Engineering a predatory bacterium as a proficient killer agent for intracellular bio-products recovery:The case of the polyhydroxyalkanoates

12p.-6 fig.-2 tab.This work examines the potential of the predatory bacterium Bdellovibrio bacteriovorus HD100, an obligate predator of other Gram-negative bacteria, as an external cell-lytic agent for recovering valuable intracellular bio-products produced by prey cultures. The bio-product targets to be recovered were polyhydroxyalkanoates (PHAs) produced naturally by Pseudomonas putida and Cupriavidus necator, or by recombinant Escherichia coli strains. B. bacteriovorus with a mutated PHA depolymerase gene to prevent the unwanted breakdown of the bio-product allowed the recovery of up to 80% of that accumulated by the prey bacteria, even at high biomass concentrations. This innovative downstream process highlights how B. bacteriovorus can be used as a novel, biological lytic agent for the inexpensive, industrial scale recovery of intracellular products from different Gram-negative prey cultures.This work was funded by the EU Seventh Framework Programme under grant agreement no. 311815 (SYNPOL), and by grants from the Comunidad de Madrid (P2013/MIT2807) and the Spanish Ministerio de Economía y Competitividad, (BIO2010-21049, BIO2013-44878-R).Peer reviewe

Editorial:Mechanisms of Prokaryotic Predation

No abstract available

Comparative Metagenomics and Network Analyses Provide Novel Insights Into the Scope and Distribution of β-Lactamase Homologs in the Environment

The β-lactams are the largest group of clinically applied antibiotics, and resistance to these is primarily associated with β-lactamases. There is increasing understanding that these enzymes are ubiquitous in natural environments and henceforth, elucidating the global diversity, distribution, and mobility of β-lactamase-encoding genes is crucial for holistically understanding resistance to these antibiotics. In this study, we screened 232 shotgun metagenomes from ten different environments against a custom-designed β-lactamase database, and subsequently analyzed β-lactamase homologs with a suite of bioinformatic platforms including cluster and network analyses. Three interrelated β-lactamase clusters encompassed all of the human and bovine feces metagenomes, while β-lactamases from soil, freshwater, glacier, marine, and wastewater grouped within a separate “environmental” cluster that displayed high levels of inter-network connectivity. Interestingly, almost no connectivity occurred between the “feces” and “environmental” clusters. We attributed this in part to the divergence in microbial community composition (dominance of Bacteroidetes and Firmicutes vs. Proteobacteria, respectively). The β-lactamase diversity in the “environmental” cluster was significantly higher than in human and bovine feces microbiomes. Several class A, B, C, and D β-lactamase homologs (blaCTX-M, blaKPC, blaGES) were ubiquitous in the “environmental” cluster, whereas bovine and human feces metagenomes were dominated by class A (primarily cfxA) β-lactamases. Collectively, this study highlights the ubiquitous presence and broad diversity of β-lactamase gene precursors in non-clinical environments. Furthermore, it suggests that horizontal transfer of β-lactamases to human-associated bacteria may be more plausible from animals than from terrestrial and aquatic microbes, seemingly due to phylogenetic similarities

Draft Genome Sequence of the Bactrocera oleae Symbiont "Candidatus Erwinia dacicola".

"Candidatus Erwinia dacicola" is a Gammaproteobacterium that forms a symbiotic association with the agricultural pest Bactrocera oleae Here, we present a 2.1-Mb draft hybrid genome assembly for "Ca. Erwinia dacicola" generated from single-cell and metagenomic data

Mutation Detection with Next-Generation Resequencing through a Mediator Genome

The affordability of next generation sequencing (NGS) is transforming the field of mutation analysis in bacteria. The genetic basis for phenotype alteration can be identified directly by sequencing the entire genome of the mutant and comparing it to the wild-type (WT) genome, thus identifying acquired mutations. A major limitation for this approach is the need for an a-priori sequenced reference genome for the WT organism, as the short reads of most current NGS approaches usually prohibit de-novo genome assembly. To overcome this limitation we propose a general framework that utilizes the genome of relative organisms as mediators for comparing WT and mutant bacteria. Under this framework, both mutant and WT genomes are sequenced with NGS, and the short sequencing reads are mapped to the mediator genome. Variations between the mutant and the mediator that recur in the WT are ignored, thus pinpointing the differences between the mutant and the WT. To validate this approach we sequenced the genome of Bdellovibrio bacteriovorus 109J, an obligatory bacterial predator, and its prey-independent mutant, and compared both to the mediator species Bdellovibrio bacteriovorus HD100. Although the mutant and the mediator sequences differed in more than 28,000 nucleotide positions, our approach enabled pinpointing the single causative mutation. Experimental validation in 53 additional mutants further established the implicated gene. Our approach extends the applicability of NGS-based mutant analyses beyond the domain of available reference genomes

A global multinational survey of cefotaxime-resistant coliforms in urban wastewater treatment plants

