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PubMed2025

SetBERT: the deep learning platform for contextualized embeddings and explainable predictions from high-throughput sequencing.

MOTIVATION: High-throughput sequencing (HTS) is a modern sequencing technology used to profile microbiomes by sequencing thousands of short genomic fragments from the microorganisms within a given sample. This technology presents a unique opportunity for artificial intelligence to comprehend the underlying functional relationships of microbial communities. However, due to the unstructured nature of HTS data, nearly all computational models are limited to processing DNA sequences individually. This limitation causes them to miss out on key interactions between microorganisms, significantly hindering our understanding of how these interactions influence the microbial communities as a whole. Furthermore, most computational methods rely on post-processing of samples which could inadvertently introduce unintentional protocol-specific bias. RESULTS: Addressing these concerns, we present SetBERT, a robust pre-training methodology for creating generalized deep learning models for processing HTS data to produce contextualized embeddings and be fine-tuned for downstream tasks with explainable predictions. By leveraging sequence interactions, we show that SetBERT significantly outperforms other models in taxonomic classification with genus-level classification accuracy of 95%. Furthermore, we demonstrate that SetBERT is able to accurately explain its predictions autonomously by confirming the biological-relevance of taxa identified by the model. AVAILABILITY AND IMPLEMENTATION: All source code is available at https://github.com/DLii-Research/setbert. SetBERT may be used through the q2-deepdna QIIME 2 plugin whose source code is available at https://github.com/DLii-Research/q2-deepdna.

Deep Learning↗
PubMed1986

An update of a dynamic model of ruminant digestion.

The progressive development of a dynamic model of ruminant digestion for evaluation of factors affecting nutritive value of feedstuffs is outlined. Significant changes have been introduced in many of the interactive subunits that accommodate the digestion of 12 chemical constituents (soluble carbohydrate, organic acids, starch, pectin, hemicellulose, cellulose, lipids, soluble protein, insoluble protein, nonprotein N, lignin and ash), microbial growth, animal interactions and summary computations. Explicit consideration of soluble carbohydrates, organic acids and pectins has been replaced by an aggregate fraction. A section has been added to follow dynamic aspects of volatile fatty acid metabolism in the rumen. Evaluations of the model were made by comparing its behavior with that observed experimentally for sheep fed a number of diets. These included an alfalfa diet fed at two intake levels either hourly or once daily, a dried subterranean clover diet fed hourly, a forage oat diet fed every 3 h and an 80% concentrate diet fed twice daily. For frequently fed diets, model estimates, in general, agreed very well with experimental estimates. Although changes in representations of protein metabolism were helpful, the pool size of ruminal ammonia N was not simulated well. Digestion and passage in the model occurred more rapidly than was observed when animals were fed high-quality forages once daily and rates of particle size reduction, fermentation and passage were lower than observed when low-quality diets were fed. It was concluded that the model can serve as a useful and adaptable tool for analyzing factors affecting nutritive value. Particle size reduction and passage from the rumen, dynamics of protein metabolism and utilization, and water dynamics were identified as areas requiring further research.

Animals↗
PubMed2006

Interaction between the CCR5 chemokine receptors and microbial HSP70.

Evidence is presented that the microbial 70-kD heat shock protein (HSP70) binds to CCR5 chemokine receptors in CCR5-transfected cell lines and in primary human cells. Significant CCR5-mediated calcium mobilization was stimulated by HSP70 and inhibited with TAK 779, which is a specific CCR5 antagonist. HSP70-mediated activation of the p38 MAPK phosphorylation signaling pathway was also demonstrated in CCR5-transfected HEK 293 cells. Direct binding of three extracellular peptides of CCR5 to HSP70 was demonstrated by surface plasmon resonance. Functional evidence of an interaction between HSP70, CCR5 and CD40 was shown by enhanced production of CCL5 by HEK 293 cells transfected with both CD40 and CCR5. Primary monocyte-derived immature DC stimulated with HSP70 produced IL-12 p40, which showed dose-dependent inhibition of >90% on treatment with both TAK 779 and anti-CD40 mAb. Stimulation of IL-12 p40 or TNF-alpha by HSP70 was related to the differential cell surface expression of CCR5 in primary human immature and mature DC, and those with the homozygous triangle DeltaDelta32 CCR5 mutation. These findings may be of significance in the interaction between HSP70 and immune responses of CCR5+ T cells in HIV-1 infection, as well as in inflammatory bowel disease.

Amides↗
PubMed2001

Inhalation of (1-->3)-beta-D-glucan causes airway eosinophilia.

