A Review of the Rumen Microbiota and the Different Molecular Techniques Used to Identify Microorganisms Found in the Rumen Fluid of Ruminants.

Variations in environments, including climate, diet, and agricultural practices, significantly impact the composition and microbial activity. A profound understanding of these adaptations allows for the improvement of nutrition and ruminant production. Therefore, this review aims to compile data from the literature on the rumen microbiota and molecular techniques for identifying the different types of microorganisms from the rumen fluid of ruminants. Analyzing the literature on rumen microbiology in different ruminants is complex due to microbial interactions, influenced by the environment and nutrition of these animals. In addition, it is worth noting that the genera of protozoa and fungi most evident in the studies used in this review on the microbiology of rumen fluid were Entodinium spp. and Aspergillus spp., respectively, and Fibrobacter spp. for bacteria. About the techniques used, it can be seen that DNA extraction, amplification, and sequencing were the most cited in the studies evaluated. Therefore, this review describes what is present in the literature and provides an overview of the main microbial agents in the rumen and the molecular techniques used.

The First Description of the Microbial Diversity in the Amarillo River (La Rioja, Argentina), a Natural Extreme Environment Where the Whole Microbial Community Paints the Landscape Yellow.

The Amarillo River in Famatina, La Rioja, Argentina, is a natural acidic river with distinctive yellow-ochreous iron precipitates along its course. While mining activities have occurred in the area, the river's natural acidity is influenced by environmental factors beyond mineralogy, where microbial species have a crucial role. Although iron-oxidising bacteria have been identified, a comprehensive analysis of the entire microbial community in this extreme environment has not yet been conducted. In this study, we employ high-throughput sequencing to explore the bacterial and fungal diversity in the Amarillo River and Cueva de Pérez terraces, considered prehistoric analogues of the current river basin. Fe(II)-enrichment cultures mimicking different environmental conditions of the river were also analysed to better understand the roles of prokaryotes and fungi in iron oxidation processes. Additionally, we investigate the ecological relationships between bacteria and fungi using co-occurrence and network analysis. Our findings reveal a diverse bacterial community in the river and terraces, including uncultured species affiliated with Acidimicrobiia, part of an uncharacterised universal microbial acidic diversity. Acidophiles such as Acidithiobacillus ferrivorans, the main iron oxidiser of the system, and Acidiphilium, which is unable to catalyse Fe(II) oxidation but has a great metabolic flexibility,, are part of the core of the microbial community, showing significant involvement in intraspecies interactions. Alicyclobacillus, which is the main Fe(II) oxidiser in the enrichment culture at 30 °C and is detected all over the system, highlights its flexibility towards the iron cycle. The prevalence of key microorganisms in both rivers and terraces implies their enduring contribution to the iron cycle as well as in shaping the iconic yellow landscape of the Amarillo River. In conclusion, this study enhances our understanding of microbial involvement in iron mineral precipitation, emphasising the collaborative efforts of bacteria and fungi as fundamental geological agents in the Amarillo River.

Microbial interactions and the homeostasis of the gut microbiome: the role of Bifidobacterium.

The human gut is home to trillions of microorganisms that influence several aspects of our health. This dense microbial community targets almost all dietary polysaccharides and releases multiple metabolites, some of which have physiological effects on the host. A healthy equilibrium between members of the gut microbiota, its microbial diversity, and their metabolites is required for intestinal health, promoting regulatory or anti-inflammatory immune responses. In contrast, the loss of this equilibrium due to antibiotics, low fiber intake, or other conditions results in alterations in gut microbiota composition, a term known as gut dysbiosis. This dysbiosis can be characterized by a reduction in health-associated microorganisms, such as butyrate-producing bacteria, enrichment of a small number of opportunistic pathogens, or a reduction in microbial diversity. Bifidobacterium species are key species in the gut microbiome, serving as primary degraders and contributing to a balanced gut environment in various ways. Colonization resistance is a fundamental property of gut microbiota for the prevention and control of infections. This community competes strongly with foreign microorganisms, such as gastrointestinal pathogens, antibiotic-resistant bacteria, or even probiotics. Resistance to colonization is based on microbial interactions such as metabolic cross-feeding, competition for nutrients, or antimicrobial-based inhibition. These interactions are mediated by metabolites and metabolic pathways, representing the inner workings of the gut microbiota, and play a protective role through colonization resistance. This review presents a rationale for how microbial interactions provide resistance to colonization and gut dysbiosis, highlighting the protective role of Bifidobacterium species.

