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Bibliography on: Microbiome

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ESP: PubMed Auto Bibliography 13 Jul 2019 at 01:45 Created: 


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: 2019-07-12

Han L, Zhang H, Chen S, et al (2019)

Intestinal microbiota can predict aGVHD following allogeneic hematopoietic stem cell transplantation.

Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation pii:S1083-8791(19)30438-0 [Epub ahead of print].

The intestinal microbiome plays an important role in the development of acute graft-versus-host disease (aGVHD). However, it has been rarely reported whether intestinal microbiota could predict the development of aGVHD. Here, we conducted a prospective study of microbiota in 141 patients post-transplantation. We found that the microbiota diversity was lower in the aGVHD group compared with non-aGVHD group at day 0 and day 15±1 (P = 0.018 and 0.009, respectively). Diversity was negatively associated with conditioning intensity (P = 0.017, day 0 and P = 0.045, day 15) and β-lactam antibiotics administration (P = 0.004, day 15). Intensified conditioning and β-lactam antibiotics were associated with a lower ratio of Treg/Th17 cells at day 15 (P = 0.030, 0.047, respectively). At day 15, the levels of the inflammatory factors (TNF-α, IL-6, IL-17A, IL-1β, and LPS) were higher in the intensified conditioning group compared with the standard group (P < 0.05). AIM score was defined as microbiota diversity and gradient of the four bacterials (Lachnospiraceae, Peptostreptococcaceae, Erysipelotrichaceae, and Enterobacteriaceae) at day 15 post-transplantation. AIM score was positively correlated with aGVHD grades (r = 0.481, P < 0.001), and the AIM score could be a predictor for the development of aGVHD (II-IV aGVHD: AUC = 0.75, P < 0.001; III-IV aGVHD: AUC = 0.84, P < 0.001). These findings suggest that intestinal microbiota and conditioning might induce aGVHD by inflammatory factors and the Treg/Th17 balance. The constitution of the intestinal microbiota at neutrophil engraftment may predict the development of aGVHD.

RevDate: 2019-07-12

Gommers LMM, Ederveen THA, van der Wijst J, et al (2019)

Low gut microbiota diversity and dietary magnesium intake are associated with the development of PPI-induced hypomagnesemia.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology [Epub ahead of print].

Proton pump inhibitors (PPIs) are used by millions of patients for the treatment of stomach acid-reflux diseases. Although PPIs are generally considered safe, about 13% of the users develop hypomagnesemia. Despite rising attention for this issue, the underlying mechanism is still unknown. Here, we examine whether the gut microbiome is involved in the development of PPI-induced hypomagnesemia in wild-type C57BL/6J mice. After 4 wk of treatment under normal or low dietary Mg2+ availability, omeprazole significantly reduced serum Mg2+ levels only in mice on a low-Mg2+ diet without affecting the mRNA expression of colonic or renal Mg2+ transporters. Overall, 16S rRNA gene sequencing revealed a lower gut microbial diversity in omeprazole-treated mice. Omeprazole induced a shift in microbial composition, which was associated with a 3- and 2-fold increase in the abundance of Lactobacillus and Bifidobacterium, respectively. To examine the metabolic consequences of these microbial alterations, the colonic composition of organic acids was evaluated. Low dietary Mg2+ intake, independent of omeprazole treatment, resulted in a 10-fold increase in formate levels. Together, these results imply that both omeprazole treatment and low dietary Mg2+ intake disturb the gut internal milieu and may pose a risk for the malabsorption of Mg2+ in the colon.-Gommers, L. M. M., Ederveen, T. H. A., van der Wijst, J., Overmars-Bos, C., Kortman, G. A. M., Boekhorst, J., Bindels, R. J. M., de Baaij, J. H. F., Hoenderop, J. G. J. Low gut microbiota diversity and dietary magnesium intake are associated with the development of PPI-induced hypomagnesemia.

RevDate: 2019-07-12

Koedooder R, Singer M, Schoenmakers S, et al (2019)

Corrigendum. The vaginal microbiome as a predictor for outcome of in vitro fertilization with or without intracytoplasmic sperm injection: a prospective study.

Human reproduction (Oxford, England) pii:5531397 [Epub ahead of print].

RevDate: 2019-07-12

Brar PC, B Kohn (2019)

Use of the microbiome in the management of children with type 2 diabetes mellitus.

Current opinion in pediatrics, 31(4):524-530.

PURPOSE OF REVIEW: The purpose of this review is to present recent data that defines our current understanding of the role of the gut microbiome in the development of T2DM.

RECENT FINDINGS: Recent studies focus on the physiology and molecular pathways of the gut microbiome-host interaction. Short-chain fatty acids (SCFAs) derived from the fermentation of plant-based nonsoluble fiber bind to G-protein-coupled receptors (GPR) GPR 41 and GPR 43 to induce enteroendocrine molecules that control appetite, and to upregulate intestinal gluconeogenesis gene expression that controls glucose regulation. "Metabolic endotexemia" reflects a state of low-grade systemic inflammation that results from lipopolysaccharide (LPS) release from the gut into the systemic circulation in response to a high-fat diet. Inflammatory pathways induced by LPS, activation of toll-like receptor-4 (TLR-4), and other inflammatory signaling pathways are mediators of systemic inflammation, insulin resistance and type II diabetes mellitus.

SUMMARY: Recent scientific data support that derangements in the composition of the microbiota, termed "microbiome dysbiosis" is a factor in the development of "metabolic endotoxemia" and T2DM. Therapeutic options that target the gut microbiome in the treatment of T2DM are explored.

RevDate: 2019-07-12

Windisch O, Frossard JL, Schiffer E, et al (2019)

Microbiologic Changes Induced by Biliary Drainage Require Adapted Antibiotic Prophylaxis during Duodenopancreatectomy.

Surgical infections [Epub ahead of print].

Background: Patients with periampullary tumors frequently undergo endoscopic biliary investigations and biliary drainage (BD) prior to surgery. Recent literature shows a shift of the biliary microbiome toward more resistant bacteria in patients having BD. This study aimed to evaluate the local microbiome and changes induced by BD and related antibiotic exposure and to consider the choice of antibiotic for peri-operative prophylaxis. Methods: A single-center retrospective cohort study included patients operated on for periampullary tumors between January 2013 and November 2017. All patients had intra-operative bile samples taken for culture and peri-operative antibiotic use as well as documentation of complications according to the Dindo-Clavien classification. Results: A total of 37 patients were included. All received pre-operative endoscopy, and 29 (78%) had BD preceded by administration of ceftriaxone or metronidazole. Intra-operative antibiotic prophylaxis consisted of cefuroxime (92%) or ceftriaxone (13%) combined with metronidazole (100%). Bacterial contamination of bile samples was more common in the BD group than in the no biliary drainage (NBD) group (93% vs 38%; p < 0.01). A shift was observed from bile containing mainly Escherichia coli and Streptococcus spp. toward Enterococcus faecalis (0 in the NBD group versus 44.8% in the BD group; p < 0.01), Enterococcus faecium (0 versus 23%; p = 0.3), and Candida albicans (0 versus 34.5%; p = 0.08). Post-operative antibiotic modifications were common. No difference was found regarding Dindo-Clavien complications, post-operative stay, or antibiotic use in the two groups, although one patient in the NBD group who had pre-operative biliary endoscopy with antibiotic prophylaxis developed a fatal septic clot caused by Escherichia coli resistant to cefuroxime. Conclusions: We observed a significant change toward colonization by enterococci and fungi in the microbiome of patients who had pre-operative biliary investigations or drainage with antibiotic prophylaxis. These findings indicate that bile samples should be obtained systematically during surgery for periampullary tumors to guide any post-operative antibiotic therapy and peri-operative antibiotic prophylaxis and might need adaptation to target the modified microbiome.

RevDate: 2019-07-12

Wilson KM, Rodrigues DR, Briggs WN, et al (2019)

Evaluation of the impact of in ovo administered bacteria on microbiome of chicks through 10 days of age.

Poultry science pii:5531588 [Epub ahead of print].

Initial inoculation and colonization of the chicken gastrointestinal tract (GIT) by microbiota have been suggested to have a major influence on the growth performance and health of birds. Commercial practices in chicken production may alter or delay microbial colonization by pioneer colonizing bacteria that can have an impact on the development and maturation of the GIT and intestinal microflora. The objective of this study was to compare the impact of apathogenic Gram-negative isolates or lactic acid bacteria (LAB) as pioneer colonizers on the microbiome at the day of hatch (DOH) and evaluate the influence through 10 D of age on ceca. At 18 embryonic days (E), the amnion of embryos was inoculated with either saline (S), approximately 102 CFU of LAB (L), Citrobacter freundii (C), or Citrobacter species (C2). Once DNA was isolated from mucosal and digesta contents, samples underwent 2 × 300 paired-end Illumina MiSeq library preparation for microbiome analysis. An increased abundance of Lactobacillaceae family and Lactobacillus genus was observed in the L group at DOH (P < 0.05), whereas the abundance of Enterococcaceae and Enterococcus was numerically decreased. While Lactobacillus salivarius was one of the pioneer colonizers in the L group at 18E, the population decreased by 10 D (39.59 to 0.09%) and replaced with a population of undefined Lactobacillus (10.36%) and Lactobacillus reuteri (3.63%). Results suggest that L treatment may have accelerated a mature microbiota. Enterobacteriaceae was the dominant family (57.44%) in C group at DOH (P < 0.05). The C2 group only showed some abundance of the C2 species (7.92%) at DOH but had the highest overall abundance of undefined Lactobacillus in the ceca by 10 D (25.28%). Taken together, different isolates provided in ovo can have an impact on the initial microbiome of the GIT, and some of these differences in ceca remain notable at 10 D.

RevDate: 2019-07-12

Ferreira JA, S Fuentes (2019)

Some comments on certain statistical aspects of the study of the microbiome.

Briefings in bioinformatics pii:5530331 [Epub ahead of print].

This note complements and clarifies part of the work of Hawinkel et al. recently published in the journal and suggests some more or less standard tools and methods for carrying out association studies of the microbiome.

RevDate: 2019-07-12

Michels N (2019)

Biological underpinnings from psychosocial stress towards appetite and obesity during youth: research implications towards metagenomics, epigenomics and metabolomics.

Nutrition research reviews pii:S0954422419000143 [Epub ahead of print].

Psychosocial stress, uncontrolled eating and obesity are three interrelated epidemiological phenomena already present during youth. This broad narrative conceptual review summarises main biological underpinnings of the stress-diet-obesity pathway and how new techniques can further knowledge. Cortisol seems the main biological factor from stress towards central adiposity; and diet, physical activity and sleep are the main behavioural pathways. Within stress-diet, the concepts of comfort food and emotional eating are highlighted, as cortisol affects reward pathways and appetite brain centres with a role for insulin, leptin, neuropeptide Y (NPY), endocannabinoids, orexin and gastrointestinal hormones. More recently researched biological underpinnings are microbiota, epigenetic modifications and metabolites. First, the gut microbiota reaches the stress-regulating and appetite-regulating brain centres via the gut-brain axis. Second, epigenetic analyses are recommended as diet, obesity, stress and gut microbiota can change gene expression which then affects appetite, energy homeostasis and stress reactivity. Finally, metabolomics would be a good technique to disentangle stress-diet-obesity interactions as multiple biological pathways are involved. Saliva might be an ideal biological matrix as it allows metagenomic (oral microbiota), epigenomic and metabolomic analyses. In conclusion, stress and diet/obesity research should be combined in interdisciplinary collaborations with implementation of several -omics analyses.

RevDate: 2019-07-12

Cӑtoi AF, Vodnar DC, Corina A, et al (2019)

Gut Microbiota, Obesity and Bariatric Surgery: Current Knowledge and Future Perspectives.

Current pharmaceutical design pii:CPD-EPUB-99476 [Epub ahead of print].

BACKGROUND: There is an urgent need for a better understanding and management of obesity and obesity-associated diseases. It is known that obesity is associated with structural and functional changes in the microbiome.

METHODS: The purpose of this review is to present current evidence from animal and human studies, demonstrating the effects and the potential efficacy of microbiota modulation in improving obesity and associated metabolic dysfunctions.

RESULTS: This review discusses possible mechanisms linking gut microbiota dysbiosis and obesity, since there is a dual interaction between the two of them. Furthermore, comments on bariatric surgery, as a favourable model to understand the underlying metabolic and inflammatory effects, as well as its association with changes in the composition of the gut microbiota, are included. Also, a possible impact of anti-obesity drugs and the novel antidiabetic drugs on the gut microbiota has been briefly discussed.

CONCLUSION: More research is needed to better understand here discussed association between microbiota modulation and obesity. It is expecting that research in this field, in the following years, will lead to a personalized therapeutic approach considering the patient's microbiome, and also give rise to the discovery of new drugs and/or the combination therapies for the management of obesity and obesity-related co-morbidities.

RevDate: 2019-07-12

Choi Y, Lee S, Kim S, et al (2019)

Vitamin E (α-tocopherol) consumption influences gut microbiota composition.

International journal of food sciences and nutrition [Epub ahead of print].

This study evaluated if vitamin E consumption affects gut microbiota. Mice were grouped into control, low vitamin E (LV), and high vitamin E (HV). LV and HV were fed DL-α-tocopherol at 0.06 mg/20 g and 0.18 mg/20 g of body weight per day, respectively, for 34 days. Body weight of mice was measured before and after vitamin E treatment. Animals were sacrificed, liver, spleen, small intestine and large intestine collected, and weight and length were measured. Composition of gut microbiota was determined by microbiome analysis. Spleen weight index of LV was the highest. However, liver weight indices and intestinal lengths were not different. Body weights of LV group were higher than those of control. Ratio of Firmicutes to Bacteroidetes was different in LV compared to control and HV. These results indicate that low-level consumption of vitamin E increases spleen and body weight, and changes gut microbiota.

RevDate: 2019-07-12

Zhang Y, Zhang Y, Kuang Z, et al (2019)

Comparison of microbiomes and resistomes in two Karst groundwater sites in Chongqing, China.

Karst groundwater is an important water resource as it accounts for about 15% of the total landscape of the earth and supplies 20% of potable water worldwide. The antibiotics resistance is an emerging global concern, and antibiotics residual and increase of antibiotic resistance genes represent serious global concerns and emerging pollutants. There is no report on the antibiotic resistance genes in groundwater. To survey resistome and microbiome in Karst groundwater, two Karst water samples were chosen for metagenome and metatranscriptome study, namely the 37th spring (C) and Dongcao spring (R) in Beibei, Chongqing, China. The two sites differ significantly in sulfur content, geochemical parameters, community structure, antibiotic resistance genes and mechanisms, and these results may be influenced by anthropogenic activities. Combining with the Antibiotic Resistance Genes Database (ARDB), three types of resistance genes baca, sul2, sul1 are present in R and C, and ant3ia, ermc, tetpa are also present in R. The number of all resistance genes in R was more than C, and Proteobacteria, Bacteroidetes, Nitrospirae are the main sources of antibiotic resistance genes. In addition, a large number of genes related to antibiotic gene transmission and drug resistance were found in both samples. Karst groundwater is an important source of drinking water and a possible venue for the transmission of microbial antibiotic resistance genes. However, few studies addressed this issue in Karst groundwater, despite its widespread and great importance to global ecosystem. Karst groundwater is a reservoir for antibiotic resistant genes, and measures to control these resistant genes are urgently needed. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-12

Mascitti M, Togni L, Troiano G, et al (2019)

Beyond Head and Neck Cancer: The Relationship Between Oral Microbiota and Tumour Development in Distant Organs.

Frontiers in cellular and infection microbiology, 9:232.

An altered oral microbiota has been linked with the development of several oral diseases, such as dental caries, periodontal disease, and oral stomatitis. Moreover, poor oral health has been linked to head and neck cancer, particularly oral cancer. In recent years a growing number of studies indicate that oral microbiota could be involved in the development of primary tumours outside of head and neck region. The aim of this article is to review the recent studies based on high-throughput technology to present evidences of a relationship between oral microbiota and "non-head and neck tumours." Oral dysbiosis seem to be more pronounced in patients with tumours of gastrointestinal tract, in particular oesophageal, gastric, pancreatic, and colorectal cancers, paving the way for developing specific oral microbiota test to allow early cancer detection. Regarding other tumour types, the results are promising but highly preliminary and still debated. Currently, there are several factors that limit the generalization of the results, such as the small sample size, the lack of adequate clinical information about patients, the different sequencing techniques used, and biological sample heterogeneity. Although only at the beginning, the analysis of oral microbiota could be the next step in the evolution of cancer therapy and will help clinicians to develop individualised approaches to cancer prevention and treatment.

RevDate: 2019-07-12

Li H, Mei X, Liu B, et al (2019)

Quantitative proteomic analysis reveals the ethanologenic metabolism regulation of Ethanoligenens harbinense by exogenous ethanol addition.

Biotechnology for biofuels, 12:166 pii:1511.

Background: H2-ethanol-coproducing bacteria, as primary fermenters, play important roles in the microbiome of bioreactors for bioenergy production from organic wastewater or solid wastes. Ethanoligenens harbinense YUAN-3 is an anaerobic ethanol-H2-fermenting bacterium. Ethanol is one of the main end-products of strain YUAN-3 that influence its fermentative process. Until recently, the molecular mechanism of metabolic regulation in strain YUAN-3 during ethanol accumulation has still been unclear. This study aims to elucidate the metabolic regulation mechanisms in strain YUAN-3, which contributes to effectively shape the microbiome for biofuel and bioenergy production from waste stream.

Results: This study reports that ethanol stress altered the distribution of end-product yields in the H2-ethanol-coproducing Ethanoligenens harbinense strain YUAN-3. Decreasing trends of hydrogen yield from 1888.6 ± 45.8 to 837 ± 64.7 mL L-1 and acetic acid yield from 1767.7 ± 45 to 160.6 ± 44.7 mg L-1 were observed in strain YUAN-3 with increasing exogenous ethanol (0 mM-200 mM). However, the ethanol yield of strain YUAN-3 increased by 15.1%, 30.1%, and 27.4% in 50 mM, 100 mM, and 200 mM ethanol stress, respectively. The endogenous ethanol accounted for 96.1% (w/w) in liquid end-products when exogenous ethanol of 200 mM was added. The molar ratio of ethanol to acetic acid increased 14 times (exogenous ethanol of 200 mM) compared to the control. iTRAQ-based quantitative proteomic analysis indicated that 263 proteins of strain YUAN-3 were differentially expressed in 50 mM, 100 mM, and 200 mM of exogenous ethanol. These proteins are mainly involved in amino acid transport and metabolism, central carbon metabolism, and oxidative stress response.

Conclusion: These differentially expressed proteins play important roles in metabolic changes necessary for growth and survival of strain YUAN-3 during ethanol stress. The up-regulation of bifunctional acetaldehyde-CoA/alcohol dehydrogenase (ADHE) was the main reason why ethanol production was enhanced, while hydrogen gas and acetic acid yields declined in strain YUAN-3 during ethanol stress. This study also provides a new approach for the enhancement of ethanologenesis by H2-ethanol-coproducing bacteria through exogenous ethanol addition.

