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Bibliography on: Microbiome

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ESP: PubMed Auto Bibliography 06 Dec 2019 at 01:46 Created: 

Microbiome

It has long been known that every multicellular organism coexists with large prokaryotic ecosystems — microbiomes — that completely cover its surfaces, external and internal. Recent studies have shown that these associated microbiomes are not mere contamination, but instead have profound effects upon the function and fitness of the multicellular organism. We now know that all MCEs are actually functional composites, holobionts, composed of more prokaryotic cells than eukaryotic cells and expressing more prokaryotic genes than eukaryotic genes. A full understanding of the biology of "individual" eukaryotes will now depend on an understanding of their associated microbiomes.

Created with PubMed® Query: microbiome[tiab] NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2019-12-05

Kuwayama H, T Higashinakagawa (2019)

The Life Cycle of Dictyostelium discoideum Is Accelerated via MAP Kinase Cascade by a Culture Extract Produced by a Synthetic Microbial Consortium.

Journal of molecular microbiology and biotechnology pii:000504442 [Epub ahead of print].

A cellular slime mold, Dictyostelium discoideum, is an amoeboid organism that has a unique life cycle consisting of distinctly separated vegetative and developmental phases. Thus, this organism presents a rare opportunity in which to examine the effects of bioactive substances on separate cellular activities. In this research, we investigated the effect of a culture extract, termed EMXG, produced by a synthetic microbial consortium. EMXG promoted proliferative response of amoeba cells. It further accelerated the developmental phase, leading to the preferred fruiting body formation from fewer cells. Furthermore, EMXG modulated biological rhythm of this organism, that is, interval of oscillation of cAMP level observed in suspension starvation was significantly shortened. Concomitantly, the level of ERKB, a MAP kinase, was found to oscillate in a similar fashion to that of cAMP. Additionally, ErkB-deficient mutant amoeboid cells did not respond to proliferative stimulation by EMXG. These lines of evidence point to a likelihood that MAP kinase cascade is involved and further that ErkB could be the molecular target of EMXG.

RevDate: 2019-12-05

Jaggar M, Rea K, Spicak S, et al (2019)

You've Got Male: Sex and the Microbiota-Gut Brain Axis Across the Lifespan.

Frontiers in neuroendocrinology pii:S0091-3022(18)30129-8 [Epub ahead of print].

Sex is a critical factor in the diagnosis and development of a number of mental health disorders including autism, schizophrenia, depression, anxiety, Parkinson's disease, multiple sclerosis, anorexia nervosa and others; likely due to differences in sex steroid hormones and genetics. Recent evidence suggests that sex can also influence the complexity and diversity of microbes that we harbour in our gut; and reciprocally that our gut microbes can directly and indirectly influence sex steroid hormones and central gene activation. There is a growing emphasis on the role of gastrointestinal microbiota in the maintenance of mental health and their role in the pathogenesis of disease. In this review, we introduce mechanisms by which gastrointestinal microbiota are thought to mediate positive health benefits along the gut-brain axis, we report how they may be modulated by sex, the role they play in sex steroid hormone regulation, and their sex-specific effects in various disorders relating to mental health.

RevDate: 2019-12-05

Tan Z, Luo L, Wang X, et al (2019)

Characterization of the cecal microbiome composition of Wenchang chickens before and after fattening.

PloS one, 14(12):e0225692 pii:PONE-D-19-16262.

The cecum of poultry harbors a complex and dynamic microbial community which plays important roles in preventing pathogen colonization, detoxifying harmful substances, nutrient processing, and harvesting of the ingestion. Understanding and optimizing microbial communities could help improve agricultural productivity. In this study, we analyzed the composition and function of cecal microbiota of Wenchang chicken (a native breed of Bantam) before and after fattening, using high throughput sequencing technology. High-throughput sequencing of the 16S rRNA genes V3-V4 hypervariable regions was used to characterize and compare the cecal microbiota of Wenchang chicken before fattening (free-range in hill) and after fattening (cage raising). Sixteen phyla were shared by the 20 samples. Firmicutes and Bacteroidetes were the top two abundant phyla being 80% of the total microbiota. Samples of chickens prior to fattening were more dispersed than those after fattening. Twenty four microbes could be considered as biomarkers and 3 phyla revealed differences by variance analysis which could distinguish the two groups. Cecal microbiota in the before fattening group had higher abundance of functions involved in digestive system and biosynthesis of other secondary metabolites. The composition and function of cecal microbiota in Wenchang chicken before and after fattening under the two feeding modes, free range in hillside and cage raising, were found to be different. These results can be attributed to the differences in feeding modes and growth stages. In-depth study on the functions and interactions of intestinal microbiota can help us in developing strategies for raising Wenchang chickens and provide valuable information for the study of microbiota in the chicken gut.

RevDate: 2019-12-05

Brandler JB, Sweetser S, Khoshbin K, et al (2019)

Colonic Manifestations and Complications Are Relatively Under-Reported in Systemic Sclerosis: A Systematic Review.

The American journal of gastroenterology, 114(12):1847-1856.

OBJECTIVES: Although systemic sclerosis (SSc) is known to affect the gastrointestinal (GI) tract, most of the literature focuses on esophageal, small intestinal, or anorectal manifestations. There have been no reviews focused on large bowel SSc complications in over 30 years. The aim of this study is to perform a systematic review of colonic manifestations and complications of SSc.

METHODS: An experienced librarian conducted a search of databases, including English and Spanish articles. The search used keywords including "systemic sclerosis," "scleroderma," and "colon." A systematic review was performed using Preferred Reporting Items for Systematic Review and Meta-Analyses guidelines. Case reports/series were screened for validity by adapting from criteria published elsewhere.

RESULTS: Of 1,890 articles, 74 met selection criteria. Fifty-nine of the 77 articles were case reports/series. The most common article topics on colonic SSc complications were constipation/dysmotility (15), colonic volvulus (8), inflammatory bowel disease (7), microscopic colitis (6), megacolon (6), and telangiectasia (6). Colonic manifestations constituted 24% of articles on GI complications of SSc. There were a total of 85 cases (84% women, with a median age of onset of colon complication of 52 years). Limited cutaneous SSc phenotype (65.6%) was more common than diffuse (26.2%). Patients frequently had poor outcomes with high mortality related to colonic complications (27%). Recent studies explore contemporary topics such as the microbiome in SSc and prucalopride for chronic constipation in SSc.

DISCUSSION: Colonic complications comprise a large proportion of the published reports on GI symptoms afflicting patients with SSc and require raised diagnostic suspicion and deliberate action to avoid potentially serious complications including death.

RevDate: 2019-12-05

Jung ES, Park JI, Park H, et al (2019)

Seven-day Green Tea Supplementation Revamps Gut Microbiome and Caecum/Skin Metabolome in Mice from Stress.

Scientific reports, 9(1):18418 pii:10.1038/s41598-019-54808-5.

Green tea supplementation has beneficial health effects. However, its underlying mechanisms, such as effects on modulating the intestinal microbiome and endogenous metabolome, particularly following short-term supplementation, are largely unclear. We conducted an integrative metabolomics study to evaluate the effects of short-term (7-day) supplementation of green tea extract (GTE) or its components, epigallocatechin gallate, caffeine, and theanine, on the caecum microbiota and caecum/skin metabolome in mice. Further, we established an integrative metabolome-microbiome model for correlating gut and skin findings. The effects of short-term supplementation with dietary compounds were evaluated with respect to UV stress response, with GTE showing the most remarkable effects. Biplot analysis revealed that Bifidobacteria and Lactobacillus spp. were considerably influenced by short-term GTE supplementation, while Clostridium butyricum was significantly increased by UV stress without supplementation. GTE supplementation helped the skin metabolome defend against UV stress. Interestingly, a significant positive correlation was observed between caecum bacteria (Bifidobacteria, Lactobacillus spp.) and metabolites including skin barrier function-related skin metabolites, caecal fatty acids, and caecal amino acids. Overall, 7-day GTE supplementation was sufficient to alter the gut microbiota and endogenous caecum/skin metabolome, with positive effects on UV stress response, providing insight into the mechanism of the prebiotic effects of GTE supplementation.

RevDate: 2019-12-05

Alesa DI, Alshamrani HM, Alzahrani YA, et al (2019)

The role of gut microbiome in the pathogenesis of psoriasis and the therapeutic effects of probiotics.

Journal of family medicine and primary care, 8(11):3496-3503 pii:JFMPC-8-3496.

The adult intestine hosts a huge number of diverse bacterial species, collectively referred to as the microbiome, that reside mainly in the lower gut, where they maintain a symbiotic relationship with their host. Recent research points to a central role of the microbiome in many biological processes. These microbial communities are influenced by multiple environmental and dietary factors and can modulate immune responses. In addition to local effects on the gastrointestinal tract, the microbiota is associated with effects on other organs and tissues, such as the skin. Indeed, an altered microbiome has been associated with skin disorders in several instances. Thus, in this review, we describe the recent advances regarding the interplay between gut microbiota and the skin. We explore how this potential link affects skin homeostasis and its influence on modulating the cutaneous immune response, focusing on psoriasis disorder. Finally, we discuss how to take advantage of this interplay to manage this disorder, particularly through probiotics administration. In the gastrointestinal tract, the microbiome has been proven to be important in the maintenance of the balance between effector T cells and regulatory T cells, and the induction of immunoglobulin A. Moreover, gut bacterial dysbiosis is associated with chronic inflammatory disorders of the skin, such as psoriasis. Thus, the microbiome can be considered an effective therapeutical target for treating this disorder. Despite some limitations, interventions with probiotics seem promising for the development of a preventive therapy by restoring altered microbiome functionality or as an adjuvant in specific immunotherapy.

RevDate: 2019-12-05

Hong X, Fang S, Huang K, et al (2019)

Characteristics of the vaginal microbiome in cross-border female sex workers in China: a case-control study.

PeerJ, 7:e8131 pii:8131.

Background: Female sex workers (FSWs) are key groups in the transmission of sexual transmitted infections (STI), and vaginal microbiome variations play an important role in transmission. We aimed to explore the characteristics of vaginal microbiome among FSWs.

Materials and Methods: A total of 24 cross-border FSWs were randomly selected from a cross-sectional survey for female sex workers in southwest China. Thirty-seven female non-sex workers (FNSWs) were randomly selected from the gynecology clinic and health examination center. Vaginal swabs were collected, bacterial DNA extracted and 16S rRNA genes were sequenced. Differences in the vaginal microbiome between both groups were compared using bioinformatics analysis.

Results: One DNA sample was excluded due to unqualified concentration, therefore 60 samples were sequenced. FSWs had significantly different vaginal microbiota β diversity, but undifferentiated α diversity when compared with non-sex workers. The average relative abundance of Sneathia, Shigella, Neisseria, Chlamydia, Prevotella, Enterococcus and Ureaplasma among FSWs was higher than FNSWs, and relative abundance of Atopobium in FSWs was lower than FNSWs. The Lactobacillus genus was the major genus in both groups. At the species level, Lactobacllus crispatus, Lactobacllus gasseri and Lactobacllus jensenii, in female sex workers, were lower when compared to FNSWs.

Conclusion: There were distinct differences in vaginal bacteria variety between FSWs and FNSWs. Some disease-related genus were also more abundant in FSWs. Based on these observations, further research is required to identify microbiome communities related to high STI risks and other diseases in these cohorts.

RevDate: 2019-12-05

Xu Q, Gill S, Xu L, et al (2019)

Comparative Analysis of Microbiome in Nasopharynx and Middle Ear in Young Children With Acute Otitis Media.

Frontiers in genetics, 10:1176.

Acute otitis media (AOM) is the most common pediatric infection for which antibiotics are prescribed in the United States. The role of the respiratory tract microbiome in pathogenesis and immune modulation of AOM remains unexplored. We sought to compare the nasopharyngeal (NP) microbiome of children 1 to 3 weeks prior to onset of AOM vs. at onset of AOM, and the NP microbiome with the microbiome in middle ear (ME). Six children age 6 to 24 months old were studied. Nasal washes (NW) were collected at healthy visits 1 to 3 weeks prior to AOM and at onset of AOM. The middle ear fluids (MEF) were collected by tympanocentesis at onset of AOM. Samples were stored in Trizol reagents or phosphate-buffered saline (PBS) at -80°C until use. The microbiome was characterized by 16S rRNA gene sequencing. Taxonomic designations and relative abundance of bacteria were determined using the RDP classifier tool through QIIME. Cumulative sum scaling normalization was applied before determining bacterial diversity and abundance. Shannon diversity index was calculated in Microsoft excel. The relative abundance of each bacteria species was compared via Mann-Whitney U test. We found that the NW microbiome of children during healthy state or at baseline was more diverse than microbiome during AOM. At AOM, no significant difference in microbiome diversity was found between NW and MEF, although some bacteria species appear to differ in MEF than in NW. The microbiome of samples stored in PBS had significant greater diversity than samples stored in Trizol reagent.

RevDate: 2019-12-05

Chen L, Li D, Shao Y, et al (2019)

Identifying Microbiota Signature and Functional Rules Associated With Bacterial Subtypes in Human Intestine.

Frontiers in genetics, 10:1146.

Gut microbiomes are integral microflora located in the human intestine with particular symbiosis. Among all microorganisms in the human intestine, bacteria are the most significant subgroup that contains many unique and functional species. The distribution patterns of bacteria in the human intestine not only reflect the different microenvironments in different sections of the intestine but also indicate that bacteria may have unique biological functions corresponding to their proper regions of the intestine. However, describing the functional differences between the bacterial subgroups and their distributions in different individuals is difficult using traditional computational approaches. Here, we first attempted to introduce four effective sets of bacterial features from independent databases. We then presented a novel computational approach to identify potential distinctive features among bacterial subgroups based on a systematic dataset on the gut microbiome from approximately 1,500 human gut bacterial strains. We also established a group of quantitative rules for explaining such distinctions. Results may reveal the microstructural characteristics of the intestinal flora and deepen our understanding on the regulatory role of bacterial subgroups in the human intestine.

RevDate: 2019-12-05

Bodein A, Chapleur O, Droit A, et al (2019)

A Generic Multivariate Framework for the Integration of Microbiome Longitudinal Studies With Other Data Types.

Frontiers in genetics, 10:963.

Simultaneous profiling of biospecimens using different technological platforms enables the study of many data types, encompassing microbial communities, omics, and meta-omics as well as clinical or chemistry variables. Reduction in costs now enables longitudinal or time course studies on the same biological material or system. The overall aim of such studies is to investigate relationships between these longitudinal measures in a holistic manner to further decipher the link between molecular mechanisms and microbial community structures, or host-microbiota interactions. However, analytical frameworks enabling an integrated analysis between microbial communities and other types of biological, clinical, or phenotypic data are still in their infancy. The challenges include few time points that may be unevenly spaced and unmatched between different data types, a small number of unique individual biospecimens, and high individual variability. Those challenges are further exacerbated by the inherent characteristics of microbial communities-derived data (e.g., sparse, compositional). We propose a generic data-driven framework to integrate different types of longitudinal data measured on the same biological specimens with microbial community data and select key temporal features with strong associations within the same sample group. The framework ranges from filtering and modeling to integration using smoothing splines and multivariate dimension reduction methods to address some of the analytical challenges of microbiome-derived data. We illustrate our framework on different types of multi-omics case studies in bioreactor experiments as well as human studies.

RevDate: 2019-12-05

Powers SE, D Thavarajah (2019)

Checking Agriculture's Pulse: Field Pea (Pisum Sativum L.), Sustainability, and Phosphorus Use Efficiency.

Frontiers in plant science, 10:1489.

Investigations regarding the incorporation of better sustainable production strategies into current agricultural-food systems are necessary to grow crops that reduce negative impacts on the environment yet will meet the production and nutritional demand of 10 billion people by 2050. The introduction of organic, alternative staple food crops, such as nutrient-dense field pea (Pisum sativum L.), to the everyday diet, may alleviate micronutrient malnutrition and incorporate more sustainable agriculture practices globally. Varieties are grown in organic systems currently yield less than conventionally produced foods, with less bioavailable nutrients, due to poor soil nutrient content. One of the most limiting nutrients for field pea is phosphorus (P) because this legume crop requires significant inputs for nodule formation. Therefore, P use efficiency (PUE) should be a breeding target for sustainable agriculture and biofortification efforts; the important role of the soil microbiome in nutrient acquisition should also be examined. The objectives of this review are to highlight the benefits of field pea for organic agriculture and human health, and discuss nutritional breeding strategies to increase field pea production in organic systems. Field pea and other pulse crops are underrepresented in agricultural research, yet are important crops for a sustainable future and better food systems. Furthermore, because field pea is consumed globally by both developed and at-risk populations, research efforts could help increase global health overall and combat micronutrient malnutrition.

RevDate: 2019-12-05

Majewska J, Kaźmierczak Z, Lahutta K, et al (2019)

Induction of Phage-Specific Antibodies by Two Therapeutic Staphylococcal Bacteriophages Administered per os.

Frontiers in immunology, 10:2607.

In therapeutic phage applications oral administration is a common and well-accepted delivery route. Phages applied per os may elicit a specific humoral response, which may in turn affect phage activity. We present specific anti-phage antibody induction in mice receiving therapeutic staphylococcal bacteriophage A3R or 676Z in drinking water. The schedule comprised: (1) primary exposure to phages for 100 days, followed by (2) diet without phage for 120 days, and (3) secondary exposure to the same phage for 44 days. Both phages induced specific antibodies in blood (IgM, IgG, IgA), even though poor to ineffective translocation of the phages to blood was observed. IgM reached a maximum on day 22, IgG increased from day 22 until the end of the experiment. Specific IgA in the blood and in the gut were induced simultaneously within about 2 months; the IgA level gradually decreased when phage was removed from the diet. Importantly, phage-specific IgA was the limiting factor for phage activity in the gastrointestinal tract. Multicopy proteins (major capsid protein and tail morphogenetic protein H) contributed significantly to phage immunogenicity (IgG), while the baseplate protein gpORF096 did not induce a significant response. Microbiome composition assessment by next-generation sequencing (NGS) revealed that no important changes correlated with phage treatment.

RevDate: 2019-12-05

Yang Y, Ashworth AJ, Willett C, et al (2019)

Review of Antibiotic Resistance, Ecology, Dissemination, and Mitigation in U.S. Broiler Poultry Systems.

Frontiers in microbiology, 10:2639.