Volatile compounds for biotechnological applications produced during competitive interactions between yeasts and fungi.

Fungi, yeasts and bacteria produce volatile compounds during their metabolism. In this study, the volatile compounds produced by yeast strains (Saccharomyces cerevisiae and Rhodotorula mucilaginosa) and fungal strains (Aspergillus carbonarius and Aspergillus ochraceus) during competitive interactions were investigated by solid-phase microextraction coupled with gas chromatography-mass spectrometry. Fifty-six volatile compounds were identified representing alcohols, aldehydes, esters, ketones, aromatic compounds, acids, furans, phenols, and nitrogen compounds, being the largest amount in the class of esters and alcohols. Eight compounds were identified only in interactive culture conditions such as 2-amino-1-propanol, isopropylamine, dimethylamine, pentyl propanoate, ethyl-2-aminopropanoate, acetone, oxalic acid, and ß-elemene and five of these were produced in cocultures including A. carbonarius. These will be developed for future biotechnological applications such as in the pharmaceutical and biological industry to produce drugs. Antimicrobial and antifungal activities; Solvent and herbicide; flavoring ingredient; solvent, plastic synthesis, nail polish remover and thinner, pesticide and herbicide; important in the complexation of minerals in the soil; and plant-environment interactions, defending predators, pathogens, and competitors.

Impact of Treatment on Host Responses in Young Individuals with Periodontitis.

Grade C periodontitis in young individuals is characterized by severe/rapid periodontal destruction, usually early onset, in systemically healthy individuals. An individual's host response, triggered by a dysbiotic subgingival biofilm, has been reported as a contributor to the tissue destruction, although mechanisms of this response and contributions to such disease remain poorly understood. Nonsurgical treatment has resulted in positive clinical responses for both localized (now molar-incisor pattern) and generalized forms of grade C periodontitis, especially when adjunctive systemic antibiotics are used. Nonsurgical treatment may also affect host responses, although mechanisms leading to significant changes in this response remain unclear. Significant effects on inflammatory response to antigens/bacteria have been described posttreatment, but evidence for long-term effects remains limited. Nonsurgical treatment in these individuals may also modulate a variety of host markers in serum/plasma and gingival crevicular fluid along with clinical parameter improvements. The impact of other adjuncts to nonsurgical treatment focusing on controlling exacerbated immunoinflammatory responses needs to be further explored in grade C periodontitis in young individuals. Recent evidence suggests that nonsurgical treatment with adjunctive laser therapy may modulate host and microbial responses in those subjects, at least in the short term. Available evidence, while very heterogeneous (including variations in disease definition and study designs), does not provide clear conclusions on this topic yet provides important insights for future studies. In this review, studies within the past decade evaluating the impact of nonsurgical treatment on systemic/local host responses in young individuals with grade C periodontitis, as well as long-term clinical responses posttreatment, will be critically appraised and discussed.

Probiotic consumption can modify the resilience of periodontal tissues in rats under experimental periodontitis.

