Intraspecies Communication Research Articles

Role of CRISPR-Cas systems in periodontal disease pathogenesis and potential for periodontal therapy: A review.

Clustered regularly interspaced short palindromic repeats (CRISPRs) are DNA sequences capable of editing a host genome sequence. CRISPR and its specific CRISPR-associated (Cas) protein complexes have been adapted for various applications. These include activating or inhibiting specific genetic sequences or acting as molecular scissors to cut and modify the host DNA precisely. CRISPR-Cas systems are also naturally present in many oral bacteria, where they aid in nutrition, biofilm formation, inter- and intraspecies communication (quorum sensing), horizontal gene transfer, virulence, inflammation modulation, coinfection, and immune response evasion. It even functions as an adaptive immune system, defending microbes against invading viruses and foreign genetic elements from other bacteria by targeting and degrading their DNA. Recently, CRISPR-Cas systems have been tested as molecular editing tools to manipulate specific genes linked with periodontal disease (such as periodontitis) and as novel methods of delivering antimicrobial agents to overcome antimicrobial resistance. With the rapidly increasing role of CRISPR in treating inflammatory diseases, its application in periodontal disease is also becoming popular. Therefore, this review aims to discuss the different types of CRISPR-Cas in oral microbes and their role in periodontal disease pathogenesis and precision periodontal therapy.

Aeromonas salmonicida AI-1 and AI-2 quorum sensing pathways are differentially regulated by rainbow trout mucins and during in vivo colonization

Aeromonas salmonicida is an opportunistic pathogen with relevance for aquaculture. Fish epithelia are covered by a mucus layer, composed mainly by highly glycosylated mucins, which are the first point of contact between fish and pathogens. Quorum sensing (QS), a bacterial communication mechanism through secreted autoinducer signals that governs gene expression, influences bacterial growth and virulence. The main A. salmonicida autoinducers are mediated by the luxS and asaI genes, corresponding to inter- and intraspecies communication, respectively. The aim of this study was to determine the effect of the mucins that pathogens encounter during colonization of the gill and skin on A. salmonicida QS. We found that expression of A. salmonicida asaI, but not luxS, was increased after culture at 20 °C compared to 10 °C. Rainbow trout gill and skin mucins up-regulated asaI expression 2-fold but down-regulated luxS 10-fold. The downregulation of luxS was reflected by a reduction in autoinducer-2 secretion. Mucins isolated from skin had a stronger inhibitory effect than mucins isolated from gills on both luxS expression and A1-2 secretion, consistent with a higher relative abundance of N-Acetylneuraminic acid on skin mucins than on gill mucins. Reduction of AI-2 production by mucins or luxS-deletion lead to a reduced A. salmonicida auto-aggregation. Furthermore, after colonization of the gill, luxS was down regulated whereas asaI expression was upregulated. Both in vivo and in vitro, the expression of luxS and asaI were thus differentially regulated, frequently in an inverse manner. The strong AI-2 inhibiting effect of the skin mucins is likely part of the mucin-based defense against pathogens.

Milk-derived exosomes in the regulation of nutritional and immune functions.

Milk-derived exosomes (MDEs), being a component of milk, have the potential to support immune system maturation in offspring and enhance immune cell proliferation. Through the transport and transmission of essential signaling molecules, MDEs contribute to the regulation of intergenerational and intraspecies communication, thereby impacting nutrient uptake and metabolic functions. A comprehensive comprehension of MDE functionalities is imperative for enhancing the quality of the dairy industry. A systematic search of the databases PubMed/Medline, Web of Science, and Scopus utilizing predetermined keywords resulted in the identification of 418 articles, of which 67 were chosen for inclusion in this review, which specifically explores the intersection of immune response and nutrition. This article provides a critical analysis of the classification of extracellular vesicles, the mechanisms underlying the biosynthesis of microvesicular dietary exosomes (MDEs), the components of MDEs, and their relevance in the contexts of nutrition and immune modulation. The primary aim of this review was to offer valuable scholarly insights to support the advancement and practical application of MDEs.

Constructions of quorum sensing signaling network for activated sludge microbial community.

