Human Microbiome and its Association With Health and Diseases

Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches

Genome-scale metabolic models (GEMs) of microbial communities offer valuable insights into the functional capabilities of their members and facilitate the exploration of microbial interactions. These models are generated using different automated reconstruction tools, each relying on different biochemical databases that may affect the conclusions drawn from the in silico analysis. One way to address this problem is to employ a consensus reconstruction method that combines the outcomes of different reconstruction tools. Here, we conducted a comparative analysis of community models reconstructed from three automated tools, i.e. CarveMe, gapseq, and KBase, alongside a consensus approach, utilizing metagenomics data from two marine bacterial communities. Our analysis revealed that these reconstruction approaches, while based on the same genomes, resulted in GEMs with varying numbers of genes and reactions as well as metabolic functionalities, attributed to the different databases employed. Further, our results indicated that the set of exchanged metabolites was more influenced by the reconstruction approach rather than the specific bacterial community investigated. This observation suggests a potential bias in predicting metabolite interactions using community GEMs. We also showed that consensus models encompassed a larger number of reactions and metabolites while concurrently reducing the presence of dead-end metabolites. Therefore, the usage of consensus models allows making full and unbiased use from aggregating genes from the different reconstructions in assessing the functional potential of microbial communities.

Analysis on Changes and Influencing Factors of the Intestinal Microbiota of Alpine Musk Deer between the Place of Origin and Migration

In China, the population of wild musk deer, belonging to the family Moschidae, has drastically decreased in recent years owing to human activities and environmental changes. During the 1990s, artificial breeding of Alpine musk deer was conducted in Xinglong Mountain, Gansu Province, China, and their ex situ conservation was explored for over a decade. Ex situ protection is beneficial for expanding the population of animals and maintaining their genetic diversity; however, it can also induce metabolic diseases and parasitic infections and reduce reproductive capacity. The gut microbiota of animals has a considerable impact on host energy metabolism and immune regulation, thereby playing a crucial role in the overall health and reproductive success of the host. In this study, by comparing the differences in the intestinal microbiome of the musk deer according to their place of origin and migration, the changes in their gut microbiota and the influencing factors were explored to provide a theoretical basis for monitoring the health status of the musk deer. We used 16S rRNA high-throughput sequencing technology to analyze the structure and diversity of the gut microbiota of Alpine musk deer in Gansu (G, place of origin) and Sichuan (S, place of migration). The results showed that the dominant bacteria and genera in the intestinal microbiome of captive musk deer were similar in the places of origin and migration, but significant differences were observed in their relative abundance (p < 0.05). Regarding Firmicutes and Actinobacteria, which are related to plant cellulose digestion, the relative abundance in group G was higher than that in group S; regarding Proteobacteria and Verrucomicrobia, which are related to fat and starch intake, the relative abundance in group S was higher than that in group G; the relative abundance of Bacillus and Clostridium sensu stricto, which are related to fiber digestibility, was higher in group G than in group S; the relative abundance of conditional pathogens Acinetobacter and Escherichia-Shigella was higher in group S than in group G. The results of α and β diversity analysis also showed significant differences between the two groups (p < 0.05). The ACE and Shannon indices of musk deer in group G were considerably higher than those in group S, and the Simpson index of musk deer in group S was greater than that in group G, indicating that the abundance and diversity of intestinal microbiome were higher in musk deer of Gansu than those of Sichuan. Comparison of the changes in the intestinal microbiome of the musk deer according to the place of origin and migration showed that the plant cellulose content in the food of the musk deer, the fat content in the concentrated feed, and changes in the feeding environment have an impact on the intestinal microbiome. Effective monitoring of the health and immunity of the musk deer is crucial for ensuring their overall health, which in turn will aid in formulating a scientific and reasonable management plan for their conservation.

Oral Bacteria: Friends and Foes?

The oral cavity is an ideal niche for microbial prosperity due to its stable temperature, suitable pH, and continuous nutrient supply [...].

Correlation Between Serum and Urine Biomarkers and the Intensity of Acute Radiation Cystitis in Patients Treated With Radiation Therapy for Localized Prostate Cancer: Protocol for the Radiotoxicity Bladder Biomarkers (RABBIO) Study

BACKGROUND

Despite improvements in radiation techniques, pelvic radiotherapy is responsible for acute and delayed bladder adverse events, defined as radiation cystitis. The initial symptoms of bladder injury secondary to pelvic irradiation are likely to occur during treatment or within 3 months of radiotherapy in approximately 50% of irradiated patients, and have a significant impact on their quality of life. The pathophysiology of radiation cystitis is not well understood, particularly because of the risk of complications associated with access to bladder tissue after irradiation, which limits our ability to study this process and develop treatments.

OBJECTIVE

It is an original study combining digital data collection to monitor patients' symptoms and biological markers during irradiation. The main objective of our study is to evaluate the correlation of biological biomarkers with the intensity of acute radiation cystitis and the quality of life of patients, assessed with the digital telemonitoring platform Cureety.

METHODS

Patients with intermediate-risk localized prostate cancer who are eligible for localized radiotherapy will be included. Inflammatory biomarkers will be analyzed in urine and blood samples before the start of radiotherapy and at weeks 4, 12, and 48 of irradiation, through quantitative methods such as a multiplex Luminex assay, flow cytometry, and enzyme-linked immunosorbent assay. We will also characterize the patients' gut and urine microbiota composition using 16S ribosomal RNA sequencing technology. Between sample collection visits, patients will complete various questionnaires related to radiation cystitis symptoms (using the International Prostate Symptom Score), adverse events, and quality of life (using the Functional Assessment of Cancer Therapy-Prostate questionnaire), using the Cureety digital remote monitoring platform. Upon receipt of the questionnaires, an algorithm will process the information and classify patients in accordance with the severity of symptoms and adverse events reported on the basis of Common Terminology Criteria for Adverse Events and International Prostate Symptom Score standards. This will allow us to correlate levels of urinary, blood, and fecal biomarkers with the severity of acute radiation cystitis symptoms and patient-reported quality of life.

RESULTS

The study started in March 2022. We estimate a recruitment period of approximately 18 months, and the final results are expected in 2024.

CONCLUSIONS

This prospective study is the first to explore the overexpression of inflammatory proteins in fluid biopsies from patients with symptoms of acute radiation cystitis. In addition, the 1-year follow-up after treatment will allow us to predict which patients are at risk of late radiation cystitis and to refer them for radioprotective treatment. The results of this study will allow us to develop strategies to limit radiation damage to the bladder and improve the quality of life of patients.

TRIAL REGISTRATION

ClinicalTrials.gov NCT05246774; https://clinicaltrials.gov/ct2/show/NCT05246774?term=NCT05246774.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

DERR1-10.2196/38362.

Changes in the Intestinal Microbiota in Patients with Chronic Pancreatitis: Systematizing Literature Data

The purpose of the review. To systematize literature data on changes in the structure of the intestinal microbiota in patients with chronic pancreatitis (CP).Key findings. The human intestinal microbiota is a dynamically changing system that is constantly undergoing qualitative and quantitative changes, especially in several pathological conditions of the digestive system. At present, the differences in the intestinal microbiota in pancreatic diseases are poorly understood. The severe CP is associated with impaired synthesis of antimicrobial peptides, bicarbonates, and digestive enzymes by the pancreas, which is a risk factor for dysbiotic changes in the intestinal microbiota, consisting in the development of small intestinal bacterial overgrowth (SIBO) and gut dysbiosis. The results of two large meta-analyses show that about a third of CP patients have SIBO. The colonic microbiota in patients with CP is also characterized by dysbiotic disorders, primarily in the reduction of alpha-diversity. Some studies have shown that these patients have an increase in Firmicutes, while Bacteroides and Faecalibacterium are reduced. In addition, as a rule, in patients with CP, the growth of Escherichia, Shigella and Streptococcus is recorded.Conclusion. In general, scientific papers have revealed significant heterogeneity in the profiles of the intestinal microbiota in patients with CP. Thus, several questions remain open, prioritizing the further study of the intestinal microbiota in patients with CP for identifying the specifics of its structure that can personalize the selection of enzyme replacement therapy and restrict the unreasonable prescription of additional pharmacotherapy (the use of proton pump inhibitors and / or antibacterial drugs).