Since the onset of land application of poultry litter, transportation of microorganisms, antibiotics, and disinfectants to new locations has occurred. While some studies provide evidence that antimicrobial resistance (AMR), an evolutionary phenomenon, could be influenced by animal production systems, other research suggests AMR originates in the environment from non-anthropogenic sources. In addition, AMR impacts the effective prevention and treatment of poultry illnesses and is increasingly a threat to global public health. Therefore, there is a need to understand the dissemination of AMR genes to the environment, particularly those directly relevant to animal health using the One Health Approach. This review focuses on the potential movement of resistance genes to the soil via land application of poultry litter. Additionally, we highlight impacts of AMR on microbial ecology and explore hypotheses explaining gene movement pathways from U.S. broiler operations to the environment. Current approaches for decreasing antibiotic use in U.S. poultry operations are also described in this review.

RevDate: 2019-12-05

Kavamura VN, Robinson RJ, Hayat R, et al (2019)

Land Management and Microbial Seed Load Effect on Rhizosphere and Endosphere Bacterial Community Assembly in Wheat.

Frontiers in microbiology, 10:2625.

Microbial community ecology studies have traditionally utilized culture-based methodologies, though the advent of next-generation amplicon sequencing has facilitated superior resolution analyses of complex microbial communities. Here, we used culture-dependent and -independent approaches to explore the influence of land use as well as microbial seed load on bacterial community structure of the wheat rhizosphere and root endosphere. It was found that niche was an important factor in shaping the microbiome when using both methodological approaches, and that land use was also a discriminatory factor for the culture-independent-based method. Although culture-independent methods provide a higher resolution of analysis, it was found that in the rhizosphere, particular operational taxonomic units (OTUs) in the culture-dependent fraction were absent from the culture-independent fraction, indicating that deeper sequence analysis is required for this approach to be exhaustive. We also found that the microbial seed load defined the endosphere, but not rhizosphere, community structure for plants grown in soil which was not wheat adapted. Together, these findings increase our understanding of the importance of land management and microbial seed load in shaping the root microbiome of wheat and this knowledge will facilitate the exploitation of plant-microbe interactions for the development of novel microbial inoculants.

RevDate: 2019-12-05

Misra P, Maji D, Awasthi A, et al (2019)

Vulnerability of Soil Microbiome to Monocropping of Medicinal and Aromatic Plants and Its Restoration Through Intercropping and Organic Amendments.

Frontiers in microbiology, 10:2604.

Cultivation of medicinal and aromatic plants (MAPs) is persistently increasing due to excessive demands of naturals. Agricultural land and its microbial diversity are primarily adapted to conventional crops, and introduction of MAP and their continuous monocropping may disturb the ecological stability of soil microbiome. Here, the effect of cultivation of MAPs on soil microbial diversity was studied. The aim of the study is to examine the effects of cultivation of MAPs on the possible shift in soil microbial diversity and to restore such impacts by using organic amendments or intercropping. Terminal restriction fragments polymorphism (TRFLP) and next-generation sequencing (NGS) studies showed that of the various selected MAPs, maximal modulation in the soil microbial diversity patterns was noticed in fields of Mentha arvensis and Artemisia annua, and the traces of essential oil/phytochemicals were detected in bulk and rhizospheric soil. In both Artemisia- and Mentha-cultivated soil, the total operating taxonomic unit (OTU) declined in both bulk and rhizospheric soil in comparison to control (Zea mays), but the bacterial richness of Mentha soil was slightly higher than that of control. However, cultivation of Mentha improved the evenness of the microbial community. The inclusion of crops like Sesbania and Chlorophytum and the application of vermicompost (VC) enhanced the microbial richness and evenness, thereby restoring the soil microbial state shift and resulting in higher productivity in the continuously Mentha cropped field. Our study concludes that long-term cultivation of some MAPs may affect the richness but promote the evenness of microbial diversity. The state shift could be restored to some extent, and crop productivity could be enhanced by the inclusion of selected crops and organic manures in cropping systems.

RevDate: 2019-12-05

Fix J, Chandrashekhar K, Perez J, et al (2019)

Association between Gut Microbiome Composition and Rotavirus Vaccine Response among Nicaraguan Infants.

The American journal of tropical medicine and hygiene [Epub ahead of print].

Rotavirus is the leading cause of childhood deaths due to diarrhea. Although existing oral rotavirus vaccines are highly efficacious in high-income countries, these vaccines have been demonstrated to have decreased efficacy in low- and middle-income countries. A possible explanation for decreased efficacy is the impact of gut microbiota on the enteric immune system's response to vaccination. We analyzed the gut microbiome of 50 children enrolled in a prospective study evaluating response to oral pentavalent rotavirus vaccination (RV5) to assess associations between relative abundance of bacterial taxa and seroconversion following vaccination. Stool samples were taken before the first RV5 dose, and microbiome composition characterized using 16S rRNA amplicon sequencing and Quantitative Insights Into Microbial Ecology software. Relative abundance of bacterial taxa between seroconverters following the first RV5 dose, those with ≥ 4-fold increase in rotavirus-specific IgA titers, and nonseroconverters were compared using the Wilcoxon-Mann-Whitney test. We identified no significant differences in microbiome composition between infants who did and did not respond to vaccination. Infants who responded to vaccination tended to have higher abundance of Proteobacteria and Eggerthella, whereas those who did not respond had higher abundance of Fusobacteria and Enterobacteriaceae; however, these differences were not statistically significant following a multiple comparison correction. This study suggests a limited impact of gut microbial taxa on response to oral rotavirus vaccination among infants; however, additional research is needed to improve our understanding of the impact of gut microbiome on vaccine response, toward a goal of improving vaccine efficacy and rotavirus prevention.

RevDate: 2019-12-05

Nuzzo A, JR Brown (2019)

The Microbiome Factor in Drug Discovery and Development.

Chemical research in toxicology [Epub ahead of print].

Here we review recent studies which illustrate three areas where the microbiome directly impacts drug development: 1) microbial effects on drug safety and efficacy; 2) the effects of drugs on causing collateral restructuring of microbiome communities and 3) the potential side-effects of novel therapies targeting the microbiome. Based on the findings of these and other studies, we advocate the systematic incorporation of microbiome analyses in early to late stage clinical trials as a strategy to increase the overall success rate of the drug discovery and development process.

RevDate: 2019-12-05

Sanyaolu LN, Oakley NJ, Nurmatov U, et al (2019)

Antibiotic exposure and the risk of colorectal adenoma and carcinoma: systematic review and meta-analysis of observational studies.

Colorectal disease : the official journal of the Association of Coloproctology of Great Britain and Ireland [Epub ahead of print].

BACKGROUND: Colorectal cancer (CRC) incidence is increasing and evidence suggests that bowel microbiome maladaptation may be associated with colorectal carcinogenesis. Antibiotic consumption may cause bowel microbiome imbalance but research assessing an association between antibiotic exposure and CRC is inconsistent. The aim of this systematic review and meta-analysis was to appraise and synthesise the available evidence.

METHODS: MEDLINE, EMBASE and CINAHL databases were searched for published observational studies. We included eight studies of 3,408,312 patients. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) for the odds of CRC following antibiotic exposure were estimated. Sensitivity analyses were performed according to exposure definition, study design and risk of bias.

RESULTS: A weak association between antibiotic exposure and CRC was demonstrated when exposure was assessed cumulatively by the number of prescriptions (OR 1.204, 95% CI 1.097-1.322, p <0.001) or duration of antibiotic exposure (OR 1.168, 95% CI 1.087-1.256, p <0.001). Antibiotic exposure assessed as a binary variable demonstrated no association with CRC.

CONCLUSION: The findings suggest a weak association between cumulative antibiotic consumption and risk of CRC but no causal conclusions can be made. Limitations include the heterogeneity and quality of the available research, particularly with regard to measurement of antibiotic exposure.

RevDate: 2019-12-05

Affinati AH, Esfandiari NH, Oral EA, et al (2019)

Bariatric Surgery in the Treatment of Type 2 Diabetes.

Current diabetes reports, 19(12):156 pii:10.1007/s11892-019-1269-4.

PURPOSE OF REVIEW: We seek to characterize the impact of bariatric surgery on diabetes mellitus by recalling its history, examining the clinical data, exploring the putative mechanisms of action, and anticipating its future.

RECENT FINDINGS: Results of clinical trials reveal that bariatric surgery induces remission of diabetes in 33-90% of individuals at 1-year post-treatment versus 0-39% of medically managed. Remission rates decrease over time but remain higher in surgically treated individuals. Investigations have revealed numerous actions of surgery including effects on intestinal physiology, neuronal signaling, incretin hormone secretion, bile acid metabolism, and microbiome changes. Bariatric surgery improves control of diabetes through both weight-dependent and weight-independent actions. These various mechanisms help explain the difference between individuals treated surgically vs. medically. They also explain differing effects of various bariatric surgery procedure types. Understanding how surgery affects diabetes will help optimize utilization of the therapy for both disease prevention and treatment.

RevDate: 2019-12-05

Walker DM, Hill AJ, Albecker MA, et al (2019)

Variation in the Slimy Salamander (Plethodon spp.) Skin and Gut-Microbial Assemblages Is Explained by Geographic Distance and Host Affinity.

Microbial ecology pii:10.1007/s00248-019-01456-x [Epub ahead of print].

A multicellular host and its microbial communities are recognized as a metaorganism-a composite unit of evolution. Microbial communities have a variety of positive and negative effects on the host life history, ecology, and evolution. This study used high-throughput amplicon sequencing to characterize the complete skin and gut microbial communities, including both bacteria and fungi, of a terrestrial salamander, Plethodon glutinosus (Family Plethodontidae). We assessed salamander populations, representing nine mitochondrial haplotypes ('clades'), for differences in microbial assemblages across 13 geographic locations in the Southeastern United States. We hypothesized that microbial assemblages were structured by both host factors and geographic distance. We found a strong correlation between all microbial assemblages at close geographic distances, whereas, as spatial distance increases, the patterns became increasingly discriminate. Network analyses revealed that gut-bacterial communities have the highest degree of connectedness across geographic space. Host salamander clade was explanatory of skin-bacterial and gut-fungal assemblages but not gut-bacterial assemblages, unless the latter were analyzed within a phylogenetic context. We also inferred the function of gut-fungal assemblages to understand how an understudied component of the gut microbiome may influence salamander life history. We concluded that dispersal limitation may in part describe patterns in microbial assemblages across space and also that the salamander host may select for skin and gut communities that are maintained over time in closely related salamander populations.

RevDate: 2019-12-05

Barrera-Vázquez OS, JC Gomez-Verjan (2019)

The Unexplored World of Human Virome, Mycobiome, and Archaeome in Aging.

The journals of gerontology. Series A, Biological sciences and medical sciences pii:5652062 [Epub ahead of print].

In the last decades, improvements in different aspects of sanitation, medical care, and nutrition, among others, have permitted an increase in the average lifespan of human population around the world. These advances have stimulated an increased interest in the study of the aging process and age-sensitive characteristics, such as the microbial community that colonizes the human body (microbiome). The human microbiome is composed of bacteria (bacteriome), archaea (archaeome), fungi (mycobiome), and viruses (virome). To date, research has mainly been centered on the composition of the bacteriome, with other members remain poorly studied. Interestingly, changes in the composition of the microbiome have been implicated in aging and age-related diseases. Therefore, in the present perspective, we suggest expanding the scope to research to include the role and the possible associations that the other members of the microbiome could have in the aging organism. An expanded view of the microbiome would increase our knowledge of the physiology of aging and may be particularly valuable for the treatment and diagnosis of age-related diseases.

RevDate: 2019-12-05

Song W, Anselmo AC, L Huang (2019)

Nanotechnology intervention of the microbiome for cancer therapy.

Nature nanotechnology, 14(12):1093-1103.

The microbiome is emerging as a key player and driver of cancer. Traditional modalities to manipulate the microbiome (for example, antibiotics, probiotics and microbiota transplants) have been shown to improve efficacy of cancer therapies in some cases, but issues such as collateral damage to the commensal microbiota and consistency of these approaches motivates efforts towards developing new technologies specifically designed for the microbiome-cancer interface. Considering the success of nanotechnology in transforming cancer diagnostics and treatment, nanotechnologies capable of manipulating interactions that occur across microscopic and molecular length scales in the microbiome and the tumour microenvironment have the potential to provide innovative strategies for cancer treatment. As such, opportunities at the intersection of nanotechnology, the microbiome and cancer are massive. In this Review, we highlight key opportunistic areas for applying nanotechnologies towards manipulating the microbiome for the treatment of cancer, give an overview of seminal work and discuss future challenges and our perspective on this emerging area.

RevDate: 2019-12-05

Greenhill C (2019)

Gut microbiome influences exercise response.

Nature reviews. Endocrinology pii:10.1038/s41574-019-0309-0 [Epub ahead of print].

RevDate: 2019-12-05

Sharma G, Rahul , Guleria R, et al (2019)

Differences in plant metabolites and microbes associated with Azadirachta indica with variation in air pollution.

Environmental pollution (Barking, Essex : 1987) pii:S0269-7491(19)31637-9 [Epub ahead of print].

Mitigation of air pollution by plants is a well-established phenomenon. Trees planted on the roadside are known to reduce particulate matter pollution by about 25%. In an urban ecosystem, especially in a metropolitan city such as Delhi, roadside trees are constantly exposed to air pollution. We, therefore, evaluated the effect of air pollution on a common Indian roadside tree, Neem (Azadirachta indica), and its associated microbes in areas with high and low levels of particulate matter (PM) pollution in Delhi. We hypothesized that alteration in the air quality index not only influences plant physiology but also its microbiome. A 100-fold increase in the number of epiphytic and 10-100 fold increase in endophytic colonies were found with 1.7 times increase in the level of pollutants. Trees in the polluted areas had an abundance of Salmonella, Proteus and Citrobacter, and showed increased secondary metabolites such as phenols and tannins as well as decreased chlorophyll and carotenoid. The number of unique microbes was positively correlated with increased primary metabolites. Our study thus indicates that, alteration in air quality affects the natural micro-environment of plants. These results may be utilized as sustainable tools for studying plant adaptations to the urban ecosystem.

RevDate: 2019-12-04

Levi YLAS, Picchi RN, Silva EKT, et al (2019)

Probiotic Administration Increases Mandibular Bone Mineral Density on Rats Exposed to Cigarette Smoke Inhalation.

Brazilian dental journal, 30(6):634-640.

Smoking is one of the main risk factor for periodontal disease, increasing its prevalence and severity. Probiotics emerged as an alternative for the prevention and treatment of many diseases, since it can modulate the host immune response and modify the modify the microbiome. Therefore, the aim of the present study is to evaluate the effects of probiotic administration on the periodontal tissues in rats exposed to cigarette smoke inhalation (CSI). Forty rats were allocated into the following groups (n=10): group C (control, without CSI and probiotic); group PROB (control+probiotic); group CSI (CSI) and group CSI+PROB (CSI+probiotic). Groups PROB and CSI+PROB received 2g of an association of probiotic microorganisms incorporated into the feed during 6 months. Groups CSI and CSI+PROB were exposed to CSI for 60 min daily. After six months all the animals were euthanized and the hemi-mandibles were collected and processed for microcomputed tomography analyses. Regarding the body weight of the animals, feed consumption was similar among the groups, however, after the second month groups C and PROB showed higher body weight gain when compared to groups CSI and CSI+PROB (p<0.05). Group CSI presented reduced bone mineral density (BMD), whereas group PROB showed the highest values (p=0.01). It can be concluded that administration of probiotics promoted an increase in BMD and, consequently, a protective effect on the mandibular bone structures in rats exposed to inhalation of cigarette smoke.

RevDate: 2019-12-04

Choi S, Lee JG, Lee AR, et al (2019)

Helicobacter pylori antibody and pepsinogen testing for predicting gastric microbiome abundance.

PloS one, 14(12):e0225961 pii:PONE-D-19-19012.

BACKGROUND: Although the high-throughput sequencing technique is useful for evaluating gastric microbiome, it is difficult to use clinically. We aimed to develop a predictive model for gastric microbiome based on serologic testing.

METHODS: This study was designed to analyze sequencing data obtained from the Hanyang University Gastric Microbiome Cohort, which was established initially to investigate gastric microbial composition according to the intragastric environment. We evaluated the relationship between the relative abundance of potential gastric cancer-associated bacteria (nitrosating/nitrate-reducing bacteria or type IV secretion system [T4SS] protein gene-contributing bacteria) and serologic markers (IgG anti-Helicobacter pylori [HP] antibody or pepsinogen [PG] levels).

RESULTS: We included 57 and 26 participants without and with HP infection, respectively. The relative abundance of nitrosating/nitrate-reducing bacteria was 4.9% and 3.6% in the HP-negative and HP-positive groups, respectively, while that of T4SS protein gene-contributing bacteria was 20.5% and 6.5% in the HP-negative and HP-positive groups, respectively. The relative abundance of both nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria increased exponentially as PG levels decreased. Advanced age (only for nitrosating/nitrate-reducing bacteria), a negative result of IgG anti-HP antibody, low PG levels, and high Charlson comorbidity index were associated with a high relative abundance of nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria. The adjusted coefficient of determination (R2) was 53.7% and 70.0% in the model for nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria, respectively.

CONCLUSION: Not only the negative results of IgG anti-HP antibody but also low PG levels were associated with a high abundance of nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria.

RevDate: 2019-12-04

Jochum MD, McWilliams KL, Pierson EA, et al (2019)

Host-mediated microbiome engineering (HMME) of drought tolerance in the wheat rhizosphere.

PloS one, 14(12):e0225933 pii:PONE-D-19-12563.

