. algae, , and ); however, all but one of the 13 environmental isolates were identified as species members outside the S. algae clade. Although all the S. algae clade isolates possessed an approximately 12,500-bp genetic region harboring , only one isolate showed carbapenem resistance. The carbapenem-resistant isolate showed a high level of transcription and β-lactamase activity compared with the carbapenem-susceptible isolates. To confirm the clinical significance and antimicrobial resistance mechanisms of the S. algae clade members, analysis involving more clinical isolates should be performed in the future.
Topics: Anti-Bacterial Agents; Carbapenems; Environment; Microbial Sensitivity Tests; Phylogeny; Shewanella; Whole Genome Sequencing; beta-Lactamases
PubMed: 34643423
DOI: 10.1128/mSphere.00593-21 -
Applied and Environmental Microbiology Feb 2008The solubility of orthophosphate (PO4(3-)) in iron-rich sediments can be exceedingly low, limiting the bioavailability of this essential nutrient to microbial... (Comparative Study)
Comparative Study
The solubility of orthophosphate (PO4(3-)) in iron-rich sediments can be exceedingly low, limiting the bioavailability of this essential nutrient to microbial populations that catalyze critical biogeochemical reactions. Here we demonstrate that dissolved extracellular DNA can serve as a sole source of phosphorus, as well as carbon and energy, for metal-reducing bacteria of the genus Shewanella. Shewanella oneidensis MR-1, Shewanella putrefaciens CN32, and Shewanella sp. strain W3-18-1 all grew with DNA but displayed different growth rates. W3-18-1 exhibited the highest growth rate with DNA. While strain W3-18-1 displayed Ca2+-independent DNA utilization, both CN32 and MR-1 required millimolar concentrations of Ca2+ for growth with DNA. For S. oneidensis MR-1, the utilization of DNA as a sole source of phosphorus is linked to the activities of extracellular phosphatase(s) and a Ca2+-dependent nuclease(s), which are regulated by phosphorus availability. Mass spectrometry analysis of the extracellular proteome of MR-1 identified one putative endonuclease (SO1844), a predicted UshA (bifunctional UDP-sugar hydrolase/5' nucleotidase), a predicted PhoX (calcium-activated alkaline phosphatase), and a predicted CpdB (bifunctional 2',3' cyclic nucleotide 2' phosphodiesterase/3' nucleotidase), all of which could play important roles in the extracellular degradation of DNA under phosphorus-limiting conditions. Overall, the results of this study suggest that the ability to use exogenous DNA as the sole source of phosphorus is widespread among the shewanellae, and perhaps among all prokaryotes, and may be especially important for nutrient cycling in metal-reducing environments.
Topics: Carbon; Chromatography, High Pressure Liquid; DNA; DNA Primers; Energy Metabolism; Iron; Mass Spectrometry; Oxidation-Reduction; Phosphorus; Polymerase Chain Reaction; Shewanella; Species Specificity
PubMed: 18156329
DOI: 10.1128/AEM.02026-07 -
Microbial Biotechnology Jul 2021The ability to directly modify native and established biofilms has enormous potential in understanding microbial ecology and application of biofilm in 'real-world'...
The ability to directly modify native and established biofilms has enormous potential in understanding microbial ecology and application of biofilm in 'real-world' systems. However, efficient genetic transformation of established biofilms at any scale remains challenging. In this study, we applied an ultrasound-mediated DNA delivery (UDD) technique to introduce plasmid to established non-competent biofilms in situ. Two different plasmids containing genes coding for superfolder green fluorescent protein (sfGFP) and the flavin synthesis pathway were introduced into established bacterial biofilms in microfluidic flow (transformation efficiency of 3.9 ± 0.3 × 10 cells in biofilm) and microbial fuel cells (MFCs), respectively, both employing UDD. Gene expression and functional effects of genetically modified bacterial biofilms were observed, where some cells in UDD-treated Pseudomonas putida UWC1 biofilms expressed sfGFP in flow cells and UDD-treated Shewanella oneidensis MR-1 biofilms generated significantly (P < 0.05) greater (61%) bioelectricity production (21.9 ± 1.2 µA cm ) in MFC than a wild-type control group (~ 13.6 ± 1.6 µA cm ). The effects of UDD were amplified in subsequent growth under selection pressure due to antibiotic resistance and metabolism enhancement. UDD-induced gene transfer on biofilms grown in both microbial flow cells and MFC systems was successfully demonstrated, with working volumes of 0.16 cm and 300 cm , respectively, demonstrating a significant scale-up in operating volume. This is the first study to report on a potentially scalable direct genetic engineering method for established non-competent biofilms, which can be exploited in enhancing their capability towards environmental, industrial and medical applications.
Topics: Bioelectric Energy Sources; Biofilms; DNA; Genetic Engineering; Shewanella
PubMed: 33993638
DOI: 10.1111/1751-7915.13823 -
Journal of Microbiology and... May 2023Identification of novel, electricity-producing bacteria has garnered remarkable interest because of the various applications of electricigens in microbial fuel cell and...
Identification of novel, electricity-producing bacteria has garnered remarkable interest because of the various applications of electricigens in microbial fuel cell and bioelectrochemical systems. BBL25, an electricity-generating microorganism, uses various carbon sources and shows broader sugar utilization than the better-known MR-1. To determine the sugar-utilizing genes and electricity production and transfer system in BBL25, we performed an in-depth analysis using whole-genome sequencing. We identified various genes associated with carbon source utilization and the electron transfer system, similar to those of MR-1. In addition, we identified genes related to hydrogen production systems in BBL25, which were different from those in MR-1. When we cultured BBL25 under anaerobic conditions, the strain produced 427.58 ± 5.85 μl of biohydrogen from pyruvate and 877.43 ± 28.53 μl from xylose. As MR-1 could not utilize glucose well, we introduced the gene from BBL25 into MR-1, resulting in a 117.35% increase in growth and a 17.64% increase in glucose consumption. The results of BBL25 genome sequencing aided in the understanding of sugar utilization, electron transfer systems, and hydrogen production systems in other species.
Topics: Bioelectric Energy Sources; Shewanella; Glucose; Carbon; Hydrogen
PubMed: 36823146
DOI: 10.4014/jmb.2212.12024