Cholecystectomy promotes the development of colorectal cancer by the alternation of bile acid metabolism and the gut microbiota

The incidence and mortality of colorectal cancer (CRC) have been markedly increasing worldwide, causing a tremendous burden to the healthcare system. Therefore, it is crucial to investigate the risk factors and pathogenesis of CRC. Cholecystectomy is a gold standard procedure for treating symptomatic cholelithiasis and gallstone diseases. The rhythm of bile acids entering the intestine is altered after cholecystectomy, which leads to metabolic disorders. Nonetheless, emerging evidence suggests that cholecystectomy might be associated with the development of CRC. It has been reported that alterations in bile acid metabolism and gut microbiota are the two main reasons. However, the potential mechanisms still need to be elucidated. In this review, we mainly discussed how bile acid metabolism, gut microbiota, and the interaction between the two factors influence the development of CRC. Subsequently, we summarized the underlying mechanisms of the alterations in bile acid metabolism after cholecystectomy including cellular level, molecular level, and signaling pathways. The potential mechanisms of the alterations on gut microbiota contain an imbalance of bile acid metabolism, cellular immune abnormality, acid-base imbalance, activation of cancer-related pathways, and induction of toxin, inflammation, and oxidative stress.

Antibiotic-induced microbiome depletion improves LPS-induced acute lung injury via gut-lung axis

AIMS

Acute lung injury (ALI) is an acute inflammatory disorder. However, the precise mechanisms underlying the pathology of ALI remain elusive. An increasing evidence suggests the role of the gut-microbiota axis in the pathology of lung injury. This study aimed to investigate whether antibiotic-induced microbiome depletion could affect ALI in mice after lipopolysaccharide (LPS) administration.

MAIN METHODS

The effects of antibiotic cocktail (ABX) on ALI in the mice after intratracheally administration of LPS (5 mg/kg) were examined. Furthermore, 16s rRNA analysis and measurement of short-chain fatty acids in feces samples and metabolomics analysis of blood samples were performed.

KEY FINDINGS

LPS significantly increased the interleukin-6 (IL-6) levels in the bronchoalveolar lavage fluid (BALF) of water-treated mice. Interestingly, an ABX significantly attenuated the LPS-induced increase in IL-6 in BALF and lung injury scores. Furthermore, ABX and/or LPS treatment markedly altered the α- and β-diversity of the gut microbiota. There were significant differences in the α- and β-diversity of the water + LPS group and ABX + LPS group. LEfSe analysis identified Enterococusfaecalis, Clostriumtertium, and Bacteroidescaecimyris as potential microbial markers for ABX + LPS group. Untargeted metabolomics analysis identified several plasma metabolites responsible for discriminating water + LPS group from ABX + LPS group. There were correlations between the relative abundance of the microbiome and plasma metabolites. Integrative network analysis showed correlations between IL-6 levels in BALF and several gut microbes (or plasma metabolites).

SIGNIFICANCE

These data suggest that ABX-induced microbiome depletion could protect against LPS-induced ALI via the gut-microbiota-lung axis.

Predicting Microbe-Disease Association Based on Multiple Similarities and LINE Algorithm

Numerous microbes have been found to have vital impacts on human health through affecting biological processes. Therefore, exploring potential associations between microbes and diseases will promote the understanding and diagnosis of diseases. In this study, we present a novel computational model, named MSLINE, to infer potential microbe-disease associations by integrating Multiple Similarities and Large-scale Information Network Embedding (LINE) based on known associations. Specifically, on the basis of known microbe-disease associations from the Human Microbe-Disease Association Database, we first increase the known associations by collecting proven associations from existing literatures. We then construct a microbe-disease heterogeneous network (MDHN) by integrating known associations and multiple similarities (including Gaussian interaction profile kernel similarity, microbe function similarity, disease semantic similarity and disease-symptom similarity). After that, we implement random walk and LINE algorithm on MDHN to learn its structure information. Finally, we score the microbe-disease associations according to the structure information for every nodes. In the Leave-one-out cross validation and 5-fold cross validation, MSLINE performs better compared to other existing methods. Moreover, case studies of different diseases proved that MSLINE could predict the potential microbe-disease associations efficiently.

Facile synthesis of nanomaterials as nanofertilizers: a novel way for sustainable crop production

Nutrient fertilization plays a major role in improving crop productivity and maintaining soil fertility. In the last few decades, the productivity of current agricultural practices highly depends on the use of chemical fertilizers. Major drawback of traditional fertilizers is their low crop nutrient use efficiency and high loss into water. Nanomaterial in agriculture is a multipurpose tool for increasing growth, development, and yield of plants. Nanotechnology facilitates the amplifying of agriculture production by reducing relevant losses and improving the input efficiency. Nanotechnology has emerged as an attractive field of research and has various agriculture applications, especially the use of nano-agrochemicals to increase nutrient use efficiency and agricultural yield. Nanofertilizers are more effective as compared to chemical fertilizers due to their cost-efficient, eco-friendly, non-toxic, and more stable in nature. Overall, this chapter focuses on synthesis of nanofertilizers through physical, chemical, and biological methods. This chapter will also explore the use of nano-enabled fertilizers to enhance the nutrient use efficiency for sustainable crop production, and global food safety.

Improving the Diagnostic Potential of Extracellular miRNAs Coupled to Multiomics Data by Exploiting the Power of Artificial Intelligence

In recent years, the clinical use of extracellular miRNAs as potential biomarkers of disease has increasingly emerged as a new and powerful tool. Serum, urine, saliva and stool contain miRNAs that can exert regulatory effects not only in surrounding epithelial cells but can also modulate bacterial gene expression, thus acting as a “master regulator” of many biological processes. We think that in order to have a holistic picture of the health status of an individual, we have to consider comprehensively many “omics” data, such as miRNAs profiling form different parts of the body and their interactions with cells and bacteria. Moreover, Artificial Intelligence (AI) and Machine Learning (ML) algorithms coupled to other multiomics data (i.e., big data) could help researchers to classify better the patient’s molecular characteristics and drive clinicians to identify personalized therapeutic strategies. Here, we highlight how the integration of “multiomic” data (i.e., miRNAs profiling and microbiota signature) with other omics (i.e., metabolomics, exposomics) analyzed by AI algorithms could improve the diagnostic and prognostic potential of specific biomarkers of disease.

Assessment of disinfectant efficacy in reducing microbial growth

The incidence of hospital- and community-acquired infections has been dramatically increased worldwide. Accordingly, hands hygiene and the use of disinfectants have been increased leading to the expansion in hand sanitizers production to meet public demand. This study was conducted to assess the efficiency of common disinfectants in the market of Riyadh, Saudi Arabia in inhibiting the microbial growth during the time of Coronavirus disease 2019 (COVID-19) pandemic. Five bacterial strains of commonly hospital-acquired infections (Pseudomonas aeruginosa, Escherichia coli, Salmonella enteritidis, Staphylococcus aureus, and Enterococcus faecalis) (ATCC reference strains and clinical isolates) were examined for their susceptibility against 18 disinfectants collected from the Saudi market. The tested 18 disinfectants were broadly clustered into different groups based on their active chemical composition as following: 12 products contained alcohol, 2 products had chlorhexidine, 3 products contained mixed concentration of alcohol/chlorhexidine and 1 product had a mixture of chlorhexidine/Hexamidine/Chlorocresol. By measuring the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC), our results revealed that all the 18 disinfectants have reduced the microbial growth of all the tested strains. Generally, the MICs and the MBCs for the clinical strains are higher than those of the reference strains. Taken together, our findings showed that all tested products have high disinfectants’ killing rate against microbes of different origins, which suggest the high quality of these disinfectants and the good surveillance practice by the local authorities in Saudi Arabia.

