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Antimicrobial-producing Pseudoalteromonas from the marine environment of Panama shows a high phylogenetic diversity and clonal structure

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Abstract

Pseudoalteromonas is a genus of marine bacteria often found in association with other organisms. Although several studies have examined Pseudoalteromonas diversity and their antimicrobial activity, its diversity in tropical environments is largely unexplored. We investigated the diversity of Pseudoalteromonas in marine environments of Panama using a multilocus phylogenetic approach. Furthermore we tested their antimicrobial capacity and evaluated the effect of recombination and mutation in shaping their phylogenetic relationships. The reconstruction of clonal relationships among 78 strains including 15 reference Pseudoalteromonas species revealed 43 clonal lineages, divided in pigmented and non‐pigmented strains. In total, 39 strains displayed moderate to high activity against Gram‐positive and Gram‐negative bacteria and fungi. Linkage disequilibrium analyses showed that the Pseudoalteromonas strains of Panama have a highly clonal structure and that, although present, recombination is not frequent enough to break the association among alleles. This clonal structure is in contrast to the high rates of recombination generally reported for aquatic and marine bacteria. We propose that this structure is likely due to the symbiotic association with marine invertebrates of most strains analyzed. Our results also show that there are several putative new species of Pseudoalteromonas in Panama to be described.

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... Our results show that all strains possess BGCs for the production of secondary metabolites, and a considerable number of distinct polyketide synthases (PKS) and NRPS clusters are present in pigmented strains. Furthermore, the molecular networking analyses revealed two new molecules produced during microbial interactions: the dibromoalterochromides D/D' (11)(12). ...
... The structures of compounds 1-8 were confirmed by manual annotation of their MS 2 spectra (Table S6, Figures S3 and S4). Additionally, we found two nodes in the bromoalterochromides cluster, m/z 860.3027 and 938.2117, (Figure 4) that could not be assigned to known compounds, hence we proceeded to a more detailed analyses of these metabolites through manual annotation of their MS 2 spectra finding out they were new compounds named bromoalterochromides D/D' (9, 10), and their dibrominated analogues (11,12) (Figures 1 and 4). ...
... The cluster includes the bromoalterochromide A series, which possesses an aryl polyene side chain of 15 carbon atoms, and the bromoalterochromide B series with an aryl polyene moiety of 17 carbon atoms that include an additional double bond ( Figure 4). The new dibromoalterochromides (11)(12) are part of bromoalterochromide A series, with an aryl polyene moiety of 15 carbon atoms. ...
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The marine bacterial genus Pseudoalteromonas is known for their ability to produce antimicrobial compounds. The metabolite-producing capacity of Pseudoalteromonas has been associated with strain pigmentation; however, the genomic basis of their antimicrobial capacity remains to be explained. In this study, we sequenced the whole genome of six Pseudoalteromonas strains (three pigmented and three non-pigmented), with the purpose of identifying biosynthetic gene clusters (BGCs) associated to compounds we detected via microbial interactions along through MS-based molecular networking. The genomes were assembled and annotated using the SPAdes and RAST pipelines and mined for the identification of gene clusters involved in secondary metabolism using the antiSMASH database. Nineteen BGCs were detected for each non-pigmented strain, while more than thirty BGCs were found for two of the pigmented strains. Among these, the groups of genes of nonribosomal peptide synthetases (NRPS) that code for bromoalterochromides stand out the most. Our results show that all strains possess BGCs for the production of secondary metabolites, and a considerable number of distinct polyketide synthases (PKS) and NRPS clusters are present in pigmented strains. Furthermore, the molecular networking analyses revealed two new molecules produced during microbial interactions: the dibromoalterochromides D/D' (11-12).
