Fighting the Enemy: One Health Approach Against Microbial Resistance

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Genome Sequence of Serratia plymuthica A153, a Model Rhizobacterium for the Investigation of the Synthesis and Regulation of Haterumalides, Zeamine, and Andrimid.

The rhizobacterium Serratia plymuthica A153 is a Gram-negative bacterium belonging to the family Enterobacteriaceae Here, we present the genome sequence of this strain, which produces multiple bioactive secondary metabolites, including the halogenated macrolide oocydin A, the polyamino antibiotic zeamine, and the bacterial acetyl-CoA carboxylase inhibitor andrimid.Work in the Salmond laboratory was supported by the Biotechnology and Biological Sciences Research Council (BBSRC, United Kingdom). Miguel A. Matilla was supported by the EU Marie-Curie intra-European Fellowship For Career Development (FP7-PEOPLE-2011-IEF) grant 298003 and the Spanish Ministry of Economy and Competitiveness Postdoctoral Research Program, Juan de la Cierva (JCI-2012-11815). The Tino Krell laboratory is supported by FEDER funds and Fondo Social Europeo through grants from the Junta de Andalucía (grant CVI-7335) and the Spanish Ministry for Economy and Competitiveness (grants BIO2013- 42297 and RTC-2014-1777-3).This is the final version of the article. It first appeared from the American Society for Microbiology via http://dx.doi.org/10.1128/genomeA.00373-1

Iron Uptake Analysis in a Set of Clinical Isolates of Pseudomonas putida

Pseudomonas putida strains are frequent inhabitants of soil and aquatic niches and they are occasionally isolated from hospital environments. As the available iron sources in human tissues, edaphic, and aquatic niches are different, we have analyzed iron-uptake related genes in different P. putida strains that were isolated from all these environments. We found that these isolates can be grouped into different clades according to the genetics of siderophore biosynthesis and recycling. The pyoverdine locus of the six P. putida clinical isolates that have so far been completely sequenced, are not closely related; three strains (P. putida HB13667, HB3267, and NBRC14164T) are grouped in Clade I and the other three in Clade II, suggesting possible different origins and evolution. In one clinical strain, P. putida HB4184, the production of siderophores is induced under high osmolarity conditions. The pyoverdine locus in this strain is closely related to that of strain P. putida HB001 which was isolated from sandy shore soil of the Yellow Sea in Korean marine sand, suggesting their possible origin, and evolution. The acquisition of two unique TonB-dependent transporters for xenosiderophore acquisition, similar to those existing in the opportunistic pathogen P. aeruginosa PAO, is an interesting adaptation trait of the clinical strain P. putida H8234 that may confer adaptive advantages under low iron availability conditions.Work in our laboratories was supported by ERANET Pathogenomics program through the ADHERS project (Ref: BIO2008-04419-E) and Fondos FEDER from the European Union through project BIO2010-17227 of the Spanish Ministry of Economy and Competitivity. The work in Abengoa Research was funded by H2020 grant Empowerputida number 65703.Peer reviewedPeer Reviewe

Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide

The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmicb. 2020.00202/full#supplementary-materialPseudomonas aeruginosa is an ubiquitous gram-negative opportunistic human pathogen which is not considered part of the human commensal gut microbiota. However, depletion of the intestinal microbiota (Dysbiosis) following antibiotic treatment facilitates the colonization of the intestinal tract by Multidrug-Resistant P. aeruginosa. One possible strategy is based on the use of functional foods with prebiotic activity. The bifidogenic effect of the prebiotic inulin and its hydrolyzed form (fructooligosaccharide: FOS) is well established since they promote the growth of specific beneficial (probiotic) gut bacteria such as bifidobacteria. Previous studies of the opportunistic nosocomial pathogen Pseudomonas aeruginosa PAO1 have shown that inulin and to a greater extent FOS reduce growth and biofilm formation, which was found to be due to a decrease in motility and exotoxin secretion. However, the transcriptional basis for these phenotypic alterations remains unclear. To address this question we conducted RNAsequence analysis. Changes in the transcript level induced by inulin and FOS were similar, but a set of transcript levels were increased in response to inulin and reduced in the presence of FOS. In the presence of inulin or FOS, 260 and 217 transcript levels, respectively, were altered compared to the control to which no polysaccharide was added. Importantly, changes in transcript levels of 57 and 83 genes were found to be specific for either inulin or FOS, respectively, indicating that both compounds trigger different changes. Gene pathway analyses of differentially expressed genes (DEG) revealed a specific FOS-mediated reduction in transcript levels of genes that participate in several canonical pathways involved in metabolism and growth, motility, biofilm formation, b-lactamase resistance, and in the modulation of type III and VI secretion systems; results that have been partially verified by real time quantitative PCR measurements. Moreover, we have identified a genomic island formed by a cluster of 15 genes, encoding uncharacterized proteins, which were repressed in the presence of FOS. The analysis of isogenic mutants has shown that genes of this genomic island encode proteins involved in growth, biofilm formation and motility. These results indicate that FOS selectively modulates bacterial pathogenicity by interfering with different signaling pathways.This work was supported by grants from the Spanish Ministry for Economy and Competitiveness (AGL2017-85270-R). CS is funded by the program Juan de la Cierva-Formación (FJCI-2015-23810)