Modulation of microbial community dynamics by spatial partitioning

Microbial communities inhabit spatial architectures that divide a global environment into isolated or semi-isolated local environments, which leads to the partitioning of a microbial community into a collection of local communities. Despite its ubiquity and great interest in related processes, how and to what extent spatial partitioning affects the structures and dynamics of microbial communities is poorly understood. Using modeling and quantitative experiments with simple and complex microbial communities, we demonstrate that spatial partitioning modulates the community dynamics by altering the local interaction types and global interaction strength. Partitioning promotes the persistence of populations with negative interactions but suppresses those with positive interactions. For a community consisting of populations with both positive and negative interactions, an intermediate level of partitioning maximizes the overall diversity of the community. Our results reveal a general mechanism underlying the maintenance of microbial diversity and have implications for natural and engineered communities.

Pharmacomicrobiomics: Exploiting the Drug-Microbiota Interactions in Antihypertensive Treatment

Hypertension is a leading risk factor for cardiovascular diseases and can reduce life expectancy. Owing to the widespread use of antihypertensive drugs, patients with hypertension have improved blood pressure control over the past few decades. However, for a considerable part of the population, these drugs still cannot significantly improve their symptoms. In order to explore the reasons behind, pharmacomicrobiomics provide unique insights into the drug treatment of hypertension by investigating the effect of bidirectional interaction between gut microbiota and antihypertensive drugs. This review discusses the relationship between antihypertensive drugs and the gut microbiome, including changes in drug pharmacokinetics and gut microbiota composition. In addition, we highlight how our current knowledge of antihypertensive drug-microbiota interactions to develop gut microbiota-based personalized ways for disease management, including antihypertensive response biomarker, microbial-targeted therapies, probiotics therapy. Ultimately, a better understanding of the impact of pharmacomicrobiomics in the treatment of hypertension will provide important information for guiding rational clinical use and individualized use.

Metataxonomic investigation of the microbial community in the trachea and oropharynx of healthy controls and diabetic patients using endotracheal tubes

BACKGROUND

Although the study of respiratory microbiota has been an active field of research, obtaining the appropriate respiratory samples for healthy controls remains to be a challenge. As such, this study aims to evaluate the use of endotracheal tube washing as a viable control for sputum samples.

METHODS

A total of 14 subjects, including 8 healthy respiratory controls and 6 diabetic patients without any respiratory disease, were enrolled in this study, during which the endotracheal tubes used in their scheduled routine surgery were collected. Pre-operative oral gargles were also collected from non-diabetic subjects.

RESULTS

16S amplicon sequencing revealed similar taxa composition in endotracheal tube washings and oral gargles in the healthy control subjects, although the relative abundance of 11 genus level operational taxonomic units was significantly different between the two sample sources. The diabetic subjects showed relatively lower diversity than those of non-diabetic subjects. The proportion range of the most abundant taxa detected in each endotracheal tube washings were 10.1-33.2%.

CONCLUSION

Endotracheal tube washing fluid may provide healthy control samples for upper respiratory investigations without incurring any additional risk to the subject.

Identifying Microbe-Disease Association Based on a Novel Back-Propagation Neural Network Model

Over the years, numerous evidences have demonstrated that microbes living in the human body are closely related to human life activities and human diseases. However, traditional biological experiments are time-consuming and expensive, so it has become a research topic in bioinformatics to predict potential microbe-disease associations by adopting computational methods. In this study, a novel calculative method called BPNNHMDA is proposed to identify potential microbe-disease associations. In BPNNHMDA, a novel neural network model is first designed to infer potential microbe-disease associations, its input signal is a matrix of known microbe-disease associations, and its output signal is matrix of potential microbe-disease associations probabilities. And moreover, in the novel neural network model, a new activation function is designed to activate the hidden layer and the output layer based on the hyperbolic tangent function, and its initial connection weights are optimized by adopting Gaussian Interaction Profile kernel (GIP) similarity for microbes, which can improve the training speed of BPNNHMDA efficiently. Finally, in order to verify the performance of our prediction model, different frameworks such as the Leave-One-Out Cross Validation (LOOCV) and k-Fold Cross Validation ( k-Fold CV) are implemented on BPNNHMDA respectively. Simulation results illustrate that BPNNHMDA can achieve reliable AUCs of 0.9242, 0.9127 ± 0.0009 and 0.8955 ± 0.0018 in LOOCV, 5-Fold CV and 2-Fold CV separately, which are superior to previous state-of-the-art methods. Furthermore, case studies of inflammatory bowel disease (IBD), asthma and obesity demonstrate that BPNNHMDA has excellent prediction ability in practical applications as well.

Threespine Stickleback: A Model System For Evolutionary Genomics

The repeated adaptation of oceanic threespine sticklebacks to fresh water has made it a premier organism to study parallel evolution. These small fish have multiple distinct ecotypes that display a wide range of diverse phenotypic traits. Ecotypes are easily crossed in the laboratory, and families are large and develop quickly enough for quantitative trait locus analyses, positioning the threespine stickleback as a versatile model organism to address a wide range of biological questions. Extensive genomic resources, including linkage maps, a high-quality reference genome, and developmental genetics tools have led to insights into the genomic basis of adaptation and the identification of genomic changes controlling traits in vertebrates. Recently, threespine sticklebacks have been used as a model system to identify the genomic basis of highly complex traits, such as behavior and host-microbiome and host-parasite interactions. We review the latest findings and new avenues of research that have led the threespine stickleback to be considered a supermodel of evolutionary genomics.

Microbial community in human gut: a therapeutic prospect and implication in health and diseases

The interest in the working and functionality of the human gut microbiome has increased drastically over the years. Though the existence of gut microbes has long been speculated for long over the last few decades, a lot of research has sprung up in studying and understanding the role of gut microbes in the human digestive tract. The microbes present in the gut are highly instrumental in maintaining the metabolism in the body. Further research is going on in this field to understand how gut microbes can be employed as potential sources of novel therapeutics; moreover, probiotics have also elucidated their significant place in this direction. As regards the clinical perspective, microbes can be engineered to afford defence mechanisms while interacting with foreign pathogenic bodies. More investigations in this field may assist us to evaluate and understand how these cells communicate with human cells and promote immune interactions. Here we elaborate on the possible implication of human gut microbiota into the immune system as well as explore the probiotics in the various human ailments. Comprehensive information on the human gut microbiome at the same platform may contribute effectively to our understanding of the human microbiome and possible mechanisms of associated human diseases.

Prioritizing Disease-Related Microbes Based on the Topological Properties of a Comprehensive Network

Many microbes are parasitic within the human body, engaging in various physiological processes and playing an important role in human diseases. The discovery of new microbe-disease associations aids our understanding of disease pathogenesis. Computational methods can be applied in such investigations, thereby avoiding the time-consuming and laborious nature of experimental methods. In this study, we constructed a comprehensive microbe-disease network by integrating known microbe-disease associations from three large-scale databases (Peryton, Disbiome, and gutMDisorder), and extended the random walk with restart to the network for prioritizing unknown microbe-disease associations. The area under the curve values of the leave-one-out cross-validation and the fivefold cross-validation exceeded 0.9370 and 0.9366, respectively, indicating the high performance of this method. Despite being widely studied diseases, in case studies of inflammatory bowel disease, asthma, and obesity, some prioritized disease-related microbes were validated by recent literature. This suggested that our method is effective at prioritizing novel disease-related microbes and may offer further insight into disease pathogenesis.