In wastewater treatment systems, the interactions among various microbes based on chemical signals, namely quorum sensing (QS), play critical roles in influencing microbial structure and function. However, it is challenging to understand the QS-controlled behaviors and the underlying mechanisms in complex microbial communities. In this study, we constructed a QS signaling network, providing insights into the intra- and interspecies interactions of activated sludge microbial communities based on diverse QS signal molecules. Our research underscores the role of diffusible signal factors in both intra- and interspecies communication among activated sludge microorganisms, and signal molecules commonly considered to mediate intraspecies communication may also participate in interspecies communication. QS signaling molecules play an important role as communal resources among the entire microbial group. The communication network within the microbial community is highly redundant, significantly contributing to the stability of natural microbial systems. This work contributes to the establishment of QS signaling network for activated sludge microbial communities, which may complement metabolic exchanges in explaining activated sludge microbial community structure and may help with a variety of future applications, such as making the dynamics and resilience of highly complex ecosystems more predictable.

Nitrile biosynthesis in nature: how and why?

Covering: up to the end of 2023Natural nitriles comprise a small set of secondary metabolites which however show intriguing chemical and functional diversity. Various patterns of nitrile biosynthesis can be seen in animals, plants, and microorganisms with the characteristics of both evolutionary divergence and convergence. These specialized compounds play important roles in nitrogen metabolism, chemical defense against herbivores, predators and pathogens, and inter- and/or intraspecies communications. Here we review the naturally occurring nitrile-forming pathways from a biochemical perspective and discuss the biological and ecological functions conferred by diversified nitrile biosyntheses in different organisms. Elucidation of the mechanisms and evolutionary trajectories of nitrile biosynthesis underpins better understandings of nitrile-related biology, chemistry, and ecology and will ultimately benefit the development of desirable nitrile-forming biocatalysts for practical applications.

Pleurosigma strigosum diatom frustule as a natural, multi-functional photonic platform

Nature provides various organisms with ordered or quasi-ordered dielectric nanostructures that enable several animals, plants, and protists to manipulate light, optimizing inter- and intra-species communication, camouflage, or solar light harvesting. In particular, diatom microalgae possess nanostructured silica cell walls, known as frustules, which efficiently interact with optical radiation through multiple diffractive, refractive, scattering, waveguiding, and frequency down-conversion mechanisms. These properties contribute to diatoms’ efficiency in photosynthesis, UV tolerance, and possibly influence the phototaxis mechanisms of motile species. In our study, we utilized several imaging, spectroscopic, and numerical techniques to explore the optical functionalities of individual frustule components in the pennate, motile diatom Pleurosigma strigosum. We discuss the implications of frustule photonic properties on the living cell, and envision the exploitation of these properties in multifunctional, bio-derived photonic devices.

Indole-3-acetic acid as a cross-talking molecule in algal-bacterial interactions and a potential driving force in algal bloom formation.

Most signaling molecules are involved in inter-or intra-species communication, and signaling involving cross-kingdom cell-to-cell communication is limited. Howerver, algae and bacteria exchange nutrients and information in a range of interactions in marine environments. Multiple signaling molecules exist between algae and bacteria, including quorum-sensing molecules, nitric oxide, and volatile organic compounds. Recently, indole-3-acetic acid (IAA), an auxin hormone that is a well-studied signaling molecule in terrestrial ecosystems, was found to act as a cue in cross-kingdom communication between algae and bacteria in aquatic environments. To increase understanding of the roles of IAA in the phycosphere, the latest evidence regarding the ecological functions of IAA in cross-kingdom communication between algae and bacteria has been compiled in this review. The pathways of IAA biosynthesis, effects of IAA on algal growth & reproduction, and potential mechanisms at phenotypic and molecular levels are summarized. It is proposed that IAA is an important molecule regulating algal-bacterial interactions and acts as an invisible driving force in the formation of algal blooms.