BACKGROUND: This study evaluated the effects of systemic administration of Bifidobacterium animalis subsp. lactis HN019 (B. lactis HN019) on experimental periodontitis (EP) in rats. METHODS: Thirty-two rats were allocated to groups C (control), C-HN019 (probiotic), EP (EP only), and EP-HN019 (EP+probiotic). From day 0, the animals of C-HN019 and EP-HN019 groups received B. lactis HN019 (1 × 109 CFU/ml) daily. On the 14th day, the animals of EP and EP-HN019 groups received silk ligature around mandibular molars. Animals were euthanized on the 28th day. Samples of oral biofilm, gingival tissues, blood serum, and mandible were obtained for microtomographic, histomorphometric, microbiological, and immunological analyses. Data were statistically analyzed (p < 0.05). RESULTS: Group EP-HN019 presented significantly less alveolar bone loss when compared with Group EP in histomorphometric and microtomographic analyses. In gingival tissue and serum, Group EP-HN019 presented lower proinflammatory/anti-inflammatory cytokines ratios than Group EP. Group EP-HN019 showed higher expression of beta-defensins and less TRAP-positive cells than Group EP. Group EP presented higher gene expression of Ifng and lower gene expression of Foxp3 when compared with Group EP-HN019 in gingival tissue. In oral biofilm, EP-HN019 group presented a lower percentage of species similar to Fusobacterium periodonticum and a higher percentage of species similar to Actinomyces gereneseriae, Actinomyces israelli, and Streptococcus gordonii when compared with Group EP. There was a significant increase of B. lactis HN019 after administration of probiotic therapy in oral biofilm of Group EP-HN019. CONCLUSION: The consumption of B. lactis HN019 promotes a protective effect against alveolar bone loss by modifying local and systemic microbiological and immunoinflammatory parameters.

Lipids from gut microbiota: pursuing a personalized treatment.

The discovery of microbiome metabolites has enlivened the field of fecal transplantation for therapeutic purposes. However, the transfer of pathogenic living organisms was recently observed to limit its therapeutic potential by increasing the risk of infection. Lipids produced by gut microbiota enter the circulation and control many phenotypic changes associated with microbiota composition. Fecal lipids significantly impact the regulation of several cell signaling pathways, including inflammation. Focusing on these molecules, we review how bioactive gut microbiota-associated lipids affect cellular functioning and clinical outcome. Here, we interrogate whether the gut microbiota can be considered a cutting-edge biotechnological tool for rapid metabolic engineering of meaningful lipids to offer a novel personalized therapy.

Modeling approaches for probing cross-feeding interactions in the human gut microbiome.

Microbial communities perform emergent activities that are essentially different from those carried by their individual members. The gut microbiome and its metabolites have a significant impact on the host, contributing to homeostasis or disease. Food molecules shape this community, being fermented through cross-feeding interactions of metabolites such as lactate, acetate, and amino acids, or products derived from macromolecule degradation. Mathematical and experimental approaches have been applied to understand and predict the interactions between microorganisms in complex communities such as the gut microbiota. Rational and mechanistic understanding of microbial interactions is essential to exploit their metabolic activities and identify keystone taxa and metabolites. The latter could be used in turn to modulate or replicate the metabolic behavior of the community in different contexts. This review aims to highlight recent experimental and modeling approaches for studying cross-feeding interactions within the gut microbiome. We focus on short-chain fatty acid production and fiber fermentation, which are fundamental processes in human health and disease. Special attention is paid to modeling approaches, particularly kinetic and genome-scale stoichiometric models of metabolism, to integrate experimental data under different diet and health conditions. Finally, we discuss limitations and challenges for the broad application of these modeling approaches and their experimental verification for improving our understanding of the mechanisms of microbial interactions.

Manipulation of the soil microbiome regulates the colonization of plants by arbuscular mycorrhizal fungi.

Arbuscular mycorrhizal fungi (AMF) are important symbionts of many plant species, facilitating the acquisition of soil nutrients by roots. We hypothesized that AMF root colonization is strongly influenced by the composition of the soil microbiome. Here, we evaluated mycorrhizal colonization of two plants, the grass Urochloa brizantha (Brachiaria) and the legume Crotalaria juncea (Crotalaria). These were cultivated in the same soil but hosting eight distinct microbiomes: natural soil (i); soil exposed to heat treatments for 1 h at 50 ºC (ii), 80 ºC (iii), or 100 ºC (iv); sterilized soil by autoclaving (AS) followed by re-inoculation of dilutions of the natural soil community at 10-1 (v), 10-3 (vi), and 10-6 (vii); and AS without re-inoculation (viii). Microbial diversity (bacteria and fungi) was assessed through 16S rDNA and ITS1 metabarcoding, respectively, and the soil acid phosphatase activity (APASE) was measured. Sequencing results showed the formation of distinct microbial communities according to the soil manipulations, which also correlated with the decline of APASE. Subsequently, seedlings of Brachiaria and Crotalaria were grown in those soils inoculated separately with three AMF (Acaulospora colombiana, Rhizophagus clarus, and Dentiscutata heterogama) which were compared to an AMF-free control treatment. Brachiaria showed higher colonization in natural soil when compared to the microbial community manipulations, regardless of the AMF species inoculated. In contrast, two mycorrhiza species were able to colonize Crotalaria under modified microbial communities at similar rates to natural soil. Furthermore, Brachiaria showed a possible inverse relationship between APASE and mycorrhization, but this trend was absent for Crotalaria. We conclude that mycorrhizal root colonization and soil acid phosphatase activity were associated with the structure of the soil microbiome, depending on the plant species evaluated.