Host-mediated microbiome engineering (HMME) is a strategy that utilizes the host phenotype to indirectly select microbiomes though cyclic differentiation and propagation. In this experiment, the host phenotype of delayed onset of seedling water deficit stress symptoms was used to infer beneficial microbiome-host interactions over multiple generations. By utilizing a host-centric selection approach, microbiota are selected at a community level, therein using artificial selection to alter microbiomes through both ecological and evolutionary processes. After six rounds of artificial selection using host-mediated microbiome engineering (HMME), a microbial community was selected that mediated a 5-day delay in the onset of drought symptoms in wheat seedlings. Seedlings grown in potting medium inoculated with the engineered rhizosphere from the 6th round of HMME produced significantly more biomass and root system length, dry weight, and surface area than plants grown in medium similarly mixed with autoclaved inoculum (negative control). The effect on plant water stress tolerance conferred by the inoculum was transferable at subsequent 10-fold and 100-fold dilutions in fresh non-autoclaved medium but was lost at 1000-fold dilution and was completely abolished by autoclaving, indicating the plant phenotype is mediated by microbial population dynamics. The results from 16S rRNA amplicon sequencing of the rhizosphere microbiomes at rounds 0, 3, and 6 revealed taxonomic increases in proteobacteria at the phylum level and betaproteobacteria at the class level. There were significant decreases in alpha diversity in round 6, divergence in speciation with beta diversity between round 0 and 6, and changes in overall community composition. This study demonstrates the potential of using the host as a selective marker to engineer microbiomes that mediate changes in the rhizosphere environment that improve plant adaptation to drought stress.

RevDate: 2019-12-04

Kim KW, Allen DW, Briese T, et al (2019)

Higher frequency of vertebrate-infecting viruses in the gut of infants born to mothers with type 1 diabetes.

Pediatric diabetes [Epub ahead of print].

BACKGROUND: Microbial exposures in utero and early life shape the infant microbiome, which can profoundly impact on health. Compared to the bacterial microbiome, very little is known about the virome. We set out to characterize longitudinal changes in the gut virome of healthy infants born to mothers with or without type 1 diabetes using comprehensive virome capture sequencing.

METHODS: Healthy infants were selected from Environmental Determinants of Islet Autoimmunity (ENDIA), a prospective cohort of Australian children with a first-degree relative with type 1 diabetes, followed from pregnancy. Fecal specimens were collected three-monthly in the first year of life.

RESULTS: Among 25 infants (44% born to mothers with type 1 diabetes) at least one virus was detected in 65% (65/100) of samples and 96% (24/25) of infants during the first year of life. In total, 26 genera of viruses were identified and > 150 viruses were differentially abundant between the gut of infants with a mother with type 1 diabetes vs without. Positivity for any virus was associated with maternal type 1 diabetes and older infant age. Enterovirus was associated with older infant age and maternal smoking.

CONCLUSIONS: We demonstrate a distinct gut virome profile in infants of mothers with type 1 diabetes, which may influence health outcomes later in life. Higher prevalence and greater number of viruses observed compared to previous studies suggests significant underrepresentation in existing virome datasets, arising most likely from less sensitive techniques used in data acquisition. This article is protected by copyright. All rights reserved.

RevDate: 2019-12-04

Sabit H, Cevik E, H Tombuloglu (2019)

Colorectal cancer: The epigenetic role of microbiome.

World journal of clinical cases, 7(22):3683-3697.

Colorectal cancer (CRC) is the third most common cancer in men (746000 cases per year) and the second most common cancer in women globally (614000 cases per year). The incidence rate of CRC in developed countries (737000 cases per year) is higher than that in less developed countries (624000 cases per year). CRC can arise from genetic causes such as chromosomal instability and microsatellite instability. Several etiologic factors underlie CRC including age, diet, and lifestyle. Gut microbiota represent a proven cause of the disease, where they play pivotal roles in modulating and reshaping the host epigenome. Several active microbial metabolites have been found to drive carcinogenesis, invasion, and metastasis via modifying both the methylation landscape along with histone structure in intestinal cells. Gut microbiota, in response to diet, can exert both beneficial and harmful functions in humans, according to the intestinal balance of number and types of these bacteria. Although the intestinal microbial community is diverse among individuals, these microbes cumulatively produce 100-fold more proteins than the human genome itself, which calls for further studies to elaborate on the complicated interaction between these microorganisms and intestinal cells. Therefore, understanding the exact role that gut microbiota play in inducing CRC will help attain reliable strategies to precisely diagnose and treat this fatal disease.

RevDate: 2019-12-04

Storm-Larsen C, Myhr KM, Farbu E, et al (2019)

Gut microbiota composition during a 12-week intervention with delayed-release dimethyl fumarate in multiple sclerosis - a pilot trial.

Multiple sclerosis journal - experimental, translational and clinical, 5(4):2055217319888767 pii:10.1177_2055217319888767.

Introduction: Patients with multiple sclerosis may have a distinct gut microbiota profile. Delayed-release dimethyl fumarate is an orally administered drug for relapsing-remitting multiple sclerosis, which has been associated with gastrointestinal side-effects in some patients.

Objectives: The purpose of this study was to determine if dimethyl fumarate alters the abundance and diversity of commensal gut bacteria, and if these changes are associated with gastrointestinal side-effects.

Methods: Thirty-six patients with relapsing-remitting multiple sclerosis received either dimethyl fumarate (n = 27) or an injectable multiple sclerosis disease-modifying therapy (glatiramer acetate or interferons, n = 9) for 12 weeks. Stool samples were collected at baseline, two and 12 weeks. We included 165 healthy individuals as controls.

Results: At baseline, 16 microbial genera were altered in multiple sclerosis patients compared with healthy controls. In the dimethyl fumarate-treated patients (n = 21) we observed a trend of reduced Actinobacteria (p = 0.03, QFDR = 0.24) at two weeks, mainly driven by Bifidobacterium (p = 0.06, QFDR = 0.69). At 12 weeks, we observed an increased abundance of Firmicutes (p = 0.02, QFDR = 0.09), mostly driven by Faecalibacterium (p = 0.01, QFDR = 0.48).

Conclusions: This pilot study did not detect a major effect of dimethyl fumarate on the gut microbiota composition, but we observed a trend towards normalization of the low abundance of butyrate-producing Faecalibacterium after 12 weeks treatment. The study was underpowered to link microbiota to gastrointestinal symptoms.

RevDate: 2019-12-04

Bich VTN, Thanh LV, Thai PD, et al (2019)

An exploration of the gut and environmental resistome in a community in northern Vietnam in relation to antibiotic use.

Antimicrobial resistance and infection control, 8:194 pii:645.

Background: Antibiotic resistance is a major global public health threat. Antibiotic use can directly impact the antibiotic resistant genes (ARGs) profile of the human intestinal microbiome and consequently the environment through shedding.

Methods: We determined the resistome of human feces, animal stools, human food and environmental (rain, well, and irrigative water) samples (n = 304) in 40 households within a community cohort and related the data to antibiotic consumption. Metagenomic DNA was isolated and qPCR was used to determine presence of mobile colistin resistance (mcr) genes, genes encoding extended-spectrum β-lactamases (ESBL), carbapenemases and quinolone resistance genes.

Results: Nearly 40 % (39.5%, 120/304) of samples contained ESBL genes (most frequent were CTX-M-9 (23.7% [72/304]), CTX-M-1 (18.8% [57/304]). Quinolone resistance genes (qnrS) were detected in all human and 91% (41/45) of animal stool samples. Mcr-1 and mcr-3 were predominantly detected in human feces at 88% (82/93) and 55% (51/93) and animal feces at 93% (42/45) and 51% (23/45), respectively. Mcr-2, mrc-4 and mcr-5 were not detected in human feces, and only sporadically (< 6%) in other samples. Carbapenemase-encoding genes were most common in water (15% [14/91]) and cooked food (13% [10/75]) samples, while their prevalence in human and animal stools was lower at 4% in both human (4/93) and animal (2/45) samples. We did not find an association between recent antibiotic consumption and ARGs in human stools. Principal component analysis showed that the resistome differs between ecosystems with a strong separation of ARGs profiles of human and animal stools on the one hand versus cooked food and water samples on the other.

Conclusions: Our study indicated that ARGs were abundant in human and animal stools in a rural Vietnamese community, including ARGs targeting last resort antibiotics. The resistomes of animal and human stools were similar as opposed to the resistomes from water and food sources. No association between antibiotic use and ARG profiles was found in a setting of high background rates of AMR.

RevDate: 2019-12-04

Pearson JA, Tai N, Ekanayake-Alper DK, et al (2019)

Norovirus Changes Susceptibility to Type 1 Diabetes by Altering Intestinal Microbiota and Immune Cell Functions.

Frontiers in immunology, 10:2654.

Environmental factors contribute to Type 1 diabetes (T1D) susceptibility. The gut microbiome, which includes bacteria, viruses, and fungi, contributes to this environmental influence, and can induce immunological changes. The gut viral component of the microbiome, related to T1D has mostly focused on coxsackieviruses and rotavirus. The role of norovirus, another common enteric virus, in susceptibility to T1D was hitherto unknown. Norovirus is highly infectious and encountered by many children. We studied the mouse norovirus 4 (MNV4), related to human noroviruses, in the Non-obese diabetic (NOD) mouse model, to determine its role in influencing susceptibility to T1D. We infected MNV-free NOD mice with MNV4 by exposing the mice to MNV4-positive bedding from an endemically-infected mouse colony to mimic a natural infection. Control MNV-free NOD mice were exposed to MNV-free bedding from the same colony. Interestingly, MNV4 infection protected NOD mice from the development of T1D and was associated with an expansion of Tregs and reduced proinflammatory T cells. We also found MNV4 significantly modified the gut commensal bacteria composition, promoting increased α-diversity and Firmicutes/Bacteroidetes ratio. To elucidate whether T1D protection was directly related to MNV4, or indirectly through modulating gut microbiota, we colonized germ-free (GF) NOD mice with the MNV4-containing or non-MNV4-containing viral filtrate, isolated from filtered fecal material. We found that MNV4 induced significant changes in mucosal immunity, including altered Tuft cell markers, cytokine secretion, antiviral immune signaling markers, and the concentration of mucosal antibodies. Systemically, MNV4-infection altered the immune cells including B cell subsets, macrophages and T cells, and especially induced an increase in Treg number and function. Furthermore, in vitro primary exposure of the norovirus filtrate to naïve splenocytes identified significant increases in the proportion of activated and CTLA4-expressing Tregs. Our data provide novel knowledge that norovirus can protect NOD mice from T1D development by inducing the expansion of Tregs and reducing inflammatory T cells. Our study also highlights the importance of distinguishing the mucosal immunity mediated by bacteria from that by enteric viruses.

RevDate: 2019-12-04

Khamis FM, Mireji PO, Ombura FLO, et al (2019)

Species-specific transcriptional profiles of the gut and gut microbiome of Ceratitis quilicii and Ceratitis rosa sensu stricto.

Scientific reports, 9(1):18355 pii:10.1038/s41598-019-54989-z.

The fruit fly species, Ceratitis rosa sensu stricto and Ceratitis quilicii, are sibling species restricted to the lowland and highland regions, respectively. Until recently, these sibling species were considered as allopatric populations of C. rosa with distinct bionomics. We used deep Next Generation Sequencing (NGS) technology on intact guts of individuals from the two sibling species to compare their transcriptional profiles and simultaneously understand gut microbiome and host molecular processes and identify distinguishing genetic differences between the two species. Since the genomes of both species had not been published previously, the transcriptomes were assembled de novo into transcripts. Microbe-specific transcript orthologs were separated from the assembly by filtering searches of the transcripts against microbe databases using OrthoMCL. We then used differential expression analysis of host-specific transcripts (i.e. those remaining after the microbe-specific transcripts had been removed) and microbe-specific transcripts from the two-sibling species to identify defining species-specific transcripts that were present in only one fruit fly species or the other, but not in both. In C. quilicii females, bacterial transcripts of Pectobacterium spp., Enterobacterium buttiauxella, Enterobacter cloacae and Klebsiella variicola were upregulated compared to the C. rosa s.s. females. Comparison of expression levels of the host transcripts revealed a heavier investment by C. quilicii (compared with C. rosa s.s.) in: immunity; energy production; cell proliferation; insecticide resistance; reproduction and proliferation; and redox reactions that are usually associated with responses to stress and degradation of fruit metabolites.

RevDate: 2019-12-04

Xi H, Shen J, Qu Z, et al (2019)

Effects of Long-term Cotton Continuous Cropping on Soil Microbiome.

Scientific reports, 9(1):18297 pii:10.1038/s41598-019-54771-1.

Verticillium wilt is a severe disease of cotton crops in Xinjiang and affecting yields and quality, due to the continuous cotton cropping in the past decades. The relationship between continuous cropping and the changes induced on soil microbiome remains unclear to date. In this study, the culture types of 15 isolates from Bole (5F), Kuitun (7F), and Shihezi (8F) of north Xinjiang were sclerotium type. Only isolates from field 5F belonged to nondefoliating pathotype, the others belonged to defoliating pathotype. The isolates showed pathogenicity differentiation in cotton. Fungal and bacterial communities in soils had some difference in alpha-diversity, relative abundance, structure and taxonomic composition, but microbial groups showed similarity in the same habitat, despite different sampling sites. The fungal phyla Ascomycota, and the bacterial phyla Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria and Gemmatimonadetes were strongly enriched. Verticillium abundance was significantly and positively correlated with AN, but negatively correlated with soil OM, AK and pH. Moreover, Verticillium was correlated in abundances with 5 fungal and 6 bacterial genera. Overall, we demonstrate that soil microbiome communities have similar responses to long-term continuous cotton cropping, providing new insights into the effects of continuous cotton cropping on soil microbial communities.

RevDate: 2019-12-05

Manuzak JA, Zevin AS, Cheu R, et al (2019)

Antibiotic-induced microbiome perturbations are associated with significant alterations to colonic mucosal immunity in rhesus macaques.

Mucosal immunology pii:10.1038/s41385-019-0238-1 [Epub ahead of print].

The diverse bacterial communities that colonize the gastrointestinal tract play an essential role in maintaining immune homeostasis through the production of critical metabolites such as short-chain fatty acids (SCFAs) and this can be disrupted by antibiotic use. However, few studies have addressed the effects of specific antibiotics longitudinally on the microbiome and immunity. We evaluated the effects of four specific antibiotics: enrofloxacin, cephalexin, paromomycin, and clindamycin, in healthy female rhesus macaques. All antibiotics disrupted the microbiome, including reduced abundances of fermentative bacteria and increased abundances of potentially pathogenic bacteria, including Enterobacteriaceae in the stool, and decreased Helicobacteraceae in the colon. This was associated with decreased SCFAs, indicating altered bacterial metabolism. Importantly, antibiotic use also substantially altered local immune responses, including increased neutrophils and Th17 cells in the colon. Furthermore, we observed increased soluble CD14 in plasma, indicating microbial translocation. These data provide a longitudinal evaluation of antibiotic-induced changes to the composition and function of colonic bacterial communities associated with specific alterations in mucosal and systemic immunity.

RevDate: 2019-12-04

Rosales SM, Miller MW, Williams DE, et al (2019)

Microbiome differences in disease-resistant vs. susceptible Acropora corals subjected to disease challenge assays.

Scientific reports, 9(1):18279 pii:10.1038/s41598-019-54855-y.

In recent decades coral gardening has become increasingly popular to restore degraded reef ecosystems. However, the growth and survivorship of nursery-reared outplanted corals are highly variable. Scientists are trying to identify genotypes that show signs of disease resistance and leverage these genotypes in restoring more resilient populations. In a previous study, a field disease grafting assay was conducted on nursery-reared Acropora cervicornis and Acropora palmata to quantify relative disease susceptibility. In this study, we further evaluate this field assay by investigating putative disease-causing agents and the microbiome of corals with disease-resistant phenotypes. We conducted 16S rRNA gene high-throughput sequencing on A. cervicornis and A. palmata that were grafted (inoculated) with a diseased A. cervicornis fragment. We found that independent of health state, A. cervicornis and A. palmata had distinct alpha and beta diversity patterns from one another and distinct dominant bacteria. In addition, despite different microbiome patterns between both inoculated coral species, the genus Sphingomonadaceae was significantly found in both diseased coral species. Additionally, a core bacteria member from the order Myxococcales was found at relatively higher abundances in corals with lower rates of disease development following grafting. In all, we identified Sphingomonadaceae as a putative coral pathogen and a bacterium from the order Myxococcales associated with corals that showed disease resistant phenotypes.

RevDate: 2019-12-04

Yoon HJ, Kim HN, Bang JI, et al (2019)

Physiologic intestinal 18F-FDG uptake is associated with alteration of gut microbiota and proinflammatory cytokine levels in breast cancer.

Scientific reports, 9(1):18273 pii:10.1038/s41598-019-54680-3.

The clinical significance of physiologic Fluorine-18-fluorodeoxyglucose (18F-FDG) intestinal uptake (IU) based on the predicted link with gut microbiota dysbiosis and inflammatory cytokine production was investigated in a cohort of breast cancer patients. A total of 114 patients were visually classified into the lower or higher IU group. The maximum and mean standardized uptake values of total bowel (TB SUVmax and TB SUVmean) were measured. The gut microbial abundance of the Citrobacter genus of the Enterobacteriaceae family showed a significant positive correlation with TB SUVmax and TB SUVmean (q = 0.021 and q = 0.010). The unclassified Ruminococcaceae showed a significant negative correlation with TB SUVmax (q = 0.010). The level of tumor necrosis factor alpha (TNF-α) was significantly increased in the high IU group (p = 0.017). The TNF-α levels showed a significant positive correlation with TB SUVmax (rho = 0.220 and p = 0.018) and TB SUVmean (rho = 0.250 and p = 0.007). Therefore, our findings suggest that the physiologic intestinal uptake may reflect subclinical inflammation and differences in the composition of the gut microbiome in breast cancer patients.

RevDate: 2019-12-04

Kong SW, C Hernandez-Ferrer (2020)

Assessment of coverage for endogenous metabolites and exogenous chemical compounds using an untargeted metabolomics platform.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 25:587-598.

Physiological status and pathological changes in an individual can be captured by metabolic state that reflects the influence of both genetic variants and environmental factors such as diet, lifestyle and gut microbiome. The totality of environmental exposure throughout lifetime - i.e., exposome - is difficult to measure with current technologies. However, targeted measurement of exogenous chemicals and untargeted profiling of endogenous metabolites have been widely used to discover biomarkers of pathophysiologic changes and to understand functional impacts of genetic variants. To investigate the coverage of chemical space and interindividual variation related to demographic and pathological conditions, we profiled 169 plasma samples using an untargeted metabolomics platform. On average, 1,009 metabolites were quantified in each individual (range 906 - 1,038) out of 1,244 total chemical compounds detected in our cohort. Of note, age was positively correlated with the total number of detected metabolites in both males and females. Using the robust Qn estimator, we found metabolite outliers in each sample (mean 22, range from 7 to 86). A total of 50 metabolites were outliers in a patient with phenylketonuria including the ones known for phenylalanine pathway suggesting multiple metabolic pathways perturbed in this patient. The largest number of outliers (N=86) was found in a 5-year-old boy with alpha-1-antitrypsin deficiency who were waiting for liver transplantation due to cirrhosis. Xenobiotics including drugs, diets and environmental chemicals were significantly correlated with diverse endogenous metabolites and the use of antibiotics significantly changed gut microbial products detected in host circulation. Several challenges such as annotation of features, reference range and variance for each feature per age group and gender, and population scale reference datasets need to be addressed; however, untargeted metabolomics could be immediately deployed as a biomarker discovery platform and to evaluate the impact of genomic variants and exposures on metabolic pathways for some diseases.