Mate calling alters expression of neuropeptide, cocaine- and amphetamine- regulated transcript (CART) in the brain of male frog Microhyla nilphamariensis

Croaking is a unique component of reproductive behaviour in amphibians which plays a key role in intraspecies communication and mate evaluation. While gonadal hormones are known to induce croaking, central regulation of sound production is less studied. Croaking is a dramatic, transient activity that sets apart an animal from non-croaking individuals. Herein, we aim at examining the profile of the neuropeptide cocaine- and amphetamine-regulated transcript (CART) in actively croaking and non-croaking frog Microhyla nilphamariensis. In anurans, this peptide is widely expressed in the areas inclusive of acoustical nuclei as well as areas relevant to reproduction. CART immunoreactivity was far more in the preoptic area (POA), anteroventral tegmentum (AV), ventral hypothalamus (vHy), pineal (P) and pituitary gland of croaking frog compared to non-croaking animals. On similar lines, tissue fragments collected from the mid region of the brain inclusive of POA, vHy, AV, pineal and pituitary gland of croaking frog showed upregulation of CART mRNA. However, CART immunoreactivity in the neuronal perikarya of raphe (Ra) was completely abolished during croaking activity. The data suggest that CART signaling in the brain may be an important player in mediating croaking behaviour in the frog.

Prevention of Psychological Stress Induced-Ulcer in rats Treated with Fruit Extract of Gymnospora montana

Gymnosporia montana (Roth) Bemth. is a traditional herbaceous plant of Celastraceous family found in different regions of India. We have earlier reported its antiulcer activity in aspirin-induced, pylorus-ligation induced, and cysteamine-induced ulcer models. As stress-induced ulcer amount to a majority of clinically evident ulcers, it was thought worthy to investigate the effects of the ethanolic extract of Gymnosporia montana in stress-induced ulcer paradigm. Psychological stress was produced by intra-species emotional communication in a jumping box. Rats were randomly divided into two groups; one was used as the ‘sender’ group that received electrical foot shocks of 10 s duration with 50 s intervallic current for the shock was increased stepwise from 10mA to 25mA. The animals showed emotional responses such as abnormal squealing and jumping. The other group called the ‘responder’ group were able to observe the ‘sender’ group mice but were not subjected to the shocks. A separate group of sender rats was used on each day. The receiver group was exposed to sender group for three consecutive days at the end of which, they were sacrificied and were observed for the presence of gastric lesions. Separate groups of rats were treated half an hour before with Ethanolic extract (500mg/kg, p.o.) and diazepam (5mg/kg, p.o.) and the protocol was repeated. At the end the ulcer index, pH of gastric contents and gastric volume was determined. Further, hisotopathology was also performed. Results revealed a good anti-ulcer activity which was comparable to that of diazepam. In conclusion, the present study affords a significant contribution in confirmation of the forklore effects of a traditional remedy.

Combining molecular modelling and experimental approaches to gain mechanistic insights into the LuxP drug target in Streptococcus pyogens

Autoinducer-2 can mediate inter- and intra-species communication signal between bacteria and these signals from AI-2 is noted from limited species of bacteria. In humans, S. pyogenes is a pathogen that causes a wide range of illnesses and can survive in the host system and transmit infection. The process by which S. pyogenes acquires the competence to live and disseminate infection remains unknown. We hypothesized that AI-2 and their receptors would play a significant role during infection, and for that present investigation provides the experimental and molecular insights. In the absence of details about the receptor LuxP and LuxQ, the screening approach provides supporting insights. The evolutionary relationship and similarities of the PBP domain (Spy 1535) and the signal transmission PDZ domain (Spy 1536) were studied in relation to their counterparts in other bacteria. Molecular docking and modeling confirmed the domain-enhanced specificity for AI-2 binding. In vitro studies showed that AI-2, which is present in the cell-free supernatant of S. pyogenes, regulates luminescence in P. luminous and biofilm development in E. coli using the LuxS reporter genes. Examination of S. pyogenes gene expression revealed modulation of virulence genes when the pathogen was exposed to V. harveyi HSL and AI-2. Therefore, S. pyogenes pathogenicity is sequentially regulated by AI-2 it acquires from other commensal bacteria. Overall, this study lays the groundwork for understanding the signalling mechanism from AI-2, which are critical to the pathogenic mechanism of S. pyogenes. Communicated by Ramaswamy H. Sarma