... These groups can therefore be considered good targets for surveys of putative beneficial micro-organisms for corals (BMCs) (Peixoto et al. 2017). In addition, some antimicrobial and antibiofilm compounds appear to be effective for controlling not only putative opportunistic coral microbes, but also for controlling clinically important micro-organisms, such as Staphylococcus aureus, Escherichia coli, Candida albicans and Aspergillus fumigatus (Gao et al. 2010;Moree et al. 2013;Atencio et al. 2018). In the following topics, we present an overview of characterized CAB compounds, their ecological importance in the coral metaorganism and their biotechnological potentials. ...
... biosynthesize several pharmaceutically important pigments of low to high molecular weights, with different antibiotic, anti-algae and antifouling properties (Bowman 2007;Kvennefors et al. 2012). Atencio et al. (2018) isolated 39 Pseudoalteromonas strains from octocoral species from Panama that show antibacterial activity against Gram-positive bacteria and high antifungal activity against C. albicans, an opportunistic pathogen present in the human gastrointestinal tract (Calderone and Clancy 2011). ...
... ;Chen et al. 2010;ElAhwany et al. 2015;Pham et al. 2016; Keller-Costa et al. 2016, Mahmoud andKalendar 2016;Ahila et al. 2017;Pereira et al. 2017;Atencio et al. 2018;Sharma et al. 2019). For example,Al-Zereini et al. (2010) first reported seven novel nitro maleimide antibacterial metabolites, termed Aqabamycins A-G, from Vibrio sp. ...
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Symbiotic relationships between corals and their associated microorganisms are essential to maintain host homeostasis. Coral‐associated bacteria (CAB) can have different beneficial roles in the coral metaorganism, such as metabolizing essential nutrients for the coral host and protecting the coral from pathogens. Many CAB exert these functions via secondary metabolites, which include antibacterial, antifouling, antitumor, antiparasitic, and antiviral compounds. This review describes how analysis of CAB has led to the discovery of secondary metabolites with potential biotechnological applications. The most commonly found types of secondary metabolites, antimicrobial and antibiofilm compounds, are emphasized and described. Recently developed methods that can be applied to enhance the culturing of CAB from shallow‐water reefs and the less‐studied deep‐sea coral reefs are also discussed. Last, we suggest how the combined use of meta‐omics and innovative growth‐diffusion techniques can vastly improve the discovery of novel compounds in coral environments.
... This species belongs to the genus of Pseudoalteromonas and the class of Gammaproteobacteria. The genus Pseudoalteromonas is a genus consisting of aerobic, Gramnegative marine bacteria and has a flagellum to push or attract bacterial cells in a liquid medium (Madigan et al. 2015) Based on a study conducted by Atencio et al. (2018), the genus Pseudoalteromonas is widely distributed in the marine environment and associated with marine organisms. ...
... P. arabiensis which is isolated from the tissues and layers of the Octocoralia mucus is capable of producing exopolysaccharide (EPS), a bioactive molecule that acts as an antifungal. These bioactive molecules make this bacteria able to help corals againts pathogenic invasions and be resistant to disease infections (Atencio et al. 2018). ...
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Agung MUK, Khairunnisa N, Astuty S, Lewaru MW, Mulyani Y. 2021. Isolation and 16S rRNA Characterization of Culturable Bacteria derived from Fire Coral Millepora intricata in Morela Coastal Waters, Maluku, Indonesia. Ocean Life 4: 1-7. Millepora, well recognized as fire coral, has nematocytes that contain toxins as self-defense, allowing the associated bacteria to have a high level of adaptation to survive in this extreme environment. This research aims to isolate and characterize fire corals Millepora intricata-associated bacteria obtained from Morela coastal waters, Maluku, Indonesia using classical culture method. Sampling of M. intricata was carried out in August 2017 from the depth of 2-3 meters. The bacteria were grown in sea water-Nutrient Agar (NA) medium, streak plate method then used until pure isolates were obtained. Molecular identification of isolates was performed using 16S rRNA gene marker. The results indicated that nine culturable pure isolates were successfully obtained from M. intricata. Three isolates (MI.P1.B; MI.P2.C; and MI.P2.D2.K) then further proceed into molecular identification and sequencing. Alignment result based on the 16S rRNA databases repositored in the genebank (NCBI) showed that isolate MI P1.B has similarity to registered sequence of Pseudoalteromonas arabiensis strain k53 (NCBI acc no. NR_113220.1) with a sequence identity of 98%. Isolate MI.P2.C has a close relationship (98%) to registered sequence of Halomonas aquamarina strain DSM 30161 (NCBI acc no. NR_042063.1). Meanwhile, isolate MI.P2.D2.K has similarity to registered sequence of Halomonas zhanjiangensis strain JSM 078169 (NCBI acc no. NR_104283.1) with a sequence identity of 99%.
