Littérature scientifique sur le sujet « Microbe-Microbe competition »

Despite the omnipresence of specific host–symbiont associations with acquisition of the microbial symbiont from the environment, little is known about how the specificity of the interaction evolved and is maintained. The bean bug Riptortus pedestris acquires a specific bacterial symbiont of the genus Burkholderia from environmental soil and harbors it in midgut crypts. The genus Burkholderia consists of over 100 species, showing ecologically diverse lifestyles, and including serious human pathogens, plant pathogens, and nodule-forming plant mutualists, as well as insect mutualists. Through infection tests of 34 Burkholderia species and 18 taxonomically diverse bacterial species, we demonstrate here that nonsymbiotic Burkholderia and even its outgroup Pandoraea could stably colonize the gut symbiotic organ and provide beneficial effects to the bean bug when inoculated on aposymbiotic hosts. However, coinoculation revealed that the native symbiont always outcompeted the nonnative bacteria inside the gut symbiotic organ, explaining the predominance of the native Burkholderia symbiont in natural bean bug populations. Hence, the abilities for colonization and cooperation, usually thought of as specific traits of mutualists, are not unique to the native Burkholderia symbiont but, to the contrary, competitiveness inside the gut is a derived trait of the native symbiont lineage only and was thus critical in the evolution of the insect gut symbiont.

ABSTRACTThe human gut is inhabited by thousands of microbial species, most of which are still uncharacterized. Gut microbes have adapted to each other's presence as well as to the host and engage in complex cross feeding. Constraint-based modeling has been successfully applied to predicting microbe-microbe interactions, such as commensalism, mutualism, and competition. Here, we apply a constraint-based approach to model pairwise interactions between 11 representative gut microbes. Microbe-microbe interactions were computationally modeled in conjunction with human small intestinal enterocytes, and the microbe pairs were subjected to three diets with various levels of carbohydrate, fat, and protein in normoxic or anoxic environments. Each microbe engaged in species-specific commensal, parasitic, mutualistic, or competitive interactions. For instance,Streptococcus thermophilusefficiently outcompeted microbes with which it was paired, in agreement with the domination of streptococci in the small intestinal microbiota. Under anoxic conditions, the probiotic organismLactobacillus plantarumdisplayed mutualistic behavior toward six other species, which, surprisingly, were almost entirely abolished under normoxic conditions. This finding suggests that the anoxic conditions in the large intestine drive mutualistic cross feeding, leading to the evolvement of an ecosystem more complex than that of the small intestinal microbiota. Moreover, we predict that the presence of the small intestinal enterocyte induces competition over host-derived nutrients. The presented framework can readily be expanded to a larger gut microbial community. This modeling approach will be of great value for subsequent studies aiming to predict conditions favoring desirable microbes or suppressing pathogens.

The human gut microbiota is transmitted from mother to infant through vaginal birth and breastfeeding. Bifidobacterium , a genus that dominates the infants’ gut, is adapted to breast milk in its ability to metabolize human milk oligosaccharides; it is regarded as a mutualist owing to its involvement in the development of the immune system. The composition of microbiota, including the abundance of Bifidobacteria, is highly variable between individuals and some microbial profiles are associated with diseases. However, whether and how birth and feeding practices contribute to such variation remains unclear. To understand how early events affect the establishment of microbiota, we develop a mathematical model of two types of Bifidobacteria and a generic compartment of commensal competitors. We show how early events affect competition between mutualists and commensals and microbe-host-immune interactions to cause long-term alterations in gut microbial profiles. Bifidobacteria associated with breast milk can trigger immune responses with lasting effects on the microbial community structure. Our model shows that, in response to a change in birth environment, competition alone can produce two distinct microbial profiles post-weaning. Adding immune regulation to our competition model allows for variations in microbial profiles in response to different feeding practices. This analysis highlights the importance of microbe–microbe and microbe–host interactions in shaping the gut populations following different birth and feeding modes.

