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Natural killer cells: emerging concepts in immunity to infection and implications for assessment of immunodeficiency.

PURPOSE OF REVIEW: As the molecular networks that connect innate and adaptive immunity are untangled, the prominence of natural killer (NK) cells in host defense continues to emerge. Herein we highlight recent findings pertaining to NK cell development, trafficking, and interactions with other innate and adaptive immune cells in the context of predicting how NK cells may be involved in a wider range of clinical immunodeficiency. RECENT FINDINGS: NK cells contribute vital roles in innate and adaptive immunity, especially in collaboration with dendritic cells (DC). Fascinating new details have been reported about cell surface integrins and receptors that regulate NK functions, as well as the cytokine/chemokine networks that provide for NK-DC interactions. Moreover, NK cells appear to play an important role in the attenuation or resolution of an immune response through either action against CD8 T cells or indirect control of certain DC. These findings shed important insights as to how NK cells and DC cooperate to control primary infections and shape the subsequent adaptive immune responses. SUMMARY: Natural killer cells are heterogeneous lymphocytes that provide an essential function in host defense. NK cells respond early to microbial assault and interact with other cells of the innate immune system, but they recognize and intercept pathogenic infections through highly specific mechanisms that are similar to T cells. Thus, NK cells are positioned as a cellular bridge between innate and adaptive immunity. It is imperative, then, to include a careful assessment of NK cell populations and functions in most cases of suspected immunodeficiency.

Animals↗

Biogeochemistry of dihydrogen (H2).

Hydrogen has had an important and evolving role in Earth's geo- and biogeochemistry, from prebiotic to modern times. On the earliest Earth, abiotic sources of H2 were likely stronger than in the present. Volcanic out-gassing and hydrothermal circulation probably occurred at several times the modern rate, due to presumably higher heat flux. The H2 component of volcanic emissions was likely buffered close to the modern value by an approximately constant mantle oxidation state since 3.9 billion years ago, and may have been higher before that, if the early mantle was more reducing. The predominantly ultramafic character of the early, undifferentiated crust could have led to increased serpentinization and release of H2 by hydrothermal circulation, as in modern ultramafic-hosted vents. At the same time, the reactive atmospheric sink for H2 was likely weaker. Collectively, these factors suggest that steady state levels of H2 in the prebiotic atmosphere were 3-4 orders of magnitude higher than at present, and possibly higher still during transient periods following the delivery of Fe and Ni by large impact events. These elevated levels had direct or indirect impacts on the redox state of the atmosphere, the radiation budget, the production of aerosol hazes, and the genesis of biochemical precursor compounds. The early abiotic cycling of H2 helped to establish the environmental and chemical context for the origins of life on Earth. The potential for H2 to serve as a source of energy and reducing power, and to afford a means of energy storage by the establishment of proton gradients, could have afforded it a highly utilitarian role in the earliest metabolic chemistry. Some origin of life theories suggest the involvement of H2 in the first energy-generating metabolism, and the widespread and deeply-branching nature of H2-utilization in the modern tree of life suggests that it was at least a very early biochemical innovation. The abiotic production of H2 via several mechanisms of water-rock interaction could have supported an early chemosynthetic biosphere. Such processes offer the continued potential for a deep, rock-hosted biosphere on Earth or other bodies in the solar system. The continued evolution of metabolic and community-level versatility among microbes led to an expanded ability to completely exploit the energy available in complex organic matter. Under the anoxic conditions that prevailed on the early Earth, this was accomplished through the linked and sequential action of several metabolic classes of organisms. By transporting electrons between cells, H2 provides a means of linking the activities of these organisms into a highly functional and interactive network. At the same time, H2 concentrations exert a powerful thermodynamic control on many aspects of metabolism and biogeochemical function in these systems. Anaerobic communities based on the consumption of organic matter continue to play an important role in global biogeochemistry even into the present day. As the principal arbiters of chemistry in most aquatic sediments and animal digestive systems, these microbes affect the redox and trace-gas chemistry of our oceans and atmosphere, and constitute the ultimate biological filter on material passing into the rock record. It is in such communities that the significance of H2 in mediating biogeochemical function is most strongly expressed. The advent of phototrophic metabolism added another layer of complexity to microbial communities, and to the role of H2 therein. Anoxygenic and oxygenic phototrophs retained and expanded on the utilization of H2 in metabolic processes. Both groups produce and consume H2 through a variety of mechanisms. In the natural world, phototrophic organisms are often closely juxtaposed with a variety of other metabolic types, through the formation of biofilms and microbial mats. In the few examples studied, phototrophs contribute an often swamping term to the H2 economy of these communities, with important implications for their overall function-including regulation of the redox state of gaseous products, and direct release of large quantities of H2 to the environment. As one of the dominant sources of biological productivity for as much as 2 billion years of Earth's history, these communities have been among the most important agents of long-term global biogeochemical change. On the modern Earth, H2 is present at only trace levels in the atmosphere and oceans. Nonetheless, its function as an arbiter of microbial interactions and chemistry ensures an important role in biogeochemical cycling. The significance of H2 in a global sense may soon increase, as the search for alternative fuels casts attention on the clean-energy potential of hydrogen fuel cells. Already, H2 utilization plays an important role in all three phylogenetic domains of life. Humans may soon add an important new term to this economy. Considerable research is focused on the H2-producing capacities of phototrophic and other microorganisms as potential contributors in this regard. Regardless of source, the large scale utilization of H2 as an energy source could carry important consequences for biogeochemistry.