Neurocognitive Impairment After Hematopoietic Stem Cell Transplant for Hematologic Malignancies: Phenotype and Mechanisms

Hematopoietic stem cell transplant (HSCT) plays a central role in the treatment of hematologic cancers. With the increasing survival of patients after HSCT, survivorship issues experienced by this population have become an important outcome. Cognitive impairment is an established sequela of HSCT, with studies to date establishing its presence, associated risk factors, and clinical phenotype. There are multiple potential contributors to cognitive impairment after HSCT. Efforts are ongoing to further characterize its clinical phenotype, associated biomarkers, and biologic underpinnings. A fundamental knowledge of post-HSCT cognitive impairment is of value for all clinicians who interface with this population, and further academic efforts are needed to more fully understand the impact of this cancer treatment on brain health. IMPLICATIONS FOR PRACTICE: As survival outcomes after hematopoietic stem cell transplant (HSCT) improve, an awareness of the post-treatment challenges faced by this population has become central to its care. HSCT can have a sustained and broad impact on brain health, causing cognitive dysfunction, fatigue, disturbed mood, and sleep. In affected patients, autonomy, return to work, relationships, and quality of life may all be affected. A fundamental fluency in this area is important for clinicians interfacing with HSCT survivors, facilitating the identification and management of cognitive dysfunction and concurrent symptom clusters, and stimulating interest in these sequelae as areas for future clinical research.

Abnormal composition of microbiota in the gut and skin of imiquimod-treated mice

Psoriasis is a chronic, inflammatory skin disease. Although the precise etiology of psoriasis remains unclear, gut-microbiota axis might play a role in the pathogenesis of the disease. Here we investigated whether the composition of microbiota in the intestine and skin is altered in the imiquimod (IMQ)-treated mouse model of psoriasis. Topical application of IMQ to back skin caused significant changes in the composition of microbiota in the intestine and skin of IMQ-treated mice compared to control mice. The LEfSe algorithm identified the species Staphylococcus lentus as potential skin microbial marker for IMQ group. Furthermore, there were correlations for several microbes between the intestine and skin, suggesting a role of skin-gut-microbiota in IMQ-treated mice. Levels of succinic acid and lactic acid in feces from IMQ-treated mice were significantly higher than control mice. Moreover, the predictive functional analysis of the microbiota in the intestine and skin showed that IMQ caused alterations in several KEGG pathways. In conclusion, the current data indicated that topical application with IMQ to skin alters the composition of the microbiota in the gut and skin of host. It is likely that skin-gut microbiota axis plays a role in pathogenesis of psoriasis.

Characterization of oral and cloacal microbial communities in cold-stunned Kemp's ridley sea turtles (Lepidochelys kempii) during the time course of rehabilitation

Microbial communities of animals play a role in health and disease, including immunocompromised conditions. In the northeastern United States, cold-stunning events often cause endangered Kemp's ridley turtles (Lepidochelys kempii) to become stranded on beaches in autumn. These sea turtles are admitted to rehabilitation facilities when rescued alive and are presumed immunocompromised secondary to hypothermia. To better understand the role that microbes play in the health of cold-stunned sea turtles, we characterized the oral and cloacal microbiome from Kemp's ridley turtles at multiple timepoints during rehabilitation, from admission to pre-release, by using Illumina sequencing to analyze the 16S rRNA gene. Microbial communities were distinct between body sites and among turtles that survived and those that died. We found that clinical parameters such as presence of pneumonia or values for various blood analytes did not correlate with oral or cloacal microbial community composition. We also investigated the effect of antibiotics on the microbiome during rehabilitation and prior to release and found that the type of antibiotic altered the microbial community composition, yet overall taxonomic diversity remained the same. The microbiome of cold-stunned Kemp's ridley turtles gradually changed through the course of rehabilitation with environment, antibiotics, and disease status all playing a role in those changes and ultimately the release status of the turtles.

The oralome and its dysbiosis: New insights into oral microbiome-host interactions

The oralome is the summary of the dynamic interactions orchestrated between the ecological community of oral microorganisms (comprised of up to approximately 1000 species of bacteria, fungi, viruses, archaea and protozoa - the oral microbiome) that live in the oral cavity and the host. These microorganisms form a complex ecosystem that thrive in the dynamic oral environment in a symbiotic relationship with the human host. However, the microbial composition is significantly affected by interspecies and host-microbial interactions, which in turn, can impact the health and disease status of the host. In this review, we discuss the composition of the oralome and inter-species and host-microbial interactions that take place in the oral cavity and examine how these interactions change from healthy (eubiotic) to disease (dysbiotic) states. We further discuss the dysbiotic signatures associated with periodontitis and caries and their sequalae, (e.g., tooth/bone loss and pulpitis), and the systemic diseases associated with these oral diseases, such as infective endocarditis, atherosclerosis, diabetes, Alzheimer's disease and head and neck/oral cancer. We then discuss current computational techniques to assess dysbiotic oral microbiome changes. Lastly, we discuss current and novel techniques for modulation of the dysbiotic oral microbiome that may help in disease prevention and treatment, including standard hygiene methods, prebiotics, probiotics, use of nano-sized drug delivery systems (nano-DDS), extracellular polymeric matrix (EPM) disruption, and host response modulators.

Fecal microbiota transplants: A review of emerging clinical data on applications, efficacy, and risks (2015-2020)

As the importance of the gut microbiota in health and disease is a subject of growing interest, fecal microbiota transplantation (FMT) was suggested as an attractive therapeutic strategy to restore homeostasis of the gut microbiota, thereby treating diseases that were associated with alteration of the gut microbiota. FMT involves the administration of fresh, frozen, or dried fecal microorganisms from the gut of a healthy donor into the intestinal tract of a patient. This rediscovery of the potential benefits of an ancient practice was accompanied by a rapid progression of our understanding of the roles and mechanisms of gut microbes in the pathogenesis of disease. With a growing number of diseases being associated with dysbiosis or the alteration of gut microbiota, FMT was suggested as an attractive therapeutic strategy to "reset the gut" and initiate clinical resolutions or remissions. The number of FMT clinical trials is increasing worldwide, but no trials are registered in the Gulf region; this suggested the need for raising awareness of the latest studies on FMT. This review presented the emergent preclinical and clinical data to give an overview of the potential clinical applications, the benefits, and inconveniences that were worth considering for eventual future testing of fecal transplants in Qatar and the Middle East. This study highlighted the diversity of methods tested and commented on the variables that can affect the assessment of the effectiveness of FMT in specific diseases. The risks associated with FMT and the threat of antimicrobial resistance for this therapeutic approach were reviewed. From gastrointestinal diseases to neurodevelopmental disorders, understanding the roles of the gut microbiota in health and disease should be at the heart of developing novel, standardized, yet personalized, methods for this ancient therapeutic approach.

SARS-CoV-2 and immune-microbiome interactions: Lessons from respiratory viral infections

By the beginning of 2020, infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had rapidly evolved into an emergent worldwide pandemic, an outbreak whose unprecedented consequences highlighted many existing flaws within public healthcare systems across the world. While coronavirus disease 2019 (COVID-19) is bestowed with a broad spectrum of clinical manifestations, involving the vital organs, the respiratory system transpires as the main route of entry for SARS-CoV-2, with the lungs being its primary target. Of those infected, up to 20% require hospitalization on account of severity, while the majority of patients are either asymptomatic or exhibit mild symptoms. Exacerbation in the disease severity and complications of COVID-19 infection have been associated with multiple comorbidities, including hypertension, diabetes mellitus, cardiovascular disorders, cancer, and chronic lung disease. Interestingly, a recent body of evidence indicated the pulmonary and gut microbiomes as potential modulators for altering the course of COVID-19, potentially via the microbiome-immune system axis. While the relative concordance between microbes and immunity has yet to be fully elucidated with regards to COVID-19, we present an overview of our current understanding of COVID-19-microbiome-immune cross talk and discuss the potential contributions of microbiome-related immunity to SARS-CoV-2 pathogenesis and COVID-19 disease progression.

Targeting the gut microbiome: A brief report on the awareness, practice, and readiness to engage in clinical interventions in Qatar

BACKGROUND

There has been a growing global interest in the role of gut microbiota in the pathogenesis of diseases and the potentials of targeting the microbiome in clinical interventions. Very few clinical studies in Qatar focused on gut microbiome. This study aimed to assess the awareness of healthcare professionals, scientists, and the general public on the role of gut microbiota in health and diseases and, more specifically, in disorders of the gut-brain axis such as neurodevelopmental disorders (NDDs) or gastrointestinal (GI) disorders. It also aimed to evaluate the readiness of the population to engage in clinical trials involving dietary interventions or fecal transplants.

