The role of host molecules in communication with the resident and pathogenic microbiota: A review

A microfluidic co-culture model for investigating colonocytes-microbiota interactions in colorectal cancer

Changes in the abundance of certain bacterial species within the colorectal microbiota correlate with colorectal cancer (CRC) development. While carcinogenic mechanisms of single pathogenic bacteria have been characterized in vitro, limited tools are available to investigate interactions between pathogenic bacteria and both commensal microbiota and colonocytes in a physiologically relevant tumor microenvironment. To address this, we developed a microfluidic device that can be used to co-culture colonocyte spheroids and colorectal microbiota. The device was used to explore the effect of Fusobacterium nucleatum, an opportunistic pathogen associated with colorectal cancer development in humans, on colonocyte gene expression and microbiota composition. F. nucleatum altered the transcription of genes involved in cytokine production, epithelial-to-mesenchymal transition, and proliferation in colonocytes in a contact-independent manner; however, most of these effects were significantly diminished by the presence of commensal microbiota. Interestingly, F. nucleatum significantly altered the abundance of multiple bacterial clades associated with mucosal immune responses and cancer development in the colon. Our results highlight the importance of evaluating the potential carcinogenic activity of pathogens in the context of a commensal microbiota, and the potential to discover novel inter-species microbial interactions in the CRC microenvironment.

The temporal fluctuations and development of faecal microbiota in commercial layer flocks

The microbiota of the gastrointestinal tract influences gut health, which in turn strongly impacts the general health and productivity of laying hens. It is essential to characterise the composition and temporal development of the gut microbiota in healthy layers raised under different management systems, to understand the variations in typical healthy microbiota structure, so that deviations from this might be recognised and correlated with production and health issues when they arise. The present investigation aimed to study the temporal development and phylogenetic composition of the gut microbiota of four commercially raised layer flocks from hatch to end of the production cycle. Non-intrusive faecal sampling was undertaken as a proxy to represent the gut microbiota. Sequencing of 16S rRNA gene amplicons was used to characterise the microbiota. Beta diversity analysis indicated that each faecal microbiota was different across the four flocks and had subtly different temporal development patterns. Despite these inter-flock differences, common patterns of microbiota development were identified. Firmicutes and Proteobacteria were dominant at an early age in all flocks. The microbiota developed gradually during the rearing phase; richness and diversity increased after 42 d of age and then underwent significant changes in composition after the shift to the production farms, with Bacteroidota becoming more dominant in older birds. By developing a more profound knowledge of normal microbiota development in layers, opportunities to harness the microbiota to aid in the management of layer gut health and productivity may be more clearly seen and realised.

First insights into the Aurelia aurita transcriptome response upon manipulation of its microbiome

Introduction

The associated diverse microbiome contributes to the overall fitness of Aurelia aurita, particularly to asexual reproduction. However, how A. aurita maintains this specific microbiome or reacts to manipulations is unknown.

Methods

In this report, the response of A. aurita to manipulations of its native microbiome was studied by a transcriptomics approach. Microbiome-manipulated polyps were generated by antibiotic treatment and challenging polyps with a non-native, native, and potentially pathogenic bacterium. Total RNA extraction followed by RNAseq resulted in over 155 million reads used for a de novo assembly.

Results

The transcriptome analysis showed that the antibiotic-induced change and resulting reduction of the microbiome significantly affected the host transcriptome, e.g., genes involved in processes related to immune response and defense mechanisms were highly upregulated. Similarly, manipulating the microbiome by challenging the polyp with a high load of bacteria (2 × 107 cells/polyp) resulted in induced transcription of apoptosis-, defense-, and immune response genes. A second focus was on host-derived quorum sensing interference as a potential defense strategy. Quorum Quenching (QQ) activities and the respective encoding QQ-ORFs of A. aurita were identified by functional screening a cDNA-based expression library generated in Escherichia coli. Corresponding sequences were identified in the transcriptome assembly. Moreover, gene expression analysis revealed differential expression of QQ genes depending on the treatment, strongly suggesting QQ as an additional defense strategy.

