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PubMed2026

Pilot metaproteomic profiling reveals bacterial diversity and potential medical and veterinary relevance of tick microbiomes in northern Algeria.

Ticks are major ectoparasites and vectors of pathogens affecting humans, livestock, and wildlife. They harbor diverse microbial communities that may influence tick biology and interactions with microorganisms; however, functional information on tick-associated microbiomes remains limited, particularly in North Africa. In this pilot study, we applied a metaproteomic approach based on high-resolution tandem mass spectrometry to characterize bacterial communities associated with three tick species collected in Algeria: Rhipicephalus sanguineus sensu lato, Hyalomma aegyptium, and Hyalomma dromedarii. Peptide spectra were assigned to taxa using a two-step database search strategy based on NCBInr, and bacterial composition and relative abundance were compared across tick species and sampling locations. A total of 40 bacterial genera belonging to 32 families and four phyla were identified. Microbiome composition differed significantly between tick genera and collection locations, suggesting an influence of species-specific and geographical factors on microbial community structure. Dominant genera included Streptomyces, Bacillus, Clostridium, Escherichia, Flavobacterium, Paenibacillus, and Providencia. Peptides related to Coxiella spp. were frequently detected, consistent with previous reports of Coxiella-like endosymbionts in ticks. This pilot study provides a first metaproteomic characterization of tick-associated communities in Algeria. The results reveal species- and location-associated differences in microbial composition and highlight the potential of metaproteomics for exploring tick-associated microbiomes in North Africa.

Animals↗
PubMed1996

Human oral microbial ecology and dental caries and periodontal diseases.

In the human oral cavity, which is an open growth system, bacteria must first adhere to a surface in order to be able to colonize. Ability to colonize a non-shedding tooth surface is necessary prior to any odontopathic or periodontopathic process. Complex microbe-host relationships occur and must be studied before the commensal-to-pathogenic nature of the human indigenous oral flora can be understood. Medical pathogens, if present in the appropriate host, always produce specific disease. Caries and periodontal diseases are conditional diseases, requiring numbers of certain indigenous species at various sites, particularly the tooth surface. In the case of caries, the condition is related to sugar consumption. Periodontal disease/s may require certain host and environmental conditions, such as local environment or nutritional factors in gingival crevicular fluids. Nonetheless, critical numbers of certain indigenous species must be present in order for these diseases to occur. The aim of this review is to understand the acquisition of the indigenous oral flora and the development of human dental plaque. The role of the salivary pellicle and adherence of indigenous bacteria to it are critical first steps in plaque development. Bacterial interactions with saliva, nutritional factors, growth factors, and microbial physiologic processes are all involved in the overall process of microbial colonization.

Bacteria↗
PubMed2001

Evaluation and refinement of tmRNA structure using gene sequences from natural microbial communities.

DNA harvested directly from complex natural microbial communities by PCR has been successfully used to predict RNase P RNA structure, and can potentially provide an abundant source of information for structural predictions of other RNAs. In this study, we utilized genetic variation in natural communities to test and refine the secondary and tertiary structural model for the bacterial tmRNA. The variability of proposed tmRNA secondary structures in different organisms and the lack of any predicted tertiary structure suggested that further refinement of the tmRNA could be useful. To increase the phylogenetic representation of tmRNA sequences, and thereby provide additional data for statistical comparative analysis, we amplified, sequenced, and compared tmRNA sequences from natural microbial communities. Using primers designed from gamma proteobacterial sequences, we determined 44 new tmRNA sequences from a variety of environmental DNA samples. Covariation analyses of these sequences, along with sequences from cultured organisms, confirmed most of the proposed tmRNA model but also provided evidence for a new tertiary interaction. This approach of gathering sequence information from natural microbial communities seems generally applicable in RNA structural analysis.

Base Sequence↗
PubMed2001

Physical and metabolic interactions of Pseudomonas sp. strain JA5-B45 and Rhodococcus sp. strain F9-D79 during growth on crude oil and effect of a chemical surfactant on them.