The skin is the largest human organ and is responsible for many important functions, such as temperature regulation, water transport, and protection from external insults. It is colonized by several microorganisms that interact with each other and with the host, shaping the microbial structure and community dynamics. Through these interactions, the skin microbiota can inhibit pathogens through several mechanisms such as the production of bacteriocins, proteases, phenol soluble modulins (PSMs), and fermentation. Furthermore, these commensals can produce molecules with antivirulence activity, reducing the potential of these pathogens to adhere to and invade human tissues. Microorganisms of the skin microbiota are also able to sense molecules from the environment and shape their behavior in response to these signals through the modulation of gene expression. Additionally, microbiota-derived compounds can affect pathogen gene expression, including the expression of virulence determinants. Although most studies related to microbial interactions in the skin have been directed towards elucidating competition mechanisms, microorganisms can also use the products of other species to their benefit. In this review, we will discuss several mechanisms through which microorganisms interact in the skin and the biotechnological applications of products originating from the skin microbiota that have already been reported in the literature.

ABSTRACTBeneficial symbioses between microbes and their eukaryotic hosts are ubiquitous and have widespread impacts on host health and development. The binary symbiosis between the bioluminescent bacterium Vibrio fischeri and its squid host Euprymna scolopes serves as a model system to study molecular mechanisms at the microbe-animal interface. To identify colonization factors in this system, our lab previously conducted a global transposon insertion sequencing (INSeq) screen and identified over 300 putative novel squid colonization factors in V. fischeri. To pursue mechanistic studies on these candidate genes, we present an approach to quickly generate barcode-tagged gene deletions and perform high-throughput squid competition experiments with detection of the proportion of each strain in the mixture by barcode sequencing (BarSeq). Our deletion approach improves on previous techniques based on splicing by overlap extension PCR (SOE-PCR) and tfoX-based natural transformation by incorporating a randomized barcode that results in unique DNA sequences within each deletion scar. Amplicon sequencing of the pool of barcoded strains before and after colonization faithfully reports on known colonization factors and provides increased sensitivity over colony counting methods. BarSeq enables rapid and sensitive characterization of the molecular factors involved in establishing the Vibrio-squid symbiosis and provides a valuable tool to interrogate the molecular dialogue at microbe-animal host interfaces.IMPORTANCE Beneficial microbes play essential roles in the health and development of their hosts. However, the complexity of animal microbiomes and general genetic intractability of their symbionts have made it difficult to study the coevolved mechanisms for establishing and maintaining specificity at the microbe-animal host interface. Model symbioses are therefore invaluable for studying the mechanisms of beneficial microbe-host interactions. Here, we present a combined barcode-tagged deletion and BarSeq approach to interrogate the molecular dialogue that ensures specific and reproducible colonization of the Hawaiian bobtail squid by Vibrio fischeri. The ability to precisely manipulate the bacterial genome, combined with multiplex colonization assays, will accelerate the use of this valuable model system for mechanistic studies of how environmental microbes—both beneficial and pathogenic—colonize specific animal hosts.

<abstract><p>This paper proposes a stochastic intestinal chemostat model considering microbial migration, intraspecific competition and stochastic perturbation. First, the extinction and persistence in mean of the intestinal microbe of the chemostat model are investigated by constructing the appropriate Lyapunov functions. Second, we explore and obtain sufficient conditions for the existence and uniqueness of an ergodic stationary distribution of the model by using ergodic theory. The results show stochastic interference has a critical impact on the extinction and sustainable survival of the intestinal microbe. Eventually, numerical simulations are carried out to verify the theoretical results.</p></abstract>