Anaerobiosis↗

Microbial ecology of the arbuscular mycorrhiza.

Arbuscular mycorrhizal (AM) fungi interact with a wide variety of organisms during all stages of their life. Some of these interactions such as grazing of the external mycelium are detrimental, while others including interactions with plant growth promoting rhizobacteria (PG PR) promote mycorrhizal functioning. Following mycorrhizal colonisation the functions of the root become modified, with consequences for the rhizosphere community which is extended into the mycorrhizosphere due to the presence of the AM external mycelium. However, we still know relatively little of the ecology of AM fungi and, in particular, the mycelium network under natural conditions. This area merits attention in the future with emphasis on the fungal partner in the association rather than the plant which has been the focus in the past.

Journal Article↗

Polysaccharides and food processing.

The rôle of polysaccharides during processing and for the quality of foods is discussed. Starch is the most important energy source for man. Most other polysaccharides are not metabolized for energy, but play an important rôle as dietary fibres. Pectins, alginates, carrageenans, and galactomannans are discussed as functional food additives in relation to their structure and their rheological behaviour, stability and interactions. Endogenous polysaccharides of fruits and vegetables and in products derived from them are responsible for such phenomena as texture (changes), press yields, ease of filtration and clarification, cloud stability, and mouth feel. To achieve desirable properties, the action of endogenous enzymes on polysaccharides must be inactivated and/or exogenous enzymes added as processing aids. This is also true for overcoming haze phenomena in clear juices or to break down undesirable microbial polysaccharides. Dough properties for bread baking can be improved by enzymic breakdown of a restrictive pentoglycan network. Network formation may come about by oxidative coupling of phenol rings of ferulic acid bound to hemicelluloses by ester links. Gels may be made by inducing oxidative coupling in natural or synthetic systems. Stagnation in development of new polysaccharide food additives is ascribed to difficulties in obtaining government approval for food use.

Carbohydrate Conformation↗

Bridging the airway microbiome and targeted therapy in bronchiectasis: multi-omics insights, endotypes and emerging therapies.

