Biology subjects

Prieto, A.

Publications and source records attributed to Prieto, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Gfa, a new integron-borne fosfomycin resistance family

Fosfomycin is increasingly used to treat multidrug-resistant Gram-negative infections, yet resistance surveillance largely relies on homology-based detection of known fos genes. Here, we identify Gfa, a previously unrecognized integron-borne fosfomycin resistance determinant uncovered through functional screening of 129 integron gene cassettes. Gfa confers high-level fosfomycin resistance across Enterobacterales and Pseudomonas aeruginosa and is resistant to phosphonoformate inhibition. Structural modelling and mutagenesis reveal a conserved cysteine-rich, zinc-organized architecture essential for activity and distinct from canonical Fos enzymes. Crude-extract assays confirm glutathione-dependent fosfomycin inactivation under metal-chelating conditions. Distant Gfa homologs also conferred resistance, although activity was restricted to a subset of proteins tested. Together, these findings establish Gfa as a previously unrecognized fosfomycin resistance family and highlight the limitations of homology-based mining for discovering novel resistance determinants and predicting which family members are functional.

microbiology↗

bioRxiv2026

Integrated valorization of glycerol and PET into lipids and PHAs using an engineered Yarrowia lipolytica strain and a Pseudomonas-Comamonas consortium

The accumulation of plastic waste necessitates innovative strategies that convert polymer carbon into value-added products. Here, we present a sequential yeast-bacterial workflow for the integrated valorisation of glycerol and amorphous polyethylene terephthalate (amPET) into triacyl glyceride (TAGs) and polyhydroxyalkanoates (PHAs). First, an engineered obese strain of Yarrowia lipolytica was cultivated on glycerol, for the simultaneous production of intracellular lipids, up to 42.9% of its cell dry weight, and secretion of a PET-depolymerizing enzymatic cocktail, composed of the cutinase from Mycothermus thermophilus (HiC) and the lipase B from Moesziomyces antarcticus (CALB). The resulting enzymatic crude hydrolysed amPET, and the released degradation products--terephthalic acid (TPA) and ethylene glycol (EG)-- served as feedstocks for a bacterial consortium composed of Comamonas testosteroni RW31 and Pseudomonas putida JM37, which naturally assimilate TPA and EG, respectively. This consortium successfully upcycled the released monomers into intracellular polyhydroxybutyrate (PHB) and medium-chain-length PHAs. Furthermore, fluorescent strains of both bacteria enabled the development of a semi-quantitative method for monitoring the consortium population dynamics. Overall, this study provides a robust proof-of-concept for a circular bioeconomy approach, successfully coupling glycerol-based enzyme and lipid production with the downstream biological conversion of PET-derived monomers into valuable bioplastics. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/729029v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1abe237org.highwire.dtl.DTLVardef@190a675org.highwire.dtl.DTLVardef@1a06dfaorg.highwire.dtl.DTLVardef@1945fe6_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2026

Integrated valorisation of PET and xylose using the oleaginous microorganisms Yarrowia lipolytica and Rhodococcus jostii

The increasing accumulation of polyethylene terephthalate (PET) waste has prompted the development of sustainable biotechnological strategies for its degradation and valorisation. This study presents an integrated approach combining enzymatic PET depolymerization by Yarrowia lipolytica, engineered to express and secrete the cutinase HiC and the lipase CalB, with the microbial valorization of PET-derived monomers, terephthalic acid (TPA) and ethylene glycol (EG), by Rhodococcus jostii RHA1. Y. lipolytica was further engineered for xylose metabolism, enabling enzyme production from low-cost lignocellulose-derived substrates. Enzymatic assays with HiC and CalB crudes effectively hydrolysate PET to TPA and EG, demonstrating functional enzymatic activity without purification steps. In addition, R. jostii RHA1 was able to use as substrate the released monomers and accumulated intracellular lipids. Overall, this work demonstrates the feasibility of coupling the production of PET degrading enzymes and microbial lipid, using an abundant monosaccharide, with the assimilation of the PET degradation products to also produce microbial lipids. This modular system provides a promising framework for the sustainable upcycling of plastic waste into value-added bioproducts within a circular economy.