Methods to enhance crude oil biodegradation by mixed bacterial cultures, for example, (bio)surfactant addition, are complicated by the diversity of microbial populations within a given culture. The physical and metabolic interactions between Rhodococcus sp. strain F9-D79 and Pseudomonas sp. strain JA5-B45 were examined during growth on Bow River crude oil. The effects of a nonionic chemical surfactant, Igepal CO-630 (nonylphenol ethoxylate), also were evaluated. Strain F9-D79 grew attached to the oil-water interface and produced a mycolic acid-containing capsule. Crude oil emulsification and surface activity were associated with the cellular fraction. Strain JA5-B45 grew in the aqueous phase and was unable to emulsify oil, but cell-free supernatants mediated kerosene-water emulsion formation. In coculture, stable emulsions were formed and strain JA5-B45 had an affinity for the capsule produced by strain F9-D79. Igepal CO-630 inhibited F9-D79 cells from adhering to the interface, and cells grew dispersed in the aqueous phase as 0.5-microm cocci rather than 2.5-microm rods. The surfactant increased total petroleum hydrocarbon removal by strain JA5-B45 from 4 to 22% and included both saturated compounds and aromatics. In coculture, TPH removal increased from 13 to 40% following surfactant addition. The culture pH normally increased from 7.0 to between 7.5 and 8.5, although addition of Igepal CO-630 to F9-D79 cultures resulted in a drop to pH 5.5. We suggest a dual role for the nonylphenol ethoxylate surfactant in the coculture: (i) to improve hydrocarbon uptake by strain JA5-B45 through emulsification and (ii) to prevent strain F9-D79 from adhering to the oil-water interface, indirectly increasing hydrocarbon availability. These varied effects on hydrocarbon biodegradation could explain some of the known diversity of surfactant effects.

Biodegradation, Environmental↗
PubMed1983

Developing standards for environmental toxicants: the need to consider abiotic environmental factors and microbe-mediated ecologic processes.

This article suggests and discusses two novel aspects for the formulation of standards for environmental toxicants. First, uniform national standards for each pollutant will be underprotective for some ecosystems and overprotective for others, inasmuch as the toxicity of a pollutant to the indigenous biota is dependent on the physicochemical properties of the recipient environment. As the number of chemicals that need regulation is immense and as microbes appear to respond similarly to pollutant-abiotic factor interactions as do plants and animals, it is suggested that microbial assays be used initially to identify those abiotic factors that most influence the toxicity of specific pollutants. Thereafter, additional studies using plants and animals can focus on these pollutant-abiotic factor interactions, and more meaningful standards can then be formulated more rapidly and inexpensively. Second, it is suggested that the response to pollutants of microbe-mediated ecologic processes be used to quantitate the sensitivity of different ecosystems to various toxicants. Such a quantification, expressed in terms of an "ecological dose 50%" (EcD50), could be easily incorporated into the methodologies currently used to set water quality criteria and would also be applicable to setting criteria for terrestrial ecosystems.

Animals↗
PubMed2002

The sewer as a bioreactor--a dry weather approach.

The sewer is a reactor for chemical and microbial transformations of wastewater. These in-sewer processes affect the quality of the wastewater and thereby the sewer itself, the subsequent treatment and the receiving water quality. The paper focuses on the interactions between the dry weather in-sewer chemical and microbial transformations of the wastewater and the corresponding processes in a downstream located treatment plant. A conceptual understanding of the sewer processes is crucial in this respect.

Bioreactors↗
PubMed2005

Pulmonary infections in swine induce altered porcine surfactant protein D expression and localization to dendritic cells in bronchial-associated lymphoid tissue.

Surfactant protein D (SP-D) is a pattern-recognition molecule of the innate immune system that recognizes various microbial surface-specific carbohydrate and lipid patterns. In vitro data has suggested that this binding may lead to increased microbial association with macrophages and dendritic cells. The aim of the present in vivo study was to study the expression of porcine SP-D (pSP-D) in the lung during different pulmonary bacterial infections, and the effect of the routes of infection on this expression was elucidated. Furthermore, the aim was to study the in vivo spatial relationship among pSP-D, pathogens, phagocytic cells and dendritic cells. Lung tissue was collected from experimental and natural bronchopneumonias caused by Actinobacillus pleuropneumoniae or Staphylococcus aureus, and from embolic and diffuse interstitial pneumonia, caused by Staph. aureus or Arcanobacterium pyogenes and Streptococcus suis serotype 2, respectively. By comparing normal and diseased lung tissue from the same lungs, increased diffuse pSP-D immunoreactivity was seen in the surfactant in both acute and chronic bronchopneumonias, while such increased expression of pSP-D was generally not present in the interstitial pneumonias. Co-localization of pSP-D, alveolar macrophages and bacteria was demonstrated, and pSP-D showed a patchy distribution on the membranes of alveolar macrophages. SP-D immunoreactivity was intracellular in dendritic cells. The dendritic cells were identified by their morphology, the absence of macrophage marker immunoreactivity and the presence of dendritic cell marker immunoreactivity. Increased expression of pSP-D in the surfactant coincided with presence of pSP-D-positive dendritic cells in bronchus-associated lymphoid tissue (BALT), indicating a possible transport of pSP-D through the specialized M cells overlying (BALT). In conclusion, we have shown that pSP-D expression in the lung surfactant is induced by bacterial infection by an aerogenous route rather than by a haematogenous route, and that the protein interacts specifically with alveolar macrophages and with dendritic cells in microbial-induced BALT. The function of the interaction between pSP-D and dendritic cells in BALT remain unclear, but pSP-D could represent a link between the innate and adaptive immune system, facilitating the bacterial antigen presentation by dendritic cells in BALT.