METHODS

A total of 156 participants were recruited to answer questionnaires-from healthcare professionals and scientists (HSs; n = 44) and the general public (n = 112). Participants from the general public self-reported their diagnosis of NDDs-autism or attention deficit hyperactivity disorder (n = 36)-or GI diseases or disorders (n = 18) or as having none of them (n = 58). Two questionnaires for HSs and for the general public were distributed, and basic descriptive and statistical analyses were conducted using the Fisher's exact test.

RESULTS

Among the participating HSs, 95% admitted that they had minimum to no knowledge on the role of gut microbes in health and diseases, and only 15.9% felt that their peers were knowledgeable about it. Nevertheless, 97.7% of HSs thought that gut microbiota should be considered when devising treatment plans as 79.1% believed that gut dysbiosis is involved in the pathogenesis of diseases. For the general public, 54% stated that they have read about studies on the potential benefits of microbes in the prevention, treatment, and management of diseases, with a higher proportion of them belonging to the GI group (p = 0.0523). The GI group was also more aware of the existence of the use of fecal transplants for treating their condition (p = 0.01935). Awareness was also reflected in participants' attempts to engage in dietary changes, as 40% tried a dietary intervention, which has noticeably changed their or their child's symptoms. This study reported a highly significant association between being exposed to multiple antibiotic courses before three years of age and being part of the NDD group (p = 0.0003). Public readiness to engage in interventions that target the gut microbiome, such as intensive dietary interventions or even fecal transplants, was perceived by HSs to be lower than what was stated by the public, with 87.96% of public being ready to engage in intensive dietary interventions and 66.98% in fecal transplants.

CONCLUSION

The study revealed that the role of gut microbes in health and diseases, and especially through the gut-brain axis, is still unclear in both the scientific community and general public. While acknowledging the importance of gut microbes, the lack of information regarding the link between lifestyle and gut microbes is considered to hold the public in the precontemplation/contemplation stages of the transtheoretical model of behavioral change. An interdisciplinary approach to new knowledge produced by microbiome studies is needed to run awareness campaigns and continue professional development activities on the benefits of lifestyle-based modulation of gut microbiome, thus engaging the general public in lifestyle changes and facilitating clinical research in human microbiome investigations in Qatar.

The Diversity of the Intestinal Flora Disturbed After Feeding Intolerance Recovery in Preterm Twins

Background: Feeding intolerance (FI) is a common condition in premature infants that results in growth retardation and even necrotizing enterocolitis. The gut microbiome is linked to FI occurrence; however, the outcome after FI recovery is unclear. Methods: Fecal samples were collected from 11 pairs of premature twins/triplets for 16S rRNA gene sequencing. Initial fecal samples were collected shortly after admission, and then every other week until 7 weeks or discharge. Results: After FI recovery, there was no significant difference in the β-diversity of the intestinal flora between the FI group and the feeding tolerance (FT) group. By contrast, there was a significant difference in the β-diversity. Proteobacteria was the predominant phylum in the microbiome of the FI group, whereas Firmicutes was the predominant phylum in the microbiome of the FT group. The predominant bacteria with LDA >4 between the two groups at 13-15 days after birth, 19-28 days after birth, and at discharge were different, with the proportions of Bacillus, Clostridium butyricum, and Clostridium being highest in the FT group and Firmicutes, unidentified_Clostridiales, and Proteobacteria being highest in the FI group. Similarly, there were significant differences in the relative abundances of KEGG pathways, such as fatty acid metabolism, DNA repair and recombination proteins, energy metabolism, and amino acid metabolism, between the two groups (P < 0.01). Conclusions: There was a significant difference in diversity of the intestinal flora after feeding intolerance recovery. Feeding intolerance may disturb the succession of the intestinal bacterial community.

Habitat disturbance influences the skin microbiome of a rediscovered neotropical-montane frog

BACKGROUND

The skin microbiome serves as a first line defense against pathogens in vertebrates. In amphibians, it has the potential to protect against the chytrid fungus Batrachochytrium dendrobatis (Bd), a likely agent of amphibian declines. Alteration of the microbiome associated with unfavorable environmental changes produced by anthropogenic activities may make the host more susceptible to pathogens. Some amphibian species that were thought to be "extinct" have been rediscovered years after population declines in the late 1980s probably due to evolved Bd-resistance and are now threatened by anthropogenic land-use changes. Understanding the effects of habitat disturbance on the host skin microbiome is relevant for understanding the health of these species, along with its susceptibility to pathogens such as Bd. Here, we investigate the influence of habitat alteration on the skin bacterial communities as well as specifically the putative Bd-inhibitory bacterial communities of the montane frog Lithobates vibicarius. This species, after years of not being observed, was rediscovered in small populations inhabiting undisturbed and disturbed landscapes, and with continuous presence of Bd.

RESULTS

We found that cutaneous bacterial communities of tadpoles and adults differed between undisturbed and disturbed habitats. The adults from disturbed habitats exhibited greater community dispersion than those from undisturbed habitats. We observed a higher richness of putative Bd-inhibitory bacterial strains in adults from disturbed habitats than in those from undisturbed habitats, as well as a greater number of these potential protective bacteria with a high relative abundance.

CONCLUSIONS

Our findings support the microbial "Anna Karenina principle", in which disturbance is hypothesized to cause greater microbial dispersion in communities, a so-called dysbiosis, which is a response of animal microbiomes to stress factors that decrease the ability of the host or its microbiome to regulate community composition. On the positive side, the high richness and relative abundance of putative Bd-inhibitory bacteria may indicate the development of a defense mechanism that enhances Bd-protection, attributed to a co-occurrence of more than 30-years of host and pathogen in these disturbed habitats. Our results provide important insight into the influence of human-modified landscapes on the skin microbiome and health implications of Bd-survivor species.

Inferring Disease-Associated Microbes Based on Multi-Data Integration and Network Consistency Projection

Plenty of microbes in our human body play a vital role in the process of cell physiology. In recent years, there is accumulating evidence indicating that microbes are closely related to many complex human diseases. In-depth investigation of disease-associated microbes can contribute to understanding the pathogenesis of diseases and thus provide novel strategies for the treatment, diagnosis, and prevention of diseases. To date, many computational models have been proposed for predicting microbe-disease associations using available similarity networks. However, these similarity networks are not effectively fused. In this study, we proposed a novel computational model based on multi-data integration and network consistency projection for Human Microbe-Disease Associations Prediction (HMDA-Pred), which fuses multiple similarity networks by a linear network fusion method. HMDA-Pred yielded AUC values of 0.9589 and 0.9361 ± 0.0037 in the experiments of leave-one-out cross validation (LOOCV) and 5-fold cross validation (5-fold CV), respectively. Furthermore, in case studies, 10, 8, and 10 out of the top 10 predicted microbes of asthma, colon cancer, and inflammatory bowel disease were confirmed by the literatures, respectively.

Predicting Microbe-Disease Association by Learning Graph Representations and Rule-Based Inference on the Heterogeneous Network

More and more clinical observations have implied that microbes have great effects on human diseases. Understanding the relations between microbes and diseases are of profound significance for disease prevention and therapy. In this paper, we propose a predictive model based on the known microbe-disease associations to discover potential microbe-disease associations through integrating Learning Graph Representations and a modified Scoring mechanism on the Heterogeneous network (called LGRSH). Firstly, the similarity networks for microbe and disease are obtained based on the similarity of Gaussian interaction profile kernel. Then, we construct a heterogeneous network including these two similarity networks and microbe-disease associations' network. After that, the embedding algorithm Node2vec is implemented to learn representations of nodes in the heterogeneous network. Finally, according to these low-dimensional vector representations, we calculate the relevance between each microbe and disease by utilizing a modified rule-based inference method. By comparison with three other methods including LRLSHMDA, KATZHMDA and BiRWHMDA, LGRSH performs better than others. Moreover, in case studies of asthma, Chronic Obstructive Pulmonary Disease and Inflammatory Bowel Disease, there are 8, 8, and 10 out of the top-10 discovered disease-related microbes were validated respectively, demonstrating that LGRSH performs well in predicting potential microbe-disease associations.

