Medicine in Microecology最新文献

Gut microbiota has emerged a major player in the pathogenesis of ulcerative colitis (UC). Targeting dysbiotic microbiota with the aim to restore intestinal homoeostasis and alleviate disease is an attractive approach in patients with UC. Results with microbiota targeted therapies including probiotics, prebiotics, and antibiotics have however been inconsistent and lack reproducibility. Faecal Microbiota Transplantation (FMT) is a novel microbiota centered therapy that has shown promise (in both efficacy and safety) with its short term use in UC. FMT appears to have bright prospects for long term management of UC due to its multi-pronged attack on the pathophysiological mechanisms involved in pathogenesis of UC. However, only limited data is available on its long term use in UC. We discuss important unsettled issues concerning use of FMT as a long term therapy. Various attributes related to FMT procedure, namely preparation of fecal slurry, frequency and duration of intervention, acceptability and safety, are analysed. Additionally we also explore the issues concerning patient and donor selection and the impact of habitual diet on results with FMT.

Fecal microbiota transplantation (FMT) has rapidly grown in notoriety and popularity worldwide as a treatment for both recurrent and refractory C. difficile infection (CDI), as well as for a myriad of other indications, with varying levels of evidence to justify its use. At present, FMT use in the U.S. has not received marketing approval from the U.S. Food and Drug Administration (FDA), but is permitted under “enforcement discretion” for CDI not responding to standard therapy. Meanwhile, the rising interest in the gut microbiome throughout mainstream media has paved the way for “do-it-yourself” (DIY) adaptations of the procedure. This access and unregulated use, often outside any clinical supervision, has quickly outpaced the medical community's research and regulatory efforts. While some studies have been able to demonstrate the success of FMT in treating conditions other than CDI—studies on ulcerative colitis have been particularly promising—little is still known about the treatment's mechanism of action or long-term side effects. Likewise, screening of donor stool is in its early stages in terms of protocol standardization. In this paper, we explore the regulatory and ethical concerns that arise from the need to balance access to a nascent but promising innovative treatment with the need for research into its efficacy, risk profile, and long-term impact.

Fecal microbiota transplantation (FMT), as an emerging therapy, can be used to treat microbiota related diseases. Progresses in donor screening, washed microbiota preparation, microbiota delivery routes, clinical administrative strategies, and long-term safety are moving FMT forward. Increasing clinical studies, especially those randomized controlled trials about ulcerative colitis and pilot real-word studies about serious inflammatory bowel disease (IBD), have been conducted. This review presents the latest findings about the efficacy, safety and methodology of FMT in treating IBD.

Tuberculosis continue to be a critical health problem causing death and illness among millions of people yearly and ranked the second leading cause of mortality among the communicable infections in the world. Therefor this work accessed the application of modelling technique to predict the inhibition activity of some prominent compounds which been reported to be efficient against Mycobacterium tuberculosis. To accomplish the purpose of this work, multiple regression and genetic function approximation were adopted to create the model. The established model was swayed with topological descriptors; AATS7s, GATS4v, nHBint3 and RDF90i which have been tested validated. More also, interactions between the compounds and the target ‘‘DNA gyrase’’ was evaluated via docking approach utilizing the PyRx and discovery studio simulated software. Meanwhile, compounds 5, 7, 10, 11, 12, 20, 25, 26, 27 and 28 were revealed to have significant bind affinities of (−6.3 to −16.5 kcal/mol) whereas, compound 12 has the most perceptible binding affinity of −16.5 kcal/mol. This implies that compound 12 could be used as a structural template when the pharmacist or the medicinal chemists aim to design new proposed drugs with more efficient activities.

Microbiota is increasingly being recognized as an important factor in human health. Alterations in the bacterial community structure have been implicated in a wide range of human diseases. Most therapeutic strategies targeting microbiota, such as probiotics, prebiotics and fecal transplantation, aim to modulate the bacterial community. Herein we demonstrate that the cell free bacterial DNAs (cfbDNAs) are extensively observed in human bloodstreams and gradually arise along with growth. Moreover, patients with immune-related diseases, e.g. inflammatory bowel disease (IBD), kawasaki disease (KD) and HIV, own higher amounts of cfbDNAs with lower microbial biodiversity compared with healthy individuals by using real-time PCR measurement and high-throughput 16S rDNA sequences analyses. Further comparisons reveal that 173 genera exhibit preferential abundance in either healthy individuals or patients, providing “molecular phenotypes” of the corresponding diseases in a manner of microbiome, especially in those IBD patients post/pre-therapy. Although the origination and function of these cfbDNAs in human circulating bloodstreams remain unclear, their taxonomic variations offer fingerprints for potential applications in noninvasive and safe pre-diagnosis or prognosis, and provide clues for further understanding of the host-microbiota interactions.