BACKGROUND: Moulds are present in a variety of environments and aerosols of fungal spores are generated when mouldy materials are handled. Molds contain (1-->3)-beta-D-glucan, a polyglucose which is present in the cell wall of fungi, certain bacteria and plants. AIM: This study was undertaken to investigate the cellular inflammatory response in the lung after inhalation of (1-->3)-beta-D-glucan and bacterial endotoxin. METHODS: Guinea pigs were exposed daily to an aerosol of pure (1-->3)-beta-D-glucan and pure endotoxin for five weeks. Lung lavage and lung interstitial cell preparations were done and the inflammatory cells counted. Histological sections were prepared from the trachea. RESULTS: There was an increase in eosinophil numbers in lung lavage, lung interstitium, and the airway epithelium of animals exposed to (1-->3)-beta-D-glucan. In animals simultaneously exposed to endotoxin, there was no increase in eosinophils. In the lung interstitium, (1-->3)-beta-D-glucan exposure caused an increase in lymphocytes, which was not found after endotoxin exposure. Endotoxin exposure caused an increase in neutrophils and macrophages in lung lavage, which was not found after (1-->3)-beta-D-glucan exposure. CONCLUSIONS: The results support previous findings that (1-->3)-beta-D-glucan causes a different response in the airways as compared to endotoxin. Endotoxin modulated the increase in eosinophils caused by (1-->3)-beta-D-glucan exposure, suggesting a complex interaction between the microbial cell wall components.

Administration, Inhalation↗
PubMed2001

Host-pathogen interactions: the attributes of virulence.

Virulence is one of a number of possible outcomes of host-microbe interaction. As such, microbial virulence is dependent on host factors, as exemplified by the pathogenicity of avirulent microbes in immunocompromised hosts and the lack of pathogenicity of virulent pathogens in immune hosts. Pathogen-centered views of virulence assert that pathogens are distinguished from nonpathogens by their expression of virulence factors. Although this concept appears to apply to certain microbes that cause disease in normal hosts, it does not apply to most microbes that cause disease primarily in immunocompromised hosts. The study of virulence is fraught with the paradox that virulence, despite being a microbial characteristic, can only be expressed in a susceptible host. Thus, the question "What is a pathogen?" begs the question, "What is the outcome of the host-microbe interaction?" We propose that host damage provides a common denominator that translates into the different outcomes of host-microbe interaction.

Animals↗
PubMed1998

In situ gene expression in mixed-culture biofilms: evidence of metabolic interactions between community members.

Microbial communities growing in laboratory-based flow chambers were investigated in order to study compartmentalization of specific gene expression. Among the community members studied, the focus was in particular on Pseudomonas putida and a strain of an Acinetobacter sp., and the genes studied are involved in the biodegradation of toluene and related aromatic compounds. The upper-pathway promoter (Pu) and the meta-pathway promoter (Pm) from the TOL plasmid were fused independently to the gene coding for the green fluorescent protein (GFP), and expression from these promoters was studied in P. putida, which was a dominant community member. Biofilms were cultured in flow chambers, which in combination with scanning confocal laser microscopy allowed direct monitoring of promoter activity with single-cell spatial resolution. Expression from the Pu promoter was homogeneously induced by benzyl alcohol in both community and pure-culture biofilms, while the Pm promoter was induced in the mixed community but not in a pure-culture biofilm. By sequentially adding community members, induction of Pm was shown to be a consequence of direct metabolic interactions between an Acinetobacter species and P. putida. Furthermore, in fixed biofilm samples organism identity was determined and gene expression was visualized at the same time by combining GFP expression with in situ hybridization with fluorescence-labeled 16S rRNA targeting probes. This combination of techniques is a powerful approach for investigating structure-function relationships in microbial communities.

Acinetobacter↗
PubMed2005

Construction of artificially structured microbial consortia (ASMC) using dielectrophoresis: examining bacterial interactions via metabolic intermediates within environmental biofilms.