Helicobacter pylori causes gastritis, peptic ulcer disease and gastric cancer. The microbe is found in the gastric mucus layer where a pH gradient ranging from acidic in the lumen to neutral at the cell surface is maintained. The aim of the present study was to investigate the effects of pH on H. pylori binding to gastric mucins from healthy individuals. At pH 3, all strains bound to the most charged MUC5AC glycoform and to a putative mucin of higher charge and larger size than subunits of MUC5AC and MUC6, irrespective of host blood-group. In contrast, at pH 7.4 only Leb-binding BabA-positive strains bound to Leb-positive MUC5AC and to smaller mucin-like molecules, including MUC1. H. pylori binding to the latter component(s) seems to occur via the H-type-1 structure. All strains bound to a proteoglycan containing chondroitin sulphate/dermatan sulphate side chains at acidic pH, whereas binding to secreted MUC5AC and putative membrane-bound strains occurred both at neutral and acidic pH. The binding properties at acidic pH are thus common to all H. pylori strains, whereas mucin binding at neutral pH occurs via the bacterial BabA adhesin and the Leb antigen/related structures on the glycoprotein. Our work shows that microbe binding to membrane-bound mucins must be considered in H. pylori colonization, and the potential of these glycoproteins to participate in signalling events implies that microbe binding to such structures may initiate signal transduction over the epithelial layer. Competition between microbe binding to membrane-bound and secreted mucins is therefore an important aspect of host–microbe interaction.

La stabilité évolutive des relations hôte-microbe est cruciale pour la symbiose. La transmission verticale des symbiotes microbiens des parents à la progéniture est bien établie, mais l'acquisition environnementale par transmission horizontale de symbiotes nécessite des adaptations spécifiques. Les insectes de l'infra-ordre Pentatomomorpha disposent d'un mécanisme efficace pour l'acquisition de leur symbiote à partir du sol. Ces insectes possèdent une architecture intestinale distinctive contenant une région postérieure, appelée M4, composée de centaines de cryptes, constituant une niche spécifique pour abriter des symbiotes intestinaux bénéfiques. Les Coreoidea sélectionnent spécifiquement des bactéries Caballeronia. Ma thèse explore la spécificité de cette association et les mécanismes bactériens sous-jacents. Trois espèces de Coreoidea (Riptortus pedestris, Leptoglossus occidentalis, Coreus marginatus) montrent une préférence pour des sous-clades spécifiques de Caballeronia, influencée par la compétition interspécifique. La région M4 est dominée par une seule espèce bactérienne, suggérant une forte pression de sélection. La spécificité de la souche est alignée avec un avantage en termes de fitness reproductif. Des criblages génétiques ont révélé des fonctions cruciales pour la colonisation des cryptes, notamment le chimiotactisme, la résistance aux peptides antimicrobiens et de la capacité à utiliser des sources de carbone néoglucogéniques, la taurine et l'inositol, suggérant que l'hôte fournit ce type de métabolites comme nutriments aux symbiotes. Ces découvertes démontrent que malgré une grande diversité microbienne environnementale, les insectes sélectionnent des symbiotes spécifiques grâce à des mécanismes multifactoriels
The evolutionary stability of host-microbe relationships is crucial for symbiosis. Vertical transmission of microbial symbionts from parents to offspring is well established, but environmental acquisition through horizontal transmission of symbionts requires specific adaptations. Insects of the infraorder Pentatomomorpha have an effective mechanism for acquiring their symbionts from the soil. These insects possess a distinctive intestinal architecture with a posterior region called M4, composed of hundreds of crypts that provide a specific niche for harboring beneficial gut symbionts. Coreoidea specifically select Caballeronia bacteria. My thesis explores the specificity of this association and the underlying bacterial mechanisms. Three species of Coreoidea (Riptortus pedestris, Leptoglossus occidentalis, Coreus marginatus) show a preference for specific subclades of Caballeronia, influenced by interspecific competition. The M4 region is dominated by a single bacterial species, suggesting strong selective pressure. Strain specificity is aligned with a reproductive fitness advantage. Genetic screenings revealed crucial functions for crypt colonization, including chemotaxis, resistance to antimicrobial peptides, and the ability to utilize neoglucogenic carbon sources such as taurine and inositol, suggesting that the host provides these metabolites as nutrients to the symbionts. These findings demonstrate that despite high environmental microbial diversity, insects select specific symbionts through multifactorial mechanisms

