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14 Oct 2019 at 01:34
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Bibliography on: Microbiome


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RJR: Recommended Bibliography 14 Oct 2019 at 01:34 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: 2019-10-12

Dubinsky V, Reshef L, Bar N, et al (2019)

Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy.

Gastroenterology pii:S0016-5085(19)41416-9 [Epub ahead of print].

BACKGROUND & AIMS: Pouchitis that develops in patients with ulcerative colitis after total proctocolectomy and ileal pouch anal anastomosis is usually treated with antibiotics. Some patients have recurrence of flares, or become antibiotic dependent, and require repeated courses or prolonged periods of antibiotic therapy. We investigated microbial factors associated with response to antibiotic treatment and development of antibiotic dependence in patients with pouchitis.

METHODS: We performed a prospective study of 49 patients who had undergone pouch surgery at a tertiary center in Israel. Disease activity was determined based on clinical, endoscopic, and histologic criteria. Pouch phenotype was defined as recurrent acute pouchitis (n=6), chronic pouchitis and Crohn's-like disease of the pouch (n=27), normal pouch from patient with ulcerative colitis (n=10), and normal pouch from patient with familial adenomatous polyposis (n=6). Fecal samples (n=234) were collected over time during or in the absence of antibiotic treatment (ciprofloxacin and/or metronidazole). Thirty-three patients were treated with antibiotics, for a median of 425 days of cumulative antibiotic therapy, during follow up. Calprotectin was measured and fecal DNA was sequenced using shotgun metagenomics and analyzed with specifically designed bioinformatic pipelines. Bacterial strains were isolated from fecal samples. We assessed their ciprofloxacin resistance and ability to induce secretion of inflammatory cytokines by human intestinal epithelial cells HT-29.

RESULTS: Most antibiotic-treated patients (79%) had a clinical response to each course of antibiotics. However, 89% of those who completed a 4-weeks course relapsed within 3 months. Median calprotectin levels decreased by 40% in response to antibiotics. Antibiotic treatment reduced disease-associated bacteria such as Clostridium perfringens, Ruminococcus gnavus, and Klebsiella pneumoniae but also beneficial species such as Faecalibacterium prausnitzii. The microbiomes of antibiotic-responsive patients were dominated by facultative anaerobic genera (Escherichia, Enterococcus, and Streptococcus), with multiple ciprofloxacin-resistance mutations in drug target genes and confirmed drug resistance. However, these strains had lower potential for virulence and did not induce secretion of inflammatory cytokines by epithelial cells. After antibiotic cessation, patients had an abrupt shift in microbiome composition, with blooms of oral and disease-associated bacteria. In addition, antibiotic treatment enriched for strains that acquired multidrug resistance loci, encoding enzymes that confer resistance to non-related antibiotics including extended-spectrum beta-lactamases.

CONCLUSIONS: The efficacy of antibiotic treatment of pouchitis might be attributed to the establishment of antibiotic-resistant microbiome with low inflammatory potential. This microbiome might provide resistance against colonization by bacteria that promote inflammation. To avoid progression to antibiotic-dependent disease and its consequences, strategies such as short-term alternating antibiotics and nutrition- and microbiome-based interventions should be considered.

RevDate: 2019-10-12

Whelan K (2019)

Diet-Microbiome Interactions and the Risk of Pouchitis in Ileal Pouch-Anal Anastomosis.

Journal of Crohn's & colitis pii:5586643 [Epub ahead of print].

RevDate: 2019-10-12

Liu Y, Shen Z, Yu J, et al (2019)

Comparison of gut bacterial communities and their associations with host diets in four fruit borers.

Pest management science [Epub ahead of print].

BACKGROUND: Microbiota that live in the gut of insects has a wide range of effects on host nutrition, physiology, and behavior. They may shape the adaptation of their hosts to different habitats and lifestyles. To characterize the gut microbiota of fruit borers comprehensively, we compared bacterial communities among Grapholita molesta, Conogethes punctiferalis, Carposina sasakii and Cydia pomonella, which are serious lepidopteran pests. We selected G. molesta as a representative pest to more explicitly test the influence of host dietary niche on the insect gut microbiome, so we also compared the bacterial microbial communities of G. molesta fed different diets (peach shoots and apple) using Illumina high-throughput sequencing technology.

RESULTS: The results showed that Proteobacteria and Firmicutes were dominant in their gut microbiota. The C. sasakii had the highest richness values and G. molesta (shoot-feeding) had the highest diversity, whereas C. pomonella and G. molesta (fruit-feeding) held the lowest bacterial richness and diversity, respectively. The ANOSIM analysis revealed significant differences in the structure of gut microbiota among different insects. In addition, G. molesta with different feeding diet had significant differences in gut microbiota composition. PICRUSt analysis indicated that most functional prediction categories were related to metabolism.

CONCLUSION: Our results showed that gut microbiota composition was affected significantly not only by host species but also host diets. An enhanced understanding of these herbivore-associated microbial symbionts is essential for understanding of the biology and ecology of the host insect and may offer new possibilities to improve integrated pest-management strategies for efficient control of fruit borers.

RevDate: 2019-10-12

Shirazi MSR, Al-Alo KZK, Al-Yasiri MH, et al (2019)

Microbiome Dysbiosis and Predominant Bacterial Species as Human Cancer Biomarkers.

Journal of gastrointestinal cancer pii:10.1007/s12029-019-00311-z [Epub ahead of print].

PURPOSE: To evaluate bacterial agents as cancer biomarkers.

METHODS AND RESULTS: Various bacterial species have been demonstrated to involve in human cancers. However, the data is not enough for better understanding of predominant specific species. Application of a rapid and early-diagnostic, cost-effective, non-invasive, and inclusive method is a crucial approach for obtaining valid results. The role of Helicobacter pylori (H. pylori) in gastric and duodenal cancer has been confirmed. From investigation among previous publications, we attempted to make it clear which bacterial species significantly and specifically increase in various cancer types. It was unraveled that there is significant change in Granulicatella adiacens (G. adiacens) in lung cancer (LC), Fusobacterium nucleatum (F. nucleatum) in colorectal cancer (CRC), H. pylori and Porphyromonas gingivalis (P. gingivalis) in pancreatic cancer, and Streptococcus spp. in oral cancer.

CONCLUSION: Alteration in the cell cycle by means of different mechanisms such as inflammation, alteration in cell signaling, invasion and immune evasion, specific niche colonization, induction of DNA damage and mutation, expression of some microRNAs, and enhancing epigenetic effects are the most common mechanisms employed by bacterial species.

RevDate: 2019-10-12

Wijarnpreecha K, Werlang ME, Watthanasuntorn K, et al (2019)

Obesity and Risk of Small Intestine Bacterial Overgrowth: A Systematic Review and Meta-Analysis.

Digestive diseases and sciences pii:10.1007/s10620-019-05887-x [Epub ahead of print].

BACKGROUND/OBJECTIVES: Recent studies have proposed that obesity may be associated with a higher risk of small intestine bacterial overgrowth (SIBO) although the results were inconsistent. The microbiome has a known metabolic role; its impact on obesity in animal models generated the hypothesis of an association between a dysfunctional microbiome and obesity. We performed this systematic review and meta-analysis to elucidate this possible association by summarizing all available data.

METHODS: A literature search utilizing MEDLINE and EMBASE databases from inception until August 2019 was conducted. Eligible studies included either cohort studies or cross-sectional studies that consisted of two groups of participants, those with obesity and those without obesity, and compared the prevalence of SIBO between the groups. Adjusted odds ratios (OR) from each study were consolidated by the generic inverse variance method of DerSimonian and Laird.

RESULTS: A total of five studies with 515 patients fulfilled eligibility criteria and were included in this meta-analysis. The risk of SIBO among individuals with obesity was higher than in individuals without obesity but did not reach statistical significance with a pooled OR of 2.08 [95% confidence interval (CI) 0.82-5.31; p = 0.12; I2 84%]. Sensitivity analysis including only studies from Western countries increased the pooled OR to 3.41 and reached statistical significance (95% CI 1.21-9.59; p = 0.02; I2 62%).

CONCLUSIONS: This meta-analysis found that the risk of SIBO was about two times higher among individuals with obesity compared to individuals without obesity, although the result did not reach statistical significance. The risk increased to threefold and reached statistical significance when only studies from Western countries were included. These observations may suggest the role of obesity as a predisposing factor for SIBO although more studies are still needed to corroborate these preliminary results.

RevDate: 2019-10-12

Kayser BD, Prifti E, Lhomme M, et al (2019)

Elevated serum ceramides are linked with obesity-associated gut dysbiosis and impaired glucose metabolism.

Metabolomics : Official journal of the Metabolomic Society, 15(11):140 pii:10.1007/s11306-019-1596-0.

INTRODUCTION: Low gut microbiome richness is associated with dyslipidemia and insulin resistance, and ceramides and other sphingolipids are implicated in the development of diabetes.

OBJECTIVES: Determine whether circulating sphingolipids, particularly ceramides, are associated with alterations in the gut microbiome among obese patients with increased diabetes risk.

METHODS: This was a cross-sectional and longitudinal retrospective analysis of a dietary/weight loss intervention. Fasted serum was collected from 49 participants (41 women) and analyzed by HPLC-MS/MS to quantify 45 sphingolipids. Shotgun metagenomic sequencing of stool was performed to profile the gut microbiome.

RESULTS: Confirming the link to deteriorated glucose homeostasis, serum ceramides were positively correlated with fasting glucose, but inversely correlated with fasting and OGTT-derived measures of insulin sensitivity and β-cell function. Significant associations with gut dysbiosis were demonstrated, with SM and ceramides being inversely correlated with gene richness. Ceramides with fatty acid chain lengths of 20-24 carbons were the most associated with low richness. Diet-induced weight loss, which improved gene richness, decreased most sphingolipids. Thirty-one MGS, mostly corresponding to unidentified bacteria species, were inversely correlated with ceramides, including a number of Bifidobacterium and Methanobrevibacter smithii. Higher ceramide levels were also associated with increased metagenomic modules for lipopolysaccharide synthesis and flagellan synthesis, two pathogen-associated molecular patterns, and decreased enrichment of genes involved in methanogenesis and bile acid metabolism.

CONCLUSION: This study identifies an association between gut microbiota richness, ceramides, and diabetes risk in overweight/obese humans, and suggests that the gut microbiota may contribute to dysregulation of lipid metabolism in metabolic disorders.

RevDate: 2019-10-12

Hess AL, Benítez-Páez A, Blædel T, et al (2019)

The effect of inulin and resistant maltodextrin on weight loss during energy restriction: a randomised, placebo-controlled, double-blinded intervention.

European journal of nutrition pii:10.1007/s00394-019-02099-x [Epub ahead of print].

PURPOSE: The objective of this study was to investigate the additive effects of combining energy restriction with dietary fibres on change in body weight and gut microbiota composition.

METHODS: The study was a 12-week randomised, placebo-controlled, double-blinded, parallel intervention trial. A total of 116 overweight or obese participants were assigned randomly either to 10 g inulin plus 10 g resistant maltodextrin or to 20 g of placebo supplementation through 400 mL of milk a day, while on a - 500 kcal/day energy restricted diet.

RESULTS: Altogether, 86 participants completed the intervention. There were no significant differences in weight loss or body composition between the groups. The fibre supplement reduced systolic (5.35 ± 2.4 mmHg, p = 0.043) and diastolic (2.82 ± 1.3 mmHg, p = 0.047) blood pressure to a larger extent than placebo. Furthermore, a larger decrease in serum insulin was observed in the placebo group compared to the fibre group (- 26.0 ± 9.2 pmol/L, p = 0.006). The intake of fibre induced changes in the composition of gut microbiota resulting in higher abundances of Parabacteroides and Bifidobacteria, compared to placebo. The effects on blood pressure and glucose metabolism were mainly observed in women, and could be attributed to a higher gut microbiota diversity after intervention. Finally, the fibre group experienced a higher degree of gastrointestinal symptoms, which attenuated over time.

CONCLUSIONS: Supplementation of inulin and resistant maltodextrin did not provide an additional weight loss during an energy-restricted diet, but reduced both systolic and diastolic blood pressure. Furthermore, the fibre supplement did stimulate the growth of potentially beneficial bacteria genera.

CLINICAL TRIAL REGISTRY: The study was registered at http://www.clinicaltrials.gov , NCT03135041.

RevDate: 2019-10-12

Mackay D, Mollard RC, Granger M, et al (2019)

The Manitoba Personalized Lifestyle Research (TMPLR) study protocol: a multicentre bidirectional observational cohort study with administrative health record linkage investigating the interactions between lifestyle and health in Manitoba, Canada.

BMJ open, 9(10):e023318 pii:bmjopen-2018-023318.

INTRODUCTION: Lifestyle factors, such as diet, physical activity and sleep, are associated with the development of many chronic diseases. The objective of The Manitoba Personalized Lifestyle Research study is to understand how these lifestyle factors interact with each other and with other factors, such as an individual's genetics and gut microbiome, to influence health.

METHODS: An observational study of adults, with extensive phenotyping by objective health and lifestyle assessments, and retrospective assessment of early life experiences, with retrospective and prospective utilisation of secondary data from administrative health records.

STUDY POPULATION: A planned non-random convenience sample of 840 Manitobans aged 30-46 recruited from the general population, stratified by sex (equal men and women), body mass index (BMI; 60% of participants with a BMI>25 kg/m2) and geography (25% from rural areas). These stratifications were selected based on Manitoba demographics.

MEASUREMENTS: Lifestyle factors assessed will include dietary pattern, physical activity, cardiovascular fitness, and sleep. Factors such as medical history, socioeconomic status, alcohol and tobacco consumption, cognition, stress, anxiety, and early life experiences will also be documented. A maternal survey will be performed. Body composition and bone density will be measured by dual energy X-ray absorptiometry. Blood pressure, pulse wave velocity, and augmentation index will be measured on two consecutive days. Chronic disease risk biomarkers will be measured in blood and urine samples. DNA will be extracted for genetic analysis. A faecal sample will be collected for microbiome analysis. Participants may provide their Manitoba personal health information number to link their study data with administrative health records.

ETHICS AND DISSEMINATION: Ethics approval has been obtained from the University of Manitoba Health Research Ethics Board (protocol # HS18951; 05/01/2016). Data analysis, release of results and publication of manuscripts are scheduled to start in early 2019. Additional information at www.TMPLR.ca.


RevDate: 2019-10-11

Cohen J, E Pennisi (2019)

DNA pushes back the microbiome frontier.

Science (New York, N.Y.), 366(6461):23.

RevDate: 2019-10-11

Lynch JB, EY Hsiao (2019)

Microbiomes as sources of emergent host phenotypes.

Science (New York, N.Y.), 365(6460):1405-1409.

Microbial communities associated with animals exert powerful influences on host physiology, regulating metabolism and immune function, as well as complex host behaviors. The importance of host-microbiome interactions for maintaining homeostasis and promoting health raises evolutionarily complicated questions about how animals and their microbiomes have coevolved, and how these relationships affect the ways that animals interact with their environment. Here, we review the literature on the contributions of host factors to microbial community structure and corresponding influences of microbiomes on emergent host phenotypes. We focus in particular on animal behaviors as a basis for understanding potential roles for the microbiome in shaping host neurobiology.

RevDate: 2019-10-11

Harris JK, Wagner BD, Zemanick ET, et al (2019)

Changes in Airway Microbiome and Inflammation with Ivacaftor Treatment in Patients with Cystic Fibrosis and the G551D Mutation.

Annals of the American Thoracic Society [Epub ahead of print].

RATIONALE: Modulation of the cystic fibrosis transmembrane conductance regulator (CFTR) protein improves clinical outcomes in patients with cystic fibrosis (CF) and specific CFTR genetic mutations. It remains unclear how improving CFTR function modifies existing airway infection and inflammation.

OBJECTIVE: To compare sputum microbiome and markers of inflammation before and after 6 months of ivacaftor treatment Methods: The study included 31 people with CF, ages 10 and older, with at least one G551D CFTR allele and an FEV1 ≥ 40% predicted who were enrolled in the G551D Observational (GOAL) study. Sputum samples were collected either by induction (n = 14) or by spontaneous expectoration (n = 17) before and 6 months after initiation of ivacaftor. Changes in bacterial community indices by sequencing of 16S rRNA amplicons, total and specific bacterial load, and a panel of proteases, antiproteases, and inflammatory cytokines were determined.

RESULTS: The cohort that spontaneously expectorated sputum had a lower FEV1, higher proportion with Pseudomonas aeruginosa infection, and higher concentrations of sputum inflammatory markers compared with the cohort that provided sputum by induction. While the overall cohort experienced significant improvements in FEV1 and reductions in sweat chloride, no significant changes in bacterial diversity, specific bacterial pathogens, or markers of inflammation were observed in these subjects. Neither total bacterial load nor presence of Pseudomonas changed significantly between paired samples with ivacaftor treatment. Younger patients experienced more shifts in their microbial communities than older patients.

CONCLUSIONS: In this multicenter cohort, six months of ivacaftor treatment were not associated with significant changes in airway microbial communities or measures of inflammation. These data suggest that concomitant antimicrobial and anti-inflammatory treatments will still be needed to manage airway disease in CF patients treated with highly effective CFTR modulator therapy, especially in older patients with more advanced disease.

RevDate: 2019-10-11

Bletz MC, Bunk B, Spröer C, et al (2019)

Amphibian skin-associated Pigmentiphaga: Genome sequence and occurrence across geography and hosts.