RevDate: 2019-07-12

Zhang Z, Yang J, Feng Q, et al (2019)

Compositional and Functional Analysis of the Microbiome in Tissue and Saliva of Oral Squamous Cell Carcinoma.

Frontiers in microbiology, 10:1439.

Oral squamous cell carcinoma (OSCC) is affected by the interaction between oral pathogen and holobionts, or the combination of the host and its microbial communities. Studies have indicated the structure and feature of the microbiome in OSCC tissue and saliva, the relationships between microbiota and OSCC sites, stages remain unclear. In the present study, OSCC tissue (T), saliva (S) and mouthwash (W) samples were collected from the same subjects and carried out the microbiome study by 16S sequencing. The results showed the T group was significantly different from the S and W groups with the character of lower richness and diversity. Proteobacteria were most enriched in the T group at the phylum level, while Firmicutes were predominant in groups S and W. At the genus level, the predominant taxa of group T were Acinetobacter and Fusobacterium, and for group S and W, the predominant taxa were Streptococcus and Prevotella. The genera related to late stage tumors were Acinetobacter and Fusobacterium, suggesting microbiota may be implicated in OSCC developing. Both compositional and functional analyses indicated that microbes in tumor tissue were potential indicator for the initiation and development of OSCC.

RevDate: 2019-07-12

Osorio C, Kanukuntla T, Diaz E, et al (2019)

The Post-amyloid Era in Alzheimer's Disease: Trust Your Gut Feeling.

Frontiers in aging neuroscience, 11:143.

The amyloid hypothesis, the assumption that beta-amyloid toxicity is the primary cause of neuronal and synaptic loss, has been the mainstream research concept in Alzheimer's disease for the past two decades. Currently, this model is quietly being replaced by a more holistic, "systemic disease" paradigm which, like the aging process, affects multiple body tissues and organs, including the gut microbiota. It is well-established that inflammation is a hallmark of cellular senescence; however, the infection-senescence link has been less explored. Microbiota-induced senescence is a gradually emerging concept promoted by the discovery of pathogens and their products in Alzheimer's disease brains associated with senescent neurons, glia, and endothelial cells. Infectious agents have previously been associated with Alzheimer's disease, but the cause vs. effect issue could not be resolved. A recent study may have settled this debate as it shows that gingipain, a Porphyromonas gingivalis toxin, can be detected not only in Alzheimer's disease but also in the brains of older individuals deceased prior to developing the illness. In this review, we take the position that gut and other microbes from the body periphery reach the brain by triggering intestinal and blood-brain barrier senescence and disruption. We also surmise that novel Alzheimer's disease findings, including neuronal somatic mosaicism, iron dyshomeostasis, aggressive glial phenotypes, and loss of aerobic glycolysis, can be explained by the infection-senescence model. In addition, we discuss potential cellular senescence targets and therapeutic strategies, including iron chelators, inflammasome inhibitors, senolytic antibiotics, mitophagy inducers, and epigenetic metabolic reprograming.

RevDate: 2019-07-12

Sanders ME, Merenstein DJ, Reid G, et al (2019)

Probiotics and prebiotics in intestinal health and disease: from biology to the clinic.

Nature reviews. Gastroenterology & hepatology pii:10.1038/s41575-019-0173-3 [Epub ahead of print].

Probiotics and prebiotics are microbiota-management tools for improving host health. They target gastrointestinal effects via the gut, although direct application to other sites such as the oral cavity, vaginal tract and skin is being explored. Here, we describe gut-derived effects in humans. In the past decade, research on the gut microbiome has rapidly accumulated and has been accompanied by increased interest in probiotics and prebiotics as a means to modulate the gut microbiota. Given the importance of these approaches for public health, it is timely to reiterate factual and supporting information on their clinical application and use. In this Review, we discuss scientific evidence on probiotics and prebiotics, including mechanistic insights into health effects. Strains of Lactobacillus, Bifidobacterium and Saccharomyces have a long history of safe and effective use as probiotics, but Roseburia spp., Akkermansia spp., Propionibacterium spp. and Faecalibacterium spp. show promise for the future. For prebiotics, glucans and fructans are well proven, and evidence is building on the prebiotic effects of other substances (for example, oligomers of mannose, glucose, xylose, pectin, starches, human milk and polyphenols).

RevDate: 2019-07-12

Zimmermann P, N Curtis (2019)

Effect of intrapartum antibiotics on the intestinal microbiota of infants: a systematic review.

Archives of disease in childhood. Fetal and neonatal edition pii:archdischild-2018-316659 [Epub ahead of print].

INTRODUCTION: The use of intrapartum antibiotic prophylaxis (IAP) has become common practice in obstetric medicine and is used in up to 40% of deliveries. Despite its benefits, the risks associated with exposing large numbers of infants to antibiotics, especially long-term effects on health through changes in the microbiota, remain unclear. This systematic review summarises studies that have investigated the effect of IAP on the intestinal microbiota of infants.

METHODS: A systematic search in Ovid MEDLINE was used to identify original studies that investigated the effect of IAP on the intestinal microbiota in infants. Studies were excluded if: they included preterm infants, the antibiotic regimen was not specified, antibiotics were used for indications other than prophylaxis, probiotics were given to mothers or infants, or antibiotics were given to infants.

RESULTS: We identified six studies, which investigated a total of 272 infants and included 502 stool samples collected up to 3 months of age. In all the studies, IAP was given for group B streptococcus (GBS) colonisation. Infants who were exposed to GBS IAP had a lower bacterial diversity, a lower relative abundance of Actinobacteria, especially Bifidobacteriaceae, and a larger relative abundance of Proteobacteria in their intestinal microbiota compared with non-exposed infants. Conflicting results were reported for the phyla Bacteroidetes and Firmicutes.

CONCLUSIONS: GBS IAP has profound effects on the intestinal microbiota of infants by diminishing beneficial commensals. Such changes during the early-life 'critical window' during which the intestinal microbiota and the immune response develop concurrently may have an important influence on immune development. The potential long-term adverse consequences of this on the health of children warrant further investigation.

RevDate: 2019-07-12

Tang W, Putluri V, Ambati CR, et al (2019)

Liver- and Microbiome-derived Bile Acids Accumulate in Human Breast Tumors and Inhibit Growth and Improve Patient Survival.

Clinical cancer research : an official journal of the American Association for Cancer Research pii:1078-0432.CCR-19-0094 [Epub ahead of print].

PURPOSE: Metabolomics is a discovery tool for novel associations of metabolites with disease. Here, we interrogated the metabolome of human breast tumors to describe metabolites whose accumulation affects tumor biology.

EXPERIMENTAL DESIGN: We applied large-scale metabolomics followed by absolute quantification and machine learning-based feature selection using LASSO to identify metabolites that show a robust association with tumor biology and disease outcome. Key observations were validated with the analysis of an independent dataset and cell culture experiments.

RESULTS: LASSO-based feature selection revealed an association of tumor glycochenodeoxycholate levels with improved breast cancer survival, which was confirmed using a Cox proportional hazards model. Absolute quantification of four bile acids, including glycochenodeoxycholate and microbiome-derived deoxycholate, corroborated the accumulation of bile acids in breast tumors. Levels of glycochenodeoxycholate and other bile acids showed an inverse association with the proliferation score in tumors and the expression of cell cycle and G2/M checkpoint genes, which was corroborated with cell culture experiments. Moreover, tumor levels of these bile acids markedly correlated with metabolites in the steroid metabolism pathway and increased expression of key genes in this pathway, suggesting that bile acids may interfere with hormonal pathways in the breast. Lastly, a proteome analysis identified the Complement & Coagulation Cascade as being up-regulated in glycochenodeoxycholate-high tumors.

CONCLUSIONS: We describe the unexpected accumulation of liver- and microbiome-derived bile acids in breast tumors. Tumors with increased bile acids show decreased proliferation, thus fall into a good prognosis category, and exhibit significant changes in steroid metabolism.

RevDate: 2019-07-12

Shen N, Caixàs A, Ahlers M, et al (2019)

Longitudinal changes of microbiome composition and microbial metabolomics after surgical weight loss in individuals with obesity.

Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery pii:S1550-7289(19)30264-3 [Epub ahead of print].

BACKGROUND: Some of the metabolic effects of bariatric surgery may be mediated by the gut microbiome.

OBJECTIVES: To study the effect of bariatric surgery on changes to gut microbiota composition and bacterial pathways, and their relation to metabolic parameters after bariatric surgery.

SETTINGS: University hospitals in the United States and Spain.

METHODS: Microbial diversity and composition by 16 S rRNA sequencing, putative bacterial pathways, and targeted circulating metabolites were studied in 26 individuals with severe obesity, with and without type 2 diabetes, before and at 3, 6, and 12 months after either gastric bypass or sleeve gastrectomy.

RESULTS: Bariatric surgery tended to increase alpha diversity, and significantly altered beta diversity, microbiota composition, and function up to 6 months after surgery, but these changes tend to regress to presurgery levels by 12 months. Twelve of 15 bacterial pathways enriched after surgery also regressed to presurgery levels at 12 months. Network analysis identified groups of bacteria significantly correlated with levels of circulating metabolites over time. There were no differences between study sites, surgery type, or diabetes status in terms of microbial diversity and composition at baseline and after surgery.

CONCLUSIONS: The association among changes in microbiome with decreased circulating biomarkers of inflammation, increased bile acids, and products of choline metabolism and other bacterial pathways suggest that the microbiome partially mediates improvement of metabolism during the first year after bariatric surgery.

RevDate: 2019-07-11

Glassner K, Quigley EM, Franco L, et al (2018)

Autoimmune liver disease and the enteric microbiome.

AIMS microbiology, 4(2):334-346 pii:microbiol-04-02-334.

The human enteric microbiome is highly complex and has more than 150 times more genes within it than its host. The host and the microbiome have a commensurate relationship that can evolve over time. The typically symbiotic relationship between the two can become pathogenic. The microbiome composition in adults reflects their history of exposure to bacteria and environmental factors during early life, their genetic background, age, interactions with the immune system, geographical location, and, most especially, their diet. Similarly, these factors are thought to contribute to the development of autoimmune disease. It is possible that alterations in the intestinal microbiome could lead to liver disease. There is emerging data for the contribution of the microbiome in development of primary sclerosing cholangitis, primary biliary cholangitis, and autoimmune hepatitis; liver disorders associated with aberrant immune function in genetically susceptible individuals.

RevDate: 2019-07-11

Barros I, Froufe H, Marnellos G, et al (2018)

Metatranscriptomics profile of the gill microbial community during Bathymodiolus azoricus aquarium acclimatization at atmospheric pressure.

AIMS microbiology, 4(2):240-260 pii:microbiol-04-02-240.

Background: The deep-sea mussels Bathymodiolus azoricus (Bivalvia: Mytilidae) are the dominant macrofauna subsisting at the hydrothermal vents site Menez Gwen in the Mid-Atlantic Ridge (MAR). Their adaptive success in such challenging environments is largely due to their gill symbiotic association with chemosynthetic bacteria. We examined the response of vent mussels as they adapt to sea-level environmental conditions, through an assessment of the relative abundance of host-symbiont related RNA transcripts to better understand how the gill microbiome may drive host-symbiont interactions in vent mussels during hypothetical venting inactivity.

Results: The metatranscriptome of B. azoricus was sequenced from gill tissues sampled at different time-points during a five-week acclimatization experiment, using Next-Generation-Sequencing. After Illumina sequencing, a total of 181,985,262 paired-end reads of 150 bp were generated with an average of 16,544,115 read per sample. Metatranscriptome analysis confirmed that experimental acclimatization in aquaria accounted for global gill transcript variation. Additionally, the analysis of 16S and 18S rRNA sequences data allowed for a comprehensive characterization of host-symbiont interactions, which included the gradual loss of gill endosymbionts and signaling pathways, associated with stress responses and energy metabolism, under experimental acclimatization. Dominant active transcripts were assigned to the following KEGG categories: "Ribosome", "Oxidative phosphorylation" and "Chaperones and folding catalysts" suggesting specific metabolic responses to physiological adaptations in aquarium environment.

Conclusions: Gill metagenomics analyses highlighted microbial diversity shifts and a clear pattern of varying mRNA transcript abundancies and expression during acclimatization to aquarium conditions which indicate change in bacterial community activity. This approach holds potential for the discovery of new host-symbiont associations, evidencing new functional transcripts and a clearer picture of methane metabolism during loss of endosymbionts. Towards the end of acclimatization, we observed trends in three major functional subsystems, as evidenced by an increment of transcripts related to genetic information processes; the decrease of chaperone and folding catalysts and oxidative phosphorylation transcripts; but no change in transcripts of gluconeogenesis and co-factors-vitamins.

RevDate: 2019-07-11

Sharma N, Bhatia S, Sodhi AS, et al (2018)

Oral microbiome and health.

AIMS microbiology, 4(1):42-66 pii:microbiol-04-01-042.

The oral microbiome is diverse in its composition due to continuous contact of oral cavity with the external environment. Temperatures, diet, pH, feeding habits are important factors that contribute in the establishment of oral microbiome. Both culture dependent and culture independent approaches have been employed in the analysis of oral microbiome. Gene-based methods like PCR amplification techniques, random amplicon cloning, PCR-RELP, T-RELP, DGGE and DNA microarray analysis have been applied to increase oral microbiome related knowledge. Studies revealed that microbes from the phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Fusobacteria, Neisseria, TM7 predominately inhabits the oral cavity. Culture-independent molecular techniques revealed the presence of genera Megasphaera, Parvimonas and Desulfobulbus in periodontal disease. Bacteria, fungi and protozoa colonize themselves on various surfaces in oral cavity. Microbial biofilms are formed on the buccal mucosa, dorsum of the tongue, tooth surfaces and gingival sulcus. Various studies demonstrate relationship between unbalanced microflora and development of diseases like tooth caries, periodontal diseases, type 2 diabetes, circulatory system related diseases etc. Transcriptome-based remodelling of microbial metabolism in health and disease associated states has been well reported. Human diets and habitat can trigger virus activation and influence phage members of oral microbiome. As it is said, "Mouth, is the gateway to the total body wellness, thus oral microbiome influences overall health of an individual".

RevDate: 2019-07-11

Abedon ST (2017)

Active bacteriophage biocontrol and therapy on sub-millimeter scales towards removal of unwanted bacteria from foods and microbiomes.

AIMS microbiology, 3(3):649-688 pii:microbiol-03-03-649.

Bacteriophages can be used as antibacterial agents as a form of biological control, e.g., such as phage therapy. With active treatment, phages must "actively" produce new virions, in situ, to attain "inundative" densities, i.e., sufficient titers to eradicate bacteria over reasonable timeframes. Passive treatment, by contrast, can be accomplished using phages that are bactericidal but incapable of generating new phage virions in situ during their interaction with target bacteria. These ideas of active versus passive treatment come from theoretical considerations of phage therapy pharmacology, particularly as developed in terms of phage application to well-mixed cultures consisting of physically unassociated bacteria. Here I extend these concepts to bacteria which instead are physically associated. These are bacteria as found making up cellular arrangements or bacterial microcolonies-collectively, clonal bacterial "clumps". I consider circumstances where active phage replication would be required to effect desired levels of bacterial clearance, but populations of bacteria nevertheless are insufficiently prevalent to support phage replication to bacteria-inundative densities across environments. Clumped bacteria, however, may still support active treatment at more local, i.e., sub-millimeter, within-clump spatial scales, and potential consequences of this are explored mathematically. Application is to the post-harvest biocontrol of foodborne pathogens, and potentially also to precise microbiome editing. Adequate infection performance by phages in terms of timely burst sizes, that is, other than just adsorption rates and bactericidal activity, thus could be important for treatment effectiveness even if bacterial densities overall are insufficient to support active treatment across environments. Poor phage replication during treatment of even low bacterial numbers, such as given food refrigeration during treatment, consequently could be problematic to biocontrol success. In practical terms, this means that the characterization of phages for such purposes should include their potential to generate new virions under realistic in situ conditions across a diversity of potential bacterial targets.

RevDate: 2019-07-11

Tang J (2017)

Microbiome in the urinary system-a review.

AIMS microbiology, 3(2):143-154 pii:microbiol-03-02-143.

Urine was considered sterile in healthy individuals for many years, and the presence of bacteria signified urinary tract infection. With the development of Expanded Quantitative Urine Culture (EQUC) and utilization of molecular techniques, the previous clinical dogma is no longer valid. Instead, healthy people harbor a considerable microbial community, or microbiota, in their urinary systems. Similar to other physiological niches where microbiota contribute to the health status of their hosts, recent studies demonstrated different microbial populations also play a crucial role in urinary health of individuals. Understanding urinary microbiome thus allows a more holistic approach in the diagnosis, treatment, and prevention of diseases and disorders in urinary system. This review article provides an overview of current findings in urinary microbiome and discusses some of the gaps for future research.

RevDate: 2019-07-11

Theuretzbacher U, LJV Piddock (2019)

Non-traditional Antibacterial Therapeutic Options and Challenges.

Cell host & microbe, 26(1):61-72.

The global challenges presented by drug-resistant bacterial infections have stimulated much activity in finding new treatments. This review summarizes the progress and setbacks of non-traditional approaches intent on circumventing bacterial drug resistance. These approaches include targeting virulence via toxin production and virulence factor secretion, impeding bacterial adhesion to host cells and biofilm formation, interrupting or inhibiting bacterial communication, and downregulating virulence. Other strategies include immune evasion, microbiome-modifying therapies, and the employment of phages as treatments or carriers. Finally, the prospects of nanoparticles, immunotherapy, antisense RNA, and drug-resistance-modulation approaches are discussed. The development of non-traditional treatments suffers similar challenges faced by developers of conventional antibiotics; however, most of these new strategies have additional and considerable hurdles before it can be shown that they are safe and efficacious for patient use. For the foreseeable future, it is likely that most of these treatments, if approved, will be used in combination with antibiotics.

RevDate: 2019-07-11

Lam KN, Alexander M, PJ Turnbaugh (2019)

Precision Medicine Goes Microscopic: Engineering the Microbiome to Improve Drug Outcomes.

Cell host & microbe, 26(1):22-34.

Despite the recognition, nearly a century ago, that the human microbiome plays a clinically relevant role in drug disposition, mechanistic insights, and translational applications are still limited. Here, we highlight the recent re-emergence of "pharmacomicrobiomics," which seeks to understand how inter-individual variations in the microbiome shape drug efficacy and side effect profiles. Multiple bacterial species, genes, and enzymes have already been implicated in the direct biotransformation of drugs, both from targeted case studies and from systematic computational and experimental analyses. Indirect mechanisms are also at play; for example, microbial interactions with the host immune system can have broad effects on immunomodulatory drugs. Finally, we discuss multiple emerging strategies for the precise manipulation of complex microbial communities to improve treatment outcomes. In the coming years, we anticipate a shift toward a more comprehensive view of precision medicine that encompasses our human and microbial genomes and their combined metabolic activities.