Actinobacillus Infections↗
PubMed1990

Procedure for the purification of streptavidin by hydrophobic interaction chromatography.

A procedure is described for the purification of hydrophobic microbial proteins such as streptavidin from Streptomyces avidinii, using Benzyl-DC bead cellulose as the column material. The separation is rapid with a high loading capacity and sufficient resolution for preparative uses. Advantages are discussed especially for industrial purposes.

Bacterial Proteins↗
PubMed1987

Surface interactions on hydrogel extended wear contact lenses: microflora and microfauna.

The microbial flora and fauna of 25 high water content nonionic "soft" contact lenses worn by patients on an extended wear basis, 4 hand-cleaned patient-worn lenses, and 4 improperly maintained lenses were compared. Almost all the patient-worn lenses (24 of 25) were free of viable microorganisms, whereas all the hand-cleaned lenses (4 of 4) were contaminated with different microorganisms. This study showed that hand contact is a major source of microbial contamination of a lens and that usually the hand-transported microorganisms do not survive permanently on the lens in a healthy, normal eye. Improperly maintained lenses demonstrated pathogenic microbial associations. Proof of the eye's potent antimicrobial environment was demonstrated. Thus, microorganism-lens associations are largely due to lens handling and inappropriate maintenance regimens. Typically there are few microorganisms on an extended wear soft lens while it is being worn.

Contact Lenses, Extended-Wear↗
PubMed2007

CD40-TRAF6 and autophagy-dependent anti-microbial activity in macrophages.

A fundamental question in host-pathogen interaction is to determine if the immune system activates fusion with the lysosomes to eradicate pathogens. We recently reported that this task is accomplished by the interaction between CD40 expressed on macrophages and CD154 expressed on activated CD4+ T cells. CD40 stimulation of macrophages induces vacuole-lysosome fusion through autophagy and results in killing of the obligate intracellular pathogen Toxoplasma gondii. This response is independent of IFN-gamma, STAT1 and p47 GTPases. We now report that vacuole-lysosome fusion is dependent on synergy between TRAF6 signaling downstream of CD40 and TNF-alpha. These studies identified a new paradigm by which T cells eradicate an intracellular pathogen within macrophages.

Amino Acid Sequence↗
PubMed2026

Upper airway microbiome interacts with GSDMB and ORMDL3 asthma risk SNPs to influence early-life wheeze risk.

BACKGROUND: Single-nucleotide polymorphisms (SNPs) in the chromosome 17q12-q21 region and, independently, early-life nasal microbiota dominated by Moraxella, Streptococcus, or Haemophilus (MSH) increase risk of chronic wheeze and asthma development. OBJECTIVE: We sought to determine whether 17q12-q21 risk SNPs and nasal microbiota interact to modulate childhood wheeze risk. METHODS: Nasal wash samples from 12-month-old infants in 2 birth cohorts, COAST (Childhood Origins of Asthma; n = 180) and URECA (Urban Environment and Childhood Asthma; n = 139), underwent 16S ribosomal RNA variable region 4 sequencing. Nasal microbiota dominated by MSH or Corynebacterium, Dolosigranulum, Staphylococcus, or Bacillus (CDSB) were assessed. Paired blood was genotyped for 9 17q12-q21 risk SNPs. Logistic regression tested interactions between 17q12-q21 SNPs and MSH or CDSB on wheeze risk in the first 3 years of life. A549 lung epithelial cells, CRISPR-edited to encode the rs7216389 risk genotype (rs7216389TT) were compared to the heterozygous (rs7216389CT) line using bulk RNA sequencing. RESULTS: SNPs, particularly those in the ORMDL3 (rs8076131; odds ratio [OR]: 1.72; 95% CI: 1.09-2.71; Pint = .031) and GSDMB (rs2305480; OR: 1.72; 95% CI: 1.09-2.71; Pint = 0.042; and rs7216389; OR: 1.73; 95% CI: 1.09-2.70; Pint = .047) genes, interact with MSH microbiota to increase early-life wheeze risk (false discovery rate Pint = .016 for all), while interactions with CDSB reduce risk. A549 airway epithelial cells homozygous for rs7216389TT exhibited decreased expression of genes involved in antimicrobial responses and neutrophil recruitment and evidence increased microbial adherence compared with the heterozygous cell line. CONCLUSION: Airway microbiota interact with SNPs at the 17q12-q21 locus in genes involved in sphingolipid metabolism and intracellular antimicrobial responses, to modulate wheeze risk.