... Coral's microbiome association mainly depends on the corals' species on which they develop a relevant role in the biosynthesis of compounds with a high degree of bioactivities, for protection against pathogenic microorganisms. Thus, the coral microbiome is an important source of antibacterial natural products [11][12][13][14]. ...
... The genetic identification of the bacterial species GA237 and BO53 was performed based on the methodology described by Atencio et al. [13]. Briefly, for DNA extraction, one milliliter of the GA237 and BO53 species were cultured on Luria Bertani (LB) broth (Difco, Michigan, MI, USA), supplemented with seawater, and grown at 25 • C for 24 h. ...
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The present research aimed to evaluate the antibacterial activity of volatile organic compounds (VOCs) produced by octocoral-associated bacteria Bacillus sp. BO53 and Pseudoalteromonas sp. GA327. The volatilome bioactivity of both bacteria species was evaluated against human pathogenic antibiotic-resistant bacteria, methicillin-resistant Staphylococcus aureus, Acinetobacter baumanni, and Pseudomonas aeruginosa. In this regard, the in vitro tests showed that Bacillus sp. BO53 VOCs inhibited the growth of P. aeruginosa and reduced the growth of S. aureus and A. baumanni. Furthermore, Pseudoalteromonas sp. GA327 strongly inhibited the growth of A. baumanni, and P. aeruginosa. VOCs were analyzed by headspace solid-phase microextraction (HS-SPME) joined to gas chromatography-mass spectrometry (GC-MS) methodology. Nineteen VOCs were identified, where 5-acetyl-2-methylpyridine, 2-butanone, and 2-nonanone were the major compounds identified on Bacillus sp. BO53 VOCs; while 1-pentanol, 2-butanone, and butyl formate were the primary volatile compounds detected in Pseudoalteromonas sp. GA327. We proposed that the observed bioactivity is mainly due to the efficient inhibitory biochemical mechanisms of alcohols and ketones upon antibiotic-resistant bacteria. This is the first report which describes the antibacterial activity of VOCs emitted by octocoral-associated bacteria.
... As a whole, the bioactive exoproducts produced by Pseudoalteromonas species possess a wide spectrum of biological activities and commercial applications such as antibacterial compounds (McCarthy et al. 1994;James et al. 1996;Isnansetyo and Kamei 2003;Franks et al. 2005;Zheng et al. 2005;Yang et al. 2007;Del Castillo et al. 2008;Chen et al. 2010;Feher et al. 2010;Aranda et al. 2012;Yu et al. 2012;Tebben et al. 2014), antifungal compounds (Kalinovskaya et al. 2004;Agarwall et al. 2014;Moree et al. 2014), antitumour (Feher et al. 2008Sobolevskaya et al. 2005;Sannino et al. 2018), antibiofilm compounds (Mai-Prochnow et al. 2006;Zeng et al. 2017;Klein et al. 2011;Daboor et al. 2019;Jouault et al. 2020), skin care cosmetics (Perez-Arcas et al. 2011), beneficial exopolysaccharides for marine invertebrate maturation (Peng et al. 2020a, b), cryoprotectants (Liu et al. 2013), and extracellular enzymes with unusual polymer hydrolytic activities (Bakunina et al. 2002;Chen et al. 2007;Zhao et al. 2008;Yu et al. 2012;Pan et al. 2019;Hettle et al. 2019;Paulsen et al. 2019;Ray et al. 2019). These valuable products, along with the ability to easily isolate the genus from the surfaces of healthy marine eukaryotic hosts, suggest that the Pseudoalteromonas genus is a key player in biofilm formation, development, and protection from pathogens (Offret et al. 2016;Atencio et al. 2018;Alker et al. 2020;Peng et al. 2020b;Chau et al. 2021). ...