synthetic biology↗

bioRxiv2026

AI-assisted improvement of Aspergillus oryzae β-galactosidase using an Ensemble of Protein Language Models

{beta}-galactosidases (BGs) are essential enzymes widely used in the food industry, particularly in the production of lactose-free products. Among them, the BG from Aspergillus oryzae is of industrial relevance due to its activity at acidic pH and moderate thermal tolerance. However, enhancing its catalytic performance remains a key challenge. Traditional enzyme engineering methods are time-consuming and resource-intensive, limiting their scalability. Recent advances in Artificial Intelligence (AI), particularly those based on Natural Language Processing, offer a promising alternative by enabling efficient exploration of protein sequence space and prediction of beneficial mutations. In this study, we introduce an ensemble-based, zero-shot Protein Language Model pipeline that reconciles predictions from six independent models (ESM2 and the five ESM1v variants) combined with a diversity-aware candidate selection strategy. Applied to the BG from A. oryzae, this approach identified beneficial mutations leading to novel enzyme variants with up to a four-fold increase in catalytic efficiency on oNPGal, a two-fold increase on lactose, and, independently, a T338I variant with markedly enhanced thermostability ({approx}80% residual activity after 24 h at 60 {degrees}C), all without requiring supervised fine-tuning on experimental fitness data. Our results demonstrate that consensus across an ensemble of PLMs can efficiently enrich beneficial substitutions in industrially relevant enzymes and substantially reduce the number of wet-lab candidates that need to be screened. Table of Contents graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/726739v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@16477baorg.highwire.dtl.DTLVardef@f071c5org.highwire.dtl.DTLVardef@1bd7777org.highwire.dtl.DTLVardef@1ee2999_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2026

Integrating Fungal-Bacterial Synergy to Enhance Circular MFC-Hydroponic Performance

Microbial fuel cells (MFCs) represent a promising technology for the simultaneous treatment of wastewater and bioelectricity generation. In this study, the MFCs are conceived as functional modules to be integrated into hydroponic cultivation systems, acting as a prosthetic rhizosphere capable of coupling wastewater treatment and bioelectrochemical activity with plant nutrition improvement. We compared the electrochemical performance of different microbial consortia comprising the electroactive bacterium Shewanella oneidensis, the plant growth promoting rhizobacterium (PGPR) Pseudomonas putida, and the plant biomass-degrading fungus Ophiostoma piceae, along with the supplementation with the quorum sensing (QS) analogue molecule 1{square} dodecanol. These microbial consortia are tested in MFCs fed with wastewater and root exudates to analyze enhanced feedstock assimilation, electricity production, and the generation of plant growth-promoting substances (PGPS). From an electrochemical perspective, we evaluated planktonic growth, anode adhesion, substrate consumption, and the production of redox-active molecules and PGPS such as flavins and siderophores respectively alongside key electrical production parameters, including current output and power. Among the different microbial configurations tested, the consortium combining S. oneidensis, P. putida, and O. piceae exhibited the highest electrical production potential. Moreover, within this framework, we detected the extracellular production of siderophores in MFCs containing P. putida, suggesting a potential role supporting hydroponic crop growth. Furthermore, the addition of 1-dodecanol led to an improvement of the bioelectrochemical parameters. These results highlight the potential of synthetic microbial consortia in MFC-based systems not only to enhance electricity generation from wastewater but also to provide added value in integrated hydroponic applications through rhizosphere-like functions.

microbiology↗

bioRxiv2026

Large-scale recovery of integron cassettes for gene discovery screens

Integrons capture and stockpile adaptive genes encoded in modular mobile genetic elements called integron cassettes (ICs). Present in 17% of bacterial genomes, integrons can harbor hundreds of cassettes, representing a hotspot of genetic variability. Some ICs encode antimicrobial or phage resistance genes, but most remain functionally uncharacterized, representing an untapped source of genes of biotechnological interest. Here, we present two tools, the cassette gatherer and hunter, that allow the swift establishment of libraries of genes either from genetically tractable strains or directly from DNA. By re-engineering a class 1 integron, these platforms capture single cassettes in a sequence and function-independent manner. When applied to Vibrio genomes, they recovered hundreds of single cassettes per assay with >99% specificity. To validate the usability of our tools for the discovery of new genes, we subjected these libraries to screens against phages ICP2 and T4, and identified nine phage-defense systems, including five previously undescribed. Hence, these tools provide a fast and simple method to recover thousands of ICs, in a way amenable to gene-discovery screens.