Humans↗
PubMed1979

Introduction to mechanisms of association of indigenous microbes.

Indigenous microorganisms of numerous types associate with epithelial surfaces in the gastrointestinal tracts of mammals and birds. Some of the microbial types, e.g., Lactobacillus sp. in the stomachs of laboratory rodents, adhere to a surface without altering it ultrastructurely. In such cases, the adherence is mediated undoubtedly by macromolecules on the bacterial surfaces, possibly polysaccharides in most cases, interacting in specific ways with receptor macromolecules on the epithelial surface. Other microbial types that associate with epithelial surfaces without altering them ultrastructurally, e.g., Clostridium 109-2 in the mouse large bowel, may adhere to the surface only weakly or not at all, and maintain the association because they are motile and attracted to the epithelium by chemotactic substances. Microbial types that alter the ultrastructure of the epithelial cells to which they attach interact intimately with the membranes of the epithelial cells. In such cases, the microbes have specialized segments or ends for adhering to the membranes, and probably elaborate systems for stabilizing the membranes and cytoplasm at the site in the epithelial cell to which they attach. Some such organisms may have evolved unique reproductive mechanisms to maintain their populations on the epithelial surface.

Adhesiveness↗
PubMed2026

Oral bacteriome in pediatric patients with malignancies prior to chemotherapy: a pilot study using full-length 16S rRNA sequencing.

OBJECTIVE: To characterize the composition, diversity, and ecological features of the oral bacteriome in pediatric patients with malignancies prior to chemotherapy initiation. METHODS: In this prospective pilot study,supragingival plaque samples were collected from 10 pediatric cancer patients prior to the initiation of chemotherapy. Bacterial genomic DNA was extracted from each sample, and the full-length 16S rRNA gene was amplified and sequenced on the PacBio Sequel II platform using circular consensus sequencing (CCS). Raw CCS reads were quality-filtered and denoised into amplicon sequence variants (ASVs) using DADA2, and taxonomic assignment was performed against the SILVA 138 reference database. Alpha diversity was assessed using the Chao1, Shannon, Simpson, and Faith's phylogenetic diversity (PD whole tree) indices, while beta diversity was evaluated through principal coordinate analysis (PCoA), and non-metric multidimensional scaling (NMDS). Microbial co-occurrence networks were constructed to characterize bacterial interactions, and functional potential was predicted using PICRUSt2, and BugBase. RESULTS: A total of 614,473 high-quality CCS reads were generated, yielding 1,697 ASVs. Alpha diversity analysis revealed substantial inter-individual variation in microbial richness and diversity among the pediatric cancer patients. The bacterial community was dominated by the phyla Firmicutes, Proteobacteria, Bacteroidota, Actinobacteriota. At the genus level, Streptococcus, Prevotella, Neisseria, and Haemophilus were the most abundant taxa. Beta diversity analysis revealed distinct clustering patterns, indicating highly individualized microbial profiles. Co-occurrence network analysis identified several keystone taxa and potential pathogenic associations within the supragingival plaque community. Functional prediction indicated that the dominant metabolic pathways were related to amino acid metabolism, carbohydrate metabolism, and membrane transport. CONCLUSION: These preliminary findings reveal a taxonomically diverse, highly individualized pre-chemotherapy oral bacteriome, providing foundational baseline profiles to guide future longitudinal investigations of chemotherapy-induced dysbiosis and personalized interventions.

Humans↗
PubMed2003

In the belly of the beast: subversion of macrophage proinflammatory signalling cascades during Toxoplasma gondii infection.

Macrophages (MØ) are used as the intracellular niche by several bacterial and protozoan microorganisms. Such microbial pathogens adopt diverse strategies to avoid MØ microbicidal effects. Recent insights into the Toxoplasma gondii-MØ interaction reveal novel ways that intracellular parasites subvert MØ function. In contrast to some microbial pathogens, Toxoplasma infection is not silent but induces rapid activation of transcription factors such as STAT-1 and NFkappaB. However, the parasite blocks nuclear translocation of both factors, and MØ cannot produce IL-12 or TNF-alpha when subsequently triggered with lipopolysaccharide. The nuclear import blockade is lifted 24 h after infection, but cells remain actively suppressed in TNF-alpha production. Nevertheless, IL-12 synthesis is initiated at this later time point. Toxoplasma gondii-induced production of this cytokine occurs through both MyD88- and CCR5-dependent pathways. The balance of cytokine subversion and stimulation during infection probably results from the parasite's need to simultaneously avoid immune elimination and trigger immunity to prevent host death.