PloS one, 14(10):e0223747 pii:PONE-D-19-14011.

The bacterial communities colonizing amphibian skin have been intensively studied due to their interactions with pathogenic chytrid fungi that are causing drastic amphibian population declines. Bacteria of the family Alcaligenaceae, and more specifically of the genus Pigmentiphaga, have been found to be associated specifically to arboreal frogs. Here we analyze their occurrence in a previously assembled global skin microbiome dataset from 205 amphibian species. Pigmentiphaga made up about 5% of the total number of reads in this global dataset. They were mostly found in unrelated arboreal frogs from Madagascar (Mantellidae and Hyperoliidae), but also occurred at low abundances on Neotropical frogs. Based on their 16S sequences, most of the sequences belong to a clade within Pigmentiphaga not assignable to any type strains of the five described species of the genus. One isolate from Madagascar clustered with Pigmentiphaga aceris (>99% sequence similarity on 16S rRNA gene level). Here, we report the full genome sequence of this bacterium which, based on 16S sequences of >97% similarity, has previously been found on human skin, floral nectar, tree sap, stream sediment and soil. Its genome consists of a single circular chromosome with 6,165,255 bp, 5,300 predicted coding sequences, 57 tRNA genes, and three rRNA operons. In comparison with other known Pigmentiphaga genomes it encodes a higher number of genes associated with environmental information processing and cellular processes. Furthermore, it has a biosynthetic gene cluster for a nonribosomal peptide syntethase, and bacteriocin biosynthetic genes can be found, but clusters for β-lactones present in other comparative Pigmentiphaga genomes are lacking.

RevDate: 2019-10-11

Darden JE, Scott EM, Arnold C, et al (2019)

Evaluation of the bacterial ocular surface microbiome in clinically normal cats before and after treatment with topical erythromycin.

PloS one, 14(10):e0223859 pii:PONE-D-19-11846.

The ocular surface microbiome of veterinary species has not been thoroughly characterized using next generation sequencing. Furthermore, alterations in the feline ocular surface microbiome over time or following topical antibiotic treatment are unknown. Aims of this study were to further characterize the ocular surface microbiome of healthy cats and to identify whether there are microbial community changes over time and following topical antibiotic use. Twenty-four eyes from twelve adult, research-bred, female spayed domestic shorthaired cats were evaluated. Erythromycin ophthalmic ointment (0.5%) was applied to the ocular surface of one randomly assigned eye per cat three times daily for 7 days, while the fellow eye served as an untreated control. The ocular surface was sampled by swabbing the inferior conjunctival fornix of both eyes prior to initiating treatment (day 0), after 1 week of treatment (day 7), and 4 weeks after concluding treatment (day 35). Genomic DNA was extracted from the swabs and sequenced using primers that target the V4 region of bacterial 16S rRNA genes. At baseline, the most common bacterial phyla identified were Proteobacteria (42.4%), Firmicutes (30.0%), Actinobacteria (15.6%), and Bacteroidetes (8.1%). The most abundant bacterial families sequenced were Corynebacteriaceae (7.8%), Helicobacteraceae (7.5%), Moraxellaceae (6.1%), and Comamonadaceae (5.6%). Alpha and beta diversity measurements were largely unchanged in both treatment and control eyes over time. However, univariate and linear discriminant analyses revealed significant and similar changes in the abundance of some bacterial taxa over time in both treatment and control eyes. Overall, the feline ocular surface microbiome remained stable over time and following topical antibiotic therapy.

RevDate: 2019-10-11

Campbell S (2019)

Microbial Treatments for the Mind.

IEEE pulse, 10(5):3-7.

For $99, you can obtain a kit that includes two cotton swabs and instructions for properly collecting your own stool sample, along with oral and skin samples. Upon shipping those specimens to the Knight Lab in La Jolla, CA, you will join the ranks of "citizen scientist," becoming a contributor to the world's largest crowd-sourced microbiome research project. In return, should you have accepted this mission, you will receive a report that offers you a "snapshot" of the microbes found in your fecal matter, and compares it to that of the rest of the population.

RevDate: 2019-10-11

Slavin M, Li HA, Frankenfeld C, et al (2019)

What is Needed for Evidence-Based Dietary Recommendations for Migraine: A Call to Action for Nutrition and Microbiome Research.

Headache, 59(9):1566-1581.

BACKGROUND: The gastrointestinal symptoms of migraine attacks have invited numerous dietary hypotheses for migraine etiology through the centuries. Substantial efforts have been dedicated to identifying dietary interventions for migraine attack prevention, with limited success. Meanwhile, mounting evidence suggests that the reverse relationship may also exist - that the biological mechanisms of migraine may influence dietary intake. More likely, the truth involves some combination of both, where the disease influences food intake, and the foods eaten impact the manifestations of the disease. In addition, the gut's microbiota is increasingly suspected to influence the migraine brain via the gut-brain axis, though these hypotheses remain largely unsubstantiated.

OBJECTIVE: This paper presents an overview of the strength of existing evidence for food-based dietary interventions for migraine, noting that there is frequently evidence to suggest that a dietary risk factor for migraine exists but no evidence for how to best intervene; in fact, our intuitive assumptions on interventions are being challenged with new evidence. We then look to the future for promising avenues of research, notably the gut microbiome.

CONCLUSION: The evidence supports a call to action for high-quality dietary and microbiome research in migraine, both to substantiate hypothesized relationships and build the evidence base regarding nutrition's potential impact on migraine attack prevention and treatment.

RevDate: 2019-10-11

Longley R, Benucci GNM, Mills G, et al (2019)

Fungal and bacterial community dynamics in substrates during the cultivation of morels (Morchella rufobrunnea) indoors.

FEMS microbiology letters pii:5585883 [Epub ahead of print].

Morel mushrooms (Morchella, Pezizales) are highly prized edible fungi. Approaches to cultivate morels indoors in pasteurized composted substrates have been successful for Morchella rufobrunnea. We used DNA amplicon sequencing of the Internal Transcribed Spacer (ITS) and 16S ribosomal DNA to follow bacterial and fungal communities in substrates during indoor morel cultivation. Our goal was to determine changes in microbial communities at key stages of morel cultivation, which included primordia development, fundament initiation, differentiation and maturation. Additionally, we compared microbial communities between trays that successfully fruited to those that produced conidia and primordia but aborted before ascocarp formation (non-fruiting). The prokaryotic community was dominated by Firmicutes belonging to Bacillus and Paenibacillus with a lower abundance of Flavobacteria. At earlier stages, the fungal community was dominated by Pezizomycetes including Morchella and other species, whereas, later in the cropping cycle Sordariomycetes dominated. Additionally, differences were observed between trays with successful fruiting, which were dominated by Gilmaniella; compared to trays that did not fruit, which were dominated by Cephalotrichum. Our findings inform understanding of microbial community dynamics during morel cultivation, and show that fungal genera such as Gilmaniella and prokaryotic genera such as Bacillus are abundant in substrates that support M. rufobrunnea fruiting.

RevDate: 2019-10-11

Klinger EG, Camp AA, Strange JP, et al (2019)

Bombus (Hymenoptera: Apidae) Microcolonies as a Tool for Biological Understanding and Pesticide Risk Assessment.

Environmental entomology pii:5585913 [Epub ahead of print].

Bumble bees provide valuable pollination services to many wild and agricultural plants. Populations of some bumble bee species are in decline, prompting the need to better understand bumble bee biology and to develop methodologies for assessing the effects of environmental stressors on these bees. Use of bumble bee microcolonies as an experimental tool is steadily increasing. This review closely examines the microcolony model using peer-reviewed published literature identified by searching three databases through November 2018. Microcolonies have been successfully used for investigating a range of endpoints including behavior, the gut microbiome, nutrition, development, pathogens, chemical biology, and pesticides/xenobiotics. Methods for the initiation and monitoring of microcolonies, as well as the recorded variables were catalogued and described. From this information, we identified a series of recommendations for standardizing core elements of microcolony studies. Standardization is critical to establishing the foundation needed to support use of this model for biological response investigations and particularly for supporting use in pesticide risk assessment.

RevDate: 2019-10-11

Mugge RL, Lee JS, Brown TT, et al (2019)

Marine biofilm bacterial community response and carbon steel loss following Deepwater Horizon spill contaminant exposure.

Biofouling [Epub ahead of print].

Steel marine structures provide foci of biodiversity when they develop into artificial reefs. Development begins with deposition of a biofilm. The effects of contaminants from oil spills on biofilm microbiomes, microbially-induced corrosion (MIC) and metal loss may impact preservation of marine metal structures. A microcosm experiment exposed biofilms on carbon steel disks (CSDs) to crude oil, dispersant, and dispersed oil to address their impacts on bacterial composition and metal loss and pitting. Biofilm diversity increased over time in all exposures. Community composition in dispersant and dispersed oil treatments deviated from the controls for the duration of a 12-week experiment. As biofilms matured, Pseudomonadaceae increased while Rhodobacteraceae decreased in abundance in dispersed oil treatments compared to the controls and dispersant treatments. Greatest mass loss and deepest pitting on CSDs were observed in dispersed oil treatments, suggesting impacts manifest as a consequence of increased MIC potential on carbon steel.

RevDate: 2019-10-11

Perez NB, Dorsen C, A Squires (2019)

Dysbiosis of the Gut Microbiome: A Concept Analysis.

Journal of holistic nursing : official journal of the American Holistic Nurses' Association [Epub ahead of print].

Background:Gut microbes influence the development several chronic conditions marking them as targets for holistic care, prevention strategies, and potential treatments. Microbiome studies are relatively new to health research and present unfamiliar terms to clinicians and researchers. "Dysbiosis" often refers to an alteration in the gut microbiome, but conceptual clarification is rarely provided. Purpose: The purpose of this study is to refine a conceptual definition of dysbiosis based on a review of nursing literature. Method: A Rodgerian approach to concept analysis was used. CINAHL, PubMed, and Web of Science were queried using "dysbiosis" through December 2018. Each article was analyzed with regard to the antecedents, attributes, and consequences of dysbiosis. Essential elements were tabulated and compared across studies to determine recurring themes and notable outliers. Findings: Analysis revealed several important antecedences, attributes, and consequences of dysbiosis. The findings also elucidated notable gaps and highlighted the co-evolving nature of the proposed definition with advances in microbiome research. Conclusion: This article adds a proposed definition of dysbiosis, offering a contribution of conceptual clarity upon which to enhance dialogue and build research. The definition emphasizes risk factors and consequences of dysbiosis as implications for holistic nursing practice.

RevDate: 2019-10-11

Brown Kav A, Rozov R, Bogumil D, et al (2019)

Unravelling plasmidome distribution and interaction with its hosting microbiome.

Environmental microbiology [Epub ahead of print].

Horizontal gene transfer, and the plasmids that are often the major transfer vectors, play a crucial role in microbial evolution. Here we present a comparative study of plasmidomes across adjacent microbial environments present in different individual rumen microbiomes. Our findings show that the rumen plasmidome displays enormous unknown functional potential currently unannotated in available databases. Nevertheless, this unknown functionality is conserved and shared with published rat gut plasmidome data. Moreover, the rumen plasmidome is highly diverse compared to microbiome that hosts these plasmids, across both similar and different rumen habitats. Our analysis demonstrates that its structure is shaped more by stochasticity than selection. Nevertheless, the plasmidome is an active partner in its intricate relationship with the host microbiome with both interacting with and responding to their environment. This study presents a unique look at the plasmidome's variation in its natural environment and its ecological role. This article is protected by copyright. All rights reserved.

RevDate: 2019-10-11

Esteban-Blanco C, Gutiérrez-Gil B, Puente-Sánchez F, et al (2019)

Microbiota characterization of sheep milk and its association with somatic cell count using 16s rRNA gene sequencing.

Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie [Epub ahead of print].

This work aimed to use 16S ribosomal RNA sequencing with the Illumina MiSeq platform to describe the milk microbiota from 50 healthy Assaf ewes. The global observed microbial community for clinically healthy milk samples analysed was complex and showed a vast diversity. The core microbiota of the sheep milk includes five genera: Staphylococcus, Lactobacillus, Corynebacterium, Streptococcus and Escherichia/Shigella. Although there are some differences, some of these genera are common with the microbiota core pattern of milk from other species, especially with dairy cows. The microbial composition of the studied samples, based on the definition of amplicon sequence variants, was analysed through a correlation network. A preliminary analysis by grouping the milk samples based on their somatic cell count (SCC), which is considered an indicator of subclinical mastitis (SM), showed certain differences for the core of the samples identified as SM. The differences in the microbiota diversity pattern among samples might also suggest that subclinical mastitis would be associated with the significant increase in some genera that are inhabitants of the mammary gland and a remarkable concomitant reduction in the microbial diversity. Additionally, we have also presented here a preliminary analysis to assess the impact of the sheep milk microbiome on SCC, as an indicator of subclinical mastitis. The results here reported provide a first characterization of the sheep milk microbiota and settle the basis for future studies in this field.

RevDate: 2019-10-11

Dobbler P, Mai V, Procianoy RS, et al (2019)

The vaginal microbial communities of healthy expectant Brazilian mothers and its correlation with the newborn's gut colonization.

World journal of microbiology & biotechnology, 35(10):159 pii:10.1007/s11274-019-2737-3.

The female lower genital tract harbors a complex microbial community essential for homeostasis and health. During pregnancy, the female body undergoes unique hormonal changes that contribute to weight gain as well as modulations in immune function that can affect microbiota composition. Several studies have described the vaginal microbiota of pregnant women from the USA, Europe and Mexico. Here we expand our knowledge about the vaginal microbial communities during the third trimester to healthy expectant Brazilian mothers. Vaginal samples were collected from patients delivering at the Hospital de Clínicas de Porto Alegre, Brazil. Microbial DNA was isolated from samples and the V4 region of the 16S rRNA gene was amplified and sequenced using the PGM Ion Torrent. Brazilian pregnant women presented three distinct types of microbial community at the time of labor. Two microbial communities, Cluster 1 and Cluster 3, presented an overall dominance of Lactobacillus while Cluster 2 tended to present higher diversity and richness, with the presence of Pseudomonas, Prevotella and other vaginosis related bacteria. About half of the Brazilian mothers sampled here had dominance of L. iners. The proportion of mothers without dominance of any Lactobacillus was higher in Brazil (22%) compared to UK (2.4%) and USA, where this community type was not detected. The vaginal microbiota showed significant correlation with the composition of the babies' gut microbiota (p-value = 0.002 with a R2 of 15.8%). Mothers presenting different vaginal microbiota shared different microorganisms with their newborns, which would reflect on initial colonizers of the developing newborns' gut.

RevDate: 2019-10-11

Li Q, Chen H, Zhang M, et al (2019)

Altered short chain fatty acid profiles induced by dietary fiber intervention regulate AMPK levels and intestinal homeostasis.

Food & function [Epub ahead of print].

The objective of this study was to investigate the effects of dietary intervention on intestinal microbiota-mediated change in short chain fatty acid (SCFA) profile and intestinal homeostasis. Sequencing of the 16S rDNA of gut bacteria, metagenomics, intestinal epithelial transcriptomics, and metabonomics were conducted. Results showed that the dietary interventions altered the microbiota composition of cecal digesta, microbiota-mediated metabolism, and the gene expression profile in intestinal epithelial cells. Compared with red meat-diet-fed mice, fiber-diet-fed mice presented a shift in the gut microbiome toward increased production of butanoate, which was accompanied by up-regulation of microbiota- and AMP-activated protein kinase (AMPK)-dependent gene expression and decrease in serum concentrations of trimethylamine N-oxide (TMAO), triglyceride (TG) and glucose (GLU). The results suggested a new regulatory mechanism via which butanoate and AMPK activation contributed to intestinal integrity and homeostasis by affecting metabolism, intestinal barrier function and transporter expression.

RevDate: 2019-10-11

Salguero MV, Al-Obaide MAI, Singh R, et al (2019)

Dysbiosis of Gram-negative gut microbiota and the associated serum lipopolysaccharide exacerbates inflammation in type 2 diabetic patients with chronic kidney disease.

Experimental and therapeutic medicine, 18(5):3461-3469.

Lipopolysaccharide (LPS), a potent endotoxin present in the outer membrane of Gram-negative bacteria, causes chronic immune responses associated with inflammation. In the present study, the association between LPS and the dysbiosis of Gram-negative bacteria in the gut microbiome was determined in patients with type 2 diabetes mellitus (T2DM) and chronic kidney disease (T2DM-CKD; stages 4 and 5, not on dialysis) compared with healthy individuals. Microbiome diversity was analyzed in patients with T2DM-CKD and healthy controls by sequencing the hypervariable sub-regions of the 16S ribosomal RNA gene from stool samples. Serum samples were assayed by ELISA for LPS, C-reactive protein (CRP), tumor necrosis factor-α (TNFα), interleukin-6 (IL6) and endothelin-1. A total of four gut Gram-negative phyla (Bacteroidetes, Proteobacteria, Fusobacteria and Verrucomicrobia) were identified in the gut microbiome of the T2DM-CKD and control groups. Proteobacteria, Verrucomicrobia and Fusobacteria exhibited significantly increased relative abundance in patients with T2DM-CKD when compared with controls (P<0.05). The levels of serum LPS were significantly increased in patients with T2DM-CKD compared with controls (P<0.05). Elevated serum LPS was significantly correlated with increased levels of TNFα, IL6 and CRP. The dysbiosis of Gram-negative bacteria in the gut microbiome of patients with T2DM-CKD may contribute to the elevated serum levels of LPS and the consequential effects on the inflammatory biomarkers in these patients. The association between the dysbiosis of Gram-negative bacteria in the gut microbiome of patients with T2DM-CKD, increased LPS levels and the effects on inflammatory biomarkers may provide insight into potential diagnostic and therapeutic approaches in the treatment of T2DM-CKD.