The construction of artificial biofilms with defined internal architectures is described. Bacterial cells are suspended in a low conductivity medium, guided to specific areas in a microelectrode array by dielectrophoresis (DEP), and then immobilised using the flocculating agent poly(ethylenimine). Multispecies biofilms can be constructed by introducing different species at different times. The rapid construction of such biofilms with defined internal architectures provides, when combined with visual reporters of gene activity, a powerful new method for the investigation of the effects of the spatial organisation on interactions between bacterial species in biofilms. To demonstrate the utility of the technique as a method for investigating metabolic interactions in biofilms, aggregates were constructed from Acinetobacter sp. C6 and Pseudomonas putida::gfp. The Acinetobacter degrades benzyl alcohol, overproducing benzoate, which in turn is consumed by the Pseudomonas strain. The P. putida has a chromosomally expressed cassette encoding a gfp downstream of the promoter which controls degradation of benzoate, making the interaction between the two strains in the metabolism of benzyl alcohol visible by the production of green fluorescent protein (GFP). Microscopic observation of the biofilms, including the use of confocal laser scanning microscopy (CLSM), confirmed that metabolic exchange occurred. In addition, it was observed that the bacteria appear to have a preferred biofilm architecture, with P. putida in the bottom layer, and Acinetobacter at the top.

Acinetobacter↗
PubMed2000

Gut bacteria may be involved in interactions between plants, herbivores and their predators: microbial biosynthesis of N-acylglutamine surfactants as elicitors of plant volatiles.

N-Acylamino acids are dominant and widespread constituents of insect oral secretions (regurgitants), serving the insect as biosurfactants in the digestive process. During feeding the conjugates may be introduced into damaged leaves and contribute there to the elicitation of plant defenses such as the induction of volatile biosynthesis. From gut segments of Spodoptera exigua, Mamestra brassicae and Agrotis segetum 23 bacterial strains were isolated, ten of which were able to synthesise typical lepidopteran N-acylamino acids from externally added precursors. Four strains, Providencia rettgeri, Ochrobactrum spec., Myroides odoratus and Acinetobacter sp. genospecies 11 were identified on the basis of their 16 S rDNA. The organisms displayed a very broad substrate tolerance, since fatty acids of different chain length and different degree of saturation were converted into N-acylamino acids. Moreover, most of the proteinogenic amino acids, but not glutamic and aspartic acid, were used as substrates. The dominant occurrence of fatty acids conjugated with glutamine may result from a preferred transport of glutamine from the hemolymph into the gut of the insects. The involvement of bacteria in the biosynthesis of compounds which play a pivotal role in the interaction of plants, herbivores and their predators adds a new trophic level to this complex network of interactions. Due to their short generation cycle and the ease of adaptation endosymbiontic bacteria may have an outstanding importance for the coevolution of plant-insect interactions.

Acylation↗
PubMed2002

Metabolic commensalism and competition in a two-species microbial consortium.

We analyzed metabolic interactions and the importance of specific structural relationships in a benzyl alcohol-degrading microbial consortium comprising two species, Pseudomonas putida strain R1 and Acinetobacter strain C6, both of which are able to utilize benzyl alcohol as their sole carbon and energy source. The organisms were grown either as surface-attached organisms (biofilms) in flow chambers or as suspended cultures in chemostats. The numbers of CFU of P. putida R1 and Acinetobacter strain C6 were determined in chemostats and from the effluents of the flow chambers. When the two species were grown together in chemostats with limiting concentrations of benzyl alcohol, Acinetobacter strain C6 outnumbered P. putida R1 (500:1), whereas under similar growth conditions in biofilms, P. putida R1 was present in higher numbers than Acinetobacter strain C6 (5:1). In order to explain this difference, investigations of microbial activities and structural relationships were carried out in the biofilms. Insertion into P. putida R1 of a fusion between the growth rate-regulated rRNA promoter rrnBP1 and a gfp gene encoding an unstable variant of the green fluorescent protein made it possible to monitor the physiological activity of P. putida R1 cells at different positions in the biofilms. Combining this with fluorescent in situ hybridization and scanning confocal laser microscopy showed that the two organisms compete or display commensal interactions depending on their relative physical positioning in the biofilm. In the initial phase of biofilm development, the growth activity of P. putida R1 was shown to be higher near microcolonies of Acinetobacter strain C6. High-pressure liquid chromatography analysis showed that in the effluent of the Acinetobacter strain C6 monoculture biofilm the metabolic intermediate benzoate accumulated, whereas in the biculture biofilms this was not the case, suggesting that in these biofilms the excess benzoate produced by Acinetobacter strain C6 leaks into the surrounding environment, from where it is metabolized by P. putida R1. After a few days, Acinetobacter strain C6 colonies were overgrown by P. putida R1 cells and new structures developed, in which microcolonies of Acinetobacter strain C6 cells were established in the upper layer of the biofilm. In this way the two organisms developed structural relationships allowing Acinetobacter strain C6 to be close to the bulk liquid with high concentrations of benzyl alcohol and allowing P. putida R1 to benefit from the benzoate leaking from Acinetobacter strain C6. We conclude that in chemostats, where the organisms cannot establish in fixed positions, the two strains will compete for the primary carbon source, benzyl alcohol, which apparently gives Acinetobacter strain C6 a growth advantage, probably because it converts benzyl alcohol to benzoate with a higher yield per time unit than P. putida R1. In biofilms, however, the organisms establish structured, surface-attached consortia, in which heterogeneous ecological niches develop, and under these conditions competition for the primary carbon source is not the only determinant of biomass and population structure.