A simple and accurate method for specific quantification of biomass in mixed cultures of filamentous fungi by quantitative PCR / Un método simple y preciso para la cuantificación específica de biomasa en cultivos mixtos de hongos filamentosos por PCR cuantitativa

Abstract Production of lignocellulolytic enzymes by filamentous fungi have a great potential at industrial level due to their widespread applications. Mixed fungal cultures and particularly mixed fungal biofilms constitute a promising fermentation system for an enhanced enzyme production. However, it has not been addressed how much of this enhancement depends on the mixed biomass proportion. In this sense, the aim of this study was to develop a method to specifically and accurately quantify mixed fungal biomass. For this purpose, mixed biofilm cultures composed of Aspergillus niger and Trichoderma reesei, two filamentous fungi used industrially for cellulase production, were collected from 48 to 120 h of growth; mycelia were pulverized, and DNA was extracted for qPCR assays with specific primers for each fungus. Primers were designed from non-conserved regions of sequences of actin and β-tubulin genes of both A. niger and T. reesei. Specificity of these primers was tested in silico and experimentally. A statistically significant correlation was obtained between qPCR-calculated biomass and dry weight biomass data. By this method, it was possible to detect changes on mycelia proportions in biofilms over time, suggesting a competitive interaction between these two fungi. In conclusion, this method allows a specific and accurate quantification of mixed fungal biomass and could be also applied to different mixed culture systems for studying microbial interactions.

Resumen La producción de enzimas lignocelulolíticas por hongos filamentosos tiene un gran potencial a nivel industrial debido a sus diversas aplicaciones. Los cultivos fúngicos mixtos y particularmente las biopelículas fúngicas mixtas constituyen un sistema de fermentación prometedor para una mayor producción enzimática. Sin embargo, no se ha abordado cuánto de esta mejora depende de la proporción de biomasa mixta. En este sentido, el objetivo de este estudio fue desarrollar un método para cuantificar de forma específica y precisa la biomasa fúngica mixta. Para este propósito, se recolectaron cultivos mixtos de biopelículas de 48 a 120 h de crecimiento compuestos por Aspergillus niger y Trichoderma reesei, dos hongos filamentosos utilizados industrialmente para la producción de celulasas; el micelio se pulverizó y el ADN se extrajo para ensayos de qPCR con cebadores específicos para cada hongo. Los cebadores se diseñaron a partir de regiones no conservadas de las secuencias de los genes de actina y β-tubulina de A. niger y T. reesei. La especificidad de estos cebadores se probó in silico y experimentalmente. Se obtuvo una correlación estadísticamente significativa entre la biomasa calculada mediante qPCR y los datos de biomasa en peso seco. Mediante este método, fue posible detectar cambios en las proporciones de los micelios en las biopelículas a lo largo del tiempo, lo que sugiere una interacción competitiva entre estos dos hongos. En conclusión, este método permite una cuantificación específica y precisa de la biomasa fúngica mixta y también podría aplicarse a diferentes sistemas de cultivo mixto para estudiar interacciones microbianas.

Vaginal microbiome diversity and preterm birth: results of a nested case-control study in Peru.