RevDate: 2019-10-11

González-Prendes R, Pena RN, Solé E, et al (2019)

Modulatory Effect of Protein and Carotene Dietary Levels on Pig gut Microbiota.

Scientific reports, 9(1):14582 pii:10.1038/s41598-019-51136-6.

In this study we investigated the impact of dietary protein and carotene levels on microbial functions and composition during the last month of purebred fattening Duroc pigs. Fecal microbiota was characterized using 16S ribosomal RNA sequencing at two points of live, 165 (T1) and 195 (T2) days. From 70 to 165 days of age, 32 pigs were divided into two groups fed either a standard-protein (SP) or a low-protein (LP) diet. In the last month (165-195 days), all pigs received a LP diet, either carotene-enriched (CE) or not (NC). Significant differences were observed between T1 and T2 at Amplicon Sequences Variants (ASVs), phylum and genus levels. In T1 group, Prevotella, Faecalibacterium and Treponema were the genera most influenced by dietary protein, together with predicted functions related with the degradation of protein. In contrast, the CE diet did not impact the microbiome diversity, although 160 ASVs were differentially abundant between CE and NC groups at T2. Weak stability of enterotype clusters across time-points was observed as consequence of medium-term dietary interventions. Our results suggest that during the last month of fattening, dietary protein have a stronger effect than carotenes on the modulation of the compositional and functional structure of the pig microbiota.

RevDate: 2019-10-11

Wang H, Latorre JD, Bansal M, et al (2019)

Microbial metabolite deoxycholic acid controls Clostridium perfringens-induced chicken necrotic enteritis through attenuating inflammatory cyclooxygenase signaling.

Scientific reports, 9(1):14541 pii:10.1038/s41598-019-51104-0.

Necrotic enteritis (NE) caused by Clostridium perfringens infection has reemerged as a prevalent poultry disease worldwide due to reduced usage of prophylactic antibiotics under consumer preferences and regulatory pressures. The lack of alternative antimicrobial strategies to control this disease is mainly due to limited insight into the relationship between NE pathogenesis, microbiome, and host responses. Here we showed that the microbial metabolic byproduct of secondary bile acid deoxycholic acid (DCA), at as low as 50 µM, inhibited 82.8% of C. perfringens growth in Tryptic Soy Broth (P < 0.05). Sequential Eimeria maxima and C. perfringens challenges significantly induced NE, severe intestinal inflammation, and body weight (BW) loss in broiler chickens. These negative effects were diminished (P < 0.05) by 1.5 g/kg DCA diet. At the cellular level, DCA alleviated NE-associated ileal epithelial death and significantly reduced lamina propria cell apoptosis. Interestingly, DCA reduced C. perfringens invasion into ileum (P < 0.05) without altering the bacterial ileal luminal colonization. Molecular analysis showed that DCA significantly reduced inflammatory mediators of Infγ, Litaf, Il1β, and Mmp9 mRNA accumulation in ileal tissue. Mechanism studies revealed that C. perfringens induced (P < 0.05) elevated expression of inflammatory mediators of Infγ, Litaf, and Ptgs2 (Cyclooxygenases-2 (COX-2) gene) in chicken splenocytes. Inhibiting the COX signaling by aspirin significantly attenuated INFγ-induced inflammatory response in the splenocytes. Consistent with the in vitro assay, chickens fed 0.12 g/kg aspirin diet protected the birds against NE-induced BW loss, ileal inflammation, and intestinal cell apoptosis. In conclusion, microbial metabolic product DCA prevents NE-induced BW loss and ileal inflammation through attenuating inflammatory response. These novel findings of microbiome protecting birds against NE provide new options on developing next generation antimicrobial alternatives against NE.

RevDate: 2019-10-11

Henning SM, Yang J, Lee RP, et al (2019)

Pomegranate Juice and Extract Consumption Increases the Resistance to UVB-induced Erythema and Changes the Skin Microbiome in Healthy Women: a Randomized Controlled Trial.

Scientific reports, 9(1):14528 pii:10.1038/s41598-019-50926-2.

In vitro and animal studies have demonstrated that topical application and oral consumption of pomegranate reduces UVB-induced skin damage. We therefore investigated if oral pomegranate consumption will reduce photodamage from UVB irradiation and alter the composition of the skin microbiota in a randomized controlled, parallel, three-arm, open label study. Seventy-four female participants (30-45 years) with Fitzpatrick skin type II-IV were randomly assigned (1:1:1) to 1000 mg of pomegranate extract (PomX), 8 oz of pomegranate juice (PomJ) or placebo for 12 weeks. Minimal erythema dose (MED) and melanin index were determined using a cutometer (mexameter probe). Skin microbiota was determined using 16S rRNA sequencing. The MED was significantly increased in the PomX and PomJ group compared to placebo. There was no significant difference on phylum, but on family and genus level bacterial composition of skin samples collected at baseline and after 12 week intervention showed significant differences between PomJ, PomX and placebo. Members of the Methylobacteriaceae family contain pigments absorbing UV irradiation and might contribute to UVB skin protection. However, we were not able to establish a direct correlation between increased MED and bacterial abundance. In summary daily oral pomegranate consumption may lead to enhanced protection from UV photodamage.

RevDate: 2019-10-11

Gouba N, Saad J, Drancourt M, et al (2019)

Genome Sequence of Enorma sp. Strain Marseille-P9525T, a Member of a Human Gut Microbiome.

Microbiology resource announcements, 8(41): pii:8/41/e00785-19.

Strain Marseille-P9525T was isolated from the gut microbiota of a 28-year-old woman and exhibits a 2.23-Mb (G+C content, 66.8%) draft genome sequence containing 1,902 protein-coding genes, 49 tRNAs, and 3 rRNAs. The 16S rRNA sequencing and in silico DNA-DNA hybridization indicated that strain Marseille-P9525T represents a new species to be described.

RevDate: 2019-10-11

Hugerth LW, Andreasson A, Talley NJ, et al (2019)

No distinct microbiome signature of irritable bowel syndrome found in a Swedish random population.

Gut pii:gutjnl-2019-318717 [Epub ahead of print].

OBJECTIVE: The ethiopathogenesis of irritable bowel syndrome (IBS) is unknown. While a link to the gut microbiome is postulated, the heterogeneity of the healthy gut makes it difficult to draw definitive conclusions. We aimed to describe the faecal and mucosa-associated microbiome (MAM) and health correlates on a community cohort of healthy and IBS individuals with no colonoscopic findings.

DESIGN: The PopCol study recruited a random sample of 3556 adults; 745 underwent colonoscopy. IBS was defined by Rome IV criteria and organic disease excluded. 16S rRNA gene sequencing was conducted on sigmoid biopsy samples from 376 representative individuals (63 IBS cases) and faecal samples from 185 individuals (32 IBS cases).

RESULTS: While sigmoid MAM was dominated by Lachnospiraceae, faeces presented a higher relative abundance of Ruminococcaceae. Microbial richness in MAM was linearly correlated to that in faeces from the same individual (R²=0.255, p<3E-11) as was diversity (R²=0.06, p=0.0022). MAM diversity decreased with increasing body mass index (BMI; Pearson's r=-0.1, p=0.08) and poorer self-rated health (r=-0.15, p=0.007), but no other health correlates. Faecal microbiome diversity was correlated to stool consistency (r=-0.16, p=0.043). Several taxonomic groups were correlated to age, BMI, depression and self-reported health, including Coprococcus catus associated with lower levels of depression (r=-0.003, p=0.00017). The degree of heterogeneity observed between IBS patients is higher than that observed between healthy individuals.

CONCLUSIONS: No distinct microbial signature was observed in IBS. Individuals presenting with low self-rated health or high BMI have lower gut microbiome richness.

RevDate: 2019-10-11

Inda ME, Broset E, Lu TK, et al (2019)

Emerging Frontiers in Microbiome Engineering.

Trends in immunology pii:S1471-4906(19)30174-7 [Epub ahead of print].

The gut microbiome has a significant impact on health and disease and can actively contribute to obesity, diabetes, inflammatory bowel disease, cardiovascular disease, and neurological disorders. We do not yet have the necessary tools to fine-tune the microbial communities that constitute the microbiome, though such tools could unlock extensive benefits to human health. Here, we provide an overview of the current state of technological tools that may be used for microbiome engineering. These tools can enable investigators to define the parameters of a healthy microbiome and to determine how gut bacteria may contribute to the etiology of a variety of diseases. These tools may also allow us to explore the exciting prospect of developing targeted therapies and personalized treatments for microbiome-linked diseases.

RevDate: 2019-10-11

Stinson LF (2019)

Establishment of the early-life microbiome: a DOHaD perspective.

Journal of developmental origins of health and disease pii:S2040174419000588 [Epub ahead of print].

The human microbiome plays a number of critical roles in host physiology. Evidence from longitudinal cohort studies and animal models strongly supports the theory that maldevelopment of the microbiome in early life can programme later-life disease. The early-life microbiome develops in a clear stepwise manner over the first 3 years of life. During this highly dynamic time, insults such as antibiotic use and formula feeding can adversely affect the composition and temporal development of the microbiome. Such experiences predispose infants for the development of chronic health conditions later in life. This review highlights key factors that disrupt the early-life microbiome and highlights major non-communicable diseases which are underpinned by early-life dysbiosis.

RevDate: 2019-10-11

Hardin SJ, Singh M, Eyob W, et al (2019)

Diet-induced chronic syndrome, metabolically transformed trimethylamine-N-oxide, and the cardiovascular functions.

Reviews in cardiovascular medicine, 20(3):121-128.

Recent studies have shown that the integrity of the gastrointestinal tract and its microbiome impact the functioning of various body systems by regulating immunological responses, extracting energy, remodeling intestinal epithelia, and strengthening the gut itself. The gastrointestinal tract microbiota includes bacteria, fungi, protozoa, viruses, and archaea which collectively comprise a dynamic community prone to alterations via influences such as the environment, illness, and metabolic processes. The idea that the host's diet possesses characteristics that could potentially alter microbiota composition is a novel notion. We hypothesize that a high fat diet leads to the alteration of the gastrointestinal microbiota composition and that metabolic transformation of the compound trimethylamine into trimethylamine-N-oxide promotes vasculopathy such as atherosclerosis and affects cardiovascular functionality. Furthermore, we hypothesize that treatment with probiotics will restore the homeostatic environment (eubiosis) of the gastrointestinal tract.

RevDate: 2019-10-11

Reddy KE, Kim HR, Jeong JY, et al (2019)

Impact of breed on the fecal microbiome of dogs under the same dietary condition.

Journal of microbiology and biotechnology pii:10.4014/jmb.1906.06048 [Epub ahead of print].

The gut microbiome influences the health and well-being of dogs. However, little is known about the impact of breed on the fecal microbiome composition in dogs. Therefore, we aimed to investigate the differences in the fecal microbiome in three breeds of dog fed and housed under the same conditions, namely eight Maltese (8.0 ± 0.1 years), eight Miniature Schnauzer (8.0 ± 0.0 years), and nine Poodle dogs (8.0 ± 0.0 years). Fresh fecal samples were collected from the dogs and used to extract metagenomic DNA. The composition of the fecal microbiome was evaluated by 16S rRNA gene amplicon sequencing on the MiSeq platform. A total of 840,501 sequences were obtained from the 25 fecal samples and classified as Firmicutes (32.3-97.3% of the total sequences), Bacteroidetes (0.1-62.6%), Actinobacteria (0.2-14.7%), Fusobacteria (0.0-5.7%), and Proteobacteria (0.0-5.1%). The relative abundance of Firmicutes was significantly lower in the Maltese dog breed than that in the other two breeds, while that of Fusobacteria was significantly higher in the Maltese than in the Miniature Schnauzer breed. At the genus level, the relative abundance of Streptococcus, Fusobacterium, Turicibacter, Succinivibrio, and Anaerobiospirillum differed significantly among the three dog breeds. These genera had no correlation with age, diet, sex, body weight, vaccination history, or parasite protection history. Within a breed, some of these genera had a correlation with at least one blood chemistry value. This study indicates that the composition of the fecal microbiome in dogs is affected by breed.

RevDate: 2019-10-11

Alsouleman K (2019)

Effect of increasing amounts of ammonium nitrogen induced by consecutive mixture of poultry manure and cattle slurry on the microbial community during thermophilic anaerobic digestion.

Journal of microbiology and biotechnology pii:10.4014/jmb.1909.09023 [Epub ahead of print].

Thermophilic anaerobic digestion (TAD) is characterized by higher biogas production rates as a result of assumedly faster microbial metabolic conversion rates compared to mesophilic AD. It was hypothesized that the thermophilic microbiome with its lower diversity than the mesophilic one is more susceptible to disturbances introduced by alterations in the operating factors, as an example, the supply of nitrogen-rich feedstock such as poultry manure (PM). Laboratory scaled TAD experiments using cattle slurry and increasing amounts of PM were carried out to investigate the (in-) stability of the process performance caused by the accumulation of ammonium and ammonia with special emphasis on the microbial community structure and its dynamic variation. The results revealed that the moderate PM addition, i.e., 25% (vol/vol based on volatile substances) PM, resulted in a reorganization of the microbial community structure which was still working sufficiently. With 50% PM application, the microbial community was further stepwise re-organized and was able to compensate for the high cytotoxic ammonia contents only for a short time resulting in consequent process disturbance and final process failure. This study demonstrated the ability of the acclimated thermophilic microbial community to tolerate a certain amount of nitrogen-rich substrate.

RevDate: 2019-10-11

Fitton HJ, Stringer DS, Park AY, et al (2019)

Therapies from Fucoidan: New Developments.

Marine drugs, 17(10): pii:md17100571.

Since our last review in 2015, the study and use of fucoidan has extended in several research areas. Clinical use of fucoidan for the treatment of renal disease has become available and human safety studies have been undertaken on radiolabeled fucoidan for the purpose of imaging thrombi. Fucoidan has been incorporated into an increasing number of commercially available supplements and topical treatments. In addition, new measuring techniques are now available to assess the biologically relevant uptake of fucoidans and to assist in production. Microbiome modulation and anti-pathogenic effects are increasingly promising applications for fucoidans, due to the need for alternative approaches to antibiotic use in the food chain. This review outlines promising new developments in fucoidan research, including potential future therapeutic use.

RevDate: 2019-10-11

Ali NABM, Mac Aogáin M, Morales RF, et al (2019)

Optimisation and Benchmarking of Targeted Amplicon Sequencing for Mycobiome Analysis of Respiratory Specimens.

International journal of molecular sciences, 20(20): pii:ijms20204991.

(1) Background: Firm consensus has yet to be established in relation to taxonomic classification and primer choice in targeted amplicon sequencing of the mycobiome. While the nuclear ribosomal internal transcribed spacer (ITS) region are recognized as the formal fungal taxonomic barcode, appraisal of different ITS sub-regions and the influence of DNA extraction methods have not been comprehensively undertaken using human respiratory specimens. (2) Methods: We performed ITS analysis of respiratory (sputum) samples by assessing (a) the effect of alternate DNA extraction techniques and (b) an evaluation of four different ITS primer pairs (ITS1F and ITS2; ITS1-30F and ITS1-217R; gITS7ngs and ITS4ng; and Fseq and Rseq) on the mycobiome profiles generated for mock fungal communities and their respective clinical (airway) specimens. (3) Results: Primer pairs varied in their resulting ITS mycobiome profiles, suggesting that particular pairs may be more relevant for analysis of respiratory samples compared to others. Assessment of DNA extraction methods highlighted lower final DNA concentrations achieved by mechanical disruption compared to enzymatic lysis. However, despite lower yields, DNA liberated by mechanical lysis more readily yielded ITS bands with highest success in combination with the Fseq and Rseq primers. (4) Conclusion: Choice of extraction method, primers used, and sequencing approach are all important considerations in sequencing the mycobiome and should be tailored to sample type. A standardization of approach to mycobiome studies using respiratory specimens will permit more reliable comparisons between studies and improve our understanding of the role of fungi in the human airway.

RevDate: 2019-10-11

Lin A, Shih CT, Huang CL, et al (2019)

Hypnotic Effects of Lactobacillus fermentum PS150TM on Pentobarbital-Induced Sleep in Mice.

Nutrients, 11(10): pii:nu11102409.

The bidirectional communication between the gastrointestinal tract and the central nervous system appears to be functionally linked to the intestinal microbiome, namely the microbiome-gut-brain axis (MGBA). Probiotics with health benefits on psychiatric or neurological illnesses are generally called psychobiotics, and some of them may also be able to improve sleep by targeting the MGBA. This study aimed to investigate the effects of a psychobiotic strain, Lactobacillus fermentum PS150TM (PS150TM), on sleep improvement by using a pentobarbital-induced sleep mouse model. Compared with the vehicle control group, the oral administration of PS150TM, but not the other L. fermentum strains, significantly decreased the sleep latency and increased the sleep duration of mice, suggesting strain-specific sleep-improving effects of PS150TM. Moreover, the ingestion of diphenhydramine, an antihistamine used to treat insomnia, as a drug control group, only increased the sleep duration of mice. We also found that the sleep-improving effects of PS150TM are time- and dose-dependent. Furthermore, the oral administration of PS150TM could attenuate a caffeine-induced sleep disturbance in mice, and PS150TM appeared to increase the expression of the gene encoding the adenosine 1 receptor in the hypothalamus of mice, as assessed by quantitative real-time polymerase chain reaction. Taken together, our results present a potential application of PS150TM as a dietary supplement for sleep improvement.