microbiology↗

bioRxiv2025

Synthetic Yarrowia lipolytica consortium for efficient conversion of lignocellulosic oligosaccharides into lipids

Lignocellulosic biomass (LCB) is an abundant and renewable feedstock for the sustainable production of bioproducts; however, its industrial exploitation is limited by its complex composition and by the lack of microbial platforms capable of simultaneously degrading and assimilating cellulose- and hemicellulose-derived oligosaccharides. Yarrowia lipolytica lacks the native enzymatic machinery required for this process. In this study, we engineered a multifunctional strain (YBXT-XR-BGL3) able to secrete fungal {beta}-glucosidase (BGL3 or BGL1) and {beta}-xylosidase (BxTw1) from Talaromyces amestolkiae, enabling the hydrolysis of cellobiose and xylooligosaccharides, respectively. In addition, a xylose reductase pathway was introduced to confer xylose assimilation. Because the construction of a single multifunctional strain may impose a significant metabolic burden and reduce fitness, we benchmarked this strain against a division-of-labor strategy. To this end, we also developed a cellobiose-specialized strain (YBGL3 or YBGL1) and a xylooligosaccharide-specialized strain (YBXT-XR). Functional characterization revealed efficient saccharification of cello- and xylooligosaccharides under acidic conditions, with BGL3 outperforming BGL1 in glucose release and BxTw1 exhibiting broad pH tolerance. Under nitrogen-limited conditions, this enabled lipid accumulation of up to 20% from cellobiose in YBGL3 and YBXT-XR-BGL3, and up to 15% from xylooligosaccharides in YBXT and YBXT-XR-BGL3. In co-culture experiments using a mixed substrate (glucose, cellobiose, and xylooligosaccharides), both the multifunctional strain and the consortium produced up to 0.67 g L{square}{superscript 1} of lipids. However, the division-of-labor approach led to higher lipid accumulation (34% versus 26.3% in the monoculture), driven by a rapid population shift: following cellobiose depletion (after 72 h), YBXT-XR became predominant and utilized the remaining xylooligosaccharides almost exclusively for lipid synthesis. Overall, this study provides the first demonstration of a Y. lipolytica system capable of simultaneously utilizing cellulose- and hemicellulose-derived oligosaccharides. Moreover, benchmarking a division-of-labor consortium against a multifunctional monoculture highlights a robust strategy to enhance lipid biosynthesis and improve process resilience for LCB valorization.

synthetic biology↗

bioRxiv2025

Biochemical Upcycling of PET via Glycolysis and Engineered Microbial Consortia

Polyethylene terephthalate (PET) waste remains a major environmental challenge due to its recalcitrance and low economic value. Here, we present an integrated biochemical approach that couples glycolysis with a synthetic microbial consortium to upcycle post-consumer PET (pcPET) into polyhydroxyalkanoates (PHA). Glycolysis efficiently depolymerized pcPET into bis(2-hydroxyethyl) terephthalate (BHET) in 2 h, circumventing the limitations of in vivo PET degradation. We engineered a two-species microbial consortium composed of Comamonas testosteroni RW31, able to metabolise terephthalic acid, and Pseudomonas putida JM37, able to consume ethylene glycol, each modified for the extracellular secretion of PET- and MHET-hydrolases, employing different plasmid architectures. This division of labour enabled rapid BHET hydrolysis and the subsequent upcycling of the released monomers into PHAs. The combination of the different strains allowed to select C. testosteroni pSEVA354-MHETase and P. putida pSEVA234-PETase as the best consortium, based on growth and PHAs content. Overall, this work proposes a strategy for PET waste depolymerisation and valorisation, highlighting the potential of mixed chemical and biological approaches and the use of non-conventional microbial chassis within engineered consortia.

