Human Microbiome Journal最新文献

Neurodegenerative diseases are estimated to afflict hundreds of thousands of Americans with vastly more worldwide. The etiologies of amyotrophic lateral sclerosis (ALS) and multiple sclerosis (MS) have yet to be established. Previous studies have suggested an association of these diseases with viruses, bacteria, and eukaryotic microbes, no new therapies have been forthcoming. High-throughput DNA sequencing has enabled the comprehensive analysis of microbial DNA profiles in diseased populations. To date, no amplicon-based next-generation DNA sequencing prokaryotic and eukaryotic community profiling studies have been completed for these diseases. Analysis of peripheral blood samples from control participants as well as ALS and MS participants was used to characterize the hematologic population of microbial DNA. Categorical and multivariate analysis with control for multiple comparisons and aged matched controls revealed differences in microbial DNA contribution in ALS patients compared to others. Notably, sequences that belonging to Ochrophyta were enriched in ALS patient samples. Mechanisms underlying this association, the role of microbial DNA sequences, and the development or progression of ALS may become a fertile subject of inquiry.

The human gastrointestinal tract exists as a complex ecosystem and contains a mycobiome and a microbiome that play central roles in host health, disease and immune system regulation. Here, we reviewed the traditional culture-dependent methods, the culturomics methods and the molecular methods used to study the gut mycobiome and microbiome. With the development of next-generation sequencing techniques, these last two methods have greatly broadened the understanding of the roles of gut bacteria in health and disease. Thus, dysbiosis of the gut microbiota and mycobiota has been found to be associated with some diseases; disruptions to the fungal and bacterial commensal communities influence the immune response and impact disease status.

Background

Advancements in sequencing capabilities have enhanced the study of the human microbiome. There are limited studies focused on the gastro-intestinal (gut) microbiome of infants, particularly the impact of diet between breast-fed (BF) versus formula-fed (FF). It is unclear what effect, if any, early feeding has on short-term or long-term composition and function of the gut microbiome.

Results

Using a shotgun metagenomics approach, differences in the gut microbiome between BF (n = 10) and FF (n = 5) infants were detected. A Jaccard distance principle coordinate analysis was able to cluster BF versus FF infants based on the presence or absence of species identified in their gut microbiome. Thirty-two genera were identified as statistically different in the gut microbiome sequenced between BF and FF infants. Furthermore, the computational workflow identified 371 bacterial genes that were statistically different between the BF and FF cohorts in abundance. Only seven genes were lower in abundance (or absent) in the FF cohort compared to the BF cohort, including CRISPR/Cas9; whereas, the remaining candidates, including autotransporter adhesins, were higher in abundance in the FF cohort compared to BF cohort.

Conclusions

These studies demonstrated that FF infants have, at an early age, a significantly different gut microbiome with potential implications for function of the fecal microbiota. Interactions between the fecal microbiota and host hinted at here have been linked to numerous diseases. Determining whether these non-abundant or more abundant genes have biological consequence related to infant feeding may aid in understanding the adult gut microbiome, and the pathogenesis of obesity.

Celiac disease is a multifactorial autoimmune enteropathy triggered by ingestion of gluten in genetically predisposed individuals. The increase of incidence in celiac disease suggests that additional environmental factors other than gluten may contribute to its onset and development. While intestinal dysbiosis has already been associated with celiac disease, the role that the blood microbiome plays in the loss of tolerance to gluten is unknown. In this study we aimed at evaluating weather celiac patients are characterized by alterations in the blood microbiome and how these changes may relate to the intestinal microbiome composition and, ultimately, to the loss of tolerance to gluten. Our data highlight alterations in the blood microbiome composition and taxonomic diversity in celiac patients as compared to healthy subjects. Although preliminary, these findings suggest that changes in the blood microbiome may contribute to the pathogenesis of celiac disease and open the possibility of new therapeutic and diagnostic tools for celiac patients.

In the last decades, studies have revealed multiple and strong correlations between the host and its commensal microbiota consisting of bacteria, protozoa, fungi and viruses. This associated microbiota can positively or negatively influence the course of a wide range of infections. Here, we review the interactions between the host and its viral microbiota and discuss new paradigms from an evolutionary perspective. The viral adaptation to a microbial environment in a co-evolutionary approach is highlighted, as well as viral cross transmission in the context of the barriers imposed by the indigenous microbiota. In addition to reviewing the host-microbiota-virus relationships, we focus the discussion on microbiota-virus interactions that could be applied to preventive and therapeutic treatments.

The human gastrointestinal tract is home to the most diverse microbial ecosystem in the human body and is made up of bacteria, viruses and eukarya. Collectively known as the gut microbiota, our knowledge of these microbial communities has historically been restricted by the relative limitations of culturing techniques. However, the recent development and utilisation of next-generation sequencing techniques has enhanced our understanding of its structure, diversity and function.