RevDate: 2019-12-04

Khan S, L Kelly (2020)

Multiclass Disease Classification from Microbial Whole-Community Metagenomes.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 25:55-66.

The microbiome, the community of microorganisms living within an individual, is a promising avenue for developing non-invasive methods for disease screening and diagnosis. Here, we utilize 5643 aggregated, annotated whole-community metagenomes to implement the first multiclass microbiome disease classifier of this scale, able to discriminate between 18 different diseases and healthy. We compared three different machine learning models: random forests, deep neural nets, and a novel graph convolutional architecture which exploits the graph structure of phylogenetic trees as its input. We show that the graph convolutional model outperforms deep neural nets in terms of accuracy (achieving 75% average test-set accuracy), receiver-operator-characteristics (92.1% average area-under-ROC (AUC)), and precision-recall (50% average area-under-precision-recall (AUPR)). Additionally, the convolutional net's performance complements that of the random forest, showing a lower propensity for Type-I errors (false-positives) while the random forest makes less Type-II errors (false-negatives). Lastly, we are able to achieve over 90% average top-3 accuracy across all of our models. Together, these results indicate that there are predictive, disease-specific signatures across microbiomes that can be used for diagnostic purposes.

RevDate: 2019-12-04

Ding Y, Wang Q, Li D, et al (2019)

Abundance of the nasopharyngeal microbiome effects pertussis diagnosis and explains the sensitivity difference between bacterial culture and real-time PCR.

European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology pii:10.1007/s10096-019-03750-5 [Epub ahead of print].

Quantitative real time PCR (qPCR)is used for pertussis diagnosis. The positive rate of qPCR is generally much higher than that of bacterial culture, which may cause confusion. The current study utilized the 16S ribosomal RNA (16S rRNA) sequencing to assess the correlation between conventional culture and qPCR and to explore the value of 16S rRNA in diagnosing pertussis. Nasopharyngeal swabs, collected from 102 children meeting clinical diagnostic criteria for pertussis, were subjected to Bordetella pertussis culture and qPCR. Bioinformatic microbiota analysis was based on 16S rRNA V3-V4 gene sequencing. Among 102 samples, 14 (13.7%) were culture-positive for Bordetella pertussis, while 61 (59.8%) were qPCR positive. Genus Bordetella was identified in 68 (66.7%) samples via 16S rRNA sequencing. When the relative abundance of Bordetella genus exceeded 0.70%, both qPCR and culture results were positive. Samples with a relative abundance of less than 0.20% exhibited positive qPCR and negative culture results. Samples with a low Bordetella abundance are the key factors underlying poor correlation between culture and qPCR results in laboratory tests.

RevDate: 2019-12-04

González-Serrano F, Pérez-Cobas AE, Rosas T, et al (2019)

The Gut Microbiota Composition of the Moth Brithys crini Reflects Insect Metamorphosis.

Microbial ecology pii:10.1007/s00248-019-01460-1 [Epub ahead of print].

Lepidoptera is a highly diverse insect order with major importance in agriculture as many species are considered pests. The role of the gut microbiota in insect physiology is still poorly understood, despite the research undertaken in recent years. Furthermore, Lepidoptera are holometabolous insects and few studies have addressed the influence of the changes taking place on the gut microbiome composition and diversity during metamorphosis, especially in monophagous species. The V3-V4 region of the 16S rRNA gene was sequenced to investigate the microbiota composition and diversity of the monophagous moth Brithys crini during three different life stages: egg, larvae (midgut and hindgut), and adult (gut). Our results showed that the microbiota composition of B. crini was stage specific, indicating that the developmental stage is a main factor affecting the gut microbiome in composition and potential functions. Moreover, the diversity of the gut microbiome reflected the developmental process, since a drop in diversity occurred between the larval and the adult phase, when the intestine is completely renewed. In spite of the changes in the gut microbiota during metamorphosis, 29 genera were conserved throughout the three developmental stages, mainly belonging to the Proteobacteria phylum, which define the core microbiome of B. crini. These genera seem to contribute to host physiology by participating in food digestion, nutrition, and detoxification mechanisms.

RevDate: 2019-12-04

Connors J, Dunn KA, Allott J, et al (2019)

The relationship between fecal bile acids and microbiome community structure in pediatric Crohn's disease.

The ISME journal pii:10.1038/s41396-019-0560-3 [Epub ahead of print].

Gut microbiome community structure is associated with Crohn's disease (CD) development and response to therapy. Bile acids (BAs) play a central role in modulating intestinal immune responses, and changes in gut bacterial communities can profoundly alter the intestinal BA pool. The liver synthesizes and conjugates primary bile acids (priBAs) that are then deconjugated, epimerized, and dehydroxylated by gut bacteria to produce secondary bile acids (secBAs). We investigated the relationship between the gut microbiome and the fecal BA pool in stool samples obtained from a well-characterized cohort of pediatric CD patients undergoing nutritional therapy to induce disease remission. We found that fecal BA composition was altered in a sub-group of CD patients who did not sustain remission. The microbial community structures associated with priBA and secBA-dominant profiles were distinct. In addition, the fecal BA concentrations were correlated with the abundance of distinct bacterial taxonomic groups. Finally, priBA dominant samples were associated with community-level decreases in enzymes for dehydroxylation but not deconjugation.

RevDate: 2019-12-04

Moon KR, van Dijk D, Wang Z, et al (2019)

Visualizing structure and transitions in high-dimensional biological data.

Nature biotechnology, 37(12):1482-1492.

The high-dimensional data created by high-throughput technologies require visualization tools that reveal data structure and patterns in an intuitive form. We present PHATE, a visualization method that captures both local and global nonlinear structure using an information-geometric distance between data points. We compare PHATE to other tools on a variety of artificial and biological datasets, and find that it consistently preserves a range of patterns in data, including continual progressions, branches and clusters, better than other tools. We define a manifold preservation metric, which we call denoised embedding manifold preservation (DEMaP), and show that PHATE produces lower-dimensional embeddings that are quantitatively better denoised as compared to existing visualization methods. An analysis of a newly generated single-cell RNA sequencing dataset on human germ-layer differentiation demonstrates how PHATE reveals unique biological insight into the main developmental branches, including identification of three previously undescribed subpopulations. We also show that PHATE is applicable to a wide variety of data types, including mass cytometry, single-cell RNA sequencing, Hi-C and gut microbiome data.

RevDate: 2019-12-04

Devika NT, K Raman (2019)

Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models.

Scientific reports, 9(1):18222 pii:10.1038/s41598-019-54696-9.

Bifidobacteria, the initial colonisers of breastfed infant guts, are considered as the key commensals that promote a healthy gastrointestinal tract. However, little is known about the key metabolic differences between different strains of these bifidobacteria, and consequently, their suitability for their varied commercial applications. In this context, the present study applies a constraint-based modelling approach to differentiate between 36 important bifidobacterial strains, enhancing their genome-scale metabolic models obtained from the AGORA (Assembly of Gut Organisms through Reconstruction and Analysis) resource. By studying various growth and metabolic capabilities in these enhanced genome-scale models across 30 different nutrient environments, we classified the bifidobacteria into three specific groups. We also studied the ability of the different strains to produce short-chain fatty acids, finding that acetate production is niche- and strain-specific, unlike lactate. Further, we captured the role of critical enzymes from the bifid shunt pathway, which was found to be essential for a subset of bifidobacterial strains. Our findings underline the significance of analysing metabolic capabilities as a powerful approach to explore distinct properties of the gut microbiome. Overall, our study presents several insights into the nutritional lifestyles of bifidobacteria and could potentially be leveraged to design species/strain-specific probiotics or prebiotics.

RevDate: 2019-12-04

Mudd AM, Gu T, Munagala R, et al (2019)

Chemoprevention of colorectal cancer by Anthocyanidins and mitigation of metabolic shifts induced by dysbiosis of the gut microbiome.

Cancer prevention research (Philadelphia, Pa.) pii:1940-6207.CAPR-19-0362 [Epub ahead of print].

Diets rich in fat, smoking, exposure to environmental pollutants and dysbiosis of gut microbiota, increase the risk of developing colorectal cancer (CRC). Much progress has been made in combating CRC. However, options for chemoprevention from environmental insult and dysbiosis of gut microbiota remains elusive. We investigated the influence of berry-derived anthocyanidins (Anthos), with and without encapsulating them in bovine milk-derived exosomes (ExoAnthos), on the chemoprevention of bacteria-driven colon tumor development. Anthos and ExoAnthos treatment of colon cancer cells showed dose-dependent decreases in cell viability. Calculated selectivity index (SI) values for Anthos and ExoAnthos suggest that both treatments selectively targeted cancer over normal colon cells. ExoAnthos treatment yielded higher SI values than Anthos. Anthos and ExoAnthos treatment of ApcMin/+ mice inoculated with ETBF bacteria led to significant decreases in colon tumor-numbers over mice receiving vehicle treatments. Western blot analysis of normal colon, colon tumor, and liver tissue lysates showed that mice inoculated with ETBF featured increased expression of phase I enzymes in normal colon tissue and decreased expression of phase II enzymes in liver tissue. Treatment with the Anthos and ExoAnthos reverted the modulation of phase I and phase II enzymes, respectively; no significant changes in phase II enzyme expression occurred in colon tumor tissue. Treatment of HCT-116 cells with benzo[a]pyrene led to similar modulation of phase I and II enzymes, which was partially mitigated by treatment with Anthos. These results provide a promising outlook on the impact of berry Anthos for prevention and treatment of bacteria- and benzo[a]pyrene-driven CRC.

RevDate: 2019-12-04

Chen L, Zhang Q, Wang Y, et al (2019)

Comparing dental plaque microbiome diversity of extrinsic black stain in the primary dentition using Illumina MiSeq sequencing technique.

BMC oral health, 19(1):269 pii:10.1186/s12903-019-0960-9.

BACKGROUND: Extrinsic black stain (EBS) is characterized by discrete dark dots or lines on the tooth surface. The relationship between EBS and oral microbiota in children remains elusive. The aim of this study was to compare dental plaque microbiome in EBS children with that in EBS-free children in the primary dentition.

METHODS: The Illumina MiSeq sequencing technique was utilized in the cross-sectional pilot study to investigate the diversity and composition of the supragingival plaque microbiota from 10 EBS-positive and 10 EBS-free children. The results were analysed with nonparametric Mann-Whitney U test, Pearson Chi-Square test, Fisher's Exact test and one-way ANOVA tests.

RESULTS: We identified 13 different phyla, 22 classes, 33 orders, 54 families, 105 genera, and 227 species from a total of 52,646 high-quality sequences. Between two groups, no statistical differences were observed in the estimators of community richness and diversity at 97% similarity, as well as in the Unweighted Unifrac principal co-ordinates analysis (PCoA). At the species level, higher level of relative abundance of Actinomyces naeslundii and lower level of relative abundance of a species belonging to Candidate_division_TM7 was observed in dental plaque of EBS-positive subjects, compared to dental plaque of EBS-free subjects (P < 0.05). This indicated that some species might be involved in the EBS process.

CONCLUSION: Changes in dental plaque microbiota is possibly relevant to the process of EBS in the primary dentition.

RevDate: 2019-12-04

Li KJ, Chen ZL, Huang Y, et al (2019)

Dysbiosis of lower respiratory tract microbiome are associated with inflammation and microbial function variety.

Respiratory research, 20(1):272 pii:10.1186/s12931-019-1246-0.

BACKGROUND: Lower respiratory tract (LRT) microbiome has been reported to associate with pulmonary diseases. Unregulated inflammation is an underlying cause of variable lung diseases. The lung microbiome may play an important role in the smoking-induced inflammatory lung diseases. What's more, the function of microbiome may be more important for understanding how microbes interact with host. Our study aims to explore the effects of smoking on the lower respiratory tract microbiome, the association between variation of lower respiratory tract microbiome and inflammation and whether smoking exposure changes the function of lower respiratory tract microbime.

METHODS: Forty male mice were randomly divided into smoking group and non-smoking group, and the smoking group was exposed to cigarette smoke for 2 h per day for 90 days. After experiment, the blood samples were collected to measure the concentration of interleukin-6 (IL-6) and C reactive protein (CRP) by ELISA. Lung tissue samples were used to detect the community and diversity of lower respiratory tract microbiome through 16S rRNA gene quantification and sequencing technology. ANOSIM and STAMP were performed to analyze the differences of the microbial community structure between smoking group and non-smoking group. SPSS 24.0 software was used to analyze the correlations between microbiome and inflammation mediators through scatter plots and Spearman correlation coefficient. Microbial metabolic function was predicted by PICRUSt based on the 16 s rRNA gene quantification and sequencing results. PATRIC database was searched for the potential pathogenic bacteria in lower respiratory tract.

RESULTS: Our results suggested that smoking had markedly effects on the microbiota structure of lower respiratory tract based on Bray-Curtis distance (R2 = 0.084, p = 0.005) and on unweighted uniFrac distance (R2 = 0.131, p = 0.002). Smoking mainly affected the abundance of microbiome which belong to Proteobacteria phyla and Firmicutes phyla. Moreover, our results also found that smoking increased the abundance of Acinetobacter, Bacillus and Staphylococcus, which were defined as pathogenic bacteria. Inflammatory mediators were observed to associate with certain microbiome at every level. Most of microbiome which were associated with inflammation belonged to Proteobacteria phyla or Firmicutes phyla. Moreover, we found that the decreased microbiome in smoking group, including Oceanospirillales, Desulfuromonadales, Nesterenkonia, and Lactobacillaceae, all were negatively correlated with IL-6 or CRP. Based on the level of inflammation, the abundance of microbiome differs. At genus level, Lactobacillus, Pelagibacterium, Geobacter and Zoogloea were significantly higher in smoking group with lower IL-6 concentration. The abundance of microbiome was not observed any statistical difference in subgroups with different weight. Three dominant genus, defined as pathogen, were found higher in the smoking group. The microbial functional prediction analysis revealed that ABC-type transport systems, transcription factors, amino acide transport and metabolism, arginine and proline metabolism et al. were distinctively decreased in smoking group, while the proportions of replication, recombination and repair, ribosome, DNA repair and recombination proteins were increased in smoking group (q < 0.05).

CONCLUSIONS: Members of Proteobacteria phyla and Firmicutes phyla played an important role in the microbial community composition and keeping a relatively balanced homeostasis. Microbiome dysbiosis might break the balance of immune system to drive lung inflammation. There might exist potential probiotics in lower respiratory tract, such as Lactobacillaceae. The altered function of Lower respiratory tract microbiome under smoking exposure may affect the physiological homeostasis of host.

RevDate: 2019-12-04

Raj G, Shadab M, Deka S, et al (2019)

Seed interior microbiome of rice genotypes indigenous to three agroecosystems of Indo-Burma biodiversity hotspot.

BMC genomics, 20(1):924 pii:10.1186/s12864-019-6334-5.

BACKGROUND: Seeds of plants are a confirmation of their next generation and come associated with a unique microbia community. Vertical transmission of this microbiota signifies the importance of these organisms for a healthy seedling and thus a healthier next generation for both symbionts. Seed endophytic bacterial community composition is guided by plant genotype and many environmental factors. In north-east India, within a narrow geographical region, several indigenous rice genotypes are cultivated across broad agroecosystems having standing water in fields ranging from 0-2 m during their peak growth stage. Here we tried to trap the effect of rice genotypes and agroecosystems where they are cultivated on the rice seed microbiota. We used culturable and metagenomics approaches to explore the seed endophytic bacterial diversity of seven rice genotypes (8 replicate hills) grown across three agroecosystems.

RESULTS: From seven growth media, 16 different species of culturable EB were isolated. A predictive metabolic pathway analysis of the EB showed the presence of many plant growth promoting traits such as siroheme synthesis, nitrate reduction, phosphate acquisition, etc. Vitamin B12 biosynthesis restricted to bacteria and archaea; pathways were also detected in the EB of two landraces. Analysis of 522,134 filtered metagenomic sequencing reads obtained from seed samples (n=56) gave 4061 OTUs. Alpha diversity indices showed significant differences in observed OTU richness (P≤0.05) across genotypes. Significant differences were also found between the individual hills of a rice genotype. PCoA analysis exhibited three separate clusters and revealed the clusters separated based on genotype, while agroecosystem showed a minimal effect on the variation of seed microbiota (adonis, R2=0.07, P=0.024). Interestingly, animal gut resident bacteria such as Bifidobacterium, Faecalibacterium, Lactobacillus, etc. were found in abundance as members of the seed microbiota.

CONCLUSION: Overall, our study demonstrates, indigenous rice genotypes of north-east India have a unique blend of endophytic bacteria in their mature seeds. While there are notable variations among plants of the same genotype, we found similarities among genotypes cultivated in completely different environmental conditions. The beta diversity variations across the seven rice genotypes were significantly shaped by their genotype rather than their agroecosystems.

RevDate: 2019-12-04

Rennison DJ, Rudman SM, D Schluter (2019)

Parallel changes in gut microbiome composition and function during colonization, local adaptation and ecological speciation.

Proceedings. Biological sciences, 286(1916):20191911.

The processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from the repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we use three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.

RevDate: 2019-12-04

Hylander BL, EA Repasky (2019)

Temperature as a modulator of the gut microbiome: what are the implications and opportunities for thermal medicine?.

International journal of hyperthermia : the official journal of European Society for Hyperthermic Oncology, North American Hyperthermia Group, 36(sup1):83-89.