PURPOSE: Preterm birth (PTB) is a major cause of neonatal mortality. The vaginal microbiome is associated with PTB, but results vary across racial/ethnic populations. Some evidence suggests gestational age affects this association. We investigated these associations in a novel population, conducting a post hoc analysis assessing if associations differed between women swabbed at different gestational ages. METHODS: We compared vaginal microbiomes from women with PTB (n = 25) to a random sample of women with term births (n = 100) among participants in the Pregnancy Outcomes, Maternal and Infant Study, conducted in Lima, Peru. Using DADA2, we identified taxa from 16S DNA sequencing and used Dirichlet multinomial mixture models to group into community state types (CSTs). RESULTS: If gestational age at sampling was not considered, no CST (diverse, Lactobacillus-dominated or Lactobacillus iners-dominated), was associated with PTB. Among women sampled before 12 weeks' gestation, women with Lactobacillus-dominated CSTs were less likely to have a PTB than those with a diverse CST. Among those swabbed between 12 and 16 weeks' gestation, the reverse was true. CONCLUSIONS: Our study supports previous literature suggesting that what constitutes a healthy vaginal microbiome varies by race/ethnicity. Longitudinal studies are necessary to disentangle effects of vaginal microbiome differences over gestation.

The Impact of Type VI Secretion System, Bacteriocins and Antibiotics on Bacterial Competition of Pectobacterium carotovorum subsp. brasiliense and the Regulation of Carbapenem Biosynthesis by Iron and the Ferric-Uptake Regulator.

The complexity of plant microbial communities provides a rich model for investigating biochemical and regulatory strategies involved in interbacterial competition. Within these niches, the soft rot Enterobacteriaceae (SRE) represents an emerging group of plant-pathogens causing soft rot/blackleg diseases resulting in economic losses worldwide in a variety of crops. A preliminary screening using next-generation sequencing of 16S rRNA comparatively analyzing healthy and diseased potato tubers, identified several taxa from Proteobacteria to Firmicutes as potential potato endophytes/plant pathogens. Subsequent to this, a range of molecular and computational techniques were used to determine the contribution of antimicrobial factors such as bacteriocins, carbapenem and type VI secretion system (T6SS), found in an aggressive SRE (Pectobacterium carotovorum subsp. brasiliense strain PBR1692 - Pcb1692) against these endophytes/plant pathogens. The results showed growth inhibition of several Proteobacteria by Pcb1692 depends either on carbapenem or pyocin production. Whereas for targeted Firmicutes, only the Pcb1692 pyocin seems to play a role in growth inhibition. Furthermore, production of carbapenem by Pcb1692 was observably dependent on the presence of environmental iron and oxygen. Additionally, upon deletion of fur, slyA and expI regulators, carbapenem production ceased, implying a complex regulatory mechanism involving these three genes. Finally, the results demonstrated that although T6SS confers no relevant advantage during in vitro competition, a significant attenuation in competition by the mutant strain lacking a functional T6SS was observed in planta. IMPORTANCE: Soft rot Enterobacteriaceae (SRE) represents important phytopathogens causing soft rot/blackleg diseases in a variety of crops leading to huge economic losses worldwide. These pathogens have been isolated alongside other bacteria from different environments such as potato tubers, stems, roots and from the soil. In these environments, SREs coexist with other bacteria where they have to compete for scarce nutrients and other resources. In this report, we show that Pectobacterium carotovorum subsp. brasiliense strain PBR1692 - Pcb1692, which represents one of the SREs, inhibits growth of several different bacteria by producing different antimicrobial compounds. These antimicrobial compounds can be secreted inside or outside the plant host, allowing Pcb1692 to effectively colonize different types of ecological niches. By analyzing the genome sequences of several SREs, we show that other SREs likely deploy similar antimicrobials to target other bacteria.

Nutrient Dependent Cross-Kingdom Interactions: Fungi and Bacteria From an Oligotrophic Desert Oasis.