RevDate: 2019-07-11

Orellana E, Davies-Sala C, Guerrero LD, et al (2019)

Microbiome network analysis of co-occurrence patterns in anaerobic co-digestion of sewage sludge and food waste.

Water science and technology : a journal of the International Association on Water Pollution Research, 79(10):1956-1965.

Addition of food waste (FW) as a co-substrate in anaerobic digesters of wastewater treatment plants is a desirable strategy towards achievement of the potential of wastewater treatment plants to become energy-neutral, diverting at the same time organic waste from landfills. Because substrate type is a driver of variations in phylogenetic structure of digester microbiomes, it is critical to understand how microbial communities respond to changes in substrate composition and concentration. In this work, high throughput sequencing was used to monitor the dynamics of microbiome changes in four parallel laboratory-scale anaerobic digesters treating sewage sludge during acclimation to an increasing amount of food waste. A co-occurrence network was constructed using data from 49 metagenomes sampled over the 161 days of the digesters' operation. More than half of the nodes in the network were clustered in two major modules, i.e. groups of highly interconnected taxa that had much fewer connections with taxa outside the group. The dynamics of co-occurrence networks evidenced shifts that occurred within microbial communities due to the addition of food waste in the co-digestion process. A diverse and reproducible group of hydrolytic and fermentative bacteria, syntrophic bacteria and methanogenic archaea appeared to grow in a concerted fashion to allow stable performance of anaerobic co-digestion at high FW.

RevDate: 2019-07-11

Carroll MW, Kuenzig ME, Mack DR, et al (2019)

The Impact of Inflammatory Bowel Disease in Canada 2018: Children and Adolescents with IBD.

Journal of the Canadian Association of Gastroenterology, 2(Suppl 1):S49-S67.

Canada has among the highest rates of childhood-onset IBD in the world. Over 7000 children and youth under 18 years old are living with IBD in Canada, and 600 to 650 children under 16 years old are diagnosed annually. While the peak age of onset of IBD is highest in the second and third decades of life, over the past two decades incidence has risen most rapidly in children under 5 years old. The treatment of children with IBD presents important challenges including therapeutic choices, risk of adverse events to medications, psychosocial impact on the child and family, increased cost of health care and the implications of the transition from pediatric to adult care. Despite the unique circumstances faced by children and their families, there is a lack of research to help understand the causes of the rising incidence and the best therapies for children with IBD. Scientific evidence-and specifically clinical trials of pharmaceuticals-are too often extrapolated from adult research. Health care providers must strive to understand the unique impact of childhood-onset IBD on patients and families, while researchers must expand work to address the important needs of this growing patient population.

Highlights: In 2018, there are over 7000 children and youth under 18 years old living with IBD in Canada, and 600 to 650 young children (under 16 years) diagnosed every year.The number of children in Canada living with IBD is growing rapidly, increasing 50% in the first decade of the 21st century.Inflammatory bowel disease is still rare in children younger than 5 years of age, but it is occurring in such young children more often than in the past.Children with IBD are different from adults. For example, delayed growth, extent of disease and difficulties encountered during adolescence are all unique to the pediatric experience.We must consider the psychosocial well-being of both children and their families, given that caring for a child with IBD can affect the global functioning of families.Treatment approaches in children sometimes differ from those in adults. However, to date, all effective therapies in adults have also been effective in children. There is great need for clinical trials of new therapies in children so that they have equal access to emerging treatments and optimal pediatric dosing can be established.

Key Summary Points: Rates of new diagnoses in children under 16 years old were increasing most rapidly in Ontario (increased 5.8% per year) and Quebec (increased 2.8% per year).Nova Scotia has the highest rate of pediatric IBD, with lower rates in Quebec and Ontario. However, even Ontario and Quebec have higher rates of pediatric IBD than most countries in the world.Inflammatory bowel disease is caused by the interaction between genes, environmental risk factors, the microbiome and the immune system. Since children experience shorter exposures and possibly fewer environmental risk factors, the interaction between these risk factors and genes may be stronger with childhood-onset IBD.The microbiome is mostly established in early childhood and is affected by a number of factors such as environment, diet, pregnancy/delivery factors and antibiotic use. Changing the microbiome to a healthier state may prevent the disease and may also be a novel therapeutic target to treat active inflammation in children with IBD.Children with IBD are different from adults. They are more likely to have extensive involvement of their intestines, especially in ulcerative colitis, and are at risk for growth impairment, osteoporosis, and psychosocial difficulties affecting their families.Children with IBD may incur more direct health costs for treatment of their IBD compared with adults. However, this is not universally true for all children because those who are very young at diagnosis (2 to 6 years old) may have milder disease or respond better to medications. This may result in decreased use of the health system, fewer hospitalizations and less risk of surgery than older children and adolescents.The choice of treatments for children with IBD may be different from that of adults. It is important to consider pediatric-specific disease considerations. Delayed growth, deficient bone development, psychosocial well-being of the child and family, disease extent, disease severity and risk of poor outcomes during transition from pediatric to adult health care are all important considerations when choosing the best treatment for children and adolescents.While the medications used are similar in children and adults with IBD, research to assess the effectiveness and safety of these medications in children (especially very young children) is sparse.Children with IBD may be more responsive to treatment than adults because they are more likely to have inflammatory (rather than stricturing) disease. Therefore, treating the inflammation earlier in the course of disease may prevent long-term complications such as strictures, obstruction, need for surgery and need for hospitalization.Some medications used in IBD have unique or more pronounced risks in children compared with adults. For example, chronic prednisone use is associated with growth impairment and stunting in children. Anti-TNF biologics are the only medications proven to improve growth in children with Crohn's disease and should be considered early in the course of disease in patients with severe IBD or those with marked growth impairment at the time of diagnosis.Some medications are used differently, depending on the sex of the patient. For example, azathioprine (with or without biologics) is associated with hepatosplenic T cell lymphoma (and other forms of lymphoma) in adolescent and young adult males more often than females. Methotrexate is associated with birth defects in the growing fetus and therefore should be avoided in adolescent and adult women of child-bearing age who are not using two or more forms of birth control.A small group of children, typically presenting in the first two years of life, have single-gene mutations that cause an IBD-like bowel disease and also immune system dysfunction. These patients may not respond to traditional IBD medications and may require therapies such as bone marrow transplant. Canada is leading research efforts to investigate, diagnose and treat this small group of very vulnerable children.Inflammatory bowel disease (especially when it is active) can affect school attendance, social interactions, concentration and learning. Schools should be aware of the implications of IBD and make allowances for these factors in children with active inflammation and symptoms to optimize their chances of academic and social success.

We have limited knowledge on what causes IBD in children and why rates are rising most rapidly in young children. We must better understand the interaction between genes, the environment, the immune system and the microbiome in order to better prevent and treat the disease.Treatment for infants with IBD-like illnesses and single-gene mutations is limited. Future research should work towards identifying these children and learning how best to treat them.There are few clinical trials for biologics in children, and most exclude very young children. Support for such trials is important to understand whether the treatments work, how they should optimally be given and whether they are safe for young children with IBD.Considering the effectiveness of dietary therapies for children with Crohn's disease (exclusive enteral nutrition), we should work to understand how diet affects intestinal inflammation and the microbiome in order to better use dietary therapies to treat IBD.Health services researchers, health care providers and policy-makers should work together to understand why variation in the access to treatment and medical care of children with IBD exists. We must work together to improve the quality of care provided to these children and ensure they have the highest quality of care.Psychosocial implications of IBD in children and their families are of importance to long-term and overall well-being. Children with a chronic, incurable disease are at risk for mental illness associated with their disease. We should design interventions to improve the psychosocial status, mental health and quality of life of children with IBD and their families.While nonlive immunizations are safe for children with IBD, we must understand how to improve their effectiveness in children who are immunosuppressed. While the peak onset of IBD occurs in the second or third decades of life, the frequency of new diagnoses in younger children is rising rapidly. In Canada, the fastest growing group of newly diagnosed people with IBD are children aged under 5 years (termed 'very early onset [VEO] IBD). These young children have not been included in clinical trials of new medications, resulting in a lack of scientific evidence of safety and effectiveness of treatments in this group, and clinical experience has shown that they do not respond to usual medications used for the majority of children with IBD. Providing children with IBD with high-quality care and social support also poses other challenges to care providers, families and the health system. This section will focus on the unique challenges facing Canadian children with IBD. A complete overview of the objectives, working committees and methodology of creating the report can be found in the supplemental file, Technical Document.

RevDate: 2019-07-11

Kaplan GG, Bernstein CN, Coward S, et al (2019)

The Impact of Inflammatory Bowel Disease in Canada 2018: Epidemiology.

Journal of the Canadian Association of Gastroenterology, 2(Suppl 1):S6-S16.

Canada has among the highest incidence and prevalence of inflammatory bowel disease (IBD) in the world. After decades of rising incidence of IBD in Canada during the 20th Century, the prevalence of IBD in 2018 is 0.7% of the Canadian population. Forecasting models predict that prevalence of IBD will continue to rise to 1.0% of the population by 2030. In 2018, the number of Canadians living with IBD is approximately 270,000 and is predicted to rise to 403,000 Canadians in 2030. Inflammatory bowel disease affects all age groups with adolescents and young adults at highest risk of diagnosis. Canadians of all ethnicities are being diagnosed with IBD including known high-risk groups such as Ashkenazi Jews and offspring of South Asian immigrants who were previously thought to be low risk. Moreover, IBD has evolved into a global disease with rising incidence in newly industrialized countries in Asia and South America. The causes of IBD remain unsolved; however, the high rates of disease in Western countries and its emergence in newly industrialized countries suggest that environmental factors associated with urbanization, modernization, or Western diets may be pertinent to understanding the pathogenesis of the disease.

Highlights: 1. Canada continues to have among the highest prevalence of IBD in the world.2. Today, approximately 270,000 Canadians live with IBD. By 2030 it is estimated that nearly 403,000 Canadians will have a diagnosis of IBD.3. Inflammatory bowel disease has become a worldwide disease with increasing rates in Asia, Africa, and South America-continents where IBD was rarely diagnosed prior to 1990.4. The causes of IBD are unknown, but the high rates of disease over the past 60 years in Western countries and the emergence of disease in developing countries suggest that factors associated with urbanization, modernization, or Western diets may be pertinent to understanding the pathogenesis of the disease.5. Many of the leading hypotheses as to the causes of IBD tie in with alteration of the gut microbiome, the suite of organisms that reside in the bowel and maintain bowel health throughout life.

Key Summary Points: 1. The incidence (the number of new diagnoses annually) of IBD rose throughout the 20th century in Canada and then stabilized at the turn of the 21st century.2. The prevalence (the total number of diagnosed persons in the population) of IBD in Canada is among the highest in the world.3. Today, 270,000 (0.7%, or 7 in 1000) Canadians are estimated to live with IBD. By 2030, that number is expected to rise to 403,000 Canadians (1% or 1 in 100).4. Inflammatory bowel disease can be diagnosed at any age. However, the age groups that are most likely to be diagnosed are adolescents and young adults from 20 to 30 years of age.5. Inflammatory bowel disease in Canada affects the lives of Canadians of all ethnicities, including known high-risk groups such as Ashkenazi Jews, and those thought previously to be at low risk, such as first-generation offspring of South Asian immigrants.6. Canadian health policy makers will need to prepare the Canadian health care system for the rising burden of IBD.7. As newly industrialized countries in Asia, Africa, and South America are transitioning to a Westernized society, IBD has emerged and its incidence in these countries is rising rapidly.8. The gut microbiome includes microorganisms that maintain digestive health. Thus, changes in the microbiome, which may change the immune system's response to triggers, may be important in initiating and perpetuating IBD.9. A number of factors can alter the gut microbiome and early childhood may be a particularly important time such that breastfeeding, early life diet, use of antibiotics, infections, and other environmental exposures may impact the gut microbiome in such a way that facilitates developing IBD.10. Smoking is associated with an increased risk and worsening disease course of Crohn's disease. Quitting smoking is associated with an increased risk of developing ulcerative colitis. Therefore, never initiating smoking can mitigate the risk for IBD. Educational programs aimed at those at-risk for IBD should emphasize the risk of starting to smoke tobacco.11. Modifying exposure to environmental risk factors associated with the Westernization of society (e.g., Western diet and lifestyles) may provide an avenue for reducing the risk of IBD in Canada and worldwide.

1. While the incidence of IBD appears to be stabilizing in some regions in Canada, IBD may be occurring more frequently in certain populations such as in children, South Asians, Ashkenazi Jews, and immigrants. Future research should focus on the changing demographics of IBD in Canada.2. The prevalence of IBD will rise steadily over the next decade. To enable better health care system planning and to respond adequately to the increasing burden of IBD, ongoing surveillance of the epidemiology and health services utilization of IBD in Canada is necessary.3. Most studies have focused on the mortality associated with IBD. Future research is necessary to assess health-adjusted life expectancy and overall life expectancy for those living with IBD.4. Analyses of resources, infrastructure, and personnel need to be modeled into the future in order to prepare our health care system for the rising burden of IBD.5. Research on the interaction between genes, microbes, and our environment will inform our understanding of the pathogenesis of IBD, information necessary to prevent IBD in the future.

RevDate: 2019-07-11

Ritschard JS, Amato L, Kumar Y, et al (2018)

The role of the surface smear microbiome in the development of defective smear on surface-ripened red-smear cheese.

AIMS microbiology, 4(4):622-641 pii:microbiol-04-04-622.

The complex smear microbiota colonizing the surface of red-smear cheese fundamentally impacts the ripening process, appearance and shelf life of cheese. To decipher the prokaryotic composition of the cheese smear microbiome, the surface of a semi-hard surface ripened cheese was studied post-ripening by culture-based and culture-independent molecular approaches. The aim was to detect potential bacterial alterations in the composition of the cheese smear microbiota resulting from cheese storage in vacuum film-prepackaging, which is often accompanied by the development of a surface smear defect. Next-generation sequencing of amplified 16S rRNA gene fragments revealed an unexpected high diversity of a total of 132 different genera from the domains Bacteria and Archaea on the cheese surface. Beside typical smear organisms, our study revealed the presence of several microorganisms so far not associated with cheese, but related to milk, farm and cheese dairy environments. A 16S ribosomal RNA based analysis from total RNA identified the major metabolically active populations in the cheese surface smear as Actinobacteria of the genera Corynebacterium, Brevibacterium, Brachybacterium and Agrococcus. Comparison of data on a higher phylogenetic level revealed distinct differences in the composition of the cheese smear microbiome from the different samples. While the proportions of Proteobacteria and Bacteroidetes were increased in the smear of prepacked samples and in particular in defective smear, staphylococci showed an opposite trend and turned out to be strongly decreased in defective smear. In conclusion, next-generation sequencing of amplified 16S rRNA genes and 16S rRNA from total RNA extracts provided a much deeper insight into the bacterial composition of the cheese smear microbiota. The observed shifts in the microbial composition of samples from defect surface smear suggest that certain members of the Proteobacteria contribute to the observed negative organoleptic properties of the surface smear of cheese after prepacking in plastic foil.

RevDate: 2019-07-11

Galbraith H, Iwanowicz D, Spooner D, et al (2018)

Exposure to synthetic hydraulic fracturing waste influences the mucosal bacterial community structure of the brook trout (Salvelinus fontinalis) epidermis.

AIMS microbiology, 4(3):413-427 pii:microbiol-04-03-413.

Production of natural gas using unconventional technologies has risen as demand for alternative fuels has increased. Impacts on the environment from waste generated from these processes are largely unexplored. In particular, the outcomes of organismal exposure to hydraulic fracturing waste have not been rigorously evaluated. We evaluated the effects of exposure to surrogate hydraulic fracturing waste (HF waste) on mucosal bacterial community structure of the brook trout (Salvelinus fontinalis) epidermis. Brook trout are fish native to streams at risk to HF waste exposure. Here, fish were exposed to four treatments (control, 0.00%; low, 0.01%; medium, 0.10%; and high, 1.0% concentrations) of surrogate HF waste synthesized to mimic concentrations documented in the field. Epidermal mucus samples were collected and assessed 15 days post-exposure to determine if the associated bacterial community varied among treatments. We observed differences in epidermal mucosal bacterial community composition at multiple taxonomic scales among treatments. These community changes reflected compositional differences in taxa dominance and community similarity rather than losses or gains in taxonomic richness. The dominant bacterial genus that explained the greatest variation in community structure between exposed and unexposed fish was Flavobacterium. Two genera associated with salmonid diseases, Flavobacterium and Pseudomonas, were statistically more abundant in high treatments than controls. These results suggest that exposure to low levels of HF waste influences bacterial colonization and may lead to a disruption that favors bacterial populations associated with fish disease.

RevDate: 2019-07-11

Afrin T, Murase K, Kounosu A, et al (2019)

Sequential Changes in the Host Gut Microbiota During Infection With the Intestinal Parasitic Nematode Strongyloides venezuelensis.

Frontiers in cellular and infection microbiology, 9:217.

Soil-transmitted helminths (STHs) are medically important parasites that infect 1. 5 billion humans globally, causing a substantial disease burden. These parasites infect the gastrointestinal tract (GIT) of their host where they co-exist and interact with the host gut bacterial flora, leading to the coevolution of the parasites, microbiota, and host organisms. However, little is known about how these interactions change through time with the progression of infection. Strongyloidiasis is a human parasitic disease caused by the nematode Strongyloides stercoralis infecting 30-100 million people. In this study, we used a closely related rodent parasite Strongyloides venezuelensis and mice as a model of gastrointestinal parasite infection. We conducted a time-course experiment to examine changes in the fecal microbiota from the start of infection to parasite clearance. We found that bacterial taxa in the host intestinal microbiota changed significantly as the infection progressed, with an increase in the genera Bacteroides and Candidatus Arthromitus, and a decrease in Prevotella and Rikenellaceae. However, the microbiota recovered to the pre-infective state after parasite clearance from the host, suggesting that these perturbations are reversible. Microarray analysis revealed that this microbiota transition is likely to correspond with the host immune response. These findings give us an insight into the dynamics of parasite-microbiota interactions in the host gut during parasite infection.

RevDate: 2019-07-11

Fasullo M, Rau P, Liu DQ, et al (2019)

Proton pump inhibitors increase the severity of hepatic encephalopathy in cirrhotic patients.

World journal of hepatology, 11(6):522-530.

BACKGROUND: Liver cirrhosis is the late stage of hepatic fibrosis and is characterized by portal hypertension that can clinically lead to decompensation in the form of ascites, esophageal/gastric varices or encephalopathy. The most common sequelae associated with liver cirrhosis are neurologic and neuropsychiatric impairments labeled as hepatic encephalopathy (HE). Well established triggers for HE include infection, gastrointestinal bleeding, constipation, and medications. Alterations to the gut microbiome is one of the leading ammonia producers in the body, and therefore may make patients more susceptible to HE.