Specific Gene Loci of Clinical Pseudomonas putida Isolates

Pseudomonas putida are ubiquitous inhabitants of soils and clinical isolates of this species have been seldom described. Clinical isolates show significant variability in their ability to cause damage to hosts because some of them are able to modulate the host’s immune response. In the current study, comparisons between the genomes of different clinical and environmental strains of P. putida were done to identify genetic clusters shared by clinical isolates that are not present in environmental isolates. We show that in clinical strains specific genes are mostly present on transposons, and that this set of genes exhibit high identity with genes found in pathogens and opportunistic pathogens. The set of genes prevalent in P. putida clinical isolates, and absent in environmental isolates, are related with survival under oxidative stress conditions, resistance against biocides, amino acid metabolism and toxin/antitoxin (TA) systems. This set of functions have influence in colonization and survival within human tissues, since they avoid host immune response or enhance stress resistance. An in depth bioinformatic analysis was also carried out to identify genetic clusters that are exclusive to each of the clinical isolates and that correlate with phenotypical differences between them, a secretion system type III-like was found in one of these clinical strains, a determinant of pathogenicity in Gram-negative bacteria.Work in the authors’ laboratories was supported by ERANET Pathogenomics programme through the ADHERS project (Ref: BIO2008-04419-E) and Fondos FEDER from the European Union through project BIO2010-17227 of the Ministry of Economy and Competitivity of Spain. Bio-Iliberis R&D provided supportPeer reviewe

Characterization of an extremophile bacterial acid phosphatase derived from metagenomics analysis

Acid phosphatases are enzymes that play a crucial role in the hydrolysis of various organophosphorous molecules. A putative acid phosphatase called FS6 was identified using genetic profiles and sequences from different environments. FS6 showed high sequence similarity to type C acid phosphatases and retained more than 30% of consensus residues in its protein sequence. A histidine-tagged recombinant FS6 produced in Escherichia coli exhibited extremophile properties, functioning effectively in a broad pH range between 3.5 and 8.5. The enzyme demonstrated optimal activity at temperatures between 25 and 50°C, with a melting temperature of 51.6°C. Kinetic parameters were determined using various substrates, and the reaction catalysed by FS6 with physiological substrates was at least 100-fold more efficient than with p-nitrophenyl phosphate. Furthermore, FS6 was found to be a decamer in solution, unlike the dimeric forms of crystallized proteins in its family.Grants from the Ministry of Science through grants from the Plan Nacional 2021 (PID2021-123469OBI00) and Transición Ecológica (TED2021129632BI00) and European Commission projects EJP soils (EJPSOIL862695) and PREPSOIL (HE/CL5SOILM/0102