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Most members of the Pseudoalteromonas genus have been isolated from living surfaces as members of epiphytic and epizooic microbiomes on marine macroorganisms. Commonly Pseudoalteromonas isolates are reported as a source of bioactive exoproducts, i.e., secondary metabolites, such as exopolymeric substances and extracellular enzymes. The experimental conditions for the production of these agents are commonly associated with sessile metabolic states such as biofilms or liquid cultures in the stationary growth phase. Despite this, the molecular mechanisms that connect biofilm formation and the biosynthesis of exoproducts in Pseudoalteromonas isolates have rarely been mentioned in the literature. This review compiles empirical evidence about exoproduct biosynthesis conditions and molecular mechanisms that regulate sessile metabolic states in Pseudoalteromonas species, to provide a comprehensive perspective on the regulatory convergences that generate the recurrent coexistence of both phenomena in this bacterial genus. This synthesis aims to provide perspectives on the extent of this phenomenon for the optimization of bioprospection studies and biotechnology processes based on these bacteria.
... The strains affiliated to this genus are often described as fast-growing bacteria, able to efficiently convert dispersed organic matter into growth substrates (Parrilli et al., 2021). It is present in all marine habitats, such as coastal, open, and deep-sea waters, sediments, is also frequently associated with healthy algae, invertebrates, and marine animals (Atencio et al., 2018). Few strains have been described as pathogenic or opportunistic being some examples of P. piscicida, P. agarivorans, and Pseudoalteromonas undina (Offret et al., 2016;Pujalte et al., 2007;Rosenberg et al., 2013). ...
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... Interestingly, the anti-fouling substances from CAMs are more potent than those derived from free-living bacteria [11]. And CAM-derived anti-microbial NPs have proven effectiveness against clinically important pathogens [10,12,13]. A focus on microbes from the SML to find new antibiotics may thus be warranted. ...
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... As discussed previously, these microorganisms would benefit by living at or near redox interfaces and/or by transitioning frequently between oxic and anoxic environments that may source terminal electron acceptors and donors, respectively, and a variety of other nutrients. Additionally, several species of Pseudoalteromonas are widely discussed in the literature as symbionts, given their diverse metabolic potential and their ability to produce a variety of antibacterial, antifungal, algicidal, and antifouling compounds (Offret et al., 2016;Atencio et al., 2018). ...
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We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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A novel exopolysaccharide-producing bacterium, designated strain k53T, was isolated from the Arabia Sea sediment in Indian Ocean. The strain was Gram-negative, motile, strictly aerobic, oxidase-positive and catalase-positive, and required Na+ for growth. Its major isoprenoid quinone was ubiquinone-8 (Q-8), and its cellular fatty acid profile mainly consisted of C16:1ω7c (26.3%), C16:0 (20.2%) and C18:1ω7c (16%). The DNA G+C content was 43 mol%. 16S rRNA gene sequence analysis suggested that strain k53T is a member of the genus Pseudoalteromonas. Strain k53T exhibited the closely phylogenetic affinity to Pseudoalteromonas lipolytica LMEB 39T (98.0%) and P. donghaensis HJ51T (97.3% sequence similarity). The DNA-DNA reassociation values between strain k53T and P. lipolytica JCM 15903T and P. donghaensis LMG 24469T were 17% and 12%, respectively. Owing to the significant differences in phenotypic and chemotaxonomic characteristics, and phylogenetic analysis based on the 16S rRNA gene sequence and DNA-DNA relatedness data, the isolate merits classification as a new species, for which the name Pseudoalteromonas arabiensis is proposed. The type strain of this species is k53T (=JCM 17292T=NCIMB 14688 T).
