Biology subjects

Jelsbak, L.

Publications and source records attributed to Jelsbak, L..

11 recordsLinked to original sources

bioRxiv2026

Beyond Antimicrobial Activity: Soil Bacteria Reveal a Biotransformation Fate for the Lanthipeptide Nisin

Natural products are central mediators of microbial interactions. However, once released into the environment, they also become available for neighboring microorganisms capable of degrading and modifying them through biotransformation. These biotransformations may fundamentally reshape metabolomes and influence community behavior, yet our understanding of these processes remains limited. Ribosomally synthesized peptides are particularly compelling in this context because their structural complexity and potent antimicrobial activity coexist with the potential to yield essential nutrients and reduced bioactivity through biotransformation. Identifying the pathways underlying these biotransformations is essential for understanding mechanisms that support microbial coexistence and nutrient recycling in soil microbiomes. Here, we used nisin as a model peptide to investigate biotransformation by soil bacteria. Selective isolation under nisin-rich, carbon-limited conditions yielded two Gram-negative isolates, Burkholderia stabilis and Pseudomonas fragi. Using growth assays and liquid chromatography-mass spectrometry, we found that both isolates grow in the presence of nisin while biotransforming and depleting the peptide. Burkholderia stabilis completely converted nisin through sequential cleavage of the C-terminus, hinge region and lanthionine ring C, whereas Pseudomonas fragi showed more limited processing restricted to the C-terminal region. Although these biotransformations dismantled structural features required for nisins antimicrobial activity, the intrinsic resistance of both isolates suggests a role beyond detoxification. We further detected nisin biosynthetic genes in the source environment, supporting nisins ecological relevance and suggesting that these bacteria may participate in its turnover in soil. Together, these findings reveal extensive microbial processing of nisin and support a role for antimicrobial peptide recycling in soil microbiomes. ImportanceNatural products are often studied through the lens of their biological activities, but much less attention has been paid to what happens to these molecules after they enter complex microbial communities. Using the lantibiotic nisin as a model system, we show that soil bacteria can extensively biotransform and deplete an antimicrobial peptide through extracellular enzymatic activity. The presence of both nisin-producing and nisin-biotransforming microorganisms in the same soil environment suggests that antimicrobial peptides may be continuously produced and recycled in nature. Our findings highlight biotransformation as an important but underexplored process governing the persistence, turnover, and ecological roles of microbial natural products.

microbiology↗

bioRxiv2025

Genetic memory devices to detect specialized metabolites in plant and soil microbiomes

Root-associated microbiomes significantly influence plant growth and resilience through intricate chemical dialogues mediated by plant- and microbe-derived specialized metabolites. These metabolites play pivotal roles in shaping the assembly, dynamics, and ecological functions of soil microbiomes. Despite advances in in vitro and DNA sequencing studies, a comprehensive understanding of in situ chemical signaling within plant and soil microbiomes remains elusive due to experimental constraints. To address this gap, we developed and tuned a set of five whole-cell biosensors in Escherichia coli for spatiotemporal, non-disruptive detection of biologically relevant specialized metabolites, including 2,4-diacetylphloroglucinol, pyoluteorin, tetracycline, salicylic acid, and naringenin. Four of these biosensors were successfully adapted to the soil-compatible Pseudomonas putida KT2440 {Delta}all-{Phi} strain. Additionally, the four sensors were shown to respond to their cognate ligand in a non-sterile soil extract medium containing the diverse microbiome found in soil. By employing genetic memory devices with DNA barcodes for readouts, our approach provides a scalable platform for sensing additional specialized metabolites in the future. This work demonstrates the potential of real-time biosensor technologies to unravel the complex chemical interactions driving soil microbiome ecology, with implications for sustainable agricultural practices.

microbiology↗

bioRxiv2025

Genome wide analyses reveal the role of mutator phenotypes in the emergence of drug resistance in Mycobacterium tuberculosis

Antimicrobial combination therapy is widely used to combat Mycobacterium tuberculosis (Mtb), yet resistance rates continue to rise. Mutator strains, with defects in DNA repair genes, are a known source of resistance in other bacterial infections, but their global role in Mtb remains unclear. Here, we provide a comprehensive overview of the contribution of single nucleotide polymorphisms (SNPs) in DNA Repair, Replication, and Recombination (3R) genes to resistance in Mtb. Through large-scale bioinformatics analysis of 53,589 whole-genomes, we identified 18 novel SNPs linked to genotypic drug resistance in 3R genes, covering 12.5% of clinical isolates/strains with available genome sequences. Notably, a number of the detected SNPs were positively selected during Mtb evolution. Experimental mutation frequency tests further indicated functional defects of these sequence variants in key DNA repair pathways. Our findings indicate that the role of mutability in 3R genes plays a significant role in Mtb resistance at the global level.