Acinetobacter↗
PubMed2005

Microbial population dynamics at effluent treatment plants.

The requirements for treated wastewater are becoming increasingly more stringent, and therefore the improved efficiency of biological treatment processes is indispensable at industrial effluent treatment plants (ETPs). Microorganisms such as bacteria play an important role in the natural cycling of materials and particularly in the decomposition of organic wastes. The knowledge of the interactions among these microbial populations needs to be harnessed for optimum evaluation and functioning of effluent treatment plants. Modern molecular techniques have revolutionized the methods of assessing these microbial populations. The combination of the results of these microbial assessments along with the on-site parameters at ETPs would favor an efficient treatment. In this review, the various approaches and importance of correlating the microbial population dynamics and treatment of wastewater at industrial ETPs has been elaborated.

Bacteria↗
PubMed2004

IIGP, a member of the IFN inducible and microbial defense mediating 47 kDa GTPase family, interacts with the microtubule binding protein hook3.

Innate immunity against intracellular pathogens is critically determined by an as yet unknown interferon (IFN)-inducible mechanism exerted by members of the 47 kDa GTPase family. The association of IGTP and IIGP with membranous compartments, the endoplasmic reticulum and, in addition in case of IIGP, the Golgi, implicate these GTPases in intracellular membrane trafficking or processing. We identified the cytoplasmic linker molecule hook3 as an interactor for IIGP by yeast two-hybrid screening. The physical complex between these molecules was present in lysates of IFNgamma-stimulated macrophages as demonstrated by co-immunoprecipitation. Only a minor subfraction of total cellular IIGP or hook3 was co-purified, indicating that this interaction is either transient and/or involves distinct subpopulations of the total cellular pools of these molecules. Binding of IIGP to hook3 depends on a GTP-bound conformation. Hook3 is a microtubule-binding protein which participates in the organization of the cis-Golgi compartment. Both proteins were detected in the Golgi-membrane-enriched fraction upon subcellular fractionation. Apart from the Golgi localization of both proteins, hook3 was detected in perinuclear regions in close spatial proximity to IIGP, associated with the endoplasmic reticulum. Our experiments identify hook3 as the first cooperation partner of a member of the 47 kDa GTPase protein family and indicate that hook3 links in an IFNgamma-inducible fashion to cytoskeleton-based membrane trafficking.

Animals↗
PubMed2005

The proportions of Streptomyces californicus and Stachybotrys chartarum in simultaneous exposure affect inflammatory responses in mouse RAW264.7 macrophages.

Adverse health outcomes associated with moisture-damaged buildings originate from an exposure consisting of complex interactions between various microbial species and other indoor pollutants. The concentrations and proportions of microbial components in such environments can vary greatly with the growth conditions. In this study, we aimed to evaluate the effects of simultaneous exposure with modified proportions of actinobacteria Streptomyces californicus and fungi Stachybotrys chartarum on inflammatory responses (cytokines macrophage inflammatory protein 2 [MIP2], interleukin 6 [IL-6] and tumor necrosis factor a [TNFa]; nitric oxide) and cytotoxicity (MTT-test and DNA content analysis) in mouse RAW264.7 macrophage cell line. Five different proportions of microbial spores were studied (Str. californicus: S. chartarum 10:1; 5:1; 1:1; 1:5; 1:10). RAW264.7 cells were coexposed to the total dose of 3x10(5) spores/ml for 24 h and also both of these microbial spores on their own at the respective doses. At least the 1.5-fold synergistic increase in cytokine production of RAW264.7 macrophages was detected when coexposure contained an equal amount or more fungal spores (S. chartarum) than bacterial spores (Str. californicus) compared to the sum response caused by these microbial spores separately. On the contrary, NO production after coexposure was nearly 40% less than the sum response induced by the microbial spores separately, when coexposure contains 5 times more bacterial than fungal spores. In addition, coexposure slightly changed the cytotoxic potency of the spores. The present results revealed that mutual proportions of fungal and bacterial spores in simultaneous exposure affect the nature of their interactions leading to increased or suppressed production of inflammatory mediators in RAW264.7 macrophages.