AIM: To investigate the relationship between the use of proton pump inhibitors (PPIs) and HE in patients with cirrhosis.

METHODS: This is a single center, retrospective analysis. Patients were included in the study with an admitting diagnosis of HE. The degree of HE was determined from subjective and objective portions of hospital admission notes using the West Haven Criteria. The primary outcome of the study was to evaluate the grade of HE in PPI users versus non-users at admission to the hospital and throughout their hospital course. Secondary outcomes included rate of infection, gastrointestinal bleeding within the last 12 mo, mean ammonia level, and model for end-stage liver disease scores at admission.

RESULTS: The HE grade at admission using the West Haven Criteria was 2.3 in the PPI group compared to 1.7 in the PPI nonuser group (P = 0.001). The average length of hospital stay in PPI group was 8.3 d compared to 6.5 d in PPI nonusers (P = 0.046). Twenty-seven (31.8%) patients in the PPI user group required an Intensive Care Unit admission during their hospital course compared to 6 in the PPI nonuser group (16.7%) (P = 0.138). Finally, 10 (11.8%) patients in the PPI group expired during their hospital stay compared to 1 in the PPI nonuser group (2.8%) (P = 0.220).

CONCLUSION: Chronic PPI use in cirrhotic patients is associated with significantly higher average West Haven Criteria for HE compared to patients that do not use PPIs.

RevDate: 2019-07-11

Zhou YH, P Gallins (2019)

A Review and Tutorial of Machine Learning Methods for Microbiome Host Trait Prediction.

Frontiers in genetics, 10:579.

With the growing importance of microbiome research, there is increasing evidence that host variation in microbial communities is associated with overall host health. Advancement in genetic sequencing methods for microbiomes has coincided with improvements in machine learning, with important implications for disease risk prediction in humans. One aspect specific to microbiome prediction is the use of taxonomy-informed feature selection. In this review for non-experts, we explore the most commonly used machine learning methods, and evaluate their prediction accuracy as applied to microbiome host trait prediction. Methods are described at an introductory level, and R/Python code for the analyses is provided.

RevDate: 2019-07-11

Ruiz L, García-Carral C, JM Rodriguez (2019)

Unfolding the Human Milk Microbiome Landscape in the Omics Era.

Frontiers in microbiology, 10:1378.

Studies conducted in the last years have demonstrated that human milk represents a continuous supply of beneficial bacteria to the infant gut, which contribute to the maturation of the digestive and immune functions in the developing infant. Nevertheless, the origin of bacterial populations in milk is not fully understood yet and they have been proposed to originate from maternal skin, infant's mouth, and (or) endogenously, from the maternal digestive tract through a mechanism involving immune cells. Understanding the composition, functions and assembly of the human milk microbiota has important implications not only for the infant gut microbiota establishment, but also for the mammary health since dysbiosis in the milk bacteria may lead to mastitis. Besides, host, microbial, medical and environmental factors may affect the composition of the human milk microbiome, with implications for the mother-infant health. Application of both culture-dependent and -independent techniques to assess the milk microbiome faces some practical limitations but, together, have allowed providing novel and complementary views on its origin, composition and functioning as summarized in this minireview. In the next future, the application of the ultimate advances in next-generation sequencing and omics approaches, including culturomics, will allow a detailed and comprehensive understanding of the composition and functions of these microbial communities, including their interactions with other milk components, expanding the opportunities to design novel microbiome-based modulation strategies for this ecosystem.

RevDate: 2019-07-11

Lopes DRG, La Reau AJ, Duarte MS, et al (2019)

The Bacterial and Fungal Microbiota of Nelore Steers Is Dynamic Across the Gastrointestinal Tract and Its Fecal-Associated Microbiota Is Correlated to Feed Efficiency.

Frontiers in microbiology, 10:1263.

The ruminant gastrointestinal tract (GIT) microbiome plays a major role in the health, physiology and production traits of the host. In this work, we characterized the bacterial and fungal microbiota of the rumen, small intestine (SI), cecum and feces of 27 Nelore steers using next-generation sequencing and evaluated biochemical parameters within the GIT segments. We found that only the bacterial microbiota clustered according to each GIT segment. Bacterial diversity and richness as well as volatile fatty acid concentration was lowest in the SI. Taxonomic grouping of bacterial operational taxonomic units (OTUs) revealed that Lachnospiraceae (24.61 ± SD 6.58%) and Ruminococcaceae (20.87 ± SD 4.22%) were the two most abundant taxa across the GIT. For the fungi, the family Neocallismastigaceae dominated in all GIT segments, with the genus Orpinomyces being the most abundant. Twenty-eight bacterial and six fungal OTUs were shared across all GIT segments in at least 50% of the steers. We also evaluated if the fecal-associated microbiota of steers showing negative and positive residual feed intake (n-RFI and p-RFI, respectively) was associated with their feed efficiency phenotype. Diversity indices for both bacterial and fungal fecal microbiota did not vary between the two feed efficiency groups. Differences in the fecal bacterial composition between high and low feed efficiency steers were primarily assigned to OTUs belonging to the families Lachnospiraceae and Ruminococcaceae and to the genus Prevotella. The fungal OTUs shared across the GIT did not vary between feed efficiency groups, but 7 and 3 OTUs were found only in steers with positive and negative RFI, respectively. These results provide further insights into the composition of the Nelore GIT microbiota, which could have implications for improving animal health and productivity. Our findings also reveal differences in fecal-associated bacterial OTUs between steers from different feed efficiency groups, suggesting that fecal sampling may represent a non-invasive strategy to link the bovine microbiota with productivity phenotypes.

RevDate: 2019-07-11

Ma W, Mao Q, Xia W, et al (2019)

Gut Microbiota Shapes the Efficiency of Cancer Therapy.

Frontiers in microbiology, 10:1050.

Systems biology provides an opportunity to discover the role that gut microbiota play in almost all aspects of human health. Existing evidence supports the hypothesis that gut microbiota is closely related to the pharmacological effects of chemical therapy and novel targeted immunotherapy. Gut microbiota shapes the efficiency of drugs through several key mechanisms: metabolism, immunomodulation, translocation, enzymatic degradation, reduction of diversity, and ecological variability. Therefore, gut microbiota have emerged as a novel target to enhance the efficacy and reduce the toxicity and adverse effects of cancer therapy. There is growing evidence to show that cancer therapy perturbs the host immune response and results in dysbiosis of the immune system, which then influences the efficiency of the therapy. Studies suggest that gut microbes play a significant role in cancer therapy by modulating drug efficacy, abolishing the anticancer effect, and mediating toxicity. In this review, we outline the role of gut microbiota in modulating cancer therapy and the implications for improving the efficacy of chemotherapy and immunotherapy in clinical practice. We also summarize the current limitations of the safety and effectiveness of probiotics in cancer therapies such as personalized cancer therapy.

RevDate: 2019-07-11

Panacer K, PJ Whorwell (2019)

Dietary Lectin exclusion: The next big food trend?.

World journal of gastroenterology, 25(24):2973-2976.

Until recently, with the exception of coeliac disease, gastroenterologists have not been particularly interested in the role of diet in the management of gastrointestinal disorders. However, patients have always felt that diet must play a part in their symptoms and, in the absence of any medical interest, have turned to alternative dietary practitioners for help, which can often have no evidence base. Fortunately, with the advent of the FODMAP diet (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) and the realisation that diet can have a profound effect on the microbiome, medical opinion is now changing. Nevertheless, research on the various diets that are now available is often completely lacking. Lectins are carbohydrate binding proteins which are widely distributed in nature and are found in a whole variety of commonly consumed foods. It seems likely that the exclusion of lectins from the diet could become the next "food fashion" for alternative practitioners to promote, especially as there is some evidence to suggest that certain lectins may be harmful to health. It is, therefore, the purpose of this viewpoint to try and stimulate research on the dietary effects of lectins, which is currently minimal, so that we can pre-empt a situation where we are unable to give patients or the public evidence based advice on this topic.

RevDate: 2019-07-11

Pagliai G, Russo E, Niccolai E, et al (2019)

Influence of a 3-month low-calorie Mediterranean diet compared to the vegetarian diet on human gut microbiota and SCFA: the CARDIVEG Study.

European journal of nutrition pii:10.1007/s00394-019-02050-0 [Epub ahead of print].

PURPOSE: We evaluated the effect of low-calorie mediterranean (MD) and vegetarian (VD) diets on gut microbiome (GM) composition and short-chain-fatty acids (SCFA) production.

METHODS: We performed next generation sequencing (NGS) of 16S rRNA and SCFA analysis on fecal samples of 23 overweight omnivores (16 F; 7 M) with low-to-moderate cardiovascular risk. They were randomly assigned to a VD or MD, each lasting 3 months, with a crossover study design.

RESULTS: Dietary interventions did not produce significant diversity in the GM composition at higher ranks (family and above), neither between nor within MD and VD, but they did it at genus level. MD significantly changed the abundance of Enterorhabdus, Lachnoclostridium and Parabacteroides, while VD significantly affected the abundance of Anaerostipes, Streptococcus, Clostridium sensu stricto, and Odoribacter. Comparison of the mean variation of each SCFA between MD and VD showed an opposite and statistically significant trend for propionic acid (+ 10% vs - 28%, respectively, p = 0.034). In addition, variations of SCFA were negatively correlated with changes of some inflammatory cytokines such as VEGF, MCP-1, IL-17, IP-10 and IL-12, only after MD. Finally, correlation analyses showed a potential relationship-modulated by the two diets-between changes of genera and changes of clinical and biochemical parameters.

CONCLUSIONS: A short-term dietary intervention with MD or VD does not induce major change in the GM, suggesting that a diet should last longer than 3 months for scratching the microbial resilience. Changes in SCFA production support their role in modulating the inflammatory response, thus mediating the anti-inflammatory and protective properties of MD.

RevDate: 2019-07-11

Okukawa M, Watanabe T, Miura M, et al (2019)

Antibacterial Activity of 1,2-Alkanediol against Staphylococcus aureus and Staphylococcus epidermidis.

Journal of oleo science [Epub ahead of print].

1,2-Alkanediol exhibits antibacterial activity against several bacteria and yeast. However, few studies have reported antimicrobial tests on skin microbiome. Bacterial microbiome on the skin surface include Staphylococcus aureus (S. aureus), which causes rough skin and inflammation in atopic dermatitis and Staphylococcus epidermidis (S. epidermidis), which enhances innate immunity. In this study, the minimal inhibitory concentration (MIC) was evaluated for 1,2-alkanediol comprising 4-12 carbon atoms against S. aureus and S. epidermidis. 1,2-Alkanediol comprising 6-12 carbon atoms exhibited antimicrobial activity against both species of Staphylococcus. The antibacterial activity depended on the alkyl chain length. In addition, the minimum bactericidal concentration (MBC) on agar was evaluated for 1,2-alkanediol comprising 6-12 carbon atoms. 1,2-Octanediol and 1,2-decanediol exhibited significant bactericidal activity.

RevDate: 2019-07-11

Tinsley N, Zhou C, Tan G, et al (2019)

Cumulative Antibiotic Use Significantly Decreases Efficacy of Checkpoint Inhibitors in Patients with Advanced Cancer.

The oncologist pii:theoncologist.2019-0160 [Epub ahead of print].

BACKGROUND: With the advent of immunotherapy, substantial progress has been made in improving outcomes for patients with advanced cancer. However, not all patients benefit equally from treatment, and confounding immune-related issues may have an impact. Several studies suggest that antibiotic use (which alters the gut microbiome) may result in poorer outcomes for patients treated with immune checkpoint inhibitors (ICI).

MATERIALS AND METHODS: This is a large, single-site retrospective review of n = 291 patients with advanced cancer treated with ICI (n = 179 melanoma, n = 64 non-small cell lung cancer, and n = 48 renal cell carcinoma). Antibiotic use (both single and multiple courses/prolonged use) during the periods 2 weeks before and 6 weeks after ICI treatment was investigated.

RESULTS: Within this cohort, 92 patients (32%) received antibiotics. Patients who did not require antibiotics had the longest median progression-free survival (PFS), of 6.3 months, and longest median overall survival (OS), of 21.7 months. With other clinically relevant factors controlled, patients who received a single course of antibiotics had a shorter median OS (median OS, 17.7 months; p = .294), and patients who received multiple courses or prolonged antibiotic treatment had the worst outcomes overall (median OS, 6.3 months; p = .009). Progression-free survival times were similarly affected.

CONCLUSION: This large, multivariate analysis demonstrated that antibiotic use is an independent negative predictor of PFS and OS in patients with advanced cancer treated with ICIs. This study highlighted worse treatment outcomes from patients with cumulative (multiple or prolonged courses) antibiotic use, which warrants further investigation and may subsequently inform clinical practice guidelines advocating careful use of antibiotics.

IMPLICATIONS FOR PRACTICE: Antibiotic use is negatively associated with treatment outcomes of immune checkpoint inhibitors (ICI) in advanced cancer. Cumulative antibiotic use is associated with a marked negative survival outcome. Judicious antibiotic prescribing is warranted in patients receiving treatment with ICI for treatment of advanced malignancy.

RevDate: 2019-07-11

Mike LA (2019)

mSphere of Influence: Systematically Decoding Microbial Chemical Communication.

mSphere, 4(4): pii:4/4/e00319-19.

Laura A. Mike works in the field of bacterial pathogenesis. In this mSphere of Influence article, she reflects on how "Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters" by P. Cimermancic et al. (Cell 158:412-421, 2014, and "A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics" by M. S. Donia et al. (Cell 158:1402-1414, 2014, made an impact on her by systematically identifying microbiome-associated biosynthetic gene clusters predicted to synthesize secondary metabolites, which may facilitate interspecies interactions.

RevDate: 2019-07-10

Ribeiro ÂM, Puetz L, Pattinson NB, et al (2019)

31° South: The physiology of adaptation to arid conditions in a passerine bird.

Molecular ecology [Epub ahead of print].

Arid environments provide ideal ground for investigating the mechanisms of adaptive evolution. High temperatures and low water availability are relentless stressors for many endotherms, including birds; yet birds persist in deserts. While physiological adaptation likely involves metabolic phenotypes, the underlying mechanisms (plasticity, genetics) are largely uncharacterized. To explore this, we took an intra-specific approach that focused on a species that is resident over a mesic to arid gradient, the Karoo scrub-robin (Cercotrichas coryphaeus). Specifically, we integrated environmental (climatic and primary productivity), physiological (metabolic rates: a measure of energy expenditure), genotypic (genetic variation underlying the machinery of energy production) and microbiome (involved in processing food from where energy is retrieved) data, to infer the mechanism of physiological adaptation. We that found the variation in energetic physiology phenotypes and gut microbiome composition are associated with environmental features as well as with variation in genes underlying energy metabolic pathways. Specifically, we identified a small list of candidate adaptive genes, some of them with known ties to relevant physiology phenotypes. Together our results suggest that selective pressures on energetic physiology mediated by genes related to energy homeostasis and possibly microbiota composition may facilitate adaptation to local conditions and provide an explanation to the high avian intra-specific divergence observed in harsh environments. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-10

Liu Y, Ajami NJ, El-Serag HB, et al (2019)

Dietary quality and the colonic mucosa-associated gut microbiome in humans.

The American journal of clinical nutrition pii:5530748 [Epub ahead of print].

BACKGROUND: Despite tremendous interest in modulating the microbiome to improve health, the association between diet and the colonic mucosa-associated gut microbiome in healthy individuals has not been examined.

OBJECTIVE: To investigate the associations between Healthy Eating Index (HEI)-2005 and the colonic mucosa-associated microbiota.

METHODS: In this cross-sectional observational study, we analyzed bacterial community composition and structure using 16S rRNA gene (V4 region) sequencing of 97 colonic mucosal biopsies obtained endoscopically from different colon segments of 34 polyp-free participants. Dietary consumption was ascertained using an FFQ. Differences in α- and β-diversity and taxonomic relative abundances between the higher and lower score of total HEI and its components were compared, followed by multivariable analyses.

RESULTS: The structure of the microbiota significantly differed by the scores for total HEI, total and whole fruits (HEI 1 and HEI 2), whole grains (HEI 6), milk products and soy beverages (HEI 7), and solid fat, alcohol, and added sugar (HEI 12). A lower score for total HEI and HEIs 2, 7, and 12 was associated with significantly lower richness. A lower score for total HEI was associated with significantly reduced relative abundance of Parabacteroides, Roseburia, and Subdoligranulum but higher Fusobacterium. A lower score for HEI 2 was associated with lower Roseburia but higher Bacteroides. A lower score for HEI 7 was associated with lower Faecalibacterium and Fusobacterium but higher Bacteroides. A lower score for HEI 12 was associated with lower Subdoligranulum but higher Escherichia and Fusobacterium (false discovery rate-adjusted P values <0.05). The findings were confirmed by multivariate analysis. Less abundant bacteria such as Alistipes, Odoribacter, Bilophila, and Tyzzerella were also associated with dietary quality.

CONCLUSIONS: A lower score for total HEI-2005 was significantly associated with reduced relative abundance of potentially beneficial bacteria but increased potentially harmful bacteria in the colonic mucosa of endoscopically normal individuals.

RevDate: 2019-07-10

Šoltys K, Planý M, Biocca P, et al (2019)

Lead soaps formation and biodiversity in a XVIII Century wax seal coloured with minium.

Environmental microbiology [Epub ahead of print].

A multidisciplinary approach was carried out in order to study the biodeterioration and the associated microbiome of a XVIII Century wax seal coloured with minium. A small wax seal fragment was observed by scanning electron microscopy combined with energy dispersive spectroscopy (SEM-EDS) in non-destructive mode. The same object was analysed by RAMAN and Fourier-transform infrared (FTIR) spectroscopy. The identification of the microbiota growing on the seal was performed with both a culture-dependent strategy, combined with hydrolytic assays, and high throughput sequencing using the MinION platform. The whole bacterial 16S rRNA gene and the fungal markers ITS and 28S rRNA were targeted. It was observed that the carnauba wax coloured with lead tetroxide (minium) was covered by a biofilm consisting of a network of filaments and other structures of microbial origin. The culture-dependent and culture-independent investigations showed the presence of a complex microbiota composed mainly by fungal members which demonstrated interesting properties related to lipids and lead processing. The formation of lead soaps and secondary biogenic minerals were also described. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-10

Li CX, You ZX, Lin YX, et al (2019)

Skin microbiome differences relate to the grade of acne vulgaris.

The Journal of dermatology [Epub ahead of print].

The skin microbiome plays important roles in the pathogenesis and development of acne. We aimed to investigate the facial skin microbiome of acne and microbiome differences related to different grades of acne. Skin swabs from nine healthy controls and 67 acne patients were collected, and the skin microbiomes were analyzed using 16S rRNA gene sequencing. Compared with healthy controls, acne patients harbored significantly altered skin microbiomes. The skin microbiomes of patients with grade 1-3 acne were similar, but patients with grade 4 acne showed a significantly different skin microbiome compared with grade 1-3 acne, including increased alpha diversity and increased proportions of four Gram-negative bacteria (Faecalibacterium, Klebsiella, Odoribacter and Bacteroides). In conclusion, acne patients harbored an altered skin microbiome, and more significant dysbiosis was found in patients with grade 4 acne (severe acne). Our findings may provide evidence for the pathogenic mechanisms of acne and microbial-based strategies to avoid and treat acne, especially grade 4 acne.