Bronchiectasis is a heterogeneous chronic airway disease primarily driven by persistent infection, microbial dysbiosis and dysregulated host immunity. While culture-based microbiology has historically informed clinical management, advances in high-throughput sequencing and multi-omic technologies have transformed our understanding of the airway ecosystem, revealing that disease activity is shaped not only by individual pathogens, but by complex and dynamic host-microbe interactions. Despite the breadth of descriptive microbiome data, translation into clinically actionable diagnostics or therapies has been limited. Importantly, cross-sectional correlations between microbiota and inflammation do not establish cause and effect, underscoring the need to embed host-microbiome profiling within both longitudinal and interventional therapeutic trials. In this review, we critically appraise current microbial and host multi-omics research in bronchiectasis, integrating microbiome studies with host inflammatory, proteomic and immunophenotyping data. We highlight themes emerging across cohorts, including low microbial diversity, pathogen dominance, loss of commensal networks and neutrophil-driven inflammation, and discuss how these features align with biological endotypes associated with exacerbations and treatment response. Drawing on lessons from host-directed therapeutic successes, we examine translational roadblocks limiting microbiome-guided care. We further review emerging microbiome-modulating strategies such as pathogen-specific biologics, bacteriophage therapy, live biotherapeutic products, biofilm-targeting adjuncts and precision antibiotic stewardship. Finally, we propose a roadmap toward microbiome-informed precision medicine through harmonised methodologies, integration of host and microbial biomarkers into clinical trials, and embedding multi-omics pipelines within large international registries. Collectively, these advances have the potential to shift bronchiectasis research and clinical management towards rationally designed, precision medicine-driven therapeutic strategies.

Humans↗

Decoding the spatiotemporal patterns of food spoilage microbial communities: Integrating multi-omics and artificial intelligence to enable precision preservation.

In the global food supply chain, food wastage caused by spoilage has resulted in significant economic losses, food shortages, and environmental pressure. This process is fundamentally driven by the spatiotemporal dynamics of microbial communities. However, traditional research methods struggle to elucidate the complex mechanisms of spatial heterogeneity, interspecies interactions, and functional succession. This limits the development of effective preservation strategies. This review systematically reviews the cutting-edge progress of integrating multi-omics technologies and artificial intelligence (AI) to study food spoilage microbial communities, breaking through this bottleneck. We propose an intelligent theoretical framework that could potentially analyze microbial metabolic activities and predict dynamic shelf life if implemented. The conceptual framework integrates multidimensional data, including spatial metabolomics, temporal metatranscriptomics, single-cell transcriptomics, and longitudinal metagenomics. It can also be combined with AI models, such as graph neural networks. The article elaborates on the principles and applications of spatio-temporal monitoring technologies, such as nano secondary ion mass spectrometry, hyperspectral imaging, and the Internet of Things sensing. Through illustrative cases of typical perishable foods, it also explores how such a multi-omics - AI system might be applied to spoilage warning and precise intervention. Additionally, the article addresses the current challenges in data coverage, model generalization, and federated learning implementation. Then the research further explores emerging areas such as engineered probiotics, edge AI, and microfluidic sensing. These areas are targeted at transforming food preservation from an empirical control approach to a data-driven, precise regulatory framework. This transformation provides theoretical support and technical approaches for developing a smart, sustainable food preservation system.

Multiomics↗

Global networking for assessment of impacts of global change on plant pests.

Global change encompasses changes in atmospheric composition, climate and climate variability, and land cover and land use. The occurrence of these changes and their interactive effects on biological systems are worldwide; thus, an effective global change research and impact assessment program must be based on international and interdisciplinary research and communication. With this in mind, several collaborative research networks with a focus on global change have been established in the biological sciences. They include the Global Change and Terrestrial Ecosystems (GCTE) Core Project of the International Geosphere-Biosphere Programme (IGBP) which aims to predict the effects of global change on terrestrial ecosystems, including agriculture and production forestry. Because of the importance of plant pests (arthropods, microbial pathogens, weeds) as yield-reducing factors in agriculture and as early indicators of global change, GCTE initiated a network Activity on "Global Change Impacts on Pests, Diseases and Weeds" with the overall goal of developing a predictive capability for impact assessment and adaptation. The network's specific objectives, contributing research projects, initial results and future challenges are discussed.

Journal Article↗

The Rhizosphere Microbiome: A Key Mediator of Crop Responses to Fertilization Strategies.

