Ilana Kolodkin-Gal | The Interdisciplinary Center, Herzliya (original) (raw)
Papers by Ilana Kolodkin-Gal
Microorganisms, Jun 18, 2024
npj Biofilms and Microbiomes
The human protozoan parasite Entamoeba histolytica is responsible for amebiasis, a disease endemi... more The human protozoan parasite Entamoeba histolytica is responsible for amebiasis, a disease endemic to developing countries. E. histolytica trophozoites colonize the large intestine, primarily feeding on bacteria. However, in the gastrointestinal tract, bacterial cells form aggregates or structured communities called biofilms too large for phagocytosis. Remarkably, trophozoites are still able to invade and degrade established biofilms, utilizing a mechanism that mimics digestive exophagy. Digestive exophagy refers to the secretion of digestive enzymes that promote the digestion of objects too large for direct phagocytosis by phagocytes. E. histolytica cysteine proteinases (CPs) play a crucial role in the degradation process of Bacillus subtilis biofilm. These proteinases target TasA, a major component of the B. subtilis biofilm matrix, also contributing to the adhesion of the parasite to the biofilm. In addition, they are also involved in the degradation of biofilms formed by Gram-ne...
bioRxiv (Cold Spring Harbor Laboratory), Sep 25, 2022
The human protozoan parasite Entamoeba histolytica is responsible for amebiasis, a disease endemi... more The human protozoan parasite Entamoeba histolytica is responsible for amebiasis, a disease endemic to developing countries. E. histolytica trophozoites are released from the cysts to colonize the large intestine, where they primarily feed on bacterial cells. In these scenarios, bacterial cells form aggregates or structured communities too large for phagocytosis. Our results show that E. histolytica can degrade pre-established biofilms of Bacillus subtilis and Escherichia coli in a dose-and time-dependent manner. Surprisingly, trophozoites incubated with B. subtilis biofilm exhibit a unique transcriptome signature compared to those incubated with planktonic cells or without bacteria. Biofilm-induced genes include cysteine proteases (CPs), and the general inhibition of CPs by E64D or by the use of specific small-RNA (sRNA)based RNA interference impairs the degradation of biofilms by E. histolytica. The degradation of B. subtilis extracellular matrix (ECM) protein TasA by CPs is associated with partial biofilm digestion and activation of the stress response in the interacting B. subtilis cells. The interaction with B. subtilis biofilms was also associated with lower levels of oxidoreductases. Oxidoreductase downregulation can be a readout of the embedding of E. histolytica trophozoites within the biofilm-produced extracellular matrix, reducing their exposure to oxidative stress (OS). Our results indicate that parasites may digest biofilms by a controlled mechanism of digestive exophagy as secretion of digestive enzymes as a conserved mechanism for biofilm degradation allows phagocytic digestion of biofilm cells. Furthermore, the partially digested biofilms can serve as an unexpected shield protecting parasites from oxidative environments and thereby may regulate the persistence and virulence of the parasite.
bioRxiv (Cold Spring Harbor Laboratory), May 30, 2022
Environmental Microbiology, Dec 10, 2018
Bacteria in nature often reside in differentiated communities termed biofilms. These communities,... more Bacteria in nature often reside in differentiated communities termed biofilms. These communities, which are composed of a number of functionally distinct cell types, are an interesting example of division of labor in microbes, and as such have been used as a system to study the evolution of cooperation. The structured population of the biofilm also plays a critical role in the persistence of infections, and biofouling of medical and industrial devices. Biofilm formation involves several stages of differentiation, which are mediated by extracellular factors secreted by cells composing the biofilm. The developmental model of biofilm formation describes this process mechanistically: specific subpopulations of cells synthesize signals within the biofilm, and promote the differentiation of other subpopulations. The handicap principle suggests that signals function because they provide reliable information regarding the state of the signaler; here we apply the handicap principle to signaling among cells composing Bacillus subtilis biofilms, emphasizing the perspective of secreted factors as sources of information rather than solely as mediators of development. Such information could facilitate competition among phenotypically similar cells composing the biofilm, affecting local organizational patterns within defined subpopulations.