RevDate: 2019-07-10

Jensen EA, Berryman DE, Murphy ER, et al (2019)

Heterogeneity spacers in 16S rDNA primers improve analysis of mouse gut microbiomes via greater nucleotide diversity.

BioTechniques [Epub ahead of print].

Illumina-based amplicon sequencing suffers from the deleterious effects of highly homogenous nucleotide composition, limiting the number of high-quality reads generated per run. We attempted to alleviate this limitation by comparing the results obtained from 16S ribosomal DNA (16S rDNA) sequencing of mouse gut microbiomes using Illumina V3-V4 primers (Run 1) and custom primers that incorporate a heterogeneity spacer (0-7 nucleotides) upstream of the 16S priming region (Run 2). Overall, Run 2 had higher quality sequences, a more diverse microbial profile, and higher precision within, and variation between, experimental groups than Run 1. Our primer design offers a simple way to increase the quality of 16S rDNA sequencing and increases the number of useable reads generated per Illumina run.

RevDate: 2019-07-10

McLean C, Jun S, A Kozyrskyj (2019)

Impact of maternal smoking on the infant gut microbiota and its association with child overweight: a scoping review.

World journal of pediatrics : WJP pii:10.1007/s12519-019-00278-8 [Epub ahead of print].

BACKGROUND: Childhood obesity is a growing public health concern with evidence demonstrating that while infant exposure to maternal smoking is linked to low birth weight at birth, there is a rapid catch up in weight and increased risk of obesity in later life. This scoping review aims to synthesize up-to-date evidence on the impact of maternal smoking on the infant gut microbiota and its association with child overweight.

METHODS: We conducted a PRISMA-compliant scoping review. Primary population-based cohort studies published between 1900 and April 2018 were included. Relevant publications were retrieved from seven databases: PubMed, Medline, Embase, Scopus, Biosis, Cochrane library, and Web of Science Core Collection.

RESULTS: A total of three prospective cohort studies were included which utilized high-throughput 16S rRNA gene sequencing to assess the gut microbiota and included a total of 1277 infant/neonatal participants. Neonates exposed to environmental smoke had a higher relative abundance of Ruminococcus and Akkermansia. Infants exposed to environmental smoke during pregnancy or postnatally were found to have increased gut bacterial richness, particularly Firmicutes at 3 months of age, while 6-month-old infants born to smoking mothers had an increased abundance of Bacteroides and Staphylococcus. Elevated Firmicutes richness at 3 months of age was associated with elevated odds of child overweight and obesity at 1 and 3 years of age.

CONCLUSION: The limited evidence to date warrants further large scale, longitudinal studies to explore the impact of maternal smoking and environmental tobacco smoke on the infant gut microbiome and its relation to child overweight.

RevDate: 2019-07-10

Youens-Clark K, Bomhoff M, Ponsero AJ, et al (2019)

iMicrobe: Tools and data-dreaiven discovery platform for the microbiome sciences.

GigaScience, 8(7):.

BACKGROUND: Scientists have amassed a wealth of microbiome datasets, making it possible to study microbes in biotic and abiotic systems on a population or planetary scale; however, this potential has not been fully realized given that the tools, datasets, and computation are available in diverse repositories and locations. To address this challenge, we developed, a community-driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with those from the broader community.

FINDINGS: The iMicrobe platform brings together analysis tools and microbiome datasets by leveraging National Science Foundation-supported cyberinfrastructure and computing resources from CyVerse, Agave, and XSEDE. The primary purpose of iMicrobe is to provide users with a freely available, web-based platform to (1) maintain and share project data, metadata, and analysis products, (2) search for related public datasets, and (3) use and publish bioinformatics tools that run on highly scalable computing resources. Analysis tools are implemented in containers that encapsulate complex software dependencies and run on freely available XSEDE resources via the Agave API, which can retrieve datasets from the CyVerse Data Store or any web-accessible location (e.g., FTP, HTTP).

CONCLUSIONS: iMicrobe promotes data integration, sharing, and community-driven tool development by making open source data and tools accessible to the research community in a web-based platform.

RevDate: 2019-07-10

Voorhies AA, Mark Ott C, Mehta S, et al (2019)

Study of the impact of long-duration space missions at the International Space Station on the astronaut microbiome.

Scientific reports, 9(1):9911 pii:10.1038/s41598-019-46303-8.

Over the course of a mission to the International Space Station (ISS) crew members are exposed to a number of stressors that can potentially alter the composition of their microbiomes and may have a negative impact on astronauts' health. Here we investigated the impact of long-term space exploration on the microbiome of nine astronauts that spent six to twelve months in the ISS. We present evidence showing that the microbial communities of the gastrointestinal tract, skin, nose and tongue change during the space mission. The composition of the intestinal microbiota became more similar across astronauts in space, mostly due to a drop in the abundance of a few bacterial taxa, some of which were also correlated with changes in the cytokine profile of crewmembers. Alterations in the skin microbiome that might contribute to the high frequency of skin rashes/hypersensitivity episodes experienced by astronauts in space were also observed. The results from this study demonstrate that the composition of the astronauts' microbiome is altered during space travel. The impact of those changes on crew health warrants further investigation before humans embark on long-duration voyages into outer space.

RevDate: 2019-07-10

Wu L, Zeng T, Zinellu A, et al (2019)

A Cross-Sectional Study of Compositional and Functional Profiles of Gut Microbiota in Sardinian Centenarians.

mSystems, 4(4): pii:4/4/e00325-19.

Sardinia, Italy, has a high prevalence of residents who live more than 100 years. The reasons for longevity in this isolated region are currently unknown. Gut microbiota may hold a clue. To explore the role gut microbiota may play in healthy aging and longevity, we used metagenomic sequencing to determine the compositional and functional differences in gut microbiota associated with populations of different ages in Sardinia. Our data revealed that the gut microbiota of both young and elderly Sardinians shared similar taxonomic and functional profiles. A different pattern was found in centenarians. Within the centenarian group, the gut microbiota was correlated with the functional independence measurement of the host. Centenarians had a higher diversity of core microbiota species and microbial genes than those in the young and elderly. We found that the gut microbiota in Sardinian centenarians displayed a rearranged taxonomic pattern compared with those of the young and elderly, featured by depletion of Faecalibacterium prausnitzii and Eubacterium rectale and enriched for Methanobrevibacter smithii and Bifidobacterium adolescentis Moreover, functional analysis revealed that the microbiota in centenarians had high capacity for central metabolism, especially glycolysis and fermentation to short-chain fatty acids (SCFAs), although the gut microbiota in centenarians was low in genes encoding enzymes involved in degradation of carbohydrates, including fibers and galactose.IMPORTANCE The gut microbiota has been proposed as a promising determinant for human health. Centenarians as a model for extreme aging may help us understand the correlation of gut microbiota with healthy aging and longevity. Here we confirmed that centenarians had microbiota elements usually associated with benefits to health. Our finding of a high capacity of glycolysis and related SCFA production represented a healthy microbiome and environment that is regarded as beneficial for host gut epithelium. The low abundance of genes encoding components of pathways involved in carbohydrate degradation was also found in the gut microbiota of Sardinian centenarians and is often associated with poor gut health. Overall, our study here represents an expansion of previous research investigating the age-related changes in gut microbiota. Furthermore, our study provides a new prospective for potential targets for gut microbiota intervention directed at limiting gut inflammation and pathology and enhancing a healthy gut barrier.

RevDate: 2019-07-10

Keij FM, Kornelisse RF, Hartwig NG, et al (2019)

RAIN study: a protocol for a randomised controlled trial evaluating efficacy, safety and cost-effectiveness of intravenous-to-oral antibiotic switch therapy in neonates with a probable bacterial infection.

BMJ open, 9(7):e026688 pii:bmjopen-2018-026688.

INTRODUCTION: High morbidity and mortality rates of proven bacterial infection are the main reason for substantial use of intravenous antibiotics in neonates during the first week of life. In older children, intravenous-to-oral switch after 48 hours of intravenous therapy has been shown to have many advantages and is nowadays commonly practised. We, therefore, aim to evaluate the effectiveness, safety and cost-effectiveness of an early intravenous-to-oral switch in neonates with a probable bacterial infection.

METHODS AND ANALYSIS: We present a protocol for a multicentre randomised controlled trial assessing the non-inferiority of an early intravenous-to-oral antibiotic switch compared with a full course of intravenous antibiotics in neonates (0-28 days of age) with a probable bacterial infection. Five hundred and fifty patients will be recruited in 17 hospitals in the Netherlands. After 48 hours of intravenous treatment, they will be assigned to either continue with intravenous therapy for another 5 days (control) or switch to amoxicillin/clavulanic acid suspension (intervention). Both groups will be treated for a total of 7 days. The primary outcome will be bacterial (re)infection within 28 days after treatment completion. Secondary outcomes are the pharmacokinetic profile of oral amoxicillin/clavulanic acid, the impact on quality of life, cost-effectiveness, impact on microbiome development and additional yield of molecular techniques in diagnosis of probable bacterial infection.

ETHICS AND DISSEMINATION: This study has been approved by the Medical Ethics Committee of the Erasmus Medical Centre. Results will be presented in peer-reviewed journals and at international conferences.


RevDate: 2019-07-10

Morley VJ, Woods RJ, AF Read (2019)

Bystander Selection for Antimicrobial Resistance: Implications for Patient Health.

Trends in microbiology pii:S0966-842X(19)30159-3 [Epub ahead of print].

Antimicrobial therapy promotes resistance emergence in target infections and in off-target microbiota. Off-target resistance emergence threatens patient health when off-target populations are a source of future infections, as they are for many important drug-resistant pathogens. However, the health risks of antimicrobial exposure in off-target populations remain largely unquantified, making rational antibiotic stewardship challenging. Here, we discuss the contribution of bystander antimicrobial exposure to the resistance crisis, the implications for antimicrobial stewardship, and some novel opportunities to limit resistance evolution while treating target pathogens.

RevDate: 2019-07-10

Uroz S, Courty PE, P Oger (2019)

Plant Symbionts Are Engineers of the Plant-Associated Microbiome.

Trends in plant science pii:S1360-1385(19)30155-4 [Epub ahead of print].

Plants interact throughout their lives with environmental microorganisms. These interactions determine plant development, nutrition, and fitness in a dynamic and stressful environment, forming the basis for the holobiont concept in which plants and plant-associated microbes are not considered as independent entities but as a single evolutionary unit. A primary open question concerns whether holobiont structure is shaped by its microbial members or solely by the plant. Current knowledge of plant-microbe interactions argues that the establishment of symbiosis directly and indirectly conditions the plant-associated microbiome. We propose to define the impact of the symbiont on the plant microbiome as the 'symbiosis cascade effect', in which the symbionts and their plant host jointly shape the plant microbiome.

RevDate: 2019-07-10

Lam TJ, Y Ye (2019)

Long reads reveal the diversification and dynamics of CRISPR reservoir in microbiomes.

BMC genomics, 20(1):567 pii:10.1186/s12864-019-5922-8.

BACKGROUND: Sequencing of microbiomes has accelerated the characterization of the diversity of CRISPR-Cas immune systems. However, the utilization of next generation short read sequences for the characterization of CRISPR-Cas dynamics remains limited due to the repetitive nature of CRISPR arrays. CRISPR arrays are comprised of short spacer segments (derived from invaders' genomes) interspaced between flanking repeat sequences. The repetitive structure of CRISPR arrays poses a computational challenge for the accurate assembly of CRISPR arrays from short reads. In this paper we evaluate the use of long read sequences for the analysis of CRISPR-Cas system dynamics in microbiomes.

RESULTS: We analyzed a dataset of Illumina's TruSeq Synthetic Long-Reads (SLR) derived from a gut microbiome. We showed that long reads captured CRISPR spacers at a high degree of redundancy, which highlights the spacer conservation of spacer sharing CRISPR variants, enabling the study of CRISPR array dynamics in ways difficult to achieve though short read sequences. We introduce compressed spacer graphs, a visual abstraction of spacer sharing CRISPR arrays, to provide a simplified view of complex organizational structures present within CRISPR array dynamics. Utilizing compressed spacer graphs, several key defining characteristics of CRISPR-Cas system dynamics were observed including spacer acquisition and loss events, conservation of the trailer end spacers, and CRISPR arrays' directionality (transcription orientation). Other result highlights include the observation of intense array contraction and expansion events, and reconstruction of a full-length genome for a potential invader (Faecalibacterium phage) based on identified spacers.

CONCLUSION: We demonstrate in an in silico system that long reads provide the necessary context for characterizing the organization of CRISPR arrays in a microbiome, and reveal dynamic and evolutionary features of CRISPR-Cas systems in a microbial population.

RevDate: 2019-07-09

Wree A, Geisler LJ, F Tacke (2019)

[Microbiome & NASH - partners in crime driving progression of fatty liver disease].

Zeitschrift fur Gastroenterologie, 57(7):871-882.

Along with the increasing prevalence of obesity, metabolic syndrome and type 2 diabetes, non-alcoholic fatty liver disease (NAFLD) is rapidly increasing and poses a major challenge for gastroenterologists. Many studies have demonstrated that the microbiome is closely associated with the progression of nutrition-related diseases, especially of fatty liver disease. Changes in the quantity and quality of the intestinal flora, commonly referred to as dysbiosis, result in altered food metabolism, increased permeability of the intestinal barrier ("leaky gut") and consecutive inflammatory processes in the liver. This favors both the progression of obesity and metabolic disorders as well as NAFLD towards non-alcoholic steatohepatitis (NASH), hepatic fibrosis, cirrhosis and hepatocellular carcinoma (HCC). Important molecular mechanisms include microbial metabolites, microbial and endogenous signaling substances (so-called PAMPs/DAMPs) as well as bile acids. Essential cellular mechanisms include immune cells in the gut and liver, especially macrophages and Kupffer cells, as well as intestinal epithelial cells and hepatocytes as central regulators of metabolism. In this review article, we briefly summarize the relevant species of the human microbiome, describe the microbial analytics, explain the most important molecular relationships between microbiome and NAFLD/NASH, and finally the opportunities and challenges of microbiome-modulating therapy for the treatment of fatty liver disease.

RevDate: 2019-07-09

Lopez SMC, Martin JM, Johnson M, et al (2019)

A method of processing nasopharyngeal swabs to enable multiple testing.

Pediatric research pii:10.1038/s41390-019-0498-1 [Epub ahead of print].

OBJECTIVE: To develop a method to perform multiple tests on single nasopharyngeal (NP) swab.

STUDY DESIGN: We collected a NP swab on children aged 2-12 years with acute sinusitis and processed it for bacterial culture, viruses, cytokine expression, and 16S ribosomal RNA gene sequencing analysis. During the course of the study, we expand the scope of evaluation to include RNA-sequencing, which we accomplished by cutting the tip of the swab.

RESULTS: Of the 174 children enrolled, 126 (72.4%) had a positive bacterial culture and 121 (69.5%) tested positive for a virus. Cytokine measurement, as judged by the adequate levels of a housekeeping enzyme (glyceraldehyde 3-phosphate dehydrogenase), appeared successful. From the samples used for 16S ribosomal sequencing we recovered, on average, 16,000 sequences per sample, accounting for a total of 2646 operational taxonomic units across all samples sequenced. Samples used for RNA-sequencing had a mean RNA integrity number of 6.0. Cutting the tip of the swab did not affect the recovery yield for viruses or bacteria, nor did it affect species richness in microbiome analysis.

CONCLUSION: We describe a minimally invasive sample collection protocol that allows for multiple diagnostic and research investigations in young children.

RevDate: 2019-07-09

Jarrett OD, Srinivasan S, Richardson BA, et al (2019)

Specific vaginal bacteria are associated with increased risk of Trichomonas vaginalis acquisition in women.

The Journal of infectious diseases pii:5530317 [Epub ahead of print].

BACKGROUND: While bacterial vaginosis has been associated with an increased risk of Trichomonas vaginalis (TV) acquisition, it is unknown if other characteristics of the vaginal microbiota, including the presence of key bacterial species, impact a woman's risk of TV.

METHODS: The pre-TV infection vaginal microbiota of 25 unique episodes of TV were compared to 50 controls who remained uninfected. Trichomonas vaginalis was detected by transcription mediated amplification. Vaginal microbiota were quantified using broad range polymerase chain reaction (PCR) and taxon-specific quantitative PCR of the 16S ribosomal RNA (rRNA) gene.

RESULTS: Trichomonas vaginalis acquisition was significantly associated with the presence of Prevotella amnii (risk ratio [RR] 2.21, 95%CI 1.12-4.38; p=.02) and Sneathia sanguinegens (RR 2.58, 95%CI 1.00-6.62; p=.049). When adjusted for menstrual phase, the association between P. amnii and TV acquisition remained similar (adjusted RR [aRR] 2.11, 95%CI 1.03-4.33; p=.04) but the association between S. sanguinegens and TV was attenuated (aRR 2.31, 95%CI 0.86-6.23; p=.10).

CONCLUSIONS: Key vaginal bacterial species may contribute to susceptibility to TV acquisition. Understanding how these bacterial species increase a woman's risk of TV could help to guide the development of novel strategies to reduce women's risk of TV infection.

RevDate: 2019-07-09

Sun L, Dicksved J, Priyashantha H, et al (2019)

Distribution of bacteria between different milk fractions, investigated using culture-dependent methods and molecular-based and fluorescent microscopy approaches.

Journal of applied microbiology [Epub ahead of print].

AIMS: To develop a protocol for DNA extraction using whole milk and further, to investigate how the use of whole instead of skimmed milk during DNA extraction affected the resulting microbial composition.

METHODS AND RESULTS: In a model study, three selected bacterial species (Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 11775 and Lactobacillus reuteri PTA 4659) were added to raw milk and their distribution between different milk fractions was examined by cultivation on selective agar plates. QPCR assays and Illumina amplicon sequencing were conducted after DNA extraction of whole milk and skimmed milk. In addition, fluorescent microscopy was used to visualise the distribution of Lactobacillus reuteri R2LC mCherry in milk samples with different fat contents. Depending on spike-in bacterial species, recovery rates of 7·4-26·5% of added bacteria were obtained in the fat fraction in culture-based enumeration. qPCR showed a 7-9 fold increase in recovery of spike-in bacteria when the milk fat fraction was combined with the pellet during the DNA extraction step. In the Illumina 16S amplicon approach, relative abundance of six out of the top 11 operational taxonomic units (OTUs) identified differed significantly when comparing skimmed milk and whole milk as starting material. Fluorescent microscopy images demonstrated that Lactobacillus reuteri R2LC mCherry was associated with fat globules in whole milk samples.