An appeasing pheromone ameliorates fear responses in the brown rat (Rattus norvegicus)

The brown rat (Rattus norvegicus) is one of the major animals both in the laboratory and in urban centers. Brown rats communicate various types of information using pheromones, the chemicals that mediate intra-species communication in minute amounts. Therefore, analyses of pheromones would further our understanding of the mode of life of rats. We show that a minute amount of 2-methylbutyric acid (2-MB) released from the neck region can ameliorate fear responses both in laboratory rats and in wild brown rats. Based on these findings, we conclude that 2-MB is an appeasing pheromone in the brown rat. A better understanding of rats themselves would allow us to perform more effective ecologically based research on social skills and pest management campaigns with low animal welfare impacts, which might contribute to furthering the advancement of science and improving public health.

Never smile at a crocodile: Gaping behaviour in the Nile crocodile at Ndumo Game Reserve, South Africa

Gaping is a regularly observed behaviour in crocodilians globally but is still poorly understood in relation to external variables which could trigger this behaviour. The occurrence of gaping behaviour was investigated in a large wild population of Nile crocodiles (Crocodylus niloticus) during the dry and wet seasons at Nyamithi Pan, Ndumo Game Reserve, South Africa. This is one of the longest crocodile gaping behaviour studies conducted in the wild, with 300 h of observations conducted over two seasons resulting in 1120 gaping behaviours recorded. The most common size class observed was between 1.5 and 2.5 m (n = 697), which accounted for 62.2% of the gaping observations. A significant decrease in gaping duration was observed as ambient temperatures increased, and the gape duration was longer at a higher degree angle. In addition, an increase in gape duration was observed as the number of neighbouring crocodiles increased. These results suggest gaping behaviour occurs when there are other crocodiles nearby and when temperatures do not necessitate thermoregulation. The study suggests that gaping could be used as a form of thermoregulation and intra-species communication.

Protocol: a simple method for biosensor visualization of bacterial quorum sensing and quorum quenching interaction on Medicago roots

BackgroundDefining interactions of bacteria in the rhizosphere (encompassing the area near and on the plant root) is important to understand how they affect plant health. Some rhizosphere bacteria, including plant growth promoting rhizobacteria (PGPR) engage in the intraspecies communication known as quorum sensing (QS). Many species of Gram-negative bacteria use extracellular autoinducer signal molecules called N-acyl homoserine lactones (AHLs) for QS. Other rhizobacteria species, including PGPRs, can interfere with or disrupt QS through quorum quenching (QQ). Current AHL biosensor assays used for screening and identifying QS and QQ bacteria interactions fail to account for the role of the plant root.MethodsMedicago spp. seedlings germinated on Lullien agar were transferred to soft-agar plates containing the broad-range AHL biosensor Agrobacterium tumefaciens KYC55 and X-gal substrate. Cultures of QS and QQ bacteria as well as pure AHLs and a QQ enzyme were applied to the plant roots and incubated for 3 days.ResultsWe show that this expanded use of an AHL biosensor successfully allowed for visualization of QS/QQ interactions localized at the plant root. KYC55 detected pure AHLs as well as AHLs from live bacteria cultures grown directly on the media. We also showed clear detection of QQ interactions occurring in the presence of the plant root.ConclusionsOur novel tri-trophic system using an AHL biosensor is useful to study QS interspecies interactions in the rhizosphere.

Microbiome engineering for bioremediation of emerging pollutants.

Axenic microbial applications in the open environment are unrealistic and may not be always practically viable. Therefore, it is important to use mixed microbial cultures and their interactions with the microbiome in the targeted ecosystem to perform robust functions towards their sustainability in harsh environmental conditions. Emerging pollutants like phthalates and hydrocarbons that are toxic to several aquatic and terrestrial life forms in the water bodies and lands are an alarming situation. The present review explores the possibility of devising an inclusive eco-friendly strategy like microbiome engineering which proves to be a unique and crucial technology involving the power of microbial communication through quorum sensing. This review discusses the interspecies and intra-species communications between different microbial groups with their respective environments. Moreover, this review also envisages the efforts for designing the next level of microbiome-host engineering concept (MHEC). The focus of the review also extended toward using omics and metabolic network analysis-based tools for effective microbiome engineering. These approaches might be quite helpful in the future to understand such microbial interactions but it will be challenging to implement in the real environment to get the desired functions. Finally, the review also discusses multiple approaches for the bioremediation of toxic chemicals from the soil environment.

