Detection of possible AI-2-mediated quorum sensing system in commensal intestinal bacteria

Deciphering the quorum-sensing lexicon of the gut microbiota

The enduring coexistence between the gut microbiota and the host has led to a symbiotic relationship that benefits both parties. In this complex, multispecies environment, bacteria can communicate through chemical molecules to sense and respond to the chemical, physical, and ecological properties of the surrounding environment. One of the best-studied cell-to-cell communication mechanisms is quorum sensing. Chemical signaling through quorum sensing is involved in regulating the bacterial group behaviors, often required for host colonization. However, most microbial-host interactions regulated by quorum sensing are studied in pathogens. Here, we will focus on the latest reports on the emerging studies of quorum sensing in the gut microbiota symbionts and on group behaviors adopted by these bacteria to colonize the mammalian gut. Moreover, we address the challenges and approaches to uncover molecule-mediated communication mechanisms, which will allow us to unravel the processes that drive the establishment of gut microbiota.

Exploring AI-2-mediated interspecies communications within rumen microbial communities

BACKGROUND

The rumen is an ecosystem with a complex microbial microflora in which microbes initiate biofilm formation by attaching to plant surfaces for plant degradation and are capable of converting feed to nutrients and energy via microbial processes. Quorum sensing (QS) is a cell-to-cell communication mechanism that allows microbes to synchronize the expression of multiple genes in the group to perform social behaviors such as chemotaxis and biofilm formation using self-synthesized QS signaling molecules. Whereas QS has been extensively studied in model microorganisms under pure culture conditions, QS mechanisms are poorly understood in complex bacterial communities, such as the rumen microflora, in which cell-to-cell communication may be common.

RESULTS

Here, we analyzed 981 rumens bacterial and archaeal genomes from the Joint Genome Institute (JGI) and GenBank databases and identified 15 types of known QS signaling molecule-related genes. The analysis of the prevalence and abundance of genes involved in QS showed that 767 microbial genomes appeared to possess QS-related genes, including 680 bacterial genomes containing autoinducer-2 (AI-2) synthase- or receptor-encoding genes. Prevotella, Butyivibrio, Ruminococcus, Oribacterium, Selenomonas, and Treponema, known abundant bacterial genera in the rumen, possessed the greatest numbers of AI-2-related genes; these genes were highly expressed within the metatranscriptome dataset, suggesting that intra- and interspecies communication mediated by AI-2 among rumen microbes was universal in the rumen. The QS processes mediated by the dCache_1-containing AI-2 receptors (CahRs) with various functional modules may be essential for degrading plants, digesting food, and providing energy and nutrients to the host. Additionally, a universal natural network based on QS revealed how rumen microbes coordinate social behaviors via the AI-2-mediated QS system, most of which may potentially function via AI-2 binding to the extracellular sensor dCache_1 domain to activate corresponding receptors involved in different signal transduction pathways, such as methyl-accepting chemotaxis proteins, histidine kinases, serine phosphatases, c-di-GMP synthases and phosphodiesterases, and serine/threonine kinases in the rumen.

CONCLUSIONS

The exploration of AI-2-related genes, especially CahR-type AI-2 receptors, greatly increased our insight into AI-2 as a potentially "universal" signal mediating social behaviors and will help us better understand microbial communication networks and the function of QS in plant-microbe interactions in complex microecosystems. Video Abstract.

Molecular interactions between the intestinal microbiota and the host

The intestine is the most densely colonized region of the body, inhabited by a diverse community of microbes. The functional significance of the intestinal microbiota is not yet fully understood, but it is known that the microbiota is implicated in numerous physiological processes of the host, such as metabolism, nutrition, the immune system, and regulation of behavior and mood. This article reviews recent findings on how bacteria of the intestinal microbiota interact with the host.