A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society

Microbes are all pervasive in their distribution and influence on the functioning and well-being of humans, life in general and the planet. Microbially-based technologies contribute hugely to the supply of important goods and services we depend upon, such as the provision of food, medicines and clean water. They also offer mechanisms and strategies to mitigate and solve a wide range of problems and crises facing humanity at all levels, including those encapsulated in the sustainable development goals (SDGs) formulated by the United Nations. For example, microbial technologies can contribute in multiple ways to decarbonisation and hence confronting global warming, provide sanitation and clean water to the billions of people lacking them, improve soil fertility and hence food production and develop vaccines and other medicines to reduce and in some cases eliminate deadly infections. They are the foundation of biotechnology, an increasingly important and growing business sector and source of employment, and the centre of the bioeconomy, Green Deal, etc. But, because microbes are largely invisible, they are not familiar to most people, so opportunities they offer to effectively prevent and solve problems are often missed by decision-makers, with the negative consequences this entrains. To correct this lack of vital knowledge, the International Microbiology Literacy Initiative–the IMiLI–is recruiting from the global microbiology community and making freely available, teaching resources for a curriculum in societally relevant microbiology that can be used at all levels of learning. Its goal is the development of a society that is literate in relevant microbiology and, as a consequence, able to take full advantage of the potential of microbes and minimise the consequences of their negative activities. In addition to teaching about microbes, almost every lesson discusses the influence they have on sustainability and the SDGs and their ability to solve pressing problems of societal inequalities. The curriculum thus teaches about sustainability, societal needs and global citizenship. The lessons also reveal the impacts microbes and their activities have on our daily lives at the personal, family, community, national and global levels and their relevance for decisions at all levels. And, because effective, evidence-based decisions require not only relevant information but also critical and systems thinking, the resources also teach about these key generic aspects of deliberation. The IMiLI teaching resources are learner-centric, not academic microbiology-centric and deal with the microbiology of everyday issues. These span topics as diverse as owning and caring for a companion animal, the vast range of everyday foods that are produced via microbial processes, impressive geological formations created by microbes, childhood illnesses and how they are managed and how to reduce waste and pollution. They also leverage the exceptional excitement of exploration and discovery that typifies much progress in microbiology to capture the interest, inspire and motivate educators and learners alike. The IMiLI is establishing Regional Centres to translate the teaching resources into regional languages and adapt them to regional cultures, and to promote their use and assist educators employing them. Two of these are now operational. The Regional Centres constitute the interface between resource creators and educators–learners. As such, they will collect and analyse feedback from the end-users and transmit this to the resource creators so that teaching materials can be improved and refined, and new resources added in response to demand: educators and learners will thereby be directly involved in evolution of the teaching resources. The interactions between educators–learners and resource creators mediated by the Regional Centres will establish dynamic and synergistic relationships–a global societally relevant microbiology education ecosystem–in which creators also become learners, teaching resources are optimised and all players/stakeholders are empowered and their motivation increased. The IMiLI concept thus embraces the principle of teaching societally relevant microbiology embedded in the wider context of societal, biosphere and planetary needs, inequalities, the range of crises that confront us and the need for improved decisioning, which should ultimately lead to better citizenship and a humanity that is more sustainable and resilient. The biosphere of planet Earth is a microbial world: a vast reactor of countless microbially driven chemical transformations and energy transfers that push and pull many planetary geochemical processes, including the cycling of the elements of life, mitigate or amplify climate change (e.g., Nature Reviews Microbiology, 2019, 17, 569) and impact the well-being and activities of all organisms, including humans. Microbes are both our ancestors and creators of the planetary chemistry that allowed us to evolve (e.g., Life's engines: How microbes made earth habitable, 2023). To understand how the biosphere functions, how humans can influence its development and live more sustainably with the other organisms sharing it, we need to understand the microbes. In a recent editorial (Environmental Microbiology, 2019, 21, 1513), we advocated for improved microbiology literacy in society. Our concept of microbiology literacy is not based on knowledge of the academic subject of microbiology, with its multitude of component topics, plus the growing number of additional topics from other disciplines that become vitally important elements of current microbiology. Rather it is focused on microbial activities that impact us–individuals/communities/nations/the human world–and the biosphere and that are key to reaching informed decisions on a multitude of issues that regularly confront us, ranging from personal issues to crises of global importance. In other words, it is knowledge and understanding essential for adulthood and the transition to it, knowledge and understanding that must be acquired early in life in school. The 2019 Editorial marked the launch of the International Microbiology Literacy Initiative, the IMiLI. HERE, WE PRESENT our concept of how microbiology literacy may be achieved and the rationale underpinning it; the type of teaching resources being created to realise the concept and the framing of microbial activities treated in these resources in the context of sustainability, societal needs and responsibilities and decision-making; and the key role of Regional Centres that will translate the teaching resources into local languages, adapt them according to local cultural needs, interface with regional educators and develop and serve as hubs of microbiology literacy education networks. The topics featuring in teaching resources are learner-centric and have been selected for their inherent relevance, interest and ability to excite and engage. Importantly, the resources coherently integrate and emphasise the overarching issues of sustainability, stewardship and critical thinking and the pervasive interdependencies of processes. More broadly, the concept emphasises how the multifarious applications of microbial activities can be leveraged to promote human/animal, plant, environmental and planetary health, improve social equity, alleviate humanitarian deficits and causes of conflicts among peoples and increase understanding between peoples (Microbial Biotechnology, 2023, 16(6), 1091–1111). Importantly, although the primary target of the freely available (CC BY-NC 4.0) IMiLI teaching resources is schoolchildren and their educators, they and the teaching philosophy are intended for all ages, abilities and cultural spectra of learners worldwide: in university education, lifelong learning, curiosity-driven, web-based knowledge acquisition and public outreach. The IMiLI teaching resources aim to promote development of a global microbiology education ecosystem that democratises microbiology knowledge.http://www.wileyonlinelibrary.com/journal/mbt2hj2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-01:No povertySDG-02:Zero HungerSDG-03:Good heatlh and well-beingSDG-04:Quality EducationSDG-06:Clean water and sanitationSDG-07:Affordable and clean energySDG-08:Decent work and economic growthSDG-12:Responsible consumption and productionSDG-13:Climate actionSDG-14:Life below wate