RevDate: 2019-10-10

Shkoporov AN, Clooney AG, Sutton TDS, et al (2019)

The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific.

Cell host & microbe, 26(4):527-541.e5.

The human gut contains a vast array of viruses, mostly bacteriophages. The majority remain uncharacterized, and their roles in shaping the gut microbiome and in impacting on human health remain poorly understood. We performed longitudinal metagenomic analysis of fecal viruses in healthy adults that reveal high temporal stability, individual specificity, and correlation with the bacterial microbiome. Using a database-independent approach that uses most of the sequencing data, we uncovered the existence of a stable, numerically predominant individual-specific persistent personal virome. Clustering of viral genomes and de novo taxonomic annotation identified several groups of crAss-like and Microviridae bacteriophages as the most stable colonizers of the human gut. CRISPR-based host prediction highlighted connections between these stable viral communities and highly predominant gut bacterial taxa such as Bacteroides, Prevotella, and Faecalibacterium. This study provides insights into the structure of the human gut virome and serves as an important baseline for hypothesis-driven research.

RevDate: 2019-10-10

Kordahi MC, RW DePaolo (2019)

Commensal Bacteria Decontaminating Your Diet.

Cell host & microbe, 26(4):446-448.

The diet-microbiome interaction can positively or negatively affect our health depending on dietary habits. In this issue of Cell Host & Microbe, Wolf et al. (2019) highlight the beneficial roles of gut commensal Collinsella in degrading potentially toxic food contaminants, called Maillard reaction products, found in processed foods.

RevDate: 2019-10-10

Dheilly NM, Martínez Martínez J, Rosario K, et al (2019)

Parasite microbiome project: Grand challenges.

PLoS pathogens, 15(10):e1008028 pii:PPATHOGENS-D-19-00607.

RevDate: 2019-10-10

Andreev VP, Liu G, Zee J, et al (2019)

Clustering of the structures by using "snakes-&-dragons" approach, or correlation matrix as a signal.

PloS one, 14(10):e0223267 pii:PONE-D-19-12477.

Biological, ecological, social, and technological systems are complex structures with multiple interacting parts, often represented by networks. Correlation matrices describing interdependency of the variables in such structures provide key information for comparison and classification of such systems. Classification based on correlation matrices could supplement or improve classification based on variable values, since the former reveals similarities in system structures, while the latter relies on the similarities in system states. Importantly, this approach of clustering correlation matrices is different from clustering elements of the correlation matrices, because our goal is to compare and cluster multiple networks-not the nodes within the networks. A novel approach for clustering correlation matrices, named "snakes-&-dragons," is introduced and illustrated by examples from neuroscience, human microbiome, and macroeconomics.

RevDate: 2019-10-10

Rashidi A, Zhu Z, Kaiser T, et al (2019)

Vancomycin-resistance gene cluster, vanC, in the gut microbiome of acute leukemia patients undergoing intensive chemotherapy.

PloS one, 14(10):e0223890 pii:PONE-D-19-21165.

Two recent reports suggested that the less common, less virulent enterococcal species, Enterococcus gallinarum and E. casseliflavus, with low-level vancomycin resistance due to chromosomally encoded vanC1 and vanC2/3, may influence host immunity. We reported that peri-transplant gut colonization with E. gallinarum and E. casseliflavus is associated with lower mortality after allogeneic hematopoietic cell transplantation (HCT). Because most acute leukemia patients undergoing HCT have received intensive chemotherapy (usually requiring prolonged hospitalization) for their underlying disease before HCT, we hypothesized that some may have acquired vanC-positive enterococci during chemotherapy. Therefore, we evaluated the presence of the vanC gene cluster using vanC1 and vanC2/3 qPCR in thrice-weekly collected stool samples from 20 acute leukemia patients undergoing intensive chemotherapy. We found that an unexpectedly large proportion of patients have detectable vanC1 and vanC2/3 (15% and 35%, respectively) in at least one stool sample. Comparing qPCR results with 16S rRNA gene sequencing results suggested that E. gallinarum may reach high abundances, potentially persisting into HCT and influencing transplant outcomes.

RevDate: 2019-10-10

Duvallet C, Zellmer C, Panchal P, et al (2019)

Framework for rational donor selection in fecal microbiota transplant clinical trials.

PloS one, 14(10):e0222881 pii:PONE-D-19-13813.

Early clinical successes are driving enthusiasm for fecal microbiota transplantation (FMT), the transfer of healthy gut bacteria through whole stool, as emerging research is linking the microbiome to many different diseases. However, preliminary trials have yielded mixed results and suggest that heterogeneity in donor stool may play a role in patient response. Thus, clinical trials may fail because an ineffective donor was chosen rather than because FMT is not appropriate for the indication. Here, we describe a conceptual framework to guide rational donor selection to increase the likelihood that FMT clinical trials will succeed. We argue that the mechanism by which the microbiome is hypothesized to be associated with a given indication should inform how healthy donors are selected for FMT trials, categorizing these mechanisms into four disease models and presenting associated donor selection strategies. We next walk through examples based on previously published FMT trials and ongoing investigations to illustrate how donor selection might occur in practice. Finally, we show that typical FMT trials are not powered to discover individual taxa mediating patient responses, suggesting that clinicians should develop targeted hypotheses for retrospective analyses and design their clinical trials accordingly. Moving forward, developing and applying novel clinical trial design methodologies like rational donor selection will be necessary to ensure that FMT successfully translates into clinical impact.

RevDate: 2019-10-10

Cribbs SK, Crothers K, A Morris (2019)

Pathogenesis of HIV-related lung disease: Immunity, infection, and inflammation.

Physiological reviews [Epub ahead of print].

Despite anti-retroviral therapy (ART), HIV-related pulmonary disease continues to be a major cause of morbidity and mortality for people living with HIV (PLWH). The spectrum of lung diseases has changed from acute opportunistic infections resulting in death to chronic lung diseases for those with access to ART. Chronic immune activation and suppression can result in impairment of innate immunity and progressive loss of T cell and B cell functionality with aberrant cytokine and chemokine responses systemically as well as in the lung. HIV can be detected in the lungs of PLWH and has profound effects on cellular immune functions. In addition, HIV-related lung injury and disease can occur secondary to a number of mechanisms including altered pulmonary and systemic inflammatory pathways, viral persistence in the lung, oxidative stress with additive effects of smoke exposure, microbial translocation, and alterations in the lung and gut microbiome. Although ART has had profound effects on systemic viral suppression in HIV, the impact of ART on lung immunology still needs to be fully elucidated. Understanding of the mechanisms by which HIV-related lung diseases continue to occur is critical to the development of new preventive and therapeutic strategies to improve lung health in PLWH.

RevDate: 2019-10-10

Pinzari F, Cornish L, AD Jungblut (2019)

Skeleton bones in museum indoor environments offer niches for fungi and are affected by weathering and deposition of secondary minerals.

Environmental microbiology [Epub ahead of print].

Large skeleton specimens are often featured as iconic open displays in Natural History Museums for example the blue whale 'Hope' at the Natural History Museum London. A study on Hope's bone surface was performed to assess the biodeterioration potential of fungi. Fungi were isolated, and a fungal ITS clone library survey was performed on dust and bone material. Mineral particles derived from bone and dust were analysed using energy dispersion spectroscopy (EDS), variable pressure scanning electron microscope (SEM) and High Vacuum SEM. Results showed that bone material, although mainly mineral in nature, and therefore less susceptible than organic materials to biodeterioration phenomena in the indoor environments, offers niches for specialised fungi and is affected by unusual and yet not so well documented mechanisms of alteration. Areas of bone surface were covered with a dense biofilm mostly composed of fungal hyphae, which produced tunnelling and extensive deposition of calcium and iron-containing secondary minerals. Airborne halophilic and xerophilic fungi including taxa grouping into Ascomycota and Basidiomycota, capable of displacing salts and overcome little water availability, were found to dominate the microbiome of the bone surface. This article is protected by copyright. All rights reserved.

RevDate: 2019-10-10

Kannt A, Papada E, Kammermeier C, et al (2019)

Mastiha (Pistacia Lentiscus) Improves Gut Microbiota Diversity, Hepatic Steatosis and Disease Activity in a Biopsy-Confirmed Mouse Model of Advanced Non-Alcoholic Steatohepatitis and Fibrosis.

Molecular nutrition & food research [Epub ahead of print].

SCOPE: As a result of the obesity epidemic, the prevalence of non-alcoholic steatohepatitis (NASH) is increasing. No drug is approved for the treatment of NASH. We have investigated the effect of a nutritional supplement, Mastiha or Chios mastic gum, on metabolic and histological parameters and on the gut microbiome in mice with NASH and fibrosis.

METHODS AND RESULTS: Advanced NASH was induced by feeding C57BL/6J mice a diet rich in fat, sucrose and cholesterol for 41 weeks. After randomization, animals received the NASH-inducing diet with or without 0.2% (w/w) Mastiha for a further eight weeks. Disease activity was assessed by liver histology and determination of plasma transaminase activities. Fecal microbiota DNA extraction and 16S rRNA amplicon sequencing were used to determine the composition of the gut microbiome. Mastiha supplementation led to a significant reduction in circulating alanine aminotransferase (ALT) activity, improvement in hepatic steatosis and collagen content and a reduction in NAFLD activity score. Furthermore, it resulted in a partial but significant recovery of gut microbiota diversity and changes in identity and abundance of specific taxa.

CONCLUSION: This is the first study demonstrating an improvement in disease activity in mice with advanced NASH with fibrosis by a diet containing Mastiha. This article is protected by copyright. All rights reserved.

RevDate: 2019-10-10

Ettamimi S, Carlier JD, Cox CJ, et al (2019)

A meta-taxonomic investigation of the prokaryotic diversity of water bodies impacted by acid mine drainage from the São Domingos mine in southern Portugal.

Extremophiles : life under extreme conditions pii:10.1007/s00792-019-01136-1 [Epub ahead of print].

The prokaryotic communities of water bodies contaminated by acid mine drainage from the São Domingos mining area in southern Portugal were analyzed using a meta-taxonomics approach with 16S rRNA gene sequences. Samples were collected in two seasonal sampling campaigns (summer and winter of 2017) from the most contaminated sites from where the water flows downstream to the freshwater reservoir of the river Chança. The physicochemical data indicate a trend of decreasing acid mine drainage contamination downstream of the mining area to the Chança's reservoir. The most contaminated sites (pH = 2.3-3.1) are distinguished by prokaryotic diversity with high abundances of operational taxonomics units related to acidophiles (genera Metallibacterium, Acidibacter, Leptospirillum, Acidobacterium, Thiomonas, Acidicapsa, Acidocella, Acidiphilium; family Acidobacteriaceae, order CPla-3 termite group). Likewise, in the transition zone in the mouth of the contaminated water flow into the Chança´s reservoir (pH = 6.4), a specific prokaryotic flora exists with some acidophiles, but notably with a cyanobacteria bloom and a high abundance of the genus Sediminibacterium (family I; order Subsection III). Moreover, the strong correlation between the abundance of acidophiles and characteristic physiochemical parameters (metals, acidity, and sulfate) confirm their potential as biomarkers of acid mine drainage pollution.

RevDate: 2019-10-10

Brunel C, Beifen Y, Pouteau R, et al (2019)

Responses of Rhizospheric Microbial Communities of Native and Alien Plant Species to Cuscuta Parasitism.

Microbial ecology pii:10.1007/s00248-019-01438-z [Epub ahead of print].

Parasitic plants have major impacts on host fitness. In the case of species of the holoparasitic Cuscuta genus, these impacts were shown to be particularly strong in some invasive alien plants, which has raised interest in the underlying mechanism. We hypothesized that Cuscuta parasitization may exert strong influence in shaping the diversity patterns in the host rhizosphere microbiome and that this may vary between native (coevolved) and alien (non-coevolved) plants. Here, we report on a field study exploring the effect of parasitization by Cuscuta australis on the rhizosphere microbiota (16S and ITS rDNA) of four plant species sharing and three plant species not sharing the parasite's native range. Despite a predominant role of the host species in shaping the rhizosphere microbiota, the role of host origin and of parasitization still appeared important in structuring microbial communities and their associated functions. Bacterial communities were more strongly influenced than fungi by the native range of the host plant, while fungi were slightly more affected than bacteria by parasitization. About 7% of bacterial phylotypes and 11% of fungal phylotypes were sensitive to Cuscuta parasitization. Parasitization also reduced the abundance of arbuscular mycorrhizal fungi by ca. 18% and of several genes related to plant growth promoting functions (e.g., nitrogen metabolism and quorum sensing). Both fungi and bacteria differentially responded to host parasitization depending on host origin, and the extent of these shifts suggests that they may have more dramatic consequences for alien than for native plants.

RevDate: 2019-10-10

Huang D, Su X, Yuan M, et al (2019)

The characterization of lung microbiome in lung cancer patients with different clinicopathology.

American journal of cancer research, 9(9):2047-2063.

There were few knowledge concerned correlation between lung microbiome and different clinicopathology of lung cancer. Bronchial washing fluid (BWF) and sputum are commonly used sample types but there was no study comparing difference of microbiome between these two in lung cancer. In this study, we aimed to compare difference of microbiome between these two sample types and characterize lung microbiome in squamous cell lung carcinoma with (SCC_M1) or without distant metastasis (SCC_M0) and lung adenocarcinoma with (AD_M1) or without distant metastasis (AD_M0). We collected 40 BWF samples and 52 sputum samples from newly diagnosed lung cancer patients. Bacterial species were sequenced via 16S rRNA sequencing. Phylum Proteobacteria in BWF samples were significantly higher than sputum samples (Wilcoxon test, P = 0.003). At phylum level, microbiome of BWF samples was more similar to that of lung cancer tissues reported in the previous literature. LEFse analysis showed that in BWF group, genera Veillonell, Megasphaera, Actinomyces and Arthrobacter in AD_M0 were significantly higher than those in SCC_M0, and genera Capnocytophaga and Rothia in AD_M1 were significantly lower than that in SCC_M1. Compared with AD_M0, genus Streptococcus of AD_M1 was significantly lower, and genera Veillonella and Rothia in SCC_M1 were significantly higher than that in SCC_M1. Our study suggested that BWF samples might better reflect the microbiome of lung cancer tissues. In different metastatic states of lung cancer, differential genera between squamous cell carcinoma and adenocarcinoma were different. And in different histologic types of lung cancer, distant metastasis-related genera were not the same.

RevDate: 2019-10-10

Figueroa-Romero C, Guo K, Murdock BJ, et al (2019)

Temporal evolution of the microbiome, immune system, and epigenome with disease progression in ALS mice.

Disease models & mechanisms pii:dmm.041947 [Epub ahead of print].

Amyotrophic lateral sclerosis (ALS) is a terminal neurodegenerative disease. Genetic predisposition, epigenetic changes, aging, and accumulated life-long environmental exposures are known ALS risk factors. The complex and dynamic interplay between these pathological influences play a role in disease onset and progression. Recently, the gut microbiome has also been implicated in ALS development. Additionally, immune cell populations are differentially expanded and activated in ALS compared to healthy individuals. However, the temporal evolution of both the intestinal flora and the immune system relative to symptom onset in ALS is presently not fully understood. To better elucidate the timeline of the various potential pathological factors, we performed a longitudinal study to simultaneously assess the gut microbiome, immunophenotype, and changes in ileum and brain epigenetic marks relative to motor behavior and muscle atrophy in the mutant superoxide dismutase 1 (SOD1G93A) familial ALS mouse model. We identified alterations in the gut microbial environment early in the life of SOD1G93A animals followed by motor dysfunction and muscle atrophy, and immune cell expansion and activation, particularly in the spinal cord. Global brain cytosine hydroxymethylation was also altered in SOD1G93A animals at disease end-stage compared to control mice. Correlation analysis confirmed interrelationships with the microbiome and immune system. This study serves as a starting point to more deeply comprehend the influence of gut microorganisms and the immune system on ALS onset and progression. Greater insight may help pinpoint novel biomarkers and therapeutic interventions to improve diagnosis and treatment for ALS patients.

RevDate: 2019-10-10

Shaikh FY, Gills JJ, CL Sears (2019)

Impact of the microbiome on checkpoint inhibitor treatment in patients with non-small cell lung cancer and melanoma.

EBioMedicine pii:S2352-3964(19)30598-5 [Epub ahead of print].

The microbiome is increasingly recognized for its role in multiple aspects of cancer development and treatment, specifically in response to checkpoint inhibitors. While checkpoint inhibitors have revolutionized cancer treatment by producing durable anti-tumor responses, only a minority of patients respond to the available immunotherapy drugs and accurate, sensitive and specific microbiome predictors of response to treatment remain elusive. Additionally, the specific mechanisms linking the microbiome and host immunological responses remain unclear. In this review, we examine the evidence for the gut microbiome's association with anti-tumor responses to checkpoint inhibitors in the treatment of melanoma, non-small cell lung cancer, and renal cell carcinoma. Furthermore, we discuss the current evidence available from murine models seeking to explain the immunological mechanisms that may drive this process. While this work is promising in defining the impact of gut microbiota in cancer treatment, many unanswered questions indicate the need for additional human and experimental studies.