Air Pollution, Indoor↗
PubMed1990

Microbial pathogenicity and host defense mechanisms--crucial parameters of posttraumatic infections.

Posttraumatic and postoperative infections which may be either localized or turn into sepsis are a major cause of morbidity and mortality in surgical patients. They derive from the imbalance between microbial pathogenicity factors and the host defense system. The virulence mechanisms include adhesion, chemotaxis, invasion, resistance, and production of toxins. In addition, local and/or systemic immune functions in these patients are altered. Unspecific as well as specific cellular and humoral defense mechanisms are affected. The interaction of defined microbial pathogenicity factors with immune effector cells results in the activation of a variety of inflammatory mediators; they are a prerequisite for protective immunity but also induce local or systemic damage in the host when they occur in excessive amounts or when their metabolism is inadequately controlled. The analysis of the pathophysiological events during infection in surgical patients by taking advantage of modern molecular and cell biological methods may contribute to the development of novel therapeutic strategies.

Bacteria↗
PubMed1993

Role of the immune system in recovery from infection.

Infection is regarded as an imbalance between microbial pathogenicity factors and the host defense system. The virulence mechanisms include adhesion, chemotaxis, invasion, resistance and production of toxins. In addition, local and/or systemic immune functions in patients undergoing infections are altered. Nonspecific as well as specific cellular and humoral defense mechanisms are affected. The interaction of defined microbial pathogenicity factors with immune effector cells results in the activation of a variety of inflammatory mediators; they are a prerequisite for protective immunity but also induce local or systemic damage in the host when they occur in excessive amounts and when their metabolism is inadequately controlled. The analysis of the pathophysiological events during infection in patients by taking advantage of modern molecular and cell-biological methods may contribute to the development of novel therapeutic strategies.

Bacteria↗
PubMed2002

Microbial composition, including the incidence of pathogens, of goat milk from the bergamo region of italy during a lactation year.

Sixty samples of raw goat milk intended for Caprino cheese-making were collected from ten farms in the Bergamo area over a 6-month period. Analyses of main microbial groups, somatic cell count (SCC) and pH were performed to determine the effect of origin (farm) and lactation period (April - September) on microbial composition and the incidence of pathogens in milk. Overall mean values were: standard plate count (SPC), 5.0 x 10(4) cfu/ml; yeasts, 2.5 x 10(2) cfu/ml; coliforms, 91 x 10(2) cfu/ml; Escherichia coli, 2.9 cells/ml: enterococci, 1.1 x 10(2) cfu/ ml; lactococci, 3 4 x 10(3) cfu/ml; lactobacilli, 3.0 x 10(3) cfu/ml; halotolerant bacteria, 8.2 x 10(3) cfu/ml; spores of mesophilic aerobic bacteria, 11 cfu/ml; SSC, 9.9 x 10(5) cells/ml; pH, 6.63. Moulds and spores of sulphite-reducing clostridia were found intermittently. Neither Salmonella spp. nor Listeria monocytogenes was detected, while Esch. coli O157: H7 was isolated from one milk sample (an incidence of 1.7%). Staphylococcus aureus was discovered at a level > 10(2) cfu/ml in 26 samples (43%) with an overall mean of 12 x 10(3) cfu/ml, whereas coagulase-negative staphylococci were found in 54 samples (90%) with an overall mean of 1.3 x 10(3) cfu/ml. Of Staph. aureus strains, 23% proved to be enterotoxinogenic with a prevalence of enterotoxin C producers. Staph. caprae was the coagulase-negative species most frequently isolated; none of the coagulase-negative staphylococci strains synthesized any of the enterotoxins tested for. Sample source was the major factor affecting the microbial composition of goat milk: significant differences (P < 0.01) were observed among samples from different farms for SPC, coliforms, lactococci, lactobacilli and halotolerant bacteria. Period of lactation had a significant effect (P < 0.025) on SCC and pH. SPC correlated well with coliforms, lactococci and lactobacilli; SSC did not reveal positive interactions with any microbial groups or pH.

Animals↗
PubMed2001

Glycan mimicry as a basis for novel anti-infective drugs.

The idea of using carbohydrate-based drugs to prevent attachment of microbial pathogens to host tissues has been around for about three decades. This concept evolved from the observation that many pathogenic microbes bind to complex carbohydrate sequences on the surface of host cells. It stands to reason, therefore, that analogs of the carbohydrate sequences pathogens bind to could be used to competitively inhibit these interactions, thereby preventing microbial damage to the host. This article will summarize some of the recent advances in developing such carbohydrate-based anti-infective drugs.

Animals↗