Sensory neuroecology and multimodal evolution across the genus Drosophila

The neural basis and genetic mechanisms for sensory evolution are increasingly being explored in depth across many closely related members of the Drosophila genus. This has, in part, been achieved due to the immense efforts toward adapting gene-editing technologies for additional, non-model species. Studies targeting both peripheral sensory variations, as well as interspecies divergence in coding or neural connectivity, have generated numerous, tangible examples of how and where the evolution of sensory-driven animal behavior has occurred. Here, we review and discuss studies that each aim to identify the neurobiological and genetic components of sensory system evolution to provide a comparative overview of the types of functional variations observed across both perceptual input and behavioral output. In addition, we examined the roles neuroecology and neuroevolution play in speciation events, such as courtship and intraspecies communication, as well as those aspects related to behavioral divergence in host navigation or egg-laying preferences. Through the investigation of comparative, large-scale trends and correlations across diverse, yet closely related species within this highly ecologically variable genus of flies, we can begin to describe the underlying pressures, mechanisms, and constraints that have guided sensory and nervous system evolution within the natural environments of these organisms.

The RNA Content of Fungal Extracellular Vesicles: At the "Cutting-Edge" of Pathophysiology Regulation.

The role of extracellular vesicles (EVs) in interkingdom communication is widely accepted, and their role in intraspecies communication has been strengthened by recent research. Based on the regulation promoted by EV-associated molecules, the interactions between host and pathogens can reveal different pathways that ultimately affect infection outcomes. As a great part of the regulation is ascribable to RNA contained in EVs, many studies have focused on profiling RNAs in fungal and host EVs, tracking their accumulation during infection, and identifying potential target genes. Herein, we overview the main classes of RNA contained in fungal EVs and the biological processes regulated by these molecules, portraying a state-of-the-art picture of RNAs loaded in fungal EVs, while also raising several questions to drive future investigations. Our compiled data show unambiguously that EVs act as key elements in signaling pathways, and play a crucial role in pathosystems. A complete understanding of the processes that govern RNA content loading and trafficking, and its effect on recipient cells, will lead to improved technologies to ward off infectious agents that threaten human health.

合成生物学应用于微生物群体感应的研究进展

<p indent="0mm">Bacteria exist as a unicellular organism with their community and systematization characteristics in the environment. Quorum sensing (QS), a language for cell-cell communication, helps bacteria regulate gene expression and community behavior, leading to adaptation to environmental changes. QS system is widespread in many kingdoms of microbiomes (bacteria, fungi, and archaea), which could manipulate various physiological behaviors, including bioluminescence, biofilm formation, producing virulence factors, and establishing symbiosis. However, due to the diversity of the microbial community structure and functional complexity in nature, there are still unknown areas for QS-mediated regulatory networks and ecological mechanisms. The recent vigorous development of synthetic biology may provide new opportunities to probe and explore QS effects. This method has made great achievements in designing genetic element libraries, assembling biological devices, designing genetic circuits, and creating predefined and predictable microbiome consortia. In parallel, synthetic biology can be used as a tool in quorum sensing to regulate the composition and function of communities. Hence, an attempt was made in this review to summarize the latest research. First, we presented several typical QS systems, their functions and signaling pathways. Second, we discussed how to design QS signaling pathways and genetic circuits and how to reduce crosstalk using synthetic biology strategies. Finally, we evaluated the assay on the synthetic QS system and its performance in microbial inter- and intraspecies communication. Thus, this review aims to sort out advanced concepts of synthetic biology, deepen the understanding of constructing a bio-calculation toolkit based on the QS system, control population density and metabolic flow, and expand the application scope of synthetic biology strategy in manipulating QS.