Environmental Microbiology, Feb 21, 2019
New Biotechnology, May 1, 2020
Computational and structural biotechnology journal, 2022
Graphical abstract
Obstetrical & Gynecological Survey, 2015
Frontiers in Microbiology, Dec 26, 2016
Objectives: This work assesses different methods to interfere with Enterococcus faecalis biofilms... more Objectives: This work assesses different methods to interfere with Enterococcus faecalis biofilms formed on human dentin slabs. Methods: First, methods are presented that select for small molecule inhibitors of biofilm targets using multi-well polystyrene biofilm plates. Next, we establish methodologies to study and interfere with biofilm formation on a medically relevant model, whereby biofilms are grown on human root dentin slabs. Results: Non-conventional D-amino acid (D-Leucine) can efficiently disperse biofilms formed on dentin slabs without disturbing planktonic growth. Cation chelators interfere with biofilm formation on dentin slabs and polystyrene surfaces, and modestly impact planktonic growth. Strikingly, sodium hypochlorite, the treatment conventionally used to decontaminate infected root canal systems, was extremely toxic to planktonic bacteria, but did not eradicate biofilm cells. Instead, it induced a viable but non-culturable state in biofilm cells when grown on dentin slabs. Conclusion: Sodium hypochlorite may contribute to bacterial persistence. A combination of the methods described here can greatly contribute to the development of biofilm inhibitors and therapies to treat Enterococcus faecalis infections formed in the root canal system.
iScience, Jun 1, 2022
In nature, bacteria reside in biofilms-multicellular differentiated communities held together by ... more In nature, bacteria reside in biofilms-multicellular differentiated communities held together by an extracellular matrix. This work identified a novel subpopulation-mineral-forming cells-that is essential for biofilm formation in Bacillus subtilis biofilms. This subpopulation contains an intracellular calcium-accumulating niche, in which the formation of a calcium carbonate mineral is initiated. As the biofilm colony develops, this mineral grows in a controlled manner, forming a functional macrostructure that serves the entire community. Consistently, biofilm development is prevented by the inhibition of calcium uptake. Our results provide a clear demonstration of the orchestrated production of calcite exoskeleton, critical to morphogenesis in simple prokaryotes.
Applied and Environmental Microbiology, Jul 1, 2019
Microbial ecosystems tightly associated with a eukaryotic host are widespread in nature. The gene... more Microbial ecosystems tightly associated with a eukaryotic host are widespread in nature. The genetic and metabolic networks of the eukaryotic hosts and the associated microbes have coevolved to form a symbiotic relationship. Both the Gram-positive Bacillus subtilis and the Gram-negative Serratia plymuthica can form biofilms on plant roots and thus can serve as a model system for the study of interspecies interactions in a host-associated ecosystem. We found that B. subtilis biofilms expand collectively and asymmetrically toward S. plymuthica, while expressing a nonribosomal antibiotic bacillaene and an extracellular protease. As a result, B. subtilis biofilms outcompeted S. plymuthica for successful colonization of the host. Strikingly, the plant host was able to enhance the efficiency of this killing by inducing bacillaene synthesis. In turn, B. subtilis biofilms increased the resistance of the plant host to pathogens. These results provide an example of how plant-bacterium symbiosis promotes the immune response of the plant host and the fitness of the associated bacteria. IMPORTANCE Our study sheds mechanistic light on how multicellular biofilm units compete to successfully colonize a eukaryote host, using B. subtilis microbial communities as our lens. The microbiota and its interactions with its host play various roles in the development and prevention of diseases. Using competing beneficial biofilms that are essential microbiota members on the plant host, we found that B. subtilis biofilms activate collective migration to capture their prey, followed by nonribosomal antibiotic synthesis. Plant hosts increase the efficiency of antibiotic production by B. subtilis biofilms, as they activate the synthesis of polyketides; therefore, our study provides evidence of a mechanism by which the host can indirectly select for beneficial microbiota members.