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In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements. In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. Alignment of up to 500 sequences using the latest SILVA SSU/LSU Ref datasets as reference MSA is offered at http://www.arb-silva.de/aligner. This page also links to Linux binaries, user manual and tutorial. SINA is made available under a personal use license.
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Yu et al. (Polar Biol. 32:1539-1547, 2009) isolated 199 Pseudoalteromonas strains from Arctic sea ice. We sequenced the genomes of six of these strains, which are affiliated to different Pseudoalteromonas species based on 16S rRNA gene sequences, facilitating the study of physiology and adaptation of Arctic sea ice Pseudoalteromonas strains.
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Primers4clades is an easy-to-use web server that implements a fully automatic PCR primer design pipeline for cross-species amplification of novel sequences from metagenomic DNA, or from uncharacterized organisms, belonging to user-specified phylogenetic clades or taxa. The server takes a set of non-aligned protein coding genes, with or without introns, aligns them and computes a neighbor-joining tree, which is displayed on screen for easy selection of species or sequence clusters to design lineage-specific PCR primers. Primers4clades implements an extended CODEHOP primer design strategy based on both DNA and protein multiple sequence alignments. It evaluates several thermodynamic properties of the oligonucleotide pairs, and computes the phylogenetic information content of the predicted amplicon sets from Shimodaira–Hasegawa-like branch support values of maximum likelihood phylogenies. A non-redundant set of primer formulations is returned, ranked according to their thermodynamic properties. An amplicon distribution map provides a convenient overview of the coverage of the target locus. Altogether these features greatly help the user in making an informed choice between alternative primer pair formulations. Primers4clades is available at two mirror sites: http://maya.ccg.unam.mx/primers4clades/and http://floresta.eead.csic.es/primers4clades/. Three demo data sets and a comprehensive documentation/tutorial page are provided for easy testing of the server's capabilities and interface.
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It is a standard practice to test for the signature of homologous recombination in studies examining the genetic diversity of bacterial populations. Although it has emerged that homologous recombination rates can vary widely between species, comparing the results from different studies is made difficult by the diversity of estimation methods used. Here, Multi Locus Sequence Typing (MLST) datasets from a wide variety of bacteria and archaea are analyzed using the ClonalFrame method. This enables a direct comparison between species and allows for a first exploration of the question whether phylogeny or ecology is the primary determinant of homologous recombination rate.
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We have examined the ability of marine Proteobacteria from the Pseudoalteromonas genus and Alteromonas macleodii to produce low-molecular-weight, biologically active compounds with antimicrobial and surface-active properties. A new marine bacterium, Pseudoalteromonas issachenkonii, exhibited a high level of biological activity and produced antifungal and hemolytic compounds. A detailed spectroscopic investigation based on UV, IR, high-resolution mass spectrometry, and 2D 1H and 13C nuclear magnetic resonance revealed that the former was indole-2,3-dione (isatin). The chemical structure of red-brown pigment (C9H7N3OS3) responsible for hemolytic activity remained unclear. Four of the 15 strains studied (P. luteoviolacea, P. rubra, P. undina, and P. issachenkonii) produced cell-bound, two (P. elaykovii and P. carrageenovora) produced extracellular, and one strain (P. citrea) produced cell-bound and extracellular fatty acids and phospholipids with surface activity. Neither peptides nor glycolipids with surface activity were detected.