Novel Forms of Immunomodulation for Cancer Therapy

In recent years immunotherapy has provided new hope for cancer patients. However, some patients eventually relapse. Immunological responses are thought to underlie the long-term effects of conventional or targeted therapies. Whether this influence emerges from direct effects on cancer cells through immunogenic cell death (ICD) or by modulating the immune environment requires further clarification. ICD-related molecular mechanisms are also shared by cell-intrinsic defense responses that combat foreign intrusions. Indeed, we could potentially mimic and harness these processes to improve cancer immunogenicity. In addition, the microbiome is materializing as a missing factor in the cancer-immune therapy axis. The emerging idea of manipulating the gut microbiota to improve responses to anticancer therapy is becoming increasingly popular, but further clinical authentication is needed.

Novel insights into cardiac regeneration based on differential fetal and adult ovine heart transcriptomic analysis

The adult mammalian cardiomyocyte has a very limited capacity to reenter the cell cycle and advance into mitosis. Therefore, diseases characterized by lost contractile tissue usually evolve into myocardial remodeling and heart failure. Analyzing the cardiac transcriptome at different developmental stages in a large mammal closer to the human than laboratory rodents may serve to disclose positive and negative cardiomyocyte cell cycle regulators potentially targetable to induce cardiac regeneration in the clinical setting. Thus we aimed at characterizing the transcriptomic profiles of the early fetal, late fetal, and adult sheep heart by employing RNA-seq technique and bioinformatic analysis to detect protein-encoding genes that in some of the stages were turned off, turned on, or differentially expressed. Genes earlier proposed as positive cell cycle regulators such as cyclin A, cdk2, meis2, meis3, and PCNA showed higher expression in fetal hearts and lower in AH, as expected. In contrast, genes previously proposed as cell cycle inhibitors, such as meis1, p16, and sav1, tended to be higher in fetal than in adult hearts, suggesting that these genes are involved in cell processes other than cell cycle regulation. Additionally, we described Gene Ontology (GO) enrichment of different sets of genes. GO analysis revealed that differentially expressed gene sets were mainly associated with metabolic and cellular processes. The cell cycle-related genes fam64a, cdc20, and cdk1, and the metabolism-related genes pitx and adipoq showed strong differential expression between fetal and adult hearts, thus being potent candidates to be targeted in human cardiac regeneration strategies.NEW & NOTEWORTHY We characterized the transcriptomic profiles of the fetal and adult sheep hearts employing RNAseq technique and bioinformatic analyses to provide sets of transcripts whose variation in expression level may link them to a specific role in cell cycle regulation. It is important to remark that this study was performed in a large mammal closer to humans than laboratory rodents. In consequence, the results can be used for further translational studies in cardiac regeneration.

Relationship Between the Gastrointestinal Side Effects of an Anti-Hypertensive Medication and Changes in the Serum Lipid Metabolome

An earlier study using a rat model system indicated that the active ingredients contained in the anti-hypertensive medication amlodipine (AMD) appeared to induce various bowel problems, including constipation and inflammation. A probiotic blend was found to alleviate intestinal complications caused by the medicine. To gain more extensive insight into the beneficial effects of the probiotic blend, we investigated the changes in metabolite levels using a non-targeted metabolic approach with ultra-performance liquid chromatography-quadrupole/time-of-fligh (UPLC-q/TOF) mass spectrometry. Analysis of lipid metabolites revealed that rats that received AMD had a different metabolome profile compared with control rats and rats that received AMD plus the probiotic blend. In the AMD-administered group, serum levels of phosphatidylcholines, lysophosphatidylcholines, sphingomyelins, triglycerides with large numbers of double bonds, cholesterols, sterol derivatives, and cholesterol esters (all p < 0.05) were increased compared with those of the control group and the group that received AMD plus the probiotic blend. The AMD-administered group also exhibited significantly decreased levels of triglycerides with small numbers of double bonds (all p < 0.05). These results support our hypothesis that AMD-induced compositional changes in the gut microbiota are a causal factor in inflammation.

Integrating omics for a better understanding of Inflammatory Bowel Disease: a step towards personalized medicine

Background

Inflammatory Bowel Disease (IBD) is a multifactorial chronic disease. Understanding only one aspect of IBD pathogenesis does not reflect the complex nature of IBD nor will it improve its clinical management. Therefore, it is vital to dissect the interactions between the different players in IBD pathogenesis in order to understand the biology of the disease and enhance its clinical outcomes.

Aims

To provide an overview of the available omics data used to assess the potential mechanisms through which various players are contributing to IBD pathogenesis and propose a precision medicine model to fill the current knowledge gap in IBD.

Results

Several studies have reported microbial dysbiosis, immune and metabolic dysregulation in IBD patients, however, this data is not sufficient to create signatures that can differentiate between the disease subtypes or between disease relapse and remission.

Conclusions

We summarized the current knowledge in the application of omics in IBD patients, and we showed that the current knowledge gap in IBD hinders the improvements of clinical decision for treatment as well as the prediction of disease relapse. We propose one way to fill this gap by implementing integrative analysis of various omics datasets generated from one patient at a single time point.

Zebrafish Models of Human Skeletal Disorders: Embryo and Adult Swimming Together

Danio rerio (zebrafish) is an elective model organism for the study of vertebrate development because of its high degree of homology with human genes and organs, including bone. Zebrafish embryos, because of the optical clarity, small size, and fast development, can be easily used in large-scale mutagenesis experiments to isolate mutants with developmental skeletal defects and in high-throughput screenings to find new chemical compounds for the ability to revert the pathological phenotype. On the other hand, the adult zebrafish represents another powerful resource for pathogenic and therapeutic studies about adult human bone diseases. In fish, some characteristics such as bone turnover, reparation, and remodeling of the adult bone tissue cannot be found at the embryonic stage. Several pathological models have been established in adult zebrafish such as bone injury models, osteoporosis, and genetic diseases such as osteogenesis imperfecta. Given the growing interest for metabolic diseases and their complications, adult zebrafish models of type 2 diabetes and obesity have been recently generated and analyzed for bone complications using scales as model system. Interestingly, an osteoporosis-like phenotype has been found to be associated with metabolic alterations suggesting that bone complications share the same mechanisms in humans and fish. Embryo and adult represent powerful resources in rapid development to study bone physiology and pathology from different points of view.

Culture-independent studies on bacterial dysbiosis in oral and oropharyngeal squamous cell carcinoma: A systematic review

Imbalance within the resident bacterial community (dysbiosis), rather than the presence and activity of a single organism, has been proposed to be associated with, and to influence, the development and progression of various diseases; however, the existence and significance of dysbiosis in oral/oropharyngeal cancer is yet to be clearly established. A systematic search (conducted on 25/01/2018 and updated on 25/05/2018) was performed on three databases (Pubmed, Web of Science & Scopus) to identify studies employing culture-independent methods which investigated the bacterial community in oral/oropharyngeal cancer patients compared to control subjects. Of the 1546 texts screened, only fifteen publications met the pre-determined selection criteria. Data extracted from 731 cases and 809 controls overall, could not identify consistent enrichment of any particular taxon in oral/oropharyngeal cancers, although common taxa could be identified between studies. Six studies reported the enrichment of Fusobacteria in cancer at different taxonomic levels whereas four studies reported an increase in Parvimonas. Changes in microbial diversity remained inconclusive, with four studies showing a higher diversity in controls, three studies showing a higher diversity in tumors and three additional studies showing no difference between tumors and controls. Even though most studies identified a component of dysbiosis in oral/oropharyngeal cancer, methodological and analytical variations prevented a standardized summary, which highlights the necessity for studies of superior quality and magnitude employing standardized methodology and reporting. Indeed an holistic metagenomic approach is likely to be more meaningful, as is understanding of the overall metabolome, rather than a mere enumeration of the organisms present.