The rhizosphere microbiome, the plant's "second genome" is pivotal for crop nutrient acquisition, health, and stress responses. While fertilization ensures high agricultural yields, a key challenge is reshaping this microbiome to boost crop performance. This review synthesizes how mineral, organic, and bio-organic/microbial inoculant fertilizers affect rhizosphere microbial structure, diversity, and function. Long-term excessive mineral fertilizers (especially nitrogen) reduce microbial diversity, diminish beneficial groups (e.g., diazotrophs, PGPR), and disrupt microbial networks via soil acidification and altered root exudates, causing continuous cropping obstacles. In contrast, organic fertilizers improve soil microenvironments, maintaining high microbial diversity, enriching beneficial taxa (e.g., Proteobacteria, Actinobacteria), and enhancing community complexity. Bio-organic fertilizers/microbial inoculants "engineer" the microbiome by introducing exogenous beneficial microbes (e.g., Bacillus, Pseudomonas, AMF), directly promoting growth, suppressing diseases, and "reconditioning" indigenous beneficial communities. We also clarify how fertilization regulates plant-microbe dialog via root exudates and rhizosphere chemistry (e.g., pH, ion balance), discuss current challenges (causality, lab-to-field translation, genotype-microbiome-fertilization interactions), and outline future directions. Integrating rhizosphere microbiome management into fertilization is crucial for reducing chemical fertilizer reliance and advancing agricultural green transformation.

fertilization strategies microbial community assem↗

Caries protocol compliance issues.

Any caries control or caries protocol program must consider compliance as a measure of success. Lower bacterial counts on saliva tests and lower defs and DMFS scores suggest that some change has occurred. However, compliance with a caries risk protocol is about more than simple and convenient clinical outcome measures. We tend to think of compliance as an individual activity, but all influences on an individual need to be considered. Change may be from external influences rather than from the individual or even from providers interacting with an individual or community. Few studies have directly addressed caries risk protocol. The paradigm change described in this manuscript suggests six key global areas--beneficiary education, health provider network education, community and state agencies, legislative commitment, access to care, and research--as significant factors to be considered in compliance. An outline of the major areas and subheadings for a global caries protocol compliance paradigm are presented.

Colony Count, Microbial↗

Crystal structure and characterization of the bismuth(III) compound with quinolone family member (ciprofloxacin). Antibacterial study.

Two bismuth(III) compounds of ciprofloxacin (cf) were synthesized. The crystal structure of one--(cfH2) (cfH) [BiCl6].2H2O (cfH2 = doubly protonated molecule of cf, cfH = protonated molecule of cf)--is presented and discussed. The compound crystallizes in the monoclinic space group P 21/c with a = 17.758(4), b = 7.600(10), c = 31.908(6) A, beta = 101.03(2)0, Z = 4. The charge of the isolated hexachlorobismuthate(III) anions is compensated with protonated of molecules (ionic interactions). One of the cf molecules is protonated at carbonyl oxygen O(1) and nitrogen N(24) of the piperazine residue, and the other at N(24) only. Two water molecules participate in the hydrogen bond network. Antimicrobial activity of this compound was tested against different microorganisms. The results of TG and FT-IR measurements are also included.

Anti-Infective Agents↗

Recombinant idiotypic TCRbeta chain immunization in mice generates antigen specific T cell response.

Vaccination remains the most cost-effective means of preventing infectious diseases. Success of vaccination depends on generation of effective memory response. Understanding the mechanism of generation and maintenance of immunological memory would help in the design of rational vaccines. T lymphocytes play a central role in the generation of protective immune response against many microbial infections. A hypothesis known as relay hypothesis was earlier proposed, which explains the maintenance of immunological memory through interaction of idiotypic and anti-idiotypic lymphocytes. In the present study, we have shown that immunization with a model antigen, chicken ovalbumin specific T cell receptor beta chain (idiotypic TCR) generates TCR specific antibody and anti-idiotypic T cell responses as well as ovalbumin specific T cell response. We further show that boosting of ovalbumin primed mice with ovalbumin specific idiotypic TCRbeta DNA or TCRbeta protein gives memory response for ovalbumin. This study provides experimental evidence for perpetuation of immunological memory through idiotypic network interactions.