evolutionary biology↗

bioRxiv2024

Serotype switching in Pseudomonas aeruginosa ST111 enhances adhesion and virulence

Evolution of the highly successful and multidrug resistant clone ST111 in Pseudomonas aeruginosa involves serotype switching from O-antigen O4 to O12. How expression of a different O-antigen serotype alters pathogen physiology to enable global dissemination of this high-risk clone-type is not understood. Here, we engineered isogenic laboratory and clinical P. aeruginosa strains that express the different O-antigen gene clusters to assess the correlation of structural differences of O4 and O12 O-antigens to pathogen-relevant phenotypic traits. We show that serotype O12 is associated with enhanced adhesion, type IV pili dependent twitching motility, and tolerance to host defense molecules and serum. Moreover, we find that serotype O4 is less virulent compared to O12 in an acute murine pneumonia infection in terms of both colonization and survival rate. Finally, we find that these O-antigen effects may be explained by specific biophysical properties of the serotype repeat unit found in O4 and O12, and by differences in membrane stability between O4 and O12 expressing cells. The results demonstrate that differences in O-antigen sugar composition can directly affect P. aeruginosa pathogenicity traits, and provide a better understanding of the potential selective advantages that underlie serotype switching and emergence of serotype O12 ST111.

microbiology↗

bioRxiv2023

Taxonomy of Pseudomonas spp determines interactions with Bacillus subtilis

Bacilli and pseudomonads are among the most well-studied microorganisms commonly found in soil, and frequently co-isolated. Despite this, no systematic approach has been employed to assess the pairwise compatibility of members from these genera. Here, we screened 720 fluorescent soil isolates for their effects on Bacillus subtilis pellicle formation in two types of media and found a predictor for interaction outcome in Pseudomonas taxonomy. Interactions were context-dependent and both medium composition and culture conditions strongly influenced interactions. Negative interactions were associated with Pseudomonas capeferrum, Pseudomonas entomophila and Pseudomonas protegens, and 2,4-diacetylphloroglucinol was confirmed as a strong (but not exclusive) inhibitor of B. subtilis. Non-inhibiting strains were closely related to Pseudomonas trivialis and Pseudomonas lini, but in this case, cocultures with increased B. subtilis pellicle formation were spatially segregated. Our study is the first to propose an overall negative outcome from pairwise interactions between B. subtilis and fluorescent pseudomonads, hence cocultures comprising members from these groups are likely to require additional microorganisms for coexistence.

microbiology↗

bioRxiv2023

Resistance towards and biotransformation of Pseudomonas-produced secondary metabolites during community invasion

The role of antagonistic secondary metabolites produced by Pseudomonas protegens in suppression of soil-borne phytopathogens has been clearly documented. However, their contribution to the ability of P. protegens to establish in soil and rhizosphere microbiomes remains ambiguous. Here, we use a four-species synthetic community to determine how antibiotic production contributes to P. protegens community invasion and identify community traits that alter the abundance of key P. protegens antimicrobial metabolites (DAPG, pyoluteorin and orfamide A). Surprisingly, mutants deficient in antimicrobial production caused similar perturbations in community composition compared to invasion by wildtype P. protegens. Intriguingly, while pyoluteorin and orfamide A are secreted at levels toxic to individual bacterial strains, community-level resistance circumvents toxicity. Here, we identify the underlying mechanism by which the cyclic lipopeptide, orfamide A, is inactivated and degraded by Rhodococcus globerulus D757 and Stenotrophomonas indicatrix D763. Altogether, the demonstration that the synthetic community constrains P. protegens invasion by detoxifying its antibiotics may provide a mechanistic explanation to inconsistencies in biocontrol effectiveness in situ.

microbiology↗

bioRxiv2022

Piperacillin-Tazobactam Resistance Mechanisms in Escherichia coli and Identification of a CTX-M-255 β-Lactamase Selectively Conferring Resistance to Penicillin/β-Lactamase Inhibitor Combinations