There is substantial research being conducted on the relationships between the gut microbiome, the immune response and health and disease. Environmental temperature and heat stress are known to modify the gut microbiome. Changes in core temperature have been linked, in multiple phyla, to altered microbiome composition and function. This raises the question of whether local/regional or whole body thermal therapies which target tumors in the abdomen, peritoneal cavity, or pelvis influence the gut microbiome. To date, there is little information on whether thermal therapy exerts positive or negative effects on the microbiome. This is an intriguing question since there is growing interest in the immunological impact of various thermal therapies. The goal of this brief review is to highlight research on how environmental conditions, particularly temperature (internal as well as external temperatures) influences the gut microbiome. Given the potential for temperature shifts to modulate gut microbe function and composition, it is likely that various forms of thermal therapy, including hyperthermic intraperitoneal chemotherapy (HIPEC), deep regional, and whole body hyperthermia influence the microbiome in ways that are currently not appreciated. More research is needed to determine whether thermal therapy induced changes in the microbiome occur, and whether they are beneficial or detrimental to the host. Currently, although approaches to microbiome modification such as dietary intervention, fecal transfer, probiotics and prebiotics are being developed, the potential of temperature manipulation has, as yet, not been explored. Therefore, new research could reveal whether perturbations of the microbiome composition that have negative health consequences (dysbiosis) could be an important target for treatment by thermal medicine.

RevDate: 2019-12-04

Martinsen TC, Fossmark R, HL Waldum (2019)

The Phylogeny and Biological Function of Gastric Juice-Microbiological Consequences of Removing Gastric Acid.

International journal of molecular sciences, 20(23): pii:ijms20236031.

Gastric juice is a unique combination of hydrochloric acid (HCl), lipase, and pepsin. Acidic gastric juice is found in all vertebrates, and its main function is to inactivate microorganisms. The phylogenetic preservation of this energy-consuming and, at times, hazardous function (acid-related diseases) reflects its biological importance. Proton pump inhibitors (PPIs) are one of the most widely used drugs in the world. Due to the reduced prevalence of Helicobacter pylori infection as well as the increased use of inhibitors of gastric acid secretion, the latter has become the most important cause of gastric hypoacidity. In the present manuscript, we review the microbiological consequences of removing gastric acidity. The resulting susceptibility to infections has not been studied extensively, and focus has mainly been restricted to bacterial and parasitic agents only. The strongest evidence concerning the relationship between hypochlorhydria and predisposition to infections relates to bacterial infections affecting the gastrointestinal tract. However, several other clinical settings with increased susceptibility to infections due to inhibited gastric acidity are discussed. We also discuss the impact of hypochlorhydria on the gut microbiome.

RevDate: 2019-12-04

Carroll-Portillo A, HC Lin (2019)

Bacteriophage and the Innate Immune System: Access and Signaling.

Microorganisms, 7(12): pii:microorganisms7120625.

Bacteriophage and the bacteria they infect are the dominant members of the gastrointestinal microbiome. While bacteria are known to be central to maintenance of the structure, function, and health of the microbiome, it has only recently been recognized that phage too might serve a critical function. Along these lines, bacteria are not the only cells that are influenced by bacteriophage, and there is growing evidence of bacteriophage effects on epithelial, endothelial, and immune cells. The innate immune system is essential to protecting the Eukaryotic host from invading microorganisms, and bacteriophage have been demonstrated to interact with innate immune cells regularly. Here, we conduct a systematic review of the varying mechanisms allowing bacteriophage to access and interact with cells of the innate immune system and propose the potential importance of these interactions.

RevDate: 2019-12-04

Moghadasian MH, Kaur R, Kostal K, et al (2019)

Anti-Atherosclerotic Properties of Wild Rice in Low-Density Lipoprotein Receptor Knockout Mice: The Gut Microbiome, Cytokines, and Metabolomics Study.

Nutrients, 11(12): pii:nu11122894.

BACKGROUND AND AIM: We previously reported the anti-atherogenic properties of wild rice in low-density lipoprotein receptor knockout (LDL-r-KO) mice. The present study aimed to discover the mechanism of action for such effects.

MATERIALS: Fecal and plasma samples from the wild rice treated and control mice were used. Fecal bacterial population was estimated while using 16S rDNA technology. The plasma samples were used to estimate the levels of 35 inflammatory markers and metabolomics, while using Meso Scale multiplex assay and liquid chromatography-mass spectrometry (LC-MS/MS) techniques.

RESULTS: Many bacteria, particularly Anaeroplasma sp., Acetatifactor sp., and Prophyromonadaceae sp., were found in higher quantities in the feces of wild rice fed mice as compared to the controls. Cytokine profiles were significantly different between the plasma of treated and control mice. Among them, an increase in the level of IL-10 and erythropoietin (EPO) could explain the anti-atherogenic properties of wild rice. Among many metabolites tested in plasma of these animals, surprisingly, we found an approximately 60% increase in the levels of glucose in the wild rice fed mice as compared to that in the control mice.

CONCLUSION: Additional studies warrant further investigation of the interplay among gut microbiome, inflammatory status, and macronutrient metabolism.

RevDate: 2019-12-03

Sureda A, Daglia M, Argüelles Castilla S, et al (2019)

Oral microbiota and Alzheimer's disease: Do all roads lead to Rome?.

Pharmacological research pii:S1043-6618(19)32483-1 [Epub ahead of print].

Alzheimer's disease (AD) is a progressive neurodegenerative pathology affecting milions of people worldwide associated with deposition of senile plaques. While the genetic and environmental risk factors associated with the onset and consolidation of late onset AD are heterogeneous and sporadic, growing evidence also suggests a potential link between some infectious diseases caused by oral microbiota and AD. Oral microbiota dysbiosis is purported to contribute either directly to amyloid protein production, or indirectly to neuroinflammation, occurring as a consequence of bacterial invasion. Over the last decade, the development of Human Oral Microbiome database (HOMD) has deepened our understanding of oral microbes and their different roles during the human lifetime. Oral pathogens mostly cause caries, periodontal disease, and edentulism in aged population, and, in particular, alterations of the oral microbiota causing chronic periodontal disease have been associated with the risk of AD. Here we describe how different alterations of the oral microbiota may be linked to AD, highlighting the importance of a good oral hygiene for the prevention of oral microbiota dysbiosis.

RevDate: 2019-12-03

Siddireddy JS, Vijay AK, Tan J, et al (2019)

Effect of Eyelid Treatments on Bacterial Load and Lipase Activity in Relation to Contact Lens Discomfort.

Eye & contact lens [Epub ahead of print].

OBJECTIVES: To evaluate the effect of microblepharon exfoliation on the number of eyelid bacteria and their lipase activity and the relationship of these to contact lens discomfort.

METHODS: Thirty experienced contact lens wearers had their eyelid margin physiology, tear properties, and comfort scores assessed. The number, type, and frequency of lower eyelid margin bacteria, and their lipase activity, were measured. Eyelids were treated with a foam cleanser or microblepharon exfoliation. Clinical and microbiological tests were repeated at each visit. Changes and correlations were examined.

RESULTS: Symptomatic lens wearers had a higher ratio for the number and frequency of gram-positive rods and cocci. Microblepharon exfoliation reduced the number and ratio of gram-positive rods to cocci from baseline for symptomatic wearers that lasted 7 to 10 days after treatment (P<0.05). Numbers of bacteria, the ratio of rods to cocci, and lipase activity correlated with lash contamination (r≥0.385; P≤0.046) and anterior blepharitis (r≥0.359; P≤0.048). Bacterial lipase correlated with meibomian gland secretions (r=0.422; P=0.038) and the tear evaporation rate (r=0.479; P=0.022). Microblepharon exfoliation produced a significant reduction in CLDEQ-8 scores and converted 10 symptomatic into asymptomatic lens wearers.

CONCLUSIONS: There was dysbiosis in the lid microbiome of symptomatic lens wearers. Microblepharon exfoliation reduced the number, frequency of isolation, and ratio of gram-positive rods and cocci. Bacterial numbers and their lipase production correlated with changes to clinical signs and symptoms. Symptomatic lens wearers could be converted to asymptomatic lens wearers after microblepharon exfoliation.

RevDate: 2019-12-03

Özdemir V (2019)

Innovating Governance for Planetary Health with Three Critically Informed Frames.

Omics : a journal of integrative biology [Epub ahead of print].

In May 2019, the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services warned that "around one million animal and plant species are now threatened with extinction." In September 2019, Naomi Klein, an astute writer on environmental change, described the interconnected social and ecological breakdowns on the planet in a new book. Ecological crises noted by these and other scholars speak well to the rise of planetary health as a new scholarship. Loss of biodiversity has manifold negative impacts on health, for example, rise of zoonotic infections and changes in healthy microbiome. But reducing our ecological footprints is not enough. We ought to change mindsets, the narrow science, and technology governance regimes that value nature and other life forms instrumentally by their usefulness to us. I describe three new, broader and critically informed, frames on governance for planetary health. First, I explain why we ought to acknowledge animal sentience, for example, as recognized in Article 13 of the Lisbon Treaty in 2009. I describe how political determinants of health, power, and agency operate at multiple sociological and planetary loci, not only among human beings but also at human and nonhuman animal interfaces. Second, planetary health calls for a shift toward ecological and political determinants beyond a narrow anthropocentric view, while resisting the entrenched dogma of exponential growth with finite planetary natural resources. Third, for critically informed governance of emerging technologies in planetary health (e.g., glycomics, artificial intelligence, health care robots), I refer to a question highlighted recently (Frodeman, 2019): "When Plato (more exactly, Juvenal) asked who guards the guardians, he was questioning whether any group can be trusted to look past its own interests for the common good." Hence, it is time we broaden the question "Who will guard the guardians?" beyond the scientific community, to actors in science policy as well. Policy questions cannot be limited to "which social issues emerge from a new technology?" but ought to include, "who should be framing science and technology policy, and why?" Youth leaders of the global climate movement such as Greta Thunberg and others are now rightly asking these epistemological questions that might contribute toward a new social contract on health for all sentient beings on planet Earth. While ecological changes accelerate and a new space industry is emerging, governance for planetary health will continue to be at the epicenter of systems thinking, responsible innovation and science policy in the 21st century.

RevDate: 2019-12-03

Lee SH, Choi N, JH Sung (2019)

Pharmacokinetic and pharmacodynamic insights from microfluidic intestine-on-a-chip models.

Expert opinion on drug metabolism & toxicology [Epub ahead of print].

Introduction: After administration, a drug undergoes absorption, distribution, metabolism, and elimination (ADME) before exerting its effect on the body. The combination of these process yields the pharmacokinetic (PK) and pharmacodynamic (PD) profiles of a drug. Although accurate prediction of PK and PD profiles are essential for drug development, conventional in vitro models are limited by their lack of physiological relevance. Recently, microtechnology-based in vitro model systems, termed "organ-on-a-chip," have emerged as a potential solution.Areas covered: Orally administered drugs are absorbed through the intestinal wall and transported to the liver before entering systemic circulation, which plays important role in the PK and PD profiles. Recently developed, chip-based in vitro models can be useful models for simulating such processes and will be covered in this paper.Expert opinion: The potential of intestine-on-a-chip models combined with conventional PK-PD modeling has been demonstrated with promising preliminary results. However, there are several challenges to overcome. Development of the intestinal wall, integration of the gut microbiome, and the provision of an intestine-specific environment must be achieved to realize in vivo-like intestinal model and enhance the efficiency of drug development.

RevDate: 2019-12-03

Hendricks AJ, Eichenfield LF, VY Shi (2019)

The Impact of Airborne Pollution on Atopic Dermatitis-A Literature Review.

The British journal of dermatology [Epub ahead of print].

BACKGROUND: The increasing prevalence of atopic dermatitis (AD) parallels a global rise in industrialization and urban living over recent decades. This shift in lifestyle is accompanied by greater cutaneous exposure to environmental pollutants during the course of daily activities. Commonly encountered forms of airborne pollution include particulate matter, traffic-related air pollution, volatile organic compounds and cigarette smoke.

OBJECTIVES: To highlight the effects of airborne pollution on epidermal barrier function, examine evidence on the relationship between pollutants and AD, synthesize a proposed mechanism for pollution-induced exacerbation of AD and identify potential methods for reduction and prevention of pollutant-induced skin damage.

METHODS: Literature review was conducted via PubMed, EMBASE and Google Scholar database searches. Search terms included combinations of "pollution", "particulate matter", "traffic-related air pollution", "volatile organic compounds", "cigarette smoke", "atopic dermatitis" and "skin barrier". Inclusion criteria were in vitro and animal studies, clinical trials and case series. Non-English publications, review articles and case reports were excluded.

RESULTS: Pollutants induce cutaneous oxidative stress and have been shown to damage skin barrier integrity by altering transepidermal water loss, inflammatory signaling, stratum corneum pH and the skin microbiome. AD represents a state of inherent barrier dysfunction, and both long- and short-term pollutant exposure have been linked to exacerbation of AD symptoms and increased AD rates in population studies.

CONCLUSIONS: Airborne pollutants have a detrimental effect on skin barrier integrity and AD symptoms, and appear to pose a multifaceted threat in AD through several parallel mechanisms including oxidative damage, barrier dysfunction, immune stimulation and propagation of the itch-scratch cycle. Future research is needed to elucidate specific mechanisms of pollution-induced epidermal barrier dysfunction and to identify efficacious methods of skin barrier repair and protection against pollutant-driven damage.

RevDate: 2019-12-03

Xu J, Zhang H, Zheng J, et al (2019)

eCAMI: simultaneous classification and motif identification for enzyme annotation.

Bioinformatics (Oxford, England) pii:5651014 [Epub ahead of print].

MOTIVATION: Carbohydrate-active enzymes (CAZymes) are extremely important to bioenergy, human gut microbiome, and plant pathogen researches and industries. Here we developed a new amino acid k-mer based CAZyme classification, motif identification, and genome annotation tool using a bipartite network algorithm. Using this tool, we classified 390 CAZyme families into thousands of subfamilies each with distinguishing k-mer peptides. These k-mers represented the characteristic motifs (in the form of a collection of conserved short peptides) of each subfamily, and thus were further used to annotate new genomes for CAZymes. This idea was also generalized to extract characteristic k-mer peptides for all the Swiss-Prot enzymes classified by the EC (enzyme commission) numbers and applied to enzyme EC prediction.

RESULTS: This new tool was implemented as a Python package named eCAMI. Benchmark analysis of eCAMI against the state-of-the-art tools on CAZyme and enzyme EC datasets found that: (i) eCAMI has the best performance in terms of accuracy and memory use for CAZyme and enzyme EC classification and annotation; (ii) the k-mer based tools (including PPR-Hotpep, CUPP, eCAMI) perform better than homology-based tools and deep-learning tools in enzyme EC prediction. Lastly, we confirmed that the k-mer based tools have the unique ability to identify the characteristic k-mer peptides in the predicted enzymes.

AVAILABILITY: https://github.com/yinlabniu/eCAMI and https://github.com/zhanglabNKU/eCAMI.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

RevDate: 2019-12-03

Nolan-Kenney R, Wu F, Hu J, et al (2019)

The association between smoking and gut microbiome in Bangladesh.

Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco pii:5651036 [Epub ahead of print].

INTRODUCTION: Epidemiological studies that investigate alterations in the gut microbial composition associated with smoking are lacking. This study examined the composition of the gut microbiome in smokers compared with non-smokers.

METHODS: Stool samples were collected in a cross-sectional study of 249 participants selected from the Health Effects of Arsenic Longitudinal Study (HEALS) in Bangladesh. Microbial DNA was extracted from the fecal samples and sequenced by 16S rRNA gene sequencing. The associations of smoking status and intensity of smoking with the relative abundance or the absence and presence of individual bacterial taxon from phylum to genus levels were examined.

RESULTS: The relative abundance of bacterial taxa along the Erysipelotrichi-to-Catenibacterium lineage was significantly higher in current smokers compared to never smokers. The odds ratio comparing the mean relative abundance in current smokers with that in never smokers was 1.91 (95% confidence interval [CI] = 1.36 to 2.69) for the genus Catenibacterium and 1.89 (95% CI = 1.39 to 2.56) for the family Erysipelotrichaceae, the order Erysipelotrichale, and the class Erysipelotrichi ((FDR-adjusted p-values = 0.0008 to 0.01). A dose-response association was observed for each of these bacterial taxa. The presence of Alphaproteobacteria was significantly greater comparing current with never smokers (OR = 4.85, FDR-adjusted p-values = 0.04).

CONCLUSIONS: Our data in a Bangladeshi population are consistent with evidence of an association between smoking status and dosage with change in the gut bacterial composition.

IMPLICATIONS: This study for the first time examined the relationship between smoking and the gut microbiome composition. The data suggest that smoking status may play an important role in the composition of the gut microbiome, especially among individuals with higher levels of tobacco exposure.

RevDate: 2019-12-03

Bond SL, Workentine M, Hundt J, et al (2019)

Effects of nebulized dexamethasone on the respiratory microbiota and mycobiota and relative equine herpesvirus-1, 2, 4, 5 in an equine model of asthma.

Journal of veterinary internal medicine [Epub ahead of print].

BACKGROUND: Prolonged exposure to environmental antigens or allergens elicits an immune response in both healthy horses and those with mild asthma. Corticosteroids often are used to treat lower airway inflammation.

OBJECTIVE: To investigate the changes in equine herpesvirus (EHV)-1,2,4,5 glycoprotein B gene expression and changes in respiratory bacterial and fungal communities after nebulized dexamethasone treatment of horses with asthma.

ANIMALS: Horses with naturally occurring mild asthma (n = 16) and healthy control horses (n = 4).

METHODS: Prospective, randomized, controlled, blinded clinical trial. Polymerase chain reaction amplification of EHV-1,2,4,5 in bronchoalveolar lavage fluid, and 16S (microbiome) and ITS2 (mycobiome) genes with subsequent sequencing was performed on DNA extracted from nasal swabs and transendoscopic tracheal aspirates before and after 13 days treatment with nebulized dexamethasone (15 mg q24h) and saline (control).

RESULTS: Nebulized dexamethasone treatment decreased microbial diversity; relative abundance of 8 genera in the upper respiratory tract were altered. For both the microbiota and the mycobiota, environment had a dominant effect over treatment. Alternaria, an opportunistic pathogen and allergen in humans recognized as a risk factor for asthma, asthma severity, and exacerbations, was increased with treatment. Treatment affected relative quantification of the equine gamma herpesviruses (EHV-2 and -5); EHV-2 DNA levels increased and those of EHV-5 decreased.

CONCLUSIONS: Nebulized dexamethasone treatment affected the upper respiratory tract microbiota, but not the mycobiota, which was overwhelmed by the effect of a sustained dusty environment.