synthetic biology↗

bioRxiv2025

Pseudomonas putida JM37 as a novel bacterial chassis for ethylene glycol upcycling

Ethylene glycol (EG), one of the main monomers of polyethylene terephthalate (PET), is an attractive target for microbial upcycling. Despite this interest, there is a limited number of described organisms that can efficiently metabolise EG. Here, we report the metabolic and biotechnological potential of Pseudomonas putida JM37 as a novel bacterial chassis for EG valorization. We show that JM37 efficiently grows on EG as the sole carbon and energy source, outperforming other Pseudomonas strains. Genome sequencing and directed mutagenesis revealed that genetic redundancies in the glyoxylate assimilation pathways underlie its robust EG metabolism. Beyond biomass generation, we demonstrated the biotechnological potential of JM37. This strain was able to accumulate medium-chain polyhydroxyalkanoates (mcl-PHAs), dominated by C10 monomers, directly from EG. Moreover, JM37 successfully expressed heterologous biosynthetic pathways, including a violacein biosynthetic operon and a PET-hydrolase which has been secreted actively into the extracellular medium. Together, our results support the use of P. putida JM37 as a versatile synthetic biology chassis for sustainable EG upcycling and as a promising platform for circular bioproduction.

synthetic biology↗

bioRxiv2025

Cell cycle dysregulation contributes to neurodegeneration in humanneurons from ALS/FTD-related C9orf72 repeat expansion carriers.

The C9orf72 hexanucleotide repeat expansion GGGGCC (G4C2) cause the most common genetic forms of ALS and frontotemporal dementia, affecting thousands of patients worldwide with uniformly fatal outcomes. C9orf72 ALS/FTD patients lack targeted treatments because druggable molecular vulnerabilities remain unidentified. Using iPSC-derived motor neurons from C9orf72 carriers and age-matched controls, we performed comprehensive cell cycle analysis, drug screening, and single-nucleus RNA sequencing validation in human brain tissue. C9orf72 neurons exhibit age-dependent cell cycle reentry with increased S-phase cells, elevated cyclin and CDK expression, and aberrant cell cycle gene signatures confirmed in patient brain excitatory neurons. Mechanistically, arginine-containing dipeptide repeat proteins (poly-GR, poly-PR) drive this cell cycle activation through CDK4/6 pathway stimulation, while C9orf72 loss-of-function alone shows no effect. Critically, the FDA-approved CDK4/6 inhibitor palbociclib normalizes cell cycle progression, reduces S-phase entry, and rescues neuronal survival with significant reduction in motor neuron death. Single-nucleus RNA-sequencing analyses from C9orf72 patient cortex reveals cell cycle-activated neuronal subclusters. Copy number variation, gene ontology and pathways analyses revealed alterations in DNA repair pathways, cell cycle regulation and cell cycle transition, validating our in vitro findings. These results identify cell cycle dysregulation as a therapeutic target in C9orf72 ALS/FTD with clinical translation potential using existing therapeutics.

neuroscience↗

bioRxiv2025

Valorization of mushroom by-products for sustainability: exploring antioxidant and prebiotic properties

Agaricus bisporus (white button mushroom), Pleurotus ostreatus (oyster mushroom), and Lentinula edodes (shiitake mushroom) are the most cultivated mushrooms in the Spanish region of Castilla-La Mancha. The increasing production of these mushrooms has created opportunities for sustainable utilization of their by-products such as undersized mushrooms, stalks, and stems. This study evaluated the antioxidant, prebiotic, and antimicrobial properties of aqueous, ethanolic and alkaline extracts derived from these by-products. Aqueous extracts from oyster mushroom, rich in glucose-polysaccharides (59.4{+/-}0.4% mushroom dw), promoted the growth and lactic acid production of the probiotic bacteria Lactocaseibacillus casei and Lactoplantibacillus plantarum. Shiitake extracts demonstrated antimicrobial activity against Pseudomonas aeruginosa, Escherichia coli and Salmonella enterica (Minimal inhibitory concentrations: 15, 7.5 and 7.5 mg/mL, respectively), and stimulated the growth of lactic acid bacteria at low concentrations (1.875 mg/mL) but inhibiting them at higher concentrations. Extracts from white button mushrooms exhibited the strongest antioxidant activity, particularly ethanolic extracts rich in phenolic compounds (0.015 mg Gallic acid/mg extract). These results highlight the potential of extracts of mushroom by-products as organic sources of antioxidants, antimicrobials, and prebiotics, creating new avenues for food product development. Reusing these by-products could encourage sustainability and assist the mushroom sector in implementing zero-waste and circular economy methods.