In den meisten Ländern Mitteleuropas gilt weniger als ein Prozent des verbleibenden Laubwaldes als ungestört und temperierte Wälder sind Herausforderungen wie Arteninvasion, Klimawandel und steigender Stickstoff(N)-Deposition ausgesetzt. In der Vergangenheit wurde gezeigt, dass hohe N-Einträge N-Limitierungen verringern, Phosphor(P)aufnahme behindern und P-Mängel in der Buche auslösen können. Die Artendiversität von Bäumen kann die Bestandsproduktivität durch die Prozesse Komplementarität und Facilitation (Wachstumserleichterung) erhöhen, wenn diese einen wachstumslimitierenden Nährstoff betreffen. Ein Schlüsselprozess im Nährstoffkreislauf ist der Weg von Nährstoffen durch die mikrobielle Biomasse während der Dekomposition. Es wurde gezeigt, dass die mikrobielle Biomasse um N bspw. mit Buchen und um P mit tropischen Moorpflanzen konkurriert. Die Buche ist eine sehr konkurrenzfähige Baumart in temperierten Waldökosystemen aber kann von der Eiche in trockenen Bereichen übertrumpft werden, während Hainbuche und Linde eine geringere Rolle spielen. Eichen erfahren jedoch in der jüngsten Vergangenheit in europäischen Wäldern einen Rückgang, der womöglich auf hohe N-Einträge zurückzuführen ist. Für diese Arbeit untersuchten wir die Nährstoff-, Konkurrenz- und strukturelle Dynamik eines unbewirtschafteten, sehr naturnahen Laubwaldes in Mitteldeutschland, der aus Buche (Fagus sylvatica), Eiche (Quercus petraea und Quercus robur), Hainbuche (Carpinus betulus) und Linde (Tilia cordata und Tilia platyphyllus) aufgebaut ist. Unsere Ziele waren (1) zu erforschen, ob Komplementarität und/oder Facilitation die Produktivität in diesem Waldökosystem erhöht, (2) festzustellen, ob es Konkurrenz um die Nährstoffe N, P und K zwischen Bäumen und mikrobieller Biomasse gibt und, (3) die Nachbarschaftsdynamik der genannten Baumarten zu untersuchen und herauszufinden, ob der Eichenrückgang mit hoher N-Deposition einhergeht. In Beständen einer Art sowie verschiedenen Mischbeständen aus je drei Arten ermittelten wir Biomasseproduktion und Nährstoffverfügbarkeit. Nährstoffnutzungseffizienzkurven (Nährstoffnutzungseffizienz = Biomasseproduktion pro verfügbare Nährstoffe) wurden genutzt um festzustellen, ob ein bestimmter Nährstoff das Baumwachstum limitiert. Die jährliche Netto-Nährstoffveränderung wurde in einer Laubbeutel-Studie als Differenz zwischen ursprünglichem und verbleibendem Nährstoffgehalt des sich zersetzenden Laubfalls nach einem Jahr kalkuliert. Die Nährstoffresorptionseffizienz berechneten wir über die Ermittlung der N-, P- und Kalium(K)-Konzentrationen in sonnenexponierten Blättern und im gefallenen Laub. Die Nachbarschaftsdynamik von Bäumen wurde über die Durchmesserverteilung, überirdische Holzbiomasse für jede Artenkombination sowie eine Polygon-Abschätzung von Wachstumsräumen erforscht. Zusätzlich wurde eine durchmesserbasierte nearest neighbor(nächster-Nachbar)-Analyse für Baumpaare durchgeführt. Ein Geographisches Informationssystem (GIS) wurde genutzt um Wachstumsraum-Polygone zu erstellen und nächste Nachbarn zu bestimmen. Auf Einzelbaum-Level, ermittelt durch einen Nachbarschaftsansatz, waren relative Wachstumsraten von Buchen im Einzelbestand geringer als in der Mischung mit Linde und Hainbuche während das Wachstum von Linde im Einzelbestand größer war als in Mischung mit Buche und Eiche. Die Nährstoffnutzungseffizienzkurve für Buche zeigte optimale P- und K-Nutzungseffizienz für die Art in Mischbeständen, während sie in Einzelbeständen  P- und K-limitiert war. Während die jährliche Netto-Nährstoffveränderung in sich zersetzendem Blattlaub die Verfügbarkeit von P und K im Boden beeinflusste, war dies für N nicht der Fall. Resorptionseffizienzen von N, P und K hingen negativ mit der jährlichen Netto-Nährstoffveränderung zusammen. In unserer Studie zur Nachbarschaftsdynamik von Bäumen fanden wir heraus, dass intraspezifische nearest neighbors gleiche Durchmesser aufwiesen und ihren Durchmesser gleichzeitig mit dem des Nachbarn vergrößerten. Im Gegensatz dazu waren die Durchmesser von interspezifischen nearest neighbors im Allgemeinen unterschiedlich und der Durchmesser des Nachbarn verringerte sich mit zunehmendem Durchmesser des Zielbaums. Eichen konnten ihren Wachstumsraum mit zunehmendem Durchmesser nicht vergrößern, aber dominierten ihre nearest neighbor über die Größe. Unsere Ergebnisse zeigten, dass im untersuchten Waldökosystem Nährstofflimitierungen artabhängig waren und dass die Nutzung von Nährstoffnutzungseffizienz und Nachbarschaftsansatz geeignete Mittel sind, den Einfluss einzelner Baumarten auf die Produktivität einer Art im Rein- und Mischbestand zu ermitteln – so wie die beobachtete Facilitation der Buche im Mischbestand. Diese Werkzeuge stellen eine wichtige Basis zur verbesserten Bewirtschaftung typischer temperierter Mischwälder dar. Wir schlussfolgerten weiterhin, dass Konkurrenz zwischen mikrobieller Biomasse und Bäumen für P und K hoch, aber für N weniger bedeutend war, was wahrscheinlich in hoher N-Deposition in diesem Waldökosystem begründet liegt, welche den internen N-Kreislauf entkoppelte. Die hohe N-Deposition trug wahrscheinlich auch zu geringer Verjüngung der Eiche bei, während ältere Eichen in unserem Untersuchungsgebiet im Wettbewerb um Licht erfolgreich waren. Die Bestandsstruktur war charakterisiert durch stärkere interspezifische verglichen mit intraspezifischer Konkurrenz. Daraus resultierend bildeten Reinbestände aus Buche, Eiche und Linde Klimaxbestände hoher Biomasse innerhalb eines sich verändernden, kleinskaligen Mosaiks verschiedener Artenzusammensetzungen. In Reaktion auf neue Bewirtschaftungsanforderungen des Globalen Wandels sind weiterführende Forschungen zu Nutzungseffizienz unterschiedlicher Ressourcen für Baumarten in verschiedenen Zusammensetzungen empfehlenswert.

碩士
中原大學
化學工程研究所
81
In this work, immobilized invertase was added into the fermenter in order to compete with microorganims for the hydrolysis of sucrose, the accumulation of monosccharides in the broth was thus controlled and the ethanol yield was enhanced. Results from batch fermentations of Z. mobilis showed that the formations of by-products; i.e., sorbitol and levan, were associ- ated with an higher sucrose concentration in the medium.The for- mation of by-products was suggested to be the reason for low ethanol yields from sucrose. As the sucrose concentration in the feed was 200g/l, the ethanol yield became only 57％ of its thro- retical value. In a combined Z. mobilis/ immobilized invertase system with 200 g/l sucrose as substrates. It was found when 0.2g immobilized invertase (activity 2100Ｕ/g)was added to a 1.2 liter batch fermenter, the ethanol yield was increased from 0.29 to 0.40 g/g (80％ of the theoretical value). High ethanol yields we also obtained from continuous cultures.When 0.2 g immobilized invertase was added, the dilution rate for the maximum ethanol productivity (10.5g/l/h) was determined as 0.2. Experimenal data showed that increasing the addition of immobilized invertase led to a low concentration of sucrose in the culture and lower rate of levan formation and sucrose hydrolysis,both were catalyzed by the extracellular exzyme levansucrase.It could be concluded that the levansucrase secreted by Z. mobilis is a sucrose inducible enzyme. In this work,the kinetic models of Z. mobilis fermentation and combined Z. mobilis/immobilized invertase system were also developed. Parameters used for model simulation were estimated from fitting the experimental data with these kinetic models.