Microbiota‐microbiota and microbiota‐host interactions are mediated by direct cell contact and by metabolites either produced by bacteria or produced by the host or the environment and metabolized by bacteria. Among them are short‐chain fatty, including butyrate, propionate, and acetate. Other examples include polyamines, linoleic acid metabolites, tryptophan metabolites, trimethylamine‐N‐oxide, vitamins, and secondary bile acids. These metabolites are involved in regulating the cell cycle, neurobiological signaling, cholesterol and bile acid metabolism, immune responses, and responses to antioxidants. Understanding the host‐microbiota pathways and their modulation will allow the identification of individualized therapeutic targets for many diseases. This overview helps to facilitate and promote further research in this field.

Hacking Commensal Bacteria to Consolidate the Adaptive Mucosal Immune Response in the Gut-Lung Axis: Future Possibilities for SARS-CoV-2 Protection

Infectious diseases caused by mucosal pathogens significantly increase mortality and morbidity. Thus, the possibility to target these pathogens at their primary entry points can consolidate protective immunity. Regarding SARS-CoV-2 infection, it has been observed that the upper respiratory mucosa is highly affected and that dysregulation of resident microbiota in the gut-lung axis plays a crucial role in determining symptom severity. Thus, understanding the possibility of eliciting various mucosal and adaptive immune responses allows us to effectively design bacterial mucosal vaccine vectors. Such design requires rationally selecting resident bacterial candidates as potential host carriers, evaluating effective carrier proteins for stimulating an immune response, and combining these two to improve antigenic display and immunogenicity. This review investigated mucosal vaccine vectors from 2015 to present, where a few have started to utilize Salmonella and lactic acid bacteria (LAB) to display SARS-CoV-2 Spike S proteins or fragments. Although current literature is still lacking for its studies beyond in vitro or in vivo efficiency, decades of research into these vectors show promising results. Here, we discuss the mucosal immune systems focusing on the gut-lung axis microbiome and offer new insight into the potential use of alpha streptococci in the upper respiratory tract as a vaccine carrier.

Quorum sensing: a new prospect for the management of antimicrobial-resistant infectious diseases

INTRODUCTION

Quorum-sensing (QS) is a microbial cell-to-cell communication system that utilizes small signaling molecules to mediates interactions between cross-kingdom microorganisms, including Gram-positive and -negative microbes. QS molecules include N-acyl-homoserine-lactones (AHLs), furanosyl borate, hydroxyl-palmitic acid methylester, and methyl-dodecanoic acid. These signaling molecules maintain the symbiotic relationship between a host and the healthy microbial flora and also control various microbial virulence factors. This manuscript has been developed based on published scientific papers.

AREAS COVERED

Furanones, glycosylated chemicals, heavy metals, and nanomaterials are considered QS inhibitors (QSIs) and are therefore capable of inhibiting the microbial QS system. QSIs are currently being considered as antimicrobial therapeutic options. Currently, the low speed at which new antimicrobial agents are being developed impairs the treatment of drug-resistant infections. Therefore, QSIs are currently being studied as potential interventions targeting QS-signaling molecules and quorum quenching (QQ) enzymes to reduce microbial virulence.

EXPERT OPINION

QSIs represent a novel opportunity to combat antimicrobial resistance (AMR). However, no clinical trials have been conducted thus far assessing their efficacy. With the recent advancements in technology and the development of well-designed clinical trials aimed at targeting various components of the, QS system, these agents will undoubtedly provide a useful alternative to treat infectious diseases.

Quorum Sensing System in Bacteroides thetaiotaomicron Strain Identified by Genome Sequence Analysis

This study is a bioinformatics assay on the microbial genome of Bacteroides thetaiotaomicron. The study focuses on the problem of quorum sensing as a result of adverse factors such as chemotherapy and antibiotic therapy. In patients with severe intestinal diseases, two strains of microorganisms were identified that were distinguished as new. Strains were investigated by conducting genome sequencing. The current concepts concerned with the quorum sensing system regulation by stationary-phase sigma factor and their coregulation of target genes in B. thetaiotaomicron were considered. The study suggested using bioinformatics data for the diagnosis of gastrointestinal disorders. In the course of the study, 402 genes having a greater than twofold change were identified with the 95% confidence level. The shortest and longest coding genes were predicted; the noncoding genes were detected. Biological pathways (KEGG pathways) were classified into the following categories: cellular processes, environmental information processing, genetic information processing, human disease, metabolism, and organismic systems. Among notable changes in the biofilm population observed in parallel to the planktonic B. thetaiotaomicron was the expression of genes in the polysaccharide utilization loci that were involved in the synthesis of O-glycans.