RevDate: 2019-10-10

Peters BA, Wilson M, Moran U, et al (2019)

Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients.

Genome medicine, 11(1):61 pii:10.1186/s13073-019-0672-4.

BACKGROUND: Recent evidence suggests that immunotherapy efficacy in melanoma is modulated by gut microbiota. Few studies have examined this phenomenon in humans, and none have incorporated metatranscriptomics, important for determining expression of metagenomic functions in the microbial community.

METHODS: In melanoma patients undergoing immunotherapy, gut microbiome was characterized in pre-treatment stool using 16S rRNA gene and shotgun metagenome sequencing (n = 27). Transcriptional expression of metagenomic pathways was confirmed with metatranscriptome sequencing in a subset of 17. We examined associations of taxa and metagenomic pathways with progression-free survival (PFS) using 500 × 10-fold cross-validated elastic-net penalized Cox regression.

RESULTS: Higher microbial community richness was associated with longer PFS in 16S and shotgun data (p < 0.05). Clustering based on overall microbiome composition divided patients into three groups with differing PFS; the low-risk group had 99% lower risk of progression than the high-risk group at any time during follow-up (p = 0.002). Among the species selected in regression, abundance of Bacteroides ovatus, Bacteroides dorei, Bacteroides massiliensis, Ruminococcus gnavus, and Blautia producta were related to shorter PFS, and Faecalibacterium prausnitzii, Coprococcus eutactus, Prevotella stercorea, Streptococcus sanguinis, Streptococcus anginosus, and Lachnospiraceae bacterium 3 1 46FAA to longer PFS. Metagenomic functions related to PFS that had correlated metatranscriptomic expression included risk-associated pathways of L-rhamnose degradation, guanosine nucleotide biosynthesis, and B vitamin biosynthesis.

CONCLUSIONS: This work adds to the growing evidence that gut microbiota are related to immunotherapy outcomes, and identifies, for the first time, transcriptionally expressed metagenomic pathways related to PFS. Further research is warranted on microbial therapeutic targets to improve immunotherapy outcomes.

RevDate: 2019-10-10

Dreisbach C, Prescott S, J Alhusen (2019)

Influence of Maternal Prepregnancy Obesity and Excessive Gestational Weight Gain on Maternal and Child Gastrointestinal Microbiome Composition: A Systematic Review.

Biological research for nursing [Epub ahead of print].

BACKGROUND: Maternal obesity is a well-known risk factor for significant obstetric and neonatal complications. The influence of the gastrointestinal microbiome in the setting of maternal obesity during pregnancy is less understood. The purpose of this systematic review is to synthesize the literature on the relationships between maternal obesity and excessive gestational weight gain (EGWG) and the composition of maternal and child gastrointestinal microbiomes.

METHOD: We searched CINHAL, OVID Medline, Web of Science, and PubMed for relevant literature using medical subject heading terms related to obesity, pregnancy, and the gastrointestinal microbiome. We assessed 249 articles for potential inclusion using the preferred reporting items for systematic review and meta-analyses framework and deemed 11 articles as relevant for this review.

RESULTS: Maternal obesity was associated with significant microbial changes in both maternal and infant fecal microbiome biospecimens including increases in Bacteroidetes, Firmicutes, and the Actinobacteria phyla and decreases in Bifidobacteria. However, inconsistencies in uniform taxonomic results across all studies mean that evidence of specific microbial associations with obesity and EGWG is inconclusive.

CONCLUSION: Our findings suggest that both maternal and child gastrointestinal microbiome composition is altered in the setting of maternal obesity and EGWG during pregnancy. Future microbiome studies should concentrate on the investigation of metagenomic sequencing to elucidate microbial function rather than solely taxonomic composition. More diverse populations of mothers should be sampled to address health disparities and adverse outcomes of underrepresented populations. Finally, analytic pipelines should be standardized across studies to aid in reproducibility.

RevDate: 2019-10-10

Rodriguez A, Trigatti BL, Mineo C, et al (2019)

Proceedings of the Ninth HDL (High-Density Lipoprotein) Workshop: Focus on Cardiovascular Disease.

Arteriosclerosis, thrombosis, and vascular biology [Epub ahead of print].

The HDL (high-density lipoprotein) Workshop was established in 2009 as a forum for candid discussions among academic basic scientists, clinical investigators, and industry researchers about the role of HDL in cardiovascular disease. This ninth HDL Workshop was held on May 16 to 17, 2019 in Boston, MA, and included outstanding oral presentations from established and emerging investigators. The Workshop featured 5 sessions with topics that tackled the role of HDL in the vasculature, its structural complexity, its role in health and disease states, and its interaction with the intestinal microbiome. The highlight of the program was awarding the Jack Oram Award to the distinguished professor emeritus G.S. Getz from the University of Chicago. The tenth HDL Workshop will be held on May 2020 in Chicago and will continue the focus on intellectually stimulating presentations by established and emerging investigators on novel roles of HDL in cardiovascular and noncardiovascular health and disease states.

RevDate: 2019-10-10

Bransfield RC, KJ Friedman (2019)

Differentiating Psychosomatic, Somatopsychic, Multisystem Illnesses, and Medical Uncertainty.

Healthcare (Basel, Switzerland), 7(4): pii:healthcare7040114.

There is often difficulty differentiating between psychosomatic, somatopsychic, multisystem illness, and different degrees of medical uncertainty. Uncommon, complex, and multisystem diseases are commonly misdiagnosed. Two case histories are described, and relevant terms differentiating psychosomatic, somatopsychic, and multisystem illnesses are identified, reviewed, and discussed. Adequate differentiation requires an understanding of the mind/body connection, which includes knowledge of general medicine, psychiatry, and the systems linking the body and the brain. A psychiatric diagnosis cannot be given solely based upon the absence of physical, laboratory, or pathological findings. Medically unexplained symptoms, somatoform disorder, and compensation neurosis are outdated and/or inaccurate terms. The terms subjective, nonspecific, and vague can be used inaccurately. Conversion disorders, functional disorders, psychogenic illness, factitious disorder imposed upon another (Munchausen's syndrome by proxy), somatic symptom disorder, psychogenic seizures, psychogenic pain, psychogenic fatigue, and delusional parasitosis can be over-diagnosed. Bodily distress disorder and bodily distress syndrome are scientifically unsupported and inaccurate. Many "all in your head" conditions may be related to the microbiome and the immune system. Better education concerning the interface between medicine and psychiatry and the associated diagnostic nomenclature as well as utilizing clinical judgment and thorough assessment, exercising humility, and maintaining our roots in traditional medicine will help to improve diagnostic accuracy and patient trust.

RevDate: 2019-10-09

Berman HL, McLaren MR, BJ Callahan (2019)

Understanding and Interpreting Community Sequencing Measurements of the Vaginal Microbiome.

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

Community-wide high throughput sequencing has transformed the study of the vaginal microbiome, and clinical applications are on the horizon. Here we outline the three main community sequencing methods: 1) amplicon sequencing, 2) shotgun metagenomic sequencing, and 3) metatranscriptomic sequencing. We discuss the advantages and limitations of community sequencing generally and the unique strengths and weaknesses of each method. We briefly review the contributions of community sequencing to vaginal microbiome research and practice. We develop suggestions for critically interpreting research results and potential clinical applications based on community sequencing of the vaginal microbiome.

RevDate: 2019-10-09

Duc D, Vigne S, Bernier-Latmani J, et al (2019)

Disrupting Myelin-Specific Th17 Cell Gut Homing Confers Protection in an Adoptive Transfer Experimental Autoimmune Encephalomyelitis.

Cell reports, 29(2):378-390.e4.

Multiple sclerosis (MS) is a common autoimmune disease of the CNS. Although an association between MS and inflammatory bowel diseases is observed, the link connecting intestinal immune responses and neuroinflammation remains unclear. Here we show that encephalitogenic Th17 cells infiltrate the colonic lamina propria before neurological symptom development in two murine MS models, active and adoptive transfer experimental autoimmune encephalomyelitis (EAE). Specifically targeting Th17 cell intestinal homing by blocking the α4β7-integrin and its ligand MAdCAM-1 pathway impairs T cell migration to the large intestine and dampens EAE severity in the Th17 cell adoptive transfer model. Mechanistically, myelin-specific Th17 cells proliferate in the colon and affect gut microbiota composition. The beneficial effect of blocking the α4β7-integrin and its ligand MAdCAM-1 pathway on EAE is interdependent with gut microbiota. Those results show that disrupting myelin-specific Th17 cell trafficking to the large intestine harnesses neuroinflammation and suggests that the gut environment and microbiota catalyze the encephalitogenic properties of Th17 cells.

RevDate: 2019-10-09

Bertucci Zoccali M, Hyman NH, Skowron KB, et al (2019)

Exposure to Anti-tumor Necrosis Factor Medications Increases the Incidence of Pouchitis After Restorative Proctocolectomy in Patients With Ulcerative Colitis.

Diseases of the colon and rectum, 62(11):1344-1351.

BACKGROUND: Pouchitis is the most frequent complication after IPAA in patients with ulcerative colitis. Antibiotics represent the mainstay of treatment, suggesting a crucial role of dysbiosis in the pathogenesis of this condition. Anti-tumor necrosis factor agents have been shown to adversely impact the gut microbiome and local host immunity.

OBJECTIVE: The aim of this study is to assess the effect of prior exposure to biologics on the development of pouchitis in patients who have ulcerative colitis.

DESIGN: This is a retrospective case-control study.

SETTINGS: This study was conducted at a tertiary-care IBD center.

PATIENTS: Consecutive patients with ulcerative colitis who underwent restorative proctocolectomy between 2000 and 2010 were included.

MAIN OUTCOME MEASURES: The primary outcome measured was the incidence of pouchitis.

RESULTS: Four hundred seventeen patients with ulcerative colitis who underwent IPAA were included. The incidence of pouchitis was 40.4%. There were no differences in patient demographics, disease-specific factors, surgical approach, and short-term postoperative complications between patients who developed pouchitis compared to those that did not. Patients exposed to anti-tumor necrosis factor agents or preoperative steroids were significantly more likely to develop pouchitis (anti-tumor necrosis factor: 47.9% vs 36.5%, p = 0.027; steroids: 41.7% vs 23.3%, p = 0.048). However, on multivariable analysis, only anti-tumor necrosis factor therapy was an independent predictor for pouchitis (p = 0.05). Pouchitis was not associated with adverse long-term outcomes.

LIMITATIONS: The retrospective design was a limitation of this study.

CONCLUSION: In a large cohort of patients undergoing IPAA for ulcerative colitis with at least a 5-year follow-up, anti-tumor necrosis factor exposure was the only independent risk factor for the development of pouchitis. These agents may "precondition" the pouch to develop pouchitis through alterations in the microbiome and/or local host immunity of the terminal ileum. See Video Abstract at http://links.lww.com/DCR/B19. LA EXPOSICIÓN A MEDICAMENTOS ANTI-TNF AUMENTA LA INCIDENCIA DE POUCHITIS DESPUÉS DE LA PROCTOCOLECTOMÍA RESTAURADORA EN PACIENTES CON COLITIS ULCEROSA:: La pouchitis es la complicación más frecuente después de la anastomosis anal de bolsa ileal en pacientes con colitis ulcerosa. Los antibióticos representan el pilar del tratamiento, lo que sugiere un papel crucial de la disbiosis en la patogénesis de esta afección. Se ha demostrado que los agentes anti-TNF tienen un impacto adverso en la microbiota intestinal y en la inmunidad local del huésped.El objetivo de este estudio es evaluar el efecto de la exposición previa a terapía biológica sobre el desarrollo de la pouchitis en pacientes con colitis ulcerosa.Estudio retrospectivo de casos y controles.Centro de tercer nivel de atención en enfermedades inflamatorias intestinales.Pacientes consecutivos con colitis ulcerosa que se sometieron a proctocolectomía restaurativa entre 2000-2010.Incidencia de pouchitis.Cuatrocientos diecisiete pacientes con colitis ulcerativa se sometieron a anastomosis anal de bolsa ileal. La incidencia de pouchitis fue del 40.4%. No hubo diferencias en la demografía del paciente, los factores específicos de la enfermedad, el abordaje quirúrgico y las complicaciones postoperatorias a corto plazo entre los pacientes que desarrollaron pouchitis en comparación con los que no lo hicieron. Los pacientes expuestos a agentes anti-TNF o esteroides preoperatorios fueron significativamente más propensos a desarrollar pouchitis (anti-TNF: 47.9% vs 36.5%, p = 0.027; esteroides: 41.7% vs 23.3%, p = 0.048). Sin embargo, en el análisis multivariable, solo la terapia anti-TNF fue un predictor independiente para la pouchitis (p = 0.05). La pouchitis no se asoció con resultados adversos a largo plazo.Diseño retrospectivo.En una gran cohorte de pacientes sometidos a anastomosis anal de bolsa ileal para la colitis ulcerosa con al menos 5 años de seguimiento, la exposición a terapía anti-TNF fue el único factor de riesgo independiente para el desarrollo de pouchitis. Estos agentes pueden "precondicionar" la bolsa para desarrollar una pouchitis a través de alteraciones en el microbioma y / o inmunidad local del huésped del íleon terminal. Vea el Resumen del video en http://links.lww.com/DCR/B19.

RevDate: 2019-10-09

Liebert A, Bicknell B, Johnstone DM, et al (2019)

"Photobiomics": Can Light, Including Photobiomodulation, Alter the Microbiome?.

Photobiomodulation, photomedicine, and laser surgery [Epub ahead of print].

Objective: The objective of this review is to consider the dual effects of microbiome and photobiomodulation (PBM) on human health and to suggest a relationship between these two as a novel mechanism. Background: PBM describes the use of low levels of visible or near-infrared (NIR) light to heal and stimulate tissue, and to relieve pain and inflammation. In recent years, PBM has been applied to the head as an investigative approach to treat diverse brain diseases such as stroke, traumatic brain injury (TBI), Alzheimer's and Parkinson's diseases, and psychiatric disorders. Also, in recent years, increasing attention has been paid to the total microbial population that colonizes the human body, chiefly in the gut and the mouth, called the microbiome. It is known that the composition and health of the gut microbiome affects many diseases related to metabolism, obesity, cardiovascular disorders, autoimmunity, and even brain disorders. Materials and methods: A literature search was conducted for published reports on the effect of light on the microbiome. Results: Recent work by our research group has demonstrated that PBM (red and NIR light) delivered to the abdomen in mice, can alter the gut microbiome in a potentially beneficial way. This has also now been demonstrated in human subjects. Conclusions: In consideration of the known effects of PBM on metabolomics, and the now demonstrated effects of PBM on the microbiome, as well as other effects of light on the microbiome, including modulating circadian rhythms, the present perspective introduces a new term "photobiomics" and looks forward to the application of PBM to influence the microbiome in humans. Some mechanisms by which this phenomenon might occur are considered.

RevDate: 2019-10-09

Peng Q, Chang H, Wang R, et al (2019)

Potassium sorbate suppresses intestinal microbial activity and triggers immune regulation in zebrafish (Danio rerio).

Food & function [Epub ahead of print].

Potassium sorbate (PS) is a class of bacteriostatic antiseptic agent widely used in the food industry; the effects of its intake on host health are currently unclear. In the present study, zebrafish (Danio rerio) were exposed to 0.1 g L-1 and 1 g L-1 aqueous solutions of PS for 2 weeks to investigate the impact of PS on the microecological balance of the intestinal microbiota and immune system. PS exposure triggered immune regulation of zebrafish, significantly reducing the content of diverse biomarkers in the gut, including Immunoglobulin G (IgG), interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α). Based on high-throughput sequencing data, it was observed that PS exposure resulted in some destabilization of the microbiome composition of the zebrafish, which mainly manifested as a reduction in the abundance of specific genera and the relative levels of transcription and carbohydrate metabolism related to microbial reproductive ability and activity. These changes were consistent with the activity index of microbiota (AIM), a novel measure that we constructed. Collectively, these results illustrate that PS can affect the immune system of zebrafish by changing the composition and function of the gut microbiota, and inhibiting the metabolism of the intestinal microbiota. Our study offers a new understanding of the toxicity of PS.

RevDate: 2019-10-09

Kaufman JH, Elkins CA, Davis M, et al (2019)

Insular Microbiogeography: Three Pathogens as Exemplars.

Current issues in molecular biology, 36:89-108 pii:v36/89 [Epub ahead of print].

Traditional taxonomy in biology assumes that life is organized in a simple tree. Attempts to classify microorganisms in this way in the genomics era led microbiologists to look for finite sets of 'core' genes that uniquely group taxa as clades in the tree. However, the diversity revealed by large-scale whole genome sequencing is calling into question the long-held model of a hierarchical tree of life, which leads to questioning of the definition of a species. Large-scale studies of microbial genome diversity reveal that the cumulative number of new genes discovered increases with the number of genomes studied as a power law and subsequently leads to the lack of evidence for a unique core genome within closely related organisms. Sampling 'enough' new genomes leads to the discovery of a replacement or alternative to any gene. This power law behaviour points to an underlying self-organizing critical process that may be guided by mutation and niche selection. Microbes in any particular niche exist within a local web of organism interdependence known as the microbiome. The same mechanism that underpins the macro-ecological scaling first observed by MacArthur and Wilson also applies to microbial communities. Recent metagenomic studies of a food microbiome demonstrate the diverse distribution of community members, but also genotypes for a single species within a more complex community. Collectively, these results suggest that traditional taxonomic classification of bacteria could be replaced with a quasispecies model. This model is commonly accepted in virology and better describes the diversity and dynamic exchange of genes that also hold true for bacteria. This model will enable microbiologists to conduct population-scale studies to describe microbial behaviour, as opposed to a single isolate as a representative.