molecular biology↗

bioRxiv2024

Anaerobiosis modulates the performance of antimicrobial resistance genes in Enterobacteriaceae

Bacteria must face and adapt to a variety of physicochemical conditions in the environment and during infection. A key condition is the concentration of dissolved oxygen, proportional to the partial pressure of oxygen (PO2), which is extremely variable among environmental biogeographical areas and also compartments of the human and animal body. Here, we sought to understand if the phenotype of resistance determinants commonly found in Enterobacterales can be influenced by oxygen pressure. To do so, we have compared the MIC in aerobic and anaerobic conditions of isogenic Escherichia coli strains containing 136 different resistance genes against 9 antibiotic families. Our results show a complex landscape of changes in the performance of resistance genes in anaerobiosis. Certain changes are especially relevant for their intensity and the importance of the antibiotic family, like the large decreases in resistance observed against ertapenem and fosfomycin among blaVIM {beta}-lactamases and certain fos genes, respectively; however, the blaOXA-48 {beta}-lactamase from the clinically relevant pOXA-48 plasmid conferred 4-fold higher ertapenem resistance in anaerobiosis. Strong changes in resistance patterns in anaerobiosis were also conserved in Klebsiella pneumoniae. Our results suggest that anaerobiosis is a relevant aspect that can affect the action and selective power of antibiotics for specific AMRs in different environments.

microbiology↗

bioRxiv2023

Targeting plasmid-encoded proteins that contain immunoglobulin-like domains to combat antimicrobial resistance.

Antimicrobial resistance (AMR) poses a significant threat to human health. Although vaccines have been developed to combat AMR, it has proven challenging to associate specific vaccine antigens with AMR. Bacterial plasmids play a crucial role in the transmission of AMR. Our recent research has identified a group of bacterial plasmids (specifically, IncHI plasmids) that encode large molecular mass proteins containing bacterial immunoglobulin-like domains. These proteins are found on the external surface of the bacterial cells, such as in the flagella or conjugative pili. In this study, we show that these proteins are antigenic and can protect mice from infection caused by an AMR Salmonella strain harboring one of these plasmids. Furthermore, we successfully generated nanobodies targeting these proteins, that were shown to interfere with the conjugative transfer of IncHI plasmids. Considering that these proteins are also encoded in other groups of plasmids, such as IncA/C and IncP2, targeting them could be a valuable strategy in combating AMR infections caused by bacteria harboring different groups of AMR plasmids. Since the selected antigens are directly linked to AMR itself, the protective effect extends beyond specific microorganisms to include all those carrying the corresponding resistance plasmids.

microbiology↗

bioRxiv2023

Maintenance of cell wall remodeling and vesicle production are connected in Mycobacterium tuberculosis

Pathogenic and nonpathogenic mycobacteria secrete extracellular vesicles (EVs) under various conditions. EVs produced by Mycobacterium tuberculosis (Mtb) have raised significant interest for their potential in cell communication, nutrient acquisition, and immune evasion. However, the relevance of vesicle secretion during tuberculosis infection remains unknown due to the limited understanding of mycobacterial vesicle biogenesis. We have previously shown that a transposon mutant in the LCP-related gene virR (virRmut) manifested a strong attenuated phenotype during experimental macrophage and murine infections, concomitant to enhanced vesicle release. In this study, we aimed to understand the role of VirR in the vesicle production process in Mtb. We employ genetic, transcriptional, proteomics, ultrastructural and biochemical methods to investigate the underlying processes explaining the enhanced vesiculogenesis phenomenon observed in the virRmut. Our results establish that VirR is critical to sustain proper cell permeability via regulation of cell envelope remodeling possibly through the interaction with similar cell envelope proteins, which control the link between peptidoglycan and arabinogalactan. These findings advance our understanding of mycobacterial extracellular vesicle biogenesis and suggest that these set of proteins could be attractive targets for therapeutic intervention.