Discussion

Overall, this study allows first insights into A. aurita's response to manipulating its microbiome, thus paving the way for an in-depth analysis of the basal immune system and additional fundamental defense strategies.

Dysbiosis of Gut Microbiota from the Perspective of the Gut-Brain Axis: Role in the Provocation of Neurological Disorders

The gut-brain axis is a bidirectional communication network connecting the gastrointestinal tract and central nervous system. The axis keeps track of gastrointestinal activities and integrates them to connect gut health to higher cognitive parts of the brain. Disruption in this connection may facilitate various neurological and gastrointestinal problems. Neurodegenerative diseases are characterized by the progressive dysfunction of specific populations of neurons, determining clinical presentation. Misfolded protein aggregates that cause cellular toxicity and that aid in the collapse of cellular proteostasis are a defining characteristic of neurodegenerative proteinopathies. These disorders are not only caused by changes in the neural compartment but also due to other factors of non-neural origin. Mounting data reveal that the majority of gastrointestinal (GI) physiologies and mechanics are governed by the central nervous system (CNS). Furthermore, the gut microbiota plays a critical role in the regulation and physiological function of the brain, although the mechanism involved has not yet been fully interpreted. One of the emerging explanations of the start and progression of many neurodegenerative illnesses is dysbiosis of the gut microbial makeup. The present understanding of the literature surrounding the relationship between intestinal dysbiosis and the emergence of certain neurological diseases, such as Alzheimer's disease, Parkinson's disease, Huntington's disease, and multiple sclerosis, is the main emphasis of this review. The potential entry pathway of the pathogen-associated secretions and toxins into the CNS compartment has been explored in this article at the outset of neuropathology. We have also included the possible mechanism of undelaying the synergistic effect of infections, their metabolites, and other interactions based on the current understanding.

Anti-cancer activity of human gastrointestinal bacteria

Malignant neoplasm is one of the most incurable diseases among inflammatory diseases. Researchers have been studying for decades to win over this lethal disease and provide the light of hope to humankind. The gastrointestinal bacteria of human hold a complex ecosystem and maintain homeostasis. One hundred trillion microbes are residing in the gastrointestinal tract of human. Disturbances in the microbiota of human's gastrointestinal tract can create immune response against inflammation and also can develop diseases, including cancer. The bacteria of the gastrointestinal tract of human can secrete a variety of metabolites and bioproducts which aid in the preservation of homeostasis in the host and gut. During pathogenic dysbiosis, on the other hand, numerous microbiota subpopulations may increase and create excessive levels of toxins, which can cause inflammation and cancer. Furthermore, the immune system of host and the epithelium cell can be influenced by gut microbiota. Probiotics, which are bacteria that live in the gut, have been protected against tumor formation. Probiotics are now studied to see if they can help fight dysbiosis in cancer patients undergoing chemotherapy or radiotherapy because of their capacity to maintain gut homeostasis. Countless numbers of gut bacteria have demonstrated anti-cancer efficiency in cancer treatment, prevention, and boosting the efficiency of immunotherapy. The review article has briefly explained the anti-cancer immunity of gut microbes and their application in treating a variety of cancer. This review paper also highlights the pre-clinical studies of probiotics against cancer and the completed and ongoing clinical trials on cancers with the two most common and highly effective probiotics Lactobacillus and Bacillus spp.

Potential Application of Living Microorganisms in the Detoxification of Heavy Metals

Heavy metal (HM) exposure remains a global occupational and environmental problem that creates a hazard to general health. Even low-level exposure to toxic metals contributes to the pathogenesis of various metabolic and immunological diseases, whereas, in this process, the gut microbiota serves as a major target and mediator of HM bioavailability and toxicity. Specifically, a picture is emerging from recent investigations identifying specific probiotic species to counteract the noxious effect of HM within the intestinal tract via a series of HM-resistant mechanisms. More encouragingly, aided by genetic engineering techniques, novel HM-bioremediation strategies using recombinant microorganisms have been fruitful and may provide access to promising biological medicines for HM poisoning. In this review, we summarized the pivotal mutualistic relationship between HM exposure and the gut microbiota, the probiotic-based protective strategies against HM-induced gut dysbiosis, with reference to recent advancements in developing engineered microorganisms for medically alleviating HM toxicity.