RevDate: 2019-12-03

Jukes CA, Ijaz UZ, Buckley A, et al (2019)

Bile salt metabolism is not the only factor contributing to Clostridioides (Clostridium) difficile disease severity in the murine model of disease.

Gut microbes [Epub ahead of print].

Susceptibility of patients to antibiotic-associated C. difficile disease is intimately associated with specific changes to gut microbiome composition. In particular, loss of microbes that modify bile salt acids (BSA) play a central role; primary bile acids stimulate spore germination whilst secondary bile acids limit C. difficile vegetative growth. To determine the relative contribution of bile salt (BS) metabolism on C. difficile disease severity, we treated mice with three combinations of antibiotics prior to infection. Mice given clindamycin alone became colonized but displayed no tissue pathology while severe disease, exemplified by weight loss and inflammatory tissue damage occurred in animals given a combination of five antibiotics and clindamycin. Animals given only the five antibiotic cocktails showed only transient colonization and no disease. C. difficile colonization was associated with a reduction in bacterial diversity, an inability to amplify bile salt hydrolase (BSH) sequences from fecal DNA and a relative increase in primary bile acids (pBA) in cecal lavages from infected mice. Further, the link between BSA modification and the microbiome was confirmed by the isolation of strains of Lactobacillus murinus that modified primary bile acids in vitro, thus preventing C. difficile germination. Interestingly, BSH activity did not correlate with disease severity which appeared linked to alternations in mucin, which may indirectly lead to increased exposure of the epithelial surface to inflammatory signals. These data confirm the role of microbial metabolic activity in protection of the gut and highlights the need for greater understanding the function of bacterial communities in disease prevention.

RevDate: 2019-12-03

Fernández-Musoles R, García Tejedor A, JM Laparra (2019)

Immunonutritional contribution of gut microbiota to fatty liver disease.

Nutricion hospitalaria [Epub ahead of print].

Non-alcoholic fatty liver disease (NAFLD) is indisputably the most widespread liver disease worldwide, leading to a significant increase in patient morbidity, mortality, and health care utilization. The gut microbiota and its genome (microbiome) have emerged as a novel modulator of the immunometabolic processes that NAFLD implies, but microbiota-targeted interventions have resulted both astounding and at the same time unsuccessful. The most relevant alteration appears to be the overgrowth of Gram-negative bacteria, characterized by an increased ratio of Firmicutes to Bacteroidetes, although current evidence indicates species- and strain-specific effects influencing energy harvest, the host's innate and adaptive immune systems, and epigenetic regulation as determinants of the immunomodulatory milieu in NAFLD. The genera Lactobacillus and Bifidobacterium deserve special attention since many of their probiotic strains are marketed for human consumption, even more so when considering that, in conjunction with prebiotics, they are potential modulators of gut microbiota composition and/or metabolic activity. Here, a better understanding of the major intestinal microbial factors with a detrimental or preventive role in NAFLD, and of the dynamic interplay between gut microbiome and host factors, appears crucial in defining the exposome for the prevention and treatment of NAFLD and associated diseases such as metabolic syndrome, type-2 diabetes, and obesity.

RevDate: 2019-12-03

Salameh M, Burney Z, Mhaimeed N, et al (2019)

The Role of Gut Microbiota in Atopic Asthma and Allergy, Implications in the Understanding of Disease Pathogenesis.

Scandinavian journal of immunology [Epub ahead of print].

Asthma is a clinical syndrome characterized by chronic airway inflammation. There is mounting evidence on the role of microbiota in the development of asthma. This review focuses on the role of microbiota in maintaining the integrity of the epithelia and their role in regulating the immune response. The review compiles data from multiple studies on the role of microbiota in the innate immune response and the development and differentiation of CD4+ T cells, a major component of the adaptive arm of the immune response. As a result of dysbiosis, invariant natural killer T cells may induce T helper 2 cell differentiation and immunoglobulin E isotype switching through the release of Interleukin-4 and Interleukin-13. Furthermore, degradation of immunoglobulin A antibodies, increased circulating mast cells and basophils, and inflammation are among other mechanisms by which dysbiosis can induce or exacerbate asthma. After explaining the underlying mechanisms, the review derives conclusions from studies that investigate dysbiosis in infancy and the development of asthma later in life. The review also includes studies that investigate asthmatic mothers and the development of asthma in children and the role of dysbiosis in that regard. Finally, the review explains the statistical relationship between eczema and asthma through multiple studies that investigate the role of dysbiosis in both atopic states. This review provides insight into the role of dysbiosis in asthma, and an understanding that is required to establish clinical trials which aim to modulate the gut microbiota as a means of preventing and treating asthma.

RevDate: 2019-12-03

Wong MS, Poon CC, Zhou LP, et al (2019)

Natural Products as Potential Bone Therapies.

Handbook of experimental pharmacology [Epub ahead of print].

Demands for natural products, in the form of botanicals, dietary supplements, and herbal medicine, for management of chronic diseases are increasing globally. Natural products might be an alternative for the management of bone health to meet the demands of a growing aging population. Different types of natural products, including Chinese herbal medicine decoctions, herbs, and isolated phytochemicals, have been demonstrated to exert bone protective effects. The most common types of bone protective bioactives are flavonoids, stilbene, triterpenoids, coumestans, lignans, and phenolic acid. The actions of natural products can be mediated by acting systemically on the hormonal axis or locally via their direct or indirect effects on osteogenesis, osteoclastogenesis, as well as adipogenesis. Furthermore, with the use of metabolomic and microbiome approaches to understand the actions of natural products, novel mechanisms that involve gut-brain-bone axis are also revealed. These studies provide evidence to support the use of natural products as bone therapeutics as well as identify new biological targets for novel drug development.

RevDate: 2019-12-03

Laster J, Bonnes SL, J Rocha (2019)

Increased Use of Emulsifiers in Processed Foods and the Links to Obesity.

Current gastroenterology reports, 21(11):61 pii:10.1007/s11894-019-0723-4.

PURPOSE OF REVIEW: The purpose of this review is to discuss the implications of the increased prevalence of emulsifiers in processed foods in daily consumption, the links to obesity both in mice and in vitro studies, and how those findings correlate with humans.

RECENT FINDINGS: There is rising interest in understanding the contributors to the obesity epidemic. One potential component recently studied has been the consumption of processed foods causing inflammatory changes leading to metabolic syndrome. This phenomenon has been shown in several mice and in vitro studies with changes in microbiome composition, elevated fasting blood glucose, hyperphagia, increased weight gain and adiposity, hepatic steatosis increased inflammatory markers, and a correlation with increased incidence of colorectal cancer. Emulsifiers are found in most foods consumed in the US population, which has increased over the years. This review focuses on understanding the initial approved safe levels of emulsifier consumption, the preceding increased use in foods with higher daily consumption than was previously tested, measuring these levels in animal models, and the positive association with obesity and metabolic syndrome. Future research will require prospectively studying emulsifier consumption more accurately along with the associated respective changes in the microbiome to determine the relationship to obesity.

RevDate: 2019-12-03

Carvalho MFMS, Cavalieri D, Do Nascimento S, et al (2019)

Cytokines Levels and Salivary Microbiome Play A Potential Role in Oral Lichen Planus Diagnosis.

Scientific reports, 9(1):18137 pii:10.1038/s41598-019-54615-y.

Oral lichen planus (OLP) is a chronic Th1-mediated inflammatory mucocutaneous disease of the skin and oral mucosa that can have various clinical presentations. Lesions are usually bilateral and often painful. While cutaneous Lichen Planus (LP) lesions are self-limiting, the oral lesions are chronic and rarely remissive. The diagnosis of oral lichen planus (OLP) is often challenging, and confirmation by histopathological criterion is generally advised. The aim of our study was to identify the cytokines present in OLP-suggestive lesions and in non-specific inflammatory lesions (NSIL) used as controls. Moreover, assess cytokines protein levels and oral microbiota composition in whole saliva samples. Histopathological analysis, immunohistochemistry and gene expression were used as techniques to analyze the oral mucosal tissue samples. ELISA was conducted to analyze salivary cytokine levels and 16S rRNA sequencing was used to determine the salivary microbiome. As a result we observed larger number of infiltrated lymphocytes (p = 0.025), as well, more T CD4 lymphocytes in the epithelial tissue (p = 0.006) in OLP samples compared to NSIL. In addition, the OLP samples displayed more apoptotic cells compared to NSIL (p = 0.047). Regarding the cytokine analysis, IFN-γ and IL-33 were more expressed in OLP lesions than in NSIL samples (p < 0.001; p = 0.026). Furthermore, our results demonstrated higher levels of IFN-γ protein expression in the saliva of OLP group compared to controls (p = 0.0156). We also observed noted differences in the oral microbiota composition between OLP and NSIL saliva samples. In conclusion, OLP lesions presented larger numbers of apoptotic and inflammatory cells, higher levels of IFN-γ and IL-33 compared to NSIL, and these lesions also differ regarding oral microbiota composition. These results are consistent with the Th-1-mediated chronic inflammation nature of oral lichen planus investigated lesions and displayed unique features that could be used as a diagnostic tool.

RevDate: 2019-12-03

Katani R, Schilling MA, Lyimo B, et al (2019)

Microbial Diversity in Bushmeat Samples Recovered from the Serengeti Ecosystem in Tanzania.

Scientific reports, 9(1):18086 pii:10.1038/s41598-019-53969-7.

Bushmeat, the meat and organs derived from wildlife species, is a common source of animal protein in the diets of those living in sub-Saharan Africa and is frequently associated with zoonotic spillover of dangerous pathogens. Given the frequent consumption of bushmeat in this region and the lack of knowledge about the microbial communities associated with this meat, the microbiome of 56 fresh and processed bushmeat samples ascertained from three districts in the Western Serengeti ecosystem in Tanzania was characterized using 16S rRNA metagenomic sequencing. The results show that the most abundant phyla present in bushmeat samples include Firmicutes (67.8%), Proteobacteria (18.4%), Cyanobacteria (8.9%), and Bacteroidetes (3.1%). Regardless of wildlife species, sample condition, season, or region, the microbiome is diverse across all samples, with no significant difference in alpha or beta diversity. The findings also suggest the presence of DNA signatures of potentially dangerous zoonotic pathogens, including those from the genus Bacillus, Brucella, Coxiella, and others, in bushmeat. Together, this investigation provides a better understanding of the microbiome associated with this major food source in samples collected from the Western Serengeti in Tanzania and highlights a need for future investigations on the potential health risks associated with the harvesting, trade, and consumption of bushmeat in Sub-Saharan Africa.

RevDate: 2019-12-03

Hao WZ, Li XJ, Zhang PW, et al (2019)

A review of antibiotics, depression, and the gut microbiome.

Psychiatry research pii:S0165-1781(19)30370-1 [Epub ahead of print].

Emerging evidence indicates that disruption of the intestinal flora play an important role in the pathogenesis of depression. As one of the causes of such disturbances, the role of antibiotics in depression risk is gradually being revealed. Herein, we review recent findings showing that the use of both single and multiple antibiotic regimens may be related to depression by changing the gut microbiota and the brain-gut axis. Based on recent discoveries, we also suggest that several brain-gut interactive mechanisms (particularly those involving nerve and glial cells, neurotransmitters, brain neurotrophic factors, inflammatory factors, short-chain fatty acids, circulating metabolites, blood-brain barrier, and oxidative stress) may help understand the effects of antibiotics on intestinal flora and its relationship with depression.

RevDate: 2019-12-03

Lee WH, Chen KP, Wang K, et al (2019)

Characterizing the cancer-associated microbiome with small RNA sequencing data.

Biochemical and biophysical research communications pii:S0006-291X(19)32294-6 [Epub ahead of print].

The microbiome is recognized as a quasi-organ in the human body. When dysbiosis of the microbiome occurs, this variation may contribute to alterations in the microenvironment, potentially inducing an inflammatory immune response and providing a niche for neoplastic growth. However, there is limited evidence regarding the correlation and interaction between the microbiome and tumorigenesis. By utilizing microRNA sequencing data of patients with colon and rectal cancer from The Cancer Genome Atlas, we designed a novel analytical process to extract non-human small RNA sequences and align them with the microbial genome to obtain a comprehensive view of the cancer-associated microbiome. In the present study, we identified >1000 genera among 630 colorectal samples and clustered these samples into three distinctive colorectal enterotypes. Furthermore, we found 12 genera from these clusters that are associated with cancer stages and revealed their putative functions. Our results indicate that the proposed analytical approach can effectively determine the cancer-associated microbiome. It may be readily applied to explore other types of cancer, in which specimens of the microbiome are difficult to collect.

RevDate: 2019-12-03

Zheng Y, X Gong (2019)

Niche differentiation rather than biogeography shapes the diversity and composition of microbiome of Cycas panzhihuaensis.

Microbiome, 7(1):152 pii:10.1186/s40168-019-0770-y.

BACKGROUND: Given their adaptation to nutrient-poor and drought environments, cycads are vital models for plant-microbiome interaction research because they are likely to host an important reservoir of beneficial microbes that may support cycad survival. However, a comprehensive understanding of the diversity and community composition of microbiome associated with different plant compartments as well as bulk soils of cycad species remains elusive.

METHOD: An extensive investigation of species diversity and community composition of bacterial and fungal microbiome in roots, seeds, unfertilized seeds, ovules, pollens, and soils of Cycas panzhihuaensis L. Zhou & S. Y. Yang has been conducted by high-through sequencing technology. Moreover, principal component analysis (PCA), hierarchical cluster analysis (HCA), and heatmap analysis were applied to test the niche-specific effect and biogeography factor among different sample types of this cycad species.

RESULTS: Highly diverse microbiota and significant variation of community structure were found among different compartments of C. panzhihuaensis. Soils exhibited a remarkable differentiation of bacterial community composition compared to the other five plant organs as revealed by PCA, HCA, and heatmap analyses. Different compartments possessed unique core microbial taxa with Pseudomonadaceae and Nectriaceae shared among them. According to the indicator species analysis, there was almost no differentiation of dominant microbiomes with regard to the geography of the host cycad. Two main transmission models existed in the C. panzhihuaensis.

CONCLUSIONS: Each sample type represented a unique niche and hosted a niche-specific core microbial taxa. Contrary to previous surveys, biogeography hardly exerted impact on microbial community variation in this study. The majority of the cycad-associated microbes were horizontally derived from soils and/or air environments with the rest vertically inherited from maternal plants via seeds. This study offers a robust knowledge of plant-microbiome interaction across various plant compartments and soils and lends guidelines to the investigation of adaptation mechanism of cycads in arid and nutrient-poor environments as well as their evolutionary conservation.

RevDate: 2019-12-03

Lauka L, Reitano E, Carra MC, et al (2019)

Role of the intestinal microbiome in colorectal cancer surgery outcomes.

World journal of surgical oncology, 17(1):204 pii:10.1186/s12957-019-1754-x.

OBJECTIVES: Growing evidence supports the role of the intestinal microbiome in the carcinogenesis of colorectal cancers, but its impact on colorectal cancer surgery outcomes is not clearly defined. This systematic review aimed to analyze the association between intestinal microbiome composition and postoperative complication and survival following colorectal cancer surgery.

METHODS: A systematic review was conducted according to the 2009 PRISMA guidelines. Two independent reviewers searched the literature in a systematic manner through online databases, including Medline, Scopus, Embase, Cochrane Oral Health Group Specialized Register, ProQuest Dissertations and Theses Database, and Google Scholar. Human studies investigating the association between the intestinal microbiome and the short-term (anastomotic leakage, surgical site infection, postoperative ileus) and long-term outcomes (cancer-specific mortality, overall and disease-free survival) of colorectal cancer surgery were selected. Patients with any stage of colorectal cancer were included. The Newcastle-Ottawa scale for case-control and cohort studies was used for the quality assessment of the selected articles.

RESULTS: Overall, 8 studies (7 cohort studies and 1 case-control) published between 2014 and 2018 were included. Only one study focused on short-term surgical outcomes, showing that anastomotic leakage is associated with low microbial diversity and abundance of Lachnospiraceae and Bacteroidaceae families in the non-cancerous resection lines of the stapled anastomoses of colorectal cancer patients. The other 7 studies focused on long-term oncological outcomes, including survival and cancer recurrence. The majority of the studies (5/8) found that a higher level of Fusobacterium nucleatum adherent to the tumor tissue is associated with worse oncological outcomes, in particular, increased cancer-specific mortality, decreased median and overall survival, disease-free and cancer-specific survival rates. Also a high abundance of Bacteroides fragilis was found to be linked to worse outcomes, whereas the relative abundance of the Prevotella-co-abundance group (CAG), the Bacteroides CAG, and the pathogen CAG as well as Faecalibacterium prausnitzii appeared to be associated with better survival.

CONCLUSIONS: Based on the limited available evidence, microbiome composition may be associated with colorectal cancer surgery outcomes. Further studies are needed to elucidate the role of the intestinal microbiome as a prognostic factor in colorectal cancer surgery and its possible clinical implications.

RevDate: 2019-12-02

Yan L, Herrmann M, Kampe B, et al (2019)

Environmental selection shapes the formation of near-surface groundwater microbiomes.

Water research, 170:115341 pii:S0043-1354(19)31115-7 [Epub ahead of print].

Hydrodynamics drives both stochastic and deterministic community assembly in aquatic habitats, by translocating microbes across geographic barriers and generating changes in selective pressures. Thus, heterogeneity of hydrogeological settings and episodic surface inputs from recharge areas might play important roles in shaping and maintaining groundwater microbial communities. Here we took advantage of the Hainich Critical Zone Exploratory to disentangle mechanisms of groundwater microbiome differentiation via a three-year observation in a setting of mixed carbonate-siliciclastic alternations along a hillslope transect. Variation partitioning of all data elucidated significant roles of hydrochemistry (35.0%) and spatial distance (18.6%) but not of time in shaping groundwater microbiomes. Groundwater was dominated by rare species (99.6% of OTUs), accounting for 25.9% of total reads, whereas only 26 OTUs were identified as core species. The proximity to the recharge area gave prominence to high microbial diversity coinciding with high surface inputs. In downstream direction, the abundance of rare OTUs decreased whereas core OTUs abundance increased up to 47% suggesting increasing selection stress with a higher competition cost for colonization. In general, environmental selection was the key mechanism driving the spatial differentiation of groundwater microbiomes, with N-compounds and dissolved oxygen as the major determinants, but it was more prominent in the upper aquifer with low flow velocity. Across the lower aquifer with higher flow velocity, stochastic processes appeared to be additionally important for community assembly. Overall, this study highlights the impact of surface and subsurface conditions, as well as flow regime and related habitat accessibility, on groundwater microbiomes assembly.