Animals↗

Role of bacterial proteinases in matrix destruction and modulation of host responses.

Recently accumulated large bodies of evidence have strongly implicated proteolytic enzymes released by subgingival plaque bacteria in the pathogenicity of periodontal disease. With regard to proteolytic power, however, the contribution from different microbial species considered as periodontal pathogens is not equal. Two of these bacteria, P. gingivalis and T. denticola, have developed an elaborate proteolytic systems composed of several surface-located or secreted enzymes, which apparently serve a role to provide bacteria with nutrients in the form of small peptides and amino acids. Of these two species, proteinases of P. gingivalis are the most intensively studied, and during the last decade an impressive array of information has been accumulated with respect to the biochemical characterization of purified proteinases and structure of the genes encoding them, the regulation of expression and the effects of these enzymes on host systems. In addition, studies on proteinase-deficient isogenic mutants has shed light on both their housekeeping functions and potential role(s) in the pathogenicity of periodontitis. Among several proteinases produced by P. gingivalis, the cysteine proteinases, referred to as gingipains, are clearly in the spotlight. They are the subject of several recent reviews and generally considered as the major virulence factors of this periodontal pathogen (59, 105, 139, 182, 183, 186, 281, 284, 286, 289). Gingipains seem to be key players in subverting host defense systems with, significantly, the complement and neutrophils being the main target. In addition, through uncontrolled activation of kallikrein/kinin pathway and coagulation cascade they contribute to local generation of bradykinin and thrombin, two synergistically working pro-inflammatory reagents with a strongly, although indirectly, stimulatory effect on bone resorption. Furthermore, the ability to interact with the cytokine networking systems has the potential to dysregulate the local inflammatory reaction. Finally, gingipains have a strong effect on mechanisms controlling host matrix metalloproteinase activity at the level of gene expression and zymogen activation (Fig. 10). Collectively, at the periodontal lesion site, the non-restrained action of gingipains, supported by other proteinases locally produced by subgingival plaque bacteria, would dysregulate most mechanisms controlling inflammatory reaction. Although successful in limiting infection to the periodontium, the ultimate effect of uncontrolled inflammatory processes would be the destruction of periodontal connective tissue, certainly the hallmark of periodontitis.

Adhesins, Bacterial↗

Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors.

MOTIVATION: Characterizing the diversity of microbial communities and understanding the environmental factors that influence community diversity are central tenets of microbial ecology. The development and application of cultivation independent molecular tools has allowed for rapid surveying of microbial community composition at unprecedented resolutions and frequencies. There is a growing need to discern robust patterns and relationships within these datasets which provide insight into microbial ecology. Pearson correlation coefficient (PCC) analysis is commonly used for identifying the linear relationship between two species, or species and environmental factors. However, this approach may not be able to capture more complex interactions which occur in situ; thus, alternative analyses were explored. RESULTS: In this paper we introduced local similarity analysis (LSA), which is a technique that can identify more complex dependence associations among species as well as associations between species and environmental factors without requiring significant data reduction. To illustrate its capability of identifying relationships that may not otherwise be identified by PCC, we first applied LSA to simulated data. We then applied LSA to a marine microbial observatory dataset and identified unique, significant associations that were not detected by PCC analysis. LSA results, combined with results from PCC analysis were used to construct a theoretical ecological network which allows for easy visualization of the most significant associations. Biological implications of the significant associations detected by LSA were discussed. We also identified additional applications where LSA would be beneficial. AVAILABILITY: The algorithms are implemented in Splus/R and they are available upon request from the corresponding author.

Bacteria↗

Rgg144/SHP144-controlled streptolancidin D mediates intra-species competition in Streptococcus pneumoniae with cumulative effect from other bacteriocins and fratricide.