Piperacillin/tazobactam (TZP) is a widely used penicillin/{beta}-lactamase inhibitor combination with broad antimicrobial activity. Recently, Escherichia coli strains resistant to TZP but susceptible to third generation cephalosporins (TZP-R/3GC-S isolates) have been increasingly identified. Here, we investigated resistance mechanisms underlying the TZP-R/3GC-S phenotype in clinical E. coli isolates. A total of 29 TZP-R/3GC-S E. coli isolates were retrieved from urinary cultures and subjected to whole genome sequencing. Resistance to TZP was confirmed by minimum inhibitory concentration determination. {beta}-lactamase activity in the presence and absence of tazobactam was determined to identify hyperproduction of {beta}-lactamase and assess susceptibility to tazobactam inhibition. A previously unrecognized {beta}-lactamase was identified and cloned to determine its resistance profile. Four different resistance mechanisms underlying the TZP-R/3-GC phenotype were identified: 1) In 18 out of 29 isolates (62%) {beta}-lactamase production was increased and in 16 of these either strong alternative promoters or increased gene copy numbers of blaTEM-1 or blaSHV-1 were identified, 2) seven isolates (24%) produced blaOXA-1, 3) three isolates (10%) produced inhibitor-resistant TEM-{beta}-lactamases, and 4) a single isolate (3%) harboured a blaCTX-M gene as the only {beta}-lactamase present. This {beta}-lactamase, CTX-M-255, only differs from CTX-M-27 by a G239S amino acid substitution. In contrast to CTX-M-27, CTX-M-255 conferred resistance to penicillin/{beta}-lactamase inhibitor combinations but remained susceptible to cephalosporins. In conclusion, hyperproduction of blaTEM was the most prevalent mechanism of TZP-resistance underlying the TZP-R/3GC-S phenotype followed by production of blaOXA-1 and inhibitor-resistant TEM-{beta}-lactamases. Furthermore, we identified a previously unrecognized CTX-M-{beta}-lactamase, CTX-M-255 that was resistant to {beta}-lactamase inhibitors.

microbiology↗

bioRxiv2021

Long-term evolution of antibiotic persistence in P. aeruginosa lung infections

Pathogenic bacteria respond to antibiotic pressure with the evolution of resistance but survival can also depend on their ability to tolerate antibiotic treatment, known as persistence. While a variety of resistance mechanisms and underlying genetics are well characterised in vitro and in vivo, the evolution of persistence, and how it interacts with resistance in situ is less well understood. We assayed for persistence and resistance with three clinically relevant antibiotics: meropenem, ciprofloxacin and tobramycin, in isolates of Pseudomonas aeruginosa from chronic cystic fibrosis lung infections spanning up to forty years of evolution. We find evidence that persistence is under positive selection in the lung and that it can particularly act as an evolutionary stepping stone to resistance. However, this pattern is not universal and depends on the bacterial clone type and antibiotic used, indicating an important role for antibiotic mode of action.

evolutionary biology↗

bioRxiv2021

Identification and differentiation of Pseudomonas species in field samples using an rpoD amplicon sequencing methodology

Species of the genus Pseudomonas are used for several biotechnological purposes, including plant biocontrol and bioremediation. To exploit the Pseudomonas genus in environmental, agricultural or industrial settings, the organisms must be profiled at species level as their bioactivity potential differs markedly between species. Standard 16S rRNA gene amplicon profiling does not allow for accurate species differentiation. Thus, the purpose of this study was to develop an amplicon-based high-resolution method targeting a 760 nt region of the rpoD gene enabling taxonomic differentiation of Pseudomonas species in soil samples. The method was benchmarked on a sixteen membered Pseudomonas species mock community. All 16 species were correctly and semi-quantitatively identified using rpoD gene amplicons, whereas 16S rRNA V3V4 amplicon sequencing only correctly identified one species. We analysed the Pseudomonas profile in thirteen soil samples in northern Zealand, Denmark, where samples were collected from grassland (3 samples) and agriculture soil (10 samples). Pseudomonas species represented up to 0.7% of the microbial community, of which each sampling site contained a unique Pseudomonas composition. Thirty culturable Pseudomonas strains were isolated from each grassland site and ten from each agriculture site and identified by Sanger sequencing of the rpoD gene. In all cases, the rpoD-amplicon approach identified more species than found by cultivation, including hard-to-culture non-fluorescent pseudomonads, as well as more than found by 16S rRNA V3V4 amplicon sequencing. Thus, rpoD profiling can be used for species profiling of Pseudomonas, and large scale prospecting of bioactive Pseudomonas may be guided by initial screening using this method. ImportanceA high throughput sequence-based method for profiling of Pseudomonas species in soil microbiomes was developed and identified more species than 16S rRNA gene sequencing or cultivation. Pseudomonas species are used as biocontrol organisms and plant-growth promoting agents, and the method will allow tracing of specific species of Pseudomonas as well as enable screening of environmental samples for further isolation and exploitation.