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The family Pseudoalteromonadaceae (class Gammaproteobacteria, order Alteromonadales) consists of three genera: the type genus Pseudoalteromonas, containing 37 species; the genus Algicola, containing two species; and the genus Psychrosphaera with one species. All species are Gram-negative rods, with the exception of Psychrosphaera saromensis which is a coccus. Historically, many species of Pseudoalteromonas were assigned to the genus Alteromonas. Similarly, both Algicola bacteriolytica and A. sagamiensis were reclassified from Pseudoalteromonas to form a separate genus. Many species of this family produce a variety of primary and secondary metabolites including hydrolytic enzymes, cyclic peptides, proteins and protein inhibitors, pigments, exopolymers, phenolic and pyrrole-containing alkaloids, and unusual brominated compounds with antibacterial and antiviral properties. Due to their versatile metabolic capacities, members of this family are highly adaptable to dissimilar ecological habitats and play important ecological roles in marine environments. © 2014 Springer-Verlag Berlin Heidelberg. All rights are reserved.
Chapter
An overview into recently identified promising marine natural products or derivatives is provided. The pipeline includes unique chemical entities from marine microorganisms, macroalgae and marine invertebrates, as well as synthetic derivatives. This glimpse into the future of marine natural products offers particular insight into the development of anticancer compounds with original mechanisms of action, a novel potent anti-HIV strategy, and new hopes for the treatment of asthma or neurological and Alzheimer's diseases. At the start of the twenty-first century, the field of marine molecules continues to provide an exciting source of new and highly potent pharmaceuticals.
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The planktonic genus Planktothrix, as other cyanobacteria, shows signals of both homologous and nonhomologous recombination. However, the frequency of recombination and its effect on Planktothrix population structuring is unknown. We isolated 290 Planktothrix strains from seven neighboring lakes in the subalpine Italian region and analyzed these using multilocus sequence typing. Four of six loci analyzed were polymorphic, resulting in 20 distinct multilocus genotypes. Association indices among alleles at different loci were suggestive of an epidemic population structure, resulting from an explosive (and temporary) dominance of one genotype against a panmictic background. ClonalFrame analyses supported this view by detecting: (i) three major clades affected by three distinct recombination events, (ii) a recombination rate about equal to the mutation rate, and (iii) the fact that recombination had an impact on introducing molecular diversity more than double the mutation rate. Furthermore, analysis of molecular variance over an annual cycle in three of seven lakes revealed that both local clonal expansion and recombination processes affected among-lake diversity. Our observations suggest that recombination affects microevolution of Planktothrix and that an epidemic structure can emerge in populations of this genus.
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Genomics, Proteomics, and Clinical Bacteriology is an accessible introduction to how genomics has and will provide novel methods for bacterial investigation and advance our understanding and knowledge of bacterial pathogenicity. The authors critically evaluate the applications of genomics to diagnostic bacteriology, highlighting both current and likely future uses, describing real-time PCR methods, and outlining the promise of microarrays in clinical bacteriology. Their discussion examines in detail genomic approaches to antibacterial discovery, the nature of pathogenicity, the discovery of new pathogens, the exploration of the concept of clonality in bacteria, and bacterial taxonomics.
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The marine environment has been a source of more than 20,000 inspirational natural products discovered over the past 50 years. From these efforts, 9 approved drugs and 12 current clinical trial agents have been discovered, either as natural products or as molecules inspired from the natural product structure. To a significant degree, these have come from collections of marine invertebrates largely obtained from shallow-water tropical ecosystems. However, there is a growing recognition that marine invertebrates are oftentimes populated with enormous quantities of "associated" or symbiotic microorganisms and that microorganisms are the true metabolic sources of these most valuable of marine natural products. Also, because of the inherently multidisciplinary nature of this field, a high degree of innovation is characteristic of marine natural product drug discovery efforts.