microbiology↗

bioRxiv2023

A singular PpaA/AerR-like protein in Rhodospirillum rubrum rules beyond the boundaries of photosynthesis in response to the intracellular redox state

Photosynthesis (PS) in Purple Non-Sulphur Bacteria (PNSB) is strictly controlled to avoid energy consumption and to prevent oxidative stress when oxygen is present. PpsR, a transcriptional repressor codified in the Photosynthetic Gene Cluster (PGC), is one of the main players in the regulation of PS related genes. In some cases, PpsR do not sense the environmental cue by itself but delegates this task to another protein like PpaA/AerR anti-repressors, which can ultimately affect PpsR affinity to some promoter regions. In this work, the effects of locus Rru_A0625 product (HP1) on PS regulation of Rhodospirillum rubrum, were studied by mutation/complementation and transcriptomic strategies. Rru_A0625 is located next to ppsR gene, just like other PpaA/AerR members, and its deletion annuls pigment synthesis in dark micro/anaerobic growth conditions. HP1 shows similarity to PpaA/AerR anti-repressors family, although it does not possess their typical cobalamin binding domain. A transcriptomic analysis of Rru_A0625 deletion mutant showed that HP1 not only has effects on bacterioclorophyll and carotenoid biosynthesis, but also many other biological processes in the cell. The most notorious is the impact on the transcription of the nitrogenase complex components and some accessory proteins. Our results suggest that this new member of the PpaA/AerR family has evolved losing the canonical cobalamin binding domain, but not the redox sensing capability, conserving a not fully understood mechanism of PS regulation. IMPORTANCERhodospirillum rubrum vast metabolic versatility places it as a remarkable model bacterium and an excellent biotechnological chassis. The key component of PS studied in this work (HP1) stands out among the other members of PpaA/AerR anti-repressors family since it lacks the most conserved motif they all share: the cobalamin B-12 binding motif. Even with a minimized and barely recognizable aminoacidic sequence, HP1 stills controls PS as the other members of the family, allowing a fast response to changes in the redox state of the cell. This work also shows that HP1 absence affects genes form relevant biological processes other than PS, including nitrogen fixation and stress response. From a biotechnological perspective, HP1 could be manipulated in approaches where PS is not necessary, such hydrogen or polyhydroxyalkanoates production, to suppress unnecessary energy burden.

microbiology↗

bioRxiv2021

Roles of proteins containing immunoglobulin-like domains in the conjugation of bacterial plasmids.

Horizontal transfer of bacterial plasmids generates genetic variability and contributes to the dissemination of the genes that enable bacterial cells to develop antimicrobial resistance (AMR). Several aspects of the conjugative process have long been known, namely, those related to the proteins that participate in the establishment of cell-to-cell contact and to the enzymatic processes associated with the processing of plasmid DNA and its transfer to the recipient cell. In this work, we describe the role of newly identified proteins that influence the conjugation of several plasmids. Genes encoding high-molecular-weight proteins that contain one or several immunoglobulin-like domains (Big) are located in the transfer regions of several plasmids that usually harbor AMR determinants. These Big proteins are exported to the external medium and target two extracellular organelles: the flagella and the conjugative pili. The plasmid-encoded Big proteins facilitate conjugation by reducing cell motility and facilitating cell-to-cell contact by binding both to the flagella and to the conjugative pilus. They use the same export machinery as that used by the conjugative pilus components. In the examples characterized in this paper, these proteins influence conjugation at environmental temperatures (i.e., 25{degrees}C). This suggests that they may play relevant roles in the dissemination of plasmids in natural environments. Taking into account that they interact with outer surface organelles, they could be targeted to control the dissemination of different bacterial plasmids carrying AMR determinants.