RevDate: 2019-12-02

Cook L, Lisko DJ, Wong MQ, et al (2019)

Analysis of flagellin-specific adaptive immunity reveals links to dysbiosis in patients with Inflammatory Bowel Disease.

Cellular and molecular gastroenterology and hepatology pii:S2352-345X(19)30167-5 [Epub ahead of print].

BACKGROUND & AIMS: Bacterial flagellin is an important antigen in Inflammatory Bowel Disease (IBD), but the role of flagellin-specific CD4+ T-cells in disease pathogenesis remains unclear. Also unknown is how changes in intestinal microbiome intersect with those in microbiota-specific CD4+ T-cells. We aimed to quantify and characterize flagellin-specific CD4+ T-cells in Crohn's disease (CD) and ulcerative colitis (UC) patients and study their relationship with intestinal microbiome diversity.

METHODS: Blood was collected from 3 cohorts which included CD and UC patients and healthy controls. Flow cytometry analysed CD4+ T-cells specific for Lachnospiraceae-derived A4-Fla2 and E. coli H18 FliC flagellins, or control vaccine antigens. Serum anti-flagellin IgG and IgA antibodies were detected by ELISA and stool samples were collected and subjected to 16S rDNA sequencing.

RESULTS: Compared to healthy controls, CD and UC patients had lower frequencies of vaccine-antigen specific CD4+ T-cells and, as a proportion of vaccine-specific cells, higher frequencies of flagellin-specific CD4+ T-cells. The proportion of flagellin-specific CD4+ T-cells that were CXCR3negCCR4+CCR6+ Th17-cells was reduced in CD and UC patients, with increased proportions of CD39+, PD-1+ and Integrin β7+ cells. Microbiome analysis revealed differentially abundant bacterial species in patient groups that correlated with immune responses to flagellin.

CONCLUSIONS: Both CD and UC patients have relative increases in the proportion of circulating Fla2-specific CD4+ T-cells, which may be associated with changes in the intestinal microbiome. Evidence that the phenotype of these cells strongly correlate with disease severity provides insight into the potential roles of flagellin-specific CD4+ T-cells in IBD.

RevDate: 2019-12-02

Ahmed N, Daniel B, Varghese J, et al (2019)

Oropharyngeal microbiome of an HIV-positive patient.

Microbial pathogenesis pii:S0882-4010(18)31956-9 [Epub ahead of print].

Studies on understanding the human microbiome continue to grow rapidly; nonetheless, reports on alterations in the microbiome post HIV infection are limited. Human microbiome is an aggregate of bacteria, fungi, viruses and archaea that have co-evolved with humans. These microbes have important roles in immune modulation, vitamin synthesis, metabolism etc. The human pharyngeal microbiome, which resides in the junction between digestive and respiratory tracts, might have a key role in the prevention of respiratory tract infections, akin to the actions of the intestinal microbiome against enteric infections. The respiratory tract is constantly exposed to various environmental and endogenous microbes; however, unlike other similar mucosal surfaces, there has been limited investigation of the microbiome of the respiratory tract. HIV infection is associated with alterations in the respiratory microbiome. The aim of this study was to use next-generation sequencing to determine the composition of the oropharyngeal microbiome in a HIV-positive individual. The bacterial composition was determined by illumina sequencing using MiSeq of partial 16S rRNA genes (V3-V4). A total of 3, 57,926 reads were analyzed. Overall, the genera Proteus, Enterococcus, Bacteroides, Prevotella and Clostridium were most prevalent bacterial populations in the oropharynx of an HIV positive patient.

RevDate: 2019-12-02

Doshi CP, Montgomery J, Quek ML, et al (2019)

"Sterile" Epididymal Abscess with Contralateral Intratesticular Recurrence.

Urology pii:S0090-4295(19)31046-5 [Epub ahead of print].

RevDate: 2019-12-02

Miller CJ, Bates ST, Gielda LM, et al (2019)

Examining transmission of gut bacteria to preserved carcass via anal secretions in Nicrophorus defodiens.

PloS one, 14(12):e0225711 pii:PONE-D-19-10903.

Direct transmission of bacteria to subsequent generations highlights the beneficial nature of host-bacteria relationships. In insects, this process is often mediated by the production of microbe-containing secretions. The objective of this study was to determine if the burying beetle, Nicrophorus defodiens, utilizes anal secretions to transmit adult digestive tract bacteria onto a small vertebrate carcass; thus creating the potential to aid in carcass preservation or pass digestive tract bacteria to their larval offspring. Using high-throughput Illumina sequencing of the 16S rRNA gene, we characterized bacterial communities of adult beetle digestive tracts, their anal secretions, and prepared mouse carcasses. We also examined unprepared carcass bacterial communities as a means to interpret community shifts that take place during carcass preservation. We found a vast reduction in diversity on prepared carcasses after anal secretion application. Overall, there was little similarity in bacterial communities among adult digestive tracts, anal secretions, and prepared carcasses, suggesting bacterial communities found in adult digestive tracts do not successfully colonize and achieve dominance on prepared carcasses by way of beetle anal secretions. We concluded that N. defodiens does not transmit their digestive tract bacterial communities to prepared carcasses in a wholesale manner, but may transmit key microbes, including core microbiome members, to preserved carcasses that may ultimately act to sustain larvae and serve as inocula for larval digestive tracts.

RevDate: 2019-12-02

Di Caro V, Alcamo AM, Cummings JL, et al (2019)

Effect of dietary cellulose supplementation on gut barrier function and apoptosis in a murine model of endotoxemia.

PloS one, 14(12):e0224838 pii:PONE-D-19-15522.

The gut plays a vital role in critical illness, and alterations in the gut structure and function have been reported in endotoxemia and sepsis models. Previously, we have demonstrated a novel link between the diet-induced alteration of the gut microbiome with cellulose and improved outcomes in sepsis. As compared to mice receiving basal fiber (BF) diet, mice that were fed a non-fermentable high fiber (HF) diet demonstrated significant improvement in survival and decreased organ injury in both cecal-ligation and puncture (CLP) and endotoxin sepsis models. To understand if the benefit conferred by HF diet extends to the gut structure and function, we hypothesized that HF diet would be associated with a reduction in sepsis-induced gut epithelial loss and permeability in mice. We demonstrate that the use of dietary cellulose decreased LPS-mediated intestinal hyperpermeability and protected the gut from apoptosis. Furthermore, we noted a significant increase in epithelial cell proliferation, as evidenced by an increase in the percentage of bromodeoxyuridine-positive cells in HF fed mice as compared to BF fed mice. Thus, the use of HF diet is a simple and effective tool that confers benefit in a murine model of sepsis, and understanding the intricate relationship between the epithelial barrier, gut microbiota, and diet will open-up additional therapeutic avenues for the treatment of gut dysfunction in critical illness.

RevDate: 2019-12-02

Hegde S, Nilyanimit P, Kozlova E, et al (2019)

CRISPR/Cas9-mediated gene deletion of the ompA gene in symbiotic Cedecea neteri impairs biofilm formation and reduces gut colonization of Aedes aegypti mosquitoes.

PLoS neglected tropical diseases, 13(12):e0007883 pii:PNTD-D-19-00160 [Epub ahead of print].

BACKGROUND: Symbiotic bacteria are pervasive in mosquitoes and their presence can influence many host phenotypes that affect vectoral capacity. While it is evident that environmental and host genetic factors contribute in shaping the microbiome of mosquitoes, we have a poor understanding regarding how bacterial genetics affects colonization of the mosquito gut. The CRISPR/Cas9 gene editing system is a powerful tool to alter bacterial genomes facilitating investigations into host-microbe interactions but has yet to be applied to insect symbionts.

To investigate the role of bacterial genetic factors in mosquito biology and in colonization of mosquitoes we used CRISPR/Cas9 gene editing system to mutate the outer membrane protein A (ompA) gene of a Cedecea neteri symbiont isolated from Aedes mosquitoes. The ompA mutant had an impaired ability to form biofilms and poorly infected Ae. aegypti when reared in a mono-association under gnotobiotic conditions. In adult mosquitoes, the mutant had a significantly reduced infection prevalence compared to the wild type or complement strains, while no differences in prevalence were seen in larvae, suggesting genetic factors are particularly important for adult gut colonization. We also used the CRISPR/Cas9 system to integrate genes (antibiotic resistance and fluorescent markers) into the symbionts genome and demonstrated that these genes were functional in vitro and in vivo.

CONCLUSIONS/SIGNIFICANCE: Our results shed insights into the role of ompA gene in host-microbe interactions in Ae. aegypti and confirm that CRISPR/Cas9 gene editing can be employed for genetic manipulation of non-model gut microbes. The ability to use this technology for site-specific integration of genes into the symbiont will facilitate the development of paratransgenic control strategies to interfere with arboviral pathogens such Chikungunya, dengue, Zika and Yellow fever viruses transmitted by Aedes mosquitoes.

RevDate: 2019-12-02

Yamanishi S, R Pawankar (2019)

Current advances on the microbiome and role of probiotics in upper airways disease.

Current opinion in allergy and clinical immunology [Epub ahead of print].

PURPOSE OF REVIEW: The prevalence of chronic upper airway inflammatory diseases such as allergic rhinitis and chronic rhinosinusitis (CRS) is increasing markedly posing a potential health threat globally. The involvement of the upper respiratory microbiota in chronic inflammatory diseases of the upper airways has been of considerable interest. The purpose of this review is to understand the characteristics of upper respiratory microbiota in both healthy and chronic inflammatory diseases of the upper airways like allergic rhinitis and CRS and to know the potential role of interventions with probiotics.

RECENT FINDINGS: We present here the studies on the nasal microbiota in healthy infants, allergic rhinitis, and CRS. The results demonstrate that there are stable and unstable profiles of microbiota during infancy. Decreased diversity or an imbalance of the microbial composition could be an important factor in the development of both allergic rhinitis and CRS. We also discuss here several recent animal and human studies that demonstrate the effect of probiotics in allergic rhinitis and chronic rhinosinusitis. Results from human studies (clinical trials) have demonstrated that probiotics may be effective for allergic rhinitis, but there are no consistent results in human CRS trials.

SUMMARY: Several strains of probiotics revealed potential efficacy for allergic rhinitis but not for CRS. Large clinical trials are essential to establish robust data on probiotics for chronic inflammatory upper airways diseases like allergic rhinitis and CRS.

RevDate: 2019-12-02

Reikvam DH, Meyer-Myklestad MH, Trøseid M, et al (2019)

Probiotics to manage inflammation in HIV infection.

Current opinion in infectious diseases [Epub ahead of print].

PURPOSE OF REVIEW: To evaluate the current scientific basis for administering probiotics to people living with HIV (PLHIV) to alleviate chronic inflammation and subsequently improve their prognosis.

RECENT FINDINGS: The gut microbiome is a potential contributing factor to low-grade inflammation in HIV infection, and there is a scientific rationale for attempting to attenuate inflammation by administering probiotics. Sixteen reports from clinical studies in antiretroviral therapy (ART)-treated PLHIV assessing inflammation after probiotic intervention have been identified; half of them randomized control trials (RCT). Some of the studies report improvement in some parameters of inflammation, but results are inconsistent. No studies report improvement of CD4 counts. None of the RCTs report improvements in any markers of inflammation when analyzed according to protocol.

SUMMARY: Current scientific evidence does not support the use of probiotics to alleviate inflammation in HIV infection. The potential effect of probiotic intervention in ART-treated PLHIV with high risk for inflammation remains to be investigated.

RevDate: 2019-12-02

Muzny CA, Van Gerwen OT, P Kissinger (2019)

Updates in trichomonas treatment including persistent infection and 5-nitroimidazole hypersensitivity.

Current opinion in infectious diseases [Epub ahead of print].

PURPOSE OF REVIEW: The purpose of this review is to update information on treatment of Trichomonas vaginalis. T. vaginalis is estimated to be the most common treatable sexually transmitted infection. In the world and is associated with poor birth outcomes, cervical cancer, sperm motility and morphology issues, and HIV acquisition and transmission.

RECENT FINDINGS: The efficacy of the recommended 2-g oral single-dose metronidazole (MTZ) for the treatment of T. vaginalis in women has recently been challenged. Two recent multicentered randomized trials and a meta-analysis have demonstrated that the 7-day dose of MTZ 500 mg twice daily was nearly two times more efficacious at clearing infection compared with the 2-g dose. Partner treatment is also essential, since up to 70% of male sexual partners can be infected and rescreening of treated women at 3 months is also recommended given the high repeat infection rates. Future studies should examine the importance of treating asymptomatic T. vaginalis, best treatment for men, the influence of the microbiome on treatment efficacy and different formulations of intravaginal treatments for hypersensitivity.

SUMMARY: 7-day 500 mg twice daily MTZ should be used as the first line treatment for T. vaginalis-infected women.

RevDate: 2019-12-02

Liu W, Huang L, Komorek R, et al (2019)

Correlative surface imaging reveals chemical signatures for bacterial hotspots on plant roots.

The Analyst [Epub ahead of print].

The rhizosphere is arguably the most complex microbial habitat on Earth, comprising an integrated network of plant roots, soil and a highly diverse microbial community (the rhizosphere microbiome). Understanding, predicting and controlling plant-microbe interactions in the rhizosphere will allow us to harness the plant microbiome as a means to increase or restore plant ecosystem productivity, improve plant responses to a wide range of environmental perturbations, and mitigate the effects of climate change by designing ecosystems for long-term soil carbon storage. To this end, it is imperative to develop new molecular approaches with high spatial resolution to capture interactions at the plant-microbe, microbe-microbe, and plant-plant interfaces. In this work, we designed an imaging sample holder that allows integrated surface imaging tools to map the same locations of a plant root-microbe interface with submicron lateral resolutions, providing novel in vivo analysis of root-microbe interactions. Specifically, confocal fluorescence microscopy, time-of-flight secondary ion mass spectrometry (ToF-SIMS), X-ray photoelectron spectroscopy (XPS), and scanning electron microscopy (SEM) were used for the first time for the correlative imaging of the Brachypodium distachyon root and its interaction with Pseudomonas SW25, a typical plant growth-promoting soil bacterium. Imaging data suggest that the root surface is inhomogeneous and that the interaction between Pseudomonas and Brachypodium roots was confined to only a few spots along the sampled root segments and that the bacterial attachment spots were enriched in Na- and S-related and high-mass organic species. We conclude that the attachment of the Pseudomonas cells to the root surface is outcompeted by strong root-soil mineral interactions but facilitated by the formation of extracellular polymeric substances (EPS).

RevDate: 2019-12-02

Fackelmann G, S Sommer (2019)

Microplastics and the gut microbiome: How chronically exposed species may suffer from gut dysbiosis.

Marine pollution bulletin, 143:193-203.

As small pieces of plastics known as microplastics pollute even the remotest parts of Earth, research currently focuses on unveiling how this pollution may affect biota. Despite increasing awareness, one potentially major consequence of chronic exposure to microplastics has been largely neglected: the impact of the disruption of the symbiosis between host and the natural community and abundance pattern of the gut microbiota. This so-called dysbiosis might be caused by the consumption of microplastics, associated mechanical disruption within the gastrointestinal tract, the ingestion of foreign and potentially pathogenic bacteria, as well as chemicals, which make-up or adhere to microplastics. Dysbiosis may interfere with the host immune system and trigger the onset of (chronic) diseases, promote pathogenic infections, and alter the gene capacity and expression of gut microbiota. We summarize how chronically exposed species may suffer from microplastics-induced gut dysbiosis, deteriorating host health, and highlight corresponding future directions of research.

RevDate: 2019-12-02

Hannula SE, Ma H, Pérez-Jaramillo JE, et al (2019)

Structure and ecological function of the soil microbiome affecting plant-soil feedbacks in the presence of a soil-borne pathogen.

Environmental microbiology [Epub ahead of print].

Interactions between plants and soil microbes are important for plant growth and resistance. Through plant-soil-feedbacks, growth of a plant is influenced by the previous plant that was growing in the same soil. We performed a plant-soil feedback study with 37 grass, forb and legume species, to condition the soil and then tested the effects of plant-induced changes in soil microbiomes on the growth of the commercially important cut-flower Chrysanthemum in presence and absence of a pathogen. We analysed the fungal and bacterial communities in these soils using next-generation sequencing and examined their relationship with plant growth in inoculated soils with or without the root pathogen, Pythium ultimum. We show that a large part of the soil microbiome is plant species-specific while a smaller part is conserved at the plant family level. We further identified clusters of plant species creating plant growth promoting microbiomes that suppress concomitantly plant pathogens. Especially soil inocula with higher relative abundances of arbuscular mycorrhizal fungi caused positive effects on the Chrysanthemum growth when exposed to the pathogen. We conclude that plants differ greatly in how they influence the soil microbiome, and that plant growth and protection against pathogens is associated with a complex soil microbial community. This article is protected by copyright. All rights reserved.

RevDate: 2019-12-02

Zhang X, Zhang X, Zhang N, et al (2019)

Airway microbiome, host immune response and recurrent wheezing in infants with severe respiratory syncytial virus bronchiolitis.

Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology [Epub ahead of print].

BACKGROUND: Early interactions between respiratory viruses and microbiota might modulate host immune responses, and subsequently contribute to later development of recurrent wheezing and asthma in childhood. We aimed to study the possible association between respiratory microbiome, host immune response, and the development of recurrent wheezing in infants with severe respiratory syncytial virus (RSV) bronchiolitis.

METHODS: Seventy-four infants who were hospitalized at Beijing Children's Hospital during an initial episode of severe RSV bronchiolitis at 6 months of age or less were included and followed for up to the age of 3 years. Sputum samples were collected, and their microbiota profiles, LPS and cytokines were analyzed by 16S rRNA-based sequencing, ELISA, and multiplex immunoassay, respectively.