Can rumen bacteria communicate to each other?

BACKGROUND

The rumen contains a myriad of microbes whose primary role is to degrade and ferment dietary nutrients, which then provide the host with energy and nutrients. Rumen microbes commonly attach to ingested plant materials and form biofilms for effective plant degradation. Quorum sensing (QS) is a well-recognised form of bacterial communication in most biofilm communities, with homoserine lactone (AHL)-based QS commonly being used by Gram-negative bacteria alone and AI-2 Lux-based QS communication being used to communicate across Gram-negative and Gram-positive bacteria. However, bacterial cell to cell communication in the rumen is poorly understood. In this study, rumen bacterial genomes from the Hungate collection and Genbank were prospected for QS-related genes. To check that the discovered QS genes are actually expressed in the rumen, we investigated expression levels in rumen metatranscriptome datasets.

RESULTS

A total of 448 rumen bacterial genomes from the Hungate collection and Genbank, comprised of 311 Gram-positive, 136 Gram-negative and 1 Gram stain variable bacterium, were analysed. Abundance and distribution of AHL and AI-2 signalling genes showed that only one species (Citrobacter sp. NLAE-zl-C269) of a Gram-negative bacteria appeared to possess an AHL synthase gene, while the Lux-based genes (AI-2 QS) were identified in both Gram-positive and Gram-positive bacteria (191 genomes representing 38.2% of total genomes). Of these 192 genomes, 139 are from Gram-positive bactreetteria and 53 from Gram-negative bacteria. We also found that the genera Butyrivibrio, Prevotella, Ruminococcus and Pseudobutyrivibrio, which are well known as the most abundant bacterial genera in the rumen, possessed the most lux-based AI-2 QS genes. Gene expression levels within the metatranscriptome dataset showed that Prevotella, in particular, expressed high levels of LuxS synthase suggesting that this genus plays an important role in QS within the rumen.

CONCLUSION

This is the most comprehensive study of QS in the rumen microbiome to date. This study shows that AI-2-based QS is rife in the rumen. These results allow a greater understanding on plant-microbe interactions in the rumen.

Challenges and Limitations of Anti-quorum Sensing Therapies

Quorum sensing (QS) is a mechanism allowing microorganisms to sense population density and synchronously control genes expression. It has been shown that QS supervises the activity of many processes important for microbial pathogenicity, e.g., sporulation, biofilm formation, and secretion of enzymes or membrane vesicles. This contributed to the concept of anti-QS therapy [also called quorum quenching (QQ)] and the opportunity of its application in fighting against various types of pathogens. In recent years, many published articles reported promising results indicating the possibility of reducing pathogenicity of tested microorganisms and their easier eradication when co-treated with antibiotics. The aim of the present article is to point to the opposite, negative side of the QQ therapy, with particular emphasis on three fundamental properties attributed to anti-QS substances: the selectivity, virulence reduction, and lack of resistance against QQ. This point of view may highlight new directions of research, which should be taken into account in the future before the widespread introduction of QQ therapies in the treatment of people.

Autoinducer 2-Dependent Escherichia coli Biofilm Formation Is Enhanced in a Dual-Species Coculture

Biofilms in nature typically consist of multiple species, and microbial interactions are likely to have crucial effects on biofilm development, structure, and functions. The best-understood form of communication within bacterial communities involves the production, release, and detection of signal molecules (autoinducers), known as quorum sensing. Although autoinducers mainly promote intraspecies communication, autoinducer 2 (AI-2) is produced and detected by a variety of bacteria, thus principally allowing interspecies communication. Here we show the importance of AI-2-mediated signaling in the formation of mixed biofilms by Enterococcus faecalis and Escherichia coli. Our results demonstrate that AI-2 produced by E. faecalis promotes collective behaviors of E. coli at lower cell densities, enhancing autoaggregation of E. coli but also leading to chemotaxis-dependent coaggregation between the two species. Finally, we show that formation of such mixed dual-species biofilms increases the stress resistance of both E. coli and E. faecalis.

IMPORTANCE The role of interspecies communication in the development of mixed microbial communities is becoming increasingly apparent, but specific examples of such communication remain limited. The universal signal molecule AI-2 is well known to regulate cell-density-dependent phenotypes of many bacterial species but, despite its potential for interspecies communication, the role of AI-2 in the establishment of multispecies communities is not well understood. In this study, we explore AI-2 signaling in a dual-species community containing two bacterial species that naturally cooccur in their mammalian hosts, i.e., Escherichia coli and Enterococcus faecalis. We show that active production of AI-2 by E. faecalis allows E. coli to perform collective behaviors at low cell densities. Additionally, AI-2- and chemotaxis-dependent coaggregation with E. faecalis creates nucleation zones for rapid growth of E. coli microcolonies in mixed biofilms and enhances the stress resistance of both species.

Roseburia spp.: a marker of health?

The genus Roseburia consists of obligate Gram-positive anaerobic bacteria that are slightly curved, rod-shaped and motile by means of multiple subterminal flagella. It includes five species: Roseburia intestinalis, R. hominis, R. inulinivorans, R. faecis and R. cecicola. Gut Roseburia spp. metabolize dietary components that stimulate their proliferation and metabolic activities. They are part of commensal bacteria producing short-chain fatty acids, especially butyrate, affecting colonic motility, immunity maintenance and anti-inflammatory properties. Modification in Roseburia spp. representation may affect various metabolic pathways and is associated with several diseases (including irritable bowel syndrome, obesity, Type 2 diabetes, nervous system conditions and allergies). Roseburia spp. could also serve as biomarkers for symptomatic pathologies (e.g., gallstone formation) or as probiotics for restoration of beneficial flora.

Chemical conversations in the gut microbiota

The gut microbiota is a complex, densely populated community, home to many different species that collectively provide huge benefits for host health. Disruptions to this community, as can result from recurrent antibiotic exposure, alter the existing network of interactions between bacteria and can render this community susceptible to invading pathogens. Recent findings show that direct antagonistic and metabolic interactions play a critical role in shaping the microbiota. However, the part played by quorum sensing, a means of regulating bacterial behavior through secreted chemical signals, remains largely unknown. We have recently shown that the interspecies signal, autoinducer-2 (AI-2), can modulate the structure of the gut microbiota by using Escherichia coli to manipulate signal levels. Here, we discuss how AI-2 could influence bacterial behaviors to restore the balance between the 2 major bacteria phyla, the Bacteroidetes and Firmicutes, following antibiotic treatment. We explore how this may impact on host physiology, community susceptibility or resistance to pathogens, and the broader potential of AI-2 as a means to redress the imbalances in microbiota composition that feature in many infectious and non-infectious diseases.

Manipulation of the quorum sensing signal AI-2 affects the antibiotic-treated gut microbiota

The mammalian gut microbiota harbors a diverse ecosystem where hundreds of bacterial species interact with each other and their host. Given that bacteria use signals to communicate and regulate group behaviors (quorum sensing), we asked whether such communication between different commensal species can influence the interactions occurring in this environment. We engineered the enteric bacterium, Escherichia coli, to manipulate the levels of the interspecies quorum sensing signal, autoinducer-2 (AI-2), in the mouse intestine and investigated the effect upon antibiotic-induced gut microbiota dysbiosis. E. coli that increased intestinal AI-2 levels altered the composition of the antibiotic-treated gut microbiota, favoring the expansion of the Firmicutes phylum. This significantly increased the Firmicutes/Bacteroidetes ratio, to oppose the strong effect of the antibiotic, which had almost cleared the Firmicutes. This demonstrates that AI-2 levels influence the abundance of the major phyla of the gut microbiota, the balance of which is known to influence human health.

Mining of luxS genes from rumen microbial consortia by metagenomic and metatranscriptomic approaches

Although rumen bacterial communities vary depending on many factors such as diet, age and physiological conditions, a core microbiota exists within the rumen. In many natural environments, some bacteria use a quorum-sensing (QS) system to regulate their physiological activities. However, very limited information is available about QS systems in rumen. To investigate the autoinducer 2 (AI-2)-mediated QS system in rumen, we detected genes (luxS) encoding the AI-2 synthase (LuxS), from three datasets embedded in metagenomics RAST server (MG-RAST) and from a metatranscriptome dataset. We collected 135 luxS genes from the metagenomic datasets, which were presumed to originate from Bacteroidetes, Firmicutes, Fusobacteria and Actinobacteria, and 34 luxS genes from the metatranscriptome dataset, which probably originated from Bacteroidetes, Firmicutes and Spirochaetes. Because the essential amino acids for LuxS activity were conserved in the LuxS homologues predicted from luxS gene sequences from both datasets, the LuxS homologues probably function in the rumen. Since the largest number of sequences of luxS genes were collected from the genera Prevotella, Ruminococcus and Eubacterium, which include many fibrolytic bacteria and constituent members of biofilm on feed particles, an AI-2-mediated QS system is likely involved in biofilm formation and fibrolytic activity in the rumen.

Microbial activities and intestinal homeostasis: A delicate balance between health and disease

The concept that the intestinal microbiota modulates numerous physiological processes including immune development and function, nutrition and metabolism as well as pathogen exclusion is relatively well established in the scientific community. The molecular mechanisms driving these various effects and the events leading to the establishment of a "healthy" microbiome are slowly emerging. The objective of this review is to bring into focus important aspects of microbial/host interactions in the intestine and to discuss key molecular mechanisms controlling health and disease states. We will discuss recent evidence on how microbes interact with the host and one another and their impact on intestinal homeostasis.

Multidirectional chemical signalling between Mammalian hosts, resident microbiota, and invasive pathogens: neuroendocrine hormone-induced changes in bacterial gene expression

Host-pathogen communication appears to be crucial in establishing the outcome of bacterial infections. There is increasing evidence to suggest that this communication can take place by bacterial pathogens sensing and subsequently responding to host neuroendocrine (NE) stress hormones. Bacterial pathogens have developed mechanisms allowing them to eavesdrop on these communication pathways within their hosts. These pathogens can use intercepted communication signals to adjust their fitness to persist and cause disease in their hosts. Recently, there have been numerous studies highlighting the ability of NE hormones to act as an environmental cue for pathogens, helping to steer their responses during host infection. Host NE hormone sensing can take place indirectly or directly via bacterial adrenergic receptors (BARs). The resulting changes in bacterial gene expression can be of strategic benefit to the pathogen. Furthermore, it is intriguing that not only can bacteria sense NE stress hormones but they are also able to produce key signalling molecules known as autoinducers. The rapid advances in our knowledge of the human microbiome, and its impact on health and disease highlights the potential importance of communication between the microbiota, pathogens and the host. It is indeed likely that the microbiota input significantly in the neuroendocrinological homeostasis of the host by catabolic, anabolic, and signalling processes. The arrival of unwanted guests, such as bacterial pathogens, clearly has a major impact on these delicately balanced interactions. Unravelling the pathways involved in interkingdom communication between invading bacterial pathogens, the resident microbiota, and hosts, may provide novel targets in our continuous search for new antimicrobials to control disease.