microbiology↗

bioRxiv2021

Predation Efficiency upon Clinical Isolates: Bdellovibrio bacteriovorus is Prey Specific and Origin Dependent

The use of predatory bacteria as live antibiotics has been proposed for managing bacterial infections, especially for those caused by antibiotic multiresistant isolates for which there are few therapeutic options. However, the current knowledge in this field is scarce, with most of the available data based on environmental isolates, with a significant lack of human clinical samples. In this study, we evaluated the predatory spectrum of the reference strain Bdellovibrio bacteriovorus 109J on 13 Serratia marcescens (5 of which were carbapenemase producers) and 78 Pseudomonas aeruginosa clinical isolates from respiratory (colonizing the lungs of patients with cystic fibrosis) or bacteremic infections, differentiated by phenotype (mucoid or not), antibiotic resistance phenotype (including multidrug-resistant isolates), and genetic lineage (frequent and rare sequence types). The source of the isolates was significantly associated with predation efficiency (100% for S. marcescens, 67% for P. aeruginosa from cystic fibrosis, and 25% for P. aeruginosa from bacteremia). In contrast, no correlation with colonial morphotype, genetic background, or antibiotic susceptibility was found. To evaluate the influence of the predator on the predation event, we employed a more aggressive B. bacteriovorus mutant 109J preying upon the same 48 bacteremic P. aeruginosa isolates. The mutants predation efficiency was higher than that of their wild-type counterpart (43% vs. 25%), pointing out that predation is specific to each prey-predator pair of isolates. Our results provide the most extensive study of clinical prey susceptibility published to date and show that the prey-predator interaction is influenced by the origin of the isolates rather than by their genetic background or their antibiotic susceptibility phenotype. IMPORTANCEThe potential usefulness of predatory bacteria in controlling human pathogens, particularly those that are multiresistant to antibiotics, is enormous. Although this possibility has long been suggested, there are still no data on predation susceptibility in clinical strains, and the possible presence of autochthonous predators of the human microbiota has not been investigated. In this study, we employed a reference predator with an environmental origin to study predation phenomena in 3 well-characterized collections of human clinical isolates. Our results demonstrated that predation is a specific consequence of each prey-predator interaction, with the origin of the strains the most relevant factor. In contrast, the genetic background, morphotype, and antibiotic resistance did not appear to influence the predation phenomenon. We also highlight the involvement of a putative polyhydroxyalkanoate depolymerase protein of B. bacteriovorus in determining prey susceptibility. To our knowledge, this study is the largest performed with strains of clinical origin, discriminating between various genera and including strains with multiresistance to antibiotics.

ecology↗

bioRxiv2021

Ancient genomes reveal hybridisation between extinct short-faced bears and the extant spectacled bear (Tremarctos ornatus)

Two genera and multiple species of short-faced bear from the Americas went extinct during or toward the end of the Pleistocene, and all belonged to the endemic New World subfamily Tremarctinae [1-7]. Two of these species were giants, growing in excess of 1,000 kg [6, 8, 9], but it remains uncertain how these extinct bears were related to the sole surviving short-faced bear: the spectacled bear (Tremarctos ornatus). Ancient mitochondrial DNA has recently suggested phylogenetic relationships among these lineages that conflict with interpretations based on morphology [1, 10-12]. However, widespread hybridisation and incomplete lineage sorting among extant bears mean that the mitochondrial phylogeny frequently does not reflect the true species tree [13, 14]. Here we present ancient nuclear genome sequences from representatives of the two extinct short-faced bear genera, Arctotherium and Arctodus. Our new data support a third hypothesis for the relationships among short-faced bears, which conflicts with existing mitochondrial and morphological data. Based on genome-wide D-statistics, we suggest that the extant spectacled bear derives substantial ancestry from Pleistocene hybridisation with an extinct short-faced bear lineage, resulting in a discordant phylogenetic signal between the mitochondrion and portions of the nuclear genome.

evolutionary biology↗