RevDate: 2019-10-09

Mashaqi S, D Gozal (2019)

Obstructive Sleep Apnea and Systemic Hypertension: Gut Dysbiosis as the Mediator?.

Journal of clinical sleep medicine : JCSM : official publication of the American Academy of Sleep Medicine, 15(10):1517-1527.

INTRODUCTION: Obstructive sleep apnea (OSA) and systemic hypertension (SH) are common and interrelated diseases. It is estimated that approximately 75% of treatment-resistant hypertension cases have an underlying OSA. Exploration of the gut microbiome is a new advance in medicine that has been linked to many comorbid illnesses, including SH and OSA. Here, we will review the literature in SH and gut dysbiosis, OSA and gut dysbiosis, and whether gut dysbiosis is common in both conditions.

METHODS: We reviewed the National Center for Biotechnology Information database, including PubMed and PubMed Central. We identified a total of 230 articles. The literature search was conducted using the phrase "obstructive sleep apnea and gut dysbiosis." Only original research articles were included. This yielded a total of 12 articles.

RESULTS: Most of the research conducted in this field was on animal models, and almost all trials confirmed that intermittent hypoxia models resulted in gut dysbiosis. Gut dysbiosis, however, can cause a state of low-grade inflammation through damage to the gut wall barrier resulting in "leaky gut." Neuroinflammation is a hallmark of the pathophysiology of OSA-induced SH.

CONCLUSIONS: Gut dysbiosis seems to be an important factor in the pathophysiology of OSA-induced hypertension. Reversing gut dysbiosis at an early stage through prebiotics and probiotics and fecal microbiota transplantation combined with positive airway pressure therapy may open new horizons of treatment to prevent SH. More studies are needed in humans to elicit the effect of positive airway pressure therapy on gut dysbiosis.

RevDate: 2019-10-09

Yanagawa Y, Arisaka T, Kawai S, et al (2019)

Case Report: Acute Amebic Colitis Triggered by Colonoscopy: Exacerbation of Asymptomatic Chronic Infection with Entamoeba histolytica Accompanied by Dysbiosis.

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

Recent data show that the gut microbiome plays a role in determining the clinical outcome of Entamoeba histolytica infection. We report the case of a patient who developed recurrent acute amebic colitis (second episode of acute colitis) after colonoscopy. Genotyping of E. histolytica revealed that she developed a second episode of acute amebic colitis with the same genotype as that of the first episode, indicating chronic infection had persisted asymptomatically for > 10 months between the first and second episodes. Analysis of the gut microbiome, in addition to the clinical findings, suggested that dysbiosis at colonoscopy induced the change in the clinical form of E. histolytica infection from asymptomatic chronic infection to symptomatic colitis.

RevDate: 2019-10-09

Winston JA, CM Theriot (2019)

Diversification of host bile acids by members of the gut microbiota.

Gut microbes [Epub ahead of print].

Bile acid biotransformation is a collaborative effort by the host and the gut microbiome. Host hepatocytes synthesize primary bile acids from cholesterol. Once these host-derived primary bile acids enter the gastrointestinal tract, the gut microbiota chemically modify them into secondary bile acids. Interest into the gut-bile acid-host axis is expanding in diverse fields including gastroenterology, endocrinology, oncology, and infectious disease. This review aims to 1) describe the physiologic aspects of collaborative bile acid metabolism by the host and gut microbiota; 2) to evaluate how gut microbes influence bile acid pools, and in turn how bile acid pools modulate the gut microbial community structure; 3) to compare species differences in bile acid pools; and lastly, 4) discuss the effects of ursodeoxycholic acid (UDCA) administration, a common therapeutic bile acid, on the gut microbiota-bile acid-host axis.

RevDate: 2019-10-09

Silva CJN, Eremina YO, Rodrigues S, et al (2018)

Detection of Fusobacterium spp in colorectal tissue samples using reverse transcription polymerase chain reaction with minor groove binder probes: an exploratory research.

Porto biomedical journal, 3(3):e22 pii:PBJ-D-18-00033.

An unhealthy microbiome is intimately correlated with several disease states, including colorectal cancer, wherein bacteria might be the key to neoplastic initiation and progression. Recent studies revealed an enrichment of Fusobacterium in colorectal tumor tissues relative to surrounding normal mucosa. Given the available evidence, we conducted an exploratory study quantifying the relative expression of Fusobacterium spp in 28 tissue samples from patients treated at Centro Hospitalar de São João belonging to 4 different groups: adenomas, paired normal tissue from patients with adenomas, carcinomas, and paired normal tissue from patients with colorectal carcinomas. To increase reverse transcription polymerase chain reaction quantification sensitivity, minor groove binders fluorescent probes were used, having in mind its implementation into routine clinical practice. Differences of Fusobacterium spp relative abundance between paired neoplastic lesions/normal tissue were examined by Wilcoxon signed-rank test and for all the other 2-group comparisons the Mann-Whitney U test was used. Most of the adenomas studied belonged to clinical specimens showing either tubular or villous low-grade dysplasia and an enrichment of Fusobacterium relative to paired normal tissue was not found (P = .180). In the carcinoma group, 57% of samples displayed a positive status for this bacterium with the highest burden of detectable Fusobacterium belonging to a specimen with positive regional lymph node metastasis. This is the first Portuguese study confirming a trend toward an overabundance of Fusobacterium in colorectal carcinomas compared to adenomas and paired samples of normal-looking mucosa, in keeping with the role of this bacterium in colorectal carcinogenesis. Further studies are needed to elucidate the relevance of Fusobacterium detection for the prevention and treatment of colorectal cancer.

RevDate: 2019-10-09

Wepking C, Badgley B, Barrett JE, et al (2019)

Prolonged exposure to manure from livestock-administered antibiotics decreases ecosystem carbon-use efficiency and alters nitrogen cycling.

Microbial communities drive soil ecosystem function but are also susceptible to environmental disturbances. We investigated whether exposure to manure sourced from cattle either administered or not administered antibiotics affected microbially mediated terrestrial ecosystem function. We quantified changes in microbial community composition via amplicon sequencing, and terrestrial elemental cycling via a stable isotope pulse-chase. Exposure to manure from antibiotic-treated cattle caused: (i) changes in microbial community structure; and (ii) alterations in elemental cycling throughout the terrestrial system. This exposure caused changes in fungal : bacterial ratios, as well as changes in bacterial community structure. Additionally, exposure to manure from cattle treated with pirlimycin resulted in an approximate two-fold increase in ecosystem respiration of recently fixed-carbon, and a greater proportion of recently added nitrogen in plant and soil pools compared to the control manure. Manure from antibiotic-treated cattle therefore affects terrestrial ecosystem function via the soil microbiome, causing decreased ecosystem carbon use efficiency, and altered nitrogen cycling.

RevDate: 2019-10-09

Strazzulli A, Cobucci-Ponzano B, Iacono R, et al (2019)

Discovery of hyperstable carbohydrate-active enzymes through metagenomics of extreme environments.

The FEBS journal [Epub ahead of print].

The enzymes from hyperthermophilic microorganisms populating volcanic sites represent interesting cases of protein adaptation and biotransformations under conditions where conventional enzymes quickly denature. The difficulties in cultivating extremophiles severely limit access to this class of biocatalysts. To circumvent this problem, we embarked on the exploration of the biodiversity of the solfatara Pisciarelli, Agnano (Naples, Italy) to discover hyperthermophilic carbohydrate-active enzymes (CAZymes) and to characterize the entire set of such enzymes in this environment (CAZome). Here we report the results of the metagenomic analysis of two mud/water pools that greatly differ in both temperature and pH (T=85°C and pH 5.5; T=92°C and pH 1.5, for Pool1 and Pool2, respectively). DNA deep sequencing and following in-silico analysis led to 14,934 and 17,652 complete ORFs in Pool1 and Pool2, respectively. They exclusively belonged to archaeal cells and viruses with great genera variance within the phylum Crenarcheaota, which reflected the difference in temperature and pH of the two Pools. Surprisingly, 30% and 62% of all of the reads obtained from Pool1 and 2, respectively, had no match in nucleotide databanks. Genes associated with carbohydrate metabolism were 15% and 16% of the total in the two Pools, with 278 and 308 putative CAZymes in Pool1 and 2, corresponding to ~2.0% of all ORFs. Biochemical characterization of two CAZymes of a previously unknown archaeon revealed a novel subfamily GH5_19 β-mannanase/β-1,3-glucanase whose hemicellulose specificity correlates with the vegetation surrounding the sampling site, and a novel NAD+ dependent GH109 with a previously unreported β-N-acetylglucosaminide/β-glucoside specificity.

RevDate: 2019-10-09

Li AL, Ni WW, Zhang QM, et al (2019)

Effect of cinnamon essential oil on gut microbiota in the mouse model of dextran sulfate sodium-induced colitis.

Microbiology and immunology [Epub ahead of print].

Increasing evidence has confirmed that the antimicrobial and anti-inflammatory effects of cinnamon essential oil (CEO) contribute to protecting against inflammatory bowel disease (IBD). The dextran sodium sulfate (DSS)-induced colitis mice model was established to investigate the correlation between the protective effects of CEO and the regulation of intestinal microflora. IBD symptoms were assessed by measuring hemoglobin content, myeloperoxidase activity, histopathological observation, cytokines and TLR4 expression. The alteration of fecal microbiome composition was analyzed by 16S rRNA gene sequencing. Results indicated that oral administration of CEO enriched with cinnamaldehyde effectively alleviated the development of DSS-induced colitis. In contrast to the inability of antibiotics to regulate flora imbalance, the mice fed with CEO improved the diversity and richness of intestinal microbiota, and modified the community composition with a decrease in Helicobacter and Bacteroides and an increase in Bacteroidales_S24-7 family and SCFA-producing bacteria (Alloprevotella and Lachnospiraceae_NK4A136_group). Moreover, correlation analysis showed TLR4 and TNF-α was positively correlated with Helicobacter, but inversely correlated with SCFA-producing bacteria. These findings indicated from a new perspective that the inhibitory effect of CEO on IBD was closely related to improving the intestinal flora imbalance. This article is protected by copyright. All rights reserved.

RevDate: 2019-10-09

Liu F, Li J, Guan Y, et al (2019)

Dysbiosis of the Gut Microbiome is associated with Tumor Biomarkers in Lung Cancer.

International journal of biological sciences, 15(11):2381-2392 pii:ijbsv15p2381.

Lung cancer is a malignancy with high morbidity and mortality worldwide. More evidences indicated that gut microbiome plays an important role in the carcinogenesis and progression of cancers by metabolism, inflammation and immune response. However, the study about the characterizations of gut microbiome in lung cancer is limited. In this study, the fecal samples were collected from 16 healthy individuals and 30 lung cancer patients who were divided into 3 groups based on different tumor biomarkers (cytokeratin 19 fragment, neuron specific enolase and carcinoembryonic antigen, respectively) and were analyzed using 16S rRNA gene amplicon sequencing. Each lung cancer group has characterized gut microbial community and presents an elimination, low-density, and loss of bacterial diversity microbial ecosystem compared to that of the healthy control. The microbiome structures in family and genera levels are more complex and significantly varied from each group presenting more different and special pathogen microbiome such as Enterobacteriaceae, Streptococcus, Prevotella, etc and fewer probiotic genera including Blautia, Coprococcus, Bifidobacterium and Lachnospiraceae. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and COG annotation demonstrated decreased abundance of some dominant metabolism-related pathways in the lung cancer. This study explores for the first time the features of gut microbiome in lung cancer patients and may provide new insight into the pathogenesis of lung cancer system, with the implication that gut microbiota may serve as a microbial marker and contribute to the derived metabolites, development and differentiation in lung cancer system.

RevDate: 2019-10-09

Zhao H, Fu S, Yu Y, et al (2019)

MetaMed: Linking Microbiota Functions with Medicine Therapeutics.

mSystems, 4(5): pii:4/5/e00413-19.

Understanding how the human microbiome affects human health has consequences for treating disease and minimizing unwanted side effects in clinical research. Here, we present MetaMed (http://metamed.rwebox.com/index), a novel and integrative system-wide correlation mapping system to link bacterial functions and medicine therapeutics, providing novel hypotheses for deep investigation of microbe therapeutic effects on human health. Furthermore, comprehensive relationships between microbes living in the environment and drugs were discovered, providing a rich source for discovering microbiota metabolites with great potential for pharmaceutical applications.

RevDate: 2019-10-09

Sakowski E, Uritskiy G, Cooper R, et al (2019)

Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019.

mSystems, 4(5): pii:4/5/e00392-19.

Accurate predictions across multiple fields of microbiome research have far-reaching benefits to society, but there are few widely accepted quantitative tools to make accurate predictions about microbial communities and their functions. More discussion is needed about the current state of microbiome analysis and the tools required to overcome the hurdles preventing development and implementation of predictive analyses. We summarize the ideas generated by participants of the Mid-Atlantic Microbiome Meet-up in January 2019. While it was clear from the presentations that most fields have advanced beyond simple associative and descriptive analyses, most fields lack essential elements needed for the development and application of accurate microbiome predictions. Participants stressed the need for standardization, reproducibility, and accessibility of quantitative tools as key to advancing predictions in microbiome analysis. We highlight hurdles that participants identified and propose directions for future efforts that will advance the use of prediction in microbiome research.

RevDate: 2019-10-09

Thiergart T, Zgadzaj R, Bozsóki Z, et al (2019)

Lotus japonicus Symbiosis Genes Impact Microbial Interactions between Symbionts and Multikingdom Commensal Communities.

mBio, 10(5): pii:mBio.01833-19.

The wild legume Lotus japonicus engages in mutualistic symbiotic relationships with arbuscular mycorrhiza (AM) fungi and nitrogen-fixing rhizobia. Using plants grown in natural soil and community profiling of bacterial 16S rRNA genes and fungal internal transcribed spacers (ITSs), we examined the role of the Lotus symbiosis genes RAM1, NFR5, SYMRK, and CCaMK in structuring bacterial and fungal root-associated communities. We found host genotype-dependent community shifts in the root and rhizosphere compartments that were mainly confined to bacteria in nfr5 or fungi in ram1 mutants, while symrk and ccamk plants displayed major changes across both microbial kingdoms. We observed in all AM mutant roots an almost complete depletion of a large number of Glomeromycota taxa that was accompanied by a concomitant enrichment of Helotiales and Nectriaceae fungi, suggesting compensatory niche replacement within the fungal community. A subset of Glomeromycota whose colonization is strictly dependent on the common symbiosis pathway was retained in ram1 mutants, indicating that RAM1 is dispensable for intraradical colonization by some Glomeromycota fungi. However, intraradical colonization by bacteria belonging to the Burkholderiaceae and Anaeroplasmataceae is dependent on AM root infection, revealing a microbial interkingdom interaction. Despite the overall robustness of the bacterial root microbiota against major changes in the composition of root-associated fungal assemblages, bacterial and fungal cooccurrence network analysis demonstrates that simultaneous disruption of AM and rhizobium symbiosis increases the connectivity among taxa of the bacterial root microbiota. Our findings imply a broad role for Lotus symbiosis genes in structuring the root microbiota and identify unexpected microbial interkingdom interactions between root symbionts and commensal communities.IMPORTANCE Studies on symbiosis genes in plants typically focus on binary interactions between roots and soilborne nitrogen-fixing rhizobia or mycorrhizal fungi in laboratory environments. We utilized wild type and symbiosis mutants of a model legume, grown in natural soil, in which bacterial, fungal, or both symbioses are impaired to examine potential interactions between the symbionts and commensal microorganisms of the root microbiota when grown in natural soil. This revealed microbial interkingdom interactions between the root symbionts and fungal as well as bacterial commensal communities. Nevertheless, the bacterial root microbiota remains largely robust when fungal symbiosis is impaired. Our work implies a broad role for host symbiosis genes in structuring the root microbiota of legumes.

RevDate: 2019-10-09

Metcalf CJE, Henry LP, Rebolleda-Gómez M, et al (2019)

Why Evolve Reliance on the Microbiome for Timing of Ontogeny?.

mBio, 10(5): pii:mBio.01496-19.

The timing of life history events has important fitness consequences. Since the 1950s, researchers have combined first principles and data to predict the optimal timing of life history transitions. Recently, a striking mystery has emerged. Such transitions can be shaped by a completely different branch of the tree of life: species in the microbiome. Probing these interactions using testable predictions from evolutionary theory could illuminate whether and how host-microbiome integrated life histories can evolve and be maintained. Beyond advancing fundamental science, this research program could yield important applications. In an age of microbiome engineering, understanding the contexts that lead to microbiota signaling shaping ontogeny could offer novel mechanisms for manipulations to increase yield in agriculture by manipulating plant responses to stressful environments, or to reduce pathogen transmission by affecting vector efficiency. We combine theory and evidence to illuminate the essential questions underlying the existence of microbiome-dependent ontogenetic timing (MiDOT) to fuel research on this emerging topic.