Microbial interactions play a key role in ecosystem functioning, with nutrient availability as an important determinant. Although phylogenetically distant bacteria and fungi commonly co-occur in nature, information on their cross-kingdom interactions under unstable, extreme environments remains poor. Hence, the aims of this work were to evaluate potential in vitro interactions among fungi and bacteria isolated from a phosphorous oligotrophic aquatic system in the Cuatro Ciénegas Basin, Mexico, and to test the nutrients-based shifts. We assessed growth changes in bacteria (Aeromonas and Vibrio) and fungi (Coprinellus micaceus, Cladosporium sp., and Aspergillus niger) on co-cultures in relation to monocultures under diverse nutrient scenarios on Petri dishes. Interactions were explored using a network analysis, and a metabolome profiling for specific taxa. We identified nutrient-dependent patterns, as beneficial interactions dominated in low-nutrients media and antagonistic interactions dominated in rich media. This suggests that cross-kingdom synergistic interactions might favor microbial colonization and growth under low nutrient conditions, representing an adaptive trait to oligotrophic environments. Moreover, our findings agree with the stress-gradient hypothesis, since microbial interactions shifted from competition to cooperation as environmental stress (expressed as low nutrients) increased. At a functional level consistent differences were detected in the production of secondary metabolites, agreeing with plate bioassays. Our results based on culture experiments, provides evidence to understand the complexity of microbial dynamics and survival in phosphorous-depleted environments.

Anti-inflammatory effect of microbial consortia during the utilization of dietary polysaccharides.

The gut microbiome has a significant impact on host health, especially at the metabolic level. Dietary compounds arriving at the colon have a large influence on the composition of the gut microbiome. High fiber diets have been associated to health benefits that are mediated in great part by short chain fatty acids (SCFA). Gut microbial interactions are relevant for the utilization of complex carbohydrates in the gut microbiome. In this work we characterized the utilization of two dietary polysaccharides by combinations of representative adult gut microbes, and the impact of their activities on a cellular inflammation model. Paired combinations of Bifidobacterium adolescentis, Bacteroides dorei, Lactobacillus plantarum, Escherichia coli and Clostridium symbiosum were grown in inulin or xylan as carbon source. Their relative abundance, substrate consumption and major SCFAs produced were determined. Higher cell growth was observed during inulin consumption, and B. adolescentis and L. plantarum were dominant in co-cultures. The co-culture of B. dorei and C. symbiosum was dominant in xylan. In several cases the combined bacterial growth was lower in co-cultures than monocultures, with a few exceptions of synergistic growth between microorganisms. Inulin fermentation resulted in larger acetate and lactate concentrations, and several combinations grown in xylan containing C. symbiosum were characterized by high amounts of butyrate. These microbial consortia were scaled to batch bioreactor fermentations reaching high cell densities and similar profiles to co-culture experiments. Interestingly, a microbial combination producing high amounts of butyrate was able to reduce IL-8 expression in HT-29 cells co-incubated with TNFα. In summary, this work shows that microbial interactions during the utilization of dietary polysaccharides are complex and substrate dependent. Moreover, certain combinations deploy potent anti-inflammatory effects, which are independent of individual microbial growth, and could be mediated in part by higher butyrate production.

Microbial interactions during sugar cane must fermentation for bioethanol production: does quorum sensing play a role?

Microbial interactions represent important modulatory role in the dynamics of biological processes. During bioethanol production from sugar cane must, the presence of lactic acid bacteria (LAB) and wild yeasts is inevitable as they originate from the raw material and industrial environment. Increasing the concentration of ethanol, organic acids, and other extracellular metabolites in the fermentation must are revealed as wise strategies for survival by certain microorganisms. Despite this, the co-existence of LAB and yeasts in the fermentation vat and production of compounds such as organic acids and other extracellular metabolites result in reduction in the final yield of the bioethanol production process. In addition to the competition for nutrients, reduction of cellular viability of yeast strain responsible for fermentation, flocculation, biofilm formation, and changes in cell morphology are listed as important factors for reductions in productivity. Although these consequences are scientifically well established, there is still a gap about the physiological and molecular mechanisms governing these interactions. This review aims to discuss the potential occurrence of quorum sensing mechanisms between bacteria (mainly LAB) and yeasts and to highlight how the understanding of such mechanisms can result in very relevant and useful tools to benefit the biofuels industry and other sectors of biotechnology in which bacteria and yeast may co-exist in fermentation processes.