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Extensive data from multilocus electrophoresis are available for many bacterial populations. In some cases, for example Neisseria gonorrhoeae, these data are consistent with the population being in linkage equilibrium. This raises the following question. What frequency of transformation, or other means of genetic recombination, is needed, relative to mutation, to produce apparent panmixis? Simulation of a finite-population model suggests that, if transformation is at least twenty times as frequent as mutation, the population structure will be indistinguishable from a panmictic one, using the best available data sets. That is, relatively infrequent transformation is sufficient to produce approximate linkage equilibrium.
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Linkage disequilibrium is an ubiquitous biological phenomenon. However a common metric for disequilibrium — the index of association or I A - is dependent on sample size. In this paper we present a modification of I A that removes this dependency. This method has been implemented in a software package.
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Bacteria and archaea reproduce clonally, but sporadically import DNA into their chromosomes from other organisms. In many of these events, the imported DNA replaces an homologous segment in the recipient genome. Here we present a new method to reconstruct the history of recombination events that affected a given sample of bacterial genomes. We introduce a mathematical model that represents both the donor and the recipient of each DNA import as an ancestor of the genomes in the sample. The model represents a simplification of the previously described coalescent with gene conversion. We implement a Monte Carlo Markov chain algorithm to perform inference under this model from sequence data alignments and show that inference is feasible for whole-genome alignments through parallelization. Using simulated data, we demonstrate accurate and reliable identification of individual recombination events and global recombination rate parameters. We applied our approach to an alignment of 13 whole genomes from the Bacillus cereus group. We find, as expected from laboratory experiments, that the recombination rate is higher between closely related organisms and also that the genome contains several broad regions of elevated levels of recombination. Application of the method to the genomic data sets that are becoming available should reveal the evolutionary history and private lives of populations of bacteria and archaea. The methods described in this article have been implemented in a computer software package, ClonalOrigin, which is freely available from http://code.google.com/p/clonalorigin/.
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The Gibbs sampler, the algorithm of Metropolis and similar iterative simulation methods are potentially very helpful for summarizing multivariate distributions. Used naively, however, iterative simulation can give misleading answers. Our methods are simple and generally applicable to the output of any iterative simulation; they are designed for researchers primarily interested in the science underlying the data and models they are analyzing, rather than for researchers interested in the probability theory underlying the iterative simulations themselves. Our recommended strategy is to use several independent sequences, with starting points sampled from an overdispersed distribution. At each step of the iterative simulation, we obtain, for each univariate estimand of interest, a distributional estimate and an estimate of how much sharper the distributional estimate might become if the simulations were continued indefinitely. Because our focus is on applied inference for Bayesian posterior distributions in real problems, which often tend toward normality after transformations and marginalization, we derive our results as normal-theory approximations to exact Bayesian inference, conditional on the observed simulations. The methods are illustrated on a random-effects mixture model applied to experimental measurements of reaction times of normal and schizophrenic patients.
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This review describes secondary metabolites that have been shown to be synthesized by symbiotic bacteria, or for which this possibility has been discussed. It includes 365 references.
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Vibrio parahaemolyticus is a marine bacterium with a worldwide distribution and is frequently associated with human outbreaks of infection. Detection and isolation of V. parahaemolyticus from natural sources is often problematical because of limitations in the analytical procedures. We evaluated a combination of conventional and molecular protocols previously described for the investigation of V. parahaemolyticus, with the aim of identifying the best procedures for improved detection of this organism in environmental matrixes. A total of 259 samples of zooplankton (103), mussels (48) and seawater (108) were investigated by an Absence-Presence method (A/P), whereas 118 samples of zooplankton (70) and mussels (48) were analyzed by the Most Probable Number (MPN) method. All samples were processed by a two-step enrichment procedure, firstly with APW broth and then with SPB as selective secondary broth. Detection of V. parahaemolyticus was by direct-PCR and by plate culture on TCBS and CHROMagar Vibrio, after sample enrichment in APW and SPB. With the A/P method, V. parahaemolyticus was detected in 23.6% samples by direct-PCR, whereas only 11.2% samples were positive with the plate culture method. With the MPN method, V. parahaemolyticus was detected in 54.2% and 27.1% of the samples by direct-PCR and plate culture respectively; this indicated the existence of 31% false negative results with the A/P method. No significant differences between the use of a single (APW) or two-step enrichment (APW+SPB) were observed by direct-PCR with A/P or MPN, although a significant higher presence of V. parahaemolyticus was detected by plate culture in both protocols with the two-step enrichment procedure. In conclusion, direct-PCR after sample enrichment in APW broth was the most successful method for detection of V. parahaemolyticus with the A/P procedure and enumeration by MPN. Better detection was obtained with MPN than with the A/P protocol. Conversely, the plate culture procedure showed better results with the two-step enrichment protocol in which CHROMagar Vibrio was used as the selective agar.