CONCLUSIONS: This study demonstrates that milk fat harbours bacterial species that might be underestimated when skimmed milk, rather than whole milk, is used for DNA extraction.

This study emphasizes the importance of using whole instead of skimmed milk for DNA extraction. A protocol for extracting DNA from whole milk is suggested. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-09

McClanahan D, Wong A, Kezic S, et al (2019)

A randomized controlled trial of an emollient with ceramide and filaggrin-associated amino acids for the primary prevention of atopic dermatitis in high-risk infants.

Journal of the European Academy of Dermatology and Venereology : JEADV [Epub ahead of print].

BACKGROUND: Skin barrier dysfunction may precede infantile development of clinical atopic dermatitis (AD). Early life emollient therapy to enhance barrier function may prevent or modify AD development in high-risk infants.

OBJECTIVES: a)To determine whether daily full-body application of an emollient with ceramide and amino acids (study emollient) can reduce the cumulative AD incidence compared to standard skin care at one year of age. b) To evaluate the study emollient's effect on skin barrier function, natural moisturizing factor and the microbiome using non-invasive biophysical and biochemical techniques.

METHODS: We performed a single center, investigator-blinded, randomized controlled trial enrolling infants at high risk for AD development determined by family history. The intervention was full-body once daily application of the study emollient. The control arm was asked to not apply full body emollient regularly and only use an emollient of their choice for dry skin. The primary outcome was the cumulative incidence of AD diagnosed at 12 months by a blinded investigator.

RESULTS: Less than half the target sample size was enrolled (n=100, goal sample was 208) with 28% lost to follow-up. Across all clinical endpoints, a numerical trend was observed in favor of the intervention, although not statistically significant likely due to lack of power from under-enrollment. AD was diagnosed in 13.2% vs. 25.0% at 12 months (P=0.204) and 19.4% vs. 31.0% at two years (P=0.296) in intervention vs. control groups, respectively. There were no significant differences between groups in skin barrier or microbiome assessments. While there were no serious adverse events, there were more cases of reported contact dermatitis in the intervention vs. control arms, 9.3% vs. 4.3%, respectively, however these events were not related to the study emollient and most mild in severity.

CONCLUSION: The observed trends suggest a protective effect of daily study emollient therapy compared to control. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-09

Meola M, Rifa E, Shani N, et al (2019)

DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products.

BMC genomics, 20(1):560 pii:10.1186/s12864-019-5914-8.

BACKGROUND: Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation of 16S reads, particularly at species rank, is still challenging due to the short size of read sequences and differently curated classification databases. The close phylogenetic relationship between species encountered in dairy products, however, makes it crucial to annotate species accurately to achieve sufficient phylogenetic resolution for further downstream ecological studies or for food diagnostics. Curated databases dedicated to the environment of interest are expected to improve the accuracy and resolution of taxonomy annotation.

RESULTS: We provide a manually curated database composed of 10'290 full-length 16S rRNA gene sequences from prokaryotes tailored for dairy products analysis ( The performance of the DAIRYdb was compared with the universal databases Silva, LTP, RDP and Greengenes. The DAIRYdb significantly outperformed all other databases independently of the classification algorithm by enabling higher accurate taxonomy annotation down to the species rank. The DAIRYdb accurately annotates over 90% of the sequences of either single or paired hypervariable regions automatically. The manually curated DAIRYdb strongly improves taxonomic annotation accuracy for microbiome studies in dairy environments. The DAIRYdb is a practical solution that enables automatization of this key step, thus facilitating the routine application of NGS microbiome analyses for microbial ecology studies and diagnostics in dairy products.

RevDate: 2019-07-09

Njoku K, EJ Crosbie (2019)

Does the vaginal microbiome drive cervical carcinogenesis?.

BJOG : an international journal of obstetrics and gynaecology [Epub ahead of print].

Since the discovery of lactic acid producing bacteria in the vagina by Albert Dodelein in 1892, multiple studies have explored the relationship between the vaginal microbiota and various physiological, infectious and malignant conditions (Łaniewski et al, Sci Rep. 2018;8(1):7593). Whether the vaginal microbiome influences the association between human papillomavirus (HPV) infection and cervical cancer is one example with several, albeit small studies assessing whether vaginal dysbiosis influences HPV acquisition, persistence and progression to cervical dysplasia and malignancy. Whilst findings from these studies have been consistent and highly suggestive of an altered vaginal microbiome (Brusselaers at al., Am J Obstet Gynaecol 2019: 221(1):9-18), compelling evidence for the specific bacterial community state type (CST) species linked with cervical disease is lacking. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-09

Bowen J, Al-Dasooqi N, Bossi P, et al (2019)

The pathogenesis of mucositis: updated perspectives and emerging targets.

Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer pii:10.1007/s00520-019-04893-z [Epub ahead of print].

Mucositis research and treatment are a rapidly evolving field providing constant new avenues of research and potential therapies. The MASCC/ISOO Mucositis Study Group regularly assesses available literature relating to pathogenesis, mechanisms, and novel therapeutic approaches and distils this to summary perspectives and recommendations. Reviewers assessed 164 articles published between January 2011 and June 2016 to identify progress made since the last review and highlight new targets for further investigation. Findings were organized into sections including established and emerging mediators of toxicity, potential insights from technological advances in mucositis research, and perspective. Research momentum is accelerating for mucositis pathogenesis, and with this has come utilization of new models and interventions that target specific mechanisms of injury. Technological advances have the potential to revolutionize the field of mucositis research, although focused effort is needed to move rationally targeted interventions to the clinical setting.

RevDate: 2019-07-09

Stanislawski MA, Dabelea D, Lange LA, et al (2019)

Gut microbiota phenotypes of obesity.

NPJ biofilms and microbiomes, 5:18 pii:91.

Obesity is a disease with a complex etiology and variable prevalence across different populations. While several studies have reported gut microbiota composition differences associated with obesity in humans, there has been a lack of consistency in the nature of the reported changes; it has been difficult to determine whether methodological differences between studies, underlying differences in the populations studied, or other factors are responsible for this discordance. Here we use 16 S rRNA data from previously published studies to explore how the gut microbiota-obesity relationship varies across heterogeneous Western populations, focusing mainly on the relationship between (1) alpha diversity and (2) Prevotella relative abundance with BMI. We provide evidence that the relationship between lower alpha diversity and higher BMI may be most consistent in non-Hispanic white (NHW) populations and/or those with high socioeconomic status, while the relationship between higher Prevotella relative abundance and BMI may be stronger among black and Hispanic populations. We further examine how diet may impact these relationships. This work suggests that gut microbiota phenotypes of obesity may differ with race/ethnicity or its correlates, such as dietary components or socioeconomic status. However, microbiome cohorts are often too small to study complex interaction effects and non-white individuals are greatly underrepresented, creating substantial challenges to understanding population-level patterns in the microbiome-obesity relationship. Further study of how population heterogeneity influences the relationship between the gut microbiota and obesity is warranted.

RevDate: 2019-07-09

Edwards RA, Vega AA, Norman HM, et al (2019)

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.

Nature microbiology pii:10.1038/s41564-019-0494-6 [Epub ahead of print].

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.

RevDate: 2019-07-09

Suenami S, Konishi Nobu M, R Miyazaki (2019)

Community analysis of gut microbiota in hornets, the largest eusocial wasps, Vespa mandarinia and V. simillima.

Scientific reports, 9(1):9830 pii:10.1038/s41598-019-46388-1.

Gut microbiota are important for various aspects of host physiology, and its composition is generally influenced by both intrinsic and extrinsic contexts of the host. Social bee gut microbiota composition is simple and highly stable hypothesized to be due to their unique food habit and social interactions. Here, we focused on hornets, the largest of the eusocial wasps - Vespa mandarinia and V. simillima. Unlike the well-studied honey bees, adult hornets are generally herbivorous but also hunt insects for broods, a unique behavior which could influence their gut microbiota. Analysis of the gut microbiome using 16S rRNA gene sequencing revealed that the two species have simple gut microbiota, composed of seven or eight consistently maintained 'core' operational taxonomic units (OTUs). While the two Vespa species shared some OTUs, the structures of their gut communities differed. Phylogenetic analysis indicated association of core OTUs with host diet. Intriguingly, prey honey bee gut microbes were detected in the V. simillima gut (and to a lesser extent in V. mandarinia), suggesting migration of microorganisms from the prey gut. This is the first report uncovering gut microbiome in hornets, giving additional insight into how food habit affects gut microbiota of social insects.

RevDate: 2019-07-09

Invernizzi R, PL Molyneaux (2019)

The contribution of infection and the respiratory microbiome in acute exacerbations of idiopathic pulmonary fibrosis.

European respiratory review : an official journal of the European Respiratory Society, 28(152): pii:28/152/190045.

Idiopathic pulmonary fibrosis (IPF) arises in genetically susceptible individuals as a result of an aberrant wound-healing response following repetitive alveolar injury. The clinical course of the disease remains both variable and unpredictable with periods of more rapid decline, termed acute exacerbation of IPF (AE-IPF), often punctuating the disease trajectory. Exacerbations carry a significant morbidity and mortality, and their exact pathogenesis remains unclear. Given the emerging evidence that disruption and alteration in the lung microbiome plays a role in the pathogenesis and progression of IPF, this review discusses the current knowledge of the contribution of infection and the respiratory microbiome to AE-IPF.

RevDate: 2019-07-09

Vandeplassche E, Tavernier S, Coenye T, et al (2019)

Influence of the lung microbiome on antibiotic susceptibility of cystic fibrosis pathogens.

European respiratory review : an official journal of the European Respiratory Society, 28(152): pii:28/152/190041.

The lungs of patients with cystic fibrosis (CF) are colonised by a microbial community comprised of pathogenic species, such as Pseudomonas aeruginosa and Staphylococcus aureus, and microorganisms that are typically not associated with worse clinical outcomes (considered as commensals). Antibiotics directed at CF pathogens are often not effective and a discrepancy is observed between activity of these agents in vitro and in the patient. This review describes how interspecies interactions within the lung microbiome might influence the outcome of antibiotic treatment targeted at common CF pathogens. Protective mechanisms by members of the microbiome such as antibiotic degradation (indirect pathogenicity), alterations of the cell wall, production of matrix components decreasing antibiotic penetration, and changes in metabolism are discussed. Interspecies interactions that increase bacterial susceptibility are also addressed. Furthermore, we discuss how experimental conditions, such as culture media, oxygen levels, incorporation of host-pathogen interactions, and microbial community composition may influence the outcome of microbial interaction studies related to antibiotic activity. Hereby, the importance to create in vitro conditions reflective of the CF lung microenvironment is highlighted. Understanding the role of the CF lung microbiome in antibiotic efficacy may help find novel therapeutic and diagnostic approaches to better tackle chronic lung infections in this patient population.

RevDate: 2019-07-09

Staudacher AG, WW Stevens (2019)

Sinus Infections, Inflammation, and Asthma.

Immunology and allergy clinics of North America, 39(3):403-415.

There is an important link between the upper and lower respiratory tracts whereby inflammation in one environment can influence the other. In acute rhinosinusitis, pathogen exposures are the primary driver for inflammation in the nose, which can exacerbate asthma. In chronic rhinosinusitis, a disease clinically associated with asthma, the inflammation observed is likely from a combination of an impaired epithelial barrier, dysregulated immune response, and potentially infection (or colonization) by specific pathogens. This review explores the associations between rhinosinusitis and asthma, with particular emphasis placed on the role of infections and inflammation.

RevDate: 2019-07-09

Insel M, M Kraft (2019)

Bacteria in Asthma Pathogenesis.

Immunology and allergy clinics of North America, 39(3):377-389.

The airways are under continuous assault from aerosolized bacteria and oral flora. The bacteria present in the airways and gastrointestinal tract of neonates promote immune maturation and protect against asthma pathogenesis. Later bacterial infections and perturbations to the microbiome can contribute to asthma pathogenesis, persistence, and severity.

RevDate: 2019-07-09

Ptaschinski C, NW Lukacs (2019)

Early Life Respiratory Syncytial Virus Infection and Asthmatic Responses.

Immunology and allergy clinics of North America, 39(3):309-319.

The infant's developing immune response is central to establishing a balanced system that reacts appropriately to infectious stimuli, but does not induce altered disease states with potential long-term sequelae. Respiratory syncytial virus may alter the immune system, affecting future responses. Early infection may have direct effects on the lung itself. Other early life processes contribute to the development of immune responses including assembly of the microbiome, which seems to have a particularly important role for establishing the immune environment. This review covers studies that have set up important paradigms and discusses recent data that direct research toward informative hypotheses.

RevDate: 2019-07-09

Lee YB, Byun EJ, AHS Kim (2019)

Potential Role of the Microbiome in Acne: A Comprehensive Review.

Journal of clinical medicine, 8(7): pii:jcm8070987.

Acne is a highly prevalent inflammatory skin condition involving sebaceous sties. Although it clearly develops from an interplay of multiple factors, the exact cause of acne remains elusive. It is increasingly believed that the interaction between skin microbes and host immunity plays an important role in this disease, with perturbed microbial composition and activity found in acne patients. Cutibacterium acnes (C. acnes; formerly called Propionibacterium acnes) is commonly found in sebum-rich areas and its over-proliferation has long been thought to contribute to the disease. However, information provided by advanced metagenomic sequencing has indicated that the cutaneous microbiota in acne patients and acne-free individuals differ at the virulent-specific lineage level. Acne also has close connections with the gastrointestinal tract, and many argue that the gut microbiota could be involved in the pathogenic process of acne. The emotions of stress (e.g., depression and anxiety), for instance, have been hypothesized to aggravate acne by altering the gut microbiota and increasing intestinal permeability, potentially contributing to skin inflammation. Over the years, an expanding body of research has highlighted the presence of a gut-brain-skin axis that connects gut microbes, oral probiotics, and diet, currently an area of intense scrutiny, to acne severity. This review concentrates on the skin and gut microbes in acne, the role that the gut-brain-skin axis plays in the immunobiology of acne, and newly emerging microbiome-based therapies that can be applied to treat acne.

RevDate: 2019-07-09

Minniti G, Rød Sandve S, Padra JT, et al (2019)

The Farmed Atlantic Salmon (Salmo salar) Skin-Mucus Proteome and Its Nutrient Potential for the Resident Bacterial Community.

Genes, 10(7): pii:genes10070515.

Norway is the largest producer and exporter of farmed Atlantic salmon (Salmo salar) worldwide. Skin disorders correlated with bacterial infections represent an important challenge for fish farmers due to the economic losses caused. Little is known about this topic, thus studying the skin-mucus of Salmo salar and its bacterial community depict a step forward in understanding fish welfare in aquaculture. In this study, we used label free quantitative mass spectrometry to investigate the skin-mucus proteins associated with both Atlantic salmon and bacteria. In particular, the microbial temporal proteome dynamics during nine days of mucus incubation with sterilized seawater was investigated, in order to evaluate their capacity to utilize mucus components for growth in this environment. At the start of the incubation period, the largest proportion of proteins (~99%) belonged to the salmon and many of these proteins were assigned to protecting functions, confirming the defensive role of mucus. On the contrary, after nine days of incubation, most of the proteins detected were assigned to bacteria, mainly to the genera Vibrio and Pseudoalteromonas. Most of the predicted secreted proteins were affiliated with transport and metabolic processes. In particular, a large abundance and variety of bacterial proteases were observed, highlighting the capacity of bacteria to degrade the skin-mucus proteins of Atlantic salmon.

RevDate: 2019-07-09

Jackson BR, Chow N, Forsberg K, et al (2019)

On the Origins of a Species: What Might Explain the Rise of Candida auris?.

Journal of fungi (Basel, Switzerland), 5(3): pii:jof5030058.

Candida auris is an emerging multidrug-resistant yeast first described in 2009 that has since caused healthcare-associated outbreaks of severe human infections around the world. In some hospitals, it has become a leading cause of invasive candidiasis. C. auris is markedly different from most other pathogenic Candida species in its genetics, antifungal resistance, and ability to spread between patients. The reasons why this fungus began spreading widely in the last decade remain a mystery. We examine available data on C. auris and related species, including genomic epidemiology, phenotypic characteristics, and sites of detection, to put forth hypotheses on its possible origins. C. auris has not been detected in the natural environment; related species have been detected in in plants, insects, and aquatic environments, as well as from human body sites. It can tolerate hypersaline environments and higher temperatures than most Candida species. We explore hypotheses about the pre-emergence niche of C. auris, whether in the environmental or human microbiome, and speculate on factors that might have led to its spread, including the possible roles of healthcare, antifungal use, and environmental changes, including human activities that might have expanded its presence in the environment or caused increased human contact.

RevDate: 2019-07-08

Aw W, S Fukuda (2019)

Protective effects of bifidobacteria against enteropathogens.

Microbial biotechnology [Epub ahead of print].

Recent major advances in metagenomics and metabolomics technologies have enabled us to collect more data on the gut microbiome and metabolome to evaluate its influence on host health. In this short opinion article, we have chosen to focus on summarizing the protective mechanisms of bifidobacteria, a highly regarded probiotic, and it's metabolite: acetate; against enteropathogens, specifically in the E. coli O157:H7 mice model. We advocate for using a novel approach metabologenomics, which is an integration of metagenomic and metabolomic information on a systems biology-wide approach to better understand this interplay between gut microbiome and host metabolism.

RevDate: 2019-07-08

Roy SM, MA Riley (2019)

Evaluation of the potential of colicins to prevent extraluminal contamination of urinary catheters by Escherichia coli.

International journal of antimicrobial agents pii:S0924-8579(19)30184-0 [Epub ahead of print].

The feasibility of using colicins to create an antimicrobial lubricant to prevent extraluminal catheter contamination during urinary catheter insertion was assessed. Levels of resistance of uropathogenic Escherichia coli to antibiotics and colicins were compared and it was revealed that antibiotics and colicins possess similar frequencies of resistance to a single drug, while colicins exhibit significantly lower levels of multi-drug resistance (22%) than antibiotics (42%). Colicins and antibiotics showed complementary inhibitory activity, with each targeting different subsets of pathogenic isolates. The collateral impact of these two antimicrobials on genera that are members of the fecal/vaginal/urinary microbiome was assessed, with colicins showing significantly less collateral damage than antibiotics. Using a novel colicin, SR4, we determined MICs for a panel of 30 uropathogenic isolates and showed that SR4 achieved the same antimicrobial efficacy as gentamicin using 20-30% less drug. Finally, we created a SR4-impregnated catheter lubricant and demonstrated its ability to prevent extraluminal urinary catheter contamination in vitro. These data argue that a colicin-impregnated lubricant may provide a viable prophylactic option for preventing catheter-associated urinary tract infections.

RevDate: 2019-07-08

Philip N, Leishman SJ, Bandara HMHN, et al (2019)

Randomized Controlled Study to Evaluate Microbial Ecological Effects of CPP-ACP and Cranberry on Dental Plaque.