In Vivo Detection and Absolute Quantification of a Secreted Bacterial Factor from Skin Using Molecularly Imprinted Polymers in a Surface Plasmon Resonance Biosensor for Improved Diagnostic Abilities

In this study, a surface plasmon resonance (SPR) biosensor was developed for the detection and quantification of a secreted bacterial factor (RoxP) from skin. A molecular imprinting method was used for the preparation of sensor chips and five different monomer-cross-linker compositions were evaluated for sensitivity, selectivity, affinity, and kinetic measurements. The most promising molecularly imprinted polymer (MIP) was characterized by using scanning electron microscopy, atomic force microscopy, and cyclic voltammetry. Limit of detection (LOD) value was calculated as 0.23 nM with an affinity constant of 3.3 × 10^-9 M for the promising MIP. Besides being highly sensitive, the developed system was also very selective for the template protein RoxP, proven by the calculated selectivity coefficients. Finally, absolute concentrations of RoxP in several skin swabs were analyzed by using the developed MIP-SPR biosensor and compared to a competitive ELISA. Consequently, the developed system offers a very efficient tool for the detection and quantification of RoxP as an early indicator for some oxidative skin diseases especially when they are present in low-abundance levels (e.g., skin samples).

Mixed Viral-Bacterial Infections and Their Effects on Gut Microbiota and Clinical Illnesses in Children

Acute gastroenteritis remains a major cause of morbidity and mortality among young children worldwide. It accounts for approximately 1.34 million deaths annually in children younger than five years. Infection can be caused by viral, bacterial and/or parasitic microorganisms. Dysbiosis due to such infections could dramatically affect disease prognosis as well as development of chronic illness. The aim of this study was to analyze gut microbiome and clinical outcomes in young children suffering from viral or mixed viral-bacterial infection. We evaluated gut microbiota composition in children suffering from viral or mixed viral-bacterial infection with two major viruses rotavirus (RV) and norovirus (NoV) and two pathogenic bacteria [Enteroaggregative E. coli (EAEC), and Enteropathogenic E. coli (EPEC)]. We sequenced 16S ribosomal RNA (V4 region) genes using Illumina MiSeq in 70 hospitalized children suffering from gastroenteric infections plus nine healthy controls. The study summarized Operational Taxonomic Unit (OTU) abundances with the Bray-Curtis index and performed a non-metric multidimensional scaling analysis to visualize microbiome similarities. We used a permutational multivariate analyses of variance to test the significance of group differences. We also analyzed the correlation between microbiome changes and clinical outcomes. Our data demonstrated a significant increase in the severity score in children with viral-bacterial mixed infections compared to those with virus infections alone. Statistical analysis by overall relative abundance denoted lesser proportions of Bacteroides in the infected children, whereas Bifidobacteriaceae richness was more prominent in the bacterial-viral mixed infections. Pairwise differences of gut microbiota were significantly higher in RV + EAEC (P = 0.009) and NoV + EAEC (P = 0.009) co-infections, compared to EPEC mixed infection with both, RV (P = 0.045) and NoV (P = 0.188). Shannon diversity index showed considerable more variation in microbiome diversity in children infected with RV cohort compared to NoV cohort. Our results highlight that richness of Bifidobacteriaceae, which acts as probiotics, increased with the severity of the viral-bacterial mixed infections. As expected, significant reduction of relative numbers of Bacteroides was characterized in both RV and NoV infections, with more reduction observed in co-infection pathogenic E. coli. Although mixed infection with EAEC resulted in significant microbiota differences compared to viral infection only or mixed infection with EPEC, the clinical condition of the children were worsened with both pathogenic E.coli co-infections. Further, in comparison with RV cohort, augmented number of differential abundant pathogenic OTUs were peculiarly noticed only with NoV mixed infection.

Feeding intolerance alters the gut microbiota of preterm infants

Feeding intolerance (FI) is a common disease in preterm infants, often causing a delay in individual development. Gut microbiota play an important role in nutrient absorption and metabolism of preterm infants. To date, few studies have focused on the community composition of gut microbiota of preterm infants with feeding intolerance. In this study, we collected fecal samples from 41 preterm infants diagnosed with feeding intolerance and 29 preterm infants without feeding intolerance, at three specific times during the development and prevalence of feeding intolerance (after birth, when feeding intolerance was diagnosed, after feeding intolerance was gone), from different hospitals for 16S rRNA gene sequencing. The gut microbiota community composition of preterm infants diagnosed with feeding intolerance was significantly different from that of preterm infants without feeding intolerance. At the time when feeding intolerance was diagnosed, the relative abundance of Klebsiella in preterm infants with feeding intolerance increased significantly, and was significantly higher than that of the preterm infants without feeding intolerance. After feeding intolerance was cured, the relative abundance of Klebsiella significantly decreased in the infants diagnosed with feeding intolerance, while the relative abundance of Klebsiella in preterm infants without feeding intolerance was not significantly altered during the development and prevalence of feeding intolerance. Furthermore, we verified that Klebsiella was effective in the diagnosis of feeding intolerance (AUC = 1) in preterm infants, suggesting that Klebsiella is a potential diagnostic biomarker for feeding intolerance.

Regulation of Adaptive Thermogenesis and Browning by Prebiotics and Postbiotics

Prebiotics are non-digestible food components able to modify host microbiota toward a healthy profile, concomitantly conferring general beneficial health effects. Numerous research works have provided wide evidence regarding the effects of prebiotics on the protection against different detrimental phenotypes related to cancer, immunity, and features of the metabolic syndrome, among others. Nonetheless, one topic less studied so far, but relevant, relates to the connection between prebiotics and energy metabolism regulation (and the prevention or treatment of obesity), especially by means of their impact on adaptive (non-shivering) thermogenesis in brown adipose tissue (BAT) and in the browning of white adipose tissue (WAT). In the present review, a key link between prebiotics and the regulation of adaptive thermogenesis and lipid metabolism (in both BAT and WAT) is proposed, thus connecting prebiotic consumption, microbiota selection (especially gut microbiota), production of microbiota metabolites, and the regulation of energy metabolism in adipose tissue, particularly regarding the effects on browning promotion, or on BAT recruitment. In this sense, various types of prebiotics, from complex carbohydrates to phenolic compounds, have been studied regarding their microbiota-modulating role and their effects on crucial tissues for energy metabolism, including adipose tissue. Other studies have analyzed the effects of the main metabolites produced by selected microbiota on the improvement of metabolism, such as short chain fatty acids and secondary bile acids. Here, we focus on state-of-the-art evidence to demonstrate that different prebiotics can have an impact on energy metabolism and the prevention or treatment of obesity (and its associated disorders) by inducing or regulating adaptive thermogenic capacity in WAT and/or BAT, through modulation of microbiota and their derived metabolites.

Association of human papillomavirus and bacterial vaginosis with increased risk of high-grade squamous intraepithelial cervical lesions

OBJECTIVE

To assess the rates of co-infections between human papillomavirus (HPV) and 13 key markers of bacterial vaginosis in cervical samples by multiplex polymerase chain reaction in a population with a high rate of abnormal cytology and a positive HPV test.

METHODS

The study included a total of 213 women aged 18-72 years screened using Papanicolaou smears for determining cervical abnormalities and for HPV and bacterial vaginosis by single-target and multiplex polymerase chain reaction.

RESULTS

A total of 83 (39%) women were negative for intraepithelial lesion or malignancy cytology and 130 (61%) had abnormal cytology. HPV-DNA prevalence was 69.9% and bacterial vaginosis was 72.7 %. Co-infections between bacterial vaginosis with HPV-DNA and high-risk HPV were associated with an increased risk for squamous intraepithelial lesions of low-grade cytology and high-grade squamous intraepithelial lesions plus cervical cancer. The most frequent bacterial vaginosis agent was Gardnerella vaginalis (33.8%), and co-infection with HPV-DNA and high-risk HPV increased the risk for squamous intraepithelial lesions of low grade cytology and high-grade squamous intraepithelial lesions plus cervical cancer. Co-infection between Megasphaera type I and high-risk HPV increased the risk for high-grade squamous intraepithelial lesions plus cervical cancer.