Advances in microbiome researches have led us to the realization that the compositions of bacterial communities of indoor environment is profoundly affected by the function of buildings, and they in turn may bring detrimental effects to the indoor environment and the occupants. These phenomena are common in biological product manufacturing, which might seriously compromise the analytical results. Thus, investigation is warranted for a deeper understanding of the potential impact of the indoor bacterial communities. Among these environments, the biological laboratories stand out because they are relatively clean and yet are highly susceptible to bacterial contaminants. However, few studies have examined the bacterial compositions of biological laboratories. In this study, we assessed the bacterial compositions of samples from the surfaces of various sites across different types of biological laboratories. We have qualitatively assessed these possible bacterial contaminants, and found distinct differences in their bacterial community composition. We also found that the types of laboratories had a larger influence than the sampling sites in shaping the bacterial community, in terms of both structure and richness. On the other hand, the public areas of the different types of laboratories shared very similar sets of bacteria. Tracing the main sources of these bacteria, we identified both environmental and human factors that are important factors in shaping the diversity and dynamics of these possible bacterial contaminations in biological laboratories. These possible bacterial contaminants that we have identified will be helpful for people who aim to eliminate them from samples.

Gut microbiota plays an important role in maintaining a healthy intestine. Escherichia coli (E.coli) is a commensal bacteria colonizes the mucous membranes of the gut, intestine, and urinary tract. However, these strains incorporate genetic elements to become pathotype and affected in hundreds of millions of people worldwide. Seven pathotypes have been categorized such as Entero-Hemorrhagic E.coli (EHEC), Entero-Aggregative E.coli (EAEC), Entero-Pathogenic E.coli (EPEC), Entero-Toxigenic E.coli (ETEC), Diffusely Adherent E.coli (DAEC), Entero-Invasive E.coli (EIEC) and Adherent-Invasive E.coli (AIEC), and each pathotype possess distinct virulence mechanism and virulence factors to disrupt the host intestinal epithelial cells that cause diarrhea and other intestinal inflammation. This review highlights the various fimbrial and afimbrial adherence mechanisms of E.coli pathovars, and how it competes with commensal bacteria in achieving pathogenicity in the host. Such adherence mechanisms are mediated by virulence proteins that have a significant impact on the outcome of intestinal inflammation.

The ongoing global pandemic of COVID-19 disease, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), mainly infect lung epithelial cells, and spread mainly through respiratory droplets. However, recent studies showed potential intestinal infection of SARS-CoV-2, implicated the possibility that the intestinal infection of SARS-CoV-2 may correlate with the dysbiosis of gut microbiota, as well as the severity of COVID-19 symptoms. Here, we investigated the alteration of the gut microbiota in COVID-19 patients, as well as analyzed the correlation between the altered microbes and the levels of intestinal inflammatory cytokine IL-18, which was reported to be elevated in the serum of in COVID-19 patients. Comparing with healthy controls or seasonal flu patients, the gut microbiota showed significantly reduced diversity, with increased opportunistic pathogens in COVID-19 patients. Also, IL-18 level was higher in the fecal samples of COVID-19 patients than in those of either healthy controls or seasonal flu patients. Moreover, the IL-18 levels were even higher in the fecal supernatants obtained from COVID-19 patients that tested positive for SARS-CoV-2 RNA than those that tested negative in fecal samples. These results indicate that changes in gut microbiota composition might contribute to SARS-CoV-2-induced production of inflammatory cytokines in the intestine and potentially also to the onset of a cytokine storm.

Accumulated evidence has shown that commensal microorganisms play key roles in human physiology and diseases. Dysbiosis of the human-associated microbial communities, often referred to as the human microbiome, has been associated with many diseases. Applying supervised classification analysis to the human microbiome data can help us identify subsets of microorganisms that are highly discriminative and hence build prediction models that can accurately classify unlabeled samples. Here, we systematically compare two state-of-the-art ensemble classifiers: Random Forests (RF), eXtreme Gradient Boosting decision trees (XGBoost) and two traditional methods: The elastic net (ENET) and Support Vector Machine (SVM) in the classification analysis of 29 benchmark human microbiome datasets. We find that XGBoost outperforms all other methods only in a few benchmark datasets. Overall, the XGBoost, RF and ENET display comparable performance in the remaining benchmark datasets. The training time of XGBoost is much longer than others, partially due to the much larger number of hyperparameters in XGBoost. We also find that the most important features selected by the four classifiers partially overlap. Yet, the difference between their classification performance is almost independent of this overlap.

Psoriasis is a chronic inflammatory skin disease associated with epidermal keratinocyte hyperplasia and epidermal immune cell over-activation. Compositions of both local skin and gut microbiome are linked to modulation of inflammation and disease severity in psoriasis. Owing to the situation that different bacteria may elicit differential immune or inflammatory responses from epidermal immune cells and keratinocytes, and to-date no single pathogen was highlighted to be responsible for psoriasis, disruption of homeostasis (dysbiosis) in the original microbial ecosystems may create a disease-promoting environment, and as a whole may be a primary causal factor. Several studies have provided evidence that the dominant IL-23/IL-17 pathogenesis pathway is regulated by metabolites produced by gut and skin microbiota. This review summarizes the approaches commonly used for functional characterization of the microbiome compositions associated with development of clinical phenotypes of psoriasis. The underlying mechanisms by which microbiota modulate immune cells and keratinocytes are also proposed.