Journal of Bacteriology, Oct 15, 2011
New Biotechnology, Oct 1, 2018
Molecular Microbiology, Sep 30, 2012
Many bacteria organize themselves into structurally complex communities known as biofilms in whic... more Many bacteria organize themselves into structurally complex communities known as biofilms in which the cells are held together by an extracellular matrix. In general, the amount of extracellular matrix is related to the robustness of the biofilm. Yet, the specific signals that regulate the synthesis of matrix remain poorly understood. Here we show that the matrix itself can be a cue that regulates the expression of the genes involved in matrix synthesis in Bacillus subtilis. The presence of the exopolysaccharide component of the matrix causes an increase in osmotic pressure that leads to an inhibition of matrix gene expression. We further show that non-specific changes in osmotic pressure also inhibit matrix gene expression and do so by activating the histidine kinase KinD. KinD, in turn, directs the phosphorylation of the master regulatory protein Spo0A, which at high levels represses matrix gene expression. Sensing a physical cue such as osmotic pressure, in addition to chemical cues, could be a strategy to non-specifically coordinate the behavior of cells in communities composed of many different species.
EMBO Reports, May 3, 2017
The linkage between regulatory elements of transcription, such as promoters, and their protein pr... more The linkage between regulatory elements of transcription, such as promoters, and their protein products is central to gene function. Promoter-protein coevolution is therefore expected, but rarely observed, and the manner by which these two regulatory levels are linked remains largely unknown. We study glutamate dehydrogenase-a hub of carbon and nitrogen metabolism. In Bacillus subtilis, two paralogues exist: GudB is constitutively transcribed whereas RocG is tightly regulated. In their active, oligomeric states, both enzymes show similar enzymatic rates. However, swaps of enzymes and promoters cause severe fitness losses, thus indicating promoter-enzyme coevolution. Characterization of the proteins shows that, compared to RocG, GudB's enzymatic activity is highly dependent on glutamate and pH. Promoter-enzyme swaps therefore result in excessive glutamate degradation when expressing a constitutive enzyme under a constitutive promoter, or insufficient activity when both the enzyme and its promoter are tightly regulated. Coevolution of transcriptional and enzymatic regulation therefore underlies paralogue-specific spatio-temporal control, especially under diverse growth conditions.
Journal of Bacteriology, Feb 1, 2011
Bacillus subtilis is able to form architecturally complex biofilms on solid medium due to the pro... more Bacillus subtilis is able to form architecturally complex biofilms on solid medium due to the production of an extracellular matrix. A master regulator that controls the expression of the genes involved in matrix synthesis is Spo0A, which is activated by phosphorylation via a phosphorelay involving multiple histidine kinases. Here we report that four kinases, KinA, KinB, KinC, and KinD, help govern biofilm formation but that their contributions are partially masked by redundancy. We show that the kinases fall into two categories and that the members of each pair (one pair comprising KinA and KinB and the other comprising KinC and KinD) are partially redundant with each other. We also show that the kinases are spatially regulated: KinA and KinB are active principally in the older, inner regions of the colony, and KinC and KinD function chiefly in the younger, outer regions. These conclusions are based on the morphology of kinase mutants, real-time measurements of gene expression using luciferase as a reporter, and confocal microscopy using a fluorescent protein as a reporter. Our findings suggest that multiple signals from the older and younger regions of the colony are integrated by the kinases to determine the overall architecture of the biofilm community.
bioRxiv (Cold Spring Harbor Laboratory), Jun 3, 2021
Beneficial and probiotic bacteria play an important role in conferring the immunity of their host... more Beneficial and probiotic bacteria play an important role in conferring the immunity of their hosts against a wide range of bacterial, viral and fungal diseases. B. subtilis is a bacterium that protects the plant from various pathogens due to its capacity to produce an extensive repertoire of antibiotics. At the same time, the plant microbiome is a highly competitive niche, with multiple microbial species competing for space and resources, a competition that can be determined by the antagonistic potential of each microbiome member. Therefore, regulating antibiotic production in the rhizosphere is of great significance to eliminate pathogens and to establish beneficial host-associated communities.In this work, we used Bacillus subtilis as a model to investigate the role of plant colonization in antibiotic production. Flow cytometry and Image-stream cytometry analysis supported the notion that A. thaliana specifically induced the transcription of the biosynthetic clusters for the non-ribosomal peptides surfactin, bacilysin and plipastatin and the polyketide bacillaene. This induction could be beneficial for the root as all clusters were shown to antagonize plant pathogens. Consistently, the root failed to induce PenP, a β-lactamase that increases only the fitness of the bacteria. Our results can be translated to improve the performance and competitiveness of beneficial members of the plant microbiome.
Microbiology spectrum, Dec 21, 2022
Mycobacterium abscessus is an emerging human pathogen belonging to the nontuberculous mycobacteri... more Mycobacterium abscessus is an emerging human pathogen belonging to the nontuberculous mycobacteria (NTM) family, causing severe pulmonary disease in compromised individuals. How this bacterium acquires iron is poorly understood.
npj Biofilms and Microbiomes
Lacticaseibacillus rhamnosus GG (LGG) is a Gram-positive beneficial bacterium that resides in the... more Lacticaseibacillus rhamnosus GG (LGG) is a Gram-positive beneficial bacterium that resides in the human intestinal tract and belongs to the family of lactic acid bacteria (LAB). This bacterium is a widely used probiotic and was suggested to provide numerous benefits for human health. However, as in most LAB strains, the molecular mechanisms that mediate the competitiveness of probiotics under different diets remain unknown. Fermentation is a fundamental process in LAB, allowing the oxidation of simple carbohydrates (e.g., glucose, mannose) for energy production under oxygen limitation, as in the human gut. Our results indicate that fermentation reshapes the metabolome, volatilome, and proteome architecture of LGG. Furthermore, fermentation alters cell envelope remodeling and peptidoglycan biosynthesis, which leads to altered cell wall thickness, aggregation properties, and cell wall composition. In addition, fermentable sugars induced the secretion of known and novel metabolites and...
Microorganisms, Jun 18, 2024
npj Biofilms and Microbiomes
The human protozoan parasite Entamoeba histolytica is responsible for amebiasis, a disease endemi... more The human protozoan parasite Entamoeba histolytica is responsible for amebiasis, a disease endemic to developing countries. E. histolytica trophozoites colonize the large intestine, primarily feeding on bacteria. However, in the gastrointestinal tract, bacterial cells form aggregates or structured communities called biofilms too large for phagocytosis. Remarkably, trophozoites are still able to invade and degrade established biofilms, utilizing a mechanism that mimics digestive exophagy. Digestive exophagy refers to the secretion of digestive enzymes that promote the digestion of objects too large for direct phagocytosis by phagocytes. E. histolytica cysteine proteinases (CPs) play a crucial role in the degradation process of Bacillus subtilis biofilm. These proteinases target TasA, a major component of the B. subtilis biofilm matrix, also contributing to the adhesion of the parasite to the biofilm. In addition, they are also involved in the degradation of biofilms formed by Gram-ne...
bioRxiv (Cold Spring Harbor Laboratory), Sep 25, 2022
The human protozoan parasite Entamoeba histolytica is responsible for amebiasis, a disease endemi... more The human protozoan parasite Entamoeba histolytica is responsible for amebiasis, a disease endemic to developing countries. E. histolytica trophozoites are released from the cysts to colonize the large intestine, where they primarily feed on bacterial cells. In these scenarios, bacterial cells form aggregates or structured communities too large for phagocytosis. Our results show that E. histolytica can degrade pre-established biofilms of Bacillus subtilis and Escherichia coli in a dose-and time-dependent manner. Surprisingly, trophozoites incubated with B. subtilis biofilm exhibit a unique transcriptome signature compared to those incubated with planktonic cells or without bacteria. Biofilm-induced genes include cysteine proteases (CPs), and the general inhibition of CPs by E64D or by the use of specific small-RNA (sRNA)based RNA interference impairs the degradation of biofilms by E. histolytica. The degradation of B. subtilis extracellular matrix (ECM) protein TasA by CPs is associated with partial biofilm digestion and activation of the stress response in the interacting B. subtilis cells. The interaction with B. subtilis biofilms was also associated with lower levels of oxidoreductases. Oxidoreductase downregulation can be a readout of the embedding of E. histolytica trophozoites within the biofilm-produced extracellular matrix, reducing their exposure to oxidative stress (OS). Our results indicate that parasites may digest biofilms by a controlled mechanism of digestive exophagy as secretion of digestive enzymes as a conserved mechanism for biofilm degradation allows phagocytic digestion of biofilm cells. Furthermore, the partially digested biofilms can serve as an unexpected shield protecting parasites from oxidative environments and thereby may regulate the persistence and virulence of the parasite.
bioRxiv (Cold Spring Harbor Laboratory), May 30, 2022
Environmental Microbiology, Dec 10, 2018
Bacteria in nature often reside in differentiated communities termed biofilms. These communities,... more Bacteria in nature often reside in differentiated communities termed biofilms. These communities, which are composed of a number of functionally distinct cell types, are an interesting example of division of labor in microbes, and as such have been used as a system to study the evolution of cooperation. The structured population of the biofilm also plays a critical role in the persistence of infections, and biofouling of medical and industrial devices. Biofilm formation involves several stages of differentiation, which are mediated by extracellular factors secreted by cells composing the biofilm. The developmental model of biofilm formation describes this process mechanistically: specific subpopulations of cells synthesize signals within the biofilm, and promote the differentiation of other subpopulations. The handicap principle suggests that signals function because they provide reliable information regarding the state of the signaler; here we apply the handicap principle to signaling among cells composing Bacillus subtilis biofilms, emphasizing the perspective of secreted factors as sources of information rather than solely as mediators of development. Such information could facilitate competition among phenotypically similar cells composing the biofilm, affecting local organizational patterns within defined subpopulations.
Environmental Microbiology, Feb 21, 2019
New Biotechnology, May 1, 2020
Computational and structural biotechnology journal, 2022
Graphical abstract
Obstetrical & Gynecological Survey, 2015
Frontiers in Microbiology, Dec 26, 2016
Objectives: This work assesses different methods to interfere with Enterococcus faecalis biofilms... more Objectives: This work assesses different methods to interfere with Enterococcus faecalis biofilms formed on human dentin slabs. Methods: First, methods are presented that select for small molecule inhibitors of biofilm targets using multi-well polystyrene biofilm plates. Next, we establish methodologies to study and interfere with biofilm formation on a medically relevant model, whereby biofilms are grown on human root dentin slabs. Results: Non-conventional D-amino acid (D-Leucine) can efficiently disperse biofilms formed on dentin slabs without disturbing planktonic growth. Cation chelators interfere with biofilm formation on dentin slabs and polystyrene surfaces, and modestly impact planktonic growth. Strikingly, sodium hypochlorite, the treatment conventionally used to decontaminate infected root canal systems, was extremely toxic to planktonic bacteria, but did not eradicate biofilm cells. Instead, it induced a viable but non-culturable state in biofilm cells when grown on dentin slabs. Conclusion: Sodium hypochlorite may contribute to bacterial persistence. A combination of the methods described here can greatly contribute to the development of biofilm inhibitors and therapies to treat Enterococcus faecalis infections formed in the root canal system.
iScience, Jun 1, 2022
In nature, bacteria reside in biofilms-multicellular differentiated communities held together by ... more In nature, bacteria reside in biofilms-multicellular differentiated communities held together by an extracellular matrix. This work identified a novel subpopulation-mineral-forming cells-that is essential for biofilm formation in Bacillus subtilis biofilms. This subpopulation contains an intracellular calcium-accumulating niche, in which the formation of a calcium carbonate mineral is initiated. As the biofilm colony develops, this mineral grows in a controlled manner, forming a functional macrostructure that serves the entire community. Consistently, biofilm development is prevented by the inhibition of calcium uptake. Our results provide a clear demonstration of the orchestrated production of calcite exoskeleton, critical to morphogenesis in simple prokaryotes.
Applied and Environmental Microbiology, Jul 1, 2019
Microbial ecosystems tightly associated with a eukaryotic host are widespread in nature. The gene... more Microbial ecosystems tightly associated with a eukaryotic host are widespread in nature. The genetic and metabolic networks of the eukaryotic hosts and the associated microbes have coevolved to form a symbiotic relationship. Both the Gram-positive Bacillus subtilis and the Gram-negative Serratia plymuthica can form biofilms on plant roots and thus can serve as a model system for the study of interspecies interactions in a host-associated ecosystem. We found that B. subtilis biofilms expand collectively and asymmetrically toward S. plymuthica, while expressing a nonribosomal antibiotic bacillaene and an extracellular protease. As a result, B. subtilis biofilms outcompeted S. plymuthica for successful colonization of the host. Strikingly, the plant host was able to enhance the efficiency of this killing by inducing bacillaene synthesis. In turn, B. subtilis biofilms increased the resistance of the plant host to pathogens. These results provide an example of how plant-bacterium symbiosis promotes the immune response of the plant host and the fitness of the associated bacteria. IMPORTANCE Our study sheds mechanistic light on how multicellular biofilm units compete to successfully colonize a eukaryote host, using B. subtilis microbial communities as our lens. The microbiota and its interactions with its host play various roles in the development and prevention of diseases. Using competing beneficial biofilms that are essential microbiota members on the plant host, we found that B. subtilis biofilms activate collective migration to capture their prey, followed by nonribosomal antibiotic synthesis. Plant hosts increase the efficiency of antibiotic production by B. subtilis biofilms, as they activate the synthesis of polyketides; therefore, our study provides evidence of a mechanism by which the host can indirectly select for beneficial microbiota members.
Journal of Bacteriology, Oct 15, 2011
New Biotechnology, Oct 1, 2018
Molecular Microbiology, Sep 30, 2012
Many bacteria organize themselves into structurally complex communities known as biofilms in whic... more Many bacteria organize themselves into structurally complex communities known as biofilms in which the cells are held together by an extracellular matrix. In general, the amount of extracellular matrix is related to the robustness of the biofilm. Yet, the specific signals that regulate the synthesis of matrix remain poorly understood. Here we show that the matrix itself can be a cue that regulates the expression of the genes involved in matrix synthesis in Bacillus subtilis. The presence of the exopolysaccharide component of the matrix causes an increase in osmotic pressure that leads to an inhibition of matrix gene expression. We further show that non-specific changes in osmotic pressure also inhibit matrix gene expression and do so by activating the histidine kinase KinD. KinD, in turn, directs the phosphorylation of the master regulatory protein Spo0A, which at high levels represses matrix gene expression. Sensing a physical cue such as osmotic pressure, in addition to chemical cues, could be a strategy to non-specifically coordinate the behavior of cells in communities composed of many different species.
EMBO Reports, May 3, 2017
The linkage between regulatory elements of transcription, such as promoters, and their protein pr... more The linkage between regulatory elements of transcription, such as promoters, and their protein products is central to gene function. Promoter-protein coevolution is therefore expected, but rarely observed, and the manner by which these two regulatory levels are linked remains largely unknown. We study glutamate dehydrogenase-a hub of carbon and nitrogen metabolism. In Bacillus subtilis, two paralogues exist: GudB is constitutively transcribed whereas RocG is tightly regulated. In their active, oligomeric states, both enzymes show similar enzymatic rates. However, swaps of enzymes and promoters cause severe fitness losses, thus indicating promoter-enzyme coevolution. Characterization of the proteins shows that, compared to RocG, GudB's enzymatic activity is highly dependent on glutamate and pH. Promoter-enzyme swaps therefore result in excessive glutamate degradation when expressing a constitutive enzyme under a constitutive promoter, or insufficient activity when both the enzyme and its promoter are tightly regulated. Coevolution of transcriptional and enzymatic regulation therefore underlies paralogue-specific spatio-temporal control, especially under diverse growth conditions.