UNLABELLED: Streptococcus pneumoniae is a major colonizer of the human nasopharynx, where inter- and intra-strain competition plays a critical role in shaping population structure and influencing vaccine outcomes. Bacteriocins are key mediators of intra-species competition, yet many of their functions and regulatory mechanisms remain poorly understood. Here, we identify and characterize streptolancidin D, a previously uncharacterized bacteriocin encoded by the sldA-T locus, and demonstrate its contribution to pneumococcal competition. Using isogenic streptolancidin-producing and non-producing variants of a naturally colonizing strain, we show that sldA-T contributes to the inhibition of competitor strains in in vitro biofilms and during murine co-colonization. Importantly, streptolancidin D also inhibited in vitro a subset of genetically diverse pneumococcal isolates representing multiple serotypes, whereas non-producing variants showed no activity. This indicates that its effect is broad and not restricted to isogenic interactions. Genomic analysis of over 7,500 pneumococcal genomes revealed that sldA-T is present in ~12% of isolates, with lineage-associated distribution patterns, and is consistently encoded downstream of the Rgg144/SHP144 quorum sensing system. We further demonstrate that sldA-T is regulated by this system, with sldA-T promoter activity abolished in a SHP-deficient background and partially restored by exogenous peptide stimulation. Finally, we show that streptolancidin D acts in concert with other bacteriocin systems and competence-mediated fratricide, highlighting a multifactorial antimicrobial strategy that enhances pneumococcal competitiveness. Overall, our findings identify a quorum sensing-regulated bacteriocin that contributes to pneumococcal competition and helps shape population dynamics. IMPORTANCE: Bacteriocins are central to bacterial competition and niche occupation, particularly in structured environments like the human nasopharynx. While several pneumococcal bacteriocins have been characterized, the functions of many remain unknown, limiting our understanding of how these systems shape strain fitness and population dynamics. We characterize streptolancidin D, a bacteriocin that enhances intraspecies competitiveness in vitro and in vivo and contributes to the inhibition of genetically diverse pneumococcal strains. We demonstrate that its expression is tightly regulated by the conserved Rgg144/SHP144 quorum sensing system and that the locus is distributed and shows synteny across multiple pneumococcal lineages. Our findings reveal that streptolancidin D operates within a broader network of bacteriocins and competence-associated mechanisms that collectively shape competitive interactions. By integrating genomic, functional, and regulatory analyses, this work expands the known repertoire of pneumococcal antimicrobial systems and provides new insights into the mechanisms underpinning competition and population structure in S. pneumoniae.

Bacteriocins↗

A network model for the organization of type IV collagen molecules in basement membranes.

Type IV collagen was solubilized from a tumor basement membrane either by acid extraction or by limited digestion with pepsin. The two forms were similar in composition and the size of the constituent chains but differed when examined by electron microscopy and in the fragment pattern produced by bacterial collagenase. The acid-soluble form showed after rotary shadowing strands mainly of a length of 320 nm which terminated in a globule, or two strands connected by a similar globule. The globule was identified as a non-collagenous domain (NC1) which under dissociating conditions could be separated into two peptides showing a monomer-dimer relationship. Higher aggregates of NC1 were visualized under non-dissociating conditions. Some of the acid-extracted molecules have retained the previously 7-S collagen domain. The pepsin-solubilized form lacked domain NC1 and consisted mainly of four triple-helical strands (length 356 nm) joined together at the 7-S domain (length 30 nm). Common to both forms of type IV collagen was a small collagenase-resistant domain NC2 which was composed of collagenous and non-collagenous elements and located between the 7-S domain and the major triple helix. These data indicate that the collagenous matrix of basement membranes consists of a regular network of type IV collagen molecules which is generated by two different interacting sites located at opposite ends of each molecule. The 7-S collagen domain connects four molecules while the NC1 domain connects two molecules. The maximal distance between identical cross-linking sites (7-S or NC1) was estimated to be about 800 nm comprising the length of two molecules.

Animals↗

Exploring the ecological drivers of bacteriophage diversity and functional viral potential in the skin of the axolotl Ambystoma altamirani.