JDR clinical and translational research [Epub ahead of print].

INTRODUCTION: Ecological approaches to dental caries prevention play a key role in attaining long-term control over the disease and maintaining a symbiotic oral microbiome.

OBJECTIVES: This study aimed to investigate the microbial ecological effects of 2 interventional dentifrices: a casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) dentifrice and the same dentifrice supplemented with a polyphenol-rich cranberry extract.

METHODS: The interventional toothpastes were compared with each other and with an active control fluoride dentifrice in a double-blinded randomized controlled trial. Real-time quantitative polymerase chain reaction (qPCR) analysis was used to determine changes in the bacterial loads of 14 key bacterial species (8 caries associated and 6 health associated) in the dental plaque of trial participants after they used the dentifrices for 5 to 6 wk.

RESULTS: From the baseline to the recall visit, significant differences were observed between the treatment groups in the bacterial loads of 2 caries-associated bacterial species (Streptococcus mutans [P < 0.001] and Veillonella parvula [P < 0.001]) and 3 health-associated bacterial species (Corynebacterium durum [P = 0.008], Neisseria flavescens [P = 0.005], and Streptococcus sanguinis [P < 0.001]). Compared to the fluoride control dentifrice, the CPP-ACP dentifrice demonstrated significant differences for S. mutans (P = 0.032), C. durum (P = 0.007), and S. sanguinis (P < 0.001), while combination CPP-ACP-cranberry dentifrice showed significant differences for S. mutans (P < 0.001), V. parvula (P < 0.001), N. flavescens (P = 0.003), and S. sanguinis (P < 0.001). However, no significant differences were observed in the bacterial load comparisons between the CPP-ACP and combination dentifrices for any of the targeted bacterial species (P > 0.05).

CONCLUSIONS: Overall, the results indicate that dentifrices containing CPP-ACP and polyphenol-rich cranberry extracts can influence a species-level shift in the ecology of the oral microbiome, resulting in a microbial community less associated with dental caries (Australian New Zealand Clinical Trial Registry ANZCTR 12618000095268).

KNOWLEDGE TRANSFER STATEMENT: The results of this randomized controlled trial indicate that dentifrices containing casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) and polyphenol-rich cranberry extracts were able to beneficially modulate the microbial ecology of dental plaque in a group of high caries-risk patients. This could contribute toward lowering the risk of developing new caries lesions, an important goal sought by patients, clinicians, and policy makers.

RevDate: 2019-07-08

Rogier R, Ederveen THA, Wopereis H, et al (2019)

Supplementation of diet with non-digestible oligosaccharides alters the intestinal microbiota, but not arthritis development, in IL-1 receptor antagonist deficient mice.

PloS one, 14(7):e0219366 pii:PONE-D-18-35700.

The intestinal microbiome is perturbed in patients with new-onset and chronic autoimmune inflammatory arthritis. Recent studies in mouse models suggest that development and progression of autoimmune arthritis is highly affected by the intestinal microbiome. This makes modulation of the intestinal microbiota an interesting novel approach to suppress inflammatory arthritis. Prebiotics, defined as non-digestible carbohydrates that selectively stimulate the growth and activity of beneficial microorganisms, provide a relatively non-invasive approach to modulate the intestinal microbiota. The aim of this study was to assess the therapeutic potential of dietary supplementation with a prebiotic mixture of 90% short-chain galacto-oligosaccharides and 10% long-chain fructo-oligosaccharides (scGOS/lcFOS) in experimental arthritis in mice. We here show that dietary supplementation with scGOS/lcFOS has a pronounced effect on the composition of the fecal microbiota. Interestingly, the genera Enterococcus and Clostridium were markedly decreased by scGOS/lcFOS dietary supplementation. In contrast, the family Lachnospiraceae and the genus Lactobacillus, both associated with healthy microbiota, increased in mice receiving scGOS/lcFOS diet. However, the scGOS/lcFOS induced alterations of the intestinal microbiota did not induce significant effects on the intestinal and systemic T helper cell subsets and were not sufficient to reproducibly suppress arthritis in mice. As expected, we did observe a significant increase in the bone mineral density in mice upon dietary supplementation with scGOS/lcFOS for 8 weeks. Altogether, this study suggests that dietary scGOS/lcFOS supplementation is able to promote presumably healthy gut microbiota and improve bone mineral density, but not inflammation, in arthritis-prone mice.

RevDate: 2019-07-08

Hernandez CJ, Yang X, Ji G, et al (2019)

Disruption of the Gut Microbiome Increases the Risk of Periprosthetic Joint Infection in Mice.

Clinical orthopaedics and related research [Epub ahead of print].

BACKGROUND: Periprosthetic joint infection (PJI) is one of the most devastating complications of total joint arthroplasty. Given the mortality and morbidity associated with PJI and the challenges in treating it, there has been increased interest in risk factors that can be modified before surgery. In this study, we used a novel mouse model to consider the role of the gut microbiome as a risk factor for PJI.

QUESTIONS/PURPOSES: (1) Does the state of the gut microbiota before surgery influence the likelihood of developing an established infection in a mouse model of PJI? (2) How does the state of the gut microbiota before surgery influence the local and systemic response to the presence of an established infection in a mouse model of PJI?

METHODS: Male C57Bl/6 mice were divided into two groups: those with modified microbiome [INCREMENT]microbiome (n = 40) and untreated mice (n = 42). In [INCREMENT]microbiome mice, the gut flora were modified using oral neomycin and ampicillin from 4 weeks to 16 weeks of age. Mice received a titanium tibial implant to mimic a joint implant and a local inoculation of Staphylococcus aureus in the synovial space (10 colony forming units [CFUs]). The proportion of animals developing an established infection in each group was determined by CFU count. The local and systemic response to established infection was determined using CFU counts in surrounding joint tissues, analysis of gait, radiographs, body weight, serum markers of inflammation, and immune cell profiles and was compared with animals that received the inoculation but resisted infection.

RESULTS: A greater proportion of animals with disrupted gut microbiota had infection (29 of 40 [73%]) than did untreated animals (21 of 42 [50%]; odds ratio, 2.63, 95% CI, 1.04-6.61; p = 0.035). The immune response to established infection in mice with altered microbiota was muted; serum amyloid A, a marker of systemic infection in mice, was greater than in mice with disrupted gut microbiota with infection (689 µg/dL; range, 68-2437 µg/dL, p < 0.05); infection associated increases in monocytes and neutrophils in the spleen and local lymph node in untreated mice but not were not observed in mice with disrupted gut microbiota.

CONCLUSIONS: The findings from this in vivo mouse model suggest that the gut microbiota may influence susceptibility to PJI.

CLINICAL RELEVANCE: These preclinical findings support the idea that the state of the gut microbiome before surgery may influence the development of PJI and justify further preclinical and clinical studies to develop appropriate microbiome-based interventions.

RevDate: 2019-07-08

Zhang Y, Dai J, Jian H, et al (2019)

The Effects of Macrolides on Airway Microbiome and Cytokine of Children with Bronchiolitis: A Systematic Review and Meta-analysis of Randomized Controlled Trials.

Microbiology and immunology [Epub ahead of print].

Macrolides may attenuate airway inflammation of bronchiolitis with anti-inflammatory and antiviral effects. But the potential mechanisms of macrolides for bronchiolitis is limited. Therefore, we conducted a meta-analysis to assess effects of macrolides on airway microbiome and cytokine of children with bronchiolitis. PubMed, Embase, Cochrane Central Register of Controlled Trials were searched until May 2018. The reference lists of included studies and pertinent reviews were checked for supplementing our search. Randomized controlled trials (RCTs) which compared macrolides versus placebo assessing the change of microbiome in airway and cytokine were included. A total of 4 RCTs were included in this review. Data analysis showed there was no significant reduction of viruses at 48 hours after azithromycin treatment(p=0.41). There were significant reductions in streptococcus pneumoniae (RR 0.28, 95% CI 0.14 to 0.6, p<0.01), haemophilus influenza (RR 0.35, 95% CI 0.2 to 0.62, p<0.01) and moraxella catarrhalis (RR 0.29, 95% CI 0.17 to 0.5, p<0.01) but no significant reduction of staphylococcus aureus(p=0.28) after the treatment of macrolides. There was a significant decrease in the serum interleukin-8 (IL-8), interleukin-4 (IL-4) and eotaxin following three weeks of clarithromycin therapy. However, there was no significant difference in serum IL-8 level at day 15 after intervention between the azithromycin and control groups, while a significant reduction of nasal lavage IL-8 level was found. The macrolides may reduce the IL-8 in airway and plasma, but failed to have an antiviral effect of macrolides for children with bronchiolitis. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-08

Amsterdam D, BE Ostrov (2018)

The Impact of the Microbiome on Immunosenescence.

Immunological investigations, 47(8):801-811.

Human microbiome investigations now provide evidence that changes in the microbiome over time and their interaction with the immune, endocrine, and nervous systems are associated with a wide array of disorders. Human immunological studies typically absent a microbiome consideration in their investigations. An area of recent exploration is the role of the microbiome as a critical partner in the development and function of the human immune system in aging. It is well known that immunologic maturation is influenced by a lifetime of interactions of the host with its companion microbiome. It is generally not well recognized that intestinal microbes play an essential role in the development and expansion of gut mucosal and systemic immune function. Gut microbial communities of elderly people have different composition and behavior compared to healthy younger adults. Comorbidities associated with microbial pathogens and an aberrant immune system tend to increase with aging. This review underscores the impact of the human-microbiome interface on the development and function of the immune system and on immunosenescence. These changes have important implications regarding health and health system utilization in the elderly population.

RevDate: 2019-07-08

Klevay LM (2019)

Copper deficiency can change the microbiome of swine.

American journal of physiology. Endocrinology and metabolism, 317(1):E183.

RevDate: 2019-07-08

Panasevich MR, RS Rector (2019)

Reply to Letter to the Editor: "Copper deficiency can change the microbiome of swine".

American journal of physiology. Endocrinology and metabolism, 317(1):E184.

RevDate: 2019-07-08

McFarlane M, Millard A, Hall H, et al (2019)

Urinary volatile organic compounds and faecal microbiome profiles in colorectal cancer.

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

BACKGROUND: Volatile organic compounds are potential biomarkers for diagnosing colorectal cancer (CRC). We characterised urinary VOCs from CRC patients, their spouses/co-habitors (spouses) and first-degree relatives (relatives) to determine any differences. Correlation with stool-derived microbiomes was also undertaken.

METHODS: Urine from 56 CRC patients, 45 spouses and 37 relatives were assayed using Liquid Chromatography: Field Asymmetric Ion Mobility Spectrometry (FAIMS): Mass Spectrometer technology. Analysis was performed using 5-fold cross-validation and a Random Forrest classifier. Faecal microbiome 16s RNA was sequenced using Illumina Miseq protocols and analysed using UPARSE and QIIME pipelines. VOC and microbiome profiles were also compared before, and after, cancer treatment.

RESULTS: Urinary VOC profiles of CRC patients were indistinguishable from either spouses or relatives. When spouses and relatives were grouped together to form a larger non-cancer control group (n=82), their VOC profiles became distinguishable from CRC patients (n=56) with 69% sensitivity and specificity, area under curve 0.72 (p<0.001). Microbiome analysis identified >1300 operational taxonomic units (OTUs) across all groups. Analysis of Similarity (ANOSIM) R value was 0.067 (p=<0.001), with significantly different bacterial abundances in 82 OTUs (6.2%) by Kruskal-Wallis testing. CRC patients' VOC or stool microbiome profiles were unchanged after treatment.

CONCLUSION: Although CRC patients' urinary VOC profiles cannot be differentiated from spouses or relatives they can be differentiated from a larger non-cancer control group. Comparison of the groups' microbiomes confirmed differences in bacterial species abundance. The current FAIMS-based assay can detect a unique, but modest, signal in CRC patients' urinary VOCs, which remains unaltered after treatment. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-08

Durante MK, Baums IB, Williams DE, et al (2019)

What drives phenotypic divergence among coral clonemates of Acropora palmata?.

Molecular ecology [Epub ahead of print].

Evolutionary rescue of populations depends on their ability to produce phenotypic variation that is heritable and adaptive. DNA mutations are the best understood mechanisms to create phenotypic variation, but other, less well-studied mechanisms exist. Marine benthic foundation species provide opportunities to study these mechanisms because many are dominated by isogenic stands produced through asexual reproduction. For example, Caribbean acroporid corals are long lived and reproduce asexually via breakage of branches. Fragmentation is often the dominant mode of local population maintenance. Thus, large genets with many ramets (colonies) are common. Here, we observed phenotypic variation in stress responses within genets following the coral bleaching events in 2014 and 2015 caused by high water temperatures. This was not due to genetic variation in their symbiotic dinoflagellates (Symbiodinium "fitti") because each genet of this coral species typically harbours a single strain of S. "fitti". Characterization of the microbiome via 16S tag sequencing correlated the abundance of only two microbiome members (Tepidiphilus, Endozoicomonas) with a bleaching response. Epigenetic changes were significantly correlated with the host's genetic background, the location of the sampled polyps within the colonies (e.g., branch vs. base of colony), and differences in the colonies' condition during the bleaching event. We conclude that long-term microenvironmental differences led to changes in the way the ramets methylated their genomes, contributing to the differential bleaching response. However, most of the variation in differential bleaching response among clonemates of Acropora palmata remains unexplained. This research provides novel data and hypotheses to help understand intragenet variability in stress phenotypes of sessile marine species.

RevDate: 2019-07-08

Sattar B, RV Chokshi (2019)

Colonic and Anorectal Manifestations of Systemic Sclerosis.

Current gastroenterology reports, 21(7):33 pii:10.1007/s11894-019-0699-0.

PURPOSE OF REVIEW: Systemic sclerosis is a chronic autoimmune disorder commonly involving the gastrointestinal tract, including the colon and anorectum. In this review, we summarize major clinical manifestations and highlight recent developments in physiology, diagnostics, and treatment.

RECENT FINDINGS: The exact pathophysiology of systemic sclerosis is unclear and likely multifactorial. The role of the microbiome on gastrointestinal manifestations has led to a better understanding of potential pathogenic gut flora. Carbohydrate malabsorption is common. Evaluation using fecal calprotectin and high-resolution anorectal manometry may broaden our understanding of the etiologies of diarrhea and fecal incontinence and help with early recognition of pathology. Prucalopride, a high-affinity 5HT4 agonist, and pyridostigmine, an acetylcholinesterase inhibitor, may help improve colonic transit in patients with constipation. Intravenous immunoglobulins have been used to target muscarinic receptor antibodies that are believed to contribute to gastrointestinal dysmotility. Colonic and anorectal manifestations of systemic sclerosis include constipation, diarrhea, and fecal incontinence, and can diminish quality of life for these patients. Recent studies regarding pathophysiology as well as diagnostic and treatment options are promising. Further targeted studies to facilitate early intervention and better management of refractory symptoms are still needed.

RevDate: 2019-07-08

Wallace RJ, Sasson G, Garnsworthy PC, et al (2019)

A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions.

Science advances, 5(7):eaav8391 pii:aav8391.

A 1000-cow study across four European countries was undertaken to understand to what extent ruminant microbiomes can be controlled by the host animal and to identify characteristics of the host rumen microbiome axis that determine productivity and methane emissions. A core rumen microbiome, phylogenetically linked and with a preserved hierarchical structure, was identified. A 39-member subset of the core formed hubs in co-occurrence networks linking microbiome structure to host genetics and phenotype (methane emissions, rumen and blood metabolites, and milk production efficiency). These phenotypes can be predicted from the core microbiome using machine learning algorithms. The heritable core microbes, therefore, present primary targets for rumen manipulation toward sustainable and environmentally friendly agriculture.

RevDate: 2019-07-08

Donowitz JR, Parikh HI, Taniuchi M, et al (2019)

Increased Fecal Lactobacillus Is Associated With a Positive Glucose Hydrogen Breath Test in Bangladeshi Children.

Open forum infectious diseases, 6(7):ofz266 pii:ofz266.

Background: Glucose hydrogen breath testing is a noninvasive test for small intestine bacterial overgrowth (SIBO). A positive glucose hydrogen breath test is common in children from low-income countries and has been found to be associated with malnutrition as measured by stunted growth. The microbiome associated with positive breath testing is relatively unstudied.

Methods: We performed 16 S V4 rDNA microbiome analysis on the stool of 90 Bangladeshi children aged 2 years from an impoverished neighborhood who were tested at the same time for SIBO by glucose hydrogen breath testing. Data were analyzed by linear discriminant analysis effect size with SIBO as the outcome. Any selected genera were tested individually by Wilcoxon's rank-sum test to ensure that linear discriminant analysis effect size results were not outlier-skewed.

Results: Linear discriminant analysis effect size analysis identified Lactobacillus (linear discriminate analysis score, 4.59; P = .03) as over-represented in 15 out of the 90 children who were SIBO positive.

Conclusions: These results suggest that glucose hydrogen breath test positivity in children from low-income settings may be due to an upper intestinal Lactobacillus bloom, potentially explaining the association of SIBO with the gut damage and inflammation that leads to malnutrition.

RevDate: 2019-07-08

Ziegler M, Han JH, Landsburg D, et al (2019)

Impact of Levofloxacin for the Prophylaxis of Bloodstream Infection on the Gut Microbiome in Patients With Hematologic Malignancy.

Open forum infectious diseases, 6(7):ofz252 pii:ofz252.

Background: We evaluated the differential impact of levofloxacin administered for the prophylaxis of bloodstream infections compared with broad-spectrum beta-lactam (BSBL) antibiotics used for the treatment of neutropenic fever on the gut microbiome in patients with hematologic malignancy.

Methods: Stool specimens were collected from patients admitted for chemotherapy or stem cell transplant in the setting of the evaluation of diarrhea from February 2017 until November 2017. Microbiome characteristics were compared among those exposed to levofloxacin prophylaxis vs those who received BSBL antibiotics.

Results: Sixty patients were included, most with acute myeloid leukemia (42%) or multiple myeloma (37%). The gut microbiome of patients with BSBL exposure had significantly reduced Shannon's alpha diversity compared with those without (median [interquartile range {IQR}], 3.28 [1.73 to 3.71] vs 3.73 [3.14 to 4.31]; P = .01). However, those with levofloxacin exposure had increased alpha diversity compared with those without (median [IQR], 3.83 [3.32 to 4.36] vs 3.32 [2.35 to 4.02]; P = .03). Levofloxacin exposure was also associated with a trend toward lower risk of dominance of non-Bacteroidetes genera compared with those without levofloxacin exposure (3 [14%] vs 15 [38%]; P = .051).

Conclusions: The impact of antibiotics on the gut microbiome varies by class, and levofloxacin may disrupt the gut microbiome less than BSBLs in this patient population.

RevDate: 2019-07-08

Lundmark A, Hu YOO, Huss M, et al (2019)

Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis.

Frontiers in cellular and infection microbiology, 9:216.