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Small-subunit ribosomal DNA sequences were determined for 17 strains belonging to the genera Alteromonas, Shewanella, Vibrio, and Pseudomonas, and these sequences were analyzed by phylogenetic methods. The resulting data confirmed the existence of the genera Shewanella and Moritella, but suggested that the genus Alteromonas should be split into two genera. We propose that a new genus, the genus Pseudoalteromonas, should be created to accommodate 11 species that were previously Alteromonas species, including Pseudoalteromonas atlantica comb. nov., Pseudoalteromonas aurantia comb. nov., Pseudoalteromonas carrageenovoa comb. nov., Pseudoalteromonas citrea comb. nov., Pseudoalteromonas denitrificans comb. nov., Pseudoalteromonas espejiana comb. nov., Pseudoalteromonas haloplanktis comb. nov. (with two subspecies, Pseudoalteromonas haloplanktis subsp. haloplanktis comb. nov. and Pseudoalteromonas haloplanktis subsp. tetraodonis comb. nov.), Pseudoalteromonas luteoviolacea comb. nov., Pseudoalteromonas nigrifaciens comb. nov., Pseudoalteromonas rubra comb. nov., and Pseudoalteromonas undina comb, nov., and one species that previously was placed in the genus Pseudomonas, Pseudoalteromonas piscicida comb. nov. We propose that P. haloplanktis (type strain, ATCC 14393) should be the type species of the genus Pseudoalteromonas. At this time the emended genus Alteromonas is restricted to a single species, Alteromonas macleodii.
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Isolates of bacterial species that are indistinguishable in genotype are assigned as a clone, with the implication that they are descended from the same recent ancestor. Clones are difficult to define with precision since bacteria are not truly asexual, and recombinational replacements result in diversification of the ancestral genotype of a clone, to produce a cluster of increasingly diverse genotypes (a clonal complex). The rate at which clonal diversification occurs depends on the extent of recombination, which varies among bacteria, so that some species have rather stable clones (e.g., Salmonella enterica), whereas in other species (e.g., Helicobacter pylori) clones may be so transient that they cannot readily be discerned. Clones and clonal complexes need to be assigned by indexing genetic variation that is selectively neutral, and currently this is best achieved using multilocus sequence typing. Some species of bacterial pathogens are very diverse, whereas others are genetically uniform, and some are, in essence, a single clone of a mother species that has been raised to species status due to the distinctiveness of the disease it causes (e.g., Yersinia pestis, Salmonella typhi, or Burkholderia mallei). The population structures of bacteria depend on the rate of recombination, and comparative measures of the extent of recombination during clonal diversification can be obtained from multilocus sequence typing data, as can measures of the longer-term impact of recombination. These studies show a wide range of recombination rates among bacterial species, and indicate that recombination in many bacteria has been sufficiently extensive that a reliable evolutionary history of the species cannot be inferred.
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This review describes natural products that are shown or suspected to be synthesized by symbiotic bacteria. It includes 349 references and covers the literature in this field through 2003.