Adaptor Proteins, Signal Transducing↗
PubMed1991

Microbial ecosystems as targets of antibiotic actions.

The old representation of the microbe-host interactions as a fight between two contenders has to be considered obsolete. Ecological studies have opened new routes to interpret symbiosis phenomena and to understand in more detail the significance of the microbial communities which are present in various niches of the skin and mucous membranes. In these ecosystems, the resident microorganisms play an important physiological role, frequently with mutualistic relationships. The great stability of these ecosystems is due to the constant composition of microbial communities. One of the main benefits that humans derive from their microbiota is protection from infections. Every change in this biological equilibrium, i.e. modifications of microbial communities (caused by exogenous or endogenous factors) can carry several negative consequences. In this context, exposure to antibiotics (either in the course of therapy or not) can produce direct changes in the target bacterial cells (adhesion, etc.) or modify the whole life of ecosystems by altering the quantitative or qualitative balance within different microbial populations. A selection of antibiotic-resistant organisms can propitiate the genetic transfer of resistance to other autochthonous or allochthonous microorganisms. Multiple-resistant organisms such as those involved in nosocomial infections have amplified the magnitude of this problem. In addition an impairment of host defences can favor infections caused by microorganisms originating from resident communities whose equilibrium has been altered by the antibiotic.

Anti-Bacterial Agents↗
PubMed2022

A graph-based approach for the visualisation and analysis of bacterial pangenomes.

BACKGROUND: The advent of low cost, high throughput DNA sequencing has led to the availability of thousands of complete genome sequences for a wide variety of bacterial species. Examining and interpreting genetic variation on this scale represents a significant challenge to existing methods of data analysis and visualisation. RESULTS: Starting with the output of standard pangenome analysis tools, we describe the generation and analysis of interactive, 3D network graphs to explore the structure of bacterial populations, the distribution of genes across a population, and the syntenic order in which those genes occur, in the new open-source network analysis platform, Graphia. Both the analysis and the visualisation are scalable to datasets of thousands of genome sequences. CONCLUSIONS: We anticipate that the approaches presented here will be of great utility to the microbial research community, allowing faster, more intuitive, and flexible interaction with pangenome datasets, thereby enhancing interpretation of these complex data.

Bacteria↗
PubMed2022

Ecological dynamics of plasmid transfer and persistence in microbial communities.

Plasmids are a major driver of horizontal gene transfer in prokaryotes, allowing the sharing of ecologically important accessory traits between distantly related bacterial taxa. Within microbial communities, interspecies transfer of conjugative plasmids can rapidly drive the generation genomic innovation and diversification. Recent studies are starting to shed light on how the microbial community context, that is, the bacterial diversity together with interspecies interactions that occur within a community, can alter the dynamics of conjugative plasmid transfer and persistence. Here, I summarise the latest research exploring how community ecology can both facilitate and impose barriers to the spread of conjugative plasmids within complex microbial communities. Ultimately, the fate of plasmids within communities is unlikely to be determined by any one individual host, rather it will depend on the interacting factors imposed by the community in which it is embedded.

Bacteria↗
PubMed1992

HS-142-1, a novel nonpeptide atrial natriuretic peptide (ANP) antagonist, blocks ANP-induced renal responses through a specific interaction with guanylyl cyclase-linked receptors.

HS-142-1, a novel microbial product, blocked 125I-labeled rat atrial natriuretic peptide (rANP) (= ANF(99-126)) binding to bovine adrenocortical membranes, where guanylyl cyclase-containing receptors are predominantly expressed. However, HS-142-1 only slightly inhibited [125I]rANP binding to bovine lung membranes where only a small portion of binding sites are coupled to guanylyl cyclase. Further, HS-142-1 only recognized the 135 kDa ANP receptor, which is considered to be the guanylyl cyclase-containing receptor based on the results obtained in affinity cross-linking studies with bovine adrenocortical and lung membranes. Under identical conditions, Atriopeptin I selectively recognized guanylyl cyclase-free receptors both in binding and affinity cross-linking experiments. When injected intravenously (1 mg/kg) to anesthetized rats, HS-142-1 abolished ANP-induced diuresis and natriuresis. These results suggest that HS-142-1 works in vivo through a specific interaction with the ANP functional receptor, and that HS-142-1 will be a powerful tool for understanding the physiological roles of ANP in distinction from its pharmacological effects.

Adrenal Glands↗