Periodontitis is a microbial-induced chronic inflammatory disease, which may not only result in tooth loss, but can also contribute to the development of various systemic diseases. The transition from healthy to diseased periodontium depends on microbial dysbiosis and impaired host immune response. Although periodontitis is a common disease as well as associated with various systemic inflammatory conditions, the taxonomic profiling of the salivary microbiota in periodontitis and its association with host immune and inflammatory mediators has not been reported. Therefore, the aim of this study was to identify key pathogens and their potential interaction with the host's inflammatory mediators in saliva samples for periodontitis risk assessment. The microbial 16S rRNA gene sequencing and the levels of inflammatory mediators were performed in saliva samples from patients with chronic periodontitis and periodontally healthy control subjects. The salivary microbial community composition differed significantly between patients with chronic periodontitis and healthy controls. Our analyses identified a number of microbes, including bacteria assigned to Eubacterium saphenum, Tannerella forsythia, Filifactor alocis, Streptococcus mitis/parasanguinis, Parvimonas micra, Prevotella sp., Phocaeicola sp., and Fretibacterium sp. as more abundant in periodontitis, compared to healthy controls. In samples from healthy individuals, we identified Campylobacter concisus, and Veillonella sp. as more abundant. Integrative analysis of the microbiota and inflammatory mediators/cytokines revealed associations that included positive correlations between the pathogens Treponema sp. and Selenomas sp. and the cytokines chitinase 3-like 1, sIL-6Rα, sTNF-R1, and gp130/sIL-6Rβ. In addition, a negative correlation was identified between IL-10 and Filifactor alocis. Our results reveal distinct and disease-specific patterns of salivary microbial composition between patients with periodontitis and healthy controls, as well as significant correlations between microbiota and host-mediated inflammatory cytokines. The positive correlations between the pathogens Treponema sp. and Selenomas sp. and the cytokines chitinase 3-like 1, sIL-6Rα, sTNF-R1, and gp130/sIL-6Rβ might have the future potential to serve as a combined bacteria-host salivary biomarker panel for diagnosis of the chronic infectious disease periodontitis. However, further studies are required to determine the capacity of these microbes and inflammatory mediators as a salivary biomarker panel for periodontitis.

RevDate: 2019-07-08

Bilotta AJ, Y Cong (2019)

Gut microbiota metabolite regulation of host defenses at mucosal surfaces: implication in precision medicine.

Precision clinical medicine, 2(2):110-119.

The gut microbiota has a well-established role in the regulation of host homeostasis. Multiple factors control the composition and function of the microbiota. The westernization of diet, a shift away from nutrient-dense foods toward diets high in saturated fats, has been implicated in the rise of chronic inflammatory diseases such as inflammatory bowel disease (IBD). Diet is critical in the development and maintenance of a healthy microbiome, where dietary fiber (found in the highest amounts in fruits, vegetables, and legumes) is metabolized by the microbiome. In turn, the bacterial metabolites of dietary fiber, short chain fatty acids (SCFAs), regulate gut homeostasis. SCFAs engage G-protein coupled receptors (GPRs) and act as histone deacetylase inhibitors (HDACi) to module epithelial and immune cell functions in the intestines, where they generally promote an anti-inflammatory state. This review highlights the functions of SCFAs and their roles in the pathogenesis of IBD to provide insights into their potential therapeutic application for the treatment of IBD for the purposes of precision medicine.

RevDate: 2019-07-08

Shi L, Sheng J, Wang M, et al (2019)

Combination Therapy of TGF-β Blockade and Commensal-derived Probiotics Provides Enhanced Antitumor Immune Response and Tumor Suppression.

Theranostics, 9(14):4115-4129 pii:thnov09p4115.

Galunisertib (Gal) is a transforming growth factor (TGF-β) blockade which is being investigated as a potential tumor immunotherapy candidate drug in clinical trials. However, primary or acquired resistance is often found in the recruited cancer patients, which limits its clinical application. Tumor immune microenvironment can be regulated by intestinal microbiota, leading to different therapeutic outcomes. It is hypothesized that manipulation of cancer patients' intestinal microbiome in the early stage of therapy may be a promising strategy to improve the therapeutic efficacy of Gal. Methods: 4T1 and H22 subcutaneous tumor bearing mice were used to evaluate the therapeutic effect. Escherichia coli strain Nissle 1917 (EcN), a widely used probiotic bacteria, was orally delivered to the tumor bearing mice daily along with Gal treatment. Antitumor effect of the combination therapy was evaluated by tumor volume, histological staining of tumor tissues. Furthermore, flow cytometry was performed to analyze the alteration of immune microenvironment in tumor bed after treatment. The suppressing effect of the combination therapy on tumor invasiveness and metastasis was evaluated in both mice and zebrafish xenografts models. Fecal sample 16S rRNA gene sequencing was conducted to analyze changes of intestinal microbial diversity. The effect of intestinal microbiota on tumor suppression after receiving EcN was further tested by fecal transplant. Results: The therapeutic outcomes in tumor growth inhibition and metastasis suppression of Gal were significantly potentiated by EcN, resulting from the strengthened antitumor immunity. EcN was able to relieve the immunosuppressive tumor microenvironment, which was evidenced by enhanced tumor-specific effector T cells infiltration and dendritic cells activation. Intestinal microbiota was modulated by EcN, illustrated by a shift of gut microbiome toward certain beneficial bacteria. Conclusion: These results suggested that Gal combined with EcN might be a novel therapeutic approach with great potential of clinical implications for cancer prevention or treatment.

RevDate: 2019-07-08

Yang Y, Misra BB, Liang L, et al (2019)

Integrated microbiome and metabolome analysis reveals a novel interplay between commensal bacteria and metabolites in colorectal cancer.

Theranostics, 9(14):4101-4114 pii:thnov09p4101.

Rationale: Colorectal cancer (CRC) is a malignant tumor with the third highest morbidity rate among all cancers. Driven by the host's genetic makeup and environmental exposures, the gut microbiome and its metabolites have been implicated as the causes and regulators of CRC pathogenesis. We assessed human fecal samples as noninvasive and unbiased surrogates to catalog the gut microbiota and metabolome in patients with CRC. Methods: Fecal samples collected from CRC patients (CRC group, n = 50) and healthy volunteers (H group, n = 50) were subjected to microbiome (16S rRNA gene sequencing) and metabolome (gas chromatography-mass spectrometry, GC-MS) analyses. The datasets were analyzed individually and integrated for combined analysis using various bioinformatics approaches. Results: Fecal metabolomic analysis led to the identification of 164 metabolites spread across 40 metabolic pathways in both groups. In addition, there were 42 and 17 metabolites specific to the H and CRC groups, respectively. Sequencing of microbial diversity revealed 1084 operational taxonomic units (OTUs) across the two groups, and there was less species diversity in the CRC group than in the H group. Seventy-six discriminatory OTUs were identified for the microbiota of H volunteers and CRC patients. Integrated analysis correlated CRC-associated microbes with metabolites, such as polyamines (cadaverine and putrescine). Conclusions: Our results provide substantial evidence of a novel interplay between the gut microbiome and metabolome (i.e., polyamines), which is drastically perturbed in CRC. Microbe-associated metabolites can be used as diagnostic biomarkers in therapeutic explorations.

RevDate: 2019-07-08

Herrmann M, Wegner CE, Taubert M, et al (2019)

Predominance of Cand. Patescibacteria in Groundwater Is Caused by Their Preferential Mobilization From Soils and Flourishing Under Oligotrophic Conditions.

Frontiers in microbiology, 10:1407.

Despite the widely observed predominance of Cand. Patescibacteria in subsurface communities, their input source and ecophysiology are poorly understood. Here we study mechanisms of the formation of a groundwater microbiome and the subsequent differentiation of Cand. Patescibacteria. In the Hainich Critical Zone Exploratory, Germany, we trace the input of microorganisms from forested soils of preferential recharge areas through fractured aquifers along a 5.4 km hillslope well transect. Cand. Patescibacteria were preferentially mobilized from soils and constituted 66% of species-level OTUs shared between seepage and shallow groundwater. These OTUs, mostly related to Cand. Kaiserbacteraceae, Cand. Nomurabacteraceae, and unclassified UBA9983 at the family level, represented a relative abundance of 71.4% of the Cand. Patescibacteria community at the shallowest groundwater well, and still 44.4% at the end of the transect. Several Cand. Patescibacteria subclass-level groups exhibited preferences for different conditions in the two aquifer assemblages investigated: Cand. Kaiserbacteraceae surprisingly showed positive correlations with oxygen concentrations, while Cand. Nomurabacteraceae were negatively correlated. Co-occurrence network analysis revealed a central role of Cand. Patescibacteria in the groundwater microbial communities and pointed to potential associations with specific organisms, including abundant autotrophic taxa involved in nitrogen, sulfur and iron cycling. Strong associations among Cand. Patescibacteria themselves further suggested that for many groups within this phylum, distribution was mainly driven by conditions commonly supporting a fermentative life style without direct dependence on specific hosts. We propose that import from soil, and community differentiation driven by hydrochemical conditions, including the availability of organic resources and potential hosts, determine the success of Cand. Patescibacteria in groundwater environments.

RevDate: 2019-07-08

Olivier-Van Stichelen S, Rother KI, JA Hanover (2019)

Maternal Exposure to Non-nutritive Sweeteners Impacts Progeny's Metabolism and Microbiome.

Frontiers in microbiology, 10:1360.

Non-nutritive sweeteners (NNS) are marketed as sugar alternatives providing sweet taste with few or no calories. Yet their consumption has been linked to metabolic dysfunction and changes in the gut microbiome. NNS exposure mostly originates from diet beverages and sweetener packages in adults or breastmilk in infants. Consequences of early life exposure remain largely unknown. We exposed pregnant and lactating mice to NNS (sucralose, acesulfame-K) at doses relevant for human consumption. While the pups' exposure was low, metabolic changes were drastic, indicating extensive downregulation of hepatic detoxification mechanisms and changes in bacterial metabolites. Microbiome profiling confirmed a significant increase in firmicutes and a striking decrease of Akkermansia muciniphila. Similar microbiome alterations in humans have been linked to metabolic disease and obesity. While our findings need to be reproduced in humans, they suggest that NNS consumption during pregnancy and lactation may have adverse effects on infant metabolism.

RevDate: 2019-07-08

Wieczorek AS, Schmidt O, Chatzinotas A, et al (2019)

Ecological Functions of Agricultural Soil Bacteria and Microeukaryotes in Chitin Degradation: A Case Study.

Frontiers in microbiology, 10:1293.

Chitin provides a valuable carbon and nitrogen source for soil microorganisms and is a major component of particulate organic matter in agricultural soils. To date, there is no information on interaction and interdependence in chitin-degrading soil microbiomes. Since microbial chitin degradation occurs under both oxic and anoxic conditions and both conditions occur simultaneously in soil, the comparison of the active microbiome members under both conditions can reveal key players for the overall degradation in aerated soil. A time-resolved 16S rRNA stable isotope probing experiment was conducted with soil material from the top soil layer of a wheat-covered field. [13CU]-chitin was largely mineralized within 20 days under oxic conditions. Cellvibrio, Massilia, and several Bacteroidetes families were identified as initially active chitin degraders. Subsequently, Planctomycetes and Verrucomicrobia were labeled by assimilation of 13C carbon either from [13CU]-chitin or from 13C-enriched components of primary chitin degraders. Bacterial predators (e.g., Bdellovibrio and Bacteriovorax) were labeled, too, and non-labeled microeukaryotic predators (Alveolata) increased their relative abundance toward the end of the experiment (70 days), indicating that chitin degraders were subject to predation. Trophic interactions differed substantially under anoxic and oxic conditions. Various fermentation types occurred along with iron respiration. While Acidobacteria and Chloroflexi were the first taxa to be labeled, although at a low 13C level, Firmicutes and uncultured Bacteroidetes were predominantly labeled at a much higher 13C level during the later stages, suggesting that the latter two bacterial taxa were mainly responsible for the degradation of chitin and also provided substrates for iron reducers. Eventually, our study revealed that (1) hitherto unrecognized Bacteria were involved in a chitin-degrading microbial food web of an agricultural soil, (2) trophic interactions were substantially shaped by the oxygen availability, and (3) detectable predation was restricted to oxic conditions. The gained insights into trophic interactions foster our understanding of microbial chitin degradation, which is in turn crucial for an understanding of soil carbon dynamics.

RevDate: 2019-07-08

Campbell LJ, Garner TWJ, Hopkins K, et al (2019)

Outbreaks of an Emerging Viral Disease Covary With Differences in the Composition of the Skin Microbiome of a Wild United Kingdom Amphibian.

Frontiers in microbiology, 10:1245.

There is growing appreciation of the important role of commensal microbes in ensuring the normal function and health of their hosts, including determining how hosts respond to pathogens. A range of infectious diseases are threatening amphibians worldwide, and evidence is accumulating that the host-associated bacteria that comprise the microbiome may be key in mediating interactions between amphibian hosts and infectious pathogens. We used 16S rRNA amplicon sequencing to quantify the skin microbial community structure of over 200 individual wild adult European common frogs (Rana temporaria), from ten populations with contrasting history of the lethal disease ranavirosis, caused by emerging viral pathogens belonging to the genus Ranavirus. All populations had similar species richness irrespective of disease history, but populations that have experienced historical outbreaks of ranavirosis have a distinct skin microbiome structure (beta diversity) when compared to sites where no outbreaks of the disease have occurred. At the individual level, neither age, body length, nor sex of the frog could predict the structure of the skin microbiota. Our data potentially support the hypothesis that variation among individuals in skin microbiome structure drive differences in susceptibility to infection and lethal outbreaks of disease. More generally, our results suggest that population-level processes are more important for driving differences in microbiome structure than variation among individuals within populations in key life history traits such as age and body size.

RevDate: 2019-07-08

Fan Y, Wang H, Liu X, et al (2019)

Crosstalk between the Ketogenic Diet and Epilepsy: From the Perspective of Gut Microbiota.

Mediators of inflammation, 2019:8373060.

Given the association between a range of neurological disorders and changes in the gut microbiota, interest in the gut microbiota has recently increased. In particular, the significant involvement of the autoimmune processes in the development of epilepsy, one of the most serious and widespread neurological diseases, has led to a suggested link with the gut microbiome. Because the constitution of the gut microbiome can be influenced by diet, dietary therapy has been shown to have a positive impact on a wide range of conditions via alteration of the gut microbiota. An example of one such diet is the ketogenic diet (KD), which promotes a diet that contains high levels of fat, adequate levels of protein, and low levels of carbohydrate. Due to the near-total elimination of carbohydrates from the individual's food in this ultra-high-fat diet, ketone bodies become an important source of energy. Although the ketogenic diet has proven successful in the treatment of refractory epilepsy and other illnesses, the underlying mechanisms of its neuroprotective effects have yet to be fully elucidated. Nevertheless, recent studies strongly indicate a role for the gut microbiota in the effective treatment of epilepsy with the ketogenic diet. The latest advances regarding the links between the ketogenic diet, gut microbiota, and epilepsy are reviewed in this article, with a particular focus on the role of the gut microbiota in the treatment outcome.

RevDate: 2019-07-07

Chen H, Li C, Liu T, et al (2019)

A Metagenomic Study of Intestinal Microbial Diversity in Relation to Feeding Habits of Surface and Cave-Dwelling Sinocyclocheilus Species.

Microbial ecology pii:10.1007/s00248-019-01409-4 [Epub ahead of print].

Light is completely absent in cave habitats, causing a shortage or lack of autochthonous photosynthesis. Thus, understanding the mechanisms underlying the ability of organisms to adapt to the unique cave habitat is of great interest. We used high-throughput sequencing of the 16S ribosomal RNA gene of intestinal microorganisms from 11 Sinocyclocheilus (Cypriniformes: Cyprinidae) species, to explore the characteristics of intestinal microorganisms and the adaptive mechanisms of Sinocyclocheilus cavefish and surface fish. We found that the α-diversity and richness of the intestinal microbiome were much higher in cavefish than in surface fish. Principal coordinate analysis showed that cavefish and surface fish formed three clusters because of different dominant gut microorganisms which are generated by different habitats. Based on PICRUSt-predicted functions, harmful substance degradation pathways were much more common in cavefish intestinal microorganisms than in those from surface fish. The intestinal microbiota of surface fish group 1 had a higher capacity for carbohydrate metabolism, whereas protein and amino acid metabolism and digestive pathways were more abundant in microorganisms from the cavefish group and surface fish group 2. Combined analysis of the intestinal microbial composition and functional predictions further revealed the structures and functions of intestinal microbial communities in Sinocyclocheilus cave and surface species. Moreover, based on their habits and intestinal microbial composition and intestinal microbial functional predictions, we inferred that the three fish groups were all omnivorous; however, surface fish group 1 preferred feeding on plants, while surface fish group 2 and cavefish preferred meat. This study improves our understanding of mechanisms of adaptation in cave habitats and may contribute to the protection of these habitats from water pollution.

RevDate: 2019-07-07

Cong L, Duan LW, Su WP, et al (2019)

Efficacy of High Specific Volume Polysaccharide - A New Type of Dietary Fiber - On Molecular Mechanism of Intestinal Water Metabolism in Rats With Constipation.

Medical science monitor : international medical journal of experimental and clinical research, 25:5028-5035 pii:916526.

BACKGROUND The aim of this study was to evaluate the effects of a new type of dietary fiber - high specific volume polysaccharide (HSVP) - on fecal properties, serum vasoactive intestinal peptide (VIP) concentration, intestinal flora count, and expression of the VIP-cAMP-PKA-AQP3 signaling pathway. MATERIAL AND METHODS Compound diphenoxylate was used in 48 healthy Wistar rats to establish a constipation model. Rats were divided into a normal control group, a constipation model group, an HSVP low-dose group, an HSVP medium-dose group, an HSVP high-dose group, and a fructose control group. We used colony count method, ELISA, WB, and RT-PCR to determine fecal moisture content, fecal hardness, fecal passage time, serum VIP concentration, number of intestinal bacteria, and VIP-cAMP-PKA-AQP3 signal pathway protein expression. RESULTS The constipation model was established successfully. HSVP (the medium dose was 10% and the high dose was 15%) improved fecal moisture content, reduced hardness, shortened fecal emptying time, increased intestinal bacteria, reduced serum VIP concentration, downregulated cAMP and PKAm RNA transcription, reduced protein expression, and reduced intestinal AQP3 expression. CONCLUSIONS HSVP improved constipation, increased the number of intestinal bacteria, and elevated expression of the VIP-cAMP-PKA-AQP3 signaling pathway. The mechanism of HSVP in regulating intestinal water metabolism in constipated rats may occur through the VIP-cAMP-PKA-AQP3 signaling pathway, and be closely related to changes in intestinal bacteria. The important role of the brain-gut-microbiome axis in the pathogenesis of constipation has been confirmed in this study.


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.

Electronic Scholarly Publishing
21454 NE 143rd Street
Woodinville, WA 98077

E-mail: RJR8222 @

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).


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


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 )