Interactions between Candida albicans and Candida glabrata in biofilms: Influence of the strain type, culture medium and glucose supplementation.

The relationship among Candida species may be influenced by several factors. Thus, this study evaluated the interactions between Candida albicans and Candida glabrata in biofilms, varying the strain type, culture medium and glucose supplementation. Biofilms were formed for 48 hours in Sabouraud dextrose broth (SDB) or RPMI 1640, supplemented with 0%, 1% or 5% glucose. Each strain of C. albicans was combined with two strains of C. glabrata, generating four biofilm associations, which were quantified by colony-forming units (CFUs), total biomass and metabolic activity. Data were analysed by ANOVA and Tukey's HSD test (α = 0.05). For CFUs, all associations were classified as indifferent for biofilms formed in RPMI 1640, while for SDB the interactions were antagonistic for C. albicans and indifferent for C. glabrata. The association of reference strains resulted in a dual-species biofilm with biomass significantly higher than that observed for each single biofilm developed in SDB. The metabolic activity of dual-species biofilms did not significantly differ from that found for single ones, except for co-culture of the reference strains. Glucose supplementation and culture media had a significant influence on all parameters. In conclusion, the strain type, culture medium and glucose supplementation influenced the interactions between C. albicans and C. glabrata.

Prebiotics Mediate Microbial Interactions in a Consortium of the Infant Gut Microbiome.

Composition of the gut microbiome is influenced by diet. Milk or formula oligosaccharides act as prebiotics, bioactives that promote the growth of beneficial gut microbes. The influence of prebiotics on microbial interactions is not well understood. Here we investigated the transformation of prebiotics by a consortium of four representative species of the infant gut microbiome, and how their interactions changed with dietary substrates. First, we optimized a culture medium resembling certain infant gut parameters. A consortium containing Bifidobacterium longum subsp. infantis, Bacteroides vulgatus, Escherichia coli and Lactobacillus acidophilus was grown on fructooligosaccharides (FOS) or 2'-fucosyllactose (2FL) in mono- or co-culture. While Bi. infantis and Ba. vulgatus dominated growth on 2FL, their combined growth was reduced. Besides, interaction coefficients indicated strong competition, especially on FOS. While FOS was rapidly consumed by the consortium, B. infantis was the only microbe displaying significant consumption of 2FL. Acid production by the consortium resembled the metabolism of microorganisms dominating growth in each substrate. Finally, the consortium was tested in a bioreactor, observing similar predominance but more pronounced acid production and substrate consumption. This study indicates that the chemical nature of prebiotics modulate microbial interactions in a consortium of infant gut species.

Microbial ecology of fermentative hydrogen producing bioprocesses: useful insights for driving the ecosystem function.

One of the most important biotechnological challenges is to develop environment friendly technologies to produce new sources of energy. Microbial production of biohydrogen through dark fermentation, by conversion of residual biomass, is an attractive solution for short-term development of bioH2 producing processes. Efficient biohydrogen production relies on complex mixed communities working in tight interaction. Species composition and functional traits are of crucial importance to maintain the ecosystem service. The analysis of microbial community revealed a wide phylogenetic diversity that contributes in different-and still mostly unclear-ways to hydrogen production. Bridging this gap of knowledge between microbial ecology features and ecosystem functionality is essential to optimize the bioprocess and develop strategies toward a maximization of the efficiency and stability of substrate conversion. The aim of this review is to provide a comprehensive overview of the most up-to-date biodata available and discuss the main microbial community features of biohydrogen engineered ecosystems, with a special emphasis on the crucial role of interactions and the relationships between species composition and ecosystem service. The elucidation of intricate relationships between community structure and ecosystem function would make possible to drive ecosystems toward an improved functionality on the basis of microbial ecology principles.