RESULTS: Twenty-six (35.1%) infants developed recurrent wheezing by the age of 3 years and 48 (64.9%) did not. The relative abundance of Haemophilus, Moraxella and Klebsiella was higher in infants who later developed recurrent wheezing than those who did not (LDA score >3.5). Airway levels of LPS (P=0.003), CXCL8 (P=0.004), CCL5 (P=0.029), IL-6 (P=0.004), and IL-13 (P<0.001) were significantly higher in infants who later developed recurrent wheezing than those who did not. Moreover, high airway abundance of Haemophilus was associated with CXCL8 (r=0.246, P=0.037) level, and that of Moraxella was associated with IL-6 level (r=0.236, P=0.046) and IL-10 level (r=0.266, P=0.024).

CONCLUSION: Our study suggests that higher abundance of Haemophilus and Moraxella in airway microbiome might modulate airway inflammation during severe RSV bronchiolitis in infancy, potentially contributing to the development of subsequent recurrent wheezing in later childhood.

RevDate: 2019-12-02

Lee W, Hayakawa T, Kiyono M, et al (2019)

Gut microbiota composition of Japanese macaques associates with extent of human encroachment.

American journal of primatology [Epub ahead of print].

In recent decades, human-wildlife interaction and associated anthropogenic food provisioning has been increasing and becoming more severe due to fast population growth and urban development. Noting the role of the gut microbiome in host physiology like nutrition and health, it is thus essential to understand how human-wildlife interactions and availability of anthropogenic food in habitats can affect an animal's gut microbiome. This study, therefore, set out to examine the gut microbiota of Japanese macaques (Macaca fuscata) with varying accessibility to anthropogenic food and the possibility of using gut microbiota as indicator for macaques' reliance on anthropogenic food. Using 16S ribosomal RNA gene sequencing, we described the microbial composition of Japanese macaques experiencing different types of human disturbance and anthropogenic food availability-captive, provisioned, crop-raiding, and wild. In terms of alpha diversity, our results showed that observed richness of gut microbiota did not differ significantly between disturbance types but among collection sites, whereas Shannon diversity index differed by both disturbance types and sites. In terms of beta diversity, captive populations harbored the most distinctive gut microbial composition, and had the greatest difference compared with wild populations. Whereas for provisioned and crop-raiding groups, the macaques exhibited intermediate microbiota between wild and captive. We identified several potential bacterial taxa at different taxonomic ranks whose abundance potentially could help in assessing macaques' accessibility to anthropogenic food. This study revealed the flexibility of the gut microbiome of Japanese macaques and provided possible indices based on the gut microbiome profile in assessing macaques' accessibility to/reliance on anthropogenic foods.

RevDate: 2019-12-02

McIlroy SE, Cunning R, Baker AC, et al (2019)

Competition and succession among coral endosymbionts.

Ecology and evolution, 9(22):12767-12778 pii:ECE35749.

Host species often support a genetically diverse guild of symbionts, the identity and performance of which can determine holobiont fitness under particular environmental conditions. These symbiont communities are structured by a complex set of potential interactions, both positive and negative, between the host and symbionts and among symbionts. In reef-building corals, stable associations with specific symbiont species are common, and we hypothesize that this is partly due to ecological mechanisms, such as succession and competition, which drive patterns of symbiont winnowing in the initial colonization of new generations of coral recruits. We tested this hypothesis using the experimental framework of the de Wit replacement series and found that competitive interactions occurred among symbionts which were characterized by unique ecological strategies. Aposymbiotic octocoral recruits within high- and low-light environments were inoculated with one of three Symbiodiniaceae species as monocultures or with cross-paired mixtures, and we tracked symbiont uptake using quantitative genetic assays. Priority effects, in which early colonizers excluded competitive dominants, were evidenced under low light, but these early opportunistic species were later succeeded by competitive dominants. Under high light, a more consistent competitive hierarchy was established in which competitive dominants outgrew and limited the abundance of others. These findings provide insight into mechanisms of microbial community organization and symbiosis breakdown and recovery. Furthermore, transitions in competitive outcomes across spatial and temporal environmental variation may improve lifetime host fitness.

RevDate: 2019-12-02

Holmes IA, Monagan IV, Rabosky DL, et al (2019)

Metabolically similar cohorts of bacteria exhibit strong cooccurrence patterns with diet items and eukaryotic microbes in lizard guts.

Ecology and evolution, 9(22):12471-12481 pii:ECE35691.

Gut microbiomes perform essential services for their hosts, including helping them to digest food and manage pathogens and parasites. Performing these services requires a diverse and constantly changing set of metabolic functions from the bacteria in the microbiome. The metabolic repertoire of the microbiome is ultimately dependent on the outcomes of the ecological interactions of its member microbes, as these interactions in part determine the taxonomic composition of the microbiome. The ecological processes that underpin the microbiome's ability to handle a variety of metabolic challenges might involve rapid turnover of the gut microbiome in response to new metabolic challenges, or it might entail maintaining sufficient diversity in the microbiome that any new metabolic demands can be met from an existing set of bacteria. To differentiate between these scenarios, we examine the gut bacteria and resident eukaryotes of two generalist-insectivore lizards, while simultaneously identifying the arthropod prey each lizard was digesting at the time of sampling. We find that the cohorts of bacteria that occur significantly more or less often than expected with arthropod diet items or eukaryotes include bacterial species that are highly similar to each other metabolically. This pattern in the bacterial microbiome could represent an early step in the taxonomic shifts in bacterial microbiome that occur when host lineages change their diet niche over evolutionary timescales.

RevDate: 2019-12-02

Mohr S, Amylidi-Mohr SK, Stadelmann P, et al (2019)

Systemic Inflammation in Pregnant Women With Periodontitis and Preterm Prelabor Rupture of Membranes: A Prospective Case-Control Study.

Frontiers in immunology, 10:2624.

Aims: Periodontal disease is associated with adverse pregnancy outcome, but the underlying pathophysiologic mechanism is still unknown. In this prospective, longitudinal, non-interventional case-control study, 45 women with preterm premature rupture of membranes and 26 controls with uncomplicated pregnancies were examined at three time-points (T1: 20-34 weeks of gestations; T2: within 48 h after delivery; T3: 4-6 weeks post partum). Examinations included subgingival, blood, vaginal, and placenta sampling for microbiologic, cytokine, and histology assessment. Objective of this study was to test the hypothesis that systemic inflammatory changes and not specific bacteria are predominantly involved in the association between periodontal disease and adverse pregnancy outcome. Results: Demographic data and gestational age at T1 were comparable between groups. While there was no correlation between vaginal and gingival fluid microbiome, cytokine levels in the assessed compartments differed between cases, and controls. Vaginal smears did not show a higher rate of abnormal flora in the cases at the onset of preterm premature rupture of membranes. Number and variety of bacteria in the case group placental membranes and vagina were higher, but these bacteria were not found in membranes at birth. Conclusions: On the basis of our results we speculate that an inflammatory pathway sequentially involving periodontal tissue, maternal serum, and finally vaginal compartment contributes to the underlying pathomechanism involved in preterm premature rupture of membranes associated with periodontitis.

RevDate: 2019-12-02

Broman E, Asmala E, Carstensen J, et al (2019)

Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter.

Frontiers in microbiology, 10:2579.

Coastal zones are important transitional areas between the land and sea, where both terrestrial and phytoplankton supplied dissolved organic matter (DOM) are respired or transformed. As climate change is expected to increase river discharge and water temperatures, DOM from both allochthonous and autochthonous sources is projected to increase. As these transformations are largely regulated by bacteria, we analyzed microbial community structure data in relation to a 6-month long time-series dataset of DOM characteristics from Roskilde Fjord and adjacent streams, Denmark. The results showed that the microbial community composition in the outer estuary (closer to the sea) was largely associated with salinity and nutrients, while the inner estuary formed two clusters linked to either nutrients plus allochthonous DOM or autochthonous DOM characteristics. In contrast, the microbial community composition in the streams was found to be mainly associated with allochthonous DOM characteristics. A general pattern across the land-to-sea interface was that Betaproteobacteria were strongly associated with humic-like DOM [operational taxonomic units (OTUs) belonging to family Comamonadaceae], while distinct populations were instead associated with nutrients or abiotic variables such as temperature (Cyanobacteria genus Synechococcus) and salinity (Actinobacteria family Microbacteriaceae). Furthermore, there was a stark shift in the relative abundance of OTUs between stream and marine stations. This indicates that as DOM travels through the land-to-sea interface, different bacterial guilds continuously degrade it.

RevDate: 2019-12-02

Miller CA, Holm HC, Horstmann L, et al (2019)

Coordinated transformation of the gut microbiome and lipidome of bowhead whales provides novel insights into digestion.

The ISME journal pii:10.1038/s41396-019-0549-y [Epub ahead of print].

Whale digestion plays an integral role in many ocean ecosystems. By digesting enormous quantities of lipid-rich prey, whales support their energy intensive lifestyle, but also excrete nutrients important to ocean biogeochemical cycles. Nevertheless, whale digestion is poorly understood. Gastrointestinal microorganisms play a significant role in vertebrate digestion, but few studies have examined them in whales. To investigate digestion of lipids, and the potential contribution of microbes to lipid digestion in whales, we characterized lipid composition (lipidomes) and bacterial communities (microbiotas) in 126 digesta samples collected throughout the gastrointestinal tracts of 38 bowhead whales (Balaena mysticetus) harvested by Alaskan Eskimos. Lipidomes and microbiotas were strongly correlated throughout the gastrointestinal tract. Lipidomes and microbiotas were most variable in the small intestine and most similar in the large intestine, where microbiota richness was greatest. Our results suggest digestion of wax esters, the primary lipids in B. mysticetus prey representing more than 80% of total dietary lipids, occurred in the mid- to distal small intestine and was correlated with specific microorganisms. Because wax esters are difficult to digest by other marine vertebrates and constitute a large reservoir of carbon in the ocean, our results further elucidate the essential roles that whales and their gastrointestinal microbiotas play in the biogeochemical cycling of carbon and nutrients in high-latitude seas.

RevDate: 2019-12-02

Willis HJ, JL Slavin (2019)

The Influence of Diet Interventions Using Whole, Plant Food on the Gut Microbiome: A Narrative Review.

Journal of the Academy of Nutrition and Dietetics pii:S2212-2672(19)31372-3 [Epub ahead of print].

Dietary intake is a key determinant of gastrointestinal microbiota composition. Studies have considered the relationship between gut microbiota and dietary patterns. It is likely that certain plant foods that contain fiber and other bioactive matter may be more likely to drive microbial changes than others; however, study design and other factors can make interpretation of the literature difficult. Fifteen well-controlled, well-defined diet interventions published between 2008 and 2018 using whole, plant foods were evaluated for their influence on gut microbiota. There was limited effect on microbial diversity across studies and modest microbial changes were noted in 10 of 15 studies. More research is needed before specific plant foods can be recommended to improve gut microbiota and ultimately health. Methodologic considerations for future diet and microbiome studies are discussed. Additional research to better understand how specific whole, plant foods influence microbe composition, functionality, and metabolite production is needed, as are mechanistic studies linking diet-induced gut microbe changes to health.

RevDate: 2019-12-01

Laster J, LA Frame (2019)

Beyond the Calories-Is the Problem in the Processing?.

Current treatment options in gastroenterology pii:10.1007/s11938-019-00246-1 [Epub ahead of print].

PURPOSE OF REVIEW: The purpose of this review is to describe the trends in dietary patterns and food quality over time along with the possible role of ultra-processed foods in obesity, chronic diseases, and all-cause mortality in the US population.

RECENT FINDINGS: There is a rising obesity epidemic, corresponding chronic diseases, and increases in ultra-processed food consumption. In mice and in vitro trials, emulsifiers, found in processed foods, have been found to alter microbiome compositions, elevate fasting blood glucose, cause hyperphagia, increase weight gain and adiposity, and induce hepatic steatosis. Recent human trials have found ultra-processed foods as a contributor to decreased satiety, increased meal eating rates, worsening biochemical markers, and more weight gain. In contrast, Blue Zone, indigenous South American, and Mediterranean populations with low meat intake, high fiber, and minimally processed foods have far less chronic diseases, obesity rates, and live longer disease-free. As the USA continues to industrialize, food has become more processed and cheaper and more convenient along with the coexistent rise in obesity prevalence. This review highlights the overall trends in food: mild improvements in dietary quality in higher socioeconomic populations, but no significant increases in whole fruit, vegetables, legumes, or nuts. Consumption of ultra-processed food is associated with weight gain and may contribute to metabolic syndrome and chronic disease. To combat this epidemic, we must create and disseminate detailed recommendations to improve diet quality and overall nutrition.

RevDate: 2019-12-01

Lee A, Arachchige BJ, Reed S, et al (2019)

Plasma from some patients with amyotrophic lateral sclerosis exhibits elevated formaldehyde levels.

Journal of the neurological sciences, 409:116589 pii:S0022-510X(19)32353-6 [Epub ahead of print].

INTRODUCTION: The aim of this study was to determine whether patients with amyotrophic lateral sclerosis (ALS) exhibit higher plasma levels of formaldehyde (FA) than controls, and to look for alterations in levels of FA precursors.

METHODS: We studied 40 heathy controls and 50 ALS patients from the Motor Neuron Disease clinic at the Royal Brisbane & Women's Hospital. Plasma FA levels were quantified using a FA detection assay. Trimethylamine (TMA) and trimethylamine oxide (TMAO) in plasma were quantified by multiple reaction monitoring (MRM) mass spectrometry. Plasma levels in patients and controls were compared using Mann-Whitney U test and Spearman's correlation test was used to assess the correlation between levels of FA, TMA, TMAO and other variables.

RESULTS: The levels of plasma FA were significantly greater in ALS subjects than controls. TMA and TMAO levels were not significantly different between healthy controls and patients, but were greater in ALS subjects with elevated FA levels than those with normal levels. Of note, levels of TMA and TMAO demonstrated a significant positive correlation with plasma FA levels (spearman's correlation coefficients of TMA with FA [r = 0.451, p = 0.010] and TMAO [r = 0.401, p = 0.023]). There was no association of FA levels with disability measured with the ALS functional rating scale, with the duration of disease or with the age of the subjects.

CONCLUSION: Elevated FA is found in some patients with ALS. FA is neurotoxic and could contribute to disease pathogenesis.

RevDate: 2019-12-01

Tansey M (2019)

Editorial for Special issue on Microbiome in neurological and psychiatric disease.

RevDate: 2019-12-01

Dixon M, Sha S, Stefil M, et al (2019)

Is it time to say goodbye to culture and sensitivity? The case for culture-independent urology.

Urology pii:S0090-4295(19)31055-6 [Epub ahead of print].

Next-Generation sequencing (NGS) has highlighted the limitations of conventional culture methods in the role of urology whilst discovering the intricate details of the role of microbiota in urologic health and disease. This review article explores: the utility and limitations of conventional culture methods; how culture-independent technologies are revolutionising medicine; and how the implementation of these technologies may lead to improved patient outcomes. Finally, this article discusses the barriers to widespread adoption of culture-independent technologies, with suggestions for how these hurdles may be overcome.

RevDate: 2019-12-01

Liu Y, Wang Y, Ni Y, et al (2019)

Gut Microbiome Fermentation Determines the Efficacy of Exercise for Diabetes Prevention.

Cell metabolism pii:S1550-4131(19)30608-4 [Epub ahead of print].

Exercise is an effective strategy for diabetes management but is limited by the phenomenon of exercise resistance (i.e., the lack of or the adverse response to exercise on metabolic health). Here, in 39 medication-naive men with prediabetes, we found that exercise-induced alterations in the gut microbiota correlated closely with improvements in glucose homeostasis and insulin sensitivity (clinicaltrials.gov entry NCT03240978). The microbiome of responders exhibited an enhanced capacity for biosynthesis of short-chain fatty acids and catabolism of branched-chain amino acids, whereas those of non-responders were characterized by increased production of metabolically detrimental compounds. Fecal microbial transplantation from responders, but not non-responders, mimicked the effects of exercise on alleviation of insulin resistance in obese mice. Furthermore, a machine-learning algorithm integrating baseline microbial signatures accurately predicted personalized glycemic response to exercise in an additional 30 subjects. These findings raise the possibility of maximizing the benefits of exercise by targeting the gut microbiota.

RevDate: 2019-12-01

Li W, Liu Y, Hou Q, et al (2019)

Lactobacillus plantarum improves the efficiency of sheep manure composting and the quality of the final product.

Bioresource technology pii:S0960-8524(19)31686-4 [Epub ahead of print].

The addition of exogenous microorganisms is one approach with potential that may also overcome the problem in northern China of slow composting in autumn and winter due to low environmental temperatures. This study investigated the use of supplements of Lactobacillus plantarum (L. plantarum), strains P-8 and LP-10, on the efficiency of sheep manure composting and the quality of the final product. The composting process lasted eight weeks and, during this time, changes in multiple physical-chemical parameters and the compost microbiome were monitored. Microbiota-encoded functions, community structure and physical-chemical parameters were distinct between the two groups. 'Composting microbiota maturation index' was proposed to quantitatively compare the impact of maturation on composting microecology. The rapid improvement in composting rate (4 weeks) and quality of the final product suggest that this approach could provide both technological and economic benefits. This work reveals the tremendous potential of L. plantarum as a promoter in composting.

RevDate: 2019-12-01

Kohn T, Wiegand S, Boedeker C, et al (2019)

Planctopirus ephydatiae, a novel Planctomycete isolated from a freshwater sponge.

Systematic and applied microbiology pii:S0723-2020(19)30317-0 [Epub ahead of print].

The microbiome of freshwater sponges is rarely studied, and not a single novel bacterial species has been isolated and subsequently characterized from a freshwater sponge to date. A previous study showed that 14.4% of the microbiome from Ephydatia fluviatilis belong to the phylum Planctomycetes. Therefore, we sampled an Ephydatia sponge from a freshwater lake and employed enrichment techniques targeting bacteria from the phylum Planctomycetes. The obtained strain spb1T was subject to genomic and phenomic characterization and found to represent a novel planctomycetal species proposed as Planctopirus ephydatiae sp. nov. (DSM 106606 = CECT 9866). In the process of differentiating spb1T from its next relative Planctopirus limnophila DSM 3776T, we identified and characterized the first phage - Planctopirus phage vB_PlimS_J1 - infecting planctomycetes that was only mentioned anecdotally before. Interestingly, classical chemotaxonomic methods would have failed to distinguish Planctopirus ephydatiae strain spb1T from Planctopirus limnophila DSM 3776T. Our findings demonstrate and underpin the need for whole genome-based taxonomy to detect and differentiate planctomycetal species.

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ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

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Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).

Timelines

ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.

Biographies

Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )