ABSTRACT
Fungi and bacteria coexist in many polymicrobial communities, yet the molecular basis of their interactions remains poorly understood. Here, we show that the fungus Candida albicans sequesters essential magnesium ions from the bacterium Pseudomonas aeruginosa. To counteract fungal Mg2+ sequestration, P. aeruginosa expresses the Mg2+ transporter MgtA when Mg2+ levels are low. Thus, loss of MgtA specifically impairs P. aeruginosa in co-culture with C. albicans, but fitness can be restored by supplementing Mg2+. Using a panel of fungi and bacteria, we show that Mg2+ sequestration is a general mechanism of fungal antagonism against gram-negative bacteria. Mg2+ limitation enhances bacterial resistance to polymyxin antibiotics like colistin, which target gram-negative bacterial membranes. Indeed, experimental evolution reveals that P. aeruginosa evolves C. albicans-dependent colistin resistance via non-canonical means; antifungal treatment renders resistant bacteria colistin-sensitive. Our work suggests that fungal-bacterial competition could profoundly impact polymicrobial infection treatment with antibiotics of last resort.
Subject(s)
Anti-Bacterial Agents , Candida albicans , Colistin , Magnesium , Pseudomonas aeruginosa , Magnesium/pharmacology , Magnesium/metabolism , Pseudomonas aeruginosa/drug effects , Anti-Bacterial Agents/pharmacology , Candida albicans/drug effects , Candida albicans/metabolism , Colistin/pharmacology , Microbial Sensitivity Tests , Polymyxins/pharmacology , Drug Resistance, Bacterial/drug effects , Microbial Interactions/drug effectsABSTRACT
Fungicides are used worldwide to improve crop yields, but they can affect non-target soil microorganisms which are essential for ecosystem functioning. Microorganisms form complex communities characterized by a myriad of interspecies interactions, yet it remains unclear to what extent non-target microorganisms are indirectly affected by fungicides through biotic interactions with sensitive taxa. To quantify such indirect effects, we fragmented a soil microbial community by filtration to alter biotic interactions and compared the effect of the fungicide hymexazol between fractions in soil microcosms. We postulated that OTUs which are indirectly affected would exhibit a different response to the fungicide across the fragmented communities. We found that hymexazol primarily affected bacterial and fungal communities through indirect effects, which were responsible for more than 75% of the shifts in relative abundance of the dominant microbial OTUs after exposure to an agronomic dose of hymexazol. However, these indirect effects decreased for the bacterial community when hymexazol doses increased. Our results also suggest that N-cycling processes such as ammonia oxidation can be impacted indirectly by fungicide application. This work sheds light on the indirect impact of fungicide exposure on soil microorganisms through biotic interactions, which underscores the need for higher-tier risk assessment. ENVIRONMENTAL IMPLICATION: In this study, we used a novel approach based on the fragmentation of the soil microbial community to determine to which extent fungicide application could indirectly affect fungi and bacteria through biotic interactions. To assess off-target effects of fungicide on soil microorganisms, we selected hymexazol, which is used worldwide to control a variety of fungal plant pathogens, and exposed arable soil to the recommended field rate, as well as to higher rates. Our findings show that at least 75% of hymexazol-impacted microbial OTUs were indirectly affected, therefore emphasizing the importance of tiered risk assessment.
Subject(s)
Bacteria , Fungi , Fungicides, Industrial , Soil Microbiology , Fungicides, Industrial/toxicity , Fungicides, Industrial/pharmacology , Fungi/drug effects , Fungi/metabolism , Bacteria/drug effects , Bacteria/metabolism , Soil Pollutants/toxicity , Microbiota/drug effects , Microbial Interactions/drug effectsABSTRACT
Colibactin is a chemically unstable small-molecule genotoxin that is produced by several different bacteria, including members of the human gut microbiome1,2. Although the biological activity of colibactin has been extensively investigated in mammalian systems3, little is known about its effects on other microorganisms. Here we show that colibactin targets bacteria that contain prophages, and induces lytic development through the bacterial SOS response. DNA, added exogenously, protects bacteria from colibactin, as does expressing a colibactin resistance protein (ClbS) in non-colibactin-producing cells. The prophage-inducing effects that we observe apply broadly across different phage-bacteria systems and in complex communities. Finally, we identify bacteria that have colibactin resistance genes but lack colibactin biosynthetic genes. Many of these bacteria are infected with predicted prophages, and we show that the expression of their ClbS homologues provides immunity from colibactin-triggered induction. Our study reveals a mechanism by which colibactin production could affect microbiomes and highlights a role for microbial natural products in influencing population-level events such as phage outbreaks.
Subject(s)
Bacteria , Bacterial Toxins , Peptides , Polyketides , Prophages , Virus Activation , Bacteria/drug effects , Bacteria/virology , Bacterial Toxins/metabolism , Bacterial Toxins/pharmacology , Bacteriolysis/drug effects , Microbial Interactions/drug effects , Peptides/metabolism , Peptides/pharmacology , Polyketides/metabolism , Polyketides/pharmacology , Prophages/drug effects , Prophages/physiology , SOS Response, Genetics/drug effects , Virus Activation/drug effectsABSTRACT
Nutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how microbial species abundances are shaped by biotic and abiotic factors. Here we show that the ribosomal RNA gene operon (rrn) copy number, a genomic trait related to bacterial growth rate and nutrient demand, decreases from the abundant to the rare biosphere in the nutrient-rich coastal sediment but exhibits the opposite pattern in the nutrient-scarce pelagic zone of the global ocean. Both patterns are underlain by positive correlations between community-level rrn copy number and nutrients. Furthermore, inter-species co-exclusion inferred by negative network associations is observed more in coastal sediment than in ocean water samples. Nutrient manipulation experiments yield effects of nutrient availability on rrn copy numbers and network associations that are consistent with our field observations. Based on these results, we propose a "hunger games" hypothesis to define microbial species abundance rules using the rrn copy number, ecological interaction, and nutrient availability.
Subject(s)
Aquatic Organisms/genetics , Microbial Interactions/genetics , Microbiota/genetics , rRNA Operon , Aquatic Organisms/drug effects , Aquatic Organisms/growth & development , Aquatic Organisms/metabolism , Ecosystem , Gene Dosage , Microbial Interactions/drug effects , Microbiota/drug effects , Nutrients/analysis , Nutrients/pharmacology , Seawater/microbiologyABSTRACT
Indoor formaldehyde (CH2O) exceeding the recommended level is a severe threat to human health. Few studies have investigated its effect on indoor surface bacterial communities, affecting habitants' health. This study used 20-L glass containers to mimic the indoor environment with bacterial inputs from human oral respiration. The behavior of bacterial communities responding to CH2O varied among the different CH2O levels. The bacterial community structure significantly changed over time in the 0.054 mg·m-3 CH2O group, which varied from the 0.1 mg·m-3 and 0.25 mg·m-3 CH2O groups. The Chao1 and Shannon index significantly increased in the 0.054 mg·m-3 CH2O group at 6 week, while they remained unchanged in the 0.25 mg·m-3 CH2O group. At 12 week, the Chao1 significantly increased in the 0.25 mg·m-3 CH2O group, while it remained unchanged in the 0.054 mg·m-3 CH2O group. Only a few Operational Taxonomic Units (OTUs) significantly correlated with the CH2O concentration. CH2O-induced OTUs mainly belong to the Proteobacteria and Firmicutes. Furthermore, bacterial communities formed at 6 or 12 weeks differed significantly among different CH2O levels. Functional analysis of bacterial communities showed that inferred genes related to chemical degradation and diseases were the highest in the 0.25 mg·m-3 CH2O group at 12 weeks. The development of nematodes fed with bacteria collected at 12 weeks was applied to evaluate the bacterial community's hazards. This showed significantly impaired growth in the 0.1 mg·m-3 and 0.25 mg·m-3 CH2O groups. These findings confirmed that CH2O concentration and exposure time could affect the indoor bacterial community and formed bacterial communities with a possibly more significant hazard to human health after long-term exposure to high CH2O levels.
Subject(s)
Air Pollution, Indoor/analysis , Formaldehyde/pharmacology , Microbial Interactions/drug effects , Anti-Bacterial Agents/metabolism , Anti-Bacterial Agents/pharmacology , Bacteria/drug effects , Bacteria/genetics , Biota/drug effects , Formaldehyde/analysis , Formaldehyde/metabolism , Humans , Microbial Consortia/drug effects , Proteobacteria/genetics , RNA, Ribosomal, 16S/geneticsABSTRACT
Vitamin D receptor (VDR) deficiency is associated with cancer, infection, and chronic inflammation. Prior research has demonstrated VDR regulation of bacteria; however, little is known regarding VDR and viruses. We hypothesize that VDR deficiency impacts on the intestinal virome and viral-bacterial interactions. We specifically deleted VDR from intestinal epithelial cells (VDRΔIEC), Paneth cells (VDRΔPC), and myeloid cells (VDRΔLyz) in mice. Feces were collected for shotgun metagenomic sequencing and metabolite profiling. To test the functional changes, we evaluated pattern recognition receptors (PRRs) and analyzed microbial metabolites. Vibrio phages, Lactobacillus phages, and Escherichia coli typing phages were significantly enriched in all three conditional VDR-knockout mice. In the VDRΔLyz mice, the levels of eight more virus species (2 enriched, 6 depleted) were significantly changed. Altered virus species were primarily observed in female VDRΔLyz (2 enriched, 3 depleted) versus male VDRΔLyz (1 enriched, 1 depleted). Altered alpha and beta diversity (family to species) were found in VDRΔLyz. In VDRΔIEC mice, bovine viral diarrhea virus 1 was significantly enriched. A significant correlation between viral and bacterial alterations was found in conditional VDR knockout mice. There was a positive correlation between Vibrio phage JSF5 and Cutibacterium acnes in VDRΔPC and VDRΔLyz mice. Also, there were more altered viral species in female conditional VDR knockout mice. Notably, there were significant changes in PRRs: upregulated TLR3, TLR7, and NOD2 in VDRΔLyz mice and increased CLEC4L expression in VDRΔIEC and VDRΔPC mice. Furthermore, we identified metabolites related to virus infection: decreased glucose in VDRΔIEC mice, increased ribulose/xylulose and xylose in VDRΔLyz mice, and increased long-chain fatty acids in VDRΔIEC and VDRΔLyz female mice. Tissue-specific deletion of VDR changes the virome and functionally changes viral receptors, which leads to dysbiosis, metabolic dysfunction, and infection risk. This study helps to elucidate VDR regulating the virome in a tissue-specific and sex-specific manner.
Subject(s)
Deficiency Diseases/physiopathology , Gastrointestinal Microbiome/drug effects , Intestines/virology , Microbial Interactions/drug effects , Receptors, Calcitriol/deficiency , Virome/drug effects , Animals , Feces/virology , Female , Male , Mice , Mice, Knockout , Myeloid Cells/drug effects , Myeloid Cells/virology , Paneth Cells/drug effects , Paneth Cells/virologyABSTRACT
Unique bacterial associations were formed in the polluted soils from territory of the industrial factories Open Joint Stock Company "The Middle Volga Chemical Plant," Chapaevsk, Russia and Open Joint Stock Company "Lubricant Producing Plant," Perm, Russia. This study evaluates the influence of the biphenyl/polychlorinated biphenyls (PCB) on the formation of aerobic bacterial associations and their biodegradative potential. Enrichment cultivation of the soil samples from the territories of these industrial factories with PCB (commercial mixture Sovol) was lead for forming aerobic bacterial enrichment cultures showing a unique composition. The dominating in these bacterial cultures was the phylum Proteobacteria (Beta- and Gammaproteobacteria). Using biphenyl as a carbon source led to decrease of biodiversity in the final stable bacterial associations. Periodic cultivation experiments demonstrated that the association PN2-B has a high degradative potential among the six studied bacterial associations. PN2-B degraded 100% mono-chlorobiphenyls (94.5 mg/L), 86.2% di-chlorobiphenyls (22.3 mg/L), 50.9% Sovol, and 38.4% Delor 103 (13.8 mg/L). Qualitative analysis of metabolites showed that association performed transformation of chlorobenzoic acids (PCB degradation intermediates) into metabolites of citrate cycle. Twelve individual strain-destructors were isolated. The strains were found to degrade 17.7-100% PCB1, 36.2-100% PCB2, 18.8-100% PCB3 (94.5 mg/L), and 15.7-78.2% PCB8 (22.3 mg/L). The strains were shown to metabolize chlorobenzoic acids formed during degradation of chlorobiphenyls. A unique ability of strains Micrococcus sp. PNS1 and Stenotrophomonas sp. PNS6 to degrade ortho-, meta-, and para-monosubstituted chlorobenzoic acids was revealed. Our results suggest that PN2-B and individual bacterial strains will be perspective for cleaning of the environment from polychlorinated biphenyls.
Subject(s)
Bacteria, Aerobic , Biodegradation, Environmental , Microbial Interactions , Polychlorinated Biphenyls , Bacteria, Aerobic/drug effects , Bacteria, Aerobic/metabolism , Biodegradation, Environmental/drug effects , Microbial Interactions/drug effects , Polychlorinated Biphenyls/analysis , Polychlorinated Biphenyls/pharmacology , Soil Microbiology , Soil Pollutants/analysis , Soil Pollutants/pharmacologyABSTRACT
Pseudomonas aeruginosa and Staphylococcus aureus are two of the most common coinfecting bacteria in human infections, including the cystic fibrosis (CF) lung. There is emerging evidence that coinfection with these microbes enhances disease severity and antimicrobial tolerance through direct interactions. However, one of the challenges to studying microbial interactions relevant to human infection is the lack of experimental models with the versatility to investigate complex interaction dynamics while maintaining biological relevance. Here, we developed a model based on an in vitro medium that mimics human CF lung secretions (synthetic CF sputum medium [SCFM2]) and allows time-resolved assessment of fitness and community spatial structure at the micrometer scale. Our results reveal that P. aeruginosa and S. aureus coexist as spatially structured communities in SCFM2 under static growth conditions, with S. aureus enriched at a distance of 3.5 µm from P. aeruginosa Multispecies aggregates were rare, and aggregate (biofilm) sizes resembled those in human CF sputum. Elimination of P. aeruginosa's ability to produce the antistaphylococcal small molecule HQNO (2-heptyl-4-hydroxyquinoline N-oxide) had no effect on bacterial fitness but altered the spatial structure of the community by increasing the distance of S. aureus from P. aeruginosa to 7.6 µm. Lastly, we show that coculture with P. aeruginosa sensitizes S. aureus to killing by the antibiotic tobramycin compared to monoculture growth despite HQNO enhancing tolerance during coculture. Our findings reveal that SCFM2 is a powerful model for studying P. aeruginosa and S. aureus and that HQNO alters S. aureus biogeography and antibiotic susceptibility without affecting fitness.IMPORTANCE Many human infections result from the action of multispecies bacterial communities. Within these communities, bacteria have been proposed to directly interact via physical and chemical means, resulting in increased disease and antimicrobial tolerance. One of the challenges to studying multispecies infections is the lack of robust, infection-relevant model systems with the ability to study these interactions through time with micrometer-scale precision. Here, we developed a versatile in vitro model for studying the interactions between Pseudomonas aeruginosa and Staphylococcus aureus, two bacteria that commonly coexist in human infections. Using this model along with high-resolution, single-cell microscopy, we showed that P. aeruginosa and S. aureus form communities that are spatially structured at the micrometer scale, controlled in part by the production of an antimicrobial by P. aeruginosa In addition, we provide evidence that this antimicrobial enhances S. aureus tolerance to an aminoglycoside antibiotic only during coculture.
Subject(s)
Anti-Bacterial Agents/pharmacology , Pseudomonas aeruginosa/drug effects , Staphylococcus aureus/drug effects , Biofilms/drug effects , Biofilms/growth & development , Coculture Techniques , Cystic Fibrosis/microbiology , Humans , Microbial Interactions/drug effects , Pseudomonas Infections/microbiology , Pseudomonas aeruginosa/growth & development , Staphylococcal Infections/microbiology , Staphylococcus aureus/growth & developmentABSTRACT
Immunotherapy has become a new paradigm in oncology, improving outcomes for several types of cancer. However, there are some aspects about its management that remain uncertain. One of the key points that needs better understanding is the interaction between immunotherapy and gut microbiome and how modulation of the microbiome might modify the efficacy of immunotherapy. Consequently, the negative impact of systemic antibiotics and corticosteroids on the efficacy of immunotherapy needs to be clarified.
Subject(s)
Adrenal Cortex Hormones/pharmacology , Anti-Bacterial Agents/pharmacology , Host Microbial Interactions , Immune Checkpoint Inhibitors/therapeutic use , Microbiota , Neoplasms/drug therapy , Probiotics , Adrenal Cortex Hormones/therapeutic use , Animals , Anti-Bacterial Agents/therapeutic use , Host Microbial Interactions/drug effects , Host Microbial Interactions/immunology , Humans , Immune Checkpoint Inhibitors/pharmacology , Immunomodulation/drug effects , Microbial Interactions/drug effects , Microbial Interactions/immunology , Microbiota/drug effects , Neoplasms/etiology , Treatment OutcomeABSTRACT
The soil bacterium Bacillus subtilis forms beneficial biofilms that induce plant defences and prevent the growth of pathogens. It is naturally found in the rhizosphere, where microorganisms coexist in an extremely competitive environment, and thus have evolved a diverse arsenal of defence mechanisms. In this work, we found that volatile compounds produced by B. subtilis biofilms inhibited the development of competing biofilm colonies, by reducing extracellular matrix gene expression, both within and across species. This effect was dose-dependent, with the structural defects becoming more pronounced as the number of volatile-producing colonies increased. This inhibition was mostly mediated by organic volatiles, and we identified the active molecules as 3-methyl-1-butanol and 1-butanol. Similar results were obtained with biofilms formed by phylogenetically distinct bacterium sharing the same niche, Escherichia coli, which produced the biofilm-inhibiting 3-methyl-1-butanol and 2-nonanon. The ability of established biofilms to inhibit the development and spreading of new biofilms from afar might be a general mechanism utilized by bacterial biofilms to protect an occupied niche from the invasion of competing bacteria.
Subject(s)
Biofilms/drug effects , Microbial Interactions/drug effects , Volatile Organic Compounds/pharmacology , 1-Butanol/metabolism , 1-Butanol/pharmacology , Bacillus subtilis/physiology , Bacterial Proteins/genetics , Biofilms/growth & development , Escherichia coli/physiology , Extracellular Polymeric Substance Matrix/drug effects , Extracellular Polymeric Substance Matrix/genetics , Gene Expression Regulation, Bacterial/drug effects , Ketones/metabolism , Ketones/pharmacology , Microbiota , Pentanols/metabolism , Pentanols/pharmacology , Volatile Organic Compounds/metabolismABSTRACT
TITLE: Le monoxyde d'azote: Une arme du système immunitaire pour brouiller les communications entre bactéries - Microorganismes et communication intercellulaire. ABSTRACT: Le dossier thématique suivant a été rédigé par les étudiantes et étudiants de Master 1 de Biologie de l'École Normale Supérieure de Lyon à l'issue de l'UE Microbiologie Moléculaire et Structurale (2019-2020). Le Master de Biologie de l'ENS de Lyon, cohabilité par l'université Claude Bernard Lyon 1, accueille chaque année environ 50 étudiants en M1 et en M2 et propose une formation de haut niveau à la recherche en biosciences. Chaque étudiant y construit son parcours à la carte, en choisissant ses options parmi un large panel de modules, favorisant ainsi une approche pluridisciplinaire des sciences du vivant, et ce en relation étroite avec les laboratoires de recherche du tissu local, national et international. En participant à diverses activités scientifiques connexes aux UE de leur formation, les étudiants préparent également l'obtention du Diplôme de l'ENS de Lyon, qui valide leur scolarité à l'ENS. La rédaction du présent dossier, qui vise à transmettre de façon claire les messages issus d'une sélection d'articles scientifiques publiés récemment dans le domaine de la microbiologie, constitue l'une de ces activités connexes proposées aux étudiants. Les bactéries peuvent vivre en communautés dont la structure est régulée par de nombreuses interactions abiotiques et biotiques. Les interactions biotiques reposent sur des communications inter-bactériennes qui participent à la mise en place de relations de collaboration, de compétition ou de prédation. Ces communautés bactériennes peuvent en outre être en interaction avec des hôtes animaux, dans le cas des bactéries du microbiote ou des bactéries pathogènes par exemple, ou avec des virus parasites, les bactériophages. Le présent dossier illustre quelques aspects nouveaux de cette communication bactérienne, et de la façon dont les interactions bactéries/hôte ou bactéries/phages peuvent impacter cette communication. Deux nouvelles s'attardent sur des découvertes récentes autour du quorum sensing, une modalité de communication bactérienne permettant l'expression coordonnée des gènes à l'échelle de la population, en fonction de la densité de la population. La nouvelle intitulée « Le monoxyde d'azote : une arme du système immunitaire pour brouiller les communications entre bactéries ¼ illustre comment le quorum sensing chez Staphylococcus aureus, une bactérie opportuniste, peut être affecté par un médiateur du système immunitaire de la souris. La nouvelle intitulée « Un bactériophage exploite le système de communication de son hôte bactérien pour entrer en cycle lytique ¼ montre une stratégie étonnante par laquelle le phage VP882 décrypte des signaux issus du quorum sensing de la bactérie qu'il infecte pour réguler son propre cycle de réplication. Au-delà du quorum sensing, deux nouvelles décrivent de nouvelles modalités de communication inter-bactérienne. La nouvelle intitulée « Les nanotubes bactériens, acteurs de la compétition entre Bacillus subtilis et Bacillus megaterium ¼ met en lumière le rôle des nanotubes, des structures de communication intercellulaire insoupçonnées jusque récemment chez les bactéries. La nouvelle intitulée « La bactérie Vibrio cholerae lyse les bactéries environnantes et assimile leur ADN qu'elle intègre dans son propre génome ¼ illustre comment un système de sécrétion, qui permet l'injection d'effecteurs bactériens dans des cellules cibles, peut être exploité pour faciliter les transferts horizontaux de gènes chez les bactéries. Enfin, pour élargir la réflexion au monde des virus eucaryotes, deux nouvelles montrent comment l'infection virale peut interférer avec la communication entre cellules eucaryotes, sur l'exemple de la communication s'effectuant par l'intermédiaire de vésicules extracellulaires. La nouvelle intitulée « La sécrétion de vésicules extracellulaires par les plaquettes activées à l'origine de la létalité de la dengue ? ¼ discute des mécanismes par lesquels le virus de la dengue déclenche la sécrétion de vésicules extracellulaires par les plaquettes, et des conséquences que cela peut avoir sur l'inflammation et le déclenchement de chocs hémorragiques. La nouvelle intitulée « Le coccolithovirus et Emiliania huxleyi : le détournement viral des vésicules extracellulaires ¼ montre enfin comment ce virus d'algue unicellulaire exploite la communication intercellulaire de son hôte pour augmenter son pouvoir de diffusion au sein de la population, et des conséquences écologiques et géochimiques que cela peut entraîner à grande échelle.
Subject(s)
Cells/microbiology , Host-Pathogen Interactions/drug effects , Microbial Interactions/drug effects , Nitric Oxide/pharmacology , Staphylococcus aureus/pathogenicity , Animals , Cell Communication/drug effects , Cells/metabolism , Nitric Oxide/metabolism , Staphylococcus aureus/drug effects , Staphylococcus aureus/metabolism , Virulence/drug effectsABSTRACT
Soil microorganisms coexist and interact showing antagonistic or mutualistic behaviors. Here, we show that an environmental strain of Bacillus subtilis undergoes heritable phenotypic variation upon interaction with the soil fungal pathogen Setophoma terrestris (ST). Metabolomics analysis revealed differential profiles in B. subtilis before (pre-ST) and after (post-ST) interacting with the fungus, which paradoxically involved the absence of lipopeptides surfactin and plipastatin and yet acquisition of antifungal activity in post-ST variants. The profile of volatile compounds showed that 2-heptanone and 2-octanone were the most discriminating metabolites present at higher concentrations in post-ST during the interaction process. Both ketones showed strong antifungal activity, which was lost with the addition of exogenous surfactin. Whole-genome analyses indicate that mutations in ComQPXA quorum-sensing system, constituted the genetic bases of post-ST conversion, which rewired B. subtilis metabolism towards the depletion of surfactins and the production of antifungal compounds during its antagonistic interaction with S. terrestris.
Subject(s)
Antifungal Agents , Ascomycota , Bacillus subtilis , Microbial Interactions , Quorum Sensing/genetics , Antifungal Agents/metabolism , Antifungal Agents/pharmacology , Ascomycota/drug effects , Ascomycota/metabolism , Bacillus subtilis/genetics , Bacillus subtilis/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Biological Products/metabolism , Ketones/metabolism , Ketones/pharmacology , Metabolome/physiology , Microbial Interactions/drug effects , Microbial Interactions/genetics , Mutation/genetics , Soil MicrobiologyABSTRACT
The dynamics of volatilomes emitted during the interaction between plant-growth-promoting bacteria (PGPB) and the phytopathogen Fusarium solani were evaluated for 5 days. The first screening was done to evaluate the antagonist activity of volatile compounds emitted by PGPB against F. solani. Volatilomes from 11 PGPB were determined individually and together with F. solani by using solid-phase microextraction coupled to gas-chromatography-mass spectrometry. Isolates of PGPB belonged to the Bacillus genus and inhibited from 18 to 24% the fungal mycelium growth. The isolates also induced morphological alterations of fungal hyphae, like small globular vesicles and the formation of chlamydospores, suggesting a stress mechanism response by the fungus. Volatilome profile showed 49 different compounds that appeared in the bacterial-fungal interaction, such as ketones, sesquiterpenes, monoterpenoids, alkanes, alkenes, carboxylic acids, and fatty acids. Some ketones and alcohols were detected in high abundance only in the interaction PGPB-fungus at 3 and 5 days. Bacillus circulans A19, Bacillus amyloliquefaciens A21, and Bacillus wiedmannii S18 shared a group of emitted alcohols and ketones when they were exposed to F. solani. F. solani produced its own volatilome profile, with the presence of sesquiterpenes, such as α-cubebene and caryophyllene, which increased significantly in co-incubation with the tested bacteria, suggesting chemical communication between them.
Subject(s)
Antifungal Agents/pharmacology , Bacteria/metabolism , Bacterial Physiological Phenomena , Fusarium/drug effects , Microbial Interactions/physiology , Plant Development/physiology , Volatile Organic Compounds/pharmacology , Alkanes/pharmacology , Alkenes/pharmacology , Antifungal Agents/chemistry , Bacillus , Bacillus amyloliquefaciens , Bacteria/drug effects , Carboxylic Acids/pharmacology , Fatty Acids/pharmacology , Fusarium/growth & development , Fusarium/pathogenicity , Ketones/pharmacology , Microbial Interactions/drug effects , Monoterpenes/pharmacology , Mycelium/growth & development , Plant Diseases/microbiology , Sesquiterpenes/pharmacology , Soil Microbiology , Volatile Organic Compounds/chemistryABSTRACT
Verona-Integron-encoded-Metallo-ß-lactamase-positive Pseudomonas aeruginosa (VIM-PA) is a cause of hard-to-treat nosocomial infections, and can colonize hospital water networks alongside Acanthamoeba. We developed an in-vitro disinfection model to examine whether Acanthamoeba castellanii can harbour VIM-PA intracellularly, allowing VIM-PA to evade being killed by currently used hospital disinfectants. We observed that A. castellanii presence resulted in significantly increased survival of VIM-PA after exposure to chlorine for 30 s or for 2 min. This undesirable effect was not observed after disinfection by 70% alcohol or 24% acetic acid. Confocal microscopy confirmed the presence of VIM-PA within A. castellanii pseudocysts. Our data indicate that A. castellanii contributes to persistent VIM-PA colonization of water systems after chlorine treatment.
Subject(s)
Acanthamoeba castellanii/microbiology , Chlorine/pharmacology , Drug Resistance, Multiple, Bacterial , Microbial Interactions/drug effects , Microbial Viability/drug effects , Pseudomonas aeruginosa/drug effects , Cross Infection/microbiology , Cross Infection/prevention & control , Disinfection , Hospitals/statistics & numerical data , Pseudomonas Infections/prevention & control , beta-LactamasesABSTRACT
With antibiotic resistance rates on the rise, it is critical to understand how microbial species interactions influence the evolution of resistance. In obligate mutualisms, the survival of any one species (regardless of its intrinsic resistance) is contingent on the resistance of its cross-feeding partners. This sets the community antibiotic sensitivity at that of the 'weakest link' species. In this study, we tested the hypothesis that weakest link dynamics in an obligate cross-feeding relationship would limit the extent and mechanisms of antibiotic resistance evolution. We experimentally evolved an obligate co-culture and monoculture controls along gradients of two different antibiotics. We measured the rate at which each treatment increased antibiotic resistance, and sequenced terminal populations to question whether mutations differed between mono- and co-cultures. In both rifampicin and ampicillin treatments, we observed that resistance evolved more slowly in obligate co-cultures of E. coli and S. enterica than in monocultures. While we observed similar mechanisms of resistance arising under rifampicin selection, under ampicillin selection different resistance mechanisms arose in co-cultures and monocultures. In particular, mutations in an essential cell division protein, ftsI, arose in S. enterica only in co-culture. A simple mathematical model demonstrated that reliance on a partner is sufficient to slow the rate of adaptation, and can change the distribution of adaptive mutations that are acquired. Our results demonstrate that cooperative metabolic interactions can be an important modulator of resistance evolution in microbial communities.
Subject(s)
Adaptation, Physiological/drug effects , Drug Resistance, Microbial/physiology , Escherichia coli/physiology , Microbial Interactions/physiology , Salmonella enterica/physiology , Adaptation, Physiological/genetics , Ampicillin/pharmacology , Anti-Bacterial Agents/pharmacology , Bacterial Proteins/genetics , Coculture Techniques , Escherichia coli/drug effects , Microbial Interactions/drug effects , Models, Theoretical , Mutation , Rifampin/pharmacology , Salmonella enterica/drug effectsABSTRACT
Bacterial adhesion on surfaces is an essential initial step in promoting bacterial mobilization for soil bioremediation process. Modification of the cell surface is required to improve the adhesion of bacteria. The modification of physicochemical properties by rhamnolipid to Pseudomonas putida KT2442, Rhodococcus erythropolis 3586 and Aspergillus brasiliensis ATCC 16404 strains was analysed using contact angle measurements. The surface energy and total free energy of adhesion were calculated to predict the adhesion of both bacteria strains on the A. brasiliensis surface. The study of bacterial adhesion was carried out to evaluate experimental value with the theoretical results. Bacteria and fungi physicochemical properties were modified significantly when treated with rhamnolipid. The adhesion rate of P. putida improved by 16% with the addition of rhamnolipid (below 1 CMC), while the increase of rhamnolipid concentration beyond 1 CMC did not further enhance the bacterial adhesion. The addition of rhamnolipid did not affect the adhesion of R. erythropolis. A good relationship has been obtained in which water contact angle and surface energy of fungal surfaces are the major factors contributing to the bacterial adhesion. The adhesion is mainly driven by acid-base interaction. This finding provides insight to the role of physicochemical properties in controlling the bacterial adhesion on the fungal surface to enhance bacteria transport in soil bioremediation.
Subject(s)
Aspergillus/drug effects , Glycolipids/pharmacology , Microbial Interactions/drug effects , Pseudomonas aeruginosa/drug effects , Rhodococcus/drug effects , Aspergillus/physiology , Bacterial Adhesion/drug effects , Pseudomonas aeruginosa/physiology , Rhodococcus/physiologyABSTRACT
OBJECTIVE: Helicobacter pylori is associated with gastric inflammation, precancerous gastric atrophy (GA) and intestinal metaplasia (IM). We aimed to identify microbes that are associated with progressive inflammation, GA and IM 1 year after H. pylori eradication. DESIGN: A total of 587 H. pylori-positive patients were randomised to receive H. pylori eradication therapy (295 patients) or placebo (292 patients). Bacterial taxonomy was analysed on 404 gastric biopsy samples comprising 102 pairs before and after 1 year H. pylori eradication and 100 pairs before and after 1 year placebo by 16S rRNA sequencing. RESULTS: Analysis of microbial sequences confirmed the eradication of H. pylori in treated group after 1 year. Principal component analysis revealed distinct microbial clusters reflected by increase in bacterial diversity (p<0.00001) after H. pylori eradication. While microbial interactions remained largely unchanged after placebo treatment, microbial co-occurrence was less in treated group. Acinetobacter lwoffii, Streptococcus anginosus and Ralstonia were enriched while Roseburia and Sphingomonas were depleted in patients with persistent inflammation 1 year after H. pylori eradication. A distinct cluster of oral bacteria comprising Peptostreptococcus, Streptococcus, Parvimonas, Prevotella, Rothia and Granulicatella were associated with emergence and persistence of GA and IM. Probiotic Faecalibacterium praustznii was depleted in subjects who developed GA following H. pylori eradication. Functional pathways including amino acid metabolism and inositol phosphate metabolism were enriched while folate biosynthesis and NOD-like receptor signalling decreased in atrophy/IM-associated gastric microbiota. CONCLUSION: This study identified that gastric microbes contribute to the progression of gastric carcinogenesis after H. pylori eradication.
Subject(s)
Bacteria , Gastritis, Atrophic , Helicobacter Infections , Helicobacter pylori , Metaplasia , Stomach , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , Bacteria/pathogenicity , Biopsy/methods , Biopsy/statistics & numerical data , Carcinogenesis , Disease Eradication/methods , Disease Eradication/statistics & numerical data , Disease Progression , Female , Gastritis, Atrophic/microbiology , Gastritis, Atrophic/pathology , Helicobacter Infections/diagnosis , Helicobacter Infections/drug therapy , Helicobacter pylori/drug effects , Helicobacter pylori/isolation & purification , Humans , Male , Metaplasia/microbiology , Metaplasia/pathology , Microbial Interactions/drug effects , Middle Aged , Sequence Analysis, RNA/methods , Stomach/microbiology , Stomach/pathologyABSTRACT
The human gut microbiota has now been associated with drug responses and efficacy, while chemical compounds present in these drugs can also impact the gut bacteria. However, drug-microbe interactions are still understudied in the clinical context, where polypharmacy and comorbidities co-occur. Here, we report relations between commonly used drugs and the gut microbiome. We performed metagenomics sequencing of faecal samples from a population cohort and two gastrointestinal disease cohorts. Differences between users and non-users were analysed per cohort, followed by a meta-analysis. While 19 of 41 drugs are found to be associated with microbial features, when controlling for the use of multiple medications, proton-pump inhibitors, metformin, antibiotics and laxatives show the strongest associations with the microbiome. We here provide evidence for extensive changes in taxonomy, metabolic potential and resistome in relation to commonly used drugs. This paves the way for future studies and has implications for current microbiome studies by demonstrating the need to correct for multiple drug use.
Subject(s)
Bacteria/classification , Bacteria/drug effects , Bacteria/metabolism , Gastrointestinal Microbiome/drug effects , Gastrointestinal Microbiome/physiology , Metagenomics , Adult , Anti-Bacterial Agents/pharmacology , Antidepressive Agents/pharmacology , Body Mass Index , Case-Control Studies , Cohort Studies , Computational Biology , Ecosystem , Feces/microbiology , Female , Humans , Irritable Bowel Syndrome/drug therapy , Irritable Bowel Syndrome/microbiology , Laxatives/pharmacology , Male , Metformin/pharmacology , Microbial Interactions/drug effects , Middle Aged , Proton Pump Inhibitors/pharmacologyABSTRACT
Airway infections associated with cystic fibrosis (CF) are polymicrobial. We reported previously that clinical isolates of Pseudomonas aeruginosa promote the growth of a variety of streptococcal species. To explore the mechanistic basis of this interaction, we performed a genetic screen to identify mutants of Streptococcus sanginuis SK36 whose growth was no longer enhanced by P. aeruginosa PAO1. Mutations in the zinc uptake systems of S. sanguinis SK36 reduced growth of these strains by 1 to 3 logs compared to that of wild-type S. sanguinis SK36 when grown in coculture with P. aeruginosa PAO1, and exogenous zinc (0.1 to 10 µM) rescued the coculture defect of zinc uptake mutants of S. sanguinis SK36. Zinc uptake mutants of S. sanguinis SK36 had no obvious growth defect in monoculture. Consistent with competition for zinc driving coculture dynamics, S. sanguinis SK36 grown in coculture with P. aeruginosa showed increased expression of zinc uptake genes compared to that of S. sanguinis grown alone. Strains of P. aeruginosa PAO1 defective in zinc transport also supported â¼2-fold more growth by S. sanguinis compared to that in coculture with wild-type P. aeruginosa PAO1. An analysis of 118 CF sputum samples revealed that total zinc levels varied from â¼5 to 145 µM. At relatively low zinc levels, Pseudomonas and Streptococcus spp. were found in approximately equal abundance; at higher zinc levels, we observed a decline in relative abundance of Streptococcus spp., perhaps as a result of increasing zinc toxicity. Together, our data indicate that the relative abundances of these microbes in the CF airway may be impacted by zinc levels.IMPORTANCE Polymicrobial infections in CF cases likely impact patient health, but the mechanism(s) underlying such interactions is poorly understood. Here, we show using an in vitro model system that interactions between Pseudomonas and Streptococcus are modulated by zinc availability, and clinical data are consistent with this model. Together with previous studies, our work supports a role for metal homeostasis as a key factor driving microbial interactions.
Subject(s)
Pseudomonas aeruginosa/metabolism , Streptococcus sanguis/metabolism , Zinc/pharmacology , Biofilms/drug effects , Coculture Techniques , Microbial Interactions/drug effects , Pseudomonas aeruginosa/drug effects , Pseudomonas aeruginosa/physiology , Streptococcus sanguis/drug effects , Streptococcus sanguis/physiologyABSTRACT
Candida albicans is a commensal of the human body and an opportunistic pathogen frequently responsible for nosocomial bloodstream infections. Most of these infections are linked to the development of a biofilm in or on implanted medical devices. C. albicans cells have the capacity to interact with bacteria within biofilms, especially by the way of chemical or metabolic indirect interactions and/or direct physical contacts involving specifically the yeast or hyphal form of the fungal cell, or more rarely involving both forms. According to the species, C. albicans-bacteria interactions can be antagonistic or synergistic, competitive or not. The polymicrobial nature of biofilms may deeply influence the physiopathology of infections as well as the efficiency of antimicrobial agents. The present review aims to focus on the current knowledge of interactions between C. albicans and major Gram-positive bacteria such as Staphylococcus aureus, coagulase negative Staphylococcus, Streptococcus spp. and Clostridium spp. within biofilms. A better understanding of this complicated, fast-paced world of multi-kingdom biofilms will contribute to develop new effective ways to fight biofilm-related infections.