Análisis del Pangenoma de Pseudomonas putida

Una especie bacteriana puede ser definida por el conjunto de todos los genes que conforman la especie o lo que es lo mismo, su pangenoma. El término pangenoma, fue utilizado por primera vez en el año 2005 por Medini. Los estudios pangenómicos surgen de la posibilidad de disponer de múltiples genomas pertenecientes a una misma especie y ofrecen una nueva aproximación a la definición de especie. El estudio del pangenoma permite determinar cuales son el conjunto de reacciones que confieren a un conjunto de microoganismos diferenciación con respecto a microrganismos de otra especie. Así mismo el pangenoma ayuda a identificar los procesos moleculares de adaptación a un nicho, que confieren las características particulares a cada cepa. Hoy en día el concepto de especie en microbiología es un concepto principalmente fenético, el cual concibe la especie como una unidad basada en el grado de semejanza entre los microrganismos que conforman dicha especie. Se tienen en cuenta tanto caracteres fenotípicos de los microorganismos, como la naturaleza del nicho ecológico y la secuencia del gen que codifica el RNA 16S. Sin embargo este concepto de especie es más real en microorganismos que tienen un nicho ecológico aislado, en el cual no prime el intercambio genético con otros microorganismos y con unas condiciones ambientales muy estables. Este no es el caso de la mayoría de los microorganismos que habitan la biosfera. La especie utilizada en el presente estudio es Pseudomonas putida, como especie modelo de microrganismo cosmopolita con cepas que habitan en distintos nichos edáficos y de agua dulce (suelo, rizosfera, lagunas, sedimentos). Esta especie está formada por bacilos Gram negativos, aerobios, móviles gracias a sus flagelos polares. Para deducir el pangenoma de esta especie se eligieron nueve cepas intentando abarcar diferentes nichos. Además también se tuvo en cuenta el grado de curación de las secuencias y el estado de su genoma en las bases de datos públicas (borrador o genoma cerrado) intentando contar con aquellas que tuviesen el grado de curación más alto.Tesis Univ. Granada. Programa Oficial de Doctorado en: Bioquímica y Biología MolecularProyectos: Análisis post-genómico functional de Pseudomonas putida KT2440, (Plan Nacional de I+D+i: BIO-2010-17227.2011-2014); Bases moleculares de la degradación y resistencia a tolueno, (Proyecto de Excelencia de la Junta de Andalucía y fondos FEDER: CVI-7391. 2012-2015); Empower: Re-programming the lifestile of Pseudomonas putida for bespoke biocatalysis, (European Union horizon PP research and innovation programme under grant agreement Nº 635536); Metafluidics. (European Union horizon PP research and innovation programme under grant agreement Nº 685474); Biorefineríes. Abengoa Research Project. (Abengoa Research S.L.