Abstract The assemblage of microbes that inhabit the plant as symbionts comprises the plant microbiome. The activities of plant roots have a great effect on the density and composition of bacteria and fungi growing around them, known as the rhizosphere effect. Plant–microbe and microbe–microbe interactions in the rhizosphere have large impacts on plant health. Rhizobia are symbiotic bacteria that fix nitrogen in association with legumes, relying on a complex signaling process that results in the production of root nodules. Mycorrhizae are plant–fungal symbioses that extend the capacity of roots to absorb nutrients and water; the four major groups are ectomycorrhizae, arbuscular mycorrhizae, ericoid mycorrhizae, and orchid mycorrhizae. Common mycorrhizal networks connect plants and result in the transfer of signals, carbon, and nutrients among individuals and even among species. Endophytic fungi and bacteria colonize all parts of plants including the phylloplane; endophytes may be commensals, parasites, or mutualists, with a variety of impacts on the hosts. Endophytes may be horizontally transmitted or vertically transmitted, colonizing seeds and then growing in the next generation of plants. Microbes in the plant microbiome interact with each other through parasitism, predation, competition, antibiosis, and sometimes syntrophy. Such microbe–microbe interactions shape access to the plant by plant pathogens.

Abstract This chapter focuses on the ways that animal and plant hosts acquire microorganisms from the external environment and other hosts, including the mother. Hosts are challenged to facilitate the colonization of beneficial microorganisms while simultaneously deterring pathogens. In humans, birth indicates the transition from a microbe-free existence to a world filled with microorganisms, while diet and social contacts could promote or resist change in the gut microbiome, which had been regarded as unique as a fingerprint. The processes involved in retaining a microbiome are complex and involve host factors (including the immune system), among-microbe interactions (such as competition and mutualisms), and chance events that result in the loss or gain of particular microbial taxa.

Iron is the fourth most abundant element in the soil, but since it forms insoluble hydroxides at neutral and basic pH, it often falls short of meeting the basic requirements of plants and microorganisms. Most aerobic and facultative aerobic microorganisms possess a high-affinity Fe transport system in which siderophores are excreted and the consequent Fe complex is taken up via a cognate specific receptor and a transport pathway. The role of the siderophore in Fe uptake by plants and microorganisms was the focus of this study. In this research Rhizopus arrhizus was found to produce a novel siderophore named Rhizoferrin when grown under Fe deficiency. This compound was purified and its chemical structure was elucidated. Fe-Rhizoferrin was found to alleviate Fe deficiency when applied to several plants grown in nutrient solutions. It was concluded that Fe-Rhizoferrin is the most efficient Fe source for plants when compared with other among microbial siderophores known to date and its activity equals that of the most efficient synthetic commercial iron fertilizer-Fe EDDHA. Siderophores produced by several rhizosphere organisms including Rhizopus Pseudomonas were purified. Monoclonal antibodies were produced and used to develop a method for detection of the siderophores produced by plant-growth-promoting microorganisms in barley rhizosphere. The presence of an Fe-ferrichrome uptake in fluorescent Pseudomonas spp. was demonstrated, and its structural requirements were mapped in P. putida with the help of biomimetic ferrichrome analogs. Using competition experiments, it was shown that FOB, Cop B and FC share at least one common determinant in their uptake pathway. Since FC analogs did not affect FOB or Cop-mediated 55Fe uptake, it could be concluded that these siderophores make use of a different receptor(s) than FC. Therefore, recognition of Cop, FOB and FC proceeds through different receptors having different structural requirements. On the other hand, the phytosiderophores mugineic acid (MA and DMA), were utilized indirectly via ligand exchange by P. putida. Receptors from different biological systems seem to differ in their structural requirements for siderophore recognition and uptake. The design of genus- or species-specific drugs, probes or chemicals, along with an understanding of plant-microbe and microbe-microbe relationships as well as developing methods to detect siderophores using monoclonal antibodies are useful for manipulating the composition of the rhizosphere microbial population for better plant growth, Fe-nutrition and protection from diseases.