RevDate: 2019-10-09

Conlan S, Lau AF, Deming C, et al (2019)

Plasmid Dissemination and Selection of a Multidrug-Resistant Klebsiella pneumoniae Strain during Transplant-Associated Antibiotic Therapy.

mBio, 10(5): pii:mBio.00652-19.

Antibiotics, which are used both to prevent and to treat infections, are a mainstay therapy for lifesaving procedures such as transplantation. For this reason, and many others, increased antibiotic resistance among human-associated pathogens, such as the carbapenem-resistant Enterobacteriaceae species, is of grave concern. In this study, we report on a hematopoietic stem cell transplant recipient in whom cultures detected the emergence of carbapenem resistance and spread across five strains of bacteria that persisted for over a year. Carbapenem resistance in Citrobacter freundii, Enterobacter cloacae, Klebsiella aerogenes, and Klebsiella pneumoniae was linked to a pair of plasmids, each carrying the Klebsiella pneumoniae carbapenemase gene (blaKPC). Surveillance cultures identified a carbapenem-susceptible strain of Citrobacter freundii that may have become resistant through horizontal gene transfer of these plasmids. Selection of a multidrug-resistant Klebsiella pneumoniae strain was also detected following combination antibiotic therapy. Here we report a plasmid carrying the blaKPC gene with broad host range that poses the additional threat of spreading to endogenous members of the human gut microbiome.IMPORTANCE Antibiotic-resistant bacteria are a serious threat to medically fragile patient populations. The spread of antibiotic resistance through plasmid-mediated mechanisms is of grave concern as it can lead to the conversion of endogenous patient-associated strains to difficult-to-treat pathogens.

RevDate: 2019-10-09

Kodavanti UP (2019)

Susceptibility Variations in Air Pollution Health Effects: Incorporating Neuroendocrine Activation.

Toxicologic pathology [Epub ahead of print].

Diverse host factors/phenotypes may exacerbate or diminish biological responses induced by air pollutant exposure. We lack an understanding of biological indicators of environmental exposures that culminate in a physiological response versus those that lead to adversity. Variations in response phenotype might arise centrally and/or at the local tissue level. In addition to genetic differences, the current evidence supports the roles of preexisting cardiopulmonary diseases, diabetes, diet, adverse prenatal environments, neurobehavioral disorders, childhood infections, microbiome, sex, and psychosocial stressors in modifying the susceptibility to air pollutant exposures. Animal models of human diseases, obesity, nutritional inadequacies, and neurobehavioral conditions have been compared with healthy controls to understand the causes of variations in susceptibility. Although psychosocial stressors have been associated with increased susceptibility to air pollutant effects, the contribution of neuroendocrine stress pathways in mediating these effects is just emerging. The new findings of neuroendocrine activation leading to systemic metabolic and immunological effects of air pollutants, and the potential contribution to allostatic load, emphasize the consideration of these mechanisms into susceptibility. Variations in susceptibility to air pollution health effects are likely to underlie host genetic and physiological conditions in concert with disrupted neuroendocrine circuitry that alters physiological stability under the influence of stressors.

RevDate: 2019-10-09

Liu XX, Jiao B, Liao XX, et al (2019)

Analysis of Salivary Microbiome in Patients with Alzheimer's Disease.

Journal of Alzheimer's disease : JAD pii:JAD190587 [Epub ahead of print].

Recent studies found that poor oral hygiene was associated with increased risk of dementia, and the number of oral bacteria significantly increased in the brain tissues of patients with Alzheimer's disease (AD), suggesting that the oral microbiota may play an important role in the pathogenesis of AD. However, the actual composition of oral bacteria communities in patients with AD and whether these oral bacteria are associated with disease severity remain largely unknown. Also, the APOEɛ4 polymorphism is a strong risk factor for sporadic AD, and it would be pertinent to see if the bacterial flora was different in those patients who were APOEɛ4 positive. A total of 78 subjects were recruited in this study, including 39 patients with AD and 39 healthy controls. Saliva was collected from each subject. 16S ribosomal RNA (16S rRNA) sequencing was conducted to analyze the salivary microbiota, and Sanger sequencing was performed to analyze the APOE genotype. There was a significantly lower richness and diversity of saliva microbiota detected in AD patients than healthy controls. The relative abundance of Moraxella, Leptotrichia, and Sphaerochaeta in the saliva of AD patients greatly increased, whereas that of Rothia was significantly reduced. Compared with APOEɛ4 (-) patients, the level of Abiotrophia and Desulfomicrobium was comparatively abundant, while Actinobacillus and Actinomyces decreased significantly in patients carrying the APOEɛ4. No bacteria were found to be associated with the severity of AD. This is the first study to analyze the salivary microorganisms in patients with AD, and we discovered that the composition of salivary microbiome was altered in AD, providing further support for the role of the oral microbiome in AD development.

RevDate: 2019-10-08

Goodwin G (2019)

Type 1 Diabetes Mellitus and Celiac Disease: Distinct Autoimmune Disorders That Share Common Pathogenic Mechanisms.

Hormone research in paediatrics pii:000503142 [Epub ahead of print].

BACKGROUND: The relatively common co-occurrence of type 1 diabetes (T1D) and celiac disease (CD) suggests these disorders share common pathogenic etiologies.

SUMMARY: T1D and CD are strongly linked to closely related high-risk human lymphocyte antigens (HLA-DR-DQ). High-risk HLA molecules bind specific fragments of gluten or the islet self-antigen(s) and present these antigens to antigen-responsive T cells. In an appropriate proinflammatory environment, the autoimmune response results in destruction of the intestinal enterocyte and/or the pancreatic beta cell. Environmental factors have been implicated in the etiology of T1D and CD because (1) identical twins are only partially concordant for these disorders and (2) incidence rates of T1D and CD have been steadily rising for decades. Prospective studies in infants genetically predisposed to T1D and CD showed that antibody positivity to both disorders begins in the first 1-3 years of life. Viral infections and early exposure to gluten or cow's milk in the infant diet have been implicated in disease pathogenesis. However, delaying introduction of gluten in the infant diet until 12 months of age had no impact on the development of islet or celiac autoimmunity. Weaning nursing infants to hydrolyzed infant formula had no impact on the development of T1D. Viral infections have been suspected of playing a role in T1D pathogenesis for decades. A large international prospective study (TEDDY) has shown increased risk of T1D autoimmunity particularly when >5 respiratory infections or febrile infections have occurred in the 9 months preceding the appearance of islet antibodies. Provocative data in animal models of T1D suggest the microbiome may play an important role in the pathogenesis of T1D. Breastfeeding, diet, infections, antibiotics, and method of birth alter the composition of the microbiome. Human data indicate subtle differences in the microbiome of children with T1D autoimmunity, while intestinal dysbiosis has been clearly demonstrated in CD. Alterations of the integrity of the intestinal mucosa plays an important role in the pathogenesis of CD, and the NOD mouse model suggests an important role of a leaky intestinal epithelium in T1D as well. Key Message: Immunogenetics and the environment are closely interrelated in the pathogenesis of T1D and CD. Large well-designed prospective studies in at-risk populations informed by scientifically rigorous studies in animal models are likely to have the greatest impact on our understanding of the complex pathogenesis of these detrimental autoimmune disorders.

RevDate: 2019-10-08

Lillington SP, Leggieri PA, Heom KA, et al (2019)

Nature's recyclers: anaerobic microbial communities drive crude biomass deconstruction.

Current opinion in biotechnology, 62:38-47 pii:S0958-1669(19)30069-2 [Epub ahead of print].

Microbial communities within anaerobic ecosystems have evolved to degrade and recycle carbon throughout the earth. A number of strains have been isolated from anaerobic microbial communities, which are rich in carbohydrate active enzymes (CAZymes) to liberate fermentable sugars from crude plant biomass (lignocellulose). However, natural anaerobic communities host a wealth of microbial diversity that has yet to be harnessed for biotechnological applications to hydrolyze crude biomass into sugars and value-added products. This review highlights recent advances in 'omics' techniques to sequence anaerobic microbial genomes, decipher microbial membership, and characterize CAZyme diversity in anaerobic microbiomes. With a focus on the herbivore rumen, we further discuss methods to discover new CAZymes, including those found within multi-enzyme fungal cellulosomes. Emerging techniques to characterize the interwoven metabolism and spatial interactions between anaerobes are also reviewed, which will prove critical to developing a predictive understanding of anaerobic communities to guide in microbiome engineering.

RevDate: 2019-10-08

Xiang Q, Zhu D, Chen QL, et al (2019)

Adsorbed sulfamethoxazole exacerbates the effects of polystyrene (~2µm) on gut microbiota and the antibiotic resistome of a soil collembolan.

Environmental science & technology [Epub ahead of print].

Microplastics pollution in the environment is now receiving worldwide attention, however, the effects of co-pollution of antibiotics and microplastics on the gut microbiome of globally distributed and functionally important non-target soil animals remain poorly understood. We studied a model collembolan (Folsomia candida) and found that the ingestion of microplastics (polystyrene, 2-2.9μm) substantially altered the gut microbiome, antibiotic resistance gene (ARG) profile and the isotopic fractionation in the soil collembolan tissue. Importantly, collembolans exposed to polystyrene microplastics loaded with sulfamethoxazole (MA) presented a distinctive gut microbiome, ARG profile and isotopic fractionation compared to those exposed to polystyrene alone (MH). We observed that the abundance of ARGs and mobile genetic elements (MGEs) in the MA-treated collembolan guts was significantly higher than in the MH and the control treatments. There were also strong interactions between the gut microbiome and ARGs in the collembolan guts. We further found that bacterial beta-diversity correlated significantly with the δ13C and δ15N values in collembolan body tissues. Together, our results indicate that changes in isotopic fractionation and ARG profiles in the collembolan were induced by the changes in gut microbiota, and suggest that microplastics from diverse sources may have profound influences on soil fauna and soil food webs.

RevDate: 2019-10-08

Eiwegger T, Hung L, San Diego KE, et al (2019)

Recent developments and highlights in food allergy.

Allergy [Epub ahead of print].

The achievement of long lasting, safe treatments for food allergy is dependent on the understanding of the immunological basis of food allergy. Accurate diagnosis is essential for management. In recent years, data from oral food challenges have revealed that routine allergy testing is poor at predicting clinical allergy for tree nuts, almonds in particular. More advanced antigen-based tests including component resolved diagnostics and epitope reactivity may lead to more accurate diagnosis and selection of therapeutic intervention. Additional diagnostic accuracy may come from cellular tests like the basophil activation test or mast cell approaches. In the context of clinical trials, cellular tests have revealed specific T-cell and B-cell populations that are more abundant in food allergic individuals with distinct mechanistic features. Awareness of clinical markers, such as the ability to eat baked forms of milk and egg, continue to inform the understanding of natural tolerance development. Mouse models have allowed for investigation into multiple mechanisms of food allergy including modification of epithelial metabolism, the induction of regulatory cell subsets and the microbiome. Increasing numbers of children who underwent food immunotherapy enlarged the body of evidence on mechanisms and predictors of treatment success. Experimental immunological markers in conjunction with clinical determinants such as lower age and lower initial specific IgE appear to be of benefit. More research on the optimal dose, preparation, and route of application integrating a high-level safety and efficacy is demanded. Alternatively, biologics blocking TSLP, IL-33, IL4 and IL13, or IgE may help to achieve that.

RevDate: 2019-10-08

Li W, ZS Ma (2019)

Diversity scaling of human vaginal microbial communities.

The composition and diversity of the human vaginal microbial community have been investigated intensively due to the diversity-stability relationship (DSR)-based hypothesis for bacterial vaginosis (BV) etiology, which was first proposed in the 1990s and has received renewed interest in recent years. Nevertheless, diversity changes (scaling) across individuals in a cohort or population have not yet been addressed, which is significant both theoretically and practically. Theoretically, biodiversity scaling is the core of biogeography, and practically, inter-subject heterogeneity is critical for understanding the etiology and epidemiology of human microbiome-associated diseases such as BV. Here we applied the diversity-area relationship (DAR), a recent extension to the classic species-area relationship (SAR), to study diversity scaling of the vaginal microbiome by reanalyzing reported data collected from 1 107 postpartum women. The model used here characterized the power-law (or its extension) relationships between accrued diversity and areas (numbers of individuals), upon which four biogeographic profiles were thus defined. Specifically, we established the DAR profile (relationship between diversity scaling parameter and so-termed diversity order (q)), similarly pair-wise diversity overlap (PDO) profile, maximal accrual diversity (MAD) profile, and ratio of individual-level to population-level diversity (RIP) profile. These four profiles offer valuable tools to assess and predict diversity scaling (changes) in the human vaginal microbiome across individuals, as well as to understand the dynamics of vaginal microbiomes in healthy women.

RevDate: 2019-10-08

Yang Y, Ashworth AJ, DeBruyn JM, et al (2019)

Soil bacterial biodiversity is driven by long-term pasture management, poultry litter, and cattle manure inputs.

PeerJ, 7:e7839 pii:7839.

Soil microorganisms are important for maintaining soil health, decomposing organic matter, and recycling nutrients in pasture systems. However, the impact of long-term conservation pasture management on soil microbial communities remains unclear. Therefore, soil microbiome responses to conservation pasture management is an important component of soil health, especially in the largest agricultural land-use in the US. The aim of this study was to identify soil microbiome community differences following 13-years of pasture management (hayed (no cattle), continuously grazed, rotationally grazed with a fenced, un-grazed and unfertilized buffer strip, and a control (no poultry litter or cattle manure inputs)). Since 2004, all pastures (excluding the control) received annual poultry litter at a rate of 5.6 Mg ha-1. Soil samples were collected at a 0-15 cm depth from 2016-2017 either pre or post poultry litter applications, and bacterial communities were characterized using Illumina 16S rRNA gene amplicon sequencing. Overall, pasture management influenced soil microbial community structure, and effects were different by year (P < 0.05). Soils receiving no poultry litter or cattle manure had the lowest richness (Chao). Continuously grazed systems had greater (P < 0.05) soil community richness, which corresponded with greater soil pH and nutrients. Consequently, continuously grazed systems may increase soil diversity, owing to continuous nutrient-rich manure deposition; however, this management strategy may adversely affect aboveground plant communities and water quality. These results suggest conservation pasture management (e.g., rotationally grazed systems) may not improve microbial diversity, albeit, buffer strips were reduced nutrients and bacterial movement as evident by low diversity and fertility in these areas compared to areas with manure or poultry litter inputs. Overall, animal inputs (litter or manure) increased soil microbiome diversity and may be a mechanism for improved soil health.

RevDate: 2019-10-08

Andoh A, Inoue R, Kawada Y, et al (2019)

Elemental diet induces alterations of the gut microbial community in mice.

Journal of clinical biochemistry and nutrition, 65(2):118-124.

The aim of the present study was to investigate elemental diet (ED)-induced alteration of the fecal and mucosal microbiome in mice. The control group was fed a normal chow and the ED group was fed normal chow containing 50% w/w Elental® (EA Pharma, Tokyo, Japan) for 28 days. Fecal and mucosal microbiome were analyzed using 16S rRNA gene sequencing. In the fecal samples, the observed species, an index for microbial richness, was significantly decreased in the ED group. Principal coordinate analysis revealed that there were significant compositional differences between the control and ED groups (PERMANOVA p = 0.0007 for unweighted and p = 0.002 for weighted UniFrac distance, respectively). In contrast, there was no significant difference in the overall structure of mucosal microbiome between the control and ED groups. In the fecal samples, abundance of the genera Adlercreutzia, Akkermansia, Streptococcus, Helicobacter, Coprobacillus and Coprococcus was significantly reduced in the ED group compared to the control group. Abundance of the genera Lactobacillus and Staphylococcus was significantly increased in the ED group. In a functional analysis using PICRUSt software, ED altered various pathways involved in amino acid metabolism of the gut microbiome. In conclusion, ED caused a reduction in bacterial diversity and altered metabolic functions.

RevDate: 2019-10-08

Zhao L, Lou H, Peng Y, et al (2019)

Comprehensive relationships between gut microbiome and faecal metabolome in individuals with type 2 diabetes and its complications.

Endocrine pii:10.1007/s12020-019-02103-8 [Epub ahead of print].

PURPOSE: As the treatment regimens such as metformin could confound the correlation between type 2 diabetes (T2D) and gut microbiome, we should revisit the relationship between gut microbiota and T2D patients who are not currently treated with metformin.

METHODS: The study recruited 65 T2D patients: 49 with and 16 without diabetic complications, and 35 healthy controls. We sequenced the 16S rRNA V3-V4 region of gut microbiota and detected metabolites based on liquid chromatography mass spectrometry (LC/MS) and gas chromatography mass spectrometry (GC/MS) in faecal samples.

RESULTS: The composition of both the gut microbiota and faecal metabolites changed significantly with T2D patients. The abundance of Proteobacteria and the ratio of Firmicutes/Bacteroidetes were higher in T2D patients than healthy subjects, and the short chain fatty acids (SCFAs), bile acids and lipids of T2D patients were significantly disordered. Moreover, the abundances of certain SCFA-producing bacteria (Lachnospiraceae and Ruminococcaceae etc.) were significantly increased in T2D patients, while the faecal SCFAs concentrations were significantly decreased. It's suggested that the role of SCFA-producing bacteria was not simply to produce SCFAs. Then we identified 44 microbial modules to explore the correlations between the gut microbiota and metabolic traits. Specially, most modules including certain SCFA-producing bacteria were comprehensively correlated to body mass index, the levels of blood glucose, blood pressure, blood cholesterol and faecal bile acids and lipids.