Impacts of Delivery Mode and Maternal Factors on Neonatal Oral Microbiota

Objectives

Initial oral microbial colonization has complicatedly interacted with growth and development. The aim of our study was to discover links between oral microbiota community structure and mode of delivery, maternal factors, such as systemic diseases, abortion history, and pregnancy complications.

Methods

A total of 177 pregnant women and their neonates were enrolled at Peking university people's hospital. We collected oral samples, medical history, and development phenotype and used a 16S rRNA gene sequence to analyze microbial diversity at all taxonomic levels, network structure, and metabolic characteristics.

Results

Firmicutes, Proteobacteria, and Actinobacteriota were the most predominant bacteria of neonatal oral samples among these phyla. Alpha-diversity of pregnant women with gestational diabetes mellitus (GDM), abortion history, and without immune diseases was higher than in control groups, and no significant dissimilarity in beta-diversity was observed between different maternal factors. Obvious separation or trend failed to be seen in different development phenotype groups. Besides, Oscillospirales were significantly more abundant in a natural delivery group than in the cesarean section group.

Conclusion

Our study indicated that maternal factors and mode of delivery influenced the oral microbial structure, but longitudinal studies were indispensable for capturing the long-term effects on neonatal development phenotype and oral microbiota.

Pseudomonas aeruginosa cytochrome P450 CYP168A1 is a fatty acid hydroxylase that metabolizes arachidonic acid to the vasodilator 19-HETE

Pseudomonas aeruginosa is a Gram-negative opportunistic human pathogen that is highly prevalent in individuals with cystic fibrosis (CF). A major problem in treating CF patients infected with P. aeruginosa is the development of antibiotic resistance. Therefore, the identification of novel P. aeruginosa antibiotic drug targets is of the utmost urgency. The genome of P. aeruginosa contains four putative cytochrome P450 enzymes (CYPs) of unknown function that have never before been characterized. Analogous to some of the CYPs from Mycobacterium tuberculosis, these P. aeruginosa CYPs may be important for growth and colonization of CF patients’ lungs. In this study, we cloned, expressed, and characterized CYP168A1 from P. aeruginosa and identified it as a subterminal fatty acid hydroxylase. Spectral binding data and computational modeling of substrates and inhibitors suggest that CYP168A1 has a large, expansive active site and preferentially binds long chain fatty acids and large hydrophobic inhibitors. Furthermore, metabolic experiments confirm that the enzyme is capable of hydroxylating arachidonic acid, an important inflammatory signaling molecule present in abundance in the CF lung, to 19-hydroxyeicosatetraenoic acid (19-HETE; K_m = 41 μM, V_max = 220 pmol/min/nmol P450), a potent vasodilator, which may play a role in the pathogen’s ability to colonize the lung. Additionally, we found that the in vitro metabolism of arachidonic acid is subject to substrate inhibition and is also inhibited by the presence of the antifungal agent ketoconazole. This study identifies a new metabolic pathway in this important human pathogen that may be of utility in treating P. aeruginosa infections.

Neuroprotective Effect of Ceftriaxone on MPTP-Induced Parkinson's Disease Mouse Model by Regulating Inflammation and Intestinal Microbiota