Bacteriophages play important roles in shaping microbial community dynamics across diverse environments. In the amphibian skin, most microbiome studies have focused on bacteria and their interactions with the fungus Batrachochytrium dendrobatidis (Bd), leaving other microbial components, including viruses, largely unexplored. Here, we present the first characterization of the viral community in the amphibian skin microbiome, focusing on ecological drivers of bacteriophage diversity and functional potential in the axolotl Ambystoma altamirani. Using public shotgun metagenomes, we found that the viral fraction was dominated by bacteriophages of the class Caudoviricetes. Bacteriophage diversity was significantly associated with local physicochemical parameters at the time of sampling, and showed a strong positive correlation with bacterial diversity, whereas no significant associations were detected with the presence of Bd. In addition, seasonality influenced the composition and properties of bacteria-bacteriophage co-abundance networks. Functional annotation of assembled bacteriophage sequences revealed a diverse functional potential, including putative auxiliary metabolic genes, superinfection exclusion, toxin-antitoxin, and virulence factors. Overall, these findings highlight the ecological relevance of bacteriophages in amphibian skin microbiomes and underscore the need for further studies on their role in the amphibian host's health.

Animals↗

Reports from the Eighth Annual Conference on Retroviruses and Opportunistic Infections. Chicago, February 4-8, 2001.

The Conference on Retroviruses and Opportunistic Infections is a research meeting created to provide a forum for basic and clinical science investigators to present, discuss, and critique developments in the field of human retrovirology and related opportunistic complications. The subjects highlighted are: virology, immunology, vaccines, pathogenesis, disease mechanisms in humans and animal models, primary/acute infection, host-virus interactions, antiretroviral therapy (preclinical, clinical, and complications), clinical pharmacology, opportunistic infections, epidemiology and infection control, microbicides, pediatric/maternal-fetal/women's health, and diagnostics. Following are digests of major reports from the conference, as compiled by the National Prevention Information Network (NPIN) of the Centers for Disease Control and Prevention (CDC).

AIDS-Related Opportunistic Infections↗

A Computational Workflow for Prioritizing Microbial Metabolite-Associated Host Genes in Constipation-Predominant Irritable Bowel Syndrome.

No standardized computational pipeline exists for systematically prioritizing microbial metabolite-associated host genes and protein-ligand complexes from publicly available chemical, genomic, and structural databases. This article describes an eight-stage workflow that accepts a user-defined set of gut microbiota-derived metabolites and produces a ranked shortlist of candidate metabolite-associated host genes, enriched biological pathways, and structurally prioritized protein-ligand complexes for experimental follow-up. The pipeline integrates (i) chemoinformatic metabolite profiling; (ii) multi-database candidate target prediction using protein-chemical interaction and ligand-based target-prediction tool and a molecular docking program; (iii) differential gene expression analysis of publicly available transcriptomic data; (iv) target-differentially expressed gene overlap; (v) protein-protein interaction network construction and pathway enrichment; (vi) molecular docking with a molecular docking program; (vii) 200 ns molecular dynamics simulation using a molecular dynamics engine with a protein force field used for molecular dynamics simulations; and (viii) MM-PBSA binding free-energy estimation. As a worked example, nine gut microbiota-derived or microbiota-modified metabolites representing short-chain fatty acids, bile acids, tryptophan-derived metabolites, and urolithin A were processed using the public IBS-C rectal mucosal transcriptomic dataset GSE36701. The workflow ranked 17 unique predicted metabolite-associated genes that were differentially expressed in this dataset. Docking, molecular dynamics simulation, and MM-PBSA analyses structurally prioritized five metabolite-protein complexes: lithocholic acid-VDR, lithocholic acid-NR1H4/FXR, ursodeoxycholic acid-NR1H4/FXR, tryptamine-HTR2A (simulated in an explicit 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer), and urolithin A-CASP3. The protocol is designed to be adaptable to other metabolite sets, disease transcriptomic datasets, and target classes; all outputs are hypothesis-generating computational predictions that require independent transcriptomic replication, protein-level validation, and functional ligand-response assays before causal or therapeutic conclusions can be drawn.

Irritable Bowel Syndrome↗