CONCLUSIONS: Our study identified the relationships between the gut microbiota and faecal metabolites, and provided a resource for future studies to understand host-gut microbiota interactions in T2D.

RevDate: 2019-10-09

Lev-Sagie A, Goldman-Wohl D, Cohen Y, et al (2019)

Vaginal microbiome transplantation in women with intractable bacterial vaginosis.

Nature medicine pii:10.1038/s41591-019-0600-6 [Epub ahead of print].

We report the results of a first exploratory study testing the use of vaginal microbiome transplantation (VMT) from healthy donors as a therapeutic alternative for patients suffering from symptomatic, intractable and recurrent bacterial vaginosis (ClinicalTrials.gov NCT02236429). In our case series, five patients were treated, and in four of them VMT was associated with full long-term remission until the end of follow-up at 5-21 months after VMT, defined as marked improvement of symptoms, Amsel criteria, microscopic vaginal fluid appearance and reconstitution of a Lactobacillus-dominated vaginal microbiome. One patient presented with incomplete remission in clinical and laboratory features. No adverse effects were observed in any of the five women. Notably, remission in three patients necessitated repeated VMT, including a donor change in one patient, to elicit a long-standing clinical response. The therapeutic efficacy of VMT in women with intractable and recurrent bacterial vaginosis should be further determined in randomized, placebo-controlled clinical trials.

RevDate: 2019-10-08

Hamilton SE, TS Griffith (2019)

A wild microbiome improves mouse modeling of the human immune response.

Lab animal pii:10.1038/s41684-019-0421-8 [Epub ahead of print].

RevDate: 2019-10-08

Dambuza IM, GD Brown (2019)

Fungi accelerate pancreatic cancer.

Nature, 574(7777):184-185.

RevDate: 2019-10-08

Schlomann BH, Wiles TJ, Wall ES, et al (2019)

Sublethal antibiotics collapse gut bacterial populations by enhancing aggregation and expulsion.

Proceedings of the National Academy of Sciences of the United States of America pii:1907567116 [Epub ahead of print].

Antibiotics induce large and highly variable changes in the intestinal microbiome even at sublethal concentrations, through mechanisms that remain elusive. Using gnotobiotic zebrafish, which allow high-resolution examination of microbial dynamics, we found that sublethal doses of the common antibiotic ciprofloxacin cause severe drops in bacterial abundance. Contrary to conventional views of antimicrobial tolerance, disruption was more pronounced for slow-growing, aggregated bacteria than for fast-growing, planktonic species. Live imaging revealed that antibiotic treatment promoted bacterial aggregation and increased susceptibility to intestinal expulsion. Intestinal mechanics therefore amplify the effects of antibiotics on resident bacteria. Microbial dynamics are captured by a biophysical model that connects antibiotic-induced collapses to gelation phase transitions in soft materials, providing a framework for predicting the impact of antibiotics on the intestinal microbiome.

RevDate: 2019-10-08

Chase C, RS Kaushik (2019)

Mucosal Immune System of Cattle: All Immune Responses Begin Here.

The Veterinary clinics of North America. Food animal practice, 35(3):431-451.

This article discusses key concepts important for mucosal immunity. The mucosa is the largest immune organ of the body. The mucosal barrier (the tight junctions and the "kill zone") along with the mucosa epithelial cells maintaining an anti-inflammatory state are essential for the mucosal firewall. The microbiome (the microorganisms that are in the gastrointestinal, respiratory, and reproductive tract) is essential for immune development, homeostasis, immune response, and maximizing animal productivity. Mucosal vaccination provides an opportunity to protect animals from most infectious diseases because oral, gastrointestinal, respiratory, and reproductive mucosa are the main portals of entry for infectious disease.

RevDate: 2019-10-08

Nielsen MC, SC Jiang (2019)

Alterations of the human skin microbiome after ocean water exposure.

Marine pollution bulletin, 145:595-603.

Skin is the body's first line of defense against invading microorganisms. The skin microbiome has been shown to provide immunity against exogenous bacterial colonization. Recreational water exposures may alter the skin microbiome and potentially induce skin infections. This study explored the link between ocean water exposures and the human skin microbiome. Skin microbiome samples were collected, using swabs, from human participants' calves before and after they swam in the ocean, and at 6 hour and 24 hour post-swim. Genomic analysis showed that skin microbiomes were different among individuals before swimming. But after swimming, microbial communities were no longer different, which was demonstrated by a decrease in inter-sample diversity. Taxonomic analysis showed that ocean bacteria, including potential pathogens, replaced the native skin bacteria and remained on the skin for at least 24 hour post-swim. This research provides insight into the relationship between the human skin microbiome and the environment.

RevDate: 2019-10-09

Amato KR, Mallott EK, McDonald D, et al (2019)

Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny.

Genome biology, 20(1):201 pii:10.1186/s13059-019-1807-z.

BACKGROUND: Comparative data from non-human primates provide insight into the processes that shaped the evolution of the human gut microbiome and highlight microbiome traits that differentiate humans from other primates. Here, in an effort to improve our understanding of the human microbiome, we compare gut microbiome composition and functional potential in 14 populations of humans from ten nations and 18 species of wild, non-human primates.

RESULTS: Contrary to expectations from host phylogenetics, we find that human gut microbiome composition and functional potential are more similar to those of cercopithecines, a subfamily of Old World monkey, particularly baboons, than to those of African apes. Additionally, our data reveal more inter-individual variation in gut microbiome functional potential within the human species than across other primate species, suggesting that the human gut microbiome may exhibit more plasticity in response to environmental variation compared to that of other primates.

CONCLUSIONS: Given similarities of ancestral human habitats and dietary strategies to those of baboons, these findings suggest that convergent ecologies shaped the gut microbiomes of both humans and cercopithecines, perhaps through environmental exposure to microbes, diet, and/or associated physiological adaptations. Increased inter-individual variation in the human microbiome may be associated with human dietary diversity or the ability of humans to inhabit novel environments. Overall, these findings show that diet, ecology, and physiological adaptations are more important than host-microbe co-diversification in shaping the human microbiome, providing a key foundation for comparative analyses of the role of the microbiome in human biology and health.

RevDate: 2019-10-08

Noonan A, TM Pawlik (2019)

Hepatocellular carcinoma: an update on investigational drugs in phase I and II clinical trials.

Expert opinion on investigational drugs [Epub ahead of print].

Introduction: Hepatocellular carcinoma (HCC) is the most common primary liver cancer and the burden of disease is increasing globally. Until recently, systemic therapies for HCC were limited and prognosis for advanced disease generally poor. Area covered: This article describes some recent phase I and II clinical trials for the treatment of HCC. We performed a search on Pubmed with keywords hepatocellular carcinoma, phase I clinical trial, phase II clinical trial, and immunotherapy. We also searched https://clinicaltrials.gov and identified relevant trials listed as active. Studies in progress or recently reported were conducted using novel therapies based on targets identified through molecular profiling of tumors or based on insights into immune system dysregulation in HCC. We also identified studies using drugs targeting recently discovered biomarkers such as endoglin or aldo-keto reductase 1c3. The major outcomes were safety and efficacy as measured by response rate, progression-free survival or overall survival. Expert Opinion: HCC is a heterogeneous disease resulting from aberrations in intracellular signaling and immune system dysregulation. Thus, a multisystem approach will be required to deliver personalized therapy. Combination therapies are likely to be future options; it is also possible that modulation of the microbiome might form part of future treatment paradigms.

RevDate: 2019-10-08

Yagishita Y, Fahey JW, Dinkova-Kostova AT, et al (2019)

Broccoli or Sulforaphane: Is It the Source or Dose That Matters?.

Molecules (Basel, Switzerland), 24(19): pii:molecules24193593.

There is robust epidemiological evidence for the beneficial effects of broccoli consumption on health, many of them clearly mediated by the isothiocyanate sulforaphane. Present in the plant as its precursor, glucoraphanin, sulforaphane is formed through the actions of myrosinase, a β-thioglucosidase present in either the plant tissue or the mammalian microbiome. Since first isolated from broccoli and demonstrated to have cancer chemoprotective properties in rats in the early 1990s, over 3000 publications have described its efficacy in rodent disease models, underlying mechanisms of action or, to date, over 50 clinical trials examining pharmacokinetics, pharmacodynamics and disease mitigation. This review evaluates the current state of knowledge regarding the relationships between formulation (e.g., plants, sprouts, beverages, supplements), bioavailability and efficacy, and the doses of glucoraphanin and/or sulforaphane that have been used in pre-clinical and clinical studies. We pay special attention to the challenges for better integration of animal model and clinical studies, particularly with regard to selection of dose and route of administration. More effort is required to elucidate underlying mechanisms of action and to develop and validate biomarkers of pharmacodynamic action in humans. A sobering lesson is that changes in approach will be required to implement a public health paradigm for dispensing benefit across all spectrums of the global population.

RevDate: 2019-10-08

Chibbar R, LA Dieleman (2019)

The Gut Microbiota in Celiac Disease and probiotics.

Nutrients, 11(10): pii:nu11102375.

Celiac disease (CeD) is an immune-mediated enteropathy, and unique in that the specific trigger is known: gluten. The current mainstay of therapy is a gluten-free diet (GFD). As novel therapies are being developed, complementary strategies are also being studied, such as modulation of the gut microbiome. The gut microbiota is involved in the initiation and perpetuation of intestinal inflammation in several chronic diseases. Intestinal dysbiosis has been reported in CeD patients, untreated or treated with GFD, compared to healthy subjects. Several studies have identified differential bacterial populations associated with CeD patients and healthy subjects. However, it is still not clear if intestinal dysbiosis is the cause or effect of CeD. Probiotics have also been considered as a strategy to modulate the gut microbiome to an anti-inflammatory state. However, there is a paucity of data to support their use in treating CeD. Further studies are needed with therapeutic microbial formulations combined with human trials on the use of probiotics to treat CeD by restoring the gut microbiome to an anti-inflammatory state.

RevDate: 2019-10-08

Janulewicz PA, Seth RK, Carlson JM, et al (2019)

The Gut-Microbiome in Gulf War Veterans: A Preliminary Report.

International journal of environmental research and public health, 16(19): pii:ijerph16193751.

Gulf War Illness (GWI) is a chronic multi-symptom disorder affecting the central nervous system (CNS), immune and gastrointestinal (GI) systems of Gulf War veterans (GWV). We assessed the relationships between GWI, GI symptoms, gut microbiome and inflammatory markers in GWV from the Boston Gulf War Illness Consortium (GWIC). Three groups of GWIC veterans were recruited in this pilot study; GWV without GWI and no gastrointestinal symptoms (controls), GWV with GWI and no gastrointestinal symptoms (GWI-GI), GWV with GWI who reported gastrointestinal symptoms (GW+GI). Here we report on a subset of the first thirteen stool samples analyzed. Results showed significantly different gut microbiome patterns among the three groups and within the GWI +/-GI groups. Specifically, GW controls had a greater abundance of firmicutes and the GWI+GI group had a greater abundance of the phyla bacteroidetes, actinobacteria, euryarchaeota, and proteobacteria as well as higher abundances of the families Bacteroidaceae, Erysipelotrichaceae, and Bifidobacteriaceae. The GWI+GI group also showed greater plasma levels of the inflammatory cytokine TNF-RI and they endorsed significantly more chemical weapons exposure during the war and reported significantly greater chronic pain, fatigue and sleep difficulties than the other groups. Studies with larger samples sizes are needed to confirm these initial findings.

RevDate: 2019-10-08

Chan S, Isbel NM, Hawley CM, et al (2019)

Infectious Complications Following Kidney Transplantation-A Focus on Hepatitis C Infection, Cytomegalovirus Infection and Novel Developments in the Gut Microbiota.

Medicina (Kaunas, Lithuania), 55(10): pii:medicina55100672.

The incidence of infectious complications, compared with the general population and the pre-transplant status of the recipient, increases substantially following kidney transplantation, causing significant morbidity and mortality. The potent immunosuppressive therapy given to prevent graft rejection in kidney transplant recipients results in an increased susceptibility to a wide range of opportunistic infections including bacterial, viral and fungal infections. Over the last five years, several advances have occurred that may have changed the burden of infectious complications in kidney transplant recipients. Due to the availability of direct-acting antivirals to manage donor-derived hepatitis C infection, this has opened the way for donors with hepatitis C infection to be considered in the donation process. In addition, there have been the development of medications targeting the growing burden of resistant cytomegalovirus, as well as the discovery of the potentially important role of the gastrointestinal microbiota in the pathogenesis of post-transplant infection. In this narrative review, we will discuss these three advances and their potential implications for clinical practice.

RevDate: 2019-09-20

Whittaker DJ, Slowinski SP, Greenberg JM, et al (2019)

Experimental evidence that symbiotic bacteria produce chemical cues in a songbird.

The Journal of experimental biology pii:jeb.202978 [Epub ahead of print].

Symbiotic microbes that inhabit animal scent glands can produce volatile compounds used as chemical signals by the host animal. Though several studies have demonstrated correlations between scent gland bacterial community structure and host animal odour profiles, none have systematically demonstrated a causal relationship. In birds, volatile compounds in preen oil secreted by the uropygial gland serve as chemical cues and signals. Here we test whether manipulating the uropygial gland microbial community affects chemical profiles in the dark-eyed junco (Junco hyemalis). We found an effect of antibiotic treatment targeting the uropygial gland on both bacterial and volatile profiles. In a second study, we cultured bacteria from junco preen oil, and found that all the cultivars produced at least one volatile compound common in junco preen oil, and that most cultivars produced multiple preen oil volatiles. In both studies, we identified experimentally generated patterns in specific volatile compounds previously shown to predict junco reproductive success. Together, our data provide experimental support for the hypothesis that symbiotic bacteria produce behaviourally relevant volatile compounds within avian chemical cues and signals.

RevDate: 2019-10-07

Moloney GM, Dinan TG, Clarke G, et al (2019)

Microbial regulation of microRNA expression in the brain-gut axis.

Current opinion in pharmacology, 48:120-126 pii:S1471-4892(19)30074-8 [Epub ahead of print].

The gut microbiome facilitates a consistent transfer of information between the gut and the brain and microRNAs may now represent a key signalling molecule that facilitates this relationship. This review will firstly examine how these small non-coding RNAs influence the gut microbiome, and secondly how the microbiome, when disturbed, may influence miRNA expression in the brain. In addition, we will examine the consequence that microbiome-related changes in miRNA expression have on neurodevelopment, behaviour and cognition. We will also discuss novel data that suggests miRNAs contained in our diet may influence our immune system in a positive manner, offering a further potential pathway for treatment of disorders of the gut-brain axis that are influenced by the microbiome.

RevDate: 2019-10-07

Silverman GJ, Azzouz DF, AV Alekseyenko (2019)

Systemic Lupus Erythematosus and dysbiosis in the microbiome: cause or effect or both?.

Current opinion in immunology, 61:80-85 pii:S0952-7915(19)30007-X [Epub ahead of print].

Throughout our lives we are immersed in, and colonized by, immense and complex microbial communities. These microbiota serve as activators and early sparring partners for the progressive construction of the layers within our immune defenses and are essential to immune homeostasis. Yet, at times imbalances within the microbiota may contribute to metabolic and immune regulatory abnormalities that underlie the development of inflammatory and autoimmune diseases. Here, we review recent progress in investigations of the microbiome, with emphasis on the gut microbiota associated with systemic autoimmunity. In particular, these studies are beginning to illuminate aspects of the pathogenesis of Systemic Lupus Erythematosus, and may suggest that interconnections with specific disease-associated patterns of dysbiosis within gut communities are bidirectional and mutually reinforcing.

RevDate: 2019-10-07

Smith RP, Easson C, Lyle SM, et al (2019)

Gut microbiome diversity is associated with sleep physiology in humans.

PloS one, 14(10):e0222394 pii:PONE-D-19-19430.

The human gut microbiome can influence health through the brain-gut-microbiome axis. Growing evidence suggests that the gut microbiome can influence sleep quality. Previous studies that have examined sleep deprivation and the human gut microbiome have yielded conflicting results. A recent study found that sleep deprivation leads to changes in gut microbiome composition while a different study found that sleep deprivation does not lead to changes in gut microbiome. Accordingly, the relationship between sleep physiology and the gut microbiome remains unclear. To address this uncertainty, we used actigraphy to quantify sleep measures coupled with gut microbiome sampling to determine how the gut microbiome correlates with various measures of sleep physiology. We measured immune system biomarkers and carried out a neurobehavioral assessment as these variables might modify the relationship between sleep and gut microbiome composition. We found that total microbiome diversity was positively correlated with increased sleep efficiency and total sleep time, and was negatively correlated with wake after sleep onset. We found positive correlations between total microbiome diversity and interleukin-6, a cytokine previously noted for its effects on sleep. Analysis of microbiome composition revealed that within phyla richness of Bacteroidetes and Firmicutes were positively correlated with sleep efficiency, interleukin-6 concentrations and abstract thinking. Finally, we found that several taxa (Lachnospiraceae, Corynebacterium, and Blautia) were negatively correlated with sleep measures. Our findings initiate linkages between gut microbiome composition, sleep physiology, the immune system and cognition. They may lead to mechanisms to improve sleep through the manipulation of the gut microbiome.


RJR Experience and Expertise


Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.


Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.


Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.


Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.


While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.


Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.


Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.


Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

short personal version

Curriculum Vitae for R J Robbins

long standard version

RJR Picks from Around the Web (updated 11 MAY 2018 )