Commensal bacteria-dependent indole production enhances epithelial barrier function in the colon

Microbiota have been shown to have a great influence on functions of intestinal epithelial cells (ECs). The role of indole as a quorum-sensing (QS) molecule mediating intercellular signals in bacteria has been well appreciated. However, it remains unknown whether indole has beneficial effects on maintaining intestinal barriers in vivo. In this study, we analyzed the effect of indole on ECs using a germ free (GF) mouse model. GF mice showed decreased expression of junctional complex molecules in colonic ECs. The feces of specific pathogen-free (SPF) mice contained a high amount of indole; however the amount was significantly decreased in the feces of GF mice by 27-fold. Oral administration of indole-containing capsules resulted in increased expression of both tight junction (TJ)- and adherens junction (AJ)-associated molecules in colonic ECs in GF mice. In accordance with the increased expression of these junctional complex molecules, GF mice given indole-containing capsules showed higher resistance to dextran sodium sulfate (DSS)-induced colitis. A similar protective effect of indole on DSS-induced epithelial damage was also observed in mice bred in SPF conditions. These findings highlight the beneficial role of indole in establishing an epithelial barrier in vivo.

LuxS influences Escherichia coli biofilm formation through autoinducer-2-dependent and autoinducer-2-independent modalities

Escherichia coli produces biofilms in response to the small molecule autoinducer-2 (AI-2), a product of the LuxS enzyme. LuxS is part of the activated methyl cycle and could also affect biofilm development by AI-2-independent effects on metabolism. A luxS deletion mutant of E. coli W3110 and an inducible plasmid-luxS-complemented strain were used to identify AI-2-independent phenotypes. Differential interference contrast microscopy revealed distinct surface colonization patterns. Confocal microscopy followed by quantitative image analysis determined differences in biofilm topography correlating with luxS expression; deletion mutant biofilms had a 'spreading' phenotype, whereas the complement had a 'climbing' phenotype. Addition of exogenous 4,5-dihydroxy-2,3-pentanedione (DPD), an AI-2 precursor, to the deletion mutant increased biofilm height and biomass, whereas addition of the methyl donor S-adenosyl methionine or aspartate prevented the luxS-complemented strain from producing a thick biofilm. The luxS-complemented strain autoaggregated, indicating that fimbriae production was inhibited, which was confirmed by transmission electron microscopy. DPD could not induce autoaggregation in the deletion mutant, demonstrating that fimbriation was an AI-2-independent phenotype. Carbon utilization was affected by LuxS, potentially contributing to the observed phenotypic differences. Overall, the work demonstrated that LuxS affected E. coli biofilm formation independently of AI-2 and could assist in adapting to diverse conditions.

Implementation of a biotechnological process for vat dyeing with woad

The traditional process for vat dyeing with woad (Isatis tinctoria L.) basically relies on microbial reduction of indigo to its soluble form, leucoindigo, through a complex fermentative process. In the 19th century, cultivation of woad went into decline and use of synthetic indigo dye and chemical reduction agents was established, with a consequent negative impact on the environment due to the release of polluting wastewaters by the synthetic dyeing industry. Recently, the ever-growing demand for environmentally friendly dyeing technologies has led to renewed interest in ecological textile traditions. In this context, this study aims at developing an environmentally friendly biotechnological process for vat dyeing with woad to replace use of polluting chemical reduction agents. Two simple broth media, containing yeast extract or corn steep liquor (CSL), were comparatively evaluated for their capacity to sustain the growth and reducing activity of the strain Clostridium isatidis DSM 15098T. Subsequently, the dyeing capacity of the CSL medium added with 140 g L−1 of woad powder, providing 2.4 g L−1 of indigo dye, was evaluated after fermentation in laboratory bioreactors under anaerobic or microaerophilic conditions. In all fermentations, a sufficiently negative oxidation/reduction potential for reduction of indigo was reached as early as 24 h and maintained up to the end of the monitoring period. However, clearly faster indigo dye reduction was seen in the broth cultures fermented under strict anaerobiosis, thus suggesting the suitability of the N2 flushing strategy for enhancement of bacterial-driven indigo reduction.