Identification of Small Regulatory RNA Transcripts in Extracellular Vesicles from Lactic Acid Bacteria

Extracellular Vesicles, also referred to as EVs, are spherical lipid membrane‐bound vesicles produced by both Gram positive and Gram negative bacteria. These vesicles are secreted into the extracellular space and play important roles in cellular and host communication, elimination of competitors, virulence, detoxification of environmental stress, and nutrient sensing. They are often packed with proteins, enzymes, lipids, nucleic acids and other biomolecules. Streptococcus thermophilus is a lactic acid bacteria (LAB), inhabiting the human digestive tract, that has been shown to produce EVs. The bacterial florae are known to influence the host immune system, metabolism, and neurological processes, but little is known about the biochemical pathways involved. Since EVs are involved in host communication, they may play a key role in affecting the biochemical processes of the host. To study the content and potential effects of EVs, we have grown different LAB strains under anaerobic conditions, including S. thermophilus, Lactobacillus acidophilus, and Lactobacillus bulgaricus. Our goal is to isolate EVs from these LAB strains and identify small regulatory RNA (sRNA) molecules that mediate communication and biochemical effects on the host systems. As part of this study, we have begun to identify sRNA genes in LAB strains that may mediate communication with other bacteria or the host. In S. thermophilus, we have focused on the AsdS sRNA transcript, that is 152 base pairs in length, and is involved in quorum sensing. This gene is conserved among other streptococcal species and in the human pathogen, S. pyogenes, a homologous sRNA, known as MarS, is associated with the regulation of virulence factors. Since S. thermophilus is a non‐pathogenic species, the AsdS gene cannot be involved in virulence, but based on functional bioinformatics predictions, it may be responsible for intraspecies communication, biofilm formation, and transport processes. Our current studies aim to identify additional sRNA transcripts that may be found in EVs and mediate effects on the host systems.

An improved spider optimization algorithm coordinated by pheromones

Swarm intelligence algorithm is an important evolutionary computation method that optimizes the objective function by imitating the behaviors of various organisms in nature. A two-stage swarm intelligence algorithm named spider pheromone coordination algorithm (SPC) is proposed in this paper. SPC tries to explore as many feasible solutions as possible on the cobweb at the positioning stage. It simulates the release and reception of different pheromones between spiders at the hunting stage, and then spiders move towards prey under the co-action of winds and pheromones. Different from the existing algorithms, SPC simulates the process that spiders accomplish intra-species communications through different pheromones and considers the impact on spider wind movement. A large number of typical benchmark functions are used in comparative numerical experiments to verify the performances of SPC. Experiments are made to compare SPC with a series of swarm intelligence algorithms, showing that SPC has higher convergence accuracy and stronger global searchability, effectively keeping the diversity of feasible solutions.

A Simple Biosensor-Based Assay for Quantitative Autoinducer-2 Analysis.

Bacteria produce and react to interspecies signaling molecules in order to control the expression of genes that are particularly beneficial when they are expressed by a bacterial community. In addition to intraspecies communication, the signaling molecule autoinducer-2 (AI-2) can also serve for interspecies communication between Gram-positive and Gram-negative bacteria and is therefore of particular interest. The analysis and quantification of AI-2 are essential for understanding population density-dependent changes in bacterial behavior and pathogenicity. However, currently available bioassays for AI-2 quantification are rather complex, have narrow detection ranges, and are very sensitive to trace components of, for example, growth media. To facilitate and improve the detection of AI-2, we have developed an Escherichia coli biosensor-based assay that is sensitive, cheap, fast, robust, and reliable in the quantification of biologically active AI-2. The bioassay is based on an lsr promoter-fluorescent reporter gene fusion cassette that we chromosomally integrated in a biosensor strain, but the cassette can also be used in a low-copy number plasmid for the application in other Gram-negative bacterial species. We show here that AI-2 quantification was possible in a concentration range from 400 nM to 100 μM and that a critical interpretation of the kinetics of the measurements can reveal sugar interference. With the help of our biosensor strain, coculture experiments were done to test the capability and kinetics of AI-2 secretion by various Gram-negative bacteria in real time. Finally, calibration curves were used to calculate the absolute AI-2 concentration in cell-free bacterial samples.