Ex vivo model for studying polymicrobial biofilm formation in root canals / Modelo ex vivo para el estudio de la formación de biopelícula polimicrobiana en conductos / Efeitos sobre a pesca nos elasmobrânquios no Pacífico colombiano

Abstract Endodontic disease has mainly a microbial origin. It is caused by biofilms capable of attaching and surviving in the root canal. Therefore, it is important to study the conditions in which those biofilms grow, develop and colonize the root canal system. However, few studies have used natural teeth as models, which would take into account the root canal anatomical complexity and simulate the clinical reality. In this study, we used human premolar root canals to standardize in vitro biofilm optimal formation conditions for microorganisms such as Enterococcus faecalis, Staphylococcus aureus and Candida albicans. 128 lower premolars underwent canal preparation using K-type files, and were treated with 5.25% sodium hypochlorite and EDTA. Samples were inoculated with microorganisms and incubated for 15, 30, 45, and 60 days under anaerobiosis (CO2 atmosphere) and aerobiosis. Microorganism presence was confirmed by Gram staining, cell culture, and electron microscopy. Exopolysaccharide matrix and microorganism aggregation were observed following 15 days of incubation. Bacterial growth towards the apical third of the root canal and biofilm maturation was detected after 30 days. CO2 atmosphere favored microbial growth the most. In vitro biofilm maturation was confirmed after 30 days of incubation under a CO2 atmosphere for both bacteria and yeast.

Resumen La enfermedad endodóntica tiene principalmente un origen microbiano. Es causada por biopelículas capaces de adherirse y sobrevivir en el conducto dental. Por ello es importante estudiar las condiciones en las que estas biopelículas crecen, se desarrollan y colonizan el conducto. Sin embargo, pocos trabajos han utilizado como modelos dientes naturales, que tengan en cuenta la complejidad anatómica de los conductos y simular la realidad clínica. En este estudio se utilizaron conductos de premolares para estandarizar las condiciones óptimas de formación in vitro de la biopelícula de microorganismos como Enterococcus faecalis, Staphylococcus aureus and Candida albicans. Se prepararon los conductos de 128 premolares inferiores usando limas para endodoncia tipo-K, y fueron tratados con 5.25 % hipodorito de sodio y EDTA. Las muestras se inocularon con microrganismos y fueron incubadas por 15, 30, 45 y 60 días en anaerobiosis (atmósfera de CO2) y aerobiosis. La presencia de microorganismos fue confirmada por tinción de Gram, cultivo celular y microscopia electrónica. Se observó una matriz de exopolisacáridos y agregación de microorganismos a los 15 días de incubación. Después de 30 días se detectó crecimiento bacteriano hacia el tercio apical del conducto, así como maduración de la biopelícula. La atmósfera de CO2 fue la que más favoreció el crecimiento microbiano. La maduración in vitro de la biopelícula se confirmó después de 30 días de incubación en atmósfera de CO2 tanto para la bacteria como para el hongo.

Resumo A doença endodôntica tem principalmente uma origem microbiana. É causada por biofilmes capazes de se fixar e sobreviver no canal radicular. Portanto, é importante estudar as condições em que esses biofilmes crescem, se desenvolvem e colonizam o sistema de canais radiculares. No entanto, poucos estudos utilizaram dentes naturais como modelo, os quais consideram a complexa anatomia dos canais radiculares e simulam a realidade clínica. Neste estudo, utilizamos canais radiculares pré- molares para padronizar as condições de formação ótima in vitro de biofilme para microrganismos como Enterococcus faecalis, Staphylococcus aureus e Candida abicans. Foram preparados os canais de 128 pré-molares inferiores usando limas odontológicas tipo K, e foram tratados com hipoclorito de sódio 5,25 % e EDTA. As amostras foram inoculadas com microrganismos e incubadas por 15, 30, 45 e 60 dias em anaerobiose (atmosfera de CO2) e aerobiose. A presença de microrganismos foi confirmada por coloração de Gram, cultura celular e microscopia eletrônica. Observou-se uma matriz de exopolisacáridos e um agregado de microrganismos depois de 15 dias de incubação. Após 30 dias de incubação foram detectados crescimento bacteriano no terço apical do canal radicular e maduração do biofilme. A atmosfera de CO2 foi a que mais favoreceu o crescimento microbiano. A maduração in vitro do biofilme foi confirmada depois de 30 dias de incubação em atmosfera de CO2 tanto para bactérias como para fungos.