Journal of Bacteriology, Feb 1, 2011
Bacillus subtilis is able to form architecturally complex biofilms on solid medium due to the pro... more Bacillus subtilis is able to form architecturally complex biofilms on solid medium due to the production of an extracellular matrix. A master regulator that controls the expression of the genes involved in matrix synthesis is Spo0A, which is activated by phosphorylation via a phosphorelay involving multiple histidine kinases. Here we report that four kinases, KinA, KinB, KinC, and KinD, help govern biofilm formation but that their contributions are partially masked by redundancy. We show that the kinases fall into two categories and that the members of each pair (one pair comprising KinA and KinB and the other comprising KinC and KinD) are partially redundant with each other. We also show that the kinases are spatially regulated: KinA and KinB are active principally in the older, inner regions of the colony, and KinC and KinD function chiefly in the younger, outer regions. These conclusions are based on the morphology of kinase mutants, real-time measurements of gene expression using luciferase as a reporter, and confocal microscopy using a fluorescent protein as a reporter. Our findings suggest that multiple signals from the older and younger regions of the colony are integrated by the kinases to determine the overall architecture of the biofilm community.
bioRxiv (Cold Spring Harbor Laboratory), Jun 3, 2021
Beneficial and probiotic bacteria play an important role in conferring the immunity of their host... more Beneficial and probiotic bacteria play an important role in conferring the immunity of their hosts against a wide range of bacterial, viral and fungal diseases. B. subtilis is a bacterium that protects the plant from various pathogens due to its capacity to produce an extensive repertoire of antibiotics. At the same time, the plant microbiome is a highly competitive niche, with multiple microbial species competing for space and resources, a competition that can be determined by the antagonistic potential of each microbiome member. Therefore, regulating antibiotic production in the rhizosphere is of great significance to eliminate pathogens and to establish beneficial host-associated communities.In this work, we used Bacillus subtilis as a model to investigate the role of plant colonization in antibiotic production. Flow cytometry and Image-stream cytometry analysis supported the notion that A. thaliana specifically induced the transcription of the biosynthetic clusters for the non-ribosomal peptides surfactin, bacilysin and plipastatin and the polyketide bacillaene. This induction could be beneficial for the root as all clusters were shown to antagonize plant pathogens. Consistently, the root failed to induce PenP, a β-lactamase that increases only the fitness of the bacteria. Our results can be translated to improve the performance and competitiveness of beneficial members of the plant microbiome.
Microbiology spectrum, Dec 21, 2022
Mycobacterium abscessus is an emerging human pathogen belonging to the nontuberculous mycobacteri... more Mycobacterium abscessus is an emerging human pathogen belonging to the nontuberculous mycobacteria (NTM) family, causing severe pulmonary disease in compromised individuals. How this bacterium acquires iron is poorly understood.
npj Biofilms and Microbiomes
Lacticaseibacillus rhamnosus GG (LGG) is a Gram-positive beneficial bacterium that resides in the... more Lacticaseibacillus rhamnosus GG (LGG) is a Gram-positive beneficial bacterium that resides in the human intestinal tract and belongs to the family of lactic acid bacteria (LAB). This bacterium is a widely used probiotic and was suggested to provide numerous benefits for human health. However, as in most LAB strains, the molecular mechanisms that mediate the competitiveness of probiotics under different diets remain unknown. Fermentation is a fundamental process in LAB, allowing the oxidation of simple carbohydrates (e.g., glucose, mannose) for energy production under oxygen limitation, as in the human gut. Our results indicate that fermentation reshapes the metabolome, volatilome, and proteome architecture of LGG. Furthermore, fermentation alters cell envelope remodeling and peptidoglycan biosynthesis, which leads to altered cell wall thickness, aggregation properties, and cell wall composition. In addition, fermentable sugars induced the secretion of known and novel metabolites and...