The World Health Organization Global Action Plan recommends integrated surveillance programs as crucial strategies for monitoring antibiotic resistance. Although several national surveillance programs are in place for clinical and veterinary settings, no such schemes exist for monitoring antibiotic-resistant bacteria in the environment. In this transnational study, we developed, validated, and tested a low-cost surveillance and easy to implement approach to evaluate antibiotic resistance in wastewater treatment plants (WWTPs) by targeting cefotaxime-resistant (CTX-R) coliforms as indicators. The rationale for this approach was: i) coliform quantification methods are internationally accepted as indicators of fecal contamination in recreational waters and are therefore routinely applied in analytical labs; ii) CTX-R coliforms are clinically relevant, associated with extended-spectrum ?-lactamases (ESBLs), and are rare in pristine environments. We analyzed 57 WWTPs in 22 countries across Europe, Asia, Africa, Australia, and North America. CTX-R coliforms were ubiquitous in raw sewage and their relative abundance varied significantly (< 0.1% to 38.3%), being positively correlated (p < 0.001) with regional atmospheric temperatures. Although most WWTPs removed large proportions of CTX-R coliforms, loads over 103 colony-forming units per mL were occasionally observed in final effluents. We demonstrate that CTX-R coliform monitoring is a feasible and affordable approach to assess wastewater antibiotic resistance status

Bdellovibrio et organismes apparentés

International audience> Les bactéries prédatrices obligatoires d'autres bactéries, les bactéries nécessitant une cellule proie Gram négatif afin de compléter leur cycle cellu-laire, appartiennent au groupe polyphylétique des Bdellovibrio et organismes apparentés (BALO). Bien que les interactions entre les bactéries prédatrices et les bactéries proies soient complexes, on commence à comprendre leur dynamique et leur impact sur les communautés bactériennes dans l'environ-nement. Les BALO ont des cycles de vie particuliers : ils grandissent soit de manière épibiotique, quand le prédateur reste attaché à l'enveloppe de sa proie, la division cellulaire étant alors binaire, ou il se déve-loppe dans le périplasme de la cellule proie. Dans ce cas, un prédateur génère plusieurs cellules. Le cycle de vie périplasmique exprime des motifs d'expres-sion géniques et protéiques ainsi que des réseaux de signalisation uniques. Cette revue explore quelques particularités de l'écologie et de la biologie cellu-laire des BALO, ainsi que leurs applications poten-tielles dans les domaines médicaux, agricoles et environnementaux. < organisms (BALO) qui inclue divers groupes monophylétiques : le genre Micavibrio et les familles Bdellovibrionaceae, Bacteriovoraceae et Peridibacteraceae [2]. Ces BALO ont pour cible des bactéries Gram négatif. La pression de prédation, pouvant conduire à la sélection de proies génétiquement résistantes, et l'existence de défenses phénoty-piques et de nature transitoire, qui constituent un mécanisme d'amor-tissement, assurent, in fine, à la fois la survie du prédateur et la capa-cité de la proie à se reconstituer [3, 4]. La dynamique des relations de type proie-prédateur entre bactéries s'avère donc complexe. S'ajoute à cette complexité, la nature mal définie du type d'interaction possible entre organismes (synergique, antagoniste, etc.). Cependant, les nouvelles technologies de séquençage, de bio-informatique et de microscopie, mais aussi le développement d'outils de manipulation génétique, permettent, aujourd'hui, une étude détaillée des méca-nismes cellulaires qui font d'une bactérie, un prédateur obligatoire. Elles offrent également une approche plus large de l'étude de leur impact écologique. Ces connaissances ouvrent de nouvelles voies vers leur application en agriculture, en aquaculture, dans la préservation de notre environnement et en médecine. Cette revue est l'occasion de synthétiser une partie des connaissances actuelles sur les BALO. Le monde méconnu des BALO On sait aujourd'hui que les BALO sont très largement distribués au sein de la biosphère et sont présents aussi bien dans les océans, les mers, les eaux côtières, les estuaires, les rivières, les lacs, que dans les bassins d'aquaculture, les stations d'épuration, l'eau d'irrigation, ou encore dans les sols, les rizières, la rhizosphère et même dans les Les bactéries constituent quantitativement le groupe dominant des organismes cellulaires. En leur sein, les bactéries prédatrices d'autres bactéries ont été très largement sous-estimées comparativement à l'action des virus ou d'autres prédateurs ou parasites euca-ryotes (flagellés, cillés, champignons). Cela est en partie dû à ce que ces bactéries ne constituent pas des populations majeures en terme d'abondance quand les bactériophages, des virus infectant les bactéries, eux, peuvent atteindre des densités dix fois supérieures aux populations bactériennes [1]. Les bactéries prédatrices obligatoires de bactéries (c'est-à-dire dépendantes de la prédation pour se reproduire) sont regroupées dans un groupe polyphylétique 1 appelé Bdellovibrio and like 1 Se dit d'un groupe composé de taxons n'ayant en commun que des convergences adap-tatives et n'ayant pas d'ancêtre commun, contrairement aux groupes monophylétiques