microbiology↗

bioRxiv2020

Development of a whole cell biosensor for detection of 2, 4-diacetylphloroglucinol (DAPG) producing bacteria from grassland soil

Fluorescent Pseudomonas spp. producing the antibiotic 2,4-diacetylphloroglucinol (DAPG) are ecologically important in the rhizosphere as they can control phytopathogens and contribute to disease suppressiveness. While studies of DAPG-producing Pseudomonas have predominantly focused on rhizosphere niches, the ecological role of DAPG as well as the distribution and dynamics of DAPG-producing bacteria remains less well understood for other environments such as bulk soil and grassland, where the level of DAPG producers are predicted to be low. Here, we construct a whole cell biosensor for detection of DAPG and DAPG-producing bacteria from environmental samples. We show that the sensor is highly specific towards DAPG, with a sensitivity in the low nanomolar range (<20 nm). This sensitivity is comparable to the DAPG levels identified in rhizosphere samples by chemical analysis. The biosensor enables guided isolation of DAPG-producing Pseudomonas. Using the biosensor, we probed the same grassland soil sampling site to isolate genetically related DAPG-producing Pseudomonas kilonensis strains over a period of 12 months. Next, we used the biosensor to determine the frequency of DAPG-producing Pseudomonads within three different grassland soil sites and show that DAPG producers can constitute part of the Pseudomonas population in the range of 0.35-17% at these sites. Finally, we show that the biosensor enables detection of DAPG produced by non-Pseudomonas species. Our studies show that a whole-cell biosensor for DAPG detection can facilitate isolation of bacteria that produce this important secondary metabolite and provide insight into the population dynamics of DAPG producers in natural grassland soil. IMPORTANCEThe interest has grown for bacterial biocontrol agents as biosustainable alternatives to pesticides to increase crop yields. Currently, we have a broad knowledge of antimicrobial compounds, such as DAPG, produced by bacteria growing in the rhizosphere surrounding plant roots. However, compared to the rhizosphere niches, the ecological role of DAPG as well as the distribution and dynamics of DAPG-producing bacteria remains less well understood for other environments such as bulk and grassland soil. Currently, we are restricted to chemical methods with detection limits and time-consuming PCR-based and probe-hybridization approaches to detect DAPG and its respective producer. In this study, we have developed a whole-cell biosensor, which can circumvent the labor-intensive screening process, as well as increase the sensitivity at which DAPG is detected. This enables quantification of relative amounts of DAPG-producers, which in turn increases our understanding of the dynamics and ecology of these producers in natural soil environments.

microbiology↗

bioRxiv2017

Host adaptation mediated by intergenic evolution in a bacterial pathogen

Bacterial pathogens evolve during the course of infection as they adapt to the selective pressures that confront them inside the host. Identification of adaptive mutations and their contributions to pathogen fitness remain a central challenge. Although mutations can either target intergenic or coding regions in the pathogen genome, studies of host adaptation have focused predominantly on molecular evolution within coding regions whereas the role of intergenic mutations remains unclear. Here, we address this issue and investigate the extent to which intergenic mutations contribute to the evolutionary response of pathogens to host environments, and if intergenic mutations have distinct roles in host adaptation. We characterize intergenic evolution in 44 lineages of a clinically important bacterial pathogen, Pseudomonas aeruginosa, as they adapt to their hosts. We identify 88 intergenic regions in which parallel evolution occur. At the genetic level, we find that mutations in these regions under selection are located primarily within regulatory elements upstream of transcriptional start sites. At the functional level, we show that these mutations both create or destroy regulatory interactions in connection to transcriptional processes, and are directly responsible for evolution of important pathogenic phenotypes including antibiotic sensitivity. Importantly, we find that intergenic mutations are more likely to be selected than coding region mutations, and that intergenic mutations enable essential genes to become targets of evolution. In summary, our results highlight the evolutionary significance of intergenic mutations in creating host-adapted variants, and that intergenic and coding regions have different qualitative and quantitative contributions to this process.\n\nSignificancePathogens adapt to their host during infection, but the contribution and function of non-coding intergenic sequences to adaptation is poorly understood. Here, genome-wide identification of adaptive mutations within intergenic regions demonstrates that these sequences constitute an important part of the genetic basis for host adaptation. We find that intergenic mutations are abundant relative to adaptive mutations within coding sequences, and can contribute directly to evolution of pathogen relevant traits. Importantly, we find that intergenic mutations modify expression of essential genes and thus make contributions that are functionally distinct from coding mutations. These results improve our understanding of the evolutionary processes in vivo, and can potentially assist in refining predictions of pathogen evolution, disease outcome, and antibiotic resistance development.

microbiology↗