Parkinson's disease (PD) is a common degenerative disease of the central nervous system. Although some drugs can alleviate the progress of PD, their long-term use will lead to complications, so it is still necessary to find new drugs to delay or cure PD effectively. In view of the difficulty in developing new drugs, it is imperative to discover new functions of existing compounds that could be used to treat PD. In this study, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) was used to induce PD symptoms in a mouse model. Subsequently, these mice were treated with the antibiotic ceftriaxone. Ceftriaxone alleviated the behavioural and neuropathological changes induced by MPTP, downregulated the expression of glial fibrillary acidic protein (GFAP) and ionised calcium-binding adapter molecule 1 (Iba1) as markers of astroglia and microglia, respectively, and reduced the expression of neuroinflammation-related Toll-like receptor 4 (TLR4), myeloid differentiation primary response 88 (MyD88), and phosphorylated nuclear factor kappa-B (p-NF-κB)/NF-κB in the brain of PD mice. In addition, ceftriaxone reduced the abundance of pathogenic bacteria of the genus Proteus and increased the abundance of probiotic Akkermansia. Finally, ceftriaxone treatment increased the expression of the tight junction proteins zona occludens-1(ZO-1) and occludin in the colon, decreased the expression of the inflammation-related proteins TLR4, MyD88, and NF-κB in the colon, and decreased the serum concentration of the proinflammatory cytokines interleukin-1β (IL-1β), IL-6, and tumour necrosis factor-α (TNF-α). These results indicate that ceftriaxone had a neuroprotective effect on MPTP-induced PD mice, and its neuroprotective effect could be through regulating inflammation and intestinal microbiota. While we showed that ceftriaxone exerts a neuroprotective effect in an MPTP-induced PD mouse model, our findings are limited to the short-term effects of ceftriaxone. Additional work using transgenic mice is required to determine the long-term effects of ceftriaxone. In addition, the dose and frequency of ceftriaxone use should be evaluated.

The complex, bidirectional role of extracellular vesicles in infection

Cells from all domains of life release extracellular vesicles (EVs), packages that carry a cargo of molecules that participate in communication, co-ordination of population behaviours, virulence and immune response mechanisms. Mammalian EVs play an increasingly recognised role to fight infection, yet may also be commandeered to disseminate pathogens and enhance infection. EVs released by bacterial pathogens may deliver toxins to host cells, signalling molecules and new DNA to other bacteria, and act as decoys, protecting infecting bacteria from immune killing. In this review, we explore the role of EVs in infection from the perspective of both the pathogen and host, and highlight their importance in the host/pathogen relationship. We highlight proposed strategies for EVs in therapeutics, and call attention to areas where existing knowledge and evidence is lacking.

Exploring the Modulatory Effects of Gut Microbiota in Anti-Cancer Therapy

In the recent decade, gut microbiota has received growing interest due to its role in human health and disease. On the one hand, by utilizing the signaling pathways of the host and interacting with the immune system, the gut microbiota is able to maintain the homeostasis in human body. This important role is mainly modulated by the composition of microbiota, as a normal microbiota composition is responsible for maintaining the homeostasis of human body, while an altered microbiota profile could contribute to several pathogenic conditions and may further lead to oncogenesis and tumor progression. Moreover, recent insights have especially focused on the important role of gut microbiota in current anticancer therapies, including chemotherapy, radiotherapy, immunotherapy and surgery. Research findings have indicated a bidirectional interplay between gut microbiota and these therapeutic methods, in which the implementation of different therapeutic methods could lead to different alterations in gut microbiota, and the presence of gut microbiota could in turn contribute to different therapeutic responses. As a result, manipulating the gut microbiota to reduce the therapy-induced toxicity may provide an adjuvant therapy to achieve a better therapeutic outcome. Given the complex role of gut microbiota in cancer treatment, this review summarizes the interactions between gut microbiota and anticancer therapies, and demonstrates the current strategies for reshaping gut microbiota community, aiming to provide possibilities for finding an alternative approach to lower the damage and improve the efficacy of cancer therapy.

Gut microbiome and Mediterranean diet in the context of obesity. Current knowledge, perspectives and potential therapeutic targets

Mediterranean Diet has been recognized as one of the healthiest and sustainable dietary patterns worldwide, based on the food habits of people living in the Mediterranean region. It is focused on a plant-based cuisine combining local agricultural products and moderate intake of fish. As eating habits seem to exert a major impact on the composition of gut microbiota, numerous studies show that an adherence to the Mediterranean diet positively influences the microbiome ecosystem network. This has a profound effect on multiple host metabolic pathways and plays a major role in immune and metabolic homeostasis. Among metabolic disorders, obesity represents a major health issue where Mediterranean Dietary regime could possibly slowdown its spread. The aim of this review is to emphasize the interaction between diet and gut microbiota and the potential beneficial effects of Mediterranean diet on metabolic disorders like obesity, which is responsible for the development of many noncommunicable diseases.