CONCLUSIONS

Our results reinforce the hypothesis that some bacterial vaginosis agents may play a role as co-factors in HPV-mediated cervical carcinogenesis, at least in some populations.

Comparative Microbiome Signatures and Short-Chain Fatty Acids in Mouse, Rat, Non-human Primate, and Human Feces

Gut microbiome plays a fundamental role in several aspects of host health and diseases. There has been an exponential surge in the use of animal models that can mimic different phenotypes of the human intestinal ecosystem. However, data on host species-specific signatures of gut microbiome and its metabolites like short-chain fatty acids (SCFAs; i.e., acetate, propionate, and butyrate) and lactate in these models and their similarities/differences from humans remain limited, due to high variability in protocols and analyses. Here, we analyze the fecal microbiota composition and the fecal levels of SCFAs and lactate in three of the most-widely used animal models, i.e., mice, rats, and non-human primates (NHPs) and compare them with human subjects, using data generated on a single platform with same protocols. The data show several species-specific similarities and differences in the gut microbiota and fecal organic acids between these species groups. Based on β-diversity, the gut microbiota in humans seems to be closer to NHPs than to mice and rats; however, among rodents, mice microbiota appears to be closer to humans than rats. The phylum-level analyses demonstrate higher Firmicutes-Bacteroidetes ratio in humans and NHPs vs. mice and rats. Human microbiota is dominated by Bacteroides followed by Ruminococcaceae and Clostridiales. Mouse gut is predominated by members of the family S24-7 followed by those from the order Clostridiales, whereas rats and NHPs have higher abundance of Prevotella compared with mice and humans. Also, fecal levels of lactate are higher in mice and rats vs. NHPs and humans, while acetate is highest in human feces. These data of host species-specific gut microbiota signatures in some of the most widely used animal models in context to the human microbiota might reflect disparities in host factors, e.g., diets, genetic origin, gender and age, and hence call for prospective studies investigating the features of gut microbiome in such animal models by controlling for these host elements.

Male Partners of Infertile Couples With Seminal Positivity for Markers of Bacterial Vaginosis Have Impaired Fertility

To access the possibility that key markers of bacterial vaginosis (KM-BV) could affect seminal parameters and thus fertility a prospective cohort study was designed (a) to develop rapid and sensitive multiplex polymerase chain reaction (M-PCR) assays to screen 13 key markers of bacterial vaginosis (KM-BV) in semen specimens, (b) to determine the prevalence of KM-BV in semen from randomized male partners of couples seeking fertility evaluation. A total of 229 semen samples were included in the study from males who visited the Sperm Analysis Section of Brazil between October 2015 and March 2016. Eligible men were 18 years or older and had a semen analysis due fertility evaluation (after failing to conceive with their partner after 1 year of unprotected intercourse). Basic seminal parameters were analyzed, and KM-BV was detected by M-PCR assays. M-PCR assays clearly distinguished 13 KM-BV in 146 semen samples (63.8%), mainly Gardnerella vaginalis (50.7%). Some important associations occurred between the presence of KM-BV in semen and changes in seminal parameters. KM-BV is commonly present in the semen of males seeking fertility evaluation and could potentially play significant roles in male subfertility and/or infertility.

Prediction of Microbe-Disease Associations by Graph Regularized Non-Negative Matrix Factorization

More and more evidence shows that microbes play crucial roles in human health and disease. The exploration of the relationship between microbes and diseases will help people to better understand the underlying pathogenesis and have important implications for disease diagnosis and prevention. However, the known associations between microbes and diseases are very less. We proposed a new method called non-negative matrix factorization microbe-disease associations (NMFMDA), which used Gaussian interaction profile kernel similarity measure, to calculate microbial similarity and disease similarity, and applied a logistic function to regulate disease similarity. And, based on the known microbe-disease associations, a graph-regularized non-negative matrix factorization model was utilized to simultaneously identify potential microbe-disease associations. Moreover, fivefold cross-validation was utilized to evaluate the performance of our method. It reached the reliable area under receiver operating characteristic curve (AUC) of 0.8891, higher than other state-of-the-art methods. Finally, the case studies on three complex human diseases (i.e., asthma, inflammatory bowel disease, and colon cancer) demonstrated the good performance of our method. In summary, our method can be considered as an effective computational model for predicting potential disease-microbe associations.

Culture-based analysis of Pristionchus-associated microbiota from beetles and figs for studying nematode-bacterial interactions

The interplay with bacteria is of crucial importance for the interaction of multicellular organisms with their environments. Studying the associations between the nematode model organisms Caenorhabditis elegans and Pristionchus pacificus with bacteria constitutes a powerful system to investigate these interactions at a mechanistic level. P. pacificus is found in association with scarab beetles in nature and recent studies revealed the succession and dynamics of this nematode and its microbiome during the decomposition of one particular host species, the rhinoceros beetle Oryctes borbonicus on La Réunion Island. However, these studies were performed using culture-free methods, with no attempt made to establish bacterial cultures from the beetle-nematode ecosystem and to investigate the effects of these microbes on life history traits in P. pacificus. Here, we establish and characterize a collection of 136 bacterial strains that have been isolated from scarab beetles and figs, another Pristionchus-associated environment, as a resource for studying their effect on various nematode traits. Classification based on 16S sequencing identified members of four bacterial phyla with the class of Gammaproteobacteria representing the majority with 81 strains. Assessing the survival of P. pacificus on individual bacteria allowed us to propose candidate groups of pathogens such as Bacillaceae, Actinobacteria, and Serratia. In combination with chemoattraction data, it was revealed that P. pacificus is able to recognize and avoid certain groups of pathogens, but not others. Our collection of bacterial strains forms a natural resource to study the effects of bacterial diet on development and other traits. Furthermore, these results will form the basis of future studies to elucidate the molecular mechanisms of recognition and pathogenicity.

From homeostasis to pathology: decrypting microbe-host symbiotic signals in the intestinal crypt

Metagenomic analysis of the human intestinal microbiome has provided a wealth of information that allowed an exceptionally detailed description of its microbial content and physiological potential. It also set the basis for studies allowing correlation of alterations in the balance of this microbiota and the occurrence of a certain number of emerging diseases, such as inflammatory bowel diseases, obesity and diabetes, and possibly colorectal cancer. The time has come to give the intestinal microbiota in symbiosis with its host an experimental dimension. This brief review summarizes our attempt at developing a cellular microbiology of the mutualistic symbiosis established between the gut microbiota and the host intestinal surface. Particular attention is paid to the intestinal crypt, due to its role in epithelial regeneration.This article is part of the themed issue 'The new bacteriology'.

Beneficial effects of a probiotic blend on gastrointestinal side effects induced by leflunomide and amlodipine in a rat model

Patients with metabolic disorders frequently suffer from side effects induced by long-term oral medications. The present study using a rat model system indicated that leflunomide (LF) and amlodipine (AMD), the active ingredients contained in the medications for rheumatoid arthritis and hypertension, respectively, appeared to induce various bowel problems including constipation and inflammation. In the small and large intestine, LF increased the expression of tumour necrosis factor (TNF)-α, interleukin (IL)-1β, and IL-6 compared to the null control and AMD increased the expression of both TNF-α and IL-1β, although its effect on IL-6 was only increased in the large intestine. It is noteworthy that the probiotic blend tested was found to alleviate intestinal complications caused by LF and AMD. Analysis of the gut microbiota revealed that AMD induced compositional changes in the gut microbiota. Namely, members of the phylum Bacteroidetes, which constituted only about 0.3% of the microbiota in the null control, made up more than 10% of the total composition in the AMD-administered rats. Interestingly, the probiotic blend was also found to normaliSe the gut microbiota.