There is emerging evidence that the gut microbiota plays a pivotal role in both health and disease. Perturbations to the structure and function of the gut microbiota are known to be associated with certain disease states. Therefore, manipulating the gut microbiota in an attempt to restore structure and function represents a promising therapeutic strategy. Recently, there has been a surge in clinical and scientific interest in manipulating the gut microbiota using a method called faecal microbiota transplantation. This increase in interest has gathered after it was shown in randomised controlled trials to be highly effective in treating recurrent Clostridium difficile infection.

Despite success in treating recurrent Clostridium difficile, there remain many unknowns about how best to optimise its preparation, regulation, mode of delivery and safety. This review aims to summarise the literature surrounding the current knowledge regarding faecal microbiota transplantation and explore potential future research avenues that aim to enhance the safety, efficacy and utilisation of faecal microbiota transplantation.

Gut microbiota (GM) is associated with metabolism, provides energy-harvesting efficiency and protection against opportunistic pathogens through competitive exclusion to the host. Previous studies highlighted the temporary as well as permanent alteration to GM resulting from different antibiotics treatment. The diverse class of antibiotics may damage the metabolic homeostasis and can alter the level of intestinal metabolites [including amino acids, bile acids (BAs), glucose, short chain fatty acids (SCFAs)] through alteration in abundance of metabolically active bacteria. The antibiotics administration causes the disturbed profile of related microbial metabolites, especially that of BAs, primary and secondary BAs (conjugated or unconjugated BAs). The antibiotics intake causes the reduced bacterial diversity that makes the individuals susceptible towards diseases. To a large extent, we tried to clarify the adverse effects of classes of antibiotics on the GM composition, and the consequent impacts of dysbiosis on the BAs feedback loop between liver and gut, which involves the farnesoid-X-receptor-fibroblast growth factor (FXR-FGF) pathway. The current review discusses the antibiotics-GM-BAs nexus during Clostridium difficile infection (CDI) and the recommended therapy includes faecal microbial transplant (FMT) in countering the exposure of harmful antibiotic and bacteriotherapy as an alternative therapeutic intervention in treating the recurrent CDI.

Bacteria that colonize the vaginal microbiota of women play an important role in health and homeostasis. Disruption of the proportion of bacteria predisposes to dysbiosis like bacterial vaginosis or severe gynecological conditions such as preterm birth, pelvic inflammatory disease and also sexually transmitted diseases. Knowledge about normal and abnormal vaginal microbiota has become a little clearer in recent years. Culture techniques have made it possible to isolate and describe many bacterial species, whereas molecular methods have highlighted the limits of culture by showing that the vagina was a complex ecosystem containing a wide range of non-cultured or difficult-to-identify bacteria. Based on an exhaustive review of the scientific literature, we built the repertoire of all the bacteria found using culture-based and/or independent methods on the human vagina. So, whether they are valid or not, we inventoried 581 bacteria identified in the human vagina distributed into 10 taxa, mainly in the phyla of Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria with 206 distinct genera classified in 96 different families. This repertoire is essential for microbiologists and clinicians and represents the starting point for a Vaginal Microbiome Project such a project aimed to map the human vaginal microbiota, to better understand the dysbioses or infections caused by its imbalance in order to offer more appropriate treatments.

In this research paper we represent a novel synthetic antibacterial phenolic polymer (pAP-DG) containing carboxylic acid group in para position. The study of poly (p-carboxylic acid phenol d-Glucose) as an antibacterial resin was focused on the development of antimicrobial polymers to clean up the water of pathogenic bacteria. The polycondensation reaction was realized between p-carboxy acid phenol (pAP) and d-Glucose (DG) as monomers; using sulfuric acid as homogeneous catalyst.

The obtained polymer was used via fecal coliform (TC), thermotolerant coliforms (CTT) and fecal streptococci (ST) bacteria to evaluate the water quality. The antibacterial activity of the synthesized resin was carried out by the contact method so the capacity of this resin was confirmed. In general, the polymer has a good antimicrobial activity against the microorganisms tested; the resulting polymer was characterized by various spectroscopy methods such as: ¹H NMR, ¹³C NMR, DSC and FTIR and a mechanism has been proposed for this polycondensation reaction.

Antibacterial agents have saved many lives and helped the growth of modern medicine over the past half century. The emergence of drug resistance, jeopardizing the effectiveness of these life-saving treatments. This clearly highlights the urgent need for new and improved antibacterial drugs with a novel target and new molecular structure agent to obviate cross-resistance. This paper reviewed the possible new ways to discover novel antibacterial agents. The most widely studied new bacterial targets for novel drug development are quorum sensor biosynthesis, bacterial virulence factor, bacteria cell division machinery, Bacterial cell wall synthesis, PDF inhibitor, isoprenoid biosynthesis, shikimate synthesis pathway, biofilm synthesis and fatty acid biosynthesis. These new discovery routes have given rise to agents that are in preclinical trials. This review also discusses the alternatives approaches that act bacteria or any approaches that target the host. The most advanced approaches that are on clinical development are phages and other approaches that are on preclinical development are antimicrobial peptides. These alternatives ways may use as adjunctive therapies, which suggest that conventional antibacterial agents are still essential.